Research conducted with the aid of the UCF ARCC covers a wide variety of disciplines including Engineering, Modeling and Simulation, Physics, Chemistry, Biology, Optics, and Nano Science.

All of these areas benefit from the UCF ARCC by allowing users to submit jobs and receive data in a timely manner that would not be possible on conventional personal computers or computational workstations. The selected list of citations below represents the work of researchers that have benefited from the use of the UCF ARCC.

  • Title: A Wavelet Domain Implementation of Sparse Representation Method for Face Recognition
    Authors: Taif Alobaidi ; Wasfy B. Mikhael
    Location: Windsor, ON, Canada, Canada

    Recently, a new discriminative sparse representation method for robust face recognition via l 2 regularization (NDSRFR) was published. In this paper, a Wavelet domain (WDNDSRFR) is presented. In particular, the Two-Dimensional Discrete Wavelet Transform implementation is given and shown to considerably reduce the computational complexity and the storage requirements while maintaining the recognition accuracy of the NDSRFR. Extensive simulations were performed on five face databases, namely, ORL, YALE, FERET, Cropped AR, and Georgia Tech and the enhanced properties of the WDNDSRFR are confirmed as shown in the given sample results.

  • Title: A Modified Discriminant Sparse Representation Method for Face Recognition
    Authors: Taif Alobaidi, Wasfy Milkhael
    Location: University of Nevada, NV, USA

    Recently, a new discriminative sparse representation method for robust face recognition that uses ℓ 2 -norm regularization was reported. In this paper, direct data-driven calculation of the balance parameter used in the objective function is presented. The modified system preserves the advantages of the original method while improving the recognition accuracy and making the system more automated, i.e., less dependent on the user's input. Extensive simulations are performed on six face databases, namely, ORL, YALE, FERET, FEI, Cropped AR, and Georgia Tech. Sample results are given demonstrating the properties of the modified system.

  • Title: Employing Vector Quantization in A Transform Domain For Face Recognition
    Authors: Taif Alobaidi, Ahmed Aldhahab, and Wasfy B. Mikhael
    Location: 2016 IEEE 7th Annual Ubiquitous Computing, Electronics & Mobile Communication Conference (UEMCON)

    A face recognition system using an integration of Discrete Cosine Transform (DCT) and Vector quantization (VQ) is proposed in this paper. The system consists of two main phases, namely, Feature Extraction and Recognition. In the first phase, the input facial image is divided into blocks with dimensions equal to the codeword dimensions. Then, DCT is applied on each block. The codebook is initialized using the Kekre Fast Codebook Generation (KFCG) method. The Final Codebook computed using VQ algorithm efficiently represents the input facial image. The second phase aims to find the recognition rates based on the Euclidean distance criterion. The system is evaluated using four different databases, namely, ORL, YALE, FERET, and FEI that have different facial variations, such as facial expressions, illuminations, etc. The experimental results are analyzed using K-fold Cross Validation (CV). The proposed system is shown to improve the storage requirements, as well as the recognition rates.

  • Title: Predicting landscape-level distributions
    Authors: Pedro Quintana-Ascencio, Stephaniem Koontz, Stacy Smith and Eric Menges
    Location: Fort Lauderdale, Florida

    Predicting landscape-level distributions: integrating demography, fire, and dryness with patch and annual variation Pedro F. Quintana-Ascencio, Stephanie Koontz, Stacy Smith, Vivienne Sclater and Eric S. Menges Department of Biology, University of Central Florida Plant Ecology Program, Archbold Biological Station ESA 2016 BACKGROUND/QUESTIONS/METHODS Demography often varies among populations, but most scientists have look at these patterns in a piecemeal way. We used a landscape level variable, relative elevation above wetlands (“dryness”) as a predictor of population variation of the perennial herb Hypericum cumulicola. Previously, we identified time-since-fire as a key driver of this species’ dynamics, but we hypothesized that dryness would explain additional variation among populations in a landscape with variable local elevation. We used data on marked plants and density plots from 1994-2014 from 14 populations, about 11K plants and 34K cases of annual vital rates, along with experiments on seed dormancy, germination and seedling survival. We used generalized linear mixed models to assess the effects of stage (first year plant or adult), plant height, time-since-fire and dryness, with random effects by population and year, on annual survival, plant growth, probability of reproduction and fecundity. Seed survival, dormancy, and germination were evaluated with general additive models. Models were then combined in an integral projection model to estimate population growth rates and other parameters. We modeled H. cumulicola occupancy in patches of various sizes and degrees of spatial isolation, comparing results to an independent dataset of patch occupancy. RESULTS/CONCLUSIONS Both fire and dryness had significant and often interacting effects on germination, seed dormancy, plant survival, plant growth, probability of reproduction, and fecundity. Population growth rates peaked about 5 years post-fire and then declined sharply through about ten years, leveling out after that. Compared to wetter areas, drier sites had higher population rates shortly after fire, lower rates at intermediate times-since-fire, and similar rates when long unburned. Observed plant densities were most closely related to model output from the drier sites. These results broadly agree with prior models on the primacy of time-since-fire in driving the population dynamics of H. cumulicola, but adds detail on how the landscape affects plant demography, likely through changes in the recovery of vegetation structure. Simulations on landscapes with realistic spatial patterns of landscape patches showed effects of fire, dryness, patch size, and isolation on occupancy. Some suitable habitat patches (in terms of fire and dryness) were usually unoccupied due to small size or isolation. Modeling across a landscape gradient can help inform management. In this case, prescribed burns can occur less often in drier than wetter parts of the landscape, to support a viable metapopu

  • Title: Large-eddy simulations of an autorotating square flat plate
    Authors: Patricia X. Coronado Domenge, Carlos A. Velez and Tuhin Das
    Location: Applied Mathematical Modelling

    Large-eddy simulation (LES) turbulence models are underdeveloped in the area of fluid-structure interaction (FSI), specifically in autorotation applications. To gain a better understanding of FSI simulations, under the influence of strong turbulent interactions, several LES simulations were conducted to study the autorotation of a thin plate and compared to experimental measurements and RANS simulations found in literature. The plate is allowed to spin freely about its center of mass and is located near the center of a wind tunnel with a free stream velocity of 5 m/s. Wall effects from the wind tunnel enclosure are neglected. In this work, a coupled Computational Fluid Dynamics (CFD) - Rigid Body Dynamics (RBD) model is proposed employing the delayed-detached-eddy simulation (DDES) and the Smagorinsky turbulence models to resolve the subgrid-scale stress (SGS). The qualitative prediction of vortex structures and the qualitative computation of pressure coefficients are in good agreement with experimental results. When compared to RANS, the results from the LES models provide better predictions of the pressure coefficient. Moreover, LES accurately captures the transient behavior of the plate and close correspondence is found between the predicted and measured moment coefficient.

  • Title: Near-Field Effects in Mesoscopic Light Transport
    Authors: R. Rezvani Naraghi, S. Sukhov, J. J. Sáenz, and A. Dogariu

    In dense multiple scattering media, optical fields evolve through both homogeneous and evanescent waves. New regimes of light transport emerge because of the near-field coupling between individual scattering centers at mesoscopic scales. We present a novel propagation model that is developed in terms of measurable far- and near-field scattering cross sections. Our quantitative description explains the increase of total transmission in dense scattering media and its accuracy is established through both full-scale numerical calculations and enhanced backscattering experiments.

  • Title: Biological Agents of Bioremediation: A Concise Review
    Authors: Karabi Biswas, Dipak Paul, Sankar Narayan Sinha
    Location: India

    g to their adulteration. Bioremediation is the use of biological organisms to destroy, or reduce the hazardous wastes on a contaminated site. Bioremediation is the most potent management tool to control the environmental pollution and recover contaminated soil. Use of biological materials, coupled to other advanced processes is one of the most promising and inexpensive approaches for removing environmental pollutants. Bioremediation technology is a beneficial alternative which leads to deg

  • Title: Biological Agents of Bioremediation: A Concise Review
    Authors: Karabi Biswas, Dipak Paul, Sankar Narayan Sinha
    Location: India

    Due to intensive agriculture, rapid industrialization and anthropogenic activities have caused environmental pollution, land degradation and increased pressure on the natural resources and contributing to their adulteration. Bioremediation is the use of biological organisms to destroy, or reduce the hazardous wastes on a contaminated site. Bioremediation is the most potent management tool to control the environmental pollution and recover contaminated soil. Use of biological materials, coupled to other advanced processes is one of the most promising and inexpensive approaches for removing environmental pollutants. Bioremediation technology is a beneficial alternative which leads to degrade of pollutants. This article presents the important biological organisms used in bioremediation technologies.

  • Title: Aeroelastic Impact of a Circumferentially Varying Tip Gap
    Authors: Canon, David & Kapat, Jayanta
    Location: ASME Power & Energy Conference

    The tip leakage flow in axial compressors is a significant factor in engine performance and a subject of investigation over the last several decades. Many studies have already shown that the vortices generated by this tip leakage can have a negative impact on the surrounding flow field and overall performance, and lead to excitations as well. This study examines the effect of these vortices on aeroelasticity, specifically, the effect of a circumferentially varying tip gap; such as that produced by casing ovalization. For this paper, a single passage, structured grid, CFD model of a compressor’s mid-stage rotor-stator configuration was analyzed using StarCCM+’s harmonic balance solver. This was a frequency domain calculation, which provided significant time savings relative to the more conventional time accurate approach. The vibratory results from an Abaqus model were incorporated into the CFD in order to calculate the aerodynamic work. The calculation modeled a circumferentially varying tip gap representative of what is seen in a real engine, and results were compared to solutions from models with circumferentially constant gaps. Furthermore, test data from an industrial gas turbine was utilized in order to recreate realistic levels of tip gap variation, as well as to validate the mechanical model’s vibratory results. The calculations showed that for the gap variation imposed, the work per cycle was increased by 59% relative to a case with constant gaps.

  • Title: QRing - a scaleable, parallel software tool for quantum transport simulations in carbon nanodevices using linear solvers on Intel Xeon/Phi and GPU architectures
    Authors: Jacj, Mark A., Prather, Ben, Byrd, Adam, Durivage, Leon W. & Encinosa, Mario R
    Location: To be submitted to Computer Physics Communications

    Not available.

  • Title: Atomic-scale simulation of space weathering in olivine and orthopyroxene
    Authors: Quadery, A. H., S. Pacheco, A. Au, N. Rizzacasa, J. Nichols, T. Le, C. Glasscock, and P. K. Schelling
    Location: Journal of Geophysical Research Planets

    Classical molecular dynamics was used to study the annealing of anion and cation Frenkel defects in olivine and orthopyroxene minerals. While it was found that for both minerals, reorganization of the Si–O bonds, often accompanied by large Si displacements, occurs to maintain the fourfold coordination of the SiO4 tetrahedra, important differences are observed in their annealing behavior. Specifically, cation defects are substantially more mobile in olivine than in orthopyroxene leading to rapid annihilation of cation Frenkel defects and formation of extended defects in olivine. By contrast, the diffusion rate of anion defects in orthopyroxene is much higher than that in olivine and also exhibits large anisotropy. Consequently, it was found that diffusion in orthopyroxene occurs without significant annihilation of anion Frenkel defects or trapping of anion interstitials or vacancies into clusters. The results obtained here are discussed in the context of space weathering of olivine and orthopyroxene. Specifically, two important observations are made which may explain previous experimental results. First, ion irradiation experiments that show reduced tolerance for radiation damage in orthopyroxene may be explained by the rapid, one-dimensional anion mobility which prevents healing of the lattice. Second, laser heating experiments which show that orthopyroxene has enhanced tolerance to reduction and the evolution of nanophase Fe inclusions could be due to the observed rapid anion diffusion in orthopyroxene, which might allow the bulk to act as a reservoir for the surface.

  • Title: Surface Roughness Parameterization of Mangroves in Central Florida
    Authors: Hovenga, P.A., Medeiros, S.C. & Hagen, S.C.
    Location: 31st ASCE EWRI Water Resources Seminar 2015, Orlando, FL, March 27, 2015

    Not available.

  • Title: Two-photon absorption and two-photon circular dichroism of hexahelicene derivatives: a study of the effect of the nature of intramolecular charge transfer
    Authors: Carlos Dıaz, Yuly Vesga, Lorenzo Echevarria, Irena G. Stara, Ivo Stary, Emmanuel Anger, Chengshuo Shen, Mehdi El Sayed Moussa, Nicolas Vanthuyne, Jeanne Crassous, Antonio Rizzo and Florencio E. Hernandez
    Location: RSC Adv., 2015, 5, 17429–17437

    Herein we report on the theoretical–experimental analysis of the one- and two-photon absorption and circular dichroism spectra of two intrinsically chiral aromatic molecules – hexahelicene derivatives – with helical chirality and intramolecular charge transfer (ICT). The primary outcomes of our investigation demonstrate that the TPA cross-section and the amplitude of the TPCD signal of this type of helicenes are strongly affected by the strength of the ICT and the nature of the extension of the electronic delocalization, i.e. beyond (EXO-ICT) or within (ENDO-ICT) the helicene core. These results were corroborated through the comparative theoretical analysis of the corresponding contributions of the magnetic dipole transition moment and the electric quadrupole transition moment to the TPA rotatory strength on a series of five similar helicene derivatives with different molecular electron delocalization disposition. Two-photon absorption (TPA) and two-photon circular dichroism (TPCD) spectra were obtained using the double L-scan technique over a broad spectral range (400–900 nm) using 90 fs pulses at a low repetition rate (2–50 Hz) produced by an amplified femtosecond system. The theoretical simulations were performed using modern analytical response theory within the Time-Dependent Density Functional Theory (TD-DFT) approach using B3LYP and CAM-B3LYP, and the aug-cc-pVDZ and 6-311++G(d,p) basis sets.

  • Title: Assessment of the tautomeric population of benzimidazole derivatives in solution: a simple and versatile theoretical– experimental approach
    Authors: Carlos Diaz, Ligia Llovera, Lorenzo Echevarria and Florencio E. Hernández
    Location: J. Comput. Aided Mol. Des., 2015, 29, 143–154

    Herein, we present a simple and versatile theoretical–experimental approach to assess the tautomeric distribution on 5(6)-aminobenzimidazole (5(6)-ABZ) derivatives in solution via one-photon absorption. The method is based on the optimized weighted sum of the theoretical spectra of the corresponding tautomers. In this article we show how the choice of exchange-correlation functional (XCF) employed in the calculations becomes crucial for the success of the approach. After the systematic analysis of XCFs with different amounts of exact-exchange we found a better performance for B3LYP and PBE0. The direct test of the proposed method on omeprazole, a well-known 5(6)-benzimidazole based pharmacotherapeutic, demonstrate its broader applicability. The proposed approach is expected to find direct applications on the tautomeric analysis of other molecular systems exhibiting similar tautomeric equilibria.

  • Title: Robust Packing Patterns and Luminescence Quenching in Mononuclear [Cu(II)(phen) 2 ] Sulfates
    Authors: Elena Melnic, Eduard B. Coropceanu, Olga V. Kulikova, Anatolii V. Siminel, Dane Anderson, Hector J. Rivera-Jacquez, Artem E. Masunov, Marina S. Fonari, & Victor Ch. Kravtsov
    Location: J. Phys. Chem. C, 2014, 118 (51), pp 30087–30100

    Three mixed-ligand Cu(II) complexes with compo- sitions [Cu(phen) 2 (SO 4 )]·CH 3 OH (1), [Cu(phen) 2 (SO 4 )]- (H 2 O) 2 (dmf) (2), and [Cu(phen) 2 H 2 O](SO 4 )(H 2 O) 4 (3), where phen = 1,10-phenanthroline and dmf = N,N′-dimethylformamide, were prepared and studied. These compounds belong to the landscape of the mononuclear Cu(phen) 2 sulfates, and the solvated complexes undergo frequent anion/water exchange at the metal center in aqueous solutions. Complexes are similar by the metal trigonal bipyramidal coordination geometry but differ by the mode of enclathration and number of protic and aprotic solvent guest molecules being accommodated in the crystal lattice. Crystal packing in 1−3 is determined by the robust supramolecular patterns that consist of stacking interactions between the planar extended phen fragments. These are observed in all three solids regardless of the interplay of other noncovalent interactions, including rather strong hydrogen bonds. The dual luminescence is detected at 580 and 470 nm for both crystals of phen and 3. Detailed analysis of singlet and triplet excitations in phen and 3 is performed by time-dependent density functional methods. Fluorescence is predicted with a low quantum yield at 386 nm, and dual phosphorescence from n−π* and π−π* triplet states is predicted at 523 and 496 nm. Emission quenching was demonstrated for 3 and explained by nonradiative decay involving supramolecular stacking and low-lying metal-centered states.

  • Title: Theoretical study of two-photon circular dichroism on molecular structures simulating aromatic amino acid residues in proteins with secondary structures
    Authors: Yuly Vesga, Carlos Diaz and Florencio E. Hernandez
    Location: RSC Adv., 2014, 4, 60974–60986

    Herein, we report on the calculation and the comparative analysis of the theoretical two-photon circular dichroism (TPCD) spectra of L-histidine (His), L-phenylalanine (Phe), and L-tyrosine (Tyr) simulating residues in proteins with secondary structures (α-helix, β-strand and random coil), down to the far-UV region (FUV). This work exposes unique signatures in the FUV for each conformer in each configuration. The outcomes of this research show how FUV-TPCD can be used to study peptide and protein structures in a region never evaluated before but packed with important structural information.

  • Title: Two-Photon Absorption Spectra Predicted by Semiempirical Methods
    Authors: Nayyar, I. H. & Masunov, A. E.
    Location: Submitted to J. Theoretical and Computational Nanoscience

    The molecular markers with large two-photon absorption cross-sections are highly sought for many applications, from photodynamic therapy to optical information processing. One may envision computational design of the chromophores combining desirable one- and two-photon absorption (1PA and 2PA) optical features with other properties important for the specific applications (solubility, toxicity etc.). Semiempirical methods are fast and seem to be well suited for the high throughput computational screening, which may be a part of such rational design strategy. Here we apply several semiempirical methods for prediction of 2PA spectra for substituted olygophenylvinylenes of donor-acceptor type. The predictions are compared to the experiment and previously reported results of the density functional theory (DFT) methods. We find ZINDO/S spectroscopic parameterization combined with single configuration interaction (CIS) method to perform far superior to the general purpose PM6 parameterization combined with various CI schemes. The poor performance in the prediction of 2PA cross-sections at PM6 level is traced to inaccurate excitation energies and incorrect transition dipoles between the 1PA and 2PA states. The state-to-state transition dipoles predicted by the ZINDO/S method are much better, as 2PA cross-sections reach the accuracy comparable to TD-DFT predictions after empirical corrections to the excitation energies. We conclude that semiempirical parameterizations can be used only for qualitative analysis of the 2PA properties. The excitation energies are in need of empirical correction, such as QSPR a linear regression for specific class of molecules. The ZINDO/S parameterization combined with multi-reference CI schemes (such as MR-CIS) could yield a good description of the intensities of 1PA and 2PA excitations, provided the right selection in reference configurations, order of excitation and active space. It can not be considered a black-box method, which makes it unsuitable choice for the high throughput screening technique.

  • Title: Predictions of the Spin Configuration in Mn 12 Molecular Magnets Made Accurate with the Help of Hubbard U on the Ligand Atoms
    Authors: Shruba Gangopadhyay, Artem E. Masunov & Svetlana Kilina
    Location: J. Phys. Chem. C, 2014, 118 (35), pp 20605–20612

    We predict Heisenberg exchange coupling J values between all metal centers for two different Mn 12 -based molecular complexes. Both wheels are reported to have the ground spin state of multiplicity 15 and weak antiferromagnetic couplings between two identical halves. The correct sign and order of the exchange couplings for all six magnetic interactions are predicted for the first time and are in agreement with experimental observations. Empirical tuning of the Hubbard repulsion term U for both metal and ligand atoms and geometrical optimization of the ground spin state were found to be crucial for accurate prediction of J values in the magnetic wheels.

  • Title: Molecular Packing in Organic Solar Cell Materials: Insights from the Emission Line Shapes of P3HT/PCBM Polymer Blend Nanoparticles
    Authors: Angela M. Crotty, Alicia N. Gizzi, Hector J. Rivera-Jacquez, Artem E. Masunov, Zhongjian Hu, Jeff A. Geldmeier & Andre J. Gesquiere
    Location: J. Phys. Chem. C, 2014, 118 (34), pp 19975–19984

    Semiconducting polymer devices have seen tremendous progress in development of material and device designs, while device efficiencies have made substantial gains. Still, the effect of material morphology on the optoelectronic properties of semiconducting polymers is not completely understood even though these materials make up the active device layer. In this study we use computational methods to simulate different poly(3-hexylthiophene) (P3HT) morphologies, predict their emission spectra, and compare them to experimentally observed emission spectra for P3HT nanoparticles. We use published X-ray diffraction data on P3HT polymorphs to build the molecular models of nanodomains that differ in the side-chain packing. The atomic and electronic structures of both nanodomains are studied with the force field, Hartree−Fock, CIS, and density functional theory methods. The results confirm the coexistence of type I and II nanodomains, where the shift of the backbones in the same stack is determined by the differences in side-chain packing. Upon excitation, the polymer chains in type II domain are free to slide to their optimal arrangement in the stack, whereas in type I domain this sliding is hindered by the steric repulsion of the side chains and the chains are essentially constrained to keep the ground state geometry. These nanodomains, therefore, differ in their emission spectra: type I emission has a single 0−0 vibronic band, while type II demonstrates pronounced vibronic progression. In agreement with Frenkel exciton theory, splitting of the excited state depends on the longitudinal shift of the π-systems. However, we find that due to the constraints arising from P3HT being confined in nanosized particles, the type I nanodomain increasingly appears as an additional emitter that exhibits J-aggregate character. As a result, a pronounced vibronic structure appears as PCBM blending ratios increase, as opposed to the changes in emission profile due to a different degree of disorder present in weakly coupled H-aggregates. These findings are distinct from those made for bulk P3HT materials.

  • Title: Polymeric Luminescent Zn(II) and Cd(II) Dicarboxylates Decorated by Oxime Ligands: Tuning the Dimensionality and Adsorption Capacity
    Authors: Lilia Croitor, Eduard B. Coropceanu, Artem E. Masunov, Hector J. Rivera-Jacquez, Anatolii V. Siminel, Vyacheslav I. Zelentsov, Tatiana Ya. Datsko & Marina S. Fonari
    Location: Cryst. Growth Des., 2014, 14 (8), pp 3935–3948

    Ten Zn(II) and Cd(II) metal−organic materials were synthesized and studied by the X-ray method. Among these 10 structures, two represent binuclear clusters, and two are one-dimensional (1D) coordination polymers, while five are laminar two-dimensional (2D) solids and one is the three-dimensional (3D) framework. The investigation has been aimed at rational design of coor- dination polymers decorated by oxime ligands to increase the accessible adsorption area in these newly synthesized solids. The ligands used include three aliphatic dicarboxylic acids, HOOC-(CH 2 ) n -COOH [n = 1, 2, 4 corresponding to malonic (H 2 mal), succinic (H 2 suc), and adipic (H 2 adi) acids], and three neutral oxime ligands [pyridine-2-aldoxime (2-pyao), pyridine-4-aldoxime (4-pyao), and 1,2- cyclohexanedionedioxime (Niox)]. These novel hybrid solids with the compositions [Zn 2 (suc) 2 (2-pyao) 4 ]·2H 2 O 1, [Cd 2 (suc)(2-pyao) 4 (H 2 O) 2 ][BF 4 ] 2 2, [Cd(suc)- (2-pyao) 2 ] n 3, [Zn(mal)(4-pyao)(H 2 O)] n 4, [Cd(mal)(4-pyao)(H 2 O)] n 5, [Zn- (suc)(4-pyao)] n 6, [Zn(adi)(4-pyao) 2 ] n 7, {[Cd(adi)(4-pyao) 2 ]·dmf} n 8, [Zn- (adi)(Niox)] n 9, and [Cd(adi)(Niox)] n 10 [dmf − N,N′-dimethylformamide] demonstrate a variable class of coordination supramolecular architectures dictated by the distinctions in the metals’ and oxime ligands’ coordination capacities and preferences, and length and flexibility of the dicarboxylic linkers. The discrete aggregates 1 and 2 differ by the components’ ratio and conformation of the bridging succinate anion; compounds 3 and 7 are 1D arrays, and compounds 4, 5, 6, 8, and 9 represent 2D layers of different topologies. Compound 10 is a 3D grid afforded by the concerted contribution of the longest in this series adipate anion, and the bigger atomic radius Cd(II) vs. Zn(II). The adsorptive properties of 7 and 9 are reported. For the laminar solid 9, the quantum chemical simulations of the adsorption capacity are in line with the experimental results. All new materials reveal dual green-blue wavelength emission in the solid state.

  • Title: Design and Electronic Structure of New Styryl Dye Bases: Steady- State and Time-Resolved Spectroscopic Studies
    Authors: N. V. Bashmakova, Ye. O. Shaydyuk, S. M. Levchenko, A. E. Masunov, O. V. Przhonska, J. L. Bricks, O. D. Kachkovsky, Yu. L. Slominsky, Yu. P. Piryatinski, K. D. Belfield, & M. V. Bondar
    Location: J Phys Chem A.;118(25):4502-9

    A comprehensive investigation of the electronic structure and fast relaxation processes in the excited states of new styryl base-type derivatives was performed using steady-state, pico-, and femtosecond time-resolved spectroscopic techniques. Linear photophysical parameters of new compounds, including steady- state absorption, fluorescence, and excitation anisotropy spectra, were obtained in a number of organic solvents at room temperature. A detailed analysis of the fluorescence lifetimes and ultrafast relaxation processes in the electronically excited state of the styryl bases revealed an important role of solvate dynamics and donor− acceptor strength of the molecular structures in the formation of their excited state absorption spectra. Experimental data were in good agreement with quantum chemical calculations at the time dependent density functional theory level, combined with a polarizable continuum model.

  • Title: Mechanism of Nonlinear Optical Enhancement and Supramolecular Isomerism in 1D Polymeric Zn(II) and Cd(II) Sulfates with Pyridine-4-aldoxime Ligands
    Authors: Lilia Croitor, Eduard B. Coropceanu, Artëm E. Masunov, Hector J. Rivera-Jacquez, Anatolii V. Siminel & Marina S. Fonari *†
    Location: J. Phys. Chem. C, 2014, 118 (17), pp 9217–9227

    Interaction of zinc(II) and cadmium(II) sulfates with pyridine-4-aldoxime (4-pyao) and pyridine-4- amidoxime (4-pyamo) ligands resulted in four 1D metal− organic materials (MOMs) with identical composition, [M(SO 4 )A 2 (H 2 O) 2 ] n , where M = Zn(II), A = 4-pyao for 1, M = Cd(II), A = 4-pyao for 2, M = Zn(II), A = 4-pyamo for 3, M = Cd(II), A = 4-pyamo for 4, and mononuclear [Zn(SO 4 )(4-pyamo) 2 (H 2 O) 3 ] 5. New coordination polymers represent the mixed-ligand supramolecular isomers different by the twisting of two pyridine-4-oxime ligands in the metal coordination environments, and crystallizing in the different space groups. Conformational preferences and nonlinear optical properties of the 4-pyao and 4-pyamo complexes were investigated using density functional theory. Spectral properties of 1−3 have been also evaluated. The solid-state emission of 1D polymers 1−3 appears to be ligand-based, as the positions of the emission maxima remain practically unchanged from free ligand to complexes. The enhancement of luminescence and two- photon absorption in polymers in comparison with the pure ligands is attributed to the chelation of the ligand to the metal center. The detailed mechanism of this enhancement upon complex formation is analyzed and can be used in future design of metal−organic nonlinear optical materials.

  • Title: Zinc deficiency induces apoptosis via mitochondrial p53- and caspase-dependent pathways in human neuronal precursor cells
    Location: India

    Previous studies have shown that zinc deficiency leads to apoptosis of neuronal precursor cells in vivo and in vitro. In addition to the role of p53 as a nuclear transcription factor in zinc deficient cultured human neuronal precursors (NT-2), we have now identified the translocation of phosphorylated p53 to the mitochondria and p53-dependent increases in the pro-apoptotic mitochondrial protein BAX leading to a loss of mitochondrial membrane potential as demonstrated by a 25% decrease in JC-1 red:green fluorescence ratio. Disruption of mitochondrial membrane integrity was accompanied by efflux of the apoptosis inducing factor (AIF) from the mitochondria and translocation to the nucleus with a significant increase in reactive oxygen species (ROS) after 24 h of zinc deficiency. Measurement of caspase cleavage, mRNA, and treatment with caspase inhibitors revealed the involvement of caspases 2, 3, 6, and 7 in zinc deficiency-mediated apoptosis. Down-stream targets of caspase activation, including the nuclear structure protein lamin and polyADP ribose polymerase (PARP), which participates in DNA repair, were also cleaved. Transfection with a dominant-negative p53 construct and use of the p53 inhibitor, pifithrin- ␮, established that these alterations were largely dependent on p53. Together these data identify a cascade of events involving mitochondrial p53 as well as p53-dependent caspase-mediated mechanisms leading to apoptosis during zinc deficiency.

  • Title: Two-photon circular dichroism of molecular structures simulating L-tryptophan residues in proteins with secondary structures
    Authors: Yuly Vesga, Carlos Diaz, Mary Higgs and Florencio E. Hernandez
    Location: Chem. Phys. Lett., 2014, 601, 6–12

    Herein, we report on the calculation and the comparative analysis of the theoretical two-photon circular dichroism (TPCD) spectra of l-tryptophan (Trp) residues in proteins with secondary structures (α-helix, β-strand and random coil) conformation, down to the far-UV region (FUV). The examination of the TPCD spectra of the different conformers in each configuration reveals distinctive fingerprints in the FUV, a dark spectral region for electronic circular dichroism (ECD). Our results show the potential of FUV-TPCD to identify and study protein structures in a region never assessed before but filled with important structural information.

  • Title: Adsorption of Glyoxal (CHOCHO) and Its UV Photolysis Products on the Surface of Atmospheric Ice Nanoparticles. DFT and Density Functional Tight-Binding Study
    Authors: Stanislav K. Ignatov, Oleg B. Gadzhiev, Alexey G. Razuvaev, Artem E. Masunov & Otto Schrems
    Location: J. Phys. Chem. C, 2014, 118 (14), pp 7398–7413

    The structures, energies, harmonic vibrational frequencies, and thermodynamic parameters of the water clusters (H 2 O) 48 , (H 2 O) 72 , and (H 2 O) 270 were calculated using the standard DFT theory (BLYP/6-31++G(d,p) for small and medium clusters) and the modern tight-binding method SCC-DFTB (DFTBA and DFTB+). The adsorption and embedding of s-cis- and s-trans-glyoxal molecules as well as its sunlight UV photolysis products (molecules CH 2 O, HCOOH, H 2 O 2 , CO, CO 2 and radicals CHO, HO, HO 2 ) on nanosized ice clusters of up to 2.5 nm in diameter were studied within the above theoretical models. The structures of adsorption complexes on different sites of ice nanoparticles, the corresponding adsorption energies and thermodynamic parameters were estimated. We found that the DFTB method is a very promising tool for the calculations of structures and energies of ice nanoparticles, when compared to both DFT and semiempirical (PM3) methods. The obtained results are discussed in relation to the possible photolysis pathways, the reaction rates in the gas phase and in the adsorbed state, and the mechanisms of glyoxal photolysis catalyzed by the ice nanoparticles in the Earth’s atmosphere.

  • Title: Giant Faraday effect due to the Pauli exclusion principle in 3D topological insulators
    Authors: Hari P. Paudel & Michael N. Leuenberger
    Location: Journal of Physics: Condensed Matter

    Experiments using ARPES, which is based on the photoelectric effect, show that the surface states in 3D topological insulators (TI) are helical. Here we consider Weyl interface fermions due to band inversion in narrow-bandgap semiconductors, such as Pb_(1-x) Sn_x Te. The positive and negative energy solutions can be identified by means of opposite helicity in terms of the spin helicity operator in 3D TI. Using the 3D Dirac equation and bandstructure calculations we show that the transitions between positive and negative energy solutions, giving rise to electron-hole pairs, obey strict optical selection rules. In order to demonstrate the consequences of these selection rules, we consider the Faraday effect due to the Pauli exclusion principle in a pump/probe setup using a 3D TI double interface of a PbTe/Pb0:31Sn0:69Te/PbTe heterostructure. For that we calculate the optical conductivity tensor of this heterostructure, which we useto solve Maxwell’s equations. The Faraday rotation angle exhibits oscillations as a function of probe wavelength and thickness of the heterostructure. The maxima in the Faraday rotation angle are of the order of millirads.

  • Title: Single-Layer MoS2 with Sulfur Vacancies: Structure and Catalytic Application
    Authors: Le, Duy and Rawal, Takat B. & Rahman, Talat S.
    Location: The Journal of Physical Chemistry C 2014 118(10) 5346-5351

    Single-layer MoS2 is proving to be a versatile material for a wide variety of electronic, optical, and chemical applications. Sulfur depletion, without destabilization of the single layer, is considered a prudent way for making the basal plane of the layer catalytically active. Based on the results of our density-functional-theory examination of vacancy structures on one side of an MoS2 layer, we show that the formation energy per sulfur vacancy is the lowest (energetically favorable) when the vacancies form a row and that the longer the row, the lower the formation energy. In addition, we find that the lowest energy barrier for the diffusion of sulfur vacancy at the row structures through the exchange of a vacancy with a nearby sulfur atom is 0.79 eV and that this barrier increases as the row elongates. We also evaluate the propensity for catalytic activity of an MoS2 layer with two types of sulfur-vacancy structures (row and patch) and find the energetics for alcohol synthesis from syngas to be more favorable for the layer with a sulfur-vacancy patch.

  • Title: Dynamics of sea level rise and coastal flooding on a changing landscape
    Authors: M.V. Bilskie, S.C. Hagen, S.C. Medeiros & D.L. Passeri
    Location: Geophysical Research Letters February 2014

    Standard approaches to determining the impacts of Sea Level Rise (SLR) on storm surge flooding employ numerical models reflecting present conditions with modified sea states for a given SLR scenario. In this study, we advance this paradigm by adjusting the model framework so that it reflects not only a change in sea state, but also variations to the landscape (morphologic changes and urbanization of coastal cities). We utilize a numerical model of the Mississippi and Alabama coast to simulate the response of hurricane storm surge to changes in sea level, Land Use Land Cover (LULC), and land surface elevation for past (1960), present (2005), and future (2050) conditions. The results show that the storm surge response to SLR is dynamic and sensitive to changes in the landscape. We introduce a new modeling framework that includes modification of the landscape when producing storm surge models for future conditions.

  • Title: Structure and properties of cerium oxides in bulk and nanoparticulate forms
    Authors: Shruba Gangopadhyay, Dmitry D. Frolov, Artëm E. Masunov, & Sudipta Seal
    Location: J. Chem. Phys. 2014 584 pp 199-208

    The experimental and computational studies on the cerium oxide nanoparticles, as well as stoichiometric phases of bulk ceria are reviewed. Based on structural similarities of these phases in hexagonal aspect, electroneutral and non-polar pentalayers are identified as building blocks of type A sesquioxide structure. The idealized core/shell structure of the ceria nanoparticles is described as dioxide core covered by a single pentalayer of sesquioxide, which explains the exceptional stability of subsurface vacancies in nanoceria. The density functional theory (DFT) predictions of the lattice parameters and elastic moduli for the Ce(IV) and Ce(III) oxides at the hybrid DFT level are also presented. The calculated values for both compounds agree with available experimental data and allow predicting changes in the lattice parameter with decreasing size of the nanoparticles. The lattice parameter is calculated as equilibrium between contraction of sesquioxide structure in the core, and expansion of dioxide structure in the shell of the nanoparticle. This is consistent with available XRD data on ceria NPs obtained in mild aqueous conditions. The core/shell model, however, breaks down when applied to the size dependence of lattice parameter in NPs obtained by the laser ablation techniques.

  • Title: Two-Photon Circular Dichroism of an Axially Dissymmetric Diphosphine Ligand with Strong Intramolecular Charge Transfer
    Authors: Carlos Diaz, Lorenzo Echevarria, Antonia Rizzo & Florencio E. Hernandez
    Location: The Journal of Physical Chemistry A 2014 118(5) pp 940-946

    In this article we report on the study of the polarization dependent two-photon absorption (TPA) of (S)-(+)-(1,1′-binaphthalene-2,2′-diyl)bis(diphenylphosphine) (S-BINAP) in solution, and the theoretical-experimental analysis of its two-photon circular dichroism (TPCD) spectrum. The comparative examination of the following two correlation functionals, using the 6-31G* basis set, showed that the Coulomb attenuated method variant of the Becke’s three-parameter exchange and the Lee–Yang–Parr (CAM-B3LYP) is more reliable than B3LYP in molecules such as S-BINAP, a heteroaromatic diphosphine chiral ligand with strong intramolecular charge transfer. To access the theoretical TPCD spectra, we employed time dependent density functional theory (TD-DFT) at the mentioned level of theory and over the first 40 electronic excited states including solvent effects by means of the polarizable continuum model (PCM). The extended calculation on twice as many electronic excited states in vacuo proved to be crucial for the correct assignment of the experimental bands. TPA measurements were performed in the femtosecond regime and over a broad spectral range using the double L-scan technique.

  • Title: Establishing Accurate High-Resolution Crystal Structures in the Absence of Diffraction Data and Single Crystals – an NMR Approach
    Authors: Keyton Kalakewich, Robbie Iuliucci & James K. Harper
    Location: Crystal Growth and Design 2013 13(12) pp 5391–5396

    Predicting accurate crystal structures from theoretical consideration has proven to be remarkably challenging. Although significant progress has been made and numerous approaches have now been investigated, selection of the correct structure as the first choice in blind studies is still rarely achieved. Here a process is described that consistently identifies the correct structure from the myriad candidates created from typical crystal structure prediction software. This approach relies on 13C solid-state NMR data and a secondary refinement process that includes lattice fields. Four structures are considered, and in all cases the correct structure is selected as the first choice and the only statistically feasible candidate. Data from 13C chemical shift tensor principal values are found to provide better selectivity, but 13C isotropic shifts also consistently identify the correct structure. This process involves only experimental NMR data and computer-generated structures, yet the structures created appear to rival the accuracy of structures derived from single crystal diffraction methods including single crystal neutron diffraction.

  • Title: Effect of aberrations in a holographic system on reflecting volume Bragg gratings
    Authors: Marc SeGall, Daniel Ott, Ivan Divliansky & Leonid B. Glebov
    Location: Applied Optics 2013 52(32) pp 7826-7831

    The effect of aberrations in the recording beams of a holographic setup is discussed regarding the deterioration of properties of a reflecting volume Bragg grating. Imperfect recording beams result in a spatially varying grating vector, which causes broadening, asymmetry, and washed out side lobes in the reflection spectrum as well as a corresponding reduction in peak diffraction efficiency. These effects are more significant for gratings with narrower spectral widths.

  • Title: Polarization dependent two-photon absorption spectroscopy on a naturally occurring biomarker (curcumin) in solution: A theoretical–experimental study
    Authors: Jose A. Tiburcio-Moreno, J.J. Alvarado-Gil, Carlos Diaz, Lorenzo Echevarria & Florencio E. Hernández
    Location: Chemical Physics Letters 2013 583 pp 160-164

    We report on the theoretical–experimental analysis of the two-photon absorption (TPA) and two-photon circular-linear dichroism (TPCLD) spectra of (1E,6E)-1,7-bis(4-hydroxy-3-methoxyphenyl)-1,6-heptadiene-3,5-dione (curcumin) in Tetrahydrofuran (THF) solution. The measurement of the full TPA spectrum of this molecule reveals a maximum TPA cross-section at 740 nm, i.e. more than 10 times larger than the maximum reported in the literature at 800 nm for the application of curcumin in bioimaging. The TPCLD spectrum exposes the symmetry of the main excited-states involved in the two-photon excitation process. TD-DFT calculations support the experimental results. These outcomes are expected to expand the application of natural-occurring dyes in bioimaging.

  • Title: Full length amylin oligomer aggregation: insights from molecular dynamics simulations and implications for design of aggregation inhibitors
    Authors: Workalemahu Mikre Berhanu & Artëm E. Masunov
    Location: Journal of Biomolecular Structure and Dynamics 2013 pp 1-19

    Amyloid oligomers are considered to play essential roles in the pathogenesis of amyloid-related degenerative diseases including type 2 diabetes. Using an explicit solvent all atomic MD simulation, we explored the stability, conformational dynamics and association force of different single-layer models of the full-length wild-type and glycine mutants of amylin (pentamer) obtained from a recent high resolution fibril model. The RMSF profile shows enhanced flexibility in the disorder (Lys1-Cys7) and turn region (Ser19-Gly23), along with smallest fluctuation at the residues (Asn14-Phe15-Leu16-Val17-His18) of β1 region and (Ala25-Ile26-Leu27-Ser28-Ser29) of the β2 region. We obtained a significant difference in backbone RMSD between the wild-type and the mutants, indicating that mutations affected the stability of the peptide. The RMSD and RMSF profiles indicate the edge and loop residues are the primary contributors to the overall conformational changes. The degree of structural similarity between the oligomers in the simulation and the fibril conformation is proposed as the possible explanation for experimentally observed shortening of the nucleation lag phase of amylin with oligomer seeding. On the basis of structure-stability findings, the β1 and β2 portions are optimal target for further anti-amyloid drug design. The MM-PBSA binding energy calculation reveals the binding of amylin: amylin strands in single layer is dominated by contributions from van der Waals interactions. The non-polar solvation term is also found to be favorable. While the electrostatic interactions and polar solvation energy was found to be favorable for the interaction for the larger aggregate and unfavorable for the smaller aggregates. A per-residue decomposition of the binding free energy has been performed to identify the residues contributing most to the self-association free energy. Residues found in the β-sheet regions were found to be key residue making the largest favorable contributions to the single-layer association. The result from our simulation could be used in rational design of new amylinomimetic agent, amylin aggregation inhibitors and amylin-specific biomarkers.

  • Title: Permanent dipole moments and energies of excited states from density functional theory compared with coupled cluster predictions: Case of para-nitroaniline
    Authors: Mikhailov, I. A., Musial, M. & Masunov, A. E.
    Location: Computation and Theoretical Chemistry

    Different ways to extract properties of excited states from time-dependent density functional theory (TD-DFT) calculations are compared to ab initio results obtained with the Equation of Motion Coupled Cluster approach. The recently proposed a posteriori Tamm–Dancoff approximation (ATDA) predicts the perma-nent dipole moments to be underestimated by 25% on average, close to the results of the relaxed density TD-DFT formalism, quadratic response formalism, and numerical energy derivatives, while the unrelaxed density approximation results are less accurate (40% overestimate). We also propose a correction for TD-DFT excitation energies, which are known to be problematic for charge transfer states. The static DFT energies evaluated on the relaxed densities of the excited states are found to be more accurate than TD-DFT excitation energies (RMSD is 0.7 eV vs. 1.1 eV, while maximum deviation is À1.0 eV vs. À2.0 eV). This validates ATDA for description of nonlinear optical properties of donor–acceptor mole-cules, exemplified by para-nitroaniline, and extends this method to improve the excitation energy predictions.

  • Title: Supramolecular step in design of nonlinear optical materials: Effect of π…π stacking aggregation on hyperpolarizability
    Authors: Kyrill Yu Suponitsky & Artëm E. Masunov
    Location: J. Chem. Phys. 2013 139

    Theoretical estimation of nonlinear optical (NLO) properties is an important step in systematic search for optoelectronic materials. Density functional theory methods are often used to predict first molecular hyperpolarizability for compounds in advance of their synthesis. However, design of molecular NLO materials require an estimation of the bulk properties, which are often approximated as additive superposition of molecular tensors. It is therefore important to evaluate the accuracy of this additive approximation and estimate the extent by which intermolecular interactions influence the first molecular hyperpolarizability β. Here we focused on the stacking aggregates, including up to 12 model molecules (p NA and ANS) and observed enhancement and suppression of molecular hyperpolarizability relative to the additive sum. We found that degree of nonadditivity depends on relative orientation of the molecular dipole moments and does not correlate with intermolecular interaction energy. Frenkel exciton model, based on dipole-dipole approximation can be used for qualitative prediction of intermolecular effects. We report on inaccuracy of this model for the molecules with long π-systems that are significantly shifted relative to each other, when dipole-dipole approximation becomes inaccurate. To obtain more detailed information on the effect of intermolecular interactions on β we proposed electrostatic approach which accounts for the mutual polarization of the molecules by each other. We measure the induced polarization of each molecule in the aggregate by the charge of its donor (or acceptor) group. The proposed approach demonstrates linear correlation β FF vs β elm (estimated by finite field theory and electrostatic model, respectively) and allows decomposition of the hyperpolarizability for a molecular aggregate into separate molecular contributions. We used this decomposition to analyze the reasons of deviation of aggregate β from additivity, as well as the cooperative effect of intermolecular interactions on hyperpolarizability for stacks of growing size. In cases of positive cooperativity (enhancement), we found 6–8 molecules to be necessary to reach the asymptotic limit. In more frequent cases of negative cooperativity two opposite factors play role. The first one consists of direct lowering of β due to repulsive dipole-dipole interactions. The second factor is originated in a decrease of molecular dipole moments, which in turn leads to a decrease of dipole-dipole repulsion, and therefore increases β. For strong intermolecular repulsive dipole-dipole interactions these effects nearly cancel each other. In such cases the trimers and even dimers are sufficient to reach the asymptotic limit of the infinite stacks. Based on the observed trends we estimated non-additive correction to β for well known NLO crystals NPAN and MNMA. In the case of NPAN, stacking effect on molecular hyperpolarizability represents the leading component of the crystal packi

  • Title: From discrete molecules to one-dimensional coordination polymers containing Mn(II) Zn(II) or Cd(II) pyridine-2-aldoxime building unit
    Authors: Croitor L., Coropceanu, E. B., Siminel, A. V., Masunov, A. E., Fonari, M. S.
    Location: Polyhedron

    The syntheses, spectroscopic characterization and crystal structures for eight coordination compounds [Cd(HCO2)2(pya)2] (1), {[M(bdc)(pya)].1.5DMF}n (M = Mn(II), Zn(II), Cd(II) (2–4), [Zn(SO4)(pya)(H2O)3](H2O) (5), [(ZnSO4)2(pya)4] DMF.2H2O (6), [Zn(SO4)(pya)(H2O)2]n (7), and [Cd(SO4)(pya)(H2O)]n (8) [pya = pyridine-2-aldoxime, bdc = 1,4-benzenedicarboxylate, DMF = N,N′-dimethylformamide] are reported. Compounds 1–4 and 6 contain two, while 5, 7, and 8 contain one neutral pya ligand coordinated in a chelate mode to the metal center through the Npyridyl and Noxime atoms. The dicarboxylic bdc anions provide an access to 1D polymeric arrays in 2–4. The hybrid sulfates including discrete mononuclear (5), binuclear (6), and 1D polymeric (7, 8) coordination arrays were obtained due to different binding modes of coordinated sulfate anion. While solid state fluorescence of new polymeric compounds 2–4 is similar to that of the H2bdc ligand, a rare dual emission is observed for compounds 7 and 8. According to TD-DFT calculations, emission at 400 and 650 nm originates from nπ∗ and ππ∗ states of the pya ligand respectively.

  • Title: Conformational Study of an Axially Chiral Salen Ligand in Solution using Two-Photon Circular Dichroism and the Fragment-Recombination Approach
    Authors: Carlos Díaz, Lorenzo Echevarria & Florencio E. Hernández
    Location: The Journal of Physical Chemistry A 2013 117(35) pp 8416–8426

    Herein we report on the conformational study of a chiral Salen ligand, AFX-155, in THF solution using two-photon absorption (TPA) and, even more importantly, two-photon circular dichroism (TPCD). The fragment-recombination approach (FRA), employed to perform computations on half-AXF-155 (AXF-169′) and the center (C-AXF-155), allowed us to overcome the current computational limitations found in calculations of the TPCD spectra of large molecules. The comparative experimental–theoretical analysis of AXF-155 showed that its TPA is mainly determined by AXF-169′ and validated, through TPCD, the presence of the two dominant Trans_R-Intra(NHB)//Trans_R-Extra(HB) and Trans_R-Intra(NHB)//Trans_R-Extra(NHB) structure in THF with a ΔΔ propeller chirality on the diphenylamine moieties at the end of each AXF-169′. The application of FRA for the analysis of the TPCD spectra of large chiral molecules has been proven to be effective.

  • Title: Preparation Characterization and Electronic Structure of Asymmetric Isonaphthalimide: Mechanism of Dual Fluorescence in Solid State
    Authors: Eduard V. Ganin, Artëm E. Masunov, Anatolii V. Siminel & Marina S. Fonari
    Location: J. Phys. Chem. C 2013 117(35) pp 18154-18162

    The asymmetric isonaphthalene imide, 3-[(4-nitrophenyl)imino]-1H,3H-benzo[de]isochromen-1-one was obtained by condensation of 1,8-naphthoylchloride with p-nitroaniline in the presence of pyridine. The crystal structure and vibrational and electronic absorption spectra are reported. The emission spectrum of the crystalline phase demonstrates dual luminescence, with short and long wavelength components, while only the short wavelength component is present in chloroform solution. The geometrical and electronic structures of the ground and excited states of the molecule are investigated using density functional theory methods. Dual fluorescence is explained in terms of the excited states of different nature. The spectroscopic properties of newly synthesized compounds for possible biosensor applications are discussed.

  • Title: Deactivation of Cu2O(100) by CO Poisoning
    Authors: Sampyo Hong, Duy Le & Talat S. Rahman
    Location: Topics in Catalysis 2013 56(12) pp 1082-1087

    We have performed kinetic Monte Carlo (KMC) simulations of 13 reaction processes for CO oxidation on the O-terminated Cu2O(100) surface to calculate the conversion rate of CO to CO2. We find that CO adsorption at O vacancy sites prevents dissociative adsorption of O2 onto the Cu2O(100) surface and accordingly CO oxidation of the Cu2O(100) surface is poisoned by CO. As a result, we could obtain a 100 % conversion rate only for a brief period of time.

  • Title: Comparison of TD-DFT Methods for the Calculation of Two-Photon Absorption Spectra of Oligophenylvinylenes
    Authors: Iffat H. Nayyar, Artëm E. Masunov, & Sergei Tretiak
    Location: J. Phys. Chem. C 2013 117(35) pp 18170–18189

    We investigate the accuracy of different formalisms within density functional theory in prediction of two-photon absorption (2PA) spectra for substituted oligophenylvinylenes compared to the experimental measurements. The quadratic response methods are compared with the recently proposed a posteriori Tamm–Dancoff approximation (ATDA) and previously published third-order coupled electronic oscillator results. Quadratic response is found to overestimate the cross sections in all cases. We trace the reasons to unreliable excited state description above the ionization threshold. In addition, quadratic response lacks the double excitations so that their contributions to the 2PA spectra are redistributed over the nearest single character excitations. This distorts the individual contributions to the 2PA response and affects the overall picture. For this reason, we do not recommend quadratic response for the essential state analysis, while ATDA can be used both for the 2PA predictions and the structure/property correlations. As an illustration for ATDA based essential state analysis, we report the mechanism of large 2PA in symmetric donor/acceptor substituted polyphenylvinylene (PPV) oligomers. While HOMO–LUMO transition provides the only bright intermediate state, the brightness of the one-photon absorption (1PA) to 2PA transition is associated with symmetric to asymmetric linear combination of the respective donor (HOMO – 1 to HOMO) or acceptor (LUMO to LUMO + 1) fragment orbitals of the donor or acceptor substituents. We also study the effect of the fraction of Hartree–Fock (HF) exchange on 2PA excitation energies and cross sections. Higher exchange (BMK and M05-2X) and range separated (CAM-B3LYP) hybrid functionals are found to yield rather inaccurate predictions both quantitatively and qualitatively. The results obtained with the long-range corrected functional LC-BLYP do not seem to be useful at all. This failure of the exchange-correlation functionals with the correct asymptotic is traced to inaccurate transition dipoles between the valence states, where only functionals with lower HF exchange succeed. A new sum over states (SOS) cutoff procedure is proposed to compensate for the collapse of the higher-lying excited states obtained with the hybrid functionals.

  • Title: Solid-State NMR Characterization of the Molecular Conformation in Disordered Methyl α-l-Rhamnofuranoside
    Authors: James K. Harper, Derek Tishler, David Richardson, John Lokvam, Robert Pendrill & Göran Widmalm
    Location: J. Phys. Chem. A 2013 117 (26) pp 5534–5541

    A combination of solid-state 13C NMR tensor data and DFT computational methods is utilized to predict the conformation in disordered methyl α-l-rhamnofuranoside. This previously uncharacterized solid is found to be crystalline and consists of at least six distinct conformations that exchange on the kHz time scale. A total of 66 model structures were evaluated, and six were identified as being consistent with experimental 13C NMR data. All feasible structures have very similar carbon and oxygen positions and differ most significantly in OH hydrogen orientations. A concerted rearrangement of OH hydrogens is proposed to account for the observed dynamic disorder. This rearrangement is accompanied by smaller changes in ring conformation and is slow enough to be observed on the NMR time scale due to severe steric crowding among ring substituents. The relatively minor differences in non-hydrogen atom positions in the final structures suggest that characterization of a complete crystal structure by X-ray powder diffraction may be feasible.

  • Title: Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics
    Authors: Gongpu Zhao, Juan R. Perilla, Ernest L. Yufenyuy, Xin Meng, Bo Chen, et. al.
    Location: Nature 497 pp. 643–646

    Retroviral capsid proteins are conserved structurally but assemble into differentmorphologies1. The mature human immunodeficiency virus-1 (HIV-1) capsid is best described by a ‘fullerene cone’model2,3, in which hexamers of the capsid protein are linked to form a hexagonal surface lattice that is closed by incorporating 12 capsid-protein pentamers. HIV-1 capsid protein contains an amino-terminal domain (NTD) comprising seven a-helices and a b-hairpin4,5, a carboxy-terminal domain (CTD) comprising four a-helices6,7, and a flexible linker with a 310-helix connecting the two structural domains8. Structures of the capsid-protein assembly units have been determined by X-ray crystallography9,10; however, structural information regarding the assembled capsid and the contacts between the assembly units is incomplete. Here we report the cryoelectron microscopy structure of a tubular HIV-1 capsid-protein assembly at 8A˚ resolution and the three-dimensional structure of a nativeHIV-1 core by cryo-electron tomography. The structure of the tubular assembly shows, at the three-fold interface11, a three-helix bundle with critical hydrophobic interactions. Mutagenesis studies confirm that hydrophobic residues in the centre of the three-helix bundle are crucial for capsid assembly and stability, and for viral infectivity. The cryo-electron-microscopy structures enable modelling by large-scale molecular dynamics simulation, resulting in all-atom models for the hexamer-of-hexamer and pentamer-ofhexamer elements as well as for the entire capsid. Incorporation of pentamers results in closer trimer contacts and induces acute surface curvature. The complete atomic HIV-1 capsid model provides a platform for further studies of capsid function and for targeted pharmacological intervention.

  • Title: Overcoming the existent computational challenges in the ab initio calculations of the two-photon circular dichroism spectra of large molecules using a fragment-recombination approach
    Authors: Carlos Diaz, Lorenzo Echevarria & Florencio E. Hernández
    Location: Chemical Physics Letters 2013 568–569 pp 176-183

    Herein we report on the development of a fragment-recombination approach (FRA) that allows overcoming the computational limitations found in the ab initio calculation of the two-photon circular dichroism (TPCD) spectra of large optically active molecules. Through the comparative analysis of the corresponding theoretical TPCD spectra of the fragments and that of the entire molecule, we prove that TPCD is an additive property. We also demonstrate that the same property apply to two-photon absorption (TPA). TPCD−FRA is expected to find great applications in the structural-analysis of large catalysts and polypeptides due to its reduced computational complexity, cost and time, and to reveal fingerprints in the obscure spectral region between the near and far UV.

  • Title: Refining crystal structures with experimental 13C NMR shift tensors and lattice-including electronic structure methods
    Authors: James K. Harper, Robbie Iuliucci, Matthew Gruber & K. Kalakewich
    Location: CrystEngComm 2013 15 8693-8704

    arge differences are found in the quality of crystal structures obtained from different diffraction methods. The most accurate studies identify all atomic sites, including hydrogens, while others lack even the resolution needed to locate individual atoms. The gauge including projector augmented wave method (GIPAW) provides a technique to further refine any of these structures under lattice constraints. Here, the sensitivity of solid-state NMR 13C shift tensor principal value data to GIPAW refinement is investigated. The refinement is shown to improve X-ray powder, X-ray single crystal and even neutron single crystal diffraction data. Convergence to a single structure is observed in most cases. Surprisingly, the final refined structures usually diverge from the original neutron diffraction coordinates – data typically viewed as the most accurate. To ensure that the structural changes represent improvements, three metrics are monitored comprising fit to 13C shift tensors, forces upon the atoms and changes in atomic positions relative to a reference structure. In all cases these parameters improve upon refinement suggesting that GIPAW creates structures surpassing the accuracy of single crystal neutron diffraction data. However, the influence of thermal motions remains unknown. Improvements are seen most strongly in forces and NMR fits and least in atom positions. This study evaluates reasonably accurate model structures to quantify improvements. However, structures obtained from lower resolution methods (e.g. electron diffraction) will benefit most from GIPAW refinement. In such structures the refinement has the potential to convert structures with questionable atom positions into coordinates rivaling neutron diffraction single crystal data.

  • Title: Rationale for the Higher Reactivity of Interfacial Sites in Methanol Decomposition on Au13/TiO2(110)
    Authors: Sampyo Hong & Talat S. Rahman
    Location: Journal of the American Chemical Society 2013 135(20) pp 7629–7635

    nterfacial and perimeter sites have been known for their high activity in various reactions on supported gold nanoparticles. We find that the higher activity of interfacial sites in Au13/TiO2(110) toward methanol decomposition originates from charge-transfer-induced Coulomb interaction among the gold, reactant, and reducible TiO2 support, brought about through the formation of an ionic O–Au bond between gold and methoxy in such sites, which turns the participating perimeter gold atom cationic. A direct result of such charge-transfer-induced repulsive interaction between cationic gold and positively charged C moiety of methoxy is activation of the positively charged C moiety of methoxy, as manifested by the pronounced elongation of O–C bond length and the tilting of the methoxy axis, which facilitate reaction of methoxy through C–H scission with the bridge oxygen atoms that are readily available from the reducible support. More generally, our proposed mechanism for the reactivity of the gold/TiO2 interface should hold for oxidation of organic molecules with the structure of R–O–R′, where R and R′ are (saturated) hydrocarbons.

  • Title: Large-Eddy Simulations of a Cylindrical Film Cooling Hole
    Authors: Perry L. Johnson & Jayanta S. Kapat
    Location: AIAA Journal of Thermophysics and Heat Transfer. April 2013.

    Large-eddy simulations are used to explore the unsteady jet-in-crossflow interactions arising from discrete hole film cooling from a cylindrical hole. The numerical grids are created using GridPro and solved in OpenFOAM. A recycling-rescaling technique is used to generate a realistic turbulent incoming boundary layer upstream of injection. The simulations match the conditions of an experiment in the open literature for the robust validation of the numerical solution and turbulence modeling. The current study tests the ability of large-eddy simulations in predicting film cooling flows using detailed experimental measurements. The large-eddy simulation results compared favorably with the experimental data except in areas close to the injection site and close to the wall. Grid resolution is discussed in terms of the percent turbulent kinetic energy resolved and related to the success of the large eddy simulation predictions in different regions of the jet. No substantial benefit was seen by using a dynamic Smagorinsky model for the subgrid turbulent heat fluxes instead of a constant subgrid Prandtl number. The trajectories, spreading rates, and large turbulent structures of the jet are discussed in terms of the hydrodynamic parameters such as velocity ratio and momentum ratio.

  • Title: Charge relaxation dynamics of an electrolytic nanocapacitor
    Authors: Vaibhav Thakore & James J. Hickman

    Understanding ion relaxation dynamics in overlapping electric double layers (EDLs) is critical for the development of efficient nanotechnology based electrochemical energy storage, electrochemomechanical energy conversion and bioelectrochemical sensing devices besides controlled synthesis of nanostructured materials. Here, using Lattice Boltzmann (LB) method, we present results from the simulations of an electrolytic nanocapacitor subjected to a step potential at t = 0 for various degrees of EDL overlap, solvent viscosities, ratios of cation to anion diffusivity and electrode separations. A continuously varying molecular speed dependent relaxation time, proposed for use with the LB equation, recovers the correct microscopic description of molecular collision phenomena and holds promise for enhancing the stability of the LB algorithm. Results for large EDL overlap showed oscillatory behavior for ionic current densities in contrast to monotonic relaxation to equilibrium for low EDL overlap. Further, at low solvent viscosities and large EDL overlap, anomalous plasma-like spatial oscillations of electric field were observed that appeared to be purely an effect of nanoscale confinement.

  • Title: Two-Photon Circular−Linear Dichroism of Perylene in Solution: A Theoretical−Experimental Study
    Authors: Marcelo G. Vivas, Carlos Diaz, Lorenzo Echevarria, Cleber R. Mendonca, Florencio E. Hernandez & Leonardo De Boni
    Location: J. Phys. Chem. B 2013 117 2742−2747

    Herein, we report on the theoretical−experimental analysis of the two-photon absorption (TPA) and twophoton circular−linear dichroism (TPCLD) spectra of a highly conjugated, rigid, and centrosymmetric molecule in solution, that is, perylene/CH2Cl2. We show how a three-energy-level diagram, under the sum-over-essential states approach, assists in the determination of the magnitude of transition electric dipole moments and the angle between them for the main TPA transitions. We demonstrate the potential of TPCLD to reveal the symmetry of excited states and the angles between their transition electric dipole moments and that of the ground state. By means of TPCLD, we explain how the overwhelming contribution of certain TPA transitions can mask important spectral features in regions where the transition electric dipole moments are perpendicular. TPCLD is expected to enhance the understanding of the photophysical properties of materials that are not accessible using conventional linear and two-photon spectroscopy. TPA and TPCLD measurements were performed employing the open-aperture Z-scan technique using an amplified femtosecond system. Time-dependent density functional theory (TD-DFT) calculations were carried out using response theory at the B3LYP level with the aug-cc-pVDZ basis set. Solvent effects were included through the polarizable continuum model (PCM).

  • Title: Topographic accuracy assessment of bare earth lidar-derived unstructured meshes
    Authors: Matthew V. Bilskie & Scott C. Hagen
    Location: Advances in Water Resources 52 (2013) 165–177

    This study is focused on the integration of bare earth lidar (Light Detection and Ranging) data into unstructured (triangular) finite element meshes and the implications on simulating storm surge inundation using a shallow water equations model. A methodology is developed to compute root mean square error (RMSE) and the 95th percentile of vertical elevation errors using four different interpolation methods (linear, inverse distance weighted, natural neighbor, and cell averaging) to resample bare earth lidar and lidar-derived digital elevation models (DEMs) onto unstructured meshes at different resolutions. The results are consolidated into a table of optimal interpolation methods that minimize the vertical elevation error of an unstructured mesh for a given mesh node density. The cell area averaging method performed most accurate when DEM grid cells within 0.25 times the ratio of local element size and DEM cell size were averaged. The methodology is applied to simulate inundation extent and maximum water levels in southern Mississippi due to Hurricane Katrina, which illustrates that local changes in topography such as adjusting element size and interpolation method drastically alter simulated storm surge locally and non-locally. The methods and results presented have utility and implications to any modeling application that uses bare earth lidar.

  • Title: Enhanced Intersystem Crossing Rate in Polymethine-Like Molecules: Sulfur-Containing Squaraines versus Oxygen-Containing Analogues
    Authors: Davorin Peceli, Honghua Hu, Dmitry A. Fishman, Scott Webster, Olga V. Przhonska, Vladimir V. Kurdyukov, Yurii L. Slominsky, Alexey I. Tolmachev, Alexey D. Kachkovski, Andrey O. Gerasov, Artëm E. Masunov, David J. Hagan & Eric W. Van Stryland
    Location: J. Phys. Chem. A 2013 117(11) pp 2333-2346

    Two different approaches to increase intersystem crossing rates in polymethine-like molecules are presented: traditional heavy-atom substitution and molecular levels engineering. Linear and nonlinear optical properties of a series of polymethine dyes with Br- and Se-atom substitution, and a series of new squaraine molecules, where one or two oxygen atoms in a squaraine bridge are replaced with sulfur atoms, are investigated. A consequence of the oxygen-to-sulfur substitution in squaraines is the inversion of their lowest-lying ππ* and nπ* states leading to a significant reduction of singlet–triplet energy difference and opening of an additional intersystem channel of relaxation. Experimental studies show that triplet quantum yields for polymethine dyes with heavy-atom substitutions are small (not more than 10%), while for sulfur-containing squaraines these values reach almost unity. Linear spectroscopic characterization includes absorption, fluorescence, quantum yield, anisotropy, and singlet oxygen generation measurements. Nonlinear characterization, performed by picosecond and femtosecond laser systems (pump–probe and Z-scan measurements), includes measurements of the triplet quantum yields, excited state absorption, two-photon absorption, and singlet and triplet state lifetimes. Experimental results are in agreement with density functional theory calculations allowing determination of the energy positions, spin–orbital coupling, and electronic configurations of the lowest electronic transitions.

  • Title: New acentric materials constructed from aminopyridines and 4-nitrophenol
    Authors: Sergiu Draguta, Marina S. Fonari, Artëm E. Masunov, Joel Zazueta, Shannon Sullivan, Mikhail Yu. Antipin & Tatiana V. Timofeeva
    Location: CrystEngComm 2013 15(23) pp 4700-4710

    Co-crystallization of 4-nitrophenol (I) with five aminopyridines (4-aminopyridine 1, 3,4-diaminopyridine 2, 2,3-diaminopyridine 3, 3-aminopyridine 4, 2-amino-6-methylpyridine 5) and 2,4-diaminopyrimidine 6 resulted in six adducts with the ratio of components 2 : 1 in five and 1 : 1 in one final compounds. Single crystals were grown by slow evaporation technique using ethanol as a solvent. Five adducts with 1–5 crystallize in acentric P21 and Pna21 space groups, and one, 2(I)·6 – in centrosymmetric P21/c space group. Compounds 2(I)·1, 2(I)·2, 2(I)·3 are isomorphous, and demonstrate similar H-bonding patterns despite the differences in aminopyridine molecules. Compound 2(I)·5 is isomorphous to two previously reported compounds. Adducts 2(I)·1, 2(I)·2, 2(I)·3, 2(I)·5, 2(I)·6 represent organic salts composed of pyridinium/pyrimidinium cation, 4-nitrophenolate anion, and 4-nitrophenol neutral molecule. The H-bonded 4-nitrophenol–4-nitrophenolate anionic dimers were found in all compounds with 2 : 1 molar ratio. In adduct I·4 both molecules are in neutral form. The IR spectral data support crystallographic conclusions on salts formation. Plane wave pseudopotential density functional theory calculations were used to predict hyperpolarizability tensor components. Our calculations suggest 2(I)·3 as the best candidate for nonlinear optical materials (14 times more active than urea).

  • Title: Superdiffusion in optically controlled active media
    Authors: Kyle M. Douglass, Sergey Sukhov & Aristide Dogariu
    Location: Nature Photonics 6 834–837 (2012)

    Active media are complex systems driven by both thermal fluctuations and additional energy sources 1, 2 and are encountered in a variety of phenomena including mobile bacteria 3, 4, protein diffusion5 or turbulent flows6, 7. However, studying the non-equilibrium dynamics of active media is often difficult because of their size and complexity 8. Here, we demonstrate that an active medium can be realized and controlled optically through dynamic coupling between multiply scattered light and colloidal particles. As a result of a strong light–matter interaction, the particles undergo diffusion upon a spatiotemporal random potential that leads to an apparent superdiffusion over timescales controlled by, among other things, both the input power and particle size. This model could serve as a convenient tool for exploring the intricacies of non-equilibrium thermodynamics of soft matter while also offering new possibilities for the coherent control of strongly coupled, complex systems 9.

  • Title: The role of van der Waals interaction in the tilted binding of amine molecules to the Au(111) surface
    Authors: D. Le, M. Aminpour, A. Kiejna & T. S. Rahman
    Location: J. Phys. Condens. Matt.

    We present the results of ab initio electronic structure calculations for the adsorption characteristics of three amine molecules on Au(111), which show that the inclusion of van der Waals interactions between the isolated molecule and the surface leads in general to good agreement with experimental data on the binding energies. Each molecule, however, adsorbs with a small tilt angle (between −5 and 9°). For the specific case of 1,4-diaminobenzene (BDA) our calculations reproduce the larger tilt angle (close to 24°) measured by photoemission experiments, when intermolecular (van der Waals) interactions (for about 8% coverage) are included. These results point not only to the important contribution of van der Waals interactions to molecule–surface binding energy, but also that of intermolecular interactions, often considered secondary to that between the molecule and the surface, in determining the adsorption geometry and pattern formation.

  • Title: Design Optimization of Liquid-Phase Flow Patterns for Microfabricated Lung on a Chip
    Authors: Long, C., Finch, C., Esch, M., Anderson, W., Shuler, M. & Hickman J.
    Location: Annals of Biomedical Engineering (2012) 40:6 1255-1267

    Microreactors experience significant deviations from plug flow due to the no-slip boundary condition at the walls of the chamber. The development of stagnation zones leads to widening of the residence time distribution at the outlet of the reactor. A hybrid design optimization process that combines modeling and experiments has been utilized to minimize the width of the residence time distribution in a microreactor. The process was used to optimize the design of a microfluidic system for an in vitro model of the lung alveolus. Circular chambers to accommodate commercial membrane supported cell constructs are a particularly challenging geometry in which to achieve a uniform residence time distribution. Iterative computational fluid dynamics (CFD) simulations were performed to optimize the microfluidic structures for two different types of chambers. The residence time distributions of the optimized chambers were significantly narrower than those of non-optimized chambers, indicating that the final chambers better approximate plug flow. Qualitative and quantitative visualization experiments with dye indicators demonstrated that the CFD results accurately predicted the residence time distributions within the bioreactors. The results demonstrate that such a hybrid optimization process can be used to design microreactors that approximate plug flow for in vitro tissue engineered systems. This technique has broad application for optimization of microfluidic body-on-a-chip systems for drug and toxin studies.

  • Title: Spontaneous Creation of Photonic States in Quantum Dots
    Authors: Tafur, S. and Leuenberger, M.
    Location: Reviews in Nanoscience and Nanotechnology 1 (2) 2012 pp. 152-161

    Models of the spontaneous emission of photons coupled to the electronic states of quantum dots are important for understanding quantum interactions in dielectric media as applied to proposed solid-state quantum computers, single photon emitters, and single photon detectors. The characteristic lifetime of photon emission is traditionally modeled in the Markovian limit. In this contribution we model the spatio-temporal evolution of photonic states by means of a Dirac-like equation for a photonic wave function within the region of interaction of a quantum source. We use discretized central-difference approximations of space and time partial derivatives to describe single photon states via single photon operators in 3 + 1 dimensions. The proposed model describes the fully quantized spontaneous emission of a photon from the excited state of a quantum dot, inclusive of near field effects in the non-Markovian regime. In this regime we derive a third order ordinary differential equation (ODE) which yields three poles associated with the creation of a photonic mode from the possibly infinite set of photonic frequencies νk that can be excited from the vacuum state.

  • Title: Large Eddy Simulations of the Hydrodynamic and Thermal Fields from a Cylindrical Film Cooling Hole
    Authors: Pery L. Johnson, Lucky V. Tranh & Jayanta S. Kapat
    Location: AIAA Thermophysics Conference. June 2012 .

    Large Eddy Simulations are used to explore the unsteady jet-in-crossflow interactions arising from discrete hole film cooling from a cylindrical hole. The numerical grids are created using GridPro and exported into OpenFOAM for solution with specified initial and boundary conditions. A recycling-rescaling technique is used to generate a realistic turbulent incoming boundary layer upstream of injection. The geometry and flow conditions are specified to match conditions of an experiment in open literature for robust validation of the numerical solution and turbulence modeling. While LES has been demonstrated to be very successful in free sheer flows, wallbounded flows remain a hot topic of research. The current study tests the ability of LES in predicting film cooling flows using detailed experimental measurements. The LES results compared favorably with the experimental data except in areas close to the injection site and close to the wall. Grid resolution is discussed in terms of the percent turbulent kinetic energy resolved and related to the success of the LES predictions in different regions of the jet. With a dynamic Smagorinsky model used for the subgrid turbulent stresses, the benefit of a dynamic procedure for the subgrid turbulent heat fluxes instead of a supplied constant Prandtl number is minimal at the current grid resolution. The trajectories, spreading rates, and large turbulent structures of the jet are discussed in terms of the hydrodynamic parameters such as velocity ratio and momentum ratio.

  • Title: Linker-induced anomalous emission of organic molecule-conjugated metal oxide nanoparticles
    Authors: V. Turkowski, S. Babu, D. Le, M. K. Haldar, A. Wagh, Z. Hu, A. S. Karakoti5, A. J. Gesquiere, B. Law, S. Mallik, T. S. Rahman, M. N. Leuenberger & S. Seal
    Location: ACS Nano ASAP

    Semiconductor nanoparticles conjugated with organic- and dye-molecules to yield high efficiency visible photoluminescence (PL) hold great potential for many future technological applications. We show that folic acid (FA)-conjugated to nanosize TiO2 and CeO2 particles demonstrates a dramatic increase of photoemission intensity at wavelengths between 500 and 700 nm when derivatized using aminopropyl trimethoxysilane (APTMS) as spacer-linker molecules between the metal oxide and FA. Using density-functional theory (DFT) and time-dependent DFT calculations we demonstrate that the strong increase of the PL can be explained by electronic transitions between the titania surface oxygen vacancy (OV) states and the low-energy excited states of the FA/APTMS molecule anchored onto the surface oxygen bridge sites in close proximity to the OVs. We suggest this scenario to be a universal feature for a wide class of metal oxide nanoparticles, including nanoceria, possessing a similar band gap (3 eV) and with a large surface-vacancy-related density of electronic states. We demonstrate that the molecule–nanoparticle linker can play a crucial role in tuning the electronic and optical properties of nanosystems by bringing optically active parts of the molecule and of the surface close to each other.

  • Title: Off-lattice pattern recognition scheme for kinetic Monte Carlo simulations
    Authors: G. Nandipati, A. Kara, S. I. Shah & T. S. Rahman
    Location: J. Comp. Phys. 231 3548 (2012)

    We report the development of a pattern-recognition scheme for the off-lattice self-learning kinetic Monte Carlo (KMC) method, one that is simple and flexible enough that it can be applied to all types of surfaces. In this scheme, to uniquely identify the local environment and associated processes involving three-dimensional (3D) motion of an atom or atoms, space around a central atom is divided into 3D rectangular boxes. The dimensions and the number of 3D boxes are determined by the accuracy with which a process needs to be identified and a process is described as the central atom moving to a neighboring vacant box accompanied by the motion of any other atom or atoms in its surrounding boxes. As a test of this method to we apply it to examine the decay of 3D Cu islands on the Cu(100) and to the surface diffusion of a Cu monomer and a dimer on Cu(111) and compare the results and computational efficiency to those available in the literature.

  • Title: Light-Controlled Plasmon Switching Using Hybrid Metal-Semiconductor Nanostructures
    Authors: Paudel, H. and Leuenberger, M.
    Location: Nano Lett. (2012)

    We present a proof of concept for the dynamic control over the plasmon resonance frequencies in a hybrid metal-semiconductor nanoshell structure with Ag core and TiO2 coating. Our method relies on the temporary change of the dielectric function ε of TiO2 achieved through temporarily generated electron–hole pairs by means of a pump laser pulse. This change in ε leads to a blue shift of the Ag surface plasmon frequency. We choose TiO2 as the environment of the Ag core because the band gap energy of TiO2 is larger than the Ag surface plasmon energy of our nanoparticles, which allows the surface plasmon being excited without generating electron–hole pairs in the environment at the same time. We calculate the magnitude of the plasmon resonance shift as a function of electron–hole pair density and obtain shifts up to 126 nm at wavelengths around 460 nm. Using our results, we develop the model of a light-controlled surface plasmon polariton switch.

  • Title: Dynamical Mean-Field Theory for Molecules and Nanostructures
    Authors: V. Turkowski, A. Kabir, N. Nayyar & T. S. Rahman
    Location: J. Chem. Phys. 136 114108 (2012)

    Dynamical mean-field theory (DMFT) has established itself as a reliable and well-controlled approximation to study correlation effects in bulk solids and also two-dimensional systems. In combination with standard density-functional theory (DFT), it has been successfully applied to study materials in which localized electronic states play an important role. It was recently shown that this approach can also be successfully applied to study correlation effects in nanostructures. Here, we provide some details on our recently proposed DFT+DMFT approach to study the magnetic properties of nanosystems [V. Turkowski, A. Kabir, N. Nayyar, and T. S. Rahman, J. Phys.: Condens. Matter 22, 462202 (2010)] and apply it to examine the magnetic properties of small FePt clusters. We demonstrate that DMFT produces meaningful results even for such small systems. For benchmarking and better comparison with results obtained using DFT+U, we also include the case of small Fe clusters. As in the case of bulk systems, the latter approach tends to overestimate correlation effects in nanostructures. Finally, we discuss possible ways to further improve the nano-DFT+DMFT approximation and to extend its application to molecules and nanoparticles on substrates and to nonequilibrium phenomena.

  • Title: Adsorption of a single layer MoS2 on the Cu(111) surface
    Authors: D. Le, D. Sun, W. Lu, L. Bartels & T. S. Rahman
    Location: Phys. Rev. B.

    First-principles calculations of the geometric and electronic structures of a single layer of molybdenum disulfide (MoS2) on Cu(111) utilizing the van der Waals density functional show three energetically equivalent stacking types and a Moiré pattern whose periodicity is in agreement with experimental findings. The layer is found not to be purely physisorbed on the surface, rather there exists a chemical interaction between it and the Cu surface atoms. We also find that the MoS2 film is not appreciably buckled, while the top Cu layer gets reorganized and vertically disordered. The sizes of Moiré patterns for a single layer of MoS2 adsorbed on other close-packed metal surfaces are also estimated by minimizing the lattice mismatch between the film and the substrate.

  • Title: Vibrations of Au13 and FeAu12 nanoparticles and the limits of the Debye temperature concept
    Authors: G. Shafai, M. Alcántara Ortigoza & T. S. Rahman
    Location: J. Phys.: Condens. Matter 24 104026 (2012)

    We present first-principles calculations of the vibrational density of states (VDOS), the specific heat and the mean-squared displacement of the five lowest-energy isomers of Au13 and of two low-energy FeAu12 nanoparticles. We find that the vibrational contributions to the Helmholtz energy do not affect the energy ordering of the isomers. As expected, for nanoparticles the vibrational density of states differs dramatically from the function proposed by the Debye model. We demonstrate that, for the nanoclusters we studied, the alternative calculations of the ‘Debye temperature’ yield significantly inconsistent results. We conclude that TD obtained from a particular thermodynamic property is neither applicable for deriving conclusions about other thermodynamic properties nor correlated with atomic bond strengths. Instead, in order to describe the temperature dependence of a nanoparticle’s mean-squared displacement and its specific-heat capacity, what is necessary is its discrete phonon spectrum.

  • Title: Observations and simulation of winds surge and currents on Florida’s east coast during Hurricane Jeanne (2004).
    Authors: Bacopoulos, P., Dally, W. R., Hagen, S. C., & Cox, A. T.
    Location: Coastal Engineering (2011)

    A novel set of measurements of winds, water levels, and currents recorded in September of 2004 captured the landfall of Hurricane Jeanne. The dataset provides a full picture of the meteorology and hydrodynamics associated with Hurricane Jeanne and are used to test the state-of-the-art in numerical modeling of storm surge. A shallow water equations model (ADCIRC) is driven by rigorously modeled winds and astronomic tides to replicate continuous hydrodynamic records at two stations, one in Melbourne Beach (Spessard) and the other inside Port Canaveral (Trident Pier), where instrumentation was located by happenstance. Simulation results represent the time-series of water surface elevations measured in the open coast off Melbourne Beach (Spessard) within 0.05 m root mean square error and within 12% of observed maximum surge elevation (1.35 m simulated vs. 1.52 m measured) and exhibit details induced by a ‘loop’ performed by the hurricane before it made landfall. Prediction of water levels inside Port Canaveral (Trident Pier) is to within 0.06 m root mean square error and includes the observed forerunner and peak surge of the hurricane. In regard to nearshore currents off Melbourne Beach (Spessard), the timing of a sudden switch in the direction of the measured (longshore) current is replicated well with the magnitude of the peak current simulated to within 14% of observation (0.96 m/s modeled vs. 1.11 m/s measured). The capability to accurately simulate the tidal and storm surge hydrodynamics during Hurricane Jeanne provides confidence in using this class of shallow water equations models in coastal engineering practice.

  • Title: Whispering gallery mode biosensor quantification of fibronectin adsorption kinetics onto alkylsilane monolayers and interpretation of resultant cellular response
    Authors: Wilson, K., Finch, C., Anderson, P., Vollmer, F. & Hickman J.
    Location: Biomaterials 33 (1) 2012 pp. 225-236

    A Whispering Gallery Mode (WGM) biosensor was constructed to measure the adsorption of protein onto alkysilane self-assembled monolayers (SAMs) at solution concentrations unattainable with other techniques. The high sensitivity was provided by a WGM resonance excited in a silica microsphere that was functionalized with alkylsilane SAMs and integrated in a microfluidic flow cell under laminar flow conditions. It was found that FN adsorbed at biologically relevant surface densities, however, the adsorption kinetics and concentration dependent saturation values varied significantly from work published utilizing alkanethiol SAMs. Mathematical models were applied to the experimental results to interpret the observed kinetics of FN adsorption. Embryonic hippocampal neurons and skeletal myoblasts were cultured on the modified surfaces, a live–dead assay was used to determine the viability of the FN surfaces for cell culture, and major differences were noted in the biological response to the different SAMs. The high sensitivity and simplicity of the WGM biosensor, combined with its ability to quantify the adsorption of any dilute protein in a label-free assay, establishes the importance of this technology for the study of surface accretion and its effect on cellular function, which can affect biomaterials for both in vivo and in vitro applications.

  • Title: A Memory Efficient Method for Structure-Based RNA Multiple Alignment
    Authors: DeBlasio, Daniel and Bruand, Jocelyne & Zhang, Shaojie
    Location: IEEE/ACM Trans. Comput. Biol. Bioinformatics 9 (1) (2012) pp. 1—11

    Structure-based RNA multiple alignment is particularly challenging because covarying mutations make sequence information alone insufficient. Existing tools for RNA multiple alignment first generate pairwise RNA structure alignments and then build the multiple alignment using only sequence information. Here we present PMFastR, an algorithm which iteratively uses a sequence-structure alignment procedure to build a structure-based RNA multiple alignment from one sequence with known structure and a database of sequences from the same family. PMFastR also has low memory consumption allowing for the alignment of large sequences such as 16S and 23S rRNA. The algorithm also provides a method to utilize a multicore environment. We present results on benchmark data sets from BRAliBase, which shows PMFastR performs comparably to other state-of-the-art programs. Finally, we regenerate 607 Rfam seed alignments and show that our automated process creates multiple alignments similar to the manually curated Rfam seed alignments. Thus, the techniques presented in this paper allow for the generation of multiple alignments using sequence-structure guidance, while limiting memory consumption. As a result, multiple alignments of long RNA sequences, such as 16S and 23S rRNAs, can easily be generated locally on a personal computer. The software and supplementary data are available at

  • Title: Large Eddy Simulations of a Cylindrical Film Cooling Holes
    Authors: Johnson, P. L. & Kapat, J. S.
    Location: AIAA Aerospace Sciences Meeting. January 2012.

    Large Eddy Simulations are used to explore the unsteady jet-in-crossflow interactions arising from discrete hole film cooling. The numerical grids are created using GridPro and exported to OpenFOAM for solution with specified initial and boundary conditions. A recycling-rescaling technique is used to generate an incoming turbulent boundary layer upstream of injection. The geometry and flow conditions are specified to match conditions of an experiment in open literature for robust validation of the numerical solution. The trajectory and spreading of the jets is discussed in terms of the insight provided by the result of the simulation.

  • Title: Thermodynamic properties of Pt nanoparticles: Size shape support and adsorbate effects
    Authors: B. Roldan Cuenya, M. Alcantara Ortigoza, L. K. Ono, F. Behafarid, S. Mostafa, J. R. Croy, K. Paredis, G. Shafai, T. S. Rahman, L. Li, Z. Zhang & J. C. Yang
    Location: Phys. Rev B 84 005400 (2011)

    This study presents a systematic investigation of the thermodynamic properties of free and γ-Al2O3-supported size-controlled Pt nanoparticles (NPs) and their evolution with decreasing NP size. A combination of in situ extended x-ray absorption fine-structure spectroscopy (EXAFS), ex situ transmission electron microscopy (TEM) measurements, and NP shape modeling revealed (i) a cross over from positive to negative thermal expansion with decreasing particle size, (ii) size- and shape-dependent changes in the mean square bond-projected bond-length fluctuations, and (iii) enhanced Debye temperatures (ΘD, relative to bulk Pt) with a bimodal size-dependence for NPs in the size range of ∼0.8–5.4 nm. For large NP sizes (diameter d >1.5 nm) ΘD was found to decrease toward ΘD of bulk Pt with increasing NP size. For NPs ≤ 1 nm, a monotonic decrease of ΘD was observed with decreasing NP size and increasing number of low-coordinated surface atoms. Our density functional theory calculations confirm the size- and shape-dependence of the vibrational properties of our smallest NPs and show how their behavior may be tuned by H desorption from the NPs. The experimental results can be partly attributed to thermally induced changes in the coverage of the adsorbate (H2) used during the EXAFS measurements, bearing in mind that the interaction of the Pt NPs with the stiff, high-melting temperature γ-Al2O3 support may also play a role. The calculations also provide good qualitative agreement with the trends in the mean square bond-projected bond-length fluctuations measured via EXAFS. Furthermore, they revealed that part of the ΘD enhancement observed experimentally for the smallest NPs (d ≤ 1 nm) might be assigned to the specific sensitivity of EXAFS, which is intrinsically limited to bond-projected bond-length fluctuations.

  • Title: The Quantum Magnetism of Individual Manganese-12-Acetate Molecular Magnets Anchored at Surfaces
    Authors: S. Kahle, Z. Deng, N. Malinowski, C. Tonnoir, A. Forment Aliaga, N. Thontasen, G. Rinke, D. Le, V. Turkowski, T. S. Rahman, S. Rauschenbach, M. Ternes & K. Kern
    Location: NanoLett. 12 518 (2012)

    The high intrinsic spin and long spin relaxation time of manganese-12-acetate (Mn12) makes it an archetypical single molecular magnet. While these characteristics have been measured on bulk samples, questions remain whether the magnetic properties replicate themselves in surface supported isolated molecules, a prerequisite for any application. Here we demonstrate that electrospray ion beam deposition facilitates grafting of intact Mn12 molecules on metal as well as ultrathin insulating surfaces enabling submolecular resolution imaging by scanning tunneling microscopy. Using scanning tunneling spectroscopy we detect spin excitations from the magnetic ground state of the molecule at an ultrathin boron nitride decoupling layer. Our results are supported by density functional theory based calculations and establish that individual Mn12 molecules retain their intrinsic spin on a well chosen solid support.

  • Title: Tailoring the Electronic Structure by Alloying: the AgnCu34-n Nanoparticle Family
    Authors: H. Yildirim, A. Kara & T. S. Rahman
    Location: J. Phys. Chem. C 116 281 (2012)

    Electronic structures of the free-standing core–shell (Cu@Ag) AgnCu34–n (n = 0–34) nanoalloy family are studied as a function of stoichiometry using ab initio total energy electronic structure calculations. Our calculations show that progressive alloying significantly alters the coordination distribution, bond lengths, formation energies, and the electronic densities of states. Changes in coordination and elemental environment are reflected in the electronic densities of states, which broaden or narrow as a result of hybridization between the Cu and the Ag atoms. The densities of states of Ag atoms in Ag-rich nanoparticles show large broadening when a single Cu atom is introduced, followed by substantial deviation of the position of the center of d states from that of the pristine (Ag34) nanoparticle. Such deviation is found to persist for nonsymmetric nanoparticles. The calculated HOMO–LUMO gaps vary between 0.2 and 0.9 eV within the family. The magnitude of the gaps is found to be strongly dependent on the geometric structure determined by the species ratio: the particles belonging to two ends of the NP family have relatively small gaps, and no overriding symmetry, whereas those toward the middle of the family exhibit high symmetry and larger gaps. The calculated ionization energies show no monotonic dependence on the Cu-to-Ag ratio and fluctuate within 500 meV as the stoichiometry changes.

  • Title: Vibrations at Surfaces
    Authors: T. S. Rahman
    Location: J. Phys.: Condens. Matter 23 (2011) 480301

    This special issue is dedicated to the phenomenon of vibrations at surfaces—a topic that was indispensible a couple of decades ago, since it was one of the few phenomena capable of revealing the nature of binding at solid surfaces. For clean surfaces, the frequencies of modes with characteristic displacement patterns revealed how surface geometry, as well as the nature of binding between atoms in the surface layers, could be different from that in the bulk solid. Dispersion of the surface phonons provided further measures of interatomic interactions. For chemisorbed molecules on surfaces, frequencies and dispersion of the vibrational modes were also critical for determining adsorption sites. In other words, vibrations at surfaces served as a reliable means of extracting information about surface structure, chemisorption and overlayer formation. Experimental techniques, such as electron energy loss spectroscopy and helium-atom-surface scattering, coupled with infra-red spectroscopy, were continually refined and their resolutions enhanced to capture subtleties in the dynamics of atoms and molecules at surfaces. Theoretical methods, whether based on empirical and semi-empirical interatomic potential or on ab initio electronic structure calculations, helped decipher experimental observations and provide deeper insights into the nature of the bond between atoms and molecules in regions of reduced symmetry, as encountered on solid surfaces. Vibrations at surfaces were thus an integral part of the set of phenomena that characterized surface science. Dedicated workshops and conferences were held to explore the variety of interesting and puzzling features revealed in experimental and theoretical investigations of surface vibrational modes and their dispersion. One such conference, Vibrations at Surfaces, first organized by Harald Ibach in Juelich in 1980, continues to this day. The 13th International Conference on Vibrations at Surfaces was held at the University of Central Florida, Orlando, in March 2010. Several speakers at this meeting were invited to contribute to the special section in this issue.As is clear from the articles in this special section, the phenomenon of vibrations at surfaces continues to be a dynamic field of investigation. In fact, there is a resurgence of effort because the insights provided by surface dynamics are still fundamental to the development of an understanding of the microscopic factors that control surface structure formation, diffusion, reaction and structural stability. Examination of dynamics at surfaces thus complements and supplements the wealth of information that is obtained from real-space techniques such as scanning tunneling microscopy. Vibrational dynamics is, of course, not limited to surfaces. Surfaces are important since they provide immediate deviation from the bulk. They display how lack of symmetry can lead to new structures, new local atomic environments and new types of dynamical modes. Nanoparticles,

  • Title: Stress balance in nanopatterned N/Cu(001) surfaces
    Authors: S. Hong, M. Alcántra Ortigoza, T. S. Rahman, E. Z. Ciftlikli & B. J. Hinch
    Location: Phys. Rev. B 84 165413 (2011)

    We employ helium-atom scattering (HAS) and density functional theory (DFT) based on the ultrasoft pseudopotential scheme and the plane-wave basis set to investigate the strain and stress balance in nanopatterned N/Cu(001) surfaces. HAS shows that, with increasing N coverage (and decreasing stripe widths), the stress-relief-driven lateral expansion of the averaged lattice parameter within finite-sized N-containing patches reduces from 3.5% to 1.8% and that, beyond a critical exposure, the lateral expansion of the patches increases again slightly, to 2.4%. The latter implies that in this higher coverage range the compressive stress is partially relieved via another mechanism, which turns out to be nucleation of Cu-vacancy trenches. In full agreement with the above and previous experimental observations, DFT calculations show that an optimized N-induced c(2?×?2) structure has a net surface stress level of 4.2 N/m and such stress is effectively relieved when stripes of clean Cu(001) form along the <100> direction or when trenchlike steps of Cu atoms form along the <110> direction. Additionally, the calculations demonstrate that (contrary to earlier suggestions) rumpling displacements within the outermost Cu layer do not act to relieve the compressive surface stress levels and that, while clocklike displacements could relieve stress levels, such displacements are energetically unstable.

  • Title: The crossover from collective motion to periphery diffusion for 2D adatom-islands on Cu(111)
    Authors: A. Karim, A. Kara, O. Trushin & T. S. Rahman
    Location: J. Phys. Condens. Matt. (Fast Track) 23 462201 (2011)

    The diffusion of two-dimensional adatom-islands (up to 100 atoms) on Cu(111) has been studied, using the self-learning kinetic Monte Carlo method (Trushin et al 2005 Phys. Rev. B 72 115401). A variety of multiple- and single-atom processes are revealed in the simulations, and the size dependences of the diffusion coefficients and effective diffusion barriers are calculated for each. From the tabulated frequencies of events found in the simulation, we show a crossover from diffusion due to the collective motion of the island to a regime in which the island diffuses through periphery-dominated mass transport. This crossover occurs for island sizes between 13 and 19 atoms. For islands containing 19–100 atoms the scaling exponent is 1.5, which is in good agreement with previous work. The diffusion of islands containing 2–13 atoms can be explained primarily on the basis of a linear increase of the barrier for the collective motion with the size of the island.

  • Title: Toward the Growth of an Aligned Single-Layer MoS2 Film
    Authors: D. Kim, D. Sun, W. Lu, Z. Cheng, Y. Zhu, D. Le & T. S. Rahman and L. Bartels
    Location: Langmuir 27 11650 (2011)

    Molybdenum disulfide (molybdenite) monolayer islands and flakes have been grown on a copper surface at comparatively low temperature and mild conditions through sulfur loading of the substrate using thiophenol (benzenethiol) followed by the evaporation of Mo atoms and annealing. The MoS2 islands show a regular Moire´ pattern in scanning tunneling microscopy, attesting to their atomic ordering and high quality. They are all aligned with the substrate high-symmetry directions providing for rotational-domain-free monolayer growth.

  • Title: Computational study of the near field spontaneous creation of photonic states coupled to few level systems
    Authors: Tafur S.
    Location: PhD dissertation, University of Central Florida, Orlando Florida (2011)

    Models of the spontaneous emission and absorption of photons coupled to the electronic states of quantum dots, molecules, N-V (single nitrogen vacancy) centers in diamond, that can be modeled as artificial few level atoms, are important to the development of quantum computers and quantum networks. A quantum source modeled after an effective few level system is strongly dependent on the type and coupling strength the allowed transitions. These selection rules are subject to the Wigner-Eckert theorem which specifies the possible transitions during the spontaneous creation of a photonic state and its subsequent emission. The model presented in this dissertation describes the spatio-temporal evolution of photonic states by means of a Dirac like equation for the photonic wave function within the region of interaction of a quantum source. As part of this aim, we describe the possibility to shift from traditional electrodynamics and quantum electrodynamics, in terms of electric and magnetic fields, to one in terms of a photonic wave function and its operators. The mapping between these will also be presented herein. It is further shown that the results of this model can be experimentally verified. The suggested method of verification relies on the direct comparison of the calculated density matrix orWigner function, associated with the quantum state of a photon, to ones that are experimentally reconstructed through optical homodyne tomography techniques. In this non-perturbative model we describe the spontaneous creation of photonic state in a non-Markovian limit which does not implement the Weisskopf-Wigner approximation. We further show that this limit is important for the description of how a single photonic mode is created from the possibly infinite set of photonic frequencies u_k that can be excited in a dielectric-cavity from the vacuum state. We use discretized central-difference approximations to the space and time partial derivatives, similar to finite-difference time domain models, to compute these results. The results presented herein show that near field effects need considered when describing adjacent quantum sources that are separated by distances that are small with respect to the wavelength of their spontaneously created photonic states. Additionally, within the future scope of this model, we seek results in the Purcell and Rabi regimes to describe enhanced spontaneous emission events from these few-level systems, as embedded in dielectric cavities. A final goal of this dissertation is to create novel computational and theoretical models that describe single and multiple photon states via single photon creation and annihilation operators.

  • Title: Effect of misfit dislocation on surface diffusion
    Authors: O.S. Trushin, M. Aminpour & T.S. Rahman
    Location: Phys. Rev. B 84 035455 (2011)

    We apply molecular dynamics and molecular static methods to study the effect of misfit dislocations on adatom diffusion in close proximity to the dislocation core in heteroepitaxial systems, using many-body interaction potentials. Our system consists of several layers (three–seven) of Cu on top of a Ni(111) substrate. The misfit dislocations are created with the core located at the interface between the Cu film and the Ni substrate, using the repulsive biased potential method described earlier. We find that presence of the defect under the surface strongly affects the adatom trajectory, creating anisotropy in atomic diffusion, independent of the thickness of the Cu film. We also calculate the potential energy surface available to the adatom and compare the energy barriers for adatom diffusion in the proximity of the core region and on the defect-free surface.

  • Title: Unstructured mesh assessment for tidal model of the South Atlantic Bight and its estuaries
    Authors: Bacopoulos, P., Parrish, D. M., and Hagen, S. C.
    Location: Journal of Hydraulic Research Special Issue on Coastal and Maritime Hydraulics (2011) 49(4) 487-502

    Localized truncation error analysis with complex derivatives was applied to compute target element sizes for tidal flow in the South Atlantic Bight (SAB) and its estuaries. An existing finite element mesh was used to generate a tidal solution that is fed into this code, which assesses the truncation error and drives it to a more uniform value through selective mesh gradation, and results in a target element size distribution for the SAB and its estuaries. The target element size distribution is compared to the element size distribution of the existing mesh. The code prescribes larger than the initial elements for the shelf and deeper waters and smaller than the initial elements for the shallow-water region. Along the coast, elements similarly sized as the initial elements are prescribed at the inlets, but larger elements are prescribed between adjacent inlets.

  • Title: Island Size Selectivity during 2D Coarsening of Ag islands on Ag (111) Surface
    Authors: G. Nandipati, A. Kara, S. Islamuddin Shah & T. S. Rahman
    Location: J. Phys. Condens. Matt. (Fast Track) 23 262001 (2011)

    We report on the early stages of submonolayer Ag island coarsening on the Ag(111) surface carried out using kinetic Monte Carlo simulations for several temperatures. Our simulations were performed using a very large database of processes identified by their local environment and whose activation barriers were calculated using the semi-empirical interaction potentials based on the embedded-atom method. We find that during the early stages, coarsening proceeds as a sequence of selected island sizes, creating peaks and valleys in the island-size distribution. This island-size selectivity is independent of initial conditions and results from the formation of kinetically stable islands for certain sizes as dictated by the relative energetics of edge atom detachment/attachment processes together with the large activation barrier for kink detachment. Our results indicate that by tuning the growth temperature it is possible to enhance the island-size selectivity.

  • Title: Toward an Understanding of Ligand Selectivity in Nanocluster Synthesis
    Authors: S. Hong, G. Shafai, M. Bertino & T. S. Rahman
    Location: J. Phy. Chem. C 115 14478 (2011)

    We performed scalar relativistic density functional theory (DFT) calculations using the projector augmented wave scheme (PAW) to examine the reactivity and selectivity of diphosphine ligands LM, with the formula PH2(CH2)MPH2 (spacer M = 3, 5), toward small-sized cationic Aun (n = 7–11) nanoclusters. By isolating the ligand-induced contribution to the stability condition, we show that such interaction selectively stabilizes the cationic Au11 cluster. Furthermore, we find that L5 with the longer spacer is more capable than L3 of relieving the strain imposed on the spacer by bidentate binding to gold clusters, which have relatively small Au–Au bond lengths. Thus L5 can interact effectively with gold clusters of various sizes, but L3 can do so only with a selected few. This result demonstrates the size-selecting power of L3 toward small gold clusters such as Au113+. To further test the validity of our results we have extended the calculation to a larger cluster, Au13, and also considered the case of a ligand with a larger spacer, M = 10, interacting with a small cluster (Au3). We find that, for Au13(L3)65+, the strain induced by the stiff L3 spacer causes the gold cluster to disintegrate. We also predict a single-end binding for the interaction of L3 with the gold trimer: one end of the diphosphine is detached from the trimer. Finally, for an ideal, highly selective ligand, we propose a two-body ligand system, in which one part of the ideal ligand provides high reactivity toward the broad range of gold clusters and the other part provides control over the reactivity. The controllable competition between the two components of an ideal, highly selective ligand system will produce a desirable selectivity for the generation of monodisperse nanoclusters of interest through tailoring process.

  • Title: Nature of the Binding of a c(2×2)-CO Overlayer on Ag(001) and Surface Mediated Intermolecular Coupling
    Authors: M. Alcántara-Ortigoza, T. S. Rahman, R. Heid & K. P. Bohnen
    Location: J. Phys. Chem. A 115 7291 (2011)

    We present a first-principles study of the nature of the binding of a c(2×2)-CO overlayer on Ag(001) and of the origin of CO–CO interactions upon adsorption. Electronic structural changes induced by molecular adsorption provide an interpretation for earlier X-ray photoemission valence band spectra of CO/Ag(001). Our results establish that CO chemisorbs on clean Ag(001) and follows the Blyholder model of donation and back-donation between CO and metal orbitals. We analyze the origin of the dispersion of the C–O stretch mode and attest that it is caused by the metal–CO coupling. Specifically, the coupling of CO to Ag, although the weakest of those between it and transition and other noble metals, greatly enhances the intermolecular force constants. We also find that the response of the charge density around CO is much stronger and of longer range when the molecule stretches than when it rigidly vibrates against the surface. This difference explains why the C–O stretch mode disperses while the Ag–CO stretch mode does not.

  • Title: Hydrodynamics of the 2004 Florida hurricanes
    Authors: Hagen, S. C., Bacopoulos, P., Cox, A. T. & Cardone, V. J.
    Location: Journal of Coastal Research (2011)

    We studied the hydrodynamic response caused by the four major hurricanes that struck Florida’s coasts in 2004: Charley, Frances, Ivan, and Jeanne. A large-scale, shallow-water-equation model was applied so as to simulate wind and tidally driven hydrodynamics from the deep ocean into the shelf and coastal waters of Florida. Hurricane Ivan served as the calibration case, where the adjusted parameter was the wind drag coefficient. We identified an “increased” wind drag coefficient to perform best and suggest it as a first approximation to the wave contribution to the hydrodynamics. The increased drag coefficient is offered to the consulting and/or forecasting communities, who are frequently without wave-modeling resources, as a pragmatic approach to approximate for waves. Hurricanes Charley, Frances, and Jeanne serve as the validation cases in which the increased wind drag coefficient was applied. Analysis was performed by inspection of maximum water-surface elevations, which are interpreted in terms of shelf and bay dynamics for the west coast hurricane cases (Charley and Ivan) and in terms of channel hydraulics for the east coast hurricane cases (Frances and Jeanne). We conclude that the broad shelf off Florida’s west coast allows the storm tide to accumulate along the open coast and that the embayments further magnify the storm tide, and that the Atlantic Intracoastal Waterway along Florida’s east coast is effective in propagating storm tide, where we show compartmentalization of the storm tide in the Indian River lagoon as caused by the flow impediment of the causeway abutments.

  • Title: Density functional theory study of small nickel clusters
    Authors: Goel, S. & Masunov, A.E.
    Location: Journal of Molecular Modeling ( 2011 ) pp. 1–8.

    The stable geometries and atomization energies for the clusters Ni n (n = 2-5) are predicted with all-electron density functional theory (DFT), using the BMK hybrid functional and a Gaussian basis set. Possible isomers and several spin states of these nickel clusters are considered systematically. The ground spin state and the lowest energy isomers are identified for each cluster size. The results are compared to available experimental and other theoretical data. The molecular orbitals of the largest cluster are plotted for all spin states. The relative stabilities of these states are interpreted in terms of superatom orbitals and no-pair bonding.

  • Title: CO-induced Diffusion of Ni Atoms to the Surface of Ni-Au Clusters on TiO2(110)
    Authors: S. A. Tenney, W. He, C. C. Roberts, J. S. Ratliff, S. I. Shah, G. S. Shafai, V. Turkowski, T. S. Rahman & D. A. Chen
    Location: J. Phys. Chem C 115 11112 (2011)

    The growth, surface composition, and chemical activity of Ni–Au clusters on TiO2(110) have been studied by scanning tunneling microscopy (STM), low energy ion scattering (LEIS), and temperature-programmed desorption (TPD), as well as density functional theory (DFT) calculations and ab initio molecular dynamics simulations. STM images of similar coverages of pure Au and pure Ni on TiO2(110) illustrate that Au clusters are larger with lower cluster densities, indicating that Au is more mobile on the surface than Ni. Consequently, bimetallic Ni–Au clusters can be grown by nucleating Au at existing Ni clusters. A sequence of STM images acquired from the same region of the surface after various depositions of Au on Ni seed clusters demonstrates that new clusters of pure Au are not formed on the surface. Furthermore, the size of the existing clusters increases with each Au deposition due to the incorporation of incoming Au atoms. For bimetallic clusters of varying compositions with a total coverage of 0.25 ML, the addition of Ni has a minor effect in suppressing cluster sintering. LEIS studies indicate that the surface of the clusters are Au-rich (85–95% Au) for bulk Au fractions =50%. For annealed bimetallic clusters, the presence of Au at the cluster surface does not significantly inhibit the encapsulation of Ni by titania, while surface Au is not encapsulated. TPD investigations of CO desorption show that CO desorbs from pure Ni clusters in a molecular peak at 400 K and a recombinant peak at 790 K. Although CO does not adsorb onto titania or pure Au clusters at room temperature, significant CO desorption occurs from bimetallic clusters even for surfaces with only a small fraction of Ni at the surface; this result suggests that CO induces the diffusion of Ni to the surface of the clusters. DFT calculations for unsupported Ni1Au121 clusters confirm that in the presence of a CO molecule, the lowest energy structure involves CO bonding to a Ni atom at the surface. In contrast, in the absence of CO, the most stable cluster surface is pure Au with all of the Ni atoms in the interior of the cluster. Ab initio molecular dynamics simulations show that Ni will migrate to the cluster surface at 300 K in the presence of CO, but Ni migration to the surface does not occur even at higher temperatures in the absence of CO.

  • Title: Theoretical Study of Photochromic Compounds: Part 3. Prediction of Thermal Stability
    Authors: Patel, P.D. & Masunov, A.E.
    Location: The Journal of Physical Chemistry C 115 20 (2011) pp 10292-10297

    Diarylethene derivatives are known to be photochromic, that is, upon irradiation they change their color because of ultrafast photocyclization. Their proposed use as nonvolatile data storage materials requires the cycloreversion process to be very slow in the dark. We apply density functional theory (DFT) methods to predict kinetics of thermal cycloreversion. The cycloreversion occurs through symmetry forbidden conrotatory electrocyclic mechanism with transition state of strong diradical character and requires the use of unrestricted broken-symmetry DFT formalism. Our results suggest that B3LYP and M05-2X are the best functionals to describe kinetics in these compounds (accurate to within 3-4 kcal/mol from the experimental values). The methods validated in this study show great promise as tools in rational design of the improved photochromic materials.

  • Title: Mass conservation analysis for the Lower St. Johns River using continuous and discontinuous Galerkin finite element methods
    Authors: Thomas, L.
    Location: MS thesis, University of Central Florida, Orlando Florida (2011)

    This thesis provides a mass conservation analysis of the Lower St. Johns River for the purpose of providing basis for future salinity transport modeling. The analysis provides an assessment of the continuous (CG) and discontinuous (DG) Galerkin finite element methods with respect to their mass conservation properties. The following thesis also presents a rigorous literature review pertaining to salinity transport in the Lower St. Johns River, from which this effort generates the data used to initialize and validate numerical simulations. Two research questions are posed and studied in this thesis: can a DG-based modeling approach produce mass conservative numerical solutions; and what are the flow interactions between the river and the marshes within the coastal region of the Lower St. Johns River? Reviewing the available data provides an initial perspective of the ecosystem. For this, salinity data are obtained and assembled for three modeling scenarios. Each scenario, High Extreme, Most Variable, and Low Extreme, is 30 days long (taken from year 12) and represents a unique salinity regime in the Lower St. Johns River. Time-series of salinity data is collected at four stations in the lower and middle reaches of the Lower St. Johns River, which provides a vantage point for assessing longitudinal variation of salinity. As an aside, precipitation and evaporation data is presented for seven stations along the entire St. Johns River, which provides added insight into salinity transport in the river. A mass conservation analysis is conducted for the Lower St. Johns River. The analysis utilizes a segmentation of the Lower St. Johns River, which divides the domain into sections based on physical characteristics. Mass errors are then calculated for the CG and DG finite element methods to determine mass conservative abilities. Also, the flow interactions (i.e., volume exchange) between the river and marshes are evaluated through the use of tidal prisms. The CG- and DG- finite element methods are then tested in tidal simulation performance, which the results are then compared to observed tides and tidal currents at four stations within the lower portion of the Lower St. Johns River. Since the results show that the DG model outperforms the CG model, the DG model is used in the tidally driven salinity transport simulations. Using four stations within the lower and middle part of the Lower St. Johns River, simulated and observed water levels and salinity concentrations are compared.

  • Title: Web-based tidal toolbox of astronomic tidal data for the Atlantic Intracoastal Waterway estuaries and continental shelf of the South Atlantic Bight
    Authors: Ruiz, A.
    Location: MS thesis, University of Central Florida, Orlando Florida (2011)

    A high-resolution astronomic tidal model has been developed that includes detailed inshore regions of the Atlantic Intracoastal Waterway and associated estuaries along the South Atlantic Bight. The unique nature of the model’s development ensures that the tidal hydrodynamic interaction between the shelf and estuaries is fully described. Harmonic analysis of the model output results in a database of tidal information that extends from a semi-circular arc (radius ~750 km) enclosing the South Atlantic Bight from the North Carolina coast to the Florida Keys, onto the continental shelf and into the full estuarine system. The need for tidal boundary conditions (elevation and velocity) for driving inland waterway models has motivated the development of a software application to extract results from the tidal database which is the basis of this thesis. In this tidal toolbox, the astronomic tidal constituents can be resynthesized for any open water point in the domain over any interval of time in the past, present, or future. The application extracts model results interpolated to a user’s exact geographical points of interest, desired time interval, and tidal constituents. Comparison plots of the model results versus historical data are published on the website at 89 tidal gauging stations. All of the aforementioned features work within a zoom-able geospatial interface for enhanced user interaction. In order to make tidal elevation and velocity data available, a web service serves the data to users over the internet. The tidal database of 497,847 nodes and 927,165 elements has been preprocessed and indexed to enable timely access from a typical modern web server. The preprocessing and web services required are detailed in this thesis, as well as the reproducibility of the Tidal Toolbox for new domains.

  • Title: Temperature-dependent properties of 147- and 309-atom iron-gold nanoclusters
    Authors: R. I. Gonzalez, G. Garcia, R. Ramirez, M. Kiwi, J. A. Valdivia & T. S. Rahman
    Location: Phys. Rev. B 83. 155425 (2011)

    The properties of several AuN and AuN-xFex nanoclusters are obtained by means of classical molecular dynamics calculations. In particular we study the configurations Au147, Au134Fe13, Au309, and Au254Fe55, which correspond to icosahedral magic numbers, for both the gold and the iron. We investigate the melting and freezing processes, atomic diffusion, hardness, vibration spectra, and specific heat of these nanoclusters. All the data obtained point toward the stability of the AuN-xFex system, with the gold atoms on the outside of the iron core.

  • Title: Production runs for the Big Bend Region of Florida
    Authors: Toro, G., Hagen, S. C., Atkinson, J., & Reed, C.
    Location: Florida Watershed Journal (2011) 4(2) 28-35.

  • Title: OneSAF Implementation on High Performance Computing Systems
    Authors: Bouwens, C., Hasan, O., Lopez, S., Smith, R., Li, J., Dere, T., Poole, J., Paschal, A. & Wiegand, P.
    Location: 2011 Spring SISO SIW Conference [Boston MA]

    Implementing One Semi Automated Forces (OneSAF(R)) (Department of the Army) on massively parallel, distributed high performance computing (HPC) systems has the potential to create large-scale events. To achieve this, users have been exploring the scalability of OneSAF in the context of distributed multi-node, multi-core systems versus the traditional networked workstation model. Such implementations would allow OneSAF to support analysis, acquisition, planning, testing, training, and experimentation on a larger scale. This paper will highlight some of the OneSAF HPC implementations to date and provide a summary of lessons learned for other users who may be interested in the use of HPCs for their forces modeling and simulation (FMS) applications. Implementations include: OneSAF on the UCF Stokes system (work by Army Research Laboratory and the University of Central Florida’s Institute for Simulation and Training (UCF IST)); Communications-Electronics Research, Development, and Engineering) Center’s (CERDEC’s) Command, Control, Communications, Computers, Intelligence Surveillance and Reconnaisance (C4ISR) and Network Modernization on Halle and Harold (U.S. Army Research Laboratory DoD Supercomputing Research Center, ARL DSRC); Space and Missile Defense Command (SMDC) and Redstone Test Center (RTC) implementations for laboratory and hardware-in-the-loop testing support.

  • Title: Deriving frictional parameters and performing historical validation for an ADCIRC storm surge model of the Florida Gulf Coast
    Authors: Atkinson, J., Roberts, H., Hagen, S. C., Zou, S., Bacopoulos, P., Medeiros, S., Weishampel, J. & Cobell, Z.
    Location: Florida Watershed Journal (2011) 4(2) 22-27.

  • Title: 1st Multidisciplinary Science Forum University of Washington Seattle USA
    Authors: Mirza, S., Doutrich, D., Hu, Y., Wickramsinghe, R., Peng, D. Sugawara, H., Kaneko, F., Win, T., Omura, A., Tanigaki, K., Palaniappan, R. & others
    Location: 1st Multidisciplinary Science Forum University of Washington Seattle USA

    This work highlights some of the on-going research in several different areas of interactive simulation using High Performance Computing (HPC) at the University of Central Florida (UCF). We are researching interactive simulation architectures and algorithms to enable scalability and analyze performance issues across multiple cores on a HPC system. UCF HPC system named “STOKES” includes 73 blades servers of Dual Xeon Quad Core Processors (648 cores) connected together by a 20 Gbps High-speed Infiniband interconnect, 1.392 TB of memory and 43 TB of raw storage space. The system is capable of 6.6 TFlops. We are investigating interactive Massive Multi-player Online gaming (MMOG) on High Performance Computing systems. Initiated by Sun Microsystems project Darkstar develops middleware/network stack for developers to seamlessly scale their games over a cluster of servers. We were able to successfully run/test the Darkstar server and client on the UCF HPC by playing a 3D multilayer game, snowman, with the server running on STOKES and clients running on laptops and workstations. We have confirmed that the multi-threaded Darkstar server, when run on a single node of STOKES uses the processing power of all the available processor cores and that a single-node server can handle 1000 simulated clients with only 10% CPU utilization. One of the limitations of current version of Darkstar server is that its multi-node capability, which scales negatively. We are proposing a new Persistence and Communication architecture based on overlapping micro-cells that will exploit the large memory and the high-speed Infiniband available on HPC systems. We demonstrate how our novel architecture implements scalability, fault tolerance, dynamic load balancing and seamless movement across cell boundaries. Another area of investigation is distribution scaling and performance issues in constructive simulations of CGFs, with a particular focus on OneSAF. We are analyzing OneSAF efficiency for large scenarios (thousands of entities) in multi-core / multi-blade configurations on the HPC. We are also exploring benchmarks that can appropriately address the scaling capabilities of distributed constructive simulation. Our final area of research is dynamic terrain on High Performance Computing systems. Dynamic terrain is an approach to increase the fidelity and interactivity of a simulation by modifying the terrain as users interact in the environment. We are implementing dynamic terrain in order to study the effects and considerations of distributing such a simulation on multi-core systems. This work will be of benefit to military large-scale war-gaming simulations.

  • Title: Tidal spectroscopy of the Lower St. Johns River from a high-resolution shallow water hydrodynamic model
    Authors: Giardino, D., Bacopoulos, P. & Hagen, S. C.
    Location: International Journal of Climate and Ocean Systems (2011) 2(1) 1-18

    The nonlinear distortion of the astronomic tide in the Lower St. Johns River is investigated. Computed tidal elevations are analyzed at various locations within the Lower St. Johns River. The modeling approach first evaluates the boundary condition applied at the open ocean with regards to it providing a complete description of the tidal elevation, followed by numerical experimentation and a tidal constituent analysis that examines the effects of finite wave amplitude, advection, and bottom friction towards distorting the tide as it propagates upriver. The distortions caused by each nonlinear source are presented in both the time and frequency domains. Analysis at observation stations reveals a river tide with more coastal characteristics near the mouth and with more considerable distortion upriver. The spectroscopy of the astronomic tide for the Lower St. Johns River is established in terms of a custom set of tidal constituents.

  • Title: Near-field enhancement of infrared intensities for ff transitions in Er 3+ ions close to the surface of silicon nanoparticles
    Authors: Borowska, L., Fritzsche, S., Kik, P.G. & Masunov, A.E.
    Location: Journal of Molecular Modeling 17 3 (2011) pp. 423–428.

    Erbium doped waveguide amplifiers can be used in optical integrated circuits to compensate for signal losses. Such amplifiers use stimulated emission from the first excited state (4 I 13/2) to the ground state (4 I 15/2) of Er3+ at 1.53 um, the standard wavelength for optical communication. Since the intra-f transitions are parity forbidden for free Er3+ ions, the absorption and the emission cross sections are quite small for such doped amplifiers. To enhance the absorption, Si nanoclusters can be embedded in silica matrix. Here we investigate the effect of the Si nanocluster on the Er3+ emission using ab initio theory for the first time. We combine multi-reference configuration interaction with one-electron spin-orbit Hamiltonian and relativistic effective core potentials. Our calculations show that the presence of a polarizable Be atom at 5? from the Er3+ ion in a crystalline environment can lead to an enhancement in the emission by a factor of three. The implications of this effect in designing more efficient optical gain materials are discussed.

  • Title: Unveiling electronic transitions in three novel chiral azo-compounds using linear and nonlinear circular dichroism: A theoretical-experimental study
    Authors: Carlos Toro, Remy Passier, Carlos Diaz, Tero Tuuttila, Kari Rissanen, Juhani Huuskonen & Florencio E. Hernandez
    Location: J. Phys. Chem. A 115 1186 ( 2011 )

    Herein, we report on the experimental and theoretically study of the linear absorption, electronic circular dichroism (ECD) spectra, as well as the two-photon absorption circular-linear dichroism measurements of three different chiral azo derivatives in dimethylsulfoxide solution. Using potential energy surfaces and frontier orbital analysis, we established the most stable conformation for each molecule and elucidated their different electronic transitions. Our theoretical calculations allowed us to unambiguously identify the spectral position of such transitions and correlate them with the spectral profiles observed in the two-photon absorption spectra. To further elucidate the characteristics of the main electronic transitions in terms of spectral shape and position, we carried out measurements of the polarization dependent two-photon absorption cross sections and determined the two-photon circular-linear dichroism spectra of these azo dyes.

  • Title: Single Photon Near Field Emission and Revival in Quantum Dots
    Authors: Tafur, S. & Leuenberger, M.N.
    Location: Arxiv preprint arXiv:1011.6566 (2010)

    Models of the spontaneous emission of photons coupled to the electronic states of quantum dots are important for understanding quantum interactions in dielectric media as applied to proposed solid-state quantum computers, single photon emitters, and single photon detectors. The characteristic lifetime of photon emission is traditionally modeled in the Weisskopf-Wigner approximation. Here we model the fully quantized spontaneous emission, including near field effects, of a photon from the excited state of a quantum dot beyond theWeisskopf-Wigner approximation. We propose the use of discretized central-difference approximations to describe single photon states via single photon operators in 3+1 dimensions. We further show herein that one can shift from the traditional description of electrodynamics and quantum electrodynamics, in terms of electric and magnetic fields to one in terms of a photonic wave function and its operators using the Dirac equation for the propagation of single photons.

  • Title: DFT+DMFT approach for Nanosystems
    Authors: V. Turkowski, A. Kabir, N. Nayyar & T.S. Rahman
    Location: J. Phys. Condens. Matt (Fast Track) 22 462202 (2010)

    We propose a combined density-functional-theory–dynamical-mean-field-theory (DFT + DMFT) approach for reliable inclusion of electron–electron correlation effects in nanosystems. Compared with the widely used DFT + U approach, this method has several advantages, the most important of which is that it takes into account dynamical correlation effects. The formalism is illustrated through different calculations of the magnetic properties of a set of small iron clusters (number of atoms 2 = N = 5). It is shown that the inclusion of dynamical effects leads to a reduction in the cluster magnetization (as compared to results from DFT + U) and that, even for such small clusters, the magnetization values agree well with experimental estimations. These results justify confidence in the ability of the method to accurately describe the magnetic properties of clusters of interest to nanoscience.

  • Title: Effective elastic properties of a van der Waals molecular monolayer at a metal surface
    Authors: D. Sun, D-H. Kim, D. Le, Ø. Borck, K. Berland, K. Kim, W. Lu, Y. Zhu, M. Luo, J. Wyrick, Z. Cheng, T. L. Einstein, T. S. Rahman, P. Hyldgaard & L. Bartels
    Location: Phys. Rev. B 82 201410 (2010)

    Adsorbing anthracene on a Cu(111) surface results in a wide range of complex and intriguing superstructures spanning a coverage range from 1 per 17 to 1 per 15 substrate atoms. In accompanying first-principles density-functional theory calculations we show the essential role of van der Waals interactions in estimating the variation in anthracene adsorption energy and height across the sample. We can thereby evaluate the compression of the anthracene film in terms of continuum elastic properties, which results in an effective Young’s modulus of 1.5 GPa and a Poisson ratio ˜0.1. These values suggest interpretation of the molecular monolayer as a porous material—in marked congruence with our microscopic observations.

  • Title: Time-dependent density-matrix functional theory for biexcitonic phenomena
    Authors: V. Turkowski, C.A. Ullrich, T.S. Rahman & M.N. Leuenberger
    Location: Phys. Rev. B 82 205208 (2010)

    We formulate a time-dependent density-matrix functional theory (TDDMFT) approach for higher-order correlation effects like biexcitons in optical processes in solids based on a reduced two-particle density-matrix formalism within the normal orbital representation. A TDDMFT version of the Schrödinger equation for biexcitons in terms of one- and two-body reduced density matrices is derived, which leads to finite biexcitonic binding energies already with an adiabatic approximation. Biexcitonic binding energies for several bulk semiconductors are calculated using a contact biexciton model.

  • Title: Thermally controlled preferential molecular aggregation state in a thiacarbocyanine dye
    Authors: Remy Passier, James P. Ritchie, Carlo Toro, Carlos Diaz, Artem E. Masunov, Kevin D. Belfield & Florencio E. Hernandez
    Location: J. Chem. Phys. 133 134508/1 (2010)

    Herein we report the experimental and theoretical study of the temperature dependence of a thiacarbocyanine dye in its monomer, H- and J-aggregates states. We demonstrate the ability to control the ratio of monomer, H- and/or J-aggregates with heat. We link such a control to the conformation dependence of the molecule. An alternative way to gain access to the dominating species without changing the concentration as a complete switching mechanism between all the present species is proposed. The results presented in this work lead to a better understanding of thiacarbocyanine dye’s behavior.

  • Title: Density functional study of oxygen vacancy formation and spin density distribution in octahedral ceria nanoparticles
    Authors: Inerbaev, T.M., Seal, S. & Masunov, A.E.
    Location: Journal of molecular modeling 16 10 (2010) pp. 1617–1623

    We report plane wave basis density functional theory (DFT) calculations of the oxygen vacancies formation energy in nanocrystalline CeO 2-x in comparison with corresponding results for bulk and (111) CeO2 surface. Effects of strong electronic correlation of Ce4f states are taken into account through the use of an effective on-site Coulomb repulsive interaction within DFT+U approach. Different combinations of exchange-correlation functionals and corresponding U values reported in the literature are tested and the obtained results compared with experimental data. We found that both absolute values and trends in oxygen vacancy formation energy depend on the value of U and associated with degree of localization of Ce4f states. Effect of oxygen vacancy and geometry optimization method on spatial spin distribution in model ceria nanoparticles is also discussed.

  • Title: Theoretical spectroscopy of carbocyanine dyes made accurate by frozen density correction to excitation energies obtained by TD-DFT
    Authors: Masunov, A.E.
    Location: International Journal of Quantum Chemistry 110 15 (2010) pp. 3095–3100

    We present long-awaited answer to the puzzling question of why the TD-DFT fails to predict the excitation energies in polymethine dyes accurately. The density functional theory methods were suspected to be inaccurate due to self interaction error inherent in exchange-correlation potentials. Here we decisively show that it is the linear response approximation that is responsible for these inaccuracies. Next, we use frozen density to evaluate the excitation energy beyond the linear response and increase the accuracy of the predictions. This recipe uniformly improves the accuracy of the first absorption maxima prediction in cyanine homologous series to within 25 nm. (C) 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010

  • Title: Ab initio calculations of the dispersion of surface phonons of a c(2×2) CO overlayer on Ag(001)
    Authors: M. Alcántara-Ortigoza, T. S. Rahman, R. Heid & K. P. Bohnen
    Location: J. Phys. Condens. Matter 22 395001 (2010).

    We examine the phonon dispersion of c(2 × 2)-CO on Ag(001) by applying density functional perturbation theory with the generalized-gradient approximation. Our calculations indicate that the c(2 × 2)-CO overlayer on Ag(001) is dynamically stable. We find that the bond length of CO is expanded and its stretch mode (?1) softened by ~ 9 meV upon adsorption on Ag(001), in excellent agreement with experiments. We show that ?1 at ar {Gamma } alone cannot gauge the metal–CO interaction since it is not entirely determined by the C–O intramolecular force constant. Further softening of ?1 on Ag(001) is obtained outside ar {Gamma } , indicative of CO–CO interactions even at a distance of ~ 4 Å. The frequency of the Ag–CO stretch mode (?2) is ~ 30 meV and it is nearly dispersionless, implying that the perturbation corresponding to this mode is short-ranged. The frustrated rotation mode of CO (?3) overlaps with the bulk band and mixes with substrate modes inside the SBZ, suggesting this as one of the key features for the enhanced diffusivity of CO on Ag surfaces over that on Cu surfaces. The frustrated translation mode of CO (?4) is everywhere below ~ 2.8 meV and therefore mixes with substrate modes in the region of the SBZ around ar {Gamma } . Depending on the q vector, vertical and in-plane surface modes may soften or stiffen with respect to their counterpart on clean Ag(001). Although the response of most Ag(001) modes to CO adsorption is similar to that of corresponding Cu(001) modes, there are some contrasting features between the dynamics of the two surfaces concerning the changes in the surface force constants and mixing of S6 with ?3 on Ag(001).

  • Title: Diffusion of the Cu monomer and dimer on Ag(111): Molecular dynamics simulations and density functional theory calculations
    Authors: S. Sikandar Hayat, M. Alcántara-Ortigoza & T. S. Rahman
    Location: Phys. Rev. B 82 085405 (2010)

    We present results of molecular dynamics (MD) simulations and density functional theory (DFT) calculations of the diffusion of Cu adatom and dimer on Ag(111). We have used potentials generated by the embedded-atom method for the MD simulations and pseudopotentials derived from the projected-augmented-wave method for the DFT calculations. The MD simulations (at three different temperatures: 300, 500, and 700 K) show that the diffusivity has an Arrhenius behavior. The effective energy barriers obtained from the Arrhenius plots are in excellent agreement with those extracted from scanning tunneling microscopy experiments. While the diffusion barrier for Cu monomers on Ag(111) is higher than that reported (both in experiment and theory) for Cu(111), the reverse holds for dimers [which, for Cu(111), has so far only been theoretically assessed]. In comparing our MD result with those for Cu islets on Cu(111), we conclude that the higher barriers for Cu monomers on Ag(111) results from the comparatively large Ag-Ag bond length, whereas for Cu dimers on Ag(111) the diffusivity is taken over and boosted by the competition in optimization of the Cu-Cu dimer bond and the five nearest-neighbor Cu-Ag bonds. Our DFT calculations confirm the relatively large barriers for the Cu monomer on Ag(111)—69 and 75 meV—compared to those on Cu(111) and hint a rationale for them. In the case of the Cu dimer, the relatively long Ag-Ag bond length makes available a diffusion route whose highest relevant energy barrier is only 72 meV and which is not favorable on Cu(111). This process, together with another involving an energy barrier of 83 meV, establishes the possibility of low-barrier intercell diffusion by purely zigzag mechanisms.

  • Title: Selective Oxidation of Ammonia on RuO2(110): a combined DFT and KMC study
    Authors: S. Hong, A. Karim, T. S. Rahman, K. Jacobi & G. Ertl
    Location: J. Catalysis 276 371 (2010)

    We have used a combination of density functional theory (DFT) and kinetic Monte Carlo (KMC) simulations to calculate the reaction rates for the selectiveoxidation of ammonia on RuO2(1 1 0). Our KMC simulations of 18 reactions among NHx(x=0–3) and OHx(x=0–2) species on RuO2(1 1 0) show 93% selectivity for NO, in close agreement with experiment (~95%). The chief factor in the high selectivity for NO on the RuO2(1 1 0) surface is the significantly reduced N diffusion (via N blocking) caused by various intermediates present on the RuO2(1 1 0) surface, which severely inhibits the recombination rate of N + N ? N2 but interfere far less with that of N + O ? NO owing to the nearby availability of O from dissociation of O2.

  • Title: Weak antiferromagnetic coupling in molecular ring is predicted correctly by density functional theory plus Hubbard U
    Authors: Gangopadhyay, S., Masunov, A.E., Poalelungi, E. & Leuenberger, M.N.
    Location: The Journal of chemical physics 132 (2010) pp. 244104

    We apply density functional theory with empirical Hubbard U parameter (DFT+U) to study Mn-based molecular magnets. Unlike most previous DFT+U studies, we calibrate U parameters for both metal and ligand atoms using five binuclear manganese complexes as the benchmarks. We note delocalization of the spin density onto acetate ligands due to ?-back bonding, inverting spin polarization of the acetate oxygen atoms relative to that predicted from superexchange mechanism. This inversion may affect the performance of the models that assume strict localization of the spins on magnetic centers for the complexes with bridging acetate ligands. Next, we apply DFT+U methodology to Mn12 molecular wheel and find antiparallel spin alignment for the weakly interacting fragments Mn6, in agreement with experimental observations. Using the optimized geometry of the ground spin state instead of less accurate experimental geometry was found to be crucial for this good agreement. The protocol tested in this study can be applied for the rational design of single molecule magnets for molecular spintronics and quantum computing applications.

  • Title: Are density functional theory predictions of the Raman spectra accurate enough to distinguish conformational transitions during amyloid formation?
    Authors: Berhanu, W.M., Mikhailov, I.A. & Masunov, A.E.
    Location: Journal of Molecular Modeling 16 6 (2010) pp. 1093–1101

    We report density functional theory (DFT) calculations of the Raman spectra for hexapepetides of glutamic acid and lysine in three different conformations (?, ? and PPII). The wave numbers of amide I, amide II and amide III bands of all three conformations predicted at B3LYP/6-31G and B3LYP/6-31G* are in good agreement with previously reported experimental values of polyglutamic acid and polylysine. Agreement with experiment improves when polarization functions are included in the basis set. Explicit water molecules, H-bonded to the backbone amide groups were found to be absolutely necessary to obtain this agreement. Our results indicate that DFT is a promising tool for assignment of the spectral data on kinetics of conformational changes for peptides during amyloid formation.

  • Title: Natural polyphenols as inhibitors of amyloid aggregation. Molecular dynamics study of GNNQQNY heptapeptide decamer
    Authors: Berhanu, W.M. & Masunov, A.E.
    Location: Biophysical chemistry 149 1-2 (2010) pp. 12–21

    Amyloid-like fibrils had been associated with many fatal diseases, and the rational design of the fibrillization inhibitors holds the great promise of finding the prevention and treatment options. The understanding of the mechanisms by which the small molecules can inhibit the aggregation plays the key role in such design. Here we present the results of MD simulations that provide the atomistic details of the process, by which the small molecules may destabilize the ordered amyloid oligomers formed by the model hexapeptide. We select a heptapeptide fragment (GNNQQNY) from Sup-35 yeast prion protein, which is capable to form both amyloid fibrils and microcrystals. Atomic-resolution structures of its crystals were reported by Eisenberg et al. (Nature 447:453, 2007). We analyze several MD trajectories describing the evolution of the decamer fragment taken from this crystal structure, both by itself and in the presence of myricetin and kaempferol (two naturally occurring polyphenols, found to be strong and weak aggregation inhibitors). While the decamer of GNNQQNY demonstrates remarkable stability of its structure after 2 ns simulation, myricretin disturbs the aggregation. The simulations show myricetin interacts with the ?-sheet due to polar interactions with side chains of the peptide weakening the interstrand hydrogen bonds, wrapping the ?-sheet and disaggregating the outer layer. Both backbone to backbone and side chain to side chain hydrogen bonds are lost, and the ?-sheets are moving away from each other. This leads to the loss of backbone H-bonding and eventual separation of one ?-strands from the outer layer. We also test several AMBER force fields and implicit solvent models for their ability to keep the decamer of GNNQQNY aggregated. The RMSDs of decamer of GNNQQNY with force field 99SB and implicit solvent models of igb2 and igb5, were maintained at less than 4.

  • Title: Theoretical calculations of hydrogen adsorption by SnO2 (110) surface: Effect of doping and calcination
    Authors: Inerbaev, T.M., Kawazoe, Y. & Seal, S.
    Location: Journal of Applied Physics 107 10 ( 2010 ) pp. 104504–104504

    A pseudopotential plane-wave based density functional theory simulations of the hydrogen adsorption on rutile SnO2 (110) surface is reported. It is found that on doping with trivalent indium, the surface becomes unstable due to the formation of bridging oxygen vacancies. At sufficiently low doping level, the surface stabilizes at an oxygen vacancy to indium ratio of 1:2. Our calculations predict that at a higher doping level of 9 at. %, this ratio becomes larger, and point out a way to synthesize p-type conducting SnO2 thin films. The binding energy of SnO2 (110) surface with adsorbed hydrogen atoms display a maximum at 3-6 at. % of indium doping. This is in good agreement with the experimental results obtained from the SnO2-based hydrogen sensor’s sensitivity measurements given by Drake etal [J. Appl. Phys. 100, 104307 (2007)]. The theoretical modeling explains that the calcinations treatment can critically affect the sensitivity of the hydrogen sensor due to the enhancement of the binding energy between the SnO2 surface and the adsorbed hydrogen atoms.

  • Title: Vibrational Dynamics of a c(2×2) phase Induced by nitrogen adsorption on Cu(001)
    Authors: E.Z. Ciftlikli, L.V. Goncharova, B.J. Hinch, M. Alcántra Ortigoza, S. Hong & T.S. Rahman
    Location: Phys. Rev. B 81 115465 (2010)

    Helium-atom scattering and density-functional perturbation theory (DFPT) calculations invoking the linear-response approximation and the pseudopotential approach have been used to study the vibrational dynamics of c(2×2)-like phases produced by nitrogen-ion implantation and subsequent annealing of Cu(001) surfaces. We find that, while the c(2×2) phonon dispersion relations are different from those of clean Cu(001), neither the acoustic nor the optical surface phonon mode energies measured along both [100] and [11¯ 0] directions are dependent on N coverage once the c(2×2) pattern is formed. We show that the dispersion of the surface phonon modes is well reproduced with an analysis of the DFPT calculations of a nonstress relieved c(2×2) structure. A marked softening of a zone center optical mode is very apparent both experimentally and in the calculations. We show this softening arises largely because of interplanar Cu surface relaxations induced by N adsorption.

  • Title: Azo-group dihedral angle torsion dependence on temperature: A theorerical-experimental study
    Authors: Leonardo De Boni, Carlos Toro, Sergio C. Zilio, Cleber R. Mendonca & Florencio E. Hernandez
    Location: Chem. Phys. Lett. 487 226 (2010)

    Quantum chemical calculations were carried out to explain the observed shifts in the absorption spectrum of different azo-aromatic compounds due to changes in the dihedral angle of the azo-group. Our results reveal that the ?-?* transition presents a hypsochromic shift and an oscillator strength drop upon increase of the dihedral angle. Nevertheless, the n-?* transition exhibits the opposite behavior. This effect is attributed to the reduction in the ?-electron conjugation length of the molecule. Experimentally, we performed temperature dependence measurements of the linear absorption spectrum. Both the theoretical and experimental results demonstrate that small energy changes are mirrored in the electronic transitions of conjugated linear molecules.

  • Title: Surface vibrational thermodynamics from ab initio calculations for fcc(100)
    Authors: H. Yildirim, A. Kara, T. S. Rahman, R. Heid & K.P. Bohnen
    Location: Surf. Sci. 604 308 (2010).

    We present vibrational dynamics and thermodynamics for the (1 0 0) surfaces of Cu, Ag, Pd, Pt and Au using a real space approach. The force field for these systems is described by density functional theory. The changes in the vibrational dynamics and thermodynamics from those in bulk are confined mostly to the first-layer. A substantial enhancement of the low-frequency end of the acoustic branch was found and is related to a loosening of the bond at the surface. The thermodynamics of the first-layer also show significant differences (higher heat capacity, lower free energy and higher mean vibrational square amplitudes) from what obtains in bulk. Comparing these results with those calculated using embedded-atom method potentials, we discovered that for Ag(1 0 0) and Cu(1 0 0), the two methods yield very similar results while for Pd(1 0 0), Pt(1 0 0) and Au(1 0 0) there are substantial differences.

  • Title: Polarization Dependent Two-photon Absorption Properties of Chiral Molecules
    Authors: Toro, C.
    Location: PhD dissertation, University of Central Florida, Orlando Florida (2010)

    Molecules that are non-superimposable on their mirror image are named chiral or optically active compound. Over the years, molecular chirality has played an essential role in the understanding of fundamental aspects associated the origin of life, drug and food technologies and, asymmetric catalysis, among others. Moreover,most of the groundbreaking discoveries and advances made in this field have happened due to the development of spectroscopic techniques based on the natural asymmetry of the enantiomers and their ability to preferentially absorb right or left polarized light. For instance, circular dichroism (CD), which measures the difference in absorption between these two states of polarized light, has emerged as one of the most useful spectroscopic methods to identify and characterize chiral compounds. Unfortunately, CD is based on linear absorption which, in most common organic molecules, takes place in the UV region of the spectrum where the majority of organic solvents absorb as well. This certainly imposes limitations in the indiscriminated applicability of this technique to the study of chiral chromophores of biological interest in non-aqueous solutions. Consequently, a systematic and comprehensive characterization of the electronic and optical properties of such molecular entities still remains a major issue to be addressed. On this regard, nonlinear optics offers new alternatives to overcome some of the shortcomings of the standard linear CD-based spectroscopy. In order to surmount the existent limitations in this field and deepen in the fundamental understanding of chiral systems, we have mainly directed the attention of our research to the experimental and theoretical study of the polarization dependent two-photon absorption (2PA) of several chiral azo-compounds and binaphthol derivatives in solution The first part of this dissertation (Chapters I-IV) covers a full characterization of the linear and nonlinear optical properties of a series of non-chiral and chiral azo derivatives. The combination of experimental techniques such as absorption, fluorescence, excitation anisotropy, circular dichroism, two-photon absorption and two-photon absorption circular-linear dichroism in combination with density functional theory calculations allowed us to unambiguously distinguish and assign the spectral position of the main electronic transitions ($n-pi^*$ and $pi-pi^*$) in azobenzene derivatives. Our results represent a major contribution to the understanding of the electronic structure of these organic chromophores which have been reported of potential interest in the design of optoelectronic devices. Then, Chapter V describes the development of a novel experimental technique called the synchronized double L-scan for the study of polarization dependent multiphoton absorption in chiral samples. The high sensitivity of this technique resides in the use of “twin” pulses to account for energy and mode fluctuations of the excitation pulse when det

  • Title: Simulation of Photochromic Compounds Using Density Functional Theory Methods
    Authors: Patel, P.D.
    Location: PhD dissertation, University of Central Florida, Orlando Florida (2010)

    This Thesis describes the systematic theoretical study aimed at prediction of the essential properties for the functional organic molecules that belong to diarylethene (DA) family of compounds. Diarylethenes present the distinct ability to change color under the influence of light, known as photochromism. This change is due to ultrafast chemical transition from open to closed ring isomers (photocyclization). It can be used for optical data storage, photoswitching, and other photonic applications. In this work we apply Density Functional Theory methods to predict 6 of the related properties: (i) molecular geometry; (ii) resonant wavelength; (iii) thermal stability; (iv) fatigue resistance; (v) quantum yield and (vi) nanoscale organization of the material. In order to study sensitivity at diode laser wavelengths, we optimized geometry and calculated vertical absorption spectra for a benchmark set of 28 diarylethenes. Bond length alternation (BLA) parameters and maximum absorption wavelengths (?max) are compared to the data presently available from X-ray diffraction and spectroscopy experiments. We conclude that TD-M05/6-31G*/PCM//M05-2X/6-31G*/PCM level of theory gives the best agreement for both the parameters. For our predictions the root mean square deviation (RMSD) are below 0.014 ? for the BLAs and 25 nm for ?max. The polarization functions in the basis set and solvent effects are both important for this agreement. Next we consider thermal stability. Our results suggest that UB3LYP and UM05- 2X functionals predict the activation barrier for the cycloreversion reaction within 3-4 kcal/mol from experimental value for a set of 7 photochromic compounds. We also study thermal fatigue, defined as the rate of undesirable photochemical side reactions. In order to predict the kinetics of photochemical fatigue, we investigate the mechanism of byproduct formation. It has been established experimentally that the by-product is formed from the closed isomer; however the mechanism was not known. We found that the thermal by-product pathway involves the bicyclohexane (BCH) ring formation as a stable intermediate, while the photochemical by product formation pathway may involve the methylcyclopentene diradical (MCPD) intermediate. At UM05-2X/6-31G* level, the calculated barrier between the closed form and the BCH intermediate is 51.2 kcal/mol and the barrier between the BCH intermediate and the by-product 16.2 kcal/mol. Next we investigate two theoretical approaches to the prediction of quantum yield (QY) for a set of 14 diarylethene derivatives at the validated M05-2X/6-31G* theory level. These include population of ground-state conformers and location of the pericycylic minimum on the potential energy surface 2-A state. Finally, we investigate the possibility of nanoscale organization of the photochromic material based on DNA template, as an alternative to the amorphous polymer matrix. Here we demonstrate that Molecular Dynamic methods are capable to describ

  • Title: Excited state absorption study in Hematoporphyrin IX
    Authors: Leonardo De Boni, Carlos Toro & Florencio E. Hernandez
    Location: The Journal of Fluorescence 20 197 (2010)

    We present the study of the excited state absorption of Hematoporphyrin IX dissolved in dimethyl sulfoxide. All measurements were carried out using open aperture Z-scan and white-light continuum pump-probe with picosecond pulses to avoid triplet excited state absorption. Without the latter contribution, the results obtained with both techniques show a transition to a high singlet excited state. The vibronic progression of the Q-band is observed due to photobleaching of the ground state. In addition, we show that the excited state presents reverse saturable absorption for most of the spectral range studied. A long relaxation component of the first singlet excited state was evidenced with the pump-probe experiment. This result is in agreement with fluorescence lifetime and fluorescence quantum yield measurements. In order to elucidate the origin of the nonlinear effects, we used a three-level energy diagram to describe the principal singlet-singlet transitions.

  • Title: Estuarine influence on tidally driven circulation in the South Atlantic Bight
    Authors: Bacopoulos, P.
    Location: PhD dissertation, University of Central Florida, Orlando Florida (2009)

    The focus of this thesis is the forcing mechanisms incorporated with salinity transport for the Lower St. Johns River. There are two primary analyses performed: a historical data analysis of primary forcing mechanisms to determine the importance of each individual influence, and a tidal hydrodynamics analysis for the Lower St. Johns River to determine the required tidal constituents for an accurate resynthesis. This thesis is a preliminary effort in understanding salinity transport for the Lower St. Johns River for engineering projects such as the dredging of navigation canals and freshwater withdrawal from the river. The analysis of the physical forcing mechanisms is performed by examining the impact of precipitation, tides, and wind advection on historical salinity measurements. Three 30-day periods were selected for the analysis, to correspond with representative peak, most-variable, and low-salinity periods for 12. The analysis displays that wind advection is the dominant forcing mechanism for the movement of salinity over a 30 day duration; however all mechanisms have an impact at some level. The dominant forcing mechanism is also dependent on the period of record examined where tidal influence is vital for durations of hours to a day, while freshwater inflow has more significance over a longer period due to climatological variation. A two-dimensional finite difference numerical model is utilized to generate a one month tidal elevations and velocities simulations that incorporates geometry, nonlinear advection and quadratic bottom friction. Several combinations of tidal constituents are extracted from this modeled tidal signal to investigate which combination of tidal constituents produces an accurate tidal resynthesis for the Lower St. Johns River. The analysis displays the need for 39 total tidal harmonic constituents to accurately resynthesize the original tidal signal. Additionally, due to the nonlinear nature of shallow water, the influence of the overtides for upstream or downstream locations in the Lower St. Johns River is shown to be spatially variable for different frequencies depending on the geometry. The combination of the constituent analysis and the historical analysis provides the basis information needed for the development of an accurate salinity transport model for the Lower St. Johns River.

  • Title: Electronic Properties of a New Two-Photon Absorbing Fluorene Derivative: The Role of Hartree–Fock Exchange in the Density Functional Theory Design of Improved Nonlinear Chromophores
    Authors: Mikhailov, I.A., Bondar, M.V., Belfield, K.D. & Masunov, A.E.
    Location: Journal of Physical Chemistry C 113, 48 (2009), pp. 20719–20724

    One- and two-photon absorption (2PA) properties of a new fluorene derivative with diphenylamino and 2-(2?-hydroxyphenyl)benzothiazole substituents were investigated theoretically using the density functional theory approach with different types of functionals and experimentally by two-photon induced fluorescence methodology. The effect of the exchange-correlation functional choice on the description of 2PA properties of fluorenes was analyzed. The best agreement of the experimental and theoretical 2PA spectra was obtained with a custom modification of the hybrid M05 functional that included 35% of Hartree-Fock exchange. This functional is recommended for reliable prediction of nonlinear optical properties of conjugated molecules. A chemical modification of the studied compound is suggested to increase the 2PA cross section.

  • Title: Computational search for nonlinear optical materials: are polarization functions important in the hyperpolarizability predictions of molecules and aggregates?
    Authors: Suponitsky, K.Y., Masunov, A.E. & Antipin, M.Y.
    Location: Mendeleev Communications 19, 6 (2009), pp. 311–313

    Hyperpolarizability of conjugated molecules with relatively long ?-system (three and more double bonds in the ?-bridge) and molecular aggregates (composed of the same molecules) can be predicted at the Density Functional Theory level with the 6-31G basis set to within 5-10% (compared to 6-31+G* results), while 6-31G* and especially MIDI! basis sets are much less accurate.

  • Title: Electronic Hyperpolarizabilities for Donor- Acceptor Molecules with Long Conjugated Bridges: Calculations versus Experiment
    Authors: Suponitsky, K.Y., Liao, Y. & Masunov, A.E.
    Location: Journal of Physical Chemistry A 113, 41 (2009), pp. 10994–11001

    We investigate the molecular first hyperpolarizability (?) for donor/acceptor (D/A) substituted ?-conjugated organic molecules with different D/A groups and ?-systems (including up to eight ?-bonds). The results of the MP2 and density functional theory (PBE0, BMK, M05, M05-2X) calculations are compared to those obtained from experimental data. The goal of this study is to select a protocol with optimal quality/cost ratio to be used for systematic prediction of molecular nonlinear optical (NLO) properties. This goal is closely related to the way in which theoretical ?s are compared to experimental ones and to the accuracy and consistency of experimental hyperpolarizabilities used to test theoretical predictions. We found that two DFT functionals with the larger fraction of Hartree-Fock exchange (BMK and especially M05-2X) provide the best agreement to the experiment, comparable to that of the MP2 method. Due to high computational cost of MP2 method, we recommend to use the M05-2X functional as a tool for systematic prediction of molecular hyperpolarizabilities.

  • Title: Symmetry breaking in cationic polymethine dyes, part 1: ground state potential energy surfaces and solvent effects on electronic spectra of streptocyanines
    Authors: Iordanov, T.D., Davis, J.L., Masunov, A.E., Levenson, A., Przhonska, O.V. & Kachkovski, A.D.
    Location: Journal of Quantum Chemistry 109, 15 (2009), pp. 3592–3601

    Charge localization and dynamics in conjugated organic molecules, as well as their spectral signatures are of great importance for photonic and photovoltaic applications. Intramolecular charge delocalization in polymethine dyes occurs through ?-conjugated bridges and contributes to the appearance of low-energy excited states that strongly influence their linear and nonlinear optical (NLO) properties. When the chain length in symmetrical cations exceeds the characteristic size of the soliton, the positive charge may localize at one of the terminal groups of the molecule and induce symmetry breaking of both the electron density distribution and molecular geometry. This charge localization is coupled with molecular vibrations and solvent effects. We investigated the mechanism of symmetry breaking in a series of cationic streptocyanines with different conjugated chain length and qualitatively predicted their electronic absorption spectra. This class of organic molecules is chosen as a model system to develop methodology which can subsequently be used to evaluate more complicated compounds for NLO applications. Our calculations show that the minimum number of vinylene groups in the conjugated chain necessary to break the symmetry of streptocyanines is eight in the gas phase and six in cyclohexane. We constructed the ground state potential energy surface (PES) in two dimensions using symmetry breaking and symmetry adapted coordinates. These were defined as the difference and the sum of the two central carbon-carbon bonds, respectively. This PES was found to have two equivalent minima for systems with symmetry breaking. The energy barrier between these two minima was estimated in the gas phase and in solution, which was taken into account by the polarizable continuum model. Charge localization in each minimum was found to be asymmetric. It is additionally stabilized by the solvent reaction field, which increases the energy barrier. The electronic absorption spectrum in solution is red shifted as compared to the gas phase. As the symmetry breaks, additional excited states with large oscillator strengths appear in the electronic spectrum. Geometry optimization and spectral predictions were also performed in a uniform external electric field in order to simulate nonequilibrium solvation effects due to the finite relaxation time of solvent molecules. Two asymmetric minima with different depths appear on the resulting PES. The lower minimum has charge localized at one of the two molecular terminal groups which is additionally stabilized by the solvent field, while the higher one has charge localized on another terminal group. This finding demonstrates the possibility that two forms with different charge distributions coexist in polar solvents. Our results suggest that nonequilibrium solvation may be a cause of absorption band broadening and splitting. This work is a first step in a larger study aimed at the analysis of the linear and nonlinear properties of

  • Title: Quantum chemistry of quantum dots: Effects of ligands and oxidation
    Authors: Inerbaev, T.M., Masunov, A.E., Khondaker, S.I., Dobrinescu, A., Plamada, A.V. & Kawazoe, Y.
    Location: Journal of chemical physics 131 (2009)

    We report Gaussian basis set density functional theory (DFT) calculations of the structure and spectra of several colloidal quantum dots (QDs) with a (CdSe)n core (n = 6,15,17), that are either passivated by trimethylphosphine oxide ligands, or unpassivated and oxidized. From the ground state geometry optimization results we conclude that trimethylphosphine oxide ligands preserve the wurtzite structure of the QDs. Evaporation of the ligands may lead to surface reconstruction. We found that the number of two-coordinated atoms on the nanoparticle’s surface is the critical parameter defining the optical absorption properties. For (CdSe)15 wurtzite-derived QD this number is maximal among all considered QDs and the optical absorption spectrum is strongly redshifted compared to QDs with threefold coordinated surface atoms. According to the time-dependent DFT results, surface reconstruction is accompanied by a significant decrease in the linear absorption. Oxidation of QDs destroys the perfection of the QD surface, increases the number of two-coordinated atoms and results in the appearance of an infrared absorption peak close to 700 nm. The vacant orbitals responsible for this near infrared transition have strong Se-O antibonding character. Conclusions of this study may be used in optimization of engineered nanoparticles for photodetectors and photovoltaic devices.

  • Title: Quantum Chemical Study of Trimolecular Reaction Mechanism between Nitric Oxide and Oxygen in the Gas Phase
    Authors: Gadzhiev, O.B., Ignatov, S.K., Razuvaev, A.G. & Masunov, A.E.
    Location: The Journal of Physical Chemistry A 113 32 (2009) pp. 9092–9101

    Singlet and triplet potential energy surfaces of the reaction between molecular oxygen and two nitric oxide(II) molecules were studied by quantum chemical methods (coupled cluster, CASSCF, and density functional theory: B3LYP, TPSS, VSXC, BP86, PBE, B2-PLYP, B2K-PLYP). Elementary steps involving various N2O4 isomers (cyclic, cis-cis-, cis-trans-, trans-trans-ONOONO, cis- and trans-ONONO2, O2NNO2) were considered, as well as weakly bound molecular clusters preceding formation of O2NNO2, and Coupe-type quasi-aromatic hexagonal ring intermediate NO2?O2N. We found that activation energy strongly depends on the conformation of ONOONO peroxide, which is formed barrierlessly. The best agreements with experimental values were achieved by the B3LYP functional with aug-pc3 basis set. The lowest transition state (TS) energies correspond to the following reaction channel: 2NO + O2 (0 kJ/mol) → cis-cis-ONOONO (-45 kJ/mol) → TS1 → NO2?O2N (-90 kJ/mol) → TS2 → cis-ONONO2 (-133 kJ/mol)→ TS3 → trans-ONONO2 (-144 kJ/mol) → TS4 → O2NNO2 (-193 kJ/mol). A valley ridge inflection (VRI) point is located on the minimum energy path (MEP) connecting NO2?O2N and cis-ONONO2. The energy landscape between NO2?O2N and CC-TS2 can be classified as a downhill valley-pitchfork VRI bifurcation according to a recent classification of bifurcation events [Quapp, W. J. Mol. Struct. 2004, 95, 695-696]. The first and second transition states correspond to barrier heights of 10.6 and 37.0 kJ/mol, respectively. These values lead to the negative temperature dependence of the rate constant. The apparent activation enthalpy of the overall reaction was calculated to be ?rH(0) = -4.5 kJ/mol, in perfect agreement with the experimental value.

  • Title: Theoretical Study of Photochromic Compounds. 1. Bond Length Alternation and Absorption Spectra for the Open and Closed Forms of 29 Diarylethene Derivatives
    Authors: Patel, P.D. & Masunov, A.E.
    Location: Journal of Physical Chemistry A 113, 29 (2009), pp. 8409–8414

    We apply several exchange-correlation functionals in combination with time-dependent density functional theory to predict the maximum wavelengths in the absorption spectra for 29 diarylethene derivatives in both open and closed isomeric forms. Solvent effects and accurate molecular geometries are found to be important to obtain good agreement with experimental absorption wavelengths. In order to evaluate the quality of geometry optimization, we compare predicted bond length alternation parameters with experimental ones. We find the TD-M05/6-31G*/PCM//M05-2x/6-31G*/PCM theory level to give the best predictions for the structural and spectral parameters of the diarylethene derivatives. Applications of the photochromic diarylethene compounds as materials for optical switching and data storage based on their photocyclization properties are also discussed.

  • Title: Structural Characterization Combined with the First Principles Simulations of Barium/Strontium Cobaltite/Ferrite as Promising Material for Solid Oxide Fuel Cells Cathodes and High-Temperature Oxygen P
    Authors: Gangopadhayay, S., Inerbaev, T., Masunov, A.E., Altilio, D. & Orlovskaya, N.
    Location: ACS Applied Materials & Interfaces 1 7 (2009) pp. 1512–1519

    Mixed ionic-electronic conducting perovskite type oxides with a general formula ABO3 (where A = Ba, Sr, Ca and B = Co, Fe, Mn) often have high mobility of the oxygen vacancies and exhibit strong ionic conductivity. They are key materials that find use in several energy related applications, including solid oxide fuel cell (SOFC), sensors, oxygen separation membranes, and catalysts. Barium/strontium cobaltite/ferrite (BSCF) Ba0.5Sr0.5Co0.8Fe0.2O3-? was recently identified as a promising candidate for cathode material in intermediate temperature SOFCs. In this work, we perform experimental and theoretical study of the local atomic structure of BSFC. Micro-Raman spectroscopy was performed to characterize the vibrational properties of BSCF. The Jahn-Teller distortion of octahedral coordination around Co4+ cations was observed experimentally and explained theoretically. Different cations and oxygen vacancies ordering are examined using plane wave pseudopotential density functional theory. We find that cations are completely disordered, whereas oxygen vacancies exhibit a strong trend for aggregation in L-shaped trimer and square tetramer structure. On the basis of our results, we suggest a new explanation for BSCF phase stability. Instead of linear vacancy ordering, which must take place before the phase transition into brownmillerite structure, the oxygen vacancies in BSCF prefer to form the finite clusters and preserve the disordered cubic structure. This structural feature could be found only in the first-principles simulations and can not be explained by the effect of the ionic radii alone.

  • Title: Towards Multiscale Simulations of Carbon Nanotube Growth Process: A Density Functional Theory Study of Transition Metal Hydrides
    Authors: Goel, S. & Masunov, A.
    Location: Computational Science–ICCS 2009 (2009) pp. 765–774

    Nanoelectronics and photonics applications of single wall carbon nanotubes (SWNT) are feasible only if SWNTs have specific chirality. The knowledge of the detailed mechanism for SWNT synthesis would allow one to optimize the chemical vapor deposition (CVD) process and may help to gain control over selectivity of SWNT synthesis. While it is not probably feasible to study this mechanism experimentally, it could be analyzed using molecular simulations. Here we propose multiscale computer modeling of CVD process. High theory level can be used for di- and tri-atomic fragments, in order to generate parameters for bond order force field. In turn, force field simulations will be used to characterize the chemical origin and thermochemical properties of the intermediates and transition states. This will allow predicting the rate constants for the elementary steps, which are then used in kinetic Monte Carlo simulations to describe SWNT growth at realistic time scales.

  • Title: Prediction of Exchange Coupling Constant for Mn 12 Molecular Magnet Using Dft+U
    Authors: Gangopadhyay, S., Masunov, A., Poalelungi, E. & Leuenberger, M.
    Location: Computational Science–ICCS 2009 (2009) pp. 151–159

    Single-molecule magnets are perspective materials for molecular spintronic applications. Predictions of magnetic coupling in these systems have posed a long standing problem, as calculations of this kind require a balanced description of static and dynamic electron correlation. The large size of these systems limits the choice of theoretical methods used. Two methods feasible to predict the exchange coupling parameters are broken symmetry Density Functional Theory (BSDFT) and DFT with empirical Hubbard U parameter (DFT+U). In this contribution we apply DFT+U to study Mn-based molecular magnets using Vanderbilt Ultrasoft Pseudopotential plane wave DFT method, implemented in Quantum ESPRESSSO code. Unlike most previous studies, we adjust U parameters for both metal and ligand atoms using two dineuclear molecular magnets [Mn2O2(phen)4]2 + and [Mn2O2(OAc)(Me4dtne)]3 + as the benchmarks. Next, we apply this methodology to Mn12 molecular wheel. Our study finds antiparallel spin alignment in weakly interacting fragments of Mn12, in agreement with experimental observations.

  • Title: Linear and nonlinear optical characterization of a monomeric symmetric squaraine-based dye in solution
    Authors: Carlos Toro, Leonardo De Boni, Sheng Yao, Artem Masunov, Kevin D. Belfield & Florencio E. Hernandez
    Location: The Journal of Chemical Physics 130 214504/1 (2009)

    The photophysical properties of a symmetric squaryllium dye, namely, 2,4-bis[4-(N,N-dibutylamino)-2-hydroxyphenyl] squaraine (SQ), in its monomer form in acetone solution, have been thoroughly studied by means of one-photon absorption (1PA) and two-photon absorption (2PA), excitation anisotropy, fluorescence emission, fluorescence quantum yield, and excited state absorption. The results show that there is a strong one-photon allowed absorption band in the near IR region associated with intramolecular charge transfer. Higher one-photon allowed and forbidden singlet excited states were also revealed by absorption and excitation anisotropy. A relatively high fluorescence quantum yield (0.44) was measured for this dye. The nonlinear optical characterization of SQ in solution confirms the ability of squaraine dyes to be used as good two-photon absorbers. Additionally, it was found that this dye presents both saturable and reverse saturable absorption effects. Density functional theory calculations of the 1PA and 2PA electronic spectra of SQ were carried out to support the experimental data. A detailed analysis of the symmetry and energy of the orbitals involved in the lowest five electronic transitions is presented and discussed in relation to the behavior observed experimentally.

  • Title: DFT-Based Methods in the Design of Two-Photon Operated Molecular Switches
    Authors: Mikhailov, I.A., Belfield, K.D. & Masunov, A.E.
    Location: Journal of Physical Chemistry A 113, 25 (2009), pp. 7080–7089

    Conjugated organic molecules with photochromic properties are being extensively studied as prospective optical switching and data storage materials. Among different photochromic compounds, diarylethenes demonstrate thermal stability, fatigue resistance, and high quantum yield. The mechanism of photoswitching in diarylethenes involves a symmetry-allowed conrotatory electrocyclic reaction, initiated by UV light. Replacement of one UV photon with two near-IR ones would offer a number of practical advantages, including drastic increase in storage capacity via three-dimensional multilayer design. For this purpose we designed a prototype molecule with a two-photon absorbing (2PA) pendant substituent, attached to the photochromic diarylethene moiety. However, this molecule was experimentally shown to have lost the photoswitching properties. We analyze reasons for this loss using quantum chemistry tools. Analysis of the nodal structure of the frontier Kohn-Sham orbitals, allowed us to trace the route of the problem to the lone pair orbital of the 2PA substituent falling within the HOMO-LUMO (highest occupied molecular orbital-lowest unoccupied molecular orbital) gap of the photoreactive diarylethene moiety. We suggest a chemical modification of the 2PA substituent in order to restore the order of the orbitals. Potential energy plots along the reaction coordinate at the M05-2X/6-31G* theory level for the prototype 2PA photochromic molecule before and after the modification confirm the predictive capability of the proposed orbital approach. The Slater transition state method was used to obtain geometries along the reaction pathway by the constrained optimization of excited states, whereas potential energy curves were plotted using the recently proposed (Mikhailov, I. A.; Tafur, S.; Masunov, A. E. Phys. Rev. A2008, 77 (1), 012510) a posteriori Tamm-Dancoff approximation to the time-dependent density functional theory in second order of the external field. We show that this combination is able to produce accurate potential surfaces for 1B and 2A excited states, as compared to available experimental data and results of high-level multireference wave function theory methods.

  • Title: Protonated nanoparticle surface governing ligand tethering and cellular targeting
    Authors: Vincent, A., Babu, S., Heckert, E., Dowding, J., Hirst, S.M., Inerbaev, T.M., Self, W.T., Reilly, C.M., Masunov, A.E., Rahman, T.S. & others
    Location: ACS nano 3, 5 (2009), pp. 1203–1211

    Nanoparticles have shown tremendous potential for effective drug delivery due to their tiny size and cell membrane penetration capabilities. Cellular targeting with nanoparticles is often achieved by surface modifications followed by ligand conjugation. However, the efficiency of the nanoparticles reaching the target cells and getting internalized depends on the stability of targeting ligands and the chemical nature of the ligand nanoparticle binding. Recent advancements in nanobiomaterials research have proven the superoxide dismutase (SOD) mimetic activity of cerium oxide nanoparticles (CNPs) in protecting cells against oxidative stress. Due to their excellent biocompatibility, CNPs can be used as a potential drug carrier that can transport and release drugs to the malignant sites. Here we combine single molecule force spectroscopy (SMFS) and density functional theory (DFT) simulations to understand the interaction between transferrin, a ligand protein overexpressed in cancer cells, and CNPs. SMFS studies demonstrate an increase in the transferrin adhesion to the nanoparticles’ surface with an increase in positive ? potential of CNPs. Binding energy values obtained from DFT calculations predict an increase in bond strength between the transferrin and CNPs upon surface protonation and charge modification. Transferrin-conjugated CNPs were tested for their binding stability and preferential cellular uptake efficiency by incubating them with human lung cancer cells (A549) and normal embryo lung cells (WI-38). The results demonstrate the importance of tuning the surface properties of nanoparticles for better ligand adsorption and cellular uptake.

  • Title: Predictions of Two Photon Absorption Profiles Using Time-Dependent Density Functional Theory Combined with SOS and CEO Formalisms
    Authors: Tafur, S., Mikhailov, I., Belfield, K. & Masunov, A.
    Location: International Conference on Computational Science–ICCS 2009, pp. 179–188

    Two-photon absorption (2PA) and subsequent processes may be localized in space with a tightly focused laser beam. This property is used in a wide range of applications, including three dimensional data storage. We report theoretical studies of 5 conjugated chromophores experimentally shown to have large 2PA cross-sections. We use the Time Dependent Density Functional Theory (TD-DFT) to describe the electronic structure. The third order coupled electronic oscillator formalism is applied to calculate frequency-dependent second order hyperpolarizability. Alternatively, the sum over states formalism using state-to-state transition dipoles provided by the a posteriori Tamm-Dancoff approximation is employed. It provides new venues for qualitative interpretation and rational design of 2PA chromophores.

  • Title: Prediction of Thermal Stability of Photochromic Materials Used for Optical Switching and Data Storage Applications
    Authors: Patel, P.D., Mikhailov, I.A. & Masunov, A.E.
    Location: International Conference on Computational Science–ICCS 2009

    Certain organic compounds posess the ability to change color under the influence of light, called photochromism. This change is often due to ultrafast chemical transition from open to closed ring isomers (photocyclization). Information thechnology applications of these photochromics require the reverse transformation to be very slow in the dark. We have applied Density Functional Theory (DFT) methods to predict kinetics of this cycloreversion. This cycloreversion occurs through symmetry forbidden conrotatory electrocyclic mechanism with transition state of strong diradical character, and requires the unrestricted broken-symmetry DFT formalism. Our results suggest that B3LYP functional describes the activation barrier for the cycloreversion process with about 1-2 kcal/mol error, while M052x functional gives an error of about 2-3 kcal/mol compared to the experimental values.

  • Title: Density Functional Theory Study of Photodegradation and Fatigue-Resistance of Photochromic Materials for Optical Switching and Data Storage Applications
    Authors: Patel, P.D., Mikhailov, I.A. & Masunov, A.E.
    Location: International Conference on Computational Science–ICCS 2009

    Photochromic compounds are promising materials for optoelectronic and photonic applications because of their ability to undergo change in color under UV/Vis illumination due to reversible chemical transition from open to closed ring isomers (photocyclization). The by-produc formation may lead to irreversible photodegradation of the material, called fatigue. We use Density Functional Theory methods to predict the rate for the by product formation for 1,2-bis(2-methyl-5-phenyl-3-thienyl)perfluorocyclopentene (PFC-2) in order to estimate its fatigue resistance. We propose a mechanism of the photofatigue for PFC-2 and explain higher fatigue resistance for its derivative. The method can become a part of rational design strategy for the new photochromic materials.

  • Title: Time-Dependent Density Functional Theory Study of Structure-Property Relationships in Diarylethene Photochromic Compounds
    Authors: Patel, P. & Masunov, A.
    Location: International Conference on Computational Science–ICCS 2009, pp. 211–220

    Photochromic compounds exhibit reversible transition between closed and open isomeric forms upon irradiation accompanied by change in their color. The two isomeric forms differ not only in absorption spectra, but also in various physical and chemical properties and find applications as optical switching and data storage materials. In this contribution we apply Density Functional Theory (DFT) and Time-Dependent DFT (TD-DFT) to predict the equilibrium geometry and absorption spectra of a benchmark set of diarylethene based photochromic compounds in open and closed forms (before and after photocyclization). Comparison of the calculated Bond Length Alternation parameters with those available from the X-ray data indicates M05-2x functional to be the best method for geometry optimization when basis set includes polarization functions. We found M05 functional accurately predicts the maximum absorption wavelength when solvent is taken into account. We recommend combined theory level TD-M05/6-31G*/PCM//M05-2x/6-31G*/PCM for prediction of geometrical and spectral parameters of diarylethene derivatives.

  • Title: Theoretical Photochemistry of the Photochromic Molecules Based on Density Functional Theory Methods
    Authors: Mikhailov, I. & Masunov, A.
    Location: Computational Science–ICCS 2009, pp. 169–178

    Mechanism of photoswitching in diarylethenes involves the light-initiated symmetry-allowed disrotatory electrocyclic reaction. Here we propose a computationally inexpensive Density Functional Theory (DFT) based method that is able to produce accurate potential surfaces for the excited states. The method includes constrained optimization of the geometry for the ground and two excited singlet states along the ring-closing reaction coordinate using the Slater Transition State method, followed by single-point energy evaluation. The ground state energy is calculated with the broken-symmetry unrestricted Kohn-Sham formalism (UDFT). The first excited state energy is obtained by adding the UDFT ground state energy to the excitation energy of the pure singlet obtained in the linear response Time-Dependent (TD) DFT restricted Kohn-Sham formalism. The excitation energy of the double excited state is calculated using a recently proposed (Mikhailov, I. A.; Tafur, S.; Masunov, A. E. Phys. Rev. A 77, 012510, 2008) a posteriori Tamm-Dancoff approximation to the second order response TD-DFT.

  • Title: High performance parallel processing algorithms for mobile communication
    Authors: Palaniappan, R., Clarke, T. & Ahmad, M.Z.
    Location: 3rd European Conference on Antennas and Propagation

    The goal of this paper is to demonstrate the development of a dynamically reconfigurable scalable high performance signal processor architecture for hand held radio applications that significantly reduce size, weight, and power over conventional technologies. The proposed software algorithms will be very useful for next generation radio and communication platforms such as joint tactical radio systems (JTRS) and other commercial software defined radios.

  • Title: Dopant-mediated oxygen vacancy tuning in ceria nanoparticles
    Authors: Babu, S., Thanneeru, R., Inerbaev, T., Day, R., Masunov, A.E., Schulte, A. & Seal, S.
    Location: Nanotechnology 20 (2009) pp. 085713

    Ceria nanoparticles with 20 and 40 at.% RE (RE = Y, Sm, Gd, and Yb) dopants were synthesized through a microemulsion method. Independently of the dopant nature and concentration, nearly monodispersed nanoparticles of size 3-5 nm were observed in high resolution transmission electron microscopic analysis. The ceria lattice either expands or contracts depending on the dopant cation ionic radii, as indicated by x-ray diffraction studies. X-ray photoelectron and Raman spectroscopic studies were used to quantify the cerium oxidation state and oxygen vacancy concentration. The results show the tunability of the oxygen vacancy and Ce3+ concentrations based on the dopant properties. First principles simulations using the free energy density functional theory method support the observed experimental trends. The reported results establish a relationship between the oxygen vacancies and oxidation states in doped ceria required for tailoring properties in catalytic and biomedical applications.

  • Title: Modeling of selective carbon nanotubes growth for non-classical memory applications
    Authors: Goel, S. & Masunov, A.E.
    Location: Quantum Nano and Micro Technologies 2009. ICQNM’09. Third International Conference on (2009) pp. 162

    Single wall carbon nanotubes (SWNT) have unique properties that make them potentially useful in wide variety of applications in nanoelectronics. However, these applications are feasible only if SWNTs have specific chirality. Therefore optimization of experimental conditions for Chemical Vapor Deposition (CVD) growth of SWNT in order to increase its selectivity is of great practical importance. This rational optimization is impossible without knowledge of mechanistic kinetics of CVD. It is not probably feasible to extract the information on mechanism for SWNT synthesis from experimental data. The chemical origin of the reaction barriers and intermediates, however, could be analyzed using molecular simulations. Here we propose multiscale computer modeling of CVD process. Our approach is to extract the structure of the intermediates from molecular dynamics trajectories, conduct the transition state search, predict the free energy activation barriers, build the kinetic model of the growth process, and implement it in kinetic Monte Carlo algorithm to predict the optimal experimental conditions necessary to produce desired chirality of SWNT.

  • Title: Analysis of the physical forcing mechanisms influencing salinity transport for the Lower St. Johns River
    Authors: Giardino, D.
    Location: MS thesis, University of Central Florida, Orlando Florida (2009)

    A high-resolution, finite element-based, shallow water equation model is developed to simulate the tides in the South Atlantic Bight. The model is constructed to include all of the estuarinefeatures along the southeastern United States seaboard: coastal inlets, rivers and tidal creeks, sounds and lagoons, intertidal zones including salt marshes and mangrove swamps, and the Atlantic Intracoastal Waterway. The estuaries are represented in the finite element mesh using triangular elements with side lengths on the order of tens of meters. Also incorporated into the model is a spatially distributed bottom friction parameterization, based on the various landcover and benthic characteristics in the domain. The motivation to use this comprehensive representation of the system was inspired by a desire to capably account for the full estuarine tidal physics. In this approach, no calibration is performed and the model is used as a tool to assess the physical processes it describes. Upon its development, the model is first validated by accurately simulating tidal hydrodynamics in the South Atlantic Bight including the described estuaries. Variants of the model are then constructed by selectively removing estuarine features from the domain. All model representations are subsequently applied in nearly identical simulations: the only differing factor between the simulations being the inland extent of the estuaries described. The solutions are compared with respect to including versus excluding the estuarine features of the domain. Where water surface elevations are shown to be unaffected by the estuarine features of the South Atlantic Bight, tidal velocities exhibit far more sensitivity. This effect is pronounced locally, with regional effects extending offshore. Further analysis is performed on cross-sectional flows recomposed locally and on tidal energetics diagnosed throughout the domain. It is discovered that the high frictional environment of the vast estuarine surface area plays a role in local and regional tidal circulation in the South Atlantic Bight.

  • Title: Potential energy curves and electronic structure of 3d transition metal hydrides and their cations
    Authors: Goel, S. & Masunov, A.E.
    Location: Journal of chemical physics 129 (2008), pp. 214302

    We investigate gas-phase neutral and cationic hydrides formed by 3d transition metals from Sc to Cu with density functional theory (DFT) methods. The performance of two exchange-correlation functionals, Boese-Martin for kinetics (BMK) and Tao-Perdew-Staroverov-Scuseria (TPSS), in predicting bond lengths and energetics, electronic structures, dipole moments, and ionization potentials is evaluated in comparison with available experimental data. To ensure a unique self-consistent field (SCF) solution, we use stability analysis, Fermi smearing, and continuity analysis of the potential energy curves. Broken-symmetry approach was adapted in order to get the qualitatively correct description of the bond dissociation. We found that on average BMK predicted values of dissociation energies and ionization potentials are closer to experiment than those obtained with high level wave function theory methods. This agreement deteriorates quickly when the fraction of the Hartree-Fock exchange in DFT functional is decreased. Natural bond orbital (NBO) population analysis was used to describe the details of chemical bonding in the systems studied. The multireference character in the wave function description of the hydrides is reproduced in broken-symmetry DFT description, as evidenced by NBO analysis. We also propose a new scheme to correct for spin contamination arising in broken-symmetry DFT approach. Unlike conventional schemes, our spin correction is introduced for each spin-polarized electron pair individually and therefore is expected to yield more accurate energy values. We derive an expression to extract the energy of the pure singlet state from the energy of the broken-symmetry DFT description of the low spin state and the energies of the high spin states (pentuplet and two spin-contaminated triplets in the case of two spin-polarized electron pairs). The high spin states are build with canonical natural orbitals and do not require SCF convergence.

  • Title: Photophysical characterization of a highly conjugated bipyridyl-based dye synthesized by a unique two-step approach
    Authors: Carlos Toro, Leonardo De Boni, Sheng Yao, Kevin D. Belfield & Florencio E. Hernandez
    Location: J. Phys. Chem. B 112, 12185 (2008)

    In this article, we present a new and simple, yet efficient, two-step approach to synthesize 4,4′-bis(dibutylaminostyrylstyryl)-2,2′-bipyridine with high yield, as well as its linear and nonlinear optical characterizations in THF and toluene solutions. We show that its one- and two-photon absorption spectra are similar in both solvents. Nevertheless, the relaxation processes of this compound exhibit dependence on the solvent polarity. The one- and two-photon induced fluorescence signal of this molecule in solution reveals that its excited state is highly stabilized in THF solution rather than in toluene. Analysis of the fluorescence quantum yield, lifetime, and radiative and nonradiative decay rates are in agreement with Lippert’s model for solute-solvent interactions. The optical measurements demonstrate that this dye is a promising candidate for multiphoton fluorescence imaging, optical limiting, and dye lasers.

  • Title: Untangling the Excited States of DR1 in Solution: An Experimental and Theoretical Study
    Authors: Leonardo De Boni, Carlos Toro, Artem E. Masunov & Florencio E. Hernandez
    Location: J. Phys. Chem. A 112, 3886 (2008)

    We report the experimental observations and the theoretical predictions of the fully separated n-pi* and pi-pi* bands of Disperse Red One in acidified methanol solution. The analysis of the linear and two-photon absorption spectra is presented in four specific solvents. We demonstrate the possibility to establish the position of the first two excited states combining linear and nonlinear spectroscopy. Calculations using density functional theory at level TD-B3LYP/6-31G*//HF/6-31G* accurately predict the spectral region of the n-pi* and pi-pi* transitions of DR1 in all solvents.

  • Title: Fluorescence Emission of Disperse Red 1 in Solution at Room Temperature
    Authors: Carlos Toro, Arthur Thibert, Leonardo De Boni, Artem Masunov & Florencio E. Hernandez
    Location: J. Phys. Chem. B 112, 929 (2008)

    In this article, we report the fluorescence emission of Disperse Red 1 in solution at room temperature and pumping at 532 nm with a 25 mW diode laser. We have measured its fluorescence quantum yield in methanol, ethylene glycol, glycerol, and phenol obtaining values as high as 10-3 in the aliphatic alcohols. The excitation spectra of Disperse Red 1 in all four solvents as well as its excitation anisotropy in glycerol are presented. Applying a Gaussian decomposition method to the absorption spectra along with the support from the excitation spectra, the positions of the different transitions in this pseudo-stilbene azobenzene dye were determined. Solvatochromic and isomerization constraint effects are discussed. Calculations using density functional theory at TD-B3LYP/6-31G*//HF/6-31G* level were performed to interpret the experimental observations.

  • Title: A photonic thermalization gap in disordered lattices
    Authors: H. Esat Kondakci, Ayman F. Abouraddy, Bahaa E. A. Saleh
    Location: Nature Physics

    The formation of gaps—forbidden ranges in the values of a physical parameter—is common to a variety of physical systems: from energy bandgaps of electrons in periodic lattices1 and their analogues in photonic2, phononic3 and plasmonic4 systems to pseudo-energy gaps in aperiodic quasicrystals5. Here, we predict a thermalization gap for light propagating in finite disordered structures characterized by disorder-immune chiral symmetry6—the appearance of the eigenvalues and eigenvectors in skew-symmetric pairs. In these systems, the span of sub-thermal photon statistics is inaccessible to input coherent light, which—once the steady state is reached—always emerges with super-thermal statistics no matter how small the disorder level. We formulate an independent constraint of the input field for the chiral symmetry to be activated and the gap to be observed. This unique feature enables a new form of photon-statistics interferometry: the deterministic tuning of photon statistics via controlled excitation symmetry breaking realized by sculpting the amplitude or phase of the input coherent field.

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