Atomistic-continuum modeling of ultrafast laser-induced melting of silicon targets

In this work, we present an atomistic-continuum model for simulations of ultrafast laser-induced melting processes in semiconductors on the example of silicon. The kinetics of transient non-equilibrium phase transition mechanisms is addressed with MD method on the atomic level, whereas the laser light absorption, strong generated electron-phonon nonequilibrium, fast heat conduction, and photo-excited free carrier diffusion are accounted for with a continuum TTM-like model (called nTTM). First, we independently consider the applications of nTTM and MD for the description of silicon, and then construct the combined MD-nTTM model. Its development and thorough testing is followed by a comprehensive computational study of fast nonequilibrium processes induced in silicon by an ultrashort laser irradiation. The new model allowed to investigate the effect of laser-induced pressure and temperature of the lattice on the melting kinetics. Two competing melting mechanisms, heterogeneous and homogeneous, were identified in our big-scale simulations. Apart from the classical heterogeneous melting mechanism, the nucleation of the liquid phase homogeneously inside the material significantly contributes to the melting process. The simulations showed, that due to the open diamond structure of the crystal, the laser-generated internal compressive stresses reduce the crystal stability against the homogeneous melting. Consequently, the latter can take a massive character within several picoseconds upon the laser heating. Due to the large negative volume of melting of silicon, the material contracts upon the phase transition, relaxes the compressive stresses, and the subsequent melting proceeds heterogeneously until the excess of thermal energy is consumed. A series of simulations for a range of absorbed fluences allowed us to find the threshold fluence value at which homogeneous liquid nucleation starts contributing to the classical heterogeneous propagation of the solid-liquid interface. A series of simulations for a range of the material thicknesses showed that the sample width we chosen in our simulations (800 nm) corresponds to a thick sample. Additionally, in order to support the main conclusions, the results were verified for a different interatomic potential. Possible improvements of the model to account for nonthermal effects are discussed and certain restrictions on the suitable interatomic potentials are found. As a first step towards the inclusion of these effects into MD-nTTM, we performed nanometer-scale MD simulations with a new interatomic potential, designed to reproduce ab initio calculations at the laser-induced electronic temperature of 18946 K. The simulations demonstrated that, similarly to thermal melting, nonthermal phase transition occurs through nucleation. A series of simulations showed that higher (lower) initial pressure reinforces (hinders) the creation and the growth of nonthermal liquid nuclei. For the example of Si, the laser melting kinetics of semiconductors was found to be noticeably different from that of metals with a face-centered cubic crystal structure. The results of this study, therefore, have important implications for interpretation of experimental data on the kinetics of melting process of semiconductors.

Molecular modelling studies of binding of DACD derivatives into G-Quadruplex DNA: comparison of force field and quantum polarized ligand docking methods

The DNA G-qadruplexes are one of the targets being actively explored for anti-cancer therapy by inhibiting them through small molecules. This computational study was conducted to predict the binding strengths and orientations of a set of novel dimethyl-amino-ethyl-acridine (DACA) analogues that are designed and synthesized in our laboratory, but did not diffract in Synchrotron light.Thecrystal structure of DNA G-Quadruplex(TGGGGT)4(PDB: 1O0K) was used as target for their binding properties in our studies.We used both the force field (FF) and QM/MM derived atomic charge schemes simultaneously for comparing the predictions of drug binding modes and their energetics. This study evaluates the comparative performance of fixed point charge based Glide XP docking and the quantum polarized ligand docking schemes. These results will provide insights on the effects of including or ignoring the drug-receptor interfacial polarization events in molecular docking simulations, which in turn, will aid the rational selection of computational methods at different levels of theory in future drug design programs. Plenty of molecular modelling tools and methods currently exist for modelling drug-receptor or protein-protein, or DNA-protein interactionssat different levels of complexities.Yet, the capasity of such tools to describevarious physico-chemical propertiesmore accuratelyis the next step ahead in currentresearch.Especially, the usage of most accurate methods in quantum mechanics(QM) is severely restricted by theirtedious nature. Though the usage of massively parallel super computing environments resulted in a tremendous improvement in molecular mechanics (MM) calculations like molecular dynamics,they are still capable of dealing with only a couple of tens to hundreds of atoms for QM methods. One such efficient strategy that utilizes thepowers of both MM and QM are the QM/MM hybrid methods. Lately, attempts have been directed towards the goal of deploying several different QM methods for betterment of force field based simulations, but with practical restrictions in place. One of such methods utilizes the inclusion of charge polarization events at the drug-receptor interface, that is not explicitly present in the MM FF.

Structure and magnetic properties of a tetranuclear Cu(II) complex containing the 2-(pyridine-2-yliminomethyl)-phenol ligand

A tetranuclear Cu(II) complex [Cu4L4(H2O)4](ClO4)4 has been synthesized using the terdentate Schiff base 2-(pyridine-2-yliminomethyl)-phenol (HL) (the condensation product of salicylaldehyde and 2-aminopyridine) and copper perchlorate. Chemical characterizations such as IR and UV/Vis of the complex have been carried out. A single-crystal diffraction study shows that the complex contains a nearly planar tetranuclear core containing four copper atoms, which occupy four equivalent five-coordinate sites with a square pyramidal environment. Magnetic measurements have been carried out over the temperature range 2–300K and with 100Oe field strengths. Analysis of magnetic susceptibility data indicates a strong antiferromagnetic (J1=−638cm−1) exchange interaction between diphenoxo-bridged Cu(II) centers and a moderate antiferromagnetic (J2=−34cm−1) interaction between N–C–N bridged Cu(II) centers. Magnetic exchange interactions (J’s) are also discussed on the basis of a computational study using DFT methodology. The spin density distribution (singlet ground state) is calculated to visualize the effect of delocalization of spin density through bridging groups.

Only subtle protein conformational adaptations are required for ligand binding to thyroid hormone receptors: Simulations using a novel multipoint steered molecular dynamics approach

Thyroid hormone receptors (TR) are hormone-dependent transcription regulators that play a major role in human health, development, and metabolic functions. The thyroid hormone resistance syndrome, diabetes, obesity, and some types of cancer are just a few examples of important diseases that are related to TR malfunctioning, particularly impaired hormone binding. Ligand binding to and dissociation from the receptor ultimately control gene transcription and, thus, detailed knowledge of binding and release mechanisms are fundamental for the comprehension of the receptor`s biological function and development of pharmaceuticals. In this work, we present the first computational study of ligand entry into the ligand binding domain (LBD) of a nuclear receptor. We report molecular dynamics simulations of ligand binding to TRs using a generalization of the steered molecular dynamics technique designed to perform single-molecule pulling simulations along arbitrarily nonlinear driving pathways. We show that only gentle protein movements and conformational adaptations are required for ligand entry into the LBDs and that the magnitude of the forces applied to assist ligand binding are of the order of the forces involved in ligand dissociation. Our simulations suggest an alternative view for the mechanisms ligand binding and dissociation of ligands from nuclear receptors in which ligands can simply diffuse through the protein surface to reach proper positioning within the binding pocket. The proposed picture indicates that the large-amplitude protein motions suggested by the apo- and holo-RXR alpha crystallographic structures are not required, reconciling conformational changes of LBDs required for ligand entry with other nuclear receptors apo-structures that resemble the ligand-bound LBDs.

Calculating the Best Dual Bound for Problems with Multiple Lagrangian Relaxations

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Um modelo de otimização inteira mista e heurísticas relax and fix para a programação da produção de fábricas de refrigerantes de pequeno porte

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Using error bounds to compare aggregated generalized transportation models

A comparative study of aggregation error bounds for the generalized transportation problem is presented. A priori and a posteriori error bounds were derived and a computational study was performed to (a) test the correlation between the a priori, the a posteriori, and the actual error and (b) quantify the difference of the error bounds from the actual error. Based on the results we conclude that calculating the a priori error bound can be considered as a useful strategy to select the appropriate aggregation level. The a posteriori error bound provides a good quantitative measure of the actual error.

Estratégias para a redução de ciclos da serra no problema de corte de estoque na indústria moveleira

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Problema integrado de dimensionamento de lotes e corte de estoque na indústria moveleira

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Análise da qualidade da tensão no ponto de conexão de uma fábrica de alumínio com o sistema interligado nacional

Apresenta-se neste trabalho uma análise da qualidade da tensão no Ponto de Acoplamento Comum (PAC) entre uma indústria de alumínio e o sistema interligado nacional, de modo a avaliar o impacto produzido por esta instalação na rede básica no que diz respeito aos fenômenos de flutuação de tensão, desequilíbrio de tensão e distorção harmônica de tensão. Os dados dos distúrbios da qualidade da energia citados anteriormente foram coletados através de uma campanha de medição com duração de 7 dias consecutivos, solicitada pelo Operador Nacional do Sistema Elétrico (ONS) em casos de cargas conectadas à rede básica que apresentem características não-lineares, como é o caso das indústrias de alumínio. Adicionalmente, um estudo computacional visando determinar os valores máximos de distorção harmônica de tensão no PAC é apresentado com o intuito de completar as análises via campanha de medição. Os programas computacionais utilizados para a realização do estudo foram o HarmZs do CEPEL e o Matlab 7.0.

Análise do impacto de conversores de frequência na qualidade da energia do sistema de distribuição de uma indústria de petróleo

Apresenta-se neste trabalho uma análise da qualidade da energia do sistema de distribuição de uma indústria de petróleo, de modo a avaliar o impacto da instalação de conversores de frequência no que diz respeito ao fenômeno de distorção harmônica. Os dados de distorção harmônica de tensão foram coletados através de duas medições com duração de sete dias consecutivos, sendo uma realizada antes e outra depois da instalação dos conversores de frequência. Adicionalmente, um estudo computacional utilizando o PTW (Power Tools for Windows) é apresentado com o intuito de simular condições futuras de instalação de novos conversores de frequência e de avaliar a influência dos bancos de capacitores na amplificação da distorção harmônica no sistema de distribuição.

Enfrentamento do problema das divergências de tradução por um sistema de tradução automática: um exercício exploratório

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Relax and cut: limitantes duais para o problema do caixeiro viajante

Pós-graduação em Matemática - IBILCE

Numerical and experimental investigations of three-dimensional container filling with Newtonian viscous fluids

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Estrutura e função da proteína YacG de Klebsiella pneumoniae e seus derivados peptídicos

Pós-graduação em Biotecnologia - IQ