Search results for "SIMULATION"
showing 10 items of 5095 documents
Computer simulations of SiO2 and GeO2
2004
Classical Molecular Dynamics (MD) simulations are used to study structural and dynamic properties of amorphous germania (GeO2) in comparison to those of silica (SiO2). The total structure factor, as obtained from these simulations, is in very good agreement with that of neutron scattering experiments, both for germania and silica. The tetrahedral network structure in silica and germania leads to a prepeak in the structure factor that appears at slightly smaller wavenumbers in GeO2 than in SiO2. At high temperatures the diffusion constants are very similar in both systems whereas at low temperatures diffusion is significantly faster in germania than in silica. We also outline the strategy fo…
Suitability ofMMGBSAfor the selection of correct ligand binding modes from docking results
2018
The estimation of the correct binding mode and affinity of a ligand into a target protein using computational methods is challenging. However, docking can introduce poses from which the correct binding mode could be identified using other methods. Here, we analyzed the reliability of binding energy estimation using the molecular mechanics-generalized Born surface area (MMGBSA) method without and with energy minimization to identify the likely ligand binding modes within docking results. MMGBSA workflow (a) outperformed docking in recognizing the correct binding modes of androgen receptor ligands and (b) improved the correlation coefficient of computational and experimental results of rescor…
Photoinduced DNA Lesions in Dormant Bacteria: The Peculiar Route Leading to Spore Photoproducts Characterized by Multiscale Molecular Dynamics
2020
International audience; Some bacterial species enter a dormant state in the form of spores to resist to unfavorable external conditions. Spores are resistant to a wide series of stress agents, including UV radiation, and can last for tens to hundreds of years. Due to the suspension of biological functions, such as DNA repair, they accumulate DNA damage upon exposure to UV radiation. Differently from active organisms, the most common DNA photoproducts in spores are not cyclobutane pyrimidine dimers, but rather the so‐called spore photoproducts. This noncanonical photochemistry results from the dry state of DNA and its binding to small, acid‐soluble proteins that drastically modify the struct…
Molecular simulation of mixed gas hydrates in astrophysical conditions
2020
In this PhD work, numerical simulation methods have been used in order to model clathrate hydrates at the molecular scale, in thermodynamic conditions typical of astrophysical contexts. The aim was to characterize the trapping abilities of those peculiar structures of water, by means of the tools used in adsorption studies. The results presented in the present thesis are focused on a couple of chemical species which are found to be abundant in our astrophysical vicinity and are quite similar: carbon monoxide, CO, and nitrogen, N2. Thus, the single-component clathrates of CO and N2, and the mixed hydrate CO-N2 have been studied, mainly using grand canonical Monte Carlo simulations. First, th…
Scatter Search—Wellsprings and Challenges
2006
I came up with the idea of editing this volume in the summer of 2002 while working on the book "Scatter search methodologies and implementations in C" with Manuel Laguna in the University of Colorado at Boulder. There, Fred Glover kindly let me use his office, where I found a copy of the "Tabu Search Methods for Optimization" special issue that he edited in 1988 for the European Journal of Operational Research. This encounter made me realize that Scatter Search has reached a level of maturity as an optimization method that has parallels with what Tabu Search was experiencing in the late eighties. So I thought that the moment was perfect to embark on this project, which has been supported en…
Novel Hydrazine Molecules as Tools To Understand the Flexibility of Vascular Adhesion Protein-1 Ligand-Binding Site: Toward More Selective Inhibitors
2011
Vascular adhesion protein-1 (VAP-1) belongs to a family of amine oxidases. It plays a role in leukocyte trafficking and in amine compound metabolism. VAP-1 is linked to various diseases, such as Alzheimer's disease, psoriasis, depression, diabetes, and obesity. Accordingly, selective inhibitors of VAP-1 could potentially be used to treat those diseases. In this study, eight novel VAP-1 hydrazine derivatives were synthesized and their VAP-1 and monoamine oxidase (MAO) inhibition ability was determined in vitro. MD simulations of VAP-1 with these new molecules reveal that the VAP-1 ligand-binding pocket is flexible and capable of fitting substantially larger ligands than was previously believ…
Customer benefits of demand-side management in the Nordic electricity market
2016
The increasing share of renewable energy sources is likely to lead to price effects in Nordic electricity market, resulting especially in increased volatility of spot and imbalance prices. The greater price volatility and amount of required balancing power increase the need for Demand-Side Management (DSM) in the electricity market and may as well increase the financial benefits of DSM participants. In this research I study the DSM in electricity mar-ket and evaluate how large the financial benefits of DSM participants could be. Monte Carlo simulation method is used to simulate imbalance prices with different volatilities for Finland and Sweden. The results show that increasing volatility m…
Robust design of a sheet stamping process: approaches to control the inner process variability
2011
The robustness investigation has become a crucial issue in the design of the sheet metal forming operations. The uncontrollable effects of some noise variables heavily influence the final process results, often evolving up to the failure of the process design. Therefore, tools able to handle such variability are worth developing with the aim to minimize the scattering of the investigated process performances despite of the process design. Moreover, the stamping process operations are usually characterized by objectives with conflicting behaviors and a set of compromise solutions, referred as Pareto front, is finally obtained instead of a global optimum. Therefore, the question becomes more …
Superfluid density and quasi-long-range order in the one-dimensional disordered Bose–Hubbard model
2015
We study the equilibrium properties of the one-dimensional disordered Bose-Hubbard model by means of a gauge-adaptive tree tensor network variational method suitable for systems with periodic boundary conditions. We compute the superfluid stiffness and superfluid correlations close to the superfluid to glass transition line, obtaining accurate locations of the critical points. By studying the statistics of the exponent of the power-law decay of the correlation, we determine the boundary between the superfluid region and the Bose glass phase in the regime of strong disorder and in the weakly interacting region, not explored numerically before. In the former case our simulations are in agreem…
Evolutionary dynamics of imatinib-treated leukemic cells by stochastic approach
2008
The evolutionary dynamics of a system of cancerous cells in a model of chronic myeloid leukemia (CML) is investigated by a statistical approach. Cancer progression is explored by applying a Monte Carlo method to simulate the stochastic behavior of cell reproduction and death in a population of blood cells which can experience genetic mutations. In CML front line therapy is represented by the tyrosine kinase inhibitor imatinib which strongly affects the reproduction of leukemic cells only. In this work, we analyze the effects of a targeted therapy on the evolutionary dynamics of normal, first-mutant and cancerous cell populations. Several scenarios of the evolutionary dynamics of imatinib-tr…