Search results for " Simulation"
showing 10 items of 4034 documents
Quantitative Analysis of the Interactions of Metal Complexes and Amphiphilic Systems: Calorimetric, Spectroscopic and Theoretical Aspects.
2022
Metals and metal-based compounds have many implications in biological systems. They are involved in cellular functions, employed in the formation of metal-based drugs and present as pollutants in aqueous systems, with toxic effects for living organisms. Amphiphilic molecules also play important roles in the above bio-related fields as models of membranes, nanocarriers for drug delivery and bioremediating agents. Despite the interest in complex systems involving both metal species and surfactant aggregates, there is still insufficient knowledge regarding the quantitative aspects at the basis of their binding interactions, which are crucial for extensive comprehension of their behavior in sol…
Fick diffusion coefficients of liquid mixtures directly obtained from equilibrium molecular dynamics.
2011
A methodology for computing Fick diffusivities directly from equilibrium molecular dynamics (MD) simulations is presented and validated for acetone-methanol and acetone-tetrachloromethane liquid mixtures. Fick diffusivities are obtained from Maxwell-Stefan (MS) diffusivities and the so-called thermodynamic factor. MS diffusivities describe the friction between different components, while the thermodynamic factor is the concentration derivative of the activity describing the deviation from ideal mixing behavior. It is important to note that all mutual diffusion experiments measure Fick diffusion coefficients, while molecular simulation provides MS diffusivities. The required thermodynamic fa…
Partial molar enthalpies and reaction enthalpies from equilibrium molecular dynamics simulation
2014
We present a new molecular simulation technique for determining partial molar enthalpies in mixtures of gases and liquids from single simulations, without relying on particle insertions, deletions, or identity changes. The method can also be applied to systems with chemical reactions. We demonstrate our method for binary mixtures of Weeks-Chandler-Anderson particles by comparing with conventional simulation techniques, as well as for a simple model that mimics a chemical reaction. The method considers small subsystems inside a large reservoir (i.e., the simulation box), and uses the construction of Hill to compute properties in the thermodynamic limit from small-scale fluctuations. Results …
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…