Search results for "molecular dynamics"

An empirical method to determine the free surface energy of solids at different deformations and temperatures regimes : An application to Al.

2005

Abstract We have performed molecular dynamics (MD) simulations using the three low index surfaces of Al to determine the variation of the surface energy as a function of deformation and temperature. We have also developed an empirical formulation for the surface free energy as a function of deformation. The observed difference between the numerical and analytical results has led us to divide the deformation into a mechanical and a thermal contribution. From this observation, we have obtained an expression for the surface free energy placing the temperature dependence on the bulk and surface elastic constants. Our simulations permitted us to analyze the multilayer relaxation for the particul…

H-2 vibrational spectral signatures in binary and ternary mixtures: theoretical model, simulation and application to CARS thermometry in high pressur…

2001

International audience; A summary of the main results obtained by the two groups in the field of H-2 vibrational spectral line signatures for various mixtures. in connection with CARS diagnostics of H-2-O-2 combustion systems, is presented. H-2-X Systems may have specific large inhomogeneous spectral features, due to the dependence of the line broadening and line shifting on the (H-2) radiator speed, particularly at high temperature. Thus, careful attention has to be paid to rigorously analyze such features, both from the experimental point of view (Dijon) and from the theoretical one (Besancon). Applications of the present results to high-pressure H-2/air flame thermometry are also briefly…

Thermodynamics and kinetics of ion permeation in wild-type and mutated open active conformation of the human α7 nicotinic receptor

2020

Molecular studies of human pentameric ligand-gated ion channels (LGICs) expressed in neurons and at neuromuscular junctions are of utmost importance in the development of therapeutic strategies for neurological disorders. We focus here on the nicotinic acetylcholine receptor nAChR-α7, a homopentameric channel widely expressed in the human brain, with a proven role in a wide spectrum of disorders including schizophrenia and Alzheimer's disease. By exploiting an all-atom structural model of the full (transmembrane and extracellular) protein in the open, agonist-bound conformation we recently developed, we evaluate the free energy and the mean first passage time of single-ion permeation using …

Dynamics of the ligand-binding domains of ionotropic glutamate receptors

2010

Targeting G-quadruplexes with Organic Dyes: Chelerythrine–DNA Binding Elucidated by Combining Molecular Modeling and Optical Spectroscopy

2019

The DNA-binding of the natural benzophenanthridine alkaloid chelerythrine (CHE) has been assessed by combining molecular modeling and optical absorption spectroscopy. Specifically, both double-helical (B-DNA) and G-quadruplex sequences&mdash

A synthetic derivative of antimicrobial peptide holothuroidin 2 from mediterranean sea cucumber (Holothuria tubulosa) in the control of Listeria mono…

2019

Due to the limited number of available antibiotics, antimicrobial peptides (AMPs) are considered antimicrobial candidates to fight difficult-to-treat infections such as those associated with biofilms. Marine environments are precious sources of AMPs, as shown by the recent discovery of antibiofilm properties of Holothuroidin 2 (H2), an AMP produced by the Mediterranean sea cucumber Holothuria tubulosa. In this study, we considered the properties of a new H2 derivative, named H2d, and we tested it against seven strains of the dangerous foodborne pathogen Listeria monocytogenes. This peptide was more active than H2 in inhibiting the growth of planktonic L. monocytogenes and was able to interf…

Molecular dynamics of electrosprayed water nanodroplets containing sodium bis(2-ethylhexyl)sulfosuccinate

2013

The behavior of aqueous solutions of sodium bis(2-ethylhexyl)sulfosuccinate (AOTNa) subject to electrospray ionization (ESI) has been investigated by molecular dynamics (MD) simulations at three temperatures (350, 500 and 800 K). We consider several types of water nanodroplets containing AOTNa molecules and composed of a fixed number of water molecules (1000), N(AOT)(0) AOT(-) anions (N(AOT)(0) =  0, 5, 10) and N(Na)(0) sodium ions (N(Na)(0) =  0, 5, 10, 15, 20): in a short time scale (less than 1 ns), the AOTNa molecules, initially forming direct micelles in the interior of the water nanodroplets, are observed in all cases to diffuse nearby the nanodroplet surface, so that the hydrophilic …

Molecular Basis for Endocrine Disruption by Pesticides Targeting Aromatase and Estrogen Receptor

2020

The intensive use of pesticides has led to their increasing presence in water, soil, and agricultural products. Mounting evidence indicates that some pesticides may be endocrine disrupting chemicals (EDCs), being therefore harmful for the human health and the environment. In this study, three pesticides, glyphosate, thiacloprid, and imidacloprid, were tested for their ability to interfere with estrogen biosynthesis and/or signaling, to evaluate their potential action as EDCs. Among the tested compounds, only glyphosate inhibited aromatase activity (up to 30%) via a non-competitive inhibition or a mixed inhibition mechanism depending on the concentration applied. Then, the ability of the thr…

The catalytic mechanism of glyceraldehyde 3-phosphate dehydrogenase from Trypanosoma cruzi elucidated via the QM/MM approach

2013

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) has been identified as a key enzyme involved in glycolysis processes for energy production in the Trypanosoma cruzi parasite. This enzyme catalyses the oxidative phosphorylation of glyceraldehyde 3-phosphate (G3P) in the presence of inorganic phosphate (Pi) and nicotinamide adenosine dinucleotide (NAD+). The catalytic mechanism used by GAPDH has been intensively investigated. However, the individual roles of Pi and the C3 phosphate of G3P (Ps) sites, as well as some residues such as His194 in the catalytic mechanism, remain unclear. In this study, we have employed Molecular Dynamics (MD) simulations within hybrid quantum mechanical/molecular …

Preorganization and reorganization as related factors in enzyme catalysis: the chorismate mutase case.

2003

In this paper a deeper insight into the chorismate-to prephenate-rearrangement, catalyzed by Bacillus subtilis chorismate mutase, is provided by means of a combination of statistical quantum mechanics/molecular mechanics simulation methods and hybrid potential energy surface exploration techniques. The main aim of this work is to present an estimation of the preorganization and reorganization terms of the enzyme catalytic rate enhancement. To analyze the first of these, we have studied different conformational equilibria of chorismate in aqueous solution and in the enzyme active site. Our conclusion is that chorismate mutase preferentially binds the reactive conformer of the substrate--that…