Search results for "Molecular Dynamic"

Theoretical study of the temperature dependence of dynamic effects in thymidylate synthase.

2010

A theoretical study of the temperature dependence of dynamic effects in the rate limiting step of the reaction catalyzed by thymidylate synthase is presented in this paper. From hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) optimizations of transition state structures within a fully flexible molecular model, free downhill molecular dynamics trajectories have been performed at four different temperatures. The analysis of the reactive and non-reactive trajectories in the enzyme environment has allowed us to study the geometric and electronic coupling between the substrate, the cofactor and the protein. The results show how the contribution of dynamic effects to the rate enhancement mea…

Self-assembly of semiflexible polymers confined to thin spherical shells

2018

Confinement effects are critical for stiff macromolecules in biological cells, vesicles, and other systems in soft matter. For these molecules, the competition between the packing entropy and the enthalpic cost of bending is further shaped by strong confinement effects. Through coarse-grained molecular dynamics simulations, we explore the self-assembly of semiflexible polymers confined in thin spherical shells for various chain lengths, chain stiffnesses, and shell thicknesses. Here, we focus on the case where the contour and persistence length of the polymers are comparable to the radius of the confining cavity. The range of ordered structures is analyzed using several order parameters to …

Collective properties of hydration: long range and specificity of hydrophobic interactions

1997

We report results of molecular dynamics (MD) simulations of composite model solutes in explicit molecular water solvent, eliciting novel aspects of the recently demonstrated, strong many-body character of hydration. Our solutes consist of identical apolar (hydrophobic) elements in fixed configurations. Results show that the many-body character of PMF is sufficiently strong to cause 1) a remarkable extension of the range of hydrophobic interactions between pairs of solute elements, up to distances large enough to rule out pairwise interactions of any type, and 2) a SIF that drives one of the hydrophobic solute elements toward the solvent rather than away from it. These findings complement re…

Solution structure of aD,L-alternating oligonorleucine as a model of double-stranded antiparallel ?-helix

2002

Conformational characteristics of alternating D,L linear peptides are of particular interest because of their capacity to form transmembrane channels with different transport properties, as some natural antibiotics do. Single- and double-stranded beta-helical structures are common for alternating D,L peptides. The stability of the beta-helix depends on several structural factors, such as the backbone peptide length, type and position of side chains, and nature of terminal groups. The NMR and molecular dynamics solution conformation of a synthetic alternating D,L-oligopeptide with 15 norleucines (XVMe) has been used as a model to get insight in to the conformational features of double-strand…

Molecular dynamics of discotic charge-transfer complexes, dielectric spectroscopy and2H NMR studie

1994

Abstract Using a combination of solid state 2H NMR spectroscopy on selectively deuteriated samples and dielectric spectroscopy, the molecular dynamics of discotic charge-transfer (CT) complexes were investigated. These complexes show particular thermodynamic and flow properties. Considered were mixtures of low molar mass donors and acceptors, low molar mass donors with main chain acceptor polymers and covalently linked donor-acceptor twins with different lengths of the spacer. A main result is that correlated rotational motions of discotic molecules or groups about the columnar axis are observed in all systems except for the twin with the short spacer. This type of motion seems to be a gene…

Molecular dynamics in ferroelectric liquid crystals: From low molar to polymeric and elastomeric systems

2007

Transport properties of 2F = F2 in a temperature gradient as studied by molecular dynamics simulations

2007

International audience; We calculate transport properties of a reacting mixture of F and F2 from results of nonequilibrium molecular dynamics simulations. The reaction investigated is controlled by thermal diffusion and is close to local chemical equilibrium. The simulations show that a formulation of the transport problem in terms of classical non-equilibrium thermodynamics theory is sound. The chemical reaction has a large effect on the magnitude and temperature dependence of the thermal conductivity and the interdiffusion coefficient. The increase in the thermal conductivity in the presence of the chemical reaction, can be understood as a response to an imposed temperature gradient, whic…

Molecular Dynamic Simulation on Polyamide6/Graphene nano-layers nanocomposites

2016

In this work results obtained from Molecular Dynamic Simulation (MDS) on Polyamide 6 (PA6) chains in graphene containing nanocomposites are presented. Through detailed MDS, the interface of complex nanocomposites systems can be fully characterized, furthermore different physical properties, such as density, end-to-end distance , and average radius of gyration of polymers chains can be predicted. This issue is useful for the design of highly value-added nanocomposites and the optimization of their production process, by defining transformation steps and status variables (temperature, time and pressure), that can also help the industrial production.

Surface-induced order and diffusion in 5CB liquid crystal confined to porous glass.

2001

Liquid crystals confined into small cavities are known to have a weak orientational order even above the nematic-isotropic transition temperature. The surface-induced order and molecular dynamics in this temperature range are studied with the aid of deuteron NMR spectra, spin relaxation times T(1) and T(2,) proton dipolar-correlation effect, and direct measurements of the effective diffusion coefficient for the liquid crystal 5CB confined to controlled-pore glasses. Our results show that an arrangement of molecules parallel to the wall is induced by local molecular interactions between the liquid crystal and solid, resulting in a weak and temperature independent surface order parameter, S(0…

Balanced dual acting compounds targeting aromatase and estrogen receptor α as an emerging therapeutic opportunity to counteract estrogen responsive b…

2021

Abstract Breast Cancer (BC) is a leading cause of death in women, currently affecting 13% of female population worldwide. First-line clinical treatments against Estrogen Receptor positive (ER+) BC rely on suppressing estrogen production, by inhibiting the aromatase (AR) enzyme, or on blocking estrogen-dependent pro-oncogenic signaling, by targeting Estrogen Receptor (ER) α with selective Modulators/Degraders (SERMs/SERDs). The development of dual acting molecules targeting AR and ERα represents a tantalizing alternative strategy to fight ER + BC, reducing the incidence of adverse effects and resistance onset that limit the effectiveness of these gold-standard therapies. Here, in silico desi…