Search results for "molecular dynamics"

The dynamic orientation of membrane-bound peptides: bridging simulations and experiments.

2007

AbstractThe structural organization in a peptide/membrane supramolecular complex is best described by knowledge of the peptide orientation plus its time-dependent and spatial fluctuations. The static orientation, defined by the peptide tilt and a rotation about its molecular axis, is accessible through a number of spectroscopic methods. However, peptide dynamics, although relevant to understand the functionality of these systems, remains largely unexplored. Here, we describe the orientation and dynamics of Trp-flanked and Lys-flanked hydrophobic peptides in a lipid bilayer from molecular dynamics simulations. A novel view is revealed, where collective nontrivial distributions of time-evolvi…

Self-Assembling of Peptide/Membrane Complexes by Atomistic Molecular Dynamics Simulations

2007

Abstract Model biological membranes consisting of peptide/lipid-bilayer complexes can nowadays be studied by classical molecular dynamics (MD) simulations at atomic detail. In most cases, the simulation starts with an assumed state of a peptide in a preformed bilayer, from which equilibrium configurations are difficult to obtain due to a relatively slow molecular diffusion. As an alternative, we propose an extension of reported work on the self-organization of unordered lipids into bilayers, consisting of including a peptide molecule in the initial random configuration to obtain a membrane-bound peptide simultaneous to the formation of the lipid bilayer. This strategy takes advantage of the…

A quantum mechanics/molecular mechanics study of the protein-ligand interaction for inhibitors of HIV-1 integrase.

2007

Human immunodeficiency virus type-1 integrase (HIV-1 IN) is an essential enzyme for effective viral replication. Diketo acids such as L-731,988 and S-1360 are potent and selective inhibitors of HIV-1 IN. In this study, we used molecular dynamics simulations, within the hybrid quantum mechanics/molecular mechanics (QM/MM) approach, to determine the protein-ligand interaction energy between HIV-1 IN and L-731,988 and 10 of its derivatives and analogues. This hybrid methodology has the advantage that it includes quantum effects such as ligand polarisation upon binding, which can be very important when highly polarisable groups are embedded in anisotropic environments, as for example in metal-c…

Conformational studies of the Emp-AKH peptide using Molecular and Langevin Dynamics methods

1998

The secondary structure of the member of the AKH/RPCH family has been studied by Molecular Dynamics and Langevin Dynamics methods. Molecular dynamics simulation were performed in vacuum, model aqueous solution and simulated membrane. Langevin dynamics simulation was performed using the friction factor γ equal to 2 ps-1. Molecular dynamics as well as Langevin Dynamics simulation were conducted at 300 K. All minimum energy conformers have similar backbone structure characterised by the turn consisted out of 3 amino acids, Thr, Pro and Asn7. Structures obtained from Molecular Dynamics simulation are characterised by the lack of hydrogen bonds whereas the structure obtained form Langevin Dynami…

Design and Optimization of Chromophores for Liquid Crystal and Photorefractive Applications

1999

ABSTRACTOrganic chromophores have been exploited for a wide range of discrete optical and electronic functions as well as a growing number of combined opto-electronic functions. We are pursuing development of organic and polymer materials for a range of applications that require properties including liquid crystallinity, second order optical nonlinearity, photorefractivity and, more recently, special nonlinear optical behavior involving molecular chirality.

Polymer Brushes on Flat and Curved Substrates: What Can be Learned from Molecular Dynamics Simulations

2017

Computer Simulation of Polymers: Physics and Methods from Specific to Universal

2004

We will discuss in this contribution several aspects of the physics of polymers on different length and time scales and the simulation methods suited for their study. A Molecular Dynamics (MD) simulation of a chemically realistic model is needed to get quantitative insight into local relaxation processes. This study will also reveal the importance of four-particle correlations in polymer dynamics resulting from the presence of dihedral potentials along the chain. Universal largescale chain relaxation can be studied by realistic models as well, but in far better statistical accuracy by Monte Carlo (MC) simulations of a coarse-grained lattice model. Finally we will present considerations for …

Highly Defined, Colloid‐Like Ionic Clusters in Solution

2012

Many societal challenges at the beginning of the 21st century lead to an apparent and growing need for functional materials and novel ways of materials synthesis and assembly. Rising to the challenge, the utilization of small, self-assembling building blocks for the bottom-up construction of new types of polymers and nanostructures has enjoyed increasing popularity among materials researchers in the recent past. Supramolecular materials like foldamers, surface films, nanoparticles, etc. are created by exploiting noncovalent forces [1] leading to an ordered arrangement of nanoscale building blocks. [2] In the search for new polymers based on noncovalent molecular forces, we are motivated by …

Phase Separation of Colloid Polymer Mixtures Under Confinement

2013

Colloid polymer mixtures exhibit vapor-liquid like and liquid-solid like phase transitions in bulk suspensions, and are well-suited model systems to explore confinement effects on these phase transitions. Static aspects of these phenomena are studied by large-scale Monte Carlo simulations, including novel “ensemble switch” methods to estimate excess free energies due to confining walls. The kinetics of phase separation is investigated by a Molecular Dynamics method, where hydrodynamic effects due to the solvent are included via the multiparticle collision dynamics method.

GPU Based Molecular Dynamics Simulations of Polymer Rings in Concentrated Solution: Structure and Scaling

2011

We report on equilibrium properties of a concentrated solution of non-concatenated ring polymers by Molecular dynamics simulations using HooMD-blue, a fast implementation on graphics processor units (GPUs). We are able to identify the intermediate scaling regime for the radius of gyration Rg ∝ N as well as indication for a crossover to Rg ∝ N for rings with chain length N in our fully flexible off-lattice polymer model. This crossover takes place between a ring size of 2500 and 7500 monomers for monomer density ρ = 0.5. Our results are in agreement with recent studies for lattice and stiff off-lattice models and show once again that this scaling is not model dependent at all. Furthermore th…