Search results for "molecular dynamics"
showing 10 items of 1075 documents
Human Inducible Hsp70: Structures, Dynamics, and Interdomain Communication from All-Atom Molecular Dynamics Simulations
2015
The 70 kDa human heat shock protein is a major molecular chaperone involved in de novo folding of proteins in vivo and refolding of proteins under stress conditions. Hsp70 is related to several "misfolding diseases" and other major pathologies, such as cancer, and is a target for new therapies. Hsp70 is comprised of two main domains: an N-terminal nucleotide binding domain (NBD) and a C-terminal substrate protein binding domain (SBD). The chaperone function of Hsp70 is based on an allosteric mechanism. Binding of ATP in NBD decreases the affinity of the substrate for SBD, and hydrolysis of ATP is promoted by binding of polypeptide segments in the SBD. No complete structure of human Hsp70 is…
How to apply the Kirkwood–Buff theory to individual species in salt solutions
2013
It is generally assumed that the Kirkwood–Buff (KB) theory cannot be applied to anions and cations individually in a solution, as one cannot simulate this system in an open ensemble due to the electroneutrality constraint. By applying our recently derived KB theory for closed systems, we show that one does have access to single-ion properties in Molecular Dynamics. Our findings are supported by simulations for a model of a salt solution in which particles interact with WCA potentials, as well as for the NaCl/water system using the Particle Mesh Ewald technique for electrostatics.
Can hydrophobic interactions be correctly reproduced by the continuum models?
1996
The ability of the continuum models to describe hydrophobic interactions is investigated. In this work we have studied the interactions between two methane molecules in aqueous solution by means of a continuum model. The resulting potential of mean force is in good agreement with those obtained using Monte Carlo and molecular dynamics techniques. The three energy contributions appearing in the continuum energy partition (electrostatic, dispersion−repulsion, and cavitation) have been analyzed. The cavitation free energy plays the most important role of the three, determining the existence of an energy barrier between the contact minimum and the separated methane monomers. This barrier, which…
Theoretical Studies of the Self Cleavage Pistol Ribozyme Mechanism
2021
AbstractRibozymes are huge complex biological catalysts composed of a combination of RNA and proteins. Nevertheless, there is a reduced number of small ribozymes, the self-cleavage ribozymes, that are formed just by RNA and, apparently, they existed in cells of primitive biological systems. Unveiling the details of these “fossils” enzymes can contribute not only to the understanding of the origins of life but also to the development of new simplified artificial enzymes. A computational study of the reactivity of the pistol ribozyme carried out by means of classical MD simulations and QM/MM hybrid calculations is herein presented to clarify its catalytic mechanism. Analysis of the geometries…
Cell-List based Molecular Dynamics on Many-Core Processors: A Case Study on Sunway TaihuLight Supercomputer
2020
Molecular dynamics (MD) simulations are playing an increasingly important role in several research areas. The most frequently used potentials in MD simulations are pair-wise potentials. Due to the memory wall, computing pair-wise potentials on many-core processors are usually memory bounded. In this paper, we take the SW26010 processor as an exemplary platform to explore the possibility to break the memory bottleneck by improving data reusage via cell-list-based methods. We use cell-lists instead of neighbor-lists in the potential computation, and apply a number of novel optimization methods. Theses methods include: an adaptive replica arrangement strategy, a parameter profile data structur…
Simulated annealing with restrained molecular dynamics using a flexible restraint potential: Theory and evaluation with simulated NMR constraints
1996
A new functional representation of NMR-derived distance constraints, the flexible restraint potential, has been implemented in the program CONGEN (Bruccoleri RE, Karplus M, 1987, Biopolymers 26:137-168) for molecular structure generation. In addition, flat-bottomed restraint potentials for representing dihedral angle and vicinal scalar coupling constraints have been introduced into CONGEN. An effective simulated annealing (SA) protocol that combines both weight annealing and temperature annealing is described. Calculations have been performed using ideal simulated NMR constraints, in order to evaluate the use of restrained molecular dynamics (MD) with these target functions as implemented i…
Force probe simulations using a hybrid scheme with virtual sites.
2017
Hybrid simulations, in which a part of the system is treated with atomistic resolution and the remainder is represented on a coarse-grained level, allow for fast sampling while using the accuracy of atomistic force fields. We apply a hybrid scheme to study the mechanical unfolding and refolding of a molecular complex using force probe molecular dynamics (FPMD) simulations. The degrees of freedom of the solvent molecules are treated in a coarse-grained manner while atomistic resolution is retained for the solute. The coupling between the solvent and the solute is provided using virtual sites. We test two different common coarse-graining procedures, the iterative Boltzmann inversion method an…
Molecular-dynamics simulation of a glassy polymer melt: Incoherent scattering function
1999
We report results of molecular-dynamics simulations for a glassy polymer melt consisting of short, linear bead-spring chains. It was shown in previous work that this onset of the glassy slowing down is compatible with the predictions of the mode coupling theory. The physical process of `caging' of a monomer by its spatial neighbors leads to a distinct two step behavior in the particle mean square displacements. In this work we analyze the effects of this caging process on the Rouse description of the melt's dynamics. We show that the Rouse theory is applicable for length and time scales above the typical scales for the caging process. Futhermore, the monomer displacement is compared with si…
Dynamics of a supercooled polymer melt above the mode-coupling critical temperature: cage versus polymer-specific effects
2000
This paper reports results of molecular dynamics simulations for a glassy polymer melt consisting of short, non-entangled chains. The temperature region studied covers the supercooled state of the melt above the mode-coupling critical temperature. The analysis focuses on the interplay of simple-liquid and polymer-specific effects. One can clearly distinguish two regimes: a regime of small and one of large monomer displacements. The first regime corresponds to motion of a monomer in its local environment. It is dominated by the cage effect and well described by the idealized mode-coupling theory. The second regime is governed by the late-β/early-α process. In this regime the connectivity of …
Time-dependent alignment of molecules trapped in octahedral crystal fields.
2006
The hindered rotational states of molecules confined in crystal fields of octahedral symmetry, and their time-dependent alignment obtained by pulsed nonresonant laser fields, are studied computationally. The control over the molecular axis direction is discussed based on the evolution of the rotational wave packet generated in the cubic crystal-field potential. The alignment degree obtained in a cooperative case, where the alignment field is applied in a favorable crystal-field direction, or in a competitive direction, where the crystal field has a saddle point, is presented. The investigation is divided into two time regimes where the pulse duration is either ultrashort, leading to nonadia…