Index of papers in April 2015 that mention
  • molecular dynamics
Nils A. Berglund, Thomas J. Piggot, Damien Jefferies, Richard B. Sessions, Peter J. Bond, Syma Khalid
Abstract
To this end, we report the first molecular dynamics simulation study of the interaction of the antimicrobial peptide, polymyxin B1 with complex models of both the inner and outer membranes of E. coli.
Discussion
Other studies have suggested that atomistic molecular dynamics simulations of AMPs require multi-microsecond timescales [36].
Discussion
The large molecular systems and extended timescales accessible to coarse-grain molecular dynamics (CG-MD) simulations provide an alternative and complementary route to studying antimicrobial peptides.
Introduction
Because of experimental difficulties associated with characterizing dynamic, heterogeneous systems such as membrane-bound AMPs, molecular dynamics (MD) simulations provide a complementary approach to studying their modes of action, in unprecedented detail [14, 15].
Simulation Parameters and Protocol
All simulations performed in this work used the GROMACS molecular dynamics software [53, 54], version 4.5.1 [55].
Simulation Systems
the axis perpendicular to the plane of the membranes) and polymyxin molecules were manually added to the systems using the Visual Molecular Dynamics (VMD) software [52].
molecular dynamics is mentioned in 6 sentences in this paper.
Topics mentioned in this paper:
Noorain Khan, Narendar Kolimi, Thenmalarchelvi Rathinavelan
Abstract
Molecular dynamics simulations on DNA hairpin stems containing A. .
Introduction
In this context, we aim here to investigate the structure and dynamics of DNA duplex containing CAG repeat using molecular dynamics (MD) simulation technique.
Methods
Subsequently, the models are subjected to a total of 1.5us molecular dynamics simulations (MD) using Sander module of AMBER 12 package [40].
Molecular dynamics simulation protocol
Molecular dynamics simulation protocol
molecular dynamics is mentioned in 4 sentences in this paper.
Topics mentioned in this paper:
Jian Tian, Jaie C. Woodard, Anna Whitney, Eugene I. Shakhnovich
Author Summary
However, commonly employed molecular dynamics simulations suffer from a limitation in accessible time scale, making it difficult to model large-scale unfolding events in a realistic amount of simulation time without employing unrealistically high temperatures.
Discussion
Estimates of protein stability using Molecular Dynamics are prohibitive for all but the smallest protein domains.
Introduction
Tm is obtainable by experiment and, in theory, from simulation, although current molecular dynamics simulations are limited in their ability to capture full folding or unfolding trajectories of most proteins (except very small fast folding domains [15]) in a tractable amount of simulation time [16].
Predicting the effects of mutations on protein stability from non-equilibrium unfolding simulations
Although the idea of obtaining equilibrium free energy differences from non-equilibrium measurements is not new [35], and protein stabilities have been calculated from molecular dynamics simulations using the Iarzynski equality, e.g., [36—38] , such simulations require application of an external steering force; in the present paper we report the use of multi-temperature Monte-Carlo unfolding simulations in obtaining protein stabilities.
molecular dynamics is mentioned in 4 sentences in this paper.
Topics mentioned in this paper:
Rodrigo Cilla, Vinodh Mechery, Beatriz Hernandez de Madrid, Steven Del Signore, Ivan Dotu, Victor Hatini
Discussion
The segmentation and tracking of AIs in 3D and the curation of vertices, edges, cells and trajectories would enable the extension of the pipeline to relate molecular dynamics with cell and tissue remodeling for multiscale analysis of epithelial tissue morphogenesis.
Introduction
These behaviors, in turn, depend on intracellular molecular dynamics that allow cells to generate and transmit mechanical forces to one another, while maintaining epithelial cohesion [1, 2].
Introduction
Live imaging of cell and molecular dynamics using fluorescently-tagged proteins is a key method to investigate these processes [4].
molecular dynamics is mentioned in 3 sentences in this paper.
Topics mentioned in this paper: