Exploring Transmembrane Diffusion Pathways With Molecular Dynamics
نویسندگان
چکیده
منابع مشابه
Exploring transmembrane diffusion pathways with molecular dynamics.
Transmembrane exchange of materials is a fundamental process in biology. Molecular dynamics provides a powerful method to investigate in great detail various aspects of the phenomenon, particularly the permeation of small uncharged molecules, which continues to pose a challenge to experimental studies. We will discuss some of the recent simulation studies investigating the role of lipid-mediate...
متن کاملExploring dynamic pathways by action-derived molecular dynamics
Action-derived molecular dynamics for the simulation of rare event and slow mode systems is reviewed. Theoretical background, implementation details, and comparison with other methods are presented. Numerical examples demonstrated include the structural formation and transformation of carbon fullerenes, and molecular reconfiguration of alanine dipeptide and valine dipeptide. It is shown that th...
متن کاملMolecular dynamics studies of straight-chain alkanes diffusion in SiO2 ceramic versus Bosanquet formula
Molecular Dynamics (MD) simulations were applied to calculate self-diffusion coefficients (Di ) and heats of adsorption for ethane, propane and n-butane. The simulations were done in temperature range of 300-525 K for various concentrations inside the pores of silicalite type zeolite. The calculated values of self-diffusion coefficients and heats of adsorption resulted from the current wo...
متن کاملEffects of Aluminum Incorporation in Tobermorite Structure on Chloride Diffusion: A Molecular Dynamics Simulation Study
In this paper, the effects of different aluminum to silicon ratios in silicate chains of calcium silicate hydrates (C-S-H) are evaluated on the diffusion coefficient of chloride ions by molecular dynamics method. Tobermorite is a crystalline phase that is used for studying C-S-H properties in nano scale, because of its analogous chemical composition to C-S-H. Aluminum incorporation in C-S-H and...
متن کاملExploring SIMD for Molecular Dynamics, Using Intel
We analyse gather-scatter performance bottlenecks in molecular dynamics codes and the challenges that they pose for obtaining benefits from SIMD execution. This analysis informs a number of novel code-level and algorithmic improvements to Sandia’s miniMD benchmark, which we demonstrate using three SIMD widths (128-, 256and 512bit). The applicability of these optimisations to wider SIMD is discu...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Physiology
سال: 2010
ISSN: 1548-9213,1548-9221
DOI: 10.1152/physiol.00046.2009