Hierarchical coarse-graining strategy for protein-membrane systems to access mesoscopic scales
نویسندگان
چکیده
منابع مشابه
Markov Methods for Hierarchical Coarse-Graining of Large Protein Dynamics
Elastic network models (ENMs) and, in particular, the Gaussian Network Model (GNM) have been widely used in recent years to gain insights into the machinery of proteins. The extension of ENMs to supramolecular assemblies presents computational challenges, because of the difficulty in retaining atomic details in mode decomposition of large protein dynamics. Here, we present a novel approach to a...
متن کاملFluctuation-preserving coarse graining for biochemical systems.
Finite stochastic Markov models play a major role in modeling biological systems. Such models are a coarse-grained description of the underlying microscopic dynamics and can be considered mesoscopic. The level of coarse-graining is to a certain extent arbitrary since it depends on the resolution of accommodating measurements. Here we present a systematic way to simplify such stochastic descript...
متن کاملA numerical strategy for coarse-graining two-dimensional atomistic models at finite temperature: the membrane case
We present a numerical strategy to compute ensemble averages of coarse-grained two-dimensional membrane-like models. The approach consists in generalizing to these two-dimensional models a one-dimensional strategy exposed in [Blanc, Le Bris, Legoll, Patz, JNLS 2010, [6]], which is based on applying the ergodic theorem to Markov chains. This may be considered as a first step towards computing th...
متن کاملCoarse graining
Multiscale simulations For nearly all systems of interest to us, the most transferrable and fundamental description of matter is one that invokes quantum mechanics. At the highest level of accuracy, this amounts to solving Schrodinger’s equation for all of the subatomic particles in a system. Computationally, many approximations need to be made in order to use ab initio methods, and even these ...
متن کاملCoarse-graining protein energetics in sequence variables.
We show that cluster expansions (CE), previously used to model solid-state materials with binary or ternary configurational disorder, can be extended to the protein design problem. We present a generalized CE framework, in which properties such as energy can be unambiguously expanded in the amino-acid sequence space. The CE coarse grains over nonsequence degrees of freedom (e.g., side-chain con...
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: Faraday Discuss.
سال: 2010
ISSN: 1359-6640,1364-5498
DOI: 10.1039/b901996k