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A Natural Coarse Graining for Simulating Large Biomolecular Motion
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ABSTRACT
Various coarse graining schemes have been proposed to speed up computer simulations of the motion within large biomolecules, which can contain hundreds of thousands of atoms. We point out here that there is a very natural way of doing this, using the rigid regions identified within a biomolecule as the coarse grain elements. Subsequently, computer resources can be concentrated on the flexible connections between the rigid units. Examples of the use of such techniques are given...
Related newspaper, magazine, and journal articles from HighBeam Research
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A Natural Coarse Graining for Simulating Large Biomolecular Motion
Biophysical Journal
; ABSTRACT Various coarse graining schemes have been proposed to speed up computer simulations of the motion within large biomolecules, which can contain hundreds of thousands of atoms. We point out here that there is a very natural way of doing this, using the rigid regions identified within a
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Predictability in a Model of Geophysical Turbulence
Journal of the Atmospheric Sciences
; ABSTRACT The nature of predictability is examined in a numerical model relevant to the midlatitude atmosphere and oceans. The approach followed is novel and uses new theoretical tools from information theory, namely entropy functionals, as measures of information content and their application to
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Coarse-graining in suspensions of charged nanoparticles *.
Pure and Applied Chemistry
; Abstract: A coarse-grain description of nanocolloidal suspensions in the presence of an added salt is presented here. It enables us to simulate trajectories of the nanoparticles from effective functions that depend on average densities of salt ions. In practice, the ion-averaged effective potential
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Fitting Low-Resolution Cryo-EM Maps of Proteins Using Constrained Geometric Simulations
Biophysical Journal
; ... experimental advances in producing density maps from cryo-electron microscopy (cryo-EM ... relevant for biological cryo-EM (5,13) and maps generated with cryo-EM are referred to commonly as "electron density maps" in the literature (7, 8,14,17-19). It ...
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Convective Forcing Fluctuations in a Cloud-Resolving Model: Relevance to the Stochastic Parameterization Problem
Journal of Climate
; ABSTRACT Idealized cloud-resolving model (CRM) simulations spanning a large part of the tropical atmosphere are used to evaluate the extent to which deterministic convective parameterizations fail to capture the statistical fluctuations in deep-convective forcing, and to provide probability
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Coarse-Grained Peptide Modeling Using a Systematic Multiscale Approach
Biophysical Journal
; ABSTRACT A systematic new approach to derive multiscale coarse-grained (MS-CG) models has been recently developed. The approach employs information from atomistically detailed simulations to derive CG forces and associated effective potentials. In this work, the MS-CG methodology is extended to
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Microscopic Simulation of Membrane Molecule Diffusion on Corralled Membrane Surfaces
Biophysical Journal
; ABSTRACT The current understanding of how receptors diffuse and cluster in the plasma membrane is limited. Data from single-particle tracking and laser tweezer experiments have suggested that membrane molecule diffusion is affected by the presence of barriers dividing the membrane into corrals.
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Effect of the Ionic Strength and pH on the Equilibrium Structure of a Neurofilament Brush
Biophysical Journal
; ABSTRACT Using the numerical model of Scheutjens and Fleer, we investigated, on a self-consistent field level, the equilibrium structure of the neurofilament brush formed by projection domains of the constituent NF-H, NF-M, and NF-L proteins. The phosphorylation of such a brush is a major
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MONTE CARLO STUDY OF DILUTE SOLUTIONS OF HETEROARM STAR COPOLYMERS IN SOLVENTS DIFFERING IN THERMODYNAMIC QUALITY
Collection of Czechoslovak Chemical Communications
; Lattice Monte Carlo simulations (an original modification of the Siepmann and Frenkel simulation variant) was used to study the conformational behavior of heteroarm star copolymers star-(polystyrene; polyisoprene), PS^sub 8^PI^sub 8^, in a common good solvent for both types of arms
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Coarse-Grained Modeling of the Actin Filament Derived from Atomistic-Scale Simulations
Biophysical Journal
; ... Reuter, J. Navaza, D. L. Stokes, and J. J. Lacapere. 2005. Normal mode-based fitting of atomic structure into electron density maps: application to sarcoplasmic reticulum Ca-ATPase. Biophys. J. 88:818-827. 38. Tama, F., O. Miyashita, and C. L. Brooks. 2004 ...
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