Friction ofN-bead macromolecules in solution: Effects of the bead-solvent interaction

Abstract

The role of the bead-solvent interaction has been studied for its influence on the dynamics of an N-bead macromolecule which is immersed into a solution. Using a Fokker-Planck equation for the phase-space distribution function of the macromolecule, we show that all the effects of the solution can be treated entirely in terms of the friction tensors which are assigned to each pair of interacting beads in the chain. For the high-density as well as for the critical solvent, the properties of these tensors are discussed in detail and are calculated by using several (realistic) choices of the bead-solvent potential. From the friction tensors, moreover, an expression for the center-of-mass friction coefficient of a (N-bead) chain macromolecule is derived. Numerical data for this coefficient for "truncated" Lennard-Jones bead-solvent potential are compared with results from molecular dynamic simulations and from the phenomenological theoretical data as found in the literature.

Hierarchical multiscale modeling of macromolecules and their assemblies

“…This has resulted in the development of coarse-grained models such as bead [7], rigid-blob [8], shape-based [9], rigid region decomposition [10], symmetry-constrained [11] and curvilinear coordinate [12] models, as well as Principle Component Analysis (PCA) and Normal Mode Analysis (NMA) guided approaches [13–14]. Simulation methodologies based on these models involve tracking a much smaller number of dynamical variables than those based on all-atom description.…”

“…Interestingly, the very hierarchical nature of macromolecular assemblies has been utilized in designing reduced dimensionality frameworks to facilitate their efficient computer simulation, but is achieved at the expense of losing atomic scale resolution. This has resulted in the development of coarse-grained models such as bead [7], rigid-blob [8], shape-based [9], rigid region decomposition [10], symmetry-constrained [11] and curvilinear coordinate [12] models, as well as Principle Component Analysis (PCA) and Normal Mode Analysis (NMA) guided approaches [13][14]. Simulation methodologies based on these models involve tracking a much smaller number of dynamical variables than those based on all-atom description.…”

Hierarchical Order Parameters for Macromolecular Assembly Simulations. 1. Construction and Dynamical Properties of Order Parameters

“…This idea has resulted in the development of coarse-grained models for macromolecules and their assemblies. An incomplete list would include bead, , shape-based, rigid region decomposition, symmetry constrained, and curvilinear coordinate models, as well as Principal Component Analysis (PCA) and Normal Mode Analysis (NMA) guided approaches. − These models have been successful in investigating structural transitions in a very rich set of biomolecules including alanine polypeptides, ligand binding proteins, transmembrane proteins, , RNA segments, , and virus capsids of different symmetries. , However, they suffer from one or more of the following difficulties: (1) Characteristic variables are not slowly varying in time. (2) Nonlinear motions like macromolecular twist are not readily accounted for.…”

High-order correlation contributions to the friction of macromolecules in solution: A semi-phenomenological Fokker-Planck approach

“…To explore the effects of the solvent onto the dynamics of macromolecules, a Fokker-Planck-type equation (FPE) has been derived recently by us for the time evolution of the phase-space distribution function of a (N -bead) macromolecule [8,10]. In this FPE, all information about the interaction among the beads of the macromolecule as well as the effects from the surrounding solvent is described by means of semi-phenomenological friction tensors which are expressed in terms of the bead-solvent 68001-p1 interaction and the dynamical structure factor of the solvent [8].…”