Formation of Collective Conformational Degrees of Freedom during Macromolecular Chain Folding Dynamics in a Viscous Mediumстатья
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Аннотация:Abstract—Computational methods were used to study the dynamics of the formation of the collective conformational
degrees of freedom in the relaxation folding of a model biopolymer chain of 50 nodes in a viscous
medium; the model has been described previously. Collective conformational motions of the nodes were
shown to arise due to friction forces in a viscous medium. The collective motions have several typical forms,
including a wave of differently directed motions of chain nodes that propagates from one end of the chain to
another (like a soliton) in response to a pertubation in terminal group position. Individual nodes located at
the middle of the chain make approximately equal contributions to the total energy dissipation rate. The end
nodes contribute approximately 2–4 times more than internal nodes to the total energy dissipation. The
results of numerical experiments are consistent with the theoretical concept developed earlier to describe the
dynamics of linear macromolecular chains in a viscous medium in the limit of a very large number of nodes.
Keywords: simulation of biopolymer dynamics, folding dynamics, principle of minimum energy dissipation
rate, energy dissipation rate distributions for conformational degrees of freedom, correlation of conformational
motions, energy funnel
DOI: 10.1134/S0006350917020233