2,921 research outputs found
On the conformational structure of a stiff homopolymer
In this paper we complete the study of the phase diagram and conformational
states of a stiff homopolymer. It is known that folding of a sufficiently stiff
chain results in formation of a torus. We find that the phase diagram obtained
from the Gaussian variational treatment actually contains not one, but several
distinct toroidal states distinguished by the winding number. Such states are
separated by first order transition curves terminating in critical points at
low values of the stiffness. These findings are further supported by
off-lattice Monte Carlo simulation. Moreover, the simulation shows that the
kinetics of folding of a stiff chain passes through various metastable states
corresponding to hairpin conformations with abrupt U-turns.Comment: 9 pages, 16 PS figures. Journal of Chemical Physics, in pres
Structure and stability of chiral beta-tapes: a computational coarse-grained approach
We present two coarse-grained models of different levels of detail for the
description of beta-sheet tapes obtained from equilibrium self-assembly of
short rationally designed oligopeptides in solution. Here we only consider the
case of the homopolymer oligopeptides with the identical sidegroups attached,
in which the tapes have a helicoid surface with two equivalent sides. The
influence of the chirality parameter on the geometrical characteristics, namely
the diameter, inter-strand distance and pitch, of the tapes have been
investigated. The two models are found to produceequivalent results suggesting
a considerable degree of universality in conformations of the tapes.Comment: 24 pages, 5 PS figures. Accepted to J. Chem. Phy
Conformational transitions of heteropolymers in dilute solutions
In this paper we extend the Gaussian self-consistent method to permit study
of the equilibrium and kinetics of conformational transitions for
heteropolymers with any given primary sequence. The kinetic equations earlier
derived by us are transformed to a form containing only the mean squared
distances between pairs of monomers. These equations are further expressed in
terms of instantaneous gradients of the variational free energy. The method
allowed us to study exhaustively the stability and conformational structure of
some periodic and random aperiodic sequences. A typical phase diagram of a
fairly long amphiphilic heteropolymer chain is found to contain phases of the
extended coil, the homogeneous globule, the micro-phase separated globule, and
a large number of frustrated states, which result in conformational phases of
the random coil and the frozen globule. We have also found that for a certain
class of sequences the frustrated phases are suppressed. The kinetics of
folding from the extended coil to the globule proceeds through non-equilibrium
states possessing locally compacted, but partially misfolded and frustrated,
structure. This results in a rather complicated multistep kinetic process
typical of glassy systems.Comment: 15 pages, RevTeX, 20 ps figures, accepted for publication in Phys.
Rev.
Hydration of a B-DNA Fragment in the Method of Atom-atom Correlation Functions with the Reference Interaction Site Model Approximation
We propose an efficient numerical algorithm for solving integral equations of
the theory of liquids in the Reference Interaction Site Model (RISM)
approximation for infinitely dilute solution of macromolecules with a large
number of atoms. The algorithm is based on applying the nonstationary iterative
methods for solving systems of linear algebraic equations. We calculate the
solvent-solute atom-atom correlation functions for a fragment of the B-DNA
duplex d(GGGGG).d(CCCCC) in infinitely dilute aqueous solution. The obtained
results are compared with available experimental data and results from computer
simulations.Comment: 9 pages, RevTeX, 9 pages of ps figures, accepted for publications in
JC
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