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