Related papers: Short-time dynamics of polypeptides
We report a numerical study of the diffusiophoresis of short polymers using non-equilibrium molecular dynamics simulations. More precisely, we consider polymer chains in a fluid containing a solute which has a concentration gradient, and…
We study quasi-particle dynamics in a quasi-periodic Ising model with temporally fluctuating transverse fields. Specifically, we calculate the dynamical exponents of the standard deviation of a quasi-particle spreading under a field chosen…
We present a method to investigate the kinetics of protein folding on a long time-scale and the dynamics underlying the formation of secondary and tertiary structures during the entire reaction. The approach is based on the formal analogy…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
We compare two recently proposed methods for the characterization of phase transitions in small systems. The validity and usefulness of these approaches are studied for the case of the q=4 and q=5 Potts model, i.e. systems where a…
A stochastic model for the dynamics of enzymatic catalysis in explicit, effective solvents under physiological conditions is presented. Analytically-computed first passage time densities of a diffusing particle in a spherical shell with…
We report on the short-time dynamics in colloidal mixtures made up of monomers and dimers highly confined between two glass-plates. At low concentrations, the experimental measurements of colloidal motion agree well with the solution of the…
The flexibility of short DNA chains is investigated via computation of the average correlation function between dimers which defines the persistence length. Path integration techniques have been applied to confine the phase space available…
We study the relation between $\alpha$-helix formation and folding for a simple artificial peptide, Ala$_{10}$-Gly$_5$-Ala$_{10}$. Our data rely on multicanonical Monte Carlo simulations where the interactions among all atoms are taken into…
By means of extensive replica-exchange simulations of generic coarse-grained models for helical polymers, we systematically investigate the structural transitions into all possible helical phases for flexible and semiflexible elastic…
Linear polymers are represented as chains of hopping reptons and their motion is described as a stochastic process on a lattice. This admittedly crude approximation still catches essential physics of polymer motion, i.e. the universal…
We use the torsional angles of the protein chain as generalized coordinates in the canonical formalism, derive canonical equations of motion, and investigate the coordinate dependence of the kinetic energy expressed in terms of the…
The boundaries of cooperative helix--coil transitions directly affect protein allostery and conformational dynamics, yet the physical origin of the persistent one-to-two-residue assignment ambiguity at these structural interfaces remains…
Two-state cooperativity is an important characteristic in protein folding. It is defined by a depletion of states lying energetically between folded and unfolded conformations. While there are different ways to test for two-state…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
The thermodynamics of a homopolymeric chain with both Van der Waals and highly-directional hydrogen bond interaction is studied. The effect of hydrogen bonds is to reduce dramatically the entropy of low-lying states and to give raise to…
Most helix-coil transition theories can be characterized by a set of three parameters: energetic, describing the (free) energy cost of forming a helical state in one repeating unit; entropic, accounting for the decrease of entropy due to…
Hybrid molecular dynamics/Monte Carlo simulations used to study melts of unentangled, thermoreversibly associating supramolecular polymers. In this first of a series of papers, we describe and validate a model that is effective in…
Using molecular dynamics simulations we examine the dynamics of a family of model polymers with varying chain length and torsional potential barriers. We focus on features of the dynamics of polymers that are seen experimentally but absent…
We have investigated the potential energy surfaces for glycine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles phi and psi, which are…