Related papers: A constant extension ensembles model of double-str…
Prestrained elastic networks arise in a number of biological and technological systems ranging from the cytoskeleton of cells to tensegrity structures. To understand the response of such a network as a function of the prestrain, we consider…
Isomorphs are curves in the thermodynamic phase diagram of invariant excess entropy, structure, and dynamics, while pseudoisomorphs are curves of invariant structure and dynamics, but not of the excess entropy. The latter curves have been…
In this study we evaluate, at full atomic detail, the folding processes of two small helical proteins, the B domain of protein A and the Villin headpiece. Folding kinetics are studied by performing a large number of ab initio Monte Carlo…
At present, there have been suggested two types of physical mechanism that may facilitate preferential pairing between DNA molecules, with identical or similar base pair texts, without separation of base pairs. One solely relies on base…
We review statistical-mechanical theories of single-molecule micromanipulation experiments on nucleic acids. First, models for describing polymer elasticity are introduced. We then review how these models are used to interpret…
Using path integral technique, we show exactly that for a semiflexible biopolymer in constant extension ensemble, no matter how long the polymer and how large the external force, the effects of short range correlations in the…
In this paper we report, clarify and broaden various recent efforts to complement the chemistry-centered models of force generation in muscles by mechanics-centered models. The physical mechanisms of interest can be grouped into two…
We study the stress distribution in a polymer brush material over a range of graft densities using molecular dynamics (MD) simulations and theory. Flexible polymer chains are treated as beads connected by nonlinear springs governed by a…
We study the impact of mutations (changes in amino acid sequence) on the thermodynamics of simple protein-like heteropolymers consisting of N monomers, representing the amino acid sequence. The sequence is designed to fold into its native…
A two-dimensional electron gas in a static external magnetic field exhibits two distinct collective excitation modes. The lower frequency mode propagates along the periphery of the domain almost freely with an extended lifetime, which is…
We investigate the folding and forced-unbinding transitions of adsorbed semiflexible polymer chains using theory and simulations. These processes describe biologically relevant phenomena that include adhesive interactions between proteins…
Heterogeneity in biological molecules, resulting in molecule-to-molecule variations in their dynamics and function, is an emerging theme. To elucidate the consequences of heterogeneous behavior at the single molecule level, we propose an…
We study the free energy of the worm-like-chain model, in the constant-extension ensemble, as a function of the stiffness for finite chains of length L. We find that the polymer properties obtained in this ensemble are "qualitatively"…
A recurring motif in the organization of biological tissues are networks of long, fibrillar protein strands effectively confined to cylindrical surfaces. Often, the fibers in such curved, quasi-2D geometries adopt a characteristic order:…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
We present a solvable model that predicts the folding kinetics of two-state proteins from their native structures. The model is based on conditional chain entropies. It assumes that folding processes are dominated by small-loop closure…
We introduce an individual-based model for fiber elements having the ability to cross-link or unlink each other and to align with each other at the cross links. We first formally derive a kinetic model for the fiber and cross-links…
Topologically constrained genome-like polymers often double-fold into tree-like configurations, which can be modelled on the level of folded (ring) polymers or on the level of the underlying random trees. For both descriptions, we have…
Conformational properties of polymer melts confined between two hard structureless walls are investigated by Monte Carlo simulation of the bond-fluctuation model. Parallel and perpendicular components of chain extension, bond-bond…
One of the most intriguing results of single molecule experiments on proteins and nucleic acids is the discovery of functional heterogeneity: the observation that complex cellular machines exhibit multiple, biologically active…