Related papers: Force spectroscopy of polymer desorption: Theory a…
Single molecule force spectroscopy provide details of the underlying energy surfaces of proteins which are essential to the understanding of their unfolding process. Recently, it has been observed experimentally that by pulling proteins in…
While stretching of most polymer chains leads to rather featureless force-extension diagrams, some, notably DNA, exhibit non-trivial behavior with a distinct plateau region. Here we propose a unified theory that connects force-extension…
A polymer chain pinned in space exerts a fluctuating force on the pin point in thermal equilibrium. The average of such fluctuating force is well understood from statistical mechanics as an entropic force, but little is known about the…
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…
We study the deformation of nano--scale polymer films which are subject to external bending forces by means of computer simulation. The polymer is represented by a generalized bead--spring--model, intended to reproduce characteristic…
In this paper we establish a new efficient method for simulating polymer-solvent systems which combines a lattice Boltzmann approach for the fluid with a continuum molecular dynamics (MD) model for the polymer chain. The two parts are…
Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In…
When injected through a contraction, high molecular weight polymer solutions exhibit a sharp increase of apparent viscosity which originates from stretching polymer chains above a critical extension rate. This chain stretching can also…
Constitutive modeling of dielectric elastomers has been of long standing interest in mechanics. Over the last two decades rigorous constitutive models have been developed that couple the electrical response of these polymers with large…
The native structures of proteins, except for notable exceptions of intrinsically disordered proteins, in general take their most stable conformation in the physiological condition to maintain their structural framework so that their…
We study the adsorption of polymer chains on a fluctuating surface. Physical examples are provided by polymer adsorption at the rough interface between two non-miscible liquids, or on a membrane. In a mean-field approach, we find that the…
Stretching response of polymer chains under external force is crucial in understanding polymer dynamics under equilibrium and non-equilibrium conditions. Here we measure the elastic response of poly(ethylene glycol) using a lock-in based…
Single-molecule force spectroscopy has opened a new field of research in molecular biophysics and biochemistry. Pulling experiments on individual proteins permit us to monitor conformational transitions with high temporal resolution and…
We propose a simple friction model for isolated polymer chains on a solid substrate. The chains are pulled at constant velocity by one end, the other end can be trapped on the solid substrate on localised sites. We focus on the energy…
We examine the thermally-induced fracture of an unstrained polymer chain of discrete segments coupled by an anharmonic potential by means of Molecular Dynamics simulation with a Langevin thermostat. Cases of both under- and over-damped…
Advanced chain-growth computer simulation methodologies have been employed for a systematic statistical analysis of the critical behavior of a polymer adsorbing at a substrate. We use finitesize scaling techniques to investigate the…
The structural dynamics of a biopolymer is governed by a process of diffusion through its conformational energy landscape. In pulling experiments using optical tweezers, features of the energy landscape can be extracted from the probability…
Dimerization and subsequent aggregation of polymers and biopolymers often occur under nonequilibrium conditions. When the initial state of the polymer is not collapsed or the final folded native state, the dynamics of dimerization can…
We derive the stochastic equations of motion for a tracer that is tightly attached to a semiflexible polymer and confined or agitated by an externally controlled potential. The generalised Langevin equation, the power spectrum, and the…
Loops undergoing thermal fluctuations are prevalent in nature. Ring-like or cross-linked polymers, cyclic macromolecules, and protein-mediated DNA loops all belong to this category. Stability of these molecules are generally described in…