Related papers: Single Chain Force Spectroscopy: Sequence Dependen…
We investigate the dynamics of a single semiflexible filament, under the action of a compressing force, using numerical simulations and scaling arguments. The force is applied along the end to end vector at one extremity of the filament,…
A framework for quantifying dependence between random vectors is introduced. With the notion of a collapsing function, random vectors are summarized by single random variables, called collapsed random variables in the framework. Using this…
Analytical relations for the mechanical response of single polymer chains are valuable for modeling purposes, on both the molecular and the continuum scale. These relations can be obtained using statistical thermodynamics and an idealized…
Treatises on vibrations devote large space to study the dynamical behavior of an elastic system subject to known external tractions. In fact, usually a "system" is not an isolated body but it is part of a chain of mechanisms which disturb…
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 present a sequence-based probabilistic formalism that directly addresses co-operative effects in networks of interacting positions in proteins, providing significantly improved contact prediction, as well as accurate quantitative…
We present a perturbative approach to disordered systems in one spatial dimension that accesses the full range of phase disorder and clarifies the connection between localization and phase information. We consider a long chain of…
Molecular dynamics simulation methods are used to study the folding of polymer chains into packed cubic states. The polymer model, based on a chain of linked sites moving in the continuum, includes both excluded volume and torsional…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…
We consider multi-chain protein native structures and propose a criterion that determines whether two chains in the system are entangled or not. The criterion is based on the behavior observed by pulling at both temini of each chain…
We revisit a model of semiflexible Gaussian chains proposed by Winkler \textit{et al}, solve the dynamics of the discrete description of the model and derive exact algebraic expressions for some of the most relevant dynamical observables,…
The results obtained from molecular dynamics simulations of the friction at an interface between polymer melts and weakly attractive crystalline surfaces are reported. We consider a coarse-grained bead-spring model of linear chains with…
Motivated by single molecule experiments on biopolymers we explore equilibrium morphologies and force-extension behavior of copolymers with hydrophobic segments using Langevin dynamics simulations. We find that the interplay between…
Modelling of single cellulose fibres is usually performed by assuming homogenous properties, such as strength and Young s modulus, for the whole fibre. Additionally, the inhomogeneity in size and swelling behaviour along the fibre is often…
We present a theoretical framework for the linear and nonlinear visco-elastic properties of reversibly crosslinked networks of semiflexible polymers. In contrast to affine models where network strain couples to the polymer end-to-end…
Many physical systems can be modelled as parameter-dependent variational problems. In numerous cases, multiple equilibria co-exist, requiring the evaluation of their stability, and the monitoring of transitions between them. Generally, the…
We study the force-induced unfolding of random disordered RNA or single-stranded DNA polymers. The system undergoes a second order phase transition from a collapsed globular phase at low forces to an extensive necklace phase with a…
DNA hairpin molecules with periodic base sequences can be expected to exhibit a regular coarse-grained free energy landscape (FEL) as function of the number of open base pairs and applied mechanical force. Using a commonly employed model,…
We examine the phase transition of polymer adsorption as well as the underlying kinetics of polymer binding from dilute solutions on a structureless solid surface. The emphasis is put on the properties of regular multiblock copolymers,…
This paper discusses the elastic behavior of a very long crosslinked polyelectrolyte chain (Debye-H\"uckel chain), which is weakly charged. Therefore the response of the crosslinked chain (network) on an external constant force $f$ acting…