Related papers: Folding and unfolding kinetics of a single semifle…
Using Langevin dynamics simulations in three dimensions (3D), we investigate the dynamics of polymer translocation into the regions between two parallel plane walls with separation $R$ under a driving force $F$, respectively. Compared with…
Understanding the role of self-propulsion on the conformational properties of active filamentous objects has relevance in biology. In this context, we consider a flexible bead-spring model polymer for which along with both attractive and…
We study the thermodynamics and kinetics of folding for a small peptide. Our data rely on Monte Carlo simulations where the interactions among all atoms are taken into account. Monte Carlo kinetics is used to study folding of the peptide at…
Solutions of semiflexible polymers confined by repulsive planar walls are studied by density functional theory and Molecular Dynamics simulations, to clarify the competition between the chain alignment favored by the wall and the depletion…
The longitudinal response of single semiflexible polymers to sudden changes in externally applied forces is known to be controlled by the propagation and relaxation of backbone tension. Under many experimental circumstances, realized, e.g.,…
We describe the effect of hydrodynamic interactions in the sedimentation of a pair of inextensible semiflexible filaments under a uniform constant force at low Reynolds numbers. We have analyzed the different regimes and the morphology of…
Recent emerging interest in experiments of single-polymer dynamics urge computational physicists to revive their understandings, particularly in the nonequilibrium context. Here we briefly discuss the currently evolving approaches of…
To what extent do general features of folding/unfolding kinetics of small globular proteins follow from their thermodynamic properties? To address this question, we investigate a new simplifed protein chain model that embodies a cooperative…
Limited-valency colloidal particles can self-assemble into polymeric structures analogous to molecules. While their structural equilibrium properties have attracted wide attention, insight into their dynamics has proven challenging. Here,…
We explore the impact of hydrodynamic interactions on the conformational and dynamical properties of wet tangentially-driven active polymers using multiparticle collision dynamics simulations. By analyzing active filaments with varying…
Brownian motion and viscoelasticity of semiflexible polymers is a subject that has been studied for many years. Still, rigorous analysis has been hindered due to the difficulty in handling the constraint that polymer chains cannot be…
We present an extremely simplified model of multiple-domains polymer stretching in an atomic force microscopy experiment. We portray each module as a binary set of contacts and decompose the system energy into a harmonic term (the…
The conformational and dynamical properties of active self-propelled filaments/polymers are investigated in the presence of hydrodynamic interactions by both, Brownian dynamics simulations and analytical theory. Numerically, a discrete…
We study the dynamics of flexible, semiflexible, and self-avoiding polymer chains moving under a Kramers metastable potential. Due to thermal noise, the polymers, initially placed in the metastable well, can cross the potential barrier, but…
Molecular dynamics study of a thin (one to five layers) lubricant film between two substrates in moving contact are performed using Langevin equations with an external damping coefficient depending on distance and velocity of atoms relative…
The folding transition of single, long semiflexible polymers was studied with special emphasis on the chain length effect using Monte Carlo simulations. While a relatively short chain (10-25 Kuhn segments) undergoes a large discrete…
We studied the dynamics of isotropic-nematic transitions in liquid crystalline polymers by integrating time-dependent Ginzburg-Landau equations. In a concentrated solution of rodlike polymers, the rotational diffusion constant Dr of the…
We have used computer simulation to study the collapse of a hydrophobic chain in water. We find that the mechanism of collapse is much like that of a first order phase transition. The evaporation of water in the vicinity of the polymer…
The conformations of semiflexible (bio)polymers are studied in flow through geometrically structured microchannels. Using mesoscale hydrodynamics simulations, we show that the polymer undergoes a rod-to-helix transition as it moves from the…
We present results of Monte Carlo computer simulations of a coarse-grained hydrophobic-polar Go-like heteropolymer model and discuss thermodynamic properties and kinetics of an exemplified heteropolymer, exhibiting two-state folding…