Related papers: Looping and reconfiguration dynamics of a flexible…
Recently single molecule experiments have shown the importance of internal friction in biopolymer dynamics. Such studies also suggested that the internal friction although independent of solvent viscosity has strong dependence on denaturant…
Loop formation between monomers in the interior of semiflexible chains describes elementary events in biomolecular folding and DNA bending. We calculate analytically the interior distance distribution function for semiflexible chains using…
We consider a phantom chain model of polymer with internal friction in a harmonic confinement and extend it to take care of effects of solvent quality following a mean field approach where an exponent $\nu$ is introduced. The model termed…
The Rouse model with internal friction (RIF), a widely used theoretical framework to interpret the effects of internal friction on conformational transitions in biomolecules, is shown to be an approximate treatment that is based on…
We study the conformational dynamics within homo-polymer globules by solvent-implicit Brownian dynamics simulations. A strong dependence of the internal chain dynamics on the Lennard-Jones cohesion strength {\epsilon} and the globule size…
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…
The folding of a protein towards its native state is a rather complicated process. However there are empirical evidences that the folding time correlates with the contact order, a simple measure of the spatial organisation of the native…
Protein folding is a universal process, very fast and accurate, which works consistently (as it should be) in a wide range of physiological conditions. The present work is based on three premises, namely: ($i$) folding reaction is a process…
The dynamics of loop formation by linear polymer chains has been a topic of several theoretical/experimental studies. Formation of loops and their opening are key processes in many important biological processes. Loop formation in flexible…
We theoretically investigate the looping dynamics of a linear polymer immersed in a viscoelastic fluid. The dynamics of the chain is governed by a Rouse model with a fractional memory kernel recently proposed by Weber et al. (S. C. Weber,…
We consider equilibrium relaxation properties of the end-to-end distance and of principal components in a one-dimensional polymer chain model with nonlinear interaction between the beads. While for the single-well potentials these…
Protein sequences serve as a natural record of the evolutionary constraints that shape their functional structures. We show that it is possible to use only sequence information to go beyond predicting native structures and global stability…
Dynamics of a polymer chain in solution gets significantly affected by the temperature and the frictional forces arising due to solvent viscosity. Here, using an explicit solvent framework for polymer simulation with the liberty to tune the…
For biologically relevant macromolecules such as intrinsically disordered proteins, internal degrees of freedom that allow for shape changes have a large influence on both the motion and function of the compound. A detailed understanding of…
Many native structures of proteins accomodate complex topological motifs such as knots, lassos, and other geometrical entanglements. How proteins can fold quickly even in the presence of such topological obstacles is a debated question in…
Packings of macroscopic granular chains capture some of the essential aspects of molecular polymer systems and have been suggested as a paradigm to understand the physics on a molecular scale. However, here we demonstrate that the…
We study the conformation and dynamics of a single polymer chain that is pulled by a constant force applied at its one end with the other end free. Such a situation is relevant to the growing technology of manipulating individual…
Chemical reactions inside cells are typically subject to the effects both of the cell's confining surfaces and of the viscoelastic behavior of its contents. In this paper, we show how the outcome of one particular reaction of relevance to…
Within the nucleus, structural maintenance of chromosome protein complexes, namely condensin and cohesin, create an architecture to facilitate the organization and proper function of the genome. Condensin, in addition to performing loop…
The folding kinetics of a number of sequences for off-lattice continuum model of proteins is studied using Langevin simulations at two values of the friction coefficient. We show that there is a remarkable correlation between folding times,…