Related papers: A protrusion can "eclipse" looping of a long self-…
We compute for the first time the effects of excluded volume on the probability for double-stranded DNA to form a loop. We utilize a Monte-Carlo algorithm for generation of large ensembles of self- avoiding worm-like chains, which are used…
We study the large-scale dynamics of event chain Monte Carlo algorithms in one dimension, and their relation to the true self-avoiding walk. In particular, we study the influence of stress, and different forms of interaction on the…
We introduce a model of self-repelling random walks where the short-range interaction between two elements of the chain decreases as a power of the difference in proper time. Analytic results on the exponent $\nu$ are obtained. They are in…
Using Brownian dynamics simulations, we study the migration of long charged chains in an electrophoretic microchannel device consisting of an array of microscopic entropic traps with alternating deep regions and narrow constrictions. Such a…
Semiflexible macromolecules in dilute solution under very good solvent conditions are modeled by self-avoiding walks on the simple cubic lattice ($d=3$ dimensions) and square lattice ($d=2$ dimensions), varying chain stiffness by an energy…
We present a new Monte Carlo scheme for the efficient simulation of multi-polymer systems. The method permits chains to be inserted into the system using a biased growth technique. The growth proceeds via the use of a retractable feeler,…
Single domain proteins are thought to be tightly packed. The introduction of voids by mutations is often regarded as destabilizing. In this study we show that packing density for single domain proteins decreases with chain length. We find…
Chain-like macromolecules in solution, whether biological or synthetic, transform from an extended conformation to a compact one when temperature or other system parameters change. This collapse transition is relevant in various phenomena,…
Proposed here is a dynamic Monte-Carlo algorithm that is efficient in simulating dense systems of long flexible chain molecules. It expands on the configurational-bias Monte-Carlo method through the simultaneous generation of a large set of…
Chromosomes are crumpled polymer chains further folded into a sequence of stochastic loops via loop extrusion. While extrusion has been verified experimentally, the particular means by which the extruding complexes bind DNA polymer remains…
A lattice model of the directed self-avoiding walk is used to estimate the possibility on the formation of an infinitely long linear semi-flexible copolymer chain. The copolymer chain is assumed to composed of four different types of the…
A polymer chain containing $N$ monomers confined in a finite cylindrical tube of diameter $D$ grafted at a distance $L$ from the open end of the tube may undergo a rather abrupt transition, where part of the chain escapes from the tube to…
We present a scaling theory and Monte Carlo (MC) simulation results for a flexible polymer chain slowly dragged by one end into a nanotube. We also describe the situation when the completely confined chain is released and gradually leaves…
Monte Carlo algorithms often aim to draw from a distribution $\pi$ by simulating a Markov chain with transition kernel $P$ such that $\pi$ is invariant under $P$. However, there are many situations for which it is impractical or impossible…
Loop extrusion convincingly describes how certain Structural Maintenance of Chromosome (SMC) proteins mediate the formation of large DNA loops. Yet, most of the existing computational models cannot reconcile recent in vitro observations…
Condensation of hundreds of mega-base-pair-long human chromosomes in a small nuclear volume is a spectacular phenomenon. This process is driven by the formation of chromosome loops. ATP consuming motor, condensin, interacts with chromatin…
We present a new Monte Carlo algorithm for studying site or bond percolation on any lattice. The algorithm allows us to calculate quantities such as the cluster size distribution or spanning probability over the entire range of site or bond…
We investigate random walks on a lattice with imperfect traps. In one dimension, we perturbatively compute the survival probability by reducing the problem to a particle diffusing on a closed ring containing just one single trap. Numerical…
We study migration of DNA molecules through a microchannel with a series of electric traps controlled by an ac electric field. We describe the motion of DNA based on Brownian dynamics simulations of a beads-spring chain. Our simulation…
We consider the properties of a self-avoiding polymer chain, adsorbed on a solid attractive substrate which is attached with one end to a pulling force. The conformational properties of such chain and its phase behavior are treated within a…