Related papers: Theoretical study of the competition between foldi…
We use the lattice model of directed walks to investigate the conformational as well as the adsorption properties of a semiflexible homopolymer chain immersed in a good solvent in two and three dimensions. To account for the stiffness in…
Various subsets of self-avoiding walks naturally appear when investigating existing methods designed to predict the 3D conformation of a protein of interest. Two such subsets, namely the folded and the unfoldable self-avoiding walks, are…
This paper presents a novel contact-implicit trajectory optimization method using an analytically solvable contact model to enable planning of interactions with hard, soft, and slippery environments. Specifically, we propose a novel contact…
Monte Carlo simulations of coarse-grained polymers provide a useful tool to deepen the understanding of conformational and statistical properties of polymers both in physical as well as in biological systems. In this study we sample compact…
The conformational and dynamical properties of active ring polymers are studied by numerical simulations. The two-dimensionally confined polymer is modeled as a closed bead-spring chain, driven by tangential forces, put in contact with a…
Phase separation has emerged as an essential concept for the spatial organization inside biological cells. However, despite the clear relevance to virtually all physiological functions, we understand surprisingly little about what phases…
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…
We suggest a new mean field method for studying the thermodynamic competition between magnetic and superconducting phases in a two-dimensional square lattice. A partition function is constructed by writing microscopic interactions that…
Random walks are powerful tools to analyze spatial-temporal patterns produced by living organisms ranging from cells to humans. At the same time, it is evident that these patterns are not completely random but are results of a convolution…
We investigate the effect of hydrodynamic interactions on the non-equilibrium drift dynamics of an ideal flexible polymer pulled by a constant force applied at one end of the polymer using the perturbation theory and the renormalization…
As robots move from the laboratory into the real world, motion planning will need to account for model uncertainty and risk. For robot motions involving intermittent contact, planning for uncertainty in contact is especially important, as…
Sensitive sequencing of biopolymers by nanopore-based translocation techniques requires extension of the time spent by the molecule in the pore. We develop an electrostatic theory of polymer translocation to show that the translocation time…
We present the results of analytic calculations and numerical simulations of the behaviour of a new class of chain molecules which we call thick polymers. The concept of the thickness of such a polymer, viewed as a tube, is encapsulated by…
A self-interacting polymer with one end attached to a sticky surface has been studied by means of a flat-histogram stochastic growth algorithm known as FlatPERM. We examined the four-dimensional parameter space of the number of monomers up…
Inspired by recent experiments on chromosomal dynamics, we introduce an exactly solvable model for the interaction between a flexible polymer and a set of motor-like enzymes. The enzymes can bind and unbind to specific sites of the polymer…
We investigate conformations and dynamics of a polymer considering its monomers to be active Brownian particles. This active polymer shows very intriguing physical behavior which is absent in an active Rouse chain. The chain initially…
We show the existence of a force induced triple point in an interacting polymer problem that allows two zero-force thermal phase transitions. The phase diagrams for three different models of mutually attracting but self avoiding polymers…
The interaction between individuals in biological populations, dilute components of chemical systems, or particles transported by turbulent flows depends critically on their contact statistics. This work clarifies those statistics under the…
We have developed a simulation model to describe particle adsorption to and desorption from liquid interfaces. Using this model we formulate a closed interfacial equation of state for repulsive elastic spheres. The effect of a long-range…
We solve a model of self-avoiding walks with up to two monomers per site on the Bethe lattice. This model, inspired on the Domb-Joyce model, was recently proposed to describe the collapse transition observed in interacting polymers [J.…