Related papers: Competitive ligand binding kinetics to linear poly…
We present a generic coarse-grained model to describe molecular motors acting on polymer substrates, mimicking, for example, RNA polymerase on DNA or kinesin on microtubules. The polymer is modeled as a connected chain of beads; motors are…
Protein binding often involves conformational changes. Important questions are whether a conformational change occurs prior to a binding event ('conformational selection') or after a binding event ('induced fit'), and how conformational…
The accurate screening of candidate drug ligands against target proteins through computational approaches is of prime interest to drug development efforts. Such virtual screening depends in part on methods to predict the binding affinity…
Ring polymers are an intriguing class of polymers with unique physical properties, and understanding their behavior is important for developing accurate theoretical models. In this study, we investigate the effect of chain stiffness and…
Single-chain elasticity is of fundamental importance in polymer physics, as it underlies many of the unique properties of polymer systems. Recently, there has been interest in characterizing the elastic properties of catenanes, molecular…
Polymer chains undergoing a continuous adsorption-desorption transition are studied through extensive computer simulations. A three-dimensional self-avoiding walk lattice model of a polymer chain grafted onto a surface has been treated for…
The prediction of protein-ligand binding affinity is of great significance for discovering lead compounds in drug research. Facing this challenging task, most existing prediction methods rely on the topological and/or spatial structure of…
We consider the dynamics of a translocation process of a flexible linear polymer through a nanopore into an environment of active rods in the {\it trans} side. Using Langevin dynamics simulations we find that the rods facilitate…
We study a blend of two kinds of homopolymers with tendency for segragation. Cross-links between the chains of different kinds do not allow macrophase separation. Instead microphase structure appears. Starting from a microscopic model we…
The field theory approach to the statistical mechanics of a system of N polymer rings linked together is generalized to the case of links that have a fixed number $2s$ of maxima and minima. Such kind of links are called plats and appear for…
We present results from extensive molecular dynamics simulations of collapse transitions of hydrophobic polymers in explicit water focused on understanding effects of lengthscale of the hydrophobic surface and of attractive interactions on…
We use inverse methods of statistical mechanics to explore trade-offs associated with designing interactions to stabilize self-assembled structures against changes in density or temperature. Specifically, we find isotropic,convex-repulsive…
We present a model to describe the concentration-dependent growth of protein filaments. Our model contains two states, a low entropy/high affinity ordered state and a high entropy/low affinity disordered state. Consistent with experiments,…
In this paper, we analyze the effect of geometrical constraint on the conformational properties of an infinitely long linear semiflexible polymer chain confined in-between two constraints under good solvent condition in two dimensions. The…
A co-polycondensation reaction is discussed analytically and by Monte-Carlo simulations where two reactive units compete for reactions with an alternating third reactive unit, whereby irreversible reactions replace bonds which are able to…
Many eukaryotic and prokaryotic cells can exhibit remarkable sensing ability under small gradient of chemical compound. In this study, we approach this phenomenon by considering the contribution of multiple ligands to the chemical kinetics…
We perform numerical simulations of isolated, partially active polymers, driven out-of-equilibrium by a fraction of their monomers. We show that, if the active beads are all gathered in a contiguous block, the position of the section along…
In this paper the number and lengths of minimal length lattice knots confined to slabs of width $L$, is determined. Our data on minimal length verify the results by Sharein et.al. (2011) for the similar problem, expect in a single case,…
Kinetic equations are analyzed for thermal degradation of polymers. The governing relations are based on the fragmentation-annihilation concept. Explicit solutions to these equations are derived in two particular cases of interest. For…
A model for the adsorption of a binary mixture on a one-dimensional infinite lattice with nearest neighbour cooperative effects is considered. The particles of the two species are both monomers but differ in the repulsive interaction…