Related papers: Competitive ligand binding kinetics to linear poly…

We present molecular dynamics simulations of a simple model for polymer melts with intramolecular barriers. We investigate structural relaxation as a function of the barrier strength. Dynamic correlators can be consistently analyzed within…

Mechanically bonded membranes of interlocked ring polymers are a significant generalization of conventional elastic sheets, where connectivity is provided by covalent bonding, and represent a promising class of topological meta-materials.…

The thermodynamics of a homopolymeric chain with both Van der Waals and highly-directional hydrogen bond interaction is studied. The effect of hydrogen bonds is to reduce dramatically the entropy of low-lying states and to give raise to…

Binding kinetic parameters can be correlated with drug efficacy, which led to the development of various computational methods for predicting binding kinetic rates and gaining insight into protein-drug binding paths and mechanisms in recent…

We have used Langevin dynamics to simulate the forced translocation of linked polymer rings through a narrow pore. For fixed size (i.e. fixed number of monomers) the translocation time depends on the link type and on whether the rings are…

A ring polymer in a confining space may exhibit at least two phases, namely an expanded (or solvent-rich phase) if its concentration is small, or a collapsed (or polymer-rich phase) when it is concentrated and compressed. These phases are…

Often a screening or selection experiment targets a cell or tissue, which presents many possible molecular targets and identifies a correspondingly large number of ligands. We describe a statistical method to extract an estimate of the…

The size of rings (also called cyclic polymers) in bidisperse blends of chemically identical rings is analyzed by computer simulations. Data of entangled ring blends and blends of interpenetrating rings are compared and it is shown that the…

A model of two interacting polymer chains has been proposed to study the effect of penetration of one chain in to the other. We show that small chain penetrates more in comparison to the long chain. We also find a condition in which both…

Topological entanglements in polymers are mimicked by sliding rings (slip-links) which enforce pair contacts between monomers. We study the force-extension curve for linear polymers in which slip-links create additional loops of variable…

The competition between the connectivity and the local or global order in model fully-flexible chain molecules is investigated by molecular-dynamics simulations. States with both missing (melts) and high (crystal) global order are…

Many variants of RNA, DNA, and even proteins can be considered semiflexible polymers, where bending stiffness, as a type of energetic penalty, competes with attractive van der Waals forces in structure formation processes. Here, we…

Associative polymer networks have shown a major promise in fabrication of self-healing and responsive materials. The can also serve as simple models to study more complex biological systems where transient interactions play an important…

Scaffold proteins organize cellular processes by bringing signaling molecules into interaction, sometimes by forming large signalosomes. Several of these scaffolds are known to polymerize. Their assemblies should therefore not be understood…

Protein-ligand binding is the process by which a small molecule (drug or inhibitor) attaches to a target protein. Binding affinity, which characterizes the strength of biomolecular interactions, is essential for tackling diverse challenges…

Elucidating the physics of a concentrated suspension of ring polymers, or of an ensemble of ring polymers in a complex environment, is an important outstanding question in polymer physics. Many of the characteristic features of these…

Using molecular dynamics simulation, we investigate the effect of confinement on a system that comprises several stiff segmented polymer chains where each chain has similar segments, but length and stiffness of the segments vary among the…

The effects of entanglement in solutions and melts of unknotted ring polymers have been addressed by several theoretical and numerical studies. The system properties have been typically profiled as a function of ring contour length at fixed…

The rate at which nodes in a network increase their connectivity depends on their fitness to compete for links. For example, in social networks some individuals acquire more social links than others, or on the www some webpages attract…

The problem of the helix-coil transition of biopolymers in explicit solvents, like water, with the ability for hydrogen bonding with solvent is addressed analytically using a suitably modified version of the Generalized Model of Polypeptide…