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In biology, there are several processes in which unfolded protein chains are transported along narrow-tube channels. Normally, without such a severe configurational constraint, unfolded polypeptides would not bind to each other. However,…
The advances in materials and biological sciences have necessitated the use of molecular simulations to study polymers. The Markov chain Monte Carlo simulations enable the sampling of relevant microstates of polymeric systems by traversing…
Compact polymers are self-avoiding random walks which visit every site on a lattice. This polymer model is used widely for studying statistical problems inspired by protein folding. One difficulty with using compact polymers to perform…
Models which include domain constraints occur in myriad contexts such as econometrics, genomics, and environmetrics, though simulating from constrained distributions can be computationally expensive. In particular, repeated sampling from…
We consider a fully directed self-avoiding walk model on a cubic lattice to mimic the conformations of an infinitely long confined flexible polymer chain; and the confinement condition is achieved by two parallel athermal plates. The…
We consider quantum particle or Gaussian polymer confinement between two surfaces and in cylinders with sinusoidal undulations. In terms of the variational method, we show that the quantum mechanical wave equations have lower ground state…
Taking into account the well known correspondence between the field theoretical O(n)-vector model in the limit $n\to 0$ and the behavior of long-flexible polymer chains in a good solvent the investigation of ideal polymer chains adsorption…
We analyze static properties of a strongly confined semiflexible polymer, i.e. either trapped in a closed space or compressed by external forces, in an athermal solvent. Like a flexible polymer case, we can resort to an analogy with the…
We present Monte Carlo simulations of a coarse-grained model for Langmuir monolayers of amphiphile molecules on a polar substrate. The molecules are modelled as chains of Lennard-Jones beads, with one slightly larger end bead confined in a…
The slip phenomena in thin polymer films confined by either flat or periodically corrugated surfaces are investigated by molecular dynamics and continuum simulations. For atomically flat surfaces and weak wall-fluid interactions, the shear…
The state space of a polymer molecule is analysed. We show how the size of the state space can be reduced on the basis of symmetry. In the reduced state space, the probability of a new state (termed below as class) is equal to the number of…
We present a new reduced-order computational method for the molecular dynamics simulation of entangled polymer systems. The polymer chains are modeled as continuous Gaussian chains. Our algorithm is based on the application of the molecular…
Polymer networks formed by cross linking flexible polymer chains are ubiquitous in many natural and synthetic soft-matter systems. Current micromechanics models generally do not account for excluded volume interactions except, for instance,…
We consider an inextensible, semiflexible polymer or worm-like chain which is confined in the transverse direction by a parabolic potential and subject to a longitudinal force at the ends, so that the polymer is stretched out and…
As an important physical quantity to understand the internal structure of polymer chains, the structure factor is being studied both in theory and experiment. Theoretically, the structure factor of Gaussian chains have been solved…
Manifold Markov chain Monte Carlo algorithms have been introduced to sample more effectively from challenging target densities exhibiting multiple modes or strong correlations. Such algorithms exploit the local geometry of the parameter…
We present a new Monte-Carlo method for estimating the chemical potential of model polymer systems. The method is based upon the gradual insertion of a penetrable `ghost' polymer into the system and is effective for large chain lengths and…
We combine parallelization and cluster Monte Carlo for hard sphere systems and present a parallelized event chain algorithm for the hard disk system in two dimensions. For parallelization we use a spatial partitioning approach into…
We discuss simulations of a simple model for polymer blends in the framework of the Rouse model. At odds with standard predictions, large dynamic asymmetry between the two components induces strong non-exponentiality of the Rouse modes for…
We present a method to generate realistic, three-dimensional networks of crosslinked semiflexible polymers. The free energy of these networks is obtained from the force-extension characteristics of the individual polymers and their…