Related papers: Re-orientational dynamics of ring polymers in dilu…
An effective medium approach together with a multiple scattering formalism is considered to study the steady-state dynamics of suspensions of spheres and rigid stiff polymer chains (Gaussian) without excluded volume interactions. The…
We consider the topologically constrained random walk model for topological polymers. In this model, the polymer forms an arbitrary graph whose edges are selected from an appropriate multivariate Gaussian which takes into account the…
Large scale molecular dynamics simulations on graphic processing units (GPUs) are employed to study the scaling behavior of ring polymers with various topological constraints in melts. Typical sizes of rings containing $3_1$, $5_1$ knots…
We investigate the translational and rotational relaxation dynamics of a crowded two-dimensional system of monodisperse Penrose kites, in which crystallization, quasi-crystallization, and nematic ordering are suppressed, from low to high…
Transport properties of metal-molecule-metal junctions containing monolayer of conjugated and saturated molecules with characteristic dimensions in the range of 30-300 nm are correlated with microscopic topography, stress and chemical…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…
Molecular topology of polymers plays a key role in determining their physical properties. We studied herein the topological effects on the static and dynamic properties of a 2D catenated network of DNA rings called a kinetoplast.…
We study the scattering properties of topological solitons on obstructions in the form of holes and barriers. We use the 'new baby Skyrme' model in (2+1) dimensions and we model the obstructions by making the coefficient of the baby skyrme…
We have studied by Molecular Dynamics computer simulations the dynamics of water confined in ionic surfactants phases, ranging from well ordered lamellar structures to micelles at low and high water loading, respectively. We have analysed…
During the life cycle of bacterial cells the non-mixing of the two ring-shaped daughter genomes is an important prerequisite for the cell division process. Mimicking the environments inside highly crowded biological cells, we study the…
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…
We consider the passage of long polymers of length N through a hole in a membrane. If the process is slow, it is in principle possible to focus on the dynamics of the number of monomers s on one side of the membrane, assuming that the two…
Macromolecules can gain special properties by adopting knotted conformations, but engineering knotted macromolecules is a challenging task. Here we surprisingly observed that knotting can be very effectively produced in active polymers.…
The theory of the dynamics of polymers in solution is developed coming from the hydrodynamic theory of the Brownian motion (BM) and the Rouse-Zimm (RZ) model. It is shown that the time correlation functions describing the polymer motion…
In the present work, four series of simulations are analyzed: entangled model networks of a) mono-disperse or b) poly-disperse weight distribution between the crosslinks, c) non-entangled phantom model networks and d) non-entangled model…
Polymer translocation in crowded environments is a ubiquitous phenomenon in biological systems. We studied polymer translocation through a pore in free, one-sided (asymmetric), and two-sided (symmetric) crowded environments. Extensive…
We investigate the process of biopolymer translocation through a narrow pore using a multiscale approach which explicitly accounts for the hydrodynamic interactions of the molecule with the surrounding solvent. The simulations confirm that…
The dynamics of ultrafast energy transfer to water clusters and to bulk water by a highly intense, sub-cycle THz pulse of duration $\approx$~150~fs is investigated in the context of force-field molecular dynamics simulations. We focus our…
Ionic transport in nano- to sub-nano-scale pores is highly dependent on translocation barriers and potential wells. These features in the free-energy landscape are primarily the result of ion dehydration and electrostatic interactions. For…
Here we report on the translocation of folded polymers through nano-pores using molecular dynamic simulations. Two cases are studied; one in which a folded molecule unfolds upon passage and one in which the folding remains intact as the…