Related papers: Polymer Translocation Dynamics in the Quasi-Static…
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…
Recent studies have suggested that the Nuclear Pore Complex (NPC) plays a significant role in mechanotransduction. When a force is exerted, the NPC's diameter widens, leading to an increased molecular flux into the nucleus. In this study,…
We develop off-lattice simulations of semiflexible polymer chains subjected to applied mechanical forces using Markov Chain Monte Carlo. Our approach models the polymer as a chain of fixed-length bonds, with configurations updated through…
Polymer-assisted ion transport underpins both energy storage technologies and emerging neuromorphic computing devices. Efficient modeling of ion migration is essential for understanding the performance of batteries and memristors, but it…
Confinement is a versatile and well-established tool to study the properties of polymers either to understand biological processes or to develop new nano-biomaterials. We investigate the conformations of a semiflexible polymer ring in weak…
The transport of deformable particles through porous media underlies a wealth of applications ranging from filtration to oil recovery to the transport and spreading of biological agents. Using direct numerical simulations, we analyze the…
A multiscale approach is used to simulate the translocation of DNA through a nanopore. Within this scheme, the interactions of the molecule with the surrounding fluid (solvent) are explicitly taken into account. By generating polymers of…
We report a numerical study of the diffusiophoresis of short polymers using non-equilibrium molecular dynamics simulations. More precisely, we consider polymer chains in a fluid containing a solute which has a concentration gradient, and…
We solve the problem of discrete translocation of a polymer through a pore, driven by the irreversible, random sequential adsorption of particles on one side of the pore. Although the kinetics of the wall motion and the deposition are…
While the dynamics of polymer chains in equilibrium media is well understood by now, the polymer dynamics in active non-equilibrium environments can be very different. Here we study the dynamics of polymers in a viscous medium containing…
The translocation of biopolymers, such as DNA and proteins, across cellular or nuclear membranes is essential for numerous biological processes. The translocation dynamics are influenced by the properties of the polymers, such as polymer…
In entangled polymer systems, there are several characteristic time scales, such as the entanglement time and the disengagement time. In molecular simulations, the longest relaxation time (the disengagement time) can be determined by the…
Using Monte Carlo dynamics and the Monte Carlo Histogram Method, the simple three-dimensional 27 monomer lattice copolymer is examined in depth. The thermodynamic properties of various sequences are examined contrasting the behavior of good…
Dimerization and subsequent aggregation of polymers and biopolymers often occur under nonequilibrium conditions. When the initial state of the polymer is not collapsed or the final folded native state, the dynamics of dimerization can…
Tunable nanopores in elastomeric membranes have been used to study the dependence of ionic current blockade rate on the concentration and electrophoretic mobility of particles in aqueous suspensions. A range of nanoparticle sizes, materials…
This paper studies the features of a homopolymer translocating through a flexible pore. The channel is modeled as a monolayer tube composed by monomers with two elastic parameters: spring-like two body interaction and bending three body…
The structure of polymer coils near interfaces between coexisting phases of symmetrical polymer mixtures (AB) is discussed, as well as the structure of symmetric diblock copolymers of the same chain length N adsorbed at the interface. The…
DNA capture with high fidelity is an essential part of nanopore translocation. We report several important aspects of the capture process and subsequent translocation of a model DNA polymer through a solid-state nanopore in presence of an…
We solve the Chapman-Kolmogorov equation and study the exact splitting probabilities of the general stochastic process which describes polymer translocation through membrane pores within the broad class of Markov chains. Transition…
Quantitative theory of interbilayer interactions is essential to interpret x-ray scattering data and to elucidate these interactions for biologically relevant systems. For this purpose Monte Carlo simulations have been performed to obtain…