Related papers: Parallel multiscale modeling of biopolymer dynamic…
Obtaining a rigorous and reliable method for linking computer simulations of polymer blends and composites at different length scales of interest is a highly desirable goal in soft matter physics. In this paper a multiscale modeling…
Polymers consisting of more than one type of monomer, known as copolymers, are vital to both living and synthetic systems. Copolymerisation has been studied theoretically in a number of contexts, often by considering a Markov process in…
Hydrodynamic interactions in systems comprised of self-propelled particles, such as swimming microorganisms, and passive tracers have a significant impact on the tracer dynamics compared to the equivalent "dry" sample. However, such…
We investigate the translocation dynamics of a folded linear polymer which is pulled through a nanopore by an external force. To this end, we generalize the iso-flux tension propagation (IFTP) theory for end-pulled polymer translocation to…
We review some recent coarse-graining and multi-scale methods, but also put forward some new ideas for addressing such issues. We find that, if one is guided by nonequilibrium statistical mechanics and thermodynamics, it is possible to…
We address in this thesis the current need to design new parallel algorithms and tools that ease the development of geodynamic modelling applications that are suited for today's and tomorrow's hardware. We present (1) the MATLAB HPC…
Force-driven translocation of a macromolecule through a nanopore is investigated by taking into account the monomer-pore friction as well as the "crowding" of monomers on the {\it trans} - side of the membrane which counterbalance the…
The impact of polymer-polymer interactions of various types on the thermodynamics, structure, and accommodation of topological constraints is addressed for systems comprising many directed polymers in two spatial dimensions. The approach is…
We present event distributions for the polymer translocation obtained by extensive Langevin dynamics simulations. Such distributions have not been reported previously and they provide new understanding of the stochastic characteristics of…
Large-scale molecular dynamics simulations are used to simulate a layer of nanoparticles diffusing on the surface of a liquid. Both a low viscosity liquid, represented by Lennard-Jones monomers, and a high viscosity liquid, represented by…
The numerical simulation of multiphase flows involving dispersed components with large scale disparities, such as the collisions between millimeter-sized bubbles and micron-sized mineral particles in flotation, poses a significant…
The transport of biomolecules across a cell membrane is an important phenomena that plays a pivotal role in the functioning of biological cells. In this paper, we investigate such processes by modeling the translocation of polymers through…
We perform two-dimensional Langevin dynamics simulations of electric-field driven polymer translocation through an attractive nanopore. We investigate the effect of the location of the attractive region using different pore patterns. This…
The presence of nanoparticles in a diblock copolymer leads to changes in the morphology and properties of the matrix and can produce highly organized hybrid materials. The resulting material properties depend not only on the polymer…
The growth dynamics of rigid biopolymers, consisting of $N$ parallel protofilaments, is investigated theoretically using simple approximate models. In our approach, the structure of a polymer's growing end and lateral interactions between…
The effect of the microscopic structure of a pore on polymer translocation is studied using Langevin dynamics simulation, and the consequence of introducing patterned stickiness inside the pore is investigated. It is found that the…
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…
Fundamental understanding of the effect of microscopic parameters on the dynamics of probe particles in different complex environments has wide implications. Examples include diffusion of proteins in the biological hydrogels, porous media,…
A new homogenization approach for the simulation of multi-phase flows in heterogeneous porous media is presented. It is based on the lattice Boltzmann method and combines the grayscale with the multi-component Shan-Chen method. Thus, it…
The self-assembly of copolymeric vesicles and micelles in micromixers is studied by External Potential Dynamics (EPD) simulations -- a dynamic density functional approach that explicitly accounts for the polymer architecture both at the…