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We use Langevin dynamics (LD) simulations to investigate single-file diffusion (SFD) in a dilute solution of flexible linear polymers inside a narrow tube with periodic boundary conditions (a torus). The transition from SFD, where the time…
We consider a model for random deposition of monomers on a line with extrinsic precursor states. As the adsorbate coverage increases, the system develops non-trivial correlations due to the diffusion mediated deposition mechanism. In a…
Physical systems with complex unsteady dynamics, such as fluid flows, are often poorly represented by a single mean solution. For many practical applications, it is crucial to access the full distribution of possible states, from which…
Living cells are characterized by the micrometric confinement of various macromolecules at high concentrations. Using droplets containing binary polymer blends as artificial cells, we previously showed that cell-sized confinement causes…
We present results of direct numerical simulation of incompressible fluid flow over a thick bed of mobile, spherically-shaped particles. The algorithm is based upon the immersed boundary technique for fluid-solid coupling and uses a…
The transport and chemical reactions of solutes are modelled as a cellular automaton in which molecules of different species perform a random walk on a regular lattice and react according to a local probabilistic rule. The model describes…
The translocation of a polymer through a pore in a membrane separating fluids of different viscosities is studied via several computational approaches. Starting with the polymer halfway, we find that as a viscosity difference across the…
The translocation dynamics of a polymer chain through a nanopore in the absence of an external driving force is analyzed by means of scaling arguments, fractional calculus, and computer simulations. The problem at hand is mapped on a one…
We present in detail a set of algorithms to carry out fluid displacements in a dynamic pore-network model of immiscible two-phase flow in porous media. The algorithms are general and applicable to regular and irregular pore networks in two…
We present here the systematic development of quantitative lattice simulations of dense polymers through a novel computational technique that allows for an efficient accounting of the chain conformations. Our approach is based on the…
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…
Molecules with complex internal structure in time-dependent periodic potentials are studied by using short Rubinstein-Duke model polymers as an example. We extend our earlier work on transport in stochastically varying potentials to cover…
We study simple lattice systems to demonstrate the influence of interpenetrating bond networks on phase behavior. We promote interpenetration by using a Hamiltonian with a weakly repulsive interaction with nearest neighbors and an…
Recent development in computer processing power leads to new paradigms of how problems in many-body physics and especially polymer physics can be addressed. GPU parallel processors can be employed to generate millions of independent…
We use molecular dynamics simulations to unravel the physics underpinning the light-induced density changes caused by the dynamic trans-cis-trans isomerization cycles of azo-mesogens embedded in a liquid crystal polymer network, an…
The rate of escape of an ideal bead-spring polymer in a symmetric double-well potential is calculated using transition state theory (TST) and the results compared with direct dynamical simulations. The minimum energy path of the transitions…
We study the propagation of tension caused by an external force along a long polymeric molecule in two different settings, namely along a free polymer in 3d space being pulled from one end, and along a pre-stretched circular polymer,…
We investigate the laminar flow of two-fluid mixtures inside a simple network of inter-connected tubes. The fluid system is comprised of two miscible Newtonian fluids of different viscosity which do not mix and remain as nearly distinct…
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…
In this article, we try to give a rather complete picture of the behavior of the free energy for a model of directed polymer in a random environment, in which the polymer is a simple symmetric random walk on the lattice $\Z^d$, and the…