Related papers: Parallel multiscale modeling of biopolymer dynamic…
We study the translocation of polymers across varying-section channels. Using systematic approximations, we derive a simplified model that reduces the problem of polymer translocation through varying-section channels to that of a point-like…
We propose a hybrid model, coupling Lattice Boltzmann and Molecular Dynamics models, for the simulation of dense fluids. Time and length scales are decoupled by using an iterative Schwarz domain decomposition algorithm. The MD and LB…
The diffusion of molecules (penetrants) of variable size, shape, and chemistry through dense crosslinked polymer networks is a fundamental scientific problem that is broadly relevant in materials, polymer, physical and biological chemistry.…
We investigate the translocation dynamics of heteropolymers driven through a nanopore using a constant temperature Langevin thermostat. Specifically, we consider heteropolymers consisting of two types of monomers labeled A and B, which are…
We use the Bond Fluctuation Model (BFM) to study the pore-blockade times of a translocating polymer of length $N$ in two dimensions, in the absence of external forces on the polymer (i.e., unbiased translocation) and hydrodynamic…
We develop an efficient parallel multiscale method that bridges the atomistic and mesoscale regimes, from nanometer to micron and beyond, via concurrent coupling of atomistic simulation and mesoscopic dynamics. In particular, we combine an…
Mathematically modeling complex transport phenomena at the molecular level can be a powerful tool for identifying transport mechanisms and predicting macroscopic properties. We use two different stochastic time series models, parameterized…
In this talk I discuss the general question of the portability of Molecular Dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision arithmetics of the today available APE platforms does…
Realistic simulations of detailed, biophysics-based, multi-scale models require very high resolution and, thus, large-scale compute facilities. Existing simulation environments, especially for biomedical applications, are designed to allow…
Modelling has become a third distinct line of scientific enquiry, alongside experiments and theory. Molecular dynamics (MD) simulations serve to interpret, predict and guide experiments and to test and develop theories. A major limiting…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
We present a novel thermodynamically guided, low-noise, time-scale bridging, and pertinently efficient strategy for the dynamic simulation of microscopic models for complex fluids. The systematic coarse-graining method is exemplified for…
Immersed boundary-lattice Boltzmann method (IB-LBM) has been widely used for simulation of particle-laden flows recently. However, it was limited to small-scale simulations with no more than O(103) particles. Here, we expand IB-LBM for…
We study the dynamics of driven polymer translocation using both molecular dynamics (MD) simulations and a theoretical model based on the non-equilibrium tension propagation on the {\it cis} side subchain. We present theoretical and…
The spreading of polymer droplets is studied using molecular dynamics simulations. To study the dynamics of both the precursor foot and the bulk droplet, large drops of ~200,000 monomers are simulated using a bead-spring model for polymers…
We successfully extend a multiscale simulation (MSS) method to nonisothermal well-entangled polymer melt flows between two coaxial cylinders. In the multiscale simulation, the macroscopic flow system is connected to a number of microscopic…
The long time dynamics of polymeric materials has been extensively studied in the past through various experimental techniques and computer simulations. While computer simulations typically treat generic, simplified models, experiments deal…
We consider the flow-driven translocation of single polymer chains through nanochannels. Using analytical calculations based on the de Gennes blob model and mesoscopic numerical simulations, we estimate the threshold flux for the…
Tissue growth underpins a wide array of biological and developmental processes, and numerical modeling of growing systems has been shown to be a useful tool for understanding these processes. However, the phenomena that can be captured are…
Recent advances in random-walk particle-tracking have enabled direct simulation of mixing and reactions on particles by allowing the particles to interact with each other using a multi-point mass transfer scheme. The mass transfer scheme…