Recently, it has become possible to unfold a single protein molecule titin, by pulling it with an atomic-force-microscope tip. In this paper, we propose and study a stochastic kinetic model of this unfolding process. Our model assumes that each immunoglobulin domain of titin is held together by six hydrogen bonds. The external force pulls on these bonds and lowers the energy barrier that preven...

The treatment of kinetic shear Alfvén waves in homogeneous magnetized plasmas by means of Vlasov simulation is examined. To this end, the driftkinetic version of the Vlasov–Maxwell equations is solved via various numerical schemes, all employing a grid in (1 + 1)D phase space. Since kinetic shear Alfvén waves are Landau damped, the use of an equidistant grid in velocity space leads to a recurre...

The newly developed high-order-accurate multidimensional gas-kinetic scheme is further investigated, including the benefit of the consideration of tangential slopes in the flux function at a cell interface, and the application of the scheme in turbulence simulation. The present study shows that in despite of increasing of computational cost, the multidimensional scheme can evidently improve the...

In this paper a new and powerful computer simulation capability for the characterization of carbonaceous nanoparticle assemblies across multiple, connected scales, starting from the molecular scale is presented. The goal is to provide a computational infrastructure that can reveal through multi-scale computer simulation how chemistry can influence the structure and function of carbonaceous asse...

The present paper is primarily concerned with modeling complex turbulent wall-bounded flow in spray-painting processes by using a commercial CFD code. Computational results of turbulent channel flow with low Reynolds numbers are compared with DNS data in order to obtain the performance of turbulence models and near wall treatments. The realizable k-ε model with the nonequilibrium wall function ...

We present a computer-assisted approach to approximating coarse optimal switching policies for systems described by microscopic/stochastic evolution rules. The “coarse timestepper” constitutes a bridge between the underlying kinetic Monte Carlo simulation and traditional, continuum numerical optimization techniques formulated in discrete time. The approach is illustrated through a simplified ki...

Full kinetic dynamics of a perpendicular collisionless shock is studied by means of a one-dimensional electromagnetic full particle simulation. The present simulation domain is taken in the shock rest frame in contrast to the previous full particle simulations of shocks. Preliminary results show that the downstream state falls into a unique cyclic reformation state for a given set of upstream p...

The melting of a 64 ion microcrystal of KCI was studied by means of a molecular dynamics computer simulation. We used a central pair interaction with an inverse power law repulsion. The thermodynamics, kinetic and structural properties such as melting temperature, latent heat, mean square displacement, diffusion constant, radial distribution function and bond angle distribution are calculated. ...

Collisionless plasma expansion is a fundamental physics problem in plasma science and has great impacts on engineering applications, such as fusion and electric propulsion. Though much more computationally expensive, the kinetic approaches are required for both electrons and ions in order to accurately solve the collisionless plasma problems. The gridbased direct kinetic simulation code with GP...