Related papers: A symplectic integrator for molecular dynamics on …
The kinetic term of the $N$-body Hamiltonian system defined on the surface of the sphere is non-separable. As a result, standard explicit symplectic integrators are inapplicable. We exploit an underlying hierarchy in the structure of the…
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…
Interfaces between two fluids are ubiquitous and of special importance for industrial applications, e.g., stabilisation of emulsions. The dynamics of fluid-fluid interfaces is difficult to study because these interfaces are usually…
Geometric integration theory can be employed when numerically solving ODEs or PDEs with constraints. In this paper, we present several one-step algorithms of various orders for ODEs on a collection of spheres. To demonstrate the versatility…
We report adaptive resolution molecular dynamics simulations of a flexible linear polymer in solution. The solvent, i.e., a liquid of tetrahedral molecules, is represented within a certain radius from the polymer's center of mass with a…
In this work, we present a hybrid simulator for space docking and robotic proximity operations methodology. This methodology also allows for the emulation of a target robot operating in a complex environment by using an actual robot. The…
Sediment transport over an erodible sediment bed is studied by particle resolved simulations with a hybrid parallel approach. To overcome the challenges of load imbalance in the traditional domain decomposition method when encountering…
We show here that molecular resolution is inherently hybrid in terms of relative separation: If molecules are close to each other, they must be characterized by a fine-grained (geometrically detailed) model, yet if molecules are far from…
We construct an explicit reversible symplectic integrator for the planar 3-body problem with zero angular momentum. We start with a Hamiltonian of the planar 3-body problem that is globally regularised and fully symmetry reduced. This…
Molecular simulation technologies have afforded researchers a unique look into the nanoscale interactions driving physical processes. However, a limitation for molecular dynamics (MD) simulations is that they must be performed on…
We study symplectic numerical integration of mechanical systems with a Hamiltonian specified in non-canonical coordinates and its application to guiding-center motion of charged plasma particles in magnetic confinement devices. The…
We investigate the feasibility of modelling turbulence via numeric functional integration. By transforming the Burgers' equation into a functional integral we are able to calculate equal-time spatial correlation of system variables using…
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…
We present two modifications of the standard cell list algorithm for nonequilibrium molecular dynamics simulations of homogeneous, linear flows. When such a flow is modeled with periodic boundary conditions, the simulation box deforms with…
We describe a lattice Boltzmann algorithm to simulate liquid crystal hydrodynamics in three dimensions. The equations of motion are written in terms of a tensor order parameter. This allows both the isotropic and the nematic phases to be…
We present the Seismic Laboratory for Imaging and Modeling/Monitoring (SLIM) open-source software framework for computational geophysics and, more generally, inverse problems involving the wave-equation (e.g., seismic and medical…
Particle-in-Cell (PIC) methods are widely used computational tools for fluid and kinetic plasma modeling. While both the fluid and kinetic PIC approaches have been successfully used to target either kinetic or fluid simulations, little was…
Emergent phenomena share the fascinating property of not being obvious consequences of the design of the system in which they appear. This characteristic is no less relevant when attempting to simulate such phenomena, given that the outcome…
Although event-driven algorithms have been shown to be far more efficient than time-driven methods such as conventional molecular dynamics, they have not become as popular. The main obstacle seems to be the difficulty of parallelizing…
Computational fluid dynamics is both a thriving research field and a key tool for advanced industry applications. The central challenge is to simulate turbulent flows in complex geometries, a compute-power intensive task due to the large…