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Step-and-project is a popular way to simulate non-penetrated deformable bodies in physically-based animation. First integrating the system in time regardless of contacts and post resolving potential intersections practically strike a good…
We test the performances of two different approaches to the computation of forces for molecular dynamics simulations on Graphics Processing Units. A "vertex-based" approach, where a computing thread is started per particle, is compared to a…
The multi-scale flow mechanism is crucial for force and heat loaded on near-space and reentry vehicles, the control of spacecraft by thrusters, the propelling and cooling of MEMS, etc. Since the continuum flow and rarefied flow often exist…
We discuss certain basic features of the equation-free (EF) approach to modeling and computation for complex/multiscale systems. We focus on links between the equation-free approach and tools from systems and control theory (design of…
The aim of this paper is to investigate the unstable nature of pressure computation focusing on incompressible flow modeling through the projection-based particle methods. A new approach from the original viewpoint of the momentum…
Kinetic equations model the position-velocity distribution of particles subject to transport and collision effects. Under a diffusive scaling, these combined effects converge to a diffusion equation for the position density in the limit of…
The stability of a galaxy model is most easily assessed through N-body simulation. Particle-mesh codes have been widely used for this purpose, since they enable the largest numbers of particles to be employed. We show that the functional…
A fast $N$-body code has been developed for simulating a stellar disk embedded in a live dark matter halo. In generating its Poisson solver, a self-consistent field (SCF) code which inherently possesses perfect scalability is incorporated…
We introduce an efficient algorithm, called partition of unity extension or PUX, to construct an extension of desired regularity of a function given on a complex multiply connected domain in $2D$. Function extension plays a fundamental role…
In this paper, we describe a numerical algorithm for the self-consistent simulations of surface water and sediment dynamics. The method is based on the original Lagrangian-Eulerian CSPH-TVD approach for solving the Saint-Venant and Exner…
Simulating Clifford and near-Clifford circuits using the extended stabilizer formalism has become increasingly popular, particularly in quantum error correction. Compared to the state-vector approach, the extended stabilizer formalism can…
An accurate force calculation with the Poisson-Boltzmann equation is challenging, as it requires the electric field on the molecular surface. Here, we present a calculation of the electric field on the solute-solvent interface that is exact…
We perform a precision calculation of the effective field theory (EFT) conditional likelihood for large-scale structure (LSS) using the saddle-point expansion method in the presence of primordial non-Gaussianities (PNG). The precision is…
Gaussian process modulated Poisson processes provide a flexible framework for modelling spatiotemporal point patterns. So far this had been restricted to one dimension, binning to a pre-determined grid, or small data sets of up to a few…
Mesoscopic numerical simulations provide a unique approach for the quantification of the chemical influences on red blood cell functionalities. The transport Dissipative Particles Dynamics (tDPD) method can lead to such effective multiscale…
This report presents a comprehensive analysis of the performance of GPU accelerated meshfree CFD solvers for two-dimensional compressible flows in Fortran, C++, Python, and Julia. The programming model CUDA is used to develop the GPU codes.…
Colloidal solutions posses a wide range of time and length scales, so that it is unfeasible to keep track of all of them within a single simulation. As a consequence some form of coarse-graining must be applied. In this work we use the…
We present a modification of the $\Delta$SCF method of calculating energies of excited states, in order to make it applicable to resonance calculations of molecules adsorbed on metal surfaces, where the molecular orbitals are highly…
We present GridFF, an efficient method for simulating molecules on rigid substrates, derived from techniques used in protein-ligand docking in biochemistry. By projecting molecule-substrate interactions onto precomputed spatial grids with…
We propose a method to efficiently determine the optimal coarse-grained force field in mesoscopic stochastic simulations of Newtonian fluid and polymer melt systems modeled by dissipative particle dynamics (DPD) and energy conserving…