相关论文: PolyHoop: Soft particle and tissue dynamics with t…

In this brief contribution to the Proceedings of the NATO-ASI on ``Electrostatic Effects in Soft Matter and Biophysics'', which took place in Les Houches from Oct. 1-13, 2000, we summarize in short aspects of the simulations methods to…

In this paper we present the results of a large-scale numerical investigation of structural properties of a model of cell membrane, simulated as a bilayer of flexible molecules in vacuum. The study was performed by carrying out extensive…

With the great development of parallel computing techniques, the particle-particle (PP) model has been successfully applied in a number of plasma applications. Comparing to particle-mesh (PM) models, for example the widely used…

The Smoothed Particles Hydrodynamics (SPH) is a particle-based, meshfree, Lagrangian method used to simulate multidimensional fluids with arbitrary geometries, most commonly employed in astrophysics, cosmology, and computational…

Creating realistic droplet simulations and animations has long been a formidable challenge for researchers and developers due to the inherent complexity of fluid dynamics. Achieving lifelike droplet splash simulations while managing…

WavePacket is an open-source program package for numerical simulations in quantum dynamics. Building on the previous Part I [Comp. Phys. Comm. 213, 223-234 (2017)] and Part II [Comp. Phys. Comm. 228, 229-244 (2018)] which dealt with quantum…

We present a new algorithm to design lightweight cellular materials with required properties in a multi-physics context. In particular, we focus on a thermo-mechanical setting, by promoting the design of unit cells characterized both by an…

The invention of three-dimensional printers has led to major innovations in tissue engineering. They have enabled the printing of complex geometries such as those that occur in natural tissues, that were not possible with traditional…

We present a physics-based framework to simulate porous, deformable materials and interactive tools with haptic feedback that can reshape it. In order to allow the material to be moulded non-homogeneously, we propose an algorithm to change…

Modern large scale cosmological hydrodynamic simulations require robust tools capable of analysing their data outputs in a parallel and efficient manner. We introduce SOAP (Spherical Overdensity and Aperture Processor), a Python package…

Stochastic models of reaction-diffusion systems are important for the study of biochemical reaction networks where species are present in low copy numbers or if reactions are highly diffusion limited. In living cells many such systems…

Event-driven molecular dynamics is a valuable tool in condensed and soft matter physics when particles can be modeled as hard objects or more generally if their interaction potential can be modeled in a stepwise fashion. Hard spheres model…

Biological tissues are complex structures composed of many elements which make light-based tissue diagnostics challenging. Over the past decades, Monte Carlo technique has been used as a fundamental and versatile approach toward modeling…

The simulation of large ensembles of particles is usually parallelized by partitioning the domain spatially and using message passing to communicate between the processes handling neighboring subdomains. The particles are represented as…

Exposing a molecule to intense light pulses may bring this molecule to a nonstationary quantum state, thus launching correlated dynamics of electronic and nuclear subsystems. Although much had been achieved in the understanding of…

We present a technique designed for parallelizing large rigid body simulations, capable of exploiting multiple CPU cores within a computer and across a network. Our approach can be applied to simulate both unilateral and bilateral…

Molecular dynamics (MD) simulations enable the description of ma- terial properties and processes with atomistic detail by numerically solv- ing the time evolution of every atom in the system. We introduce Poly- merModeler, a…

We present the results from a two-day study in which we discussed various implementations of Smooth Particle Hydrodynamics (SPH), one of the leading methods used across a variety of areas of large-scale astrophysical simulations. In…

picFoam is a fully kinetic electrostatic Particle-in-Cell(PIC) solver, including Monte Carlo Collisions(MCC), for non-equilibrium plasma research in the open-source framework of OpenFOAM. The solver's modular design, based on the same…

In a world made of atoms, the computer simulation of molecular systems, such as proteins in water, plays an enormous role in science. Software packages that perform these computations have been developed for decades. In molecular…