Related papers: PolyHoop: Soft particle and tissue dynamics with t…
We introduce a particle-based simulation method for granular material in interactive frame rates. We divide the simulation into two decoupled steps. In the first step, a relatively small number of particles is accurately simulated with a…
Polylab is a MATLAB toolbox for multivariate polynomial scalars and polynomial matrices with a unified symbolic-numeric interface across CPU and GPU-oriented backends. The software exposes three aligned classes: MPOLY for CPU execution,…
The present work presents a density-functional microscopic model of soft biological tissue. The model was based on a prototype molecular structure from experimentally resolved collagen peptide residues and water clusters and has the…
This paper introduces a library of algorithms for representing cloud microphysics in numerical models. The library is written in C++, hence the name libcloudph++. In the current release, the library covers three warm-rain schemes: the…
We investigate morphologies of proliferating cellular tissues using a newly developed numerical simulation model for mechanical cell division and migration in 2D. The model is applied to a bimodal mixture consisting of stiff cells with a…
We describe collective-move Monte Carlo algorithms designed to approximate the overdamped dynamics of self-assembling nanoscale components equipped with strong, short-ranged and anisotropic interactions. Conventional Monte Carlo simulations…
We develop an algorithm suitable for parallel molecular dynamics simulations in $d$ spatial dimensions and describe its implementation in C++. All routines work in arbitrary $d$; the maximum simulated $d$ is limited only by available…
In virtual Hand-Object Interaction (HOI) scenarios, the authenticity of the hand's deformation is important to immersive experience, such as natural manipulation or tactile feedback. Unrealistic deformation arises from simplified hand…
Multiparticle collision dynamics (MPCD) is a flexible and robust mesoscale computational technique for simulating solvent-mediated hydrodynamic interactions in soft materials. Here, we provide a critical overview of the MPCD method and…
Many animals, and an increasing number of artificial agents, display sophisticated capabilities to perceive and manipulate objects. But human beings remain distinctive in their capacity for flexible, creative tool use -- using objects in…
Number-conserving cellular automata are discrete dynamical systems that simulate interacting particles like e.g. grains of sand. In an earlier paper, I had already derived a uniform construction for all transition rules of one-dimensional…
Scaffold hopping is a drug discovery strategy to generate new chemical entities by modifying the core structure, the \emph{scaffold}, of a known active compound. This approach preserves the essential molecular features of the original…
A holographic microscope captures interference patterns, or holograms, that encode three-dimensional (3D) information about the object being viewed. Computation is essential to extracting that 3D information. By wrapping low-level…
Mesoscopic molecular dynamics simulations are used to determine the large scale structure of several binary polymer mixtures of various chemical architecture, concentration, and thermodynamic conditions. By implementing an analytical…
Molecular dynamics computer simulations are used to investigate thedynamics of a binary mixture of charged (Yukawa) particles with a size-ratio of 1:5. We find that the system undergoes a phase transition where the large particles…
Droplets form a cornerstone of the spatiotemporal organization of biomolecules in cells. These droplets are controlled using physical processes like chemical reactions and imposed gradients, which are costly to simulate using traditional…
Dynamical maps describe general transformations of the state of a physical system, and their iteration can be interpreted as generating a discrete time evolution. Prime examples include classical nonlinear systems undergoing transitions to…
We present an easy-to-use and lightweight surface and volume mesh sampling standalone application tailored for the needs of particle-based simulation. We describe the surface and volume sampling algorithms used in LEAVEN in a…
Polymer syntactic foams are transforming materials that will shape the future of next-generation aerospace and marine structures. When manufactured using traditional processes, like compression molding, syntactic foams consist of a solid…
Modeling plasma accelerators is a computationally challenging task and the quasi-static particle-in-cell algorithm is a method of choice in a wide range of situations. In this work, we present the first performance-portable, quasi-static,…