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Multiparticle collision dynamics is a modern coarse-grained simulation technique to treat the hydrodynamics of Newtonian fluids by solving the Navier-Stokes equations. Naturally, it also includes thermal noise. Initially it has been applied…
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…
The previously described methodology for hierarchical grouping of objects through iterative averaging has been used for simulation of cooperative interactions between objects of a system with the purpose of investigation of the…
Soft particles at fluid interfaces play an important role in many aspects of our daily life, such as the food industry, paints and coatings, and medical applications. Analytical methods are not capable of describing the emergent effects of…
Robustly handling collisions between individual particles in a large particle-based simulation has been a challenging problem. We introduce particle merging-and-splitting, a simple scheme for robustly handling collisions between particles…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
A new methodology is developed to integrate numerically the equations of motion for classical many-body systems in molecular dynamics simulations. Its distinguishable feature is the possibility to preserve, independently on the size of the…
Intraoperative observation of tissue internal structure is often difficult. Hence, real-time soft tissue deformation is essential for the localization of tumor and other internal structures. We propose a method to simulate the internal…
A mesoscopic colloid model is developed in which a spherical colloid is represented by many interacting sites on its surface. The hydrodynamic interactions with thermal fluctuations are taken accounts in full using Dissipative Particle…
Discrete particle simulations have become the standard in science and industrial applications exploring the properties of particulate systems. Most of such simulations rely on the concept of interacting spherical particles to describe the…
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…
Active matter exhibits striking behaviour reminiscent of living matter and molecular fluids, and has promising applications in drug delivery or mixing at the micron scale. Active colloidal systems provide important models with simple and…
The presence of surfactants alters the dynamics of viscous drops immersed in an ambient viscous fluid. This is specifically true at small scales, such as in applications of droplet based microfluidics, where the interface dynamics become of…
We derive from first principles a three-dimensional theory of self-propelled particle swarming in a viscous fluid environment. Our model predicts emergent collective behavior that depends critically on fluid opacity, mechanism of…
Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…
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 show that polar molecules driven by microwave fields give naturally rise to strong three-body interactions, while the two-particle interaction can be independently controlled and even switched off. The derivation of these effective…
Molecular Dynamics simulations are becoming a powerful tool for examining and predicting atomic and molecular processes in various environment. The present review shows how, in the fields of plasma physics, chemistry and interactions with…
Videos of the molecular dynamics simulations of a colliding hard disk reactive medium. A simple event-driven algorithm is used to simulate these colliding hard disks allowing for the study of detonations at the microscopic level. This video…
A particle-based model for mesoscopic fluid dynamics is used to simulate steady and unsteady flows around a circular and a square cylinder in a two-dimensional channel for a range of Reynolds number between 10 and 130. Numerical results for…