Related papers: Fast simulation of Brownian dynamics in a crowded …
Exploiting the efficiency and stability of Position-Based Dynamics (PBD), we introduce a novel crowd simulation method that runs at interactive rates for hundreds of thousands of agents. Our method enables the detailed modeling of per-agent…
In crowded environments, individuals must navigate around other occupants to reach their destinations. Understanding and controlling traffic flows in these spaces is relevant for coordinating robot swarms and designing infrastructure for…
Brownian motion is a central scientific paradigm. Recently, due to increasing efforts and interests towards miniaturization and small-scale physics or biology, the effects of confinement on such a motion have become a key topic of…
Chemical reactions inside cells are generally considered to happen within fixed-size compartments. Needless to say, cells and their compartments are highly dynamic. Thus, such stringent assumptions may not reflect biochemical reality, and…
Stochastic models of diffusion with excluded-volume effects are used to model many biological and physical systems at a discrete level. The average properties of the population may be described by a continuum model based on partial…
It is now well established that the cell is a highly crowded environment. Yet, the effects of crowding on the dynamics of signaling pathways, gene regulation networks and metabolic networks are still largely unknown. Crowding can alter both…
The modeling of complex reaction-diffusion processes in, for instance, cellular biochemical networks or self-assembling soft matter can be tremendously sped up by employing a multiscale algorithm which combines the mesoscopic Green's…
With the continuous growth of processing power for scientific computing, first principles Born-Oppenheimer molecular dynamics (MD) simulations are becoming increasingly popular for the study of a wide range of problems in materials science,…
Simulating chemical reaction networks is often computationally demanding, in particular due to stiffness. We propose a novel simulation scheme where long runs are not simulated as a whole but assembled from shorter precomputed segments of…
A computer simulation has to be fast to be helpful, if it is employed to study the behavior of a multicomponent dynamic system. This paper discusses modeling concepts and algorithmic techniques useful for creating such fast simulations.…
The phoretic Brownian dynamics method is shown here to be an effective approach to simulate the properties of colloidal chemophoretic based systems. The method is then optimized to allow for the comparison with results from multiparticle…
Models invoking the chemical master equation are used in many areas of science, and, hence, their simulation is of interest to many researchers. The complexity of the problems at hand often requires considerable computational power, so a…
Explicit simulations of fluid mixtures of highly size-dispersed particles are constrained by numerical challenges associated with identifying pair-interaction neighbors. Recent algorithmic developments have ameliorated these difficulties to…
The network of biochemical reactions inside living organisms is characterized by an overwhelming complexity which stems from the sheer number of reactions and from the complicated topology of biochemical cycles. However the high speed of…
During the life cycle of bacterial cells the non-mixing of the two ring-shaped daughter genomes is an important prerequisite for the cell division process. Mimicking the environments inside highly crowded biological cells, we study the…
We use computer simulations to study the onset of collective motion in systems of interacting active particles. Our model is a swarm of active Brownian particles with internal energy depot and interactions inspired by the dissipative…
Turbulent flows laden with small bubbles are ubiquitous in many natural and industrial environments. From the point of view of numerical modeling, to be able to handle a very large number of small bubbles in direct numerical simulations,…
This study investigates the evolution of nanoparticle populations undergoing Brownian coagulation in a spatial mixing layer. The dynamics of particle size distribution and number concentration are analyzed using a coupled Eulerian approach…
This study uses a combination of stochastic optimization, statistical mechanical theory, and molecular simulation to test the extent to which the long-time dynamics of a single tracer particle can be enhanced by rationally modifying its…
We present a simple modification of the direct-forcing immersed boundary method (IBM) proposed by Uhlmann [J. Comput. Phys, 2005] in order to enable it to be applied to particulate flows with solid-to-fluid density ratios around unity. The…