Related papers: Fast simulation of Brownian dynamics in a crowded …
Most biochemical reactions in living cells rely on diffusive search for target molecules or regions in a heterogeneous overcrowded cytoplasmic medium. Rapid re-arrangements of the medium constantly change the effective diffusivity felt…
The reaction-diffusion master equation (RDME) is a model that allows for efficient on-lattice simulation of spatially resolved stochastic chemical kinetics. Compared to off-lattice hard-sphere simulations with Brownian Dynamics (BD) or…
An efficient technique to simulate turbulent particle-laden flow at high mass loadings within the four-way coupled simulation regime is presented. The technique implements large eddy simulation, discrete phase simulation, a deterministic…
In recent years, several particle-based stochastic simulation algorithms (PSSA) have been developed to study the spatially resolved dynamics of biochemical networks at a molecular scale. A challenge all these approaches have to address is…
Product formulas can be used to simulate Hamiltonian dynamics on a quantum computer by approximating the exponential of a sum of operators by a product of exponentials of the individual summands. This approach is both straightforward and…
In recent years modelling crowd and evacuation dynamics has become very important, with increasing huge numbers of people gathering around the world for many reasons and events. The fact that our global population grows dramatically every…
Complex biological and physical transport processes are often described through systems of interacting particles. Excluded-volume effects on these transport processes are well studied, however the interplay between volume exclusion and…
We consider a system of classical Brownian particles interacting via a smooth long-range potential in the mean-field regime, and we analyze the propagation of chaos in form of sharp, uniform-in-time estimates on many-particle correlation…
Evacuation plans have been historically used as a safety measure for the construction of buildings. The existing crowd simulators require fully-modeled 3D environments and enough time to prepare and simulate scenarios, where the…
A simple and efficient algorithm of the molecular-dynamics simulation of the hard disk system based on the Event-Driven method is developed. From the analysis of algorithm, the complexity is O(log N) per 1 event, and the constant…
The efficiency of atomic simulations of materials and molecules can rapidly deteriorate when large free energy barriers exist between local minima. We propose smooth basin classification, a universal method to define reaction coordinates…
Using Brownian dynamics simulations, the motion of active Brownian particles (ABPs) in the presence of fuel (or 'food') sources is studied. It is an established fact that within confined stationary systems, the activity of ABPs generates…
We present a new algorithm to simulate dynamic group behaviors for interactive multi-agent crowd simulation. Our approach is general and makes no assumption about the environment, shape, or size of the groups. We use the least effort…
Diffusion in bidisperse Brownian hard-sphere suspensions is studied by Stokesian Dynamics (SD) computer simulations and a semi-analytical theoretical scheme for colloidal short-time dynamics, based on Beenakker and Mazur's method [Physica…
We present a new Eulerian framework for the computation of turbulent compressible multiphase channel flows, specifically to assess turbulence modulation by dispersed particulate matter in dilute concentrations but with significant mass…
In the coarse grained Brownian Dynamics simulation method the many solvent molecules are replaced by random thermal kicks and an effective friction acting on the particles of interest. For Brownian Dynamics the friction has to be so strong…
Crowd simulation models are used to assess the performance and safety of crowd systems. In some systems, wheelchairs and other moving objects are present in the crowd. The different size and speed of the wheelchairs could significantly…
Simulation of biomolecular networks is now indispensable for studying biological systems, from small reaction networks to large ensembles of cells. Here we present a novel approach for stochastic simulation of networks embedded in the…
The analysis of non-equilibrium steady states of biochemical reaction networks relies on finding the configurations of fluxes and chemical potentials satisfying stoichiometric (mass balance) and thermodynamic (energy balance) constraints.…
Fluctuating hydrodynamics based techniques have been developed in recent years for the simulation of Brownian motion of particles. These mesoscale simulation tools are viable approaches for problems where molecular dynamics simulations may…