Related papers: Wavelet Monte Carlo dynamics: a new algorithm for …
Brownian Dynamics simulations are an important tool for modeling the dynamics of soft matter. However, accurate and rapid computations of the hydrodynamic interactions between suspended, microscopic components in a soft material is a…
Brownian dynamics of colloidal particles on complex surfaces has found important applications in diverse physical, chemical and biological processes. However, current Brownian dynamics simulation algorithms mostly work for relatively simple…
In the Ermak-McCammon algorithm for Brownian Dynamics, the hydrodynamic interactions (HI) between N spherical particles are described by a 3N x 3N diffusion tensor. This tensor has to be factorized at each timestep with a runtime of O(N^3),…
We present a hybrid Brownian dynamics / Monte Carlo algorithm for simulating solutions of highly entangled semiflexible polymers or filaments. The algorithm combines a Brownian dynamics time-stepping approach with an efficient scheme for…
We put forward a simple procedure for extracting dynamical information from Monte Carlo simulations, by appropriate matching of the short-time diffusion tensor with its infinite-dilution limit counterpart, which is supposed to be known.…
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 present a revision to the well known Stormer-Verlet algorithm for simulating second order differential equations. The revision addresses the inclusion of linear friction with associated stochastic noise, and we analytically demonstrate…
Molecular simulations of many particles which move rather according to a brownian than a newtonian type of dynamics, nevertheless, can be performed by means of a "velocity-Verlet-like" algorithm. The derivation of this algorithm requires…
We introduce a `virtual-move' Monte Carlo (VMMC) algorithm for systems of pairwise-interacting particles. This algorithm facilitates the simulation of particles possessing attractions of short range and arbitrary strength and geometry, an…
We present a new efficient method for Monte Carlo simulations of diffusion-reaction processes. First introduced by us in [Phys. Rev. Lett., 97:230602, 2006], the new algorithm skips the traditional small diffusion hops and propagates the…
Dynamics simulations of constrained particles can greatly aid in understanding the temporal and spatial evolution of biological processes such as lateral transport along membranes and self-assembly of viruses. Most theoretical efforts in…
We study the phenomenon of the "walking droplet", by means of numerical fluid dynamics simulations using the Smoothed Particle Hydrodynamics numerical method. This phenomenon occurs when a millimetric drop is released on the surface of an…
We present numerical and analytical results describing the effect of hydrodynamic interactions on the dynamics of a short polymer chain in solution. A molecular dynamics algorithm for the polymer is coupled to a direct simulation Monte…
Colloids have a striking relevance in a wide spectrum of industrial formulations, spanning from personal care products to protective paints. Their behaviour can be easily influenced by extremely weak forces, which disturb their…
We have presented a new and alternative algorithm for noise reduction using the methods of discrete wavelet transform and numerical differentiation of the data. In our method the threshold for reducing noise comes out automatically. The…
Simulating the static and dynamic properties of semidilute polymer solutions with Brownian dynamics (BD) requires the computation of a large system of polymer chains coupled to one another through excluded-volume and hydrodynamic…
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…
The conformational and dynamical properties of active Brownian polymers embedded in a fluid depend on the nature of the driving mechanism, e.g., self-propulsion or external actuation of the monomers. Implementations of self-propelled and…
Random batch algorithms are constructed for quantum Monte Carlo simulations. The main objective is to alleviate the computational cost associated with the calculations of two-body interactions, including the pairwise interactions in the…
We consider the aeroelastic simulation of flexible mechanical structures submerged in subsonic fluid flows at low Mach numbers. The nonlinear kinematics of flexible bodies are described in the total Lagrangian formulation and discretized by…