相关论文: Parallel computing and molecular dynamics of biolo…

Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a…

Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modelling of such systems.…

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…

Developers of Molecular Dynamics (MD) codes face significant challenges when adapting existing simulation packages to new hardware. In a continuously diversifying hardware landscape it becomes increasingly difficult for scientists to be…

Particle-in-cell methods couple mesh-based methods for the solution of continuum mechanics problems, with the ability to advect and evolve particles. They have a long history and many applications in scientific computing. However, they have…

Membrane computing is a well-established and successful research field which belongs to the more general area of molecular computing. Membrane computing aims at defining parallel and non-deterministic computing models, called membrane…

Modern analog computers are ideally suited to solving large systems of ordinary differential equations at high speed with low energy consumtion and limited accuracy. In this article, we survey N-body physics, applied to a simple water model…

Stochastic simulation methods can be applied successfully to model exact spatio-temporally resolved reaction-diffusion systems. However, in many cases, these methods can quickly become extremely computationally intensive with increasing…

Although event-driven algorithms have been shown to be far more efficient than time-driven methods such as conventional molecular dynamics, they have not become as popular. The main obstacle seems to be the difficulty of parallelizing…

Liposomes that achieve a heterogeneous and spatially organized surface through phase separation have been recognized to be a promising platform for delivery purposes. However, their design and optimization through experimentation can be…

We provide a mathematically proven parallelization scheme for particle methods on distributed-memory computer systems. Particle methods are a versatile and widely used class of algorithms for computer simulations and numerical predictions…

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…

The numerical simulation of large-scale multiphase flow in porous media is of considerable importance across various application fields, particularly in the petroleum industry. The fully implicit method is preferred in reservoir simulations…

We introduce a simulation strategy to consistently couple continuum biomembrane dynamics to the motion of discrete biological macromolecules residing within or on the membrane. The methodology is used to study the diffusion of integral…

Recent developments in lipid membrane models for simulations are reviewed. To reduce computational costs, various coarse-grained molecular models have been proposed. Among them, implicit solvent (solvent-free) molecular models are…

Owing to the computational complexity of electronic structure algorithms running on classical digital computers, the range of molecular systems amenable to simulation remains tightly circumscribed even after many decades of work. Quantum…

This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization…

Particle-in-cell merging algorithms aim to resample dynamically the six-dimensional phase space occupied by particles without distorting substantially the physical description of the system. Whereas various approaches have been proposed in…

This article introduces a highly parallel algorithm for molecular dynamics simulations with short-range forces on single node multi- and many-core systems. The algorithm is designed to achieve high parallel speedups for strongly…

We present Monte Carlo simulations of an ultra coarse-grained lipid bilayer with different number of lipids on both leaflets. In the simulations, we employ a new method for measuring the elastic parameters of the membrane, including the…