Related papers: Event-Driven Molecular Dynamics in Parallel
The latest trends in high-performance computing systems show an increasing demand on the use of a large scale multicore systems in a efficient way, so that high compute-intensive applications can be executed reasonably well. However, the…
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…
Neuromorphic computing aims to incorporate lessons from studying biological nervous systems in the design of computer architectures. While existing approaches have successfully implemented aspects of those computational principles, such as…
We introduce a scheme for molecular simulations, the Deep Potential Molecular Dynamics (DeePMD) method, based on a many-body potential and interatomic forces generated by a carefully crafted deep neural network trained with ab initio data.…
Conventional molecular dynamics (MD) simulations struggle when simulating particles with steeply varying interaction potentials, due to the need to use a very short time step. Here, we demonstrate that an event-driven Monte Carlo (EDMC)…
We describe a new model for the study of weakly-collisional, magnetized plasmas derived from exploiting the separation of the dynamics parallel and perpendicular to the magnetic field. This unique system of equations retains the particle…
We report the results of intensive numerical calculations for four atomic H2+H2 energy transfer collision. A parallel computing technique based on LAM/MPI functions is used. In this algorithm, the data is distributed to the processors…
Brownian dynamics algorithms integrate numerically Langevin equations and allow to probe long time scales in simulations. A common requirement for such algorithms is that interactions in the system should vary little during an integration…
Optimal multiple sequence alignment by dynamic programming, like many highly dimensional scientific computing problems, has failed to benefit from the improvements in computing performance brought about by multi-processor systems, due to…
Dynamical systems see widespread use in natural sciences like physics, biology, chemistry, as well as engineering disciplines such as circuit analysis, computational fluid dynamics, and control. For simple systems, the differential…
Although poor for small dynamic scales, the Particle-Mesh (PM) model allows in astrophysics good insight for large dynamic scales at low computational cost. Furthermore, it is possible to employ a very high number of particles to get high…
Molecular docking is an essential tool for drug design. It helps the scientist to rapidly know if two molecules, respectively called ligand and receptor, can be combined together to obtain a stable complex. We propose a new multi-objective…
With the growing complexity and capability of contemporary robotic systems, the necessity of sophisticated computing solutions to efficiently handle tasks such as real-time processing, sensor integration, decision-making, and control…
We introduce and analyze the stability of a class of event-triggered extremum-seeking algorithms designed to solve resource-aware, model-free, optimization problems. Leveraging recent advances in Lie-Bracket Averaging for hybrid systems, we…
Parallelism of tight-binding molecular dynamics simulations is presented by means of the order-N electronic structure theory with the Wannier states, recently developed (J. Phys. Soc. Jpn. 69,3773 (2000)). An application is tested for…
In a world made of atoms, the computer simulation of molecular systems, such as proteins in water, plays an enormous role in science. Software packages that perform these computations have been developed for decades. In molecular…
In this era of large-scale data, distributed systems built on top of clusters of commodity hardware provide cheap and reliable storage and scalable processing of massive data. Here, we review recent work on developing and implementing…
A previous study of MD algorithms designed for GPU use is extended to cover more recent developments in GPU architecture. Algorithm modifications are described, together with extensions to more complex systems. New measurements include the…
Quantum computing has the potential to reduce the computational cost required for quantum dynamics simulations. However, existing quantum algorithms for coupled electron-nuclear dynamics simulation either require fault-tolerant devices, or…
Increasing complexity and data-generation rates in cyber-physical systems and the industrial Internet of things are calling for a corresponding increase in AI capabilities at the resource-constrained edges of the Internet. Meanwhile, the…