Related papers: DynamO: A free O(N) general event-driven molecular…
We suggest a simple model for the dynamics of granular particles in suspension which is suitable for an event driven algorithm, allowing to simulate $N=\mathcal{O}(10^6)$ particles or more. As a first application we consider a dense…
Time- and frequency resolved optical signals provide insights into the properties of light harvesting molecular complexes, including excitation energies, dipole strengths and orientations, as well as in the exciton energy flow through the…
Ordinary Differential Equations (ODE) are used throughout science where the capture of rates of change in states is sought. While both pieces of commercial and open software exist to study such systems, their efficient and accurate usage…
We provide an introduction to molecular dynamics simulations in the context of the Kob-Andersen model of a glass. We introduce a complete set of tools for doing and analyzing the results of simulations at fixed NVE and NVT. The modular…
Non-Markovian dynamics arising from the strong coupling of a system to a structured environment is essential in many applications of quantum mechanics and emerging technologies. Deriving an accurate description of general quantum dynamics…
The recent progress of linear-scaling or O(N) methods in the density functional theory (DFT) is remarkable. We expect that first-principles molecular dynamics (FPMD) simulations based on DFT can now treat more realistic and complex systems…
A new numerical method is presented to efficiently simulate the inelastic hard sphere (IHS) model for granular media, when fluid and frozen regions coexist in the presence of gravity. The IHS model is extended by allowing particles to…
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…
This paper presents the design, development, and application of a novel space simulation environment for rapidly prototyping and testing flight software for distributed space systems. The environment combines the flexibility, determinism,…
We present a comprehensive end-to-end framework for simulating the real-time dynamics of chemical systems on a fault-tolerant quantum computer, incorporating both electronic and nuclear quantum degrees of freedom. An all-particle simulation…
Computer simulations have become a very powerful tool for scientific research. Given the vast complexity that comes with many open scientific questions, a purely analytical or experimental approach is often not viable. For example,…
An N-component continuous-time dynamic system is considered whose components evolve autonomously all the time except for in discrete asynchronous instances of pairwise interactions. Examples include chaotically colliding billiard balls and…
The most difficult aspect of the realistic modeling of granular materials is how to capture the real shape of the particles. Here we present a method to simulate granular materials with complex-shaped particles. The particle shape is…
Computer simulations have become a very powerful tool for scientific research. In order to facilitate research in computational biology, the BioDynaMo project aims at a general platform for biological computer simulations, which should be…
Several physical systems in condensed matter have been modeled approximating their constituent particles as hard objects. The hard spheres model has been indeed one of the cornerstones of the computational and theoretical description in…
We propose and implement a priority queue suitable for use in event driven molecular dynamics simulations. All operations on the queue take on average O(1) time per collision. In comparison, previously studied queues for event driven…
In the study of open quantum systems, one typically obtains the decoherence dynamics by solving a master equation. The master equation is derived using knowledge of some basic properties of the system, the environment and their interaction:…
Many real-world problems require sequential decisions under uncertainty: when to inject or withdraw gas from storage, how to rebalance a pension portfolio each month, what temperature profile to run through a pharmaceutical reactor chain.…
In this paper we present the event-chain algorithms, which are fast Markov-chain Monte Carlo methods for hard spheres and related systems. In a single move of these rejection-free methods, an arbitrarily long chain of particles is…
A great deal of research has been conducted in the consideration of meta-heuristic optimisation methods that are able to find global optima in settings that gradient based optimisers have traditionally struggled. Of these, so-called…