Related papers: Complex step-size dependences in tracking a simple…
Many recently introduced enhanced sampling techniques are based on biasing coarse descriptors (collective variables) of a molecular system on the fly. Sometimes the calculation of such collective variables is expensive and becomes a…
Computer simulations have become an important tool across the biomedical sciences and beyond. For many important problems several different models or hypotheses exist and choosing which one best describes reality or observed data is not…
Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is…
Single-molecule tracking is a powerful way to look at the dynamic organization of plasma membranes. However, there are some limitations to its use. For example, it was recently observed, using numerical simulation, that time-averaging…
The modern study of the dynamics of stellar systems requires the use of high-performance computers. Indeed, an accurate modelization of the structure and evolution of self-gravitating systems like planetary systems, open clusters, globular…
We show that the exact exchange-correlation potential of time-dependent density-functional theory displays dynamical step structures that have a spatially non-local and time non-local dependence on the density. Using one-dimensional…
Contemporary statistical publications rely on simulation to evaluate performance of new methods and compare them with established methods. In the context of meta-analysis of log-odds-ratios, we investigate how the ways in which simulations…
Discrete simulation methods are efficient tools to investigate the complex behaviors of complex fluids made of either dry granular materials or dilute suspensions. By contrast, materials made of soft and/or concentrated units (emulsions,…
The dynamics of biological systems, from proteins to cells to organisms, is complex and stochastic. To decipher their physical laws, we need to bridge between experimental observations and theoretical modeling. Thanks to progress in…
The simulation of quantum systems has been a key aim of quantum technologies for decades, and the generalisation to open systems is necessary to include physically realistic systems. We introduce an approach for quantum simulations of open…
Inspired by the need for effective stochastic models to describe the complex behavior of biological motor proteins that move on linear tracks exact results are derived for the velocity and dispersion of simple linear sequential models (or…
Dual-unitary circuits have emerged as a minimal model for chaotic quantum many-body dynamics in which the dynamics of correlations and entanglement remains tractable. Simultaneously, there has been intense interest in the effect of…
Coarse-graining of fully atomistic molecular dynamics simulations is a long-standing goal in order to allow the description of processes occurring on biologically relevant timescales. For example, the prediction of pathways, rates and…
With the advent of digital and analog quantum simulation experiments, it is now possible to experimentally simulate dynamics of quantum many-body lattice systems and make site-resolved measurements. These experiments make it pertinent to…
We propose a computational method to quantitatively evaluate the systematic uncertainties that arise from undetectable sources in biological measurements using live-cell imaging techniques. We then demonstrate this method in measuring…
System identification aims to build models of dynamical systems from data. Traditionally, choosing the model requires the designer to balance between two goals of conflicting nature; the model must be rich enough to capture the system…
The exact study of small systems can guide us toward measures for extracting information about many-body physics as we move to more complex systems capable of quantum information processing or quantum analog simulation. We use exact…
Molecular dynamics computer simulations are used to investigate thedynamics of a binary mixture of charged (Yukawa) particles with a size-ratio of 1:5. We find that the system undergoes a phase transition where the large particles…
Studying systems where many individual bodies in motion interact with one another is a complex and interesting area. Simple mechanisms that may be determined for biological, chemical, or physical reasons can lead to astonishingly complex…
Stochastic quantization offers the opportunity to simulate field theories with a complex action. In some theories unstable trajectories are prevalent when a constant stepsize is employed. We construct algorithms for generating an adaptive…