Related papers: Linear-scaling calculation of experimental observa…
Molecular dynamics (MD) simulation is a widely used technique to simulate molecular systems, most commonly at the all-atom resolution where equations of motion are integrated with timesteps on the order of femtoseconds…
The application of molecular dynamics (MD) simulations to quasistatic loading is severely limited by the large separation between atomic vibration timescales and experimentally relevant deformation rates. In this work we employ the…
Molecular dynamics (MD) simulations provide detailed insight into atomic-scale mechanisms but are inherently restricted to small spatio-temporal scales. Coarse-grained molecular dynamics (CGMD) techniques allow simulations of much larger…
Simulating the time evolution of physical systems is pivotal in many scientific and engineering problems. An open challenge in simulating such systems is their multi-resolution dynamics: a small fraction of the system is extremely dynamic,…
The dynamics of complex systems often involve thermally activated barrier crossing events that allow these systems to move from one basin of attraction on the high dimensional energy surface to another. Such events are ubiquitous, but…
Molecular dynamics (MD) simulations present a data-mining challenge, given that they can generate a considerable amount of data but often rely on limited or biased human interpretation to examine their information content. By not asking the…
A variational method is used to derive a self-consistent macro-particle model for relativistic electromagnetic kinetic plasma simulations. Extending earlier work [E. G. Evstatiev and B. A. Shadwick, J. Comput. Phys., vol. 245, pp. 376-398,…
Dynamic Mode Decomposition (DMD) is a powerful data-driven method used to extract spatio-temporal coherent structures that dictate a given dynamical system. The method consists of stacking collected temporal snapshots into a matrix and…
Molecular dynamics simulates the~movements of atoms. Due to its high cost, many methods have been developed to "push the~simulation forward". One of them, metadynamics, can hasten the~molecular dynamics with the~help of variables describing…
We present a novel algorithm which can overcome the drawbacks of the conventional linear scaling method with minimal computational overhead. This is achieved by introducing additional constraints, thus eliminating the redundancy of the…
Biased sampling of collective variables is widely used to accelerate rare events in molecular simulations and to explore free energy surfaces. However, computational efficiency of these methods decreases with increasing number of collective…
We present an approach to solving problems in micromechanics that is amenable to massively parallel calculations through the use of graphical processing units and other accelerators. The problems lead to nonlinear differential equations…
Conformational dynamics is crucial for ribonucleic acid (RNA) function. Techniques such as nuclear magnetic resonance, cryo-electron microscopy, small- and wide-angle X-ray scattering, chemical probing, single-molecule F\"orster resonance…
Estimating free energy differences quantifies thermodynamic preferences in molecular interactions, which is central to chemistry and drug discovery. Despite fruitful progress, existing methods still face key limitations: classical…
Enhanced sampling algorithms have emerged as powerful methods to extend the utility of molecular dynamics simulations and allow the sampling of larger portions of the configuration space of complex systems in a given amount of simulation…
Linear solvers for large and sparse systems are a key element of scientific applications, and their efficient implementation is necessary to harness the computational power of current computers. Algebraic MultiGrid (AMG) preconditioners are…
The multi-wavelength anomalous diffraction (MAD) method is used to determine phase information in x-ray crystallography by employing dispersion corrections from heavy atoms on coherent x-ray scattering. X-ray free-electron lasers (FELs)…
Simulating the dynamics of ions near polarizable nanoparticles (NPs) using coarse-grained models is extremely challenging due to the need to solve the Poisson equation at every simulation timestep. Recently, a molecular dynamics (MD) method…
Time-evolving perforated domains arise in many engineering and geoscientific applications, including reactive transport, particle deposition, and structural degradation in porous media. Accurately capturing the macroscopic behavior of such…
Simulating large-scale articulated assemblies poses a significant challenge due to the numerical stiffness and geometric complexity of jointed structures. Conventional rigid body solvers struggle with the high nonlinearity induced by…