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Condense phase molecular systems organize in wide range of distinct molecular configurations, including amorphous melt and glass as well as crystals often exhibiting polymorphism, that originate from their intricate intra- and…
Computational fluid dynamics (CFD) simulations are broadly applied in engineering and physics. A standard description of fluid dynamics requires solving the Navier-Stokes (N-S) equations in different flow regimes. However, applications of…
We describe a project-based introduction to reproducible and collaborative neuroimaging analysis. Traditional teaching on neuroimaging usually consists of a series of lectures that emphasize the big picture rather than the foundations on…
Molecular dynamics simulations provide a mechanistic description of molecules by relying on empirical potentials. The quality and transferability of such potentials can be improved leveraging data-driven models derived with machine learning…
Studies Beyond the Standard Model (BSM) will become more and more important in the near future with a rapidly increasing amount of data from different experiments around the world. The full study of BSM models is in general an extremely…
Decades of hardware, methodological, and algorithmic development have propelled molecular dynamics (MD) simulations to the forefront of materials-modeling techniques, bridging the gap between electronic-structure theory and continuum…
Non-adiabatic molecular dynamics (NAMD) simulations have become an indispensable tool for investigating excited-state dynamics in solids. In this work, we propose a general framework, N$^2$AMD which employs an E(3)-equivariant deep neural…
The development of reliable and extensible molecular mechanics (MM) force fields -- fast, empirical models characterizing the potential energy surface of molecular systems -- is indispensable for biomolecular simulation and computer-aided…
A computational method for magnetically guided drug delivery is presented and the results are compared for the aggregation process of magnetic particles within a fluid environment. The model is developed for the simulation of the…
The partitioning of small molecules in cell membranes---a key parameter for pharmaceutical applications---typically relies on experimentally-available bulk partitioning coefficients. Computer simulations provide a structural resolution of…
We propose a multiscale computational method for thin-layer flows of complex fluids, termed the synchronized molecular dynamics (SMD) method, which directly couples local molecular dynamics (MD) simulations with a macroscopic lubrication…
Exascale computing holds great opportunities for molecular dynamics (MD) simulations. However, to take full advantage of the new possibilities, we must learn how to focus computational power on the discovery of complex molecular mechanisms,…
Molecular simulations can provide microscopic insight into the physical and chemical driving forces of complex molecular processes. Despite continued advancement of simulation methodology, model errors may lead to inconsistencies between…
Most approaches in Lagrangian fluid dynamics simulations proceed from the definition of particle volumes, from which discrete versions of the spatial differential operators are derived. Recently, Gallou\"et and M\'erigot [1] simultaneously…
Machine learning techniques not only offer efficient tools for modelling dynamical systems from data, but can also be employed as frontline investigative instruments for the underlying physics. Nontrivial information about the original…
Classical Computational Fluid Dynamics (CFD) of long-time processes with strongly separated time scales is computationally extremely demanding if not impossible. Consequently, the state-of-the-art description of such systems is not capable…
Accelerated molecular dynamics (MD) simulations are implemented to model the sliding process of AFM experiments at speeds close to those found in experiment. In this study the hyperdynamics method, originally devised to extend MD time…
In this paper we investigate the approximation properties of the coarse-graining procedure applied to kinetic Monte Carlo simulations of lattice stochastic dynamics. We provide both analytical and numerical evidence that the hierarchy of…
Molecular simulations in an open environment, involving ion exchange, are necessary to study various systems, from biosystems to confined electrolytes. However, grand-canonical simulations are often computationally demanding in condensed…
Monte Carlo statistical ray-tracing methods are commonly employed to simulate carrier transport in nanostructured materials. In the case of a large degree of nanostructuring and under linear response (small driving fields), these…