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Classical molecular dynamics simulations of hydrogen plasmas have been performed with emphasis on the analysis of equilibration process. Theoretical basis of simulation model as well as numerically relevant aspects -- such as the proper…
A QM/MM implementation for periodic systems is reported. This is done for the case of molecules and for systems with two and three-dimensional periodicity, which is suitable to model electrolytes in contact with electrodes. Tests on…
A roughly constant temperature over a wide range of densities is maintained in molecular clouds through radiative heating and cooling. An isothermal equation of state is therefore frequently employed in molecular cloud simulations. However,…
The diffuse medium in and around galaxies can exist in a multi-phase state: small, cold gas clouds contributing significantly to the total mass embedded in pressure equilibrium with a hotter, more diffuse volume-filling component. Modeling…
Scientific computing applications have benefited greatly from high performance computing infrastructure such as supercomputers. However, we are seeing a paradigm shift in the computational structure, design, and requirements of these…
Droplets form a cornerstone of the spatiotemporal organization of biomolecules in cells. These droplets are controlled using physical processes like chemical reactions and imposed gradients, which are costly to simulate using traditional…
Interactions between quantum particles, such as electrons, are the source of important effects, ranging from superconductivity, to the formation of molecular bonds, or the stability of elementary compounds at high-energies. In this article,…
Numerical simulation of fluids plays an essential role in modeling many physical phenomena, such as weather, climate, aerodynamics and plasma physics. Fluids are well described by the Navier-Stokes equations, but solving these equations at…
Long ranged electrostatic interactions are time consuming to calculate in molecular dynamics and Monte-Carlo simulations. We introduce an algorithmic framework for simulating charged particles which modifies the dynamics so as to allow…
Virtually all aspects of many-body atomic physics are challenging: experiments are technically demanding, datasets have become enormous, and the memory and CPU requirements for classical simulation of generic quantum systems often scale…
High resolution molecular dynamics simulations with full Coulomb interactions of electrons are used to investigate field emission in planar nanodiodes. The effects of space charge and emitter radius are examined and compared to previous…
Monoclonal antibodies are among the most promising therapeutic agents in modern medicine, yet their formulation into high-concentration solutions for subcutaneous self-administration poses a major challenge. A key obstacle is the marked…
Hydrodynamic simulations have become irreplaceable in modern cosmology for exploring complex systems and making predictions to steer future observations. In Chapter 1, we begin with a philosophical discussion on the role of simulations in…
Machine learning techniques are essential tools to compute efficient, yet accurate, force fields for atomistic simulations. This approach has recently been extended to incorporate quantum computational methods, making use of variational…
We use molecular dynamics simulations to study the evaporation of particle-laden droplets on a heated surface. The droplets are composed of a Lennard-Jones fluid containing rigid particles which are spherical sections of an atomic lattice,…
Many aspects of the study of protein folding and dynamics have been affected by the recent advances in machine learning. Methods for the prediction of protein structures from their sequences are now heavily based on machine learning tools.…
Constant potential method molecular dynamics simulation (CPM MD) enables the accurate modelling of atomistic electrode charges when studying the electrode-electrolyte interface at the nanoscale. Here we extend the theoretical framework of…
The ever increasing demands placed upon machine performance have resulted in the need for more comprehensive particle accelerator modeling. Computer simulations are key to the success of particle accelerators. Many aspects of particle…
Oxide-water interfaces govern a wide range of physical and chemical processes fundamental to many fields like catalysis, geochemistry, corrosion, electrochemistry, and sensor technology. Near solid oxide surfaces, water behaves differently…
Energy functions for pure and heterogenous systems are one of the backbones for molecular simulation of condensed phase systems. With the advent of machine learned potential energy surfaces (ML-PESs) a new era has started. Statistical…