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Accurate interatomic potentials (IAPs) are essential for modeling the potential energy surfaces (PES) that govern atomic interactions in materials. However, most existing IAPs are developed for bulk materials and often struggle to…
The molecular simulations solve the equation of motion of molecular systems, making 3D shapes of molecules four-dimensional by adding the time coordinate. These methods have a great potential in drug discovery because they can realistically…
System dynamics (SD) is an effective approach for helping reveal the temporal behavior of complex systems. Although there have been recent developments in expanding SD to include systems' spatial dependencies, most applications have been…
Dynamic programming (DP) is a fundamental and powerful algorithmic paradigm taught in most undergraduate (and many graduate) algorithms classes. DP problems are challenging for many computer science students because they require identifying…
Material processing with femtosecond lasers has attracted enormous attention because of its potential for technology and industrial applications. In parallel, time-resolved x-ray diffraction has been successfully used to study ultrafast…
We derive and validate a partition function for low-dimensional systems interacting with a heat bath, addressing the general issue of thermodynamic modeling of nanoscale systems. In contrast to bulk systems in the canonical (NVT) ensemble…
Dissipative particle dynamics (DPD) is a novel particle method for mesoscale modeling of complex fluids. DPD particles are often thought to represent packets of real atoms, and the physical scale probed in DPD models are determined by the…
Controlling the interaction graph between spins or qubits in a quantum simulator allows user-controlled tailoring of native interactions to achieve a target Hamiltonian. The flexibility of engineering long-ranged phonon-mediated spin-spin…
This article presents a comparison of various implementations of the Lattice Discrete Particle Model (LDPM) for the numerical simulation of concrete and other heterogeneous quasibrittle materials. The comparison involves the use of…
Matter at extreme temperatures and pressures -- commonly known as warm dense matter (WDM) in the literature -- is ubiquitous throughout our Universe and occurs in a number of astrophysical objects such as giant planet interiors and brown…
Sintering, as a thermal process at elevated temperature below the melting point, is widely used to bond contacting particles into engineering products such as ceramics, metals, polymers, and cemented carbides. Modelling and simulation as…
At present, many laboratories are performing experiments to simulate theoretical models of strongly correlated systems using cold atoms in optical lattices, a program referred to as "Quantum Simulation". It is hoped that these experiments…
The discovery and study of new material systems rely on molecular simulations that often come with significant computational expense. We propose MDDM, a Molecular Dynamics Diffusion Model, which is capable of predicting a valid output…
We present OpenMM-Python-Force, a plugin designed to extend OpenMM's functionality by enabling integration of energy and force calculations from external Python programs via a callback mechanism. During molecular dynamics simulations, data…
PolyMAPS is an open-source library that helps researchers to initialize LAMMPS molecular dynamics simulations. It introduces an integrated workflow by combining preparation, launching, visualization, and analysis into a single Jupyter…
In context of highly complex energy system experiments, sensitivity analysis is gaining more and more importance to investigate the effects changing parameterization has on the outcome. Thus, it is crucial how to design an experiment to…
In nuclear engineering studies, uncertainty and sensitivity analyses of simulation computer codes can be faced to the complexity of the input and/or the output variables. If these variables represent a transient or a spatial phenomenon, the…
DynamicGEM is an open-source Python library for learning node representations of dynamic graphs. It consists of state-of-the-art algorithms for defining embeddings of nodes whose connections evolve over time. The library also contains the…
PyDDC is a particle tracking reservoir simulator capable of solving non-linear density driven convection of single phase carbon-dioxide ($\mathrm{CO_2}$)--brine fluid mixture in saturated porous media at the continuum scale. In contrast to…
Understanding many processes, e.g. fusion experiments, planetary interiors and dwarf stars, depends strongly on microscopic physics modeling of warm dense matter (WDM) and hot dense plasma. This complex state of matter consists of a…