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The transport and manipulation of particles and cells in microfluidic devices has become a core methodology in domains ranging from molecular biology to manufacturing and drug design. The rational design and operation of such devices can…
Routine applications of electronic structure theory to molecules and periodic systems need to compute the electron density from given Hamiltonian and, in case of non-orthogonal basis sets, overlap matrices. System sizes can range from few…
We have developed an open-source software package (SedSimple) for stratigraphic forward modeling. It is aimed for use in research and education. The package uses ASCII files for input and output to facilitate understanding, debugging and…
MADNESS (multiresolution adaptive numerical environment for scientific simulation) is a high-level software environment for solving integral and differential equations in many dimensions that uses adaptive and fast harmonic analysis methods…
A reliable and user-friendly characterisation of nano-objects in a target material is presented here in the form of a software data analysis package for interpreting small-angle X-ray scattering (SAXS) patterns. When provided with data on…
We develop a multiscale hybrid scheme for simulations of soft condensed matter systems, which allows one to treat the system at the particle level in selected regions of space, and at the continuum level elsewhere. It is derived…
Deep learning methods have gained popularity in high energy physics for fast modeling of particle showers in detectors. Detailed simulation frameworks such as the gold standard Geant4 are computationally intensive, and current deep…
The physical processes at the interface of a low-temperature plasma and a solid are extremely complex. They involve a huge number of elementary processes in the plasma, in the solid as well as charge, momentum and energy transfer across the…
The MeMC is an open-source software package for monte-carlo simulation of elastic shells. It is designed as a tool to interpret the force-distance data generated by indentation of biological nano-vesicles by atomic force microscopes. The…
Microscopy, in particular scanning probe and electron microscopy, has been pivotal in improving our understanding of structure-function relationships at the nanoscale and is by now ubiquitous in most research characterization labs and…
Context. The Spectroscopy Made Easy (SME) package has become a popular tool for analyzing stellar spectra, often in connection with large surveys or exoplanet research. SME has evolved significantly since it was first described in 1996, but…
Computer simulation has become one of the most important tools in scientific research in many disciplines. Benefiting from the dynamical trajectories regulated by versatile interatomic interactions, various material properties can be…
Coarse-grained modeling and efficient computer simulations are critical to the study of complex molecular processes with many degrees of freedom and multiple spatiotemporal scales. Variational implicit-solvent model (VISM) for biomolecular…
Accurate and efficient simulation tools are essential in robotics, enabling the visualization of system dynamics and the validation of control laws before committing resources to physical experimentation. Developing physically accurate…
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 Probe-Particle Model combine theories designed for the simulation of scanning probe microscopy experiments, employing non-reactive, flexible tip apices to achieve sub-molecular resolution. In the article we present the latest version of…
Recent advances in deep learning have inspired numerous works on data-driven solutions to partial differential equation (PDE) problems. These neural PDE solvers can often be much faster than their numerical counterparts; however, each…
Empirical potential structure refinement (EPSR) is a neutron scattering data analysis algorithm and a software package. It was developed by the British spallation neutron source (ISIS) Disordered Materials Group in 1980s, and aims to…
Polarized Resonant Soft X-ray scattering (P-RSoXS) has emerged as a powerful synchrotron-based tool that combines principles of X-ray scattering and X-ray spectroscopy. P-RSoXS provides unique sensitivity to molecular orientation and…
Modern systems are increasingly connected and more integrated with other existing systems, giving rise to \textit{systems-of-systems} (SoS). An SoS consists of a set of independent, heterogeneous systems that interact to provide new…