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Simulation of atomic resolution image formation in scanning transmission electron microscopy can require significant computation times using traditional methods. A recently developed method, termed plane-wave reciprocal-space interpolated…
We describe two means by which XSTAR, a code which computes physical conditions and emission spectra of photoionized gases, has been parallelized. The first is pvm_xstar, a wrapper which can be used in place of the serial xstar2xspec script…
Proteinoids are solidified gels made from poly(amino acids) based polymers that exhibit oscillatory electrical activity. It has been proposed that proteinoids are capable of performing analog computing as their electrical activity can be…
Spectroscopy is a central pillar of materials characterization, providing useful information on properties like structure, composition, or excited state dynamics of a system. However, many spectroscopic techniques present challenges in…
Machine learning (ML) is increasingly becoming a common tool in computational chemistry. At the same time, the rapid development of ML methods requires a flexible software framework for designing custom workflows. MLatom 3 is a program…
We develop a Python-based open-source package to analyze the results stemming from ab initio molecular-dynamics simulations of fluids. The package is best suited for applications on natural systems, like silicate and oxide melts,…
PACKMOL is a widely utilized molecular modeling tool within the computational chemistry community. However, its perceivable advantages have been impeded by the long-standing lack of a robust open-source graphical user interface (GUI) that…
Structure determination by chemical-shift-driven NMR crystallography relies on comparing chemical shieldings measured in solid-state NMR experiments with simulations. However, computational cost limits the accuracy of shielding predictions,…
Large language models (LLMs) are increasingly recognized as powerful tools for scientific discovery, particularly in molecular science. A fundamental requirement for these models is the ability to accurately understand molecular structures,…
We present MXtalTools, a flexible Python package for the data-driven modelling of molecular crystals, facilitating machine learning studies of the molecular solid state. MXtalTools comprises several classes of utilities: (1) synthesis,…
Identifying which design patterns already exist in source code can help maintenance engineers gain a better understanding of the source code and determine if new requirements can be satisfied. There are current techniques for mining design…
We have developed and demonstrated a scheme to achieve rotationally-closed photon cycling in polyatomic molecules with complex hyperfine structure and sensitivity to hadronic symmetry violation, specifically $^{171}$YbOH and $^{173}$YbOH.…
We present the python package DiPolMol-Py, which can be used to calculate the rotational and hyperfine structure of $^2\Sigma$ molecules. The calculations can be performed in the presence of dc magnetic fields, dc electric fields and far…
Merlin++ is a C++ charged-particle tracking library developed for the simulation and analysis of complex beam dynamics within high energy particle accelerators. Accurate simulation and analysis of particle dynamics is an essential part of…
A procedure is described for storing a 2D pattern consisting of 32x32 = 1024 bits in a spin state of a molecular system and then retrieving the stored information as a stack of NMR spectra. The system used is a nematic liquid crystal, the…
High precision atomic data is indispensable for experiments involving studies of fundamental interactions, astrophysics, atomic clocks, plasma science, and others. We develop new parallel atomic structure codes and explore the difficulties…
We formulate a computationally efficient time-independent method based on the multi-electron molecular R-matrix formalism. This method is used to calculate transition matrix elements for the multi-photon ionization of atoms and molecules…
We develop a model for predicting fine- and hyperfine intensities in the direct photoionization of molecules based on the separability of electron and nuclear spin states from vibrational-electronic states. Using spherical tensor algebra,…
Most modern optical display and sensing devices utilize a limited number of spectral units within the visible range, based on human color perception. In contrast, the rapid advancement of machine-based pattern recognition and spectral…
An algorithm and numerical code for the up-sampling of a system of particles, from a smaller to a larger number, is described. The method introduces a Poissonian `shot-noise' to the up-sampled distribution, typical of the noise statistics…