Related papers: Development of simulation package for atomic proce…
Mathematical models implemented on a computer have become the driving force behind the acceleration of the cycle of scientific processes. This is because computer models are typically much faster and economical to run than physical…
The nuclear shell model is one of the prime many-body methods to study the structure of atomic nuclei, but it is hampered by an exponential scaling on the basis size as the number of particles increases. We present a shell-model quantum…
The availability of open-source molecular simulation software packages allows scientists and engineers to focus on running and analyzing simulations without having to write, parallelize, and validate their own simulation software. While…
We present a formalism for coupling a density functional theory-based quantum simulation to a classical simulation for the treatment of simple metallic systems. The formalism is applicable to multiscale simulations in which the part of the…
This paper presents the simulation of the GLAST high energy gamma-ray telescope. The simulation package, written in C++, is based on the Geant4 toolkit, and it is integrated into a general framework used to process events. A detailed…
The Simulation Environment for Atomistic and Molecular Modeling (SEAMM) is an open-source software package written in Python that provides a graphical interface for setting up, executing, and analyzing molecular and materials simulations.…
Macroscopic theories of nucleation such as classical nucleation theory envision that clusters of the bulk stable phase form inside the bulk metastable phase. Molecular dynamics simulations are often used to elucidate nucleation mechanisms,…
Linear scaling methods, or O(N) methods, have computational and memory requirements which scale linearly with the number of atoms in the system, N, in contrast to standard approaches which scale with the cube of the number of atoms. These…
Computer models are widely used to study complex real world physical systems. However, there are major limitations to their direct use including: their complex structure; large numbers of inputs and outputs; and long evaluation times.…
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…
Molecular simulation is a scientific tool dealing with challenges in material science and biology. This is reflected in a permanent development and enhancement of algorithms within scientific simulation packages. Here, we present…
An effective method for the quantitative description of the electronic excited states of polyatomic systems is developed by using computer technology. The proposed method allows calculating various properties of matter at the atomic level…
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,…
The dynamic emulation of non-linear deterministic computer codes where the output is a time series, possibly multivariate, is examined. Such computer models simulate the evolution of some real-world phenomenon over time, for example models…
With the rise of service-oriented computing, applications are more and more based on coordination of autonomous services. Envisioned over largely distributed and highly dynamic platforms, expressing this coordination calls for alternative…
The integration of large language models (LLMs) into materials science offers a transformative opportunity to streamline computational workflows, yet current agentic systems remain constrained by rigid, carefully crafted domain-specific…
This paper introduces QuanUML, an extension of the Unified Modeling Language (UML) tailored for quantum software systems. QuanUML integrates quantum-specific constructs, such as qubits and quantum gates, into the UML framework, enabling the…
Electronic structure calculations have been instrumental in providing many important insights into a range of physical and chemical properties of various molecular and solid-state systems. Their importance to various fields, including…
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a…
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…