Related papers: A Set of Tutorials for the LAMMPS Simulation Packa…
Machine learning interatomic potentials (MLIPs) enable atomistic simulations with near ab initio accuracy at significantly reduced computational cost, but their broader adoption is often limited by fragmented tooling, limited scalability,…
Background and Objective: Computational ultrasound imaging has become a well-established methodology in the ultrasound community. Simulations of ultrasound sequences and images allow the study of innovative techniques in terms of emission…
This paper introduces a random-batch molecular dynamics (RBMD) package for fast simulations of particle systems at the nano/micro scale. Different from existing packages, the RBMD uses random batch methods for nonbonded interactions of…
Machine-learned interatomic potentials (MLIPs) promise to significantly advance atomistic simulations by delivering quantum-level accuracy for large molecular systems at a fraction of the computational cost of traditional electronic…
relentless is an open-source Python package that enables the optimization of objective functions computed using molecular dynamics simulations. It has a high-level, extensible interface for model parametrization; setting up, running, and…
We present TTCF4LAMMPS, a toolkit for performing non-equilibrium molecular dynamics (NEMD) simulations to study fluid behaviour at low shear rates using the LAMMPS software. By combining direct NEMD simulations and the transient-time…
Large Language Models (LLMs) have revolutionized human-AI interaction by enabling intuitive task execution through natural language prompts. Despite their potential, designing effective prompts remains a significant challenge, as small…
Particle-Mesh (PM) codes are still very useful tools for testing predictions of cosmological models in cases when extra high resolution is not very important. We release for public use a cosmological PM N-body code. We provide a complete…
Despite their ability to understand chemical knowledge, large language models (LLMs) remain limited in their capacity to propose novel molecules with desired functions (e.g., drug-like properties). In addition, the molecules that LLMs…
PLUMED-GUI is an interactive environment to develop and test complex PLUMED scripts within the Visual Molecular Dynamics (VMD) environment. Computational biophysicists can take advantage of both PLUMED's rich syntax to define collective…
Molecular dynamics simulations are an essential tool in understanding protein structure, dynamics, and function at the atomic level. However, preparing high quality input files for MD simulations can be a time consuming and error prone…
Only a small fraction of the data generated in state-of-the-art all-atom multi-microsecond molecular dynamics (MD) simulations is typically analyzed. With femtosecond integration steps, microsecond simulations generate billions of time…
CHEMSMART (Chemistry Simulation and Modeling Automation Toolkit) is an open-source, Python-based framework designed to streamline quantum chemistry workflows for homogeneous catalysis and molecular modeling. By integrating job preparation,…
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,…
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…
Atomistic simulations are essential tools in chemistry and materials science, accelerating the discovery of novel catalysts, energy storage materials, and pharmaceuticals. However, running these simulations remains challenging due to the…
Pre-trained on extensive text and image corpora, current Multi-Modal Large Language Models (MLLM) have shown strong capabilities in general visual reasoning tasks. However, their performance is still lacking in physical domains that require…
Molecular dynamics (MD) simulations allow atomistic insights into chemical and biological processes. Accurate MD simulations require computationally demanding quantum-mechanical calculations, being practically limited to short timescales…
Multi-scale computer simulations combine the computationally efficient classical algorithms with more expensive but also more accurate ab-initio quantum mechanical algorithms. This work describes one implementation of multi-scale…
Quantum simulation is a leading candidate for demonstrating practical quantum advantage over classical computation, as it is believed to provide exponentially more compute power than any classical system. It offers new means of studying the…