Related papers: AMDAT: An Open-Source Molecular Dynamics Analysis …
We propose the first multi agent framework for computational fluid dynamics that enables fully automated, end to end simulations directly from natural language queries. The approach integrates four specialized agents Pre processing, Prompt…
We describe an open-source toolkit for neural machine translation (NMT). The toolkit prioritizes efficiency, modularity, and extensibility with the goal of supporting NMT research into model architectures, feature representations, and…
Atomic probe tomography (APT), based on the work of Erwin Mueller, is able to generate three-dimensional chemical maps in atomic resolution. The required instruments for APT have evolved over the last 20 years from an experimental to an…
Warm dense matter systems created in the laboratory are highly dynamical. In such cases electron dynamics is often needed to accurately simulate the evolution and properties of the system. Large systems force one to make simple…
Merging natural language interfaces with computational fluid dynamics (CFD) workflows presents transformative opportunities for both industry and research. In this study, we introduce OptMetaOpenFOAM - a novel framework that bridges…
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.…
Molecule-and-text cross-modal representation learning has emerged as a promising direction for enhancing the quality of molecular representation, thereby improving performance in various scientific fields. However, most approaches employ a…
Machine-learned interatomic potentials have revolutionized molecular dynamics simulations by providing quantum-mechanical accuracy at empirical-potential speeds. The graphics processing unit molecular dynamics (GPUMD) package, featuring the…
Molecular dynamics (MD) is a powerful and popular tool for understanding the dynamical evolution of materials at the nano and mesoscopic scales. There are various flavors of MD ranging from the high fidelity albeit computationally expensive…
LAMMPS is a widely popular classical Molecular Dynamics package. It was designed for materials modeling but it is well prepared for simulations in Soft Matter. The use packages like LAMMPS has advantages and disadvantages. The main…
Atomistic simulations have become a powerful tool in materials research due to the extremely fine spatial and temporal resolution provided by such techniques. In order to understand the fundamental principles which govern material behavior…
Simulation of non-adiabatic dynamics of a quantum system coupled to dissipative environments poses significant challenges. New sophisticated methods are regularly being developed with an eye towards moving to larger systems and more…
Atomic and molecular data for the transitions of a number of astrophysically interesting species are summarized, including energy levels, statistical weights, Einstein A-coefficients and collisional rate coefficients. Available collisional…
Traditional VMAT optimization often ignores dynamic machine limits, treating delivery time as an emergent property rather than a steerable parameter. This work introduces Dynamic Modulated Arc Therapy (DMAT), an intent-driven framework that…
Crystal Toolkit is an open source tool for viewing, analyzing and transforming crystal structures, molecules and other common forms of materials science data in an interactive way. It is intended to help beginners rapidly develop web-based…
We present sMolBoxes, a dataflow representation for the exploration and analysis of long molecular dynamics (MD) simulations. When MD simulations reach millions of snapshots, a frame-by-frame observation is not feasible anymore. Thus,…
Recent works in dataset distillation seek to minimize training expenses by generating a condensed synthetic dataset that encapsulates the information present in a larger real dataset. These approaches ultimately aim to attain test accuracy…
We present AMADA, an interactive web application to analyse multidimensional datasets. The user uploads a simple ASCII file and AMADA performs a number of exploratory analysis together with contemporary visualizations diagnostics. The…
Recent progress of deep generative models in the vision and language domain has stimulated significant interest in more structured data generation such as molecules. However, beyond generating new random molecules, efficient exploration and…
Molecular dynamics simulations have a prominent role in biophysics and drug discovery due to the atomistic information they provide on the structure, energetics and dynamics of biomolecules. Specialized software packages are required to…