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Designing molecules with specific properties is a long-lasting research problem and is central to advancing crucial domains such as drug discovery and material science. Recent advances in deep graph generative models treat molecule design…
Chemical modelling serves two purposes in dynamical models: accounting for the effect of microphysics on the dynamics and providing observable signatures. Ideally, the former must be done as part of the hydrodynamic simulation but this…
Molecular editing aims to modify a given molecule to optimize desired chemical properties while preserving structural similarity. However, current approaches typically rely on string-based or continuous representations, which fail to…
Molecular dynamics simulations, an indispensable research tool in computational chemistry and materials science, consume a significant portion of the supercomputing cycles around the world. We focus on multi-body potentials and aim at…
The mechanisms of physical and chemical interactions of low temperature plasmas with surfaces can be fruitfully explored using molecular dynamics (MD) simulations. MD simulations follow the detailed motion of sets of interacting atoms…
The application of machine learning (ML) techniques, especially neural networks, has seen tremendous success at processing images and language. This is because we often lack formal models to understand visual and audio input, so here neural…
Multimodal large language models (MLLMs) have made impressive progress in many applications in recent years. However, chemical MLLMs that can handle cross-modal understanding and generation remain underexplored. To fill this gap, we propose…
We report the development of a user-friendly nano-visualization software program which can acquaint high-school students with nanotechnology. The visual introduction to atoms and molecules, which are the building blocks of this technology,…
Scientific computing applications have benefited greatly from high performance computing infrastructure such as supercomputers. However, we are seeing a paradigm shift in the computational structure, design, and requirements of these…
We introduce MolMiner, a fragment-based, geometry-aware, and order-agnostic autoregressive model for molecular design. MolMiner supports conditional generation of molecules over twelve properties, enabling flexible control across…
Generating precise 3D molecular geometries is crucial for drug discovery and material science. While prior efforts leverage 1D representations like SELFIES to ensure molecular validity, they fail to fully exploit the rich chemical knowledge…
An important aspect of astrophysical MHD turbulence research is developing diagnostics to connect simulations with the observable universe. Turbulent systems are by definition structurally complex in all fluid variables (density, velocity,…
Drug discovery aims at designing novel molecules with specific desired properties for clinical trials. Over past decades, drug discovery and development have been a costly and time consuming process. Driven by big chemical data and AI, deep…
Molecular dynamics (MD) simulations are essential tools in computational chemistry and drug discovery, offering crucial insights into dynamic molecular behavior. However, their utility is significantly limited by substantial computational…
This paper presents the development of a real-time simulator for the validation of controlling a large vehicle manipulator. The need for this development can be justified by the lack of such a simulator: There are neither open source…
Visualizations play a critical role in validating and improving statistical models. However, the design space of model check visualizations is not well understood, making it difficult for authors to explore and specify effective graphical…
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…
In the field of chemical structure recognition, the task of converting molecular images into machine-readable data formats such as SMILES string stands as a significant challenge, primarily due to the varied drawing styles and conventions…
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD)…
Virtual observatories allow the means by which an astronomer is able to discover, access, and process data seamlessly, regardless of its physical location. However, steep learning curves are often required to become proficient in the…