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This report synthesizes findings from the November 2024 Community Workshop on Practical Reproducibility in HPC, which convened researchers, artifact authors, reviewers, and chairs of reproducibility initiatives to address the critical…
Designing enzymes with substrate-binding pockets is a critical challenge in protein engineering, as catalytic activity depends on the precise interaction between pockets and substrates. Currently, generative models dominate functional…
To facilitate rational molecular and materials design, this research proposes an integrated computational framework that combines stochastic simulation, ab initio quantum chemistry, and molecular docking. The suggested workflow allows…
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.…
The properties and fundamental limits of chemical computers have recently attracted significant interest as a model of computation, an unifying principle of cellular organisation and in the context of bio-engineering. As of yet, research in…
Information and communication technologies account for a growing portion of global environmental impacts. While emerging technologies, such as emerging non-volatile memories (eNVM), offer a promising solution to energy efficient computing,…
Optimization problems associated with the interaction of linked particles are at the heart of polymer science, protein folding and other important problems in the physical sciences. In this review we explain how to recast these problems as…
The optimal design of compounds through manipulating properties at the molecular level is often the key to considerable scientific advances and improved process systems performance. This paper highlights key trends, challenges, and…
Climate change is profoundly affecting nearly all aspects of life on earth, including human societies, economies and health. Various human activities are responsible for significant greenhouse gas emissions, including data centres and other…
All-atom molecular dynamics has been recently proven a useful tool for the study of supramolecular polymers. While the high resolution offered by the atomistic models may allow for deep comprehension of the assembled structure, obtaining a…
The evolution of molecular dynamics (MD) simulations has been intimately linked to that of computing hardware. For decades following the creation of MD, simulations have improved with computing power along the three principal dimensions of…
Enzyme mining is rapidly evolving as a data-driven strategy to identify biocatalysts with tailored functions from the vast landscape of uncharacterized proteins. The integration of machine learning into these workflows enables…
On August 9-10, 2023, a workshop was convened at the Pacific Northwest National Laboratory (PNNL) in Richland, WA that brought together a group of internationally recognized experts in metabolomics, natural products discovery, chemical…
Model merging aims to integrate multiple task-specific fine-tuned models derived from a shared pre-trained checkpoint into a single multi-task model without additional training. Despite extensive research, task interference remains a major…
Quantum computers have the potential to advance material design and drug discovery by performing costly electronic structure calculations. A critical aspect of this application requires optimizing the limited resources of the quantum…
Quantitative methods and mathematical modeling are playing an increasingly important role across disciplines. As a result, interdisciplinary mathematics courses are increasing in popularity. However, teaching such courses at an advanced…
Computational methods are the most effective tools we have besides scientific experiments to explore the properties of complex biological systems. Progress is slowing because digital silicon computers have reached their limits in terms of…
Approximate computing is a computation domain which can be used to trade time and energy with quality and therefore is useful in embedded systems. Energy is the prime resource in battery-driven embedded systems, like robots. Approximate…
We report an experimental evaluation of the "input-output surface" for a biochemical AND gate. The obtained data are modeled within the rate-equation approach, with the aim to map out the gate function and cast it in the language of logic…
The shift from a linear to a circular economy has the potential to simultaneously reduce uncertainties of material supplies and waste generation. However, to date, the development of robotic and, more generally, autonomous systems have been…