Related papers: The need to implement FAIR principles in biomolecu…
This paper is a brief update on developments in the BioDynaMo project, a new platform for computer simulations for biological research. We will discuss the new capabilities of the simulator, important new concepts simulation methodology as…
Nonadiabatic molecular dynamics simulations aim to describe the coupled electron-nuclear dynamics of molecules in excited electronic states. These simulations have been applied to understand a plethora of photochemical and photophysical…
Biobanks are indispensable resources for medical research collecting biological material and associated data and making them available for research projects and medical studies. For that, the biobank data has to meet certain criteria which…
Event-driven molecular dynamics is a valuable tool in condensed and soft matter physics when particles can be modeled as hard objects or more generally if their interaction potential can be modeled in a stepwise fashion. Hard spheres model…
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…
In many healthcare settings, it is both critical to consider fairness when building analytical applications but also uniquely unacceptable to lower model performance for one group to match that of another (e.g. fairness cannot be achieved…
Machine learning (ML) is an increasingly important scientific tool supporting decision making and knowledge generation in numerous fields. With this, it also becomes more and more important that the results of ML experiments are…
Foundational Models (FMs) are gaining increasing attention in the biomedical AI ecosystem due to their ability to represent and contextualize multimodal biomedical data. These capabilities make FMs a valuable tool for a variety of tasks,…
Machine learning force fields have emerged as promising tools for molecular dynamics (MD) simulations, potentially offering quantum-mechanical accuracy with the efficiency of classical MD. Inspired by foundational large language models,…
Along with recent progress in structural biology and genome biology, structural dynamics of molecular systems including nucleic acids has attracted attention in the context of gene regulation. Structure-function relationship is an important…
The physical processes at the interface of a low-temperature plasma and a solid are extremely complex. They involve a huge number of elementary processes in the plasma, in the solid as well as charge, momentum and energy transfer across the…
According to the FAIR (findability, accessibility, interoperability, and reusability) principles, scientific data should always be stored with machine-readable descriptive metadata. Existing solutions to store data with metadata, such as…
Integrative biological simulations have a varied and controversial history in the biological sciences. From computational models of organelles, cells, and simple organisms, to physiological models of tissues, organ systems, and ecosystems,…
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…
Materials discovery and biomedical translation increasingly require models that can reason across composition, processing, structure, biological response, manufacturability, safety, and governance constraints. Existing materials and…
This paper extends the FAIR (Findable, Accessible, Interoperable, Reusable) guidelines to provide criteria for assessing if software conforms to best practices in open source. By adding 'USE' (User-Centered, Sustainable, Equitable),…
Modern epidemiological analyses to understand and combat the spread of disease depend critically on access to, and use of, data. Rapidly evolving data, such as data streams changing during a disease outbreak, are particularly challenging.…
Scientists strive to make their datasets available in open repositories, with the goal that they be findable, accessible, interoperable, and reusable (FAIR). Although it is hard for most investigators to remember all the guiding principles…
We describe a framework for interactive molecular dynamics in a multiuser virtual reality environment, combining rigorous cloud-mounted physical atomistic simulation with commodity virtual reality hardware, which we have made accessible to…
Machine learning (ML) has emerged as a pervasive tool in science, engineering, and beyond. Its success has also led to several synergies with molecular dynamics (MD) simulations, which we use to identify and characterize the major…