Related papers: H5MD: a structured, efficient, and portable file f…
More and more massive parallel codes running on several hundreds of thousands of cores enter the computational science and engineering domain, allowing high-fidelity computations on up to trillions of unknowns for very detailed analyses of…
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…
The FITS (Flexible Image Transport System) data format has been the de facto data format for astronomy-related data products since its inception in the late 1970s. While the FITS file format is widely supported, it lacks many of the…
Scientific datasets are known for their challenging storage demands and the associated processing pipelines that transform their information. Some of those processing tasks include filtering, cleansing, aggregation, normalization, and data…
The field of structural bioinformatics has seen significant advances with the use of Molecular Dynamics (MD) simulations of biological systems. The MD methodology has allowed to explain and discover molecular mechanisms in a wide range of…
In High Energy Physics (HEP), experimentalists generate large volumes of data that, when analyzed, helps us better understand the fundamental particles and their interactions. This data is often captured in many files of small size,…
Nowadays simulations can produce petabytes of data to be stored in parallel filesystems or large-scale databases. This data is accessed over the course of decades often by thousands of analysts and scientists. However, storing these volumes…
Scientific data is often stored in files because of the simplicity they provide in managing, transferring, and sharing data. These files are typically structured in a specific arrangement and contain metadata to understand the structure the…
In this work, a new algorithm based on the application of higher-order dynamic mode decomposition (HODMD) is proposed for feature selection and variables clustering in reacting flow simulations. The hierarchical HODMD (h-HODMD) performs a…
Molecular dynamics (MD) simulations present a data-mining challenge, given that they can generate a considerable amount of data but often rely on limited or biased human interpretation to examine their information content. By not asking the…
The RMPCDMD software package performs hybrid Molecular Dynamics simulations, coupling Multiparticle Collision Dynamics to model the solvent and Molecular Dynamics to model suspended colloids, including hydrodynamics, thermal fluctuations,…
Molecular dynamics (MD) has long been the de facto choice for simulating complex atomistic systems from first principles. Recently deep learning models become a popular way to accelerate MD. Notwithstanding, existing models depend on…
Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…
The integration of molecular and natural language representations has emerged as a focal point in molecular science, with recent advancements in Language Models (LMs) demonstrating significant potential for comprehensive modeling of both…
Systems composed of soft matter (e.g., liquids, polymers, foams, gels, colloids, and most biological materials) are ubiquitous in science and engineering, but molecular simulations of such systems pose particular computational challenges,…
ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales,…
Computer simulation is an important tool for scientific progress, especially when lab experiments are either extremely costly and difficult or lack the required resolution. However, all of the simulation methods come with limitations. In…
The increasingly collaborative, globalized nature of scientific research combined with the need to share data and the explosion in data volumes present an urgent need for a scientific data management system (SDMS). An SDMS presents a…
Metal-organic frameworks (MOFs) are porous materials composed of metal ions and organic linkers. Due to their chemical diversity, MOFs can support a broad range of applications in chemical separations. However, the vast amount of structural…
Photon-HDF5 is an open-source and open file format for storing photon-counting data from single molecule microscopy experiments, introduced to simplify data exchange and increase the reproducibility of data analysis. Part of the Photon-HDF5…