Related papers: H5MD: a structured, efficient, and portable file f…
The complexities of today's materials simulations demand computer codes which are both powerful and highly flexible. A researcher should be able to readily choose different geometries, different materials and different algorithms without…
The FITS (Flexible Image Transport System) data format was developed in the late 1970s for storage and exchange of astronomy-related image data. Since then, it has become a standard file format not only for images, but also for radio…
We present a data format for the output of general N-body simulations, allowing the presence of individual time steps. By specifying a standard, different N-body integrators and different visualization and analysis programs can all share…
Molecular dynamics (MD) simulation is one of the past decade's most important tools for enabling biology scientists and researchers to explore human health and diseases. However, due to the computation complexity of the MD algorithm, it…
The purpose of this document is to specify the basic data types required for storing electrophysiology and optical imaging data to facilitate computer-based neuroscience studies and data sharing. These requirements are being developed…
Materials science is undergoing profound changes due to advances in characterization instrumentation that have resulted in an explosion of data in terms of volume, velocity, variety and complexity. Harnessing these data for scientific…
In order to allow different software applications, in constant evolution, to interact and exchange data, flexible file formats are needed. A file format specification for different types of content has been elaborated to allow communication…
Molecular dynamics simulation is a proven technique for computing and visualizing the time-resolved motion of macromolecules at atomic resolution. The MDsrv is a tool that streams MD trajectories and displays them interactively in web…
Modelling has become a third distinct line of scientific enquiry, alongside experiments and theory. Molecular dynamics (MD) simulations serve to interpret, predict and guide experiments and to test and develop theories. A major limiting…
Open material databases storing hundreds of thousands of material structures and their corresponding properties have become the cornerstone of modern computational materials science. Yet, the raw outputs of the simulations, such as the…
Magnetic particle imaging (MPI) is a tomographic method to determine the spatio-temporal distribution of magnetic nanoparticles. In this document, a file format for the standardized storage of MPI and magnetic particle spectroscopy (MPS)…
Dataset storage, exchange, and access play a critical role in scientific applications. For such purposes netCDF serves as a portable and efficient file format and programming interface, which is popular in numerous scientific application…
Molecular dynamics simulations yield large amounts of trajectory data. For their durable storage and accessibility an efficient compression algorithm is paramount. State of the art domain-specific algorithms combine quantization, Huffman…
In this work, the application of the multi-dimensional higher order dynamic mode decomposition (HODMD) is proposed for the first time to analyse combustion databases. In particular, HODMD has been adapted and combined with other…
Conventional molecular dynamics (MD) simulation approaches, such as $\textit{ab initio}$ MD (AIMD) and empirical force field MD (EFFMD), face significant trade-offs between physical accuracy and computational efficiency. This work presents…
We present an unsupervised data processing workflow that is specifically designed to obtain a fast conformational clustering of long molecular dynamics simulation trajectories. In this approach we combine two dimensionality reduction…
The high-performance computing (HPC) community has recently seen a substantial diversification of hardware platforms and their associated programming models. From traditional multicore processors to highly specialized accelerators, vendors…
Scientific applications produce vast amounts of data, posing grand challenges in the underlying data management and analytic tasks. Progressive compression is a promising way to address this problem, as it allows for on-demand data…
Raw data sizes are growing and proliferating in scientific research, driven by the success of data-hungry computational methods, such as machine learning. The preponderance of proprietary and shoehorned data formats make computations slower…
Molecular dynamics simulations have emerged as a potent tool for investigating the physical properties and kinetic behaviors of materials at the atomic scale, particularly in extreme conditions. Ab initio accuracy is now achievable with…