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Effective data visualization is a key part of the discovery process in the era of big data. It is the bridge between the quantitative content of the data and human intuition, and thus an essential component of the scientific path from data…
Simulation ensembles are a common tool in physics for understanding how a model outcome depends on input parameters. We analyze an active particle system, where each particle can use energy from its surroundings to propel itself. A…
For over half a century, the computer mouse has been the primary tool for interacting with digital data, yet it remains a limiting factor in exploring complex, multi-scale scientific images. Traditional 2D visualization methods hinder…
Measuring similarity between molecules is an important part of virtual screening (VS) experiments deployed during the early stages of drug discovery. Most widely used methods for evaluating the similarity of molecules use molecular…
Acupuncture is a form of medicine that involves inserting needles into targeted areas of the body and requires knowledge of both Traditional Chinese Medicine (TCM) and Evidence-Based Medicine (EBM). The process of acquiring such knowledge…
Scientists often explore and analyze large-scale scientific simulation data by leveraging two- and three-dimensional visualizations. The data and tasks can be complex and therefore best supported using myriad display technologies, from…
Agent-based modeling (ABM) is a well-established paradigm for simulating complex systems via interactions between constituent entities. Machine learning (ML) refers to approaches whereby statistical algorithms 'learn' from data on their…
Mixed Reality (MR) and Virtual Reality (VR) simulations are hampered by requirements for hand controllers or attempts to perseverate in use of two-dimensional computer interface paradigms from the 1980s. From our efforts to produce more…
A large number of powerful, high-quality, and open-source simulation packages exist to efficiently perform molecular dynamics simulations, and their prevalence has greatly accelerated discoveries across a wide range of scientific domains.…
Interpreting biological networks becomes challenging when molecular components, such as genes or proteins, participate in numerous interactions, resulting in densely connected regions and overlapping interactions that obscure functional…
The common techniques to study protein-protein proximity in vivo are not well-adapted to the capabilities and the expertise of a standard proteomics laboratory, typically based on the use of mass spectrometry. With the aim of closing this…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…
PolyMAPS is an open-source library that helps researchers to initialize LAMMPS molecular dynamics simulations. It introduces an integrated workflow by combining preparation, launching, visualization, and analysis into a single Jupyter…
Advanced manufacturing creates increasingly complex objects with material compositions that are often difficult to characterize by a single modality. Our collaborating domain scientists are going beyond traditional methods by employing both…
It is desired to equip robots with the capability of interacting with various soft materials as they are ubiquitous in the real world. While physics simulations are one of the predominant methods for data collection and robot training,…
The ionic environment of biomolecules strongly influences their structure, conformational stability, and inter-molecular interactions.This paper introduces GIBS, a grand-canonical Monte Carlo (GCMC) simulation program for computing the…
Biological laboratory automation can reduce repetitive manual work and improve reproducibility, but reliable embodied execution in wet-lab environments remains challenging. Protocols are often unstructured, labware is frequently transparent…
Summary: VTX is a molecular visualization software capable to handle most molecular structures and dynamics trajectories file formats. It features a real-time high-performance molecular graphics engine, based on modern OpenGL, optimized for…
This paper introduces a random-batch molecular dynamics (RBMD) package for fast simulations of particle systems at the nano/micro scale. Different from existing packages, the RBMD uses random batch methods for nonbonded interactions of…
There will be a paradigm shift in chemical and biological research, to be enabled by autonomous, closed-loop, real-time self-directed decision-making experimentation. Spectrum-to-structure correlation, which is to elucidate molecular…