Related papers: Dataflow programming for the analysis of molecular…
Dataflow programming is a popular and convenient programming paradigm in systems modelling, optimisation, and machine learning. It has a number of advantages, for instance the lacks of control flow allows computation to be carried out in…
Supporting the interactive exploration of large datasets is a popular and challenging use case for data management systems. Traditionally, the interface and the back-end system are built and optimized separately, and interface design and…
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…
Interprocedural data-flow analyses form an expressive and useful paradigm of numerous static analysis applications, such as live variables analysis, alias analysis and null pointers analysis. The most widely-used framework for…
We introduce the Visual Data Management System (VDMS), which enables faster access to big-visual-data and adds support to visual analytics. This is achieved by searching for relevant visual data via metadata stored as a graph, and enabling…
Understanding the complex combustion dynamics within scramjet engines is critical for advancing high-speed propulsion technologies. However, the large scale and high dimensionality of simulation-generated temporal flow field data present…
Domain-specific languages (DSLs) for visualization aim to facilitate visualization creation by providing abstractions that offload implementation and execution details from users to the system layer. Therefore, DSLs often execute…
We provide an introduction to molecular dynamics simulations in the context of the Kob-Andersen model of a glass. We introduce a complete set of tools for doing and analyzing the results of simulations at fixed NVE and NVT. The modular…
Modern scientific applications are increasingly decomposable into individual functions that may be deployed across distributed and diverse cyberinfrastructure such as supercomputers, clouds, and accelerators. Such applications call for new…
Machine learning methods have been extensively used to study the dynamics of complex fluid flows. One such algorithm, known as adaptive neural fuzzy inference system (ANFIS), can generate data-driven predictions for flow fields but has not…
Recent years have seen an increased interest in large-scale analytical dataflows on non-relational data. These dataflows are compiled into execution graphs scheduled on large compute clusters. In many novel application areas the predominant…
ABACUS (Atomic-orbital Based Ab-initio Computation at USTC) is an open-source software for first-principles electronic structure calculations and molecular dynamics simulations. It mainly features density functional theory (DFT) and…
In this paper we show how advanced visualization tools can help the researcher in investigating and extracting information from data. The focus is on VisIVO, a novel open source graphics application, which blends high performance…
Efficient molecular dynamics (MD) simulation is vital for understanding atomic-scale processes in materials science and biophysics. Traditional density functional theory (DFT) methods are computationally expensive, which limits the…
Psychological research often involves understanding psychological constructs through conducting factor analysis on data collected by a questionnaire, which can comprise hundreds of questions. Without interactive systems for interpreting…
Molecular Dynamics (MD) simulations are ubiquitous in cutting-edge physio-chemical research. They provide critical insights into how a physical system evolves over time given a model of interatomic interactions. Understanding a system's…
Large language model (LLM) agents are increasingly capable of orchestrating complex tasks in low-code environments. However, these agents often exhibit hallucinations and logical inconsistencies because their inherent reasoning mechanisms…
IVISIT is a generic interactive visual simulation tool that is based on Python/Numpy and can be used for system simulation, parameter optimization, parameter management, and visualization of system dynamics as required, for example,for…
Large language models are moving scientific research from text assistance toward agentic workflows, yet biological research requires strong object validation, methodological suitability, reproducibility, and auditability. Prompt…
Metal-organic frameworks (MOFs) offer a vast design space, and as such, computational simulations play a critical role in predicting their structural and physicochemical properties. However, MOF simulations remain difficult to access…