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Molecular dynamics simulations have a prominent role in biophysics and drug discovery due to the atomistic information they provide on the structure, energetics and dynamics of biomolecules. Specialized software packages are required to…
Interactive visualization can support fluid exploration but is often limited to predetermined tasks. Scripting can support a vast range of queries but may be more cumbersome for free-form exploration. Embedding interactive visualization in…
Molecular dynamics (MD) simulations provide detailed insight into atomic-scale mechanisms but are inherently restricted to small spatio-temporal scales. Coarse-grained molecular dynamics (CGMD) techniques allow simulations of much larger…
Large language models (LLMs) are changing the way researchers interact with code and data in scientific computing. While their ability to generate general-purpose code is well established, their effectiveness in producing scientifically…
An accurate treatment of the structures and dynamics that lead to enhanced chemical reactivity in enzymes requires explicit treatment of both electronic and nuclear quantum effects. The former can be captured in ab initio molecular dynamics…
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…
Molecular dynamics (MD) simulations are a crucial computational tool for researchers to understand and engineer molecular structure and function in areas such as drug discovery, protein engineering, and material design. Despite their…
Recent advances in generative AI have accelerated the discovery of novel chemicals and materials. However, scaling these discoveries to industrial production remains a major bottleneck due to the synthesis gap -- the need to develop…
Recent developments in many-body potential energy representation via deep learning have brought new hopes to addressing the accuracy-versus-efficiency dilemma in molecular simulations. Here we describe DeePMD-kit, a package written in…
Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of…
Molecular Vibe Coding, a paradigm where chemists interact with LLMs to generate executable programs for molecular tasks, has emerged as a flexible alternative to chemical agents with predefined tools, enabling chemists to express…
We create a Python GUI scripting interface working under Windows in addition to (UNIX/Linux). The GUI has been built around the Python open-source programming language. We use the Python's GUI library that so called Python Mega Widgets…
With the rapid advancement of large language models (LLMs) and vision-language models (VLMs), significant progress has been made in developing open-vocabulary robotic manipulation systems. However, many existing approaches overlook the…
CLPGUI is a graphical user interface for visualizing and interacting with constraint logic programs over finite domains. In CLPGUI, the user can control the execution of a CLP program through several views of constraints, of finite domain…
Text-to-image generative models like DALL-E and Stable Diffusion have revolutionized visual content creation across various applications, including advertising, personalized media, and design prototyping. However, crafting effective textual…
The Simulation Environment for Atomistic and Molecular Modeling (SEAMM) is an open-source software package written in Python that provides a graphical interface for setting up, executing, and analyzing molecular and materials simulations.…
Background and Objective: Hemodynamic analysis of blood flow through arteries and veins is critical for diagnosing cardiovascular diseases, such as aneurysms and stenoses, and for investigating cardiovascular parameters, such as turbulence…
Molecular dynamics is crucial for understanding molecular systems but its applicability is often limited by the vast timescales of rare events like protein folding. Enhanced sampling techniques overcome this by accelerating the simulation…
Modeling of turbulent combustion system requires modeling the underlying chemistry and the turbulent flow. Solving both systems simultaneously is computationally prohibitive. Instead, given the difference in scales at which the two…
Graphical user interface (GUI) has become integral to modern society, making it crucial to be understood for human-centric systems. However, unlike natural images or documents, GUIs comprise artificially designed graphical elements arranged…