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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.…
This study employed an artificial intelligence-enhanced molecular simulation framework to enable efficient Path Integral Molecular Dynamics (PIMD) simulations. Owing to its modular architecture and high-throughput capabilities, the…
The advent of immersive Virtual Reality applications has transformed various domains, yet their integration with advanced artificial intelligence technologies like Visual Language Models remains underexplored. This study introduces a…
The adoption of detailed mechanisms for chemical kinetics often poses two types of severe challenges: First, the number of degrees of freedom is large; and second, the dynamics is characterized by widely disparate time scales. As a result,…
An approach for incorporating embedded simulation and analysis capabilities in complex simulation codes through template-based generic programming is presented. This approach relies on templating and operator overloading within the C++…
Molecular dynamics simulations provide a mechanistic description of molecules by relying on empirical potentials. The quality and transferability of such potentials can be improved leveraging data-driven models derived with machine learning…
Computational Grids are emerging as a popular paradigm for solving large-scale compute and data intensive problems in science, engineering, and commerce. However, application composition, resource management and scheduling in these…
Enhanced sampling simulations make the computational study of rare events feasible. A large family of such methods crucially depends on the definition of some collective variables (CVs) that could provide a low-dimensional representation of…
Human expertise in chemistry and biomedicine relies on contextual molecular understanding, a capability that large language models (LLMs) can extend through fine-grained alignment between molecular structures and text. Recent multimodal…
MuSim is a new user-friendly program designed to interface to many different particle simulation codes, regardless of their data formats or geometry descriptions. It presents the user with a compelling graphical user interface that includes…
The potential of virtual reality (VR) to contribute to drug design and development has been recognised for many years. Hardware and software developments now mean that this potential is beginning to be realised, and VR methods are being…
Prompt-driven image analysis converts a single natural-language instruction into multiple steps: locate, segment, edit, and describe. We present a practical case study of a unified pipeline that combines open-vocabulary detection,…
Synthetic biology is a rapidly emerging research area, with expected wide-ranging impact in biology, nanofabrication, and medicine. A key technical challenge lies in embedding computation in molecular contexts where electronic…
In modern data-driven science, reproducibility and reusability are key challenges. Scientists are well skilled in the process from data to publication. Although some publication channels require source code and data to be made accessible,…
The "IMP Science Gateway Portal" (http://scigate.imp.kiev.ua) for complex workflow management and integration of distributed computing resources (like clusters, service grids, desktop grids, clouds) is presented. It is created on the basis…
Utilizing Graphic User Interface (GUI) for human-computer interaction is essential for accessing a wide range of digital tools. Recent advancements in Vision Language Models (VLMs) highlight the compelling potential to develop versatile…
The computer programs most users interact with daily are driven by a graphical user interface (GUI). However, many scientific applications are used with a command line interface (CLI) for the ease of development and increased flexibility…
Rapid developments of AI tools are expected to offer unprecedented assistance to the research of natural science including chemistry. However, neither existing unimodal task-specific specialist models nor emerging general large multimodal…
As molecular scientists have made progress in their ability to engineer nano-scale molecular structure, we are facing new challenges in our ability to engineer molecular dynamics (MD) and flexibility. Dynamics at the molecular scale differs…
Simulation of non-adiabatic dynamics of a quantum system coupled to dissipative environments poses significant challenges. New sophisticated methods are regularly being developed with an eye towards moving to larger systems and more…