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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…
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…
Highly customized graphical user interfaces play a major role in today's software applications. There exist many technologies that support developing them. But these technologies demand writing a significant amount of unintuitive code to…
A data structure and toolkit are presented here that allow for the description and manipulation of mathematical models of three-manifolds and their interactive display from multiple viewpoints via the OpenGL 3D graphics package. The data…
Neural network potentials (NNPs) are rapidly changing the landscape of state-of-the-art molecular dynamics (MD) simulations. To make full use of this development, the community needs flexible, easy-to-use interfaces firmly integrated with…
Capturing molecular knowledge with representation learning approaches holds significant potential in vast scientific fields such as chemistry and life science. An effective and generalizable molecular representation is expected to capture…
We present a user-friendly software for photonic analog quantum computing with an installable MATLAB package and the graphical user interface (GUI) that allows for convenient operation without requiring programming skills. Arbitrary…
In this and the associated article 'BioBlender: A Software for Intuitive Representation of Surface Properties of Biomolecules', (Andrei et al) we present BioBlender as a complete instrument for the elaboration of motion (here) and the…
We introduce TofuML, an interactive system designed to make machine learning (ML) concepts more accessible and engaging for non-expert users. Unlike conventional GUI-based systems, TofuML employs a physical and spatial interface consisting…
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…
Foundation models (FMs) have transformed computational pathology by providing powerful, general-purpose feature extractors. However, adapting and benchmarking individual FMs for specific diagnostic tasks is often time-consuming and…
Although Raman spectroscopy is widely used for the investigation of biomedical samples and has a high potential for use in clinical applications, it is not common in clinical routines. One of the factors that obstruct the integration of…
Molecular simulations are an important tool for research in physics, chemistry, and biology. The capabilities of simulations can be greatly expanded by providing access to advanced sampling methods and techniques that permit calculation of…
Making quantum mechanical equations and concepts come to life through interactive simulation and visualization are commonplace for augmenting learning and teaching. However, graphical visualizations nearly always exhibit a set of hard-coded…
We present a perspective on molecular machine learning (ML) in the field of chemical process engineering. Recently, molecular ML has demonstrated great potential in (i) providing highly accurate predictions for properties of pure components…
Drug discovery can be viewed as a combinatorial search over an immense chemical space, motivating the development of deep generative models for de novo molecular design. Among these, GPT-based molecular language models (MLM) have shown…
We report the development of a user-friendly nano-visualization software program which can acquaint high-school students with nanotechnology. The visual introduction to atoms and molecules, which are the building blocks of this technology,…
Artificial intelligence (AI) techniques are widely applied in the life sciences. However, applying innovative AI techniques to understand and deconvolute biological complexity is hindered by the learning curve for life science scientists to…
Pulgon-tools is an open-source software package providing building blocks for the analysis and modeling of quasi-one-dimensional (quasi-1D) periodic systems based on line-group theory. While mature libraries exist for space-group detection…
Current multimodal large language models (MLLMs) face significant challenges in visual document understanding (VDU) tasks due to the high resolution, dense text, and complex layouts typical of document images. These characteristics demand a…