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We present the VECMA toolkit (VECMAtk), a flexible software environment for single and multiscale simulations that introduces directly applicable and reusable procedures for verification, validation (V&V), sensitivity analysis (SA) and…
Scientific Machine Learning (SciML) has advanced recently across many different areas in computational science and engineering. The objective is to integrate data and physics seamlessly without the need of employing elaborate and…
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…
This article introduces a metamodel for the Business Model Canvas (BMC) using the Unified Modelling Language (UML), together with a dedicated Domain-Specific Modelling Language (DSML) tool. Although the BMC is widely adopted by both…
Atomic-scale simulations have progressed tremendously over the past decade, largely due to the availability of machine-learning interatomic potentials. These potentials combine the accuracy of electronic structure calculations with the…
We introduce \textsc{qcmath}, a user-friendly quantum chemistry software tailored for electronic structure calculations, implemented using the Wolfram Mathematica language and available at \url{https://github.com/LCPQ/qcmath}. This…
Mayavi is an open-source, general-purpose, 3D scientific visualization package. It seeks to provide easy and interactive tools for data visualization that fit with the scientific user's workflow. For this purpose, Mayavi provides several…
The convergence of statistical learning and molecular physics is transforming our approach to modeling biomolecular systems. Physics-informed machine learning (PIML) offers a systematic framework that integrates data-driven inference with…
Molecular dynamics (MD) simulations are essential tools in computational chemistry and drug discovery, offering crucial insights into dynamic molecular behavior. However, their utility is significantly limited by substantial computational…
The extraction of molecular structures and reaction data from scientific documents is challenging due to their varied, unstructured chemical formats and complex document layouts. To address this, we introduce MolMole, a vision-based deep…
Graphical User Interface (GUI) element grounding (precisely locating elements on screenshots based on natural language instructions) is fundamental for agents interacting with GUIs. Deploying this capability directly on resource-constrained…
Advances in large language models (LLMs) and real-time speech recognition now make it possible to issue any graphical user interface (GUI) action through natural language and receive the corresponding system response directly through the…
3D modeling is becoming a well-developed field of medicine, but its applicability can be limited due to the lack of software allowing for easy utilizations of generated 3D visualizations. By leveraging recent advances in virtual reality, we…
Survival prediction is a critical task in pathology. In clinical practice, pathologists often examine multiple cases, leveraging a broader spectrum of cancer phenotypes to enhance pathological assessment. Despite significant advancements in…
In this paper, we describe a Graphical User Interface (GUI) designed to manage large quantities of image data of a biological system. After setting the design requirements for the system, we developed an ecology quantification GUI that…
A software platform for global optimisation, called PaGMO, has been developed within the Advanced Concepts Team (ACT) at the European Space Agency, and was recently released as an open-source project. PaGMO is built to tackle…
Molecular Dynamics (MD) simulations are essential for understanding the atomic-level behavior of molecular systems, giving insights into their transitions and interactions. However, classical MD techniques are limited by the trade-off…
We report an implementation of a program for visualizing complex-valued molecular orbitals. The orbital phase information is encoded on each of the vertices of triangle meshes using the standard color wheel. Using this program, we…
Decades of hardware, methodological, and algorithmic development have propelled molecular dynamics (MD) simulations to the forefront of materials-modeling techniques, bridging the gap between electronic-structure theory and continuum…
Ensuring the correctness of quantum programs is crucial for quantum software quality assurance. Although various effective verification methods exist for classical programs, they cannot be applied to quantum programs due to the fundamental…