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Biological regulatory networks can be represented by computational models, which allow the study and analysis of biological behaviours, therefore providing a better understanding of a given biological process. However, as new information is…
Background: To understand protein function, it is important to study protein- protein interaction networks. These networks can be represented in network diagrams called protein interaction maps that can lead to better understanding by…
-Molecular simulations allow the study of properties and interactions of molecular systems. This article presents an improved version of the Adaptive Resolution Scheme that links two systems having atomistic (also called fine-grained) and…
Molecular "fingerprints" encoding structural information are the workhorse of cheminformatics and machine learning in drug discovery applications. However, fingerprint representations necessarily emphasize particular aspects of the…
I present a Python package developed for fitting Voigt profiles to absorption lines. The software fits multiple components for various atomic lines simultaneously allowing parameters to be tied and fixed. Moreover, the code is able to…
Large Language Models (LLMs) with their strong task-handling capabilities have shown remarkable advancements across a spectrum of fields, moving beyond natural language understanding. However, their proficiency within the chemistry domain…
In this paper we address the problem of protein classification starting from a multi-view 2D representation of proteins. From each 3D protein structure, a large set of 2D projections is generated using the protein visualization software…
We present PyWolf, an open-source software capable of performing numerical simulations of partially coherent light propagation from two-dimensional light sources. PyWolf computes the evolution of a user-defined cross-spectral density…
Boxplots and related visualization methods are widely used exploratory tools for taking a first look at collections of univariate variables. In this note an extension is provided that is specifically designed to detect and display…
Procedural materials, represented as functional node graphs, are ubiquitous in computer graphics for photorealistic material appearance design. They allow users to perform intuitive and precise editing to achieve desired visual appearances.…
Multimodal molecular models often suffer from 3D conformer unreliability and modality collapse, limiting their robustness and generalization. We propose MuMo, a structured multimodal fusion framework that addresses these challenges in…
Magboltz is widely used to compute electron transport properties in gas mixtures for detector applications. Its text-based workflow, however, can be a barrier for routine use, especially for users who are not already familiar with the…
Graph representations of programs are commonly a central element of machine learning for code research. We introduce an open source Python library python_graphs that applies static analysis to construct graph representations of Python…
This paper introduces pycvxset, a new Python package to manipulate and visualize convex sets. We support polytopes and ellipsoids, and provide user-friendly methods to perform a variety of set operations. For polytopes, pycvxset supports…
The advent of language implementation tools such as PyPy and Truffle/Graal have reinvigorated and broadened interest in topics related to automatic compiler generation and optimization. Given this broader interest, we revisit the Futamura…
A visual programming language uses pictorial tools such as diagrams to represent its structural units and control stream. It is useful for enhancing understanding, maintenance, verification, testing, and parallelism. This paper proposes a…
Molecular Property Prediction (MPP) plays a pivotal role across diverse domains, spanning drug discovery, material science, and environmental chemistry. Fueled by the exponential growth of chemical data and the evolution of artificial…
The Cellular Potts Model (CPM) is a widely used simulation paradigm for systems of interacting cells that has been used to study scenarios ranging from plant development to morphogenesis, tumour growth and cell migration. Despite their wide…
HOOMD-blue is a particle simulation engine designed for nano- and colloidal-scale molecular dynamics and hard particle Monte Carlo simulations. It has been actively developed since March 2007 and available open source since August 2008.…
Large language models (LLMs) are increasingly recognized as powerful tools for scientific discovery, particularly in molecular science. A fundamental requirement for these models is the ability to accurately understand molecular structures,…