Related papers: Computer-aided modelling of complex physical syste…
We examine several currently used techniques for visualizing complex-valued functions applied to modular forms. We plot several examples and study the benefits and limitations of each technique. We then introduce a method of visualization…
When modeling complex, hierarchical, and time-dynamic systems, such as biological systems, good computational tools are essential. Current tools, while powerful, often lack comprehensive frameworks for modular model composition,…
The (py)LIon package is a set of tools to simulate the classical trajectories of ensembles of ions in electrodynamic traps. Molecular dynamics simulations are performed using LAMMPS, an efficient and feature-rich program. (py)LIon has been…
Automated searches for strong gravitational lensing in optical imaging survey datasets often employ machine learning and deep learning approaches. These techniques require more example systems to train the algorithms than have presently…
Python has become the de-facto language for training deep neural networks, coupling a large suite of scientific computing libraries with efficient libraries for tensor computation such as PyTorch or TensorFlow. However, when models are used…
Multiscale models provide a unique tool for studying complex processes that study events occurring at different scales across space and time. In the context of biological systems, such models can simulate mechanisms happening at the…
We demonstrate that for a broad class of physical systems that can be described using classical field theory, automated runtime translation of the physical equations to parallelized finite-element numerical simulation code is feasible. This…
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…
In the field of affective computing, where research continually advances at a rapid pace, the demand for user-friendly tools has become increasingly apparent. In this paper, we present the AffectToolbox, a novel software system that aims to…
Machine learning solutions are very popular in the field of chemoinformatics, where they have numerous applications, such as novel drug discovery or molecular property prediction. Molecular fingerprints are algorithms commonly used for…
We present PyMoosh, a Python-based simulation library designed to provide a comprehensive set of numerical tools allowing to compute essentially all optical characteristics of multilayered structures, ranging from reflectance and…
An easy way to define and visualize geometry for PHITS input files introduced. Suggested FitsGeo Python package helps to define surfaces as Python objects and manipulate them conveniently. VPython assists to view defined geometry…
In this paper, we present a novel general framework grounded in the factor graph theory to solve kinematic and dynamic problems for multi-body systems. Although the motion of multi-body systems is considered to be a well-studied problem and…
In this paper, we introduce PhotoHolmes, an open-source Python library designed to easily run and benchmark forgery detection methods on digital images. The library includes implementations of popular and state-of-the-art methods, dataset…
We describe a numerical technique and accompanying open-source Python software package called RydIQule. RydIQule uses a directional graph, relying on adjacency matrices and path-finding to generate a Hamiltonian for multi-level atomic…
This paper describes an Open Source Software (OSS) project: PythonRobotics. This is a collection of robotics algorithms implemented in the Python programming language. The focus of the project is on autonomous navigation, and the goal is…
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…
Mathematical and numerical modeling is an increasingly important, yet often neglected, topic for biology students. We have found Glowscript to facilitate teaching and introducing computer simulations to students. In particular, the built-in…
fgivenx is a Python package for functional posterior plotting, currently used in astronomy, but will be of use to scientists performing any Bayesian analysis which has predictive posteriors that are functions. The source code for fgivenx is…
We present Conedy, a performant scientific tool to numerically investigate dynamics on complex networks. Conedy allows to create networks and provides automatic code generation and compilation to ensure performant treatment of arbitrary…