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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.…
Many cytoskeletal systems are now sufficiently well known to permit their precise quantitative modelling. Microtubule and actin filaments are well characterized, and the associated proteins are often known, as well as their abundance and…
Small and wide angle x-ray scattering tensor tomography are powerful methods for studying anisotropic nanostructures in a volume-resolved manner, and are becoming increasingly available to users of synchrotron facilities. The analysis of…
We introduce the Unity Perception package which aims to simplify and accelerate the process of generating synthetic datasets for computer vision tasks by offering an easy-to-use and highly customizable toolset. This open-source package…
Numerical end-to-end simulation in Adaptive Optics (AO) is a key tool in the development of complex systems, from the initial design to the commissioning phase. Based on our previous experience with PASSATA, we decided to develop a new AO…
This paper describes a 2D and 3D simulation engine that quantitatively models the statics, dynamics, and non-linear deformation of heterogeneous soft bodies in a computationally efficient manner. There is a large body of work simulating…
Recent advances in both theory and computational power have created opportunities to simulate biomolecular processes more efficiently using adaptive ensemble simulations. Ensemble simulations are now widely used to compute a number of…
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…
The soon-to-be-realized, global network of neutrino telescopes will allow new opportunities for collaboration between detectors. While each detector is distinct, they share the same underlying physical processes and detection principles.…
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…
Modern precision experiments trapping low-energy particles require detailed simulations of particle trajectories and spin precession to determine systematic measurement limitations and apparatus deficiencies. We developed PENTrack, a tool…
In computer experiments, a mathematical model implemented on a computer is used to represent complex physical phenomena. These models, known as computer simulators, enable experimental study of a virtual representation of the complex…
Simulations with high accuracy are an essential part of scientific research to accelerate the innovation process. They are especially useful for finding novel approaches or optimizing existing methods. Today, powerful software tools are…
We consider different approaches to simulate a modern X-ray beamline. Several methodologies with increasing complexity are applied to discuss the relevant parameters that quantify the beamline performance. Parameters such as flux,…
This paper presents Virtual Simulation Objects (VSO) concept which forms theoretical basis for building tools and framework that is developed for system-level simulations using existing software modules available within…
The analysis of experimental results with Python often requires writing many code scripts which all need access to the same set of functions. In a common field of research, this set will be nearly the same for many users. The qspec Python…
Multimodal deep sensor fusion has the potential to enable autonomous vehicles to visually understand their surrounding environments in all weather conditions. However, existing deep sensor fusion methods usually employ convoluted…
As space exploration advances, underground environments are becoming increasingly attractive due to their potential to provide shelter, easier access to resources, and enhanced scientific opportunities. Although such environments exist on…
AutoDRIVE is envisioned to be an integrated research and education platform for scaled autonomous vehicles and related applications. This work is a stepping-stone towards achieving the greater goal of realizing such a platform.…
In this article we present PARSIR (PARallel SImulation Runner), a package that enables the effective exploitation of shared-memory multi-processor machines for running discrete event simulation models. PARSIR is a compile/run-time…