Related papers: Simulated single molecule microscopy with SMeagol
The simulation of many-particle systems often requires the detailed knowledge of proximity relations to reduce computational complexity and to provide a basis for specific calculations. Here we describe the basic scheme of a simulator of…
Developing foundation models in medical imaging requires continuous monitoring of downstream performance. Researchers are burdened with tracking numerous experiments, design choices, and their effects on performance, often relying on…
Developing complex biomolecular workflows is not always straightforward. It requires tedious developments to enable the interoperability between the different biomolecular simulation and analysis tools. Moreover, the need to execute the…
As data science and machine learning methods are taking on an increasingly important role in the materials research community, there is a need for the development of machine learning software tools that are easy to use (even for nonexperts…
The exchange of large and complex slide microscopy imaging data in biomedical research and pathology practice is impeded by a lack of data standardization and interoperability, which is detrimental to the reproducibility of scientific…
The-Bodega is a Matlab-based toolbox for simulating ground-truth datasets for Ultrasound Localization Microscopy (ULM)-a super resolution imaging technique that resolves microvessels by systematically tracking microbubbles flowing through…
Modules for Experiments in Stellar Astrophysics (MESA; (Paxton2011, 2013, 2015, 2018, 2019, Jermyn 2023) is a widely used open-source software for modelling stellar evolution. In many studies, the computational grids covers thousands of…
Molecular dynamics simulations have a prominent role in biophysics and drug discovery due to the atomistic information they provide on the structure, energetics and dynamics of biomolecules. Specialized software packages are required to…
Molecular Dynamics (MD) simulations are ubiquitous in cutting-edge physio-chemical research. They provide critical insights into how a physical system evolves over time given a model of interatomic interactions. Understanding a system's…
The complexity of biological systems and processes, spanning molecular to macroscopic scales, necessitates the use of multiscale simulations to get a comprehensive understanding. Quantum mechanics/molecular mechanics (QM/MM) molecular…
The scintillator-strip electromagnetic calorimeter (ScECAL) is one of the calorimeter technic for the ILC. To achieve the fine granularity from the strip-segmented layers the strips in odd layers are orthogonal with respect to those in the…
The Saliency Model Implementation Library for Experimental Research (SMILER) is a new software package which provides an open, standardized, and extensible framework for maintaining and executing computational saliency models. This work…
Toward the goal of using Scientific Machine Learning (SciML) emulators to improve the numerical representation of aerosol processes in global atmospheric models, we explore the emulation of aerosol microphysics processes under cloud-free…
The sensitivity analysis and validation of simulation models require specific approaches in the case of spatial models. We describe the spatialdata scala library providing such tools, including synthetic generators for urban configurations…
ScopeSim is a flexible multipurpose instrument data simulation framework built in Python. It enables both raw and reduced observation data to be simulated for a wide range of telescopes and instruments quickly and efficiently on a personal…
The paper introduces the software Spectangular for spectral disentangling via singular value decomposition with global optimisation of the orbital parameters of the stellar system or radial velocities of the individual observations. We will…
The accurate ab initio simulation of molecules and periodic solids with diagrammatic perturbation theory is an important task in quantum chemistry, condensed matter physics, and materials science. In this article, we present the…
We present an open source software package SpectroLab a Matlab-based tool developed in 2018 for the analysis of spectroscopic data. In this package, there are tools for derivative analysis, stacked energy contours, stacked plots for theory,…
This paper presents a 2D/3D Free Surface Lattice Boltzmann Method simulation package called LBfoam for the simulation of foaming processes. The model incorporates the essential physics of foaming phenomena: gas diffusion into nucleated…
Computational micromagnetics requires numerical solution of partial differential equations to resolve complex interactions in magnetic nanomaterials. The Virtual Micromagnetics project described here provides virtual machine simulation…