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We introduce QCLAB, an object-oriented MATLAB toolbox for constructing, representing, and simulating quantum circuits. Designed with an emphasis on numerical stability, efficiency, and performance, QCLAB provides a reliable platform for…

PhysiBoSS is an open-source platform that integrates agent-based modeling of cell populations with intracellular stochastic Boolean networks, enabling multiscale simulations of complex biological behaviors. To promote model sharing and…

Three-dimensional cardiovascular fluid dynamics simulations typically require computation of several cardiac cycles before they reach a periodic solution, rendering them computationally expensive. Furthermore, there is currently no…

CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular and biological systems. It is especially aimed at massively-parallel and linear-scaling…

We present Clinica (www.clinica.run), an open-source software platform designed to make clinical neuroscience studies easier and more reproducible. Clinica aims for researchers to i) spend less time on data management and processing, ii)…

This PhD thesis introduces the concept of meta-electrodes coupled with laser optoporation for high quality intracellular signals from hiPSCs-CM. These signals can be recorded on high-density commercial CMOS-MEAs from 3Brain characterized by…

We describe a general-purpose computational toolkit for simulating open quantum systems, which provides numerically exact solutions for composites of zero-dimensional quantum systems that may be strongly coupled to multiple, quite general…

The introduction of computational models in cardiovascular sciences has been progressively bringing new and unique tools for the investigation of the physiopathology. Together with the dramatic improvement of imaging and measuring devices…

By generating synthetic biosignals, the quantity and variety of health data can be increased. This is especially useful when training machine learning models by enabling data augmentation and introduction of more physiologically plausible…

Electronic-photonic integrated circuits (EPICs) offer transformative potential for next-generation high-performance AI but require interdisciplinary advances across devices, circuits, architecture, and design automation. The complexity of…

Ultrasound is a key technology in healthcare, and it is being explored for non-invasive, wearable, continuous monitoring of vital signs. However, its widespread adoption in this scenario is still hindered by the size, complexity, and power…

Molecular dynamics is widely used to study various phenomena, such as diffusion, shock wave propagation, and plasma dynamics. A wide range of software packages supports the expanding scope of molecular dynamics applications. However, the…

We study the problem of adding native pulse-level control to heterogeneous High Performance Computing-Quantum Computing (HPCQC) software stacks, using the Munich Quantum Software Stack (MQSS) as a case study. The goal is to expand the…

Computational ultrasound imaging has become a well-established methodology in the ultrasound community. In the accompanying paper (part I), we described a new ultrasound simulator (SIMUS) for Matlab, which belongs to the Matlab UltraSound…

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 has become an essential tool in academia and industry to support fundamental research and the design and development of devices. Consequently, computational micromagnetics is widely used in the community, and…

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…

Many parts of human body generate internal sound during biological processes, which are rich sources of information for understanding health and wellbeing. Despite a long history of development and usage of stethoscopes, there is still a…

In this paper we present SimCommSys, a Simulator of Communication Systems that we are releasing under an open source license. The core of the project is a set of C++ libraries defining communication system components and a distributed Monte…

Motivation: This paper presents libRoadRunner 2.0, an extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models expressed using Systems Biology Markup Language SBML). Results:…