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The cryogenic buffer gas beam (CBGB) is an important tool in the study of cold and ultracold molecules. While there are known techniques to enhance desired beam properties, such as high flux, low velocity, or reduced divergence, they have…
Simulated ultrasound image sequences are key for training and validating machine learning algorithms for left ventricular strain estimation. Several simulation pipelines have been proposed to generate sequences with corresponding ground…
The article describes parallel multiphysics simulations of charged particles in microfluidic flows with the waLBerla framework. To this end, three physical effects are coupled: rigid body dynamics, fluid flow modelled by a lattice Boltzmann…
In this paper, we are concerned with the simulation of blood flow in microvascular networks and the surrounding tissue. To reduce the computational complexity of this issue, the network structures are modeled by a one-dimensional graph,…
SMeagol is a software tool to simulate highly realistic microscopy data based on spatial systems biology models, in order to facilitate development, validation, and optimization of advanced analysis methods for live cell single molecule…
Determining brain hemodynamics plays a critical role in the diagnosis and treatment of various cerebrovascular diseases. In this work, we put forth a physics-informed deep learning framework that augments sparse clinical measurements with…
The regulation of intestinal blood flow is critical to gastrointestinal function. Imaging the intestinal mucosal micro-circulation in vivo has the potential to provide new insight into the gut physiology and pathophysiology. We aimed to…
Fast and realistic coupling of blood flow and vessel wall is of great importance to virtual surgery. In this paper, we propose a novel data-driven coupling method that formulates physics-based blood flow simulation as a regression problem,…
Computational fluid dynamics (CFD) studies have been increasingly used for blood flow simulations in intracranial aneurysms (ICAs). However, despite the continuous progress of body-fitted CFD solvers, generating a high quality mesh is still…
Direct numerical simulation of liquid-gas-solid flows is uncommon due to the considerable computational cost. As the grid spacing is determined by the smallest involved length scale, large grid sizes become necessary -- in particular if the…
A recent reformulation [1] of the problem of Coulomb gases in the presence of a dynamical dielectric medium showed that finite temperature simulations of such systems can be accomplished on the basis of completely local Hamiltonians on a…
Intracardiac flow patterns are shaped by the coupled motion of the cardiac chambers and heart valves and provide important information about cardiac function. However, clinical flow imaging remains limited by exam times, noise, resolution,…
Soft matter materials and polymers are widely used in the controlled delivery of drugs. Simulation and modeling provide insight at the atomic scale enabling a level of control unavailable to experiments. We present a workflow protocol for…
We developed a computer vision-based methodology to achieve precise 3D segmentation and tracking of superbubbles within magnetohydrodynamic simulations of the supernova-driven interstellar medium. Leveraging advanced 3D transformer models,…
The design of gaseous detectors for accelerator, particle and nuclear physics requires simulations relying on multi-physics aspects. In fact, these simulations deal with the dynamics of a large number of charged particles interacting in a…
An arteriovenous fistula, created by artificially connecting segments of a patient's vasculature, is the preferred way to gain access to the bloodstream for kidney dialysis. The increasing power and availability of supercomputing…
Segmentation of medical images is a fundamental task with numerous applications. While MRI, CT, and PET modalities have significantly benefited from deep learning segmentation techniques, more recent modalities, like functional ultrasound…
We present a versatile and fast MATLAB program (UmUTracker) that automatically detects and tracks particles by analyzing video sequences acquired by either light microscopy or digital in-line holographic microscopy. Our program detects the…
Recently, hybrid models have emerged that combine microscopic and mesoscopic regimes in a single stochastic reaction-diffusion simulation. Microscopic simulations track every individual molecule and are generally more accurate. Mesoscopic…
Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…