Related papers: A typical workflow to simulate cytoskeletal system…
The proper functions of tissues depend on the ability of cells to withstand stress and maintain shape. Central to this process is the cytoskeleton, comprised of three polymeric networks: F-actin, microtubules, and intermediate filaments.…
Tissue remodelling in diverse developmental contexts require cell shape changes that have been associated with pulsation and flow of the actomyosin cytoskeleton. Here we describe the dynamics of the actomyosin cytoskeleton as a confined…
The study of motor protein dynamics within cytoskeletal networks is of high interest to physicists and biologists to understand how the dynamics and properties of individual motors lead to cooperative effects and control of overall network…
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…
Our understanding of the physics of biological molecules, such as proteins and DNA, is limited because the approximations we usually apply to model inert materials are not in general applicable to soft, chemically inhomogeneous systems. The…
While self-supervised pretraining has reduced vision systems' reliance on synthetic data, simulation remains an indispensable tool for closed-loop optimization and rigorous out-of-distribution (OOD) evaluation. However, modern simulation…
We present AccaSim, a simulator for workload management in HPC systems. Thanks to AccaSim's scalability to large workload datasets, support for easy customization, and practical automated tools to aid experimentation, users can easily…
In active matter systems, self-propelled particles can self-organize to undergo collective motion, leading to persistent dynamical behavior out of equilibrium. In cells, cytoskeletal filaments and motor proteins self-organize into complex…
Coarse-grained modeling and efficient computer simulations are critical to the study of complex molecular processes with many degrees of freedom and multiple spatiotemporal scales. Variational implicit-solvent model (VISM) for biomolecular…
Microfluidic devices have been the subject of considerable attention in recent years. The development of novel microfluidic devices, their evaluation, and their validation requires simulations. While common methods based on Computational…
Modeling spinal motion is fundamental to understanding human biomechanics, yet remains underexplored in computer vision due to the spine's complex multi-joint kinematics and the lack of large-scale 3D annotations. We present a…
Xsuite is a newly developed modular simulation package combining in a single flexible and modern framework the capabilities of different tools developed at CERN in the past decades, notably Sixtrack, Sixtracklib, COMBI and PyHEADTAIL. The…
Under many physiological and pathological conditions such as division and migration, cells undergo dramatic deformations, under which their mechanical integrity is supported by cytoskeletal networks (i.e. intermediate filaments, F-actin,…
The cytoskeleton in eukaryotic cells plays several crucial roles. In terms of intracellular transport, motor proteins use the cytoskeletal filaments as a backbone along which they can actively transport biological cargos such as vesicles…
Labelling data is expensive and time consuming especially for domains such as medical imaging that contain volumetric imaging data and require expert knowledge. Exploiting a larger pool of labeled data available across multiple centers,…
Image simulation remains under-exploited for the most widely used biological phase microscopy methods, because of difficulties in simulating partially coherent illumination. We describe an open-source toolbox, microlith…
Cells control fluid flows with a spatial and temporal precision that far exceeds the capabilities of current microfluidic technologies. Cells achieve this superior spatio-temporal control by harnessing dynamic networks of cytoskeleton and…
Computer simulations have become a very powerful tool for scientific research. In order to facilitate research in computational biology, the BioDynaMo project aims at a general platform for biological computer simulations, which should be…
Ensemble datasets are ever more prevalent in various scientific domains. In climate science, ensemble datasets are used to capture variability in projections under plausible future conditions including greenhouse and aerosol emissions. Each…
Contractile cytoskeletal structures such as fine actomyosin meshworks and stress fibers are essential force-generators for mechanical phenomena in live cells, including motility, morphogenesis, and mechanosensing. While there have been many…