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Purpose: Protoplasmic tubes of Physarum polycephalum, also know as Physarum Wires (PW), have been previously suggested as novel bio- electronic components. Until recently, practical examples of electronic circuits using PWs have been…
In mesh-based numerical simulations, sweep is an important computation pattern. During sweeping a mesh, computations on cells are strictly ordered by data dependencies in given directions. Due to such a serial order, parallelizing sweep is…
Multiview light sheet fluorescence microscopy (LSFM) allows to image developing organisms in 3D at unprecedented temporal resolution over long periods of time. The resulting massive amounts of raw image data requires extensive processing…
The Simulation Environment for Atomistic and Molecular Modeling (SEAMM) is an open-source software package written in Python that provides a graphical interface for setting up, executing, and analyzing molecular and materials simulations.…
The "cosmic web", the filamentary large-scale structure in a cold dark matter Universe, is readily apparent via galaxy tracers in spectroscopic surveys. However, the underlying dark matter structure is as of yet unobservable and mapping the…
We present DiSH-Sim, a simulator for large discrete models of biological signal transduction pathways, capable of simulating networks with multi-valued elements in both deterministic and stochastic manner. We focus on order of update and…
The transport and manipulation of particles and cells in microfluidic devices has become a core methodology in domains ranging from molecular biology to manufacturing and drug design. The rational design and operation of such devices can…
The evolution of multicellular organisms from monocellular ancestors represents one of the greatest advances of the history of life. The assembly of such multicellular organisms requires signalling and response between cells: over millions…
Unconventional computing devices are increasingly of interest as they can operate in environments hostile to silicon-based electronics, or compute in ways that traditional electronics cannot. Mechanical computers, wherein information…
Mycelium is a promising biomaterial based on fungal mycelium, a highly porous, nanofibrous structure. Scanning electron micrographs are used to characterize its network, but the currently available tools for nanofibrous microstructures do…
In resent years, the software ecosystem for numerical simulation still remains fragmented, with different algorithms and discretization methods often implemented in isolation, each with distinct data structures and programming conventions.…
PySEMTools is a Python-based library for post-processing simulation data produced with high-order hexahedral elements in the context of the spectral element method in computational fluid dynamics. It aims to minimize intermediate steps…
PyMembrane is a software package for simulating liquid and elastic membranes using a discretisation of the continuum description based on unstructured triangulated two-dimensional meshes embedded in three-dimensional space. The package is…
Computer models of humans are ubiquitous throughout computer animation and computer vision. However, these models rarely represent the dynamics of human motion, as this requires adding a complex layer that solves body motion in response to…
This article presents MuMFiM, an open source application for multiscale modeling of fibrous materials on massively parallel computers. MuMFiM uses two scales to represent fibrous materials such as biological network materials (extracellular…
Existing indoor SLAM datasets primarily focus on robot sensing, often lacking building architectures. To address this gap, we design and construct the first dataset to couple the SLAM and BIM, named SLABIM. This dataset provides BIM and…
Fluorescence lifetime imaging microscopy (FLIM) is a powerful technique in biomedical research that uses the fluorophore decay rate to provide additional contrast in fluorescence microscopy. However, at present, the calculation, analysis,…
Mesoscale molecular assemblies on the cell surface, such as cilia and filopodia, integrate information, control transport and amplify signals. Synthetic devices mimicking these structures could sensitively monitor these cellular functions…
Scalable and efficient numerical simulations continue to gain importance, as computation is firmly established as the third pillar of discovery, alongside theory and experiment. Meanwhile, the performance of computing hardware grows through…
Simulations of biomolecules have enormous potential to inform our understanding of biology but require extremely demanding calculations. For over twenty years, the Folding@home distributed computing project has pioneered a massively…