Related papers: Simulated single molecule microscopy with SMeagol
The ribosome is a macromolecular complex which is responsible for protein synthesis in all living cells according to their transcribed genetic information. Using X-ray crystallography and, more recently, cryo-electron microscopy (cryo-EM),…
Recent advances in electron microscopy have enabled the imaging of single cells in 3D at nanometer length scale resolutions. An uncharted frontier for in silico biology is the ability to simulate cellular processes using these observed…
The Smoothed Particles Hydrodynamics (SPH) is a particle-based, meshfree, Lagrangian method used to simulate multidimensional fluids with arbitrary geometries, most commonly employed in astrophysics, cosmology, and computational…
A modular, maintainable and extensible particle beam simulation architecture is presented. Design considerations for single particle, multi particle, and rms envelope simulations (in two and three dimensions) are outlined. Envelope…
The distortion of light's degrees of freedom when passing through complex random media is of great interest across a diversity of fields, e.g., scattering in biological studies. Emulating such media in a controlled laboratory setting…
Soft X-ray tomography provides detailed structural insight into whole cells but is hindered by experimental artifacts such as the missing wedge and by limited availability of annotated datasets. We present SimAQ, a simulation pipeline that…
Blood clotting involves the coupled processes of platelet aggregation and coagulation. Simulating clotting under flow in complex geometries is challenging due to multiple temporal and spatial scales and high computational cost. clotFoam is…
Large language models excel at interpreting complex natural language instructions, enabling them to perform a wide range of tasks. In the life sciences, single-cell RNA sequencing (scRNA-seq) data serves as the "language of cellular…
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…
The giant single-celled slime mould Physarum polycephalum has inspired rapid develop- ments in unconventional computing substrates since the start of this century. This is primarily due to its simple component parts and the distributed…
This manual accompanies the release of the particle data for 24 simulations of the EAGLE suite of cosmological hydrodynamical simulations of galaxy formation by the virgo consortium. It describes how to download these snapshots and how to…
Simourg is a software based on the Geant4 toolkit and provides the Monte Carlo simulation of nuclear spectrometric setups with simple geometries for such applications as nuclear decay research, radiation safety, and nuclear medicine. With…
Here we report on a set of programs developed at the ZMBH Bio-Imaging Facility for tracking real-life images of cellular processes. These programs perform 1) automated tracking; 2) quantitative and comparative track analyses of different…
Multiplex tissue immunostaining is a technology of growing relevance as it can capture in situ the complex interactions existing between the elements of the tumor microenvironment. The existence and availability of large, annotated image…
We present MASSCLEAN, a new, sophisticated and robust stellar cluster image and photometry simulation package. This visualization tool is able to create color-magnitude diagrams and standard FITS images in any of the traditional optical and…
The basis for most vision based applications like robotics, self-driving cars and potentially augmented and virtual reality is a robust, continuous estimation of the position and orientation of a camera system w.r.t the observed environment…
We describe a web-based tool, MakeSBML (https://sys-bio.github.io/makesbml/), that provides an installation-free application for creating, editing, and searching the Biomodels repository for SBML-based models. MakeSBML is a client-based web…
In the era of data-driven science, conducting computational experiments that involve analysing large datasets using heterogeneous computational clusters, is part of the everyday routine for many scientists. Moreover, to ensure the…
This paper presents libRoadRunner, an extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models \ expressed using Systems Biology Markup Language (SBML). SBML is the most widely…
In fluorescence microscopy, Single Molecule Localization Microscopy (SMLM) techniques aim at localizing with high precision high density fluorescent molecules by stochastically activating and imaging small subsets of blinking emitters.…