ArticleScientific reports2020
FluoSim: simulator of single molecule dynamics for fluorescence live-cell and super-resolution imaging of membrane proteins.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed.
- Single molecule dynamics in a virtual cell combining a 3-dimensional matrix model with random walks.Scientific reports · 2024Article
- Sub-membrane actin rings compartmentalize the plasma membrane.The Journal of cell biology · 2024Article
- Development of AI-assisted microscopy frameworks through realistic simulation with pySTED.Nature machine intelligence · 2024Article
- Physically informed Monte Carlo simulation of dual-wedge prism-based spectroscopic single-molecule localization microscopy.Journal of biomedical optics · 2024Article
- What's past is prologue: FRAP keeps delivering 50 years later.Biophysical journal · 2023Review
- Single molecule imaging simulations with advanced fluorophore photophysics.Communications biology · 2023Article
- A generative model to simulate spatiotemporal dynamics of biomolecules in cells.Biological imaging · 2023Article
- Precise measurement of nanoscopic septin ring structures with deep learning-assisted quantitative superresolution microscopy.Molecular biology of the cell · 2022Article
- In vitro reconstitution of Escherichia coli divisome activation.Nature communications · 2022Article
- Article
- Emerin self-assembly and nucleoskeletal coupling regulate nuclear envelope mechanics against stress.Journal of cell science · 2022Article
- High-Resolution Fluorescence Imaging Combined With Computer Simulations to Quantitate Surface Dynamics and Nanoscale Organization of Neuroligin-1 at Synapses.Frontiers in synaptic neuroscience · 2022Article
- An Efficient GUI-Based Clustering Software for Simulation and Bayesian Cluster Analysis of Single-Molecule Localization Microscopy Data.Frontiers in bioinformatics · 2021Article
- PySTACHIO: Python Single-molecule TrAcking stoiCHiometry Intensity and simulatiOn, a flexible, extensible, beginner-friendly and optimized program for analysis of single-molecule microscopy data.Computational and structural biotechnology journal · 2021Article
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5 authors.
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Abstract
Fluorescence live-cell and super-resolution microscopy methods have considerably advanced our understanding of the dynamics and mesoscale organization of macro-molecular complexes that drive cellular functions. However, different imaging techniques can provide quite disparate information about protein motion and organization, owing to their respective experimental ranges and limitations. To address these issues, we present here a robust computer program, called FluoSim, which is an interactive simulator of membrane protein dynamics for live-cell imaging methods including SPT, FRAP, PAF, and FCS, and super-resolution imaging techniques such as PALM, dSTORM, and uPAINT. FluoSim integrates diffusion coefficients, binding rates, and fluorophore photo-physics to calculate in real time the localization and intensity of thousands of independent molecules in 2D cellular geometries, providing simulated data directly comparable to actual experiments. FluoSim was thoroughly validated against experimental data obtained on the canonical neurexin-neuroligin adhesion complex at cell-cell contacts. This unified software allows one to model and predict membrane protein dynamics and localization at the ensemble and single molecule level, so as to reconcile imaging paradigms and quantitatively characterize protein behavior in complex cellular environments.
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