Summary of 6-Arjunan-MolDyn

SSBD:database URL
Relase date
Updated date
Quantitative data based on Simulation
Number of Datasets
1 ( Image datasets: 0, Quantitative data datasets: 1 )
Size of Datasets
190.8 MB ( Image datasets: 0 bytes, Quantitative data datasets: 190.8 MB )

E. coli

single molecule dynamics
Molecular Function (MF)
Biological Process (BP)
cellular protein localization
Cellular Component (CC)
Biological Imaging Method
XYZ Scale
XY: 1.0 micrometer/pixel, Z: 1.0 micrometer/frame
T scale
0.5 microsecond for each time interval

Image Acquisition
Experiment type
Microscope type
Acquisition mode
Contrast method
Microscope model
Detector model
Objective model
Filter set

Related paper(s)

Satya Nanda Vel Arjunan, Masaru Tomita (2010) A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E. coli MinE to E-ring formation., Systems and synthetic biology, Volume 4, Number 1, pp. 35-53

Published in 2010 Mar (Electronic publication in Dec. 10, 2009, midnight )

(Abstract) UNLABELLED: Many important cellular processes are regulated by reaction-diffusion (RD) of molecules that takes place both in the cytoplasm and on the membrane. To model and analyze such multicompartmental processes, we developed a lattice-based Monte Carlo method, Spatiocyte that supports RD in volume and surface compartments at single molecule resolution. Stochasticity in RD and the excluded volume effect brought by intracellular molecular crowding, both of which can significantly affect RD and thus, cellular processes, are also supported. We verified the method by comparing simulation results of diffusion, irreversible and reversible reactions with the predicted analytical and best available numerical solutions. Moreover, to directly compare the localization patterns of molecules in fluorescence microscopy images with simulation, we devised a visualization method that mimics the microphotography process by showing the trajectory of simulated molecules averaged according to the camera exposure time. In the rod-shaped bacterium Escherichia coli, the division site is suppressed at the cell poles by periodic pole-to-pole oscillations of the Min proteins (MinC, MinD and MinE) arising from carefully orchestrated RD in both cytoplasm and membrane compartments. Using Spatiocyte we could model and reproduce the in vivo MinDE localization dynamics by accounting for the previously reported properties of MinE. Our results suggest that the MinE ring, which is essential in preventing polar septation, is largely composed of MinE that is transiently attached to the membrane independently after recruited by MinD. Overall, Spatiocyte allows simulation and visualization of complex spatial and reaction-diffusion mediated cellular processes in volumes and surfaces. As we showed, it can potentially provide mechanistic insights otherwise difficult to obtain experimentally. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11693-009-9047-2) contains supplementary material, which is available to authorized users.

Satya Nanda Vel Arjunan , Keio University , Institute for Advanced Biosciences
Satya Nanda Vel Arjunan, Masaru Tomita

Dataset List of 6-Arjunan-MolDyn

Dataset ID
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# 484
Datast ID Eco_MinE_AS
Dataset Kind Quantitative data
Dataset Size 190.8 MB
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