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May 30, 2023 317 likes •446 views

Enabling Grids for E-sciencE Construction of a Mathematical Model of a Cell as a Challenge for Science in the 21 Century and EGEE Project Victor Lakhno Institute of Mathematical Problems of Biology RAS EGEE User Forum CERN, 01-03.03.2006

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INFSO-RI-508833

Enabling Grids for E-sciencE

www.eu-egee.org

Construction of a Mathematical Model of a Cell as a Challenge for Science in the 21 Century and EGEE Project

Victor Lakhno

Institute of Mathematical Problems of Biology RAS EGEE User Forum CERN, 01-03.03.2006

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www.mathcell.ru

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The project "MATHEMATICAL CELL" is directed on creation of the multipurpose environment for studies in biology of a living cell by integration of mathematical models, resources in bioinformatics, and computational facilities. It will help to produce a new knowledge about a living cell, as self-consistent dynamic system. The project is carried out by the Institute

f Mathematical Problems of Biology

in frames of the EGEE project. It leads to the gradual deployment of new applications in computational biology

n EGEE infrastructure.

About the project

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3D model of the cell

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ENCYCLOPAEDIA

Encyclopedia

physical and mathematical knowledge biological knowledge

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Links

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Library of mathematical models

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Сharge transfer in DNA

In order to estimate the average value of macroscopic physical parameters

ne has to calculate the large number of realizations.

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Charge transfer in mytochondrion membrane

Cytochrom C Ubiquinon Membrane Protein complexes, built in a membrane

Simulation models

Real mytochondrion membrane

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Cellular metabolism

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Mathematical modeling of cell metabolism

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Future development of MathCell

In the near future IMPB RAS is planning to deploy in EGEE a software tool to calculate a charge transfer on inner membranes of some compartments of eukaryotic cells (mitochondria and chloroplasts) through direct simulation of charge transfer with regard to the detailed structure of biomembranes containing various molecular

complexes. Next on the agenda is a software tool to calculate

metabolic reaction pathways in compartments of a cell as well as the dynamics of gene networks. Further development of the MathCell project implies integration of individual components of the model into an integrated program system which would enable modeling of cell processes at all levels – from microscopic to macroscopic scales and from picoseconds to the scales comparable with the cell lifetime. Such modeling will naturally require combining of computational and commutation resources provided by EGEE project and their merging into an integrated computational medium.