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The Problem

The Problem. Ion Moraru Jim Schaff Boris Slepchenko. The Virtual Cell Project. Rashad Badrawi John Carson Yung-Sze Choi Ann Cowan Fei Gao Susan Krueger Anu Lakshminarayana Daniel Lucio Frank Morgan Igor Novak Diana Resasco Dong-Guk Shin John Wagner NIGMS NSF.

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The Problem

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  1. The Problem

  2. Ion Moraru Jim Schaff Boris Slepchenko The Virtual Cell Project • Rashad Badrawi • John Carson • Yung-Sze Choi • Ann Cowan • Fei Gao • Susan Krueger • Anu Lakshminarayana • Daniel Lucio • Frank Morgan • Igor Novak • Diana Resasco • Dong-Guk Shin • John Wagner • NIGMS • NSF

  3. Hypothesis (Model) • What are the initial concentrations, diffusion coefficients and locations of all the implicated molecules? • What are the rate laws and rate constants for all the biochemical transformations? • What are the membrane fluxes and how are they regulated? • How are the forces controlling cytoskeletal mechanics regulated? Quantitative Cell Biology Experiment Predictions Dynamics of Cellular Structures and Molecules Simulation Trends in Cell Biology 13:570-576 (2003)

  4. The Virtual Cell – Modeling Reactions and Diffusion kf kr A + B C C C x B A C

  5. Physiology Applications Applications Applications Math Description Math Description Math Description Applications Molecular Species Compartment Topology Topology Geometry, Initial Conditions, Boundary Conditions, Diffusion Coefficients, Pseudo-steady, Enable/Disable Reactions Topology Geometry, Initial Conditions, Boundary Conditions, Diffusion Coefficients, Pseudo-steady, Enable/Disable Reactions Topology Geometry, Initial Conditions, Boundary Conditions, Diffusion Coefficients, Pseudo-steady, Enable/Disable Reactions Topology Geometry, Initial Conditions, Boundary Conditions, Diffusion Coefficients, Pseudo-steady, Enable/Disable ReactionsElectrophysiology Protocols VCMDL Reactions and Fluxes Simulations Images Images Images Simulations Simulations Simulations Timestep, Mesh Size, Parameter Searches, Sensitivity Timestep, Mesh Size, Parameter Searches, Sensitivity Images Timestep, Mesh Size, Parameter Searches, Sensitivity Timestep, Mesh Size, Parameter Searches, Sensitivity Results Results Results Results

  6. VCDB

  7. Experiment Bradykinin Induced Calcium Wave in a Neuroblastoma Cell Simulation C. Fink et al., JCB, 1999 C. Fink et al., BJ, 2000

  8. Other model examples • Model of Stress-Dependent Focal Adhesion Dynamics: (Novak) • Modeling mpf activation at fertilization: stochastic modeling (Slepchenko and Terasaki) • Modeling active intracellular transport in sea urchin (advection) (Rodionov) • Intracellular trafficking of RNA granules (stochastic modeling) Carson • Diffusion Processes in Mitochondria (Moraru) • TIR FRAP experiment at ribbon synapses • Calcium wave at fertilization in Xenopus eggs (Nuccitelli) • Nuclear envelope breakdown at fertilization (Terasaki & Slepchenko)

  9. What we can't do yet – but are working on…. • Diffusion within the membrane • 2D in final testing • 3D coming next • Stochasitc events/discrete particles (large scale) • In Math Interface, not in Biology Interface • Changing geometries • Very hard, in deep development • Input spatial changes in species concentrations directly from images. http://vcell.org

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