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VCell Project: Enabling Technologies

VCell Project: Enabling Technologies. Jim Schaff 2010 NRCAM Advisory Committee Meeting. SmolDyn integration. SmolDyn is a Brownian dynamics modeling and simulation package

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VCell Project: Enabling Technologies

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  1. VCell Project:Enabling Technologies Jim Schaff 2010 NRCAM Advisory Committee Meeting

  2. SmolDyn integration • SmolDyn is a Brownian dynamics modeling and simulation package Andrews, S. S., Bray, D. (2004) “Stochastic simulation of chemical reactions with spatial resolution and single molecule detail”, Phys Biol, vol 1, issue 3-4, pp 137-51. SmolDyn Simulation VCell Model

  3. SmolDyn integration • VCell model  SmolDyn data model  SmolDyn file  simulator. • 3D Geometry (compartments, surfaces, domain types) • Surfaces: polygonal tessellation or primatives (explicit surfaces). • Compartments: Interior volume points specified (implicit volumes). • Domain Types: like VCell’s subvolumes (groups multiple regions) • VCell Geometry is volume sampled, surfaces are generated, volume region centroid determined. • Molecular Species • Individual molecules without complex state. • diffusion, drift (x,y,z), number of molecules, domain(s) • spatial distributions or positions for initial conditions. • Reactions • VCell mass action kinetics supported.

  4. Level set integration • Example: normal membrane velocity proportional to concentration of intracellular species. • “water intake from local osmotic pressure?”

  5. Level Set Implementation(with Charles Wolgemuth, CCAM) • VCell Model  Motility Data Model  Matlab code generation. • Multiple Phases • Constitutive law (e.g. LinearMaxwell) • 2 phase Gel - fluid or 1 phase viscoelastic (supports N phases). • Frame of reference for contained molecules. • Level Set Geometry • Segmented image  Low pass filter  extension to accurate distance map (Mark Zajac) • 2D – but 3D a trivial extension (for geometry!) • Species • Phase, diffusion rate, reaction rate, initial conditions • Membrane velocity • Explicit expression (normal to surface) Wolgemuth, C. W., Zajac, M. (2009) “The moving boundary node method: a level set-based, finite volume algorithm with applications to cell motility”, J. Comput. Phys. (submitted).

  6. Generalized Topology Update • Refined abstractions • Prototype for SBML spatial extension • New reaction diagram editor (layout similar to ProcessDB)

  7. bases responsefunction 1 sampled at each collocation point image responsefunction 1 Averagedover each 2D image ROI Inverse PDE – bases/responses Mesh refinement “fields” – resolve near membranes and bleach region Concentration due to impulse (“Green’s”function) Fluorescence due to impulse (pre-convolved with PSF) volume bases and collocation pointsrefined along isosurfaces in field.

  8. SBML Spatial Extension • Jim is an SBML editor – 3 year term • Working toward reconciliation of • level-set • analytic volume functions & R-functions • geometric primitives • Polygonal surfaces • CSG. • New Java libSBML for prototyping • Uses “generalized topology” branch to validate concepts an ensure compatability.

  9. Other Technology • Completed VC metadata infrastructure (native RDF), in VCell 4.8 alpha. • Evaluating VTK / ParaView / VisIt for VCell data visualization

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