1 / 9

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

sari
Télécharger la présentation

VCell Project: Enabling Technologies

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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

More Related