看了看不见细胞模拟人类科学.pptVIP

Acknowledgements Michael Ellison Joel Weiner David Arndt Robert Yang Joseph Cruz Peter Tang Funding – bottle drives, bake sales and lemonade stands SimCell is available at: http://wishart.biology.ualberta.ca/SimCell/ Read about it in this month’s issue of ISB! M9-Glucose MOPS Mixture Compound A Compound B Compound C Spectral Deconvolution of a Mixture Containing Compounds A, B and C Fitting NMR Spectra with Eclipse Succinate Production Acetate Glycerol Pyruvate Acetate Glycerol Pyruvate Succinate Succinate Metabolic Responses Three Types of Simulation Atomic Scale 0.1 - 1.0 nm Coordinate data Dynamic data 0.1 - 10 ns Molecular dynamics Meso Scale 1.0 - 10 nm Interaction data Kon, Koff, Kd 10 ns - 10 ms Mesodynamics Continuum Model 10 - 100 nm Concentrations Diffusion rates 10 ms - 1000 s Fluid dynamics Meso Continuum Dynamics Meso-scale dynamics also requires solving MD equations (stochastic DE’s) Continuum dynamics require solving fluid dynamics and flux equations (more differential equations) 3 Different methods to simulate at 3 different scales Isn’t there a better way? Cell-Sim CA or Agent-based simulation system Designed to permit easy set-up (4-step set-up Wizard) Allows for general dynamic, stochastic modelling of almost all cellular processes (enzyme kinetics, diffusion, metabolism, operon activity) Allows real time monitoring (graphing) and animation of the system Cell-Sim Four types of molecules: Proteins Small Molecules DNA Molecules Membrane Molecules Two types of rules: Molecule interaction rules - protein-protein, protein-small molecule, protein-DNA interactions. Membrane interaction rules - protein-membrane, small molecule-membrane interactions. Cell-Sim Set-up Wizards Simple Enzyme-Substrate Reaction E + S ? E + P time # molecules (P) SimCell Java application that uses Dynamic Cellular Automata (DCA) to model motions, interactions, transport and transformations at the meso-scale (10-8 to 10-6 m) Uses a square, 2D lattice to model processes, l