100Final%20conclusions

100Final%20conclusions - Modeling Molecular and Cellular...

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1 Modeling Molecular and Cellular systems Modeling Nature’s laws -1 st law -2 nd law - Mass conservation Experimental data - Model constants - Estalishing new relationships - Verify model predictions - Establish empirical Eqn in the model Hypotheses - e.g., law of mass action in this course What is covered in this course? Where to go from here? 1. Rates and kinetics of chemical reactions 2. Simplification of kinetic analysis 3. Enzyme kinetics and its regulation 4. Cell signaling 5. Cell growth kinetics 6. Regulation of gene expression 7. First and second laws of thermodynamics 8. Phase transition of pure substances 9. Standard State and Gibbs Energy 10. Simple mixtures 11. Chemical Equilibrium 12. Equilibrium DNA binding analysis 13. Receptor-mediated endocytosis Biological Systems at Multiple Scales Organ level (L = 10 -3 –10 -1 m) Body level (L = 1 m) Tissue and Cell levels (L = 10 -5 –10 -4 m) Molecular level (L = 10 -9 –10 -7 m)
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2 Multi-scale Modeling Body Tissue Cell Molecule Multi-scales Advantage: - Providing detailed analysis of a system. - Revealing mechanisms  dV r v F r F S f F F D t F ) sin( ) ( ) exp( ) ( ) (  Challenges: - Knowing detailed information of the system. - Dealing with complex system and nonlinear interactions Feasibility: - 5-6 orders of magnitude in spatial and temporal changes in simple systems. - 2-3 orders of magnitude changes in complex systems. Mechanistic modeling of a system often involves multiple scales in L and t. Images are from http://en.wikipedia.org/ 1 st and 2 nd laws (Mass) = 0 1 st and 2 nd laws (Mass) = 0 1 st and 2 nd laws (Mass) = 0 1 st and 2 nd laws (Mass) = 0 1 st and 2 nd laws (Mass) = 0 Phenomenological Modeling Input Output Input Output Input Output Input Output Input Output Advantage: - A general approach to modeling of all different systems. - Providing average properties of the systems (e.g., H, E, S, G, or Diffusion Coefficient). Disadvanges: - Cannot provide mechanisms and predict individual processes in the system. - The concepts are often abstract.
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100Final%20conclusions - Modeling Molecular and Cellular...

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