2.1_BioBodeDetails

2.1_BioBodeDetails - Danger bad scholarship ahead Huge...

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Danger: bad scholarship ahead • Huge literatures going back a century (at least) hat I don’t know all that well (not my main research) – That I don t know all that well (not my main research) – Bewildering amount of domain details ersistent mysteries (and controversy) Persistent mysteries (and controversy) – Exist consistent, coherent components of the story – Even experts know only small fraction • Large teams of collaborators (i.e. the real talent) •V e r y “new” results – Not “written up” yet, just the slides you see (sort of) – Intended to be universal/accessible (but aren’t yet) – Illustrate principles beyond the domains – Pedagogy, not depth
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Universals in complex, robust networks Today’s focus on fundamentals oncepts: Complexity, robustness, and fragility Concepts: Complexity, robustness, and fragility • Theory: Fundamental laws, constraints, tradeoffs etwork architecture Network architecture • Illustrate with “simple” and familiar case studies • Warm up with some (hopefully familiar) example
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[ a system ] can have property bust r [ a property ] robust for [ a set of perturbations ] Fragile Yet be fragile for [a different property] Robust Or [ a different perturbation ] Robust yet fragile = fragile robustness
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ad Complementary approaches bad asteful Find and x bugs wa Sharpen fix bugs hard bounds fragile
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signaling gene expression metabolism source receiver lineage Biological athways pathways
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signaling gene expression metabolism source receiver lineage ontrol control nergy energy materials More omplex complex feedback
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source receiver ontrol control nergy energy materials Autocatalytic feedback
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signaling gene expression metabolism source receiver lineage What theory is relevant to ese more complex ontrol these more complex feedback systems? control nergy energy materials More omplex complex feedback
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Inside every cell atabolism rsors Nucleotides Catabolism Precu r Carriers Core metabolic bowtie
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Core metabolism atabolism rsors Nucleotides Catabolism Precu r Carriers Inside every ell ( 0 30 cell ( 10 )
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atabolism rsors Catabolism Precu r Carriers
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Gly atabolism G1P G6P F6P Catabolism F1-6BP Gly3p 13BPG ATP TCA Pyr Oxa Cit ACA PEP 3PG 2PG NADH
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Gly 1P G1P G6P ursors F6P 1 BP Prec u metabolites F1-6BP Gly3p 13BPG 3PG TCA Pyr Oxa ACA PEP 2PG Cit
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Gly 1P nzymatically G1P G6P Enzymatically catalyzed reactions F6P 1 BP F1-6BP Gly3p 13BPG 3PG TCA PEP Pyr 2PG Oxa ACA Cit
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Gly 1P Autocatalytic G1P G6P F6P 1 BP consumed Rest of cell F1-6BP Gly3p ATP 13BPG 3PG produced TCA Pyr Oxa ACA PEP 2PG NADH Cit
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Gly 1P G1P G6P Feedbacks F6P 1 BP Autocatalysis F1-6BP Gly3p ATP Control 13BPG 3PG TCA PEP Pyr 2PG NADH Oxa ACA Cit
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Gly G1P G6P F6P F1-6BP Gly3p 3BPG Oxa 13BPG 3PG TCA Pyr Cit ACA PEP 2PG
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Gly G1P Unreadable G6P F6P F1-6BP hy so complex?
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This note was uploaded on 01/04/2012 for the course CDS 212 taught by Professor Tarraf,d during the Fall '08 term at Caltech.

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2.1_BioBodeDetails - Danger bad scholarship ahead Huge...

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