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By W. C. Reynolds, R. W. MacCormack

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All cells of a multicellular organism contain the same genetic material. Nevertheless, the use made of it varies widely between different tissues. The current state of a cell is determined by the proteins it contains; it changes when new proteins are produced by decoding genetic information. Understanding the dynamic behavior of gene regulatory systems is a challenge to computational systems biology. The molecular actors within these networks interact nondeterministically. Given a particular condition, one can never tell with certainty which among several thinkable reactions will follow next.

OR2_vacant(or1) ::= pro ? {id,init}, if id=cro then up_or2_prm ! {cro}, up_or2_pr ! {cro}, (new release(Kd_or2_cro)) init ! {release}, OR2_cro(or1,release) else up_or2_prm ! {rep}, up_or2_pr ! {rep}, (new release(infinite)), init ! {release}, if or1=rep then OR2_rep_high(release) else OR2_rep_low(or1,release) + up_or1_or2 ? {new_or1}, OR2_vacant(new_or1) + up_or2_pr ? {new_pr}, if new_pr=polymerase then up_or2_prm ! {blocked}, OR2_blocked else OR2_vacant(or1). OR2_cro(or1,release) ::= release ?

Coli cell volume. We need to divide by A · V for reactions involving two reactants, such as binding; for reactions that transform a single reactant as unbinding, the macroscopic and mesoscopic rates coincide. Note that we assume the cell volume to be constant while ignoring cell growth. 155/ sec We can now quantify the effects of cooperative binding between repressors at OR1 and OR2 . Cooperativity adds a favorable term of −2 kcal mol to the Gibbs binding energy of Rep at OR2 [41] 5 . 155, the same value as for OR1 .

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