Numerical integration of the rate equations of the MerB reaction mechanism

2015-06-12T15:48:42Z (GMT) by Pedro Silva
<p>Source code, Windows executable, and outputs.</p> <p> </p> <p>Syntax is:</p> <p> </p> <p>HgMerB_kinetics [initial concentration of organomercurial (optional)] [number of steps with timestep tightening] [initial_timestep][pH] [type of molecule] [how many seconds of kinetic information you want] [HgMerB (or free MerB) concentration] [concentration of the Hg-removing molecules tested] [barriers in kcal.mol-1 for the 38 reaction steps] [name of output file]</p> <p> </p> <p>Type of molecule is : 1 for MerA, 2 for dithiothreitol, 3 for GSH or other monothiols</p> <p>Notes on the algorithm:</p> <p> </p> <p>A) concentrations are output whenever :</p> <p>A1) concentration of HgMerB decreases by 1%, or</p> <p>A2) concentration of product increases by 1% of initial MerB concentration, or</p> <p>A3) 10^7 integration timesteps have elapsed since the last output (or 3*10^5, if less than 10^7 integration timestpes have elapsed since the beginning of the simulation)</p> <p> </p> <p>B) Integration timestep is scaled to ensure that the concentration of every intermediate does not increase more than 10% of its previous concentration. After product concentration increases above 0.1% of initial enzyme concentration, this test is disabled.  </p> <p>C) Further scaling is always performed to prevent concentrations of any intermediate  from becoming negative.</p> <p>C) Numerical noise (or even outright integration error) may occur if the reaction quotient of any reaction changes too abruptly due to numerical increase in the reactant concentrations above the real equilibrium concentrations or (less commonly) extensive depletion of products. This is most likey to occur when consecutive rection steps have extremely small activation energies.The option of setting a number of  "Timestep tightening cycles" is present to help overcome these issues. In each of these cycles, the timestep is decreased to ensure that, in the next cycle, the intermediates which  currently have positive derivatives (of concentration w.r.t. time) still  have positive derivatives. The requested number of  integration timesteps with  timestep-tightening cycles is performed every time that concentrations are output to disk.</p> <p> </p>