TY - DATA T1 - Numerical integration of the rate equations of the MerB reaction mechanism PY - 2015/06/12 AU - Pedro Silva UR - https://figshare.com/articles/dataset/Numerical_integration_of_the_rate_euqations_of_the_MerB_reaction_mechanism/1433993 DO - 10.6084/m9.figshare.1433993.v10 L4 - https://ndownloader.figshare.com/files/3339974 L4 - https://ndownloader.figshare.com/files/3339980 L4 - https://ndownloader.figshare.com/files/3339983 L4 - https://ndownloader.figshare.com/files/3339989 L4 - https://ndownloader.figshare.com/files/3339995 L4 - https://ndownloader.figshare.com/files/3339998 L4 - https://ndownloader.figshare.com/files/3340004 L4 - https://ndownloader.figshare.com/files/3340010 L4 - https://ndownloader.figshare.com/files/3340013 L4 - https://ndownloader.figshare.com/files/3340019 L4 - https://ndownloader.figshare.com/files/3340025 L4 - https://ndownloader.figshare.com/files/3340031 L4 - https://ndownloader.figshare.com/files/3340037 L4 - https://ndownloader.figshare.com/files/3340043 L4 - https://ndownloader.figshare.com/files/3340049 L4 - https://ndownloader.figshare.com/files/3340055 L4 - https://ndownloader.figshare.com/files/3340061 L4 - https://ndownloader.figshare.com/files/3340067 L4 - https://ndownloader.figshare.com/files/3340070 L4 - https://ndownloader.figshare.com/files/3340076 L4 - https://ndownloader.figshare.com/files/3340082 L4 - https://ndownloader.figshare.com/files/3340088 L4 - https://ndownloader.figshare.com/files/3340094 L4 - https://ndownloader.figshare.com/files/3340103 L4 - https://ndownloader.figshare.com/files/3340109 L4 - https://ndownloader.figshare.com/files/3340115 L4 - https://ndownloader.figshare.com/files/3340118 L4 - https://ndownloader.figshare.com/files/3340124 L4 - https://ndownloader.figshare.com/files/3340130 L4 - https://ndownloader.figshare.com/files/3340136 L4 - https://ndownloader.figshare.com/files/3340142 L4 - https://ndownloader.figshare.com/files/3340148 L4 - https://ndownloader.figshare.com/files/3340151 L4 - https://ndownloader.figshare.com/files/3340157 L4 - https://ndownloader.figshare.com/files/3340163 L4 - https://ndownloader.figshare.com/files/3340169 L4 - https://ndownloader.figshare.com/files/3340175 L4 - https://ndownloader.figshare.com/files/3340181 L4 - https://ndownloader.figshare.com/files/3340187 L4 - https://ndownloader.figshare.com/files/3340193 L4 - https://ndownloader.figshare.com/files/3340199 L4 - https://ndownloader.figshare.com/files/3340202 L4 - https://ndownloader.figshare.com/files/3340208 L4 - https://ndownloader.figshare.com/files/3340214 L4 - https://ndownloader.figshare.com/files/3340220 L4 - https://ndownloader.figshare.com/files/3340226 L4 - https://ndownloader.figshare.com/files/3340232 L4 - https://ndownloader.figshare.com/files/3340238 L4 - https://ndownloader.figshare.com/files/3340241 L4 - https://ndownloader.figshare.com/files/3340247 L4 - https://ndownloader.figshare.com/files/3340253 L4 - https://ndownloader.figshare.com/files/3340259 L4 - https://ndownloader.figshare.com/files/3340265 L4 - https://ndownloader.figshare.com/files/3340271 L4 - https://ndownloader.figshare.com/files/3340277 L4 - https://ndownloader.figshare.com/files/3340283 L4 - https://ndownloader.figshare.com/files/3340289 L4 - https://ndownloader.figshare.com/files/3340295 L4 - https://ndownloader.figshare.com/files/3340301 L4 - https://ndownloader.figshare.com/files/3340307 L4 - https://ndownloader.figshare.com/files/3340310 L4 - https://ndownloader.figshare.com/files/3340316 L4 - https://ndownloader.figshare.com/files/3340322 L4 - https://ndownloader.figshare.com/files/3340328 L4 - https://ndownloader.figshare.com/files/3340334 L4 - https://ndownloader.figshare.com/files/3340340 L4 - https://ndownloader.figshare.com/files/3340346 L4 - https://ndownloader.figshare.com/files/3340352 L4 - https://ndownloader.figshare.com/files/3340358 L4 - https://ndownloader.figshare.com/files/3340364 L4 - https://ndownloader.figshare.com/files/3340370 L4 - https://ndownloader.figshare.com/files/3340376 L4 - https://ndownloader.figshare.com/files/3340382 L4 - https://ndownloader.figshare.com/files/3340388 L4 - https://ndownloader.figshare.com/files/3340766 L4 - https://ndownloader.figshare.com/files/3340772 L4 - https://ndownloader.figshare.com/files/3340769 L4 - https://ndownloader.figshare.com/files/3340775 L4 - https://ndownloader.figshare.com/files/3340778 L4 - https://ndownloader.figshare.com/files/3340784 L4 - https://ndownloader.figshare.com/files/3340790 L4 - https://ndownloader.figshare.com/files/3340787 L4 - https://ndownloader.figshare.com/files/3340796 L4 - https://ndownloader.figshare.com/files/3340793 L4 - https://ndownloader.figshare.com/files/3340799 L4 - https://ndownloader.figshare.com/files/3340802 L4 - https://ndownloader.figshare.com/files/3340805 L4 - https://ndownloader.figshare.com/files/3340808 L4 - https://ndownloader.figshare.com/files/3340811 L4 - https://ndownloader.figshare.com/files/3340814 L4 - https://ndownloader.figshare.com/files/3340823 L4 - https://ndownloader.figshare.com/files/3340817 L4 - https://ndownloader.figshare.com/files/3340826 L4 - https://ndownloader.figshare.com/files/3340829 L4 - https://ndownloader.figshare.com/files/3340832 L4 - https://ndownloader.figshare.com/files/3340835 L4 - https://ndownloader.figshare.com/files/3340838 KW - methylmercury KW - enzyme KW - Biochemistry N2 - Source code, Windows executable, and outputs.   Syntax is:   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]   Type of molecule is : 1 for MerA, 2 for dithiothreitol, 3 for GSH or other monothiols Notes on the algorithm:   A) concentrations are output whenever : A1) concentration of HgMerB decreases by 1%, or A2) concentration of product increases by 1% of initial MerB concentration, or 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)   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.   C) Further scaling is always performed to prevent concentrations of any intermediate  from becoming negative. 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.   ER -