//genesis // kkit Version 8 flat dumpfile // Saved on Thu Dec 12 12:36:50 2002 include kkit {argv 1} FASTDT = 1e-05 SIMDT = 0.0001 CONTROLDT = 1 PLOTDT = 0.1 MAXTIME = 100 TRANSIENT_TIME = 2 VARIABLE_DT_FLAG = 1 DEFAULT_VOL = 1e-06 VERSION = 8.0 setfield /file/modpath value /home2/bhalla/scripts/modules kparms //genesis initdump -version 3 -ignoreorphans 1 simobjdump table input output alloced step_mode stepsize x y z simobjdump xtree path script namemode sizescale simobjdump xcoredraw xmin xmax ymin ymax simobjdump xtext editable simobjdump xgraph xmin xmax ymin ymax overlay simobjdump xplot pixflags script fg ysquish do_slope wy simobjdump group xtree_fg_req xtree_textfg_req plotfield expanded movealone \ link savename file version md5sum mod_save_flag x y z simobjdump kpool CoTotal CoInit Co n nInit nTotal nMin vol slave_enable notes \ xtree_fg_req xtree_textfg_req x y z simobjdump kreac kf kb notes xtree_fg_req xtree_textfg_req x y z simobjdump kenz CoComplexInit CoComplex nComplexInit nComplex vol k1 k2 k3 \ keepconc usecomplex notes xtree_fg_req xtree_textfg_req link x y z simobjdump stim level1 width1 delay1 level2 width2 delay2 baselevel trig_time \ trig_mode notes xtree_fg_req xtree_textfg_req is_running x y z simobjdump xtab input output alloced step_mode stepsize notes editfunc \ xtree_fg_req xtree_textfg_req baselevel last_x last_y is_running x y z simobjdump kchan perm gmax Vm is_active use_nernst notes xtree_fg_req \ xtree_textfg_req x y z simobjdump proto x y z simobjdump linkinfo xtree_fg_req xtree_textfg_req uplink downlink x y z simobjdump uplink xtree_fg_req xtree_textfg_req x y z simobjdump downlink xtree_fg_req xtree_textfg_req x y z simobjdump mirror notes xtree_fg_req x y z simundump kpool /kinetics/E 0 10 1e-05 1e-05 5.9999e+09 5.9999e+09 5.9999e+15 \ 0 5.9999e+14 0 "" blue black -6 -1 0 simundump kpool /kinetics/E.S1.S2 0 0 0 0 0 0 0 0 5.9999e+14 0 "" 26 black 2 \ -1 0 simundump kpool /kinetics/E.S1_in 0 0 0 0 0 0 0 0 5.9999e+14 0 "" blue black \ -2 5 0 simundump kpool /kinetics/E.S1 0 0 0 0 0 0 0 0 5.9999e+14 0 "" blue black -2 \ 1 0 simundump kpool /kinetics/E.S2 0 0 0 0 0 0 0 0 5.9999e+14 0 "" 47 black -2 -3 \ 0 simundump kpool /kinetics/E_in 0 0 0 0 0 0 0 0 5.9999e+14 0 "" blue black -6 \ -7 0 simundump kreac /kinetics/k5 0 2.6e-05 0 "" white black -2 3 0 simundump kreac /kinetics/k1 0 3.3334e-17 6 "" white black -4 0 0 simundump kreac /kinetics/k1_prime 0 1.6667e-15 10 "" white black 0 0 0 simundump kreac /kinetics/k1_prime_2 0 1.6667e-15 10 "" white black -4 -2 0 simundump kreac /kinetics/k5_2 0 2.6e-05 0 "" white black -6 -5 0 simundump kreac /kinetics/k5_3 0 2.6e-05 0 "" white black -2 -5 0 simundump kreac /kinetics/k5_4 0 2.6e-05 0 "" white black 2 -5 0 simundump kreac /kinetics/k2 0 30 0 "" white black 4 -1 0 simundump kpool /kinetics/E.P1 0 0 0 0 0 0 0 0 5.9999e+14 0 "" 1 black 6 -1 0 simundump kpool /kinetics/AMP 0 0 0 0 0 0 0 0 5.9999e+14 0 "" blue black 4 -3 \ 0 simundump kpool /kinetics/E.P 0 0 0 0 0 0 0 0 5.9999e+14 0 "" 58 black 10 -1 \ 0 simundump kreac /kinetics/k3 0 10 0 "" white black 8 -1 0 simundump kpool /kinetics/photon 0 0 0 0 0 0 0 0 5.9999e+14 0 "" blue black 8 \ -3 0 simundump kreac /kinetics/k6 0 0.0003 0 "" white black 10 -5 0 simundump kpool /kinetics/E.P_in 0 0 0 0 0 0 0 0 5.9999e+14 0 "" blue black \ 10 -7 0 simundump kpool /kinetics/E.S2_in 0 0 0 0 0 0 0 0 5.9999e+14 0 "" blue black \ -2 -7 0 simundump kpool /kinetics/E.S1.S2_in 0 0 0 0 0 0 0 0 5.9999e+14 0 "" blue \ black 2 -7 0 simundump kreac /kinetics/k4 0 0.1 1.6667e-15 "" white black 10 3 0 simundump kpool /kinetics/P 0 0 0 0 0 0 0 0 5.9999e+14 0 "" blue black 12 -1 \ 0 simundump kpool /kinetics/S1 0 1e+05 1000 1000 5.9999e+17 5.9999e+17 \ 5.9999e+19 0 5.9999e+14 0 "" blue black -6 0 0 simundump kpool /kinetics/S2 0 100 100 100 5.9999e+16 5.9999e+16 5.9999e+16 0 \ 5.9999e+14 0 "" blue black 2 0 0 simundump kreac /kinetics/k1_2 0 3.3334e-17 6 "" white black 0 -2 0 simundump xgraph /graphs/conc1 0 0 100 0 1.0776e+08 0 simundump xgraph /graphs/conc2 0 0 100 0 4.8924e-07 0 simundump xplot /graphs/conc2/E.S1.Co 3 524288 \ "delete_plot.w ; edit_plot.D " blue 0 0 1 simundump xplot /graphs/conc2/E.P1.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 1 0 0 1 simundump xplot /graphs/conc2/E.P.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 58 0 0 1 simundump xgraph /moregraphs/conc3 0 -1 100 0 9.7826e-06 0 simundump xgraph /moregraphs/conc4 0 0 100 0 5e-08 0 simundump xplot /moregraphs/conc3/E.Co 3 524288 \ "delete_plot.w ; edit_plot.D " blue 0 0 1 simundump xplot /moregraphs/conc3/E.S1.S2.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 26 0 0 1 simundump xplot /moregraphs/conc4/E.S2.Co 3 524288 \ "delete_plot.w ; edit_plot.D " 47 0 0 1 simundump xcoredraw /edit/draw 0 -8 14 -9 7 simundump xtree /edit/draw/tree 0 \ /kinetics/#[],/kinetics/#[]/#[],/kinetics/#[]/#[]/#[][TYPE!=proto],/kinetics/#[]/#[]/#[][TYPE!=linkinfo]/##[] \ "edit_elm.D ; drag_from_edit.w " auto 0.6 simundump xtext /file/notes 0 1 xtextload /file/notes \ "This model is based on L. Yu Brovko et al 1994," \ "Biochemistry (Moscow) 59(2):1994." \ "The model is according to their reaction scheme and rates, but" \ "there are discrepancies both with the simulated (fig 4) and" \ "with the experimental data in their paper. The overall time-course" \ "and luciferase dependence of luminescence (figs 1, 2, 3a) are" \ "reasonable semi-quantitative matches." addmsg /kinetics/k1 /kinetics/E REAC A B addmsg /kinetics/k1_prime_2 /kinetics/E REAC A B addmsg /kinetics/k5_2 /kinetics/E REAC A B addmsg /kinetics/k4 /kinetics/E REAC B A addmsg /kinetics/k1_prime /kinetics/E.S1.S2 REAC B A addmsg /kinetics/k5_4 /kinetics/E.S1.S2 REAC A B addmsg /kinetics/k2 /kinetics/E.S1.S2 REAC A B addmsg /kinetics/k1_2 /kinetics/E.S1.S2 REAC B A addmsg /kinetics/k5 /kinetics/E.S1_in REAC B A addmsg /kinetics/k5 /kinetics/E.S1 REAC A B addmsg /kinetics/k1 /kinetics/E.S1 REAC B A addmsg /kinetics/k1_prime /kinetics/E.S1 REAC A B addmsg /kinetics/k1_prime_2 /kinetics/E.S2 REAC B A addmsg /kinetics/k5_3 /kinetics/E.S2 REAC A B addmsg /kinetics/k1_2 /kinetics/E.S2 REAC A B addmsg /kinetics/k5_2 /kinetics/E_in REAC B A addmsg /kinetics/E.S1 /kinetics/k5 SUBSTRATE n addmsg /kinetics/E.S1_in /kinetics/k5 PRODUCT n addmsg /kinetics/E /kinetics/k1 SUBSTRATE n addmsg /kinetics/E.S1 /kinetics/k1 PRODUCT n addmsg /kinetics/S1 /kinetics/k1 SUBSTRATE n addmsg /kinetics/E.S1 /kinetics/k1_prime SUBSTRATE n addmsg /kinetics/E.S1.S2 /kinetics/k1_prime PRODUCT n addmsg /kinetics/S2 /kinetics/k1_prime SUBSTRATE n addmsg /kinetics/E /kinetics/k1_prime_2 SUBSTRATE n addmsg /kinetics/E.S2 /kinetics/k1_prime_2 PRODUCT n addmsg /kinetics/S2 /kinetics/k1_prime_2 SUBSTRATE n addmsg /kinetics/E /kinetics/k5_2 SUBSTRATE n addmsg /kinetics/E_in /kinetics/k5_2 PRODUCT n addmsg /kinetics/E.S2 /kinetics/k5_3 SUBSTRATE n addmsg /kinetics/E.S2_in /kinetics/k5_3 PRODUCT n addmsg /kinetics/E.S1.S2 /kinetics/k5_4 SUBSTRATE n addmsg /kinetics/E.S1.S2_in /kinetics/k5_4 PRODUCT n addmsg /kinetics/E.S1.S2 /kinetics/k2 SUBSTRATE n addmsg /kinetics/E.P1 /kinetics/k2 PRODUCT n addmsg /kinetics/AMP /kinetics/k2 PRODUCT n addmsg /kinetics/k2 /kinetics/E.P1 REAC B A addmsg /kinetics/k3 /kinetics/E.P1 REAC A B addmsg /kinetics/k2 /kinetics/AMP REAC B A addmsg /kinetics/k3 /kinetics/E.P REAC B A addmsg /kinetics/k6 /kinetics/E.P REAC A B addmsg /kinetics/k4 /kinetics/E.P REAC A B addmsg /kinetics/E.P1 /kinetics/k3 SUBSTRATE n addmsg /kinetics/E.P /kinetics/k3 PRODUCT n addmsg /kinetics/photon /kinetics/k3 PRODUCT n addmsg /kinetics/k3 /kinetics/photon REAC B A addmsg /kinetics/E.P /kinetics/k6 SUBSTRATE n addmsg /kinetics/E.P_in /kinetics/k6 PRODUCT n addmsg /kinetics/k6 /kinetics/E.P_in REAC B A addmsg /kinetics/k5_3 /kinetics/E.S2_in REAC B A addmsg /kinetics/k5_4 /kinetics/E.S1.S2_in REAC B A addmsg /kinetics/E.P /kinetics/k4 SUBSTRATE n addmsg /kinetics/P /kinetics/k4 PRODUCT n addmsg /kinetics/E /kinetics/k4 PRODUCT n addmsg /kinetics/k4 /kinetics/P REAC B A addmsg /kinetics/k1 /kinetics/S1 REAC A B addmsg /kinetics/k1_2 /kinetics/S1 REAC A B addmsg /kinetics/k1_prime /kinetics/S2 REAC A B addmsg /kinetics/k1_prime_2 /kinetics/S2 REAC A B addmsg /kinetics/E.S2 /kinetics/k1_2 SUBSTRATE n addmsg /kinetics/E.S1.S2 /kinetics/k1_2 PRODUCT n addmsg /kinetics/S1 /kinetics/k1_2 SUBSTRATE n addmsg /kinetics/E.S1 /graphs/conc2/E.S1.Co PLOT Co *E.S1.Co *blue addmsg /kinetics/E.P1 /graphs/conc2/E.P1.Co PLOT Co *E.P1.Co *1 addmsg /kinetics/E.P /graphs/conc2/E.P.Co PLOT Co *E.P.Co *58 addmsg /kinetics/E /moregraphs/conc3/E.Co PLOT Co *E.Co *blue addmsg /kinetics/E.S1.S2 /moregraphs/conc3/E.S1.S2.Co PLOT Co *E.S1.S2.Co *26 addmsg /kinetics/E.S2 /moregraphs/conc4/E.S2.Co PLOT Co *E.S2.Co *47 enddump // End of dump call /kinetics/E.S1/notes LOAD \ "S1 is ATP. E.S1 is luciferase.ATP" call /kinetics/E.S2/notes LOAD \ "S2 is Luciferin." call /kinetics/photon/notes LOAD \ "The photon pool is equivalent to the cumulative photon count." \ "The time derivative of this pool count (in number of photons, not" \ "in terms of concentration) will give the rate of production" \ "of photons." call /kinetics/S1/notes LOAD \ "S1 is ATP" \ "" call /kinetics/S2/notes LOAD \ "S2 = LH2" complete_loading