//genesis
// kkit Version 9 flat dumpfile
 
// Saved on Mon Aug 18 17:00:52 2003
 
include kkit {argv 1}
 
FASTDT = 0.0001
SIMDT = 0.005
CONTROLDT = 10
PLOTDT = 10
MAXTIME = 3000
TRANSIENT_TIME = 2
VARIABLE_DT_FLAG = 1
DEFAULT_VOL = 2e-08
VERSION = 9.0
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 transport input output alloced step_mode stepsize dt delay clock \
  kf 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 group /kinetics/Transcription 0 61 black x 1 0 "" Transcription \
  /home2/bhalla/scripts/modules/Transcription_0.g 0 0 0 29 0 0
simundump kreac /kinetics/Transcription/Complex_Formation 0 1.5167e-11 0 "" \
  white 61 23 -1 0
simundump kpool /kinetics/Transcription/RNAP 0 0.083333 0.0375 0.0375 4.5e+11 \
  4.5e+11 1e+12 0 1.2e+13 0 "" 16 61 22 -3 0
simundump kpool /kinetics/Transcription/TrRNAP 0 0 0 0 0 0 0 0 1.2e+13 0 "" \
  blue 61 24 1 0
simundump kreac /kinetics/Transcription/In_Transcription 0 3.75e-19 0 "" \
  white 61 25 -1 0
simundump kpool /kinetics/Transcription/N 0 1000 1000 1000 1.2e+16 1.2e+16 \
  1.2e+16 0 1.2e+13 0 "" blue 61 26 1 0
simundump kpool /kinetics/Transcription/P 0 0.025 0.025 0.025 3e+11 3e+11 \
  3e+11 0 1.2e+13 0 "" 15 61 24 -3 0
simundump kpool /kinetics/Transcription/mRNA 0 0 0 0 0 0 0 0 1.2e+13 0 "" \
  blue 61 22 -7 0
simundump transport /kinetics/Transcription/mRNA_synthesis 4 1431 7.799e+07 1 \
  6 0 0.25 425 4 0.0002 yellow 61 17 -6 0
loadtab /kinetics/Transcription/mRNA_synthesis table 1 1700 0 1700 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 
loadtab -continue \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 
loadtab -continue \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 
loadtab -continue \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 
loadtab -continue \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 
loadtab -continue \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 
loadtab -continue \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 
loadtab -continue \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 
loadtab -continue \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
simundump kreac /kinetics/Transcription/RNAPdecay 0 1e-05 0 "" white 61 21 -1 \
  0
simundump kreac /kinetics/Transcription/mRNA_Decay 0 1e-05 0 "" 15 61 21 -5 0
simundump kpool /kinetics/Transcription/decayed_mRNA 0 0 0 0 0 0 0 0 1.2e+13 \
  0 "" blue 61 20 -3 0
simundump kpool /kinetics/Transcription/decayed_RNAP 0 0 0 0 0 0 0 0 1.2e+13 \
  0 "" blue 61 22 1 0
simundump kpool /kinetics/Transcription/RBS 0 0 0 0 0 0 0 0 1.2e+13 0 "" 36 \
  61 26 -3 0
simundump kreac /kinetics/Transcription/RBS_Decay 0 1e-05 0 "" white 61 27 -5 \
  0
simundump kpool /kinetics/Transcription/decayed_RBS 0 0 0 0 0 0 0 0 1.2e+13 0 \
  "" blue 61 28 -3 0
simundump xtab /kinetics/noOligo 0 -600 0 1 2 0 "" edit_xtab white red 0 0 0 \
  0 36 -9 0
loadtab /kinetics/noOligo table 0 2500 0 2500 \
 24.5 24.6797 24.8594 25.0391 25.2188 25.6955 26.2346 26.7737 27.3128 26.8353 \
 25.817 24.7987 23.7804 23.537 24.136 24.735 25.334 25.384 24.186 22.988 \
 21.79 20.908 22.106 23.304 24.502 25.7 24.4298 23.0521 21.6744 20.2967 \
 20.705 21.6035 22.502 23.4005 24.116 24.715 25.314 25.913 26.5906 27.3693 \
 28.148 28.9267 29.0734 27.4561 25.8388 24.2215 22.7932 23.2724 23.7516 \
 24.2308 24.71 24.9147 25.0944 25.2741 25.4538 26.123 26.9616 27.8002 28.6388 \
 28.2839 27.026 25.7681 24.5102 23.6552 23.4156 23.176 22.9364 23.0426 \
 24.3604 25.6782 26.996 28.1949 27.0568 25.9187 24.7806 23.6425 24.4956 \
 25.6337 26.7718 27.9099 27.242 25.8044 24.3668 22.9292 22.7872 23.8055 \
 24.8238 25.8421 26.3092 25.7701 25.231 24.6919 24.25 24.25 24.25 24.25 \
 24.256 25.1545 26.053 26.9515 27.85 27.7006 27.3412 26.9818 26.6224 25.868 \
 24.9096 23.9512 22.9928 22.5873 22.767 22.9467 23.1264 23.4744 24.1932 \
 24.912 25.6308 26.3164 26.7956 27.2748 27.754 28.2332 27.4986 26.7199 \
 25.9412 25.1625 25.5688 26.2876 27.0064 27.7252 26.853 24.9961 23.1392 \
 21.2823 20.7022 21.7205 22.7388 23.7571 24.5162 24.5761 24.636 24.6959 \
 24.7036 24.2244 23.7452 23.266 22.7868 23.4689 24.2476 25.0263 25.805 \
 26.2245 26.524 26.8235 27.123 27.25 27.25 27.25 27.25 27.2259 27.166 27.1061 \
 27.0462 26.9863 26.9264 26.8665 26.8066 26.7236 26.2444 25.7652 25.286 \
 24.8068 23.7468 22.6087 21.4706 20.3325 21.8656 24.5012 27.1368 29.7724 \
 30.488 29.5296 28.5712 27.6128 26.8056 26.2665 25.7274 25.1883 24.9628 \
 26.1009 27.239 28.3771 29.4936 29.0144 28.5352 28.056 27.5768 27.1982 \
 26.8388 26.4794 
loadtab -continue \
 26.12 25.7207 25.3014 24.8821 24.4628 25.0465 26.6638 28.2811 29.8984 \
 31.0382 31.158 31.2778 31.3976 31.3869 30.6082 29.8295 29.0508 28.2721 \
 27.4934 26.7147 25.936 25.1573 25.717 26.6155 27.514 28.4125 28.3012 27.5824 \
 26.8636 26.1448 26.182 27.1404 28.0988 29.0572 29.8828 30.362 30.8412 \
 31.3204 31.688 31.089 30.49 29.891 29.292 29.0829 28.9032 28.7235 28.5438 \
 28.3188 28.0792 27.8396 27.6 28.3376 29.7752 31.2128 32.6504 33.8185 34.5972 \
 35.3759 36.1546 36.9615 37.86 38.7585 39.657 40.4334 39.3552 38.277 37.1988 \
 36.1206 39.7772 44.0301 48.283 52.5359 54.2208 54.8797 55.5386 56.1975 \
 57.8608 60.3766 62.8924 65.4082 67.308 68.1466 68.9852 69.8238 70.8248 \
 72.502 74.1792 75.8564 77.578 81.4715 85.365 89.2585 93.152 97.4511 101.824 \
 106.196 110.569 114.055 117.11 120.165 123.22 126.215 129.15 132.085 135.02 \
 139.262 146.21 153.159 160.107 166.455 169.45 172.445 175.44 178.435 184.36 \
 190.35 196.34 202.33 207.356 212.148 216.94 221.732 226.562 231.414 236.266 \
 241.118 246.189 251.52 256.851 262.182 268.924 279.227 289.53 299.832 \
 309.726 316.315 322.904 329.493 336.082 337.566 338.704 339.842 340.98 \
 348.333 357.618 366.903 376.187 385.472 394.756 404.041 413.325 421.165 \
 426.976 432.786 438.596 444.464 450.514 456.564 462.614 468.955 479.258 \
 489.561 499.864 510.166 521.595 533.155 544.716 556.277 561.876 565.171 \
 568.465 571.76 578.99 589.472 599.955 610.438 620.92 631.402 641.885 652.367 \
 661.326 664.201 667.076 669.952 672.955 680.622 688.289 695.956 703.624 \
 713.284 723.287 733.29 743.294 748.454 751.329 754.204 757.079 765.651 \
 779.787 793.924 
loadtab -continue \
 808.06 818.893 823.086 827.279 831.472 835.361 837.637 839.913 842.19 \
 844.466 851.757 859.125 866.492 873.86 890.024 908.234 926.444 944.653 \
 955.07 961.06 967.05 973.04 978.641 983.792 988.944 994.095 999.055 1003.55 \
 1008.04 1012.53 1017.77 1028.61 1039.45 1050.29 1061.13 1064.24 1066.87 \
 1069.51 1072.14 1082.85 1095.96 1109.08 1122.2 1132.68 1141.36 1150.05 \
 1158.73 1162.79 1160.51 1158.24 1155.96 1158.24 1174.3 1190.35 1206.4 \
 1221.99 1231.88 1241.76 1251.64 1261.53 1265.63 1269.11 1272.58 1276.05 \
 1282.89 1290.97 1299.06 1307.15 1315.63 1324.44 1333.24 1342.05 1347.77 \
 1348.49 1349.21 1349.93 1353.58 1368.43 1383.29 1398.14 1412.62 1416.28 \
 1419.93 1423.58 1427.24 1432.23 1437.44 1442.65 1447.86 1454.97 1462.93 \
 1470.9 1478.87 1488.28 1499.06 1509.84 1520.62 1528.14 1529.27 1530.41 \
 1531.55 1534.19 1544.44 1554.68 1564.92 1575.16 1575.73 1576.2 1576.68 \
 1577.16 1586.51 1597.83 1609.15 1620.47 1635.46 1652.47 1669.49 1686.5 \
 1697.73 1702.46 1707.19 1711.92 1715.87 1717.97 1720.07 1722.16 1725 1733.09 \
 1741.17 1749.26 1757.34 1766.17 1775.04 1783.9 1792.77 1800.93 1808.9 \
 1816.87 1824.83 1825.51 1821.38 1817.24 1813.11 1813.71 1820.59 1827.48 \
 1834.37 1844.04 1861.83 1879.62 1897.41 1914.8 1927.62 1940.44 1953.25 \
 1966.07 1971 1975.14 1979.27 1983.4 1983.44 1982.01 1980.57 1979.13 1982.8 \
 1990.47 1998.14 2005.8 2014.56 2025.04 2035.53 2046.01 2056.2 2065.3 2074.41 \
 2083.51 2092.41 2096.42 2100.44 2104.45 2108.46 2114.24 2120.29 2126.34 \
 2132.39 2139.52 2147.13 2154.74 2162.34 2168.24 2172.55 2176.86 2181.18 \
 2185.35 2189.24 2193.13 2197.03 2202.38 2214.78 2227.18 
loadtab -continue \
 2239.58 2251.98 2259.3 2266.6 2273.91 2281.22 2295.84 2312.01 2328.18 \
 2344.36 2347.04 2342.48 2337.93 2333.38 2336.49 2347.99 2359.49 2370.99 \
 2378.02 2374.78 2371.55 2368.31 2368.1 2388.04 2407.99 2427.94 2447.88 \
 2445.6 2442.3 2439.01 2435.71 2442.32 2451.66 2461.01 2470.35 2480.72 \
 2491.74 2502.76 2513.78 2524.15 2533.67 2543.2 2552.72 2558.31 2552.79 \
 2547.28 2541.77 2537.4 2544.7 2552.01 2559.32 2566.63 2582.81 2599.82 \
 2616.84 2633.85 2639 2640.02 2641.04 2642.06 2641.96 2641 2640.04 2639.08 \
 2645.13 2661.96 2678.8 2695.63 2708.33 2706.41 2704.49 2702.58 2701.42 \
 2715.8 2730.17 2744.55 2758.93 2766.92 2773.99 2781.06 2788.13 2798.34 \
 2809.9 2821.46 2833.02 2838.85 2839.51 2840.16 2840.82 2841.25 2841.25 \
 2841.25 2841.25 2843.44 2855.72 2868 2880.28 2892.52 2896.71 2900.91 2905.1 \
 2909.29 2916.27 2923.82 2931.37 2938.92 2945.44 2951.43 2957.42 2963.41 \
 2970.5 2978.77 2987.03 2995.3 3001.58 3003.43 3005.29 3007.15 3009.52 \
 3015.15 3020.78 3026.41 3032.04 3029.54 3026.72 3023.91 3021.09 3033.51 \
 3049.98 3066.45 3082.92 3095.6 3105.9 3116.2 3126.51 3129.63 3123.7 3117.77 \
 3111.84 3111.06 3124.3 3137.53 3150.77 3164.07 3177.97 3191.87 3205.76 \
 3219.66 3218.87 3216.84 3214.8 3212.76 3218.66 3227.22 3235.79 3244.35 \
 3246.49 3243.85 3241.22 3238.58 3240.53 3249.33 3258.14 3266.94 3278.16 \
 3297.56 3316.97 3336.38 3355.22 3363.96 3372.71 3381.45 3390.2 3381.66 \
 3370.76 3359.86 3348.95 3353.91 3365.47 3377.04 3388.6 3392.47 3389.59 \
 3386.72 3383.84 3390.73 3415.05 3439.37 3463.69 3482.38 3476.33 3470.28 \
 3464.23 3458.23 3456.37 3454.51 3452.66 3450.8 3460.94 3473.4 
loadtab -continue \
 3485.86 3498.32 3504.21 3506.79 3509.36 3511.94 3522.98 3542.81 3562.64 \
 3582.46 3593.78 3586.77 3579.76 3572.75 3568.19 3578.19 3588.19 3598.2 \
 3608.2 3611.52 3614.64 3617.75 3620.87 3622.64 3624.08 3625.52 3626.96 \
 3636.45 3650.83 3665.2 3679.58 3683.22 3673.7 3664.17 3654.65 3652.65 \
 3670.44 3688.23 3706.02 3722.38 3726.16 3729.93 3733.71 3737.48 3741.09 \
 3744.68 3748.27 3751.87 3761.52 3773.14 3784.76 3796.38 3801.01 3800.59 \
 3800.17 3799.75 3802.55 3810.04 3817.52 3825.01 3827.59 3814.05 3800.51 \
 3786.97 3775.91 3803.59 3831.26 3858.93 3886.61 3874.51 3857.32 3840.13 \
 3822.94 3837 3863.66 3890.31 3916.97 3927.31 3923.72 3920.12 3916.53 3920.14 \
 3936.25 3952.37 3968.48 3981.27 3980.07 3978.87 3977.68 3976.35 3967.96 \
 3959.57 3951.19 3942.8 3963.51 3989.57 4015.62 4041.68 4058.37 4070.47 \
 4082.57 4094.67 4099.38 4096.62 4093.87 4091.11 4094.59 4111.06 4127.53 4144 \
 4155.11 4135.88 4116.66 4097.43 4078.2 4078.8 4079.88 4080.96 4082.04 \
 4092.11 4104.39 4116.67 4128.95 4137.87 4144.82 4151.77 4158.72 4160.53 \
 4156.22 4151.91 4147.6 4143.25 4138.82 4134.38 4129.95 4129.63 4163.05 \
 4196.48 4229.9 4263.32 4246.07 4225.28 4204.5 4183.71 4195.58 4217.68 \
 4239.78 4261.89 4276 4284.5 4293.01 4301.52 4306.28 4305.74 4305.2 4304.66 \
 4306.4 4315.32 4324.25 4333.17 4341.44 4340.61 4339.77 4338.93 4338.09 \
 4345.17 4353.2 4361.22 4369.25 4377.88 4386.74 4395.61 4404.47 4398.04 \
 4378.87 4359.7 4340.53 4332.8 4344.36 4355.93 4367.49 4376.56 4375.6 4374.64 \
 4373.68 4373.26 4393.5 4413.75 4434 4454.24 4470.1 4485.2 4500.29 4515.39 \
 4512.25 4500.45 4488.65 4476.85 4466.26 4456.85 
loadtab -continue \
 4447.45 4438.05 4439.71 4463.79 4487.87 4511.95 4531.06 4523.45 4515.84 \
 4508.23 4500.63 4501.62 4502.76 4503.9 4505.03 4512.72 4521.94 4531.17 \
 4540.39 4547.14 4552.47 4557.8 4563.13 4567.16 4569.68 4572.19 4574.71 \
 4579.34 4589.16 4598.98 4608.81 4618.53 4627.52 4636.5 4645.49 4654.48 \
 4638.08 4620.11 4602.14 4584.17 4602.36 4631.47 4660.58 4689.69 4700.61 \
 4699.11 4697.62 4696.12 4687.69 4669.72 4651.75 4633.78 4623.76 4637.95 \
 4652.15 4666.35 4679.76 4683.23 4686.7 4690.18 4693.65 4699.34 4705.27 \
 4711.2 4717.13 4722.06 4726.61 4731.16 4735.71 4744.2 4755.89 4767.57 \
 4779.25 4780.94 4766.26 4751.59 4736.91 4728.56 4744.67 4760.78 4776.9 \
 4792.25 4784.34 4776.44 4768.53 4760.62 4785.61 4816.04 4846.47 4876.9 \
 4870.67 4847.55 4824.43 4801.31 4793.79 4801.22 4808.65 4816.08 4824.07 \
 4833.18 4842.28 4851.38 4860.89 4872.45 4884.01 4895.57 4907.13 4897.29 \
 4887.22 4877.16 4867.1 4876.55 4890.38 4904.22 4918.06 4909.6 4888.76 \
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 0 0
simundump xgraph /graphs/conc1 0 0 3000 0 6233.3 0
simundump xgraph /graphs/conc2 0 0 3000 0 0.015347 0
simundump xplot /graphs/conc1/PMT_count.Co 3 524288 \
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simundump xplot /graphs/conc1/noOligo.output 3 524288 \
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simundump xplot /graphs/conc2/mRNA.Co 3 524288 \
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simundump xplot /graphs/conc2/E.Co 3 524288 \
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simundump xgraph /moregraphs/conc3 0 -1 3000 0 9.7826e-06 0
simundump xgraph /moregraphs/conc4 0 0 3000 0 5e-08 0
simundump xcoredraw /edit/draw 0 -2 39 -34 3
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simundump xtext /file/notes 0 1
xtextload /file/notes \
"Input rate at translation is = 0.00016" \
"" \
"Based on B_binding6.g." \
"Fixed dumping of location of transporters." \
""
addmsg /kinetics/Transcription/P /kinetics/Transcription/Complex_Formation SUBSTRATE n 
addmsg /kinetics/Transcription/RNAP /kinetics/Transcription/Complex_Formation SUBSTRATE n 
addmsg /kinetics/Transcription/TrRNAP /kinetics/Transcription/Complex_Formation PRODUCT n 
addmsg /kinetics/Transcription/Complex_Formation /kinetics/Transcription/RNAP REAC A B 
addmsg /kinetics/Transcription/RNAPdecay /kinetics/Transcription/RNAP REAC A B 
addmsg /kinetics/Transcription/mRNA_synthesis /kinetics/Transcription/RNAP MM_PRD output 
addmsg /kinetics/Transcription/In_Transcription /kinetics/Transcription/TrRNAP REAC A B 
addmsg /kinetics/Transcription/Complex_Formation /kinetics/Transcription/TrRNAP REAC B A 
addmsg /kinetics/Transcription/TrRNAP /kinetics/Transcription/In_Transcription SUBSTRATE n 
addmsg /kinetics/Transcription/N /kinetics/Transcription/In_Transcription SUBSTRATE n 
addmsg /kinetics/Transcription/P /kinetics/Transcription/In_Transcription PRODUCT n 
addmsg /kinetics/Transcription/RBS /kinetics/Transcription/In_Transcription PRODUCT n 
addmsg /kinetics/Transcription/In_Transcription /kinetics/Transcription/N REAC A B 
addmsg /kinetics/Transcription/Complex_Formation /kinetics/Transcription/P REAC A B 
addmsg /kinetics/Transcription/In_Transcription /kinetics/Transcription/P REAC B A 
addmsg /kinetics/Transcription/mRNA_Decay /kinetics/Transcription/mRNA REAC A B 
addmsg /kinetics/Transcription/mRNA_synthesis /kinetics/Transcription/mRNA MM_PRD output 
addmsg /kinetics/Translation/Rib_RNA_Complex /kinetics/Transcription/mRNA REAC A B 
addmsg /kinetics/Translation/Prot_synthesis /kinetics/Transcription/mRNA MM_PRD output 
addmsg /kinetics/Translation/Rib_mRNA-decay /kinetics/Transcription/mRNA REAC B A 
addmsg /kinetics/Transcription/RBS /kinetics/Transcription/mRNA_synthesis SUBSTRATE n 
addmsg /kinetics/Transcription/RNAP /kinetics/Transcription/RNAPdecay SUBSTRATE n 
addmsg /kinetics/Transcription/decayed_RNAP /kinetics/Transcription/RNAPdecay PRODUCT n 
addmsg /kinetics/Transcription/mRNA /kinetics/Transcription/mRNA_Decay SUBSTRATE n 
addmsg /kinetics/Transcription/decayed_mRNA /kinetics/Transcription/mRNA_Decay PRODUCT n 
addmsg /kinetics/Transcription/mRNA_Decay /kinetics/Transcription/decayed_mRNA REAC B A 
addmsg /kinetics/Transcription/RNAPdecay /kinetics/Transcription/decayed_RNAP REAC B A 
addmsg /kinetics/Transcription/In_Transcription /kinetics/Transcription/RBS REAC B A 
addmsg /kinetics/Transcription/RBS_Decay /kinetics/Transcription/RBS REAC A B 
addmsg /kinetics/Transcription/RBS /kinetics/Transcription/RBS_Decay SUBSTRATE n 
addmsg /kinetics/Transcription/decayed_RBS /kinetics/Transcription/RBS_Decay PRODUCT n 
addmsg /kinetics/Transcription/RBS_Decay /kinetics/Transcription/decayed_RBS REAC B A 
addmsg /kinetics/luciferase/k5 /kinetics/luciferase/E.S1_in REAC B A 
addmsg /kinetics/luciferase/E.S1 /kinetics/luciferase/k5 SUBSTRATE n 
addmsg /kinetics/luciferase/E.S1_in /kinetics/luciferase/k5 PRODUCT n 
addmsg /kinetics/luciferase/k5 /kinetics/luciferase/E.S1 REAC A B 
addmsg /kinetics/luciferase/k1 /kinetics/luciferase/E.S1 REAC B A 
addmsg /kinetics/luciferase/k1_prime /kinetics/luciferase/E.S1 REAC A B 
addmsg /kinetics/luciferase/k1 /kinetics/luciferase/S1 REAC A B 
addmsg /kinetics/luciferase/k1_2 /kinetics/luciferase/S1 REAC A B 
addmsg /kinetics/luciferase/E /kinetics/luciferase/k1 SUBSTRATE n 
addmsg /kinetics/luciferase/E.S1 /kinetics/luciferase/k1 PRODUCT n 
addmsg /kinetics/luciferase/S1 /kinetics/luciferase/k1 SUBSTRATE n 
addmsg /kinetics/luciferase/k1 /kinetics/luciferase/E REAC A B 
addmsg /kinetics/luciferase/k1_prime_2 /kinetics/luciferase/E REAC A B 
addmsg /kinetics/luciferase/k5_2 /kinetics/luciferase/E REAC A B 
addmsg /kinetics/luciferase/k4 /kinetics/luciferase/E REAC B A 
addmsg /kinetics/Translation/Prot_synthesis /kinetics/luciferase/E MM_PRD output 
addmsg /kinetics/Translation/Protein_Decay /kinetics/luciferase/E REAC A B 
addmsg /kinetics/luciferase/E.S1 /kinetics/luciferase/k1_prime SUBSTRATE n 
addmsg /kinetics/luciferase/E.S1.S2 /kinetics/luciferase/k1_prime PRODUCT n 
addmsg /kinetics/luciferase/S2 /kinetics/luciferase/k1_prime SUBSTRATE n 
addmsg /kinetics/luciferase/k1_prime /kinetics/luciferase/S2 REAC A B 
addmsg /kinetics/luciferase/k1_prime_2 /kinetics/luciferase/S2 REAC A B 
addmsg /kinetics/luciferase/E.P /kinetics/luciferase/k4 SUBSTRATE n 
addmsg /kinetics/luciferase/P /kinetics/luciferase/k4 PRODUCT n 
addmsg /kinetics/luciferase/E /kinetics/luciferase/k4 PRODUCT n 
addmsg /kinetics/luciferase/k1_prime /kinetics/luciferase/E.S1.S2 REAC B A 
addmsg /kinetics/luciferase/k5_4 /kinetics/luciferase/E.S1.S2 REAC A B 
addmsg /kinetics/luciferase/k2 /kinetics/luciferase/E.S1.S2 REAC A B 
addmsg /kinetics/luciferase/k1_2 /kinetics/luciferase/E.S1.S2 REAC B A 
addmsg /kinetics/luciferase/E.S1.S2 /kinetics/luciferase/k2 SUBSTRATE n 
addmsg /kinetics/luciferase/E.P1 /kinetics/luciferase/k2 PRODUCT n 
addmsg /kinetics/luciferase/AMP /kinetics/luciferase/k2 PRODUCT n 
addmsg /kinetics/luciferase/k2 /kinetics/luciferase/E.P1 REAC B A 
addmsg /kinetics/luciferase/k3 /kinetics/luciferase/E.P1 REAC A B 
addmsg /kinetics/luciferase/E.P1 /kinetics/luciferase/k3 SUBSTRATE n 
addmsg /kinetics/luciferase/E.P /kinetics/luciferase/k3 PRODUCT n 
addmsg /kinetics/luciferase/photon /kinetics/luciferase/k3 PRODUCT n 
addmsg /kinetics/luciferase/k3 /kinetics/luciferase/E.P REAC B A 
addmsg /kinetics/luciferase/k6 /kinetics/luciferase/E.P REAC A B 
addmsg /kinetics/luciferase/k4 /kinetics/luciferase/E.P REAC A B 
addmsg /kinetics/luciferase/k4 /kinetics/luciferase/P REAC B A 
addmsg /kinetics/luciferase/E /kinetics/luciferase/k1_prime_2 SUBSTRATE n 
addmsg /kinetics/luciferase/E.S2 /kinetics/luciferase/k1_prime_2 PRODUCT n 
addmsg /kinetics/luciferase/S2 /kinetics/luciferase/k1_prime_2 SUBSTRATE n 
addmsg /kinetics/luciferase/E.S2 /kinetics/luciferase/k1_2 SUBSTRATE n 
addmsg /kinetics/luciferase/E.S1.S2 /kinetics/luciferase/k1_2 PRODUCT n 
addmsg /kinetics/luciferase/S1 /kinetics/luciferase/k1_2 SUBSTRATE n 
addmsg /kinetics/luciferase/k1_prime_2 /kinetics/luciferase/E.S2 REAC B A 
addmsg /kinetics/luciferase/k5_3 /kinetics/luciferase/E.S2 REAC A B 
addmsg /kinetics/luciferase/k1_2 /kinetics/luciferase/E.S2 REAC A B 
addmsg /kinetics/luciferase/k2 /kinetics/luciferase/AMP REAC B A 
addmsg /kinetics/luciferase/k3 /kinetics/luciferase/photon REAC B A 
addmsg /kinetics/luciferase/E /kinetics/luciferase/k5_2 SUBSTRATE n 
addmsg /kinetics/luciferase/E_in /kinetics/luciferase/k5_2 PRODUCT n 
addmsg /kinetics/luciferase/E.S2 /kinetics/luciferase/k5_3 SUBSTRATE n 
addmsg /kinetics/luciferase/E.S2_in /kinetics/luciferase/k5_3 PRODUCT n 
addmsg /kinetics/luciferase/E.S1.S2 /kinetics/luciferase/k5_4 SUBSTRATE n 
addmsg /kinetics/luciferase/E.S1.S2_in /kinetics/luciferase/k5_4 PRODUCT n 
addmsg /kinetics/luciferase/photon /kinetics/luciferase/num_photons SUMTOTAL n nInit 
addmsg /kinetics/luciferase/photon /kinetics/luciferase/PMT_count SUMTOTAL n nInit 
addmsg /kinetics/luciferase/E.P /kinetics/luciferase/k6 SUBSTRATE n 
addmsg /kinetics/luciferase/E.P_in /kinetics/luciferase/k6 PRODUCT n 
addmsg /kinetics/luciferase/k6 /kinetics/luciferase/E.P_in REAC B A 
addmsg /kinetics/luciferase/k5_4 /kinetics/luciferase/E.S1.S2_in REAC B A 
addmsg /kinetics/luciferase/k5_3 /kinetics/luciferase/E.S2_in REAC B A 
addmsg /kinetics/luciferase/k5_2 /kinetics/luciferase/E_in REAC B A 
addmsg /kinetics/Translation/Rib_RNA_Complex /kinetics/Translation/Ribosome REAC A B 
addmsg /kinetics/Translation/RibosomeDecay /kinetics/Translation/Ribosome REAC A B 
addmsg /kinetics/Translation/Prot_synthesis /kinetics/Translation/Ribosome MM_PRD output 
addmsg /kinetics/Translation/Ribosome /kinetics/Translation/Rib_RNA_Complex SUBSTRATE n 
addmsg /kinetics/Transcription/mRNA /kinetics/Translation/Rib_RNA_Complex SUBSTRATE n 
addmsg /kinetics/Translation/Rib_mRNA /kinetics/Translation/Rib_RNA_Complex PRODUCT n 
addmsg /kinetics/Translation/Rib_RNA_Complex /kinetics/Translation/Rib_mRNA REAC B A 
addmsg /kinetics/Translation/Rib_mRNA-decay /kinetics/Translation/Rib_mRNA REAC A B 
addmsg /kinetics/Translation/B-subunit-bind-to_ribosome /kinetics/Translation/Rib_mRNA REAC A B 
addmsg /kinetics/Translation/decayed_Rib_mRNA /kinetics/Translation/Rib_mRNA-decay PRODUCT n 
addmsg /kinetics/Transcription/mRNA /kinetics/Translation/Rib_mRNA-decay PRODUCT n 
addmsg /kinetics/Translation/Rib_mRNA /kinetics/Translation/Rib_mRNA-decay SUBSTRATE n 
addmsg /kinetics/Translation/Ribosome /kinetics/Translation/RibosomeDecay SUBSTRATE n 
addmsg /kinetics/Translation/decayed_Ribosome /kinetics/Translation/RibosomeDecay PRODUCT n 
addmsg /kinetics/Translation/RibosomeDecay /kinetics/Translation/decayed_Ribosome REAC B A 
addmsg /kinetics/Translation/B-subunit /kinetics/Translation/B-subunit-bind-to_ribosome SUBSTRATE n 
addmsg /kinetics/Translation/Rib_mRNA /kinetics/Translation/B-subunit-bind-to_ribosome SUBSTRATE n 
addmsg /kinetics/Translation/primed-mRNA /kinetics/Translation/B-subunit-bind-to_ribosome PRODUCT n 
addmsg /kinetics/Translation/B-subunit-bind-to_ribosome /kinetics/Translation/primed-mRNA REAC B A 
addmsg /kinetics/Translation/Rib_mRNA-decay /kinetics/Translation/decayed_Rib_mRNA REAC B A 
addmsg /kinetics/Translation/decayed_protein /kinetics/Translation/Protein_Decay PRODUCT n 
addmsg /kinetics/luciferase/E /kinetics/Translation/Protein_Decay SUBSTRATE n 
addmsg /kinetics/Translation/Protein_Decay /kinetics/Translation/decayed_protein REAC B A 
addmsg /kinetics/Translation/B-subunit-bind-to_ribosome /kinetics/Translation/B-subunit REAC A B 
addmsg /kinetics/Translation/primed-mRNA /kinetics/Translation/Prot_synthesis SUBSTRATE n 
addmsg /kinetics/luciferase/PMT_count /graphs/conc1/PMT_count.Co PLOT Co *PMT_count.Co *51 
addmsg /kinetics/noOligo /graphs/conc1/noOligo.output PLOT output *noOligo.output *white 
addmsg /kinetics/Transcription/mRNA /graphs/conc2/mRNA.Co PLOT Co *mRNA.Co *blue 
addmsg /kinetics/luciferase/E /graphs/conc2/E.Co PLOT Co *E.Co *54 
enddump
// End of dump

setfield /kinetics/noOligo table->dx 1
setfield /kinetics/noOligo table->invdx 1
call /kinetics/Transcription/Complex_Formation/notes LOAD \
"Smita Patel et al." \
"Biochemistery 2002,41, 3586-3595"
call /kinetics/Transcription/TrRNAP/notes LOAD \
"Open complex of DNA and RNApolymerase"
call /kinetics/Transcription/In_Transcription/notes LOAD \
"Initiation Of Transcription" \
"The forward rate is 0.45 nucleotides/second." \
"We are assuming that this step represents 100 nucleotides." \
"We are considering that there are 1.2e16 nucleotides to get" \
"the kf = 3.33e-17"
call /kinetics/Transcription/N/notes LOAD \
"nucleotide "
call /kinetics/Transcription/P/notes LOAD \
"Promotor." \
"Assume conc of promoter is 25 nM."
call /kinetics/Transcription/mRNA_synthesis/notes LOAD \
"I scale down the input rate to 2/sec assuming that the space between" \
"successive RNA Pols is 20 bases." \
"The mRNA is 1700 bases long." \
"Promega says that the amount of mRNA" \
"produced after 1 hour should be about" \
"equal to the amount of DNA originally added." \
"Temperature dependence means that the actual" \
"amount will be less."
call /kinetics/Transcription/mRNA_Decay/notes LOAD \
"There are inhibitors in the reaction mix, so decay rate is 1e-6/sec"
call /kinetics/Transcription/RBS_Decay/notes LOAD \
"Same as mRNA decay"
call /kinetics/luciferase/E.S1/notes LOAD \
"S1 is ATP. E.S1 is luciferase.ATP"
call /kinetics/luciferase/S1/notes LOAD \
"S1 is ATP" \
"Conc as specified by Promega."
call /kinetics/luciferase/S2/notes LOAD \
"S2 = LH2 = luciferin." \
""
call /kinetics/luciferase/E.S2/notes LOAD \
"S2 is Luciferin."
call /kinetics/luciferase/PMT_count/notes LOAD \
"Volume is scaled so that 1 photon gives a Co equivalent of 0.0031," \
"which is the collection efficiency." \
"" \
"vol = 1.6667e-21 / 0.0031 = 5.37e-19" \
""
call /kinetics/Translation/Rib_RNA_Complex/notes LOAD \
"Formation Of RBS and Ribosome Complex" \
"Rate taken from Kierzek et al." \
"Kf=100" \
"Kb=2.25"
call /kinetics/Translation/Protein_Decay/notes LOAD \
"Assuming same rate as Kierzek et al." \
""
call /kinetics/Translation/Prot_synthesis/notes LOAD \
"The synthesis rate is assumed at 15 nucleotides (5 AAs) per second." \
"This gives a total synthesis time of 120 sec as" \
"600 AAs/5 per sec." \
"" \
"The open parameter is input rate, which defines how closely spaced the " \
"ribosomes are upon the mRNA. At a rate of 0.1, there are 150 nucleotides" \
"between ribomes (1/(0.067 * 0.1))" \
""
complete_loading