(* The Transcription/RNA Splcing Coupling Model for T7 RNA Polymerase *)

<<myPadRight.m ; <<cellerator.m ; <<kMech.m ; Off[General :: "spell1"] ; Off[General :: "spell"] ;

myPadRight Version 0.3 for Cellerator Loaded.

Cellerator™ 1.4.6 (30-July-2004) loaded 9-Dec-2004 00:32 using Mathematica Version 5.0 for Microsoft Windows (June 11, 2003)

 kMech is loaded

(* Start Transcription/RNA Splcing Coupling Simulation *)(* NE1 : RNA polymera ... kf10, kr11, kcat12}},  {{Overscript[mRNA⇄NMP, NEd], kf13, kr14, kcat15}} ] ;

{myODEs,myVars}=interpret[mRNASplcing]

{{DNA^′[t]  -kf1 DNA[t] NE1[t] NTP[t] + kcat3 $Complex$NE1$DNA$NTP$[t] + kr2 $Co ... $NE1$DNA$NTP$, $Complex$NEs$premRNA$, $Complex$premRNA$NEd$, $Complex$$Complex$NEs$premRNA$$NEd$}}

Lamda = 1 ;  RowBox[{myKs, =, RowBox[{{, , , RowBox[{RowBox[{KmNE1$DNA ... 2754;Kf[KmNEd$mRNA, kcat15, Lamda], ,, , kr14Kr[kcat15, Lamda]}], , }}]}]

RowBox[{{, RowBox[{RowBox[{kf1, , 5.35714*10^-9}], ,, kr20, ,, RowBox[{kf4, &# ... , , 0.001}], ,, kr110, ,, RowBox[{kf13, , 0.001}], ,, kr140}], }}]

RowBox[{RowBox[{myICs, =, RowBox[{{, , RowBox[{DNA[0] 12, ,, , NTP[0]  ... s$premRNA$$NEd$[0] 0, ,, , $Complex$mRNA$NEd$[0] 0}], , }}]}], ;}]

tmax = 150 ; mySolution = NDSolve[Join[myODEs/.myKs, myICs], myVars, {t, 0, tmax}, MaxSteps3000]

RowBox[{{, RowBox[{{, RowBox[{RowBox[{DNA, , TagBox[RowBox[{InterpolatingFunction, [,  ... x[{{, RowBox[{0., ,, 150.}], }}], }}], ,, <>}], ]}], False, Editable -> False]}]}], }}], }}]

orderedVars={DNA,NTP,premRNA,mRNA,NMP,NE1,NEs,NEd,$Complex$NE1$DNA$NTP$,
$Complex$NEs$premRNA$,$Complex$premRNA$NEd$,$Complex$mRNA$NEd$};

Show[GraphicsArray[
    Partition[
      Map[Plot[#[t]/.mySolution,{t,0,tmax},PlotLabel→#,
            PlotRange→All,DisplayFunction→Identity]&,orderedVars],3]
    ]
  ];

[Graphics:HTMLFiles/Splcing_T7_14.gif]

RowBox[{RowBox[{FormalPlot[varName_, displayTime_, YplotRange_], :=, , RowBox[{Plot, [ ... ,, RowBox[{AxesStyle, , RowBox[{{, RowBox[{Thickness, [, 0.0006, ]}], }}]}]}], ]}]}], ;}]

totalPremRNA[t_] = premRNA[t] + $Complex$NEs$premRNA$[t] + $Complex$premRNA$NEd$[t] ;

RowBox[{RowBox[{P1, =, RowBox[{DotPlot, [, RowBox[{mRNA, ,, tmax, ,, RowBox[{{, RowBox[{0, ,,  ...   , RowBox[{{, RowBox[{0, ,, 0.1}], }}]}], ,, DisplayFunction$DisplayFunction}], ]}], ;}]

<<Graphics`MultipleListPlot`(* Time points (min) : 15, 40, 65, 90, 115,  ... ,, RowBox[{AxesStyle, , RowBox[{{, RowBox[{Thickness, [, 0.0006, ]}], }}]}]}], ]}]}], ;}]

[Graphics:HTMLFiles/Splcing_T7_19.gif]

RowBox[{RowBox[{Show, [, RowBox[{P3, ,, P1, ,, P2, ,, RowBox[{PlotRange, ,  , RowBox[{{, RowBox[{0, ,, 0.1}], }}]}], ,, DisplayFunction$DisplayFunction}], ]}], ;}]

(* KmNEs$premRNA = 8 *)

[Graphics:HTMLFiles/Splcing_T7_23.gif]

(* KmNEs$premRNA = 80 *)

[Graphics:HTMLFiles/Splcing_T7_25.gif]

(* KmNEs$premRNA = 800 *)

[Graphics:HTMLFiles/Splcing_T7_27.gif]


Created by Mathematica  (December 16, 2004)