enzyme2.mdl

biomedical stuffs...

Model {
  Name			  "enzyme2"
  Version		  2.20
  SimParamPage		  Solver
  SampleTimeColors	  off
  InvariantConstants	  off
  WideVectorLines	  on
  ShowLineWidths	  off
  StartTime		  "0.0"
  StopTime		  "8000"
  Solver		  ode15s
  RelTol		  "1e-3"
  AbsTol		  "1e-3"
  Refine		  "1"
  MaxStep		  "0.2"
  InitialStep		  "auto"
  FixedStep		  "auto"
  MaxOrder		  5
  OutputOption		  RefineOutputTimes
  OutputTimes		  "[]"
  LoadExternalInput	  off
  ExternalInput		  "[t, u]"
  SaveTime		  off
  TimeSaveName		  "tout"
  SaveState		  off
  StateSaveName		  "xout"
  SaveOutput		  off
  OutputSaveName	  "yout"
  LoadInitialState	  off
  InitialState		  "xInitial"
  SaveFinalState	  off
  FinalStateName	  "xFinal"
  LimitMaxRows		  off
  MaxRows		  "1000"
  Decimation		  "1"
  AlgebraicLoopMsg	  warning
  MinStepSizeMsg	  warning
  UnconnectedInputMsg	  warning
  UnconnectedOutputMsg	  warning
  UnconnectedLineMsg	  warning
  ConsistencyChecking	  off
  ZeroCross		  on
  SimulationMode	  normal
  RTWSystemTargetFile	  "grt.tlc"
  RTWInlineParameters	  off
  RTWPlaceOutputsASAP	  off
  RTWRetainRTWFile	  off
  RTWTemplateMakefile	  "grt_default_tmf"
  RTWMakeCommand	  "make_rtw"
  RTWGenerateCodeOnly	  off
  ExtModeMexFile	  "ext_comm"
  ExtModeBatchMode	  off
  BlockDefaults {
    Orientation		    right
    ForegroundColor	    black
    BackgroundColor	    white
    DropShadow		    off
    NamePlacement	    normal
    FontName		    "Helvetica"
    FontSize		    10
    FontWeight		    normal
    FontAngle		    normal
    ShowName		    on
  }
  AnnotationDefaults {
    HorizontalAlignment	    center
    VerticalAlignment	    middle
    ForegroundColor	    black
    BackgroundColor	    white
    DropShadow		    off
    FontName		    "Helvetica"
    FontSize		    10
    FontWeight		    normal
    FontAngle		    normal
  }
  LineDefaults {
    FontName		    "Helvetica"
    FontSize		    9
    FontWeight		    normal
    FontAngle		    normal
  }
  System {
    Name		    "enzyme2"
    Location		    [-3, 72, 781, 548]
    Open		    on
    ToolBar		    on
    StatusBar		    on
    ScreenColor		    white
    PaperOrientation	    landscape
    PaperPositionMode	    auto
    PaperType		    usletter
    PaperUnits		    inches
    Block {
      BlockType		      SubSystem
      Name		      "INFORMATION"
      Ports		      [0, 0, 0, 0, 0]
      Position		      [632, 315, 755, 352]
      ForegroundColor	      white
      BackgroundColor	      black
      ShowPortLabels	      off
      MaskDisplay	      "disp('Double-click for info')"
      MaskIconFrame	      on
      MaskIconOpaque	      on
      MaskIconRotate	      none
      MaskIconUnits	      autoscale
      System {
	Name			"INFORMATION"
	Location		[10, 175, 630, 580]
	Open			off
	ToolBar			off
	StatusBar		off
	ScreenColor		black
	PaperOrientation	landscape
	PaperPositionMode	auto
	PaperType		usletter
	PaperUnits		inches
	Annotation {
	  Position		  [272, 317]
	  VerticalAlignment	  top
	  Text			  "where,  A = alpha,  G = gamma"
	}
	Annotation {
	  Position		  [292, 277]
	  VerticalAlignment	  top
	  Text			  "Phi = {A*(1+A)*(1+G)^2}/{L + (1+A)^2 + (1+G"
")^2}\nFn = G^n/(K^n + G^n)"
	}
	Annotation {
	  Position		  [277, 242]
	  VerticalAlignment	  top
	  Text			  "dA/dt = V - Sigma-M*Phi + Sigma-i*Fn\ndG/dt"
" = q*Sigma-M*Phi - Sigma-i*Fn - ks*G"
	}
	Annotation {
	  Position		  [157, 217]
	  VerticalAlignment	  top
	  Text			  "Equations of model:"
	}
	Annotation {
	  Position		  [297, 67]
	  VerticalAlignment	  top
	  Text			  "This model simulates a product-activated en"
"zyme reaction with\nrecycling of product into substrate. "
	}
	Annotation {
	  Position		  [317, 107]
	  VerticalAlignment	  top
	  Text			  " Many biochemical reactions are of this typ"
"e.\nOne prominent reaction is the glycolosis pathway, in which ADP is convert"
"ed into\nATP. "
	}
	Annotation {
	  Position		  [327, 152]
	  VerticalAlignment	  top
	  Text			  " Athough this pathway has been modeled in m"
"uch more detail, this two component\nmodel captures its essential behavior.  "
"See (Goldbeter and Moran, Eur. Biophys. J.,\n15: 277-287, 1988.)"
	}
      }
    }
    Block {
      BlockType		      SubSystem
      Name		      "INSTRUCTIONS"
      Ports		      [0, 0, 0, 0, 0]
      Position		      [621, 370, 766, 404]
      ForegroundColor	      white
      BackgroundColor	      green
      ShowPortLabels	      off
      MaskDisplay	      "disp('Double-click for instructions')"
      MaskIconFrame	      on
      MaskIconOpaque	      on
      MaskIconRotate	      none
      MaskIconUnits	      autoscale
      System {
	Name			"INSTRUCTIONS"
	Location		[35, 273, 490, 578]
	Open			on
	ToolBar			off
	StatusBar		off
	ScreenColor		green
	PaperOrientation	landscape
	PaperPositionMode	auto
	PaperType		usletter
	PaperUnits		inches
	Annotation {
	  Position		  [242, 207]
	  VerticalAlignment	  top
	  Text			  "The net input, v, and the two outputs, alph"
"a and gamma,\nwill be sent to the workspace.  By default, they are sampled\na"
"t 1.0 Hz for 8000 seconds."
	}
	Annotation {
	  Position		  [232, 167]
	  VerticalAlignment	  top
	  Text			  "To set the amplitude of the sinusoidal inpu"
"t, double-click\nthe VA block and set the value."
	}
	Annotation {
	  Position		  [232, 132]
	  VerticalAlignment	  top
	  Text			  "Note that the frequency should be specified"
" in radians/sec."
	}
	Annotation {
	  Position		  [232, 97]
	  VerticalAlignment	  top
	  Text			  "To set the frequency of the sinusoidal inpu"
"t, double-click\nthe 'Substrate rate, AC' block and set the value."
	}
	Annotation {
	  Position		  [227, 52]
	  VerticalAlignment	  top
	  Text			  "To set the magnitude of the step input, dou"
"ble-click\nthe V0 block and set the value."
	}
      }
    }
    Block {
      BlockType		      SubSystem
      Name		      "Phi"
      Ports		      [2, 1, 0, 0, 0]
      Position		      [285, 372, 315, 423]
      ForegroundColor	      magenta
      ShowPortLabels	      off
      System {
	Name			"Phi"
	Location		[-5, 363, 600, 603]
	Open			off
	ToolBar			off
	StatusBar		off
	ScreenColor		white
	PaperOrientation	landscape
	PaperPositionMode	auto
	PaperType		usletter
	PaperUnits		inches
	Block {
	  BlockType		  Inport
	  Name			  "in_1"
	  Position		  [95, 30, 115, 50]
	  Port			  "1"
	  PortWidth		  "-1"
	  SampleTime		  "-1"
	}
	Block {
	  BlockType		  Inport
	  Name			  "in_2"
	  Position		  [75, 30, 95, 50]
	  Port			  "2"
	  PortWidth		  "-1"
	  SampleTime		  "-1"
	}
	Block {
	  BlockType		  Sum
	  Name			  "1+alpha"
	  Ports			  [2, 1, 0, 0, 0]
	  Position		  [150, 80, 170, 100]
	  Inputs		  "++"
	}
	Block {
	  BlockType		  Sum
	  Name			  "1+gamma"
	  Ports			  [2, 1, 0, 0, 0]
	  Position		  [150, 135, 170, 155]
	  Inputs		  "++"
	}
	Block {
	  BlockType		  Fcn
	  Name			  "Fcn1"
	  Position		  [255, 70, 295, 90]
	  Expr			  "u*u"
	}
	Block {
	  BlockType		  Fcn
	  Name			  "Fcn2"
	  Position		  [255, 125, 295, 145]
	  Expr			  "u*u"
	}
	Block {
	  BlockType		  Fcn
	  Name			  "Fcn3"
	  Position		  [445, 145, 485, 165]
	  Expr			  "1/u"
	}
	Block {
	  BlockType		  Constant
	  Name			  "L"
	  Position		  [285, 175, 305, 195]
	  Value			  "5000000"
	}
	Block {
	  BlockType		  Constant
	  Name			  "One"
	  Position		  [55, 105, 75, 125]
	  Value			  "1"
	}
	Block {
	  BlockType		  Product
	  Name			  "Phi"
	  Ports			  [2, 1, 0, 0, 0]
	  Position		  [535, 108, 565, 132]
	  ForegroundColor	  magenta
	  Inputs		  "2"
	}
	Block {
	  BlockType		  Product
	  Name			  "Product1"
	  Ports			  [3, 1, 0, 0, 0]
	  Position		  [445, 57, 475, 93]
	  Inputs		  "3"
	}
	Block {
	  BlockType		  Sum
	  Name			  "Sum2"
	  Ports			  [3, 1, 0, 0, 0]
	  Position		  [350, 97, 370, 133]
	  Inputs		  "+++"
	}
	Block {
	  BlockType		  Outport
	  Name			  "out_1"
	  Position		  [585, 110, 605, 130]
	  Port			  "1"
	  OutputWhenDisabled	  held
	  InitialOutput		  "0"
	}
	Line {
	  SrcBlock		  "Fcn3"
	  SrcPort		  1
	  Points		  [15, 0; 0, -30]
	  DstBlock		  "Phi"
	  DstPort		  2
	}
	Line {
	  SrcBlock		  "Product1"
	  SrcPort		  1
	  Points		  [20, 0; 0, 40]
	  DstBlock		  "Phi"
	  DstPort		  1
	}
	Line {
	  SrcBlock		  "Sum2"
	  SrcPort		  1
	  Points		  [30, 0; 0, 40]
	  DstBlock		  "Fcn3"
	  DstPort		  1
	}
	Line {
	  SrcBlock		  "Fcn2"
	  SrcPort		  1
	  Points		  [15, 0]
	  Branch {
	    Points		    [0, -20]
	    DstBlock		    "Sum2"
	    DstPort		    2
	  }
	  Branch {
	    Points		    [15, -50]
	    DstBlock		    "Product1"
	    DstPort		    3
	  }
	}
	Line {
	  SrcBlock		  "1+alpha"
	  SrcPort		  1
	  Points		  [30, 0; 0, -10]
	  Branch {
	    DstBlock		    "Fcn1"
	    DstPort		    1
	  }
	  Branch {
	    Points		    [0, -30; 175, 0; 0, 25]
	    DstBlock		    "Product1"
	    DstPort		    2
	  }
	}
	Line {
	  SrcBlock		  "in_1"
	  SrcPort		  1
	  Points		  [0, 25]
	  Branch {
	    Points		    [0, 20]
	    DstBlock		    "1+alpha"
	    DstPort		    1
	  }
	  Branch {
	    DstBlock		    "Product1"
	    DstPort		    1
	  }
	}
	Line {
	  SrcBlock		  "L"
	  SrcPort		  1
	  Points		  [20, -5; 0, -50]
	  DstBlock		  "Sum2"
	  DstPort		  3
	}
	Line {
	  SrcBlock		  "Fcn1"
	  SrcPort		  1
	  Points		  [15, 0; 0, 25]
	  DstBlock		  "Sum2"
	  DstPort		  1
	}
	Line {
	  SrcBlock		  "1+gamma"
	  SrcPort		  1
	  Points		  [30, 0; 0, -10]
	  DstBlock		  "Fcn2"
	  DstPort		  1
	}