Figure 1: AND, OR, XOR Logic Gates

plots[1]=Plot3D[If[x>0&&y>0,1,0],{x,-1,1},{y,-1,1},Evaluate@fig1Opts,Evaluate@opts];
plots[2]=Plot3D[If[x>0||y>0,1,0],{x,-1,1},{y,-1,1},Evaluate@fig1Opts,Evaluate@opts];
plots[3]=Plot3D[If[x>0&&y<0||x<0&&y>0,1,0],{x,-1,1},{y,-1,1},Evaluate@fig1Opts,Evaluate@opts];
Grid[Map[Show[#,ImageSize->Medium]&,{{plots[1],plots[2],plots[3]}},{2}]]

figureNames={"fig1A.png","fig1B.png","fig1C.png"};
Export[FileNameJoin[{$figurePath,"Panels",figureNames[[#]]}],Rasterize[plots[#],"Image",RasterSize->2000,Background->None]]&/@Range@Length@figureNames;

Figure 3C: Examples of AND and OR

plotA=With[{KdA=2.5 (10^(-8)),KdI=1.5 (10^(-4)),βΔϵ=-14.2},
KdA1=KdA2=KdA;
KdI1=KdI2=KdI;
Plot3D[(((1+L1norm)(1+L2norm))/((1+L1norm)(1+L2norm)+(E^(-βΔϵ))(1+L1norm(KdA1/KdI1))(1+L2norm(KdA2/KdI2)))),{L1norm,(10^(-1)),(10^5)},{L2norm,(10^(-1)),(10^5)},ScalingFunctions->{"Log","Log",Identity},PlotRange->{0,1},ImageSize->350,Ticks->ticksFig3,Evaluate@opts3]
];
plotB=With[{KdA=2.5 (10^(-8)),KdI=1.5 (10^(-4)),βΔϵ=-5},
KdA1=KdA2=KdA;
KdI1=KdI2=KdI;
Plot3D[(((1+L1norm)(1+L2norm))/((1+L1norm)(1+L2norm)+(E^(-βΔϵ))(1+L1norm((KdA1/KdI1)))(1+L2norm((KdA2/KdI2))))),{L1norm,(10^(-1)),(10^5)},{L2norm,(10^(-1)),(10^5)},ScalingFunctions->{"Log","Log",Identity},PlotRange->{0,1},ImageSize->350,Ticks->ticksFig3,Evaluate@opts3]
];
grid=Grid[{{plotA,plotB}}]

Export[FileNameJoin[{$figurePath,"Panels","fig3_AND.png"}],Rasterize[plotA,"Image",RasterSize->2000,Background->None]];
Export[FileNameJoin[{$figurePath,"Panels","fig3_OR.png"}],Rasterize[plotB,"Image",RasterSize->2000,Background->None]];

Figure 3D: Quality of Gates

dϵ=(-5-(-14.2))/3;
ϵMin=-14.2-dϵ;
ϵMax=-5+3*dϵ;
plotA=SliceDensityPlot3D[((1/(1+(10^(γ1log)) (10^(γ2log)) (E^(-βΔϵ)))))(1-(1/(1+(E^(-βΔϵ)))))(1-(1/(1+(10^(γ1log)) (E^(-βΔϵ)))))(1-(1/(1+(10^(γ2log)) (E^(-βΔϵ))))),{"ZStackedPlanes",6},{γ1log,-7.5,7.5},{γ2log,-7.5,7.5},{βΔϵ,ϵMin,ϵMax},PlotRange->{0,1},AxesEdge->{{-1,-1},{-1,-1},{1,-1}},ColorFunction->"BlueGreenYellow",ColorFunctionScaling->False,ImageSize->290,ViewPoint->{-0.77478,-2.9928,1.3751},ViewVertical->{-0.99753,-0.065097,0.026049},Ticks->ticksFig3D,Evaluate@opts,BoxRatios->{1,1,1.5}];
plotAwithPoint=Show[plotA,ListPointPlot3D[{{Log10[2.5*(10^(-8))/(1.5*(10^(-4)))],Log10[2.5*(10^(-8))/(1.5*(10^(-4)))],-14.2}}]];plotB=SliceDensityPlot3D[((1/(1+(10^(γ1log)) (10^(γ2log)) (E^(-βΔϵ)))))((1/(1+(10^(γ1log)) (E^(-βΔϵ)))))((1/(1+(10^(γ2log)) (E^(-βΔϵ)))))(1-(1/(1+ (E^(-βΔϵ))))),{"ZStackedPlanes",6},{γ1log,-7.5,7.5},{γ2log,-7.5,7.5},{βΔϵ,ϵMin,ϵMax},PlotRange->{0,1},AxesEdge->{{-1,-1},{-1,-1},{1,-1}},ColorFunction->"BlueGreenYellow",ColorFunctionScaling->False,ImageSize->290,ViewPoint->{-0.77478,-2.9928,1.3751},ViewVertical->{-0.99753,-0.065097,0.026049},Ticks->ticksFig3D,Evaluate@opts,BoxRatios->{1,1,1.5}];
plotBwithPoint=Show[plotB,ListPointPlot3D[{{Log10[2.5*(10^(-8))/(1.5*(10^(-4)))],Log10[2.5*(10^(-8))/(1.5*(10^(-4)))],-5}}]];
leg=BarLegend["BlueGreenYellow",LabelStyle->{FontSize->fontSize+2}];
grid=Grid[{{plotAwithPoint,plotBwithPoint,leg}},Spacings->0.5,Alignment->{{Top,Top,Automatic}}]

Export[FileNameJoin[{$figurePath,"Panels","fig3_QualityAND.png"}],Rasterize[plotAwithPoint,"Image",RasterSize->2000,Background->None]];
Export[FileNameJoin[{$figurePath,"Panels","fig3_QualityOR.png"}],Rasterize[plotBwithPoint,"Image",RasterSize->2000,Background->None]];
Export[FileNameJoin[{$figurePath,"Panels","fig3_QualityLegend.png"}],Rasterize[leg,"Image",RasterSize->2000,Background->None]];

Figure 4: General 2-Ligand MWC Response

(* === Panel A Parameters === *)
βΔϵ=0;
{KdA1,KdI1,KdA2,KdI2}={1,0.0526,1,9.};
{L1min,L1max}={(10^(-10)),(10^10)};
{L2min,L2max}={(10^(-10)),(10^10)};
dx=1.07;
meshX=meshY=Table[{Log[(10^valuesLog)]},{valuesLog,Union[Range[0,10,dx],Range[0,-10,-dx]]}];
meshX=Join[meshX,{{Log[transitionL1[βΔϵ,KdA1,KdI1,KdA2,KdI2,0]],Directive[Thickness[0.008],]},{Log[transitionL1[βΔϵ,KdA1,KdI1,KdA2,KdI2,∞]],Directive[Thickness[0.008],Dashed,]}}];
meshY=Join[meshY,{{Log[transitionL2[βΔϵ,KdA1,KdI1,KdA2,KdI2,0]],Directive[Thickness[0.008],]},{Log[transitionL2[βΔϵ,KdA1,KdI1,KdA2,KdI2,∞]],Directive[Thickness[0.008],Dashed,]}}];
plotA=Plot3D[(((1+(L1/KdA1))(1+(L2/KdA2)))/((1+(L1/KdA1))(1+(L2/KdA2))+(E^(-βΔϵ))(1+(L1/KdI1))(1+(L2/KdI2)))),{L1,L1min,L1max},{L2,L2min,L2max},ScalingFunctions->{"Log","Log",Identity},Ticks->ticksFig5A,PlotRange->{{(10^(-7.1)),(10^7.1)},{(10^(-7.1)),(10^7.1)},{0,1}},ImageSize->1.5*imageSize4,Mesh->{meshX,meshY},Evaluate@opts];
(* === Panel B Parameters === *)
βΔϵ=0;
{KdA1,KdI1,KdA2,KdI2}={1,(10^(-4)),1,(10^4)};
{L1min,L1max}={(10^(-6)),(10^2)};
{L2min,L2max}={(10^(-2)),(10^6)};
dx=0.62;
meshX=meshY=Table[{Log[(10^valuesLog)]},{valuesLog,Union[Range[0,10,dx],Range[0,-10,-dx]]}];
plotB=Plot3D[(((1+(L1/KdA1))(1+(L2/KdA2)))/((1+(L1/KdA1))(1+(L2/KdA2))+(E^(-βΔϵ))(1+(L1/KdI1))(1+(L2/KdI2)))),{L1,L1min,L1max},{L2,L2min,L2max},ScalingFunctions->{"Log","Log",Identity},Ticks->ticksFig5B,PlotRange->{0,1},ImageSize->1.5*imageSize4,Evaluate@opts4,MeshFunctions->{#3&},Mesh->9,MeshStyle->Directive[Thickness[0.007]]];
grid=Grid[{{plotA,plotB}},Spacings->2]

vp=Options[Graphics3D,ViewPoint][[1,2]];
Make3dYZ[plot_,height_,isDashed_,color_]:=Module[
{newplot},newplot=First@Graphics[plot];
newplot=N@newplot/.{x_?AtomQ,y_?AtomQ}:>{x,height,y};
If[isDashed,newplot[[1]][[1]][[3]][[1]][[1]]=Directive[Opacity[1.0],AbsoluteThickness[1.6`],Dashed,Thickness[0.008`],color],
newplot[[1]][[1]][[3]][[1]][[1]]=Directive[Opacity[1.0],AbsoluteThickness[1.6`],Thickness[0.008`],color]];
newplot]
Make3dXZ[plot_,height_,isDashed_,color_]:=Module[
{newplot},newplot=First@Graphics[plot];
newplot=N@newplot/.{x_?AtomQ,y_?AtomQ}:>{height,x,y};
If[isDashed,newplot[[1]][[1]][[3]][[1]][[1]]=Directive[Opacity[1.0],AbsoluteThickness[1.6`],Dashed,Thickness[0.008`],color],
newplot[[1]][[1]][[3]][[1]][[1]]=Directive[Opacity[1.0],AbsoluteThickness[1.6`],Thickness[0.008`],color]];
newplot
]
L10=transitionL1[βΔϵ,KdA1,KdI1,KdA2,KdI2,0];
L1∞=transitionL1[βΔϵ,KdA1,KdI1,KdA2,KdI2,∞];
L20=transitionL2[βΔϵ,KdA1,KdI1,KdA2,KdI2,0];
L2∞=transitionL2[βΔϵ,KdA1,KdI1,KdA2,KdI2,∞];
opts2d=Sequence@@{ScalingFunctions->{"Log",Identity},PlotStyle->Directive[Thickness[0.008]],PlotRange->All,Ticks->ticksFig5B};
plot2dL10=Plot[(((1+(L10/KdA1))(1+(L2/KdA2)))/((1+(L10/KdA1))(1+(L2/KdA2))+(E^(-βΔϵ))(1+(L10/KdI1))(1+(L2/KdI2)))),{L2,L20,L2∞},Evaluate@opts2d];
plot2dL1∞=Plot[(((1+((L1∞)/KdA1))(1+(L2/KdA2)))/((1+((L1∞)/KdA1))(1+(L2/KdA2))+(E^(-βΔϵ))(1+((L1∞)/KdI1))(1+(L2/KdI2)))),{L2,L20,L2∞},Evaluate@opts2d];
plot2dL20=Plot[(((1+(L1/KdA1))(1+(L20/KdA2)))/((1+(L1/KdA1))(1+(L20/KdA2))+(E^(-βΔϵ))(1+(L1/KdI1))(1+(L20/KdI2)))),{L1,L10,L1∞},Evaluate@opts2d];
plot2dL2∞=Plot[(((1+(L1/KdA1))(1+((L2∞)/KdA2)))/((1+(L1/KdA1))(1+((L2∞)/KdA2))+(E^(-βΔϵ))(1+(L1/KdI1))(1+((L2∞)/KdI2)))),{L1,L10,L1∞},Evaluate@opts2d];
𝒟1=ImplicitRegion[L1min≤x≤L10∨L1∞≤x≤L1max,{x}];
𝒟2=ImplicitRegion[L2min≤x≤L20∨L2∞≤x≤L2max,{x}];
plot2dL10outside=Plot[(((1+(L10/KdA1))(1+(L2/KdA2)))/((1+(L10/KdA1))(1+(L2/KdA2))+(E^(-βΔϵ))(1+(L10/KdI1))(1+(L2/KdI2)))),{L2}∈𝒟2,Evaluate@opts2d];
plot2dL1∞outside=Plot[(((1+((L1∞)/KdA1))(1+(L2/KdA2)))/((1+((L1∞)/KdA1))(1+(L2/KdA2))+(E^(-βΔϵ))(1+((L1∞)/KdI1))(1+(L2/KdI2)))),{L2}∈𝒟2,Evaluate@opts2d];
plot2dL20outside=Plot[(((1+(L1/KdA1))(1+(L20/KdA2)))/((1+(L1/KdA1))(1+(L20/KdA2))+(E^(-βΔϵ))(1+(L1/KdI1))(1+(L20/KdI2)))),{L1}∈𝒟1,Evaluate@opts2d];
plot2dL2∞outside=Plot[(((1+(L1/KdA1))(1+((L2∞)/KdA2)))/((1+(L1/KdA1))(1+((L2∞)/KdA2))+(E^(-βΔϵ))(1+(L1/KdI1))(1+((L2∞)/KdI2)))),{L1}∈𝒟1,Evaluate@opts2d];

(*lightCol=RGBColor[127/255,127/255,127/255];*)
lightCol=RGBColor[160/255,160/255,160/255];
lightCol=;
plotB2color=Show[{plotB,
Graphics3D[Make3dYZ[plot2dL20,Log[L20],False,]],
Graphics3D[Make3dYZ[plot2dL2∞,Log[L2∞],True,]],
Graphics3D[Make3dXZ[plot2dL10,Log[L10],False,]],
Graphics3D[Make3dXZ[plot2dL1∞,Log[L1∞],True,]],
Graphics3D[Make3dYZ[plot2dL20outside,Log[L20],False,lightCol]],
Graphics3D[Make3dYZ[plot2dL2∞outside,Log[L2∞],True,lightCol]],
Graphics3D[Make3dXZ[plot2dL10outside,Log[L10],False,lightCol]],
Graphics3D[Make3dXZ[plot2dL1∞outside,Log[L1∞],True,lightCol]]
},Axes->True,ViewPoint->vp]

Export[FileNameJoin[{$figurePath,"Panels","fig4_general.png"}],Rasterize[plotA,"Image",RasterSize->2000,Background->None]];
Export[FileNameJoin[{$figurePath,"Panels","fig4_ratiometric.png"}],Rasterize[plotB,"Image",RasterSize->2000,Background->None]];
Export[FileNameJoin[{$figurePath,"Panels","fig4_ratiometric_2color.png"}],Rasterize[plotB2color,"Image",RasterSize->2000,Background->None]];

Figure 5: AND->OR Switching (Increasing n)

plotANDn1=With[{KdA=2.5 (10^(-8)),KdI=2.5 (10^(-6)),βΔϵ=-7},
KdA1=KdA2= KdA;
KdI1=KdI2=KdI;
Plot3D[(((1+L1norm)(1+L2norm))/((1+L1norm)(1+L2norm)+(E^(-βΔϵ))(1+L1norm(KdA1/KdI1))(1+L2norm(KdA2/KdI2)))),{L1norm,(10^(-2)),(10^5)},{L2norm,(10^(-2)),(10^5)},ScalingFunctions->{"Log","Log",Identity},PlotRange->{0,1},Ticks->ticksFig6,ImageSize->350,Evaluate@opts5]
];
plotORn=With[{KdA=2.5 (10^(-8)),KdI=2.5 (10^(-6)),βΔϵ=-7,n=4},
KdA1=KdA2= KdA;
KdI1=KdI2=KdI;
Plot3D[(((((1+L1norm))^n)(((1+L2norm))^n))/((((1+L1norm))^n)(((1+L2norm))^n)+(E^(-βΔϵ))(((1+L1norm(KdA1/KdI1)))^n)(((1+L2norm(KdA2/KdI2)))^n))),{L1norm,(10^(-2)),(10^5)},{L2norm,(10^(-2)),(10^5)},ScalingFunctions->{"Log","Log",Identity},PlotRange->{0,1},Ticks->ticksFig6,ImageSize->350,Evaluate@opts5]
];
Grid[{plotANDn1,plotORn}]

Export[FileNameJoin[{$figurePath,"Panels","fig5_AND_n1.png"}],Rasterize[plotANDn1,"Image",RasterSize->2000,Background->None]];
Export[FileNameJoin[{$figurePath,"Panels","fig5_OR_n4.png"}],Rasterize[plotORn,"Image",RasterSize->2000,Background->None]];

Figure 6: AND->OR Switching (saturating [L3])

plotANDlow=With[{KdA=2.5 (10^(-8)),KdI=2.5 (10^(-4)),βΔϵ=-12},
KdA1=KdA2=KdA3 = KdA;
KdI1=KdI2=KdI;
KdI3 = KdI;
L3 = 0;
Plot3D[(((1+L1norm)(1+L2norm)(1+(L3/KdA3)))/((1+L1norm)(1+L2norm)(1+(L3/KdA3))+(E^(-βΔϵ))(1+L1norm(KdA1/KdI1))(1+L2norm(KdA2/KdI2))(1+(L3/KdI3)))),{L1norm,(10^(-2)),(10^5)},{L2norm,(10^(-2)),(10^5)},ScalingFunctions->{"Log","Log",Identity},PlotRange->{0,1},Ticks->ticksFig6,ImageSize->350,Evaluate@opts5]
];
plotORhigh=With[{KdA=2.5 (10^(-8)),KdI=2.5 (10^(-4)),βΔϵ=-12},
KdA1=KdA2=KdA3 = KdA;
KdI1=KdI2=KdI;
KdI3 = KdI;
L3 = 0.00025;
Plot3D[(((1+L1norm)(1+L2norm)(1+(L3/KdA3)))/((1+L1norm)(1+L2norm)(1+(L3/KdA3))+(E^(-βΔϵ))(1+L1norm(KdA1/KdI1))(1+L2norm(KdA2/KdI2))(1+(L3/KdI3)))),{L1norm,(10^(-2)),(10^5)},{L2norm,(10^(-2)),(10^5)},ScalingFunctions->{"Log","Log",Identity},PlotRange->{0,1},Ticks->ticksFig6,ImageSize->350,Evaluate@opts5]
];
plotANDlow2=With[{KdA=2.5  (10^(-8)),KdI=2.5 (10^(-4)),KdI23=2.5 (10^(-6)),βΔϵ=-12},
KdA1=KdA2=KdA3 = KdA;
KdI1=KdI;
KdI2=KdI23;
KdI3 = KdI23;
L3 = 0;
Plot3D[(((1+L1norm)(1+L2norm)(1+(L3/KdA3)))/((1+L1norm)(1+L2norm)(1+(L3/KdA3))+(E^(-βΔϵ))(1+L1norm(KdA1/KdI1))(1+L2norm(KdA2/KdI2))(1+(L3/KdI3)))),{L1norm,(10^(-2)),(10^5)},{L2norm,(10^(-2)),(10^5)},ScalingFunctions->{"Log","Log",Identity},PlotRange->{0,1},Ticks->ticksFig6,ImageSize->350,Evaluate@opts5]
];
plotYES1high=With[{KdA= 2.5  (10^(-8)),KdI= 2.5 (10^(-4)),KdI23= 2.5 (10^(-6)),βΔϵ=-12},
KdA1=KdA2=KdA3 = KdA;
KdI1=KdI;
KdI2=KdI23;
KdI3 = KdI23;
L3 = 0.00025;
Plot3D[(((1+L1norm)(1+L2norm)(1+(L3/KdA3)))/((1+L1norm)(1+L2norm)(1+(L3/KdA3))+(E^(-βΔϵ))(1+L1norm(KdA1/KdI1))(1+L2norm(KdA2/KdI2))(1+(L3/KdI3)))),{L1norm,(10^(-2)),(10^5)},{L2norm,(10^(-2)),(10^5)},ScalingFunctions->{"Log","Log",Identity},PlotRange->{0,1},Ticks->ticksFig6,ImageSize->350,Evaluate@opts5]
];
Grid[{{plotANDlow,plotORhigh},{plotANDlow2,plotYES1high}}]

Export[FileNameJoin[{$figurePath,"Panels","fig6_AND_lowL3.png"}],Rasterize[plotANDlow,"Image",RasterSize->2000,Background->None]];
Export[FileNameJoin[{$figurePath,"Panels","fig6_OR_highL3.png"}],Rasterize[plotORhigh,"Image",RasterSize->2000,Background->None]];

Export[FileNameJoin[{$figurePath,"Panels","fig6_ANDtoYES_AND.png"}],Rasterize[plotANDlow2,"Image",RasterSize->2000,Background->None]];
Export[FileNameJoin[{$figurePath,"Panels","fig6_ANDtoYES_YES.png"}],Rasterize[plotYES1high,"Image",RasterSize->2000,Background->None]];

Figure S1: NAND, NOR, XNOR Logic Gates

plots[4]=Plot3D[If[x>0&&y>0,0,1],{x,-1,1},{y,-1,1},Evaluate@fig1Opts,Evaluate@opts];
plots[5]=Plot3D[If[x>0||y>0,0,1],{x,-1,1},{y,-1,1},Evaluate@fig1Opts,Evaluate@opts];
plots[6]=Plot3D[If[x>0&&y<0||x<0&&y>0,0,1],{x,-1,1},{y,-1,1},Evaluate@fig1Opts,Evaluate@opts];
Grid[Map[Show[#,ImageSize->Medium]&,{{plots[4],plots[5],plots[6]}},{2}]]

figureNames={"figS1A.png","figS1B.png","figS1C.png"};
Export[FileNameJoin[{$figurePath,"Panels",figureNames[[#-3]]}],Rasterize[plots[#],"Image",RasterSize->2000,Background->None]]&/@Range[4,6];

Figure S2: XOR Gate

plot=With[{KdA=1,KdI=0.6 (10^4),βΔϵ=-5,βϵAcoop=15,βϵIcoop=0},
KdA1=KdA2=KdA;
KdI1=KdI2=KdI;
Plot3D[((1+(L1/KdA1)+(L2/KdA2)+(L1/KdA1)(L2/KdA2)(E^(-βϵAcoop)))/(1+(L1/KdA1)+(L2/KdA2)+(L1/KdA1)(L2/KdA2)(E^(-βϵAcoop))+(E^(-βΔϵ))(1+(L1/KdI1)+(L2/KdI2)+(L1/KdI1)(L2/KdI2)(E^(-βϵIcoop))))),{L1,(10^(-2.5)),(10^10.5)},{L2,(10^(-2.5)),(10^10.5)},ScalingFunctions->{"Log","Log",Identity},PlotRange->{0,1},ImageSize->350,Ticks->ticksS3,Evaluate@opts]
]

Export[FileNameJoin[{$figurePath,"Panels","figS2.png"}],Rasterize[plot,"Image",RasterSize->2000,Background->None]];

Old Version

plot=With[{KdA=2.5 (10^(-8)),KdI=1.5 (10^(-4)),βΔϵ=-5,βϵAcoop=15,βϵIcoop=0},
KdA1=KdA2=KdA;
KdI1=KdI2=KdI;
Plot3D[((1+(L1/KdA1)+(L2/KdA2)+(L1/KdA1)(L2/KdA2)(E^(-βϵAcoop)))/(1+(L1/KdA1)+(L2/KdA2)+(L1/KdA1)(L2/KdA2)(E^(-βϵAcoop))+(E^(-βΔϵ))(1+(L1/KdI1)+(L2/KdI2)+(L1/KdI1)(L2/KdI2)(E^(-βϵIcoop))))),{L1,(10^(-10)),(10^3)},{L2,(10^(-10)),(10^3)},ScalingFunctions->{"Log","Log",Identity},PlotRange->{0,1},AxesLabel->axesLabel3,ImageSize->250,Ticks->ticksS3,Evaluate@opts]
]

Figure S3: Beyond Logic Gates

Can we get the different figures in Antebi 2017?

imageSize=300;
plotS3[1]=Plot3D[Which[Abs[x-y]<0.3,1,True,0],{x,-1,1},{y,-1,1},ImageSize->imageSize,Ticks->ticksS4A,Evaluate@fig1Opts,Evaluate@opts];
plotS3[2]=With[{KdA=1.5 (10^(-4)),KdI=2.5 (10^(-8)),βΔϵ=5,βϵAcoop=-15,βϵIcoop=0},
KdA1=KdA2=(KdA/KdA);
KdI1=KdI2=(KdI/KdA);
{min,max}=(({(10^(-11)),(10^(-3))})/KdA);
Plot3D[((1+(L1/KdA1)+(L2/KdA2)+(L1/KdA1)(L2/KdA2)(E^(-βϵAcoop)))/(1+(L1/KdA1)+(L2/KdA2)+(L1/KdA1)(L2/KdA2)(E^(-βϵAcoop))+(E^(-βΔϵ))(1+(L1/KdI1)+(L2/KdI2)+(L1/KdI1)(L2/KdI2)(E^(-βϵIcoop))))),{L1,min,max},{L2,min,max},ScalingFunctions->{"Log","Log",Identity},PlotRange->{0,1},ImageSize->imageSize,Ticks->ticksS4B,Evaluate@opts]
];
plotS3[3]=Plot3D[Which[x<y,1,True,0],{x,-1,1},{y,-1,1},ImageSize->imageSize,Ticks->ticksS4C,Evaluate@fig1Opts,Evaluate@opts];
plotS3[4]=With[{KdA=(10^(-8)),KdI=(10^(-4)),βΔϵ=0},
KdA1=KdI2=KdI;
KdI1=KdA2=KdA;
(* Normalize the concentration axes *)
{KdA1,KdI1}=(({KdA1,KdI1})/KdA1);
{KdA2,KdI2}=(({KdA2,KdI2})/KdA2);
{L1min,L1max}={(10^(-6)),(10^2)};
{L2min,L2max}={(10^(-2)),(10^6)};
Plot3D[(((1+(L1/KdA1))(1+(L2/KdA2)))/((1+(L1/KdA1))(1+(L2/KdA2))+(E^(-βΔϵ))(1+(L1/KdI1))(1+(L2/KdI2)))),{L1,L1min,L1max},{L2,L2min,L2max},ScalingFunctions->{"Log","Log",Identity},Ticks->ticksS4D,PlotRange->{0,1},ImageSize->imageSize,Evaluate@opts]
];
grid=Grid[{{plotS3[1],plotS3[2]},{plotS3[3],plotS3[4]}}]

Export[FileNameJoin[{$figurePath,"Panels","figS3A.png"}],Rasterize[plotS3[1],"Image",RasterSize->2000,Background->None]];
Export[FileNameJoin[{$figurePath,"Panels","figS3B.png"}],Rasterize[plotS3[2],"Image",RasterSize->2000,Background->None]];

Initialization

Figure Styles

(* To format String expressions *)
font[text_,size_:12,opts___]:=Style[text,size,opts,FontFamily->"Lucida Sans"];
fontAxes[text_,size_:12,opts___]:=Style[text,size,opts,FontFamily->"Lucida Sans",SingleLetterItalics->False];

imageSize4=300;

(* Label sizes for plots *)
fontSize=12;
titleSize=14;
captionLetterSize=14;

fig1Opts={Ticks->{ticksLin0toInf,ticksLin0toInf,ticksLin0to1}};

opts3=Sequence@@{(*ViewPoint->{1.6981305868309342`,-2.1706593909582557`,1.9633110600498234`},*)AxesEdge->{{-1,-1},{1,-1},{-1,-1}},ViewVertical->{0,0,1},ColorFunction->Function[{x,y,z},Blend[colors,z]],AxesStyle->Black,TicksStyle->Directive[14]};
opts4=Sequence@@{(*ViewPoint->{1.6981305868309342`,-2.1706593909582557`,1.9633110600498234`},*)AxesEdge->{{-1,-1},{1,-1},{-1,-1}},ViewVertical->{0,0,1},ColorFunction->Function[{x,y,z},Blend[colors,z]],AxesStyle->Black,TicksStyle->Directive[14]};
optsOpaque=Sequence@@{(*ViewPoint->{1.6981305868309342`,-2.1706593909582557`,1.9633110600498234`},*)AxesEdge->{{-1,-1},{1,-1},{-1,-1}},ViewVertical->{0,0,1},AxesStyle->Black,TicksStyle->Directive[14]};

opts5=Sequence@@{AxesEdge->{{-1,-1},{1,-1},{-1,-1}},ViewVertical->{0,0,1},ColorFunction->Function[{x,y,z},Blend[colors,z]],AxesStyle->Black,TicksStyle->Directive[19]};

opts=Sequence@@{(*ViewPoint->{1.6981305868309342`,-2.1706593909582557`,1.9633110600498234`},*)AxesEdge->{{-1,-1},{1,-1},{-1,-1}},ViewVertical->{0,0,1},ColorFunction->Function[{x,y,z},Blend[colors,z]],AxesStyle->Black,TicksStyle->Directive[14]};

axesLabel1=fontAxes[#,fontSize]&/@{(*"[(Subscript[L, 1])]","[(Subscript[L, 2])]"*)(*,Rotate["(Subscript[p, active])",π/2]*)};
axesLabel2=fontAxes[#,fontSize]&/@{"(Subscript[γ, 1])","(Subscript[γ, 2])",Rotate["(Subscript[Δϵ, AI]) ((Subscript[k, B])T)",π/2]};
axesLabel3=fontAxes[#,fontSize]&/@{"[(Subscript[L, 1])]/(Subscript[K, A, 1])","  [(Subscript[L, 2])]/(Subscript[K, A, 2])",Rotate["(Subscript[(Overscript[p, ,]), active])         ",π/2]};
axesLabel4=fontAxes[#,fontSize]&/@{"   [(Subscript[L, 1])]/(Subscript[K, A, 1])","[(Subscript[L, 2])]/(Subscript[K, A, 2])",Rotate["(Subscript[(Overscript[p, ,]), active])         ",π/2]};

{labelS1A,labelS1B,labelS1C,labelS1D}=fontAxes[#,titleSize]&/@{"AND Quality","OR Quality","NAND Quality","NOR Quality"};

colors=RGBColor@@@({{235,164,139},{186,217,125}}/255);

(* Labels for multiple plots *)
aLabel=font["(A)",captionLetterSize];
bLabel=font["(B)",captionLetterSize];
cLabel=font["(C)",captionLetterSize];
dLabel=font["(D)",captionLetterSize];
eLabel=font["(E)",captionLetterSize];
fLabel=font["(F)",captionLetterSize];
gLabel=font["(G)",captionLetterSize];
hLabel=font["(H)",captionLetterSize];
iLabel=font["(I)",captionLetterSize];

Frame Ticks

(* From Mark Caprio's CustomTicks package which I put in "C:\\Program Files\\Wolfram Research\\Mathematica\\10.1\\AddOns\\Packages\\CustomTicks" *)
<<CustomTicks`
SetOptions[LogTicks,LogPlot->True];

tickSize1=20;
tickSize2=18;
tickSize3=18;
tickSize3D=14;
tickSize4=1.5*14;
tickSizeS3First=14;
tickSizeS3Second=15;
tickSize5=14;
tickSize6=12;
ticksLin0toInf={{-0.9,Style["0",tickSize1],{0.01`,0}},{0.9,Style["∞",tickSize1],{0.01`,0}}};
ticksLin0to1={{0.`,Style["0.0",tickSize2],{0.01`,0},{}},{0.5`,Style["0.5",tickSize2],{0.01`,0},{}},{1.0`,Style["1.0",tickSize2],{0.01`,0},{}},{0.1`,"",{0.005`,0},{}},{0.2`,"",{0.005`,0},{}},{0.3`,"",{0.005`,0},{}},{0.4`,"",{0.005`,0},{}},{0.6`,"",{0.005`,0},{}},{0.7`,"",{0.005`,0},{}},{0.8`,"",{0.005`,0},{}},{0.9`,"",{0.005`,0},{}}};
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ticksLog10to3={{1.`*^-10,"(10^(-10))",{0.02`,0},{}},{1.`*^-9,""(*"(10^(-9))"*),{0.02`,0},{}},{1.`*^-8,"(10^(-8))",{0.02`,0},{}},{1.`*^-7,""(*"(10^(-7))"*),{0.02`,0},{}},{1.`*^-6,"(10^(-6))",{0.02`,0},{}},{0.00001`,""(*"(10^(-5))"*),{0.02`,0},{}},{0.0001`,"(10^(-4))",{0.02`,0},{}},{0.001`,""(*"(10^(-3))"*),{0.02`,0},{}},{2.0000000000000003`*^-10,"",{0.01`,0},{}},{3.000000000000001`*^-10,"",{0.01`,0},{}},{4.000000000000001`*^-10,"",{0.01`,0},{}},{4.999999999999999`*^-10,"",{0.01`,0},{}},{6.000000000000003`*^-10,"",{0.01`,0},{}},{7.000000000000002`*^-10,"",{0.01`,0},{}},{8.000000000000003`*^-10,"",{0.01`,0},{}},{9.000000000000007`*^-10,"",{0.01`,0},{}},{2.`*^-9,"",{0.01`,0},{}},{3.0000000000000012`*^-9,"",{0.01`,0},{}},{4.000000000000001`*^-9,"",{0.01`,0},{}},{4.999999999999999`*^-9,"",{0.01`,0},{}},{6.000000000000003`*^-9,"",{0.01`,0},{}},{7.0000000000000015`*^-9,"",{0.01`,0},{}},{8.000000000000004`*^-9,"",{0.01`,0},{}},{9.000000000000006`*^-9,"",{0.01`,0},{}},{2.0000000000000004`*^-8,"",{0.01`,0},{}},{3.000000000000001`*^-8,"",{0.01`,0},{}},{4.0000000000000014`*^-8,"",{0.01`,0},{}},{4.999999999999999`*^-8,"",{0.01`,0},{}},{6.000000000000003`*^-8,"",{0.01`,0},{}},{7.000000000000002`*^-8,"",{0.01`,0},{}},{8.000000000000003`*^-8,"",{0.01`,0},{}},{9.000000000000006`*^-8,"",{0.01`,0},{}},{2.0000000000000002`*^-7,"",{0.01`,0},{}},{3.000000000000001`*^-7,"",{0.01`,0},{}},{4.000000000000001`*^-7,"",{0.01`,0},{}},{5.`*^-7,"",{0.01`,0},{}},{6.000000000000003`*^-7,"",{0.01`,0},{}},{7.000000000000002`*^-7,"",{0.01`,0},{}},{8.000000000000003`*^-7,"",{0.01`,0},{}},{9.000000000000007`*^-7,"",{0.01`,0},{}},{2.0000000000000003`*^-6,"",{0.01`,0},{}},{3.0000000000000013`*^-6,"",{0.01`,0},{}},{4.000000000000001`*^-6,"",{0.01`,0},{}},{4.9999999999999996`*^-6,"",{0.01`,0},{}},{6.000000000000003`*^-6,"",{0.01`,0},{}},{7.000000000000002`*^-6,"",{0.01`,0},{}},{8.000000000000003`*^-6,"",{0.01`,0},{}},{9.000000000000007`*^-6,"",{0.01`,0},{}},{0.00002`,"",{0.01`,0},{}},{0.00003000000000000001`,"",{0.01`,0},{}},{0.00004000000000000001`,"",{0.01`,0},{}},{0.000049999999999999996`,"",{0.01`,0},{}},{0.00006000000000000003`,"",{0.01`,0},{}},{0.00007000000000000002`,"",{0.01`,0},{}},{0.00008000000000000003`,"",{0.01`,0},{}},{0.00009000000000000007`,"",{0.01`,0},{}},{0.00020000000000000004`,"",{0.01`,0},{}},{0.00030000000000000014`,"",{0.01`,0},{}},{0.00040000000000000013`,"",{0.01`,0},{}},{0.0004999999999999999`,"",{0.01`,0},{}},{0.0005999999999999997`,"",{0.01`,0},{}},{0.0007000000000000001`,"",{0.01`,0},{}},{0.0007999999999999995`,"",{0.01`,0},{}},{0.0008999999999999998`,"",{0.01`,0},{}}};

Folder Paths

$figurePath=NotebookDirectory[];