Appendix E

Tetrahedral Lattice .pddf file

# Another example pddf ... spheres in a diamond-style tetrahedral

# lattice structure

#

Model Diamond

{

Sphere a 1.0 <0,0,0> red

#site name <position> <direction> twist

site Aside <1,1,1> <1,1,1> <0,1,-1>

site Bside <1,-1,-1> <1,-1,-1> <0,-1,1>

site Cside <-1,-1,1> <-1,-1,1> <0,1,1>

site Dside <-1,1,-1> <-1,1,-1> <0,-1,-1>

State unbound

State bound

colour a = blue

Event bind { } unbound -> bound

Event break { all } bound -> unbound

}

# unbound links

Binding Diamond Aside unbound to Diamond Aside unbound = 0.001 0

Binding Diamond Aside unbound to Diamond Bside unbound = 0.001 0

Binding Diamond Aside unbound to Diamond Cside unbound = 0.001 0

Binding Diamond Aside unbound to Diamond Dside unbound = 0.001 0

Binding Diamond Bside unbound to Diamond Aside unbound = 0.001 0

Binding Diamond Bside unbound to Diamond Bside unbound = 0.001 0

Binding Diamond Bside unbound to Diamond Cside unbound = 0.001 0

Binding Diamond Bside unbound to Diamond Dside unbound = 0.001 0

Binding Diamond Cside unbound to Diamond Aside unbound = 0.001 0

Binding Diamond Cside unbound to Diamond Bside unbound = 0.001 0

Binding Diamond Cside unbound to Diamond Cside unbound = 0.001 0

Binding Diamond Cside unbound to Diamond Dside unbound = 0.001 0

Binding Diamond Dside unbound to Diamond Aside unbound = 0.001 0

Binding Diamond Dside unbound to Diamond Bside unbound = 0.001 0

Binding Diamond Dside unbound to Diamond Cside unbound = 0.001 0

Binding Diamond Dside unbound to Diamond Dside unbound = 0.001 0

# half bound links

Binding Diamond Aside bound to Diamond Aside unbound = 0.9 0

Binding Diamond Aside bound to Diamond Bside unbound = 0.9 0

Binding Diamond Aside bound to Diamond Cside unbound = 0.9 0

Binding Diamond Aside bound to Diamond Dside unbound = 0.9 0

Binding Diamond Bside bound to Diamond Aside unbound = 0.9 0

Binding Diamond Bside bound to Diamond Bside unbound = 0.9 0

Binding Diamond Bside bound to Diamond Cside unbound = 0.9 0

Binding Diamond Bside bound to Diamond Dside unbound = 0.9 0

Binding Diamond Cside bound to Diamond Aside unbound = 0.9 0

Binding Diamond Cside bound to Diamond Bside unbound = 0.9 0

Binding Diamond Cside bound to Diamond Cside unbound = 0.9 0

Binding Diamond Cside bound to Diamond Dside unbound = 0.9 0

Binding Diamond Dside bound to Diamond Aside unbound = 0.9 0

Binding Diamond Dside bound to Diamond Bside unbound = 0.9 0

Binding Diamond Dside bound to Diamond Cside unbound = 0.9 0

Binding Diamond Dside bound to Diamond Dside unbound = 0.9 0

# unbound links

Binding Diamond Aside unbound to Diamond Aside bound = 0.9 0

Binding Diamond Aside unbound to Diamond Bside bound = 0.9 0

Binding Diamond Aside unbound to Diamond Cside bound = 0.9 0

Binding Diamond Aside unbound to Diamond Dside bound = 0.9 0

Binding Diamond Bside unbound to Diamond Aside bound = 0.9 0

Binding Diamond Bside unbound to Diamond Bside bound = 0.9 0

Binding Diamond Bside unbound to Diamond Cside bound = 0.9 0

Binding Diamond Bside unbound to Diamond Dside bound = 0.9 0

Binding Diamond Cside unbound to Diamond Aside bound = 0.9 0

Binding Diamond Cside unbound to Diamond Bside bound = 0.9 0

Binding Diamond Cside unbound to Diamond Cside bound = 0.9 0

Binding Diamond Cside unbound to Diamond Dside bound = 0.9 0

Binding Diamond Dside unbound to Diamond Aside bound = 0.9 0

Binding Diamond Dside unbound to Diamond Bside bound = 0.9 0

Binding Diamond Dside unbound to Diamond Cside bound = 0.9 0

Binding Diamond Dside unbound to Diamond Dside bound = 0.9 0

#bound links

Binding Diamond Aside bound to Diamond Aside bound = 0.9 0

Binding Diamond Aside bound to Diamond Bside bound = 0.9 0

Binding Diamond Aside bound to Diamond Cside bound = 0.9 0

Binding Diamond Aside bound to Diamond Dside bound = 0.9 0

Binding Diamond Bside bound to Diamond Aside bound = 0.9 0

Binding Diamond Bside bound to Diamond Bside bound = 0.9 0

Binding Diamond Bside bound to Diamond Cside bound = 0.9 0

Binding Diamond Bside bound to Diamond Dside bound = 0.9 0

Binding Diamond Cside bound to Diamond Aside bound = 0.9 0

Binding Diamond Cside bound to Diamond Bside bound = 0.9 0

Binding Diamond Cside bound to Diamond Cside bound = 0.9 0

Binding Diamond Cside bound to Diamond Dside bound = 0.9 0

Binding Diamond Dside bound to Diamond Aside bound = 0.9 0

Binding Diamond Dside bound to Diamond Bside bound = 0.9 0

Binding Diamond Dside bound to Diamond Cside bound = 0.9 0

Binding Diamond Dside bound to Diamond Dside bound = 0.9 0

# environment constants

Temperature 310

Viscosity 0.69

TimeScale 100

# Finally, specify the mix of molecules in solution.

Mix Diamond 100%