Supplementary Materials for "DNA Templating as an Investigative Technique"

S1 - Simulation of patchy model assembling on a periodic ring.


This is the patchy model, simulated assembling on a periodic ring, using this code, parameters unchanged.
S2 - Simulation of conformational model assembling on a periodic ring.


This is the conformational model, simulated assembling on a periodic ring, using this code, parameters unchanged. Green represents the protein in "closed" configuration (t=0), blue represents the protein in "open" configuration" (t=1).
S3 - Simulation of patchy model assembling on an alternately spaced periodic ring.


This is the patchy model, simulated assembling on an alternately spaced periodic ring, using this code, parameters unchanged.
S4 - Simulation of conformational model assembling on an alternately spaced periodic ring.


This is the conformational model, simulated assembling on an alternately spaced periodic ring, using this code, parameters unchanged. Green represents the protein in "closed" configuration (t=0), blue represents the protein in "open" configuration" (t=1).
S5 - Simulation of the collapse of the patchy model on a linear template.


This is the patchy model, initiated as an assembled oligomer on a linear template (depicted as a circle "missing" a site) too small to maintain stability, using this code, parameters unchanged.
S6 - Simulation of the assembly of the patchy model on a linear template.


This is the patchy model, assembling from solution on a linear template (depicted as a circle "missing" a site) large enough to maintain stability, using this code, parameters unchanged.
S7 - Simulation of the collapse of the conformational model on a linear template.


This is the conformational model, initiated as an assembled oligomer on a linear template (depicted as a circle "missing" a site) too small to maintain stability, using this code, parameters unchanged. Green represents the protein in "closed" configuration (t=0), blue represents the protein in "open" configuration" (t=1).
S8 - Simulation of the assembly of the conformational model on a linear template.


This is the conformational model, assembling from solution on a linear template (depicted as a circle "missing" a site) large enough to maintain stability, using this code, parameters unchanged. Green represents the protein in "closed" configuration (t=0), blue represents the protein in "open" configuration" (t=1).
S9 - Simulation of anisotropic patchy model assembling on a periodic ring.


This is the anisotropic patchy model, simulated assembling on a periodic ring, using this code, parameters unchanged. Green corresponds to a left-facing protein (p=0), blue a right-facing protein (p=1).
S10 - Simulation of anisotropic conformational model assembling on a periodic ring.


This is the anisotropic conformational model, simulated assembling on a periodic ring, using this code, parameters unchanged. Note the change in colour scheme: Green corresponds to a left-facing protein (p=0), blue a right-facing protein (p=1). Here, circles correspond to "closed" proteins (t=0), crosses to "open" proteins (t=1).
S11 - Simulation of patchy "Janus particle" model assembling on a periodic ring.


This is the patchy "Janus particle" model, simulated assembling on a periodic ring, using this code, parameters unchanged. Green corresponds to a left-facing protein (p=0), blue a right-facing protein (p=1). The proteins assemble into pairs - note the unoccupied site left over by the odd-numbered nature of the template.
S12 - Simulation of patchy model assembling on a periodic ring in the presence of finite solute.


This is the patchy model, simulated assembling on a periodic ring in the presence of finite solute, using this code, parameters unchanged. Note the steady state with an incomplete tempate - the oligomer "runs out" of material with which to build.
S13 - Simulation of conformational model assembling on a periodic ring in the presence of finite solute.


This is the conformational model, simulated assembling on a periodic ring in the presence of finite solute, using this code, parameters unchanged. Green represents the protein in "closed" configuration (t=0), blue represents the protein in "open" configuration" (t=1). Note the steady state with an incomplete tempate - the oligomer "runs out" of material with which to build.
S14 - Mathematica notebooks with analytical solutions of models.

A Mathematica notebook featuring analytical solutions of the patchy and conformational models on a complete ring can be found here.
A Mathematica notebook featuring analytical solutions of the patchy and conformational models on an alternately spaced ring can be found here.
A Mathematica notebook featuring analytical solutions of the patchy and conformational models on a finite linear template can be found here.
A Mathematica notebook featuring analytical solutions of the anisotropic patchy and conformational models on a complete ring can be found here.