Computation with molecules
Computation with molecules
What is the data structure to store information?
What is the data structure to store information?
You make a particular molecule
You have a certain distribution of molecular concentrations
? There is a certain multiway graph of transformations
You have a certain distribution of molecular concentrations
? There is a certain multiway graph of transformations
How do we characterize “what’s going on a cell”?
How do we characterize “what’s going on a cell”?
Looking at how much of particular proteins get produced
Interactome
State of cell:
concentrations
? spatial information
concentrations
? spatial information
[ e.g. CA running in microtubules ]
Spatial information
Spatial information
Coordinates by string matching : genome, docking, etc.
E.g. in bronchial trees, dendritic trees
What kinds of molecules to use?
What kinds of molecules to use?
Success story: biology [DNA + proteins]
Modular synthesis?
[[ a few repeating units ]]
Combinatorial chemistry [30-50 types of amines, ...]
Drug discovery: mostly shape + charge distribution
Sample goal : generate the primes with molecules
Sample goal : generate the primes with molecules
Generate only molecular sizes that are prime...
Generate only molecular sizes that are prime...
E.g. maybe there only certain buckyballs that are possible ; cf tiling problem
Set up constraints that are only satisfied by the result you want....
In[]:=
ResourceFunction["BuckyballGraph"][2]
Out[]=
Cf. find the ground state of a spin glass ... cf traveling salesman problem [[ with a substrate ]]
< Specifying the program with a substrate >
Is there a substrate [that we can make, as a metamaterial] so that we get e.g. the primes
Generate successive primes
Generate successive primes
Analogous example: freezing of complicated molecules
Analogous example: freezing of complicated molecules
When don’t things crystallize? [Becomes amorphous]
In[]:=
EntityValue[EntityClass["Chemical",{"HillFormulaString"->"C8H18"}],"MeltingPoint"]
Out[]=
{,,,,,,,,,,,,,,,,,}
In[]:=
KeyMap[Molecule,EntityValue[EntityClass["Chemical",{"HillFormulaString"->"C8H18"}],"MeltingPoint","EntityAssociation"]]
Out[]=
Molecule,Molecule,Molecule,Molecule,Molecule,Molecule,Molecule,Molecule,Molecule,Molecule,Molecule,Molecule,Molecule,Molecule,Molecule,Molecule,Molecule,Molecule
Simpler goal: make the Thue-Morse sequence
Simpler goal: make the Thue-Morse sequence
Can there be a computation encoded in the chemical network?
Can there be a computation encoded in the chemical network?
Cf. circadian rhythm networks
Cf. circadian rhythm networks
BZ reaction : reaction/diffusion
BZ reaction : reaction/diffusion
Cicadas
Cicadas
http://mariomarkus.com/save/biological-primes.pdf
Perturbations in multiway graphs
Perturbations in multiway graphs
Are there topologically stable structures in multiway graphs
[ Particles in branchial space? ]
How do you program the chemical system?
How do you program the chemical system?
Put in certain initial compounds
Put in certain initial compounds
Flash light at it, etc. / magnetic fields / temperature
Flash light at it, etc. / magnetic fields / temperature
Change pH / wash in some other compound
Change pH / wash in some other compound
[ Flow through a tube ]
[ Flow through a tube ]
Given a background multiway structure ... what is the “effective physics” of making certain perturbations
Given a background multiway structure ... what is the “effective physics” of making certain perturbations
Computation is through certain ?persistent perturbations etc.