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CS594- FinalPresentation:ChemicalComputation

TyVaughanDecember1,2017

ChemicalComputation:Overview1. BriefHistory

2. WhatisChemicalComputation?

3. RealvsArtificialChemicalComputation

4. ProgrammingParadigmofChemicalComputation

5. ArtificialChemicalComputationExample

6. CurrentTechnology

7. FutureAdvances

8. Conclusion

BriefHistoryIntheearly1900s,scientistswerestillgaininganunderstandingofhowtoquantifycertainchemicalpropertiesandinteractions

Inthe1920s,theoreticalcalculationsforchemicalandquantumphysicswerebeingpublishedthatacceleratedprogress◦ Schrodinger’swaveequation◦ Hiesenberg’s establishmentofquantummechanics

Asimprovementsincomputertechnologyescalatedbythe60s,researchforhowtoprogramchemicalexperimentsincreased.

In1971,Hendricksonpublishedoneofthefirstdesignsforachemicalprogram.Theprogramwasforcomputer-assistedsynthesisoforganicmaterials.

BriefHistory(Cont.)Moreprogramsbegantobedeveloped,andin1978,thetwoofthefirstcompaniesdedicatedtochemicalcomputationhardwareandsoftwareemerged.

Fromthe1980son,manymorecompaniesandindividualsbegandevelopingsoftwaretoolsforchemicalcomputation.

Now,computationalpoweristhemainlimitingforceformanyoftheanalysesabletobeperformedforchemicalproblems.

Unconventionalcomputationwithrealchemicalsgrewasafieldtowardstheendofthe1900s.OneexampleisDNAcomputation,whichwasofficiallyestablishedwithAdleman’s 1994publicationofhisDNAHamiltonianpathsolver.

Advancesinquantumcomputingarelookeduponasoneofthebiggestimprovementstofurtherthefield.

ChemicalComputation:Overview1. BriefHistory

2. WhatisChemicalComputation?

3. RealvsArtificialChemicalComputation

4. ProgrammingParadigmofChemicalComputation

5. ArtificialChemicalComputationExample

6. CurrentTechnology

7. FutureAdvances

8. Conclusion

WhatisChemicalComputation?

ChemicalComputationiscomputationthatfocusesonmodeling/computingchemicalpropertiesandreactionsItrequirestheprogrammertodefineabasisofinterpretation◦ Canbestraightforward◦ Canbemoreabstract

ChemicalComputation:Overview1. BriefHistory

2. WhatisComputationalChemistry?

3. RealvsArtificialChemicalComputation

4. ProgrammingParadigmofChemicalComputation

5. ArtificialChemicalComputationExample

6. CurrentTechnology

7. FutureAdvances

8. Conclusion

TwoTypesofChemicalComputationTherearetwocategoriesofchemicalcomputation1.RealChemicalComputation:◦ Useofactualmoleculesandchemicalsintypicalreactions◦ Useofacomputertosimulateandcomputechemical/quantumalgorithms

2.ArtificialChemicalComputation:◦ Theapplicationofthefundamentalcomponentsofchemicalreactionstoabstractlyperformproblems.

◦ The“ChemicalMetaphor”forproblemsolving◦ Unconventionalformofcomputation

ChemicalComputation:Overview1. BriefHistory

2. WhatisComputationalChemistry?

3. RealvsArtificialChemicalComputation

4. ProgrammingParadigmofChemicalComputation

5. ArtificialChemicalComputationExample

6. CurrentTechnology

7. FutureAdvances

8. Conclusion

ChemicalcomputationHowcanwemodelchemicalproblemsinsoftware?

•Differentaspectstoconsider•Differentelementstodefine

•Differentapproachestobeused•Differentmodelstoapply

AspectsofChemicalComputationScope1.MicroscopicSystem:◦ Achangeofstateintheoverallsystemisdescribedbyachangeofstateoftheindividualcomponentsofthesystem.

◦ Ex:Dittrich’sprimenumbergenerator2.MacroscopicSystem:◦ Thestateoftheoverallsystemisdescribedbyallcomponentsinthesystem◦ Ex:Dittrich’srobotcontroller

AspectsofChemicalComputationDeterminism1.DeterministicSystem:◦ Orderofoperationsisknown.◦ Ex:testingthepropertiesofachemical

2.StochasticSystem:◦ Orderofoperationsisnotguaranteed◦ Ex:biologicalsystems

AspectsofChemicalComputationOpenness1.OpenSystem:◦ Chemicalreactionsinthesystemdonotneedtobebalanced.◦ Componentscanbeintroducedfromorreleasedbacktotheenvironment

2.ClosedSystem:◦ Chemicalreactionsinthesystemarebalanced◦ Componentsdonotdisappearfromthesystem

ElementsofChemicalComputationTherearethreemainelementsthatneedtobedefined:1.Molecules:◦ thesecomposethestateofthesystemandarethemaincomponentsofcomputationinthesystem

2.Reactions:◦ thesearethepossibleinteractionsthatcanoccurbetweenmoleculesandbetweenmoleculesandtheenvironment

3.Dynamics(Environment):◦ thisdetermineshowreactionsbegin,whentheyoccur,andwhichreactionsarepossible

ElementsofChemicalComputation

ApproachestoChemicalComputationTherearetwogeneralapproachestosettingupchemicalcomputationproblems:1.Explicitdefinitionofmoleculesandreactions◦ Morefavorableforsimplesystemswhereeachreactioncanbeexplicitlystated

2.Implicitdefinitionofmoleculesandreactions◦ Morefavorableforcomplex,dynamicsystemsthatcanoperategivenonlyafewgeneralrules

◦ Largerreactionsandmoleculescanbeperformed,composedofdefinedreactionsandmolecules

ModelsForChemicalComputationTheaforementionedaspects,elements,andapproachescanbecombinedinfivegeneralmodelsforchemicalcomputation1.RewritingorProductionModel◦ Sequences/patternsareusedtorepresentthestateofthesystem.◦ Allreactionsinvolvechangingorrearrangingthedifferentsequences◦ SimilartohowDNAcomputationisperformed◦ Ex:Adleman’s AlgorithmforHamiltonianpaths◦ Ex:Lipton’sSATalgorithm

ModelsForChemicalComputationTheaforementionedaspects,elements,andapproachescanbecombinedinfivegeneralmodelsforchemicalcomputation2.ArithmeticModel◦ Arithmeticsymbolsandoperationsrepresentmoleculesandreactions◦ Ex:Dittrich’s PrimeNumberGenerator

3.AbstractAutomataModel◦ Moleculesarerepresentedbysymbolsandbits◦ Reactionsperformedarebasedonthemolecule’ssymbols◦ Somemoleculescanrepresentthestatesoftheautomata,otherscaninteractwiththestatemolecules

◦ Ex:Benenson’sDNAFSMforenzymaticcomputation

ModelsForChemicalComputationTheaforementionedaspects,elements,andapproachescanbecombinedinfivegeneralmodelsforchemicalcomputation4. AssemblerAutomataModel◦ Assemblerautomatamachineisused– highlyparallel◦ Molecules,reactions,andenvironmentareallspecifiedandcompeteforCPU◦ Ex:Tierra– parisitic organismsimulation

5. LatticeModel◦ Unitgridisgenerated,moleculesexistwithinthegrid◦ Moleculesandreactionsarespecified,andthedynamicscanbedifferentforeachlattice◦ Ex:Astor’sneuralnetworkdevelopmentmodel

AdvantagesandDisadvantagesForChemicalComputationAdvantages:◦ Complexproblems/algorithmscanbeexplainedwithsimplernotation◦ Canexpressproblemsinaformthattakesadvantageofmassiveparallelism◦ Ifperformedwithrealchemicals,itdrasticallyreducesthepowerneededforcomputation

Disadvantages:◦ Electronicreal/artificialcomputationrequiresalotofpower◦ Althoughproblemsmaybemorescalablegiventheirspecifications,theydonotscalewellinhardware

ChemicalComputation:Overview1. BriefHistory

2. WhatisComputationalChemistry?

3. RealvsArtificialChemicalComputation

4. ProgrammingParadigmofChemicalComputation

5. ArtificialChemicalComputationExample

6. CurrentTechnology

7. FutureAdvances

8. Conclusion

ExampleDynamicNeuralNetworkGenerationUsingChemicalComputation◦ Stochasticsystem,latticemodel

Threeelements:◦ Molecules:celltypes- input,neurons,output◦ Reactions:allowthecellstocommunicate◦ Dynamics:eachgridcellcontainsdifferentsubstrates(initialorgeneratedbycells)

Cellscommunicateviasubstrates,form/loseconnections,reproduce/die

ChemicalComputation:Overview1. BriefHistory

2. WhatisComputationalChemistry?

3. RealvsArtificialChemicalComputation

4. ProgrammingParadigmofChemicalComputation

5. ArtificialChemicalComputationExample

6. StateoftheArt

7. FutureAdvances

8. Conclusion

StateoftheArtQuantumComputing:OpenFermion (Google)◦ Chemicalcomputationlibrariesforquantumcomputing◦ Platformfortranslatingconventionalcodetoquantumcode◦ Opensource

AdvancesinAlgorithms◦ Timedependentdensityfunctionaltheorymeasurements– Berkeleylabs◦ Allowscientiststostudytheresonantfrequencyofmolecules,whichdescribeitspropertiesandbehaviorinreactions

◦ Newalgorithmreducestheamountofcomputationalresourcesandtimeneededbyusingaccurateapproximations

ChemicalComputation:Overview1. BriefHistory

2. WhatisComputationalChemistry?

3. RealvsArtificialChemicalComputation

4. ProgrammingParadigmofChemicalComputation

5. ArtificialChemicalComputationExample

6. CurrentTechnology

7. FutureAdvances

8. Conclusion

FutureAdvancesQuantumComputation◦ Providesthemassiveparallelismneededforrealandartificialchemicalcomputation

◦ Forrealchemicalcomputations,onlyafewqubitsareneededtosimulatesimpleatoms.

◦ BerkeleyLabs– intenseresearchtodevelopquantumprocessors,compilers,optimizations,andalgorithmsspecificallytargetedathandlingchemicalcomputations

ChemicalComputation:Overview1. BriefHistory

2. WhatisComputationalChemistry?

3. RealvsArtificialChemicalComputation

4. ProgrammingParadigmofChemicalComputation

5. ArtificialChemicalComputationExample

6. CurrentTechnology

7. FutureAdvances

8. Conclusion

Conclusion/ThankYou!