cs 594 -final presentation: chemical computationweb.eecs.utk.edu › ~bmaclenn › classes ›...
TRANSCRIPT
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!