Biomolecular Information Processing: From Logic Systems to Smart Sensors and Actuators

368 Pages·2012·5.73 MB·English

Editedby
EvgenyKatz
BiomolecularInformationProcessing
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Edited by Evgeny Katz
Biomolecular Information Processing
From Logic Systems to Smart Sensors and Actuators
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V
Contents
Preface XIII
ListofContributors XV
1 BiomolecularComputing:FromUnconventionalComputingto‘‘Smart’’
BiosensorsandActuators – EditorialIntroduction 1
EvgenyKatz
References 5
2 Peptide-BasedComputation:Switches,Gates,andSimple
Arithmetic 9
ZehavitDadon,ManickasundaramSamiappan,NathanielWagner,
NuritAshkenasy,andGonenAshkenasy
2.1 Introduction 9
2.2 Peptide-BasedReplicationNetworks 10
2.2.1 Template-AssistedReplication 10
2.2.2 TheoreticalPredictionoftheNetworkConnectivity 11
2.2.3 DenovoDesignedSyntheticNetworks 12
2.3 LogicGateswithinTernaryNetworks 13
2.3.1 UniformDesignPrinciplesofAllTwo-InputGates 13
2.3.2 ORLogic 14
2.3.3 ANDLogic 15
2.3.4 NANDLogic 15
2.3.5 XORLogic 15
2.4 SymmetryandOrderRequirementsforConstructingtheLogic
Gates 16
2.4.1 SymmetryandOrderinPeptide-BasedCatalyticNetworks 16
2.4.2 HowSymmetryandOrderAffecttheReplicationofRNA
Quasispecies 17
2.5 TakingtheStepstowardMoreComplexArithmetic 19
2.5.1 ArithmeticUnits 19
2.5.2 NetworkMotifs 20
VI Contents
2.6 ExperimentalLogicGates 21
2.6.1 ORLogic 21
2.6.2 NOT,NOR,andNOTIFLogic 21
2.6.3 AdditionalLogicOperations 23
2.7 AdaptiveNetworks 24
2.7.1 ChemicalTriggering 24
2.7.2 LightTriggering 24
2.7.3 Light-InducedLogicOperations 25
2.8 Peptide-BasedSwitchesandGatesforMolecularElectronics 28
2.9 SummaryandConclusion 29
Acknowledgments 30
References 30
3 BiomolecularElectronicsandProtein-BasedOpticalComputing 33
JordanA.Greco,NicoleL.Wagner,MatthewJ.Ranaghan,
SanguthevarRajasekaran,andRobertR.Birge
3.1 Introduction 33
3.2 BiomolecularandSemiconductorElectronics 34
3.2.1 SizeandSpeed 34
3.2.2 Architecture 36
3.2.3 NanoscaleEngineering 37
3.2.4 Stability 38
3.2.5 Reliability 38
3.3 BacteriorhodopsinasaPhotonicandHolographicMaterial
forBioelectronics 40
3.3.1 TheLight-InducedPhotocycle 40
3.3.2 TheBranchedPhotocycle 42
3.4 FourierTransformHolographicAssociativeProcessors 42
3.5 Three-DimensionalOpticalMemories 45
3.5.1 Write,Read,andEraseOperations 46
3.5.2 EfficientAlgorithmsforDataProcessing 48
3.5.3 MultiplexingandErrorAnalysis 50
3.6 GeneticEngineeringofBacteriorhodopsinforDevice
Applications 51
3.7 FutureDirections 53
Acknowledgments 54
References 54
4 BioelectronicDevicesControlledbyEnzyme-BasedInformation
ProcessingSystems 61
EvgenyKatz
4.1 Introduction 61
4.2 Enzyme-BasedLogicSystemsProducingpHChanges
asOutputSignals 62
Contents VII
4.3 InterfacingoftheEnzymeLogicSystemswithElectrodesModified
withSignal-ResponsivePolymers 64
4.4 SwitchableBiofuelCellsControlledbytheEnzymeLogicSystems 68
4.5 BiomolecularLogicSystemsComposedofBiocatalytic
andBiorecognitionUnitsandTheirIntegrationwithBiofuelCells 70
4.6 ProcessingofInjuryBiomarkersbyEnzymeLogicSystemsAssociated
withSwitchableElectrodes 74
4.7 SummaryandOutlook 77
Acknowledgments 78
References 78
5 EnzymeLogicDigitalBiosensorsforBiomedicalApplications 81
EvgenyKatzandJosephWang
5.1 Introduction 81
5.2 Enzyme-BasedLogicSystemsforIdentificationofInjury
Conditions 82
5.3 MultiplexingofInjuryCodesfortheParallelOperationofEnzyme
LogicGates 85
5.4 ScalingUptheComplexityoftheBiocomputingSystemsfor
BiomedicalApplications – MimickingBiochemicalPathways 89
5.5 ApplicationofFilterSystemsforImprovingDigitalization
oftheOutputSignalsGeneratedbyEnzymeLogicSystems
forInjuryAnalysis 94
5.6 ConclusionsandPerspectives 96
Acknowledgments 98
Appendix 98
References 99
6 InformationSecurityApplicationsBasedonBiomolecular
Systems 103
GuinevereStrack,HeatherR.Luckarift,GlennR.Johnson,
andEvgenyKatz
6.1 Introduction 103
6.2 MolecularandBio-molecularKeypadLocks 104
6.3 AntibodyEncryptionandSteganography 108
6.4 Bio-barcode 113
6.5 Conclusion 114
Acknowledgments 114
References 114
7 Biocomputing:ExploreItsRealizationandIntelligent
LogicDetection 117
MingZhouandShaojunDong
7.1 Introduction 117
7.2 DNABiocomputing 119
VIII Contents
7.3 AptamerBiocomputing 121
7.4 EnzymeBiocomputing 124
7.5 ConclusionsandPerspectives 128
References 129
8 SomeExperimentsandModelsinMolecularComputing
andRobotics 133
MilanN.StojanovicandDarkoStefanovic
8.1 Introduction 133
8.2 FromGatestoProgrammableAutomata 133
8.3 FromRandomWalkertoMolecularRobotics 139
8.4 Conclusions 142
Acknowledgments 143
References 143
9 BiomolecularFiniteAutomata 145
TamarRatner,SivanShoshani,RonPiran,andEhudKeinan
9.1 Introduction 145
9.2 BiomolecularFiniteAutomata 146
9.2.1 TheoreticalModelsofaMolecularTuringMachine 146
9.2.2 TheFirstRealizationofanAutonomousDNA-Based
FiniteAutomaton 150
9.2.3 Three-Symbol-Three-StateDNA-BasedAutomata 155
9.2.4 MolecularCryptosystemforImagesbyDNAComputing 157
9.2.5 MolecularComputingDeviceforMedicalDiagnosis
andTreatmentInVitro 159
9.2.6 DNA-BasedAutomatonwithBacterialPhenotypeOutput 161
9.2.7 MolecularComputingwithPlantCellPhenotype 163
9.3 BiomolecularFiniteTransducer 167
9.4 ApplicationsinDevelopmentalBiology 172
9.5 Outlook 176
References 178
10 InVivoInformationProcessingUsingRNAInterference 181
YaakovBenenson
10.1 Introduction 181
10.1.1 RegulatoryPathwaysasComputations 181
10.1.2 AComputationVersusaComputer 182
10.1.3 PriorWorkonSyntheticBiomolecularComputingCircuits 182
10.2 RNAInterference-BasedLogic 183
10.2.1 GeneralConsiderations 183
10.2.2 LogicCircuitBlueprint 184
10.2.3 ExperimentalConfirmationoftheComputationalCore 188
10.3 BuildingtheSensoryModule 189
10.3.1 DirectControlofsiRNAbymRNAInputs 191
Contents IX
10.3.2 ComplexTranscriptionalRegulationUsingRNAi-BasedCircuits 194
10.4 Outlook 195
References 197
11 BiomolecularComputingSystems 199
HarishChandran,SudhanshuGarg,NikhilGopalkrishnan,
andJohnH.Reif
11.1 Introduction 199
11.1.1 OrganizationoftheChapter 199
11.2 DNAasaToolforMolecularProgramming 200
11.2.1 DNAStructure 200
11.2.2 ReviewofDNAReactions 200
11.3 BirthofDNAComputing:Adleman’sExperiment
andExtensions 203
11.3.1 NP-CompleteProblems 203
11.3.2 HamiltonianPathProblemviaDNAComputing 204
11.3.3 OtherModelsofDNAComputing 204
11.3.4 ShortcomingsandNonscalabilityofSchemesUsingDNA
ComputationtoSolveNP-CompleteProblems 204
11.4 ComputationUsingDNATiles 205
11.4.1 TAM:anAbstractModelofSelf-Assembly 205
11.4.2 AlgorithmicAssemblyviaDNATilingLattices 206
11.4.2.1 SourceofErrors 206
11.4.3 AlgorithmicErrorCorrectionSchemesforTilings 207
11.5 ExperimentalAdvancesinPurelyHybridization-Based
Computation 209
11.6 ExperimentalAdvancesinEnzyme-BasedDNAComputing 212
11.7 BiochemicalDNAReactionNetworks 217
11.8 Conclusion:ChallengesinDNA-BasedBiomolecular
Computation 218
11.8.1 ScalabilityofBiomolecularComputations 218
11.8.2 EaseofDesignandProgrammabilityofBiomolecular
Computations 220
11.8.3 InVivoBiomolecularComputations 220
11.8.4 Conclusions 220
Acknowledgments 221
References 221
12 EnumerationApproachtotheAnalysisofInteractingNucleic
AcidStrands 225
SatoshiKobayashiandTakayaKawakami
12.1 Introduction 225
12.2 DefinitionsandNotationsforSetandMultiset 226
12.3 ChemicalEquilibriumandHybridizationReactionSystem 227
12.4 SymmetricEnumerationMethod 230
X Contents
12.4.1 EnumerationGraph 230
12.4.2 PathMappings 231
12.4.3 EnumerationScheme 232
12.4.4 AnExampleofEnumerationScheme – Folding
ofanRNAMolecule 233
12.4.5 ConvexProgrammingProblemforComputingEquilibrium 235
12.5 ApplyingSEMtoNucleicAcidStrandsInteraction 236
12.5.1 TargetSecondaryStructures 237
12.5.2 IntroducingBasicNotations 237
12.5.3 DefinitionofEnumerationGraphStructure 239
12.5.4 AssociatedWeightFunctions 241
12.5.5 SymmetricProperties 242
12.5.6 ComplexityIssues 242
12.6 Conclusions 243
References 244
13 RestrictionEnzymesinLanguageGeneration
andPlasmidComputing 245
TomHead
13.1 Introduction 245
13.2 WetSplicingSystems 246
13.3 DrySplicingSystems 249
13.4 SplicingTheory:ItsOriginalMotivationandItsExtensive
UnforeseenDevelopments 252
13.5 ComputingwithPlasmids 253
13.6 FluidMemory 254
13.7 ExamplesofAqueousComputations 255
13.8 FinalCommentsaboutComputingwithBiomolecules 260
References 261
14 DevelopmentofBacteria-BasedCellularComputingCircuits
forSensingandControlinBiologicalSystems 265
MichaelaA.TerAvest,ZhongjianLi,andLargusT.Angenent
14.1 Introduction 265
14.2 CellularComputingCircuits 267
14.2.1 GeneticToolbox 267
14.2.1.1 EngineeredGeneRegulation 267
14.2.1.2 QuorumSensing 269
14.2.2 Implementations 269
14.2.2.1 Oscillators 269
14.2.2.2 Switches 270
14.2.2.3 ANDLogicGates 270
14.2.2.4 EdgeDetector 271
14.2.2.5 ComplexLogicFunctionswithMultipleStrains 272
14.2.3 TransitiontoInSilicoRationalDesign 273