Table Of ContentPaul Pop · Mirela Alistar
Elena Stuart · Jan Madsen
Fault-Tolerant
Digital
Microfl uidic
Biochips
Compilation and Synthesis
Fault-Tolerant Digital Microfluidic Biochips
Paul Pop • Mirela Alistar • Elena Stuart
Jan Madsen
Fault-Tolerant Digital
Microfluidic Biochips
Compilation and Synthesis
123
PaulPop MirelaAlistar
DepartmentofAppliedMathematics DepartmentofAppliedMathematics
andComputerScience andComputerScience
TechnicalUniversityofDenmark TechnicalUniversityofDenmark
KongensLyngby,Denmark KongensLyngby,Denmark
ElenaStuart JanMadsen
NetcompanyA/S DepartmentofAppliedMathematics
Copenhagen,Denmark andComputerScience
TechnicalUniversityofDenmark
KongensLyngby,Denmark
ISBN978-3-319-23071-9 ISBN978-3-319-23072-6 (eBook)
DOI10.1007/978-3-319-23072-6
LibraryofCongressControlNumber:2015947496
SpringerChamHeidelbergNewYorkDordrechtLondon
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Acronyms
ACCC Area-ConstrainedCompilationwithContaminationavoidance
BFS Breadth-FirstSearch
CAD Computer-AidedDesign
CCD Charge-CoupledDevice
CPA ColorimetricProteinAssay
CRM Circular-RouteModule
DAC Droplet-AwareCompilation
DAG DirectedAcyclicGraph
DEP Dielectrophoresis
DMB DigitalMicrofluidicBiochip
DNA DeoxyribonucleicAcid
EWOD Electrowetting-on-dielectric
FA-LSR Fault-AwareListSchedulingandRouting
FTC Fault-TolerantCompilation
FTP FastTemplatePlacement
FTSG Fault-TolerantSequencingGraph
FT-BBC Fault-TolerantBlack-BoxCompilation
FT-DAC Fault-TolerantDroplet-AwareCompilation
GFTA GeneralizedFault-TolerantApplication
GRASP GreedyRandomizedAdaptiveSearchProcedure
IDP InterpolationDilutionofaProtein
ILB IncrementalLibraryBuild
ILP IntegerLinearProgramming
ITO IndiumTinOxide
IVD In-VitroDiagnostics
LB LocalBranching
LED Light-EmittingDiode
LS ListScheduling
LSPR ListScheduling,PlacementandRouting
MBC Module-BasedCompilation
OIA Operation-Interdependency-Awarecompilation
v
vi Acronyms
ONC OnlineCompilation
OS OptimalSynthesisapproach
PCB PrintedCircuitBoard
PCR PolymeraseChainReaction
PCR/M MixingstageofthePolymeraseChainReaction
PDNA samplepreparationforPlasmidDNA
QSC Quasi-StaticCompilation
RBC Routing-BasedCompilation
RBCC Routing-BasedCompilationwithContaminationavoidance
RCL RestrictedCandidateList
ROS RedundancyOptimizationStrategy
RRT RectangularRouteofvaryingThickness
SA SimulatedAnnealing
SB SyntheticBenchmark
SF Straight-forwardapproach
SFS Straight-forwardScheduling
TGFF TaskGraphsForFree
TNT Trinitrotoluene
TS TabuSearch
VLSI VeryLarge-ScaleIntegration
Notations
A Allocation
Arch Biochiparchitecture
B Binding
C Setofelectrodes
c Electrode
i
C Operationexecutiontimewithoutfault-tolerance
i
Ck Operationexecutiontimeincaseofkpermanentfaults
i
CMk ExecutiontimeofoperationO onmoduleM
i i k
Chain Chainofelectrodes
i
D Detectionoperation
i
DR DetectionoperationneededtodetectanerrorduringR
i i
E Setofdependenciesbetweentheoperationsinagivengraph
E Intrinsicerrorlimitfordilutionoperation
Dlt
E Intrinsicerrorlimitfordispensingoperation
Ds
E Conditionofafaultoccurrence
i
E Conditionofanofaultoccurrence
i
E Intrinsicerrorlimitformixingoperation
Mix
E Intrinsicerrorlimitforsplitoperation
Slt
E Errorthreshold
Thr
E Intrinsicerrorlimitfortransportoperation
Trans
F Fluidiclibrary
F Setoffaultyelectrodes
G0,G Biochemicalapplicationgraphwithoutfault-tolerance
GC BiochemicalapplicationgraphG0withthedetectionoperations
GR Biochemicalapplicationgraphwithredundancy
I Inputoperationerrorlimit
i
InB Dispensingreservoirforbuffer
InR Dispensingreservoirforreagent
InS Dispensingreservoirforsample
k Numberofpermanentfaults
vii
viii Notations
L Modulelibrary
M Componentlibrary
M Circular-routemodule
i
mi;j Binary variable defining if a storage is requiredfor operationOi at time
stept
j
n Numberofsensors
sns
O Operation
i
OR Redundantoperation
i
Oi:x ThexthcopyoftheoperationOi
P Placement
p0 Percentagetowardsoperationcompletionforaforwardmovementofone
1
electrode
p0 Percentage towards operation completion for a forward movement of at
2
leasttwoconsecutiveelectrodes
p180 Percentagetowardsoperationcompletionforabackwardmovement
p90 Percentagetowardsoperationcompletionfora90ıturn
p0 Percentage towards operation completion for a cycle when there are no
cycle
faults
pf Percentagetowardsoperationcompletionfora cycleincase off perma-
cycle
nentfaults
q Numberoftransientfaultsinalltypesofoperations
R Routing
R RecoverysubgraphforO
i i
RSpace Recoverysubgraphforspaceredundancy
i
RTime Recoverysubgraphfortimeredundancy
i
RF ReusabilityfactorforoperationO
i i
S Scheduleofoperations
s Numberoftransientfaultsinsplitoperations
tstart StarttimeforoperationO
i i
tfinish FinishtimeforoperationO
i i
tfinish Finishingtimeofthesinknodeoftheapplicationgraph
sink
TI Initialtemperature
TL Temperaturelength
W Penaltyweight
zi;j;k;l BinaryvariabledefiningatwhattimestepjoperationOi
startsexecuting,onwhatmoduleM ,andthecellc usedasabottom-left
k l
cornerforplacingmoduleM
k
ıG Applicationcompletiontime
ıs Applicationcompletiontimeincaseofsfaultsinsplitoperations
G
ık Applicationcompletiontimeincaseofkpermanentfaults
G
(cid:2) Coolingratio
(cid:3) Implementationofanapplicationonagivenmicrofluidicbiochip
i
Contents
1 Introduction................................................................. 1
1.1 Motivation............................................................ 5
1.2 Overview.............................................................. 6
References.................................................................... 9
PartI Preliminaries
2 DesignMethodologyforDigitalMicrofluidicBiochips................. 13
2.1 CompilationofBiochemicalApplications.......................... 15
2.2 RelatedWork......................................................... 16
2.2.1 CompilationMethods ...................................... 17
2.2.2 DropletRoutingMethods .................................. 18
2.2.3 MethodsforPin-ConstrainedBiochips.................... 20
2.2.4 MethodsforCross-ContaminationAvoidance............ 21
2.2.5 CompilationMethodsforFault-Tolerance
andVariability .............................................. 22
2.2.6 MethodsforBiochipArchitectureSynthesis.............. 24
References.................................................................... 25
3 BiochipArchitectureModel............................................... 29
3.1 DropletActuation .................................................... 30
3.2 TypicalDigitalMicrofluidicBiochipArchitectures................ 32
3.3 FaultModels.......................................................... 34
3.3.1 CrossContamination....................................... 37
3.4 OperationExecution:Modulevs.Routing.......................... 38
3.5 CharacterizingRouting-BasedOperationExecution............... 40
3.6 DynamicModules.................................................... 42
3.7 Non-RectangularModules........................................... 42
3.8 Circular-RouteModule .............................................. 43
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