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Table of Contents
Preface; Contents; 1 Introduction; 1.1 Overview of Digital Microfluidics; 1.1.1 Theory of Electrowetting-on-Dielectric; 1.1.2 Hardware Platform; 1.1.3 Sensing Systems; 1.1.3.1 Droplet Visualization System; 1.1.3.2 Capacitive Sensors; 1.1.3.3 Photodetectors and Optical Sensing; 1.1.4 Fault Models; 1.2 Computer-Aided Design and Optimization; 1.2.1 Design Flow for Digital Microfluidic Biochips; 1.2.2 Testing Techniques; 1.2.3 Error Recovery; 1.2.4 Pin-Assignment Methods; 1.2.5 Chip-Level Design; 1.3 Outline of the Book; References; 2 Error-Recovery in Cyberphysical Biochips
2.1 Motivation and Related Prior Work2.2 Overview of Cyberphysical Biochips; 2.2.1 Sensing Systems; 2.2.2 ``Physical-Aware'' Software; 2.2.3 Interfaces Between Biochip and Control Software; 2.3 Reliability-Driven Error-Recovery; 2.3.1 Error Recovery Strategies; 2.3.2 Reliability Consideration in Error-Recovery; 2.3.3 Comparison Between Two Sensing Schemes; 2.4 Error Recovery and Dynamic Re-synthesis; 2.4.1 Off-Line Data Preparation Before Bioassay Execution; 2.4.2 On-Line Monitoring of Droplets and Re-synthesis of the Bioassay; 2.4.2.1 Step 1: Error Identification
2.4.2.2 Step 2: Update of Sequencing Graph2.4.2.3 Step 3: Dynamic Re-synthesis; 2.5 Simulation Results; 2.5.1 Preparation of Plasmid DNA; 2.5.2 Protein Assays: Interpolating Mixing and Exponential Dilution; 2.6 Chapter Summary and Conclusions; References; 3 Real-Time Error Recovery Using a Compact Dictionary; 3.1 Motivation and Related Prior Work; 3.2 Generation of the Error Dictionary; 3.2.1 Dictionary Entry for Error-Free Case; 3.2.2 Dictionary Entries for Single-Operation Errors; 3.2.3 Dictionary Entries for Multiple-Operation Errors
3.2.4 Consideration of Error-Recovery Cost and Reduction in the Number of Dictionary Entries3.3 Actuation Matrix; 3.4 Estimation for the Percentage of Non-zero Elements in Actuation Matrices; 3.5 Compaction of the Error Dictionary; 3.5.1 Compaction of the Actuation Matrix; 3.5.2 De-Compaction of the Error Dictionary; 3.6 Implementation of Dictionary-Based Error Recovery on FPGA; 3.6.1 Sensing Module; 3.6.2 Memory for Storage of the Error Dictionary; 3.6.3 FSM Module; 3.6.4 De-Compaction Module; 3.6.5 Resource Report for Synthesized Modules
3.7 Fault Simulation in the Presence of Chip-Parameter Variations3.8 Simulation Results; 3.8.1 Exponential Dilution of a Protein Sample; 3.8.1.1 Generating Error Dictionaries; 3.8.1.2 Compaction for Error Dictionaries; 3.8.1.3 Fault Simulation Results; 3.8.2 Interpolation Dilution of a Protein Sample; 3.8.3 Mixing Tree Bioassay; 3.8.4 PCR Bioassay; 3.8.5 Flash Chemistry; 3.9 Chapter Summary and Conclusions; References; 4 Biochemistry Synthesis Under Completion-Time Uncertainties in Fluidic Operations; 4.1 Introduction; 4.2 Biochips with Multiple Clock Frequencies
2.1 Motivation and Related Prior Work2.2 Overview of Cyberphysical Biochips; 2.2.1 Sensing Systems; 2.2.2 ``Physical-Aware'' Software; 2.2.3 Interfaces Between Biochip and Control Software; 2.3 Reliability-Driven Error-Recovery; 2.3.1 Error Recovery Strategies; 2.3.2 Reliability Consideration in Error-Recovery; 2.3.3 Comparison Between Two Sensing Schemes; 2.4 Error Recovery and Dynamic Re-synthesis; 2.4.1 Off-Line Data Preparation Before Bioassay Execution; 2.4.2 On-Line Monitoring of Droplets and Re-synthesis of the Bioassay; 2.4.2.1 Step 1: Error Identification
2.4.2.2 Step 2: Update of Sequencing Graph2.4.2.3 Step 3: Dynamic Re-synthesis; 2.5 Simulation Results; 2.5.1 Preparation of Plasmid DNA; 2.5.2 Protein Assays: Interpolating Mixing and Exponential Dilution; 2.6 Chapter Summary and Conclusions; References; 3 Real-Time Error Recovery Using a Compact Dictionary; 3.1 Motivation and Related Prior Work; 3.2 Generation of the Error Dictionary; 3.2.1 Dictionary Entry for Error-Free Case; 3.2.2 Dictionary Entries for Single-Operation Errors; 3.2.3 Dictionary Entries for Multiple-Operation Errors
3.2.4 Consideration of Error-Recovery Cost and Reduction in the Number of Dictionary Entries3.3 Actuation Matrix; 3.4 Estimation for the Percentage of Non-zero Elements in Actuation Matrices; 3.5 Compaction of the Error Dictionary; 3.5.1 Compaction of the Actuation Matrix; 3.5.2 De-Compaction of the Error Dictionary; 3.6 Implementation of Dictionary-Based Error Recovery on FPGA; 3.6.1 Sensing Module; 3.6.2 Memory for Storage of the Error Dictionary; 3.6.3 FSM Module; 3.6.4 De-Compaction Module; 3.6.5 Resource Report for Synthesized Modules
3.7 Fault Simulation in the Presence of Chip-Parameter Variations3.8 Simulation Results; 3.8.1 Exponential Dilution of a Protein Sample; 3.8.1.1 Generating Error Dictionaries; 3.8.1.2 Compaction for Error Dictionaries; 3.8.1.3 Fault Simulation Results; 3.8.2 Interpolation Dilution of a Protein Sample; 3.8.3 Mixing Tree Bioassay; 3.8.4 PCR Bioassay; 3.8.5 Flash Chemistry; 3.9 Chapter Summary and Conclusions; References; 4 Biochemistry Synthesis Under Completion-Time Uncertainties in Fluidic Operations; 4.1 Introduction; 4.2 Biochips with Multiple Clock Frequencies