Optimization of Trustworthy Biomolecular Quantitative Analysis Using Cyber-Physical Microfluidic Platforms

ISBN-13: 9780367223526 / Angielski / Twarda / 2020 / 349 str.

Mohamed Ibrahim; Krishnendu Chakrabarty

Opis

This book creates a new research field as it bridges the technical skills gap between microfluidic systems and molecular biology protocols but viewed from the perspective of an electronic/systems engineer.

Spis treści

1 Introduction 1.1 Overview of Digital Microfluidics 1.2 Overview of Continuous-Flow Microfluidics 1.3 Design Automation and Optimization of Micro fluidic Biochips 1.4 Cyber-physical Adaptation for Quantitative Analysis 1.5 Security Assessment of Biomolecular Quantitative Analysis 1.6 Proposed Research Methodology 1.7 Book Outline I Real-Time Execution of Multi-Sample Biomolecular Analysis 2 Synthesis for Multiple Sample Pathways: Gene-Expression Analysis 2.1 Benchtop Protocol for Gene-Expression Analysis 2.2 Digital Microfluidics for Gene-Expression Analysis 2.3 Spatial Reconfiguration 2.4 Shared-Resource Allocation2.5 Firmware for Quantitative Analysis 2.6 Simulation Results 2.7 Chapter Summary 3 Synthesis of Protocols with Temporal Constraints: Epigenetic Analysis3.1 Miniaturization of Epigenetic-Regulation Analysis3.2 System Model 3.3 Task Assignment and Scheduling 3.4 Simulation Results and Experimental Demonstration 3.5 Chapter Summary 4 A Micro fluidics-Driven Cloud Service: Genomic Association Studies 4.1 Background 4.2 Biological Pathway of Gene Expression and Omic Data 4.3 Case Study: Integrative Multi-Omic Investigation of Breast Cancer4.4 The Proposed Framework: BioCyBig4.5 BioCyBig Application Stack4.6 Design of Microfluidics for Genomic Association Studies 4.7 Distributed-System Interfacing and Integration 4.8 Chapter Summary II High-Throughput Single-Cell Analysis 5 Synthesis of Protocols with Indexed Samples: Single-Cell Analysis 5.1 Hybrid Platform and Single-Cell Analysis5.2 Mapping to Algorithmic Models5.3 Co-Synthesis Methodology 5.4 Valve-Based Synthesizer 5.5 Protocol Modeling Using Markov Chains 5.6 Simulation Results5.7 Chapter Summary 6 Timing-Driven Synthesis with Pin Constraints: Single-Cell Screening 6.1 Preliminaries 6.2 Multiplexed Control and Delay6.3 Sortex: Synthesis Solution6.4 Experimental Results 6.5 Chapter Summary III Parameter-Space Exploration and Error Recovery7 Synthesis for Parameter-Space Exploration: Synthetic Bio-circuits 7.1 Background 7.2 PSE Based on MEDA Biochips 7.3 Sampling of Concentration Factor Space7.4 Synthesis Methodology 7.5 High-Level Synthesis 7.6 Physical-Level Synthesis 7.7 Simulation Results 7.8 Chapter Summary 8 Fault-Tolerant Realization of Biomolecular Assays 8.1 Physical Defects and Prior Error-Recovery Solutions 8.2 Adaptation of the C5 Architecture to Error Recovery 8.3 System Design8.4 Dictionary-Based Error Recovery 8.5 Experiment Results and Demonstration 8.6 Chapter Summary IV Security Vulnerabilities and Countermeasures 9 Security Vulnerabilities of Quantitative-Analysis Frame-works 9.1 Threats Assessment of DMFBs 9.2 Manipulation Attacks on Glucose-Test Results 9.3 Attacks in the Presence of Cyber-Physical Integration 9.4 DNA-Forgery Attacks on DNA Preparation 9.5 Chapter Summary10 Security Countermeasures of Quantitative-Analysis Frame-works 10.1 Microfluidic Encryption 10.2 Aging Reinforces DMFB Security 10.3 Encryption Security Analysis and Simulation Results 10.4 DNA Barcoding as a Biochemical-Level Defense Mechanism 10.5 Benchtop Demonstration of DNA Barcoding 10.6 Chapter Summary 11 Conclusion and Future Outlook 11.1 Book Summary 11.2 Future Research Directions Appendix A Proof of Theorem 5.1: A Fully Connected Routing Crossbar Appendix B Modeling a Fully Connected Routing Crossbar Appendix C Proof of Lemma 6.1: Derivation of Control Delay Vector Appendix D Proof of Theorem 6.1: Derivation of Control LatencyAppendix E Proof of Lemma 7.1: Properties of Aliquot-Generation Trees E.1 Overlapping-Subproblems Property E.2 Optimal-Substructure Property Appendix F Proof of Theorem 7.1: Recursion in Aliquot-Generation Trees Bibliography