Optimization of Trustworthy Biomolecular Quantitative Analysis Using Cyber-Physical Microfluidic Platforms
Mohamed Ibrahim ; Krishnendu Chakrabarty
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However, as the applications of molecular biology grow, the adoption of microfluidics in many applications has not grown at the same pace, despite the concerted effort of microfluidic systems engineers. Recent studies suggest that state-of-the-art design techniques for microfluidics have two major drawbacks that need to be addressed appropriately: (1) current lab-on-chip systems were only optimized as auxiliary components and are only suitable for sample-limited analyses; therefore, their capabilities may not cope with the requirements of contemporary molecular biology applications; (2) the integrity of these automated lab-on-chip systems and their biochemical operations are still an open question since no protection schemes were developed against adversarial contamination or result-manipulation attacks. Optimization of Trustworthy Biomolecular Quantitative Analysis Using Cyber-Physical Microfluidic Platforms provides solutions to these challenges by introducing a new design flow based on the realistic modeling of contemporary molecular biology protocols. It also presents a microfluidic security flow that provides a high-level of confidence in the integrity of such protocols. In summary, this book creates a new research field as it bridges the technical skills gap between microfluidic systems and molecular biology protocols but it is viewed from the perspective of an electronic/systems engineer.
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 Allocation
2.5 Firmware for Quantitative Analysis
2.6 Simulation Results
2.7 Chapter Summary
3 Synthesis of Protocols with Temporal Constraints: Epigenetic
Analysis
3.1 Miniaturization of Epigenetic-Regulation Analysis
3.2 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 Cancer
4.4 The Proposed Framework: BioCyBig
4.5
BioCyBig Application Stack
4.6 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 Analysis
5.2 Mapping to Algorithmic Models
5.3 Co-Synthesis Methodology
5.4 Valve-Based Syn