Ebook: Design and Analysis of Biomolecular Circuits: Engineering Approaches to Systems and Synthetic Biology

This book is devoted to the design and analysis of biomolecular circuits as considered in systems biology and synthetic biology. The aim of the book is to present in a coherent framework some of the most recent work on the analysis, simulation and design of biomolecular circuits and systems, reflecting the interdisciplinary and collaborative nature of the field. The results discussed range from how these systems should be modeled and analyzed, to how they should be physically designed and implemented.

Drawing parallels to electronic circuit design, this book’s contents are organized to reflect what the editors believe are the important, necessary steps to build complex synthetic circuits. Coverage includes analysis and simulation, modularity and abstraction, design and standardization, and enabling technologies. Each of these themes is organized in different chapters that are self-contained so that they can be read individually by experts but also read sequentially by someone wanting to get an overview of the field. This book is intended for computational scientists, e.g. mathematicians, physicists, computer scientist or engineers as well as for researchers from the life sciences. Every effort has been made to make the presentation accessible to a broad, multi-disciplinary audience.

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This book is devoted to the design and analysis of biomolecular circuits as considered in systems biology and synthetic biology. The aim of the book is to present in a coherent framework some of the most recent work on the analysis, simulation and design of biomolecular circuits and systems, reflecting the interdisciplinary and collaborative nature of the field. The results discussed range from how these systems should be modeled and analyzed, to how they should be physically designed and implemented.

Drawing parallels to electronic circuit design, this book’s contents are organized to reflect what the editors believe are the important, necessary steps to build complex synthetic circuits. Coverage includes analysis and simulation, modularity and abstraction, design and standardization, and enabling technologies. Each of these themes is organized in different chapters that are self-contained so that they can be read individually by experts but also read sequentially by someone wanting to get an overview of the field. This book is intended for computational scientists, e.g. mathematicians, physicists, computer scientist or engineers as well as for researchers from the life sciences. Every effort has been made to make the presentation accessible to a broad, multi-disciplinary audience.

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This book is devoted to the design and analysis of biomolecular circuits as considered in systems biology and synthetic biology. The aim of the book is to present in a coherent framework some of the most recent work on the analysis, simulation and design of biomolecular circuits and systems, reflecting the interdisciplinary and collaborative nature of the field. The results discussed range from how these systems should be modeled and analyzed, to how they should be physically designed and implemented.

Drawing parallels to electronic circuit design, this book’s contents are organized to reflect what the editors believe are the important, necessary steps to build complex synthetic circuits. Coverage includes analysis and simulation, modularity and abstraction, design and standardization, and enabling technologies. Each of these themes is organized in different chapters that are self-contained so that they can be read individually by experts but also read sequentially by someone wanting to get an overview of the field. This book is intended for computational scientists, e.g. mathematicians, physicists, computer scientist or engineers as well as for researchers from the life sciences. Every effort has been made to make the presentation accessible to a broad, multi-disciplinary audience.


Content:
Front Matter....Pages i-xiii
Front Matter....Pages 1-1
Continuous Time Markov Chain Models for Chemical Reaction Networks....Pages 3-42
Stochastic Simulation for Spatial Modelling of Dynamic Processes in a Living Cell....Pages 43-62
Graph-Theoretic Analysis of Multistability and Monotonicity for Biochemical Reaction Networks....Pages 63-72
From Structure to Dynamics in Biological Networks....Pages 73-92
Contraction Theory for Systems Biology....Pages 93-114
Front Matter....Pages 115-115
Toward Modularity in Synthetic Biology: Design Patterns and Fan-out....Pages 117-138
Retroactivity as a Criterion to Define Modules in Signaling Networks....Pages 139-159
The Impact of Retroactivity on the Behavior of Biomolecular Systems....Pages 161-181
Modularity, Retroactivity, and Structural Identification....Pages 183-200
Front Matter....Pages 201-201
Computer-Aided Design for Synthetic Biology....Pages 203-224
High-Level Programming Languages for Biomolecular Systems....Pages 225-252
Rational Design of Robust Biomolecular Circuits: from Specification to Parameters....Pages 253-279
Data Model Standardization for Synthetic Biomolecular Circuits and Systems....Pages 281-293
DNA Assembly Method Standardization for Synthetic Biomolecular Circuits and Systems....Pages 295-314
Front Matter....Pages 315-315
Gene Synthesis – Enabling Technologies for Synthetic Biology....Pages 317-335
On the Construction of Minimal Cell Models in Synthetic Biology and Origins of Life Studies....Pages 337-368
Fluorescent-Based Quantitative Measurements of Signal Transduction in Single Cells....Pages 369-393
Back Matter....Pages 395-402

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This book is devoted to the design and analysis of biomolecular circuits as considered in systems biology and synthetic biology. The aim of the book is to present in a coherent framework some of the most recent work on the analysis, simulation and design of biomolecular circuits and systems, reflecting the interdisciplinary and collaborative nature of the field. The results discussed range from how these systems should be modeled and analyzed, to how they should be physically designed and implemented.

Drawing parallels to electronic circuit design, this book’s contents are organized to reflect what the editors believe are the important, necessary steps to build complex synthetic circuits. Coverage includes analysis and simulation, modularity and abstraction, design and standardization, and enabling technologies. Each of these themes is organized in different chapters that are self-contained so that they can be read individually by experts but also read sequentially by someone wanting to get an overview of the field. This book is intended for computational scientists, e.g. mathematicians, physicists, computer scientist or engineers as well as for researchers from the life sciences. Every effort has been made to make the presentation accessible to a broad, multi-disciplinary audience.


Content:
Front Matter....Pages i-xiii
Front Matter....Pages 1-1
Continuous Time Markov Chain Models for Chemical Reaction Networks....Pages 3-42
Stochastic Simulation for Spatial Modelling of Dynamic Processes in a Living Cell....Pages 43-62
Graph-Theoretic Analysis of Multistability and Monotonicity for Biochemical Reaction Networks....Pages 63-72
From Structure to Dynamics in Biological Networks....Pages 73-92
Contraction Theory for Systems Biology....Pages 93-114
Front Matter....Pages 115-115
Toward Modularity in Synthetic Biology: Design Patterns and Fan-out....Pages 117-138
Retroactivity as a Criterion to Define Modules in Signaling Networks....Pages 139-159
The Impact of Retroactivity on the Behavior of Biomolecular Systems....Pages 161-181
Modularity, Retroactivity, and Structural Identification....Pages 183-200
Front Matter....Pages 201-201
Computer-Aided Design for Synthetic Biology....Pages 203-224
High-Level Programming Languages for Biomolecular Systems....Pages 225-252
Rational Design of Robust Biomolecular Circuits: from Specification to Parameters....Pages 253-279
Data Model Standardization for Synthetic Biomolecular Circuits and Systems....Pages 281-293
DNA Assembly Method Standardization for Synthetic Biomolecular Circuits and Systems....Pages 295-314
Front Matter....Pages 315-315
Gene Synthesis – Enabling Technologies for Synthetic Biology....Pages 317-335
On the Construction of Minimal Cell Models in Synthetic Biology and Origins of Life Studies....Pages 337-368
Fluorescent-Based Quantitative Measurements of Signal Transduction in Single Cells....Pages 369-393
Back Matter....Pages 395-402
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