2011

Design and Analysis of Biomolecular Circuits

Engineering Approaches to Systems and Synthetic Biology

ISBN: 978-1-4419-6765-7 (Print) 978-1-4419-6766-4 (Online)

Table of contents (17 chapters)

  1. Front Matter

    Pages i-xiii

  2. Analysis and simulation

    1. Front Matter

      Pages 1-1

    2. No Access

      Book Chapter

      Pages 3-42

      Continuous Time Markov Chain Models for Chemical Reaction Networks

    3. No Access

      Book Chapter

      Pages 43-62

      Stochastic Simulation for Spatial Modelling of Dynamic Processes in a Living Cell

    4. No Access

      Book Chapter

      Pages 63-72

      Graph-Theoretic Analysis of Multistability and Monotonicity for Biochemical Reaction Networks

    5. No Access

      Book Chapter

      Pages 73-92

      From Structure to Dynamics in Biological Networks

    6. No Access

      Book Chapter

      Pages 93-114

      Contraction Theory for Systems Biology

  3. Modularity and abstraction

    1. Front Matter

      Pages 115-115

    2. No Access

      Book Chapter

      Pages 117-138

      Toward Modularity in Synthetic Biology: Design Patterns and Fan-out

    3. No Access

      Book Chapter

      Pages 139-159

      Retroactivity as a Criterion to Define Modules in Signaling Networks

    4. No Access

      Book Chapter

      Pages 161-181

      The Impact of Retroactivity on the Behavior of Biomolecular Systems

    5. No Access

      Book Chapter

      Pages 183-200

      Modularity, Retroactivity, and Structural Identification

  4. Design and standardization

    1. Front Matter

      Pages 201-201

    2. No Access

      Book Chapter

      Pages 203-224

      Computer-Aided Design for Synthetic Biology

    3. No Access

      Book Chapter

      Pages 225-252

      High-Level Programming Languages for Biomolecular Systems

    4. No Access

      Book Chapter

      Pages 253-279

      Rational Design of Robust Biomolecular Circuits: from Specification to Parameters

    5. No Access

      Book Chapter

      Pages 281-293

      Data Model Standardization for Synthetic Biomolecular Circuits and Systems

    6. No Access

      Book Chapter

      Pages 295-314

      DNA Assembly Method Standardization for Synthetic Biomolecular Circuits and Systems

  5. Enabling technologies

    1. Front Matter

      Pages 315-315

    2. No Access

      Book Chapter

      Pages 317-335

      Gene Synthesis – Enabling Technologies for Synthetic Biology

    3. No Access

      Book Chapter

      Pages 337-368

      On the Construction of Minimal Cell Models in Synthetic Biology and Origins of Life Studies

    4. No Access

      Book Chapter

      Pages 369-393

      Fluorescent-Based Quantitative Measurements of Signal Transduction in Single Cells

  6. Back Matter

    Pages 395-402