Design and Analysis of Biomolecular Circuits

1. Front Matter

   Pages i-xiii

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2. Analysis and Simulation

   1. Front Matter

      Pages 1-1

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3. Analysis and simulation

   1. Continuous Time Markov Chain Models for Chemical Reaction Networks

      • David F. Anderson, Thomas G. Kurtz

      Pages 3-42

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

      • Kevin Burrage, Pamela M. Burrage, André Leier, Tatiana Marquez-Lago, Dan V. Nicolau Jr

      Pages 43-62

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

      • Gheorghe Craciun, Casian Pantea, Eduardo D. Sontag

      Pages 63-72

   4. From Structure to Dynamics in Biological Networks

      • Murad Banaji

      Pages 73-92

   5. Contraction Theory for Systems Biology

      • Giovanni Russo, Mario di Bernardo, Jean Jacques Slotine

      Pages 93-114

4. Modularity and Abstraction

   1. Front Matter

      Pages 115-115

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5. Modularity and abstraction

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

      • Kyung Hyuk Kim, Deepak Chandran, Herbert M. Sauro

      Pages 117-138

   2. Retroactivity as a Criterion to Define Modules in Signaling Networks

      • Julio Saez-Rodriguez, Holger Conzelmann, Michael Ederer, Ernst Dieter Gilles

      Pages 139-159

   3. The Impact of Retroactivity on the Behavior of Biomolecular Systems

      • Domitilla Del Vecchio

      Pages 161-181

   4. Modularity, Retroactivity, and Structural Identification

      • Eduardo D. Sontag

      Pages 183-200

6. Design and Standardization

   1. Front Matter

      Pages 201-201

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7. Design and standardization

   1. Computer-Aided Design for Synthetic Biology

      • Deepak Chandran, Frank T. Bergmann, Herbert M. Sauro, Douglas Densmore

      Pages 203-224

   2. High-Level Programming Languages for Biomolecular Systems

      • Jacob Beal, Andrew Phillips, Douglas Densmore, Yizhi Cai

      Pages 225-252

   3. Rational Design of Robust Biomolecular Circuits: from Specification to Parameters

      • Marc Hafner, Tatjana Petrov, James Lu, Heinz Koeppl

      Pages 253-279

   4. Data Model Standardization for Synthetic Biomolecular Circuits and Systems

      • Michal Galdzicki, Deepak Chandran, John H. Gennari, Herbert M. Sauro

      Pages 281-293

   5. DNA Assembly Method Standardization for Synthetic Biomolecular Circuits and Systems

      • Nathan J. Hillson

      Pages 295-314

8. Enabling Technologies

   1. Front Matter

      Pages 315-315

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9. Enabling technologies

   1. Gene Synthesis – Enabling Technologies for Synthetic Biology

      • Michael Liss, Ralf Wagner

      Pages 317-335

The book deals with engineering aspects of the two emerging and intertwined fields of synthetic and systems biology. Both fields hold promise to revolutionize the way molecular biology research is done, the way today’s drug discovery works and the way bio-engineering is done. Both fields stress the importance of building and characterizing small bio-molecular networks in order to synthesize incrementally and understand large complex networks inside living cells. Reminiscent of computer-aided design (CAD) of electronic circuits, abstraction is believed to be the key concept to achieve this goal. It allows hiding the overwhelming complexity of cellular processes by encapsulating network parts into abstract modules. This book provides a unique perspective on how concepts and methods from CAD of electronic circuits can be leveraged to overcome complexity barrier perceived in synthetic and systems biology.

• Bio-molecular circuits
• BioBricks
• ChIP-chip
• Circuit Design
• Circuits and Systems
• DNA Synthesis
• Synthetic Biology
• Systems Biology
• iGEM

From the reviews:

“This collection of papers is an excellent reference for anyone who would like to learn more about the engineering and computing side of systems and synthetic biology. … this clear and detailed volume will help to introduce mathematicians, engineers, and computer scientists to an application of their fields in biology. It will also serve biologists who want to know more about how in silico technologies can be an important part of the arsenal used to understand and create biological systems.” (Sara Kalvala, ACM Computing Reviews, June, 2012)

• , Automatic Control Laboratory, ETH Zurich, Zurich, Switzerland

  Heinz Koeppl

• ARCES, Università di Bologna, Bologna, Italy

  Gianluca Setti

• Università di Napoli Federico II, Napoli, Italy

  Mario di Bernardo

• , Department of Electrical and Computer En, Boston University, Boston, USA

  Douglas Densmore

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