Design and Analysis of Biomolecular Circuits Engineering Approaches to Systems and Synthetic Biology 1st edition by Heinz Koeppl, Douglas Densmore, Gianluca Setti, Mario di Bernardo ISBN 1441967656 978-1441967657

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ISBN 10: 1441967656
ISBN 13:  978-1441967657
Author: Heinz Koeppl, Douglas Densmore, Gianluca Setti, Mario di Bernardo

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.

Design and Analysis of Biomolecular Circuits  Engineering Approaches to Systems and Synthetic Biology 1st Table of contents:

1. Introduction to Synthetic Biology and Biomolecular Circuits

• Overview of synthetic biology and systems biology
• The intersection of engineering and biology
• History and evolution of biomolecular circuits
• Key concepts and principles in the field

2. Mathematical Foundations of Systems Biology

• Basic mathematical tools for modeling biological systems
• Differential equations and network analysis
• Feedback loops and dynamical systems
• Nonlinear dynamics in biomolecular circuits

3. Biomolecular Circuit Design

• Basic building blocks of biomolecular circuits
• Gene expression systems and regulatory networks
• Construction and design principles for biomolecular circuits
• Design challenges and strategies

4. Engineering Principles in Synthetic Biology

• Engineering approaches to creating biological devices
• Modular design, standardization, and abstraction
• The role of standard biological parts (BioBricks)
• Synthetic biology tools for circuit construction

5. Modeling Biomolecular Circuits

• Introduction to modeling biomolecular circuits
• Stochastic vs. deterministic models
• Kinetic models for gene regulatory networks
• Computational tools for simulating biomolecular circuits

6. Circuit Analysis and Validation

• Techniques for analyzing the behavior of biomolecular circuits
• Experimental validation and testing of synthetic circuits
• Tools for measuring circuit performance in living cells
• Feedback and error correction in biomolecular circuits

7. Applications of Biomolecular Circuits

• Engineering circuits for therapeutic applications
• Biosensors and diagnostic tools
• Biomolecular circuits in environmental monitoring
• Synthetic biology in industrial biotechnology

8. Synthetic Biology and Evolution

• The role of evolution in synthetic biology
• Engineering evolutionary stability in synthetic circuits
• Evolutionary algorithms for optimizing biomolecular designs
• Case studies in evolutionary design of circuits

9. Ethics and Regulation of Synthetic Biology

• Ethical considerations in synthetic biology research
• Public policy and regulatory frameworks for synthetic biology
• Safety protocols and biosecurity concerns
• The future of synthetic biology in society

10. Future Directions in Biomolecular Circuit Design

• Emerging trends and cutting-edge research
• Integration of synthetic biology with other fields (e.g., nanotechnology, artificial intelligence)
• The promise of autonomous synthetic circuits
• Potential for large-scale applications in medicine, industry, and environmental sustainability

11. Conclusion: Towards a New Era of Engineering Biology

• Summary of key principles in biomolecular circuit design
• Challenges and opportunities ahead in the field of synthetic biology
• Bridging the gap between engineering and life sciences for innovation

12. Appendices

• Detailed mathematical derivations and equations
• Protocols for experimental techniques
• Key resources for further study and research

13. Index

• Index for quick reference of terms, topics, and key concepts

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