Chapter 1 Computational protein design methods for synthetic biology.

Chapter 3 Computational design of RNA parts, devices, and transcripts with kinetic folding algorithms implemented on multiprocessor clusters.

Chapter 4 Regulatory RNA design through evolutionary computation and strand displacement.

Chapter 5 Programming Languages for Circuit Design

Chapter 6 Kappa Rule-Based Modeling in Synthetic Biology

Chapter 7 Modular Design of Synthetic Gene Circuits with Biological Parts and Pools

Chapter 8 Computationally Guided Design of Robust Gene Circuits

Chapter 9 Chemical Master Equation Closure for Computer-Aided Synthetic Biology

Chapter 10 Feedback loops in biological networks.

Chapter 11 Efficient Analysis Methods in Synthetic Biology

Chapter 12 Using computational modeling and experimental synthetic perturbations to probe biological circuits.

Chapter 13 In silico control of biomolecular processes.

Chapter 14 Stochastic modular analysis for gene circuits: interplay among retroactivity, nonlinearity, and stochasticity.

Chapter 15 Distributed Model Construction with Virtual Parts

Chapter 16 The synthetic biology open language.

Chapter 17 Computational Methods for the Construction, Editing, and Error Correction of DNA Molecules and Their Libraries