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<span class="menu-text"><span class="chapter-number">1</span> <span class="chapter-title">Introduction to biological circuit design</span></span></a>
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<span class="menu-text"><span class="chapter-number">7</span> <span class="chapter-title">Two component systems enable robust linear amplification</span></span></a>
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<span class="menu-text"><span class="chapter-number">8</span> <span class="chapter-title">Signaling cascades can give ultrasensitivity</span></span></a>
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<span class="menu-text"><span class="chapter-number">9</span> <span class="chapter-title">Kinetic proofreading: Multi-step processes reduce error rates in molecular recognition</span></span></a>
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<span class="menu-text"><span class="chapter-number">10</span> <span class="chapter-title">Blinking bacteria: The repressilator enables self-sustaining oscillations</span></span></a>
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<span class="menu-text"><span class="chapter-number">13</span> <span class="chapter-title">Molecular titration generates ultrasensitive responses in biological circuits</span></span></a>
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<span class="menu-text"><span class="chapter-number">15</span> <span class="chapter-title">MultiFate enables expandable and controllable multistability</span></span></a>
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<span class="menu-text">Noise: Bug and feature</span></a>
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<span class="menu-text"><span class="chapter-number">17</span> <span class="chapter-title">Bursty gene expression</span></span></a>
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<span class="menu-text"><span class="chapter-number">18</span> <span class="chapter-title">Cellular bet-hedging</span></span></a>
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<span class="menu-text"><span class="chapter-number">21</span> <span class="chapter-title">Turing patterns</span></span></a>
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<span class="menu-text"><span class="chapter-number">22</span> <span class="chapter-title">Scaling reaction-diffusion patterns</span></span></a>
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<span class="menu-text">Technical appendices</span></a>
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<span class="menu-text">Technical Appendix 2a: Approximate solutions of autorepressive dynamics</span></a>
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<span class="menu-text">Technical Appendix 2b: Numerical solutions to ODEs with SciPy</span></a>
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<span class="menu-text">Technical Appendix 2c: Interactive plotting with Bokeh</span></a>
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<span class="menu-text">Technical Appendix 3a: Nondimensionalization</span></a>
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<span class="menu-text">Technical Appendix 4a: Numerical solution of FFLs</span></a>
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<span class="menu-text">Technical Appendix 6a: Michaelis-Menten enzyme kinetics</span></a>
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<span class="menu-text">Technical Appendix 8a: Signaling cascades</span></a>
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<span class="menu-text">Technical Appendix 8b: Cascades of multiply phosphorylated signaling molecules</span></a>
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<span class="menu-text">Technical Appendix 8c: Phosphorylation cascade with saturation</span></a>
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<span class="menu-text">Technical Appendix 10a: Fixed points and composite functions</span></a>
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<span class="menu-text">Technical Appendix 10b: Linear stability analysis</span></a>
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<span class="menu-text">Technical Appendix 10c: Numerical one-dimensional bounded root finding</span></a>
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<span class="menu-text">Technical Appendix 11a: Stability diagrams by numerical computation of eigenvalues</span></a>
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<span class="menu-text">Technical Appendix 11b: The Greshgorin circle theorem</span></a>
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<span class="menu-text">Technical Appendix 11c: Numerical solution of delay differential equations</span></a>
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<span class="menu-text">Technical Appendix 11d: Linear stability analysis of delay differential equations</span></a>
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<span class="menu-text">Technical Appendix 17a: Stochastic (Gillespie) simulation</span></a>
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<span class="menu-text">Technical Appendix 17b: Profiling code for speed and an application of the Gillespie algorithm</span></a>
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<span class="menu-text">Technical Appendix 20a: Lateral Inhibition: Spontaneous symmetry breaking to form a spatial pattern of cells</span></a>
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<span class="menu-text">Exercise 1.1: Strategies for controlling protein expression</span></a>
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<span class="menu-text">Exercise 1.2: Separation of time scales</span></a>
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<span class="menu-text">Exercise 1.3: Rate of production of gene product by an activator</span></a>
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<span class="menu-text">Exercise 1.4: Activators vs. repressors</span></a>
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<span class="menu-text">Exercise 1.5: Bound and unbound promoter regions</span></a>
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<span class="menu-text">Exercise 2.1: Cost of a steady state</span></a>
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<span class="menu-text">Exercise 2.2: Event handling for discontinuous derivatives</span></a>
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<span class="menu-text">Exercise 3.1: Modes of bistability</span></a>
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<span class="menu-text">Exercise 3.2: Controlling an autoactivation circuit</span></a>
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<span class="menu-text">Exercise 3.3: Autoactivation, bistability, and the importance of leakage</span></a>
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<span class="menu-text">Exercise 3.4: Modeling inducers in a toggle switch</span></a>
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<span class="menu-text">Exercise 3.5: Negative autoregulation including mRNA dynamics</span></a>
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<span class="menu-text">Exercise 3.6: Noncooperative bistability with a growth-determined positive feedback circuit</span></a>
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<span class="menu-text">Exercise 3.7: Design principles for toggles</span></a>
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<span class="menu-text">Exercise 4.1: Accelerated responses with FFLs</span></a>
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<span class="menu-text">Exercise 4.2: Statistics of random genetic circuits</span></a>
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<span class="menu-text">Exercise 4.3: XOR gates</span></a>
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<span class="menu-text">Exercise 5.1: Robustness in a C1-FFL</span></a>
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<span class="menu-text">Exercise 6.1: Co-substrate compensation</span></a>
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<span class="menu-text">Exercise 7.1: Interpretations of sensitivity</span></a>
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<span class="menu-text">Exercise 7.2: Signal propagation in a kinase cascade</span></a>
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<span class="menu-text">Exercise 7.3: Dependence of signaling response on total histidine kinase and response regulator concentrations</span></a>
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<span class="menu-text">Exercise 9.1: Kinetic proofreading in the immune system</span></a>
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<span class="menu-text">Exercise 10.1: Coupled repressilators</span></a>
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<span class="menu-text">Exercise 10.2: The KaiABC clock</span></a>
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<span class="menu-text">Exercise 10.3: Linear stability analysis of the repressilator with mRNA</span></a>
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<span class="menu-text">Exercise 11.1: Tuning delay oscillators with positive feedback</span></a>
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<span class="menu-text">Exercise 11.2: Controlling p53 levels</span></a>
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<span class="menu-text">Exercise 12.1: Temporal gene expression and inferring a circuit</span></a>
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<span class="menu-text">Exercise 14.1: Programming cellular response</span></a>
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<span class="menu-text">Exercise 15.1: A tri-stable cell-fate determinant circuit</span></a>
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<span class="menu-text">Exercise 17.1: Dynamics of noise</span></a>
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<span class="menu-text">Exercise 17.2: Noise in a switchable promoter</span></a>
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<span class="menu-text">Exercise 17.3: A possible mechanism for bursty gene expression</span></a>
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<span class="menu-text">Exercise 22.1: Turing patterns with expanders</span></a>
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<span class="menu-text"><span class="chapter-number">A</span> <span class="chapter-title">Configuring your computer to use Python for scientific computing</span></span></a>
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<span class="menu-text">Appendix B1: Hello, world.</span></a>
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<span class="menu-text">Appendix B2: Variables, operators, and types</span></a>
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<span class="menu-text">Appendix B3: Lists and tuples</span></a>
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<span class="menu-text">Appendix B4: Iteration</span></a>
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<span class="menu-text">Appendix B5: Introduction to functions</span></a>
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<span class="menu-text">Appendix B6: String methods</span></a>
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<span class="menu-text">Appendix B7: Dictionaries</span></a>
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<span class="menu-text">Appendix B8: Comprehensions</span></a>
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<span class="menu-text">Appendix B9: Packages and modules</span></a>
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<span class="menu-text">Appendix B10: Errors and exception handling</span></a>
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<span class="menu-text">Appendix B11: Introduction to Numpy and Scipy</span></a>
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<span class="menu-text">Appendix B12: Introduction to Pandas</span></a>
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<span class="menu-text">Appendix B13: Tidy data and split-apply-combine</span></a>
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<span class="menu-text">Appendix B14: Making plots</span></a>
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<span class="menu-text"><span class="chapter-number">D</span> <span class="chapter-title">Regulatory functions and their derivatives</span></span></a>
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<h1 class="title">References</h1>
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<div class="quarto-title-meta">
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