Stuff(t)�(or the Protocol of Biological Dynamics)
Quantitative Biology Bootcamp
Fall 2025
The Incredible Diversity of Time Scales in Biological Processes
Stuff(t) Pervades All of Science�Galileo and Falling Bodies
[The universe] cannot be read until we have learnt the language and become familiar with the characters in which it is written. It is written in mathematical language, and the letters are triangles, circles and other geometrical figures…
Galileo Galilei
Stuff(t) Pervades All of Science�Newton, Linking Galileo and Kepler, and Falling Into Orbit
Stuff(x,t) Pervades All of Science�The Belousov–Zhabotinsky Reaction
Stuff(t) Pervades All of Science�Human Impacts and the Keeling Curve
Stuff(t) Pervades All of Science�Dynamics of the Immune System
Stuff(t) Pervades All of Science�Dynamics of Embryonic Development
Update Rules: A Revolution Enabled by Newton
The Step-In-Time Protocol
Stuff(t) Pervades All of Science�Dynamics of Bacterial Growth
Neidhardt and His Lifelong Love for dN/dt
Measuring Growth Dynamics in Bulk
What Does This Data Tell Us?
Bacterial Growth Dynamics Revealed the Great Insight from Monod and Jacob: Genes That Control Other Genes
Monod (1949)
Single-Cell Bacterial Growth in High Throughput: The Mother Machine
Suckjoon Jun @ UCSD
The Mathematics of Change
A Model of Bacterial Growth
A Probabilistic View of Bacterial Growth
Probabilistic and Bulk Bacterial Growth
A Recurring Theme: Divide and Conquer�The Example of Riemann Integrals
Divide and Conquer in Time to Integrate Differential Equations Using the Euler Method
Our First Key Equation: Exponential Growth
A Feeling for Exponential Growth
Logistic Growth Accounts for the Carrying Capacity of a Cell Culture
Logistic Growth
Measuring Colony Growth and Fitting for the Growth Rate
Stuff(t) Leads Us to “Dynamical Systems”�Differential Equations as Update Rules
Our First Exercise In Mathematicizing�Our Pathetic Thinking
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