MCB137/237 Spring 2024

Physical Biology of the Cell

Biology is being revolutionized by new experimental techniques that have made it possible to quantitatively query the inner workings of molecules, cells and multicellular organisms in ways that were previously unimaginable. The objective of this course is to respond to this deluge of quantitative data through quantitative models and the use of biological numeracy. The course will explore the description of a broad array of topics from modern biology using the language of physics and mathematics. One style of thinking we will emphasize imagines the kinds of simple calculations that one can do with a stick in the sand.

We will draw examples from broad swaths of modern biology from our department and beyond including cell biology (signaling and regulation, cell motility), physiology (metabolism, swimming), developmental biology (patterning of body plans, how size and number of organelles and tissues are controlled), neuroscience (action potentials and ion channel gating) and evolution (population genetics) in order to develop theoretical models that make precise predictions about biological phenomena. These predictions will be tested through the hands-on analysis of experimental data and by performing numerical simulations using Python. Physical biology will be introduced as an exciting new tool to complement other approaches within biology such as genetics, genomics and structural biology. The course will introduce students to the enabling power of biological numeracy in scientific discovery and make it possible for them to use these tools in their own future research.

  • Hernan Garcia - Instructor

    hggarcia@berkeley.edu
    Office Hours:
    Mondays 3:30pm - 4:30pm @ 505 Weill Hall and on Zoom


  • Nick Gravina - GSI

    nick_gravina@berkeley.edu
    Office Hours:
    Fridays 1pm - 2pm @ 505 Weill Hall, Discussion: Fridays 12-1 pm in 259 Dwinelle


The class as a whole will meet twice a week for one hour and a half: Tuesdays and Thursdays from 2pm-3:30pm in 251 Dwinelle. This time will be devoted to lectures, discussions and hands-on activities including Python exercises. Further, the class will be split into weekly one-hour lab sessions. During these lab sessions, students will work closely with the GSIs to implement the concepts they learned in class in the context of different biological problems. Homework assignment will be given every week and will represent 70% of the final grade. At the end of the semester, students will prepare a written project. The project will be based on performing an estimate based on an extensive list we will provide. Attending class and office hours
If you miss classes, it is your responsibility to get notes from one of your classmates. You cannot expect the instructor or GSI to redo the lecture during office hours.
Being able to attend office hours are a key to success. If you cannot attend any of the three offered office hours, you might want to reconsider taking this course.

Homework assignments
Homeworks are due at the beginning of class one week after they are posted.
Homeworks should be submitted through Gradescope to the GSIs in PDF form. Any other form of homework submission will not be accepted. No late homeworks. Time management is key. Start to work on your homework assignments early and make use of office hours and our availability over Piazza.
It is important to describe your reasoning. Just writing an equation or drawing a plot does not constitute a satisfactory answer to a homework problem. All plots in the homeworks need to have labeled axes. All code used needs to be submitted through GraceScope by the homework due date. You can work in groups, but the answers should be your own. This includes the code!

Grading
Regrading is done only until a week after the homework solutions are posted. If you ask us to regrade an answer in a homework assignment, we reserve the right to regrade all the answers it that homework assignment. Your two worst scoring homeworks will not be considered for the final grade. We do not grade on a curve or anything like that.
Title Due Date Required Materials Solutions
Homework 1 1/25 at 2:00 PM
Homework 2 2/01 at 2:00 PM
Homework 3 2/13 at 2:00 PM
Homework 4 2/20 at 2:00 PM
Homework 5 2/27 at 2:00 PM
Homework 6 3/5 at 2:00 PM
Homework 7 3/12 at 2:00 PM
Homework 8 3/19 at 2:00 PM
Homework 9 4/2 at 2:00 PM
Homework 10 4/09 at 2:00 PM
Homework 11 4/16 at 2:00 PM
Homework 12: Final Project 4/30 at 2:00 PM
Homework 13: Extra Credit 5/7 at 2:00 PM

A pdf of the full course syllabus can be found here.

Number Date Topics Materials Discussion Videos
1 1/16 Lecture @ 251 Dwinelle.
  • A feeling for the numbers in biology.
  • Street-Fighting Mathematics: Order-of-magnitude estimates as a tool for discovery in the living world.
  • What sets the scale of X?
2 1/18 Lecture @ 251 Dwinelle
  • A Feeling for the Numbers in Biology, Part II.
3 1/23 Lecture @ 251 Dwinelle
  • Stuff(t) or the Protocol of Biological Dynamics, Part I.
    • Time evolution in biology.
    • Bacterial growth dynamics: Solving bacterial growth analytically and numerically.
4 1/25 Lecture @ 251 Dwinelle
  • Stuff(t) or the Protocol of Biological Dynamics, Part II.
    • Bacterial growth dynamics: Solving bacterial growth numerically.
5 1/30 Lecture @ 251 Dwinelle
  • Stuff(t) or the Protocol of Biological Dynamics, Part III.
    • Bacterial growth dynamics: Mechanisms of bacterial size control.
6 2/1 Lecture @ 251 Dwinelle
  • Stuff(t) or the Protocol of Biological Dynamics, Part IV.
    • Bacterial growth dynamics: Mechanisms of bacterial size control.
7 2/6 Lecture @ 251 Dwinelle
  • Null Hypotheses in Biology: The Poisson Distribution, Part I.
    • The Great Probability Distributions of Biology
    • The constitutive promoter.
8 2/8 Lecture @ 251 Dwinelle
  • Null Hypotheses in Biology: The Poisson Distribution, Part II.
    • Chemical master equation of the constitutive promoter.
9 2/13 Lecture @ 251 Dwinelle
  • Null Hypotheses in Biology: The Poisson Distribution, Part III.
    • The Poisson Distribution: Bombs over London, constitutive promoters, and sequencing the human genome.
    • Synthetic transcriptomes and the single-cell sequencing revolution.
10 2/15 Lecture @ 251 Dwinelle
  • Null Hypotheses in Biology: The Exponential Distribution.
    • Waiting times for photobelaching and ion channel dynamics.
11 2/20 Lecture @ 251 Dwinelle
  • Diffusion as Biology's Null Hypothesis for Dynamics, Part I.
    • Diffusion and axonal transport.
12 2/22 Lecture @ Zoom
  • Diffusion as Biology's Null Hypothesis for Dynamics, Part II.
    • Diffusion by coin flips.
13 2/27 Lecture @ 251 Dwinelle
  • Diffusion as Biology's Null Hypothesis for Dynamics, Part III.
    • Solving diffusion using chemical master equations.
    • FRAP: Measuring diffusion using photobleaching
    • A universal diffusion speed limit for enzyme catalysis and other reactions
14 2/29 Lecture @ 251 Dwinelle
  • Diffusion as Biology's Null Hypothesis for Dynamics, Part IV.
    • A universal diffusion speed limit for enzyme catalysis and other reactions.
15 3/5 Lecture @ 251 Dwinelle
  • Phase Transitions in Biology, Part I.
    • Entropy maximization
16 3/7 Lecture @ 251 Dwinelle
  • Phase Transitions in Biology, Part II.
    • Free Energy Minimization.
    • Drawing Phase Diagrams.
17 3/12 Lecture @ 251 Dwinelle
  • Phase Transitions in Biology, Part III.
    • A dynamical systems view of phase separation
    • Scaling of nucleolar size
18 3/14 Lecture @ 251 Dwinelle
  • The Boltzmann Distribution and Statistical Mechanics, Part I.
    • The ubiquitous nature of binding problems in biology
    • Regulatory biology: the constitutive promoter revisited
19 3/19 Lecture @ 251 Dwinelle
  • The Boltzmann Distribution and Statistical Mechanics.
    • Regulatory biology: simple repression
20 3/21 Lecture @ 251 Dwinelle
  • The Boltzmann Distribution and Statistical Mechanics.
    • Simple Activation
    • Cooperativity
    • Logic Gates
21 4/2 Lecture @ Zoom
  • Defiance Is the Secret of Life: Burning Energy for Fun and Profit, Part I.
    • Energy estimates in biology.
    • Biological batteries
22 4/4 Lecture @ Zoom
  • Defiance Is the Secret of Life: Burning Energy for Fun and Profit, Part II.
    • Defying diffusion: Paying for positional information using degradation vs. transport
23 4/9 Lecture @ 251 Dwinelle
  • Defiance Is the Secret of Life: Burning Energy for Fun and Profit, Part III.
    • Charging up the ATP battery.
    • Using the ATP battery
24 4/11 Lecture @ 251 Dwinelle
  • Defiance Is the Secret of Life: Burning Energy for Fun and Profit, Part IV.
    • Regulatory defiance.
25 4/16 Lecture @ 251 Dwinelle
  • Biological Networks.
    • A life-or-death decision: the Lambda switch.
    • Epidemiology and the SIR model
26 4/18 Lecture @ 251 Dwinelle
  • Biological Networks.
    • A life-or-death decision: the Lambda switch.
    • Epidemiology and the SIR model
27 4/23 Lecture @ 251 Dwinelle
  • Physical Biology of the Cell
28 4/25 Lecture @ 251 Dwinelle
  • Study Hall - No Lecture