EST 5053 CCBS 2026
Course materials for EST 5053 - Control and Computation in Biological Systems, Fall 2026
Control and Computation in Biological Systems · Fall 2026
Tue & Thu 10:40–12:15, E10-305, Yungu campus. 16 lectures, 1 September–3 November.
Lecturer: Fangzhou Xiao. Office hour: one hour/week by email appointment, E1-321.
TAs: Wenqin Zhou and Xinyu Wang.
How this course works · Submission repository
Schedule update · 19 September. With School of Engineering approval, no lecture on 29 September. Lecture 9 moves to 8 October and each later lecture moves one meeting later. The final lecture is 3 November. Presenter assignments, class time and room are unchanged. The research essay is now due 10 November, 23:59. Revised mini-essay deadlines.
Teaching-format update · 11 September. From Lecture 5, each student teaches one concrete point in roughly 10 minutes or less, within a lecture led by Fangzhou. Preparation lead times follow the revised lecture dates below. More points need rehearsal approval and earn +5 course points only with a full normal score of 3. A whole lecture is an exceptional request requiring Fangzhou’s approval. Format and preparation details · Grading.
About the course
Three schools provide our tools: physics asks what life is as an object, systems asks how it works as a machine, and industry asks how to make it useful. We learn to estimate, model, simulate and reason about biological systems, from molecules to cells and populations. No prior background is required.
Lectures 1–7 build the tools. Lecture 8 develops the course’s central research position: the cell as a machine composed of binding and catalysis. Lectures 9–16 apply and question that framework. Throughout, use AI to investigate and build, then verify the claims, reproduce the calculations and explain the result yourself.
Schedule
Fangzhou leads the lectures and hands over when each student’s agreed point comes. All 17 enrolled students have a teaching assignment, based on the final 11 September roster. † marks a lecturer-assigned slot: complete your GitHub signup and contact Fangzhou if you need to change it. Lectures without student presenters are taught entirely by Fangzhou.
Materials: the core is the lecture guide, posted a week ahead. A core (stub) fixes scope but is not yet a complete guide. Lecturer-written expositions develop the lecture. Student materials are labeled separately and appear after submission and staff review. Lineage traces the ideas’ history. Audience extensions synthesize students’ weekly mini-essays with attribution. Lineage and all extension essays normally appear after the lecture day. Lecture 7’s lineage is released alongside its core with lecturer approval.
| # | Date | Topic and materials | Student presenter(s) |
|---|---|---|---|
| 1 | 1 Sep (Tue) | How this course works, and order of magnitude: the physics how this course works · core · exposition · extension example · audience extension · lineage | Lecturer only |
| 2 | 3 Sep (Thu) | From order of magnitude in biology to binding and catalysis core · exposition · lineage · extension example · audience extension | Lecturer only |
| 3 | 8 Sep (Tue) | From reactions to systems: how biochemical behavior emerges core · exposition · lineage · audience extension | Lecturer only |
| 4 | 10 Sep (Thu) | Dynamics: from simulations to possible behaviors core · lecturer exposition · lineage · audience extension Álvaro’s slides (PDF, as submitted) | Álvaro Bátrez Original format |
| 5 | 15 Sep (Tue) | Stochastic dynamics: the master equation and Gillespie core · lecturer exposition · lineage · audience extension student slides (PDF, as submitted) | 郎可菡 · Kehan Lang 施延庆 · Leo Sin |
| 6 | 17 Sep (Thu) | Timescale separation: QSSA and the telegraph model core · lecturer exposition · lineage · audience extension | 吴新宇 · Xinyu Wu |
| 7 | 22 Sep (Tue) | From stationary dynamics to equilibrium weights core · lecturer exposition · lineage | 方利培 · Lipei Fang |
| 8 | 24 Sep (Thu) | The cell as a biomachine: binding and catalysis core · lecturer exposition · lineage | 李常凯 · Changkai Li 薛顺康 · Shunkang Xue |
| 25 Sep–7 Oct | Mid-Autumn / National Day course break. No class on 29 September, 1 October or 6 October. | ||
| 9 | 8 Oct (Thu) | Closing the loop: five behaviors of binding and catalysis core · lecturer exposition · lineage | 王菲 · Fei Wang † |
| 10 | 13 Oct (Tue) | The adaptation biomachine core · lecturer exposition · lineage · research essay | Weihan Luo † |
| 11 | 15 Oct (Thu) | Analysis of binding and catalysis via reaction-order geometry core | Lecturer only |
| 12 | 20 Oct (Tue) | The computation biomachine core | 朱小萌 · Xiaomeng Zhu † |
| 13 | 22 Oct (Thu) | The metabolic biomachine core | 金城炜 · Chengwei Jin 王子轩 · Zixuan Wang 苏芃 · Peng Su |
| 14 | 27 Oct (Tue) | The growth biomachine core (stub) | 郑豪波 · Haobo Zheng 王思恒 · Siheng Wang |
| 15 | 29 Oct (Thu) | Introduction to protein design core (stub) | 闫润梓 · Runzi Yan 李艺冰 · Yibing Li |
| 16 | 3 Nov (Tue) | Foundational virtual cells that are fully mechanistic core (stub) | Lecturer only |
Assignments
The ordinary weights are unchanged. Full instructions and deadlines are in the course guide.
| Assignment | Weight | When |
|---|---|---|
| Teaching: prepare, rehearse and teach one point, then submit its exposition. One excellent point can earn full ordinary marks. | 40% | Your assigned lecture. Rehearse Friday for Tuesday, Monday for Thursday. Final materials the day before. |
| Extension mini-essays: one point taken beyond each listed lecture pair, clearly explained, illustrated and sourced. Best 6 of 8, five points each. Short worked example. | 30% | Mondays 23:59. Rounds 5–8 now due 19 Oct, 26 Oct, 2 Nov and 9 Nov. See the eight dates. |
| Research essay: a standalone HTML essay with a clear problem, challenge, approach, proof and significance. | 20% | 10 November, 23:59 |
| Participation: questions, discussion, exercises and peer ratings. | 10% | Throughout the course |
The optional teaching bonus is five points on the 100-point total, at most once, with the final total capped at 100. The entire approved contribution is graded normally, including additional points. This does not change the weekly extension mini-essay assignment.
Submit by fork → add your file → pull request to the submission repository. Passing checks normally merge the PR automatically. A merge records receipt, not a grade, approval of teaching scope or website publication. Use this schedule for current teaching assignments if older repository records differ.
Tools and further reading
The course has no required textbook. The core pages are self-contained. These resources offer further explanations and tools.
- AI and writing: Westlake AI Campus · research-essay skill · Research with AI · Fangzhou’s essays
- Modeling and control: Biomolecular Feedback Systems · Feedback Systems · An Introduction to Systems Biology · Biocircuits
- Quantitative foundations: Cell Biology by the Numbers · Nonlinear Dynamics and Chaos · Foundations of Chemical Reaction Network Theory
- Course history: Why the teaching format changed and the previous guide · 2025 course