- Jonathan Scholey, Professor (BSc Cell and Molecular Biology; PhD Molecular Biology), firstname.lastname@example.org
- Gul Civelekoglu-Scholey, Associate Project Scientist (BSc Mathematics; PhD Applied Math), email@example.com
This class will be taught in two integrated sections that combine; Part (i) lectures and reading on the physical and chemical principles by which atoms and molecules form living, moving, reproducing cells; with Part (ii) the application of mathematical and computational techniques for modeling the molecular mechanisms of these fundamental cell biological processes. We will supplement lectures with reading material from the primary literature, online seminars and problem sets or written paper assignments. Matlab programing will be introduced at the beginning of the second part of the course, and simple algorithms associated with topics selected from part I of the class will be developed. Students will thus learn how to perform “hands-on” modeling of processes such as cell locomotion and mitosis on their lap-tops using Matlab codes. Grades will be based on participation in class, take-home problem sets and papers.
Lectures will be held every Wednesday from 1-3pm and Friday from 1-2pm. They will be organized roughly as follows;
Part (i) Wednesday – formal lecture on the topic mentioned. Students may watch the assigned approximately one-hour iBioseminar in their own time. Friday – a less formal instructor-led discussion of the week’s iBioseminar and assignment of homework. iBioseminars are available at: http://www.ibiology.org/ibioseminars.html
Part (ii) Wednesday – formal lecture on mathematical modeling in cell and molecular biology. Friday – more “hands-on” discussion involving student participation in model development, and assignment of homework.
Part I: Building the Living, Moving, Reproducing Cell (JS)
Week 1. Origin and Nature of Cellular Life.
- W. Sept 25: Introductory lecture: Molecular Basis of Cell Organization.
- F. Sept 27: Origin of Cellular Life on Earth (Szostak iBioseminar).
Week 2. Physical Nature and Organization of Cytoplasm.
- W. October 2: The Physical Nature of the Intracellular Environment: Thermal Energy, Diffusion and the Low Reynold’s Number World.
- F. October 4: Organization of Cytoplasm (Hyman iBioseminar).
Week 3. Protein Machines.
- W. October 9: Enzyme Action: a paradigm for conformational changes in cytoskeletal motors.
- F. October 11: G-proteins as molecular switches (Wittinghofer iBioseminar).
Week 4. Kurban Bayrami October 14th-18th
Week 5. Cell Locomotion.
- W. October 23: Polymer Ratchets and Cell Crawling.
- F. October 25: Cell Motility (Theriot iBioseminar).
Week 6. Research Discussion.
- W. October 29: – REPUBLIC DAY
- F. November 1: Discussion of Previous Friday Scholey Research Seminar – “Motors Adapted for Mitosis and Ciliogenesis”.
Week 7. Biological Motors and Intracellular Transport Systems.
- W. November 6: Intracellular and Intraflagellar Transport Motors.
- F. November 8: Cytoskeletal motors (Vale iBioseminar).
Week 8. Mechanisms of Mitosis and Cell Division.
- W. November 13: Mitotic Motors and Chromosome Segregation.
- F. November 15: Control of the Cell Cycle (Morgan iBioseminar).
Part II: Modeling the Living Cell (G C-S)
Week 9. Introduction to Mathematical Modeling of Subcellular Processes.
- W. November 20: Introduction to Dynamical Systems: Discrete and Continuous Approaches. Examples of basic discrete and continuous models (differential equations), and their analysis: phase plane, steady states, stability, elementary bifurcations, oscillations introduced with examples.
- F. November 22: Overview of (i) Analytical and Computational approaches for studying dynamical systems, (ii) Deterministic versus Stochastic Modeling approaches.
Week 10. Introduction to Matlab for Cell and Molecular Biology.
- W. November 27: Introduction to Matlab, using built-in differential equation solvers, examples of classic models in cell biology solved by Matlab ODE solvers.
- F. November 29: Deterministic versus Stochastic Models in cell biology. Separation of time scales, non-dimensionalization. Monte-Carlo simulations.
Week 11. How to Write Matlab Codes for Modeling the Living Cell.
- W. December 4: Methods of discretization and algorithm design for efficient computation.
- F. December 6: Presentation of results: Graphics and videos showing simulations of results.
Week 12. Modeling Cell Locomotion.
- W. December 11: Modeling the Brownian Ratchet.
- F. December 13: Dendritic nucleation model and the actin tail of Listeria monocytogenes.
Week 13. Modeling molecular motors.
- W. December 25: Physical properties and forces generated by MT-based ATPases in Modeling cargo movements by MT-based molecular motors.
- F. December 27: Modeling coordination or competition of same polarity or opposing polarity MT-based molecular motors.
Week 14. Modeling Mitosis.
- W. December 18: Modeling spindle length control.
- F. December 20: Modeling anaphase B spindle elongation and chromosome separation.