Download a PDF of the syllabus with detailed course policies.
Below is a schedule of lectures, homeworks, and readings for the course. The content and scheduling will change as the course goes along, but will generally follow the below. The table below will be updated as we go though the course.
| M, 01/06 | L1: Why biology is a quantitative science; course overview; biology by the numbers I | PBoC2 Ch. 1; CBBTN introduction | Phillips, et al., 2009 | Moran, et al., 2010 | ||
| W, 01/08 | L2: Biology by the numbers II; principles of estimation | HW1 posted | PBoC2 2.1, 2.2, 3.1, 3.2 | CBBTN Ch. 1 (see HW1) | Milo, 2013 |
| M, 01/13 | L3: Dimensional analysis; mathematizing cartoons | Mahajan Ch. 1 | Goldreich Ch. 2 | ||
| W, 01/15 | L4: Statistical mechanics of molecular interactions | HW1 due; HW2 posted | PBoC2 Ch. 6 | CBBTN Ch. 5 (see HW2) | Dill and Bromberg |
| F, 01/17 | Makeup lecture, L5: Two-state models | PBoC2 Ch. 7 | ||
| M, 01/20 | No class: Martin Luther King, Jr. Day | |||
| W, 01/22 | L6: Allostery and the Monod-Wyman-Changeux model | HW2 due; HW3 posted | Marzen, Garcia, Phillips, 2013 | CBBTN Ch. 2 (see HW3) | |
| M, 01/27 | L7: States and weights I: application of statistical mechanics to gene expression regulation | PBoC2 19.1 and 19.2 | Boedicker, Garcia, Phillips, 2013 | Bintu, et al., 2005 | |
| W, 01/29 | L8: States and weights II: dynamics of regulation of gene expression and genetic switches | HW3 due; HW4 posted | PBoC2 19.3-19.5 | CBBTN Ch. 3 (see HW4) | |
| M, 02/03 | L9: Mass conservation, random walks, and diffusion | PBoC2 Ch. 13 | Berg, Ch. 2 and Ch. 3 | |
| W, 02/05 | L10: Introduction to biopolymers; beam theory and the wormlike chain | PBoC2 8.1-8.3 and 10.1-10.3 | Howard Ch. 6 | |
| M, 02/10 | L11: DNA looping; DNA packaging in nuclei and viruses | PBoC2 10.4 | ||
| W, 02/12 | L12: Introduction to fluid mechanics; bacterial swimming and foraging | HW4 due; HW5 posted | PBoC2 Ch. 12 | Purcell, 1977 | |
| F, 02/14 | Makeup lecture, L13: Introduction to actin and microtubules | PBoC2 10.5, 15.1, 15.3-15.5 | ||
| M, 02/17 | No class: Presidents' Day | |||
| W, 02/19 | L14: Buckling and length control of cytoskeletal filaments | HW5 due; HW6 posted | Howard Ch. 9 | |
| M, 02/24 | L15: Molecular motors: active transport and force generation | PBoC2 Ch. 16 | Howard Ch. 13 and 15 | |
| W, 02/26 | L16: The actin cytoskeleton and cellular integrity; viscoelasticity | HW6 due | Kasza, et al., 2007 | Chaudhuri, et al., 2007 | |
| M, 03/03 | L17: Active viscoelastic materials | HW7 and HW8 posted | Wottawah, et al., 2005 | |
| W, 03/05 | L18: Microtubules: spindle formation and positioning | Grill, et al., 2001 | Grill, et al., 2005 | ||
| M, 03/10 | L19: Introduction to biological membranes: composition and mechanics | PBoC2 Ch. 11 | ||
| W, 03/12 | L20: Course recap | HW7 due | PBoC2 Ch. 22 | |
| F, 03/19 | No class | HW8 due |
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Physical Biology of
the Cell (2nd ed) ISBN: 0815344503 This is our primary text for the course. Much of the course material draws heavily from this book, and we highly recommend you buy your own copy. We'll call this book PBoC2 throughout the term. |
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Cell Biology by the Numbers Download a draft here. This book is in the early stages of being written and is complemented by the BioNumbers website. We will have reading assignments from this text and ask for your comments. We will call this book CBBTN. |
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Essential Cell Biology, 4th Ed. ISBN: 0815344546 This book is an excellent reference for cell biology in general, and is a great companion for PBoC2. |
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Random Walks in Biology ISBN: 0691000646 This book gives a fun, intuitive, and instructive treatment on transport processes in biology that can be described as random walks. A very valuable resource for this class. On reserve in SFL. |
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Mechanics of the Cell, 2nd Ed. ISBN: 0521130697 This book contains a nice colLection of insights on mechanics in cells, from DNA to the cytoskeleton to membranes. On reserve in SFL. |
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Molecular Driving Forces: Statistical Thermodynamics in Biology, Chemistry, Physics, and Nanoscience, 2nd Ed. ISBN: 0815344309 Dill and Bromberg give a clear, pedagogical introduction to statistical mechanics and its use in biological applications. On reserve in SFL. |
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Mechanics of Motor Proteins and the Cytoskeleton ISBN: 0878933336 Howard gives a quite complete and throughtful treatise on cytoskeletal mechanics. It is clearly written and will be a great help during the part of the cours dealing with the cytoskeleton. On reserve in SFL. |