APH 161


Download a PDF of the syllabus with detailed course policies.


Course schdeule

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



Physical Biology of the Cell

Physical Biology of the Cell (2nd ed)
by Rob Phillips, Jané Kondev, Julie Theriot and Hernán Garcia

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.

Cell Biology by the Numbers

Cell Biology by the Numbers
by Ron Milo and Rob Phillips

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.

Essential Cell Biology, 4th Ed.

Essential Cell Biology, 4th Ed.
by Bruce Alberts, et al.

ISBN: 0815344546

This book is an excellent reference for cell biology in general, and is a great companion for PBoC2.

Random Walks in Biology

Random Walks in Biology
by Howard Berg

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.

Mechanics of the Cell

Mechanics of the Cell, 2nd Ed.
by David Boal

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.

Molecular Driving Forces: Statistical Thermodynamics in Biology, Chemistry, Physics, and Nanoscience, 2nd Ed.

Molecular Driving Forces: Statistical Thermodynamics in Biology, Chemistry, Physics, and Nanoscience, 2nd Ed.
by Ken Dill and Sarina Bromberg

ISBN: 0815344309

Dill and Bromberg give a clear, pedagogical introduction to statistical mechanics and its use in biological applications. On reserve in SFL.

Mechanics of Motor Proteins and the Cytoskeleton

Mechanics of Motor Proteins and the Cytoskeleton
by Joe Howard

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.