PHYS 444 Physical Biology: From Molecules to Cells

Fall 2014
Course Information
1.

Introduction:

When: Class Tuesday/Thursday 2:00 3:50 pm. Office Hours Thursdays 1:00 2:00 p.m.
Who: You and me (Moh El-Naggar, x 0-2394, mnaggar@usc.edu, SSC 215C)
Where: Class KAP 146, Office Hours SSC 215C
What: An introductory biological physics class. Our text will be Physical Biology of the Cell,
2nd edition, by Phillips, Kondev, Theriot, and Garcia. You can find it at the bookstore, or get it
somewhere online.
Prerequisite: PHYS 152 or PHYS 162
Recommended Preparation: A background in cell biology at the level of BISC 220 is
recommended, but not required.

2.

Course Description

The last few decades have witnessed historical advances in cell, molecular, and structural
biology, driven at least partially by powerful physical approaches. As new experimental
measurements and techniques continue to emerge, this has become fertile ground for physicists
to explore the fundamental laws and organizational principles behind biological function.
This new 4-unit course bridges the No Mans Land between the quantitative modeling of
idealized systems that physics students are typically exposed to, and the complexity of real cell
biology that biologists appreciate. This course is now the cornerstone of the undergraduate
biophysics major, offered by the Department of Physics and Astronomy. In addition to
biophysics and physics majors, the target audience includes quantitatively-minded biology
majors, as well as students from the physical/chemical sciences and engineering interested in
applying physical concepts to achieve a quantitative understanding of biological systems. The
course is also appropriate for graduate students seeking an introduction to biophysics. Success
will be measured by our ability to make quantitative and predictive statements about complex
biological processes using simple physical tools.
Our goal is to cover the following topics. The courses blackboard page will be routinely updated
to point to the corresponding chapters (or sections) from the Phillips book as well as any
additional reading (see below). Please note that this list is subject to small changes and tweaks
throughout the semester depending on the level of interest and student response, we may
choose to delve more deeply into certain topics.

The basic components and construction plans of life. Length, time, and energy scales of life.
Order of magnitude estimates in biology
Case studies of quantitative model building in biology
Thermodynamics in biology (can we invoke equilibrium?)
Statistical mechanics in biology: predicting equilibrium, two-state systems, ion channels,
cooperative binding, random walks, and biomolecular structures

Physics 444, Fall 2014, Page 1 of 6

Electrostatics of salty environments

3.

Books, Supplementary Reading, and Guest lecturers

The textbook by Phillips et al is a pedagogical triumph. The books organization sets it apart
from all other books on the subject. While most authors organize topics according to biological
function, our textbook presents similar information organized based on their proximity in the
physical biology / quantitative modeling perspective. Most topics follow a familiar pattern: 1)
Introduce a problem, 2) Make an order of magnitude estimate, 3) Propose a crude (but
quantitative model), and 4) Refine the model to the point where it matches biological
observations with the hope that it serves as a predictive model.
We will stick closely to the book in the first few weeks of the semester. However, it is critical
that you read the book as we go along. The book aside, this is a reading intensive class. I will
post reading assignments from current and classical literature as we go along. In addition, I will
routinely point you to a number of books for either an interesting take on biophysics, or an indepth treatment of specific topics:*
B. Alberts, D. Bray, A. Johnson, J. Lewis, M. Ra, K. Roberts and P. Walter, Essential Cell
Biology, Garland Publishing, 2003. A great reference book.
D. Boal, Mechanics of the Cell, Cambridge University Press, 2001. Boal has assembled a very
nice collection of insights into the ways in which mechanics can be applied to the living world.
K. Sneppen and G. Zocchi, Physics in Molecular Biology, Cambridge University Press, 2005.
This book is one of a growing number of attempts on the part of physicists to make a case for the
role of quantitative analysis and physical reasoning in attacking real biological problems. There
are many interesting topics scattered throughout the book.
S. Carroll, Endless Forms Most Beautiful, W. W. Norton and Company, 2005. An absolutely
amazing treatment.
M. Kirschner and J. Gerhart, The Plausibility of Life, Yale University Press, 2005. This book is
similar in spirit to that of Carroll and discusses the insights that modern molecular and
developmental biology have provided into evolution.
A. Murray and T. Hunt, The Cell Cycle, Oxford University Press, 1993. This book is by two of
the leaders in this eld and, though it is probably dated, it is full of interesting facts and ideas.
J. Howard, Mechanics of Motor Proteins and the Cytoskeleton, Sinauer Associates, 2001.
O. Mouritsen, Life - As a Matter of Fat, Springer, 2005. This book gives a number of insights
into the role of lipids.
*

Most of this is picked directly from Caltechs Aph 161 taught by the books author:

Physics 444, Fall 2014, Page 2 of 6

R. Burton, Physiology by Numbers, Cambridge University Press, 2000. This book attempts to
take stock of many of the processes of physiology from the perspective of a feeling for the
numbers, as we will do in the class.
R. Schleif, Genetics and Molecular Biology, Johns Hopkins University Press, 1993.
P. Nelson, Biological Physics: Energy, Information, Life, W. H. Freeman and Company, 2004.
Phil Nelsons book represents a view of parts of biology from a fully quantitative perspective
and makes for enlightening reading.
Ptashne, M., A Genetic Switch, Blackwell Science, 1992 and Ptashne, M. and Gann, A., Genes
and Signals, Cold Spring Harbor Laboratory Press, 2002. Absolutely amazing. The clarity of the
thinking and the far-reaching vision which attempts to tame the complexity of biological
specicity is truly inspiring. I also encourage you to listen to Ptashnes lectures at
Rockefeller University which you can nd online.
Dill, K. and Bromberg, S., Molecular Driving Forces, Garland Publishing, 2002. This fantastic
book gives a proper description of the power and versatility of statistical mechanics as opposed
to the schoolboy exercises that make for the main substance of most books on statistical
mechanics. The applications to real world problems in biology and chemistry are as refreshing as
they are enlightening (Note from ME-N: I use this book occasionally in my undergraduate
statistical thermodynamics class, and the physics majors love it)
Carroll S. B., Grenier J. K. and Weatherbee, S. D., From DNA to Diversity, Blackwell Science,
2001. This book is of the same high quality as those by Ptashne (and indeed, was inspired by
Ptashnes A Genetic Switch). Like Ptashne, these authors try to follow one key idea to its
extreme, namely, the idea that animals share the same genetic toolkit that dictate body pattern.
G. Fain, Sensory Transduction, Sinauer Associates, 2003. Fains book describes how organisms
take external stimuli and do something with it. Two related books that will touch on the
processing of information are G. Matthews, Cellular Physiology of Nerve and Muscle and M.
Blaustein, J. Kao and D. Matteson, Cellular Physiology.
A. Lesk, Introduction to Bioinformatics, Oxford University Press, 2002. Want to know the
dierences between wooly mammoths and elephants, etc? Read this book.
A. Y. Grosberg and A. R. Khokhlov, Statistical Physics of Macromolecules, AIP Press, 1994.
Full of interesting insights into the ways in which polymer physics can be used to explore
problems of biological interest.
J. M. Berg, J. L. Tymoczko and L. Stryer, Biochemistry, W. H. Freeman and Company, 2002.
There are a host of interesting books on biochemistry and the hope is that you will overcome any
distaste you might have for the mindless memorization that seems to dictate the pedagogy that
many of us have been exposed to, and be open to the many beautiful problems in this area.
I. M. Klotz, Ligand-Receptor Energetics, John Wiley and Sons, 1997 and Introduction to
Biomolecular Energetics, Academic Press, 1986. Like Ptashne, Klotz brings personality,
originality and clarity to his books. Klotz works very hard to teach us how to think about
molecules in interaction, and as he points out in the preface, it is only when viewed through the
prism of their interactions that molecules are of interest to life.
J. D. Watson, T. A. Baker, S. P. Bell, A. Gann, M. Levine and R. Losick, Molecular Biology of
the Gene, Cold Spring Harbor Laboratory Press, 2004.
Physics 444, Fall 2014, Page 3 of 6

E. Bier, The Coiled Spring: How Life Begins, Cold Spring Harbor Laboratory Press, 2000.
J. Israelachvili, Intermolecular and Surface Forces, Academic Press, 1992. The subject of this
book is much larger than is implied by the title. We will make reference to Israelachvilis
discussion both when discussing forces in the material world and also in the context of selfassembly.
C. R. Calladine and H. R. Drew, Understanding DNA, Academic Press, 1999. This book
provides a window on DNA which makes a good deal of contact with the perspective that will be
brought to this important molecule in the course.
M. Doi, Introduction to Polymer Physics, Oxford University Press, 1996. This book is short and
sweet and provides a readable introduction to many of the ideas from polymer physics that we
will borrow in our attempt to understand the mechanics of biological macromolecules.
P.-G. de Gennes, Scaling Concepts in Polymer Physics, Cornell University Press, 1979. de
Gennes classic epitomizes the appeal of universal insights.
A. Y. Grosberg and A. R. Khokhlov, Giant Molecules, Academic Press, 1997. A very nice
introduction to the physics of macromolecules. Describes many of the arguments that will be
made in our course.
U. Seifert, Congurations of uid membranes and vesicles, Adv. Phys., 46, 13 (1997). Seifert
provides a detailed description of the elasticity of membranes as well as insights into the current
understanding of equilibrium shapes.
H. C. Berg, Random Walks in Biology, Princeton University Press, 1993. A must read. Berg has
all sorts of fun and interesting things to say.
M. Doi and S. F. Edwards, The Theory of Polymer Dynamics, Clarendon Press, 1986. Doi and
Edwards have some important discussions of the motion of polymers in crowded environments.
H. Echols, Operators and Promoters and H. F. Judson, The Eighth Day of Creation. Two very
interesting books on the history of molecular biology. Judsons book is instructive both on the
science and on the types of personalities that did that science. Echols was a molecular biologist
himself and tells the story of the development of molecular biology in very compelling terms - if
you read this book you will learn much biology.
To the extent possible, I will be inviting special guest lecturers throughout the semester to
give you special insight into current research topics. I hope you will enjoy these
appearances.

4.

Demonstrations

Biophysics is advancing rapidly, mostly because of experiments. Throughout the course, I will
constantly explain and refer to experimental techniques. In addition, I will hopefully organize a
few experimental demonstrations using my own laboratory at USC. I hope this will give you a
unique flavor of experimental biophysics.

5.

Online Course Support

The PHYS 444 home page is maintained at http://blackboard.usc.edu. Under the home page you
will find a copy of this course syllabus, lecture slides, assigned reading (check it every week),
Physics 444, Fall 2014, Page 4 of 6

solutions to problems discussed in class, current homework assignments together with some
hints, solutions to completed homeworks, handouts, grades and perhaps other, hopefully useful,
information.

6.

Homework Assignments

Homework assignments complement the lectures and constitute an integral part of this course.
Theyre weighted quite heavily in this course (60% of the total grade). The solutions to the
written assignments are due in class at the beginning, not the end, of the Thursday lecture. Do
not bother trying to hand in a late HW. If for a very strong reason you are unable to finish your
homework on time, you need to send me an e-mail and ask for an extension before the
homework is due (the reason better be good). Please do not slide your homework under my door
or drop it in my mailbox without prior authorization.
I beg you to talk to your colleagues and classmates as you work on problem sets. The solutions
should be written up legibly with enough details so that anybody, not just the author, can
understand what is going on. Specifically, be sure to show all intermediate steps and use words,
not just equations, to explain the solution. A solution consisting of a string of equations with no
comments, a figure if required, or some minimal explanation will be considered unsatisfactory.
Please make sure to staple together multiple homework sheets, as all work submitted as loose, or
clipped together pages will not be graded. Finally, please note that you are not allowed to look
up solutions in a solutions manual or on the web. Graded homework will be returned in class and
solutions will be posted on the course home page.

7.

Project

During the last few weeks of classes, you will be organized into teams of ~ 2 students per team.
Each team will work collaboratively on one of the serious/longer problems in the textbook, or
some other problem of my choosing (preferably an open ended serious problem of current
interest in the field i.e. current scientific literature). Alternatively, if some random problem
tickles your interest, run it by me. If I like it as well, we can discuss making it into a project. You
will then work out the details, and make a brief (20 30 minute) presentation to the class on the
results, as well as a nice poster. Ill provide more details on project topics and logistics by the
middle of the semester. The point is to have fun, work in a team, and get into some serious
research problem that we can all explore together

8.

Grading

The final course grade will be determined according to the following distribution:
Homework
60%
Project
20%
Class participation 20%
Class participation is essentially about you being involved in class. I will teach this class seminar
style, and it has to be a two-way street. Letter grades are entirely at my discretion i.e. I do not use
rigid percentage marks (such as e.g., a rule that 90% would correspond to A- or similar). Further
details about the grading procedure are given in class.

Physics 444, Fall 2014, Page 5 of 6

9.

Miscellaneous

Academic Integrity
Students who violate university standards of academic integrity are subject to disciplinary
sanctions, including failure in the course and suspension from the university. Since dishonesty in
any form harms the individual, other students and the university, policies on academic integrity
will be strictly enforced. We expect you will familiarize yourself with the USC academic
integrity guidelines.
The Trojan Integrity Guide can be found at
http://www.usc.edu/student-affairs/SJACS/forms/tio.pdf.
The Undergraduate Guide for Avoiding Plagiarism can be found at
http://www.usc.edu/student-affairs/SJACS/forms/tig.pdf.
A Guide for Graduate Students can be found at
http://www.usc.edu/student-affairs/SJACS/forms/GradIntegrity.pdf.
Students with Disabilities
Students who need to request accommodations based on a disability are required to register each
semester with the Disability Services and Programs. In addition, a letter of verification to the
instructor from the Disability Services and Programs is needed for the semester you are enrolled
in this course. If you have any questions concerning this procedure, please contact the course
instructor and Disability Services and Programs at (213) 740-0776, STU 301.

10.

Important Dates

Labor day: Monday, September 1

Physics 444, Fall 2014, Page 6 of 6