Introduces the physics of biological systems. Topics vary according to instructor and student interest, but may include physics of proteins and nucleic acids, biomolecular motors, and diffusional signaling and sensing. Important experimental tools such as magnetic resonance and synchrotron x-ray crystallography will also be discussed. (WR)
A few supplementary texts are suggested here, in no particular order. These should all be available in the Marston Science Library:
The goal of this course is to introduce some key concepts in the study
of the physics of biological systems. We will study some of the ways
that the mathematical and physical models and approaches shed useful
light on the functional principles of important biological systems: How
do you write down a quantitative, physics-based model that captures the
behavior of a biological system in an enlightening and predictive way?
The textbook develops statistical ideas and models, dimensional analysis,
simple model systems, dynamical equations, and other such tools and
then shows how they can be applied in biology. The first half of the
course introduces a set of foundational statistical ideas with important
applications in the study of biological systems. The second half will
apply these tools to a diverse set of examples in biology, centered
largely around the role of light in biology.
This course is intended to be
accessible to most undergraduate students in science and engineering
disciplines, especially those who have had some basic physics (mechanics
and electromagnetism in particular) and who are comfortable with calculus
of one variable (differentiation and integration).
The textbook author also has a website with datasets and other materials relevant to the homework and examples: Click here for details. Specific datasets are available here.
Homework will be collected in class. It will not be accepted out
of class. Please do not slide it under my office door or place it in
my mailbox. Each homework assignment will be graded on a 3-point scale
(0-3 points). Late homework will not be graded and missed assignments
cannot be made up. I will provide some sort of HW drop scheme at the
end of the semester, so there is no need for you to provide an excuse
for missed homework.
As there are no makeups available for the final exam, you should make
no plans to leave campus prior to the scheduled exam date, 7:30-9:30 am, Friday
May 4, 2012 (Exam group 4A).
Please plan carefully. Check all deadline and exam
dates carefully before you make any plans to travel away from campus
during the semester. If you purchase an airline ticket to travel during
the semester, and you later realize that your travel conflicts with a
scheduled deadline or exam, you will have a problem.
Some students may nevertheless suffer from a severe personal or
family emergency that forces them to miss a quiz or homework:
Therefore, the two lowest quiz/homework scores will be dropped when final grades
are calculated.
It is the policy of the University of Florida that the student, not the
instructor, is responsible for arranging accommodations when needed. The
instructor will not remind the student to schedule accommodations prior
to each quiz or exam. If you require extra time for in-class work, you
must initiate this request at least seven days before the exam or quiz.
What does
"academic dishonesty" mean? Although it is normal and appropriate for
students in this course to work together on homework assignments, certain
other activities are inappropriate: these include plagiarism,
fabricating data or information, giving or receiving any
unauthorized assistance on quizzes or exams, and interfering with
the academic work of other students. Submitting homework solutions
that were simply copied or transcribed from another student, a book,
or a website is clearly dishonesty, because it is not your own work.
Supplying a false or fabricated excuse for missed academic work is also
academic dishonesty. If the incident is the student's first offense
at UF, the student will receive a failing grade in PHY4710. If not,
the Dean of Students Office will decide the appropriate sanction.
The Dean of Students Office website has further details on
academic honesty policies at UF.
Prof. Steve Hagen
Office: 2362 NPB
Email: sjhagen (at) ufl.edu
Office hours: TBA (and also by appointment)
Tues/Thurs 5th-6th period (11:45 am - 1:45 pm)
(Although the schedule indicates 4 hrs/wk, we will only use 3 hrs/wk in the classroom.)
Room 1216 NPB
Part I
Ch 1 - Introduction
Ch 2 - Tools for biophysical modeling
Ch 3 - Look ahead
Ch 4 - Discrete randomness
Ch 5 - Useful discrete distributions
Ch 6 - Continuous distributions
Ch 7 - Poisson processes
Ch 8 - What is light?
Part II
Ch 9 - Color vision
Ch 10 - How photons know where to go
Ch 11 - Direct and diffractive imaging
Ch 12 - Randomness in chemical reactions
Ch 13 - Genetic control networks
Ch 14 - More general control networks
Ch 15 - Noise in gene regulatory networks
Ch 16 - What happens in photoreceptors
This is a course in biological physics. It is not a course in
bioengineering, clinical medicine, medical physics, diagnostic imaging,
medical devices, orthopedics, nuclear medicine, sports medicine, or
radiation oncology. If you are interested in those topics, you might
find the course interesting. But we will not cover those topics.
It is also not an introduction to biology for physicists,
or an introduction to physics for biologists.
So you may ask, What is it?
Very tentative schedule for the first half of the semester:
The calendar (and all current information) will be posted on the
UF Sakai website.
You can also access the site
through the UF E-learning Services. You will
need to log in with your Gatorlink ID. On the website you will find the
course calendar along with the syllabus, homework and quiz problems and
solutions, and various other timely information. The instructor will
assume that all students visit the website regularly and are
familiar with the information and announcements that are posted there.
The only way to learn physics is to work a large number
of homework problems. Regular homework is therefore at the heart of
this course. Work with a friend if you like. Solutions will
also be posted online. But make sure that you understand each problem and
that you can present your solution. People who don't seriously engage
with the homework usually do poorly in physics courses. If you don't
have time to do homework, then you don't have time to
study physics and you should not be taking this course.
Many of the book's homework and examples use Matlab, a
mathematical analysis and graphics software package that is very
widely used in the natural sciences. The datasets for the homework are provided as Matlab (*.mat) files as well as CSV. Therefore you will probably want to use Matlab (or
similar software, such as Octave) for some of the homework. Matlab is
very useful, so you will not regret learning how to use it. If you do
not already have access to Matlab, your options are:
(1) Obtain access to the physics computer lab (1212 NPB) by requesting a signup form from the Student Services office (1210 NPB). Fill out the form and then bring it to Mr David Hansen in room 2122 NPB;
(2) Get a copy of Octave, a free Matlab clone that should work just fine with all of our files;
(3) Try out the Student Edition of Matlab and consider buying yourself a copy (about $60-70).
(4) Find another computer facility on campus that offers student Matlab access.
The final course grade will be determined by a combination of
homework, a term paper, and a final examination. We may also have
an occasional quiz, which will count as homework. This is a Gordon Rule 2 class, and so the term paper is 3000 words
(roughly ten pages doublespaced in 12 point Roman). To complete the
term paper assignment you must (1) Choose and present your topic,
(2) Submit a complete and polished draft, (3) Submit the final paper.
Details and deadlines will be announced. Therefore your final grade in
PHZ4710 is calculated as follows:
The Instructor believes that make-ups are intrinsically
unfair. This unfairness can be mitigated (but not eliminated)
by keeping the number of make-ups to an absolute minimum.
Therefore there will be no makeups for missed quizzes or homework.
A make-up for a missed exam will be granted only in a truly dire situation.
(A student who lacks diligence in contacting the instructor once
this dire situation arises is unlikely to be granted the make-up.)
Regular class attendance is definitely expected. Mastery of the course
material will require each student to make a sustained and consistent
investment of effort throughout the semester. Class attendance is part
of that effort. Poor attendance or frequent lateness will result in
a reduced final grade, or even a failing grade. A student who stops
participating in the class - i.e. who ceases attending class, doing
homework, communicating with the instructor, taking quizzes/exams - should
drop the course, because otherwise a failing grade is certain. No special
end-of-semester arrangements (such as make-up work, late-drop petitions,
incomplete grades, signatures on various forms, etc.) will be provided
to any student who simply disappeared for a substantial portion of the
semester. Such accommodations are only available to students who have
participated in class and kept in regular contact with the instructor
during the term.
Unfortunately the instructor cannot approve requests to audit
PHZ4710. Every student must register formally and take the class for
credit. Coursework of unregistered students is not graded.
Student academic records are confidential, under federal
law. I will not answer emailed questions about your grades or other
academic matters, unless the email comes from your UF email or
Sakai (E-learning) account. Parents (and others) cannot ask instructors
for information on a student's attendance, grades, performance, etc,
either by phone or email. Even your UFID is confidential.
Students who will require a classroom accommodation for a disability must
contact the Dean of Students Office and request proper documentation. Upon
bringing that documentation to the Instructor, the student will be
given the appropriate accommodations. No accommodations are available to
students who lack this documentation.
It is a sad commentary on the 21st century that some people
need to be reminded of appropriate classroom behavior. Frequent lateness,
entering and leaving the classroom during the lecture, listening to
headphones or reading the ALLIGATOR during class, checking messages and
viewing Facebook during class, cellphone rings, etc. ... are all
rude and disruptive behaviors. They distract the teacher and the
other students in the classroom - a direct violation of the Student Conduct Code. In fact it is
the view of this instructor that student use of laptops, iPods, tablet
computers, and all other electronic devices is almost always detrimental
to student learning and attention. Please show courtesy and respect for
yourself, your colleagues, and your institution by turning OFF electronic
devices and avoiding other distracting behaviors.
All students are required to abide by the
principles of academic honesty expressed in the Student Honor Code.
Consistent with university policy, any incident of academic dishonesty in
this course will be reported to the Dean of Students Office.
Major religious observances will be accommodated. It is university
policy, however, that the student must inform the instructor of religious
observances that will conflict with class attendance or other activities,
prior to the class or the occurrence of that activity.
Since major religious holidays are usually based on astronomical calendars -
which can be calculated hundreds of years in advance - the instructor
will expect the student to provide at least 7-14 days of advance
notice of any upcoming religious observance.
The UF Code of Student Conduct (6C1-4.041, section 3(i)
Unauthorized Recordings) prohibits a student from making any
type of recording of any class or activity without express authorization
from the instructor and from other participants. Please also note that
the instructor of this course holds the copyright to all course
materials other than the textbook and the associated homework.
That includes lecture notes and classroom audio/video. The textbook,
homework questions, and written homework solutions are the intellectual
property of the textbook author and the copyright is owned by the author
and his publisher. Permission to redistribute, reuse, recycle, share,
upload, copy, duplicate, sell etc. any course materials in any form
is denied. Period. That means for example that it is illegal
to copy or upload homework solutions or classroom audio/video to any
website or distribute them to any third party for any purpose.