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)
*However, see also Math skills, below
This course aims to introduce some key concepts in the physics of
biological systems. We will study some of the ways that 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? What are some
fundamental physical principles that limit the performance of biological
systems?
Because we have to start somewhere, we will focus largely on the physics
of the cell. That will mean a heavy emphasis on bacteria, their growth,
motility, sensing, and gene regulation behaviors. However we will
discuss some other (i.e. eukaryotic) systems from time to time, when
it serves our purposes. Because physics is an experimental science, we
will also discuss some of the modern tools that biologists and biological
physicists use to study living systems in the laboratory.
This course is intended to be accessible to most undergraduate students in
science and engineering disciplines. No particular background in biology
or chemistry (beyond your high school classes) is assumed or expected.
You will need to know basic university physics (primarily mechanics and
electromagnetism) and be comfortable with routine use of basic calculus
(see Math Skills, above). Mathematical expectations are not extremely
high, but if you don't like using your calculus skills then you will not be
happy in this course.
Physical Biology of the Cell
You are welcome to buy the hardcopy instead of the E-book, but the 180-day rental of the E-book is a lot cheaper at $73.00
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. Late homework will not be graded and missed assignments
cannot be made up. (See Make-up policy below.)
Homework assignments will consist largely of end-of-chapter
problems from the Physical Biology of the Cell textbook.
In-class activities may consist of a small computer (Matlab) project,
a homework question or a set of questions about a reading assignment.
This is a Gordon Rule 2 class, and so you will need to submit
3000 words of original writing over the full semester (equivalent to
ten pages doublespaced in 12 point Roman). You will accomplish this by
writing about 5-6 article summaries, each roughly 500-600 words
in length, over the semester. An article summary is a short essay
describing the contents of a scientific article that is relevant to
the textbook and or class lectures. Details on the article summaries
will be provided in class.
The final examination will be a comprehensive in-class
exam that will focus on the material covered in the above assignments
and in lecture. As there are no makeups available for the final exam,
you should make no plans to leave campus prior to the scheduled exam
date, Tuesday April 30, 2013 at 7:30-9:30 AM (Exam group 30A).
Please plan carefully. Check 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.
A make-up for a missed final 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.)
No make-ups will be granted for missed article summaries.
Specific due dates and times will be specified for homework and
other assignments, and these deadlines are firm. Deadlines are a fact
of life in all types of professional environments, and we all need to
learn to meet them. The fact that one has other concurrent deadlines or
obligations in other spheres is not an excuse for missing deadlines in
this course. Consequently, late work will not be accepted in general. Work
that is very slightly late may (at the instructor or grader's
discretion) be accepted with a grade penalty.
Note that computer problems of various types (hard drive crash, software
incompatibility, Sakai down, loss of internet connection, etc.) are not
acceptable excuses for late work, as the fallibility of technology in
general is widely recognized. A decision to leave your work to the last
minute only sets you up for disaster when one of these minor incidents
occurs. Similarly, common medical problems such as minor and transient
illnesses can strike at any time, and so we cannot use them as an excuse
for missing deadlines that were assigned well in advance. Success in a
professional work environment requires working comfortably ahead of
deadlines, so that chance occurences, technical difficulties, or other
malfunctions arising at the last minute do not derail one's efforts.
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? As in most physics courses, it
is normal and appropriate for students in PHZ4710 to work together on
homework assignments. However 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. These acts are
dishonest. Supplying a false or fabricated excuse for missed academic work
is also academic dishonesty. Students are often tempted to plagiarize
small amounts of text from various sources - but any amount of
direct copying or plagiarism in any assignment is regarded as a
deliberate violation of the academic honesty code. Plagiarizing any
portion of an article summary from any source (including the article
itself) is academic dishonesty. 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. If you
collaborate with a friend on the homework, you must still write up your
solution in your own words, in a way that you understand. Most students
have no trouble understanding the difference between collaboration on
homework (which is okay) and copying homework (which is not okay) --
but if you find it confusing just let me know.
The Dean
of Students Office website has further details on academic honesty
policies at UF.
Although PHY2053/2054 is formally acceptable as a prerequisite, a strong background in calculus is definitely expected.
Calculus 1, Calculus
2 and Calculus 3 are used extensively.
We will routinely use integrals and derivatives,
trig functions and logarithms, sums and series, functions of several variables, partial
derivatives, and vectors.
Prof. Steve Hagen
Office: 2362 NPB
Office hours: to be announced (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
This course is an introduction to biological physics. It is
not a course in biochemistry. It is also not a course in
bioengineering, medical physics, medical imaging, radiation oncology,
or the mechanics of sports. If you are interested in such topics, you
might find this course very interesting. But we will not cover those topics.
Second edition (2012)
By R. Phillips, J. Kondev, J. Theriot, H. Garcia
Ebook version: ISBN 9781134111589
Published by Garland Science / Taylor and Francis
Online resources for this textbook
Note that you can also purchase individual electronic chapters as needed for $9.00 - this might be a good option if you are on a tight budget, as we are unlikely to cover all 22 chapters. (However I cannot promise that this will ultimately prove to be cheaper than the 180 day rental. The absolute cheapest option is probably to rent a hardcopy from Amazon.) A few supplementary texts are suggested here, in no particular order. These should all be available in the Marston Science Library:
Topics
this semester include
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. I 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. A common reason why some students do poorly
in physics courses is that they do not attempt to master the homework.
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 Excel (*.xls) files, which
are easily read and manipulated in Matlab. Matlab is vastly superior to Excel for most scientific computing work, and so 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
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 make-ups
for missed homework or in-class activities. If you experience a severe
personal or family emergency that prevents you from attending class or
submitting your homework, please do not request a make-up. Instead,
I will make some allowance at the end of the semester to drop the one
or two lowest assignment scores. (The number will depend on how many
assignments were given.)
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.
This is
an upper-division, university classroom and so we expect professional
behavior from everyone. Frequent lateness, entering and leaving the
classroom during the lecture, listening to headphones or reading the
ALLIGATOR during class, texting, websurfing, emailing 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 this instructor believes that clasroom use
of laptops, iPods, phones, tablet computers, and virtually all other
electronic devices is almost always detrimental to student learning
and attention. There may be times when we use laptop computers for a
classroom activity - but at all other times, please do not use them in
class. Please show courtesy and respect for yourself, your colleagues,
and your institution by putting away all your electronic devices at the
start of class, and by 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. No warnings and no exceptions. If the
incident is the student's first offense at UF, the student will receive
a failing grade in PHZ4710. If not, the Dean of Students Office will
decide the appropriate sanction.
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.