PHZ4710 - Introduction to Biological Physics
Section 3812 - Spring 2016
Physics Department, University of Florida
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)
Office: 2362 NPB (Located on the 2nd floor of Physics Building)
Office hours: I set aside time each week to meet with students in my
office. I strongly encourage you to come and talk with me if you have
any questions about the course or the assignments. The data show that
students who come to office hours earn (on average) higher final grades
than students who do not. The exact time and day of my office hours
will change each week; this allows me to accomodate the different schedules of more students.
If you cannot attend at the scheduled time you are welcome
to make an appointment for a different time. Come and talk with me right
before or after class and we can make an appointment. Or just send me
an email suggesting some days/times that are convenient for you:
The course aims to introduce some key concepts in the physics of
biological systems. It explores a set of physical and mathematical
principles that help us to understand quantitatively the ways that
biological systems regulate their function,
process and store information, and sense and adapt to their environment.
This course is intended to be accessible to most undergraduate students in
science and engineering disciplines. No particular background in biology
or chemistry assumed or expected - other than basic high school chemistry
and biology (What is an amino acid? What is DNA? What is a chromosome?).
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). In recent years the composition of the class
have been about 30-35% physics majors, 40% chemistry majors, and 25-30% other
science majors (biology, microbiology, engineering ...).
The course also aims to teach some aspects of good technical writing:
You will be asked to write clearly and thoughtfully about the
reading assignments. Mathematical expectations are not extremely high,
but if you are uncomfortable using your calculus skills then you will
not be happy in this course.
Topics this semester (draft):
A "course packet" (actually a book of lecture notes) will be provided via Target Copy, 1412 W. University Avenue,
Gainesville Florida 32603. It is a spiral-bound book of about 125 pages, sold
for just under $20. Call Target at 352-376-3826 for details. (FYI The price reflects the retail cost of printing.
Your instructor receives no royalty, commission, compensation,
kickback, etc. from the sale of this course packet). That is the only required
purchase.
A few other books are recommended but optional - see below.
The books by Nelson are especially recommended. These should all be
available in the Marston Science Library:
In Spring 2016 we will discuss (1) breakthough technologies
in biological microscopy, with emphasis on the superresolution methods
that were recently recognized with the 2014 Nobel Prize. Although the
prize was awarded in Chemistry, this topic really involves a lot of
physics and it has applications across biology. We will continue on
in the vein of optics and biology by discussing (2) vision and the eye, with
emphasis on information collection and processing by the photoreceptor
cells of the retina. Along the way we will discuss Poisson statistics,
photon counting by the retina, and the theory of information. We
will (3) introduce some of the biological physics of biomacromolecules,
including the structure, assembly, stability and information content of
DNA and protein. We will also (4) explore bacterial signaling and chemotaxis,
which is an interesting example of information sensing and processing
at the bacterial (micron) size scale. As time permits, we
will (5) explore some aspects of gene regulation, including models for
transcription and translation, noise and stochasticity, feedback and
nonlinearity. With all of these topics we will see examples of the
physical and mathematical principles that can bring deeper understanding
of complex biological systems. Along the way we will from time to time
discuss technical aspects of experimental work, including microscopy,
optical detectors, fluorescence, photon counting, optical tweezers, etc.
Some work (article summaries for example) can be submitted electronically,
but paper or hardcopy homework will only 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 be prepared by the instructor. You are welcome to come to office hours and discuss the HW if you are having trouble.
In-class activities may consist of a short written assignment regarding a recent reading assignment, a HW question, or another question about a recent topic discussed in class.
This course meets the State of Florida undergraduate writing requirement (Gordon Rule 2) by which you must submit
at least 2000 words of original writing over the full semester. You will accomplish this by
writing about 5 article summaries, each 600-800 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 course and the lectures. Details on the article summaries
is available at this link. 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 26, 2016. See Canvas for details of time and place.
Check 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, Canvas 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. The UF Library has a training module on avoiding plagiarism and you are advised to read it. 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.
A familiarity with calculus is required, as Calculus 1 and
Calculus
2 are used extensively. Calculus 3
is also used occasionally. You will need to be familiar with integrals
and derivatives of simple functions (polynomials, exponentials, trig
functions), as well as basic properties of sums and series, the Taylor
expansion, limits, exponentials and logarithms. We will make some
limited use of functions of several variables, partial derivatives,
and simple differential equations. Concepts related to probability and statistics, such as the Gaussian (normal) distribution and Poisson statistics,
will also be introduced and discussed.
Prof. Steve Hagen
Tues/Thurs 5th-6th period (11:45 am - 1:45 pm)
(Although the schedule indicates 4 hrs/wk, we will often 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, medical physics, medical imaging,
exercise physiology, etc. If you are interested in such topics, you might
find this course very interesting. But we will not cover those topics.
The calendar (and all current information) will be posted on the
UF Canvas 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.
I will assign reading as homework and I will also assign HW problems
from time to time. I do expect students to keep up with the HW by doing
the reading and working out the problems. You may work with a friend
if you like. Solutions to written problems will eventually 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.
We will make some use of data analysis/modeling software such as
Matlab,
It is highly recommended that you gain some facility with a data analysis package during your undergraduate career, if you wish to participate in undergraduate research or go to graduate school.
If you do not already have access to Matlab, you can access it through
UFApps, using
through your web browser and Gatorlink login.
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
grade allowance at the end of the semester by dropping one or two of the
lowest assignment scores - this will help people who missed just one or
two assignments.
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.
Consistently poor attendance or lateness will result in a sharply
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 Canvas/E-learning) account
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.