- Course Data
PHZ4710 - Introduction to Biological Physics
Section 3812 - Spring 2014
Physics Department, University of Florida
- Catalog Description
Credit: 3; Prereq: one year of introductory physics (PHY 2053/2054,
PHY 2048/2049, or the equivalent) and calculus (MAC 2311/2312 or the
equivalent).
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)
- Math Prerequisite
In prior years PHY2053/2054 was the only formally required prerequisite and there was no mathematics prerequisite. However calculus is added this year as a prereq as Calculus 1 and Calculus
2 are used extensively. Calculus 3 is also used occasionally. If you have not used calculus in some time then you will need to review integrals and derivatives,
trig functions and logarithms, sums and series, functions of several variables, partial
derivatives, and vectors.
- Instructor
Prof. Steve Hagen
Office: 2362 NPB
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 higher final grades on average
than students who do not. The exact time and day of my office hours
will change each week - check the Sakai page for this week's schedule.
Varying my office hours helps me accomodate more students with different
schedules.
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:
Grader: Alejandro (Pedro) Quintero Cabra: paquintero@phys.ufl.edu
- Class Meetings
Tues/Thurs 5^{th}-6^{th} 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
- Goals
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.
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.
- Textbook
We will use Physical Models of Biological Systems ("PMBS") by Prof Philip
Nelson of the University of Pennsylvania. PMBS is a new textbook that
explores the mathematical and conceptual tools needed for developing
physics-based quantitative models of biological systems - especially
(but not exclusively) at the molecular and cellular levels.
As the PMBS book is not yet completely finished, and consequently
not yet published, we will be using the book in manuscript form.
Spiral bound copies of the book should be available from Target Copy,
1412 W Univ Ave, Gainesville FL, tel. (352) 376-3826, starting in the
late afternoon of Tuesday January 6. The price will be just under 25
dollars. Unfortunately, owing to the publisher's legitimate concerns
about electronic piracy, we cannot provide the book in electronic form.
If you are interested in a different perspective on biological physics, the textbook by Rob Phillips et al. is optional but recommended:
Physical Biology of the Cell
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
A few additional, optional texts are suggested here, in no particular order. These should all be available in the Marston Science Library:
- Schedule of topics:
Topics
this semester may include
- Simple dynamical models for biological systems
- Review of basic concepts in probability and statistics
- Bayes theorem, the binomial distribution, and their applications in biology
- Poisson statistics in biology - transposons, pythons, etc.
- Single photon detection in vision
- Maximum likelihood estimation
- Methods - Superresolution microscopy in biology
- The Luria-Delbruck problem in bacterial mutation
- Bacterial growth, chemostats, and related kinetic models
- Simulating random processes such as protein or RNA production
- Measuring protein production molecule-by-molecule in vivo
- Simple models for gene circuits and regulation
- Cellular oscillators, circadian cycles, etc.
- Noise and information
- Methods - Optical tweezers
- Methods - Fluorescence and reporters
- Methods - Single molecule detection
- Website & Calendar
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.
- Homework
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.
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.)
- Matlab
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) Use UFApps to access Matlab through your web browser and Gatorlink login.
(5) Find another computer facility on campus that offers student
Matlab access.
- Exams and Grades
The final course grade will be determined by
- 40% - Homework assignments, in-class writings and activities
- 35% - Article summaries / synopses
- 25% - Final Examination
- 100% - Total
Homework assignments will consist largely of end-of-chapter
problems from the PMBS 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 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 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, Friday May 2, 2014 at 12:30 - 2:30 pm (Exam group 2C).
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.
- Make-ups, Late work, Deadlines, etc.
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.
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.
- Attendance
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.
- Auditing the course
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.
- Privacy
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.
- Disabilities (Accomodations)
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 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.
- Professional Behavior
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.
- Academic Honesty
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.
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.
- Religious Holidays
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.
- Copyright
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.