Physics 320: Intermediate Physics for the Biosciences
Spring Semester, 2006
Course Syllabus
Instructor: Prof.
Daniel Reich
Office: Bloomberg
347
Tel: 516-7899
email: reich@jhu.edu
Lab: Bloomberg
010
Lab Tel: 516-6030
Office Hours: Tuesday, 1-3 PM
TA: Vivek
Thampy
Office: Bloomberg
363
Tel: 516-8933
email vivek@pha.jhu.edu
Office Hours: Tuesday 3-5
This is the second semester of a two-semester course
designed for students in the biosciences who desire or require a second course
in physics beyond the standard
³Physics 1² curriculum.
This semester will focus on wave phenomena and biological probes that depend on
the interaction of electromagnetic radiation with matter. Topics will include:
Waves
and Fourier Analysis
X-ray
diffraction and crystallography
Optics the physics of modern light microscopy
Quantum
mechanics
NMR
and MRI
Class Schedule:
Lectures: Mon.,
Tues., Wed., 9-10AM
Bloomberg 361.
Section: Thursday 12-1
Bloomberg 176
Labs: TBD
Prerequisites: Physics
171:101-102, 171:103-104 or 171.105-106; Calculus II 110. 109.
Physics 319, or permission of the instructor.
Course Website:
The course website is in the JHU WebCT system. You can access it at
You can find a link to it on the Dept of Physics and Astronomyıs home page at:
http://physics.jhu.edu/
This will the syllabus, schedule, late-breaking news,
and copies of the homework assignments and solution sets. Lecture notes and links to other
on-line supplementary material will be available.
Course Materials:
There is no single textbook that covers the course material at the appropriate level. Therefore, we will be working with a variety of sources.
1. Required Textbooks: (available in campus bookstore)
1.
R. K. Hobbie, Intermediate Physics for Medicine and Biology, 3rd
Ed., AIP Press.
2. Recommended Textbook: (available in campus bookstore)
1.
C. E. Swartz, Used
Math
3. Other Useful Books
Waves
F. S. Crawford, Waves, McGraw Hill
H. J. Pain, The Physics of Vibrations and Waves,
Wiley
Diffraction and Crystallography
C.
Kittel, Introduction
to Solid State Physics, 6th or 7th ed. Wiley
G. Rhodes, Crystallography Made Crystal Clear,
2nd ed. Academic Press
Quantum Mechanics
R. Harris, Nonclassical Physics, Addison
Wesley
Others
will made available as needed.
Fairly extensive lecture notes will be available on
the P320 website.
Various
supplementary reading will be handed out in class
Requirements and Grading:
When %of grade
Homework
Weekly 25
Labs TBD 5
Midterm
exam 1 Wed.
March 1 15*
Midterm
exam 2 Wed.
April 12 15*
Final
Exam Tues
May 16 40*
* If a student's grade on the Final exam is higher than his or her average
on the midterm exams, the final exam will be counted for 55% of the grade, and
the studentıs worst midterm exam score will be dropped. It is expected that students will attend all lectures, labs, and
sections, and complete all assignments, and exams.
Senior Option:
In recent years, seniors in this class have managed
to convince (snooker, hoodwink, cajole, sweet-talk) me into honoring the
somewhat dubious JHU tradition of the ³Senior Option,² wherein graduating
seniors are sometimes excused from taking the final exam in Spring Term
courses. This year I am attempting
to make the ground rules for this clear from the outset. Graduating seniors who have done all
homeworks, attended all labs, and taken both midterms will be eligible to elect
the Senior Option. Such
individualsı grades will be determined by a revised scoring scheme wherein each
Midterm exam is counted for 35% of the grade. Students who wish to consider Senior Option can find out
what their grade would be before deciding what to do. Those who elect it will need to inform the Professor by
email. Those who decline Senior
Option and take the final exam may not revert to Senior Option in the event of
mishap on the final.
Homework:
Homework will be due on Wednesdays in class with
the first problem set due on Feb 8.
Solution sets will be available in Section, and on the Course website.
As part of the homework, there will be exercises that
require use of a computer. While some of these will just require a good
plotting program, some will require more sophistication. To this end, we will be using the
program Mathematica. This will be
made available to you for free (with a temporary license), or you may buy it
through HITS. Alternatively, Mathematica is available on the machines in the
Physics Undergraduate Computer (PUC) lab in Bloomberg. As a student in Physics 320, you are
entitled to access to the PUC lab.
Please see Brian Schriver in Bloomberg 366G (Dept office) for an application form for PUC lab
privileges.
Labs:
There will be periodic laboratory exercises. These will be scheduled at mutually agreed upon times. These will be of an informal nature, but they are instructive and perhaps even fun. Attendence and participation is mandatory, but extensive lab write-ups etc will not be required. A tentative schedule of the labs is given below. We may have to shift the dates of one or more lab.
Physics 320 Policy on Collaboration: Doing the homework is crucial to learning the
material in this class. Working
together can be useful and productive, and hence is not discouraged, provided
that all parties put in equal efforts. It is strongly recommended that you not collaborate
until you have each thought about and tried the homework. If you do not put this effort in
on your own, you will not learn the material, and it will be readily apparent
on the exams.
Official University Statement
on Academic Ethics: The strength of the university depends on academic and
personal integrity. In this
course, you must be honest and truthful.
Ethical violations include cheating on exams, plagiarism, reuse of
assignments, improper use of the Internet and electronic devices, unauthorized
collaboration, alterations of graded assignments, forgery and falsification,
lying, facilitating academic dishonesty, and unfair competition.
Report any violations you witness
to the instructor. You may consult
the associate dean of students and/or the chairman of the Ethics Board
beforehand. See the guide on
³Academic Ethics for Undergraduates,² and the Ethics Board Web site (http://ethics.jhu.edu) for more information.
Intermediate Physics for the Biosciences
Spring 2006
Approximate Schedule
Week Dates Topics Notes
1 1/30-2/1 Basic
wave props
Start
Fourier analysis
2 2/6-8 Fourier
Analysis Section
Wed in class,
Lecture
during section
3 2/13-15 Digital
signal processing Lab
1: Sound and
Physics
of Hearing Fourier
Synthesis
4 2/20-22 Intro
to Electromagnetic waves Lab
2: Beats, Digital
Interference
and Diffraction in 1D Signal
Measurement
Aliasing
5 2/27-3/1 Diffraction
in 2D and 3D Midterm
1: 3/1
6 3/6-8 X-ray
Crystallography Lab
3: Interference
Structure
of DNA and
Diffraction
7 3/13-15 Geometrical
Optics Lab
4: Optical
vision, basic microscopy simulation
of DNA
diffraction
3/20 JHU
SPRING BREAK
8 3/27-29 Physical
Optics
Numerical
Aperture and all that
9 4/3-5 Fancy
microscopy phase contrast, Lab
5: Inside an
DIC, image processing. optical
microscope
10 4/10-12 Quantum
mechanics Midterm
2: 4/12
11 4/17-19 Quantum
mechanics applications
Basic
NMR
12 4/24-26 Pulsed
and FT NMR Lab
6: Pulsed NMR
MRI
13 5/1-3 MRI
14 5/8-10 Reading
period Review Session TBA
15 5/16 FINAL
EXAM: Tuesday 5/16 9-Noon