Syllabus
Physics 598BP Biophysics Lab
Spring 2016
Updated
Jan 22,
2016
Instructors: Paul Selvin (selvin@illinois.edu) and Jaya Yodh (jyodh@illinois.edu )
Prerequisites: None; Credit: 4 hrs;
Lectures: Mon 4:00-4:50 pm, Loomis 464
Lab: Tues or Thur 1:00-4:50 pm (see location below)
Groups A-D consist of 3 students each for Groups A-C and 4 students in Group D
Website: https://courses.physics.illinois.edu/phys598BP/
Format: 5 experimental labs will be offered in total. Each experimental lab is taught over 2 weeks to 4 groups of 3-4
students each.. The hands-on experiments and analysis will be mixed over each 2 week period (for example – 6 hrs total
of taking data & 2 hrs of analysis). Students will be expected to do the remainder of the analysis on their own and turn in
a lab report for each lab. Lectures for each lab will be taught on Mondays.
Ensemble Fluorescence
Location - Loomis Selvin Lab; Instructor(s) - Marco Tjioe, tjioe2@gmail.com
Part 1: Dye absorption, emission, lifetime, anisotropy
Part 2: Bulk FRET, donor-acceptance donor
Bright Field & Fluorescence Microscopy
Location – IGB; Instructor - Jaya Yodh (jyodh@illinois.edu)
Part 1: Brightfield, Kohler illumination DIC, Phase Contrast, Color, Fluorescence Microscopy
Part 2: Widefield fluorescence 3D stack and deconvolution
smFRET
Location – Loomis 108B ; Instructors - Digvijay Singh (digvijay.in1@gmail.com) and Jaba Mitra (jmitra2@illinois.edu)
Part 1: TIRF optics, Slide Pegylation, Chamber Setup, smFRET experiment intro
Part 2: GQ folding experiment and Fret histogram, trace and HaMMy analysis
FIONA
Location - Loomis Selvin Lab; Instructor(s) - Marco Tjioe, tjioe2@gmail.com
Part 1: Photobleaching Lifetime Dye-DNA,
Part 2: Kinesin Q-dot step size measurement; Matlab Code and FIONA analysis* (may extend into STORM)
STORM/PALM
Location - Loomis Selvin Lab; Instructors – Duncan Nall (nall2@illinois.edu) and
Part 1: Microtubule-Cy3b imaging using PALM principles. Imaging and Analysis
Part 2: Microtubule Ab-label (2-color) STORM. Imaging and Analysis
Final week possible demo/labs
Light Sheet Microscopy
Location – IGB; Instructor Duncan Nall (nall2@illinois.edu)
Optical Trapping
Location - Loomis, Chemla lab; Instructor - Roshni Bano (bano2@illinois.edu)
1
Lecture & Lab Schedule Spring 2016
Week (M-F)
Monday
(4:00-4:50 pm,
Loomis 464)
Tuesday
(1:00-4:50 pm)
Thursday
(1:00-4:50 pm)
Jan 18-22,
2016
1/19/16 No
Lecture
(Holiday)
Lecture 1:00-2:30pm, Loomis 464
Lecture 1:00-2:30 pm, Loomis 464
Lecture
Ensemble Fluorescence Part 1 (Group A)
Bright Field & Fluorescence Microscopy
Part 1 (Group B)
Ensemble Fluorescence Part 1 (Group C)
Bright Field & Fluorescence Microscopy
Part 1 (Group D)
Lecture
Ensemble Fluorescence Part 2 (Group A)
Bright Field & Fluorescence Microscopy
Part 2 (Group B)
Jan 25-29,
2016
Feb 1-5, 2016
Feb 8-12, 2016
Lecture
Feb 15-19,
2016
Lecture
Ensemble Fluorescence Part 1 (Group B)
Bright Field & Fluorescence Microscopy
Part 1 (Group A)
Ensemble Fluorescence Part 2 (Group B)
Bright Field & Fluorescence Microscopy
Part 2 (Group A)
Feb 22-26,
2016
Lecture
FIONA Part 1 (Group A)
STORM Part 1 (Group B)
Feb 29-Mar 5,
2016
Mar 7-11,
2016
Ensemble Fluorescence Part 2 (Group C)
Bright Field & Fluorescence Microscopy
Part 2 (Group D)
Ensemble Fluorescence Part 1 (Group D)
Bright Field & Fluorescence Microscopy
Part 2 (Group C)
Ensemble Fluorescence Part 2 (Group D)
Bright Field & Fluorescence Microscopy
Part 2 (Group C)
FIONA Part 1 (Group C)
STORM Part 1 (Group D)
BPS Meeting from February 27-March 2 No Lecture/Labs
smFRET Part 1 (Groups A and B)
Note - This lab will likely also include an
Lecture
evening session
smFRET Part 1 (Groups C & D)
Note - This lab will likely also include an
evening session
smFRET Part 2 (Groups A and B)
This lab may have an evening session also
smFRET Part 2 (Groups C & D)
This lab may have an evening session also
Lecture
FIONA Part 2 (Group A)
STORM Part 2 (Group B)
FIONA Part 2 (Group C)
STORM Part 2(Group D)
Apr 4-8, 2016
Lecture
FIONA Part 1 (Group B)
STORM Part 1 (Group A)
FIONA Part 1 (Group D)
STORM Part 1 (Group C)
Apr 11-15,
2016
NO LECTURE
FIONA Part 2 (Group B)
STORM Part 2 (Group A)
FIONA Part 2 (Group D)
STORM Part 2(Group C)
Apr 18-22,
2016
Lecture
Light Sheet Microscopy or Optical
Trapping (Groups A & B)
Light Sheet Microscopy or Optical
Trapping (Groups C & D)
Apr 25-29,
2016
Lecture
Light Sheet Microscopy or Optical
Trapping (Groups A & B)
Student
Presentations
Student Presentations
Light Sheet Microscopy or Optical
Trapping (Groups C & D)
No Class Last Day of Instruction is Wed
May 4
Reading period begins Thurs. May 5
Mar 14-18
2016 (APS)
Mar 21-25,
2016
Mar 28- Apr 1,
2016
May 2-6, 2016
May 9-13
2016
NO LECTURE
Spring Break
NO FINAL EXAM; May 20, 2016 GRADES DUE
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