Physics 173/BGGN 266
Overview of the Course (Report on years 1 to 5; 0.5Mb PDF)
This laboratory course consists of "table-top" experiments in biological physics, biophotonics, nuclear magnetic resonance, optics, and soft condensed matter physics.
The experiments in this course have been funded through internal UCSD sources, donations from the UCSD research laboratories of the late Theodore Bullock, Harvey Karten, David Kleinfeld, Mu-ming Poo and Douglas Smith, grants from the NSF (PHY to David Kleinfeld and IGERT to Terrance Sejnowski), and HHMI/NIBIB and NIBIB training grants (to Andrew McCulloch). This course was initiated by Prof. David Kleinfeld in 2001 and offered in 2001-06 (David Kleinfeld), 2008-12 (David Kleinfeld), 2013-14 (Philbert S. Tsai), and 2015 (Jeremie A. Palacci); Prof. Palacci will transform the class with projects in soft condenced matter physics.
Course Schedule through 2012 (0.1Mb PDF)
The class meets Tuesday and Thursday from 2:00 PM to 6:00 PM during the Spring Quarter in Mayer Hall. Tutorials and presentations are in room 2623 and the laboratory is in room 3722, with an annex in room 3129. There are typicaly seven tutorials, each of which lasts about one hour. One tutorial is an introduction to Matlab, three are on optics and microscopy, one is on electrical measurement, and two are on spectral analysis. The tutorials are associated with formal exercises. On all non-tutorial days, the period from 2:00 PM to 2:40 PM consists of student presentations and round-table discussions.
Exercises
| Optics and Optical Bench Design | |
| Matrix Methods Lecture Handout: | (3.0Mb PDF) |
| Lab Manual - Basics: | (0.1Mb PDF) |
| Lab Manual - Laser Scanning Microscopy: | (0.1Mb PDF) |
| Lab Manual - Brightfield Microscopy: | (0.5Mb PDF) |
| Electronics | |
| Primer on OpAmp Basics: | (1.2Mb PDF) |
| Primer on Filters and Modularity: | (2.1Mb PDF) |
| Primer on Nonlinear OpAmp Circuits: | (0.2Mb PDF) |
| Spectral Methods in Data Analysis | |
| Basics: | (1.1Mb PDF) |
| Applications: | (3.2Mb PDF) |
Experiments (reprints and a subset of past reports through 2014)
| Belousov-Zhabotinskii Reaction | |
| Reprint: | (0.7Mb PDF) |
| Past Reports: | |
| 2003 | (0.3Mb PDF) |
| 2006 | (0.3Mb PDF) |
| 2014 | (5.8Mb PDF) |
| Bioluminescence | |
| Publications: | (2.7Mb PDF) |
| (0.4Mb PDF) | |
| Past Report: | |
| 2009 | (0.7Mb PDF) |
| Chaotic Circuits | |
| Past Reports: | |
| 2003 | (0.7Mb PDF) |
| 2006 | (1.0Mb PDF) |
| 2012 | (0.8Mb PDF) |
| Coherent Light Scattering | |
| A study of Brownian motion using light scattering, by Clark, Lunacek & Webb. | PDF (1.6 Mb) |
| Canonical data. | PDF (0.1 Mb) |
| Past Reports: | |
| 2002 | (0.3Mb PDF) |
| 2003 | (1.0Mb PDF) |
| 2010a | (1.3Mb PDF) |
| 2010b | (0.5Mb PDF) |
| Software: | (0.1Mb G code) |
| Continuous Nuclear Magnetic Resonance Spectroscopy (discontinued) | |
| Past Reports | |
| 2002 | (2.0Mb PDF) |
| Electroencephalography | |
| Past Report: | |
| 2012 | (0.8Mb PDF) |
| Electromyography | |
| Past Reports: | |
| 2013 | (0.8Mb PDF) |
| 2014 | (1.2Mb PDF) |
| Electrophysiology with Leech Neurons | |
| Past Reports: | |
| 2004 | (1.9Mb PDF) |
| 2006 | (0.3Mb PDF) |
| 2010 | (1.8Mb PDF) |
| 2014 | (1.84Mb PDF) |
| Electrophysiology with Oocytes | |
| Manual (preliminary): | (1.6 Mb PDF) |
| Past Reports: | |
| 2002 | (0.1 Mb PDF) |
| 2003 | (0.5 Mb PDF) |
| Endoscopy | |
| Past Report: | |
| 2014 | (0.6Mb PDF) |
| Fluorescent Imaging of Structure and Function | |
| Past Reports: | |
| 2009 | (1.8Mb PDF) |
| 2010 | (3.7Mb PDF) |
| 2013 | (15.7Mb PDF) |
| Holography | |
| Manual | ;(0.3Mb PDF) |
| Red Star Holography Film | (0.1Mb PDF) |
| Introduction to Holography, by Givens | (0.3Mb PDF) |
| Image Location & Magnification by Givens | (0.9Mb PDF) |
| Point Source Holography | (0.7Mb PDF) |
| Holography of Pennies | (0.7Mb PDF) |
| Holography for Modal Analysis | (0.5Mb PDF) |
| Past Reports: | |
| 2002 | (0.1Mb PDF) |
| 2008 | (4.2Mb PPT) |
| 2011 | (1.9Mb PDF) |
| 2012 | (2.5Mb PDF) |
| 2013 | (12.2Mb PDF) |
| Laser Doppler Flowometry | |
| Past Reports: | |
| 2006 | (2.5Mb PDF) |
| 2009 | (0.7Mb PDF) |
| 2010 | (0.4Mb PDF) |
| 2014 | (1.0Mb PDF) |
| Mossbauer Spectroscopy (discontinued) | |
| Past Reports: | |
| 2001 | (0.4Mb PDF) |
| mRNA Synthesis and Expression in Oocytes | |
| mRNA Synthesis and Expression in Oocytes | (1.3Mb PDF) |
| Past Report: | |
| 2001 | (0.4Mb PDF) |
| Microfluidics | |
| Past Reports: | |
| 2013 | (1.6Mb PDF) |
| 2014 | (3.4Mb PDF) |
| Neuromorphic Circuits | |
| Past Reports: | |
| 2008 | (1.0Mb PDF) |
| 2009 | (0.5Mb PDF) |
| 2010 | (0.1Mb PDF) |
| 2011 | (3.1Mb PDF) |
| Optical Sectioning | |
| Past Report: | |
| 2002 | (0.5Mb PDF) |
| Optical Tweezers | |
| Manual (preliminary): | (0.7Mb PDF) |
| Polysciences Microspheres Data Sheet | (0.3Mb PDF) |
| Past Reports: | |
| 2002 | (0.2Mb PDF) |
| 2003 | (0.2Mb PDF) |
| 2008 | (3.0Mb PDF) |
| 2009 | (1.1Mb PDF) |
| 2010 | (3.2Mb PDF) |
| 2012 | (1.2Mb PDF) |
| 2014 | (1.7Mb PDF) |
| Pulsed Nuclear Magnetic Resonance Spectroscopy | |
| Past Reports: | |
| 2004 | (1.2Mb PDF) |
| 2006 | (0.2Mb PDF) |
| 2008 | (2.1Mb PDF) |
| 2012 | (0.4Mb PDF) |
| 2014 | (0.6Mb PDF) |
| Second Harmonic Generation | |
| In vivo two-photon laser scanning microscopy with concurrent plasma-mediated ablation: Principles and hardware realization, by Tsai & Kleinfeld. | (6.2 Mb PDF) |
| Past Reports: | |
| 2006 | (0.4Mb PDF) |
| 2008 | (0.6Mb PDF) |
| 2009 | (1.6Mb PDF) |
| Two Photon Microscopy | |
| In vivo two-photon laser scanning microscopy with concurrent plasma-mediated ablation: Principles and hardware realization, by Tsai & Kleinfeld. | PDF (6.2 Mb) |
| Past Reports: | |
| 2006 | (0.4Mb PDF) |
| 2010 | (6.2Mb PDF) |
| 2012 | (0.4Mb PDF) |
| 2013 | (8.2Mb PDF) |
| 2014 | (3.1Mb PDF) |
| Visual Coding in the Fly | |
| Past Reports: | |
| 2001 | (0.4Mb PDF) |
| 2002 | (1.4Mb PDF) |
| 2004 | (0.8 Mb PDF) |
| 2006 | (9.7Mb HTML) |
| 2008 | (0.7Mb PDF) |
| 2009 | (0.7Mb DOCX) |
| 2011 | (0.4Mb PDF) |
| 2012 | (0.3Mb PDF) |
| 2013 | (0.3Mb PDF) |
| 2014 | (0.7Mb PDF) |
| Zeeman Effect in Mercury | |
| Handout: | (1.6Mb PDF) |
| Past Reports: | |
| <1980 | (1.4Mb PDF) |
| 2002 | (0.1Mb PDF) |
| 2003 | (0.5Mb PDF) |
Equipment Manuals
| Andor iXon 885 EMCCD Brochure | |
| Andor iXon 885 EMCCD User Guide | |
| Andor iXon 885 EMCCD System Guide | |
| Andor Quick Launch Computer Guide | |
| Axoprobe 1A Amplifier | |
| Bioelectric Amplifier | |
| Burleigh Actuator Manual | |
| Cambridge Scanner Manual | |
| Cambridge Driver Manual | |
| CrystaLaser User Manual | |
| ENMA 72-XXXX Power Supply Manual | |
| Eppendorf Photometer | |
| Fisher pH meter | |
| Hamamatsu PMT R4220 | |
| Hamamatsu PMT R6357 | |
| Ithaco 427 Current Amplifier Manual | |
| JDS Uniphase He-Ne Laser | |
| Kinetic Systems Vibraplane Manual | |
| Narashigee MO-203 Hydraulic Manipulator | |
| National Instruments ADC Board | |
| Newport CMA Actuator Instructions | |
| Nikon SMZ645 Manual | |
| Olympus CH-RFL Fluorescence Manual | |
| Olympus IX-FLA Fluorescence Manual | |
| Olympus IX50-IX70 Microscope Manual | |
| Orion 210A pH Meter | |
| Orion 91-XX Combination pH Electrode | |
| Research ElectroOptics He-Ne Laser | |
| SOMA MC300 Motion Controller | |
| SOMA Micromanipulator Manual | |
| SOMA MX1100L Diagram | |
| SOMA MX1100R Diagram | |
| Spectral Physics Tsunami Manual | |
| Spectral Physics Millennia Manual | |
| ST4 Camera Manual | |
| Sutter P-97 Micropipette Puller | |
| Sutter Laser Puller Programs | |
| Sutter Micropipette Cookbook | |
| ThorLabs LDC 500 Manual | |
| Measurement Computing USB-1208fs | |
| Warner LPF-8 Low Pass Filter Manual | |
| Warner OC-725C Oocyte Clamp Manual | |
| Warner 20 Oocyte Chamber | |
| World Precision Instr DAM-80 Amplifier Manual | |
| World Precision Instr ISO-80 Amplifier Manual | |
