http://openwetware.org/index.php?title=Dunn&action=feed&wikifeed=atom 2013-06-19T21:59:51Z MediaWiki 1.13.2 via WikiArticleFeeds 0.6.3 http://openwetware.org/wiki/Dunn 2013-05-27T21:03:46Z

<br /> <br /> <a name="Welcome_to_the_Dunn_Lab_homepage.21"></a><br /> <br /> WELCOME TO THE DUNN LAB HOMEPAGE!<br /> <br /> Our lab is interested in studying [http://openwetware.org/inde [1]

http://openwetware.org/wiki/Dunn:Education/Outreach/ChemE_Car 2013-05-06T07:33:33Z

<br /> <br /> The ChemE Car is a competition hosted by the American Institute of Chemical Engineers (AIChE) where students must design cars that use chemical reactions as their power. Cars must travel specific distances using only the energy from chemical reactions as their "fuel." <br /> <br /> [1] <br /> <br /> In 2013, Stanford's ChemE Car Team placed 5th out of 10 teams at the Western Regional Conference/Competition in San Diego, CA. The car was run off of a magnesium-lemon juice redox reaction and stopped with a vitamin C - iodine clock reaction. If you ask me, this vitamin C-iodine clock reaction seems like a pretty clever way to time the reaction appropriately. <br /> <br /> The team was 5 meters short of the target 15 meters. The winners were 1.5 meters short. (To put in perspective, the Stanford team has previously achieved 13 and 14 inches away from the target line.) They had 15 magnesium-

http://openwetware.org/wiki/Dunn:Education/Outreach 2013-05-06T07:11:21Z

<br /> <br /> CONTENTS<br /> <br /> * 1 Science is Elementary (SIE) [1]<br /> * 2 East Palo Alto Tennis and Tutoring (EPATT) [2]<br /> * 3 Maker Faire [3]<br /> * 4 Splash at Stanford [4]<br /> * 5 AIChE ChemE Car! [5]<br /> <br /> <a name="Science_is_Elementary_.28SIE.29"></a><br /> <br /> SCIENCE IS ELEMENTARY (SIE) [6]<br /> <br /> <a name="East_Palo_Alto_Tennis_and_Tutoring_.28EPATT.29"></a><br /> <br /> EAST PALO ALTO TENNIS AND TUTORING (EPATT) [7]<br /> <br /> <a name="Maker_Faire"></a><br /> <br /> MAKER FAIRE [8]<br /> <br /> <a name="Splash_at_Stanford"></a><br /> <br /> SPLASH AT STANFORD [9]<br /> <br /> <a name="AIChE_ChemE_Car.21"></a><br /> <br /> AICHE CHEME CAR! [10]<br /> <br />

http://openwetware.org/wiki/Dunn:People 2013-05-06T06:58:14Z

<br /> <br /> <a name="Lab_Members_.28Scroll_down.29"></a><br /> <br /> LAB MEMBERS (SCROLL DOWN)<br /> <br /> [1] [2] <a name="Roster"></a><br /> <br /> ROSTER<br /> <br /> [3] <br /> <br /> Alex Dunn [4], Assistant Professor, Chemical Engineering, alex.dunn(at)stanford.edu [5] <br /> <br /> Diego "Don\'t FRET" Ramallo [6], Graduate Student, Biophysics, ramalldf(at)stanford.edu [7] <br /> <br /> Jack "Mr. Sunshine" Chai, Graduate Student, Chemical Engineering, jackchai(at)stanford.edu [8] <br /> <br /> Arjun Adhikari, Graduate Student, Chemical Engineering, asarjun(at)stanford.edu, CV [9] <br /> <br /> [10] <br /> <br /> Craig Buckley, Graduate Student, Chemical Engineering, buckley2(at)stanford.edu [11] <br /> <br /> Olga Shcherbakova, Research Associate, olia(at)stanford.edu Michael Kri <br /> <br />

http://openwetware.org/wiki/Dunn:Publications 2012-08-31T05:07:17Z

<br /> <br /> <a name="Publications"></a><br /> <br /> PUBLICATIONS<br /> <br /> 26. Borghi N, Sorokina M, Shcherbakova OG, Weis WI, Pruitt BL, Nelson WJ, DUNN AR. "E-cadherin is under constitutive actomyosin-generated tension that is increased at cell-cell contacts upon externally applied stretch." PNAS. 2012 July 16. Link [1] [2] <br /> <br /> 25. Adhikari AS, Glassey E, DUNN AR. "Conformational Dynamics Accompanying the Proteolytic Degradation of Trimeric Collagen I by Collagenases." JACS. 2012 June 21. Link [3] <br /> <br /> 24. Adhikari AS, Chai J, DUNN AR. "Multiplexed Single-molecule Force Proteolysis Measurements Using Magnetic Tweezers." JoVE. 2012. Link [4] <br /> <br /> 23. Adhikari AS, Mekhdjian AH, DUNN AR. "Strain Tunes Proteolytic Degradation and Diffusive Transp

http://openwetware.org/wiki/Dunn:Education/Outreach/Maker_Faire 2012-04-11T16:04:32Z

<br /> <br /> This was our second year participating in in Maker Faire [1], a two-day festival of art, science, and engineering that draws over 100,000 people from around the world. “Single molecules for the masses” is our goal and the title of the work we presented. Maker Faire showcases creations of all kinds and sizes, but our demonstration was one of the smallest, just several-billionth-of-a-meter in size. We explained how our lab uses "magnetic tweezers" to pull on single DNA and protein molecules.<br /> Surprisingly, magnetic tweezers are quite easy to build. Our display allowed participants to reach out and "touch" a single DNA molecule with the help of a refrigerator magnet and a simple light microscope. I think people really liked it! They could twist the DNA molecules by themselves, and then watch the DNA rewind in real time. The whole lab enjoyed sharing the ideas that we'r

http://openwetware.org/wiki/Dunn:Tools/Calendars 2011-11-14T20:15:17Z

<br /> <br /> <a name="Calendar_2011_.28edit.29"></a><br /> <br /> CALENDAR 2011 (EDIT [1])<br /> <br />

http://openwetware.org/wiki/Dunn:Education/Biophysics_Education_Blog 2011-10-19T09:54:53Z

<br /> <br /> <a name="4.2F14.2F10:_Testing_out_embedded_wordpress_blog"></a><br /> <br /> 4/14/10: TESTING OUT EMBEDDED WORDPRESS BLOG<br /> <br /> Sorry for the long delay between posts, lots of stuff occurred since the end of the last quarter and this one, but we'll have to explain in the next post. For now, we're just trying to see what the blog will look like with a wordpress interface embedded inside our OWW homepage. I think it works because we can have the best of both worlds: <br /> <br /> * Lab toolbar up top to continue navigating OWW <br /> * Wordpress interface that has a calendar, tag list, search bar <br /> <br /> For now, this will only be a test, but look out for newer posts as we test out the wordpress page. --Ramalldf [1] 06:27, 14 April 2010 (EDT) <a name="2.2F10.2F10:_Nerding_out_over_hair_cells"></a><br /> <br /> 2/10/10: NERDING OUT OVER HAIR CELLS<br /> <br /> Sorry about the delay in updates, but everyone in lab has been quite busy with lab work and classes. Ne

http://openwetware.org/wiki/Dunn:People/Raj 2011-10-14T06:47:01Z

<br /> <br /> EDUCATIONAL HISTORY: <br /> <br /> B.Tech, Electrical Engineering, Calicut University <br /> <br /> PhD, Biomedical Engineering (specialization: Biophysics/Biotechnology), University of Michigan, Ann Arbor (Thesis Topic: Thermal Fluctuations of Single Molecules of dsDNA) <br /> <br /> WORK HISTORY: Postdoctoral Research, Dept. of Cell and Dev. Biology, Vanderbilt University (Research Topics: Unconventional Myosins, T-Helper Cell/Epithelial Cell Membrane Mechanics) <br /> <br /> GENERAL SCIENTIFIC INTERESTS: Force Transducers, Microscopy, Spectroscopy, Motor Proteins, Membrane/Transmembrane Proteins, Single Molecule Biophysics, Cell/Dev Biology, Mathematical Models of Biological Systems, the Vertebrate Immune System. <br /> <br /> HOBBIES/INTERESTS: Constantly Evolving (nature/wildlife, birding, gardening, classical literature, poetry, history, science fiction, robots/AI, metaphysics/philosophy/fringe science, current events/world news, punk rock &c.)

http://openwetware.org/wiki/Dunn:People/Armen%21 2011-10-11T07:53:04Z

<br /> <br /> Hello World! This will be the start of personal pages for all our lab members.

http://openwetware.org/wiki/Dunn:Education/Outreach/Splash_at_Stanford 2011-10-06T04:35:42Z

<br /> <br /> Splash is a program that brings high school and middle school students from around the Bay Area to Stanford's campus for a two-day learning extravaganza (per the description). Starting last year, our lab members, graduate and undergraduate, have helped teach classes in Non-Newtonian fluids, general chemistry, and biophysics. <br /> <br /> Updates (including pictures and videos) will be posted soon! Stay tuned! <br /> <br /> Splash at Stanford! [1]

http://openwetware.org/wiki/Dunn:Projects 2011-02-11T00:07:46Z

<br /> <br /> <a name="Uncovering_previously_unrecognized_functions_of_mechanical_force_in_extracellular_matrix_remodeling."></a><br /> <br /> UNCOVERING PREVIOUSLY UNRECOGNIZED FUNCTIONS OF MECHANICAL FORCE IN EXTRACELLULAR MATRIX REMODELING.<br /> <br /> [1] [2] [3] [4] <br /> <br /> _The stiff, the hard, and the brittle are harbingers of death._ – Tao Te Ching trans. Stan Rosenthal The benefits of flexibility, both literal and metaphorical, have been recognized for over 2,500 years. The material properties of our own bodies is governed largely by the extracellular matrix, a complex protein and carbohydrate network that gives shape to tissues and organs. Previously, the ECM was dismissed as passive glue that simply held cells together. We now know that failure to<br /> maintain the ECM leads not only to aching knees and wrinkles, but also to atherosclerosis, aneurism, and other cardiovascular diseases. Furthermore, the key step in cancer metastasis is the dissolution of the local ECM so that the cancer cells can escape to coloniz

http://openwetware.org/wiki/Dunn:Contact 2011-01-07T18:58:52Z

<br /> <br /> <a name="Contact"></a><br /> <br /> CONTACT<br /> <br /> If you have any questions you can contact the following people: <br /> <br /> PROFESSOR DUNN by email at alex.dunn@stanford.edu <br /> <br /> VICTORIA LEE (lab administrator): Phone: 650.723.7503, Fax: 650.724.0451, Email: vhlee@stanford.edu <br /> <br /> DIEGO RAMALLO [1] (webpage guy): ramalldf@stanford.edu <br /> <br /> You can also visit the Chemical Engineering department website [2] to find additional contact information for the department. <a name="Location"></a><br /> <br /> LOCATION<br /> <br /> Our main lab is located in the third floor of the Keck building, right across the street from the Cantor Arts Center and the Lokey building. Here's our mailing address: Stauffer III 381 North South Mall Stanford University Stanford, CA 94305-5025

http://openwetware.org/wiki/Dunn:Projects/Support 2010-12-19T09:05:45Z

<br /> <br /> <a name="Funding"></a><br /> <br /> FUNDING<br /> <br /> * National Institutes of Health (2010) [1] <br /> * Stanford Cardiovascular Institute (2010-2011) <br /> * Stanford Graduate Fellowship (2010) <br /> * NSF Graduate Research Fellowship Program (2009, 2010) <br /> * Digestive Disease Center, Stanford University (2010) <br /> * Burroughs Wellcome Career Award at the Scientific Interface (2008) <br /> <br />

http://openwetware.org/wiki/Dunn:Tools/Protocols/Instrument_Setup/Microscopy/Building_a_single-molecule_device_and_measuring_the_diffusion_constant_of_ZSYellow 2010-11-25T02:09:30Z

<br /> <br /> [1] Download (courtesy of David Altman) [2] .

http://openwetware.org/wiki/Dunn:Tools/Protocols/Wetlab_protocols 2010-06-09T18:57:00Z

<br /> <br /> Molecular Biology [1] <br /> <br /> caption <br /> CELL PROTOCOLS<br /> DNA <br /> PROTEIN <br /> SOFTWARE <br /> HOUSEKEEPING <br /> <br /> E. Coli Liquid Cultures [2] <br /> Miniprep [3] <br /> Protein Expression [4] <br /> Sequencher [5] <br /> Washing Dishes [6] <br /> <br /> cell <br /> <br />

http://openwetware.org/wiki/Dunn:Tools/Wiki_Tutorial 2010-06-09T08:34:13Z

<br /> <br /> [1] <a name="Quick_Intro"></a><br /> <br /> QUICK INTRO<br /> <br /> * This page needs a lot of work, but touches on a lot of the tools that might be useful to the people that use OWW. I basically gathered information from a lot of different places on the internet and put them together here. Most of the sources are linked, so if you're looking for something that isn't mentioned here, it might be a good idea to visit that site directly. <br /> * Anyone on OWW is more than free to edit this page, but please leave your signature when you do decide to modify it. If we end up with something that is superhelpful in a few months, maybe we'll try to make a polished version for the OWW main page. --Ramalldf [2] <br /> <br /> <a name="Setting_up_your_User_page"></a><br /> <br /> SETTING UP YOUR USER PAGE<br /> <br /> * The Openwetware (OWW) site has a grea <br /> <br />

http://openwetware.org/wiki/Dunn:Tools/Protocols 2010-05-08T05:17:06Z

<br /> <br /> <a name="Instrumentation"></a><br /> <br /> INSTRUMENTATION [1]<br /> <br /> <a name="Wetlab_protocols"></a><br /> <br /> WETLAB PROTOCOLS [2]<br /> <br /> MORE COMING SOON!

http://openwetware.org/wiki/Dunn:Tools/Protocols/Molecular_Biology 2010-05-07T23:39:02Z

<br /> <br />

http://openwetware.org/wiki/Dunn:Recent_Updates 2010-04-16T06:28:48Z

<br /> <br /> <a name="Recent_Updates_to_OWW_by_our_members"></a><br /> <br /> RECENT UPDATES TO OWW BY OUR MEMBERS<br /> <br />

http://openwetware.org/wiki/Dunn:Contact/Openings 2009-09-02T05:45:17Z

<br /> <br /> <a name="Openings"></a><br /> <br /> OPENINGS<br /> <br /> <a name="Postdocs"></a><br /> <br /> POSTDOCS<br /> <br /> [1] [2] <br /> <br /> We are currently recruiting postdoctoral scholars who enjoy a collaborative environment and have a strong record of creative research. Topics and techniques of interest include (but are not limited to) computational protein design, single molecule instrumentation, and mammalian cell culture. <a name="Graduate_Students"></a><br /> <br /> GRADUATE STUDENTS<br /> <br /> [3] [4] <br /> <br /> In addition to students from Chemical Engineering, I'm interested in advising students from Biophysics, Bioengineering, Chemistry, Physics, Applied Physics, and Computer Science. If you think you might be interested in our research please contact me via email: alex dot dunn at stanford dot edu. <br /> <br /> _Photos courtesy of www.JohnTodd.com_

http://openwetware.org/wiki/Dunn:Tools/Useful_Links 2009-09-12T17:00:11Z

<br /> <br /> COMING SOON!

http://openwetware.org/wiki/Dunn:Tools/Tutorials 2009-07-22T04:14:37Z

<br /> <br /> * Here we'll have something like David's tutorial for aligning the excitation and emission pathways for our TIRF setup. <br /> <br />

http://openwetware.org/wiki/Dunn:Education/Biophysics_education 2010-04-07T06:01:02Z

<br /> <br /> <a name="2.2F10.2F10:_Nerding_out_over_hair_cells"></a><br /> <br /> 2/10/10: NERDING OUT OVER HAIR CELLS<br /> <br /> Sorry about the delay in updates, but everyone in lab has been quite busy with lab work and classes. Next week we go to the Biophys. Conference, so we're trying to run our final experiments before then since we won't have many chances to perform them during that week. <br /> <br /> Today I wanted to post about some material from a class that I am currently taking called "Biology by the Numbers" (BIOC236). One thing that drew me to biophysics as an undergrad was the curiosity and wonder that overtook me whenever I saw something like this cochlear hair cell in action: <br /> <br />

http://openwetware.org/wiki/Dunn:Education/Outreach/SIE 2010-01-20T04:47:47Z

<br /> <br /> <a name="Purpose"></a><br /> <br /> PURPOSE<br /> <br /> Another one of our members has also worked here for about two semesters. We give very cool science demonstrations to elementary school students once a month. If you want to learn more about them, here is their site [1].

http://openwetware.org/wiki/Dunn:Education/Teaching 2010-04-07T06:29:21Z

<br /> <br /> CONTENTS<br /> <br /> * 1 Graduate Level Courses Taught [1] <br /> <br /> * 1.1 CHEMENG 320 - Chemical Kinetics and Reaction Engineering [2]<br /> <br /> * 2 Undergraduate Level Courses Taught [3] <br /> <br /> * 2.1 CHEMENG 183 - Biochemistry II [4]<br /> <br /> <a name="Graduate_Level_Courses_Taught"></a><br /> <br /> GRADUATE LEVEL COURSES TAUGHT<br /> <br /> <a name="CHEMENG__320_-_Chemical_Kinetics_and_Reaction_Engineering"></a><br /> <br /> CHEMENG 320 - CHEMICAL KINETICS AND REACTION ENGINEERING<br /> <br /> Theoretical and experimental tools useful in understanding and manipulating reactions mediated by small-molecules and biological catalysts. Theoretical: first classical chemical kinetics and transition state theory; then RRKM theory and Monte Carlo simulations. Experimental approaches include practical application of modern spectroscopic techniques, stopped-flow measurements, temperature-jump experiments, and single-molecule approaches to chemical and biological systems. Both theory and<br /> application are framed with regard to systems of particular interest, including industrially relevant enzymes, organometallic catalysts, heterogeneous catalysis, electron transfer reactions, and chemical kinetics within living cells. <a name="Undergraduate_Level_Courses_Taught"></a><br /> <br /> UNDERGRADUATE LEVEL COURSES TAUGHT<br /> <br /> <a name="CHEMENG_183_-_Biochemistry_II"></a><br /> <br /> CHEMENG 183 - BIOCHEMISTRY II <br /> <br /> Focus on metabolic biochemistry: the study of chemical reactions that provide the cell

http://openwetware.org/wiki/Dunn:Tools/Protocols/Instrument_Setup/Microscopy 2010-04-07T21:26:17Z

<br /> <br /> Building a single-molecule device and measuring the diffusion constant of ZSYellow [1]

http://openwetware.org/wiki/Dunn:Tools/Protocols/Instrument_Setup 2010-04-08T23:01:12Z

<br /> <br /> <a name="Microscopy"></a><br /> <br /> MICROSCOPY [1]<br /> <br /> * A few protocols for aligning lasers and other things. <br /> <br />

http://openwetware.org/wiki/Dunn:Education/Biophysics_Research_Blog 2010-02-11T08:17:57Z

<br /> <br /> <a name="2.2F10.2F10:_Nerding_out_over_hair_cells"></a><br /> <br /> 2/10/10: NERDING OUT OVER HAIR CELLS<br /> <br /> Sorry about the delay in updates, but everyone in lab has been quite busy with lab work and classes. Next week we go to the Biophys. Conference, so we're trying to run our final experiments before then since we won't have many chances to perform them during that week. <br /> <br /> Today I wanted to post about some material from a class that I am currently taking called "Biology by the Numbers" (BIOC236). One thing that drew me to biophysics as an undergrad was the curiosity and wonder that overtook me whenever I saw something like this cochlear hair cell in action: <br /> <br />

http://openwetware.org/wiki/Dunn:Education 2010-04-09T07:41:36Z

<br /> <br /> CONTENTS<br /> <br /> * 1 Teaching [1]<br /> * 2 Outreach [2]<br /> * 3 Biophysics Education Blog [3]<br /> * 4 ChemE Car Team [4]<br /> <br /> <a name="Teaching"></a><br /> <br /> TEACHING [5]<br /> <br /> <a name="Outreach"></a><br /> <br /> OUTREACH [6]<br /> <br /> <a name="Biophysics_Education_Blog"></a><br /> <br /> BIOPHYSICS EDUCATION BLOG [7]<br /> <br /> <a name="ChemE_Car_Team"></a><br /> <br /> CHEME CAR TEAM [8]<br /> <br /> MORE COMING SOON!