Welcome to TiddlyWiki created by Jeremy Ruston, Copyright © 2007 UnaMesa Association
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To get started with this blank TiddlyWiki, you'll need to modify the following tiddlers:
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* MainMenu: The menu (usually on the left)
* DefaultTiddlers: Contains the names of the tiddlers that you want to appear when the TiddlyWiki is opened
You'll also need to enter your username for signing your edits: <<option txtUserName>>
These InterfaceOptions for customising TiddlyWiki are saved in your browser
Your username for signing your edits. Write it as a WikiWord (eg JoeBloggs)
<<option txtUserName>>
<<option chkSaveBackups>> SaveBackups
<<option chkAutoSave>> AutoSave
<<option chkRegExpSearch>> RegExpSearch
<<option chkCaseSensitiveSearch>> CaseSensitiveSearch
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Also see AdvancedOptions
The elastic response of a polymer is uniquely sensitive to its structure and the interactions it has with the solution in which it is bathed. We study the elasticity of single polymers (particularly single- and double-stranded DNA), with an eye towards understanding the solution physics that governs biopolymer activity //in vivo//. We have particularly pioneered the study of polymer elasticity at very low (sub-picoNewton) forces, discovering novel regimes of polymer behavior that have given new insight into the long-standing problem of charged polymer behavior.
!!!Related publications
#J. Lin, F. Persson, J. Fritzsche, J. O. Tegenfeldt & O. A. Saleh. [[Bandpass Filtering of DNA Elastic Modes Using Confinement and Tension|http://dx.doi.org/doi:10.1016/j.bpj.2011.11.4014]]. //Biophysical Journal// ''102'', 96-100 (2012).
#Y. Yang, J. Lin, B. Kaytanli, O. A. Saleh & M. T. Valentine. [[Direct correlation between creep compliance and deformation in entangled and sparsely crosslinked microtubule networks|http://dx.doi.org/10.1039/C2SM06745E]]. //Soft Matter// ''8'', 1776-1784 (2012).
#A. Dittmore, D. B. ~McIntosh, S. Halliday & O. A. Saleh. [[Single-Molecule Elasticity Measurements of the Onset of Excluded Volume in Poly(Ethylene Glycol)|http://link.aps.org/doi/10.1103/PhysRevLett.107.148301]]. //Physical Review Letters// ''107'', 148301 (2011).
#D. B. ~McIntosh & O. A. Saleh. [[Salt Species-Dependent Electrostatic Effects on ssDNA Elasticity|http://pubs.acs.org/doi/abs/10.1021/ma1028196]]. //Macromolecules// ''44'', 2328-2333 (2011).
#P. Pincus & O.A. Saleh. [[Polyelectrolytes: The de Gennes Legacy.|http://www.worldscibooks.com/physics/7395.html]] in //P.-G. de Gennes' Impact in Science, Vol. 2// (eds. J. Bok, J. Prost & F. ~Brochard-Wyart) (2009).
#D.B. ~McIntosh, N. Ribeck & O.A. Saleh. [[Detailed scaling analysis of low-force polyelectrolyte elasticity|http://link.aps.org/abstract/PRE/v80/e041803]]. //Physical Review E// ''80'', 041803 (2009).
#O.A. Saleh, D.B. ~McIntosh, P. Pincus & N. Ribeck. [[Nonlinear Low-Force Elasticity of Single-Stranded DNA Molecules|http://link.aps.org/doi/10.1103/PhysRevLett.102.068301 ]]. //Phys. Rev. Lett.// ''102'', 068301-4 (2009).
Befitting UCSB's reputation as a highly-interdisciplinary research university, groups researching biophysics (broadly defined) can be found in many departments. Many, but not all, of those groups are associated with the [[BMSE|http://www.bmse.ucsb.edu/]] program. Some of the other labs with significant biophysics efforts are (listed by principal investigator):
[[Safinya|http://www.mrl.ucsb.edu/mrl/faculty/safinya.html]], [[Pincus|http://www.mrl.ucsb.edu/mrl/faculty/pincus.html]], [[Israelachvili|http://www.mrl.ucsb.edu/mrl/faculty/israelachvili.html]], [[Brown|http://www.chem.ucsb.edu/%7Ebrowngroup/]], [[Shea|http://www.chem.ucsb.edu/~sheagroup/]], [[Fygenson|http://www.physics.ucsb.edu/~deborah/]], [[Lipman|http://www.physics.ucsb.edu/~lipman/]], [[Shraiman|http://www.kitp.ucsb.edu/~shraiman/]],
[[Valentine|http://www.me.ucsb.edu/valentinelab/]]
|!Dr. Saleh||
| email| saleh *at* engr.ucsb.edu|
| office| 3031 MRL|
| tel| 805.893.8814|
| fax| 805.893.8486|
|!the lab||
| location| 1207 Engineering II|
| tel| 805.893.5105|
|!Mailing address| Materials Dept., UCSB|
|~| Santa Barbara, CA 93106-5050|
[[Campus map|http://www.aw.id.ucsb.edu/maps/]]
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!!! Thermodynamic Foundation of Materials
[[Syllabus| http://www.engr.ucsb.edu/~saleh/Teaching/200AF11/Mat200ASyllabus2011.pdf]]
!!! Complex fluids
This course covers the science of complex fluids, i.e. solutions composed of a solvent and one or more solutes that, while large relative to the solvent, are still strongly affected by thermal fluctuations. We cover the unique interactions that govern solution behavior, and describe the effect of those potentials on polymeric and colloidal systems. This framework is then applied to the structure and interactions of bio-polymers.
[[2012 Course syllabus|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/271B%20W12%20syllabus.pdf]]
!!! Problem sets
[[Pset one|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/W12%20271B%20pset%20one.pdf]]; [[Data for Pset1#3|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/ParticleDistributionData.zip]]; [[Solutions|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/W12%20271B%20pset%20one-sol.pdf]]
[[Pset two|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/W12%20271B%20pset%20two.pdf]]; [[Solutions|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/W12%20271B%20pset%20two-sol.pdf]]
[[Pset three|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/W12%20271B%20pset%20three.pdf]]; [[Solutions|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/W12%20271B%20pset%20three-sol.pdf]]
[[Pset four|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/W12%20271B%20pset%20four.pdf]]; [[Solutions|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/W12%20271B%20pset%20four-sol.pdf]]
[[Pset five|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/W12%20271B%20pset%20five.pdf]]; [[Solutions|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/W12%20271B%20pset%20five-sol.pdf]]
!!! Lecture outlines
Here are the typed-up outlines; these cover the same information as the hand-written notes below, but in a easier-to-read fashion (though lacking sketches).
[[Lecture 1 overview|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/271B%20W12%20Lecture%20One%20Overview.pdf]]
[[Lecture 2 overview|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/271B%20W12%20Lecture%20Two%20Overview.pdf]]
[[Lecture 3 overview|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/271B%20W12%20Lecture%20Three%20Overview.pdf]]
[[Lecture 4 overview|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/271B%20W12%20Lecture%20Four%20Overview.pdf]]
[[Lecture 5 overview|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/271B%20W12%20Lecture%20Five%20Overview.pdf]]
[[Lecture 6 overview|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/271B%20W12%20Lecture%20Six%20Overview.pdf]]
[[Lecture 7 overview|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/271B%20W12%20Lecture%20Seven%20Overview.pdf]]
[[Lecture 8 overview|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/271B%20W12%20Lecture%20Eight%20Overview.pdf]]
[[Lecture 9 overview|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/271B%20W12%20Lecture%20Nine%20Overview.pdf]]
[[Lecture 10 overview|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/271B%20W12%20Lecture%20Ten%20Overview.pdf]]
[[Lecture 11 overview|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/271B%20W12%20Lecture%20Eleven%20Overview.pdf]]
[[Lecture 12 overview|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/271B%20W12%20Lecture%20Twelve%20Overview.pdf]]
[[Lecture 13 overview|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/271B%20W12%20Lecture%20Thirteen%20Overview.pdf]]
[[Lecture 14 overview|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/271B%20W12%20Lecture%20Fourteen%20Overview.pdf]]
[[Lecture 15 overview|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/271B%20W12%20Lecture%20Fifteen%20Overview.pdf]]
[[Lecture 16 overview|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/271B%20W12%20Lecture%20Sixteen%20Overview.pdf]]
[[Lecture 17 overview|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/271B%20W12%20Lecture%20Seventeen%20Overview.pdf]]
[[Lecture 18 overview|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/271B%20W12%20Lecture%20Eighteen%20Overview.pdf]]
[[Lecture 19 overview|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/271B%20W12%20Lecture%20Nineteen%20Overview.pdf]]
!!!Lectures notes
Here are the notes on which the course will be based. I will likely adjust some as we go along.
[[Lecture 1|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/W12%20271B%20lec1.PDF]]
[[Lecture 2|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/W12%20271B%20lec2.PDF]]
[[Lecture 3|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/W12%20271B%20lec3.PDF]]
[[Lecture 4|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/W12%20271B%20lec4.PDF]]
[[Lecture 5|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/W12%20271B%20lec5.PDF]]
[[Lecture 6|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/W12%20271B%20lec6.PDF]]
[[Lecture 7|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/W12%20271B%20lec7.PDF]]
[[Lecture 8|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/W12%20271B%20lec8.PDF]]
[[Lecture 9|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/W12%20271B%20lec9.PDF]]
[[Lecture 10|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/W12%20271B%20lec10.PDF]]
[[Lecture 11|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/W12%20271B%20lec11.PDF]]
[[Lecture 12|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/W12%20271B%20lec12.PDF]]
[[Lecture 13|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/W12%20271B%20lec13.PDF]]
[[Lecture 14|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/W12%20271B%20lec14.PDF]]
[[Lecture 15|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/W12%20271B%20lec15.PDF]]
[[Lecture 16|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/W12%20271B%20lec16.PDF]]
[[Lecture 17|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/W12%20271B%20lec17.PDF]]
[[Lecture 18|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/W12%20271B%20lec18.PDF]]
[[Lecture 19|http://www.engr.ucsb.edu/~saleh/Teaching/271BW12/W12%20271B%20lec19.PDF]]
!!!Mechanical Force and Biomolecules
This course gives an overview of the importance of mechanical processes in biomolecular behavior. It reviews both modern instrumental techniques, and the theories that attempt to account for mechanical biomolecular behavior. The course places a heavy emphasis on the recent literature of this still-developing subject.
[[Course syllabus|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2012/bioforce2012%20syllabus.pdf]]
[[List of papers for final presentation|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2012/2012BioForcePaperList.pdf]]
[[Archive (.zip) of paper pdf's|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2012/Bioforce2012-Papers.zip]]
[[Problem set one|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2012/bioforce2012-ps1.pdf]],
[[pset 1 Solutions|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2012/bioforce2012-ps1-sol.pdf]]
[[Problem set two|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2012/bioforce2012-ps2.pdf]]
|!File downloads|>|>|>|
|!Lecture #|!Slides|!Notes|!Papers and other references|
| 1|[[slides 1|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2012/bioforce2012%20Lecture%201.pptx]]|[[notes 1|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2012/lecture 1 notes.pdf]]|[[Woese, 2004|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2012/woese2004.pdf]]; [[Anderson, 1972|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2012/anderson1972.pdf]]|
| 2|[[slides 2|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2012/bioforce2012%20Lecture%202.ppt]]|[[notes 2|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2012/Lecture 2 notes.pdf]]||
| 3|[[slides 3|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2012/bioforce2012%20Lecture%203.ppt]]|[[notes 3|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2012/Lecture 3 notes.pdf]]|[[Dill et al., 1995|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2012/dill1995-OCR.pdf]]; [[Binnig et al., 1985|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2012/binnig1985.pdf]]; [[Strick et al., 1996|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2012/strick1996.pdf]]; [[Gosse and Croquette, 2002|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2012/gosse2002.pdf]] |
| 4|[[Valentine slides|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2009/valentine optical trap lecture.pdf]]|[[notes 4|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2012/Lecture 4 notes.pdf]]|[[Neuman and Block, 2004|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2012/neuman2004.pdf]]; [[Langevin handout|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2012/langevin2012.pdf]]|
| 5||[[notes 5|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2012/Lecture 5 notes.pdf]]|[[Langevin handout|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2012/langevin2012.pdf]]|
| 6||[[notes 6|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2012/Lecture 6 notes.pdf]]|[[Langevin handout|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2012/langevin2012.pdf]]; [[Garcia, 2007|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2012/garcia2007.pdf]]; [[Marko and Siggia, 1995|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2012/marko1995.pdf]]|
| 7||[[notes 7|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2012/lecture 7 notes.pdf]]||
| 8||[[notes 8|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2012/lecture 8 notes.pdf]]||
| 9||[[notes 9|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2012/Lecture 9 notes.pdf]]||
| 10||[[notes 10|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2012/Lecture 10 notes.pdf]]||
| 11||[[notes 11|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2012/Lecture 11 notes.pdf]]||
| 12||[[notes 12|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2012/Lecture 12 notes.PDF]]||
| 13||[[notes 13|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2012/Lecture 13 notes.pdf]]||
| 14||[[notes 14|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2012/Lecture 14 notes.pdf]]||
| 15||[[notes 15|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2012/Lecture 15 notes.pdf]]||
| 16||[[notes 16|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2012/Lecture 16 notes.pdf]]||
!!Various links of interest:
!!!Books online
If you are looking for basic background information about biochemistry or a biological system, these online book resources are a good place to start.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Books
The NCBI bookshelf, which allows you to perform online searches of many biology textbooks, including Stryer, Lodish, Alberts....
http://books.google.com/
Google’s book search
!!!Online journal searches:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi
http://www.isiknowledge.com
Pubmed and Web of Science, the standard electronic journal search engines; these resources make it trivial to find articles related to your final presentation.
!!Thermodynamic Foundations of Materials
This is a rigorous graduate-level course that covers, during the first half, the statistical mechanics principles that underly thermodynamics, and then, in the second half, the application of those principles to basic issues of materials science. It is a required course for all 1st year materials graduate students; the 200A/B/C sequence forms the core classwork of the Ph.D. program.
[[Course syllabus|http://www.engr.ucsb.edu/~saleh/Teaching/200AF09/Mat200ASyllabus2009.pdf]]
[[Welcome]]
[[Publications]]
[[The Group]]
[[Omar A. Saleh]]
[[Teaching]]
[[Contact]]
[[Biophysics at UCSB]]
Motor proteins are fascinating enzymes that accomplish the neat trick of transducing chemical energy into mechanical work. They are workhorses of molecular biology, accomplishing a huge range of active, mechanical tasks, including the storage, sequestration, and replication of the genome. We use precision single-molecule measurements to understand the workings of motor proteins, particular those that act on DNA. This work has implications both for the motors' biological roles and their extraordinary physics. A major feature of this work is developing new, faster, and more precise instrumentation to capture motor dynamics.
!!!Related publications
#B. M. Lansdorp & O. A. Saleh. [[Power spectrum and Allan variance methods for calibrating single-molecule video-tracking instruments|http://link.aip.org/link/doi/10.1063/1.3687431]]. //Rev. Sci. Instrum.// ''83'', 025115-025110 (2012).
#N. Ribeck, D.L. Kaplan, I. Bruck, I. & O.A. Saleh. [[DnaB Helicase Activity Is Modulated by DNA Geometry and Force|http://dx.doi.org/10.1016/j.bpj.2010.07.039]]. //Biophysical Journal// ''99'', 2170-2179 (2010).
#M. Manosas, A. Meglio, M. M. Spiering, F. Ding, S. J. Benkovic, F.-X. Barre, O. A. Saleh, J. F. Allemand, D. Bensimon & V. Croquette.[[Magnetic Tweezers for the Study of DNA Tracking Motors|http://dx.doi.org/10.1016/S0076-6879(10)75013-8]] in //Methods Enzymol.// ''475'' (ed G. Walter Nils; Academic Press, 2010).
#K. Kim & O.A. Saleh. [[A high-resolution magnetic tweezer for single-molecule measurements|http://nar.oxfordjournals.org/cgi/content/abstract/gkp725v1]]. //Nucl. Acids Res.//, gkp725 (2009).
#N. Ribeck & O.A. Saleh. [[Multiplexed single-molecule measurements with magnetic tweezers|http://link.aip.org/link/?RSINAK/79/094301/1]]. //Rev. Sci. Instrum.//, ''79'', 094301 (2008). <html>*</html>,<html>†</html>
#K. Kim & O.A. Saleh. [[Stabilizing method for reflection interference contrast microscopy|http://www.opticsinfobase.org/abstract.cfm?uri=ao-47-12-2070]]. //Appl. Opt.// ''47'', 2070-2075 (2008). <html>†</html>,<html>‡</html>
#T. Lionnet, J.F. Allemand, A. Revyakin, T.R. Strick, O.A. Saleh, D. Bensimon & V. Croquette. [[Single-Molecule Studies Using Magnetic Traps|http://www.cshlpress.com/default.tpl?action=full&cart=12191010033090908&--eqskudatarq=643]], in //~Single-Molecule Techniques: A Laboratory Manual// (eds. T. Ha & P.R. Selvin; CSHL Press, 2008).
#J.-F. Allemand, D. Bensimon, G. Charvin, V. Croquette, G. Lia, T. Lionnet, K.C. Neuman, O.A. Saleh, & H. Yokota. [[Studies of DNA-Protein Interactions at the Single Molecule Level with Magnetic Tweezers|http://www.springerlink.com/content/k12rm776k3h57171/?p=4008e358e53d48ac93560d2bd2798ae5&pi=0]]. //Lect. Notes Phys.// ''711'', 123-140 (2007).
#S. Bigot, O.A. Saleh, F. Cornet, J.F. Allemand & F.X. Barre. [[Oriented loading of FtsK on KOPS|http://www.nature.com/nsmb/journal/v13/n11/abs/nsmb1159.html]]. //Nat. Struct. Mol. Biol.// ''13'', 1026-1028 (2006).
#T. Lionnet, A. Dawid, S. Bigot, F.X. Barre, O.A. Saleh, F. Heslot, J.F. Allemand, D. Bensimon & V. Croquette. [[DNA mechanics as a tool to probe helicase and translocase activity.|http://nar.oxfordjournals.org/cgi/content/abstract/34/15/4232]] //Nucleic Acids Res.// ''34'', 4232-4244 (2006).
#K.C. Neuman, O.A. Saleh, T. Lionnet, G. Lia, J.F. Allemand, D. Bensimon & V. Croquette. [[Statistical determination of the step size of molecular motors.|http://www.iop.org/EJ/abstract/0953-8984/17/47/012]] //Journal of Physics: Condensed Matter// ''17'', S3811 (2005).
#S. Bigot, O.A. Saleh, C. Lesterlin, C. Pages, M. El Karoui, C. Dennis, M. Grigoriev, J.-F. Allemand, F.-X. Barre & F. Cornet. [[KOPS: DNA motifs that control E. coli chromosome segregation by orienting the FtsK translocase.|http://www.nature.com/emboj/journal/v24/n21/abs/7600835a.html]] //EMBO J.// ''24'', 3770-3780 (2005).
#O.A. Saleh, J.F. Allemand, V. Croquette & D. Bensimon. [[Single-molecule manipulation measurements of DNA transport proteins.|http://www3.interscience.wiley.com/cgi-bin/abstract/110476115/ABSTRACT?CRETRY=1&SRETRY=0]] //Chemphyschem// ''6'', 813-818 (2005).
#O.A. Saleh, S. Bigot, F.X. Barre & J.F. Allemand. [[Analysis of DNA supercoil induction by FtsK indicates translocation without groove-tracking.|http://www.nature.com/nsmb/journal/v12/n5/abs/nsmb926.html]] //Nat. Struct. Mol. Biol.// ''12'', 436-440 (2005).
#O.A. Saleh, C. Perals, F.-X. Barre & J.-F. Allemand. [[Fast, DNA-sequence independent translocation by FtsK in a single-molecule experiment.|http://www.nature.com/emboj/journal/v23/n12/full/7600242a.html]] //EMBO J.// ''23'', 2430-2439 (2004).
Omar Saleh received a B.S. in Physics from M.I.T. in 1997, then attended Princeton University for his graduate studies. For his thesis, he developed novel biosensors based on methods of micro- and nano-fabrication. He received his Ph.D. from the physics department in 2003, and then moved into the field of single-molecule biophysics. His post-doctoral research took place at the École Normale Supérieure in Paris, France, where he studied the properties of the motor protein ~FtsK. He arrived at UCSB in September 2005, where he is currently an associate professor in the [[Materials Department|http://www.materials.ucsb.edu/]] and [[Biomolecular Science and Engineering Program|http://www.bmse.ucsb.edu/]].
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All Saleh lab publications, in reverse chronological order. Follow links, or [[contact|Contact]] us, for full-text versions.
#B. M. Lansdorp & O. A. Saleh. [[Power spectrum and Allan variance methods for calibrating single-molecule video-tracking instruments|http://link.aip.org/link/doi/10.1063/1.3687431]]. //Rev. Sci. Instrum.// ''83'', 025115-025110 (2012).
#J. Lin, F. Persson, J. Fritzsche, J. O. Tegenfeldt & O. A. Saleh. [[Bandpass Filtering of DNA Elastic Modes Using Confinement and Tension|http://dx.doi.org/doi:10.1016/j.bpj.2011.11.4014]]. //Biophysical Journal// ''102'', 96-100 (2012).
#Y. Yang, J. Lin, B. Kaytanli, O. A. Saleh & M. T. Valentine. [[Direct correlation between creep compliance and deformation in entangled and sparsely crosslinked microtubule networks|http://dx.doi.org/10.1039/C2SM06745E]]. //Soft Matter// ''8'', 1776-1784 (2012).
#A. Dittmore, D. B. ~McIntosh, S. Halliday & O. A. Saleh. [[Single-Molecule Elasticity Measurements of the Onset of Excluded Volume in Poly(Ethylene Glycol)|http://link.aps.org/doi/10.1103/PhysRevLett.107.148301]]. //Physical Review Letters// ''107'', 148301 (2011).
#D. B. ~McIntosh & O. A. Saleh. [[Salt Species-Dependent Electrostatic Effects on ssDNA Elasticity|http://pubs.acs.org/doi/abs/10.1021/ma1028196]]. //Macromolecules// ''44'', 2328-2333 (2011).
#N. Ribeck, D.L. Kaplan, I. Bruck, I. & O.A. Saleh. [[DnaB Helicase Activity Is Modulated by DNA Geometry and Force|http://dx.doi.org/10.1016/j.bpj.2010.07.039]]. //Biophysical Journal// ''99'', 2170-2179 (2010).
#M. Manosas, A. Meglio, M. M. Spiering, F. Ding, S. J. Benkovic, F.-X. Barre, O. A. Saleh, J. F. Allemand, D. Bensimon & V. Croquette.[[Magnetic Tweezers for the Study of DNA Tracking Motors|http://dx.doi.org/10.1016/S0076-6879(10)75013-8]] in //Methods Enzymol.// ''475'' (ed G. Walter Nils; Academic Press, 2010).
#P. Pincus & O.A. Saleh. [[Polyelectrolytes: The de Gennes Legacy.|http://www.worldscibooks.com/physics/7395.html]] in //P.-G. de Gennes' Impact in Science, Vol. 2// (eds. J. Bok, J. Prost & F. ~Brochard-Wyart) (2009).
#D.B. ~McIntosh, N. Ribeck & O.A. Saleh. [[Detailed scaling analysis of low-force polyelectrolyte elasticity|http://link.aps.org/abstract/PRE/v80/e041803]]. //Physical Review E// ''80'', 041803 (2009).
#K. Kim & O.A. Saleh. [[A high-resolution magnetic tweezer for single-molecule measurements|http://nar.oxfordjournals.org/cgi/content/abstract/gkp725v1]]. //Nucl. Acids Res.//, gkp725 (2009).
#O.A. Saleh, D.B. ~McIntosh, P. Pincus & N. Ribeck. [[Nonlinear Low-Force Elasticity of Single-Stranded DNA Molecules|http://link.aps.org/doi/10.1103/PhysRevLett.102.068301 ]]. //Phys. Rev. Lett.// ''102'', 068301-4 (2009).
#N. Ribeck & O.A. Saleh. [[Multiplexed single-molecule measurements with magnetic tweezers|http://link.aip.org/link/?RSINAK/79/094301/1]]. //Rev. Sci. Instrum.//, ''79'', 094301 (2008).
#K. Kim & O.A. Saleh. [[Stabilizing method for reflection interference contrast microscopy|http://www.opticsinfobase.org/abstract.cfm?uri=ao-47-12-2070]]. //Appl. Opt.// ''47'', 2070-2075 (2008).
#T. Lionnet, J.F. Allemand, A. Revyakin, T.R. Strick, O.A. Saleh, D. Bensimon & V. Croquette. [[Single-Molecule Studies Using Magnetic Traps|http://www.cshlpress.com/default.tpl?action=full&cart=12191010033090908&--eqskudatarq=643]], in //~Single-Molecule Techniques: A Laboratory Manual// (eds. T. Ha & P.R. Selvin; CSHL Press, 2008).
#J.-F. Allemand, D. Bensimon, G. Charvin, V. Croquette, G. Lia, T. Lionnet, K.C. Neuman, O.A. Saleh, & H. Yokota. [[Studies of DNA-Protein Interactions at the Single Molecule Level with Magnetic Tweezers|http://www.springerlink.com/content/k12rm776k3h57171/?p=4008e358e53d48ac93560d2bd2798ae5&pi=0]]. //Lect. Notes Phys.// ''711'', 123-140 (2007).
#S. Bigot, O.A. Saleh, F. Cornet, J.F. Allemand & F.X. Barre. [[Oriented loading of FtsK on KOPS|http://www.nature.com/nsmb/journal/v13/n11/abs/nsmb1159.html]]. //Nat. Struct. Mol. Biol.// ''13'', 1026-1028 (2006).
#T. Lionnet, A. Dawid, S. Bigot, F.X. Barre, O.A. Saleh, F. Heslot, J.F. Allemand, D. Bensimon & V. Croquette. [[DNA mechanics as a tool to probe helicase and translocase activity.|http://nar.oxfordjournals.org/cgi/content/abstract/34/15/4232]] //Nucleic Acids Res.// ''34'', 4232-4244 (2006).
#K.C. Neuman, O.A. Saleh, T. Lionnet, G. Lia, J.F. Allemand, D. Bensimon & V. Croquette. [[Statistical determination of the step size of molecular motors.|http://www.iop.org/EJ/abstract/0953-8984/17/47/012]] //Journal of Physics: Condensed Matter// ''17'', S3811 (2005).
#S. Bigot, O.A. Saleh, C. Lesterlin, C. Pages, M. El Karoui, C. Dennis, M. Grigoriev, J.-F. Allemand, F.-X. Barre & F. Cornet. [[KOPS: DNA motifs that control E. coli chromosome segregation by orienting the FtsK translocase.|http://www.nature.com/emboj/journal/v24/n21/abs/7600835a.html]] //EMBO J.// ''24'', 3770-3780 (2005).
#O.A. Saleh, J.F. Allemand, V. Croquette & D. Bensimon. [[Single-molecule manipulation measurements of DNA transport proteins.|http://www3.interscience.wiley.com/cgi-bin/abstract/110476115/ABSTRACT?CRETRY=1&SRETRY=0]] //Chemphyschem// ''6'', 813-818 (2005).
#O.A. Saleh, S. Bigot, F.X. Barre & J.F. Allemand. [[Analysis of DNA supercoil induction by FtsK indicates translocation without groove-tracking.|http://www.nature.com/nsmb/journal/v12/n5/abs/nsmb926.html]] //Nat. Struct. Mol. Biol.// ''12'', 436-440 (2005).
#O.A. Saleh, C. Perals, F.-X. Barre & J.-F. Allemand. [[Fast, DNA-sequence independent translocation by FtsK in a single-molecule experiment.|http://www.nature.com/emboj/journal/v23/n12/full/7600242a.html]] //EMBO J.// ''23'', 2430-2439 (2004).
#O.A. Saleh & L.L. Sohn. [[An On-Chip Artificial Pore for Molecular Sensing. in Handbook of BioMEMs and Biomedical Nanotechnology|http://www.springer.com/engineering/biomedical+eng/book/978-0-387-25561-3]], Vol IV: Biomolecular Sensing, Processing and Analysis (eds. R. Bashir & S. Wereley) (Kluwer Academic Publishers, 2004).
#O.A.Saleh. [[A novel resistive pulse sensor for biological measurements.|http://www1.engr.ucsb.edu/~saleh/Research/Saleh_Omar_Thesis.pdf]] Ph.D. thesis, Princeton University (2003).
#O.A. Saleh & L.L. Sohn. [[An artificial nanopore for molecular sensing.|http://pubs.acs.org/cgi-bin/abstract.cgi/nalefd/2003/3/i01/abs/nl0255202.html]] //Nano Letters// ''3'', 37-38 (2003).
#O.A. Saleh & L.L. Sohn. [[Direct detection of antibody-antigen binding using an on-chip artificial pore.|http://www.pnas.org/cgi/content/abstract/100/3/820]] //Proc. Natl. Acad. Sci. U. S. A.// ''100'', 820-824 (2003).
#O.A. Saleh & L.L. Sohn. [[Correcting off-axis effects in an on-chip resistive-pulse analyzer.|http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=RSINAK000073000012004396000001&idtype=cvips&gifs=Yes]] //Rev. Sci. Instrum.// ''73'', 4396-4398 (2002).
#O.A. Saleh & L.L. Sohn. [[Quantitative sensing of nanoscale colloids using a microchip Coulter counter.|http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=RSINAK000072000012004449000001&idtype=cvips&gifs=Yes]] //Rev. Sci. Instrum.// ''72'', 4449-4451 (2001).
# L.L. Sohn, O.A. Saleh, G.R. Facer, A.J. Beavis, R.S. Allan & D.A. Notterman. [[Capacitance cytometry: Measuring biological cells one by one.|http://www.pnas.org/cgi/content/abstract/97/20/10687]] //Proc. Natl. Acad. Sci. U. S. A.// ''97'', 10687-10690 (2000).
Micro-mechanical studies of biomolecular and soft-matter systems
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<<tabs txtMainTab "Timeline" "Timeline" TabTimeline "All" "All tiddlers" TabAll "Tags" "All tags" TabTags "More" "More lists" TabMore>>
|!Quarter|!Course|
|Spring 2012|[[MAT/BMSE 272]]: Mechanical Force and Biomolecules|
|Winter 2012|[[MAT 271B]]: Complex Fluids|
|Fall 2011|[[MAT 200A]]: Thermodynamic Foundation of Materials|
|!Principal Investigator|>|>|
|[[Dr. Omar A. Saleh|Omar A. Saleh]]|>|>|
|!Post Docs|>|>|
|Chang Young Park |Mechanics of gels |>|
|!Grad students|>|>|
|Andrew Dittmore|Manipulation of proteins | Materials student|
|Dustin ~McIntosh|Low-force polymer elasticity | Physics student|
|John Berezney|Bacterial chromosome structure | Materials student|
|Bob Lansdorp|High resolution tracking of motor proteins | Materials student|
|!Undergraduate students|>|>|
|Gina E. ~McFarlane|Electrostatics of intermediate-stiffness polymers| Physics student|
|Johanna Palmstrom|Structure and dynamics of braided DNA | Physics student|
''We study the physics of soft matter systems, with a focus on the active and passive micro-mechanics of biomolecules and polymers. We pursue these studies primarily using custom-built instrumentation that manipulates single molecules by stretching them with picoNewton-scale forces, and measuring their elastic response with nanometer-scale resolution.''
Our work currently focuses on the following two areas:
* [[The mechanics of (bio)polymers|(Bio)Polymer Mechanics]]
* [[The mechanics of motor proteins|Motor Proteins]]
Click the links above, or peruse all of our publications ([[here|Publications]] or [[here|http://scholar.google.com/citations?user=jiQnYRkAAAAJ]]) for more details.
!!!Support
Funding for the lab is currently obtained from [[NSF|http://www.nsf.gov]], [[NIH|http://www.nih.gov]] and the [[UCSB MRL|http://www.mrl.ucsb.edu/]].
Open-source [[tiddlywiki|http://www.tiddlywiki.com/]] design downloaded from [[tiddlythemes|http://tiddlythemes.com/]]