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To get started with this blank [[TiddlyWiki]], you'll need to modify the following tiddlers:
* [[SiteTitle]] & [[SiteSubtitle]]: The title and subtitle of the site, as shown above (after saving, they will also appear in the browser title bar)
* [[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>>
<<importTiddlers>>
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<link rel='alternate' type='application/rss+xml' title='RSS' href='index.xml' />
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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]]
<<option chkAnimate>> [[EnableAnimations]]

----
Also see [[AdvancedOptions]]
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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 nucleic acids), 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. P. Berezney & O. A. Saleh. [[Locked nucleic acid oligomers as handles for single molecule manipulation|http://dx.doi.org/10.1093/nar/gku760]]. //Nucleic Acids Research// (2014).
#A. Dittmore, J. Landy, A. A. Molzon & O. A. Saleh. [[Single-Molecule Methods for Ligand Counting: Linking Ion Uptake to DNA Hairpin Folding|http://dx.doi.org/10.1021/ja500094z]]. //Journal of the American Chemical Society// ''136'', 5974-5980 (2014).
#D. B. ~McIntosh, G. Duggan, Q. Gouil & O. A. Saleh. [[Sequence-Dependent Elasticity and Electrostatics of Single-Stranded DNA: Signatures of Base-Stacking|http://dx.doi.org//10.1016/j.bpj.2013.12.018]]. //Biophysical Journal// ''106'', 659-666 (2014).
#D. R. Jacobson, D. B. ~McIntosh & O. A. Saleh. [[The Snakelike Chain Character of Unstructured RNA|http://dx.doi.org/10.1016/j.bpj.2013.10.019]]. //Biophysical Journal// ''105'', 2569-2576 (2013).
#M. J. Stevens, D. B. ~McIntosh & O. A. Saleh. [[Simulations of Stretching a Strong, Flexible Polyelectrolyte: Using Long Chains To Access the Pincus Scaling Regime|http://dx.doi.org/10.1021/ma401211w]]. //Macromolecules// ''46'', 6369-6373 (2013).
#J. Landy, D. B. ~McIntosh & O. A. Saleh. [[Quantifying Screening Ion Excesses in Single-Molecule Force-Extension Experiments|http://prl.aps.org/abstract/PRL/v109/i4/e048301]]. //Physical Review Letters// ''109'', 048301 (2012).
#M. J. Stevens, D. B. ~McIntosh & O. A. Saleh. [[Simulations of Stretching a Strong, Flexible Polyelectrolyte|http://dx.doi.org/10.1021/ma300899x]]. //Macromolecules// (2012).
#J. Landy, D. B. ~McIntosh, O. A. Saleh & P. Pincus. [[Ionic excesses and entropies in mean-field screening models|http://dx.doi.org/10.1039/C2SM25608H]]. //Soft Matter// (2012).
#J. Lin, F. Persson, J. Fritzsche, J.&nbsp;O. Tegenfeldt & O.&nbsp;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/]]
Below, you can download code for ~GPU-based particle tracking described in the following article:
Lansdorp, Tabrizi, Dittmore and Saleh. __A high-speed magnetic tweezer beyond 10,000 frames per second__. In press, //Rev. Sci. Instrum.// (2013).

|//Link to code//|//Comments//|
|[[v2|http://www.engr.ucsb.edu/~saleh/Tracking%20Demo2.zip]]|Fixed discretization error in lateral tracking|
|[[v1|http://www.engr.ucsb.edu/~saleh/Tracking%20Demo.zip]]|Initial release|
|!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/]]
[[Welcome]]
<<closeAll>><<permaview>><<newTiddler>><<newJournal 'DD MMM YYYY'>><<saveChanges>><<slider chkSliderOptionsPanel OptionsPanel 'options »' 'Change TiddlyWiki advanced options'>> <<slider chkSliderContents [[TabContents]] 'contents »' 'contents'>>
!!! 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]]


!!! 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]], 

[[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]]||
!!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
#N. Ribeck & O. A. Saleh. [[DNA Unwinding by Ring-Shaped T4 Helicase gp41 Is Hindered by Tension on the Occluded Strand|http://dx.doi.org/10.1371/journal.pone.0079237]]. //PLOS ONE// ''8'', e79237 (2013).
#B. M. Lansdorp, S. J. Tabrizi, A. Dittmore & O. A. Saleh. [[A high-speed magnetic tweezer beyond 10,000 frames per second|http://dx.doi.org/10.1063/1.4802678]]. //Review of Scientific Instruments// ''84'', 044301 (2013).
#D. L. Kaplan, N. Ribeck & O. A. Saleh. [[Single-molecule and bulk approaches to the DnaB replication fork helicase|http://dx.doi.org/10.2741/4097]]. //Frontiers in Bioscience, Landmark// ''18'', 224-240 (2013).
#O. J. N. Bertrand, D. K. Fygenson & O. A. Saleh. [[Active, motor-driven mechanics in a DNA gel|http://dx.doi.org/10.1073/pnas.1208732109]]. //Proceedings of the National Academy of Sciences// ''109'', 17342-17347 (2012).
#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).
##B. M. Lansdorp & O. A. Saleh. [[Erratum: “Power spectrum and Allan variance methods for calibrating single-molecule video-tracking instruments” [Rev. Sci. Instrum.83, 025115 (2012)]|http://dx.doi.org/10.1063/1.4860059]]. //Review of Scientific Instruments// ''85'', - (2014).
#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>&#x2A</html>,<html>&#x2020</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>&#x2020</html>,<html>&#x2021</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).
[[Full CV (pdf)| http://www.engr.ucsb.edu/~saleh/8-2014%20Saleh%20CV.pdf]]

//Brief Biography//
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 worked with Lydia Sohn to develop 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 focused on magnetic-tweezer studies of motor protein dynamics, and took place at the &Eacute;cole Normale Sup&eacute;rieure in Paris, France, with Vincent Croquette, David Bensimon and ~Jean-Francois Allemand. 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 (BMSE) Program|http://www.bmse.ucsb.edu/]]. In 2013, he became director of the BMSE program.
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All Saleh lab publications, in reverse chronological order. Follow links, or [[contact|Contact]] us, for full-text versions.

#C.-Y. Park & O. A. Saleh [[Image-based synchronization of force and bead motion in active electromagnetic microrheometry|http://dx.doi.org/10.1088/0957-0233/25/12/125010]]. //Measurement Science and Technology// ''25'', 125010 (2014).
#J. P. Berezney & O. A. Saleh. [[Locked nucleic acid oligomers as handles for single molecule manipulation|http://dx.doi.org/10.1093/nar/gku760]]. //Nucleic Acids Research// (2014).
#A. Dittmore, J. Landy, A. A. Molzon & O. A. Saleh. [[Single-Molecule Methods for Ligand Counting: Linking Ion Uptake to DNA Hairpin Folding|http://dx.doi.org/10.1021/ja500094z]]. //Journal of the American Chemical Society// ''136'', 5974-5980 (2014).
#D.&nbsp;B. ~McIntosh, G. Duggan, Q. Gouil & O.&nbsp;A. Saleh. [[Sequence-Dependent Elasticity and Electrostatics of Single-Stranded DNA: Signatures of Base-Stacking|http://dx.doi.org//10.1016/j.bpj.2013.12.018]]. //Biophysical Journal// ''106'', 659-666 (2014).
#D. R. Jacobson, D. B. ~McIntosh & O. A. Saleh. [[The Snakelike Chain Character of Unstructured RNA|http://dx.doi.org/10.1016/j.bpj.2013.10.019]]. //Biophysical Journal// ''105'', 2569-2576 (2013).
#N. Ribeck & O. A. Saleh. [[DNA Unwinding by Ring-Shaped T4 Helicase gp41 Is Hindered by Tension on the Occluded Strand|http://dx.doi.org/10.1371/journal.pone.0079237]]. //PLOS ONE// ''8'', e79237 (2013).
#M. J. Stevens, D. B. ~McIntosh & O. A. Saleh. [[Simulations of Stretching a Strong, Flexible Polyelectrolyte: Using Long Chains To Access the Pincus Scaling Regime|http://dx.doi.org/10.1021/ma401211w]]. //Macromolecules// ''46'', 6369-6373 (2013).
#B. M. Lansdorp, S. J. Tabrizi, A. Dittmore & O. A. Saleh. [[A high-speed magnetic tweezer beyond 10,000 frames per second|http://dx.doi.org/10.1063/1.4802678]]. //Review of Scientific Instruments// ''84'', 044301 (2013).
#D. L. Kaplan, N. Ribeck & O. A. Saleh. [[Single-molecule and bulk approaches to the DnaB replication fork helicase|http://dx.doi.org/10.2741/4097]]. //Frontiers in Bioscience, Landmark// ''18'', 224-240 (2013).
#O. J. N. Bertrand, D. K. Fygenson & O. A. Saleh. [[Active, motor-driven mechanics in a DNA gel|http://dx.doi.org/10.1073/pnas.1208732109]]. //Proceedings of the National Academy of Sciences// ''109'', 17342-17347 (2012).
#J. Landy, D. B. ~McIntosh & O. A. Saleh. [[Quantifying Screening Ion Excesses in Single-Molecule Force-Extension Experiments|http://prl.aps.org/abstract/PRL/v109/i4/e048301]]. //Physical Review Letters// ''109'', 048301 (2012).
#M. J. Stevens, D. B. ~McIntosh & O. A. Saleh. [[Simulations of Stretching a Strong, Flexible Polyelectrolyte|http://dx.doi.org/10.1021/ma300899x]]. //Macromolecules// (2012).
#J. Landy, D. B. ~McIntosh, O. A. Saleh & P. Pincus. [[Ionic excesses and entropies in mean-field screening models|http://dx.doi.org/10.1039/C2SM25608H]]. //Soft Matter// (2012).
#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).
##B. M. Lansdorp & O. A. Saleh. [[Erratum: “Power spectrum and Allan variance methods for calibrating single-molecule video-tracking instruments” [Rev. Sci. Instrum.83, 025115 (2012)]|http://dx.doi.org/10.1063/1.4860059]]. //Review of Scientific Instruments// ''85'', - (2014).
#J. Lin, F. Persson, J. Fritzsche, J.&nbsp;O. Tegenfeldt & O.&nbsp;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
The Saleh Lab at UCSB
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<<tabs txtMainTab "Timeline" "Timeline" TabTimeline "All" "All tiddlers" TabAll "Tags" "All tags" TabTags "More" "More lists" TabMore>>
Dr. Saleh teaches courses in Thermodynamics, Complex Fluids, Biophysics and Introductory Materials Science. Course materials are available on ~GauchoSpace for registered students. 
|!Principal Investigator|>|>|
|[[Dr. Omar A. Saleh|Omar A. Saleh]]|>|>|
|!Post Docs|>|>|
|Chang Young Park |Mechanics of active gels |>|
|!Grad students|>|>|
|David Jacobson|RNA elasticity and electrostatics | Physics student|
|John Berezney|Polyelectrolyte elasticity | Materials student|
|Bob Lansdorp|High resolution tracking of motor proteins | Materials student|
|Dan Nguyen|Mechano-genetic DNA gels | BMSE student|
|!Undergraduate students|>|>|
|Zach Lotze|Elastic response of a crowded polymer| Physics student|
|Dan Knox|Mechano-genetic DNA gels| Chemical Engineering 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/]].

!!!Code
Code we have released can be found [[here|Code]]
Open-source [[tiddlywiki|http://www.tiddlywiki.com/]] design downloaded from [[tiddlythemes|http://tiddlythemes.com/]]