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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>>
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
Befitting UCSB's reputation as a highly-interdisciplinary research university, groups researching biophysics (loosely 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/]]
|!Dr. Saleh||
| email| saleh *at* engineering.ucsb.edu|
| office| 1361A Engineering II|
| 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 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.

[[2007 course syllabus|http://www.engr.ucsb.edu/~saleh/Teaching/200AF07/Mat200ASyllabus2007.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.

[[2007 Course syllabus|http://www.engr.ucsb.edu/~saleh/Teaching/271BW07/syllabus.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.

[[2008 Course syllabus|http://www.engr.ucsb.edu/~saleh/Teaching/bioforce2008/2008%20bioforce%20syllabus.pdf]]

|!2008 File downloads|>|>|>|
|!Lecture #|!Slides|!Notes|!Papers|
| 1|[[slides 1|http://www.engr.ucsb.edu/~saleh/Spring2006/Lecture 1.pdf]]|[[notes 1|http://www.engr.ucsb.edu/~saleh/Spring2006/lecture 1 notes.pdf]]|[[Woese, 2004|http://www.engr.ucsb.edu/~saleh/Spring2006/woese2004.pdf]]; [[Anderson, 1972|http://www.engr.ucsb.edu/~saleh/Spring2006/anderson1972.pdf]]|
| 2|[[slides 2|http://www.engr.ucsb.edu/~saleh/Spring2006/Lecture 2.pdf]]|[[notes 2|http://www.engr.ucsb.edu/~saleh/Spring2006/Lecture 2 notes.pdf]]||
| 3|[[slides 3|http://www.engr.ucsb.edu/~saleh/Spring2006/Lecture 3.pdf]]|[[notes 3|http://www.engr.ucsb.edu/~saleh/Spring2006/Lecture 3 notes.pdf]]|[[Dill et al, 1995|http://www.engr.ucsb.edu/~saleh/Spring2006/dill1995-OCR.pdf]];[[Neuman and Block, 2004|http://www.engr.ucsb.edu/~saleh/Spring2006/neuman2004.pdf]] |
| 4||[[notes 4|http://www.engr.ucsb.edu/~saleh/Spring2006/Lecture 4 notes.pdf]]|[[Langevin handout|http://www.engr.ucsb.edu/~saleh/Spring2006/langevin2008.pdf]]|
| 5||[[notes 5|http://www.engr.ucsb.edu/~saleh/Spring2006/Lecture 5 notes.pdf]]||
| 6|[[slides 6|http://www.engr.ucsb.edu/~saleh/Spring2006/lecture 6.pdf]]|[[notes 6|http://www.engr.ucsb.edu/~saleh/Spring2006/Lecture 6 notes.pdf]]|[[Garcia, 2007|http://www.engr.ucsb.edu/~saleh/Spring2006/garcia2007.pdf]]; [[Marko and Siggia, 1995|http://www.engr.ucsb.edu/~saleh/Spring2006/marko1995.pdf]]|

[[Problem set 1|http://www.engr.ucsb.edu/~saleh/Spring2006/bioforce2008-ps1.pdf]]

!!!Papers for final presentation
[[List of papers|http://www.engr.ucsb.edu/~saleh/Spring2006/bioforce2008 papers.doc]]; pdfs of all papers as a [[.zip archive|http://www.engr.ucsb.edu/~saleh/Spring2006/2008bioforcepapers.zip]] or a [[.tar archive|http://www.engr.ucsb.edu/~saleh/Spring2006/2008bioforcepapers.tar]]

!!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
!!!Protein and Nucleic Acid Structures
http://www.rcsb.org/pdb/ 
The protein data bank
http://ndbserver.rutgers.edu/
The nucleic acids database
http://www.fli-leibniz.de/IMAGE.html
The Jena Library of Biological Macromolecules; good intro material
!!!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.
[[Welcome]]
[[Publications]]
[[The Group]]
[[Omar A. Saleh]]
[[Teaching]]
[[Contact]]
[[Biophysics at UCSB]]

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 &Eacute;cole Normale Sup&eacute;rieure 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 assistant 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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Dr. Saleh's publications, in reverse chronological order. Follow links, or [[contact|Contact]] us, for full-text versions.

#J.-F. Allemand, D. Bensimon, G. Charvin, V. Croquette, G. Lia, T. Lionnet, K.C. Neuman, O.A. Saleh, and 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).







exploring molecular biophysics since 2005






The Saleh Lab at UCSB






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|!Quarter|!Course|
|Spring 2008|[[MAT 287B/BMSE 257]]: Mechanical Force and Biomolecules|
|Fall 2007|[[MAT 200A]]: Thermodynamic Foundations of Materials|
|Winter 2007|[[MAT 271B]]: Complex Fluids|






|!Principal Investigator|>|>|
|[[Dr. Omar A. Saleh|Omar A. Saleh]]|>|>|
|!Post-docs|>|>|
|[[Dr. Kipom Kim|http://www.materials.ucsb.edu/~kpkim/]] | High-resolution instrumentation| Physics Ph.D|
|!Grad students|>|>|
|Noah Ribeck | Dynamics of replication proteins | Physics student|
|Jun Lin| Visualizing DNA properties| BMSE student|
|Andrew Dittmore| Dynamics of replication proteins| Materials student|
|!Undergrads|>|>|
|Natalia Shabaltas| Visualizing DNA properties| CCS student|






!!!Research
We study the physics of biomolecular systems, with a focus on developing instruments capable of measuring and manipulating the properties of single biomolecules and their interactions. Current projects include: developing single-molecule tracking methods with sub-nanometer resolution; visualizing the elastic properties of DNA; and determining the physical mechanisms of DNA replication. Peruse our [[publications|Publications]] for more details.

!!!Support
Funding for the lab is currently obtained from [[HFSP|http://www.hfsp.org]], [[NSF|http://www.nsf.gov]] and [[NIH|http://www.nih.gov]].

!!!Positions
We are always on the lookout for good people! Interested applicants should [[contact|Contact]] Omar, preferably by emailing a CV and cover letter.






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