The Kondev group is interested in mechanical and statistical
properties of biopolymers, such as DNA and globular proteins.
Simple mathematical models of these macromolecules are developed
in order to elucidate their structure and dynamics. Given
the recent advances in developing quantitative probes (laser
tweezers, AFM, fluorescence, etc.) for measuring properties
of single molecules such as proteins, DNA, and RNA, mathematical
models have an important role to play in analyzing and interpreting
data, as well as formulating new hypothesis. In our work
we make use of analytical (statistical mechanics, field
theory, etc.) and computational tools (Monte-Carlo, transfer
matrix, etc.). Specific projects we are currently pursuing
include:
|
i.
|
Transcriptional regulation of gene expression
|
|
ii.
|
Chromosome structure in bacteria |
|
iii.
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Mating switching in yeast |
|
iv.
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Voltage sensing by ion channels |
|
v.
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Chemical reactions in crowded and confined
environments |
Selected Publications
Garcia HG, Grayson P, Han L, Inamdar M, Kondev J, Nelson
PC, Phillips R, Widom J, Wiggins PA. (2007) Biological consequences
of tightly bent DNA: The other life of a macromolecular
celebrity. Biopolymers. 2007 Feb;85(2):115-30. [abstract]
Oberdorf R, Ferguson A, Jacobsen JL, Kondev J. (2006) Secondary
structures in long compact polymers. Phys Rev E Stat
Nonlin Soft Matter Phys. 2006 Nov;74(5 Pt 1):051801.
[abstract]
Prasad A, Hori Y, Kondev J. (2005) Elasticity of semiflexible
polymers in two dimensions. Phys Rev E Stat Nonlin Soft
Matter Phys. 2005 Oct;72(4 Pt 1):041918. Epub 2005 Oct
18. [abstract]
Bintu L, Buchler NE, Garcia HG, Gerland U, Hwa T, Kondev
J, Kuhlman T, Phillips R. (2005) Transcriptional regulation
by the numbers: applications, Curr Opin Genet Dev.,
15:125-35. [abstract]
Jacobsen JL, Kondev J. (2004) Continuous melting of compact
polymers. Phys Rev Lett. 2004 May 28;92(21):210601.
Epub 2004 May 28. [abstract]
Phillips R, Kondev J, Pruohit PK. (2004) Mechanics of Biological
Nanotechnology, Nanotechnology Handbook, B. Bhushan
(ed.), Springer-Verlag (2004).
Purohit PK, Kondev J, Phillips R. (2003) Mechanics of DNA
packaging in viruses. Proc Natl Acad Sci U S A. 2003
Mar 18;100(6):3173-8. Epub 2003 Mar 10. [abstract]
Last review:
February 15, 2007. E-mail comments or questions to the webmaster.
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