Philip Nelson, Biological Physics, University of Pennsylvania



 








Phil Nelson

Physics and Astronomy
University of Pennsylvania
Philadelphia, PA 19104
USA

phone:   (215) 898-7001
fax:         (215) 898-2010


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Quote of the moment (come back later for more):

`Nature' is what we see --
The Hill -- the Afternoon --
Squirrel -- Eclipse -- the Bumble bee --
Nay -- Nature is what we hear --
The Bobolink -- the Sea --
Thunder -- the Cricket --
Nay -- Nature is Harmony --
Nature is what we know --
Yet have no art to say --
So impotent Our Wisdom is
To her simplicity. 
  -- Emily Dickinson

I am a physicist.
I teach some courses.
I'm also interested in K-12 education.
See our group's homepage.
Here is my boring official home page (with credo) and my vita.
Cool schools and conferences:
2008 Boulder Summer School on "Strongly Correlated Materials" June 30 - July 18, 2008.
I'm a member of Penn's Nano-Bio Interface Center, and the Institute for Medicine and Engineering.

Plain-English Articles

Physics in the cell: Spring theory by Brendan Maher (Nature 448, 984-986 (30 August 2007)).
The great hunt for extra compliance by Jan Liphardt (Biophys. J. 2007).
Teaching Biological Physics, Physics Today 58:3 46 (March 2005).
Excerpt from a review of my book, published in The American Journal of Physics.
And another review published in Nature.
Here's one published in Biomedical Computation Review.
DNA Elasticity, in McGraw-Hill Yearbook of Science and Technology 1999.
Statistical Mechanics of Membranes, from McGraw-Hill Yearbook of Science and Technology 1995.

Recent Talks

A course on physical models of biological systems (Biophysical Society Meeting, 2008).

Journal Publications

The research in these publications was funded in part by The National Science Foundation and by the Human Frontier Science Program. "Any opinions, findings, confusions, contusions, contortions, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation."

[picture] ?
The Role of Microtubule Movement in Bidirectional Organelle Transport. With Kulic, Brown, Kim, Kural, Blehm, Selvin, and Gelfand.PNAS, in press.

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First-principles calculation of DNA looping in tethered particle experiments. With Towles, Beausang, Garcia, and R. Phillips. coming soon. [picture]

[picture] When experiments seem to imply that the stiffness of DNA depends on its length, what's really going on?
Elasticity of short DNA molecules: Theory and experiment for contour lengths of 0.6--7 um. With Seol, Li, Perkins, and Betterton. Biophys. J. 93 4360 (2007).

How accurately can we infer the length of a long molecule from the motion of a bead on its end?
Colloidal Particle Motion as a Diagnostic of DNA Conformational Transitions. Current Opinion in Colloid and Interface Science 12 307 (2007). [picture]

[picture] Are there long-lived kinetic substates in DNA looping?
Diffusive hidden Markov model characterization of DNA looping dynamics in tethered particle experiments . With Beausang. Physical Biology 4 205 (2007).

How can you extract kinetics from noisy data without binning?
DNA looping kinetics analyzed using diffusive hidden Markov model . With Beausang, Zurla, Manzo, Dunlap, and Finzi. Biophys. J. 92, L64 (2007). [picture]

[picture] Are there hidden regularities in "random" Brownian motion?
Elementary simulation of tethered Brownian motion. With Beausang, Zurla, Sullivan, and Finzi. Am. J. Phys. 75, 520 (2007).

What energy source squirts viral DNA into a host cell?
Biological Consequences of Tightly Bent DNA: The Other Life of a Macromolecular Celebrity . With Garcia, Grayson, Han, Inamdar, Kondev, Phillips, Widom, and Wiggins. Biopolymers 85, 115 (2007). [picture]

[picture] If DNA is a stiff elastic rod, how can it form those tight regulatory loops?
High flexibility of DNA on short length scales probed by atomic force microscopy. With Wiggins, van der Heijden, Moreno-Herrero, Spakowitz, Phillips, Widom, and Dekker.Nature Nanotechnology 1, 137 (2006) A commentary appears here.
See the Erratum to this article.

Do cells transport vesicles using active conveyor belts?
Hitchhiking Through the Cytoplasm. With Kulic. Europhys. Lett. 81, 18001-(1--6) (2008). [picture]

[picture] How can you see protein binding in real time?
Entropic elasticity of DNA with a permanent kink. With Betterton and Li. Macromolecules 39 8816 (2006).

When you twist a string, how does that affect loop formation?
Effect of supercoiling on formation of protein mediated DNA loops. With Purohit. Phys. Rev. E74, art. no. 061907 (14 pages) (2006).
See the Erratum to this article. [picture]

How can you detect DNA looping in real time, when you can't even see DNA?
Tethered particle motion as a diagnostic of DNA tether length. With Zurla, Brogioli, Beausang, Finzi, and Dunlap. Journal of Physical Chemistry B110, 17260 (2006). [picture]

[picture] How can fluorescence tell us about molecular mechanics?
Generalized theory of semiflexible polymers. With Wiggins. Phys. Rev. E73, art. number 031906 (2006).

What can a balloon in a hurricane tell us about gene regulation?
Excluded-Volume Effects in Tethered-Particle Experiments: Bead Size Matters. With Segall and Phillips. Phys. Rev. Lett. 96 art. number 088306 (2006). [picture]

[picture] How does DNA spontaneously form gene regulatory complexes with "impossibly" tight loops?
Exact theory of kinkable elastic polymers . With Wiggins and Phillips. Phys. Rev. E71 art. number 021909 (2005).

Is single-stranded DNA really a freely jointed chain?
Theory of High-Force DNA Stretching and Overstretching. With Storm. Phys. Rev. E67 (2003) art. number 051906 (Erratum ibid. 70, 013902 (2004)). [picture]

[picture] What's going on when DNA stretches to 1.6 times its "maximum" length?
The bend stiffness of S-DNA. With Storm. Europhys. Lett. 62 (2003) 760.