David Nelson

Professor of Biophysics and of Physics and Applied Physics

Harvard University
19 Oxford St., Lyman 234
Cambridge, MA 02138
Tel: 617-495-4331
Email: nelson@physics.harvard.edu

Website:

http://www.physics.harvard.edu/people/facpages/nelson.html
Lab Size: Between 5 and 10

Summary

Much of Nelson's recent research has focused on problems that bridge the gap between the physical and biological sciences. Early work explored population dynamics in the presence of varying growth rates and convection, leading to universal predictions for the spreading and transverse profile of populations in space- and time-dependent environments. Together with his student, David Lubensky, Nelson developed a theory of force-induced denaturation of double-stranded DNA. Sequence heterogeneity dominates the dynamics of the un-zipping fork (with possible implications for DNA replication in prokaryotes) over a large of forces above an unzipping transition. Energy barriers near the transition scale as the square root of the genome size. Recent observations of jumps and plateaus in the unzipping of lambda phage DNA at constant force (the result of a collaboration with his colleague, Mara Prentiss) are consistent with these predictions. Sequence heterogeneity was also predicted to have a re-markable effect on the dynamics of motor proteins such as helicases, exonulceases and RNA polymerases, leading to sublinear drift in time of these complex enzymes and a possible expla-nation for the nearly horizontal velocity-force curves observed near the stall force in experi-ments on RNA polymerase. Nelson and colleagues have also studied the shapes of viruses, showing that the icosahedral packing of protein capsomeres of spherical viruses becomes un-stable to faceting for sufficiently large virus size. A parametization of the architecture of virus shells in terms of single dimensionless "von Karman number" shows why small viruses are round and large ones are faceted, and allows important information about the elastic constants to be extracted from electron micrographs. Professor Nelson's current interests include population genetics, gene surfing, cooperation and competition

Publications

D.R. Nelson and N. Shnerb, "Non-Hermitian localization and population biology", Phys. Rev. E58, 1383 (1998).

D. K. Lubensky and D.R. Nelson, "Single molecule statistics and the polynucleotide unzipping transition", Phys. Rev. E 65, 03917 (2002).

C. Danilowicz, V. W. Coljee, C. Bouzigues, D. K. Lubensky, D. R. Nelson and M. Prentiss, "DNA unzipped under a constant force exhibits multiple metastable intermediates", Proc. Natl. Acad. Sci. V100, 1694 (2003).

J. Lidmar, L. Mirny and D. R. Nelson, "Virus shapes and buckling transitions in spherical shells", Phys. Rev. E68, 051910 (2003).

Y. Kafri, D.K. Lubensky and D. R. Nelson, "Dynamics of molecular motors and polymer translocation with sequence heterogeneity", Biophys. J. V86, 3373 (2004).