Harvard University - Department of Molecular & Cellular Biology

DAVID R NELSON

Nelson
Arthur K. Solomon Professor of Biophysics; Professor of Physics and Applied Sciences

Email: nelson@physics.harvard.edu
Phone: 617-495-4331

Mail: Lyman 325

Members of the Nelson Lab

Courses

MCB 199. Statistical Thermodynamics and Quantitative Biology
Catalog Number: 9072  View Course Website
Term: [Spring Term 2014-2015.]   Credit: Half course.
Instructor: David Nelson
Course Level: For Undergraduates and Graduates
Description: Course seeks to develop an understanding of thermodynamics and statistical mechanics, with applications to quantitative problems in biology such as configurations of biopolymers, equilibrium states of matter, chemical reactions and protein transport, using the concepts of entropy, free energy, adsorption, chemical kinetics and molecular diffusion.
Prerequisite(s): Two terms of college calculus, a calculus-based physics course, and some exposure to molecular and cellular biology. Experience with statistics and differential equations not essential, but helpful.
Meetings: M., W., F., at 11
APPHY 367. Topics on Condensed Matter Physics
Catalog Number: 6975  View Course Website
Term: Fall Term; Repeated Spring Term 2013-2014.   Credit: Half course.
Instructor: David Nelson
Course Level: Graduate Course
APPHY 368. Topics on Condensed Matter Physics
Catalog Number: 4173  View Course Website
Term: Fall Term; Repeated Spring Term 2013-2014.   Credit: Half course.
Instructor: David Nelson
Course Level: Graduate Course
PHYSICS 251b. Advanced Quantum Mechanics II
Catalog Number: 2689  View Course Website
Term: Spring Term 2013-2014.   Credit: Half course.
Instructor: David Nelson
Course Level: Primarily for Graduates
Description: Potential topics include Heisenberg picture; time-dependent perturbations; inelastic scattering; electrons in a uniform magnetic field; quantized radiation field; absorption and emission of radiation; identical particles and second quantization; nuclear magnetic resonance; Feynman path integrals for quantum spins.
Prerequisite(s): Physics 251a.
Meetings: M., W., F., at 12
PHYSICS 269r. Topics in Statistical Physics and Physical Biology
Catalog Number: 6214  View Course Website
Term: [Spring Term 2014-2015.]   Credit: Half course.
Instructor: David Nelson
Course Level: Primarily for Graduates
Description: Introduction to strongly interacting soft condensed matter and biophysical systems. We begin with the physics of cells and related single molecule experiments on bio-polymers such as DNA, RNA and proteins. A major part of the course will then focus on genetic engineering, and the non-equilibrium statistical dynamics of genetic circuits and neural networks.
Prerequisite(s): Physics 262, Applied Physics 284 or equivalent.
Meetings: M., W., F., at 11
PHYSICS 327a. Topics in Condensed Matter Physics
Catalog Number: 5969  View Course Website
Term: Fall Term; Repeated Spring Term 2013-2014.   Credit: Half course.
Instructor: David Nelson
Course Level: Graduate Course
PHYSICS 327b. Topics in Condensed Matter Physics
Catalog Number: 6524  View Course Website
Term: Fall Term; Repeated Spring Term 2013-2014.   Credit: Half course.
Instructor: David Nelson
Course Level: Graduate Course
(View all MCB Courses)

Research

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.

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).

J. Mathe, A. Aksimnetiev, D. R. Nelson, K. Schulten, and A. Meller, "Orientation discrimination of single stranded DNA inside the alpha-hemolysin membrane channel", PNAS, 102, 12377 (2005).

updated: 04/22/2014