Jonathan Whitmer

Research Associate


  • B.S. Physics and B. S. Mathematics, Summa Cum Laude, Kansas State University, 2005
  • M.S. Physics, University of Illinois, 2009
  • Ph.D. Physics, University of Illinois, 2011

Research Interests

Recent developments in DNA sequencing have shown the promise of direct single-molecule analyses. Many such methods rely on the ability to stretch DNA molecule, where hydrodynamic flows and microchannel confinement may be utilized. I am interested in elucidating the mechanical and thermodynamic effects facilitating DNA elongation through the use of simulations.

As DNA is a highly charged, complicated molecule, study of large-scale effects is facilitated by coarse-graining into a more simple mesoscopic description. I am currently developing coarse-grained models for use in the study of DNA both in bulk solution and in confinement.

Additionally, the self-assembly of DNA-nanoparticle conjugates has shown to be a useful method for the selection and design of self-assembled nanoparticle superstructures. I am further interested in understanding the dynamic and thermodynamic limits to using DNA hybridization, among other self-assembly methods, to assemble macroscopic superstructures of nanoparticles and colloids.


Dr. Jonathan Whitmer
Department of Chemical and Biological Engineering
University of Wisconsin-Madison
3105 Engineering Hall
1415 Engineering Drive
Madison, WI 53706-1691
tel: +1 608 265-4926
fax: +1 608 262-5434
email: Jonathan Whitmer