Johan Strumpfer
MailTheoretical and Computational Biophysics Group
Beckman Institute, Room 3115
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801
Emailjohanstr [at] ks . uiuc . edu
DeptBiophysics

Education



Research



A little Latex class

A new Kindle 3 has prompted me to write a basic latex class that can produce pdfs in the correct size and format. The class file can be found here along with an example pdf. Care must be taken with equations as the small Kindle screen width often results in them running off the page. The page size may be a little small for the dx, but the class file can easily be modified for a sligtly larger screen.

Video formats for presentations

After making some animations for papers and presentations, I have spent time finding the best codecs for different uses. As expected, for high quality videos, it’s best to use the H264 codec due to it’s excellent compression. On the other hand, this codec usually requires some additional software to be installed before it will play on most computers.

After some experimentation it is clear that the best codec to use for playback across most platforms in both Keynote and Powerpoint is mpeg1. This usually means larger file sizes, but videos can be played without installing extra codecs in both QuickTime and Windows Media Player. I’ve written a short tcsh script for encoding with ffmpeg 0.4.8, available here.

Publications

Photosynthesis:

Publications Database Excited state dynamics in photosynthetic reaction center and light harvesting complex 1. Johan Strümpfer and Klaus Schulten. Journal of Chemical Physics, 137:065101, 2012. (8 pages). Open quantum dynamics calculations with the hierarchy equations of motion on parallel computers. Johan Strümpfer and Klaus Schulten. Journal of Chemical Theory and Computation, 8:2808-2816, 2012. Juxtaposing density matrix and classical path-based wave packet dynamics. Mortaza Aghtar, Jörg Liebers, Johan Strümpfer, Klaus Schulten, and Ulrich Kleinekathöfer. Journal of Chemical Physics, 136:214101, 2012. (9 pages). How quantum coherence assists photosynthetic light harvesting. Johan Strumpfer, Melih Sener, and Klaus Schulten. Journal of Physical Chemistry Letters, 3:536-542, 2012. Theory and simulation of the environmental effects on FMO electronic transitions. Carsten Olbrich, Johan Strümpfer, Klaus Schulten, and Ulrich Kleinekathoefer. Journal of Physical Chemistry Letters, 2:1771-1776, 2011. From atomistic modeling to excitation transfer and two-dimensional spectra of the FMO light-harvesting complex. Carsten Olbrich, Thomas L. C. Jansen, Jörg Liebers, Mortaza Aghtar, Johan Strümpfer, Klaus Schulten, Jasper Knoester, and Ulrich Kleinekathoefer. Journal of Physical Chemistry B, 115(26):8609-8621, 2011. The effect of correlated bath fluctuations on exciton transfer. Johan Strümpfer and Klaus Schulten. Journal of Chemical Physics, 134:095102, 2011. (9 pages). Förster energy transfer theory as reflected in the structures of photosynthetic light harvesting systems. Melih Sener, Johan Strümpfer, Jen Hsin, Danielle Chandler, Simon Scheuring, C. Neil Hunter, and Klaus Schulten. ChemPhysChem, 12:518-531, 2011. The light-harvesting apparatus in purple photosynthetic bacteria, introduction to a quantum biological device. Johan Strümpfer, Jen Hsin, Melih Sener, Danielle Chandler, and Klaus Schulten. In Benoit Roux, editor, Molecular Machines, chapter 2, pp. 19-48. World Scientific Press, 2011. Quest for spatially correlated fluctuations in the FMO light-harvesting complex. Carsten Olbrich, Johan Strümpfer, Klaus Schulten, and Ulrich Kleinekathoefer. Journal of Physical Chemistry B, 115:758-764, 2011. Energy transfer dynamics in an RC-LH1-PufX tubular photosynthetic membrane. Jen Hsin, Johan Strümpfer, Melih Sener, Pu Qian, C. Neil Hunter, and Klaus Schulten. New Journal of Physics, 12:085005, 2010. (19 pages). Self-assembly of photosynthetic membranes. Jen Hsin, Danielle E. Chandler, James Gumbart, Christopher B. Harrison, Melih Sener, Johan Strumpfer, and Klaus Schulten. ChemPhysChem, 11:1154-1159, 2010. Photosynthetic vesicle architecture and constraints on efficient energy harvesting. Melih Sener, Johan Strumpfer, John A. Timney, Arvi Freiberg, C. Neil Hunter, and Klaus Schulten. Biophysical Journal, 99:67-75, 2010. Light harvesting complex II B850 excitation dynamics. Johan Strümpfer and Klaus Schulten. Journal of Chemical Physics, 131:225101, 2009. (9 pages).

Mechanical Proteins:

Publications Database Identification of an N-terminal inhibitory extension as the primary mechanosensory regulator of twitchin kinase. Eleonore von Castelmur, Johan Strümpfer, Barbara Franke, Julijus Bogomolovas, Sonia Barbieri, Hiroshi Qadota, Petr V. Konarev, Dmitri I. Svergun, Siegfried Labeit, Guy M. Benian, Klaus Schulten, and Olga Mayans. Proceedings of the National Academy of Sciences, USA, 109:13608-13613, 2012. Mutation of conserved histidines alters the tertiary structure and nanomechanics of consensus ankyrin repeats. Whasil Lee, Johan Strümpfer, Vann Bennett, Klaus Schulten, and Piotr E. Marszalek. Journal of Biological Chemistry, 287:19115-19121, 2012. Molecular origin of the hierarchical elasticity of titin: simulation, experiment and theory. Jen Hsin, Johan Strümpfer, Eric H. Lee, and Klaus Schulten. Annual Review of Biophysics, 40:187-203, 2011.

Protein Folding:

Publications Database Structural characterization of l-repressor folding from all-atom molecular dynamics simulations. Yanxin Liu, Johan Strümpfer, Peter L. Freddolino, Martin Gruebele, and Klaus Schulten. Journal of Physical Chemistry Letters, 3:1117-1123, 2012.