Welcome to the Brooks Group Website!

Research in the group of Charles L. Brooks III in the Department of Chemistry and Biophysics Program at the University of Michigan is focused on the application of statistical mechanics, quantum chemistry and computational methods to chemically and physically oriented problems in biology. Current research interests include:

  • multi-scale modeling applied to dynamics and assembly of complex biological assemblies, e.g., viruses, ribosome, myosin
  • development of constant pH molecular dynamics with applications to pH dependent conformational changes: folding, unfolding and aggregation of proteins and nucleic acids
  • RNA structure, function and folding processes using all atom and coarse-grained models
  • free energy based methods for inhibitor screening and optimization, including lambda-dynamics, ligand docking, protein stability and continuum based free energy approximations
  • coupling between protein motion and enzyme catalysis in DHFR, AdK, DNA polymerases, including QM/MM investigations of enzyme catalysis
  • coarse-grained modeling of molecular machines: ribosome, viruses, helicases
  • development of new polarizable force fields for proteins, lipids and small molecules
  • protein folding using all atom and simplified off lattice models, including unfolded states of proteins
  • protein structure prediction, ab initio folding, homology modeling

In addition, we are oversee the development and support of the CHARMM molecular mechanics and modeling software. Our efforts in software development focus on new methods for the problems noted above and high performance computing on large parallel and distributed supercomputers, including accelerated molecular dynamics using GPUs.


November 5, 2015 - Congrats To Efrosini For Passing Her Candidacy Exam In Flying Colors!
A big hurrah to Efrosini for an excellent candidacy presentation and defense. Now the fun starts!
September 3, 2015 - Congratulations To Liz
Congrats to Liz in passing her candidacy exam today! One more hurdle down.
September 2, 2015 - Welcome Maral Budak Rotation Student In Biophysics
We all wish Maral a hearty welcome as she joins us for a rotation this semester. Maral is a PIBS Biophysics student.
September 2, 2015 - Refreshed Faces Return! Welcome Back Blair
Blair Whittington, now a sophomore, returns for the fall semester. Great to see her in group meeting - we need representation from Walled Lake :-)
September 1, 2015 - Welcome To New Postdoc Ryan Hayes
The Brooks Group welcomes Ryan Hayes to the group. Ryan recently finished his Ph.D. with Jose' Onuchic at Rice University.
August 26, 2015 - Charlie Named 2016 Fellow Of The Biophysical Society
Congratulations to the "fearless leader" Charlie, who was elected to the 2016 class of Fellows of the Biophysical Society. Charlie will receive his award/recognition at the LA BPS Meeting in February, 2016. (Link)
August 17, 2015 - Tony Mustoe, Former Brooksian Wins Beckman Postdoctoral Fellowship
Tony was recently awarded the Beckman Postdoctoral Fellowship for the Postdoctoral work he is carrying-out with Kevin Weeks at UNC, Chapel Hill. Congratulations Tony! (Link)
August 7, 2015 - Introducing Dr. Jessica Gagnon, Ph.D.
Congratulations on an excellent Ph.D. thesis defense by Jessica Gagnon!
August 6, 2015 - Alexis, Biophysics REU, Presents Work At REU Symposium
Congratulations to Alexis Okainski on a successful summer REU. Alexis presented her work at the REU symposium to an audience of Physicists and Biophysicists. Alexis worked with Logan and Alex over the summer on coarse graining of protein-protein interactions.
July 17, 2015 - Charlie Attends Annual CHARMM Developer Meeting In Vienna, Austria
Charlie helped run sessions at the annual CHARMM Developers meeting. This year hosted by Stefan Boresh in Vienna, Austria.
Funding from the following agencies: