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.


July 7, 2014 - Sean And Jessica Publish In Proc. Natl. Acad. Sci. U. S. A.!
Their work, conducted in collaboration with Dr. Anna Mapp, presented novel methods for studying allostery using a coarse-grained model and provided new insights into the allosteric regulation of IDPs. Congratulations, Sean and Jessica!

July 7, 2014 - Karunesh Publishes Work In Proc. Natl. Acad. Sci. U. S. A.!
This collaborative work examined frustration in the folding of the CheY protein through the innovative use of coarse-grained simulations to study circular permutants of CheY. Congratulations, Karunesh!

July 4, 2014 - Congratulations To Xiancheng And Dai On The Birth Of Their Daughter!
Liyi (栎伊), was born on Independence Day , weighing in at 7lb 2oz!

July 1, 2014 - Xinqiang Ding Joins The Group As A New Graduate Student
Welcome to the group, Xinqiang!
June 16, 2014 - Charlie Awarded Gilda Loew Memorial Award From The International Society Of Quantum Biology And Pharmacology
Congratulations Charlie!
June 6, 2014 - Logan Wins NIH NRSA Postdoctoral Grant
Congratulations to Logan for receiving an NIH NRSA Postdoctoral Fellowship. Great job Logan!
June 3, 2014 - Elizabeth (Liz) Gichana Joins The Group As A New PIBS Graduate Student
Welcome aboard Liz! Fold your ancestors!
June 2, 2014 - Summer REUs Arrive
Welcome Aiman Sherani, biophysics REU, physics major from Wellesley College, and Nathan Jenkins, med chem REU, chemistry/comp sci major, New Mexico State University. Looking forward to a successful summer!
May 30, 2014 - Protein Folding Consortium Meeting Held In Ann Arbor
The Brooks Group helped organize and participated in the Protein Folding Consortium Meeting, May 30 - June 1 here in Ann Arbor. Poster presentations by Karunesh, Alex, Sean, Logan, Jessica and Liz. Alex gave an "Ignite talk" - 20 slides, self-advancing every 15 seconds, 5 minutes total - awesome job.
April 23, 2014 - Undergraduate Students Present Work In UROP Spring Research Symposium
Five students presented their research in collaboration with UROP sponsors Aaron, Garrett, Karunesh, and Logan.

Funding from the following agencies: