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.

News


March 11, 2014 - Congratulations To Aaron And Noorie On The Birth Of Their Son
Aaron and his wife welcomed Azmeer Terrence Abbasi-Frank to their family. Mother and baby are doing well.

March 1, 2014 - Brooks And Feig Lab Ski Trip
The Brooks and Feig labs meet in between Ann Arbor and East Lansing for a Saturday ski trip at Mt. Brighton.

February 26, 2014 - Karunesh Receives First Independent Funding From NIH
In a collaborative project with Bob Matthews on the folding of TIM barrel proteins, Karunesh receives funding for his contributions in NIH grant. Congratulations "special K".
February 24, 2014 - Karunesh Submits First Independent NIH Grant
Congratulations to Karunesh for submitting his first NIH grant as PI. Good luck!
January 13, 2014 - Sean, Garrett, Logan, And Charlie Presented Their Work At The 2014 Protein Folding Gordon Research Conference.
We presented our work focusing on complex and pH-dependent folding processes.
December 20, 2013 - First XSEDE Grant Goes To Fox And Garrett
Congratulations to Fox and Garrett in winning their grant for supercomputing time of ~5M processor hours.
September 22, 2013 - Group Outing
Members of the Brooks lab (and Professor Zimmerman) take a Sunday trip to Detroit to watch a baseball game between the Tigers and the Chicago White Sox.

September 9, 2013 - Elena Laricheva Presents Work At ACS National Meeting
Elena gave an invited talk in the Phys Division of ACS at the National meeting in Indianapolis on her recently published work describing the mechanism of pH-mediated switching from inactive to active forms of rhodopsin.
August 19, 2013 - Congratulations Dr (Joseph) Yesselman For An Excellent Thesis Defense
Joe did an excellent job defending his dissertation yesterday and now joins the rank of Ph.D.'s who have been associated with the Brooks Group. Congratulations to Joe and good luck in your new position in California!
August 16, 2013 - Jessica And Garrett Present At The Vaughn Symposium
Graduate students, Garrett Goh and Jessica Gagnon both presented posters at the 2013 Vaughn Symposium.

Funding from the following agencies: