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.


January 21, 2014 January 19, 2015 - Alex and Isabella welcome a new Brooksian to the group!

Congratulations to Alex and Isabella on the birth of Florence Elizabeth de Barbaro at 8:12 PM, January 19. She’s 8 lbs 12 oz and she, mom and Alex are doing great. It’s wonderful to welcome a new Brooks group member into the world:-)
January 15, 2015 - Shanshan Has Third Paper Of 2015 = PCAlign In Press In BMC Bioinformatics
Congratulations Shanshan.
January 7, 2015 - Congratulations To Fox And Tuli Mukhopadhyay On Getting The Second Paper Of The Year Accepted - In PNAS
Our paper "Residue level resolution of alphavirus envelope protein interactions in pH dependent fusion" was accepted for publication in PNAS. Great job Fox and Tuli!
January 6, 2015 - First Paper Of The Year Accepted In JMB!
The paper by Logan, Alex and Sean - Multiscale Modeling of a Conditionally Disordered pH-Sensing Chaperone - will appear in JMB shortly. This paper outlines a complete multi-scale approach for examining structure-function relationships in the conditionally disordered HdeA protein chaperone. Congratulations guys!
January 1, 2015 - Happy And Prosperous New Year!
The Brooks Group Wishes Everyone a Happy and Prosperous New Year
November 26, 2014 - We Wish A Fond Farewell To Visiting Scientist Huiyu
Huiyu Li is heading back to her faculty position in China this weekend. She will continue her collaborative research with the group. We wish her well on her return home, and will miss her.
November 14, 2014 - Congratulations To Summer Biophysics UROP Student Aiman Sherani For Winning A Travel Award To Participate In The 2015 Emerging Researchers National (ERN) Conference In STEM In Washington, DC
Great job Aiman! Good luck with your school year at Wellesley.
October 24, 2014 - We Bid Farewell To Afra
Afra moves to BU in a teaching-postdoc position with John Straub. Good luck Afra!
September 21, 2014 - Welcome Annie Wang - Shanshan's beautiful daughter!

The Brooks group congratulates Shanshan ( Sunshine ) on the birth of her daughter Annie ( Zixuan Ann Wang ) at 3:35 AM Monday morning ( September 21). Shanshan, daughter and family are doing well, though somewhat sleep deprived. Mazel tov!
September 15, 2014 - Biophysics Graduate Student Efrosini Artikis Joins For Rotation Semester
Efrosini joins the lab for a rotation. Welcome Efrosini!
Funding from the following agencies: