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


December 10, 2019 - Congratulations To Former Lab Member Xinqiang Ding For Paper In Nature Communications
Machine learning and protein sequences! Deciphering protein evolution and fitness landscapes with latent space models (Link)
December 6, 2019 - Congratulations To Tricia - DEI Scientific Spotlight
Check out the great story about Tricia! (Link)
December 6, 2019 - Congratulations To Tricia - DEI Scientific Spotlight
Check out the great story about Tricia! (Link)
November 25, 2019 - Welcome Back Nick!
The Brooks Group welcomes back Nick following his leave, and the birth of his new son. Glad you're back Nick and congratulations.
November 22, 2019 - Big Congratulations To "candidate" Yujin
Yujin successfully passed his candidacy exam with flying colors. Great job!
November 22, 2019 - Fond Farewell To Marc
We are sad to see Marc finish his temporary assignment in the group, taking over for Nick during his leave. Thanks Marc!
September 19, 2019 - Congratulations To Yanming On Publication Of JPC Lett Paper On Allostery And Electrostatics
Yanming's paper exploring the role of electrostatics in allostery and a novel HREX method are described in his latest accepted paper in JPC Lett (just accepted)!
September 19, 2019 - Congrats To Sara And Troy For JPC Paper On Radical-coupled Electron Transfer Mechanism!
Exciting new paper from Sara and Troy as part of Narayan/ZImmerman collaboration, see https://pubs.acs.org/doi/abs/10.1021/acs.jpcb.9b08178
September 3, 2019 - Arghya Chakravorty joins the group for a postdoc.
Arghya Chakravorty comes to us from Clemson to workon amyloid beta simulations.
August 29, 2019 - Yanming, Tricia And Jonah Present At ACS Fall Symposium In San Diego
Yanming and Jonah presented excellent posters on their work on GPU accelerated Generalized Born models (Yanming) and MSLD bench marking on BACE I. Tricia and Jonah presented exceptional talks on ML -MATCH and Gibbs Sampler MSLD. Great job from all!
Funding from the following agencies: