Biological Physics @ CMU

The Biological Physics Initiative
Carnegie Mellon University, Department of Physics

www.cmu.edu
 
     

Welcome to the Biological Physics Group at CMU!

Biological Physics at CMU is expanding ...

  • 2 new faculty members (Deserno, Evilevitch)

  • theory and simulation (Deserno, Nagle, Swendsen, Widom) complement experimental approaches (Evilevitch, Garoff, Heinrich, Lösche, Mandal, Nagle, Tristram-Nagle)

Research focus areas include:

  • Biomembrane structure, dynamics and reorganization
  • Physical virology: Viral assembly and genome packaging
  • Peptide or protein interaction with membranes in biomedical research
  • Folding and unfolding of single protein and RNA molecules
  • Collective vibrational modes in biomacromolecules
  • Transport and rheology in biopolymer gels
  • Interactions and structure of supramolecular assemblies

Research opportunities at Large Scale Facilities:

  • TeraGrid computing
  • Synchrotron x-ray scattering
  • Neutron diffraction and reflectometry

Our funding sources include:

Interdisciplinary collaborations with:

 

 

Lab briefs (click investigator name)

Markus Deserno


412-268-4401
deserno@andrew.cmu.edu
lab website

Research topics

  • Biophysical properties of proteins using computational models
  • Coarse-grained lipid membranes
  • Membrane-mediated forces between proteins

Lab members

  • Karpur Shukla (undergrad)
  • Senthilkumar Muthiah (undergrad)
  • Kunting (Eddie) Chua (undergrad)
  • Tristan Bereau (grad student)
  • Cem Yolcu (grad student)
  • Mingyang Hu (grad student)
  • Zunjing Wang (post-doc)
  • Xiaofei Li (post-doc)

Representative publications

  • M Deserno, Macromol. Rapid. Comm. 30 752 (2009).
  • BJ Reynwar, G Illya, et al., Nature 447 461 (2007).

Key project collaborators

  • C. Peters (MPI-P, Mainz, Germany)
  • R. Faller (UC Davis, CA)
  • M. Karttunen (U Western Ontario, Canada)
Alex Evilevitch


412-268-2748
alexe@andrew.cmu.edu
lab website

Research topics

  • Viral genome packaging and ejection
  • Self-assembly and mechanical properties of viral capsids and packaging motors
  • Nanocontainers and molecular devices modeled after viral capsids

Lab members

  • Muwen Kong (grad student)
  • Meerim Jeembaeva (grad student)
  • Loubna Bendrioua (grad student)
  • Elmar Nurmemmedov (post-doc)

Representative publications

  • M Jeembaeva, M Castelnovo, F Larsson, A Evilevitch, J. Mol. Biol. 381 310 (2008).
  • I Ivanovska, G. Wuite, B Jönsson, A Evilevitch, Proc. Natl. Acad. Sci. USA 104 9603 (2007).

Key project collaborators

  • J. Conway (U Pittsburgh Med School)
  • J.E. Johnson (Scripps Res. Inst., San Diego, CA)
  • G.J.L. Wuite (Free University, Amsterdam, The Netherlands)
Stephen Garoff


412-268-6877
sg2e@andrew.cmu.edu
lab website

Prof. Garoff is also a faculty member in the CMU Dept. of Chemical Engineering and a member of the Complex Fluids Engineering Group

Research topics

  • Surfactant formulations for self-dispersing aerosol drug carriers

Lab members

  • Alex Marakov (undergrad)
  • Austin Good (ChemE undergrad)
  • Kevin Koch (grad student)
  • Amsul Khanal (BME grad student)

Representative publications

  • AL Marcinkowski, S Garoff, et al., Aerosol Med. Pulm. Drug Deliv. 21, 361 (2008).

Key project collaborators

  • T.E. Corcoran, J.E. Pilewski (U Pittsburgh Med School)
  • T.M. Przybycien, R.D. Tilton (CMU BME)
Frank Heinrich


301-975-4507
fheinrich@cmu.edu

lab website

Dr. Heinrich is a permanent staff member at the NIST Center for Neutron Research (NCNR).

Research topics

  • Surface-supported bilayer membranes
  • Peptide-membrane interactions in Alzheimer's disease
  • Neutron scattering

Lab members

  • Prabhanshu Shekhar (grad student)

Representative publications

  • F Heinrich, T Ng, et al., Langmuir 25 4219 (2009).
  • SA Holt, AP Le Brun, et al., Soft Matter 5 2576 (2009).

Key project collaborators

  • J.E. Hall (UC Irvine, CA)
  • G. Valincius (Inst Biochemistry, Vilnius, LT)
  • C.F. Majkrzak (NIST Center f Neutron Research, MD)
Mathias Lösche


412-268-2735

lab website


Prof. Lösche is also a faculty member in the CMU Dept. of Biomed. Engineering and a NIST Associate at the NCNR.

Research topics

  • Bilayer membrane models near solid surfaces
  • Amyloid-β impact on membranes in Alzheimer's disease
  • Biophysical and structural studies of protein-membrane interaction in viral assembly, aging and cell signalling

Lab members

  • Siddharth Shenoy (grad student)
  • Prabhanshu Shekhar (grad student)
  • Agnieszka Kalinowski (MD/PhD student)
  • Haw Zan Goh (grad student)
  • Sam Rauhala (grad student)
  • Radu Moldovan (post-doc)
  • Matteo Broccio (post-doc)

Representative publications

  • DJ McGillivray, G Valincius, et al., Biophys. J. 96 1547 (2009).
  • G Valincius, F Heinrich, et al., Biophys. J. 95 4845 (2008).

Key project collaborators

  • J.E. Hall (UC Irvine)
  • G. Valincius (Inst Biochemistry, Vilnius, LT)
  • K.N. Dahl (CMU BME)

 

Maumita Mandal


412-268-4213
mandal@cmu.edu
lab website


Prof. Mandal is a faculty member of the CMU Dept. of Chemistry and an associated faculty member of the Depts. of Physics and Biomed. Engineering.

Research topics

  • Single molecule manipulations of RNA folding with optical tweezers
  • Self-assembly and structural studies of RNA–ligand and RNA–protein interactions
  • Riboswitches and transcriptional regulation
  • Nucleic acid-based molecular motors

Lab members

  • Ha Pham (grad student)
  • Muwen Kong (grad student)
  • Jonathan Wert (grad student)
  • Sang Kwon Seo (undergrad student)

Representative publications

  • DJ Mandal, B Boese, et al., Cell 113 577 (2003).
  • M Mandal, M Lee, et al., Science 306 275 (2004).

Key project collaborators

  • Steven Smith (UC Berkeley)

 

John F. Nagle


412-268-2764
nagle@andrew.cmu.edu
lab website

Prof. Nagle is also a faculty member in the CMU Dept. of Biological Sciences
.

Research topics

  • Lipid bilayer structure
  • Interaction between model membranes
  • X-ray and neutron scattering

Lab members

  • Pradeep Uppamoochikkal (post-doc)

Representative publications

  • J Pan, S Tristram-Nagle, JF Nagle, Phys. Rev. E 80 021931 (2009).
  • TT Mills, J Huang, GW Feigenson, JF Nagle, Gen. Physiol. Biophys. 28 126 (2009).

Key project collaborators

  • N. Kucerka (NRC Canada, Chalk River)
  • J. Sachs (U Minnessota)


Robert H. Swendsen


412-268-5211
swendsen+@andrew.cmu.edu

Research topics

  • Algorithms for exploration of computer-generated data

Representative publications

  • T Bereau, RH Swendsen, J. Comput. Phys. 228, 6119 (2009).
  • RH Swendsen, Am. J. Phys. 76 643 (2008).

Monographs

  • DC Mattis, RH Swendsen, Statistical Mechanics made Simple, World Scientific, NJ 2008

 

Stephanie Tristram-Nagle


412-268-3174
stn@cmu.edu
lab website

Research topics

  • Lipid membrane structure
  • Cholesterol/lipid interactions in raft domains
  • HIV peptide/membrane interactions

Lab members

  • Yuriy Zubovsky (undergrad)
  • Danny Kim (undergrad)
  • Rob Chan (undergrad)
  • Pradeep Uppamoochikkal (post-doc)

Representative publications

  • J Pan, DP Tieleman, et al., Biochim. Biophs. Acta 1788 1387 (2009).
  • SD Guler, DD Ghosh, et al., Chem. Phys. Lipids 160 33 (2009).

Key project collaborators

  • D.P. Tieleman (U Calgary, CA)
  • J. Mathai, M. Zeidel (Harvard U Med School)


Michael Widom


412-268-7645
widom@andrew.cmu.edu

Research topics

  • Elasticity and mechanical response of viral capsids
  • Secondary structure and function of noncoding RNA

Lab members

  • Ben Sauerwine (grad student)

Representative publications

  • Z Yang, I Bahar and M Widom, Biophys. J. 96 4438 (2009).
  • M Widom, J Lidmar, DR Nelson, Phys. Rev. E 76 031911 (2007).

Key project collaborators

  • I. Bahar (U Pitt Med School)
  • M. Mandal (CMU Chemistry)

 

 

 

Lab Websites or departmental pages

Deserno (theory/sim)

Evilevitch (exp)

Garoff (exp)

Lösche/Heinrich (exp)

Mandal (exp)

Nagle (exp/theory)

Swendsen (simulation)

Tristram-Nagle (exp)

Widom (theory)

related links

Prospective Graduate Students

Positions to fill

Physics Department

CMU main