Research
Scientific publications
- Real time observations of single bacteriophage λ DNA ejections in vitro. Paul Grayson, Lin Han, Tabita Winther, and Rob Phillips. PNAS, September 5, 2007. [supplementary information]
- Is phage DNA “injected” into cells - biologists and physicists can agree. Paul Grayson and Ian J. Molineux. Current Opinion in Microbiology, August 20, 2007.
- Biological Consequences of Tightly Bent DNA: The Other Life of a Macromolecular Celebrity. Hernan G. Garcia, Paul Grayson, Lin Han, Mandar Inamdar, Jané Kondev, Philip C. Nelson, Jonathan Widom and Paul A. Wiggins. Biopolymers 85(2):115-130 (2007).
- The Effect of Genome Length on Ejection Forces in Bacteriophage Lambda. Paul Grayson, Alex Evilevitch, Mandar M. Inamdar, Prashant K. Purohit, William M. Gelbart, Charles M. Knobler, and Rob Phillips. Virology, 2006, 348(2):430-436, 2006.
- Forces During Bacteriophage DNA Packaging and Ejection. Prashant Purohit, Mandar Inamdar, Paul Grayson, Todd Squires, Jané Kondev, and Rob Phillips. Biophysical Journal, 88:851-866, 2005.
- Conductance and physical asymmetry of the Escherichia coli glycerol facilitator GlpF. Deyu Lu, Paul Grayson, and Klaus Schulten. Biophysical Journal, 85:2977-2987, 2003.
- Mechanisms of selectivity in channels and enzymes studied with interactive molecular dynamics. Paul Grayson, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 85:36-48, 2003.
- A System for Interactive Molecular Dynamics Simulation. John E. Stone, Justin Gullingsrud, Klaus Schulten, Paul Grayson. In 2001 ACM Symposium on Interactive 3D Graphics, John F. Hughes and Carlo H. Sequin, editors, pages 191-194, New York, 2001, ACM SIGGRAPH.
External Presentations
- Watching phage λ ejection: towards a single-molecule Hershey-Chase experiment. Thesis defense, Caltech, May 14, 2007.
- Real time visualization of genome ejection from bacteriophages. Single Molecule Biophysics Conference, Aspen, CO, 2007.
- The role of pressure in DNA ejection from bacteriophage λ. Poster for PCAMB Conference, Puebla, Mexico, 2007. (1200k PDF)
- Real time visualization of genome ejection from bacteriophage lambda: how internal pressure drives the translocation of DNA. Special Biophysics Seminar, Northwestern University, Evanston, IL, 2006.
-
Pressure in bacteriophages. Theoretical Biophysics Seminar, University of Illinois, Urbana, IL, 2005.
- Viruses: designed by evolution, constrained by physics. Guest lecture for Nature’s Designs, an undergraduate course at the Art Center, Pasadena, CA, 2005.
- Pressure in bacteriophages. Phage/Virus Assembly Meeting, Winter Park, CO, 2005.
- Measurements of pressurized DNA in phage capsids. Poster for Biophysical Society Meeting, 2005. (800k PDF)
Education
- Ph.D. in Physics, with Prof. Rob Phillips. California Institute of Technology, 2002-2007.
- Studied the role of internal pressure in DNA delivery by viruses, focusing on the tailed dsDNA bacteriophage family, including phages lambda, phi29, T5, and P22. We successfully measured the internal pressure of lambda at 20-25 atm and observed DNA ejection in real time, determining a velocity of up to 60 kbp/s. This kind of analysis required a variety of bulk and single-molecule techniques including theoretical modeling of phages at many levels.
- Graduate research with Prof. Klaus Schulten. University of Illinois,
Urbana-Champaign, 2001-2002.
- Implemented the new technique Interactive Molecular Dynamics,
interfacing molecular dynamics simulations to haptic force-feedback to
allow users to literally feel simulated molecules. Contributed this
feature to the source code of VMD and NAMD, the group’s molecular
visualization and simulation software, in parallel with scientific
studies on the bacterial aquaglyceroporin GlpF and glycerol kinase.
- Implemented the new technique Interactive Molecular Dynamics,
interfacing molecular dynamics simulations to haptic force-feedback to
allow users to literally feel simulated molecules. Contributed this
feature to the source code of VMD and NAMD, the group’s molecular
visualization and simulation software, in parallel with scientific
studies on the bacterial aquaglyceroporin GlpF and glycerol kinase.
- S.B. in Physics with Electrical Engineering. Massachusetts Institute of Technology, 2001.
- S.B. in Mathematics. Massachusetts Institute of Technology, 2001.
Erdős path
- The Effect of Genome Length on Ejection Forces in Bacteriophage Lambda. Paul Grayson, Alex Evilevitch, Mandar M. Inamdar, Prashant K. Purohit, William M. Gelbart, Charles M. Knobler, and Rob Phillips. Virology, 2006, 348(2):430-436, 2006.
- Gelbart, William M.; Rice, Stuart A.; Freed, Karl F. Stochastic theory of vibrational relaxation and dissociation. J. Chem. Phys. 52 1970 5718–5732.
- Helfand, Eugene; Rice, Stuart A. Principle of corresponding states for transport properties. H. Chem. Phys. 32 1960 1642–1644.
- Kac, M.; Helfand, E. Study of several lattice systems with long-range forces. J. Mathematical Phys. 4 1963 1078–1088.
- Erdös, P.; Kac, M. The Gaussian law of errors in the theory of additive number theoretic functions. Amer. J. Math. 62, (1940). 738–742.