LABORATORY OF ROBERT S. EISENBERG

Department of Molecular Biophysics & Physiology

Bob Eisenberg is interested in studying ion channels as physical objects, trying to use the tools of physics, chemistry, engineering, and applied mathematics to understand how they work. Ion channels are proteins with a hole down their middle that are the gatekeepers for cells. Ion channels control an enormous range of biological function in health and disease. But ion channels have simple enough structure that they can be analyzed with the usual tools of physical science. With that analysis in hand, Bob and John Tang, with gifted collaborators, are trying to design practical machines that use ion channels.

What is physiology all about?

Brief autobiography

Full Length CV

PNP online is a web-based software for running Poisson Nernst Planck theory.

A complete list of publications:  Many are available on-line by clicking the link named PDF.

Selected references:

Eisenberg, R.S., Klosek, M.M., and Schuss, Z. (1995) Diffusion as a chemical reaction: stochastic trajectories between fixed concentrations. J. Chem. Phys., 102(4): 1767-1780.

Elber, R., Chen, D., Rojewska, D., and Eisenberg, R.S. (1995) Sodium in gramicidin: an example of a permion. Biophysical Journal, 68: 906-924.

Chen, D., Eisenberg, R., Jerome, J., and Shu, C. (1995) Hydrodynamic model of temperature change in open ionic channels. Biophysical J. 69: 2304-2322.

Barkai, E., Eisenberg, R.S., and Schuss, Z. (1996)A bidirectional shot noise in a singly occupied channel. Physical Review E(2), 54 1161-1175.

Chen, D., Lear, J., and Eisenberg, B. (1997) Permeation through an Open channel. Poisson-Nernst-Planck Theory of a Synthetic Ionic Channel. Biophysical Journal, 72, 97-116.

Barcilon, V., Chen, D.-P., Eisenberg, R.S., and J.W. Jerome. (1997) Qualitative properties of steady-state Poisson-Nernst-Planck systems: perturbation and simulation study. SIAMJ.Appl.Math. 57(3) 631-648.

Chen, D.; Xu, L.; Tripathy, A.; Meissner, G.; Eisenberg, B. (1997) Permeation through the Calcium Release Channel of Cardiac Muscle. with an appendix Rate Constants in Channology. Biophys. J. 73(3) 1337-1354.

Nonner, W.; Chen, D.; Eisenberg, B. (1998) Anomalous Mole Fraction Effect, Electrostatics, and Binding.Biophys. J. 74 2327-2334.

Nonner, W. and Eisenberg, B. (1998) Ion Permeation and Glutamate Residues Linked by Poisson-Nernst-Planck Theory in L-type Calcium Channels.Biophys. J. 75:1287-1305.

Chen, D.; Xu, L.; Tripathy, A.; Meissner, G.; Eisenberg, B. (1998) Selectivity and Permeation in Calcium Release Channel of Cardiac Muscle: Alkali Metal Ions. (submitted to Biophysical Journal)

Gardner, C., Jerome, J. and Eisenberg, B. (1998) Electrodiffusion Model of Rectangular Current Pulses in Ionic Channels of Cellular Membranes. (submitted to Phys. Rev. Letters)

Eisenberg, R.S. (1996) Atomic Biology, Electrostatics and Ionic Channels.Ch.5, p. 269-357, in: New Developments and Theoretical Studies of Proteins. Edited by Ron Elber in the Advanced Series in Physical Chemistry, Vol. 7.World Scientific, Philadelphia.

Eisenberg, R.S. (1996) Computing the field in proteins and channels. J. Membrane Biol. 150:1-25.

Eisenberg, Bob (1998). Ionic channels in biological membranes. Natural nanotubes. Accounts of Chemical Research 31:117-125.

Eisenberg, Bob (1998). Ionic Channels in Biological Membranes: Natural Nanotubes described by the Drift-Diffusion Equations. (Invited by and accepted by VLSI Design) Proceedings of the Fifth International Workshop on Computational Electronics.8:75-78.

Eisenberg, Bob (1998). Ionic channels in biological membranes. Electrostatic analysis of a natural nanotube. Contemporary Physics, 39 (6) 447 - 466

Nonner, Wolfgang, Chen, Duan, and Bob Eisenberg.(1999). Progress and prospects in permeation. Journal of General Physiology 113: 773-782

Eisenberg, R.S. (1999). From Structure to Function in Open Ionic Channels. Journal of Membrane Biology 171 1-24.

Nonner, Wolfgang, and Bob Eisenberg.(2000) Electrodiffusion in Ionic Channels of Biological Membranes. Journal of Molecular Fluids 87:149-162.

Eisenberg, Bob. (2000). Permeation as a Diffusion Process. Chapter 4 in Biophysics Textbook On Line “Channels Receptors, and Transporters” Louis J. DeFelice, Volume Editor. http://www.biophysics.org/btol/channel.html#5

Eisenberg, R. (2000) Ionic channels: natural nanotubes described by the drift diffusion equations. Superlattices and Microstructuers.27 (5/6) 545-549.

Z.Schuss, B.Nadler, R.S.Eisenberg.(2001) Derivation of Poisson and Nernst-Planck equations in a bath and channel from a molecular model. PHYSICAL REVIEW E,VOLUME 64,036116.

Wolfgang Nonner, Dirk Gillespie, and R.S.Eisenberg (2001). Ion Accumulation in a Biological Calcium Channel: Effects of Solvent and Confining, J. Phys. Chem. B 2001, 105, 6427-6436

Dirk Gillespie,R.S.Eisenberg. Physical descriptions of experimental selectivity measurements in ion channels.EurBiophys J (2002) 31: 454–466

Dirk Gillespie,Robert S. Eisenberg (2002) Physical descriptions of experimental selectivity measurements, EurBiophys J (2002) 31: 454–466

Bob Eisenberg (2003) Proteins, channels and crowded ions, Biophysical Chemistry 100 (2003) 507–517

DezsoBoda, David D. Busath, Bob Eisenberg, Douglas Henderson and Wolfgang Nonner (2002) Monte Carlo simulations of ion selectivity in a biological Na channel: Charge–space competition, Phys. Chem. Chem. Phys., 4, 5154–5160

Dirk Gillespie, Wolfgang Nonner, Douglas Henderson and Robert S. Eisenberg (2002) A physical mechanism for large-ion selectivity of ion channels , Phys. Chem. Chem. Phys., 4, 4763–4769

Dirk Gillespie, WolfgangNonner, and Robert S. Eisenberg (2002) Coupling Poisson–Nernst–Planck and density functional theory to calculate ion flux, J. Phys.: Condens. Matter 14 (2002) 12129–12145

Additional resources, including downloadable files,  are available from the following locations:

The interactive version of PNP can be found at http://www.pnponline.org/

The general directory for anonymous ftp is ftp://ftp.rush.edu/pub/Eisenberg   (see the INDEX).

The early versions of PNP are found in ftp://ftp.rush.edu/pub/Eisenberg/PNP and were written by Duan Chen.

Later versions are in ftp://ftp.rush.edu/pub/Eisenberg/Nonner and were written by Wolfgang Nonner using code written by Duan Chen for location dependent diameter, diffusion coefficient and permittivity (dielectric 'constant').

The later versions in more user friendly form are in ftp://ftp.rush.edu/pub/Eisenberg/Hollerbach and were rewritten and annotated and tested by UweHollerbach so they will compile on almost any C compiler (we hope).

http://www2.phys.rush.edu/files/Eisenberg contains a number of papers.

ftp://ftp.rush.edu/pub/Eisenberg/noise contains files for studying single channels in noise, written by Rick Levis.