Office: 3-120 Knudsen
Phone: (310) 825-8539
Education: Vrije Universiteit, Amsterdam, B.S. in Physics.(19.74).
Rijks-Universiteit Utrecht, M.S. in Physics (1976).
University of Southern California., Ph.D. in Physics (1979).
Positions Held: Postdoctoral Fellow, Harvard University 1979-1980.
Research Associate, Brookhaven National Lab.1980-1982.
Visiting Scientist, IBM Research Center, Yorktown, 1982-1984.
Assistant Professor of Physics, University of California, 1984-1988.
Associate Professor of Physics, University of California, 1988-1990.
Chair, Theoretical Physics for the Life Sciences, Leiden University, 2000-2001.
Full Professor of Physics, University of California, 1990-2008.
Distinguished Professor of Physics, University of California, 2008-2012.
Honors: Pierre et Marie Curie Visiting Professorship (E.S.P.C.I.) (1994)
Rothschild Foundation Fellowship (1996)
Distinguished Lecturer, College de France (1999)
Fellow American Physical Society (2001)
Hans-Fischer Fellowship, Technical University Munich, (2011)
Elasticity theory and shape transitions of viral shells, T. T. Nguyen, R. F. Bruinsma, and W. M. Gelbart, Elasticity theory and shape transitions of viral shells, Phys. Rev. E 72, 051923 (2005).
Abstract: From decades of high-resolution crystallography and electron microsopy studies, viral capsids have been shown to exhibit a cross-over – upon increase in radius – from spherical to faceted icosahedral structures. Lidmar, Mirny and Nelson showed in 2003 that this “buckling” transition can be accounted for by continuum elasticity theory in terms of a competition between stretching and bending energies of the curved, closed, protein shells. Nguyen et al. generalize this approach by allowing for nonzero spontaneous curvature of the shell, and for nonicosahedral shapes. They find a continuous or weakly first-order transition from icosahedral to spherocylindrical symmetry near the onset of the buckling transition, driven by increase in the ratio of stretching to bending modulus, consistent with experimentally observed variations in the shapes of a variety of viral capsids. PDFs: shape transitions.pdf (7.44 MB) PNGs: Elasticity theory and shape transitions of viral shells.png (201.05 KB)
Research category: Cellular mechanics
Nonlinear-dynamics theory of up-down transitions in neocortical neural networks
Abstract: The neurons of the neocortex show ∼1-Hz synchronized transitions between an active up state and a quiescent down state. The up-down state transitions are highly coherent over large sections of the cortex, yet they are accompanied by pronounced, incoherent noise. We propose a simple model for the up-down state oscillations that allows analysis by straightforward dynamical systems theory. An essential feature is a nonuniform network geometry composed of groups of excitatory and inhibitory neurons with strong coupling inside a group and weak coupling between groups. The enhanced deterministic noise of the up state appears as the natural result of the proximity of a partial synchronization transition. The synchronization transition takes place as a function of the long-range synaptic strength linking different groups of neurons.
JPEGs: levine_nonlineardynamics.jpg (319.59 KB)
Research categories: Neuroscience, Nonequilibrium physics
Propulsion of African trypanosomes is driven by bihelical waves with alternating chirality separated by kinks, Jose A. Rodrígueza, Miguel A. Lopez, Michelle C. Thayer, Yunzhe Zhao, Michael Oberholzer, Donald D. Chang, Neville K. Kisalu, Manuel L. Penichet, Gustavo Helguera, Robijn Bruinsma, Kent L. Hill, and Jianwei Miao
Abstract: Trypanosoma brucei, a parasitic protist with a single flagellum, is the causative agent of African sleeping sickness. Propulsion of T. brucei was long believed to be by a drill-like, helical motion. Using millisecond differential interference-contrast microscopy and analyzing image sequences of cultured procyclic-form and bloodstream-form parasites, as well as bloodstream-form cells in infected mouse blood, we find that, instead, motility of T. brucei is by the propagation of kinks, separating left-handed and right-handed helical waves. Kink-driven motility, previously encountered in prokaryotes, permits T. brucei a helical propagation mechanism while avoiding the large viscous drag associated with a net rotation of the broad end of its tapering body. Our study demonstrates that millisecond differential interference-contrast microscopy can be a useful tool for uncovering important short-time features of microorganism locomotion.
PDFs: zpq19322.pdf (15.10 MB) PNGs:
Propulsion of African trypanosomes is drivenby bihelical waves with alternating chiralityseparated by kinks.png (903.81 KB)
Research categories: Tissues and Organisms, Nonequilibrium physics
Nucleosome Switches, David Schwab, Robijn F. Bruinsma, and Joseph Rudnick
Abstract: Nucleosomes” are groups of eight proteins (“histones”) around which genomic DNA is wound (see figure) as a means of “condensing” DNA. Jonathan Widom had demonstrated that the positioning of these nucleosomes is encoded by the DNA itself. We applied an exactly soluble one-dimensional statistical mechanics model that could predict the locations of the the nucleosomes based on the DNA sequence. Based on this model, we found that nucleosome positioning can act as “switches” regulating gene expression. PDFs: nihms-124886.pdf (3.95 MB) PNGs: Nucleosome Switches.png (440.41 KB) Research category: Biological Macromolecules Origin of icosahedral symmetry in viruses, Roya Zandi, David Reguera, Robijn F. Bruinsma, William M. Gelbart, and Joseph Rudnick Abstract: With few exceptions, the shells of most viruses have the symmetry of one of the Platonic Solids: the icosahedron. The shells are composed of coat proteins (subunits) assembled in special motifs, the T-number structures. The figure shows a T=3 viral shell and the reconstruction of the protein positions. Using Monte Carlo simulation we found that a very simple statistical mechanical model can reproduce all the structures of viruses in vivo (T-number icosahedra) as well as important nonicosahedral structures (with octahedral and cubic symmetry) that had been observed in the laboratory.
PDFs: PNAS-2004-Zandi-15556-60.pdf (4.79 MB)
PNGs: Origin of icosahedral symmetry in viruses.png (1.50 MB) Research category: Viruses