Department Research Activities:
Biophysics is a growing field of great intellectual activity and progress. Researchers are addressing such major questions as how the brain functions, and how nature's nanomachines, motor proteins and enzymes, move to do their work. The exciting new development is that rapid progress is now being made on these very old questions.
Biophysics is a wonderful area for invention and instrumentation. For example, the basic inventions are now being made that will enable diagnostic arrays to be produced and read out. The science and technology necessary for DNA delivery for gene therapy, and to study individual protein molecules in action is also undergoing rapid development.
Frank Brown's interests center around the theoretical study of biological membranes and single molecule spectroscopy. His work involves a combination of analytical and numerical calculations and coarse-grained simulations. His group is currently interested in the development of continuum level (elastic, hydrodynamic) theories and simulation algorithms for the study of biomembranes and lipid bilayers and the theoretical description of photon counting spectroscopy experiments. Recent work in the group has applied these models to the study of protein diffusion on the surface of human red blood cells, the fluctuation dynamics of inter-membrane junctions and the dynamics of single enzymes in solution.
Jean Carlson has been working on theoretical foundations for complex systems theory, merging concepts from statistical physics, biological evolution, and robust control theory from engineering. Her interests include adaptation and sorting in ecosystems subject to disturbance (e.g. fire prone terrestrial ecosystems), and the role of robustness in evolutionary biology from the intracellular level to populations.
Deborah Fygenson's group works on mechanics and dynamics of macromolecular assemblies. Her group performs experiments using techniques of light microscopy, electron microscopy and micromanipulation, complimented by standard tools from biophysical chemistry and molecular biology. Over the last few years, the group's focus has been on naturally occuring biological nanofibers known as microtubules. They have quantified characteristics of molecular transport within large bundles of microtubules and are developing techniques for measuring diffusion/transport down the axis of single microtubules. Recently, in collaboration with Paul Hansma's group, they have begun studying collagen fibrils as well. Their collaboration has shed a surprising new light on the nanoscopic structure of the fibrils, demonstrating that mechanically the fibrils behave as tubes. To better grasp and control the physical constraints at work in nanofibers of biomolecules, the Fygenson group, in collaboration with Erik Winfree's group at Caltech, is pursuing the characterization of macromolecular tubes designed from first principles and assembled out of DNA. By playing around with classic, well studied, biomaterials, like microtubules, collagen and DNA, the Fygenson group seeks fresh insights that can open channels for analyzing and inventing macromolecular architectures or machinery either within or without biology.
Helen Hansma focuses on biological applications of the Atomic Force Microscope. Her recent work (in collaboration Paul Hansma) on imaging DNA transcription as it occurs has demonstrated that the AFM can image even complex and sensitive individual enzyme molecules like RNA polymerase in action. This work has been featured in news stories in Science magazine and Science News, among others. The work is part of her group's continuing research on DNA-protein interactions as well as DNA condensation for gene therapy. She has also recently begun investigating substructures and elastic properties of synaptic vesicles in collaboration with Stan Parson's group in Chemistry.
Paul Hansma's group works on the development of scanning probe microscopes for biophysical applications. His group designed and built a series of Atomic Forces Microscopes, AFMs, that have included prototypes for commercially successful AFMs developed and marketed by Digital Instruments, a Santa Barbara company. These prototype AFMs and their commercial versions have been used at UCSB and by other biophysics groups around the world. The Hansma group has also worked on other scanning probe microscopes. They invented the Scanning Ion Conductance Microscope, SICM, which can measure the ion conductance through pores in membranes. Recently, Hansma, in collaboration with Galen Stucky's group in Chemistry and Dan Morse's group in the Department of Molecular, Cellular and Developmental Biology has used the SICM together with the AFM to develop a new paradigm for sea shell growth: mineral bridges thru pores in membranes rather than hetero-epitaxial nucleation.
Everett Lipman's group develops and uses ultrasensitive optical methods to study the self-assembly and function of biological molecules. With single-molecule resonance energy transfer, they have measured the folding of small proteins and the flexibility of biopolymers. The group has combined single-molecule fluorescence detection with microfluidic diffusive mixers, and this technique is used to observe protein folding under non-equilibrium conditions and to identify minute quantities of specific biomolecules.
The Lipman group takes full advantage of the unique collaborative environment at UCSB. Work is presently underway to study functional RNA with Professors Luc Jaeger and Joan-Emma Shea from the Chemistry Department, and to study molecular motors with Professors Omar Saleh in Materials and Kevin Plaxco in Chemistry.
Phil Pincus has been concerned with theoretical problems at the interface between soft condensed matter and issues of biomolecular relevance. Over the last few years, his group has been considering the properties of fluid membranes with incorporated inclusions which may be viewed as membrane-bound proteins. More recently, the focus has been on electrostatic interactions between charged membranes, biopolymers, and charged colloidal particles. The biophysical motivation is associated with gene therapy applications in which anionic DNA must overcome the Coulomb barrier to transfect cells.
Distinguished scientists in other departments at UCSB are also working on biophysical problems.
Cyrus Safinya in the Materials Department (with a joint appointment in Physics) is working with X-ray diffraction and enhanced video microscopy to study mixed systems with lipids and biomolecules, such as DNA. Joe Zasadinski in Chemical Engineering is using electron and scanning probe microscopes to study lung surfactants and model lipid systems. Jacob Israelachvili in Chemical Engineering and Materials is working with the Surface Forces Apparatus to study the forces between surfaces coated with systems of biological relevance, such as model membrane systems.
Research in the Shea Group focuses on developing and applying the techniques of statistical and computational physics to the study of biological problems. Current work involves the investigation of cellular processes including in-vivo protein folding and protein aggregation.
Boris Shraiman's research interests focus on statistical mechanics of non-equilibrium systems, quantitative systems biology and bioinformatics.