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Faculty in the Biophysics program share a common interest in understanding the physical principles that underlie biological phenomena. Research in the program involves two overlapping branches of biophysics: the application of physical and chemical principles and methods to solving biological problems, and the development of new methods. Research areas include the molecular basis of macromolecular function including structural biology, single molecule analysis, and computational biology; the quantitative relationship between molecular properties and higher-level cell and tissue properties; and emerging areas of quantitative cell and organ biology. Methodologies include imaging at all biological scales: single-molecule analysis; x-ray diffraction, electron microscopy, NMR and other spectroscopic methods for determining three-dimensional structure; and cellular and tissue-level MRI. The training program includes graduate-level coursework in physical and biological sciences, participation in seminar series, and most importantly independent research.
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For more information contact:
Kathleen Guan
Biophysics Program
Fairchild Building, D118
Stanford, CA 94305-5126
(650) 723-7576
(650) 723-8464 (fax)
biophysics@med.stanford.edu
http://med.stanford.edu/biophysics/
Faculty and their Research Interests
Russ Altman. BioMedical informatics: understanding of macromolecular structural ensembles.
Steven M. Block. Properties of proteins or nucleic acids at the level of single macromolecules and molecular complexes. Experimental tools include laser-based optical traps (“optical tweezers”) and a variety of state-of-the-art fluorescence techniques, in conjunction with custom-built instrumentation for the nanometer-level detection of displacements and piconewton-level detection of forces.
http://www.stanford.edu/group/blocklab/
Steven Boxer. Electrostatics and dynamics in proteins; membranes biotechnology and applications; excited state processes in GFP and photosynthesis.
Axel Brunger. Our goal is to understand the molecular mechanism of synaptic neurotransmission. Our primary tools are x-ray crystallography, solution nuclear magnetic resonance, cryo-electron microscopy, and single-molecule fluorescence spectroscopy. We are particularly interested in the structure and function of key players in the synaptic vesicle fusion machinery. Our lab is also working on the p97/VCP ATPase involved in endoplasmic reticulum-associated degradation, and the sec6/8 complex involved in cell polarization. These investigations are aimed at a molecular understanding of these complex protein machineries, which may ultimately lead to improved therapeutics. http://atb.slac.stanford.edu
Douglas Brutlag. Genomics and bioinformatics. We apply bioinformatics and machine learning methods to discover conserved structural and functional motifs in proteins and conserved regulatory motifs near genes. These motifs can be used to predict structure and function in newly sequenced proteins and gene regulatory networks in newly sequenced genomes.
Zev Bryant. My laboratory seeks to understand the physical mechanisms by which biological molecular motors convert chemical energy into mechanical work. We use single molecule tracking and manipulation techniques to observe and perturb substeps in the mechanochemical cycles of individual motors. Protein engineering helps us to explore relationships between molecular structures and mechanical functions. Topics of current interest include torque generation by DNA-associated ATPases and mechanical adaptations of unconventional myosins.
Xiaoyuan (Shawn) Chen. A chemist/radiochemist interested in developing and validating molecular probes for multimodality imaging of tumor angiogenesis and metastasis. He is also keen on molecular targeted delivery of chemo-, radio-, and gene therapeutics.
Gilbert Chu. Mechanisms for how cells recognize and respond to DNA damage.
Jennifer Cochran. Protein engineering of ligands and receptors to investigate molecular mechanisms of cell signaling and develop novel therapeutics. Techniques include molecular evolution, biophysical analyses,and NMR spectroscopy of altered proteins.
Mark Davis. Immunology; T cell recognition in the development of immune responses.
Sebastian Doniach. Protein and RNA folding, applications of synchrotron x-ray scattering to study changes in biomolecular structure.
James Ferrell, Jr. Quantitative aspects of cell signaling and cell cycle regulation.
Judith Frydman. The mechanism of protein folding has become a central problem in biology. We wish to understand the pathways and regulation of protein folding in eukaryotic cells. Knowledge of how proteins actually fold in the cell should eventually provide the basis for controlling protein function under normal conditions and during abnormal conditions of environmental stress and disease.
http://www.stanford.edu/group/frydman/
K. Christopher Garcia. Structural and functional aspects of cell surface receptor recognition and activation, in receptor/ligand systems relevant to human health and disease.
Gary Glover. Development of magnetic resonance imaging methods, especially for demonstrating and characterizing brain function.
Miriam Goodman. Research in the Goodman lab is directed toward the discovery of the molecular events responsible for the sensation of touch and temperature in the nematode worm, Caenorhabditis elegans. Our approach is to combine techniques in genetics, quantitative behavioral analysis, in vivo electrophysiology, and biophysical studies of ion channel proteins required for sensation. In a collaboration with the Pruitt lab in Mechanical Engineering, our studies of touch sensation include analysis of tissue biomechanics. Additionally, we are investigating the cellular basis for the worm’s ability to associate food and temperature.
Philip C. Hanawalt. Philip Hanawalt discovered repair replication of DNA, the major process by which all living cells deal with damage to their genetic material. His research group studies the mechanisms by which living cells maintain their genomes in the face of endogenous DNA damage and environmental radiations and chemical carcinogens.
http://www.stanford.edu/~hanawalt/
Pehr Harbury. Structural determinants of protein folding, design and small molecule recognition.
Daniel Herschlag. RNA folding: Kinetics and thermodynamics. Mechanisms of catalysis by RNA and protein enzymes. System biology of RNA processing.
Keith Hodgson. X-ray absorption spectroscopy to investigate the metal constituents in macromolecular systems.
Ted Jardetzky. Studying of the structures and mechanisms of macromolecular complexes important in viral pathogenesis, allergic hypersensitivities and the regulation of cellular growth and differentiation, with an interest in uncovering novel conceptual approaches to intervening in disease processes. Ongoing research projects include studies of paramyxovirus and herpesvirus entry mechanisms, IgE-receptor structure and function and TGF-beta ligand signaling pathways.
Chaitan Khosla. Biosynthesis and engineering of polyketide natural products. Pharmacology of Celiac Sprue.
Brian Kobilka. Molecular structure of adrenergic receptors and conformational changes that mediate signal transduction. Intracellular targeting and trafficking of adrenergic receptors. Analysis of adrenergic subtype diversity in transgenic mice.
Eric Kool. Chemical and structural mechanisms of DNA replication and repair. Telomere structure and biology. Design of probes for imaging cellular RNAs.
Ron Kopito. Cell Biology of protein folding and misfolding. Protein aggregation and aggregation disorders. Mechanisms of intracellular protein degradation.
Roger Kornberg. Biochemical and crystallographic approaches to gene activation and transcription in yeast.
Craig Levin. The molecular imaging instrumentation laboratory develops novel instrumentation and methods for in vivo imaging of molecular signals of disease in humans and small laboratory animals.
Michael Levitt. Molecular modeling and dynamics of protein structure and folding.
Richard Lewis. Calcium signaling mechanisms in lymphocytes. Gene-ration of calcium dynamics by channels, pumps and organelles, and effects of on the specificity of gene expression. Biophysics and regulation of store-operated calcium channels. Imaging T-cell signaling and development in vivo with 2-photon microscopy.
Merritt Maduke. Mechanisms of ion channels and transporters.
David McKay. Study of molecular chaperones, RNA helicases and ribozymes using crystallographic and biophysical approaches.
Jack McMahan. We use electron microscope tomography to study the three-dimensional organization and behavior of macromolecules at the nervous systems’s synapses. The information we obtain provides in-sights unobtainable in any other way about the molecular mechanism involved in synaptic impulse transmission and the sequence of steps in synapse formation. To augment our studies we maintain extensive programs aimed at developing methods for localizing known proteins to specific macromolecules and for the quantitative analysis of tomographic data, technologies that can be applied to the investigation of macromolecules in any tissue.
Tobias Meyer. Cell signaling, intracellular signal transduction.
W.E. Moerner. Single-molecule spectroscopy and imaging, novel fluorophores and labeling strategies for single-molecule detection in cells, and trapping of nanoparticles and biomolecules in solution.
Vijay Pande. Computational biophysics and structural biology: simulations of protein folding in vitro and vivo, protein dynamics, and protein-ligand binding.
Norbert Pelc. Magnetic resonance imaging techniques and their bio-medical application.
Joseph Puglisi. RNA structure and function, mechanism of translation, NMR spectroscopy.
Stephen Quake. Quake’s interests lie at the nexus of physics, biology and biotechnology. His group pioneered the development of Microfluidic Large Scale Integration (LSI), demonstrating the first integrated microfluidic devices with thousands of mechanical valves. Throughout his career, Quake has also been active in the field of single molecule biophysics; he has focused on precision force measurements on single molecules, and in 2003 his group demonstrated the first successful single molecule DNA sequencing experiments.
Jianghong Rao. Cellular and molecular imaging of living subjects. We are interested in developing biosensors to image gene expression, mRNA and protein dynamics in single living cells.
Mark Schnitzer. In vivo fluorescence optical imaging and electrophysiological studies of the mammalian brain towards understanding biophysical aspects of learning and memory. We are developing and applying novel imaging approaches such as multiphoton fluorescence endoscopy for examining individual neutrons and dendrites, with emphasis on experiments in awake behaving animals.
Stephen J. Smith. Dynamics of brain development, neural circuit architectures and dynamics, imaging methods.
Ed Solomon. Spectroscopy, electronic structure and function of transition metal active sites in proteins, enzymes and drugs.
James Spudich. Mechanism by which the molecular motor myosin facilitates muscle contraction, cytokinesis, and cell movement.
Julie Theriot. Cell biology of host-pathogen interactions.
William Weis. Molecular basis of cell adhesion, Wnt signaling, and intracellular vesicle trafficking.
Richard Zare. Analyzing single cells for chemical contents; proteomic studies using mass spectrometry.
