Biophysics
Contact Information
Faculty and their Research Interests
Lysteria in motion.
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.
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.
Annelise E. Barron. The Barron lab is designing, creating and applying novel families of synthetic and biological polymers for applications in medicine and biotechnology. Our integrated approach to creating new and useful biomimetics and bioconjugates involves molecular design, chemical and/or biological synthesis, physical characterization, and finally, rigorous in vitro and in vivo testing of the new oligomers or polymers for their intended medical or biotechnological use.
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 and their impact on enzyme mechanisms, folding, and ligand binding; membrane biotechnology and applications to membrane fusion, ultrahigh resolution optical imaging of membrane protein conformational changes, and imaging membrane organization by mass spectrometry; excited state processes in GFP and photosynthesis.
Axel Brunger. Our goal is to understand the molecular mechanism of synaptic neurotransmission using x-ray crystallography, single-molecule fluorescence microscopy, and macromolecular computer simulation. We are particularly interested in the structure and function of key players in the synaptic vesicle fusion machinery, including the SNARE complex, synaptotagmin, complexin, and other factors.
http://atbweb.stanford.edu
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.
Manish Butte. The goal of my lab is to address fundamental and therapeutic questions in immunology using innovative biophysical and bioengineering approaches to visualize and manipulate cells. Our primary focus is on understanding at a molecular level the signals that balance T cell activation versus tolerance. We are using soft lithography, microfluidics, TIRF/confocal microscopy, and biological scanning probe/atomic force microscopy to image and control the molecules that mediate T cell activation. The ultimate aim of our work is to manipulate T cell signaling pathways to control immunologically-mediated diseases.
Lynette Cegelski. Assembly, architecture, and function of macromolecular systems, and interference with assembly processes. Particular interests include functional bacterial amyloid, cell walls, and biofilms, with an emphasis on “whole-cell NMR†and chemical biology.
Gilbert Chu. studies responses of human cells to DNA damage. One focus is the molecular basis for non-homologous end joining, the pathway that repairs double-strand breaks created by ionizing radiation and V(D)J recombination; a second focus is methods for analyzing microarray data to understand the damage response.
http://cmgm.stanford.edu/~chu/
Jennifer Cochran. Jennifer Cochran. Protein engineering of ligands and receptors to investigate molecular mechanisms of cell signaling and to develop novel therapeutics. Techniques include molecular evolution, biophysical analyses,and NMR spectroscopy of engineered proteins.
http://www.stanford.edu/group/cochrangroup/
Bianxiao Cui. We focus on developing quantitative tools to study the molecular mechanisms of axonal transport in normal and diseased neurons. Methods of interest include single molecule fluorescence imaging, optical trapping, multi-layer soft lithography, microfluidic neuronal network, and planar micro-electrode patterning.
Rhiju Das. Strives to predict how sequence codes for structure in proteins, nucleic acids, and heteropolymers whose folds have yet to be explored. The Das group uses new computational and experimental tools to tackle the de novo modeling of protein and RNA folds, the high-throughput structure mapping of riboswitches and random RNAs, and the design of self-knotting and self-crystallizing nucleic acids.
Mark Davis. Immunology. We are interested in the molecular basis of T lymphocyte recognition of foreign versus self antigens that underlies most immune responses. We have used biochemical and structural approaches, and particularly, single molecule and other types of advanced imaging methods to characterize the key molecular interactions that occur.
Adam de la Zerda. The expression of many biomolecules changes in time, space and local environments. We build optical imaging instrumentation to visualize these complex behaviors in cancer and ophthalmic disease animal models. Visualizing these changes in the context of living tissues may give rise to new diagnostic and therapeutic approaches, and can further reveal new molecular mechanisms not otherwise visible in traditional biochemical studies. Our research efforts span both basic science and clinically translatable work.
Sebastian Doniach. Research on structure-function relationships for small functional RNAs such as ribowsitches and ribozymes using small angle x-ray scattering (SAXS). Low resolution atomic scale structures are derived using a variety of computer simulation tools.
Alex Dunn. The Dunn lab studies how protein motion contributes to biological function. Long-term research goals include developing molecular force sensors for in vivo imaging and elucidating how motor proteins convert chemical energy into directed motion.
Liang Feng. Structure, dynamics and function of membrane transport proteins and enzymes.
James Ferrell, Jr. Quantitative aspects of cell signaling and cell cycle regulation.
Daniel Fisher. Theoretical research in cell biology, particularly dynamical phenomena, and quantitative aspects of evolutionary dynamics focussing on microbes.
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. Our goal is to discover the molecular events responsible for the sensation of touch and temperature using the nematode worm, Caenorhabditis elegans, as a model system. We combine genetic dissection with tools in structural biology (electron microscopy), biophysics (single-channel and whole-cell patch clamp recording), and mechanical biology (MEMS-based force sensors and analysis of body mechanics).
http://wormsense.stanford.edu
William Greenleaf. Our lab develops methods to probe the genome and epigenome at the single-cell and single-molecule levels. Our efforts are split between building new tools to leverage the power of high-throughput sequencing and cutting-edge optical microscopes, and bringing these new technologies to bear against basic biological questions of genetic and epigenetic inheritance and variation within populations.
http://greenleaf.stanford.edu/
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. Physical and chemical studies of biomolecular processes, focusing on fundamental properties and quantitative descriptions of RNA and protein catalysis and of RNA folding in vitro and in vivo. Techniques include single molecule flourescence, x-ray crystallography, NMR, vibrational spectroscopy, small angle x-ray scattering, and pre-steady state kinetics.
Keith Hodgson. X-ray absorption spectroscopy to investigate the metal constituents in macromolecular systems.
KC Huang. Our laboratory is interested in the relationships among cell shape detection, determination, and maintenance in bacteria. We are integrating computational physics-based models with evolutionary and synthetic biology approaches to control morphogenesis and cellular organization.
http://whatislife.stanford.edu
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. The goal of our research is to understand the structural basis for G protein coupled receptor activation. We use a variety of approaches to obtain high resolution structural information, as well as to characterize dynamic aspects of receptor structure and ligand-induced conformational changes.
Eric Kool. Eric Kool studies the mechanisms by which genetic sequence information is communicated in the pathways of DNA replication, DNA repair, and in RNA interference. This is accomplished by designing modified nucleosides and nucleic acids to be used as tools, and studying their properties in vitro and in vivo.
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 cellular and molecular signatures of disease in humans and small laboratory animals.
Michael Levitt. Computational biology with emphasis on molecular structure, which extends from detailed quantum mechanical simulations of simple solutes in water to a global analysis of the nature of the protein universe. In between, we focus on molecular modeling, structure morphing, dynamics and refinement of protein structure and folding of proteins and nucleic acids.
Richard Lewis. Molecular mechanisms that control store-operated calcium channels. Decoding calcium dynamics to control the specificity of gene expression. Applying 2-photon microscopy to study T-cell signaling and development in immune tissue.
Jin Billy Li. RNA editing: identification, regulation, and function.
Sharon R. Long. Molecular, genetic, and biochemical techniques are used to study how Rhizobium cells recognize and form nodules on their plant hosts. The association is highly specific: individual species of Rhizobium are classified according to the particular legumes they are able to nodulate.
http://cmgm.stanford.edu/biology/long/
Merritt Maduke. Mechanisms of ion channels and transporters.
Tobias Meyer. Cell signaling, intracellular signal transduction.
W.E. Moerner. We use single-molecule spectroscopy and imaging combined with novel fluorophores and labeling strategies for biophysical studies of proteins and enzymes in membranes, bacteria, and eukaryotic cells. In the area of methods, we are using a new type of trap to explore single biomolecules in solution, and we are developing new methods for 3-dimensional super-resolution imaging using single-molecule active control, optical nonlinearity, and PSF engineering.
Vijay Pande. Our research fuses biophysics, structural biology, theoretical physical chemistry, Bayesian statistics, and computer science in order to tackle challenging problems in molecular biophysics. In particular, we have interests in protein folding, RNA folding, protein-ligand binding, and protein structure refinement as well as the behavior of large macromolecular complexes such as ribosomes and chaperonins.
Norbert Pelc. Computed tomography (CT), especially the physics, engineering and mathematics of these systems. Current projects aims to develop volumetric CT systems, multi-energy CT imaging and understanding and optimizing the performance limitations of CT, especially with respect
to dose efficiency.
Beth Pruitt. The Pruitt microsystems lab works on custom measurements and analysis systems for small scale biomechanics and mechanotransduction. We study the mechanics and biology of the sense of touch in C. elegans, the mechanisms and forces of cell adhesion, and the development and response of stem cells and cardiac myocytes to mechanical loading. To this end, we are interested in the reliable manufacture and operation of micromachined sensors and actuators in harsh environments, measuring nanoscale mechanical behavior, and the analysis, design, and control of integrated electro-mechanical systems. We leverage custom microscale tools to answer novel questions in our lab in the areas of physiology, biology, stem cells, neuroscience and cardiology with an eye toward quantitative and fundamental biophysics.
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.
Ingmar H. Riedel-Kruse. Our research focus is on:
(1) Engineering and applications of biotic games for education and large scale science; (2) Biophysics of vertebrate (zebrafish) development with focus on oscillatory patterning dynamics in multi-cellular genetic networks. Lab website:
http://www.stanford.edu/group/riedel-kruse/
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.
Jan Skotheim. Our lab aims to find the principles underlying the function and evolution of genetic circuits through detailed studies and then comparisons of several natural systems. Our favorite models are the budding and fission yeast cell cycles, which due to their extensive biochemical and genetic characterization, are ideal platforms for the systems-level study of genetic control circuits.
Stephen J. Smith. The Smith laboratory is exploring the molecular architecture and connectivity of neural circuits in the cerebral cortex. Their experimental approach relies upon mice engineered to facilitate both structural and physiological study, a novel high-resolution, high-throughput imaging method called array tomography, and advanced image analysis and data-mining methods. More information is available at:
http://smithlab.stanford.edu
Edward Solomon. Spectroscopy, electronic structure and function of transition metal active sites in proteins, enzymes and drugs.
Andrew Spakowitz. Our lab utilizes a combination of analytical theory and computational techniques to understand the underlying physical phenomena in biological systems and complex fluids. Focusing on experimental systems that are of scientific and technological importance, we study a range of topics in DNA biophysics, protein self assembly, and charge transport in conjugated polymers.
James Spudich. Our research interests include the molecular basis of energy transduction that leads to ATP-driven myosin movement on actin, the roles of the myosin family of molecular motors in eukaryotic cells, and the regulation of myosin function in vivo.
Mary Teruel. Systems biology of cell differentiation and cell signaling in metabolism, cancer, and obesity.
http://med.stanford.edu/labs/mary-teruel/
Julie Theriot. Cell biology of host-pathogen interactions.
William Weis. Our laboratory is interested in the molecular mechanisms that underlie the development and maintenance of cell and tissue structure. Structural, biophysical and biochemical methods are used to study cell-cell adhesion, the Wnt signaling pathway, and intracellular membrane trafficking.
Richard Zare. Analyzing single cells for proteins and nucleic acids; using fast mass spectrometry for solution kinetics; applying surface plasmon resonance spectroscopy for molecular recognition; and synthesizing organic nanoparticles and studying their efficacy for drug delivery.