School of Engineering
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Professor of Biochemistry and, by courtesy, of Chemical Engineering and of Chemistry
Current Research and Scholarly InterestsOur research is aimed at understanding the chemical and physical behavior underlying biological macromolecules and systems, as these behaviors define the capabilities and limitations of biology. Toward this end we study folding and catalysis by RNA, as well as catalysis by protein enzymes.
James H. Clark Professor in the School of Engineering and Professor of Chemical Engineering and of Bioengineering
BioUsing and Understanding Cell-Free Biology
Swartz Lab General Research Focus:
The current and projected research in the Swartz lab balances basic research in microbial metabolism, protein expression, and protein folding with a strong emphasis on compelling applications. The power and versatility of cell-free methods coupled with careful evaluation and engineering of these new systems enables a whole new range of applications and scientific investigation. Fundamental research on: the mechanisms and kinetics of ribosomal function, fundamental bioenergetics, basic mechanisms of protein folding, functional genomics, and metabolic pathway analysis is motivated by a variety of near- and medium term applications spanning medicine, energy, and environmental needs.
Swartz Lab Application Focus:
In the medical area , current research addresses the need for patient-specific vaccines to treat cancer. Particularly for lymphomas, there is a strong need to be able to make a new cancer vaccine for each patient. Current technologies are not practical for this demanding task, but cell-free approaches are rapid and inexpensive. We have already demonstrated feasibility in mouse tumor challenge studies and are now expanding the range of applications and working to improve the relevant technologies. Experience with these vaccines has also suggested a new and exciting format for making inexpensive and very potent vaccines for general use.
To address pressing needs for a new and cleaner energy source, we are working towards an organism that can efficiently capture solar energy and convert it into hydrogen. The first task is to develop an oxygen tolerant hydrogenase using cell-free technology to express libraries of mutated enzymes that can be rapidly screened for improved function. Even though these are very complex enzymes, we have produced active hydrogenases with our cell-free methods. We are now perfecting the screening methods for rapid and accurate identification of improved enzymes. After these new enzymes are identified, the project will progress toward metabolic engineering and bioreactor design research to achieve the scales and economies required.
To address environmental needs, we are developing an improved water filters using an amazing membrane protein, Aquaporin Z. It has the ability to reject all other chemicals and ions except water. We have efficiently expressed the protein into lipid bilayer vesicles and are now working to cast these membranes on porous supports to complete the development of a new and powerful water purification technology. The same lessons will be applied toward the development of a new class of biosensors that brings high sensitivity and selectivity.
Jennifer R. Cochran
Shriram Chair of Bioengineering, Associate Professor of Bioengineering and, by courtesy, of Chemical Engineering
Current Research and Scholarly InterestsMolecular Bioengineering, Protein Biochemistry, Biotechnology, Cell and Tissue Engineering, Molecular Imaging, Chemical Biology
Jagdeep and Roshni Singh Professor in the School of Engineering, Senior Associate Dean for Faculty & Academic Affairs, Senior Fellow at Precourt and Professor, by courtesy, of Materials Science & Eng, of Electrical Eng and of Chemistry
BioThe research in the Bent laboratory is focused on understanding and controlling surface and interfacial chemistry and applying this knowledge to a range of problems in semiconductor processing, micro- and nano-electronics, nanotechnology, and sustainable and renewable energy. Much of the research aims to develop a molecular-level understanding in these systems, and hence the group uses of a variety of molecular probes. Systems currently under study in the group include functionalization of semiconductor surfaces, mechanisms and control of atomic layer deposition, molecular layer deposition, nanoscale materials for light absorption, interface engineering in photovoltaics, catalyst and electrocatalyst deposition.
W. M. Keck, Sr. Professor in Engineering and Professor, by court, of Materials Science and Engineering and of Chemistry
BioThe properties of ultrathin polymer films are often different from their bulk counterparts. We use spin casting, Langmuir-Blodgett deposition, and surface grafting to fabricate ultrathin films in the range of 100 to 1000 Angstroms thick. Macromolecular amphiphiles are examined at the air-water interface by surface pressure, Brewster angle microscopy, and interfacial shear measurements and on solid substrates by atomic force microscopy, FTIR, and ellipsometry. A vapor-deposition-polymerization process has been developed for covalent grafting of poly(amino acids) from solid substrates. FTIR measurements permit study of secondary structures (right and left-handed alpha helices, parallel and anti-parallel beta sheets) as a function of temperature and environment.
A broadly interdisciplinary collaboration has been established with the Department of Ophthalmology in the Stanford School of Medicine. We have designed and synthesized a fully interpenetrating network of two different hydrogel materials that have properties consistent with application as a substitute for the human cornea: high water swellability up to 85%,tensile strength comparable to the cornea, high glucose permeability comparable to the cornea, and sufficient tear strength to permit suturing. We have developed a technique for surface modification with adhesion peptides that allows binding of collagen and subsequent growth of epithelial cells. Broad questions on the relationships among molecular structure, processing protocol, and biomedical device application are being pursued.
Fletcher Jones II Professor in the School of Engineering
BioThe processing of complex liquids (polymers, suspensions, emulsions, biological fluids) alters their microstructure through orientation and deformation of their constitutive elements. In the case of polymeric liquids, it is of interest to obtain in situ measurements of segmental orientation and optical methods have proven to be an excellent means of acquiring this information. Research in our laboratory has resulted in a number of techniques in optical rheometry such as high-speed polarimetry (birefringence and dichroism) and various microscopy methods (fluorescence, phase contrast, and atomic force microscopy).
Another application of orientation dynamics is in the development of solar cells. The efficiency of second-generation solar cells fabricated with conjugated polymers is limited by photoelectron transport within the polymer film. Inspired by electrorheological fluids, an external electric field is applied to the film to induce anisotropy in polymer crystallites, which is expected to enhance electron mobility.
The microstructure of polymeric and other complex materials also cause them to have interesting physical properties and respond to different flow conditions in unusual manners. In our laboratory, we are equipped with instruments that are able to characterize these materials such as shear rheometer, capillary break up extensional rheometer, and 2D extensional rheometer. Then, the response of these materials to different flow conditions can be visualized and analyzed in detail using high speed imaging devices at up to 2,000 frames per second.
There are numerous processes encountered in nature and industry where the deformation of fluid-fluid interfaces is of central importance. Examples from nature include deformation of the red blood cell in small capillaries, cell division and structure and composition of the tear film. Industrial applications include the processing of emulsions and foams, and the atomization of droplets in ink-jet printing. In our laboratory, fundamental research is in progress to understand the orientation and deformation of monolayers at the molecular level. These experiments employ state of the art optical methods such as polarization modulated dichroism, fluorescence microscopy, and Brewster angle microscopy to obtain in situ measurements of polymer films and small molecule amphiphile monolayers subject to flow. Langmuir troughs are used as the experimental platform so that the thermodynamic state of the monolayers can be systematically controlled. For the first time, well characterized, homogeneous surface flows have been developed, and real time measurements of molecular and microdomain orientation have been obtained. These microstructural experiments are complemented by measurements of the macroscopic, mechanical properties of the films.
Alfred M. Spormann
Professor of Civil and Environmental Engineering, of Chemical Engineering and, by courtesy, of Biology
Current Research and Scholarly InterestsMetabolism of anaerobic microbes in diseases, bioenergy, and bioremediation
Associate Professor of Materials Science and Engineering and, by courtesy, of Chemical Engineering and of Bioengineering
Current Research and Scholarly InterestsProtein engineering
Associate Professor of Chemical Engineering
Current Research and Scholarly InterestsMy lab is deeply interested in understand how living cells sense and respond to mechanical stimuli.
Robert M. Waymouth
Robert Eckles Swain Professor in Chemistry and, by courtesy, of Chemical Engineering
BioRobert Eckles Swain Professor in Chemistry Robert Waymouth investigates new catalytic strategies to create useful new molecules, including sustainable polymers, synthetic fuels, and bioactive molecules. In one such breakthrough, Professor Waymouth and IBM researcher Jim Hedrick opened a new path for production of environmentally sustainable plastics and improved plastics recycling, earning recognition in the 2012 Presidential Green Chemistry Award.
Born in 1960 in Warner Robins, Georgia, Robert Waymouth studied chemistry and mathematics at Washington and Lee University in Lexington, Virginia (B.S. and B.A., respectively, both summa cum laude, 1982). He developed an interest in synthetic and mechanistic organometallic chemistry during his doctoral studies in chemistry at the California Institute of Technology under Professor R.H. Grubbs (Ph.D., 1987). His postdoctoral research with Professor Piero Pino at the Institut fur Polymere, ETH Zurich, Switzerland, focused on catalytic hydrogenation with chiral metallocene catalysts. He joined the Stanford University faculty as assistant professor in 1988, becoming full professor in 1997 and in 2000 the Robert Eckles Swain Professor of Chemistry.
Today, the Waymouth Group applies mechanistic principles to develop new concepts in catalysis, with particular focus on the development of organometallic and organic catalysts for the synthesis of complex macromolecular architectures. In organometallic catalysis, the group devised a highly selective alcohol oxidation catalyst that selectively oxidizes unprotected polyols and carbohydrates to alpha-hyroxyketones. The Waymouth group pioneered the development of catalysts that can access multiple kinetic states during a polymerization reaction in order to control sequence distribution. They devised a novel strategy for the synthesis of elastomeric polypropylene utilizing a metallocene catalyst whose structure was designed to interconvert between chiral and achiral coordination geometries on the timescale of the synthesis of a single polymer chain.
In collaboration with Jim Hedrick of IBM laboratories, the Waymouth Group has developed an extensive platform of organic catalysts for the controlled ring-opening polymerization of lactones, carbonates and other heterocyclic monomers. Mechanistic studies of nucleophilic N-heterocyclic carbene catalysts revealed an unusual zwitterionic ring-opening polymerization method which enabled the synthesis of high molecular weight cyclic polymers, a novel topology for these biodegradable and biocompatible macromolecules. In collaboration with the Wender group, the Waymouth group has devised selective organocatalytic strategies for the synthesis of functional degradable polymers and oligomers that function as "molecular transporters" to deliver drugs and probes into cells. These efforts combine elements of mechanistic organic and organometallic chemistry, polymer synthesis, and homogeneous catalysis to rationally design new macromolecular structures.