Senior Thesis and Independent Research Requirements: Advisors

Finding a Thesis Advisor

The following is a list of faculty members who have expressed willingness to take on Engineering Biology students for Independent Research or Senior Thesis Projects. Check with these faculty about their availability and specific projects.

Professor Leland Allen, Chemistry

Electronic Structure Aspects of Enzyme Catalysis

Background: Projects in my research group have included identifying the electronic role of active site residues in metalloproteins. Carbonic anhydrase, liver alcohol dehydrogenase, and carboxypeptidase A are examples of zinc enzymes we have studied. One result has been design of carbonic anhydrase inhibitors for use in the treatment of glaucoma.

Another project has been the study of possible mechanisms to understand the catalytic action of RNAs.

Student Research Project: A current interest, and possible project for undergraduate research, is the electronic structure of nitrogenase, the enzyme which catalyzes the transformation of N2 to ammonia. Recent determination of the crystal structure for this enzyme has significantly advanced the possibility of fruitful electronic structure calculations for this long-standing and very important biological problem. It is also a practical problem of great interest to chemical engineers: simulation of the nitrogenase mechanism would lead to a major new chemical industry.

A simple method to determine atomic charges has been devised and can be readily understood and applied by undergrad Chemical Engineering students.

Professor Ahmet S. Cakmak, Department of Civil Engineering

Wave propagation and scattering problems in earthquake engineering; the establishment of a data base for strong motion accelerograms, use of such a data base for determining soil parameters for modeling ground motions by statistical methods seismic structural damage assessment. Numerical methods in the solution of soil-structure interaction problems. Study of the tectonics and seismicity of Turkey and Japan.

Professor Jannette Carey, Department of Chemistry

Basic Research in Biophysical Chemistry with Potential Overlap to Chemical Engineering

The research interests of our group center around understanding the interactions of biological macromolecules. We study protein-protein, protein-nucleic acid, and protein-small ligand interactions, as well as protein folding, which we consider a special case of molecular recognition in which the partners are distant parts of the same chain. We are investigating the underlying physical chemical principles that govern these interactions in order to understand the molecular basis for their features. Out expertise is in biochemical and biophysical analysis of binding equilibria and conformational transitions using a wide variety of tools. The following project areas offer the possibility of overlap to chemical engineering, and inquiries about collaborative projects are most welcome.

Engineering ligand-binding affinity and specificity of proteins.
Enhancing protein stability by mechanisms that are not protein-specific.
Surface deposition of proteins in specific orientations.
Ordered self-assembly of proteins from peptide fragments.
Influence of solvent interactions on biopolymer conformation.
Engineering proteins with new properties.

Professor Charles Dismukes, Department of Chemistry

Bioinorganic & Biophysical Chemistry

Photosynthesis and the Environment

a. Water splitting enzyme. The mechanism of water oxidation which is responsible for all of the dioxygen in our atmosphere is being investigated at the atomic level using spectroscopic methods: electron spin resonance spectroscopy to examine the paramagnetic radicals produced during the photochemical charge separation events, NMR spectroscopy to identify the protein coordination environment surrounding the catalytic sites.

b. Water oxidation catalysts. Synthesis of functionally active catalysts for non-photosynthetic water oxidation would greatly benefit the environment by enabling use of dioxygen instead of air in many industrial processes and combustions. There are no commercially available catalysts for this process. Our approach is based on mimicking the structure of the active site of the photosynthetic enzyme which splits water into dioxygen and protons.

Human Immunodeficiency Virus type l(HIV-1)

The human immunodeficiency virus type l(HIV-1) is the etiologic agent of AIDS. Replication of the HIV-1 virus, and hence infection, requires DNA synthesis by a retrovirus-encoded RNA-dependent DNA polymerase, or reverse transcriptase (RT). HIV-1-RT is a multi-functional enzyme required, not only, for the synthesis of the double-stranded proviral DNA from the single-stranded retroviral RNA genome, but also, cleavage of the retroviral RNA polymer in the form of a hybrid DNA-RNA intermediate (ribonuclease H or RNAase H activity) that allows transcription of the RNA fragments to proceed. We are working with the pharmaceutical industry to characterize the pair of metal ions that comprise the catalytic site of the RNAase subdomain and several mutant proteins. A second project involves the HIV-1 integrase, an enzyme responsible for integration of the virus' DNA into the host's genome. One of the important goals is to kill the AIDS virus by developing specific inhibitors of the metal sites of these enzymes.

Anti-oxidant Enzymes-Catalase

Nature has provided us with two different classes of enzymes, called catalases, which protect us against the destructive effects of hydrogen peroxide which forms during normal cellular biochemistry to an appreciable extent. We study the rare catalase produced by thermophillic bacteria. It has a novel binuclear Mn center at its active site. We are working on the mechanism of catalysis using magnetic resonance methods. This research is aimed at developing both a fundamental understanding of catalysis and a practical application to develop high temperature enzymes for applications in bleaching. The insights discovered from the enzyme studies are being used to synthesize small molecule catalysts for selective oxidations.

Hydrolytic Enzymes-Arginase

The dimanganese enzyme, arginase, is responsible for metabolism of the amino acid L-arginine, a product of protein metabolism. It may also be linked to formation of the intracellular messenger nitric oxide. We are exploring the mechanism of catalysis of this hydrolysis reaction using biochemical and magnetic resonance techniques.

Inorganic Chemistry

We have a program in the synthesis of multinuclear metal complexes as models for arginase, manganese catalase and the water oxidase. We are also developing these catalysts for applications in environmental clean oxidations such as for chlorine-free domestic laundry, paper/pulp bleaching and hydrocarbon oxidations.

Professor Enoch Durbin, Department of Mechanical & Aerospace Engineering

Alternate fuels, vehicle engines-emissions from vehicles.

Professor J.T. Groves, Department of Chemistry

Catalysis
Biocatalysis
Biomaterials

Professor Bart Hoebel, Department of Psychology

Neural basis of motivation: eating and drug abuse. Research in rats using brain lesions, stimulation, drug injections and microdialysis.

Professor Niraj K. Jha, Electrical Engineering

DNA Based Computing: Using tools of Molecular Biology to find solutions to combinatorial problems in Computer Engineering/Science.

Professor M.G. Littman. Department of Mechanical & Aerospace Engineering

Anthropomorphic robots, Hierarchical autonomous control, Parallel computing, human motor control. In addition, I will also supervise students wishing to work with disabled children in developing better man-machine interfaces for communication devices (in conjunction with N.J. Dept. of Education).

Professor Vincent Poor, Department of Electrical Engineering

Application of passive acoustic signal detection methods to the noninvasive detection of Coronary Artery Disease.

Application of finite-field wavelet transforms in biosequence analysis.

Professor Robert K. Prud'homme, Department of Chemical Engineering

Microstructures Templated Gel

Our interest is in being able to create nanoporous structured materials by using surfactant self-assembly to provide a template for the polymerization of gels. These materials have potential applications in biomedical controlled release, in the immobilization of enzymes, as gel chromotography supports, and as super-absorbents. Our work will consist of creating and polymerizing these three-dimensional micropore systems, measuring pore sizes using X-Ray scattering and then studying the swelling and mechanical properties of these gels using rheological measurements.

Novel Polymers for DNA Gel Electrophoresis Supports and for Enzyme Encapsulation

This is a project with FMC Corporation in Princeton. We will be looking at a new polymer they have developed that could be used for gel electrophoresis. Current aqueous polymers used for DNA gel electrophoresis need to be heated to melt them and that heating process results in damage to DNA fragments that are to be recovered from the gels. This new material has the unique property of liquefying upon cooling: Therefore the DNA could be removed from these gels by cutting out the sample and placing in the refrigerator to liquefy the sample. The mechanism of this liquefaction is not well understand and no one, as of yet, has tried these gel separations with this new material. Another area is enzyme encapsulation, the idea here is that enzymes can be dispersed in gel particles and then the fine gel particles can be put in non-aqueous media to do chemical reactions. Non-aqueous enzymology has been done Professor Klibinov at MIT. However, they have not developed techniques to disperse the enzymes and the efficiency of their process are very low. The goal of this work is to see if by embedding the enzymes in gels, we can both increase accessibility of the enzyme to the nonaqueous substrates and therefore increase the yield. In addition, gels can be condensed around enzymes to enhance their thermal stability. This "shrink wrapping" technique offers the promise of making stable enzymes for diagnostic sensors and chemical synthesis.

Structure: Properties of absorbent Gels

Superabsorbent polyacrylate gels are the largest single use of water soluble gels. The fundamental relationships between molecular structure, synthesis conditions, and function are not well understood. In this project we would like to use several new techniques to synthesize and characterize gels:

A thermal expansion technique from the ceramics industry to measure permeability,
An osmotic pressure technique from the biophysics literature to determine swelling potential,
An interfacial polymerization technique from the electronics industry to make core-shell gel beads.

Professor William B. Russel, Department of Chemical Engineering

Interested in transport phenomena in complex systems whether polymeric, colloidal, or biological.

Professor Jean Schwarzbauer, Department of Molecular Biology

Research directions include extracellular matrix structure and function, matrix protein interactions with cell adhesion receptors particularly integrins, and mechanisms of action of anti-adhesive matrix proteins. Systems include cell culture and the nematode C. elegans. Recombinant proteins are used to dissect function; several different procaryotic and eucaryotic expressions systems are used.

Professor Giacinto Scoles, Department of Chemistry

Surface structure and chemical properties of organic thin film.
Polymerization of organic monolayers.
Two-dimensional crystallization of proteins and other molecules of biological interest.

Professor Rob Socolow, Center for Energy and Environmental Studies

Please see Hema Ramamurthy in A201 (Chemical Engineering) for a complete listing of independent work projects available.

Professor M. Gerard Waters, Department of Molecular Biology

Study of the molecular mechanisms of membrane traffic in the eukaryotic cell. This process results in the generation of distinct protein and lipid compositions in different intracellular organelles, as well as the secretion of proteins from cells. It is a highly ordered process that requires the formation of membrane vesicles from intracellular organelles (for example, the endoplasmic reticulum), followed by specific docking to a recipient organelle (for example, the Golgi apparatus), and finally fusion of the vesicle and organelle membrane bilayers.