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Research Projects

Taylor, John

Project Description

Many proteins and protein fragments (peptides) are known to form aggregated insoluble structures called beta fibrils.  Some of these insoluble structures are closely associated with disease states such as Altzheimer’s and Parkinson’s.  Short peptide segments of such proteins that retain the ability to form beta-fibrils in aqueous solution will be synthesized and studied, together with analogs designed to investigate the structural requirements for aggregation.

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Ebright, Richard H.

Project Description

We have identified multiple new "drug targets" within the structure of bacterial RNA polymerase, the enzyme that mediates bacterial gene expression.  Each of these new targets can serve as a binding site for compounds that inhibit bacterial gene expression and thereby kill bacteria.  For each of these new targets, we have identified at least one "lead compound" that binds to the new target and have characterized the activity of the lead compound.  Several of the lead compounds exhibit exceptionally high promise, exhibiting potent activity against a broad spectrum of priority public-health bacterial pathogens and priority biodefense bacterial pathogens (including the pathogens responsible for tuberculosis, staph infections, strep infections, anthrax, and plague), and exhibiting no cross resistance with current antibiotics.

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Lee, Jeehiun Katherine

Project Description

Bioorganic and organic reactivity is examined using analytical methods, including computational chemistry and mass spectrometry.  Specific projects include the study of damaged DNA, carbene reactivity, and catalysis.

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Baum, Jean

Project Description

The student will work on characterizing the mechanism of aggregation of proteins that are involved in neurodegenerative disease.  One protein that will be studied is a-synuclein, the primary protein component found in Parkinson’s disease.  Methods of characterization include fluorescence, NMR and Transmission Electron Microscopy.  Students will be exposed to methods in molecular biology and will learn how to purify and express the proteins.

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Khare, Sagar D.

Project Description

Starting September 2012, projects will focus on the computational design of novel enzymes and small molecule binding proteins. Through billions of years of evolution, nature has come up with enzyme catalysts with exquisitely high and finely tuned efficiencies and selectivities. We will design new catalysts for natural and non-natural (not catalyzed by existing enzymes) reactions by mimicking the process of biological evolution on the computer and in the laboratory. Some questions that projects will attempt to answer are:

  1. How do new enzymatic activities arise from existing ones? Can we design an enzyme activity not found in nature into an existing enzyme?
  2. How do natural proteins signal that they have bound a small molecule ligand? Can we design molecular on-off switches?

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York, Darrin M.

Project Description

Molecules of RNA have recently come into the spotlight, due to recent discoveries of the breadth of their biological roles that range from acting as a messenger of the genetic code, to performing important regulatory functions and acting as a catalyst for complex chemical transformations, including peptide synthesis.  My group develops and applies theoretical and computational methods to study the structure, dynamics and mechanisms of RNA molecules in order to understand their fundamental biophysical properties.  These properties allow us to build up a basic understanding of the biological function of RNA molecules, and gain new insight that may guide the design of future biotechnology.  In particular, my group performs quantum chemical calculations and high-level molecular dynamics simulations whereby the molecules are able to change conformations, interact with other molecules and even react, in a realistic solvated environment, like that encountered in a laboratory, or even in a cell.  These simulations are validated against experiments, such as X-ray crystallography, NMR spectroscopy, kinetic isotope measurements and other experiments performed by our collaborators.  Ultimately, the detail afforded by computer simulations provide a wealth of atomic-level detail that cannot be observed directly by any experiment.

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Lee, Ki-Bum

Project Description

The primary research interest of our group is to develop nanomaterial-based approaches to control and modulate cellular behaviors of stem cells and cancer cells. In particular, we are interested in studying the function of microenvironmental cues (e.g. soluble signals, cell-cell interactions, and insoluble/physical signals) towards stem cell and cancer cell fate. For example, our work involves both approaches from nanotechnology, the “top-down” pattering of extracellular matrix (ECM) and signal molecules in combinatorial ways (e.g. ECM compositions, pattern  geometry, pattern density, and gradient patterns), and the “bottom-up” synthesis of multifunctional nanoparticles and their modification with specific signal molecules-should for investigating complex cellular behaviors. Collectively, our research projects are directly relevant to matters concerning biomaterials, nanomedicine, chemical biology and stem/cancer cell biology.

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Olson, Wilma K.

Project Description

All of the processes necessary for the survival of a living system hinge on its ability to store and read the genetic information encoded in its DNA. The packaging of the long human genome into the very small confines of the nucleus is complicated by the necessity of maintaining the accessibility of the DNA for genetic processing. The Olson group is establishing new chemistry- and physics-based computational methodologies to unravel the mystery of how genomes can at once be tightly packed and yet available for read-out. Aside from the fundamental importance to an understanding of biology, knowledge of the interplay between local and large-scale biomolecular structure and genetic function could transform life-science technologies. That is, if certain environmental pressures perturb genomic structure and switch genes on or off, then perhaps one might be able to engineer such changes in an organism and correct diseased states or optimize production of desired products.

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Marcotrigiano, Joseph

Project Description

Hepatitis C virus (HCV) represents a major public health problem, infecting an estimated 2% of the world’s population (approximately 123-170 million people). In fact, there are 3 to 4 times more individuals chronically infected with HCV than HIV. In most cases, HCV infection becomes chronic and can persist for decades, leading to cirrhosis, end-stage liver disease, and hepatocellular carcinoma. There is no vaccine against HCV and the current approved treatments has limited efficacy on the many HCV genotypes. HCV is an enveloped virus with two glycoproteins (E1 and E2) that form the outer shell of the virus particle. As in the case of other enveloped viruses, HCV infection requires fusion between viral and host cell membrane before the viral genome can be released into the host cell cytosol. This critical step is thought to occur in the endosomal compartment, is triggered by low pH, and likely requires structural rearrangement of the glycoproteins. In addition to its role in membrane fusion, E2 is essential for cell targeting by recognition of host cellular receptors and for immune evasion. Our laboratory is focused on studying the structure and function HCV E1 and E2, in the hopes of developing 1) a better understanding of how HCV enters a host cell, 2) small molecule inhibitors, and 3) a protective HCV vaccine to stop spread of the virus.

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Herzog, Greg

Project Description

Measuring how long it takes meteorites to come to Earth from asteroids.

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Case, David

Project Description

Our group carries out molecular dynamics simulations of proteins and nucleic acids, and helps to develop the Amber suite of computer codes that facilitates such investigations.  One feature of computer work is that it is relatively easy to start projects in various areas, and we have group members looking at collagen (a connective tissue protein, in a collaboration with Prof. Jean Baum), at small peptide crystals, at RNA enzymes (in a collaboration with Prof. Darrin York), and at computational drug design, targeted at the SARS virus and other pathogens.

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Warmuth, Ralf

Project Description

Research in the Warmuth group involves the multi-component assembly of molecular containers and nanocapsules using Schiff base chemistry and the application of these capsules in molecular recognition, catalysis, as nanoreactors and for drug delivery. A possible undergraduate student project would involve the synthesis of suitable building blocks and the optimization of reaction conditions for their assembly into molecular capsules. As part of this, the student will get insight into the design of multi-step synthesis of small organic molecules and learn diverse laboratory techniques that are common to synthesis, isolation, purification and characterization of small and medium-sized organic molecules. The student will also get hands-on experience in the recording and interpretation of NMR and mass spectra, and in analytical techniques such as HPLC and gel permeation chromatography. Undergraduate students will be supervised by graduate students in the Warmuth group and are expected to work more and more independently as their project progresses.

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Asefa, Tewodros (Teddy)

Project Description

The research programs for undergraduate students in Asefa lab are intended to teach and train the students with various research topics and concepts on fundamental and applied chemistry and materials science. Furthermore, projects in Asefa lab are designed to enable undergraduate students obtain research experience related to nanomaterials, nanoscience, nanotechnology and nanobiotechnology. Specific applications of interest of the works they do include developing novel nanocatalysts for transformation of raw materials and fine chemicals into synthetic materials and pharmaceuticals as efficiently as possible; novel nanomedicines for cancer treatment and diagnostics; and nanomaterials for solar cells. The following two projects for undergraduates are currently undergoing:

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Garfunkel, Eric L.

Project Description

Nanoscience, thin films and surfaces, whatever….

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Williams, Lawrence J.

Project Description

The mission of our laboratory is to advance new methods and strategies of chemical synthesis and bring them to bear on issues of human health. Our research aims to understand the relation between molecular structure and reactivity and how these relate to the functional properties of compounds and materials. Specific projects range from the application of computational methods for understanding structure and reactivity to new reaction development, motif building, the synthesis of natural products and natural product congeners, and collaborative studies in the areas of chemical biology, antimicrobial agents, cancer biology, and materials science.

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Romsted, Laurence S.

Background and Projects

    Our research probes the non-covalent intermolecular interactions that control the self-assembly of surfactant molecules (also known as soaps, detergents, and in biology, phospholipids) in solution.  Surfactants spontaneously assemble into micelles and form a variety of aggregate structures such as spherical and rod-like micelles, lamellar and cubic mesophases, and reverse micelles in oil/water mixtures. The results from our research program are leading to new models for the balance of forces controlling aggregate self-assembly, antioxidant distributions in emulsions and someday perhaps, protein organization in membranes. Surfactant solutions wash your dishes, clean your clothes, and some assemble into vesicles that organize cell function. The forces responsible for self-assembly are the same ones that drive protein coiling and the formation of biological membranes. The forces controlling these interactions are weak, on the order of the strengths of hydrogen bonds or less, and include hydration, polarization, Van der Waals, electrostatic and ion specific interactions. The contributions of each to the balance of forces controlling self-assembly are still not understood.
    Our primary research tool for investigating the properties of self-assembled surfactant aggregates is a chemical trapping reaction using a hydrophobic arenediazonium ion probe that associates very strongly with surfactant aggregates and is chemically trapped by water, alcohols, urea and peptide bonds, halide ions and other weakly basic nucleophiles.  This reaction provides estimates of the molarities of water, counterions, and other weakly nucleophile molecules in the interfacial regions and provides new insight into changing interfacial concentrations with changing aggregate structures, for example, the transition for spherical to rod-like micelles. We also use, UV/VIS, NMR, light scattering, chemical kinetics to probe the aggregates, and periodically synthesize new molecules.

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Knapp, Spencer

Project Description

Organic synthesis:

  • Total synthesis of natural products
  • New synthetic methods
  • New drug delivery systems
  • New anti-malarials
  • Enzyme inhibitors, models, and mechanism

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Goldman, Alan

Project Description

Organometallic chemistry: Synthetic, mechanistic and/or computational.

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Castner, Jr., Edward W.

Project Description

Physical and chemical properties of ionic liquids:  novel materials for energy-related applications.

Our projects combine several aspects of modern chemistry that include several physical measurements, occasional chemical synthesis, computational and theoretical chemistry.

We use ultrafast time-resolved laser spectroscopy to initiate and probe photo-induced electron-transfer reactions in ionic liquids, to understand how the unique chemical and physical environment of these molten salts affect the outcomes of the simplest chemical reactions, and those that we must use to capture sunlight for renewable electrical and chemical energy supplies.  We also apply several advanced NMR methods to measure the self-diffusion coefficient of the cations and anions comprising these liquids.  This information is crucial for more efficient design of both next-generation batteries and ultra-capacitors, where the ionic liquids serve as the electrolytes.  The other major research approach involves using x-rays from the national synchrotron light sources such as those at Argonne and Brookhaven National Labs.  We do a variety of x-ray scattering, diffraction and spectroscopy experiments there, which provides information about the intermediate-range order present in many of the ionic liquids.  Chemical synthesis is required either to generate a novel ionic liquid to test a new hypothesis, or to provide an ultra-pure sample for the laser spectroscopy experiments.

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Dismukes, Charles

Project Description

  1. Solar energy conversion and chemical catalysis for renewable energy applications
  2. Microbial biology for bioenergy and biofuel applications

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Hinch, Jane

Project Description

To simulate ion trajectories in a new mass spectrometer design, (a Rutgers invention).  The objective is to understand the experimental factors that govern the sensitivity and resolution of various prototypical mass specs.  An investigation of initial ion trajectory phase space is to determine the next generation of devices.  Construction and testing of the new instruments is to follow.  Commercial interest in design improvements and optimization of an intrinsically simple trap design adds impetus to this project.  The future extension to inexpensive mass spec design drives towards university and even high school teaching projects.

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Brennan, John

Project Background

The actinide and lanthanide elements form numerous complexes with organic compounds. Presently, the CSD contains approximately 3,000 actinide and 20,000 lanthanide structures. This represents a wealth of information that could enhance our understanding of their chemistry. The project will involve analyzing their crystal structure data for correlations and trends.

An understanding of these complexes will enable the design of better molecules that can make nuclear reprocessing safer [1], to help us recycle rare earth metals [2] and to clean up contaminated waste sites. Such work will have implications for the nation’s security, safety and energy independence.

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O’Carroll, Deirdre

Project Description

Conventional lasers are limited in how small they can be made because the feedback component for photons in a laser, the optical resonator, must be at least half the size of the wavelength of the laser light. Photons cannot be confined to areas with dimensions much smaller than half their wavelength, or about 250 nanometers, thus limiting the extent to which optical devices can be integrated in complex circuitry. Miniaturization of lasers lies in the use of resonating noble metal particles which can support surface plasmon excitations. Surface plasmons can be confined in significantly smaller spaces than photons and can be converted into conventional light waves. When combined with gain-materials such as polyfluorene conjugated polymers or quantum dots, surface plasmons can be amplified, creating of a sub-wavelength scale device that produces intense, coherent emission of light. The term coined for this device is “SPASER” (surface plasmon amplification by stimulated emission of radiation). It is the SPASER that many photonics experts assert is the key component that will usher in the age of nanophotonics, and would facilitate dramatic increases in computing speeds (in the Terahertz regime) through the development of on-chip lasers and all-optical data processing. These innovations will simultaneously increase computing and energy efficiency. This project will address the design, synthesis and characterization of sub-wavelength light amplification devices consisting of silver nanoparticles and a variety of high-optical-gain materials.

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Greenblatt, Martha

Project Description

Synthesis and characterization of new inorganic transition metal oxides with interesting and useful electronic and magnetic properties.

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Li, Jing

Project Description

Synthesis characterization of new materials for energy related applications.

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Jimenez, Leslie

Project Description

The synthesis of 2,8-dihydroxyadenine in three steps from 4,6-diamino-2-mercaptopyrimidine.

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