Research Projects
Asefa, Tewodros (Teddy) - Multifunctional Nanomaterials for Targeted Delivery of Anticancer Drugs & Synthesis of high-surface area multifunctional nanoporous materials for catalysis and photocatalysis
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:
Baum, Jean - Characterizing the Mechanism of Aggregation of Proteins that are Involved in Neurodegenerative Disease
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.
Brennan, John - Structural Informatics Application in Actinide/Rare Earth Chemistry
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.
Case, David - Molecular Dynamics Simulations of Proteins and Nucleic Acids
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.
Dismukes, Charles - Renewable Energy, Bioenergy and Biofuel Applications
Project Description
- Solar energy conversion and chemical catalysis for renewable energy applications
- Microbial biology for bioenergy and biofuel applications
Ebright, Richard - Bacterial RNA Polymerase
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 compound that binds to the new target and have characterized the activity of the compound. Several of the compounds exhibit high promise, exhibiting either potent anti-tuberculosis activity or potent broad spectrum antibacterial activity, and exhibiting no cross resistance with current anti-tuberculosis drugs and broad-spectrum antibacterial drugs.
Garfunkel, Eric L. - Nanoscience, Thin Films and Surfaces
Project Description
Nanoscience, thin films and surfaces, whatever….
Goldman, Alan - Organometallic chemistry: Synthetic, mechanistic and/or computational
Project Description
Organometallic chemistry: Synthetic, mechanistic and/or computational.
Greenblatt, Martha - Synthesis and Characterization of New Inorganic Transition Metal Oxides
Project Description
Synthesis and characterization of new inorganic transition metal oxides with interesting and useful electronic and magnetic properties.
Gu, Yuwei - Macromolecular Biomimicry
Project Description
It is difficult to imagine human society without polymers—from biomacromolecules that form the basics of life, to synthetic polymers that have revolutionized our daily life since their inception in the late 19th century. While biomacromolecules seem to possess a greater level of functional complexity compared to synthetic polymers, they share similar macromolecular features and their behaviors are thus governed by the same sets of rules in polymer physics.
Hinch, Jane - Simulate Ion Trajectories in a New Mass Spectrometer Design
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.
Jimenez, Leslie - Synthesis of 2,8-dihydroxyadenine in three steps from 4,6-diamino-2-mercaptopyrimidine
Project Description
The synthesis of 2,8-dihydroxyadenine in three steps from 4,6-diamino-2-mercaptopyrimidine.
Khare, Sagar D. - Computational Design of Novel Enzymes and Small Molecule Binding Proteins
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:
- How do new enzymatic activities arise from existing ones? Can we design an enzyme activity not found in nature into an existing enzyme?
- How do natural proteins signal that they have bound a small molecule ligand? Can we design molecular on-off switches?
Knapp, Spencer - Organic Synthesis and New Drug Delivery Systems
Project Description
Organic synthesis:
- Total synthesis of natural products
- New synthetic methods
- New drug delivery systems
- New anti-malaria and anti-inflammatory drug candidates
- Enzyme inhibitors, models, and mechanism
Lee, Jeehiun Katherine - Bioorganic and Organic Reactivity
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.
Lee, Ki-Bum - Develop Nanomaterial-based Approaches to Control and Modulate Cellular Behaviors of Stem and Cancer Cells
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.
Li, Jing - Synthesis Characterization of New Materials for Energy Related Applications
Project Description
Our research interests and activities are primarily in the development of solid-state inorganic and inorganic-organic hybrid materials that are both fundamentally and practically important. Our current work focuses mainly on the design, synthesis, characterization, functionalization, and optimization of two material families, namely metal-organic frameworks (MOFs) and inorganic-organic hybrid semiconductor materials. These materials are potentially useful for applications related to clean and renewable energies and environmental remediation, including but not limited to photovoltaics, solid-state lighting, gas storage, capture and separation and chemical sensing and imaging. Undergraduate students will participate in various aspects of the synthesis, structure characterization and property studies of these materials.
O’Carroll, Deirdre - Surface Plasmon Amplification using High-Gain Organic Semiconductors
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.
Olson, Wilma K. - Genetic Information Encoded in DNA
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.
Remsing, Richard
Background and Projects
Research in the Remsing group combines computer simulations with the development and application of physics-based theories to model a variety of molecular systems. Current areas of research includes modeling electronic properties of materials for energy applications, interfaces relevant to catalysis and environmental processes, astrobiology/prebiotic chemistry, and self-assembly processes in materials science and biomolecular systems. These research areas involve varying levels of quantum mechanics and thermodynamics, depending on the project. Students in the group learn computer programming to setup and analyze their simulations, and they learn how to carry out molecular simulations using supercomputers.
Shi, Zheng
Background and Projects
The Shi lab combines biophysical, photochemical, and optogenetic tools to study the properties of biomolecular assemblies such as cell membranes and biomolecular condensates. We aim to understand the mechanical behavior of cell membranes and how the mechanics of cell membranes interact with downstream biochemical signaling pathways. We also develop quantitative techniques and theoretical models to understand the material properties of biomolecular condensates that are associated with neurodegeneration.
Wang, Lu
Background and Projects
In the Wang lab, the undergraduate students will learn to use quantum chemistry calculations and molecular dynamics simulations to solve biologically relevant problems. For example, the students will use molecular dynamics simulation to study how enzymes work by examining the interactions between small molecules and enzymes and calculating the infrared spectra in the binding process. Using similar methods, the students will study how charge transfer processes enhance enzyme functions.
As we are a computational chemistry group, the undergraduate students will use a supercomputer server and pre-installed software packages to carry out the calculations and visualize the results. The analysis process often involves programming, so the students are encouraged to gain some programming experiences before jointing the group.
Warmuth, Ralf - Multi-Component Assembly of Molecular Containers and Nanocapsules
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.
Williams, Lawrence J. - New Methods and Strategies of Chemical Synthesis
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.
York, Darrin M. - Develop and Apply Theoretical and Computational Methods to Study the Structure, Dynamics and Mechanisms of RNA Molecules
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.
Zhang, Jason
Project Description
Precise structural control is critical for scientists to harness the optical, magnetic, chemical and biological properties of nanomaterials and nanomedicines. In nanoscience, precise bottom-up synthesis bridging the microscopic and macroscopic world is an ultimate goal. To this end, identifying precise building blocks and understanding how their functionalization are fundamental. Fullerenes and their close relatives, endohedral metallofullerenes (EMFs) reside at the boundary between inorganic and organic worlds, and between small-molecules and nanomaterials. They have defined molecular structures, and can be functionalized with robust C-C bonds. Our group focuses on the chemistry of these molecules, and the application of them as functional materials.
