Past Projects

Research in our laboratory consists of the development and application of computational methods to diverse systems of interest. The research projects are interdisciplinary in nature, including subjects from organic chemistry, physical chemistry, analytical chemistry, inorganic chemistry and biochemistry. The group utilizes various computational tools such as Gaussian 98/03, GAMESS, CHARMM, AMBER, MOE, CAChe, UHBD, NAMD, and DL_POLY. Students in the group interact with faculty members within the Department as well as faculty from Pitt and PSC. Students also work with and visit scientists at IBM Almaden and the Pittsburgh National Energy Technology Laboratory.

CdS Project

CdS Project

Description: This project centers on the structure and electronic properties of encapsulated cadmium sulfide nanoparticles. Our interest is to understand the fundamental principles that lead to stable, functionalized quantum dots. The challenge of creating functionalized, robust quantum confined group II-VI semiconductor nanoclusters (NC’s) involves the ability to realize size-controlled and size-stable nanocrystallites. The objective is […]

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Oligosaccharide – Protein Interactions

Oligosaccharide – Protein Interactions

Description: A multi-disciplinary research project that is exploring sugar – protein interactions and is developing fundamental scientific discoveries and advances leading to a new understanding of biochemistry. This project is a collaborative project between a biochemistry group at the University of South Alabama and here. The computational component being undertaken at Duquesne along with some basic physical […]

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CO2 Sequestration in Brines and Coal

CO2 Sequestration in Brines and Coal

Description: The combustion of fossil fuels releases large amounts of carbon dioxide into the atmosphere, which is known to cause global warming. One idea to get rid of the excess CO2 is to use brine aquifers to sequester the gas by using mineral trapping in brine aquifers, where the CO2 is introduced into solution, converted […]

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Metals in Biology

Metals in Biology

Description: Recent studies have shown that cells use proteins called “metallochaperones” to perform the routing of metal ions to protect the cell and to ensure delivery to nascent enzymes. However, the mechanism of binding and relese of metals by these metallochaperones is not well understood. The largest protein of the copper chaperone family has a […]

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Nitrile Anion Structure and Reactivity

Nitrile Anion Structure and Reactivity

Description: The nitrile functional group is a small, under-utilized unit in organic synthesis. However, it has been demonstrated that this functional group can be used in the synthesis of complex organic compounds. In particular the stereochemistry of cis/trans decalin systems. Fundamental insight on how nitrile anions operate is not fully realized. Computational methods are being applied to study these […]

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Proteins at Ice/Water Interfaces

Proteins at Ice/Water Interfaces

Description: Antifreeze Proteins (AFPs) found in fish, plants and insects help the organisms to survive cold temperatures. Various applications of such molecules are in agricultural (grain preservation and transgenic plants), medicine (organ preservation and cryosurgery), aerospace (wing de-icers) and other industries. Goals: The goal of this project is to apply various computational techniques such as MM, […]

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Proteins and Inorganic Crystals at Lipid/Water Interfaces

Proteins and Inorganic Crystals at Lipid/Water Interfaces

Description: This project investigates a) the mechanism of inflammatory diseases such as arthritis and pseudogout and b) the mechanism of protection of lipid membrane by antifreeze proteins. Our interest is to understand the mechanism of interaction of different molecules with lipid membranes. Goals: The goals of this project are to apply computational techniques to determine the […]

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Melatonin Receptors

Melatonin Receptors

Description: This project involves creating structures of G-Protein Coupled Receptors (GPCRs) through a technique called “comparative modeling.” The GPCRs of interest are the melatonin receptors (MT1 and MT2), which belong to the rhodopsin family. Specific, highly conserved motifs of these models that contain key mutations are being analyzed in order to elucidate their function. Currently, there is collaboration […]

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HIV-RT Inhibitors

HIV-RT Inhibitors

Description: HIV-1 reverse transcriptase (RT) is an important target for drugs used in the treatment of AIDS. Drugs known as non-nucleoside RT inhibitors (NNRTI) appear to alter the structural and dynamical properties of RT which in turn inhibit RTs ability to transcribe. Molecular dynamics, principal component analysis and binding free energy simulations are employed to […]

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Methane Hydrates

Methane Hydrates

Description: Gas clathrates are viable energy resources. Methane stored in naturally occurring clathrates potentially hold enough methane to ensure supply for many years; methane clathrates are also known to cause blockage in the natural gas pipelines. Clathrates have also been discussed as possible storage sites in CO2 sequestration. Although these have been known about for […]

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