Projects

Computational Study of the Serotonin Transporter (SERT) and other Central Nervous System (CNS) Targets

Computational Study of the Serotonin Transporter (SERT) and other Central Nervous System (CNS) Targets

An area of interest in the lab is CNS disorders such as depression. One of the primary targets of treating depression is the serotonin transporter, which is responsible for the reuptake of serotonin into the cell from the synaptic cleft. There are no known crystal structures for this protein at this moment. The lab’s focus […]

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Computational Drug Design

Computational Drug Design

Fragment based drug design has become a cost and time efficient means to screen for lead compounds in drug discovery. By computationally simulating binding, affinities of ligands to the receptor can be calculated and used as a springboard to further develop novel, high affinity compounds. Our group utilizes the published Dopamine D3 receptor crystal structure […]

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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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Computational Materials Science

Computational Materials Science

One avenue of our research is focused on computational materials science. Here, we use several plane-wave algorithms to elucidate the electronic structure of various extended solids. Ultimately, in studying a materials electronic structure, we can gain valuable insight to optical and thermoelectric properties. Utilizing density functional theory (DFT) and the linearized-augmented plane-wave (LAPW) method in […]

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Investigation of Polyglutamine (PolyQ) Peptides via Molecular Dynamics Simulations

Investigation of Polyglutamine (PolyQ) Peptides via Molecular Dynamics Simulations

We use molecular dynamics simulations to investigate the properties of polyglutamine (polyQ) peptides. PolyQ peptides aggregate in neurons to form fibrils, which are thought to be major contributors towards the symptoms of Huntingtons disease.We seek to understand the underlying causes of polyQ aggregation through identifying their conformational ensemble, which we achieve by exploring the polyQ […]

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Free Energy Calculations of Serotonin Transporters (SERT)

Free Energy Calculations of Serotonin Transporters (SERT)

The serotonin transporter (SERT) exists as the primary target for treating depression. We are conducting free energy calculations to find potential inhibitors of SERT. Absolute binding free energy calculations will accurately calculate the binding energy of protein-ligand complexes. Compounds that result in favorable free energy calculations are synthesized and experimental binding assays are performed to […]

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Molecular Dynamics Simulations of solvated poly(n-isopropylacrylamide) (PNIPAM)

Molecular Dynamics Simulations of solvated poly(n-isopropylacrylamide) (PNIPAM)

We are using molecular dynamics simulations to model the conformational changes of solvated poly(n-isopropylacrylamide) (PNIPAM) at temperatures above the lower critical solution temperature (LCST). We are interested in determining how the side chains interact with the surrounding water. Madeline Galbraith, Undergraduate Student

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Conformational Change and Transport of the Monoamine Transporters

Conformational Change and Transport of the Monoamine Transporters

Depleted neurotransmitter concentration in the synaptic cleft can lead to a variety of psychological diseases, notably depression, anxiety, and addiction. Neurotransmitter sodium symporter proteins are responsible for reuptake of neurotransmitters to the presynaptic neuron. Understanding transport mechanisms and conformations of these proteins can help in the development of drugs to combat these diseases. Our work […]

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