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Position TitleAmyloid formation in the presence of lipds
SummaryConsiderable evidence points to a role for membrane-associated production and propagation of oligomers in the progression of Alzheimer’s disease. An example for such lipid-catalyzed oligomers are the Large Fatty Acid-derived Aβ Oligomers (LFAOs) studied in the Lab of our collaborator Vijay Rangachari (University of Southern Missisippi). However, neither the structure of LFAOs nor their mechanism of propagation is known in detail. Deriving both, and modeling their dependence on sequence and interfacial environment, will help us to understand the mechanism by which amyloid strains become predominant in patient brains.
Job DescriptionGuided by experimental data from the Rangachari Lab, the student will use a new technique (replica-exchange with tunneling), developed in our lab to enhance sampling of amyloid simulations, to determine the ensemble of LFAO structures and their structure-dependent propagation as function of sequence and environmental conditions.
Use of Blue WatersSimulations of an in-home extension of Gromacs that implements a variant of replica-exchange molecular dynamics developed in our Lab. We are considering to migrate to NAMD, but for the first half the student will have to use present code. Some simulations will be also done on our local resources, the SCHOONER cluster at OU.
Conditions/QualificationsMust be an Undergraduate at OU, must have programming experience
Start Date05/31/2018
End Date05/31/2019
LocationDepartment of Chemistry and Biochemistry
Elliott Vanderford