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Project TitleMolecular Modeling of Amyloid Aggregation
SummaryThe self-assembly of amyloidogenic peptides into cytotoxic oligomers and amyloid fibrils is associated with several progressive diseases including Alzheimer’s disease (AD) and type II diabetes (T2D). The details of this self-assembly and the effects of these oligomers, especially low molecular weight oligomers (dimers to dodecamers), on plasma membranes is largely unknown. By investigating the molecular details and interactions associated with oligomer assembly and the interactions of the oligomers with membranes, we can provide insight into mechanistic details relevant to toxicity. This project investigates the formation of low-molecular weight oligomers in a range of sizes to determine key size and environmental influences on the fibril formation and perturbation of model membranes by the oligomers.
Job DescriptionThe intern will be engaged in the entire research process. The intern will build the systems needed to address the research questions of this project, run the simulations on Blue Waters, and perform the analysis of the simulation data. The intern will make connections between results and the literature and write up the results in a scientifically appropriate way. These tasks all fall in line with the undergraduate research project that the mentor has developed and published in Biochemistry and Molecular Biology Education. Training in scientific writing, presentation, and collaboration will be provided, along with mentorship on both research and career goals. As appropriate, the intern will be exposed to workshops on software usage on supercomputing and scripting.
Use of Blue WatersMolecular dynamics simulations are often limited in their scope by the size of the system and the amount of real time required to run simulations that are sufficiently long to address interesting questions. The power of Blue Waters will enable us to build more complex systems and use existing or updated sampling techniques to examine interactions relevant to amyloid self-assembly and the effect of the oligomers on membranes. The dedicated time that the intern will receive on Blue Waters will greatly enhance the feasibility of performing simulations of these complex systems.
Conditions/QualificationsMust be an undergraduate at Virginia Tech
Start Date05/15/2017
End Date05/15/2018
LocationBevan/Brown Research Lab, Department of Biochemistry, Virginia Tech, Blacksburg, VA
David Barto