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Examining the structure of proteins that contribute to neurodegenerative diseases

The toll that neurodegenerative diseases can take on patients and their loved ones can be daunting. Our uncertainty about what causes such diseases creates uncertainty about how to treat them, but researchers have been working to change this by studying the biochemistry of the brain and learning more about the delicate interplay of neurons and chemical signals that give life to the mind.

One major research focus concern show the brain’s biochemistry is affected by the mutation of proteins associated with neuron growth and intracellular signaling. Here at Rutgers, our research group is investigating why certain gene mutations are tied to aging, stress-related disorders and lower tolerance for drugs.

Molecular dynamics simulations are an indispensable tool for understanding how mutations affect the structure and dynamics of proteins. Since large proteins are modeled atom by atom and require long simulation times, their dynamical behavior must be followed using a large number of computer cores. Such hardware is necessary to run the computational experiments efficiently and get meaningful results.

Role of Caliburn

Caliburn’s nodes, which each contain 18 cores, are perfectly suited for providing parallelism. With partitions that allow numerous simultaneous node usages, researchers can run single massively parallel simulations as well as ensemble workflows.

principal investigator

Principal Investigator:
Grace Brannigan – View her personal lab page.
Student: Ruchi Lohia, PhD Candidate
Institution: Rutgers University–Camden, Center for Computational and Integrative Biology and Department of Physics