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Multiscale Dynamics Simulations of Membrane Proteins


Shodor > NCSI > XSEDE EMPOWER > XSEDE EMPOWER Positions > Multiscale Dynamics Simulations of Membrane Proteins

Status
Completed
Mentor NameHai Lin
Mentor's XSEDE AffiliationResearch Allocation
Mentor Has Been in XSEDE Community4-5 years
Project TitleMultiscale Dynamics Simulations of Membrane Proteins
SummaryMembrane proteins are attached to or associated with membranes, and they perform a wide range of functions from signal transduction to membrane fusion that are vital to cell growth, replication, and movement. Here, we develop and apply highly accurate and efficient methods for multiscale simulations of critical membrane proteins in order to gain insights into their acting mechanisms and underlying dynamics.
Job DescriptionStudent will construct models of membrane proteins, equilibrate the model systems, carry out combined QM/MM dynamics simulations, visualize the trajectories, and analyze the data. Computer programs to be used including NAMD, Gaussian, and our in-house codes. The students may need to write codes in Python or Fortran for specific tasks including for machine learning tasks.
Computational ResourcesComet
Contribution to Community
Position TypeApprentice
Training PlanThe student will be given an intensive 2-week training at the beginning of the project. The training will cover multiscale simulation algorithms, relevant programs including our in-house codes, how to use HPC, and backgrounds of the specific membrane proteins.
Student Prerequisites/Conditions/QualificationsStudents should be familiar with Linux operating system, and have Python or Fortran coding experiences.
DurationSummer
Start Date05/25/2020
End Date07/31/2020

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