NCSI: Multiscale Simulations of Membrane Proteins

Status	Completed
Mentor Name	Hai Lin
Mentor's XSEDE Affiliation	Research Allocation
Mentor Has Been in XSEDE Community	4-5 years
Project Title	Multiscale Simulations of Membrane Proteins
Summary	Membrane 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 Description	Student will construct models of membrane proteins, equilibrate the model system, 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 Resources	Comet
Contribution to Community
Position Type	Apprentice
Training Plan	A student new to the project 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/Qualifications	Students should have knowledge of quantum-chemistry calculations, are familiar with Linux operating system, and have Python or Fortran coding experiences.
Duration	Semester
Start Date	09/01/2020
End Date	11/21/2020