NCSI: Dynamic Mechanisms of Membrane Channel Gating

Status	Completed
Mentor Name	Steve Reichow
Mentor's XSEDE Affiliation	Research Allocation
Mentor Has Been in XSEDE Community	Less than 1 year
Project Title	Dynamic Mechanisms of Membrane Channel Gating
Summary	The Reichow Lab uses cryo-electron microscopy (CryoEM) and molecular dynamics (MD) simulations to understand the fundamental relationship between structure, dynamics and function in complex biomolecular systems. We are keenly interested in understanding how cell-to-cell communication is facilitated and dynamically regulated by a class of intercellular membrane channels, known as gap junctions. We aim to apply GPU-accelerated MD simulations using XSEDE resources to understand the molecular function of these intercellular channels.
Job Description	The student will use the scripting language TK/Tcl, along with the program visual molecular dynamics (VMD) to prepare MD simulation systems. They will perform all-atom equilibrium and non-equilibrium MD simulations using the GPU-enabled nanoscale molecular dynamics (NAMD) engine to simulate the permeation of biologically relevant solutes through gap junction intercellular channels. The student will be expected to write analytical scripts in Tcl, BASH, and Python to extract pertinent data from the simulations, and analyze the data using standard scientific libraries such as numpy, pandas, and matplotlib. The student will present the results of their experiments at weekly meetings with the PI and at regular group meetings.
Computational Resources	Our lab has resource allocation to the GPU-nodes on SDSU-Comet and PSC-Bridges. Each node on Comet contains dual Xeon CPUs, with four Nvidia-P100 GPUs. Each node on PSC-Bridges contains dual Xeon CPUs, with two Nvidia-P100 GPUs. We have allocated storage on SDSU-Oasis, and PSC-Pylon. Additionally, student will have access to PSUÃ¢ÂÂs COEUS cluster, OHSUÃ¢ÂÂs Exacloud GPU-cluster, and local GPU/CPU-workstations for data analysis.
Contribution to Community
Position Type	Apprentice
Training Plan	o Background in biochemistry, molecular biology, or biophysics o Computer languages (basic understanding): Python, TK/Tcl, BASH o Student must be familiar with basic command line tools. o Student will be trained to execute MD simulations with the NAMD software, and will be trained throughout the summer to perform equilibrium and non-equilibrium MD simulations on complex bio-molecular systems. o Student will be trained to manipulate protein structures, analyze MD trajectories and render professional images and movies with VMD for the purposes of disseminating results. o Student will present their results at weekly meetings with the PI, monthly group meetings and local conferences when appropriate/available.
Student Prerequisites/Conditions/Qualifications
Duration	Summer
Start Date	06/15/2019
End Date	08/23/2019