NCSI: Molecular Dynamics Simulations of Gap Junction Intercellular Channels

Status	Completed
Mentor Name	Steve Reichow
Mentor's XSEDE Affiliation	Research Allocation
Mentor Has Been in XSEDE Community	1-2 years
Project Title	Molecular Dynamics Simulations of Gap Junction Intercellular Channels
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. Gap junctions are large protein channels that span the membranes of two neighboring cells, connecting their cytosols. We aim to use GPU-accelerated MD simulations to understand the molecular requirements underlying solute permeation through these intercellular channels
Job Description	The student will perform all atom, equilibrium MD simulations of gap junctions and derived mutants associated with disease. The student will apply the scripting language TK/Tcl, along with the program visual molecular dynamics (VMD) to prepare gap junction simulation systems. They will then perform MD simulations using the nanoscale molecular dynamics (NAMD) engine, optimized for GPU-computing. The student will then be expected to write analytical scripts in Tcl, Python, and BASH to extract pertinent data from the simulations, and analyze the data using standard scientific libraries such as numpy, pandas, and matplotlib. This position requires a commitment of 10 weeks, 30h per week
Computational Resources	Our lab has access to the GPU-nodes on SDSU-Comet, and PSC-Bridges for benchmarking studies. 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. The student will have access to PSU's COEUS cluster, OHSU's Exacloud GPU/CPU-cluster, and local GPU-workstations for simulation and data analysis. This work will build off of simulations done under our start-up XSEDE allocation (Dynamic Mechanisms of Membrane Channel Gating). An XSEDE resource allocation is under preparation and planned to be submitted for the upcoming deadline (April 15, 2020).
Contribution to Community
Position Type	Intern
Training Plan	The training plan will include regular (daily) meetings with a lead graduate student to discuss research agenda and data analyis. In addition, the trainee will meet with the PI on a weekly basis to discuss on-going research and professional development plans. Furthermore, the trainee will gain experience in the dissemination of research through participation in weekly group meetings, and local and regional symposiums/conferences. Technical training: o Required Languages (Intermediate-advanced): o Python o TK/Tcl o BASH o Student is expected to conduct simulations and analysis with supplemental supervision o Student will be trained on advanced molecular dynamics techniques/theories such as: Markov-State Models, enhanced-sampling algorithms, free-energy calculations. o Student will be trained to manipulate molecules, and render professional images with VMD.
Student Prerequisites/Conditions/Qualifications	Responsible and respectful of a diverse working environment
Duration	Summer
Start Date	06/15/2020
End Date	08/23/2020