NCSI: Dynamics of Gap Junction Intercellular Communication Channels

Status	Completed
Mentor Name	Steve Reichow
Mentor's XSEDE Affiliation	Research Allocation
Mentor Has Been in XSEDE Community	1-2 years
Project Title	Dynamics of Gap Junction Intercellular Communication 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, enabling direct cell-to-cell communication of chemical signals. We aim to use GPU-accelerated MD simulations to understand the molecular principles underlying solute permeation and selectivity of these intercellular communication pathways.
Job Description	The student will perform all-atom equilibrium MD simulations using the GPU-enabled nanoscale molecular dynamics (NAMD) engine to simulate various gap junction intercellular channels, in the presence of physiological substrates, to understand how specific chemical messages are discriminated. The student will use the scripting language TK/Tcl, along with the program visual molecular dynamics (VMD) to prepare gap junction simulation systems. The student will also be expected to write analytical scripts in Tcl, Python, and BASH to extract pertinent data from the simulation trajectories, and analyze the data using standard scientific libraries such as numpy, pandas, and matplotlib. Student is expected to conduct simulations and analysis with supplemental supervision Required Languages (Intermediate-advanced):  Python  TK/Tcl  BASH
Computational Resources	This work will build off of simulations done under our start-up XSEDE allocation (Dynamic Mechanisms of Membrane Channel Gating), which provided access 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. A new XSEDE resource allocation is under preparation and will be submitted for the Spring deadline (Dec-13). The student will also have access to PSU's COEUS CPU-cluster, OHSU's Exacloud GPU/CPU-cluster, and local GPU-workstations for simulation and data analysis.
Contribution to Community
Position Type	Intern
Training Plan	Training: o Student will be trained on advanced molecular dynamics techniques, theories and analytical methods; such as: Markov-State Models, enhanced-sampling algorithms, free-energy calculations. o Student will be trained to manipulate biological macromolecules, and render professional images with VMD o Student will receive training in dissemination of results (oral and written), and exposed to other professional development activities (e.g., presentations at conferences/symposia) as appropriate
Student Prerequisites/Conditions/Qualifications
Duration	Quarter
Start Date	01/15/2020
End Date	03/15/2020