Submission Number: 77
Submission ID: 109
Submission UUID: 27112b5f-952f-4a65-94f5-3dd997b497d2
Submission URI: /form/project

Created: Wed, 11/11/2020 - 15:44
Completed: Wed, 11/11/2020 - 15:49
Changed: Tue, 08/02/2022 - 15:05

Remote IP address: 165.230.224.167
Submitted by: Galen Collier
Language: English

Is draft: No
Webform: Project
Electrostatics of the GABA(A) receptor pore
CAREERS
eprotein.jpg
bash (242), molecular-dynamics (288), namd (290), programming (5), programming-best-practices (49), scripting (243), slurm (71)
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Project Leader

Grace Brannigan
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Project Personnel

Galen Collier
Jesse Sandberg
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Project Information

The coronavirus E protein is an ion channel in the membrane envelope that is important for maintaining viral shape as well as conducting ions. We aim to run coarse-grained and atomistic molecular dynamics simulation of E proteins, in order to test two distinct hypotheses for how the protein shapes the membrane. The student would both run simulations using open-source, highly developed existing packages, and write their own analysis and signal processing code.

Project Information Subsection

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Grad or undergrad
Interested in structural biology research
Experienced Linux or Unix user
Comfortable working in a remote Linux environment (HPC cluster)
Some experience with Python programming
Structural modeling experience (understanding general concepts) will be helpful
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Some hands-on experience
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Rutgers University–Camden
303 Cooper St
Camden, New Jersey. 08102
CR-Rutgers
11/01/2020
No
Already behind3Start date is flexible
6
02/10/2021
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11/19/2021
  • Milestone Title: Run simulations
    Milestone Description: Run coarse-grained simulations of the E protein in 8 different lipid bilayers
    Completion Date Goal: 2021-02-10
    Actual Completion Date: 2021-02-10
  • Milestone Title: Analyze results for deformations
    Milestone Description: Analyze elastic deformations of membranes for different systems
    Completion Date Goal: 2021-03-10
    Actual Completion Date: 2021-03-10
  • Milestone Title: Analyze results for lipid sorting
    Milestone Description: Analyze lipid sorting in each bilayer
    Completion Date Goal: 2021-04-14
    Actual Completion Date: 2021-04-14
  • Milestone Title: Run follow-up sorting simulations
    Milestone Description: Based on results from milestones 1-3, run additional simulations to test role of lipid chains vs headgroups in sorting
    Completion Date Goal: 2021-05-12
  • Milestone Title: Run general interactions simulations
    Milestone Description: Run atomistic simulations to confirm potential interactions are stable
    Completion Date Goal: 2021-06-09
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One publication on the role of hydrophobic mismatch in driving the effect of E proteins on membrane shape.
The student will learn how to run coarse-grained and atomistic simulations, analyze simulations using VMD and python, and the underlying elastic theory for the proposed mechanism.
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Effort involved in recruiting and training junior-level research software engineers.
We will apply for time on the State of New Jersey's "Caliburn" system at Rutgers University
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Final Report

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