Submission information
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
| Project Title | Electrostatics of the GABA(A) receptor pore |
|---|---|
| Program | CAREERS |
| Project Image |
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| Tags | bash (242), molecular-dynamics (288), namd (290), programming (5), programming-best-practices (49), scripting (243), slurm (71) |
| Status | Complete |
| Project Leader | Grace Brannigan |
| grace.brannigan@rutgers.edu | |
| Mobile Phone | |
| Work Phone | |
| Mentor(s) | Galen Collier |
| Student-facilitator(s) | Jesse Sandberg |
| Mentee(s) | |
| Project Description | 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 Deliverables | |
| Project Deliverables | |
| Student Research Computing Facilitator Profile | 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 |
| Mentee Research Computing Profile | |
| Student Facilitator Programming Skill Level | Some hands-on experience |
| Mentee Programming Skill Level | |
| Project Institution | Rutgers University–Camden |
| Project Address | 303 Cooper St Camden, New Jersey. 08102 |
| Anchor Institution | CR-Rutgers |
| Preferred Start Date | 11/01/2020 |
| Start as soon as possible. | No |
| Project Urgency | Already behind3Start date is flexible |
| Expected Project Duration (in months) | 6 |
| Launch Presentation | |
| Launch Presentation Date | 02/10/2021 |
| Wrap Presentation | |
| Wrap Presentation Date | 11/19/2021 |
| Project Milestones |
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| Github Contributions | |
| Planned Portal Contributions (if any) | |
| Planned Publications (if any) | One publication on the role of hydrophobic mismatch in driving the effect of E proteins on membrane shape. |
| What will the student learn? | 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. |
| What will the mentee learn? | |
| What will the Cyberteam program learn from this project? | Effort involved in recruiting and training junior-level research software engineers. |
| HPC resources needed to complete this project? | We will apply for time on the State of New Jersey's "Caliburn" system at Rutgers University |
| Notes | |
| What is the impact on the development of the principal discipline(s) of the project? | |
| What is the impact on other disciplines? | |
| Is there an impact physical resources that form infrastructure? | |
| Is there an impact on the development of human resources for research computing? | |
| Is there an impact on institutional resources that form infrastructure? | |
| Is there an impact on information resources that form infrastructure? | |
| Is there an impact on technology transfer? | |
| Is there an impact on society beyond science and technology? | |
| Lessons Learned | |
| Overall results |