Submission information
Submission Number: 23
Submission ID: 40
Submission UUID: 0287b732-8e95-426e-afe8-d094b74639d1
Submission URI: /form/project
Created: Tue, 09/03/2019 - 13:46
Completed: Tue, 09/03/2019 - 13:48
Changed: Mon, 10/21/2024 - 18:57
Remote IP address: 130.215.55.243
Submitted by: Juan Vanegas
Language: English
Is draft: No
Webform: Project
| Project Title | Understanding Mechanical Properties of Bio-interfaces with HPC Molecular Simulations |
|---|---|
| Program | Northeast |
| Project Leader | Juan Vanegas |
| jvanegas@uvm.edu | |
| Mobile Phone | 5415805322 |
| Work Phone | 8026560049 |
| Mentor(s) | |
| Student-facilitator(s) | Ali Razavi |
| Mentee(s) | |
| Project Description | Molecular simulations are emerging as a new form of “microscopy” that can uniquely probe the behavior of biomolecules and interfacial systems such as biomembranes at the nanometer scale. High resolution techniques such as classical and first principles molecular dynamics (MD) can be used to understand the connection between molecular structure, biological function, and mechanical properties of biomaterials. In this project, students will use high performance MD simulation engines such as GROMACS (www.gromacs.org) to model biological interfaces and use custom local stress codes to characterize the mechanical properties of these systems. |
| Project Deliverables | 1. Ali will use UVM's VACC HPC cluster "DeepGreen" with the simulation engine such GROMACS (www.gromacs.org) to model biological interfaces. 2. After Ali learns to use the cluster and software he will custom local stress codes to characterize the mechanical properties of these systems. |
| Project Deliverables | |
| Student Research Computing Facilitator Profile | Students with backgrounds in biology and/or physics, and basic experience with linux/unix systems. |
| Mentee Research Computing Profile | |
| Student Facilitator Programming Skill Level | |
| Mentee Programming Skill Level | |
| Project Institution | University of Vermont |
| Project Address | 82 University Place Discovery Bldg W428 Burlington, Vermont. 05408 |
| Anchor Institution | NE-University of Vermont |
| Preferred Start Date | 04/10/2019 |
| Start as soon as possible. | No |
| Project Urgency | Already behind3Start date is flexible |
| Expected Project Duration (in months) | |
| Launch Presentation | |
| Launch Presentation Date | |
| Wrap Presentation | |
| Wrap Presentation Date | |
| Project Milestones |
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| Github Contributions | |
| Planned Portal Contributions (if any) | |
| Planned Publications (if any) | |
| What will the student learn? | In this project students will learn how to set up molecular dynamics simulations, create batch scripts to submit jobs to an HPC scheduler, use analysis tools to characterize MD trajectories, and visualize results. |
| What will the mentee learn? | |
| What will the Cyberteam program learn from this project? | |
| HPC resources needed to complete this project? | HPC facilities at the Vermont Advanced Computing Core and the Vanegas CPU/GPU Cluster |
| Notes | |
| What is the impact on the development of the principal discipline(s) of the project? | By using coarse-grained simulations rather than the more computationally expensive atomistic models, we were able to explore a much larger configurational space over a broader range of time-scales. The coarse-grained model we employed can run 1 microsecond of simulation time in a single gpu-accelerated node in roughly 1 day, while the equivalent atomistic system would require about 3 weeks to run on the same hardware. Although less chemically accurate, the coarse-grained model allowed us to rapidly explore a range of membrane/protein configurations under constant volume and simulation. Now that we have a better overall physical picture of the behavior of the system, we can run more accurately atomistic simulations in special regions of interest. |
| 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? | The tutorials created during the course of this project will allow new students interested in molecular dynamics simulations to more quickly setup systems of interest to study biological systems. |
| 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? | Understanding the interactions between proteins and lung surfactant at the molecular level could help develop new treatments to help patients with respiratory issues related the development and maintenance of lung surfactant monolayer. |
| Lessons Learned | |
| Overall results | The student research computing facilitator generated a set of coarse-grained molecular dynamics simulations to study the interactions between lipid monolayers that mimic lung surfactants and one of the surfactant proteins (SP-C) found in the lungs. The various simulations included different concentrations of protein to understand how SP-C affects the surface tension of the monolayer and its role during the expansion and collapse of the surfactant layer during breathing. In addition to the simulations, he also developed a set of basic simulation tutorials to help new students learn how to setup and run basic coarse-grained simulations using the GROMACS package. The tutorials are publicly available on the web at: https://github.com/vanegasj/MDTutorials . |