Investigating Protein Folding using Knapsack Minimization Algorithms on High Performance Computers and Quantum Computers

Project Title: Investigating Protein Folding using Knapsack Minimization Algorithms on High Performance Computers and Quantum Computers
Program:
CAREERS (323)

Project Image: https://support.access-ci.org/system/files/webform/project/200/A-B-C.jpg
Tags:
ai (271), benchmarking (400), bioinformatics (277), biology (515), computational-chemistry (81), deep-learning (303), hpc-arch-and-perf (467), jupyterhub (214), machine-learning (272), optimization (509), proposal-development (341), python (69), quantum-mechanics (281), scikit-learn (273), singularity (23)

Status: Halted
Project Leader
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Project Leader:
Avery Leider

Email: al43110n@pace.edu
Mobile Phone: 917-991-5235
Work Phone: 917-991-5235

Project Personnel
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Mentor(s):
Avery Leider (652)

Student-facilitator(s):
Gio Abou Jaoude (612), MLDL Vermont (1378), Siddh Agarwal (653)

Mentee(s):
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Project Information
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Project Description:
Investigating Protein Folding using Knapsack Minimization Algorithms on High Performance Computers and Quantum Computers.  Protein folding and unfolding in nature appears to use the forward thinking greedy algorithm of Knapsack Minimization.  Understanding this and then enhancing it with sorting can help us find new medicines swiftly, instead of the incremental approach that is currently the method for the pharmaceutical sciences, such as bioinformatics and biotechnology.  We seek to understand how to use our current bioinformatics tools on the AiMOS high performance computer (HPC) and the Q-Experience quantum computers of IBM available to researchers.

Project Information Subsection
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Project Deliverables:
Write code in Python and post it in Google Colab to share and collaborate.  Use greedy algorithm template for code.  Check on 

Project Deliverables:
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Student Research Computing Facilitator Profile:
Seeking biological informatics and quantum computing curious.

Mentee Research Computing Profile:
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Student Facilitator Programming Skill Level: Can work with any level
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Project Institution: Pace University
Project Address:
861 Bedford Rd
Pleasantville, New York. 10570

Anchor Institution: CR-Rensselaer Polytechnic Institute
Preferred Start Date: {Empty}
Start as soon as possible.: Yes
Project Urgency: Already behind3Start date is flexible
Expected Project Duration (in months): 6 months
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Launch Presentation Date: 09/08/2021
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Wrap Presentation Date: 02/09/2022
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What will the student learn?:
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What will the Cyberteam program learn from this project?:
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HPC resources needed to complete this project?:
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Notes:
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Final Report
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What is the impact on the development of the principal discipline(s) of the project?:
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Is there an impact on the development of human resources for research computing?:
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Is there an impact on society beyond science and technology?:
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Lessons Learned:
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Overall results:
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