Submission Number: 89
Submission ID: 126
Submission UUID: 674e748a-fc62-4de4-a3be-d1339ef69afa
Submission URI: /form/project

Created: Thu, 02/18/2021 - 22:41
Completed: Thu, 02/18/2021 - 23:09
Changed: Tue, 08/02/2022 - 15:12

Remote IP address: 108.4.141.235
Submitted by: Jeremy Feldblyum
Language: English

Is draft: No
Webform: Project
Project Title Computational Simulation of One-Dimensional Porous Polymers
Program CAREERS
Project Image Picture1.jpg
Tags computational-chemistry (81), materials-science (516), monte-carlo (343)
Status In Progress
Project Leader Jeremy Feldblyum
Email jfeldblyum@albany.edu
Mobile Phone
Work Phone 5184424426
Mentor(s) Michael Strickler, Neil McGlohon
Student-facilitator(s) Parameshwaran Pasupathy
Mentee(s)
Project Description In this project, we are using computation to optimize the design of one-dimensional porous polymers. We aim to relate chemical motifs with pore size and internal surface area. Our workflow consists of polymer design, construction, and incorporation into quasi-amorphous periodic cells that enable determination of pore size and surface area via established Monte Carlo methods. We are currently using Materials Studio for our work, however, we are seeking a Mentor who can offer expertise in areas including streamlining our workflow via scripts, leveraging high-performance computing resources to which we currently lack access, and insight into other potential software options that may improve our ability to screen large numbers of polymers with a minimum of manual intervention.
Project Deliverables - Access to high-performance computing resources that are compatible with our workflow
- Improvement of workflow to minimize need for manual intervention
- Suggestions for and training with alternative software that may improve accuracy and speed of calculations, and speed of workflow, as relevant to our work
Project Deliverables
Student Research Computing Facilitator Profile Student willing to learn basics of geometry optimization, simulated annealing, and determination of pore characteristics of porous materials via simulation. Software of use will be LAMMPS.
Mentee Research Computing Profile
Student Facilitator Programming Skill Level Some hands-on experience
Mentee Programming Skill Level
Project Institution The University at Albany, SUNY
Project Address Chemistry, Room 029
1400 Washington Ave.
Albany, New York. 12222
Anchor Institution CR-Rensselaer Polytechnic Institute
Preferred Start Date
Start as soon as possible. No
Project Urgency Already behind2Start date is flexible
Expected Project Duration (in months) 6
Launch Presentation
Launch Presentation Date 05/11/2022
Wrap Presentation
Wrap Presentation Date
Project Milestones
  • Milestone Title: Reproduce Results on AiMOS
    Milestone Description: This milestone will be complete when the undergraduate student obtains access to RPI's AiMOS supercomputer and is able to reproduce our preliminary results using AiMOS. Specifically, we have calculated geometric accessible surface areas for several polymers simulated using desktop computing resources. Our current workflow requires several modules available in Materials Studio, and being able to reproduce this work using supercomputing resources would be a significant advance for us, as it would significantly improve the accuracy and throughput of our work. This may require the use of other software such as LAMMPS.
    Completion Date Goal: 2021-05-21
  • Milestone Title: Automate Simulation Workflow
    Milestone Description: Our workflow requires several manual interventions that slow progress considerably. For this milestone to be complete, code would be established that would execute the following tasks in an automated fashion:


    1. Starting from a user-defined monomer, form a polymer of a user-input degree of polymerization.
    2. Perform geometry optimization of the user-defined monomer
    2. Form a user-specified number of conformations of that polymer via simulated annealing.
    3. Place a user-specified number of annealed polymer chains (from step 2) in an "amorphous cell," a periodic system containing stochastically inserted chains that to not overlap.
    4. Perform simulated annealing on the periodic system from step 3 until a user-defined density is reached (this density can be a single user-defined value, or be defined in terms of the extent of convergence of density).
    5. The periodic system from step 4 should then be analyzed for porosity and pore size distribution PoreBlazer or other similar software. Doing so requires converting the system from step 4 into a file that PoreBlazer can interpret.

    Completion Date Goal: 2021-08-09
  • Milestone Title: Properties of Porous Ferrocene-Based Polymers
    Milestone Description: With a streamlined workflow established with milestones 1 and 2, the third milestone of the project will focus on the chemical building blocks used to form these polymers. Specifically, we are interested in examining the porosity of ferrocene-containing polymers. We have experimental evidence for porosity in this class of polymers, but only computation is suitable for rapidly establishing design rules that maximize porosity in this class of materials. Completion of the third milestone will be achieved when chemical insights can be gained from polymers simulated by the methods developed in the first two milestones. Specifically, we aim to relate porosity and pore size distribution to the polymer structural features such as the distance between ferrocene units, the presence or absence of ansa linkages, and the identity of side-chains.
    Completion Date Goal: 2021-10-01
Github Contributions
Planned Portal Contributions (if any)
Planned Publications (if any) We are wrapping up experimental work on this class of polymers and hope to publish in early summer. Computational work will be featured in part or in whole as a second publication following our experimental work.
What will the student learn? Polymer chemistry, porous materials, Monte Carlo simulation, DFT-based geometry optimization and annealing, periodic vs. amorphous systems, Materials Studio, scripting
What will the mentee learn?
What will the Cyberteam program learn from this project? Unlike crystalline porous materials (MOFs, zeolites, etc.), porous polymers lack experimentally-derived structural models from which properties can be simulated. We are developing a route to simulating these polymers and deriving structure-property relationships based on simulation. We aim to follow success in the initial stages of our work by developing more sophisticated algorithms to computer-driven polymer modification (that is, without human intervention), leading to large datasets that can be used to discover structure-property relationships in these materials that would be too cumbersome to reveal with manual design.
HPC resources needed to complete this project? Likely; we look forward to discussing options with project Mentor
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