NCSI: Replica-Exchange Molecular Dynamics (REMD) Simulations of Highly Ordered Polycyclic Aromatic Hydrocarbon (PAH) Foldamers

Status	Completed
Mentor Name	Bohdan Schatschneider
Mentor's XSEDE Affiliation	Previous research allocation recipient and currently applying for more time
Mentor Has Been in XSEDE Community	4-5 years
Project Title	Replica-Exchange Molecular Dynamics (REMD) Simulations of Highly Ordered Polycyclic Aromatic Hydrocarbon (PAH) Foldamers
Summary	This position has three aspects: 1) Assembly of polycyclic aromatic hydrocarbon (PAH) oligomers/polymers in a visualization software package 2) calculation of the native confirmation of the polymer in a solvent box using replica-exchange molecular dynamics software (REMD) and 3) calculation of the intermolecular orbital overlap of neighboring monomers in the oligomer/polymer chain using fragment orbital density functional theory (FO-DFT). This job will necessitate the coordination of two undergraduate researchers (UGRs) to run the calculations and assemble the data in one file for later analysis.
Job Description	Undergraduate researchers (UGRs) will generate PAH foldamers structures in the visualization software, ChemDraw Pro (2D representtaions) and Chem 3D (allows for manipulation of monomer orientations in 3D space). Since each PAH monomer has several linkage sites, many permutations of different site linkages will be performed. All monomer to monomer linkages will be homogeneous in these initial stages of the project in order to systematically understand which morphologies develop the highest amount of secondary (folding) order within the materials. UGRs will then insert the oligomers into solvent boxes (periodic cell containing solvent molecules) using the Amorphous Cell module within Materials Studio. The solvated oligomers will then be placed into the GROMACS freeware package where REMD simulations will be conducted on the Open Science Grid. Once the REMD simulations are complete, both UGRs will perform FO-DFT on the resulting foldamers (polymers with significant secondary ordering in the structure) in the freeware package NWChem. The FO-DFT calculations will provide the intermolecular orbital overlap of the neighboring monomeric units within the foldamers chain, providing insight into the charge transfer capabilities of the material.
Computational Resources	We have applied for a startup allocation on the Open Science Grid resource in order to run the REMD simulations. This startup allocation is also slotted for use with two other project running through the EMPOWER program entitled: “Establishing the Electronic Genome of Functionalized Polycyclic Aromatic Hydrocarbons (PAHs) using High-throughput DFT and Machine Learning” and “High-Throughput Investigation of Organic Molecular Crystal Energy Frameworks an Intermolecular Orbital Overlap”. If the 200,000 core-hr allocation is used up between the three projects, we will apply for more time. In addition, we have a high-performance computing cluster here at CPP that we can use to complete the work.
Contribution to Community
Position Type	Learner
Training Plan	This position will require the UGRs to use ChemDraw, Chem 3D, Amorphous Cell, GROMACS, and NWChem. One of the UGRs slated for this investigation (Israel Estrada) has been using ChemDraw, Chem 3D, Amouphous Cell, and GROMACS extensively since last summer. He will train the incoming UGR, Diego Henriquez, on the use of these programs. The PI will work with both UGRs to teach them the proper usage of FO-DFT within the NWChem package.
Student Prerequisites/Conditions/Qualifications
Duration
Start Date	06/01/2019
End Date	08/20/2019