NCSI: Exploring the Structures and Synergic Properties of Mixed Palladium Copper (PdnCum; n+m ≤ 8) Clusters

Status	Completed
Mentor Name	Jonathan Lyon
Mentor's XSEDE Affiliation	Research Allocation and Campus Champion
Mentor Has Been in XSEDE Community	4-5 years
Project Title	Exploring the Structures and Synergic Properties of Mixed Palladium Copper (PdnCum; n+m ≤ 8) Clusters
Summary	In this position, the student will study strongly bound mixed transition metal clusters as models for real world heterogeneous catalytic systems. Specifically, we will investigate mixed palladium - copper clusters here, searching the cluster potential energy surfaces for local and global minima and exploring the relationship of cluster size and dopant concentration on different cluster properties. The results from this investigation will then be compared with related cluster systems.
Job Description	The student will begin by performing a literature search for this system, which will allow the student to pick an appropriate level of theory to conduct this investigation. This level will be chosen by performing calculations on the PdCu diatomic cluster (and select other sizes based on the results of the literature search) and comparing the predictions with experimentally determined spectroscopic data (e.g., bond length, stretching frequency, etc.). The student will then perform theoretical chemistry calculations using the Gaussian 16 and NBO 7 programs on the EXPANSE cluster housed at the San Diego Supercomputing Center (SDSC). First, this student will generate candidate structures for each cluster size and composition using two global optimization procedures. One program utilizes the artificial bee colony algorithm, whereas the second basin hoping program is written and compiled in-house using Fortran code. Additional structures will be generated by hand from our prior knowledge. All candidate structures will then be further optimized by this student at the appropriate level determined at the start of the semester. Higher level (e.g., double hybrid density functional theory) calculations will also be performed as further confirmation of the predicted results. Various results from output files will be visualized with the Avogadro, Gabedit, and Gaussview programs on a local machine.
Computational Resources	This project will make use of the EXPANSE high performance computing cluster at the SDSC through XSEDE allocation CHE-130094. This computer cluster has the Gaussian 16 program and required compilers already installed. The NBO 7 program, which will also be utilized in this project, was purchased and installed on the EXPANSE cluster in 2021. Output files from all programs will be transferred to a local desktop in PI Lyon's research laboratory for analysis, visualization, and long term storage.
Contribution to Community	This project will contribute to the XSEDE community in several ways. First, it is expected the results from this project will be of significant interest to the scientific community. It is anticipated this project will result in a presentation by the student at a scientific meeting, a presentation by the mentor, and a manuscript submitted for publication to a peer reviewed journal. Second, it is likely the student applying for this position will come from a group typically underrepresented in science and computing fields. This program will allow for the mentoring of this next-generation researcher in computer science and computational chemistry. Lastly, this project will occur at Murray State University, an EPSCoR institution.
Position Type	Intern
Training Plan	It is anticipated the student applying for this position will have already been trained in the computer models, completed all safety requirements for work with PI Lyon, and successfully have completed an EMPOWER program in a prior semester. Regardless, a refresher training will be performed by the mentor at the start of the semester to quickly catch the student up to speed after the break between semesters. If needed after this refresher training with PI Lyon, the “Expanse 101 Webinar” recorded on 10/8/2020 and the Cornell University’s “Introduction to Linux Virtual Workshop,” both of which are available on the XSEDE training site, will be utilized as additional training supplements for this student. Any additional new or refresher training needed by the student throughout the remainder of the semester will be performed by the mentor. Although scheduled weekly meetings will occur between the student and mentor where progress and problems encountered will be discussed, in person interactions will likely occur more frequently every day or two as they have in the past. Monthly progress reports for Shodor will be prepared by the student and discussed with the mentor before all formal deadlines. Dr. Lyon has trained several undergraduate students in the past in similar techniques, including previously successful EMPOWER program participants.
Student Prerequisites/Conditions/Qualifications	The student applicant should be familiar with navigating through Linux operating systems. Student should be a chemistry major, or suitable equivalent. Student should be able to work independently at times on the tasks of this project (i.e., they should have a good working knowledge of the project and techniques), while also being willing to work with and help assist younger group members as needed. While a prior knowledge of physical chemistry is beneficial, it is not required. A desire and willingness to learn physical chemistry concepts as needed is more important.
Duration	Semester
Start Date	01/18/2022
End Date	05/13/2022