NCSI: Adsorption of Amino Acids and Nucleic Acids at Nanomaterials

Status	Completed
Mentor Name	Luiz Oliveira
Mentor's XSEDE Affiliation	Startup Allocation (Planning to submit a larger Research Allocation request during the Sep 15 - Oct 15 submission period)
Mentor Has Been in XSEDE Community	3-4 years
Project Title	Adsorption of Amino Acids and Nucleic Acids at Nanomaterials
Summary	The interaction of biomolecules with nanomaterials is present in a large range of applications, including, nanomedicine, biosensing, nanobioelectronics, and bioelectrochemistry. To refine such technologies, it is important to gain a deeper molecular comprehension of the properties of nano-bio interfaces. With this goal in mind, the apprentice will study the adsorption of selected amino acids, DNA, and RNA fragments onto gold nanoclusters and single-walled carbon nanotubes.
Job Description	To achieve the goals described above, the student will utilize CP2K to perform molecular dynamics (MD) simulations, as well as, VMD and python scripts to post-process the MD simulations. MD simulations will be performed on the SDSC EXPANSE. Output files will be transferred to local machines for post-processing analysis. It is also expected that the student will actively communicate with the PI, prepare monthly reports and, with the PI supervision, prepare a poster for presentation at a local symposium for undergraduate research.
Computational Resources	This project will initially utilize resources from an XSEDE Startup project (CHE190029) to perform benchmark simulations for our specific systems of interest. Such simulations will provide sufficient information to prepare for a Research request during the submission period, Sep 15 - Oct 15.
Contribution to Community	This project will stimulate the interest of students in computational molecular science. Students will expand their knowledge by learning and utilizing molecular modeling, programming languages, and high-performance computing techniques. Dr. Oliveira plans to submit a proposal to promote the apprentice to intern in Spring 2022. Furthermore, the results from the Fall 2021 and Spring 2022 semesters are expected to be presented at the 2022 Molecular Education and Research Consortium in Undergraduate computational chemistRY (MERCURY) conference and at the 52nd Midwest Theoretical Chemistry Conference (MWTCC). A long-term contribution is to attract more undergraduate students from MVNU to be part of the XSEDE community in the future.
Position Type	Apprentice
Training Plan	The student sought for this position is currently acquiring the skills necessary for this project. This is a volunteered work being performed during Summer 2021. Therefore, during the Fall 2021 semester, the student will be proficient in the utilization of CP2K and VMD after the completion of several tutorials and weekly discussions with the PI. Throughout the duration of the present project, we plan to keep meeting at least once per week, and more frequently if necessary, to discuss the progress and possible issues of the simulations.
Student Prerequisites/Conditions/Qualifications	The student should be familiar with MD simulations, the Linux operating systems, and CP2K and VMD software.
Duration	Semester
Start Date	08/23/2021
End Date	11/12/2021