Teaching Assistant, Physical Chemistry of Biomolecules & Techniques of Chemical Measurement II
Research Summary:
The broad view of my research focuses on developing machine learning methods that combine theory and experiment to tackle problems in structural biology and cheminformatics. My first original research proposal resulted in a first authorship and a submission to the SAMPL7 challenge. Since then, I have submitted in the SAMPL8 physical property challenge to study the effects of various machine learning models using our in-house database that I curated. In addition, with the help of some lab members, we have just recently submitted in the SAMPL9 host-guest challenge. The main focus of my dissertation research is centered around the algorithm BICePs (Bayesiain Inference of conformational populations), which is designed for force field validation and parameterization.
The BICePs has recently been turned into a Python 3 module and labeled BICePs 2.0 with documentation, enhanced analysis and MCMC convergence checking.
My current work
Robert M. Raddi
Theoretical Chemist/Graduate Research Assistant
Summary
I'm a theoretical chemist from the greater Philadelphia area who loves experiencing diverse cultures, meeting new people, hiking, and programming. The broad view of my research focuses on developing scientific software packages that use machine learning/physical based approaches to tackle problems in chemistry and structural biology. Currently, I work in the Voelz Lab as a graduate research assistant in pursuit of obtaining a Ph.D. in Theoretical/Physical Chemistry from Temple University.
Philadelphia, PA
267-312-0604
Education
Temple University
Doctor of Philosophy — PhD, Theoretical Chemistry; Advisor: Dr. Vincent Voelz
Doctor of Philosophy — PhD, Theoretical Chemistry; Advisor: Dr. Vincent Voelz
2018 - 2023
Temple University
Bachlors of Science — B.S, Chemistry;
Bachlors of Science — B.S, Chemistry;
2013 - 2017
History/Experience
January 2020 - April 2020 Teaching Assistant, Temple University
Assignment: Physical Chemistry of Biomolecules & Techniques of Chemical Measurement II
September 2019 - December 2019 Teaching Assistant, Temple UniversityAssignment: Physical Chemistry of Biomolecules & General Chemistry I laboratory
Awards: the Guy Allen award for outstanding teaching
May 2019 - September 2019 Graduate Research Assistant, Temple UniversityDevelopment of BICePs 2.0 & Was awarded Teaching in Higher Education Certification;
June 2019 - June 2019 Academic Intern for Computing & Statistics Workshop, Temple UniversityThis 2-week graduate level summer workshop of ~30 students was organized by Matthew Newby (Physics), Vincent Voelz (Chemistry) and Adrienn Ruzsinszky (Physics). I contributed to some lecture material (spdes), helped students one-on-one and answered various questions regarding Python, Bash, Jupyter Notebooks, GitHub, etc. (basic programming fundamentals). Website: sites.temple.edu/compstat
January 2019 - April 2019 Teaching Assistant, Temple UniversityAssignment: Chemistry for Engineers recitation & General Chemistry II laboratory
September 2018 - December 2018 Teaching Assistant, Temple UniversityAssignment: General Chemistry I recitation & laboratory
December 2016 - September 2018 Undergraduate Research, Temple UniversityHistory/Experience
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Jan. 2020 - Apr. 2020
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21st Jun 2019
Honors, Awards & Certificates
1$^{st}$ place poster presentation at ACS EUS YCC Research Symposium
August 2021
Guy Allen award for outstanding teaching
December 2019
Teaching in Higher Education Certification
May 2019
Publications
- Raddi, Robert, and Vincent Voelz. "Stacking Gaussian Processes to Improve pKa Predictions in the SAMPL7 Challenge." (2021).
- Voelz, Vincent A., Yunhui Ge, and Robert M. Raddi. "Reconciling simulations and experiments with BICePs: a review." Frontiers in Molecular Biosciences 8 (2021): 325.
- Robert M. Raddi, Yunhui Ge, and Voelz, Vincent A. "BICePs 2.0: new tools for Bayesian Inference of Conformational Populations from Theory and Experiment."
submitted - Robert M. Raddi, Tim Marshall, Yunhui Ge, and Voelz, Vincent A. "BICePs RepX: Force Field Validation by Bayesian Inference."
in preparation - Robert M. Raddi, Richard Baxter, and Voelz, Vincent A. "Reconciling simulated ensembles of Serotransferrin with experimental SAXS intensities."
in preparation
Skills & Programming Languages
Primary Programming Languages: Python, C/C++, Bash, Visual Basic for Applications (Microsoft Excel macros)
Markup Languages: Markdown, HTML/CSS, LaTex
High performance computing (Owlsnest), Distributed computing platform (Folding@home)
Proficient with the following programs: LabView & AutoCAD (engineering software), Gromacs & OpenMM(molecular dynamics simulations), Chimera & VMD-Visual Molecular Dynamics (interactive molecular visualization), mMASS (Mass spectrometry data acquisition and processing), TopSpin (NMR data acquisition and processing)
Other Experience: