Jonathan Barnes, Phd Email & Phone Number

- Filtered dataset of 500+ KP4 homolog sequences to then process through phylogenetic likelihoodanalysis pipeline to reduce to representative sampling of systems. Processed resulting systems throughrigorous molecular dynamics pipeline to ascertain similarity and probability of functionality as antifungals.- Performed molecular dynamics simulations with GROMACS on a large protein-antibody system(Respiratory Syncytial Virus bound to Motavizumab) to investigate epistatic effects of two empiricallydetermined antibody escape mutations.- Manipulated two datasets to develop and include new features then used R and Python to perform multinomial regression analysis and determine which physical attributes determine the sign of epistatic interactions in protein systems. Combined with a prior model to predict double mutational effects given computationally predicted single mutations.

Remote

- Performed contract software development for sensor integration on a commercial UAS platform.- Developed multi-threaded sensor control client/server software and API to interface with multiple types of physical sensors, with both command-line and GUI clients

- Collaborated with community members across multiple countries and backgrounds to build, test, and deploy services and software. - Maintained, managed, and secured back-end server infrastructure for web services like explorers, lightwallets, websites, and API endpoints. - Developed and deployed APIs written in Python to interface with blockchain daemons. - Created and maintained custom monitoring for back-end infrastructure (45+ nodes) using Zabbix.

- Cleaned and processed datasets for protein binding affinity (7085) and folding stability (3735) to curatesubsets that met desired criteria. Compiled data and physical attributes corresponding to the subsetprotein systems and mutations to then perform multivariate statistical analysis using R and Python todetermine the best-fit model that mechanistically explained epistasis in protein systems.- Processed structural data from molecular dynamics simulations to provide features for linear statisticalmodels built in R to predict spectral sensitivities in opsin proteins.- Generated conformational snapshots using OpenMM on two antibodies in a complex with SARS-CoV-2-Sprotein to feed through FoldX and PyRosetta pipelines to predict potential antibody escape variants.- Built library of helper scripts in Python and Bash to automate data processing and cleaning, figuregeneration, simulation preparation, and cluster job operation.- Communicated research findings to broad audiences via presentations, posters, and publications.

Moscow, Id

- Collaborated with 4+ TAs and 1 lab manager to prepare laboratory equipment and facilitate instruction.- Instructed physics laboratories, consisting of 3+ sections per semester with 24 students per class with lectures, demonstrations, and one-on-one assistance.- Assisted faculty with proctoring and grading of exams, quizzes, and homework.

- Built templates and automated pipeline for LATEX report generation.- Deployed web services using docker and NGINX for administration and asset tracking.- Automated large batch data processing for metadata using Python.- Developed software with python for real-time data collection and analysis over non-local networks.- Implemented AI techniques with Python and Neurala for image processing.

-Managed two distinct physics laboratories including setup and calibration of various equipment-Facilitated physics laboratories consisting of 4+ sections per quarter with 24+ students per class-Assessed student understanding of material and analyzed grades via excel and custom Python tools

-Codesigned and built custom apparatus: Programmed controlling arduino and wrote analysis software with Python for material testing.-Prototyped and constructed components for testing apparatus, winding equipment, and line setups using 3 cartesian 3D printers via OpenSCAD-Created and developed production plastics with exotic properties on a team of 3-Managed chemical neutralization and disposal, maintained glassware, followed laboratory safety and chemical handling and testing protocols.

Doctor Of Philosophy - Phd, Physics

Master Of Science - Ms, Physics

Bachelor Of Science (B.S.), Physics

Graudated cum laude.