CV

Curriculum vitae.

Summary

  • Ph.D. candidate (expected Summer 2026) in theoretical and computational chemistry developing multiscale, atomistic models of P-type ATPases.
  • Expertise in time-series data including: molecular dynamics (enhanced sampling, free energy), hybrid Quantum Mechanical/Molecular Mechanics for chemical steps.
  • Recent AI/ML internship applying computational neuroscience to build a synthetic olfactory engine.

General Information

Full Name Jose Luis Guerra
Email Jlguerra@uchicago.edu
LinkedIn jlguerraphd
Profile

Education

  • Expected May 2026

    Chicago, IL

    Ph.D. in Chemistry
    University of Chicago
    • NSF Graduate Research Fellow
    • Dissertation: Multiscale Modeling of P-type ATPase Pumps
    • Relevant coursework: Mathematical Foundations of Machine Learning; Machine Learning in Chemistry; Agents for Science
  • May 2021

    Stony Brook, NY

    B.S. in Biochemistry (Honors)
    Stony Brook University
    • Minor in Chemistry and Music
    • Honors thesis: Molecular Dynamics of Mismatched Base Pairs in a B-family DNA Polymerase

Research & Professional Experience

  • Jan 2022 – Present

    Chicago, IL

    Graduate Researcher
    Roux Lab, University of Chicago
    • Built an atomistic 40+ microstate model of the Na+,K+-ATPase transport cycle; computed step-wise displacement charge and linked mechanism to measurable observables.
    • Designed enhanced-sampling and free-energy workflows integrated with QM/MM to study ATP hydrolysis and dephosphorylation.
    • Built reproducible Python pipelines processing and validating more than 1 TB of simulation data.
  • Jul 2025 – Sep 2025

    Remote

    AI/ML Intern (Independent Contractor)
    Aurat Aroma LLC
    • Supported the Synthetic Olfactory Engine with computational neuroscience models and supporting algorithms.
    • Developed production-quality Python code and technical documentation for new components.
    • Contributed to back-end infrastructure and data pipelines; translated requirements into implementable tasks.
  • Summer 2021

    New York, NY

    Summer Research Intern (Amgen Scholars Program)
    Columbia University
    • Established protocols for high-speed AFM imaging of biomechanical properties.
  • Jan 2018 – May 2021

    Stony Brook, NY

    Undergraduate Researcher
    Simmerling Lab, Stony Brook University
    • Simulated protein–nucleic acid interactions using AMBER/NAMD and Python; validated results via statistical analyses and targeted in silico mutations.

Technical Skills

Programming
Python
Bash
R
C
Fortran
ML / Analysis
NumPy, pandas, SciPy, scikit-learn, PyTorch
Data curation and model evaluation
Simulation
NAMD, AMBER, OpenMM
Gaussian, TeraChem
Enhanced sampling and free-energy methods
HPC / Workflow
Linux clusters
PBS, Slurm
Domain
Ion transport, electrostatics, protein–ligand interactions, structure-based modeling

Leadership & Service

  • Dec 2023 – May 2025

    Chicago, IL

    Graduate Student Intern
    UChicago PSD Office of Diversity and Inclusion
    • Developed a web-scraping pipeline to gather and analyze population data from R1 institutions.
    • Evaluated partnerships with R1 and R2 minority-serving institutions to inform targeted recruitment and outreach.
  • 2021 – 2024

    Remote

    Graduate School Application Mentor
    Científico Latino
    • Provided resume and cover letter feedback, conducted mock interviews, and supported applicants applying to STEM Ph.D. programs.

Selected Publications & Presentations

Awards & Honors