CV

Education

Graduate:

Undergraduate:

  • B.A. – Physics – CMC ’15
    • Thesis Advisors:
      • Yun Lyna Luo
      • Scot Gould
    • Mentor:
      • Paul S. Nerenberg

Publications

Peer reviewed:

  • Wych, David C., et al. “Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein.” Structural Dynamics 6.6 (2019): 064704.

    • Abstract:
      • To gain insight into crystalline protein dynamics, we performed molecular-dynamics (MD) simulations of a periodic 2 × 2 × 2 supercell of staphylococcal nuclease. We used the resulting MD trajectories to simulate X-ray diffraction and to study collective motions. The agreement of simulated X-ray diffraction with the data is comparable to previous MD simulation studies. We studied collective motions by analyzing statistically the covariance of alpha-carbon position displacements. The covariance decreases exponentially with the distance between atoms, which is consistent with a liquidlike motions (LLM) model, in which the protein behaves like a soft material. To gain finer insight into the collective motions, we examined the covariance behavior within a protein molecule (intraprotein) and between different protein molecules (interprotein). The interprotein atom pairs, which dominate the overall statistics, exhibit LLM behavior; however, the intraprotein pairs exhibit behavior that is consistent with a superposition of LLM and rigid-body motions (RBM). Our results indicate that LLM behavior of global dynamics is present in MD simulations of a protein crystal. They also show that RBM behavior is detectable in the simulations but that it is subsumed by the LLM behavior. Finally, the results provide clues about how correlated motions of atom pairs both within and across proteins might manifest in diffraction data. Overall, our findings increase our understanding of the connection between molecular motions and diffraction data and therefore advance efforts to extract information about functionally important motions from crystallography experiments.
    • Selected as a Featured Article by the Editors
    • Highlighted by the AIP in the SciLight newsletter

Not peer reviewed:

  • Wych, David C., Yun “Lyna” Luo. “Molecular Dynamics Simulation Study of PTEN Binding to Calpain Isoforms.” CMC Senior Thesis.

Presentations:

  • Molecular Dynamics Simulation Workflows for Macromolecular Crystallography
    • OpenEye CUP XXI – March 2022
  • Molecular Dynamics Simulations of Protein X-ray Crystallographic Diffuse Scattering
    • American Crystallographic Association (ACA) Annual Meeting 2019 – July 2019
  • Non-negative Matrix Factorization for Structural Dynamics Clustering of Electron Density Trajectory
    • AML Summer Fellowship Presentation Series

Research Experience

  • Post-doctoral Researcher | Los Alamos National Lab (LANL)
    • August 2021 – present
    • Mentor: Michael E. Wall
    • Crystalline MD Simulations, Crystallography, Diffuse Scattering, Exasale Computing, and Large-scale QM/MM
  • Graduate Student Researcher | University of California, Irvine (UCI)
    • December 2016 – July 2021
    • Advisor: David L. Mobley
    • Crystalline MD Simulations, Crystallography Diffuse Scattering
  • CNLS Virtual Summer Intern | Los Alamos National Lab (LANL)
    • June – August 2020
    • Mentor: Michael E. Wall
    • Crystalline MD Simulations, Diffuse Scattering, Disorder Modelling
  • Graduate Student Assistant | Los Alamos National Lab (LANL)
    • January – August 2019
    • Mentor: Michael E. Wall
    • Crystalline MD Simulations, Diffuse Scattering, Disorder Modelling
  • Applied Machine Learning Summer Fellow | Los Alamos National Lab (LANL)
    • June – August 2018
    • Mentor: Michael E. Wall
    • Crystalline MD Simulations, Diffuse Scattering, Machine Learning, Non-negative Matrix Factorization
  • Undergraduate Student Researcher | Claremont McKenna College (CMC) and Western University of Health Sciences
    • Advisors: Paul S. Nerenberg (now at Cal State LA) and Yun Lyna Luo (WesternU)
    • Solutions State Molecular Dynamics, Force-field Development
  • REU Summer Researcher | Columbia University
    • Savin Lab
    • Astrochemistry, Ion Simulation, Ultra-high Vacuum, Apparatus Modification

Instruction

  • Instructor – Physical Biochemistry
    • Fall 2019 and 2020 | UCI
    • Taught class of 120 students online and in person
    • Full overhaul of course materials: lectures, exams, homework, etc.

Research Focus, Interest Areas, and Relevant Skills

  • Primarily focused on crystalline MD simulations of protein crystals for the study of diffuse (continuous) scattering in macromolecular X-ray crystallography
  • More recently focused on electron density analysis using crystalline MD simulations for prediction of water structure, improvement of modelling and refinement techniques, and MD forcefield improvement.
  • Experienced in MD simulation using GROMACS, AMBER, and auxiliary software: Python, MdTraj, OpenEye tools, cctbx, DIALS, Lunus, Phenix, C, shell scripting, and OpenMP/MPI high-performance parallel computing. 
  • Cooking, music, mathematics, dog training, and Greek mythology for fun.