David Wych

CV

SUMMARY

David C. Wych is a postdoctoral research associate in the Computer, Computational, and Statistical Sciences Division (CCS-3) and the Center for Non-Linear Studies (CNLS) at Los Alamos National Laboratory (LANL).

His research focus involves using molecular-dynamics (MD) and quantum mechanics(QM) simulations of proteins, in both the crystalline and solution state, to better understand and improve the modeling of protein/solvent structure and disorder in X-ray crystallography (specifically, the “diffuse scattering”), developing High-performance Computing methods for crystallographic modeling and refinement, and using QM-MD simulations to probe protein structure and dynamics beyond what is possible with classical MD.

EDUCATION

Ph.D. – Pharmacological Sciences – University of California, Irvine – 2021

B.A. – Physics – Claremont McKenna College (CMC) – 2015

PROFESSIONAL EXPERIENCE

Postdoctoral Research Associate – LANL – Computer, Computational and Statistical Sciences Division (CCS-3) and the Center for Non-linear Studies (CNLS) – 2021-present

Graduate Student Researcher – UCI – Pharmaceutical Sciences – 2016-2021

Virtual Summer Intern – LANL – CNLS – Summer 2020

Graduate Student Assistant – LANL – CCS-3 – Winter-Fall 2019

Professional Tutor – Revolution Prep

TEACHING EXPERIENCE

Course Instructor:

Physical Biochemistry (300-level, Pharm. Sci.) – UCI – Fall 2020 – Virtual (COVID19)

Physical Biochemistry (300-level, Pharm. Sci.) – UCI – Fall 2019 – In Person

Course description and responsibilities:

Teaching Assistant:

Physical Biochemistry (PHARMSCI 171) – 2018

Introductory Chemistry Laboratory (CHEM 1L) – 2017

Professional Tutor:

Revolution Prep – 2015 - 2016

Course Tutor:

Scripps College – 2014 - 2015

Keck Science Department of the Claremont Colleges – 2013 - 2015

PUBLICATIONS

Peer-reviewed Publications

Pre-print and in-review

HONORS AND AWARDS

CNLS Postdoctoral Fellowship – LANL – 2021

Applied Machine Learning Summer Fellowship – LANL – 2018

PROFESSIONAL ACTIVITIES AND AFFILIATIONS

Invited Lecturer and Workshop Leader/Organizer at the 57th Course of the Erice International School of Crystallography on Diffuse Scattering: the crystallography of dynamics, defects, and disorder. (2022)

Reviewer for the Journal of Chemical Informatics and Modeling (JCIM) (2022)

Member of the American Chemical Society (ACS), Biophysical Society (BPS), and American Crystallographic Association (ACA) (since 2019)

COMPUTATIONAL EXPERTISE

⋅ GROMACS (9 yrs.)

⋅ AMBER (9 yrs.)

⋅ CHARMM (2 yrs.)

⋅ NAMD (1 yr.)

⋅ LATTE (1 yr.)

⋅ OpenEye toolkits

⋅ MDTraj

⋅ ParmEd

⋅ PyEMMA

⋅ ChimeraX

⋅ PyMOL

⋅ VMD

⋅ cctbx (4 yrs.)

⋅ phenix (3 yrs.)

⋅ ccp4 (3 yrs.)

⋅ coot

⋅ lunus

⋅ Python (10 yrs.)

⋅ NumPy

⋅ SciPy

⋅ pandas

⋅ Matplotlib

⋅ Jupyter

⋅ C++ (2 yrs.)

⋅ bash/zsh (10 yrs.)

⋅ slurm (9 yrs.)

⋅ LaTeX

⋅ Mathematica

⋅ Maple

⋅ MATLAB

PROFESSIONAL PRESENTATIONS

“Analysis of Molecular Dynamics Simulations of Protein Crystals”

“Molecular Dynamics Simulation Methods for Macromolecular Crystallography”

“Molecular Dynamics Simulations of Protein X-ray Crystallographic Diffuse Scattering”