Hello world

This is my first post. I’m Alex. I’m from the Northern Virginia area. I like chemical engineering, chemistry, computer science, and scientific computing/data science.

• Undergraduate: University of Virginia (2016), high honors
  • Major: Chemical engineering and economics
  • Minor: Computer science
  • Activities: Rowing, lion dance, attempted case competitions, attempted apps
  • Research: Molecular dynamics simulation and metadynamics to study protein folding and structure.
    • GROMACS, PLUMED
• Graduate: Vanderbilt University
  • Chemical Engineering
  • Research: Molecular dynamics simulation of lipid bilayers (membranes) and membrane permeability. Coarse-grained model development
  • Many, many open source packages (as broad as the SciPy ecosystem, as niche as molecular modeling)

What to expect

I want to talk about grad school, molecular modeling, and other academic/personal thoughts worth sharing with the internet. I’m going to avoid intense technical detail, but hopefully have just enough detail to understand the bigger picture and purpose of some topics and packages. More application than theory.

More importantly, in the molecular modeling community, I’ve found there’s a degree of craftsmanship or art in working with the field. Explaining some of these software packages or ideas is like trying to explain conspiracy theories

For molecular modeling, the theories are well-established, and the popular packages have enough documentation to understand the input and output arguments. There are plenty of examples and tutorials for people to copy code and refactor to fit their needs, but there isn’t good discussion on the design and engineering behind these packages.

In my experience, to get the most out of these packages, you could spend years coming up to speed about a package’s core data structures before you feel comfortable actually running with it (beyond the examples) or contributing a good pull request.

Hopefully I can do a good job introducing this material to the budding molecular modeler.