siver_john

"spirit and the letter (of the law)" is a common phrase in English. For the next part IANAL.

It appears in the US that generally the letter of the law matters more in legal proceedings than the spirit of what was written. Though there is sometimes debate (especially around the constitution) as to what the words meant at the time the law was written which give a little legal freeway to the spirit. From what I have seen though these cases generally deal more with rights/civil liberties than laws which affect corporations/tax codes/processes/etc. There is greater freedom to interpret the spirit of the law in criminal cases (e.g. jury nullification).

I mean the passenger train from Lebanon, TN to Nashville, TN is quite busy. I rode it over a decade ago and it was quite used and my partner rides it now and it is much the same. If it still ran at night like it did back then, I'd probably take it into downtown (and go downtown more often) for events. I don't believe the train left the station a long time ago, we just simply shifted it off the tracks.

Biased: Was a researcher in this field...

For MD, specifically the type talked about here, we aren't taking in all the quantum effects, and that is known. Crystalizing molecules, especially large either dynamic proteins or ones in lipids is hard. Crystalizing during transitory states is orders of magnitude more difficult. MD allows us to visualize those transitory states and was used, for example, to observe the unfolding of the spike protein in Sars-Cov2 to assist in designing mRNA vaccines, because the important amino acids could be observed.

There is a lot of times where it is good enough, outpaces current experimental techniques, etc that it is the tool for the job. But it is not perfect and very rarely can stand completely on its own, in say drug discovery or other fields.

Sent an email =)

Depends on how deep you want to go. The pioneering work in this field is the "The multiscale coarse-graining method." series of papers kicked off by Noid. Who is still a person to pay attention to in this field.

I also believe the work of Frank Noe is someone to watch for in the ML potential space for proteins.

I'm also always happy to talk about CG.

Amazing article on Molecular dynamics, in the infinite number of things they could add is a small segment on coarse graining. Though I'm biased (and have been thinking about writing one myself).

Granted wished this had been around when I started my journey instead of having to delve into things like the Amber manual... (which I will grant is wonderful for its information but the organization isn't as convenient).

Went to a show in Nashville with some friends, I think last year. And drones were definitely incorporated in (interestingly showing Star Wars and then US military assets), but it was done in tandem with the fireworks. Which as a distraction during transitional elements does seem like a good use for them.

Honestly I think the biggest threat is also fireworks NIMBYism, people don't like the loud sounds disturbing their lives, their pets, etc combined with the general pressure of bigger and better exacerbating those problems.

God I love einsum so much. I discovered it in grad school and it made my life so much nicer, definitely recommend learning it, you can do some wicked powerful stuff. (One of the first things I asked one of the NVIDIA guys when they were showing off cuPy a few years back was whether it had einsum.)

Honestly, seeing this on the front page had my hopes up they had found out a way forward but alas.

I applied to the backend position last month but could fit for other positions, should I apply to those directly as well?

I am a computational biophysicist turned generalist, I enjoy solving the weird problems everyone hates. Undocumented code on a system built from decades old software where it's held up by toothpicks? My jam! Need me to build a jet engine from duct tape, super glue, and balsa wood? Let's go! From being in academia I've worked on large and diverse teams and from being a contractor I've been both part of smaller teams and left to my own devices, I excel no matter what.

  Location: Nashville, TN

  Remote: Yes

  Willing to relocate: No

  Technologies: React, Python, NodeJS, Postgres, SQLAlchemy, Flask, Numba, CUDA, Go, Bash, Scala, Amber, AmberTools, Schrodinger Suite, PyMol, Tensorflow, Neural Networks, Physics Informed Neural Networks, SQL, AWS, Docker, Linux

  Résumé/CV: https://biophysvertex.com/Jonathon_Ferrell_Resume.pdf

  Email: jbferrell [at] biophysvertex [dot] com

Open to contract and full time employment.

This is extraneous to your comment, but as someone who speaks some Japanese, if you ever want someone to practice English with, I am more than happy to lend a hand.