Hacker News: siver_john

New comment by siver_john in "Dolly Parton's Dollywood Express"

siver_john — Wed, 11 Jun 2025 17:45:30 +0000

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.

New comment by siver_john in "A Primer on Molecular Dynamics"

siver_john — Wed, 11 Jun 2025 15:43:26 +0000

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.

New comment by siver_john in "A Primer on Molecular Dynamics"

siver_john — Wed, 11 Jun 2025 15:35:15 +0000

Sent an email =)

New comment by siver_john in "A Primer on Molecular Dynamics"

siver_john — Wed, 11 Jun 2025 13:56:46 +0000

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.

New comment by siver_john in "A Primer on Molecular Dynamics"

siver_john — Tue, 10 Jun 2025 15:24:54 +0000

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).

New comment by siver_john in "Drone shows: Will they overtake firework displays?"

siver_john — Tue, 10 Jun 2025 15:16:17 +0000

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.

Pre-orders are now open in the US

siver_john — Thu, 10 Apr 2025 17:04:51 +0000

Article URL: https://frame.work/blog/framework-laptop-12-pre-orders-are-now-open

Comments URL: https://news.ycombinator.com/item?id=43645939

Points: 3

# Comments: 0

New comment by siver_john in "Reversible Computing Escapes the Lab"

siver_john — Tue, 14 Jan 2025 13:52:01 +0000

This is really cool, I never expected to see reversible computation made in electrical systems. I learned about it undergrad taking a course by Bruce MacLennan* though it was more applied to "billiard ball" or quantum computing. It was such a cool class though.

*Seems like he finally published the text book he was working on when teaching the class: [https://www.amazon.com/dp/B0BYR86GP7?ref_=pe_3052080_3975148...

New comment by siver_john in "Einsum in Depth"

siver_john — Mon, 06 Jan 2025 18:52:20 +0000

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.)

New comment by siver_john in "A Gentle Introduction to Graph Neural Networks"

siver_john — Fri, 20 Dec 2024 15:08:03 +0000

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

New comment by siver_john in "Ask HN: Who is hiring? (December 2024)"

siver_john — Mon, 09 Dec 2024 19:53:33 +0000

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

New comment by siver_john in "Ask HN: Who wants to be hired? (December 2024)"

siver_john — Tue, 03 Dec 2024 00:55:58 +0000

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.

New comment by siver_john in "The English Paradox: Four decades of life and language in Japan"

siver_john — Thu, 07 Nov 2024 16:46:13 +0000

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.

New comment by siver_john in "Trump wins presidency for second time"

siver_john — Wed, 06 Nov 2024 21:52:36 +0000

Here I'll bite:

Didn't fill existing positions for monitoring pandemic diseases arising in China that were put in place by Bush then strengthened by Obama, allowing for a slower response to what would become covid[1].

Huge corporate tax cuts that lead to stock buy backs, which enriched the wealthy while doing little to nothing below (buying stocks back and raising stock value generally does not help the average/low income individual beyond maybe their 401k).[2]

[1]https://www.theatlantic.com/politics/archive/2020/06/how-whi...

[2] For just the tax information later, there are plenty of articles about stock buybacks at that time if you don't trust the org. https://itep.org/one-legacy-of-the-trump-tax-law-big-tax-bre...

New comment by siver_john in "Life expectancy rise in rich countries slows down: took 30 years to prove"

siver_john — Wed, 16 Oct 2024 14:01:45 +0000

From my friends who are on ozempic, yes it has literally done just that. Along with the fact because they are driven to eat less they, in general are less snacky (and thus eat less chips) and tend to avoid greasy/fried foods because combined with the medicine it leaves them feeling worse afterwards than eating a similar "healthier meal".

Yes N=2, small sample sizes, but I could also see how being less snacky makes one less likely to eat chips. (Why I almost pathologically don't keep easy to eat food in my pantry, granted this can also backfire too).

New comment by siver_john in "Chemistry Nobel: Computational protein design and protein structure prediction"

siver_john — Wed, 09 Oct 2024 15:53:42 +0000

They had to put David Baker on here, his work on protein design if nothing else was ground breaking. I've expected him to win it at some point in a, it's not a matter of if but of when.

Doom Ported to Run Atop AMD ROCm and LLVM Libc To Run On AMD GPUs

siver_john — Mon, 30 Sep 2024 19:33:19 +0000

Article URL: https://www.phoronix.com/news/DOOM-ROCm-LLVM-Port

Comments URL: https://news.ycombinator.com/item?id=41701122

Points: 4

# Comments: 0

New comment by siver_john in "Ask HN: Should we bring software dev in-house?"

siver_john — Fri, 09 Aug 2024 14:13:58 +0000

Just wanted to add in, even as someone who isn't super experienced in the field (1.5 years of contracting on top of 6ish years programming in grad school), I find logistics an incredibly interesting field. So yes even from youngish guys you'll be attractive even being a "non-glamorous industry."

Also I believe a large swath of developers just enjoy problem solving regardless of the application as long as solving the problem itself is a challenge. While others like steady routine, and I think both are useful to your ends. Of course there are some that like to be on the cutting edge (though IMHO logistics can very much include that, though I recognize that isn't your needs currently) and those people will choose a different company.

New comment by siver_john in "Ask HN: Who wants to be hired? (April 2024)"

siver_john — Mon, 08 Apr 2024 17:53:07 +0000

Seeking Contract Or Long Term Employment

  Location: Nashville, TN, US
  Remote: Yes
  Willing to relocate: Most likely, no
  Technologies: Python, Tensorflow, CUDA, Node.JS, Docker, SQL, AMBER, Schrodinger, Linux
  Website: https://biophysvertex.com
  Resume/CV: https://biophysvertex.com/Jonathon_Ferrell_Resume.pdf
  Email: jbferrell [at] biophysvertex [dot] com

I have a deep background in computational biology/chemistry with extensive coding experience especially around Neural Networks. My background in academia and recent work has set me to be very comfortable in working with old, outdated, poorly documented software and massaging it to work in current workflows. I also have strong experience developing new projects and software.

New comment by siver_john in "Ask HN: Freelancer? Seeking freelancer? (April 2024)"

siver_john — Mon, 08 Apr 2024 15:55:16 +0000

SEEKING WORK, REMOTE

Remote: Yes, I have only worked with US clients but would be willing to work with international clients.

Willing to relocate: No

- Technologies: Python, Tensorflow, CUDA, Javascript, General AI, SQL, Docker

- CV/Resume: https://biophysvertex.com/Jonathon_Ferrell_Resume.pdf

- Website: https://biophysvertex.com/

- Email: jbferrell [at] biophysvertex [dot] com

I am an incredibly flexible and adaptable worker. I can quickly learn new programming languages, software, etc and I specialize in dealing with old and poorly maintained code. I thrive on problems that seem insurmountable. Of course I am happy to work on easier problems too.