41–48 of 48 posts
Earlier quoted context omitted.
Good point, and while SV does have a lot of obscure references, this one may be a bit too obscure. Happy coincidence perhaps.
Gilfoyle refers to himself as a LaVeyan satanist early on in the show.
Now seems as good a time as any to share a replica of an Antoine van Leeuwenhoek microscope that my father made. The lens he made in the same way as the original... heating up glass to a semi molten stake, then letting a drop fall through the air. By the time it had landed and cooled...voila! A spherical lens. https://www.dropbox.com/s/in4x3vjysw1o1wc/IMG_0291.JPG?dl=0
Now seems as good a time as any to share a replica of an Antoine van Leeuwenhoek microscope that my father made. The lens he made in the same way as the original... heating up glass to a semi molten stake, then letting a drop fall through the air. By the time it had landed and cooled...voila! A spherical lens. https://www.dropbox.com/s/in4x3vjysw1o1wc/IMG_0291.JPG?dl=0
Can we please have more information about this? And better pictures?
https://www.dropbox.com/s/qhs8qf2qw5e4n35/micro_01.jpg?dl=0 From the back
https://www.dropbox.com/s/4vl3rbfkelf1nv9/micro_02.jpg?dl=0 Same, but annotated. 1 = The lens housing 2 = The 'stage'. Basically, just a pin that you stick the subject onto 3 = The handle. using this, the assembly is positioned in front of a strong light.
https://www.dropbox.com/s/4xra81bu2qdsxj9/micro_03.jpg?dl=0 The front, showing the viewing hole
The whole thing actually works. The lens is hit or miss (literally), and it shows. Plenty of chromatic aberration. Basically just a droplet of glass. He tried many times to get it right.
Why did he make it? Well... he has a fascination with old technology. He was a founding member of the British Vintage Wireless Society, and has written a book on the subject of old radios. Also one on ancient navigation techniques. He is an old fashioned polymath. Also have in my possession a replica of Galileo's first telescope. Also works fine.
“The performance of a 512-node Anton machine is over 17,000 nanoseconds of simulated time per day for a protein-water system consisting of 23,558 atoms.[5] In comparison, MD codes running on general-purpose parallel computers with hundreds or thousands of processor cores achieve simulation rates of up to a few hundred nanoseconds per day on the same chemical system.” 17,000 ns of simulation per day sounds crazy small…
[Disclaimer: I used to work at D. E. Shaw Research from 2011-2016] The early Anton 1 numbers of 17us/day on 100K atoms were huge leap forward then. At that time, GPU-based simulations (e.g. GROMACS/Desmond on GPU) were doing single digit ns/day. Remember, even for 'fast-folding' proteins, the relaxation time is on the order of us and you need 100s of samples before you can converge statistical properties, like foldin…
Nonetheless, I'm thankful for both DESMOND and Anton, which helped push the MD community out of its moribund state in the early 2000s. I still don't think MD simulations produce anything that exceeds the opportunity value of the power they consume, and it seems unclear that they ever will, although I still would love to know the answer to the question: "could sophisticated classic forcefields with reasonable O(nlogn) scaling every be truly valuable as a virtual screening feature generator/evaluation mechanism".
Earlier quoted context omitted.
[Disclaimer: I used to work at D. E. Shaw Research from 2011-2016] The early Anton 1 numbers of 17us/day on 100K atoms were huge leap forward then. At that time, GPU-based simulations (e.g. GROMACS/Desmond on GPU) were doing single digit ns/day. Remember, even for 'fast-folding' proteins, the relaxation time is on the order of us and you need 100s of samples before you can converge statistical properties, like foldin…
I think it's still an open question whether you truly need an ensemble of long simulations (versus many shorter ones that can be generated in embarassingly parallel mode on GPUs). Nonetheless, I'm thankful for both DESMOND and Anton, which helped push the MD community out of its moribund state in the early 2000s. I still don't think MD simulations produce anything that exceeds the opportunity value of the power they…
On the other hand, DESRES had been focusing on a lot of acceleration methods that involved hardware optimized HMC-esque methodologies that had reasonably good parallelism. AFAICT the only public description of this work is in the appendices of this paper [0].
At the end of the day, you probably need both techniques because the pure sampling approaches lose fine structure (e.g. binding pockets opening up with anomalous frequency due to water clusters) whereas the standalone MD model has too long of a decorrelation time to get averages to converge.
Earlier quoted context omitted.
Can we please have more information about this? And better pictures?
My pleasure. Thanks for taking an interest: https://www.dropbox.com/s/qhs8qf2qw5e4n35/micro_01.jpg?dl=0 From the back https://www.dropbox.com/s/4vl3rbfkelf1nv9/micro_02.jpg?dl=0 Same, but annotated. 1 = The lens housing 2 = The 'stage'. Basically, just a pin that you stick the subject onto 3 = The handle. using this, the assembly is positioned in front of a strong light. https://www.dropbox.com/s/4xra81bu2qdsxj9/micr…
