--- Log opened Wed Sep 21 00:00:25 2022
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08:30 < kanzure> https://diyhpl.us/~bryan/papers2/nanotech/Mechanical%20computing%20systems%20using%20only%20links%20and%20rotary%20joints%20-%202018.pdf
08:30 < kanzure> a version based on axles/rotors would be nice given https://www.bakerlab.org/wp-content/uploads/2022/04/science.abm1183.pdf
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08:31 < kanzure> or gears.
08:33 < kanzure> ralph merkle seems to have lost his merkle.com domain
08:34 < kanzure> oh, it was https://ralphmerkle.com/ ?
08:36 < kanzure> hmm... no.
08:36 < kanzure> http://web.archive.org/web/20220302020252/http://www.merkle.com/
09:31 < kanzure> "In 2015 a consortium of 12 laboratories in eight countries developed a cultivar that displayed a rudimentary form of C4 photosynthesis (C4P) to boost growth by capturing carbon dioxide and concentrated it in specialized leaf cells. C4P is the reason corn and sugarcane grow so rapidly. Engineering C4 photosynthesis into rice could increase yields per hectare by roughly 50 percent. The current ...
09:31 < kanzure> ...cultivar still relies primarily on C3 photosynthesis. To get them to completely adopt C4P, the plants must produce specialized cells in a precise arrangement: one set of cells to capture the carbon dioxide and to surround other cells that concentrate it. Some (possibly dozens of) genes involved in producing these cells remain to be identified. Other C3P crops that could exploit such knowledge ...
09:31 < kanzure> ...include wheat, potatoes, tomatoes, apples and soybeans.[25]"
10:03 < docl> nice! there's a fast growing tree called paulownia that uses C4. it's more common in grasses, e.g. bamboo. I wonder why rice and wheat are C3
10:07 < docl> maybe there's a complexity penalty so it doesn't tend to evolve to C4 unless something is in a hypercompetitive niche where photosynthesis efficiency/growth rate matters a lot
10:22 < docl> well, the complexity penalty is discussed in that quote -- specialized cells in a certain arangement are needed. apparently the main pressure is low humidity rather than growth rate, as respiration loses water. so plants not in a dry environment wouldn't tend to evolve it
10:27 < kanzure> .tw https://twitter.com/aubreydegrey/status/1572532506926387200
10:27 < saxo> Here's my talk announcng the new foundation: https://www.youtube.com/watch?v=Ucw19Wc5K-o (@aubreydegrey)
10:27 < Muaddib> [Ucw19Wc5K-o] HUGE announcement by Aubrey de Grey at Longevity Summit Dublin 2022 (23:27)
11:26 < kanzure> speech recognition https://github.com/openai/whisper https://news.ycombinator.com/item?id=32927360
11:27 < fenn> can you imagine growing up around this kind of stuff http://web.archive.org/web/20220220003831/http://www.merkle.com/pluto/pluto.html
11:42 < fenn> 50% yield increase is nothing to sneeze at
11:42 < nmz787> https://github.com/ucberkeley-ee290c/osci-sky130
11:43 < nmz787> .title
11:43 < saxo> GitHub - ucberkeley-ee290c/osci-sky130: osci-sky130
11:43 < nmz787> This chip consists of a CPU and an ADC. The ADC writes data to an 8-bit memory-mapped register, which the CPU reads from.
11:43 < nmz787> chipyard contains the Chisel source and VLSI back-end configuration for the digital half of the SoC. (And is also a fork of https://github.com/ucb-bar/chipyard.)
11:43 < nmz787> bag-workspace contains the BAG generator code for the Python-generated analog portions of the SoC, plus the OpenAccess views of all other custom-designed portions, including the top integration levels. This is a fork of the starter Berkeley Wireless Research Center Sky130 BAG Workspace, which includes both Sky130-tech-specific and BWRC-site-specific setup.
11:43 < nmz787> caravel_user_project_analog is a fork of eFabless's Caravel (Analog) User-Project Starter. It serves as a delivery area, meeting eFabless's expectations for directory and file layout. Note many of its sub-directories targeted for specific tools (magic, xschem, etc) are left empty or unmodified from the template version.
11:43 < fenn> what is a BAG?
11:44 < nmz787> hm, whatever it is, it's seemingly not available anymore
11:44 < nmz787> both links fail
11:45 < nmz787> https://github.com/ucberkeley-ee290c/osci-sky130-bag-workspace
11:45 < nmz787> hmm, empty with readme only commit
11:46 < nmz787>  Berkeley Analog Generator (BAG)
11:46 < nmz787> https://github.com/google/skywater-pdk-libs-sky130_bag3_pr
11:47 < nmz787> https://skywater-pdk.readthedocs.io/en/main/analog.html?highlight=berkeley%20analog%20generator
11:47 < nmz787> ugh, "TODO: analog/bag¶
11:48 < nmz787> https://github.com/ucb-art/bag
11:48 < nmz787> BAG, a recursive acronym which stands for "BAG AMS Generator", is a fork and successor of the BAG_framework.
11:49 < nmz787> AMS == analog mixed signal
11:49 < nmz787> I believe
11:50 < fenn> BAG, a recursive acronym which stands for BAG Acronym Game, is deprecated
11:54 < fenn> so is it better than a TV tuner SDR?
13:15 < nmz787> it's for generating silicon layout I believe
13:16 < nmz787> https://www2.eecs.berkeley.edu/Pubs/TechRpts/2019/EECS-2019-23.html
13:17 < nmz787> Analog and mixed signal IC design is notoriously difficult and slow due in large part to the layout. Modern integrated circuit fabrication with such small devices can have significant interconnect parasitics that can drastically affect the behavior of a circuit’s design. The implication is that simulations of circuit’s behavior are unreliable until after the interconnect parasitics are extracted 
13:17 < nmz787> from the layout and included in the simulation. The Berkeley Analog Generator (BAG) is a Python-based tool that interfaces with the Cadence Virtuoso software [3] that aims to solve the above problem. BAG allows the user to write parametrizable generator scripts that will automatically generate the entire layout and schematic, as well as run the layout-versus-schematic (LVS) and post-layout extraction 
13:17 < nmz787> (PEX) tools and export the results in a time that ranges from seconds to minutes based on circuit complexity.
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14:32 < kanzure> https://www.vipergen.com/yoctoreactor-yr-libraries/
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14:52 < kanzure> .wik Z-DNA
14:52 < saxo> "Z-DNA is one of the many possible double helical structures of DNA. It is a left-handed double helical structure in which the helix winds to the left in a zigzag pattern, instead of to the right, like the more common B-DNA form." - https://en.wikipedia.org/wiki/Z-DNA
14:57 < kanzure> https://gnusha.org/logs/2018-12-19.log
14:57 < kanzure> 12:14 < fenn> i swear they make the DNA left-handed just to piss off any scientists who might happen to be reading
14:57 < nmz787> hmm, so mechanosynthesis via DNA origami, basically
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16:10 < fenn> it's never Z-DNA, which has a much shallower helix angle and wouldn't look right
16:10 < fenn> and besides nobody who is making those illustrations even knows what Z-DNA is
16:46 < kanzure> "Bringing microscopy-by-sequencing into view" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6943198/
16:46 < kanzure> nearly forgot about DNA nanoscopy ...
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17:10 < kanzure> "Advanced unconventional techniques for sub-100 nm nanopatterning" (2022) https://onlinelibrary.wiley.com/doi/pdf/10.1002/inf2.12323
17:17 < kanzure> "Three-dimensional nanolithography guided by DNA modular epitaxy" https://sci-hub.se/https://www.nature.com/articles/s41563-021-00930-7
17:17 < kanzure> ".. Single-run reactive ion etching then transfers the DNA patterns to a Si substrate at a lateral critical dimension of 7 nm and a vertical critical dimension of 2 nm."
17:25 < kanzure> fluorescent protein sequencing technique https://www.erisyon.com/technology/
17:28 < kanzure> oh yeah, talli somekh
17:29 < kanzure> "fluorosequencing" ok
17:31 < kanzure> http://www.museaventures.com/portfolio/ not bad... also didn't know his family was the "founding donor" of biobricks foundation.
17:37 < maaku> fenn: left handedness is the right handedness
17:54 < fenn> well whatever you call it when the helix goes clockwise away from you
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19:06 < kanzure> .wik punched tape
19:06 < saxo> "Punched tape or perforated paper tape is a form of data storage that consists of a long strip of paper in which holes are punched." - https://en.wikipedia.org/wiki/Punched_tape
19:09 < kanzure> https://en.wikipedia.org/wiki/History_of_numerical_control
19:10 < fenn> going to make a molecular NC machine?
19:10 < fenn> fortunately atomic lattices are quantized
19:10 < fenn> all integers makes the math easy
19:18 < kanzure> more accurately i'm avoiding work at the moment :p
--- Log closed Thu Sep 22 00:00:26 2022