--- Log opened Tue Sep 26 00:00:29 2017
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02:44 < kanzure> .wik SELEX
02:44 < yoleaux> "Disambiguation: SELEX" — https://en.wikipedia.org/wiki/SELEX
02:45 < kanzure> .wik systematic evolution of ligands by exponential enrichment
02:45 < yoleaux> "Systematic evolution of ligands by exponential enrichment (SELEX), also referred to as in vitro selection or in vitro evolution, is a combinatorial chemistry technique in molecular biology for producing oligonucleotides of either single-stranded DNA or RNA that specifically bind to a target ligand or ligands." — https://en.wikipedia.org/wiki/Systematic_evolution_of_ligands_by_exponential_enrichment
02:47 < kanzure> your "barcode per cell" idea is essentially the same thing as mapseq or synseq which zador lab has been doing
02:47 < kanzure> http://diyhpl.us/~bryan/papers2/neuro/Using%20high-throughput%20barcode%20sequencing%20to%20efficiently%20map%20connectomes%20-%20v3%20-%202017.pdf
02:50 < kanzure> cheapo laminar flow hood (targeted to the amateur fungi grower community) http://www.fungi.com/product-detail/product/the-series-i-laminar-flow-hood-230v50hz.html
02:53 < fenn> fig 4f is pretty cool
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03:04 < kanzure> yeah i guess it would be cheaper to record all the mRNA transcripts inside of a cell, into an internal polymer chain, rather than coat the internal brain surface with dna molecules and read everything out.
03:04 < kanzure> you only need to know relative 'weights' and which receptors are win which neurons-- and presumably receptors do not live for decades or whatever, they are probably replaced on a regular schedule?
03:05 < kanzure> and presumably you don't need to know the relative positioning of each receptor (and types) against all the other receptors on the same neuronal membrane.... if that's a requirement then maybe we really are screwed.
03:06 < fenn> i'd rather have an off-brain backup
03:06 < kanzure> russell is still doing his gold nanoparticle x-ray stuff
03:07 < fenn> getting the sequence out of the brain is better than only recording internally
03:07 < kanzure> there's a non-zero amount of dna in the bloodstream... just secrete out the polymers from each neuron, target the bloodstream, then put a nanopore sequencing array in the heart to grab all the free floating dna.
03:07 < fenn> it could be packaged up as a virus and put into the blood for filtering by artificial antibodies
03:08 < fenn> sure you could use an implant too
03:14 < kanzure> musics https://www.youtube.com/watch?v=-9pgIVcB3rk
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06:51 < kanzure> ayup.
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07:10 < kanzure> pasky: grognor has died.
07:12 < kanzure> "Detecting DNA cytosine methylation using nanopore sequencing" http://www.nature.com/nmeth/journal/v14/n4/full/nmeth.4184.html
07:16 < pasky> who's grognor?
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07:32 < mindsForge> if anyone is interested the Google dev Human/AI interaction livestream is talking about feed algos: https://www.youtube.com/watch?v=w3zSffhPUz0
07:33 < kanzure> pasky: author of that blog post you were looking at
07:35 < pasky> Oh, the twitter suns. Well, I was kinda confused by that one. But all deaths are sad. :(
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07:57 < kanzure> gene-hacker: has hod lipson abducted you yet?
07:58 < kanzure> oh wait he's at columbia now
07:58 < gene-hacker> nope
07:58 < gene-hacker> pittsburgh
07:59 < gene-hacker> got abducted by another computational synthesist though
07:59 < kanzure> ah okay. cool.
07:59 < gene-hacker> \msg kanzure test
08:03 < kanzure> wrong /
08:05 < heath> hm, the schedule online (http://dna23ut.org) is slightly different from what's in the booklet. oh well
08:06 < gene-hacker> yeah I got it
08:07 < gene-hacker> did you get my message?
08:09 < gene-hacker> guess you di
08:09 < gene-hacker> *did
08:10 < gene-hacker> NIAC 2017 starting up at 10:20 mountain time
08:10 < gene-hacker> https://www.nasa.gov/sites/default/files/atoms/files/2017_niac_symposium_agenda.pdf
08:10 < gene-hacker> https://livestream.com/viewnow/NIAC2017
08:10 < kanzure> "optical mining of asterois"
08:10 < kanzure> *asteroids
08:12 < kanzure> and the torpor presentation on wednesday, that looks ok
08:13 < gene-hacker> yeah optical mining was yesterday
08:13 < gene-hacker> where was that optical sorting paper?
08:13 < gene-hacker> area of effect soft robots for asteroids was interesting
08:14 < gene-hacker> though in my opinion it could have used less soft robots
08:14 < gene-hacker> soft robotics is just a buzzword
08:14 < kanzure> soft robotics is just su8 lizard overlords trying to take over the world
08:14 < kanzure> pdms/su8 overlords
08:15 < gene-hacker> nah
08:15 < gene-hacker> these days it's dragon skin
08:15 < gene-hacker> but I've no gripe with using commercially available elastomers
08:15 < gene-hacker> it's the actuators I have a problem with
08:16 < gene-hacker> we don't have a good way to make soft actuators
08:17 < gene-hacker> the thermodynamics just simply doesn't make pneumatic soft robots practical for much of anything
08:21 < superkuh> sci-hub seems offline.
08:21 < kanzure> superkuh: http://sci-hub.ac/
08:22 < kanzure> gene-hacker: have you seen inkjet printable actuators stuff? http://diyhpl.us/~bryan/papers2/mems/Inkjet%20printing%20of%20micro-electro-mechanical%20systems%20(MEMS)%20-%202017.pdf
08:22 < superkuh> Yeah, that too.
08:22 < kanzure> superkuh: that link works for me
08:22 < superkuh> Ah. I'll try different IPs on my end.
08:23 < superkuh> I'm getting the cloudflare  site is down message.
08:23 < gene-hacker> that's not a good sign
08:24 < gene-hacker> wow
08:24 < superkuh> Oh, yeah, the main page loads.
08:24 < gene-hacker> that paper's pretty good
08:24 < gene-hacker> whole lot of showing off
08:24 < superkuh> But no results. I always just type, http://sci-hub.whatever/10.2514/1.8554
08:26 < heath> superkuh: not having problemss over here with .cc
08:27 < kanzure> superkuh: try this, https://sci-hub.ac/https://arc.aiaa.org/doi/abs/10.2514/1.8554
08:27 < heath> i do have problems when i typing in a name, but pasting the doi has always worked
08:27 < heath> s/typing/type
08:27 < kanzure> ah yes it really is down
08:27 < kanzure> https://moscow.sci-hub.ac/f698d04e3d388f3001659e75dd02ddbd/mcguire2005.pdf?download=true
08:28 < kanzure> superkuh: this one is up,
08:28 < kanzure> https://moscow.sci-hub.ac/f698d04e3d388f3001659e75dd02ddbd/mcguire2005.pdf?download=true
08:28 < kanzure> er... sorry.
08:28 < kanzure> https://ocean.sci-hub.ac/f698d04e3d388f3001659e75dd02ddbd/mcguire2005.pdf?download=true
08:28 < heath> hm. .cc is down now. i just used it 5 mins ago
08:28 < kanzure> ocean not moscow
08:29 < kanzure> file downloaded for me when using the ocean mirror instead of moscow mirror
08:29 < superkuh> Yes. Thanks.
09:18 < fltrz> kanzure: can you take a look at the pdf here https://www.researchgate.net/publication/272095393_Direct_Design_of_an_Energy_Landscape_with_Bistable_DNA_Origami_Mechanisms
09:19 < fltrz> look at the first figure of the bistable potential energy well
09:19 < fltrz> the resonance frequency of a well depends on the curvature of the wells bottom
09:20 < fltrz> note S1 and S2 in the diagram, those would be different resonance frequencies
09:20 < fltrz> let me denote their frequencies f1 and f2, to transition from S1 to S2, you produce vibration at frequency f1 while absorbing any frequency at f2
09:21 < fltrz> to transition from S2 to S1, you produce frequency f2 and absorb any f1 vibrations
09:22 < fltrz> irrespective if the vibrations are caused by phonons (tiny piezo?) , IR photons (focused dot), or polaritons (perhaps an on-nanopore-chip polariton transmission line ending near the nanopore)
09:23 < fltrz> so it should be possible to set or reset (i.e. overwrite) the bit encoded in secondary structures
09:24 < fltrz> in their example the mechanism design is very bar & linkage inspired
09:24 < fltrz> but the software used to determine stable secondary structure energies should be able to calculate resonance frequencies at each stable conformation as well
09:27 < fltrz> so the bistable single bit 'monomer' (which is actually an oligomer sequence on the biopolymer tape with 2 or more stable secondary structures) doesn't need to be designed from the perspective of bars and joints
09:28 < fltrz> assuming given: software that computes from biopolymer sequence -> stable conformations energies + frequencies
09:28 < fltrz> we can write a loop that instructs to compute these for all possible sequences up to length N and select the best candidates
09:29 < fltrz> i.e. where 2 stable states have similar low energy levels, where the barrier between the 2 states is high/wide enough to prevent thermal fluctuations from erasing the bit
09:29 < fltrz> etc
09:29 < fltrz> and such that the frequencies are accessible to be delivered
09:29 < fltrz> and absorbed
09:30 < fltrz> (absorption of say phonons on a piezo can be modulated by matching a load impedance to the piezo, and opening or closing the circuit)
09:32 < fltrz> first versions of the write head might have the writing zone substantially larger than the single bit length on the biopolymer tape
09:32 < fltrz> so first versions might actually be writing say 100 of the bistable elements at once
09:33 < fltrz> then it is a matter of miniaturization to try to stimulate only one bistable bit on the polymer
09:34 < fltrz> f1 and f2 can be supplied by seperate piezo's or if close together enough, by the same piezo, and the circuit impedance can be made frequency dependent
09:35 < fltrz> so that the same single piezo can alternate between producing f1 & absorbing f2 OR producing f2 and absorbing f1 OR inactivity
09:36 < fltrz> i.e. writing S2 when the bit is already in S2 does not switch it back to S1, ... since the bistable system will not resonate with f1 when it is in S2
09:38 < fltrz> if you don't understand parts of my proposal just ask
09:44 < gene-hacker> what's your proposal?
09:48 < kanzure> data storage technique using a biopolymer tape
09:49 < kanzure> fltrz: describe write resolution or storage/retrieval resolution. if you use a giant 15 nm laser spot, then your write density ain't so good...
09:49 < kanzure> or is write density irrelevant as long as you have high storage/retrieval density?
09:50 < gene-hacker> DNA is also sort of fragile
09:50 < gene-hacker> also note the scale bar
09:50 < kanzure> gene-hacker: i was at a meeting earlier this month organized by IARPA because they want to do molecular information storage on DNA. they were asking me how to scale it up to write many exabytes of data into less than 1 kg of DNA.
09:50 < fltrz> kanzure: correct, but it could still count as a proof of concept, where the write head needs replacing with say polariton transmission line
09:51 < kanzure> gene-hacker: DNA (or other polymers) is an OK data storage medium, yea it's fragile in some circumstances, but there's a lot of research regarding how to handle DNa.
09:51 < kanzure> gene-hacker: you can imagine storing data in DNA molecules by e.g. methyl groups and then shooting off the methyl groups with electrons using a nanopore, or storing data based on the sequence of nucleotides, and other methods.
09:52 < fltrz> an alternative is to find enough bistable sequences, such that you can alternate them, say a 1000 different kinds, such that using f1,499 and damping f2,499 does not affect the 500 bits before and after
09:52 < gene-hacker> so again these DNA molecules are pretty big
09:52 < fltrz> and the 500 after
09:52 < gene-hacker> how do you read them
09:52 < kanzure> gene-hacker: well a bunch of dna data storage proposals use dna molecules that are 20 bp to 200 bp in length, and some use longer molecules like 100 kbp (which are not as regularly synthesized these days, although people are hopeful that we will switch)
09:52 < gene-hacker> also how did you get involved with IARPA
09:53 < kanzure> some guy named "metreon cascade" at IARPA recommended me, i dunno
09:53 < fltrz> I think proof of concept of reagentless mass storage (with prospect of decreasing the constant of atoms/bit, with prospect of decreasing write spot size) would be convincing
09:53 < kanzure> they are worried about impending data storage apocalypse (running out of pure silicon, which is obviously a requirement for flash memory devices which top out at about 1 picogram per 1 bit)
09:54 < gene-hacker> well if you want bistable
09:54 < gene-hacker> rotaxanes are an interesting option
09:54 < fltrz> gene-hacker: I propose reading them with nanopores, so secondary structure S1 and secondary structure S2 would need to have different nanopore profile
09:54 < gene-hacker> http://rsta.royalsocietypublishing.org/content/roypta/365/1855/1607.full.pdf
09:55 < gene-hacker> how do you read a linkage with a nanopore?
09:55 < kanzure> i saw a rotaxane the other day.... i think they are often used for the molecular nanomachine walkers?
09:55 < kanzure> nanopore dna sequencing is a very popular technique these days
09:55 < fltrz> say orienting more parallel vs perpendicular to the average nanotape length direction
09:55 < fltrz> that would differentially block current through the nanopore
09:55 < kanzure> you run a current through the molecule and you can detect which nucleotide is at that location in the dna molecule. then you run the dna molecule through the nanopore at about 1kbp/sec.
09:55 < fltrz> gene-hacker: I don't propose to use this linkage
09:56 < kanzure> oh you mean fltrz's linkage
09:56 < adlai> kanzure: thank you for sharing http://diyhpl.us/~bryan/papers2/luminous.pdf - but if all the .pdf contains is text, why not .txt?
09:56 < gene-hacker> a nanopore would be a silly way to read it
09:56 < kanzure> "Designing bistable [2]rotaxanes for molecular electronic devices" http://rsta.royalsocietypublishing.org/content/roypta/365/1855/1607.full.pdf
09:56 < gene-hacker> especially when you can do FRET
09:56 < fltrz> I am not familiar with rotaxanes
09:56 < kanzure> FRET requires optics ya?
09:56 < gene-hacker> you can put photophores in the right place on your DNA linkage
09:56 < gene-hacker> and you could figure out what state it is in with that
09:57 < gene-hacker> yes
09:57 < kanzure> gene-hacker: yes fluorescence is used in some dna sequencing techniques, called "sequencing by synthesis"
09:57 < gene-hacker> so you could use a beefed up optical disk
09:57 < gene-hacker> writing would still be interesting
09:58 < kanzure> well even with, say, inkjet dna synthesiers... the write density is low. so you have to do lots of parallel reactions (100 million different inkjet-targeted spots on a surface).  and then you store the dna in a more compact form (giant pool of liquid, then you use PCR to pull out the data you want later).
09:59 < gene-hacker> so rotaxanes you can electrically switch and electrically ready
09:59 < gene-hacker> the challenge is wiring them all up
09:59 < kanzure> electrical switching -> conformational change?
09:59 < fltrz> thanks all for the rotaxanes mention! i have some more reading to do then
09:59 < gene-hacker> yes
10:00 < kanzure> well maybe you could put a rotaxane in a protein or enzyme.  easy to hook up proteins to electrodes or nanopores.
10:00 < gene-hacker> you move a ring up and down a rod
10:00 < gene-hacker> then you lose storage capacity
10:01 < gene-hacker> there are a number of molecules that switch when electricity is applied
10:01 < fltrz> kanzure: if they fear running out of high purity silicon, any system where device usage (as opposed to manufacture) consumes reagents is not going to sound pleasant to them
10:01 < kanzure> gene-hacker: i'm most familiar with azobenzenes, which switch in the presence of photons or optical stimulation
10:01 < gene-hacker> but it is really hard to wire them up
10:01 < kanzure> fltrz: well the ultimate form of dna data storage is just use food or whatever the autotrophs do
10:02 < kanzure> gene-hacker: azobenzenes have been used in custom amino acids, so you can deliver an optically-inducible conformational change into any protein or enzyme
10:02 < gene-hacker> yeah
10:03 < gene-hacker> but again, how do you individually write them?
10:03 < gene-hacker> and read them?
10:03 < fltrz> right, but that island seems far away *for now*, a reagentless biopolymer with a bistable 'monomer' as repetition unit, seems like a compromise, an island along the way
10:04 < kanzure> i have not thought about genetically-encoded azobenzenes in the context of data storage.  i think there's some potential there.  you can combine them with dna-modifying/binding enzymes.
10:05 < gene-hacker> what do you need a biopolymer for?
10:05 < kanzure> dna is a biopolymer
10:05 < kanzure> it's the highest density information storage mechanism that we know about
10:05 < gene-hacker> when you could spray something bistable on disk and read them?
10:05 < fltrz> gene-hacker: because its tape
10:06 < fltrz> * tape-ish
10:06 < kanzure> you can't spray at that density
10:06 < fltrz> and nanopore is the tape reader
10:06 < gene-hacker> yes you can
10:06 < gene-hacker> see self assembling monolayers
10:06 < kanzure> elaborate
10:07 < fltrz> gene-hacker: the read/write spot size is typically orders of magnitude greater (lets call it T for thousandish) than the bistable system, with linear tape that would only be T, in 2 dimensions that becomes T^2 is millionish
10:08 < fltrz> so the number of atoms per bit would be order of T wastefull with spot size T on a linear biopolymer, but would be T^2 wasteful in atoms per bit on 2d surface
10:08 < kanzure> also dna can fold up and be stored very compactly
10:09 < fltrz> kanzure: thats actually the same argument but you put it better
10:09 < kanzure> i'm debugging some bitcoin errors at the moment so i'm not really paying attention sorry
10:09 < gene-hacker> with a SAM, you could have the rotaxanes or whatever packed very densely
10:09 < gene-hacker> again
10:09 < kanzure> well your rotaxanes were hard to manipulate individually right?
10:10 < gene-hacker> how do you read and write for the DNA linkage thing?
10:10 < fltrz> i.e. consider a write zone length of T bistable units, in 2 dimensions you could fold that tape back and forth and form a square of T^2, and that would be individual adressable bistable unit on surface tech
10:10 < kanzure> not sure about linkage sorry.   i can describe general DNA read/write.
10:10 < gene-hacker> how do you fold the tape without changing the state
10:11 < fltrz> gene-hacker: I was considering resonance, consider nanopore where the electrodes are across the pore, then any net electrical polarization in the bistable unit could be used for electrically coupling the mechanical resonance
10:11 < gene-hacker> yeah I'm aware of the DNA data storage stuff
10:12 < fltrz> gene-hacker: I am ignoring the tertiary structure, i.e. just letting float in solution
10:12 < gene-hacker> well if it's just floating in solution then it's going to change shape
10:12 < gene-hacker> on it's own
10:13 < fltrz> well the bistable unit would be selected such that the barrier between S1 and S2 is high enough, for thermal vibrations in contact with solvent, or itself
10:14 < fltrz> some errors are inevitable, and its why every data storage format uses error correcting codes
10:14 < fltrz> or do you mean something like the dna getting in a knot?
10:14 < gene-hacker> DNA has about the structural properties of jello
10:15 < fltrz> yes, its why one should use correct jello software that calculates the energies and resonances for DNA origami correctly
10:20 < fltrz> semiconductor has about the same conductive properties as seawater
10:24 < fltrz> these are 3 open source DNA origami softwares https://en.wikipedia.org/wiki/Ascalaph_Designer https://en.wikipedia.org/wiki/MDynaMix https://dna.physics.ox.ac.uk/index.php/Main_Page
10:26 < kanzure> also cadnano
10:26 < kanzure> and https://github.com/kanzure/nanoengineer
10:27 < fltrz> as soon as the excitation mechanism starts to approach the size of a single repetition unit of the biopolymer, this repetition unit should not propagate the f1 and f2 frequencies along the biopolymer, so that neighbouring bits dont get altered along
10:27 < fltrz> but as long as T is large enough, we can ignore this issue in the selection of repetition unit
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10:30 < fltrz> kanzure: I did not include all the design softwares like cadnano, since they don't actually simulate, they are used as starting points, to be verified with biopolymer simulation software
10:31 < fltrz> does nanoengineer simulate? does it work well on biopolymers?
10:33 < fltrz> for a suitable bistable repetition unit the 2 stable states should also have the same length, and rotation, such that switching state does not significantly pull/push torsion/rotate the 2 large sections of dna on either side
10:34 < fltrz> for fast/energy efficient switching, for not disturbing neighbouring bits
10:35 < fltrz> the software probably need some custom tailoring to include these requirements in simulation
10:37 < kanzure> nanoengineer does simulation using other software like gromacs
10:38 < fltrz> ok, I consider that good enough (Ascalaph designer also delegates the actual simulation to other software packages)
10:50 < fltrz> gene-hacker: thx for mentioning the rotaxanes, they're awesome
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11:18 < fltrz> for excitation/absorption, consider silicon nanopore with this kind of polariton transmissionline right to the edge of the pore: https://www.researchgate.net/publication/305502108_On-chip_sub-terahertz_surface_plasmon_polariton_transmission_lines_with_mode_converter_in_CMOS
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11:45 < archels> http://voxeu.org/article/rise-robots-german-labour-market
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12:58 < fltrz> lol this Hodges science-slave is like his electricity test animal https://web.archive.org/web/20120314115000/http://www.lateralscience.co.uk/VicN2/vicN2.html
13:00 < fltrz> his suffering just never stops? "Hodges` hand was still smoking when I started the sketch, I hurried somewhat, as he was pleading to go to the horse doctor."
13:01 < fltrz> the text is about the accidental discovery of nitrogen TEA laser, in victorian era, although they didn't even know the concept of a laser, so they did not understand what they saw...
13:02 < fltrz> and what Hodges again was of course blinded by
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13:05 < fltrz> ah its not real, its written as if...
13:08 < kanzure> did you fall into the wrong time line again?
13:09 < kanzure> "Getting started with openbsd device driver development" https://www.openbsd.org/papers/eurobsdcon2017-device-drivers.pdf
13:22 < nmz787> kanzure: you're never gonna get a 15nm laser spot... unless you have some crazy hologram or insane diffractive optics
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14:16 < kanzure> what spot size should i use when i want to refer to an appropriate laser spot size
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14:49 < fltrz> kanzure: what do you mean with what spot size? gaussian waist?
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15:18 < fltrz> one dimensional 50nm lens 10 years ago http://sci-hub.cc/10.1364/OE.15.006947
15:19 < fltrz> non scihub link http://circuit.ucsd.edu/~zhaowei/Journals/Optics_exp_planb%20tilted%20lines.pdf
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15:46 < kanzure> tree style tabs now works on recent versions of firefox again https://news.ycombinator.com/item?id=15342362
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16:42 < nmz787> kanzure: well without crazy diffractive/holographic lenses, you're limited to diffraction limit, which would be basically the wavelength of the photons
16:52 < kanzure> we don't have crazy diffractive optics for optical data write?
16:52 < kanzure> i guess it doesn't matter, it will always lose out to more compact forms of data storage
16:55 < nmz787> CD/DVD/bluray is all at-diffraction-limit
16:55 < nmz787> and the wavelength color of each's laser got smaller
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18:00 < kanzure> hrmm i have at least 30 papers to review (and accept/reject) for scalingbitcoin.org stanford
18:08 < fltrz> you have early access to scaling proposals?
18:17 < kanzure> i am the program committee
18:20 < kanzure> http://media.comicbook.com/2016/12/dredd-movie-karl-urban-sequel-217152-1280x0.jpg
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18:48 < kanzure> .title https://news.ycombinator.com/item?id=15342840
18:48 < yoleaux> BOOM v2: an open-source out-of-order RISC-V core | Hacker News
18:48 < kanzure> https://www2.eecs.berkeley.edu/Pubs/TechRpts/2017/EECS-2017-157.html
18:49 < kanzure> https://www2.eecs.berkeley.edu/Pubs/TechRpts/2015/EECS-2015-167.pdf
18:49 < nmz787> hybrid human:raccoon could be cool
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18:50 < kanzure> "Avoiding ISA bloat in RISC-V" https://arxiv.org/abs/1607.02318
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18:55 < kanzure> risc-v cores in bluespec https://github.com/csail-csg/riscy
18:56 < kanzure> https://github.com/csail-csg/riscy/blob/master/procs/riscy-lib/RVMulDiv.bsv
18:57 < kanzure> and one using spinalhdl https://github.com/SpinalHDL/VexRiscv
18:57 < kanzure> and this one in verilog https://github.com/cliffordwolf/picorv32
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19:05 < nmz787> https://lirias.kuleuven.be/bitstream/123456789/496274/1/thesis.pdf
19:05 < nmz787> "As stated, a nanopore is basically a nanometer-sized version of the Coulter Counter."
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19:31 < nmz787> http://domino.research.ibm.com/library/cyberdig.nsf/papers/6482D3B7D94062B785257384005D2882/$File/rc24242.pdf
19:33 < nmz787> "Our DNA transistor is a nanopore defined in an atomically precise sandwich of metal elec- trodes and insulators. Application of external voltages to the electrodes creates a potential well inside DNA transistor that is capable of trapping the polymer molecule with a trap- ing energy in the range of a few k B T range. Variation of applied voltages leads to trans- location of the DNA molecule by one
19:33 < nmz787> nucleotide with high probability. We called this effect digital electrophoresis and estimate that it can run at ~500 MHz range frequencies."
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19:40 < kanzure> nmz787: i was thinking, apply a current to a dna molecule and knock out a methyl group... and that's your write.
19:40 < kanzure> just a long cytosine chain, with methyl groups, or something
19:41 < nmz787> reversible somehow?
19:42 < kanzure> well..... there's methlytransferase and demethylase enzymes.
19:42 < kanzure> i know that's not an answer to your question. but sort of.
19:46 < kanzure> yeah maybe we need some more nanopore friends
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19:53 < kanzure> gene-hacker: tell me nanopore things
19:54 < gene-hacker> they're small
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19:59 < nmz787> gene-hacker: know anyone around your way doing nanofluidics or single-molecule stuff?
20:13 < gene-hacker> some of the people in our office do DNA origami
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22:48 < nmz787_> "In Section II we explain the operation principle of the DNA transistor – electrostatic control over ionized phosphate groups of DNA backbone"
23:13 < nmz787_> .tw https://twitter.com/whitequark/status/912419697181822977
23:13 < nmz787_> .tw
23:13 < yoleaux> okay so I sequenced my whole genome and published it under CC-BY-NC https://doi.org/10.5281/zenodo.995635 https://doi.org/10.5281/zenodo.995725 (some assembly required) (@whitequark)
23:13 < yoleaux> okay so I sequenced my whole genome and published it under CC-BY-NC https://doi.org/10.5281/zenodo.995635 https://doi.org/10.5281/zenodo.995725 (some assembly required) (@whitequark)
23:16 < nmz787_> what does the sequence of M D M D M  at the bottom of this image mean? https://youtu.be/pKi30ai35mU?t=24   ?
23:17 < nmz787_> .title
23:17 < yoleaux> DNA Transistor - YouTube
23:26 < nmz787_> kanzure: so we need to call out diffs between ssDNA and dsDNA... and also how to deal with the persistence length being like 10X shorter with ssDNA (or something like that, I read it earlier but it didn't have numbers)... so kinks and such will form in wide-enough channels unless complexed (with a complement), or maybe in some salt solution or something.
23:27 < nmz787_> I guess we could require two synthesis reactions be paired...
23:27 < nmz787_> or have a polymerase hanging out to do it in the next chamber/section over
23:28 < nmz787_> i guess tdt is a polymerase technically
23:32 < nmz787_> but then later during search, we might need some matching enzyme to unzip and aid the search... possibly locking on to all 3 for long enough to filter the whole big mass from the non-result soup
23:34 < nmz787_> .tell yashgaroth is there an enzyme that will take a primer and search a soup of dsDNA, then lock on to all 3 (easily reversible, but stays on long enough to filter/electrophorese away, etc, then remove after that...)
23:34 < yoleaux> nmz787_: I'll pass your message to yashgaroth.
23:36 < nmz787_> kanzure: also we should probably get similar 'retention' times (longevity, stability, etc..) for enzymes like polymerases and nucleotide kinases... the DNA might be stable, but what about these/any proposed enzymes?
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