--- Log opened Tue Jul 19 00:00:01 2016 00:33 -!- drewbot [~cinch@ec2-174-129-100-67.compute-1.amazonaws.com] has quit [Remote host closed the connection] 00:33 -!- drewbot [~cinch@ec2-50-16-54-38.compute-1.amazonaws.com] has joined ##hplusroadmap 00:48 -!- ebowden_ [~ebowden@2001:8003:100e:c500:2468:9f3b:3509:2100] has quit [Remote host closed the connection] 00:49 -!- ebowden_ [~ebowden@CPE-101-180-249-107.lnse3.cha.bigpond.net.au] has joined ##hplusroadmap 00:57 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 01:08 -!- augur [~augur@2601:645:c100:63f1:291d:3d8f:a53:97b3] has quit [Remote host closed the connection] 01:50 -!- zeroach [~CharlieNo@97-85-242-17.static.stls.mo.charter.com] has quit [Ping timeout: 240 seconds] 01:51 < chris_99> Anyone know of a database of visibile/IR spectrums, for assorted chemicals/materials etc 02:04 -!- PatrickRobotham [uid18270@gateway/web/irccloud.com/x-qhdlvnlbduauhdvv] has joined ##hplusroadmap 02:16 -!- jtimon [~quassel@55.31.134.37.dynamic.jazztel.es] has joined ##hplusroadmap 02:30 -!- jtimon [~quassel@55.31.134.37.dynamic.jazztel.es] has quit [Ping timeout: 244 seconds] 03:31 < nmz787> chris_99: might try CRC manual 03:31 < nmz787> chris_99: or torrents or something :/ 03:31 < ebowden_> nmz787, any idea how to contact authors of a paper? 03:33 < ebowden_> The relevant paper is in future med chem. 03:40 < chris_99> nmz787, CRC manual? 03:40 < ebowden_> chris_99, have you any idea how I might contact the author of a paper? 03:40 < chris_99> this - http://www.hbcpnetbase.com/ ? 03:40 < chris_99> ebowden_, do they not list the email address on their paper 03:44 < ebowden_> Oh fucking derp, I didn't see the author for correspondence email address. 03:46 < chris_99> heh 03:54 < ebowden_> God damn it. 04:09 < chris_99> https://en.wikipedia.org/wiki/Heavy_water#Production just reading that, i wonder how hard it is to extract with electrolysis 04:11 < TMA> chris_99: it's not very energy efficient in the first phases, when the deuterium contents is very low 04:11 < chris_99> ahh 04:11 < chris_99> could you do it though, given enough time, from tap water 04:12 < TMA> chris_99: you most certainly can. 04:13 < chris_99> neat 04:15 < TMA> chris_99: be prepared to pay huge electricity bills though 04:16 < chris_99> heh yeah 04:16 < TMA> chris_99: (you might save a bit if you burn the resulting hydrogen and use the heat in a distillation step) 04:18 -!- CheckDavid [uid14990@gateway/web/irccloud.com/x-rjvjprdwtrcswnxq] has joined ##hplusroadmap 04:18 < chris_99> i need to read about how the electrolysis works, as normally you get H and O right, so what happens to the D, how is that actually seperated 04:21 < TMA> chris_99: when you split water into hydrogen and oxygen, the splitting occurs first with 1H (because it is lighter) the remaining water contains more 2H = D than the water you have put in 04:23 < chris_99> ah interesting 04:23 < TMA> chris_99: so after you reduce the volume of the input water to some fraction, the liquid fraction is more concentrated than the input; lather rinse repeat :) 04:23 < chris_99> heh 04:23 < chris_99> how do you measure the % of H2O to D2O 04:24 < Jenda`> maybe by density, D2O has about 1100 kg/m3 04:24 < Jenda`> mass spectrometer would be more precise, but most people don't have it at home 04:25 < chris_99> mm, density sounds a good waay 04:28 < TMA> chris_99: it is difficult to measure precisely in the early phases 04:28 < chris_99> ah makes sense 04:29 < chris_99> with D2 is the same amount of energy released as H2, during combustion out of interest 04:31 < TMA> makes sense -- the chemical bond energy is the same 04:31 < chris_99> aha 04:32 < TMA> even in the electrolysis you need the same amount of energy to dissociate the water molecule 04:32 < chris_99> so i'm slightly confused, does the D2 not get released at all during electrolysis 04:32 < TMA> but due to the weight differential the dissociated H+ moves faster than dissociated D+ 04:33 < TMA> therefore it is less likely to be recaptured by another molecule 04:34 < TMA> chris_99: it is released. but the release of D is slower (hence you want the electrolysis to stop at the right moment) 04:34 < chris_99> ah 04:35 < chris_99> hmm does the D2O sink to the bottom of a pool of tap water? 04:36 < TMA> chris_99: in tap water the H:D ratio is 6420:1 ; after a single run of the electrolysis it might be like 6400:1, the reduction is very slow especially in the initial phases 04:37 < chris_99> ah eek 04:37 < TMA> chris_99: if in sufficient concentration, otherwise it is knocked upwards by brown motion 04:37 < chris_99> gotcha 04:38 < TMA> there is a reason why D2O is about 1000 €/kg 04:38 < chris_99> heh 04:39 < chris_99> there isn't another way to create it, doing something to Hydrogen, to turn it into D? 04:39 < Jenda`> I don't think a neutron capture can occur 04:39 < TMA> chris_99: put it in a reactor, it will capture neutrons 04:40 < chris_99> interesting 04:40 < Jenda`> Business plan: if cars on hydrogen become popular, collect leftovers from electrolysis 04:40 < chris_99> heh 04:40 < Jenda`> TMA: I don't think reactors produce significant amount of deuterium 04:41 < Jenda`> well, year, Temelín (local nuclear power plant) releases tritium, but I don't know if it's from hydrogen or if it's a fissile product 04:41 < TMA> Jenda`: it is less economically viable, but they do 04:42 < TMA> Jenda`: Temelin uses light water, the tritium is partly from neutron capture 04:43 < Jenda`> hm, so the water in the primary circuit slowly turns into D2O and then to T2O? 04:43 < TMA> Jenda`: exactly 04:44 < Jenda`> well, but how do they routinely release it, when the primary circuit is closed (and contaminated)? 04:44 -!- jtimon [~quassel@55.31.134.37.dynamic.jazztel.es] has joined ##hplusroadmap 04:45 < TMA> Jenda`: T for nuclear weapons was made by irradiating D2O in heavy water in a breeder reactor 04:45 -!- jtimon [~quassel@55.31.134.37.dynamic.jazztel.es] has quit [Remote host closed the connection] 04:45 < Jenda`> ah, ok, they really clean and release water from primary circuit: https://www.cez.cz/cs/vyroba-elektriny/jaderna-energetika/jaderne-elektrarny-cez/ete/technologie-a-zabezpeceni/11.html 04:46 < Jenda`> I thought that they fill the primary circuit once and never drain/refill it 04:48 < Jenda`> chris_99: maybe electrolysing water from rivers near a nuclear power plant would be a better start than electrolysing regular tap water https://www.cez.cz/edee/content/img/energie-a-zivotni-prostredi/jaderna-energetika-elektrarny-cez-ete-technologie-a-zabezpeceni-tritium.gif 04:49 < chris_99> what's Bq/l mean? 04:50 < chris_99> oh becquerel 04:51 < Jenda`> red line = activity during drought, yellow = average activity; x-axis: kilometers 04:52 < chris_99> interesting 05:31 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has quit [Quit: quit message] 05:55 -!- bluebear_ [~chatzilla@80.95.97.194] has joined ##hplusroadmap 06:00 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Quit: Leaving] 06:02 < fenn> TMA: i'd imagine the methods used for uranium enrichment work just fine on H2 gas as well, namely laser enrichment and microfluidic single-turn centrifuge/separators i.e. https://commons.wikimedia.org/wiki/File:Aerodynamic_enrichment_nozzle.svg 06:06 < TMA> fenn: it might work directly with steam 06:06 < TMA> i.e. no need to prepare H2 HD D2 mixture beforehand 06:07 < TMA> fenn: do you have any idea how to compute the best geometry? 06:08 < fenn> "Separation of Isotopes by Laser Excitation (SILEX)" jeez no wonder i was confused about SELEX 06:09 < fenn> sorry i don't know very much about it, i imagine it's pretty similar to a mass spectrometer 06:09 -!- eudoxia [~eudoxia@r167-56-138-115.dialup.adsl.anteldata.net.uy] has joined ##hplusroadmap 06:09 < fenn> without the magnetic field of course 06:10 -!- Aurelius_Work [~cpopell@209.48.69.2] has joined ##hplusroadmap 06:19 < fenn> enrichment nozzles are really small, i discovered it while reading about high aspect ratio silicon etching processes for MEMS 06:21 < fenn> i remember seeing a bottle of D20 in a university chemistry lab sitting on a shelf, it can't be that expensive 06:22 < TMA> fenn: the diagram on wikipedia has 1 mm bar for size comparison. I gather that the radius and aperture shall be different for diferent isotope separation tasks 06:26 < TMA> fenn: university labs are well stocked -- the only reason they are not broken into more often is that the market for the more expensive reagents is small and the burglars are stupid 06:28 < xentrac> I think there are much easier ways to separate deuterium, including mere chemical reactions and crystallization 06:28 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 06:32 < fenn> ah D20 is used for proton NMR solvents which makes sense for a chemistry department 06:37 < xentrac> ah, D₂O 06:37 < xentrac> I was picturing icosahedra 06:37 < ebowden_> I really, really like tiny containers. I hope to see an NMR tube one day. 06:44 -!- eudoxia [~eudoxia@r167-56-138-115.dialup.adsl.anteldata.net.uy] has quit [Quit: Leaving] 06:49 < fenn> "According to the WNA, there are currently 436 operable reactors around the world with ~380 GWe generating capacity. Another 67 reactors are under construction in 14 countries, including 24 in China, 6 in India, and 5 in the USA. A further 166 reactors are on order or planned and 322 reactors are proposed to be built." 06:50 < fenn> wow i didn't realize the USA is building new reactors 06:56 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Remote host closed the connection] 06:56 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 06:59 < chris_99> http://www.economist.com/news/science-and-technology/21702343-individual-atoms-offer-ultra-dense-information-storage-scientists-pave-way wonder if they could just use lots of heads, maybe they already do 07:08 < chris_99> http://phoenixnuclearlabs.com/products/ 07:31 -!- Cory [~C@unaffiliated/cory] has quit [Max SendQ exceeded] 07:31 -!- EnabrinTain [sid11525@gateway/web/irccloud.com/x-efunkusmefmxhuip] has quit [Max SendQ exceeded] 07:31 -!- btcdrak [uid165369@gateway/web/irccloud.com/x-pembnhmtevagqsfy] has quit [Max SendQ exceeded] 07:31 -!- kanzure [~kanzure@unaffiliated/kanzure] has quit [Max SendQ exceeded] 07:32 -!- kanzure [~kanzure@unaffiliated/kanzure] has joined ##hplusroadmap 07:34 -!- EnabrinTain [sid11525@gateway/web/irccloud.com/x-ebeudlxdqajwvwrq] has joined ##hplusroadmap 07:34 -!- btcdrak [uid165369@gateway/web/irccloud.com/x-csjodsspivzyrwkg] has joined ##hplusroadmap 07:35 -!- Cory [~C@unaffiliated/cory] has joined ##hplusroadmap 07:38 < JayDugger> fenn, does that include military reactors in subs and carriers, or just civilian? 07:40 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Quit: Leaving] 07:46 -!- ebowden_ [~ebowden@CPE-101-180-249-107.lnse3.cha.bigpond.net.au] has quit [Remote host closed the connection] 08:06 -!- Regex__ [~Cara@2601:1c0:8501:d159:510b:d746:751f:b86c] has joined ##hplusroadmap 08:07 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has joined ##hplusroadmap 08:10 -!- Regex_ [~Cara@2601:1c0:8501:d159:510b:d746:751f:b86c] has quit [Ping timeout: 250 seconds] 08:31 < kanzure> researchgate spams you every time someone reads any of your publications? ugh 08:50 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has joined ##hplusroadmap 09:16 < kanzure> "Possible existence of optical communication channels in the brain" http://arxiv.org/abs/1607.02969 09:17 < kanzure> "Given that many fundamental questions in neuroscience are still open, it seems pertinent to explore whether the brain might use other physical modalities than the ones that have been discovered so far. In particular it is well established that neurons can emit photons, which prompts the question whether these biophotons could serve as signals between neurons, in addition to the well-known electro-chemical signals. For such communication ... 09:17 < kanzure> ... to be targeted, the photons would need to travel in waveguides. Here we show, based on detailed theoretical modeling, that myelinated axons could serve as photonic waveguides, taking into account realistic optical imperfections. We propose experiments, both \textit{in vivo} and \textit{in vitro}, to test our hypothesis. We discuss the implications of our results, including the question whether photons could mediate long-range quantum ... 09:17 < kanzure> ... entanglement in the brain." 09:21 -!- PatrickRobotham [uid18270@gateway/web/irccloud.com/x-qhdlvnlbduauhdvv] has quit [Quit: Connection closed for inactivity] 09:29 < kanzure> protein graph repository http://wjdi.bioinfo.uqam.ca/ they have converted all PDB proteins into graph data 09:29 < kanzure> "PGR: A Graph Repository of Protein 3D-Structures" http://arxiv.org/abs/1604.00045 09:29 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has quit [Remote host closed the connection] 09:30 < kanzure> "mammalian poly(A) polymerase" http://wjdi.bioinfo.uqam.ca/data/explore.html?graphId=113067 09:36 -!- JayDugger [~jwdugger@108.19.186.58] has quit [Quit: Leaving.] 10:00 -!- zeroach [~CharlieNo@97-85-242-17.static.stls.mo.charter.com] has joined ##hplusroadmap 10:04 < kanzure> "A theoretical model for template-free synthesis of long DNA sequence" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2735642/ (2009) 10:04 < kanzure> "This theoretical scheme is intended to formulate a potential method for high fidelity synthesis of Nucleic Acid molecules towards a few thousand bases using an enzyme system. Terminal Deoxyribonucleotidyl Transferase, which adds a nucleotide to the 3′OH end of a Nucleic Acid molecule, may be used in combination with a controlled method for nucleotide addition and degradation, to synthesize a predefined Nucleic Acid sequence. A pH ... 10:04 < kanzure> ... control system is suggested to regulate the sequential activity switching of different enzymes in the synthetic scheme. Current practice of synthetic biology is cumbersome, expensive and often error prone owing to the dependence on the ligation of short oligonucleotides to fabricate functional genetic parts. The projected scheme is likely to render synthetic genomics appreciably convenient and economic by providing longer DNA ... 10:04 < kanzure> ... molecules to start with." 10:11 < kanzure> the "molecular assemblies, inc." patent references that paper https://www.google.com/patents/US9279149 10:14 -!- zer0ach [~CharlieNo@97-85-242-17.static.stls.mo.charter.com] has joined ##hplusroadmap 10:18 -!- zeroach [~CharlieNo@97-85-242-17.static.stls.mo.charter.com] has quit [Ping timeout: 240 seconds] 10:20 < kanzure> "(It is estimated that the annual demand for oligonucleotide synthesis is responsible for greater than 300,000 gallons of hazardous chemical waste, including acetonitrile, trichloroacetic acid, toluene, tetrahydrofuran, and pyridine. See LeProust et al., Nucleic Acids Res., vol. 38(8), p. 2522-2540, (2010), " 10:22 < kanzure> "Another embodiment for using non-template dependent polymerase/transferase enzymes would be to using protein engineering or protein evolution to modify the enzyme to remain tightly bound and inactive to the nascent strand after each single nucleotide incorporation, thus preventing any subsequent incorporation until such time as the polymerase/transferase is released from the strand by use of a releasing reagent/condition. Such ... 10:22 < kanzure> ... modifications would be selected to allow the use of natural unmodified dNTPs instead of reversible terminator dNTPs. Releasing reagents could be high salt buffers, denaturants, etc. Releasing conditions could be high temperature, agitation, etc. For instance, mutations to the Loop1 and SD1 regions of TdT have been shown to dramatically alter the activity from a template-independent activity to more of a template dependent activity. ... 10:23 < kanzure> ... Specific mutations of interest include but are not limited to Δ3384/391/392, del loop1 (386→398), L398A, D339A, F401A, and Q402K403C404→E402R403S404. Other means of accomplishing the goal of a post-incorporation tight binding (i.e., single turnover) TdT enzyme could include mutations to the residues responsible for binding the three phosphates of the initiator strand including but not limited to K261, R432, and R454." 10:28 < kanzure> hm 10:29 < kanzure> you could have capactive labels on nucleotides that have a certain electrical signal in response to optical illumination, e.g. to make a really strong signal for electrical detection 10:29 < kanzure> or making a really specific signature i mean 10:35 -!- eudoxia [~eudoxia@r167-56-137-106.dialup.adsl.anteldata.net.uy] has joined ##hplusroadmap 10:39 -!- FourFire [4d289e64@gateway/web/freenode/ip.77.40.158.100] has joined ##hplusroadmap 10:39 < FourFire> Aubrey is having an AMA now 10:40 < FourFire> Anyone care to criticise my questions for him: https://www.reddit.com/r/Futurology/comments/4t65ay/aubrey_de_grey_ama_ask_about_the_quest_to_cure/d5icja5 10:54 -!- ArturSha1 [~ArturShai@37.218.162.107] has quit [Ping timeout: 276 seconds] 11:20 -!- sandeepkr__ [~sandeep@111.235.64.4] has quit [Ping timeout: 250 seconds] 11:29 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 11:35 -!- jaboja [~jaboja@vps.jaboja.pl] has joined ##hplusroadmap 11:37 < kanzure> "To date, CRISPR Therapeutics has raised $154 million through the sale of equity. The company banked another $75 million last October from Boston’s Vertex Pharmaceuticals, which licensed the rights to as many as six CRISPR-based therapies and promised to pay as much as $420 million for each down the road." 11:37 -!- bsm117532 [~mcelrath@38.121.165.30] has quit [Remote host closed the connection] 11:37 -!- bsm117532 [~mcelrath@38.121.165.30] has joined ##hplusroadmap 11:42 -!- bluebear_ [~chatzilla@80.95.97.194] has quit [Quit: ChatZilla 0.9.92 [Firefox 47.0/20160606113944]] 11:43 -!- nildicit [~nildicit@unaffiliated/nildicit] has quit [Ping timeout: 264 seconds] 11:44 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has joined ##hplusroadmap 11:47 < kanzure> "Techniques used to study the DNA polymerase reaction pathway" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2846202/ 11:47 < kanzure> "Despite the focus of fluorescence studies on the prechemistry steps of the DNA polymerase mechanism, the nature of the slow step that is rate-limiting for dNTP incorporation remains a mystery. In some cases, as described earlier for T7 DNA polymerase, it is possible that a more detailed analysis of the reaction pathway will reveal that the chemical step itself is rate-limiting [18]. In others, exemplified by Klenow fragment, the ... 11:47 < kanzure> ... rate-limiting step may involve relatively subtle structural changes and consequently be fluorescently silent with the probes that have been used. A stopped-flow fluorescence experiment, in which Ca2+ was used instead of Mg2+, suggests that the rate-limiting prechemistry step of Klenow fragment could involve the entry into the active site of the metal ion that activates the primer 3′OH [29]. Likewise, it has been suggested that ... 11:47 < kanzure> ... entry of the second catalytic metal ion could take place immediately before chemistry in the DNA polymerase β mechanism [22, 23]." 11:50 < kanzure> figure 8 and figure 9 are diagrams of the chemical reaction pathway provided by dna polymerase 11:51 -!- eudoxia [~eudoxia@r167-56-137-106.dialup.adsl.anteldata.net.uy] has quit [Quit: Leaving] 11:52 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Quit: Leaving...] 11:58 < kanzure> .wik scanning ion conductance microscopy 11:58 < yoleaux> "Scanning ion-conductance microscopy (SICM) is a scanning probe microscopy technique that uses an electrode as the probe tip. SICM allows for the determination of the surface topography of micrometer and even nanometer-range structures in aqueous media conducting electrolytes." — https://en.wikipedia.org/wiki/Scanning_ion-conductance_microscopy 11:58 < kanzure> .wik scanning electrochemical microscopy 11:58 < yoleaux> "Scanning electrochemical microscopy (SECM) is a technique within the broader class of scanning probe microscopy (SPM) that is used to measure the local electrochemical behavior of liquid/solid, liquid/gas and liquid/liquid interfaces. Initial characterization of the technique was credited to University of Texas electrochemist, Allen J." — https://en.wikipedia.org/wiki/Scanning_electrochemical_microscopy 11:59 -!- Jawmare [~Jawmare@unaffiliated/jawmare] has quit [Read error: Connection reset by peer] 12:01 < kanzure> "Role of conformational motions in enzyme function - Selected methodologies and case studies" http://www.mdpi.com/2073-4344/6/6/81/pdf 12:04 < kanzure> "DNA polymerase conformational dynamics and the role of fidelity-conferring residues: Insights from computational simulations" http://journal.frontiersin.org/article/10.3389/fmolb.2016.00020/full 12:04 < kanzure> "We report a comprehensive atomic resolution study of wild type and mutant enzymes in different bound states and starting from different crystal structures, using extensive molecular dynamics (MD) simulations that cover a total timespan of ~5 ms. [...] Our results show that the presence of fidelity-decreasing mutations or the binding of incorrect nucleotides in ternary complexes tend to favor transitions from closed toward open ... 12:04 < kanzure> ... structures, passing through an ensemble of semi-closed intermediates." 12:05 -!- Jawmare [~Jawmare@unaffiliated/jawmare] has joined ##hplusroadmap 12:14 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has joined ##hplusroadmap 12:14 < kanzure> "Molecular events during translocation and proofreading extracted from 200 static structures of DNA polymerase" http://nar.oxfordjournals.org/content/early/2016/06/20/nar.gkw555.full 12:15 < kanzure> "This enzyme catalyzes incorporation of hundreds of nucleotides each second in host cells. That is to say, its fingers domain is wagging between the open and closed positions at a frequency of several hundred Hz during normal elongation (300 Hz is used in calculations throughout this paper). The fingers domain acts as an oscillator just like one in a mechanical clock and is responsible for power management of both translocation and ... 12:15 < kanzure> ... processive active site switching. Once this oscillation is established, each leaving pyrophosphate (PPi) bound to the fingers in the closed conformation replenishes energy to maintain the oscillation. With each push from a newly cleaved PPi resulting from dNTP hydrolysis, the closed fingers accelerate to adopt an open conformation. At the end of a large swing, the fingers slam into the N-terminal domain. When the motion of the ... 12:15 < kanzure> ... fingers is completely halted at the open position, their momentum is transferred to power the translocation. The motion of the thumb drives a back-and-forth displacement of the product duplex during translocation. The structural events during translocation and active site switching share much of the same conformational pathway until they branch out at an advanced stage." 12:16 < kanzure> hmm we should email this guy 12:16 < kanzure> zren@uic.edu 12:22 -!- hazirafel [~hazirafel@bzq-79-183-46-171.red.bezeqint.net] has quit [Read error: Connection reset by peer] 12:24 < chris_99> https://thescribblepen.com/ -- wonder how that works, if it isn't a scam 12:26 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has quit [Quit: hacked by sjw] 12:29 < xentrac> chris_99: such systems have been commonplace in paint stores for decades, mixing at a liter scale rather than microliter 12:30 < chris_99> i can only think it could use some kind of microfludic chip maybe? 12:31 < xentrac> is that the part that puzzles you? I think nanoliter-resolution pumps have been available for decades now 12:32 < xentrac> for e.g. medical devices like implanted insulin pumps 12:32 < chris_99> well i guess you could use a piezo head 12:34 < chris_99> but to do all that in the space of a pen 12:36 < xentrac> it's kind of a fat pen 12:38 < chris_99> true 12:38 < chris_99> http://www.dolomite-microfluidics.com/webshop/pumps-piezo-pumps-c-38_50/stainless-steel-piezoelectric-pump-p-231 that looks pretty small 12:48 < CaptHindsight> another ghetto fluid handling project http://www.3ders.org/articles/20160714-ai-biosciences-repurposes-low-cost-printrbot-3d-printer-into-high-quality-bio-extraction-instrument.html 12:55 < CaptHindsight> chris_99: CMYK inks + pumps 12:55 < chris_99> CaptHindsight, how would the mixing work 12:55 < chris_99> thoo 12:55 < CaptHindsight> mix right before the tip 12:56 < xentrac> yeah, mix in the tip 12:56 < chris_99> using microfluidic type stuff? 12:56 < CaptHindsight> If I had one I could probably tell you how much before based on how long it takes to change colors 12:56 < xentrac> sort of by definition, yeah, but it isn't really any more microfluidic than a regular ballpoint pen 12:57 < xentrac> mixing becomes easier at microfluidic scales and regular human timescales because the distance across the cavity is small compared to the diffusion rate 12:57 < CaptHindsight> I couldn't make it through the videos... 12:57 < CaptHindsight> do they show what happens when you change from one color to the next? 12:58 < CaptHindsight> do you need to blot the tip until the color changes? 12:58 < chris_99> conventiantly they don't show 12:58 < chris_99> that 12:59 < CaptHindsight> Scribble's ink cartridge connects to a smart micro pump that recreates the color you have scanned. 13:02 -!- nildicit [~nildicit@unaffiliated/nildicit] has joined ##hplusroadmap 13:06 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has joined ##hplusroadmap 13:06 < xentrac> you could do the blotting internally and robotically but they probably don't bother for the first release 13:11 -!- bsm117532 [~mcelrath@38.121.165.30] has quit [Read error: Connection reset by peer] 13:12 -!- bsm117532 [~mcelrath@38.121.165.30] has joined ##hplusroadmap 13:12 -!- bsm117532 [~mcelrath@38.121.165.30] has quit [Client Quit] 13:14 -!- bsm117532 [~mcelrath@38.121.165.30] has joined ##hplusroadmap 13:17 < CaptHindsight> Scribble Gene Pen, change your the color and shape of your eyes, skin and hair easily in your own home 13:19 < CaptHindsight> no more running to the Gene Salon 13:39 < kanzure> unfortunately since it wont have an instantaneous effect, users will think it doesn't work 13:45 -!- bsm117532 [~mcelrath@38.121.165.30] has quit [Remote host closed the connection] 13:45 -!- bsm117532 [~mcelrath@38.121.165.30] has joined ##hplusroadmap 13:53 -!- nmz787_i [~ntmccork@134.134.139.83] has joined ##hplusroadmap 13:54 < nmz787_i> kanzure: that is probably the best biophoton paper I 13:54 < nmz787_i> I've read* 13:54 < nmz787_i> also the bangladeshi paper on pH control is pretty interesting 13:54 < kanzure> pH control is unlikely to be real-timey enough though 13:55 < nmz787_i> yeah, interesting since we actually mentioned that on call 13:55 < nmz787_i> and in general their view was pretty formal 13:55 < nmz787_i> (which is becoming more interesting to me as of late, getting into the SAT solver stuff) 13:56 < kanzure> did you see the pacbio patent yesterday about capactive and inductive sensing of a polymerase enzyme? 13:57 < nmz787_i> hrmm, not sure 13:57 < kanzure> that sort of technique is probably going to require lots of signals sent over the CMOS traces to get an individual per-wire level view of what sort of noise is happening, otherwise you probably wont be able to see each individual base incorporation at any relevant level of detail 14:00 < nmz787_i> luckily electrical traces aren't as hard for fabs as MEMS/fluidics seem to be 14:01 < nmz787_i> I'll take a look 14:01 < kanzure> nmz787_i: https://www.google.com/patents/US20150065353 pacbio dna sequencing by electrical conductance measurement of dna polymerase 14:01 < kanzure> notes http://gnusha.org/logs/2016-07-18.log 14:01 < nmz787_i> https://www.google.com/patents/US20050147979 14:02 < nmz787_i> not quite the one I am remembering 14:02 < nmz787_i> but it seems they made a series of similar claims 14:03 < nmz787_i> http://www.google.com/patents/US20040110208 14:03 < nmz787_i> that's it 14:06 < nmz787_i> well they mention the FET on-chip, which is what I assumed would probably be needed... this complicates things from a "little guy prototyping" standpoint... but it might not be deadly (maybe there are some CSP, chip scale package, FETs available... etc... that could stand-in for a prototype) 14:19 < xentrac> https://www.youtube.com/watch?v=Wex_yKfrTo4 AvE generates refractory carbon foam by charring bread 14:19 < xentrac> white bread 14:20 -!- FourFire [4d289e64@gateway/web/freenode/ip.77.40.158.100] has left ##hplusroadmap [] 14:23 < xentrac> hmm, video has some NSFW parts, if you care 14:25 < xentrac> original paper http://phys.org/news/2016-07-multi-use-stiff-carbon-foam-bread.html 14:25 < xentrac> well, OK, news article on original paper 14:26 < xentrac> original paper http://pubs.acs.org/doi/abs/10.1021/acsami.6b03985 14:28 < xentrac> 3.6 MPa compressive strength, .29 g/cc, 121 MPa compressive modulus 14:28 < xentrac> .06 W/m/K thermal conductivity 14:29 < xentrac> wonder if you could do metal casting in it 14:30 < xentrac> heh, "recently, carbon foams based on biomass (such as watermelon, lignin, bagasse, pomelo peel, banana peel, bacterial fiber, bacterial cellulose, et al) have been successfully fabricated by different methods" 14:37 < kanzure> i suspect polymerase does not operate at higher frequency because the resource requirements would be too toxic to cells 14:37 < nmz787_i> I wonder if it would get too hot 14:38 < nmz787_i> or yeah be too hungry, and starve some other required-for-life part of the cell 14:38 < kanzure> well that metal ion for example, is that used once per incorporation 14:38 < kanzure> so lots of metal would be ungood.... for many reasons.. 14:39 -!- Aurelius_Work [~cpopell@209.48.69.2] has quit [Ping timeout: 240 seconds] 14:42 < kanzure> "FRET is analogous to near-field communication, in that the radius of interaction is much smaller than the wavelength of light emitted. In the near-field region, the excited chromophore emits a virtual photon that is instantly absorbed by a receiving chromophore. These virtual photons are undetectable, since their existence violates the conservation of energy and momentum, and hence FRET is known as a radiationless mechanism" 14:43 < kanzure> wat 14:53 -!- ebowden_ [~ebowden@2001:8003:100e:c500:195a:ae3a:6569:8c2f] has joined ##hplusroadmap 14:57 -!- ebowden_ [~ebowden@2001:8003:100e:c500:195a:ae3a:6569:8c2f] has quit [Ping timeout: 260 seconds] 14:58 < CaptHindsight> nmz787_i: making tools to make devices with a few gates at a few nm should not be a problem 14:59 < CaptHindsight> tools for large devices with billions of gates is another story 14:59 < CaptHindsight> the nanorap should do it, FDM on the nanoscale 15:00 < CaptHindsight> easily deposits metal oxides on silicon with nm features 15:01 < CaptHindsight> only the software will be buggy after a few uses and it will require constant realignment every print or two :) 15:01 < xentrac> I've also prepared carbon foam by heating sugar in a spoon on a gas burner. My dad was a little mad because I never could get all the carbon off the spoon 15:01 < xentrac> CaptHindsight: nanorap? 15:02 < CaptHindsight> xentrac: a teeny tiny reprap for printing electronics 15:02 < CaptHindsight> you could fit 100 across the width of your hair 15:03 < CaptHindsight> now to work on how to get woodgrain shrunk down to the nanoscale? 15:04 < xentrac> does it work? 15:04 < xentrac> I'm skeptical about this idea of FDM on the nanoscale 15:06 < CaptHindsight> how else will 100nm high Yoda heads be manufactured? 15:06 < CaptHindsight> 2-photon polymerization? 15:06 < xentrac> I will shit them out 15:07 < xentrac> thoughts on the bread? 15:07 < xentrac> having just watched a YouTube video of some Canadian roughneck melting aluminum castings with a torch on top of carbonized bread, I'm stoked 15:08 < CaptHindsight> does it also work on Starbucks coffee? 15:09 -!- chris_99 [~chris_99@unaffiliated/chris-99/x-3062929] has quit [Quit: Leaving] 15:10 < xentrac> what, like spent coffee grounds? if it works on bagasse, banana peel, and watermelon, it'll probably work on coffee grounds too 15:11 < xentrac> not sure you'll have a very strong foam though 15:11 < xentrac> maybe if you add a little bit of sugar as a binder 15:13 < CaptHindsight> Starbucks sells coffee flavored carbon water 15:15 -!- ebowden_ [~ebowden@2001:8003:100e:c500:195a:ae3a:6569:8c2f] has joined ##hplusroadmap 15:32 < nmz787_i> xentrac: FIB is essentially FDM 15:33 < xentrac> heh, at a certain layer of abstraction, yes 15:33 < xentrac> in the same way that bread is essentially a watermelon 15:33 < ebowden_> lol 15:33 < nmz787_i> umm 15:33 < ebowden_> What is FIB? 15:33 < xentrac> focused-ion-beam lithography 15:33 < nmz787_i> I literally told someone yesterday that FIB is essentially a nano milling machine + 3d printer 15:34 < xentrac> sure, I'll agree with that 15:34 < nmz787_i> made no mention of bread and watermelon analogies 15:34 < nmz787_i> no analogies whatsoever other than to a 3d printer 15:34 < nmz787_i> (and milling machine) 15:35 < xentrac> ebowden_: you accelerate a beam of ions with a high voltage and focus them to a point with a magnetic field, just as in an electron microscope, except using ions instead of electrons 15:35 < nmz787_i> I /have/ in the past likened it to shooting a gun at a firing range, and when you want to deposit/3d-print... you make some ducks/small-birds fly across the gun range... and when they get shot the bullet is so energetic it pushes them to the target wall, and smashes them there, where they may accumulate 15:36 < nmz787_i> xentrac: actually most ion optics use electrostatic lensing 15:36 < xentrac> this allows you to implant the ions into the surface, stick them to the surface, or vaporize the surface, depending on the energy and how many of them there are 15:36 < xentrac> oh! thanks! I didn't realize that 15:36 < xentrac> SEMs usually use magnetic lensing, no? or am I confused about that too? 15:38 < xentrac> I didn't know about the duck deposition either; I just figured you just directly accelerated ions of whatever you wanted to deposit 15:39 < xentrac> the acceleration is just with a static electric field, right? or do you use a cyclotron or synchrotron approach to get higher energies on those fat, slow ions? 15:40 -!- ebowden_ [~ebowden@2001:8003:100e:c500:195a:ae3a:6569:8c2f] has quit [Remote host closed the connection] 15:42 < nmz787_i> SEMs use magnetics usually 15:42 -!- eudoxia [~eudoxia@r186-50-155-214.dialup.adsl.anteldata.net.uy] has joined ##hplusroadmap 15:43 < nmz787_i> pretty sure it's just a static e-field... the voltage between the hot solder-like metal-source and the bottom of the column 15:44 < nmz787_i> the duck analogy is a bit off... really the bullets would probably scatter, imparting its energy on the duck, and also burning it's feathers off so it couldn't fly away (vaporizing carbonyl tail usually) 15:46 < nmz787_i> I think its a carbonyl 15:47 < nmz787_i> hmm, suppliers show Trimethyl(methylcylopentadienyl)Platinum(IV) 15:48 < nmz787_i> I can't remember the generic class of metal-carbon these fall in, or where I thought they did 15:54 < CaptHindsight> have to make a MyFirst FIB Fab 15:55 < CaptHindsight> make your own nanoscale devices, electronics, machines, Yoda Heads 15:56 -!- zer0ach [~CharlieNo@97-85-242-17.static.stls.mo.charter.com] has quit [Ping timeout: 244 seconds] 15:58 < nmz787_i> in time, maybe 15:59 < CaptHindsight> it's near the top of my list 15:59 < CaptHindsight> new POSAM first 16:01 < CaptHindsight> the ChinaCo Epson printers are too poorly made to be able use them 16:02 < CaptHindsight> new droplet sorter http://phys.org/news/2016-07-surface-tension-droplets-biomedical-applications.html 16:02 < CaptHindsight> with video 16:03 < CaptHindsight> http://pubs.rsc.org/en/Content/ArticleLanding/2016/LC/C6LC00673F#!divAbstract 16:03 < xentrac> CaptHindsight: to use them for what? 16:04 < CaptHindsight> sort blue DNA from Green DNA for example 16:04 < CaptHindsight> oligos in brine 16:15 -!- ebowden1 [~ebowden@1.152.97.24] has joined ##hplusroadmap 16:16 -!- ebowden [~ebowden@1.136.97.38] has quit [Ping timeout: 244 seconds] 16:56 -!- eudoxia [~eudoxia@r186-50-155-214.dialup.adsl.anteldata.net.uy] has quit [Quit: Leaving] 17:00 -!- ebowden1 [~ebowden@1.152.97.24] has quit [Ping timeout: 258 seconds] 17:06 -!- nmz787_i [~ntmccork@134.134.139.83] has quit [Ping timeout: 258 seconds] 17:47 -!- jaboja [~jaboja@vps.jaboja.pl] has quit [Ping timeout: 272 seconds] 17:52 -!- justanotheruser [~Justan@unaffiliated/justanotheruser] has quit [Read error: Connection reset by peer] 17:52 -!- justanot1eruser [~Justan@unaffiliated/justanotheruser] has joined ##hplusroadmap 17:54 -!- justanot1eruser is now known as justanotheruser 18:02 < kanzure> hrmph 18:04 < kanzure> we should have a library of standard conformational changes, caused by charge transform or something upon electrical stimulation or optical illumination. and then we need components that do 90 degree angles and other weird motions. 18:15 -!- SloanOnLinux [~sloan@162.72.132.128] has joined ##hplusroadmap 18:15 < SloanOnLinux> Hi there 18:17 -!- SloanOnLinux [~sloan@162.72.132.128] has left ##hplusroadmap ["Once you know what it is you want to be true, instinct is a very useful device for enabling you to know that it is"] 18:17 -!- SloanOnLinux [~sloan@162.72.132.128] has joined ##hplusroadmap 18:18 < kanzure> SloanOnLinux: hi. 18:19 < SloanOnLinux> This channel seems to be about things I'm interested in 18:20 < SloanOnLinux> So yeah I'm new here, sup? 18:38 < maaku> Welcome. 18:38 < maaku> Maybe start with your interests and skills? 18:46 < SloanOnLinux> I am interested in computers, politics, biohacking, open source, I have dabbled in python and reverse engineering. I came here to learn. 18:52 -!- PatrickRobotham [uid18270@gateway/web/irccloud.com/x-hsvyfvmyvfnqtudu] has joined ##hplusroadmap 18:52 -!- zer0ach [~CharlieNo@97-85-242-17.static.stls.mo.charter.com] has joined ##hplusroadmap 18:57 -!- zer0ach [~CharlieNo@97-85-242-17.static.stls.mo.charter.com] has quit [Ping timeout: 250 seconds] 19:09 -!- sandeepkr [~sandeep@111.235.64.4] has joined ##hplusroadmap 19:09 -!- flappynerd [~flappyner@unaffiliated/flappynerd] has joined ##hplusroadmap 19:21 -!- flappynerd [~flappyner@unaffiliated/flappynerd] has left ##hplusroadmap ["Leaving"] 19:22 < nmz787> SloanOnLinux: what kind of reverse engineering? computers, mechanical systems, electronics, dolphin brains (etc)? 19:24 < SloanOnLinux> I took schtuph apart when I was a kid, then when I experienced internet for the first time I hacked a game with cheat engine 19:30 < kanzure> SloanOnLinux: cheat engine is fun. here is a thing i did: https://github.com/kanzure/pokecrystal 19:39 -!- gaydude [be168908@gateway/web/freenode/ip.190.22.137.8] has joined ##hplusroadmap 19:39 -!- zer0ach [~CharlieNo@97-85-242-17.static.stls.mo.charter.com] has joined ##hplusroadmap 19:55 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has quit [Ping timeout: 260 seconds] 20:11 -!- hylleddin [~hylleddin@2604:a880:1:20::b2:d001] has quit [Ping timeout: 264 seconds] 20:16 -!- ArturSha1 [~ArturShai@37.218.162.107] has joined ##hplusroadmap 20:26 -!- ebowden [~ebowden@2001:8003:100e:c500:b55c:8f3e:8089:1a76] has joined ##hplusroadmap 20:38 -!- hylleddin [~hylleddin@2604:a880:1:20::b2:d001] has joined ##hplusroadmap 20:40 -!- fleshtheworld [~fleshthew@2602:306:cf0f:4c20:d8db:b4ec:dda3:ea6d] has joined ##hplusroadmap 20:49 < SloanOnLinux> kanzure: Cool, how long did it take for you to do that_ 20:51 < kanzure> bunch of other people got involved, no idea 20:52 < justanotheruser> greetings 20:52 < SloanOnLinux> Oh 20:52 < SloanOnLinux> Hi 20:52 < justanotheruser> hi SloanOnLinux, what are you working on 20:53 < SloanOnLinux> Nothing 20:55 < SloanOnLinux> Hbu_ 20:55 < SloanOnLinux> ?* 20:56 < SloanOnLinux> Can I help with anything, justanotheruser? 20:57 < kanzure> you could read logs and write summaries on the wiki, that would be really helpful http://gnusha.org/logs/ 21:03 -!- Aurelius_Home2 [~cpopell@c-73-200-185-48.hsd1.va.comcast.net] has joined ##hplusroadmap 21:04 -!- Aurelius_Home [~cpopell@c-73-200-185-48.hsd1.va.comcast.net] has quit [Ping timeout: 276 seconds] 21:08 < SloanOnLinux> Where do I submit these summaries 21:08 -!- Malvolio [~Malvolio@unaffiliated/malvolio] has joined ##hplusroadmap 21:10 < kanzure> SloanOnLinux: our wiki http://diyhpl.us/wiki/ 21:28 < kanzure> "repurposing the ribosome to do DNA synthesis" actually this might be possible, since the ribosome is a ribozyme, and there's a ribozyme polymerase..... 21:37 -!- SloanOnLinux [~sloan@162.72.132.128] has quit [Read error: Connection reset by peer] 21:38 -!- SloanOnLinux [~sloan@162.72.132.128] has joined ##hplusroadmap 21:52 -!- Aurelius_Work [~cpopell@c-73-200-185-48.hsd1.va.comcast.net] has joined ##hplusroadmap 22:54 -!- Malvolio is now known as CatherineIII 23:00 -!- Aurelius_Work [~cpopell@c-73-200-185-48.hsd1.va.comcast.net] has quit [Ping timeout: 272 seconds] 23:07 -!- augur [~augur@noisebridge130.static.monkeybrains.net] has quit [Remote host closed the connection] 23:11 -!- CatherineIII is now known as Malvolio 23:27 -!- nmz787_i [~ntmccork@134.134.139.76] has joined ##hplusroadmap 23:52 -!- augur [~augur@2601:645:c100:63f1:f49e:dd53:596a:5e15] has joined ##hplusroadmap 23:54 -!- ebowden [~ebowden@2001:8003:100e:c500:b55c:8f3e:8089:1a76] has quit [Remote host closed the connection] 23:58 -!- ebowden [~ebowden@2001:8003:100e:c500:bc63:c401:c220:91ed] has joined ##hplusroadmap --- Log closed Wed Jul 20 00:00:02 2016