2015-02-26.log

--- Log opened Thu Feb 26 00:00:03 2015
--- Day changed Thu Feb 26 2015
nmz787i see keyword 'brushes'00:00
nmz787ah00:04
nmz787.wik Electronic correlation00:04
yoleaux"Electronic correlation is the interaction between electrons in the electronic structure of a quantum system." — http://en.wikipedia.org/wiki/Electronic_correlation00:04
nmz787i thin kthat is what I mean by 'electronics'00:04
nmz787paperbot: http://pubs.acs.org/doi/abs/10.1021/jp505105a00:06
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paperbothttp://diyhpl.us/~bryan/papers2/paperbot/In-Silico%20Design%20of%20a%20DonorAntennaAcceptor%20Supramolecular%20Complex%20for%20Photoinduced%20Charge%20Separation.txt00:07
nmz787http://diyhpl.us/~nmz787/pdf/In-Silico_Design_of_a_DonorAntennaAcceptor_Supramolecular_Complex_for_Photoinduced_Charge_Separation.pdf00:07
nmz787the name COSMO is so cool.00:09
nmz787.title http://arxiv.org/abs/1306.262700:10
yoleaux[1306.2627] Electronic structure and charge transfer excited states of a multichromophoric antenna00:10
nmz787https://www.ocb.ch.tum.de/fileadmin/w00bes/www/_migrated_content_uploads/1-deGroot_AnnuRevBiophys13.pdf00:11
nmz787Solid-State NMR of Nanomachines Involved in Photosynthetic Energy Conversion00:11
nmz787"Many scientists believe that it will be possible to apply the principles of light harvesting, charge separation, and multielectron catalysis in photosynthesis to the chemical design and synthesis of responsive matrices for the production of hydrogen- or carbon-based solar fuel on a large scale, using water and CO2 as raw materials (53). Natural photosynthesis converts the equivalent of 100–200 TW of power, which is about ten times more ...00:13
nmz787... than the ∼14 TW that is currently dissipated by our economies."00:13
nmz787yoink http://diyhpl.us/~nmz787/pdf/Solid-State_NMR_of_Nanomachines_Involved_in_Photosynthetic_Energy_Conversion.pdf00:19
genehackerthere are also molecular logic gates based around something like that00:20
genehackerthey aren't very useful thought00:20
nmz787Quantum Simulation Study of DNA nucleotide Thymine for use00:22
nmz787in Molecular Devices     http://www.iosrjournals.org/iosr-jece/papers/vol1-issue1/A0110106.pdf00:22
nmz787paperbot: http://onlinelibrary.wiley.com/doi/10.1560/IJC.49.2.149/abstract00:24
nmz787http://www.victoria.ac.nz/raman/publis/pablo/pdf/2010_amjp_78_300.pdf00:25
nmz787'Electronic structure, Raman tensors, and resonance phenomena in a simple molecular model'00:25
nmz787"II. THE TOY MOLECULE"00:25
nmz787no one tells the run-time of the DFT it seems00:27
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/789a13a9cadc4e483c5c49355a7aa4b3.txt00:28
nmz787http://diyhpl.us/~nmz787/pdf/A_Quantum_Chemistry_Study_of_Binding_Carotenoids_in_the_Bacterial_Light-Harvesting_Complexes.pdf00:31
genehackeryeah, because it takes a long time00:31
nmz787http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3199570/pdf/nihms-189250.pdf00:31
paperbothttp://libgen.info/scimag/get.php?doi=10.1021%2Fja803074y00:31
genehackerit's probably why no one has done good quantum chemistry of diamonoid mechanosynthesis yet00:31
nmz787'Differential Tuning of the Electron Transfer Parameters in 1,3,5- Triarylpyrazolines: A Rational Design Approach for Optimizing the Contrast Ratio of Fluorescent Probes'00:31
nmz787http://www.rfreitas.com/Nano/McK68141.pdf00:33
nmz787'Challenges of Molecular Nanotechnology for Space Exploration'00:33
nmz787http://www.rfreitas.com/Nano/JNNDimerTool.pdf00:34
nmz787'Theoretical Analysis of a Carbon-Carbon Dimer Placement Tool for Diamond Mechanosynthesis'00:35
nmz787hmm, http://www.vasp.at/00:37
nmz787.wik Vienna Ab-initio Simulation Package00:37
yoleaux"The Vienna Ab-initio Simulation Package, better known as VASP, is a package for performing ab initio quantum mechanical molecular dynamics (MD) using either Vanderbilt pseudopotentials, or the projector augmented wave method, and a plane wave basis set." — http://en.wikipedia.org/wiki/Vienna_Ab-initio_Simulation_Package00:37
nmz787"A slightly lower level of theory (in which the geometry is optimized at HF/3-21G∗) has a mean absolute deviation of 0.14 eV"00:38
nmz787"Thermal noise at room temperature is about 0.02 eV; in conventional positionally uncontrolled chemistry, errors on the order of 0.14 eV might well influence reaction rates and the dominant reaction pathway taken when multiple alternative reaction pathways are present. H"00:38
nmz787"The DCB6-X family of dimer placement tools, for X = Si, Ge, Sn, and Pb, should be stable in a vacuum when used at room temperature, and possibly at significantly higher temperatures."00:40
nmz787we'd better start computing now if we ever want to make any progress since we don't have supercomputers00:41
* nmz787 sleeps00:41
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archels.gc "deep.learning"02:51
yoleauxarchels: Sorry, that command (.gc) crashed.02:51
archelsfrack02:52
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archelshmmm this article takes "supervised training on millions of object-labelled images" to be a defining property of deep learning02:54
FourFirenmz787, on the contrary: arxiv.org/pdf/astro-ph/991220202:57
FourFireset an end date, precommit to actually reach it, and spend the time in between optimizing your code and earning more money02:58
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archelsI am apparently having lunch with Stefan Sorgner in 5 minutes03:34
archelsany pointed questions I should ask him?03:34
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archelskanzure: to come back to that question of how to define complexity, these guys define it as 1/λ. where λ is a regularisation parameter04:47
archelsI guess that makes sense as regularisation is considered a penalty for complexity04:48
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kanzuresup06:31
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archelsphilosophers. I am surrounded by them06:56
kanzurehere's a trick: call them a p-zombie and say "you can't explain that" three times fast. they will vanish in a smokey poof of indignation.06:58
cluckjthe very existence of philosophers negates solipsism06:59
kanzurecluckj: perhaps your next thesis should be about the half-life of bad philosophy. how long will i have to wait for all the bad philosophy to die off?07:01
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JayDuggerGood morning.07:10
cluckjkanzure, noooooope07:13
cluckjbook #2 might be about anti-vaccinators07:13
kanzureuh, why?07:14
cluckjthe rhetoric is interesting07:15
cluckjI was also thinking about diabetes biohackers07:16
chris_99anyone need a new head - http://www.dailymail.co.uk/sciencetech/article-2969375/Could-doctors-REALLY-transplant-head-body-2-years-time-Italian-surgeon-confident-perform-7-5milllion-operation-help-paralysed-patients-like-Christopher-Reeve.html07:18
cluckjthe rhetoric that I find interesting in anti-vax and diy bio was that both groups get labeled as "a threat to the social body"07:18
cluckjwhich I find to be a really troublesome and crypto-fascist metaphor07:18
kanzureanti-vax is too broad in that context though07:18
cluckjyeah07:19
cluckjI wouldn't even do any research on it for like 5 years, so I'm not too concerned with the specifics right now :)07:19
kanzureanti-vax is like 90% parents that are upset with themselves and the world, and then some subset that are interested in pondering the great questions of the universe like "why should the government do x"07:19
cluckjlol07:19
cluckjhttp://gas.sagepub.com/content/early/2014/05/09/0891243214532711.full.pdf+html?ijkey=fUokCLKdAFzI2&keytype=ref&siteid=spgas07:21
paperbothttp://libgen.info/scimag/get.php?doi=10.1177%2F089124321453271107:21
cluckjthanks paperbot07:21
cluckjthat's a pretty interesting article about anti-vax07:22
cluckjthe visceral anti-anti-vax stuff is what I find more interesting and a little bit scarier07:27
FourFirechris_99, meh, I'll check back in 3.5 years, the likely time it will actually take to do such a procedure07:42
FourFire3-5*07:43
kanzurecluckj: "i object to everyone incubating viruses and microbes that might later infect me. therefore i demand that everyone becomes an emulation in the computational butt cloud."07:44
cluckjhah08:01
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archels.title http://www.nature.com/nature/journal/v518/n7540/full/nature14236.html08:39
yoleauxHuman-level control through deep reinforcement learning : Nature : Nature Publishing Group08:39
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kanzurehttp://i.imgur.com/MKMgbiM.png09:06
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nmz787_iarchels: presumably your algorithm had file-based intermediates so you could swap hardware and get the best of both worlds. But I guess that paper was talking about reducing cost, not reducing overall time.09:46
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nmz787_ipaperbot: http://pubs.rsc.org/en/content/articlelanding/2014/lc/c4lc00833b#!divAbstract10:39
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/On-demand%20control%20of%20microfluidic%20flow%20via%20capillary-tuned%20solenoid%20microvalve%20suction.pdf10:40
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nmz787_i"The suction effect was innovatively employed as a stable and controllable driving force for the manipulation of the microfluidic system by connecting a piece of capillary between the microvalve and the microfluidic chip, which caused significant hydrodynamic resistance differences among the solenoid valve ports and changed the flowing mode inside the valve. The volume of sucked liquid could be controlled from microliters even10:42
nmz787_idown to picoliters either by decreasing the valve energized duration (from a maximum energized duration to the valve response time of 20 ms) or by increasing the inserted capillary length (i.e., its hydrodynamic resistance). Several important microfluidic unit operations such as cell/droplet sorting and on-demand size-controllable droplet generation have been demonstrated on the developed platform and both simulations and10:42
nmz787_iexperiments confirmed that this platform has good controllability and stability"10:42
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delinquentmeUH.11:26
delinquentmekanzure,11:26
delinquentmeyou. need to watch Full mejal alchemist11:26
delinquentmeRULF. new contracts too11:26
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kanzurefull metal is boring11:54
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maakuhttp://www.fastcompany.com/3042861/the-y-combinator-chronicles/the-secret-million-that-y-combinator-invests-in-all-its-startups12:02
maaku.title12:02
yoleauxThe Secret Million That Y Combinator Invests In All Its Startups | Fast Company | Business + Innovation12:02
maakuhuh bad title. half about transcriptic, half about yc12:02
maakudelinquentme: why FMA?12:02
kanzurejust a whiney story about state-sponsored alchemy12:03
chris_99whats the full-metal part refer to12:04
maakuyeah i saw it when i was younger. interesting, but could have been much better12:04
maakuchris_99: the main character's brother, who had his soul affixed to a suit of armor12:05
maakuor the main character who had a mechanical arm, i don't remember12:05
chris_99aha, cheers.  It's in Japanese i'm assuming12:05
maakuyes12:05
maakua Full-Metal Rationalist would be interesting (hint hint yudkowski)12:06
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delinquentmemaaku, because i love the song at the ending credits12:12
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maakuhah ok12:12
maakuwhich one? don't they change it up?12:12
cluckjkanzure, "working knowledge"?12:15
kanzurewhat about it?12:15
kanzureit's like telling someone you know a secret, and they can't really verify it12:16
kanzureit's a principal agent problem12:16
kanzureand probably something about lemons and markets12:16
cluckjwat12:16
kanzureexpertise?12:16
kanzurewhat are we talking about?12:16
cluckjyes12:17
kanzureclaims of expertise are very difficult or impossible to verify12:17
kanzureand verification itself is all sorts of broken too12:18
cluckjI'm trying to come up with a phrase that isn't nearly as pedantic and goofy as "expertise, as a verb"12:18
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kanzureadroiting12:19
cluckjthe problem I'm having writing this bit is that there's a whole language attached to "expertise" that is difficult to avoid if I keep saying expertise12:20
cluckjhmm12:20
kanzureif the concept is wrong for public communication (eg., it doesn't work: no good reasons to tell people you are an expert, really), then maybe it also has no application in the other way you are attempting to write about12:21
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cluckjit's a very entrenched concept, and I can't ignore it because it's a part of what my discipline talks about12:27
cluckjthere's a lot of power dynamics in expertise/authority that pervade how american society works, much of which is invisible12:28
cluckjthe power, not american society12:30
kanzuresounds like people are really upset by the idea that people can do things without institutional authority12:41
kanzurewhy is it so surprising though12:41
cluckjyep12:42
cluckjbecause it undercuts institutions12:42
kanzurethat's not surprising though12:43
kanzurethe ability for institutions to do things is only because it is possible for individuals to do things, not the other way around12:43
cluckjthe other way around is how the institutionally-entrenched think12:44
cluckjlike you can't do medical research, or any real science at all, without a million dollar budget12:45
cluckjand to handle that size of a budget you need an institution, QED you can only do things in institutions12:46
kanzureheh, the weird thing is that a million bucks is no big deal, hell i know a few people in here who have signing authority for that much in their day job, easily12:47
kanzurealthough probably not single check signing authority for that amount of course :)12:47
cluckjright12:47
cluckjI bet that job is in some kind of institution though :P12:47
kanzurehuh?12:48
kanzurewhy would that matter?12:48
kanzurei was trying to emphasize the difference there, where it's not a big deal, whereas academia makes it out to be a big deal12:49
cluckjI'm saying it matters because of the connection between authority, power, and institutions...if you can do the same or similar scientific research that Merck is doing in their billion-dollar laboratories for $100 in your kitchen, it freaks people out12:50
kanzurei could go on a money rant here if you would like12:51
kanzureover time it should be only natural for small amounts of money to do more things. that shows an increase in capability for lower amounts of savings activity.12:51
kanzureinstead what we see though is larger and larger amounts of money being spent to do totally trivial things (or sometimes what /ought/ to be trivial things)12:52
maaku"that's the cost of doing business"12:53
cluckjit freaks the FBI and the FDA out because there's no "institutional oversight" (which I guess makes everything super safe for them), it freaks the medical-industrial complex out because they've built up this argument that they need to charge so much for drugs because they're spending tons of cash on research12:53
maakuworst rationalization ever12:53
cluckjkanzure, definitely12:53
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cluckjlots of people believe the medical-industrial complex on that lie because those companies are the only ones doing that kind of research at the moment12:55
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kanzurecluckj: i think that the system should be architected so that over time an individual is able to investigate more things on their own12:59
kanzurecluckj: because in genreal we need the costs of basic research to be going down significantly if we want to cover as many things as we plan to13:00
cluckjso when DIY starts undercutting one part of the "WE NEED INSTITUTIONS TO GET ANYTHING DONE" rhetoric, people who are invested in those institutions get very nervous13:00
cluckjyes13:00
kanzurenobody seriously cares if a college vanishes-- i mean if a college was to go underwater, someone or some other institution would just buy it, no big deal13:01
cluckjcolleges aren't the only institutions that do research13:03
kanzureso what are they nervous about13:03
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cluckjthey're nervous that the authority and power that their institution provides is going to disappear13:03
cluckjthat their investment in the institutional structures is going to be wasted13:04
Mokstaryou really think DIY research is on their radar?13:04
cluckjif people are going to start doing their own medical research, and experimenting on themselves, do we really need the FDA anymore?13:04
kanzuresunk cost fallacy?13:04
kanzurethat's not what the FDA was originally setup for :P13:04
cluckjkanzure, yes13:05
kanzurehttp://diyhpl.us/wiki/fda/13:05
cluckjMokstar, yes13:05
kanzurei don't think it's "on their radar" in that sense, it's more like a... "what does this mean and why is that happening" sense13:06
kanzureand then wider existential crises13:06
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kanzurethe fda is not really because people are worried about people taking medicine, it's more of a regulation/authority/government/market thing..13:07
cluckjkanzure, they're worried because they're supposed to ensure public safety about medicines...if people are making their own (or collectively making it), they can't really regulate it13:08
kanzure"public safety" is sort of a broken concept in a few places13:09
kanzurehave you read about "the proactionary principle" from max more?13:09
cluckjDIY research is definitely on the radar of several companies and the federal government13:09
kanzureanother thing that i would recommend, and this may sound stupid, is "site:mises.org fda" heh13:09
cluckjya13:10
kanzurehttp://mises.org/library/we-cannot-predict-many-ways-freedom-will-improve-our-lives13:10
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cluckjyes....it's the unknown unknown13:13
kanzurehttp://www.maxmore.com/proactionary.html13:13
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cluckjoh dear, the forward march of progress13:15
kanzurewell, there's some context here, it's not intended to sound like that13:15
cluckjhaha13:15
kanzurethe context is that he was trying to explain why the precautionary principle is not good13:15
cluckjyes13:18
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cluckjI'm saying it's about losing power and control, not about public safety13:19
cluckjthe way that the FDA currently regulates is tied up with other institutions, and DIY stuff disrupts that13:20
cluckjso they're going to be freaking out about it until someone figures out a way to regulate DIY13:20
cluckjwhich is to be honest, a kind of creepy prospect in every way I can think of13:21
cluckjthe way the FBI is 'regulating' DIY bio is extremely creepy13:21
kanzurethere was an idea somewhere about turning the fda into something you opt into... don't know where that idea came from..13:22
cluckjew?13:23
kanzurewell it's better than them telling you that you can't buy a heart or whateer13:24
kanzure*whatever13:24
cluckjthey need to find a way to regulate that doesn't exclusively require a formalized institution13:24
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cluckjI'm okay with not being able to buy a heart13:26
kanzurehave fun being heartless13:27
cluckj...is someone going to steal mine from me?13:28
kanzureno, but yours might break13:30
cluckjI do have a bad track record of organs breaking without much notice13:31
cluckjI'd rather grow one at genspace than buy one, though13:38
kanzuregenspace isn't very do-it-yourslef13:39
cluckjoh?13:40
cluckjI mean I wouldn't want to grow a heart for myself by myself13:41
cluckjI have no idea wtf I am doing13:41
kanzureit's a community lab company.13:41
kanzurei didn't claim you should grow your own heart; my comment was about buying hearts.13:41
kanzureyou mentioned genspace and i thought that may have been because DIY reasons13:42
kanzureand thus my comment about categorizing genspace13:42
cluckjhaha13:42
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kanzure.title https://news.ycombinator.com/item?id=911415914:57
yoleaux20n (YC W15) Uses Software To Engineer Microbes For Chemical-Making | Hacker News14:57
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kanzurewhy?14:59
kanzureeveryone and their dog does metabolic pathway engineering stuff. so what makes this any different?14:59
kanzure"Optimizing for large scale production is indeed what most of the field works on. There have been many success stories: an anti-malarial drug through yeast (Artemisinin by Amyris+Sanofi), a plastic precursor through bacteria (1,4-BDO by Genomatica+DuPont), and more. What they are missing is the whole spectrum of what could be made biologically. We will create microbes for the most valuable chemicals and then partner with existing ...15:00
kanzure... optimization companies that have industrial fermenters running. Think beer fermentation, just instead of the alcohol yeast, you use our yeast."15:00
kanzurehuh? that's missing?15:00
kanzurewhat? "Defensibility for us: microbes we build, and the platform they form. Our software-driven engineering is significantly faster than the state-of-the-art: human's looking at metabolic maps. People will start building on top of our initial microbes and improving them. These initial microbes form the "platform" from which to enable more bioproduction apps."15:00
kanzurehow is that defensibility15:00
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kanzuremaybe there's a business model to be had related to the private delivery of private strains (not even patented strains, just straight up private)15:04
kanzurehmm but that doesn't explain enough..15:04
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kanzurewhat?? "Their special sauce is their software platform. While there are companies that license ways to create bacteria that produce specialty chemicals, the process of identifying how to create these microbes is tedious."15:09
kanzuresomething doesn't add up here15:09
kanzure"With the specialty chemical industry being worth $980 billion, licenses for these microbes can start in the hundreds of thousands of dollars. 20n already has several contracts in negotiation."15:09
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kanzure"Protein folding, 50 years on" http://web.iitd.ac.in/~nkurur/2012-13/IIsem/cyl110/protfoldprob50.pdf15:18
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dpkpaperbot: http://link.springer.com/article/10.1007%2Fs12119-000-1011-y17:00
paperbothttp://diyhpl.us/~bryan/papers2/paperbot/10c4f9b63dc8cdcb20e82d42278b881.txt17:00
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delinquentmekanzure,  you shuld publish a weekly thinger on whos doing what thats cool17:46
delinquentmePLZ17:46
delinquentmepz.17:46
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kanzurea blog? no thanks18:10
kanzurehttp://en.wikipedia.org/wiki/Carterfone#Landmark_regulatory_decision18:10
kanzure"This ruling (13 F.C.C.2d 420) created the possibility of selling devices that could connect to the phone system using a protective coupler, and opened the market to customer-owned equipment. The decision is often referred-to as "any lawful device", allowing later innovations like answering machines, fax machines, and modems (which initially used the same type of manual acoustic coupler as the Carterfone) to proliferate."18:11
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nmz787kanzure: nah you need to 'tweet' it I think18:29
nmz787or better yet, post it to myspace18:29
nmz787then need some love18:29
nmz787each post has to be in the form of metal music18:29
nmz787and you need to scream the cool news at the sudience18:29
nmz787audience*18:29
nmz787what is the state of pdfparanoia? did you ever succeed in getting a congealed critical-mass of librarians to hang out on IRC and chat about this sort of stuff?18:31
kanzurethat's #code4lib18:34
nmz787any suggestions for what I should think about working on for a talk at defcon?18:36
nmz787i'm thinking a simple electromicrofluidic with spectroscopy18:36
nmz787made a capillary electrophoresis rig18:36
nmz787using a microscope for lithography stage and also detection of chromatography eluents18:37
nmz787then throw some FIB shit in there somehow, probably most likely relating to plating the electrical traces (though I might be able to do that with normal lithography then gold sputtering)18:38
nmz787s/made/maybe/18:40
nmz787huh, rich pell had something to do with that arduino thermal cycler18:56
cluckjyes19:08
nmz787he seems like a decent guy19:09
nmz787his museuem was fun to visit19:09
nmz787museum*19:09
cluckjhe's a really great dude19:10
cluckjI still haven't made it to the museum yet19:10
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nmz787yeah I think I went twice19:11
nmz787once maybe just for a second19:12
nmz787I can't really remember19:12
cluckjlol19:12
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cluckjI need to get to pittsburgh when it's not the holidays so I can do19:20
cluckjerr go19:20
nmz787i took my dad19:30
nmz787:P19:30
cluckjoh god19:30
cluckjwas he prepared for the weird?19:30
nmz787he thought it was strange that I photographed the entire row of books (so i could get the titles)19:31
nmz787oh, yeah I think so19:31
nmz787he seemed to enjoy it19:31
nmz787we went out to dinner after with rich19:31
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cluckjhe's having a baby, dunno when it's due19:32
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cluckjmy partner told me like....earlier this month? so maybe in 5 or 6 months from now19:35
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nmz787i think he had it last month19:46
nmz787or they19:46
cluckjit does take two, usually19:47
cluckjno, it's way too early19:50
cluckjI'll ask her in the morning19:51
cluckjmaybe what she said was "rich had a baby" instead of "rich is having a baby"20:08
nmz787hah20:08
cluckjwhateva20:09
nmz787are you from pgh?20:09
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cluckjno20:09
cluckjmy partner was friends with him at CMU for undergrad, then she and him ended up at RPI (with me) at the same time20:10
JayDugger...20:11
cluckj?20:13
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nmz787niceeee20:26
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nmz787http://diyhpl.us/~nmz787/pdf/DFT_flavor_of_coordination_chemistry.pdf20:49
nmz787DFT... mmm, Donut Flavor Technology20:50
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nmz787http://diyhpl.us/~nmz787/pdf/Realistic_Modeling_of_Nanostructures_Using_Density_Functional_Theory.pdf22:06
nmz787"standard, state-of-the-art electronic-structure approaches based on density functional theory (DFT) have computational costs that scale as the second power of the number of atoms studied for the memory required in a calculation, and as the third power for the CPU time."22:20
nmz787as of 200622:20
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