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fenn | i take back my praise for the 'cleverness' of the arduino LCD+buttons shield | 03:22 |
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fenn | they actually did it wrong, so you can't press more than one button at once | 03:23 |
fenn | what were they thinking! | 03:23 |
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fenn | http://imagebin.org/46068 PCR idea | 07:14 |
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kanzure | fenn: funny how there is more engineering on diybio in the last day than there has been on OM, ever | 10:02 |
kanzure | or maybe that's sad. my meter is kind of messed up. | 10:02 |
kanzure | heh in situ adaptive PCR control via adding SYBR green and detecting intensity every 0.5 s | 10:50 |
kanzure | increased intensity -> increased number of strands | 10:50 |
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kanzure | why not just find favorable thermozymes that let us do pcr without having to have a machine. | 11:15 |
kanzure | just sayin' | 11:15 |
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kanzure | oh right. I was trying to find a cell life cycle phase that amplifies DNA, and then some mutant of that phase that can't stop doing that; then apply the photoporation technique, and you're good to go if you can bare to run some .. blah, what are those extractions of gel runs called? whatever it is you do to the gels to recover DNA. | 11:56 |
cis-action | hey | 11:57 |
cis-action | kanzure: http://jb.asm.org/cgi/content/full/182/13/3673 | 11:58 |
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kanzure | cis-action: hey. | 15:02 |
cis-action | hi | 15:02 |
kanzure | 15:02 | |
kanzure | ComP, a Pilin-Like Protein Essential for Natural Competence in Acinetobacter sp. Strain BD413: Regulation, Modification, and Cellular Localization | 15:02 |
kanzure | ah, neat | 15:02 |
kanzure | but is this the only protein necessary? | 15:02 |
* cis-action read the last part of the abstract | 15:03 | |
cis-action | or did you already? | 15:04 |
kanzure | "dna binding and uptake" hr | 15:05 |
kanzure | hrm | 15:05 |
kanzure | "A deletion of comP completely abolished natural transformation but had no effect on piliation, as revealed by electron microscopy (33)." | 15:06 |
kanzure | this is pretty neat. :) | 15:06 |
kanzure | "Expression of ComP in E. coli from plasmids pMP1 and pMP2 resulted in malE::comP fusion products of 58 and 53 kDa, respectively." | 15:08 |
cis-action | Ahh! I meant to say, read the last part of the discussion / conlusion. | 15:10 |
cis-action | conclusion* | 15:10 |
kanzure | "Our data rather suggest that the comP promoter responds to nutrient limitations" | 15:10 |
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kanzure | Hey DrTread. | 15:11 |
kanzure | cis-action: hrm. well. looks like ComP might not be our guy. | 15:12 |
kanzure | but that's why I suggested comB8, comB9, comB10 and maybe comB7. | 15:12 |
DrTread | hola | 15:14 |
DrTread | what's the sub-topic for today? | 15:16 |
kanzure | I've been hunting down genes necessary to make an organism automagically take up DNA that happens to be floating by | 15:17 |
DrTread | ah. a retrovirus sort if thingy. | 15:18 |
kanzure | nope | 15:18 |
kanzure | holes in the membrane that DNA can go through | 15:18 |
DrTread | oh! ok. anthrax. creates lovely holes. | 15:19 |
DrTread | usually fatal, tho. :( | 15:19 |
kanzure | hm, the ComG genes look interesting too. (ComG-3, ComG-4, ComG-5) | 15:20 |
DrTread | trouble is that you need a stable hole, not just a hole. | 15:21 |
kanzure | DrTread: there are specific organisms that have evolved these genes for the purpose of uptake of DNA | 15:22 |
kanzure | or at least it seems to be for the purpose of uptake of DNA (because that's what they do) | 15:22 |
kanzure | so it's a matter of importing the genes over, more or less, as long as the membrane composition is somewhat similar methinks | 15:22 |
kanzure | hm. I like this one: "All seven comG ORFs are required for DNA binding during transformation of competent Bacillus subtilis" | 15:23 |
DrTread | these things must be handled delicately. iirc, anthrax uses 4 genes, but many subunits. | 15:24 |
DrTread | genes are big things. | 15:25 |
kanzure | it would be ideal if I could find a single gene that encodes a single protein that enables this activity | 15:25 |
cis-action | The DNA import machinery seems to be powered by the transmembrane proton gradient and seems to take dsDNA, chop one strand up, and suck the other strand through the cell as ssDNA | 15:26 |
kanzure | in which case? | 15:26 |
kanzure | there are multiple systems I've been looking at. visP, comB, comP, comG, etc. | 15:27 |
kanzure | some papers are telling me that some ecoli has natural competence | 15:31 |
kanzure | with some homologs of the com genes of H. influenzae | 15:31 |
DrTread | going to work (play) on my blinkey lights. | 15:38 |
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kanzure | the paper called "Internalizing DNA" is good and includes a nice chart. | 16:16 |
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kanzure | sonication leads to DNA fracture? | 16:50 |
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cis-action | ok, signing off to get ready for the talk | 16:56 |
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kanzure | you get bonus points for speaking only in nucleotides | 16:57 |
kanzure | blah | 16:57 |
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kanzure | Hey ericzhang. | 17:04 |
ericzhang | hey kanzure | 17:04 |
kanzure | mac just stepped out to give a presentation at codecon | 17:05 |
ericzhang | i see. | 17:06 |
ericzhang | funny topic name here, haha. | 17:06 |
kanzure | :) | 17:06 |
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kanzure | welcome back? | 17:09 |
ericzhang | sorry...browser issues. | 17:09 |
-!- ericzhang is now known as junglistric | 17:10 | |
junglistric | *name change | 17:10 |
kanzure | hrm. this sucks. ADP1 uses 16 genes for the natural competence mechanism. | 17:11 |
kanzure | why can't it be one gene. blah. | 17:11 |
junglistric | haha. | 17:12 |
fenn | hello eric | 17:12 |
kanzure | "comE and comF mutants exhibit 10- and 1,000-fold reduced transformation frequencies" | 17:12 |
junglistric | hi fenn | 17:13 |
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fenn | diy-ish laptop: http://benheck.com/03-03-2009/darksiders-xbox-360-laptop-for-thq | 17:20 |
fenn | his other mod is cooler though: http://benheck.com/04-05-2009/commodore-64-original-hardware-laptop#more-496 | 17:20 |
fenn | er, scroll up | 17:21 |
junglistric | the first one is just a portable xbox...2nd one is pretty cool. | 17:23 |
junglistric | what one does with a comm64 these days, i dunno. | 17:23 |
kanzure | brag | 17:23 |
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junglistric | or play ThunderBlade and brag | 17:25 |
kanzure | competence proteins of ADP1: | 17:26 |
kanzure | http://heybryan.org/books/papers/competence_proteins_ADP1.jpg | 17:26 |
kanzure | what the setup looks like in Heliobacter pylori: http://heybryan.org/books/papers/Natural%20transformation%20in%20Helicobacter%20pylori%20-%20DNA%20transport%20in%20an%20unexpected%20way.pdf.1.jpeg | 17:26 |
kanzure | and what it looks like in a cousin of ADP1: http://heybryan.org/books/papers/Acquisition%20of%20foreign%20DNA%20by%20natural%20transformation%20in%20Acinetobacter%20baylyi%20-%20introgression%20process.pdf.1.jpg | 17:27 |
fenn | looks about the same except they used letters instead of numbers | 17:30 |
fenn | of course colored blobs doesn't really tell you much | 17:31 |
kanzure | SCIENCE! | 17:31 |
kanzure | a blobby thingy works here by doing something like a blob | 17:31 |
fenn | i'm going to start doing technical diagrams with colored blobs in them for no particular reason | 17:32 |
kanzure | actually I was surprised (and happy) to see that some people correctly guessed that there were various hydrophilic-domains of the amino acids that are specifically used in a "DNA sensor/grabber thingy" | 17:32 |
kanzure | heh | 17:32 |
kanzure | this mechanism is fairly complicated | 17:32 |
kanzure | I was expecting a single protein to make up the pore. | 17:32 |
kanzure | all sorts of wild/funky regulation going on of each individual protein's expression too.. | 17:33 |
kanzure | for instance, apparently only some species are naturally competent during log phase growth | 17:33 |
kanzure | however gonororrhea is naturally competent all the time | 17:33 |
fenn | skyhook wireless maps wifi MAC addresses to geolocation.. eek | 17:35 |
kanzure | going in the wrong direction. | 17:35 |
fenn | apparently they had 200 drivers go around with GPS and wifi antenna | 17:35 |
kanzure | wasn't skyhook some sort of james bond movie military research study codename? | 17:35 |
kanzure | "operation skyhook" | 17:35 |
fenn | meh | 17:35 |
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fenn | skyhook is hans moravec's idea for an orbital space tether | 17:35 |
kanzure | you'd fire some sort of flair and a skyhook would come down and swing you away | 17:36 |
fenn | oh, was that called skyhook too? | 17:36 |
* kanzure nods | 17:36 | |
kanzure | I keep thinking of cows on hooks in slaughter houses though. that seems to be the result of trying to hitch a ride with a fast-moving "sky hook" | 17:36 |
junglistric | haha | 17:37 |
kanzure | also found some weird stuff on naturally competent ecoli in water | 17:39 |
kanzure | http://heybryan.org/books/papers/Natural%20plasmid%20transformation%20in%20ecoli.pdf | 17:39 |
kanzure | oh, B. subtilis competence proteins diagram: http://heybryan.org/books/papers/Internalizing_DNA.pdf.B_subtilis_competence_proteins.gif | 17:40 |
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kanzure | what is supercoiled monomeric or linear concatemeric DNA? as opposed to linear monomeric DNA. | 17:41 |
kanzure | is supercoiled monomeric == "plasmid" ? | 17:42 |
fenn | fancy words | 17:43 |
fenn | A concatemeric DNA is the product of multiple replication and recombination. The result of this multiple replication is a molecule which contains many copies of the same DNA connected end-to-end. | 17:43 |
fenn | supercoiled usually means plasmid | 17:44 |
junglistric | plasmids have more than 1 type of 2ndary structure | 17:44 |
junglistric | yeah | 17:44 |
fenn | chromatin keeps DNA in a supercoiled state but it's not in a loop | 17:44 |
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kanzure | I want a gene pool rss feed. | 17:48 |
junglistric | thanks for the ADP1 stuff Bryan. doesn't seem so complex when you can just click and buy some competent cells. | 17:48 |
kanzure | junglistric: it's not diy if you get to buy your way to success :) | 17:49 |
junglistric | that's the new motto right there | 17:49 |
kanzure | new? | 17:49 |
genehacker | talk going on today? | 17:49 |
kanzure | genehacker: in san francisco, codecon. | 17:49 |
genehacker | hmmmmm... | 17:50 |
genehacker | coordinates? | 17:50 |
kanzure | check codecon.org for coords | 17:50 |
genehacker | kanzure supercoiled is what you get when you twist a ruberband a lot and it starts to kink | 17:51 |
genehacker | haven't you ever played with deformed elastomer powered vehicles? | 17:52 |
kanzure | I doubt the biologists are using proper terminology | 17:52 |
genehacker | oops | 17:53 |
junglistric | http://en.wikipedia.org/wiki/File:Circular_DNA_Supercoiling.png | 17:53 |
genehacker | http://chemistry.umeche.maine.edu/CHY431/Supercoil3.gif | 17:53 |
genehacker | this is super coiling | 17:53 |
junglistric | plectonemic rubber bands | 17:53 |
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genehacker | http://chemistry.umeche.maine.edu/CHY431/Nucleic5.html | 17:54 |
junglistric | dna might coil in different ways ex vivo | 17:55 |
junglistric | like in a gel | 17:55 |
junglistric | sometimes when you run plasmids, you see these bands that don't migrate as they should | 17:56 |
kanzure | right | 17:56 |
kanzure | I've had gel streaking issues before | 17:56 |
junglistric | or 2-3 distinct bands | 17:56 |
junglistric | different supercoils | 17:57 |
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junglistric | streaking tends to happen when your DNA is just obliterated | 17:57 |
junglistric | a spectrum of lengths | 17:57 |
kanzure | IIRC it was due to contamination and i.e. trusting invitrogen's DNA or something | 17:58 |
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junglistric | it could be that the DNA is just degraded somehow | 17:58 |
junglistric | sometimes you want to fragment DNA, when you're building a library | 17:59 |
junglistric | for diff. applications | 17:59 |
junglistric | sequencing for example | 18:00 |
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junglistric | hm dinner time. | 18:01 |
junglistric | later guys. | 18:01 |
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kanzure | hm | 20:18 |
kanzure | 1.6 terabits/in^2 via an AFM in room temperature in air, 8 nm bits are written at a rate of 5 kbits/sec | 20:18 |
kanzure | is it enough to shine a photodiode to detect some change in cantilever angle ? | 20:19 |
nsh | enough? | 20:25 |
nsh | i assume it's a pretty damn complicated instrument | 20:26 |
kanzure | not really | 20:27 |
kanzure | piezoelectric crystal with sample on it. | 20:27 |
kanzure | a giant cantilever thingy with a sharp point | 20:27 |
kanzure | laser pointing at the cantilever | 20:27 |
kanzure | some way of reading the deflection | 20:27 |
fenn | photodiode will only give you a point signal | 20:27 |
fenn | you need a camera sensor | 20:28 |
kanzure | wikipedia suggests an array of photodiodes | 20:28 |
fenn | or photodiode strip | 20:28 |
kanzure | yay | 20:28 |
fenn | why photodiode btw? | 20:28 |
kanzure | dunno? | 20:28 |
fenn | ok.. just remember there are megapixel camera sensors for $10 | 20:28 |
kanzure | wonder how much resolution that would give me. | 20:29 |
fenn | 1000 per axis | 20:29 |
kanzure | erm, no, I mean in terms of .. nevermind. | 20:29 |
fenn | you mean 'how much dynamic range would that give me' | 20:29 |
fenn | or something | 20:29 |
kanzure | or something, yes. | 20:30 |
fenn | whats the AFM writing on? | 20:31 |
fenn | and doesnt the tip get dull really quickly? | 20:31 |
kanzure | titanium | 20:31 |
kanzure | it seems to be some sort of oxidization process | 20:31 |
fenn | oh | 20:32 |
kanzure | what material should be used for the cantilever? | 20:33 |
kanzure | it's basically a "spring" but I really don't know | 20:33 |
kanzure | ideally, running a silver-coated hair would be awesome, but it wouldn't necessarily stay put | 20:34 |
kanzure | I guess I have to wonder about how much bend you get per nanoNewton of force or something on a metal bar? | 20:34 |
kanzure | "the AFM can only imnage a maximum height on the order of micrometers and a maximum scanning area of around 150 by 150 micrometers" | 20:36 |
kanzure | videoAFM heh | 20:37 |
fenn | you and your hair obsession | 20:40 |
fenn | dont you know hair varies by a factor of 10 in thickness | 20:41 |
genehacker | http://blog.reprap.org/2009/04/first-reprapped-circuit.html | 20:58 |
genehacker | you talking about the millipede? | 20:59 |
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kanzure | fenn: I can't help it, I grow so much of it | 21:04 |
kanzure | hm. | 21:06 |
kanzure | http://en.wikipedia.org/wiki/File:Atomic_Force_Microscope_Science_Museum_Lond.jpg | 21:06 |
kanzure | erm | 21:06 |
kanzure | http://en.wikipedia.org/wiki/File:Atomic_Force_Microscope_Science_Museum_London.jpg | 21:06 |
genehacker | http://www.youtube.com/watch?v=Wnu4lmOnX00&feature=related | 21:10 |
kanzure | genehacker: that was linked in the comments on the last link you linked to.. | 21:10 |
genehacker | yeah | 21:11 |
genehacker | it's cool nonetheless | 21:11 |
genehacker | that solder pump sounds a bit insidious | 21:11 |
kanzure | hey, what are those alligator clip thingies that are made entirely out of metal? the ones that clip. | 21:13 |
fenn | alligator clips | 21:15 |
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kanzure- | open flame + micropipette tip = bent AFM cantilever tip. then glue a sparkle-glitter-thingy on the bent part and shine the laser. | 21:48 |
kanzure- | is there non-deflection AFM? | 21:49 |
fenn | i dont know anything about AFM | 21:55 |
fenn | besides what you've dosed me with | 21:56 |
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fenn | why do they use lasers vs for example a capacitive probe? | 21:57 |
fenn | to detect bending of the cantilever | 21:57 |
kanzure- | it's weird, I thought I knew what AFM was too | 22:02 |
kanzure- | but I never heard of just watching for the bending angle or whatever | 22:03 |
kanzure- | what do you mean a capacitive probe? | 22:03 |
kanzure- | a capacitor? | 22:03 |
fenn | like a touchpad | 22:05 |
fenn | capacitor is two metal plates in close proximity | 22:05 |
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fenn | the capacitance varies with the distance | 22:05 |
fenn | you set up a resonant circuit and measure the frequency | 22:05 |
fenn | frequency is proportional to capacitance is proportional to distance | 22:05 |
fenn | it's not linear though | 22:06 |
kanzure- | good news, somebody already patented "scanning capacitance microscopy" | 22:06 |
kanzure- | hand over a million dollars. or else. | 22:06 |
kanzure- | 1989 | 22:07 |
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fenn | seems people dont really go after patent infringers unless they've already made a lot of money on it | 22:08 |
genehacker | micropippette tips are pretty big | 22:08 |
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kanzure- | huh you must be in the clear then | 22:08 |
* kanzure- snickers | 22:08 | |
fenn | i should infringe more patents | 22:08 |
genehacker | you can only infringe on patents if you make it and sell it | 22:09 |
genehacker | trading it on the other hand... | 22:09 |
kanzure- | genehacker: according to who | 22:09 |
fenn | genehacker: not true | 22:09 |
genehacker | those fuckers | 22:09 |
fenn | if you build and use it you're infringing | 22:09 |
kanzure- | it's a living hell | 22:09 |
genehacker | LETS INFRINGE SOME PATENTS FOR THE LULZ | 22:10 |
fenn | kanzure i need you to apply your massive social networking skills towards getting me more money | 22:10 |
genehacker | http://www.ifpi.org/ | 22:10 |
genehacker | check it out | 22:10 |
kanzure- | wait, wait, I have social networking skills? | 22:11 |
genehacker | yeah | 22:11 |
fenn | something like that | 22:11 |
genehacker | you know a bunch of transhumanists | 22:11 |
kanzure- | nobody that has any money. | 22:11 |
kanzure- | fenn: I'll look into it. | 22:11 |
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kanzure- | hrm, I'd like to capacitance scanning microscopy except my upload isn't all that good | 22:13 |
fenn | is that a book? | 22:13 |
kanzure- | no. wireless just sucks here. | 22:13 |
kanzure- | oh look, it jumped up to 8.2 kb/sec | 22:14 |
fenn | wowza | 22:14 |
fenn | time to eat some pringles | 22:14 |
fenn | don't buy a bunch of stuff from deal extreme if you expect to get it any time soon | 22:16 |
kanzure- | fenn, how soon do you need monies? | 22:17 |
kanzure- | scanning capacitance microscopy: http://heybryan.org/books/papers/Scanning%20capacitance%20microscopy%20on%20a%2025%20nm%20scale.pdf | 22:18 |
fenn | just in general | 22:18 |
fenn | there's a lot of things i could be working on right now if i had cash to throw around | 22:18 |
kanzure- | andrew hessel suggested I needed a patron | 22:19 |
kanzure- | do they make those any more? | 22:19 |
fenn | good question. tell me if you find out | 22:19 |
fenn | it makes a lot more sense than paying for specific art objects as if they were products | 22:20 |
kanzure- | I think that paper is exactly what you were thinking of | 22:21 |
fenn | does it measure capacitance between the tip and the surface of interest? | 22:22 |
fenn | because that's not what i meant | 22:22 |
kanzure- | works for both insulators and conductors | 22:22 |
kanzure- | so I would assume it's not tip-surface capacitance measurements | 22:22 |
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fenn | it measures capacitance between tip and surface | 22:31 |
kanzure- | ouch. | 22:37 |
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fenn | anyway that's cool as it gives you another dimension to image | 22:42 |
fenn | you could use the same tip for STM, AFM, and capacitance microscopy, right? | 22:42 |
kanzure- | why do people and papers complain about having to switch out tips all the time then? | 22:42 |
katsmeow | they crash them? the tips oxidize? | 22:43 |
kanzure- | ok, that's reasonable. | 22:43 |
fenn | afm wears out the tips doesn't it? | 22:43 |
fenn | it sounds like capacitance microscopy isnt used very much | 22:44 |
kanzure- | you need a better name for your version of capacitance microscopy | 22:44 |
fenn | it's not 'my version of capacitance microscopy' | 22:44 |
kanzure- | then what is it? | 22:45 |
fenn | it's just a bend sensor for a standard AFM cantilever | 22:45 |
kanzure- | huh? I thought you said the distance between a sample-holding plate and the cantilever tip | 22:45 |
kanzure- | oh well. I was wrong | 22:46 |
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kanzure- | I can't seem to find piezo nanowires. am I missing out on some good search terms? | 23:05 |
katsmeow | piezo nanowires? never heard of it | 23:05 |
katsmeow | piezo implies crystal, which isn't a wire? | 23:06 |
kanzure- | you can't have a crystal wire? | 23:06 |
fenn | The International Federation of the Phonographic Industry (IFPI): introducing and improving copyright laws, anti-piracy enforcement, anti-piracy litigation, internet monitoring and closing of illegal sites (Censorship), marketing and public relations efforts, and working to create new forms of Digital Rights Management. | 23:06 |
katsmeow | umm,, i think it would shatter easily | 23:06 |
kanzure- | fenn: is that supposed to be funny, sad, or none of the above | 23:07 |
fenn | In mid-October 2007, after the IFPI let the ifpi.com domain registration lapse, ownership of the ifpi.com domain was transferred to The Pirate Bay, under the backronym "International Federation of Pirates Interests, | 23:07 |
fenn | then they tried to switch to ifpi.org but the DNS was hacked again | 23:08 |
fenn | er, hacked twice (first time was just stupidity by ifpi) | 23:08 |
katsmeow | kanzure http://ltn.vbnlive.com/site/upload/document/Microsoft_PowerPoint_-_9._Paul_Beecher_Nokia.pdf | 23:08 |
kanzure- | katsmeow: what is it? | 23:09 |
katsmeow | an url | 23:09 |
kanzure- | .. | 23:09 |
katsmeow | to nanowire touch sensor | 23:09 |
kanzure- | please don't make me click stuff | 23:09 |
katsmeow | Microsoft PowerPoint - 9. Paul Beecher Nokia.ppt | 23:09 |
katsmeow | ZnO Nanowires for flexible tactile arrays. Characteristics for sensor | 23:09 |
katsmeow | applications. • Uniaxial piezoelectric response. • Enabler of novel touch sensor | 23:09 |
katsmeow | ... | 23:09 |
katsmeow | http://ltn.vbnlive.com/site/upload/document/Microsoft_PowerPoint_-_9._Paul_Beecher_Nokia.pdf | 23:09 |
kanzure- | hm. | 23:09 |
kanzure- | neat. | 23:09 |
katsmeow | or | 23:09 |
katsmeow | http://www-mcr.trinhall.cam.ac.uk/wiki/Aron_Rachamim | 23:10 |
katsmeow | Research | 23:10 |
katsmeow | I am investigating the use of zinc oxide nanowires in touch sensor devices (e.g. displays on mobile phones). Zinc oxide nanowires are piezoelectric so compression of them generates a voltage. Conversely application of a voltage causes them to extend so there is also potential for touch feedback to the user (e.g. they could press on the screen to call someone and the screen could vibrate so they could feel that the call is taking p | 23:10 |
katsmeow | This research is being funded by Nokia. | 23:10 |
kanzure- | so .. resolution anyone? | 23:10 |
kanzure- | gah, wireless sucks here | 23:10 |
katsmeow | sorry i mentioned it was for wireless devices | 23:11 |
kanzure- | no, my wireless connection | 23:11 |
kanzure- | because I can't download anything quickly, or upload | 23:11 |
katsmeow | ah | 23:11 |
fenn | where's "here"? | 23:12 |
kanzure- | dorm | 23:12 |
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