--- Log opened Thu Oct 19 00:00:37 2017
--- Day changed Thu Oct 19 2017
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00:01 < nmz787> is there a test procedure?
00:01 < nmz787> you mentioned a low-powered LED
00:02 < nmz787> how would I know how much to start with?
00:02 < nmz787> I mean, what if the x-rays have much different sensitivity to my choice of LED
00:04 < fltrz> the low powered led is to test and verify the amplifier stages, i.e. the gain as a function of frequency
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00:07 < fltrz> if you want to do spectroscopy, and you see a similar pulse height distribution after your amplifier(s) as in the opengeiger.de picture, you need some sources of xrays of 2 energies and then its practically a linear fit for pulse height per gamma energy
00:09 < nmz787> another thing was I could never really figure out what frequency to target
00:09 < fltrz> for the amplifiers?
00:10 < nmz787> how could I know how often a photon would arrive, or how quickly I'd need to respond when it came in (as fast as I can go, while still being below noise tolerance)
00:10 < nmz787> tolerance/threshold
00:11 < nmz787> I'd assume it would have something to do with the number of FIB ions impinging on the material for PIXE to occur... and how many FIB ions might depend on the accelerating voltage of the beam or something
00:12 < nmz787> but them as you move the beam, or as the material mills away, you might also have signal changes
00:12 < nmz787> so again... not sure how to calc the needed frequency
00:12 < nmz787> of the amps, yeah
00:12 < fltrz> so you want to limit the bandwidth of the amplifier, because then there is less noise being amplified
00:12 < nmz787> and any filtering/feedback stuff I guess too
00:13 < nmz787> like, there's the bandwidth of the op-amps, but then also the feedback design and values for the amplification
00:13 < fltrz> let me restart
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00:14 < fltrz> to do spectroscopy, you need to amplify individual pulses, and measure their heights,... above a certain radiation rate and hence pulse rate the exponentially decaying pulses start overlapping
00:14 < fltrz> and at some point you dont see individual pulses, an hence cant do spectroscopy
00:15 < fltrz> so if you want to know the number gammas per second you don't care about spectroscopy, and can go up to very high count rates
00:16 < fltrz> but if you want to do spectroscopy, you need to limit the gamma count rate so that your electronics can distinguish individual pulses
00:17 < fltrz> so at what point do these pulses start overlapping? it depends on the decay speed of the exponential pulse
00:17 < fltrz> this is determined by the capacitance of the photodiode
00:18 < fltrz> (this depends on reverse bias voltage)
00:18 < fltrz> look at figure 6 page 3 of http://www.vishay.com/docs/81521/bpw34.pdf
00:20 < nmz787> sure, I remember the reverse biasing
00:21 < fltrz> so that gives about 17pF
00:21 < fltrz> ok, the driven load resistor together with this capacitance determines the 'half-life' of the RC filter they form
00:22 < fltrz> so that fundamentally sets the highest rate at which your detector+circuit will be able to count
00:23 < fltrz> so amplifying any signal above this frequency just contributes noise
00:24 < nmz787> hmm
00:24 < fltrz> (the resistors all contribute johnson nyquist noise, the rms value of which is proportional to bandwidth)
00:24 < nmz787> there are so many kinds of noise :P
00:26 < fltrz> yes, thats why we look up the different noise contributions in operational amplifiers, http://www.analog.com/media/en/training-seminars/tutorials/MT-047.pdf this one first for quick intro
00:26 < fltrz> then http://www.ti.com/lit/an/slyt094/slyt094.pdf for rigorous noise total
00:30 < fltrz> make sure to read the quick intro pdf first, because they just give the example with noise from 1 resistor and compare it with voltage noise, amplifier current noise, johnson noise
00:30 < fltrz> these are the 3 kinds of noises
00:31 < fltrz> but there are more sources per kind
00:31 < nmz787> this is a good 3-part series
00:31 < nmz787> .g design femtoampere site:edn.com
00:31 < yoleaux> https://www.edn.com/design/analog/4395651/Design-femtoampere-circuits-with-low-leakage---Part-3--Low-current-design-techniques
00:31 < fltrz> look at figure 4 of http://www.analog.com/media/en/training-seminars/tutorials/MT-047.pdf they compare 3 noise sources in 3 situations
00:31 < nmz787> well google those keywords anyway
00:32 < fltrz> yes that series is good
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00:37 < fltrz> in slyt094.pdf at the end they suggest using a spreadsheet program, so that in the future you can simply plug in the different values and observe their effect
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00:38 < nmz787> that opengeiger.de site seems pretty good
00:38 < fltrz> yes it is
00:38 < nmz787> will have to look into this all more again, soon
00:40 < nmz787> lots of different stuff going on lately, not as much need for the x-ray detector, but it would definitely still be useful to have, as well as get some sense of accomplishment from finishing this project idea
00:40 < nmz787> and gaining some more skills and knowledge
00:40 < nmz787> any sources you would recommend for calibrating?
00:40 < fltrz> regarding your question for amplifaction level, it just determines the upper bound of the energy window for spectroscopy, and the pulse discriminator / trigger level determines the lower bound of the energy window
00:40 < nmz787> you mentioned smoke detector and banana?
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00:41 < fltrz> to be honest, I knew the concept of calibration as we did it in university with a pulse channel analyzer
00:41 < fltrz> but I am not sure what range of energies the pin photodiode are suitable for
00:42 < fltrz> I think the maxim application note in your folder says it somewhere IIRC from long ago
00:42 < fltrz> so once you know what every range the photodiode can detect
00:43 < fltrz> you can select typical radioactive sources on the basis of them releasing a gamma in this range
00:43 < fltrz> I think forums/websites for calibrating these devices are easier to find the knowledge (i postpone this part until afterwards)
00:44 < fltrz> *what energy range
00:45 < nmz787> mm
00:45 < nmz787> well thanks for the new reading
00:46 < nmz787> I have a lot more in a another folder which I didn't commit, but can if you think it would be useful/good
00:49 < fltrz> I would check it out if you did, but not really sure how happy github is with including materials of third party?
00:49 < nmz787> meh, who knows
00:50 < fltrz> true
00:50 < nmz787> guess they'll email me and complain that I suck at open-source
00:52 < fltrz> I think jameco used the FET because the LM358 has unspecified (probably crap) input current noise
00:53 < nmz787> yeah I had no idea of the signal levels
00:54 < fltrz> when selecting op-amp just sort them by input current noise, and select low fA/sqrtHz range
00:55 < nmz787> earlier you mentioned 17pF, and that setting the max freq of the response, which would be pointless to aim for faster amplifiers (right?) (and by faster amplifiers, I mean the bandwidth specs they quote, usually at unity)
00:55 < fltrz> (if you want to do spectroscopy)
00:55 < fltrz> correct
00:55 < nmz787> what about just dosimetry
00:55 < fltrz> but
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00:56 < fltrz> higher GBP is still desirable, because you can amplify more for the same bandwidth
00:56 < nmz787> (as opposed to "if you want to do spectroscopy")
00:56 < nmz787> I figured it meant faster slew rate
00:56 < nmz787> and wouldn't the edge of a photon be the speed of light
00:56 < nmz787> or the freq of a photon (THz)
00:57 < fltrz> with edge you mean the leading side of the pulse?
00:57 < fltrz> THz is far infrared :)
00:57 < nmz787> I guess, like the speed of light briging that whole particle into the detector and inducing photoelectric effect (and conversion to electrons)
00:57 < nmz787> well visible is THz
00:57 < nmz787> so is x-ray
00:58 < fltrz> visible is more like PHz
00:58 < nmz787> "A typical human eye will respond to wavelengths from about 390 to 700 nm. In terms of frequency, this corresponds to a band in the vicinity of 430–770 THz."
00:58 < nmz787> I mean, I guess it's near Peta
00:58 < fltrz> ok right
00:59 < fltrz> but x-ray is way higher up
00:59 < nmz787> 10^-1 PHz range
00:59 < nmz787> "X-rays are electromagnetic waves with wavelengths in the range of 0.01 to 10 nanometers, corresponding to frequencies in the range 30 petahertz to 30 exahertz "
00:59 < nmz787> hmm
01:00 < nmz787> yeah, anyway, with those kinda numbers, GBP seems like I need at least that much for shannon information theory sort of stuff
01:00 < nmz787> idk
01:00 < fltrz> nono
01:00 < nmz787> it definitely get's confusing when starting from scratch
01:01 < fltrz> theres a difference between the frequency of the electromagnetic wave like these PHz
01:01 < fltrz> and the frequency of photon arrivals
01:01 < fltrz> like say 20kHz
01:02 < fltrz> well decay rate would be a better terminology I guess
01:02 < fltrz> so the response time of the detector sets the maximum number of nuclear disintegrations per second
01:02 < fltrz> before the pulses start overlapping due to response time
01:03 < nmz787> but I guess if you had PHz amps and sensing... you might see less overlap right?
01:03 < fltrz> higher rates of radiation would cause the pulses to overlap, and spectroscopy is impossible, but dosimetry still is possible
01:04 < fltrz> if we had PHz amps and sensing, we would be able to measure the electric field of photons directly, like how we can do this at radio frequencies with antennas
01:04 < nmz787> or I guess I imagined you could somehow deconvolve the overlapping detections, to try and unobfuscate things
01:05 < fltrz> nmz787: yes, in software it should be possible to deconvolve somewhat
01:05 < fltrz> but I don't think its a good idea to try any of this with a first geiger counter
01:07 < nmz787> :P
01:07 < nmz787> :/
01:08 < fltrz> for spectroscopy the noise level is important, because noise causes pulse height to be wrongly measured, so it blurs energy levels
01:08 < nmz787> yes, I tend to overwhelm myself with depth-first searches/learning
01:08 < fltrz> nmz787: I have the same problem
01:08 < fltrz> but its not a problem if you only do it mentally
01:08 < nmz787> I did however buy an electrometer that I thought should help me test/debug
01:08 < fltrz> its good to explore and understand possible approaches
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01:19 < fltrz> instead of trying to make extremely high pulse readings possible, people just choose a less active source, i.e. a smaller part of a rock, or bigger distance between source and detector
01:22 < fltrz> but most of the time people are measuring much less radioactive sources, and the problem never presents, to the contrary, they wait couple of minutes to let the spectrum build up. i.e. at first the graph is flat with all channels at 0 counts, then the setup is detecting pulses, and each pulse increases one of the energy bins with 1... so supposing a graph of width and height of 1000, and a single pixel increase in height for each
01:23 < fltrz> it can take a while to build up a graph with sufficient counts per bin in order to get accurate relative spectroscopic heights in order to do dating etc
01:24 < fltrz> also they let it run for a while and subtract the background (no sample) spectrum in order to get the spectrum of the sample
01:25 < fltrz> so the graph could build up faster with higher count rate circuits, one also would need a stronger sample to supply gammas at this rate... which obviously... people somewhat avoid
01:26 < fltrz> also, when you try to date a piece of painting, you just dont want to cut a large piece of the painting away
01:33  * nmz787 sleeps
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03:10 < adlai> i'd like to say a few brief words about Grognor, if that's alright.
03:10 < adlai> i read once on the web that he was a voice actor, along with other gigs
03:10 < adlai> dunno if he did this under the same name we know him by today
03:11 < adlai> once he called me on skype to test a microphone, and literally hung up the moment he could hear me hear him
03:11 < adlai> fellow really seemed to know what he wanted out of life, and i hope he got it, too.
03:12 < adlai> .tw https://twitter.com/Grognor/status/874375747510702084
03:12 < yoleaux> person B means a lot to person A, but person A means nothing to person B. I'm person A a lot. it makes me very sad (@Grognor)
03:12  * adlai hopes he's less sad, now. that is all.
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06:01 < kanzure> .title https://www.nytimes.com/2017/10/18/health/immunotherapy-cancer-kite.html
06:01 < yoleaux> F.D.A. Approves Second Gene-Altering Treatment for Cancer - The New York Times
06:01 < kanzure> $375k. hm.
06:02 < kanzure> adlai: have you checked the hplusroadmap logs when he appeared in here?
06:02 < kanzure> before he died
06:06 < kanzure> adlai: someone is asking me whether you are a weird sun on twitter
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07:13 < ebowden> Before who died?
07:13 < ebowden> kazure, ^
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07:49 < kanzure> i'm not sure how that could be confusing
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09:15  * heath wonders how the $375k figure was calculated
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11:09 < heath> speaking with a guy who was previously a process engineer developing nanotube afm probes
11:11 < heath> seems he also built a plasma generator for nasa
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12:12 < kanzure> 12:06 < kuudes> could we try to prevent intelligence explosion by limiting the amount of intelligence always small enough?
12:12 < kanzure> 12:07 < kuudes> maybe. if we can metalearn the measure of intelligence before we deploy it?
12:12 < kanzure> 12:12 < kanzure> the more you try to prevent intelligence explosion, the more i try to do it anyway
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14:07 < fltrz> for energy storage, one actively researched candidate are flywheel energy storage systems (FES). the shape and size of FES is limited by the tensile strength of the rotor material
14:08 < fltrz> FES have the highest energy density when they are small and rotate at higher speeds
14:08 < fltrz> this limitation on tensile strength... imho stems from trying to spin them in vacuum (to reduce friction)
14:10 < fltrz> imagine a frictionless fluid, then the centrifugal force that needs to be balanced with tensile strength could be balanced with pressure as well, in order to reach higher rotational speeds
14:11 < fltrz> conceptually, imagine a pressurized superfluid instead of a vacuum surrounding the rotor, then as long as the superfluid can remain in the superfluid state, we can have the rotor reach arbitrary rotational speeds by increasing the pressure of the superfluid, which presses inward on the rotor
14:12 < fltrz> i.e. instead of centrifugal force balanced with tensile strength: centrifugal force balanced with (tensile strength + pressure)
14:13 < fltrz> this may seem to displace the problem to the walls of the container, but with a (super)fluid acting as a low friction bearing between rotor and stator
14:14 < fltrz> but the crux is that the stator is now no longer moving, and can have arbitrarily thick walls to support the fluid presssure!
14:15 < fltrz> https://en.wikipedia.org/wiki/Flywheel_energy_storage
14:17 < fltrz> in vacuum you cant provide inward support to the rotor .. because there is no pressure in vacuum
14:19 < fltrz> perhaps instead of a superfluid, an air bearing (along the whole surface of the rotor) could suffice, even if there is some friction: while it might decay its energy faster than the vacuum versions (and none of them are perfect either) it could reach higher storage density by allowing faster rotors
14:21 < heath> .title https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4068291/
14:21 < yoleaux> DNA polymerases drive DNA sequencing-by-synthesis technologies: both past and present
14:35 < fenn> is energy density important if you're reinforcing with huge thick walls?
14:36 < fenn> utility flywheels are buried a few meters below ground in a concrete lined vault, so i guess it doesn't matter for that application
14:37 < fenn> the other main use is for electric launch catapults on aircraft carriers, and ship mounted railguns
14:38 < fenn> i guess energy density is important in those applications, but it's probably not the main consideration
14:39 < fenn> what about compressive magnetic bearings instead of an air bearing?
14:39 < fenn> or something like a mag lev track turned in a circle
14:40 < fenn> i think this would need superconductors to prevent losses due to the eddy currents, but there's more experience with superconductors than superfluid bearings
14:42 < fenn> another important consideration is cost per watt and cost per joule, if you can't beat lithium ion batteries there's not much point. adding super* components tends to add cost
14:43 < fenn> .wik compulsator
14:43 < yoleaux> "A compensated pulsed alternator, also known by the portmanteau compulsator, is a form of power supply." — https://en.wikipedia.org/wiki/Compulsator
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15:13 < fltrz> the walls wouldnt necessarily need to be huge, just strong enough to contain the pressure without itself rotating... when a flywheel shatters it is the outermost part that shatters first because it is furthest from the axis of rotation, furthermore most flywheels are buried underground in order to contain such an explosion event anyway
15:13 < fltrz> so yeah like you said
15:14 < fltrz> fenn, perhaps compressive magnetic bearings could work, I thought about it myself, but not sure if that would induce eddy current losses
15:15 < fltrz> I think it would
15:16 < fltrz> I think they are cheaper in cost per watt already, but not per joule
15:18 < fltrz> hence their (potential) utilization for regenerative breaking (every time car decelerates only to accelerate afterwards, with dissipative braking, its energy multiple times, heat generated, brakes wearing out, dust generated)
15:21 < fltrz> but mostly the repeated expenditure of energy because of braking then accelerating, compare 2 cars, one fossil fuel say, and one with regenerative braking, but both initially increase the same weight car to 100kJ (1000kg car 10m/s), every time the car stops and speeds up to the same speed again, say 30 times in a trip
15:22 < fenn> are you talking about a mechanical CVT linkage, or using electric motors/generators
15:22 < fltrz> the first car will expend 3MJ, while the second will expend 100kJ in the trip (plus some regenerative losses)
15:23 < fltrz> so while the energy density may be lower for the FES-in-a-car, it may need to expend much less energy over the average representative trip
15:23 < fenn> apparently most garbage trucks already use hydraulic accumulators and vane motors to recover energy
15:24 < fenn> vehicle mounted flywheels have problems because of gyroscopic effects
15:24 < fltrz> yes, for garbage trucks even a very lossy regenerative system is helpful since they stop every few houses
15:25 < fltrz> how many stop-start cycles would a garbage truck do on a typical run?
15:25 < fenn> hundreds
15:25 < fltrz> if not more, theres also recovery opportunity in slight deceleration and slight acceleration
15:26 < fltrz> so while the complicated system currently used on garbage trucks isn't justified on consumer vehicles
15:27 < fltrz> the FES might be for 30-ish (a number I made up) stop-start cycles on average consumer car trip
15:28 < fltrz> also when parking the car the energy in the FES can be slowly loaded back into current style (but smaller) batteries
15:28 < fltrz> do electric cars do regenerative breaking back into the battery? or are the currents to high?
15:28 < fenn> the flywheel only needs to be big enough to absorb stopping from cruising speed once
15:28 < fltrz> right
15:29 < fenn> i think toyota prius does something like this but with batteries
15:29 < fltrz> cars need to be able to brake very fast
15:29 < fltrz> perhaps they can do it already with batteries, all in parallel or smth
15:30 < fenn> it's rare that a car actually needs to brake fast
15:30 < fltrz> fenn: there may still be utility in large flywheel than cruising speed to full stop
15:30 < fenn> if drivers were rewarded for braking slowly they would adapt
15:30 < fltrz> for hilly terrain, uphill downhill
15:31 < fenn> meh it's an 80/20 situation as usual
15:31 < fenn> a small flywheel with a small power rating would handle 80% of loads
15:32 < fenn> i think the time for vehicle mounted flywheels has passed though, with modern lithium batteries
15:33 < fltrz> I'm not entirely certain, in the long run construction may be cheaper for flywheels
15:33 < fltrz> and if maintenance cost is lower than for batteries... batteries only last x years/cycles
15:33 < fenn> eh batteries last thousands of cycles
15:34 < fltrz> every time we make a flywheel and bury it
15:34 < fltrz> it could last much longer than batteries
15:35 < fenn> probably it could, but by then we will have better batteries
15:35 < fltrz> I hope so
15:36 < fenn> i'm not a fan of disposable technology, but batteries are enough of a commodity that there will definitely be an aftermarket
15:36 < fenn> so it should be possible to upgrade old cars to new batteries
15:38 < fltrz> since the wikipedia page provides nothing like pressurized fluid to provide supporting pressure for the flywheel for higher speeds, I assume it's been thought of and ruled out due to friction?
15:39 < fenn> i don't know, i've never heard of it, but i'm not an expert on flywheels
15:39 < fltrz> or should I contact one of the random flywheel scientists, and ask if their may be utility of it?
15:46 < fenn> 15:42 < garit> fenn: at 500 m/s you will be holding a tank with 3000 atm, while air bearing can hold 10 atm or so
15:46 < nmz787> I was just looking at the 2018 mitsubishi outlander (or highlander, something like that)... but it was saying that it could work as a series-hybrid or parallel-hybrid
15:46 < fenn> 15:43 < garit> maglev can hold 4 atm squared per tesla
15:46 < fenn> 15:45 < garit> So, your idea just needs a hundred times better bearing than the ones we have. And may be 10 times better than the best we can make in theory in a lab
15:48 < fenn> garit's argument seems to assume a particular mass density, but the surface area to mass ratio of a flywheel is somewhat arbitrary
15:50 < fenn> 15:49 < garit> I assumed a solid cylinder
15:50 < fenn> 15:50 < garit> but you get the idea. Increasing the surface area by a factor of 100 will make the energy disappear in a matter of seconds/minutes
15:52 < fltrz> "while air bearing can hold 10 atm or so" that is the pressure it can support, or is that the gas pressure?
15:55 < fltrz> what channel is this garit?
15:55 < fenn> ##engineering
16:00 < fenn> https://arstechnica.com/information-technology/2017/09/bluetooth-bugs-open-billions-of-devices-to-attacks-no-clicking-required/  seems like they should deploy a self-replicating exploit patcher
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16:39 < kanzure> http://diyhpl.us/~bryan/papers2/bio/Eric_Drexler_Adam_Marblestone_09-01-16_(public).pdf
16:41 < fenn> what's the one sentence summary?
16:42 < kanzure> i don't know, i was actually looking for http://diyhpl.us/~bryan/papers2/neuro/marblestone.stanford.cs379c.04-29-13.pdf
16:43 < fenn> "creating a self-assembling biomolecular device capable of functioning as a 3D printer with 1 nm resolution, a conversation"
16:47 < fenn> "contrary to a widespread misconception, atomically precise manufacturing does not require the manipulation of individual atoms"
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16:56 < kanzure> hmm almost sounds like biology coughcoughcough
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17:34 < juul> anyone want to go to this tonight? i have an extra ticket https://www.calacademy.org/nightlife/extraterrestrial-nightlife
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17:37 < mrdata-> where
17:37 < juul> San Francisco
17:37 < mrdata-> i'm a 5 hr flight away
17:38 < mrdata-> i think i missed it
17:39 < kanzure> fenn: you want it?
17:45 < fenn> no
17:48 < fenn> i have been to previous cal academy night life events, and they were fun, but i'm not feeling up to it today
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18:27 < kanzure> "Design of coiled-coil protein-origami cages that self-assemble in vitro and in vivo" https://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3994.html https://twitter.com/NatureBiotech/status/921048075145269248
18:28 < kanzure> "Polypeptides and polynucleotides are natural programmable biopolymers that can self-assemble into complex tertiary structures. We describe a system analogous to designed DNA nanostructures in which protein coiled-coil (CC) dimers serve as building blocks for modular de novo design of polyhedral protein cages that efficiently self-assemble in vitro and in vivo. We produced and characterized ...
18:28 < kanzure> ...>20 single-chain protein cages in three shapes—tetrahedron, four-sided pyramid, and triangular prism—with the largest containing >700 amino-acid residues and measuring 11 nm in diameter. Their stability and folding kinetics were similar to those of natural proteins. Solution small-angle X-ray scattering (SAXS), electron microscopy (EM), and biophysical analysis confirmed agreement of the ...
18:28 < kanzure> ...expressed structures with the designs. We also demonstrated self-assembly of a tetrahedral structure in bacteria, mammalian cells, and mice without evidence of inflammation. A semi-automated computational design platform and a toolbox of CC building modules are provided to enable the design of protein cages in any polyhedral shape."
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18:29 < kanzure> .tw https://twitter.com/antonioregalado/status/920771720318988289
18:29 < yoleaux> Gates: "Biology is software" Collins: "Mmm huh." (@antonioregalado)
18:30 < kanzure> "Neo: This new citizen science game invites you to team up with other heroes of neuroscience to strategically decipher the spectacular spiny dendrites and vast axons of neurons found in neocortex of a mouse brain. We aim to discover never-before-charted circuits and reveal insights into how the brain’s primary visual cortex encodes the beginnings of perception."  ...
18:30 < kanzure> ...http://blog.eyewire.org/announcingneo/ http://blog.eyewire.org/neuron-bundle-neo-update/
18:31 < kanzure> ( https://twitter.com/neobraingame/status/920645964490211328 )
18:33 < kanzure> "Dynamic control of aptamer-ligand activity using strand displacement reactions" http://pubs.acs.org/doi/10.1021/acssynbio.7b00277 https://twitter.com/BiochemPhD/status/920701825577299969
18:33 < kanzure> "Nucleic acid aptamers are an expandable toolkit of sensors and regulators. To employ aptamer regulators within non-equilibrium molecular networks, the aptamer-ligand interactions should be tunable over time, so that functions within a given system can be activated or suppressed on demand. This is accomplished through complementary sequences to aptamers, which achieve programmable ...
18:33 < kanzure> ...aptamer-ligand dissociation by displacing the aptamer from the ligand. We demonstrate the effectiveness of our simple approach on light-up aptamers as well as on aptamers inhibiting viral RNA polymerases, dynamically controlling the functionality of the aptamer-ligand complex. Mathematical models allow us to obtain estimates for the aptamer displacement kinetics. Our results suggest that ...
18:33 < kanzure> ...aptamers-kleptamer pairs could be used to build dynamic nucleic acid networks with direct control over a variety of aptamer-controllable enzymes and their downstream pathways."
18:33 < kanzure> hmm.
18:34 < kanzure> "Computational design of small transcription activating RNAs for versatile and dynamic gene regulation" https://www.nature.com/articles/s41467-017-01082-6 https://twitter.com/LucksLab/status/921041057458065409
18:35 < kanzure> "... Of the many regulatory molecules available, RNA regulators offer the intriguing possibility of de novo design—allowing for the bottom-up molecular-level design of genetic control systems. Here we present a computational design approach for the creation of a bacterial regulator called Small Transcription Activating RNAs (STARs) and create a library of high-performing and orthogonal ...
18:35 < kanzure> ...STARs that achieve up to ~ 9000-fold gene activation. We demonstrate the versatility of these STARs—from acting synergistically with existing constitutive and inducible regulators, to reprogramming cellular phenotypes and controlling multigene metabolic pathway expression. Finally, we combine these new STARs with themselves and CRISPRi transcriptional repressors to deliver new types of ...
18:35 < kanzure> ...RNA-based genetic circuitry that allow for sophisticated and temporal control of gene expression."
18:36 < kanzure> so anyway,
18:36 < kanzure> if those polyhedral protein cages are working then we can do basically any 3d model/object -> polyhedral protein cage
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18:50 < kanzure> some defensive patent pool stuff:
18:50 < kanzure> https://defensivepatentlicense.org/
18:50 < kanzure> http://www.rpxcorp.com/rpx-network/
18:50 < kanzure> http://www.openinventionnetwork.com/about-us/
18:51 < kanzure> https://en.wikipedia.org/wiki/Defensive_patent_aggregation
18:58 < kanzure> juul: do you have any other links for open-source synthetic biology licenses and patent defense stuff? i am putting together some suggestions for gp-write (i'm on their intellectual property group, have a call w/ them tomorrow morning)
18:59 < kanzure> i guess there's the cambia thing ...?
19:01 < juul> Well beside the OpenMTA this just went live: https://biobricks.org/pdc/
19:01 < juul> Otherwise ask linda@biobricks.org
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19:02 < kanzure> .title https://biobricks.org/pdc/
19:02 < yoleaux> Public Domain Chronicle | BioBricks Foundation
19:03 < kanzure> "PDC recombines elements of Open-Source-style public licensing, open-access publishing, open data, and defensive publication. Contributors can secure a new finding for the public domain by completing a mercifully short disclosure form, adding metadata to help situate their finding in context, and applying two new short, plain-language legal tools: a public declaration of intent to claim ...
19:03 < kanzure> ...discoveries for the commons, and a public license to make record of that contribution free for redistribution, processing, and search. These disclosures, tuned to effectively build the public domain, become public prior art immediately, with automatically applied and corroborated timestamps.
19:03 < kanzure> juul: btw you should use https://opentimestamps.org/ for timestamping
19:04 < kanzure> (i timestamp all of my git commits these days.)
19:04 < kanzure> hmm "The software powering PDC is Open Source, available under the terms of The Apache License, Version 2.0. Anyone can host a PDC server, receive contributions, and republish contributions to other servers automatically. Flexible by design, PDC servers can be tuned for ease of use in specific scientific areas. BioBricks will host a server tuned for best possible ease of use in synthetic ...
19:04 < kanzure> ...biology, such as for genetic functions. We look forward to seeing the system adapted for chemistry, materials science, and other areas."
19:04 < kanzure> https://github.com/publicdomainchronicle/
19:04 < kanzure> so why is a separate server required?
19:11 < juul> It is because the open source'ish patent regime stuff is contract based and requires someone to keep the contracts. It could be a single central thing but that goes against biobricks values and also some orgs want to customize and integrate their contract keeper system
19:11 < juul> Kemitchell is the hacker lawyer who wrote it. He is on irc and can tell you the details
19:12 < juul> Usually on #sudoroom
19:12 < kanzure> huh, alright. cool.
19:12 < juul> I will look at open timestamps
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19:13 < juul> I am at the grocery store on phone so not ideal for long explanations
19:13 < kanzure> ah yeah irc is also how i spend my time at grocery stores, 100% understandable.
19:14 < juul> I get notifications on mention :)
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19:35 < heath> patenleft stuff https://www.redhat.com/en/about/patent-promise
19:37 < heath> http://www.iam-media.com/blog/detail.aspx?g=af275128-57ca-4590-b62b-a3164a37f8de
19:37 < heath> "The new promise also borrows one element from the License on Transfer Network: if Red Hat were to transfer a patent to a third party, the promise would transfer with the patent. "
19:37 < heath> http://lotnet.com
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