<kanzure>
also, any papers you can contribute on #homecmos would be welcomed
<azonenberg>
very nice
<azonenberg>
and well, my work has actually mostly been in MEMS
<azonenberg>
my lab notes are in the google code repository in the topic
<kanzure>
etching processes are pretty similar in a few places
<kanzure>
sometimes microfluidics requires gold electrodes and other crap
<azonenberg>
Yeah
<kanzure>
but has the same geometry/layout problems that you need to consider
<azonenberg>
And larger
<azonenberg>
Which is a huge benefit for home / low budget fab
<kanzure>
yes, well, i'm not complaining about that
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<comeon>
why are nitrides like silicon nitride or titanium nitride such good "barrier" layer materials?
<azonenberg>
comeon: Mostly because they're denser, i think
<azonenberg>
I'm a little less up on the transistor side of things as i've mostly studied MEMS
<azonenberg>
I dont see Si3N4 used as a barrier as much
<azonenberg>
TiN and TaN i see used
<comeon>
nonstoichiometric silicon nitride is pecvd at low temperatures on gaas after doping gaas so that during an lattice damage removal annealing heat treatment the as doesn't float away
<comeon>
fuckin nazis on ##chemistry and ##physics quieted me
<azonenberg>
I assume by non-stoichiometric they mean Si rich and not N rich
<azonenberg>
but i'm not sure of the exact characteristics of pecvd nitride's formulation
<azonenberg>
but makes sense
<azonenberg>
also just fyi this is the unofficial microfab / semiconductor channel on freenode
<azonenberg>
not just home fab
<comeon>
then rename it
<azonenberg>
I might
<azonenberg>
Just saying, discussion of cleanroom fab on "real" tools is not offtopic
<comeon>
well i only asked because the bigger channels quieted me
<comeon>
but you're the only person who ever talks here anyway
<comeon>
might as well call it #azonenberg
<azonenberg>
Lol
<azonenberg>
Other people do talk
<azonenberg>
But they idle a lot
<azonenberg>
the community is small
<azonenberg>
Not many people interested in semiconductors
<azonenberg>
and even less know anything about them
<azonenberg>
even less are on freenode
<comeon>
freenode has a lot of software cocksuckers
<azonenberg>
lol
<azonenberg>
Hey, dont knock software TOO much
<azonenberg>
my undergraduate degree is in computer science
<comeon>
psh
<azonenberg>
and i'm going for a PhD in the same
<comeon>
why
<azonenberg>
My research is in computer architecture
<azonenberg>
and operating system security
<comeon>
that sounds super boring
<azonenberg>
Not at all
<azonenberg>
my advisor is a crypto guy and i'm not too into the intense theory but when it comes time to prototype stuff its fun
<comeon>
whatever floats your boat dude
<azonenberg>
I just do hardware stuff for fun lol
<comeon>
there is a dude in ##electronics who literally floats in a boat
<azonenberg>
starting to take EE classes because i've taken most of the ones CS offers adn am not interested in the rest
<comeon>
geckosenator or something
<azonenberg>
interesting, i've heard of the guy but didnt know he lived on a boat
<comeon>
he cooks his own shit for fuel
<azonenberg>
lol
<comeon>
super greenie weirdo
<soul-d>
lol
<soul-d>
i din't want to know that
<azonenberg>
i assume he's online via a solar-powered laptop
<azonenberg>
with a satellite or 3g connection?
<comeon>
and the asshole lives on food stamps
<comeon>
cuz he doesn't want to work a real job
<comeon>
just float on a boat and leech off society
<azonenberg>
furrywolf is mostly off-grid too, he/she (i think wolfy is a female) runs almost entirely on solar
<soul-d>
i think most people in here are just to steal azonenberg's idea's for world domination
<soul-d>
at least i am
<azonenberg>
soul-d: they'll be waiting a long time
<comeon>
got to milk them nerds
<soul-d>
no key is nano bots :P
<azonenberg>
this isnt ##world-domination
<azonenberg>
my world domination plans are occurring elsewhere
<azonenberg>
i dont drink but i wanted to get a picture of me and a bottle of alcohol on my 21st
<soul-d>
he does what he likes
<comeon>
you don't drink?
<comeon>
like at all?
<azonenberg>
Nope
<comeon>
why not?
<azonenberg>
totally clean
<comeon>
are you a moralfag?
<azonenberg>
and i just dont feel the need to alter my neurotransmitters at all
<azonenberg>
i like 'em just the way they are
<azonenberg>
if it's not broken dont fix it
<comeon>
but it's fun
<azonenberg>
anyway so i showed the pic to my doctoral advisor and he thought it was hilarious
<azonenberg>
comeon: maybe you think it is, and if so you're welcome to do it
<azonenberg>
while you're off puking your guts up i'll be doing FPGA design
<comeon>
have you tried it at least?
<comeon>
you don't have to drink to you puke your guts
<azonenberg>
I know i wouldnt like it
<azonenberg>
my mind cant handle downtime
<azonenberg>
after i graduated college i went with my family down the shore for a vacation
<azonenberg>
By the end of the second or third day i couldnt take it anymore
<azonenberg>
pulled out my laptop and started doing mask layout for a MEMS comb drive
<comeon>
you need to get laid
<azonenberg>
i need to be doing something intellectual every waking hour, basically, or i go nuts
<kanzure>
i don't talk much in here because of the other diybio channel ##hplusroadmap
<kanzure>
but that one is called ##kanzure not #azonenberg
<azonenberg>
lol
<kanzure>
also, that channel is full of neurofags doing nootropics
<kanzure>
but i think you were talking about alcohol
<kanzure>
so nevermind
* kanzure
sleeps
<comeon>
what
<comeon>
i don't know man. you need to lighten up
<azonenberg>
comeon: lighten up? What is that going to do for me
<azonenberg>
i'm 21, most of my friends havent even graduated yet, and i have companies beating a path to my door basically offering me jobs
<comeon>
there's more to life than companies and stuff
<azonenberg>
i'm in a PhD program at a well known engineering school doing work i love, with enough spare time to do crazy research and projects on the side
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<azonenberg>
comeon: suffice it to say, ten years from now i think i'll be very happy with where i am
<comeon>
where is that?
<soul-d>
in a position he can look back
<soul-d>
and be proud on
<soul-d>
instead of wasted time
<soul-d>
drinking
<soul-d>
complaining
<soul-d>
telling others tehy don't have a lvie becasue you don;t have one
<azonenberg>
High paying job at a R&D lab for some big tech company or national lab, living in a house/lab i built from the ground up with my own two hands
<azonenberg>
loaded with tools and equipment rivaling a small university
<azonenberg>
all the toys i could ever want, from a SEM to a class 1000 cleanroom to a machine shop
<azonenberg>
by that point i will likely have large submicron (750nm or so) CMOS fab working
<azonenberg>
oh, and out in the country so i can enjoy the outdoors and not be bothered by neighbors living too close
<soul-d>
azonenberg, whenever your company put's out stocks give me pm id like to take some
<azonenberg>
though still within a commuting distance of wherever i work
<azonenberg>
soul-d: lol, the last company i owned closed its doors when my partner took a full time offer and i left for grad school
<azonenberg>
so thats a ways out
<comeon>
do you have friends in real life?
<azonenberg>
comeon: sure - my roommates, most of the electronics club
<soul-d>
given your personality comeon i doubt you have any real friends
<azonenberg>
i dont go out drinking with them, more likely i'll wander into the living room at 2 AM and find one of them working in the lab
<soul-d>
just friendly to your face till you are gone
<azonenberg>
or etching a PCB in the fume hood
<azonenberg>
And you know what? I wouldnt have it any other way
<comeon>
soul-d: i don't get teetotalers
<soul-d>
who said he was and why are you obseesed by it
<soul-d>
maybe he understands the chemical formula
<comeon>
in small quantities it's healthier than completely abstaining
<azonenberg>
and get away from studying for my upcoming PhD qualifying exam
<soul-d>
did he say he did and why are you intrested in why are you obsessed with an online persons life ?
<soul-d>
and why do you want to change it
<soul-d>
somthing to do with just respecting people's choices
<comeon>
what's with the whiteknight?
<azonenberg>
i dont need anyone to defend me, he's just having fun poking the troll
<comeon>
you don't have to respect people's choices especially if they are super different than everyone else
* azonenberg
pops lid of "troll food" can and throws it toward ##conspiracy-theory
<soul-d>
i don't take people that use the word "super" very seriously
<comeon>
i don't take people that use the word "very" super seriously
<azonenberg>
And for the record i do not care what you think about me whatsoever, i am perfectly happy with where i am in life and am not "missing out" on anything
<azonenberg>
as a result of spending my evenings designing microprocessors instead of going out drinking
<soul-d>
one establisches brain networks and makes you measurably smarter other
<soul-d>
...
<soul-d>
you can guess
<azonenberg>
If you enjoy going out and ingesting near-toxic levels of ethanol, thats your decision
<azonenberg>
One less person to compete for my job
<azonenberg>
But i find joy in intellectual stimulation and there's absolutely nothing wrong with that
<soul-d>
and i can tell from experience
<soul-d>
that it's better tehn waking up in a ditch
<Sync>
kanzure: I probably can get you a DLP devkit
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<kanzure>
Sync: what are the details
<kanzure>
also, can you possibly get me one that can also do UV
<Sync>
they are sillicon imaging dev boards iirc
<kanzure>
azonenberg: i'm a little disappointed that you're in school :)
<azonenberg>
kanzure: why? Lol
<azonenberg>
thought i was some 14-year-old kid?
<kanzure>
Sync: link?
<kanzure>
azonenberg: that would be the ideal case yes
<azonenberg>
Lol
<kanzure>
azonenberg: but more to the point that you feel university is necessary at all
<azonenberg>
Oh
<azonenberg>
I needed a piece of paper that says "bachelor of science" to get some employers to even look at me
<azonenberg>
cant say i've learned much from class, i dont find lectures a good way to learn
<kanzure>
are those the types of people that you really want to work for
<kanzure>
your employment requirements should just be money, imho
<azonenberg>
No, but
<azonenberg>
they'd pay the bills while i looked for the *right* people
<Sync>
I don't know which ones gotta find them first
<kanzure>
i saw some pretty cheap dlp dev kits for $300ish
<kanzure>
but they didn't do UV
<kanzure>
UV would be nice so that i can do DNA quantification by raman absorption spectroscopy or something
<azonenberg>
They specifically said no uv, or they didnt say they did?
<azonenberg>
And depends on the wavelength
<kanzure>
their support varies, i've looked at some spec sheets.. whatever
<azonenberg>
for lithography using DNQ-novolac photoresist you can get stuff that responds at 405 or even 450nm (my resist is 405 peak)
<kanzure>
there's a few problems with dna synthesis, maybe you have some ideas
<azonenberg>
which is actually on the edge of the visible spectrum
<kanzure>
if i explain what the process is.
<azonenberg>
Well, i understand at a very basic level how dna replication works
<azonenberg>
but when you say synthesis
<kanzure>
nah this is different
<kanzure>
*different
<azonenberg>
you want to take a bunch of raw nucleotides and make a piece of dna?
<azonenberg>
with a specific sequence?
<kanzure>
you can use dna polymerase to make new sequences but you can't control what nucleotides it chooses
<kanzure>
there's a few different chemistries for adding nucleotides to a growing single strand
<kanzure>
this is generally called oligonucleotide synthesis
<kanzure>
the most popular solid phase oligonucleotide synthesis method is phosphoramidite chemistry
<azonenberg>
ok
<kanzure>
there's also a version of this phosphoramidite chemistry that uses photolabile protecting groups on the ddNTPs
<azonenberg>
Bear in mind my ochem knowledge is relatively limited
<azonenberg>
i have more experience with inorganic and even that is somewhat limitd
<kanzure>
so you shine some light to decap, and hope a reaction occurs to add that nucleotide to the end of the growing strand
<kanzure>
wash step. then some other capping/decapping steps.
<kanzure>
the wash step is the main pain in the ass for me
<kanzure>
it's not a complicated step, but i mean from a practical standpoint
<azonenberg>
Ok, let me see if i have this straight
<azonenberg>
Start with a single nucleotide, attach chemical A to one end and B to the other
<azonenberg>
B is stable and A degrades under UV
<azonenberg>
Use UV to remove A, add a small amount of your second nucleotide and attach to that end of the strand
<azonenberg>
remove unreacted nucleotide somehow, add more A to cap it?
<kanzure>
more or less, yes
<kanzure>
"remove unreacted nucleotide" is a giant wash step
<azonenberg>
Yeah, i can imagine that'd be fun to do without taking out your target strands
<azonenberg>
no clue where to start myself lol
<kanzure>
most microfluidic devices use continuous flow, so they just flow the wash chemistry by all of the 'array units'
<azonenberg>
Anyway so why do you need lithography-style patterning for this?
<azonenberg>
are you talking for building a microfluidic unit?
<kanzure>
most of the time this chemistry is done on solid supports (beads)
<kanzure>
so you can imagine an array of beads and DLP/DMD using different wavelengths to activate different nucleotides at different locations (beads in physically separate chambers)
<kanzure>
hrm, i'm not explaining this well. there's a few more points to mention
<kanzure>
1) you can do this in continuous flow with an array of these reactions, but they have to all be growing the same sequence so that you don't contaminate different reactions
<kanzure>
2) you theoretically want to do dna synthesis of different sequences in parallel; but you'd have to keep each reaction physically isolated
<azonenberg>
Hmm
<kanzure>
if you are doing this in continous flow with a shared reagent/wash bath for all beads (on which this reaction is occurring),
<kanzure>
hmm no. the point i am trying to make is that because of the error rate of this chemistry you want to monitor each bead and make sure the sequence is correct
<azonenberg>
Ooh, interesting
<kanzure>
if you are in a continous flow situation, how do you physically move an individual bead to lead it down the path to, say, sequencing
<azonenberg>
By raman spectroscopy?
<azonenberg>
(monitoring)
<kanzure>
well, that's one way, but i haven't seen a paper doing that yet
<kanzure>
the most basic version of all of this is don't use DLP/DMD, do only one oligonucleotide synthesis at a time on a single solid support bead, don't do anything parallel and hope for the best..
<kanzure>
but this loses the advantages of microscopic features
<kanzure>
i mean why not just pick up a syringe and do it, at that point ;)
<azonenberg>
Hmm, i'm not familiar enough with the techniques to suggest much at this point lol
<kanzure>
yeh i just need to rant to someone heh
<kanzure>
i mean, i guess it's not too disastrous if i have an unmonitored collection of a million beads simultaneously (but if it's unmonitored, and under continous flow, i don't need the photochemistry and all the sequences would (hopefully) be the same)
<kanzure>
and then hope that at least one of the beads has at least one strand of DNA that ends up being correct
<azonenberg>
Lol
<azonenberg>
How do you find it'
<azonenberg>
and separate it
<kanzure>
whether or not "finding it and separating it" is a problem depends on which method you're using
<kanzure>
for instance, if you are under continous flow where all beads get the same reagants/wash simultaneously, you hope for the best that all beads are synthesizing/growing the same sequence
<kanzure>
when you force the beads out of the system, you wouldn't care which one is which
<kanzure>
since they all theoretically are the same
<azonenberg>
But in practice?
<kanzure>
in practice- in that method- there are definitely going to be certain strands that are wrong
<kanzure>
oligonucleotide chemistry has error rates as bad as 1 in 250 bp wrong
<kanzure>
(enzymes like dna polymerase make 1 error in 10,000...)
<kanzure>
so what if you're synthesizing a 800 bp strand.. and the 750th bp is wrong. you're going to be pissed off.
<azonenberg>
Lol, yeah
<azonenberg>
Can you make say four 200bp strands separately
<azonenberg>
verify each
<azonenberg>
then concatenate?
<azonenberg>
kinda like Xilinx does with their virtex 7 chips
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<kanzure>
yes you can concatenate
<kanzure>
this is called ligation
<azonenberg>
ok
<kanzure>
verification is its own can of worms
<azonenberg>
Is it worth doing to boost yieldss?
<azonenberg>
And the way i'd verify would be
<kanzure>
you can verify by dna sequencing on a microfluidic chip ;)
<azonenberg>
to PCR each of the test strands
<azonenberg>
then sequence some of it
<kanzure>
right
<kanzure>
pcr on a chip is really amazing.. my favorite method is LED-assisted heating of a droplet of water. it's like 20x faster than lab equipment since the volume is so small
<kanzure>
so, dna sequencing needs as much optimizing as dna synthesis, so it basically doubles the complexity of the project
<kanzure>
but dna sequencing is important to me so i'm willing to overlook that
<azonenberg>
i see
<azonenberg>
Yeah, i've never done full sequencing
<azonenberg>
only simple fingerprinting by gel electrophoresis
<kanzure>
you have to select what you are going to sequence. in a continous flow situation with DLP, how would you move beads out to individually test (or rather- how would you send the "detach from bead" chemistry to only that bead)
<azonenberg>
looking for presence or absence of one or two SNPs
<kanzure>
if i can't come up with a "access a specific bead under continuous flow" solution, then the DLP is more or less useless :P
<azonenberg>
Hmm, i see
<kanzure>
"just put 1000s of valves in your circuit and it'll be fine"
<kanzure>
one possibility is to use droplets instead (water-in-oil).. a set of beads per droplet. store each droplet at an xy location. the wash step would involve.. uh.
<kanzure>
i guess a droplet wash step would involve (1) a clean drop of water + (2) wash chemistry + (3) a way to dilute the bead/droplet's water enough times over?
<azonenberg>
Hmm
<kanzure>
my connection sucks today.
<kanzure>
i think i've found a good solution
<kanzure>
i'll store 100~ beads per droplet. water-in-oil microfluidics.
<kanzure>
store each droplet in a register specific to the next reaction that it needs to have. i.e., store all the "give this a G" together.
<kanzure>
move the droplets out of the register into a continuous flow channel. space them out by distance, so that 100 beads from droplet 1 are physically separated from 100 beads from droplet 2
<kanzure>
magnetize the beads, do continuous flow microfluidics to do the synthesis cycle/steps, waste water output
<kanzure>
turn off waste; redirect flow to a feature that re-forms a droplet based on timing, so that the beads from the original droplets end up in separate droplets again
<kanzure>
depending on the length of the reaction channel maybe you'll react 100s of different sequences simultaneously
<kanzure>
then you cycle between doing A, C, T and G reactions in the continuous flow "reaction channel" to build up your final sequence, based on what you have loaded into the reaction channel at the moment
<azonenberg>
Hmm
<azonenberg>
So each of those 100 beads are considered equivalent?
<kanzure>
yeah; there can be any number (but hopefully at least one) growing oligo per bead
<kanzure>
maybe there's 10,000 strands of dna growing on a single bead
<kanzure>
but adding beads is nice for redundancy's sake
<azonenberg>
Ok
<azonenberg>
But you cant grab one bead separately from the others
<azonenberg>
only drop from drop
<kanzure>
yes, because of the spacing/timing when the other beads were released into the reaction channel
<kanzure>
i.e. release first droplet, let the droplet break up and go downstream for 10-20 ms (or whatever the bead formation time constant is...)
<kanzure>
*droplet formation
<azonenberg>
Yeah, makes sense
<kanzure>
in this scenario, you hope that each bead within the same droplet is growing the same oligo
<kanzure>
so if you want to sequence a droplet, you take just one bead out and go pcr it and do other things
<azonenberg>
And then keep the other beads going
<azonenberg>
interesting
<azonenberg>
how big are these beads?
<azonenberg>
tens of microns?
<azonenberg>
single microns?
<kanzure>
tons of companies sell tons of different beads
<kanzure>
look up polystyrene beads on google scholar
<kanzure>
but yes i've seen 10 micron beads, definitely
<kanzure>
interestingly enough there are microfluidic devices capable of manufacturing polystyrene beads as well...
<azonenberg>
what i meant was, more, what is a typical size
<azonenberg>
or size range
<azonenberg>
and are they porous or pretty solid
<kanzure>
dunno. 1 micron beads exist too.
<kanzure>
solid
<azonenberg>
And the DNA just sticks on the surface?
<kanzure>
there's some chemistry for that
<kanzure>
i'm really bad at magnetism, i don't know if a magnetic microbead could be kept in place with an electromagnet directly under it, or if the flow forces would sweep it away
<azonenberg>
Depends on the conditions, there's no definite yes or no
<azonenberg>
depends on cross section, flow velocity, amoutn of magnetic mateiral in the bead, strength of the electromagnet's field
<kanzure>
flow velocity can be varied by me, so that's not a relevant variable
<kanzure>
actually, if the overall flow velocity is low enough, i bet a bead couldn't be moved
<azonenberg>
Well, in that case i'd say it can definitely be done
<azonenberg>
the question is how strong a magnet will you need
<azonenberg>
and how magnetic you can make the bead
<kanzure>
they wouldn't have to be magnetic if i'm ok with very low velocities
<kanzure>
and then increase the flow rate when i want to move them
<kanzure>
ah but that would make the beads closer to the "top" move first, sadly
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<kanzure>
hi gene_hacker
<kanzure>
gene_hacker: azonenberg is around now, you had some questions..
<gene_hacker>
is azonenberg here right now?
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<azonenberg>
lol, missed him again
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