Sharpie microfluidics

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Bryan Bishop

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Mar 2, 2009, 12:05:04 PM3/2/09
to diy...@googlegroups.com, Open Manufacturing, kan...@gmail.com
Hey all,

Saturday afternoon, I was in the lab playing around with that
microfluidics paper archive. I really recommend you guys go read
through it. In particular, I have come across a method for
constructing microfluidic devices cheaply, with materials you probably
have laying around your home or the office. Basically, you need 2
glass microscopy slides, tape, and a sharpie. It would also help if
you have some alligator clamps. Metal paperclips don't work and just
scratch/destroy the slides, don't bother.

Ideally, you need to make the slides super hydrophobic by soaking them
in piranha for 12 hours, which is a 3 to 1 ratio concoction of H2SO4
and hydrogen peroxide (respectively), but it's really nasty and I
wouldn't recommend it. Also, I didn't seem to have to do that to make
this work, although I am confident it would help and be worth the
trouble. Maybe doing big baths or batch-runs of soaking the glass
would be more practical? Don't worry- that's the most complicated step
in this whole process, and you get to ignore it (yay!).

So here's what you do.

(1) Draw your pattern in sharpie on two slides. In other words, the
two slides should have a mirror image of each other, so that they can
be stacked together, such that the sharpie pattern is facing itself on
both sides. You can do this with stencils, freehand- which I
successfully did for a design with 2 parallel lines as well as 2
circles (using a dime, sort of).

(2) Take a small piece of tape and loop it, so that it is connected to
itself. Put this loop on the left side of one of the slides. Do this
again for the right side.

(3) Sandwhich the two slides together, such that the two patterns meet
up, and such that you're basically unable to distinguish which side
you started with :-).

(4) To see it in action, micropipette a drop of water into an opening
at the top that you declare the input. You can try squirting water,
but it will not work very well unless you made the slides super
hydrophobic-- for droplets, this works fine. So, for large volumes of
fluid, like deposited via a straw or leaky squirt bottle nozzle, it
will flood over the lines simply because the glass isn't all that
hydrophobic- however you will see that the water still stays away from
the sharpie-drawn lines, so it's a hint as to what will happen if you
go use piranha, or something- I'm sure someone can help figure out an
alternative, more readily available concoction for making the slides
hydrophobic.

You can see a diagram here:
http://heybryan.org/books/papers/microfluidics/sharpie.png

I promise I'll make a video and get some photographs very very soon. :-)

I last mentioned microfluidics in a recent post about $100 DNA
sequencing in 5 years via nanofluidics from BioNanoMatrix:
http://groups.google.com/group/diybio/browse_frm/thread/4b1efc2d0033fc10#
archive: http://heybryan.org/books/papers/microfluidics_2009.zip

Some videos (not from me):
microfluidic pin-ball via lasers: http://www.youtube.com/watch?v=w-ruyV2Lak4
more: http://www.youtube.com/watch?v=QOYdn8Ft_IU
droplet formation: http://www.youtube.com/watch?v=OK1xNcAObjA
surface tension-confined microfluidics:
http://www.youtube.com/watch?v=1HrRuaLFGmY (somewhat the same as
sharpie microfluidics)
sandwhich for microscale reactions: http://www.youtube.com/watch?v=QQ8rjO0FpZc

The sharpie-based method can be found here: "Performing chemical
reactions in virtual capillary of surface tension-confined
microfluidic devices". But that's about it. Nobody has cited that
paper apparently. What's the deal?

There are many papers out there about "labs on a chip". I think it is
interesting that an amateur can now start drawing their labs on a
chip, and perform many of the experiments and reactions that otherwise
require huge equipment. Many microfluidic devices have been mentioned
in the literature that do PCR, thermocycling, DNA sequencing, DNA
synthesis, in vitro cell-free protein synthesis, immunoassays,
emulsions, particle separation/filtration, even simple procedures like
gel electrophoresis can be done with microfluidic devices via an array
of dots (maybe- this needs to be tested some more methinks).

So what's next? Well, I think I need a stamp, or a (sharpie) pen
plotter, or some better stencils, or something. Originally I was
trying to do this with nail polish, because some nail polish cures in
UV light. There are some epoxies and paints that work here too
apparently. Anyway, if that would have gone better, then I would have
printed out some circuits from a printer, laminated it, and then done
UV mask lithography on a small surface layer of nail polish, and then
wash away the rest of it. Maybe somebody with actual nail polish
experience can figure out a way to make this work? I bought some
supplies for $14, it's not much. (Also, wax is hydrophobic, so a wax
printer or just melting wax from a candle and then imprinting the
pattern of some bent metal from a paperclip would work, but it's not
as awesome as using sharpies.)

That still leaves the question as to what's next open though. What is
this going to be used for? I was confining algae in bubbles and moving
it around with the sharpie patterns. That's one possible use. But then
how are we going to actuate the bubbles? You can use a heat gradient
by heating one side and cooling the other, salt water plus electrical
conduction, pneumatic pumps, laser-actuated movement of droplets, etc.
There have been some papers in the past about applying a force
perpendicular to the surface just before the droplet and this
apparently causing movement to occur, so that's something to look
into. There's also the question of how to get inputs and outputs into
this system: I'm thinking straws, and then superglue or chewing gum to
seal it (sort of). Another option is to find plastic hydrophobic
slides and just use a needle to poke holes in the top/bottom for
letting fluid flow outwardly.

That's all I have for now.

= Microfluidics bibliography, especially DIY-friendly =

A Brownian dynamics-finite element method for simulating DNA
electrophoresis in nonhomogeneous electric fields - complicated
geometries
Accumulating particles at the boundaries of a laminar flow
A "do-it-yourself" array biosensor
A Dry Process for Production of Microfluidic Devices Based on the
Lamination of Laser-Printed Polyester Films
A Gravity-Driven Microfluidic Particle Sorting Device with
Hydrodynamic Separation Amplification
A high rate flow-focusing foam generator
AlgalBiophysics_TBPS_2003
A microfabricated thermal field-flow fractionation system
A microfluidic abacus channel for controlling the addition of droplets
A microfluidic bioreactor for increased active retrovirus output
An optical toolbox for total control of droplet microfluidics with lasers
Applications of microfluidics for neuronal studies
A simple pneumatic setup for driving microfluidics
A soft lithographic approach to fabricate patterned microfluidic channels
Bonding of glass-based microfluidic chips at low- or room-temperature
in routine laboratory
Bonding of glass microfluidic chips at room temperatures
Bonding of soda-lime glass microchips at low temperature (65 celsius)
Boosting migration of large particles by solute contrasts
Brownian dynamics simulations of a DNA molecule colliding with a small
cylindrical post
Capillary flow control using hydrophobic patterns
Capture of DNA in microfluidic channel using magnetic beads -
increasing capture efficiency with integrated mixer
Capture of particles of dust by convective flow - PhysFluids_17_063302
Cell infection within a microfluidic device using virus gradients
Cell separation by non-inertial force fields in microfluidic systems
Cell Stimulus and Lysis in a Microfluidic Device with Segmented Gas-Liquid Flow
CFD - CFD in microfluidic systems - MATLAB source code
CFD - Computational Fluid Dynamics in Microfluidic Systems
CFD - Designing microfluidic components for enhanced surface delivery
using a genetic algorithm search - automated design
CFD - Elmer
CFD for Microfluidics - examples
CFD - Proprietary CFD software tools for microfluidic applications - a
case study
CFD - Simulations of Microfluidic Systems - Friedhelm Schonfeld
CFD - Theory and numerical simulation of droplet dynamics in complex
flows--a review
CFD - TINY3D - A robust solver for incompressible flow on cartesian
grids with colocated variables
CFD - Toolbox for the design of optimized microfluidic components -
without solving flow equations
CFD - Toolbox for the design of optimized microfluidic components -
without solving flow equations - supplementary
Conformational Preconditioning by Electrophoresis of DNA through a
Finite Obstacle Array
Construction of refreshable microfluidic channels and electrophoresis along them
Continuous flow separations in microfluidic devices
Continuous particle separation in a microchannel having asymmetrically
arranged multiple branches
Continuous particle separation in spiral microchannels using dean
flows and differential migration
Continuous Particle Separation Through Deterministic Lateral Displacement
Correlations of droplet formation in T-junction microfluidic devices:
from squeezing to dripping
Critical particle size for fractionation by deterministic lateral displacement
Design and evaluation of a Dean vortex-based micromixer - separations
Design and numerical simulation of a DNA electrophoretic stretching device
Discrete magnetic microfluidics on superhydrophobic surfaces using
magnetic fields
Does Thermophoretic Mobility Depend on Particle Size?
Droplet microfluidics
Droplet traffic in microfluidic networks: A simple model for
understanding and designing
Dynamic patterning programmed by DNA tiles captured on a DNA origami substrate
Effective mixing of laminar flows at a density interface by an
integrated ultrasonic transducer - on a PCB
Effect of contact angle hysteresis on thermocapillary droplet actuation
Effects of flow and diffusion on chemotaxis studies in a
microfabricated gradient generator
Effects of Separation length and voltage on Isoelectric focusing in a
plastic microfluidic device_Journal_In Press2006
Electrophoresis - Design and Optimization of Compact Microscale
Electrophoretic Separation Systems
Enhanced particle filtration in straight microchannels using
shear-modulated inertial migration
Fabrication inside microchannels using fluid flow
Fabrication of microsensors using unmodified office inkjet printers
Field gradient electrophoresis
FLASH: A rapid method for prototyping paper-based microfluidic devices
Flat fluidics - acoustically driven planar microfluidic devices
Flows of concentrated suspensions through an asymmetric bifurcation
Formation of simple and compound drops in microfluidic devices
Frontal photopolymerization for microfluidic applications - CabralLangmuir_2004
Fully integrated miniature device for automated gene expression DNA
microarray processing
Generating fixed concentration arrays in a microfluidic device
Generation of complex concentration profiles in microchannels in a
logarithmically small number of steps
Generation of dynamic temporal and spatial concentration gradients
using microfluidic devices
Generation of gradients having complex shapes using microfluidic networks
High resolution DNA separations using microchip electrophoresis
Human neural stem cell growth and differentiation in a
gradient-generating microfluidic device
Hydrodynamic metamaterials: Microfabricated arrays to steer, refract,
and focus streams of biomaterials.
Ice-lithographic fabrication of concave microwells and a microfluidic
network - ice droplets for structure formation in PDMS
Inertial migration of neutrally buoyant particles in a square duct -
an investigation of multiple equilibrium positions
Inertial migration of rigid spherical particles in Poiseuille flow
Inertial migration of spherical particles in circular Poiseuille flow
at moderately high Reynolds numbers
Integration of polymer and metal microstructures using liquid-phase
photopolymerization
Lab on paper
Lecithin-Based Water-In-Oil Compartments as Dividing Bioreactors - in
vitro protein synthesis
Light-induced shape-memory polymers
Marangoni flows
Maskless photolithography using UV LEDs
Membrane-free microfiltration by asymmetric inertial migration -
spirals - bifurcations
Membraneless microseparation by asymmetry in curvilinear laminar flows
Microbioreactors for bioprocess development
Microbubble or pendant drop control described by a general phase diagram
Microchannels Constructed on Rough Hydrophobic Surfaces
Microfluidic assembly blocks
Microfluidic bubble logic - Gershenfeld
Microfluidic chip-based valveless flow injection analysis system with
gravity-driven flows
Microfluidic logic gates and timers
Microfluidic manipulation via Marangoni forces
Microfluidics of complex fluids
Microfluidic sorting in an optical lattice
Micropatterning of biomedical polymer surfaces by novel UV
polymerization techniques
Microvortex for focusing, guiding and sorting of particles
Microwave welding of polymeric-microfluidic devices
Mixing-induced activity in open flows
Modeling shapes and dynamics of confined bubbles
Nanomaterials and chip-based nanostructures for capillary
electrophoretic separations of DNA
Nonlithographic fabrication of microfluidic devices
On-chip cell lysis by local hydroxide generation
Particle Continuous Separation by Evaporation Force on Microfluidic System
Patterned Superhydrophobic Surfaces: Toward a Synthetic Mimic of the
Namib Desert Beetle
Pattern formation in acoustic cavitation
Patterning of flow and mixing in rotating radial microchannels
PCR - A circular ferrofluid driven microchip for rapid polymerase chain reaction
PCR - An inexpensive and portable microchip-based platform for
integrated RT-PCR and capillary electrophoresis
PCR - Disposable real-time microPCR device: lab-on-a-chip at a low cost
PCR - Droplet-based micro oscillating-flow PCR chip
PCR - Integrated Portable Polymerase Chain Reaction-Capillary
Electrophoresis Microsystem for Rapid Forensic Short Tandem Repeat
Typing
PCR - Nanodroplet real-time PCR system with laser assisted heating
PCR - On-chip, real-time, single-copy polymerase chain reaction in
picoliter droplets
Performing chemical reactions in virtual capillary of surface
tension-confined microfluidic devices - sharpies - nail polish - glass
surfaces - hydrophobicity
Photosensitive Polymer from Ionic Self-Assembly of Azobenzene Dye and
Poly(ionic liquid) and Its Alignment Characteristic toward Liquid
Crystal Molecules
PNAS-2008-Morton-7434-8
Polymer embossing tools for rapid prototyping of plastic microfluidic devices
Pressure drops for droplet flows in microfluidic channels
Principles of microfluidic actuation by modulation of surface stresses
Protein fabrication automation
Rapid fabrication of microfluidic devices in poly(dimethylsiloxane) by
photocopying
Rapid method for design and fabrication of passive micromixers in
microfluidic devices using a direct-printing process
Rapid prototyping of microfluidic devices with a wax printer
Rapid prototyping of microfluidic systems using a laser-patterned tape
Recent advances of microfluidics in Mainland China
Refreshable microfluidic channels constructed using an inkjet printer
Room Temperature Microchannel Fabrication for Microfluidic System -
see evaporation force paper
Separation enhancement in pinched flow fractionation
Separation of suspended particles by asymmetric arrays of obstacles in
microfluidic devices
Shrinky-Dink microfluidics: 3D polystyrene chips
Shrinky-Dink microfluidics: rapid generation of deep and rounded patterns
Simple, robust storage of drops and fluids in a microfluidic device
Simultaneous cell lysis and bead trapping in a continuous flow
microfluidic device
Stacking of beads into monolayers by flow through flat microfluidic chambers
Step-and-scan maskless lithography for ultra large scale DNA chips
Surface Effects on PCR Reactions in Multichip Microfluidic Platforms
Surface-Tension-Confined Microfluidics
Synthesis - Gene synthesis on microchips - review
Synthesis - Impact of microdrops on solid surfaces for DNA synthesis
Synthesis - Integrated two-step gene synthesis in a microfluidic
device (1k bp, 1 error per 250 bp)
Synthesis - Microfluidic PicoArray synthesis of oligodeoxynucleotides
and simultaneous assembling of multiple DNA sequences (10 kb)
Synthesis - Parallel gene synthesis in a microfluidic device (1 kb,
but parallelizable) - CBA
Synthesis - Solvent resistant microfluidic DNA synthesizer
Systematic modeling of microfluidic concentration gradient generators
The design and fabrication of autonomous polymer-based surface
tension-confined microfluidic platforms
The impact of diffusion on confined oscillated bubbly fluid
The lateral migration of neutrally-buoyant spheres transported through
square microchannels
The origins and the future of microfluidics - Whitesides - 2006
The pressure drop along rectangular microchannels containing bubbles
Thermocapillary manipulation of droplets using holographic beam
shaping: Microfluidic pin ball
Thermophoresis: moving particles with thermal gradients
Three-dimensional microfluidic devices fabricated in layered paper and tape
Trends - Droplets as Microreactors for High-Throughput Biology
Trends - miniautirising the laboratory in emulsion droplets
Ultra rapid prototyping of microfluidic systems using liquid phase
photopolymerization (5 min)
Use of polystyrene spin-coated compact discs for microimmunoassaying
Valves for autonomous capillary systems - droplets - delay valves -
abruptly changing geometries
Versatile stepper based maskless microlithography using a liquid
crystal display for direct write of binary and multilevel
microstructures
Xurography: rapid prototyping of microstructures using a cutting
plotter - vinyl cutters

= Papers related to BioNanoMatrix's DNA sequencing tech =
see also: http://heybryan.org/mediawiki/index.php/DNA_sequencing
http://heybryan.org/mediawiki/index.php/DNA_sequencing#Microfluidic_DNA_sequencing

DNA prism for high-speed continuous fractionation of large DNA molecules
A nanoelectrode lined nanochannel for single-molecule DNA sequencing
A nanofluidic railroad switch for DNA
An experimental study of DNA rotational relaxation time in nanoslits
Design and numerical simulation of a DNA electrophoretic stretching device
Diffusion mechanisms of localised knots along a polymer
DNA confined in nanochannels: Hairpin tightening by entropic depletion
Electrical Detection of DNA and Integration with Nano-fluidic Channels
Electrophoretic stretching of DNA molecules using microscale T junctions
** Fabrication of 10 nm enclosed nanofluidic channels
Fabrication of Size-Controllable Nanofluidic Channels by
Nanoimprinting and Its Application for DNA Stretching
Nanofilter array chip for fast gel-free biomolecule separation
Polymers in Confined Geometry
The dynamics of genomic-length DNA molecules in 100-nm channels
The shape of a flexible polymer in a cylindrical pore

- Bryan
http://heybryan.org/
1 512 203 0507

Dan

unread,
Mar 2, 2009, 2:01:24 PM3/2/09
to DIYbio
Bryan - good post, haven't had time to parse all of it but wanted to
make a quick correction. You're mixing up hydrophillic and
hydrophobic. Piranha cleaned glass will be extremely hydrophillic.
I've found you can get the same by cleaning glass in a heated alconox
(strong detergent) bath with scrubbing and cleaning under DI water
while wearing gloves to prevent recontamination by skin oils.

Glass is naturally hydrophillic because it has a large amount of
oxygen in it that terminates as OH groups at the surface that water
can bind to.

The sharpie will be very hydrophobic as it is composed of orgamic
molecules that are non-polar and do not bind water strongly.

PS: this is a good way to see how good your labware cleaning protocol
is. Glass should have water that very slowly runs off in a smooth
sheet and never completely leaves until it dries off. (Some glass can
be chemically modified to be hydrophobic but all normal lab glass
should hold water) If you see water running off of the glass quickly
and leaving behind areas where it is dry or covered with small
droplets, you have surface contamination.

Conversely, all polypropylene (what most lab plasticware is made from)
is very hydrophobic and when clean, water should run off very quickly
and leave a perfectly dry surface. Any sheeting or droplets left
behind indicate that you have surface contamination. (this is
somewhat dependent on the processing of the polypropylene - plastic
can be made hydrophillic through plasma treatment or if there are
microscopic pits in it that can retain water)

Jeswin John

unread,
Mar 2, 2009, 5:38:23 PM3/2/09
to diy...@googlegroups.com
Hey Bryan (very catchy)
Can you tell me which articles in your archive are a must read? I hate reading articles on my computer and would rather print them out. Interesting stuff. I might try them out this week if I can find some supplies.

Thanks
--
*-----------------------------------------------------------*
Join the Revolution

http://diybio.org/
http://homebrewbioscience.blogspot.com/
*------------------------------------------------------------*

Bryan Bishop

unread,
Mar 3, 2009, 9:19:03 AM3/3/09
to diy...@googlegroups.com, kan...@gmail.com
On Mon, Mar 2, 2009 at 4:38 PM, Jeswin John <phill...@gmail.com> wrote:
> Can you tell me which articles in your archive are a must read? I hate
> reading articles on my computer and would rather print them out. Interesting
> stuff. I might try them out this week if I can find some supplies.

That's a hard question to answer. There are so many good papers here.
Sorry about the bad formatting on the bibliography- newlines were
appended and broke up paper titles, and it's hard to rapidly can
through that list with almost randomly alternating upper/lowercase, so
here's a fixed version:

http://heybryan.org/mediawiki/index.php/Microfluidics

Fixed formatting below. Asterisks mark the beginning of a paper title.
Anybody that throws this into (full- title, authors, journal id, page
number-fledged) BibTeX automagically becomes my best friend, or
something.

I'll probably add my annotations to the wiki page above. I've done
that before for some other topics, for instance:
http://heybryan.org/mediawiki/index.php/Polymerase
http://heybryan.org/mediawiki/index.php/Sustained_attention
.. but I don't know if you'll find that helpful or not, it seems to
add rather than compress. :-)

So which would be the most important papers to read? Most importantly,
look at the surface tension microfluidics paper:

* Performing chemical reactions in virtual capillary of surface
tension-confined microfluidic devices

And if you want to read more on that topic, but not about sharpie
microfluidics, see-
* Surface-Tension-Confined Microfluidics
* Microchannels Constructed on Rough Hydrophobic Surfaces
* Principles of microfluidic actuation by modulation of surface stresses
* The design and fabrication of autonomous polymer-based surface
tension-confined microfluidic platforms

Various other somewhat DIY-friendly fabrication techniques:
* A Dry Process for Production of Microfluidic Devices Based on the


Lamination of Laser-Printed Polyester Films

* FLASH: A rapid method for prototyping paper-based microfluidic devices
* Polymer embossing tools for rapid prototyping of plastic microfluidic devices
* Rapid fabrication of microfluidic devices in poly(dimethylsiloxane)
by photocopying
* Rapid method for design and fabrication of passive micromixers in


microfluidic devices using a direct-printing process

* Rapid prototyping of microfluidic devices with a wax printer
* Rapid prototyping of microfluidic systems using a laser-patterned tape
* Shrinky-Dink microfluidics: 3D polystyrene chips
* Shrinky-Dink microfluidics: rapid generation of deep and rounded patterns
* Ultra rapid prototyping of microfluidic systems using liquid phase
photopolymerization (5 min)
* Xurography: rapid prototyping of microstructures using a cutting
plotter - vinyl cutters
* Three-dimensional microfluidic devices fabricated in layered paper and tape
* Ice-lithographic fabrication of concave microwells and a


microfluidic network - ice droplets for structure formation in PDMS

General trends about microfluidics
* Droplets as Microreactors for High-Throughput Biology
* Miniautirising the laboratory in emulsion droplets
* The origins and the future of microfluidics (Whitesides)

There are so many other papers, it's hard to sort and categorize.
Dan's post was very helpful--- David Treadwell has suggested looking
into Rain-X or Kemxert ultraviolet glass adhesive ($21 for 1 oz.,
maybe not so great). Also, it turns out that some people do not know
what a sharpie is:

http://helpyourdoc.files.wordpress.com/2008/10/sharpie.jpg

Just a permanent marker. I guarantee that you have one nearby
somewhere. Anyway, for those who are still clueless as to what's going
on here, this is a way to guide liquids and bubbles on glass surfaces
and in other microfluidic devices, which can mean lab equipment,
experiments, and so on.

= Microfluidics bibliography, especially DIY-friendly =

* A Brownian dynamics-finite element method for simulating DNA


electrophoresis in nonhomogeneous electric fields - complicated
geometries

* Accumulating particles at the boundaries of a laminar flow
* A "do-it-yourself" array biosensor
* A Dry Process for Production of Microfluidic Devices Based on the


Lamination of Laser-Printed Polyester Films

* A Gravity-Driven Microfluidic Particle Sorting Device with
Hydrodynamic Separation Amplification
* A high rate flow-focusing foam generator
* AlgalBiophysics_TBPS_2003
* A microfabricated thermal field-flow fractionation system
* A microfluidic abacus channel for controlling the addition of droplets
* A microfluidic bioreactor for increased active retrovirus output
* An optical toolbox for total control of droplet microfluidics with lasers
* Applications of microfluidics for neuronal studies
* A simple pneumatic setup for driving microfluidics
* A soft lithographic approach to fabricate patterned microfluidic channels
* Bonding of glass-based microfluidic chips at low- or
room-temperature in routine laboratory
* Bonding of glass microfluidic chips at room temperatures
* Bonding of soda-lime glass microchips at low temperature (65 celsius)
* Boosting migration of large particles by solute contrasts
* Brownian dynamics simulations of a DNA molecule colliding with a
small cylindrical post
* Capillary flow control using hydrophobic patterns
* Capture of DNA in microfluidic channel using magnetic beads -


increasing capture efficiency with integrated mixer

* Capture of particles of dust by convective flow - PhysFluids_17_063302
* Cell infection within a microfluidic device using virus gradients
* Cell separation by non-inertial force fields in microfluidic systems
* Cell Stimulus and Lysis in a Microfluidic Device with Segmented
Gas-Liquid Flow
* CFD - CFD in microfluidic systems - MATLAB source code
* CFD - Computational Fluid Dynamics in Microfluidic Systems
* CFD - Designing microfluidic components for enhanced surface


delivery using a genetic algorithm search - automated design

* CFD - Elmer
* CFD for Microfluidics - examples
* CFD - Proprietary CFD software tools for microfluidic applications -
a case study
* CFD - Simulations of Microfluidic Systems - Friedhelm Schonfeld
* CFD - Theory and numerical simulation of droplet dynamics in complex
flows--a review
* CFD - TINY3D - A robust solver for incompressible flow on cartesian
grids with colocated variables
* CFD - Toolbox for the design of optimized microfluidic components -
without solving flow equations
* CFD - Toolbox for the design of optimized microfluidic components -


without solving flow equations - supplementary

* Conformational Preconditioning by Electrophoresis of DNA through a
Finite Obstacle Array
* Construction of refreshable microfluidic channels and
electrophoresis along them
* Continuous flow separations in microfluidic devices
* Continuous particle separation in a microchannel having
asymmetrically arranged multiple branches
* Continuous particle separation in spiral microchannels using dean
flows and differential migration
* Continuous Particle Separation Through Deterministic Lateral Displacement
* Correlations of droplet formation in T-junction microfluidic


devices: from squeezing to dripping

* Critical particle size for fractionation by deterministic lateral displacement
* Design and evaluation of a Dean vortex-based micromixer - separations
* Design and numerical simulation of a DNA electrophoretic stretching device
* Discrete magnetic microfluidics on superhydrophobic surfaces using
magnetic fields
* Does Thermophoretic Mobility Depend on Particle Size?
* Droplet microfluidics
* Droplet traffic in microfluidic networks: A simple model for
understanding and designing
* Dynamic patterning programmed by DNA tiles captured on a DNA origami substrate
* Effective mixing of laminar flows at a density interface by an


integrated ultrasonic transducer - on a PCB

* Effect of contact angle hysteresis on thermocapillary droplet actuation
* Effects of flow and diffusion on chemotaxis studies in a
microfabricated gradient generator
* Effects of Separation length and voltage on Isoelectric focusing in


a plastic microfluidic device_Journal_In Press2006

* Electrophoresis - Design and Optimization of Compact Microscale
Electrophoretic Separation Systems
* Enhanced particle filtration in straight microchannels using
shear-modulated inertial migration
* Fabrication inside microchannels using fluid flow
* Fabrication of microsensors using unmodified office inkjet printers
* Field gradient electrophoresis
* FLASH: A rapid method for prototyping paper-based microfluidic devices
* Flat fluidics - acoustically driven planar microfluidic devices
* Flows of concentrated suspensions through an asymmetric bifurcation
* Formation of simple and compound drops in microfluidic devices
* Frontal photopolymerization for microfluidic applications -
CabralLangmuir_2004
* Fully integrated miniature device for automated gene expression DNA
microarray processing
* Generating fixed concentration arrays in a microfluidic device
* Generation of complex concentration profiles in microchannels in a


logarithmically small number of steps

* Generation of dynamic temporal and spatial concentration gradients
using microfluidic devices
* Generation of gradients having complex shapes using microfluidic networks
* High resolution DNA separations using microchip electrophoresis
* Human neural stem cell growth and differentiation in a
gradient-generating microfluidic device
* Hydrodynamic metamaterials: Microfabricated arrays to steer,


refract, and focus streams of biomaterials.

* Ice-lithographic fabrication of concave microwells and a


microfluidic network - ice droplets for structure formation in PDMS

* Inertial migration of neutrally buoyant particles in a square duct -


an investigation of multiple equilibrium positions

* Inertial migration of rigid spherical particles in Poiseuille flow
* Inertial migration of spherical particles in circular Poiseuille


flow at moderately high Reynolds numbers

* Integration of polymer and metal microstructures using liquid-phase
photopolymerization
* Lab on paper
* Lecithin-Based Water-In-Oil Compartments as Dividing Bioreactors -
in vitro protein synthesis
* Light-induced shape-memory polymers
* Marangoni flows
* Maskless photolithography using UV LEDs
* Membrane-free microfiltration by asymmetric inertial migration -
spirals - bifurcations
* Membraneless microseparation by asymmetry in curvilinear laminar flows
* Microbioreactors for bioprocess development
* Microbubble or pendant drop control described by a general phase diagram
* Microchannels Constructed on Rough Hydrophobic Surfaces
* Microfluidic assembly blocks
* Microfluidic bubble logic - Gershenfeld
* Microfluidic chip-based valveless flow injection analysis system
with gravity-driven flows
* Microfluidic logic gates and timers
* Microfluidic manipulation via Marangoni forces
* Microfluidics of complex fluids
* Microfluidic sorting in an optical lattice
* Micropatterning of biomedical polymer surfaces by novel UV
polymerization techniques
* Microvortex for focusing, guiding and sorting of particles
* Microwave welding of polymeric-microfluidic devices
* Mixing-induced activity in open flows
* Modeling shapes and dynamics of confined bubbles
* Nanomaterials and chip-based nanostructures for capillary
electrophoretic separations of DNA
* Nonlithographic fabrication of microfluidic devices
* On-chip cell lysis by local hydroxide generation
* Particle Continuous Separation by Evaporation Force on Microfluidic System
* Patterned Superhydrophobic Surfaces: Toward a Synthetic Mimic of
the Namib Desert Beetle
* Pattern formation in acoustic cavitation
* Patterning of flow and mixing in rotating radial microchannels
* PCR - A circular ferrofluid driven microchip for rapid polymerase
chain reaction
* PCR - An inexpensive and portable microchip-based platform for


integrated RT-PCR and capillary electrophoresis

* PCR - Disposable real-time microPCR device: lab-on-a-chip at a low cost
* PCR - Droplet-based micro oscillating-flow PCR chip
* PCR - Integrated Portable Polymerase Chain Reaction-Capillary


Electrophoresis Microsystem for Rapid Forensic Short Tandem Repeat
Typing

* PCR - Nanodroplet real-time PCR system with laser assisted heating
* PCR - On-chip, real-time, single-copy polymerase chain reaction in
picoliter droplets
* Performing chemical reactions in virtual capillary of surface


tension-confined microfluidic devices - sharpies - nail polish - glass
surfaces - hydrophobicity

* Photosensitive Polymer from Ionic Self-Assembly of Azobenzene Dye


and Poly(ionic liquid) and Its Alignment Characteristic toward Liquid
Crystal Molecules

* PNAS-2008-Morton-7434-8
* Polymer embossing tools for rapid prototyping of plastic microfluidic devices
* Pressure drops for droplet flows in microfluidic channels
* Principles of microfluidic actuation by modulation of surface stresses
* Protein fabrication automation
* Rapid fabrication of microfluidic devices in poly(dimethylsiloxane)
by photocopying
* Rapid method for design and fabrication of passive micromixers in


microfluidic devices using a direct-printing process

* Rapid prototyping of microfluidic devices with a wax printer
* Rapid prototyping of microfluidic systems using a laser-patterned tape
* Recent advances of microfluidics in Mainland China
* Refreshable microfluidic channels constructed using an inkjet printer
* Room Temperature Microchannel Fabrication for Microfluidic System -
see evaporation force paper
* Separation enhancement in pinched flow fractionation
* Separation of suspended particles by asymmetric arrays of obstacles
in microfluidic devices
* Shrinky-Dink microfluidics: 3D polystyrene chips
* Shrinky-Dink microfluidics: rapid generation of deep and rounded patterns
* Simple, robust storage of drops and fluids in a microfluidic device
* Simultaneous cell lysis and bead trapping in a continuous flow
microfluidic device
* Stacking of beads into monolayers by flow through flat microfluidic chambers
* Step-and-scan maskless lithography for ultra large scale DNA chips
* Surface Effects on PCR Reactions in Multichip Microfluidic Platforms
* Surface-Tension-Confined Microfluidics
* Synthesis - Gene synthesis on microchips - review
* Synthesis - Impact of microdrops on solid surfaces for DNA synthesis
* Synthesis - Integrated two-step gene synthesis in a microfluidic


device (1k bp, 1 error per 250 bp)

* Synthesis - Microfluidic PicoArray synthesis of


oligodeoxynucleotides and simultaneous assembling of multiple DNA
sequences (10 kb)

* Synthesis - Parallel gene synthesis in a microfluidic device (1 kb,
but parallelizable) - CBA
* Synthesis - Solvent resistant microfluidic DNA synthesizer
* Systematic modeling of microfluidic concentration gradient generators
* The design and fabrication of autonomous polymer-based surface
tension-confined microfluidic platforms
* The impact of diffusion on confined oscillated bubbly fluid
* The lateral migration of neutrally-buoyant spheres transported
through square microchannels
* The origins and the future of microfluidics - Whitesides - 2006
* The pressure drop along rectangular microchannels containing bubbles
* Thermocapillary manipulation of droplets using holographic beam
shaping: Microfluidic pin ball
* Thermophoresis: moving particles with thermal gradients
* Three-dimensional microfluidic devices fabricated in layered paper and tape
* Trends - Droplets as Microreactors for High-Throughput Biology
* Trends - miniautirising the laboratory in emulsion droplets
* Ultra rapid prototyping of microfluidic systems using liquid phase
photopolymerization (5 min)
* Use of polystyrene spin-coated compact discs for microimmunoassaying
* Valves for autonomous capillary systems - droplets - delay valves -
abruptly changing geometries
* Versatile stepper based maskless microlithography using a liquid


crystal display for direct write of binary and multilevel
microstructures

* Xurography: rapid prototyping of microstructures using a cutting
plotter - vinyl cutters


= Papers related to BioNanoMatrix's DNA sequencing tech =

* DNA prism for high-speed continuous fractionation of large DNA molecules
* A nanoelectrode lined nanochannel for single-molecule DNA sequencing
* A nanofluidic railroad switch for DNA
* An experimental study of DNA rotational relaxation time in nanoslits
* Design and numerical simulation of a DNA electrophoretic stretching device
* Diffusion mechanisms of localised knots along a polymer
* DNA confined in nanochannels: Hairpin tightening by entropic depletion
* Electrical Detection of DNA and Integration with Nano-fluidic Channels
* Electrophoretic stretching of DNA molecules using microscale T junctions


* Fabrication of 10 nm enclosed nanofluidic channels

* Fabrication of Size-Controllable Nanofluidic Channels by


Nanoimprinting and Its Application for DNA Stretching

* Nanofilter array chip for fast gel-free biomolecule separation
* Polymers in Confined Geometry
* The dynamics of genomic-length DNA molecules in 100-nm channels
* The shape of a flexible polymer in a cylindrical pore

Jeswin John

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Mar 3, 2009, 11:39:35 AM3/3/09
to diy...@googlegroups.com
Rain X. We use it on the car so I got a bottle at home. What the title on that article?

http://homebrewbioscience.blogspot.com/
*------------------------------------------------------------*

Dan

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Mar 3, 2009, 1:20:49 PM3/3/09
to DIYbio
RainX would be a great way to render glass hydrophobic but that leaves
the difficulty in patterning the stuff at small dimensions. I haven't
tried this for microfluidics but it works well for making circuit
boards. Laser print a pattern onto Staples brand extra glossy inkjet
photo paper. Put it face down on a substrate and proceed to iron the
everloving crap out of it. The printer toner will melt onto the
substrate and you can then use water and a bit of soap to carefully
remove the photo paper.

I've used this method to get 0.5 mm features fairly reliably. i knw
the toner transfer marks are hydrophobic but don't know if they are
hydrophobic enough for these purposes.

Sharpie, despite the appeal of simplicity, is problematic because itis
essentially impossible to get a consistent thickness coating from it.
I tried using sharpie for circuit board making and found that every
hesitation and twitch in my hand while drawing caused thin spots in
the sharpie trace where there was almost no coating. These
irregularities are difficult to spot by eye. Some of the fluid holdup
and difficulty in moving samples around is likely caused by this.

Jeswin John

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Mar 4, 2009, 6:52:09 PM3/4/09
to diy...@googlegroups.com
I did it today. It was pretty fun and showed some basic concepts of microfluidics. Now you got me hooked on this stuff, Bryan. Maybe someone could hack an inkjet printer to print on slides. Sharpie lines are a bit thick. I see alot of potential especially for seperating proteins by their sizes or shape. Is this already done? I think this has great DIYbio potential.
IMG_0524.JPG
IMG_0521.JPG

Bryan Bishop

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Mar 4, 2009, 7:06:02 PM3/4/09
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On Wed, Mar 4, 2009 at 5:52 PM, Jeswin John wrote:
> I did it today. It was pretty fun and showed some basic concepts of

Woah, your droplet is huge. How did you manage that? Was that with
Rain-X, or the nasty piranha method, or something else?

> microfluidics. Now you got me hooked on this stuff, Bryan. Maybe someone
> could hack an inkjet printer to print on slides. Sharpie lines are a bit

You don't have to do much hacking to make an inkjet usable for this.
Apparently you can just print out circuits and then proceed to
laminate them. There were a few papers about this. See:

A Dry Process for Production of Microfluidic Devices Based on the

Lamination of Laser Printed Polyester Films

Rapid prototyping of micropatterned substrates using conventional laser printers

Fabrication of microsensors using unmodified office inkjet printers

Rapid prototyping of microfluidic devices with a wax printer

Refreshable microfluidic channels constructed using an inkjet printer

> thick. I see alot of potential especially for seperating proteins by their


> sizes or shape. Is this already done? I think this has great DIYbio
> potential.

Hell yeah, it's been done many many times- though not yet with sharpie
microfluidics. It's been done on the millimeter scale, mind you.
Consider the case of the hydrodynamic+gravity studies of mass-based
particle filtration methods. Anything written by Yamada in this area
is going to be good. But my most favorite paper is this one-

A Gravity-Driven Microfluidic Particle Sorting Device with
Hydrodynamic Separation Amplification

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2527745#R31
pdf: http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=2527745&blobtype=pdf

See also references #32-38. The big issue is that these papers and
studies are usually done for microliters and sometimes mL over the
period of an hour, which might be okay if you do microfluidic
reactions for your biology experiments, but if you're trying to make a
20 gallon barrel of stock, this is not the way to do it.

Jeswin John

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Mar 4, 2009, 7:40:43 PM3/4/09
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What do you mean the drop is huge? The distance between the lines is large therefore the drops will be huge. Correct? How big were yours? No chemicals, just same way you described

In regards to diy protein separation with microfluidics, I was referring to the microscale level. Whats a good way to print lanes small enough to separate proteins? How big would the lanes have to be? I can't remember the average size of a protein, at least their range of sizes.

Bryan Bishop

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Mar 4, 2009, 7:57:26 PM3/4/09
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On Wed, Mar 4, 2009 at 6:40 PM, Jeswin John <phill...@gmail.com> wrote:
> What do you mean the drop is huge? The distance between the lines is large
> therefore the drops will be huge. Correct? How big were yours? No chemicals,
> just same way you described

Ah, well, I didn't measure the distance between the lines I was first
using, so that would explain it, wouldn't it? And there have been a
few times where I was reckless, so too much water was added to the
system, flooding over the lines. Also, I was using masking tape, which
is thicker, I'll be sure to try scotch tape next.

> In regards to diy protein separation with microfluidics, I was referring to
> the microscale level. Whats a good way to print lanes small enough to
> separate proteins? How big would the lanes have to be? I can't remember the
> average size of a protein, at least their range of sizes.

The lanes need to have a width in the 100 micrometers to 1000
micrometer (1 mm) range-- but I suspect larger channels are going to
be okay. Most researchers test microfluidic devices with fluorescent
polystyrene beads purchased from nearly any science supply company.
Also consider dye, like a food coloring. Any of the papers in that
archive that have these words in the title are going to be about
particle filtration/separation: hydrodynamic, asymmetric, dean
vortex/vortices, bifurcation, gradient, separation, filter,
filtration, etc.

Yesterday, a friend showed me his (broken) lego pen plotter kit. Too
bad it was only two-axis (no ability to lift up the pen or sharpie)-
though this could be corrected with some lego building.

Jeswin John

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Mar 4, 2009, 8:06:49 PM3/4/09
to diy...@googlegroups.com
"Yesterday, a friend showed me his (broken) lego pen plotter kit. Too
bad it was only two-axis (no ability to lift up the pen or sharpie)-
though this could be corrected with some lego building."

Was it complicated to make?

The scotch tape made the distance between the slides very thin. I noticed this principle between cover slips and microscope slides. In that case, the liquid fills the whole square but here its path is restricted.

What would happen to liquids between a hydrophobic and a hydrophillic slide? Maybe an experiment for another day

Bryan Bishop

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Mar 5, 2009, 9:36:54 AM3/5/09
to diy...@googlegroups.com, kan...@gmail.com
On Wed, Mar 4, 2009 at 6:57 PM, Bryan Bishop wrote:

> On Wed, Mar 4, 2009 at 6:40 PM, Jeswin John wrote:
>> In regards to diy protein separation with microfluidics, I was referring to
>> the microscale level. Whats a good way to print lanes small enough to
>> separate proteins? How big would the lanes have to be? I can't remember the
>> average size of a protein, at least their range of sizes.
>
> The lanes need to have a width in the 100 micrometers to 1000
> micrometer (1 mm) range-- but I suspect larger channels are going to
> be okay. Most researchers test microfluidic devices with fluorescent
> polystyrene beads purchased from nearly any science supply company.
> Also consider dye, like a food coloring. Any of the papers in that
> archive that have these words in the title are going to be about
> particle filtration/separation: hydrodynamic, asymmetric, dean
> vortex/vortices, bifurcation, gradient, separation, filter,
> filtration, etc.

Specifically:

* Continuous flow separation of particles within an asymmetric
microfluidic device
* Hydrodynamic filtration for on-chip particle concentration and
classification utilizing microfluidics
* Continuous cell partitioning using an aqueous two-phase flow system
in microfluidic devices
* Microfluidic particle sorter employing flow splitting and recombining
* In-channel focusing of flowing microparticles utilizing hydrodynamic
filtration
* Pinched Flow Fractionation - Continuous Size Separation of Particles
Utilizing a Laminar Flow Profile in a Pinched Microchannel
* Characterization of microseparator-classifier with a simple arc microchannel
* High Throughput Membrane-less Water Purification
* Modular microfluidics for gradient generation
* Numerical simulation of multiple species detection using
hydrodynamic and electrokinetic focusing
* Thermocapillary valve for droplet production and sorting
* Controlling drop size and polydispersity using chemically patterned
surfaces - sort drops by size via parallel hydrophilic lines of
varying width
* (maybe) Pressure drops for droplet flows in microfluidic channels
* (maybe) Modeling shapes and dynamics of confined bubbles


* Design and evaluation of a Dean vortex-based micromixer - separations

* High resolution DNA separations using microchip electrophoresis

* Boosting migration of large particles by solute contrasts

* Generation of dynamic temporal and spatial concentration gradients
using microfluidic devices
* Generation of complex concentration profiles in microchannels in a
logarithmically small number of steps

* Systematic modeling of microfluidic concentration gradient generators

* Thermophoresis: moving particles with thermal gradients

* Effects of flow and diffusion on chemotaxis studies in a
microfabricated gradient generator

* Generation of gradients having complex shapes using microfluidic networks

* Generating fixed concentration arrays in a microfluidic device

* Particle Continuous Separation by Evaporation Force on Microfluidic System

* Inertial migration of rigid spherical particles in Poiseuille flow

* Separation enhancement in pinched flow fractionation

* Inertial migration of spherical particles in circular Poiseuille
flow at moderately high Reynolds numbers

* The lateral migration of neutrally-buoyant spheres transported
through square microchannels

* Inertial migration of neutrally buoyant particles in a square duct -
an investigation of multiple equilibrium positions

* Membrane-free microfiltration by asymmetric inertial migration -
spirals - bifurcations

* Enhanced particle filtration in straight microchannels using
shear-modulated inertial migration

* Continuous particle separation in spiral microchannels using dean
flows and differential migration

* Membraneless microseparation by asymmetry in curvilinear laminar flows

* Microvortex for focusing, guiding and sorting of particles

* A Gravity-Driven Microfluidic Particle Sorting Device with
Hydrodynamic Separation Amplification


* Critical particle size for fractionation by deterministic lateral displacement

* Continuous flow separations in microfluidic devices
* Continuous particle separation in a microchannel having
asymmetrically arranged multiple branches

* Continuous Particle Separation Through Deterministic Lateral Displacement

* Hydrodynamic metamaterials: Microfabricated arrays to steer,
refract, and focus streams of biomaterials

* Separation of suspended particles by asymmetric arrays of obstacles
in microfluidic devices

* Accumulating particles at the boundaries of a laminar flow

* Flows of concentrated suspensions through an asymmetric bifurcation

This bibliography is also mentioned on the web here:
http://heybryan.org/mediawiki/index.php/Microfluidics#Microfluidic_particle_filtering_devices

> Yesterday, a friend showed me his (broken) lego pen plotter kit. Too
> bad it was only two-axis (no ability to lift up the pen or sharpie)-
> though this could be corrected with some lego building.

Which, btw, was a lego kit, so by definition it's not going to be
particularly hard. I have never come across a hard lego kit. Usually
they provide step-by-step instructions in the form of graphical media
[which is actually something that I've been hoping to do with
leocad/ldraw for a while now, automatically, but I just haven't got
around to this].

EJ

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Mar 5, 2009, 12:18:19 PM3/5/09
to DIYbio
The paper you link at the bottom is dealing with particles that are
much larger than protein molecules. The smallest particle was 3
micrometers. Protein diameters are typically in the nanometer range.

Some examples:

cytochrome c (diameter 3.1nm)
myoglobin (diameter 3.5nm)
hemoglobin (diameter 5.5nm)
catalase (diameter 10.5nm)
ferritin (diameter 12.2nm)
earthworm hemoglobin (diameter 30nm)
> pdf:http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=2527745&blobtyp...
>
> See also references #32-38. The big issue is that these papers and
> studies are usually done for microliters and sometimes mL over the
> period of an hour, which might be okay if you do microfluidic
> reactions for your biology experiments, but if you're trying to make a
> 20 gallon barrel of stock, this is not the way to do it.
>
> - Bryanhttp://heybryan.org/
> 1 512 203 0507

Bryan Bishop

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Mar 5, 2009, 12:49:38 PM3/5/09
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On Thu, Mar 5, 2009 at 11:18 AM, EJ <ellenjo...@aol.com> wrote:
> The paper you link at the bottom is dealing with particles that are
> much larger than protein molecules. The smallest particle was 3
> micrometers. Protein diameters are typically in the nanometer range.

Take a look at the other papers. "Spiral microfluidic nanoparticle
separators" is another good one- they did 590 nm particles in a spiral
filter with 95% of the particles migrating to a particular exit point
in the spiral channels. The microchannel width was 100 micrometers and
spacing between loops was 250 micrometers, radius of curvature = 3 mm
and number of loops = 5. Not exactly easy (or perhaps even possible)
to draw with a sharpie, but still worth pointing out.

> cytochrome c (diameter 3.1nm)
> myoglobin (diameter 3.5nm)
> hemoglobin (diameter 5.5nm)
> catalase (diameter 10.5nm)
> ferritin (diameter 12.2nm)
> earthworm hemoglobin (diameter 30nm)

- Bryan

EJ

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Mar 5, 2009, 1:17:34 PM3/5/09
to DIYbio
Is there a way to click on the papers in your list and open them? The
only one I was able to access via hypertext was the I commented on
below. When I cut and pasted the title of the one you suggested I look
at into Google, I can get the abstract but not whole paper.

On Mar 5, 12:49 pm, Bryan Bishop <kanz...@gmail.com> wrote:
> - Bryanhttp://heybryan.org/
> 1 512 203 0507

William Heath

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Mar 5, 2009, 2:00:24 PM3/5/09
to diy...@googlegroups.com
Hi All,

I am very interested in doing electrophoresis with this approach.  Anyone know how to do it?

-Tim

Bryan Bishop

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Mar 5, 2009, 3:18:41 PM3/5/09
to diy...@googlegroups.com, kan...@gmail.com
On Thu, Mar 5, 2009 at 12:17 PM, EJ <ellenjo...@aol.com> wrote:
> Is there a way to click on the papers in your list and open them? The
> only one I was able to access via hypertext was the I commented on
> below. When I cut and pasted the title of the one you suggested I look
> at into Google, I can get the abstract but not whole paper.

Yes, there is. I linked to an image the other day-
heybryan.org/books/papers/microfluidics/diybio.png
.. and if you check the directory, that's where the papers are.
However, I would prefer not to link to it openly on the mailing list,
since then naughty search engines will ignore my robots.txt file. I'll
also send you the link off-list and to anyone else who asks.

- Bryan

Bryan Bishop

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Mar 6, 2009, 2:03:50 PM3/6/09
to diy...@googlegroups.com, EJ, kan...@gmail.com
On Fri, Mar 6, 2009 at 8:27 AM, <EllenJo...@aol.com> wrote:
> I was actually thinking about this on the train this morning, and I was
> wondering if you could somehow use a human hair to make a really thin DIY
> microfluidics channel- like stretch it over the glass and then run the
> sharpie over it? But I guess the ink would probably run all around it. Maybe
> you could figure out some other way...paint a thin film of something over it
> and then pull it out?

So, I tried short human hair. I held it down with two fingers, I
clamped it with two alligator clamps, I taped it down with scotch
tape, I even wrapped it around glass, and even dangled the alligator
clips while the hair was stretched over a slide, but alas I was only
rarely ever able to get straight channels, and even then, the
beginnings/ends were too messy, and the vibrations in the hair due to
this contraption effectively being a micron guitar were far too great
to do any serious work with. Anyone with seriously ridiculously long
hair might want to give this a try, though I don't think anything will
come of it. Wikipedia says that hair is from 18 to 180 micrometers in
diameter, and the first transistor was 10 micrometers in width-- so
it's certainly something fun to play with.

However, if you draw and fill in a giant square with sharpie, you can
then run your fingernail or the pointy end of a (metal) paperclip or
the graphite of a mechanical pencil, and this allows you to make clean
channels. In fact, with an ultra fine point sharpie tip, you can just
run it back and forth over itself and the sharpie ink fluid will be
swept away and so only the edges of the effective size of the tip will
be present, although there is still a small residue present where the
sharpie has been before, and it's not really easy to control with your
hand. At the moment, a really sharp pointy tip of either a metal
paperclip, paperclip, or one of those pricklies that tend to attach
themselves to your shoes- any of these will be good to experiment
with.

http://heybryan.org/books/papers/microfluidics/macgyver_multitool.jpg

Bonus points for anyone who can figure out how to get the same pattern
on two slides with the paperclip, or even hair method. Seriously- it's
hard enough just getting the same pattern when you're drawing it by
hand.

- Bryan

Jeswin John

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Mar 6, 2009, 3:56:25 PM3/6/09
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I tried to do some things with the sharpie slide such as understand how particles behave through the channels. I didn't have any small insoluble particles so I carefully took the smallest pieces of dirt particles from soil and mixed with water. I learned 2 things:
1) The soil Particles suspend in the water but also go with the flow of water. I tried to make capturing areas with large entry point but narrow exit points. This was difficult and I gave up half way.
2) I noticed that the water started to pull off the ink and tear up the lines. I'm not sure what happened but I have two theories. One is that the distance between the 2 slides was reduced and the other is that I made the channel width smaller. These are 2 things I did differently from my first microfluidics slide.

I will have to test this later.
Bryan, You mentioned alligator clips in your first post. How did you use them? To hold the slides together?

Bryan Bishop

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Mar 6, 2009, 7:02:18 PM3/6/09
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On Fri, Mar 6, 2009 at 2:10 PM, <EllenJo...@aol.com> wrote:
> LOL, I can see where the scraping method would be preferable. Could you
> maybe take a comb-like device with little sharp metal bits embedded in the
> sides of the comb teeth, and glass slides stacked in between so that when
> you move the comb spine and the glass plates effectively move between the
> teeth you duplicate the same pattern on all?

Ah, what might make more sense is to have a "foot" that you attach to
the end of a long stick- think of a plunger, or a broom, except in
this case it's a doubly-pronged hook with sharp pointy tips. And then
this foot would scrape the top and bottom slides simultaneously. You
want only the "foot" to scrape so that you can backtrack or attempt to
do curves, or something. This might even be doable for when you have
two slides sandwhiched together with tape already- in fact, it should
probably be done like that so that there's no positional displacement
of the slides with respect to one another. Doing this would require
making a large rectangular area of sharpie material- which is not a
big deal- and the scratch-off method might work with hair too,
although I haven't tried it. Prototyping on scotch tape works really
well, except of course it's not glass and so if you make a super
amazing pattern, you're boned. Repeatability! Repeatability!

Also on my todo list is trying to just smash hair between two slides
with dark rectangles of sharpie. Maybe it will (not) work. Anybody
with an inkjet printer and access to a lamination machine should be
thinking about trying the double lamination ("polyester") layer
microfluidics method instead of sharpies, since that means we'd be
able to just print off designs. What's the maximum resolution on
inkjet printer outputs these days? Can we do 100 micrometer channels
with them?

ben lipkowitz

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Mar 6, 2009, 8:09:52 PM3/6/09
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On Fri, 6 Mar 2009, Bryan Bishop wrote:

> Anybody
> with an inkjet printer and access to a lamination machine should be
> thinking about trying the double lamination ("polyester") layer
> microfluidics method instead of sharpies, since that means we'd be
> able to just print off designs. What's the maximum resolution on
> inkjet printer outputs these days? Can we do 100 micrometer channels
> with them?

you have to use a laser printer. the channel walls are formed by melted
toner, which is basically plastic. inkjet ink won't melt like this.

Mackenzie Cowell

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Mar 6, 2009, 8:43:50 PM3/6/09
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Is transparency "paper" hydrophilic?  Because I know there are certain types that you can run directly through a laser printer.  That would avoid the hot-iron mediated toner transfer step.

Mac

ben lipkowitz

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Mar 6, 2009, 8:49:48 PM3/6/09
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there is no toner transfer step, you just run it through the printer.
there's special "laser printer" transparencies but i dont see much
difference in practice.

Bryan Bishop

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Mar 6, 2009, 10:53:24 PM3/6/09
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On Fri, Mar 6, 2009 at 6:02 PM, Bryan Bishop <kan...@gmail.com> wrote:
> Also on my todo list is trying to just smash hair between two slides
> with dark rectangles of sharpie. Maybe it will (not) work.

That worked, and I ended up with a clean microchannel. In particular,
I was using "Sanford Permanent Vis-a-Vis Overhead Projector Pen DO NOT
SHAKE", and I smashed the hair between the two slides and then slowly
pulled it out from one end. This was only with one "sharpie blotch" on
one of the slides, not on both. I've found though that the edge of a
metal paperclip or small staple can provide even more thin
microchannels than hair.

You do not have to draw the circuit twice. Draw it once on a glass
slide (or "flaky" side of a CD) and then attach the spacers and place
it on to the side of a CD-R (RW?) that does not flake when you take a
knife to it-- "the shiny side", which is the hydrophobic side of a CD.
The other, flaky side is aluminum, and if you're careful to not do too
much damage when you flake it, you can make it so that you can see
through it. So, you can draw your circuit on another CD, the
aluminum/flaky/not-shiny side, place the spacers on it, attach it to
another CD, and then on the other side you flake off the aluminum and
then you can see through it to get a visual on what is happening in
your circuit- I recommend using a dye to help with the visualization
since the plastic is going to be all shredded up. Overall, you only
draw the circuit just once, and it works just as well as it did with
the glass sandwich method that I outlined earlier.

Bryan Bishop

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Mar 7, 2009, 3:19:41 AM3/7/09
to Andrew Hessel, diy...@googlegroups.com, kan...@gmail.com
On Sat, Mar 7, 2009 at 1:38 AM, Andrew Hessel <ahe...@gmail.com> wrote:
> This so reminds me of using an old Etch-a-Sketch.  Just a really tiny one.
> :)

Someone here in Austin made a "CNC etch-a-sketch" a few weeks ago. As
you can imagine, it physically looks like one of those engineering
projects way too over the top.

http://instruct1.cit.cornell.edu/courses/ee476/FinalProjects/s2004/jml66/EAS_final.htm
http://www.hektor.ch/
http://lists.puremagic.com/pipermail/robotgroup/2007-October/007177.html
http://lists.puremagic.com/pipermail/robotgroup/2004-July/000690.html

In particular, it was the "CNC Magic Screen Machine":
http://lists.puremagic.com/pipermail/robotgroup/2009-February/011999.html
http://www.unfocusedbrain.com/projects/2009/cncmagicscreenmachine/
image: http://www.unfocusedbrain.com/projects/2009/cncmagicscreenmachine/dscn3737_small.jpg

Jeswin John

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Mar 7, 2009, 8:46:10 AM3/7/09
to diy...@googlegroups.com
"You do not have to draw the circuit twice. Draw it once on a glass
slide (or "flaky" side of a CD) and then attach the spacers and place
it on to the side of a CD-R (RW?) that does not flake when you take a
knife to it-- "the shiny side", which is the hydrophobic side of a CD.
The other, flaky side is aluminum, and if you're careful to not do too
much damage when you flake it, you can make it so that you can see
through it. So, you can draw your circuit on another CD, the
aluminum/flaky/not-shiny side, place the spacers on it, attach it to
another CD, and then on the other side you flake off the aluminum and
then you can see through it to get a visual on what is happening in
your circuit- I recommend using a dye to help with the visualization
since the plastic is going to be all shredded up. Overall, you only
draw the circuit just once, and it works just as well as it did with
the glass sandwich method that I outlined earlier."

This is a bit hard for me to understand. You used one slide and one CD?

My problem was trying to get the tiny channels drawn at the place on the 2 sldes and that was very hard.

I also noticed that using a paperclip to remove the ink left small traces of it on the surface.Have you been able to get water to flow through such small openings?

Bryan Bishop

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Mar 7, 2009, 10:01:19 AM3/7/09
to diy...@googlegroups.com, kan...@gmail.com
On Sat, Mar 7, 2009 at 7:46 AM, Jeswin John <phill...@gmail.com> wrote:
> This is a bit hard for me to understand. You used one slide and one CD?

Yes. But you can also use two CDs sandwiched together.

> My problem was trying to get the tiny channels drawn at the place on the 2
> sldes and that was very hard.

Yes, so now you only have to draw the channels once.

> I also noticed that using a paperclip to remove the ink left small traces of
> it on the surface.

What do you mean?

> Have you been able to get water to flow through such small openings?

Nope, but I also have not tried it yet. I'll take a look at it under
the microscope when I get back into a lab later today. Maybe it
requires very small volumes of water that are hard to see? I need to
go buy myself a dye from the convenience store.

Jeswin John

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Mar 12, 2009, 11:24:03 AM3/12/09
to diy...@googlegroups.com
What I have learned so far:

  • If the space is too small i.e. made by scratching a thin line with a pencil perpendicular to a thick sharpie line, the water will flood the lines and overflow rather than go through the tiny opening.
  • Dipping a pencil graphite in isopropanol will better facilitate removal of sharpie line. I used an Eagle HB2 pencil and this doesn't leave any pieces of graphite or graphite lines on the glass.

Next I will try the effects of Rain X. The bottle says it is denatured alcohol (MEOH or ETOH? can't remember if it said)

Bryan Bishop

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Mar 12, 2009, 12:25:49 PM3/12/09
to diy...@googlegroups.com, kan...@gmail.com
On Thu, Mar 12, 2009 at 10:24 AM, Jeswin John <phill...@gmail.com> wrote:
> If the space is too small i.e. made by scratching a thin line with a pencil
> perpendicular to a thick sharpie line, the water will flood the lines and
> overflow rather than go through the tiny opening.

The brief bisection of the hydrophobic line, representing the conduit
into which you want the water to flow, isn't going to allow for water
flow because essentially the surface tension effects make it apear
like an entirely straight line, as far as the motion of the fluid is
concerned. To test this hypothesis, we could draw lines with
decreasing width and test whether or not fluid will flow into each
channel. It might be that you can't see the water that flows into the
channels, or that it needs to go down a funnel, or something.

Aaron Hicks

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Mar 12, 2009, 3:52:51 PM3/12/09
to diy...@googlegroups.com
EtOH + IPA:

http://www.windtrax.com/images/MSDS/RX11169_MSDS.pdf

No additional denaturants listed, although I suspect the IPA is probably sufficient to make BATF happy.

-AJ

Jeswin John

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Mar 12, 2009, 6:48:14 PM3/12/09
to diy...@googlegroups.com
My bottle states "Caution: Denatured Alcohol" (Something like that)

What does it mean for alcohol to be denatured?

Aaron Hicks

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Mar 12, 2009, 8:37:10 PM3/12/09
to diy...@googlegroups.com
It is to render it unsafe for consumption, meaning it does not need a tax stamp. There's a huge list of the different formulas for denaturing alcohol:

http://edocket.access.gpo.gov/cfr_2005/aprqtr/pdf/27cfr21.32.pdf

The idea is that something is added that makes it unsuitable for consumption, but cannot readily be separated- frequently by adding something that co-distills when heated.

-AJ

JonathanCline

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Mar 13, 2009, 1:55:25 PM3/13/09
to DIYbio, jcl...@ieee.org
On Mar 12, 11:25 am, Bryan Bishop <kanz...@gmail.com> wrote:
>
> we could draw lines with
> decreasing width and test whether or not fluid will flow into each
> channel. It might be that you can't see the water that flows into the
> channels, or that it needs to go down a funnel, or something.

Can you explain what you guys are eventually trying to do? So you've
got a method for allowing a water-based culture to wick horizontally
or vertically (how high vertically?). Is this meant for measuring
volumes (if so, how to dispense the solution)? For directing into
micro-reactors (if so, how to drain the reactor)? For size-sorting
objects in solution into a separate vessel? or..?


## Jonathan Cline
## jcl...@ieee.org
## Mobile: +1-805-617-0223
########################

Bryan Bishop

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Mar 13, 2009, 4:39:02 PM3/13/09
to diy...@googlegroups.com, kan...@gmail.com
On Fri, Mar 13, 2009 at 12:55 PM, JonathanCline <jnc...@gmail.com> wrote:
> On Mar 12, 11:25 am, Bryan Bishop <kanz...@gmail.com> wrote:
>> we could draw lines with
>> decreasing width and test whether or not fluid will flow into each
>> channel. It might be that you can't see the water that flows into the
>> channels, or that it needs to go down a funnel, or something.
>
> Can you explain what you guys are eventually trying to do?  So you've
> got a method for allowing a water-based culture to wick horizontally
> or vertically (how high vertically?).  Is this meant for measuring
> volumes (if so, how to dispense the solution)?  For directing into
> micro-reactors (if so, how to drain the reactor)?  For size-sorting
> objects in solution into a separate vessel?   or..?

I have no immediate project in mind at the moment. However, many
papers have gone over using microfluidic devices for PCR, DNA
separation, DNA sequencing, DNA synthesis, electroporation,
microreactors, micromixers, in situ fabrication, cell-free protein
expression, nano/micro mas spec, capillary force lithography, and so
many other techniques under the disguise of the "lab on a chip"
buzzword.

Volume measurement might be possible. I guess you would measure out
your lines with a ruler, and then measure out the right amount of
tape, and tape it in just the right way to make the correct space
between two plates so that you can confirm that any liquid mass
filling the volume will in fact be the right amount. So there's that.
For dispensing, you can do micropipettes, or use some of the designs
for droplet production from a continuous stream of liquid (i.e.,
pouring).

For draining, capillary force works, but the problem is that there is
some amount of material left over, so either things are going to be
one-time use (or "few-time use"), or we'll have to come up with a
cleaning operation, or whatever- as was previously observed, sometimes
it's too easy to get the sharpie to diffuse into the water, although
this still has to be tested on the microscale with the large
microchannels that you can draw with the edge of a paperclip and so
on.

Size-sorting of nanoparticles has also been done in previous
literature, such as in the hydrodynamics+gravity paper. If all you
need is very small volumes of the substances in relatively pure
conditions, such as for further microreactions for lab experiments,
then this might be the way to go. :-)

Jeswin John

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Mar 13, 2009, 4:49:05 PM3/13/09
to diy...@googlegroups.com
You reminded me. If it's not known but you could make the water flow at a faster rate by connecting the exit point with paper towels or absorbent material.

My reason for playing around with this is that it is very easy for me to work with. I got slides, a Sharpie, some alcohol and water.

Here's an idea that just popped in my head right now: Grow individual organisms on a slide fed by a flow of nutrient water. Not sure what use it is or if it could work.

Jeswin John

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Mar 13, 2009, 4:50:07 PM3/13/09
to diy...@googlegroups.com
"For draining, capillary force works"

Sorry missed that part. I guess you used the paper trick also?

Bryan Bishop

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Mar 13, 2009, 5:12:04 PM3/13/09
to diy...@googlegroups.com, kan...@gmail.com
On Fri, Mar 13, 2009 at 3:49 PM, Jeswin John <phill...@gmail.com> wrote:
> You reminded me. If it's not known but you could make the water flow at a
> faster rate by connecting the exit point with paper towels or absorbent
> material.

I haven't tried this, no. Have you done this? How do you set this up-
just tear off a piece of paper and water will be pulled through your
circuit? By the way, there was also a paper about fabrication of
components by evaporation, surface tension and capillary force.
Evaporation in this situation might not be appropriate- since you want
the fluid- but if you're going to put some of the resultant fluid in
an absorbent material, I guess you don't care about the fluid that you
could otherwise use for evaporation?

> Here's an idea that just popped in my head right now: Grow individual
> organisms on a slide fed by a flow of nutrient water. Not sure what use it
> is or if it could work.

All sorts of fun stuff. Growing life in specific patterns. Large-scale
arrays for directed evolution experiments. etc.

Jeswin John

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Mar 13, 2009, 5:37:03 PM3/13/09
to diy...@googlegroups.com
"I guess you don't care about the fluid that you
could otherwise use for evaporation?"

Yep, Right now, I'm just observing how water behaves.

 I still have a hard time with getting water through ≤1mm openings.

Bryan Bishop

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Mar 19, 2009, 3:52:58 PM3/19/09
to diy...@googlegroups.com, kan...@gmail.com
On Fri, Mar 6, 2009 at 10:53 PM, Bryan Bishop <kan...@gmail.com> wrote:
> On Fri, Mar 6, 2009 at 6:02 PM, Bryan Bishop <kan...@gmail.com> wrote:
>> Also on my todo list is trying to just smash hair between two slides
>> with dark rectangles of sharpie. Maybe it will (not) work.
>
> You do not have to draw the circuit twice. Draw it once on a glass
> slide (or "flaky" side of a CD) and then attach the spacers and place
> it on to the side of a CD-R (RW?) that does not flake when you take a
> knife to it-- "the shiny side", which is the hydrophobic side of a CD.
> The other, flaky side is aluminum, and if you're careful to not do too
> much damage when you flake it, you can make it so that you can see
> through it. So, you can draw your circuit on another CD, the
> aluminum/flaky/not-shiny side, place the spacers on it, attach it to
> another CD, and then on the other side you flake off the aluminum and
> then you can see through it to get a visual on what is happening in
> your circuit- I recommend using a dye to help with the visualization
> since the plastic is going to be all shredded up. Overall, you only
> draw the circuit just once, and it works just as well as it did with
> the glass sandwich method that I outlined earlier.

So, I'd thought I'd update the diybio peeps with something that is
also just as exciting regarding the use of CDs. Apparently someone has
done stamps with CDs. Here's the paper:

Patterning Design in Color at the Submicron Scale - Arun Chattopadhyay
- stamps via CDs (pdf)
http://tinyurl.com/ddv4wd

Speaking of that, here's a list of researchers in this area that
should be paid attention to:
* Arun Chattopadhyay
* Hong H. Lee
* Kahp Y. Suh

Every time I come across an amazingly useful paper, one of those three
is the main culprit behind it. Simply amazing the work that they're
doing.

So, the CD stamp paper. Here's what they did. They pressed a CD down
on a splotch of sharpie or permanent pen ink (within one minute of
drawing the splotch), and based off of the applied pressure were able
to make different grooves with a width of 0.8 and depth of 0.5
micrometers.

"""
A CD is typically made of a polycarbonate disk on which
patterns are drilled in the form of a single spiral track. The
typical width and depth of each line in the spiral track are
0.8 and 0.5 µm, respectively, and separation between two
such lines is about 1.6 µm. [20] The diameter of a typical CD
is much larger than the separation between two lines and
hence under an optical microscope the lines appear parallel
with nearly infinite radii of curvatures. The aluminum coating
on the polycarbonate membrane also has the structural
patterns that appear as parallel lines under an optical
microscope.
The polycarbonate disk and the aluminum foil could
be separated and be independently used as molds for
two-dimensional pattern generation. For our experiments
we have used parts of both the aluminum foil and the
polycarbonate disk to imprint patterns. Optical micrographs
of patterns found in polycarbonate disc and aluminum foil
in a CD are shown in Figure 1. It is clear that even after the
CD is dismantled, the original lines remain intact and hence
could be used as molds. A schematic view of the present
method of imprinting patterns on various surfaces is shown
in Figure 2.
[..]
Here, we have demonstrated a method of imprinting lines
and arrays of various colors on glass slides and OHP films.
Parallel lines with submicron dimensions could be imprinted
on such substrates by using polycarbonate and Al foil molds
of a CD. Also, microarrays of ink spots positioned at
predetermined angles and spacing determined by the separa-
tion of lines in the mold could be generated. Even though
the dimensions of the lines and arrays are in and around the
micron range, the resolution could further be increased using
a mold with lines and patterns of higher resolution. The same
principle could be used for imprinting designed arrays of
various materials on plastic and glass substrates in accordance
with their use. The use of flexible plastic material like OHP
paper enhances the possibility of storing designs in foldable
substrates.
"""

Does anyone know what size the grooves are in DVDs?

And has anyone tried the laser printer + lamination procedure yet?

Another paper I've been glancing over today--

Contact Electrochemical Replication of Hydrophilic-Hydrophobic
Monolayer Patterns
http://is.gd/o2Kq

"""
Contact electrochemical replication (CER) is a novel pattern
replication methodology advanced in this laboratory that offers the
unprecedented capability of direct one-step reproduction of monolayer
surface patterns consisting of hydrophilic domains surrounded by a
hydrophobic monolayer background (hydrophilic @ hydrophobic monolayer
patterns), regardless of how the initial "master" pattern was created.
CER is based on the direct electrochemical transfer of information,
through aqueous electrolyte bridges acting as an information transfer
medium, between two organosilane monolayers self-assembled on smooth
silicon wafer surfaces. Upon the application of an appropriate voltage
bias between a patterned monolayer/silicon specimen playing the role
of "stamp" and a monolayer/silicon specimen playing the role of
"target", the hydrophilic features of the stamp are copied onto the
hydrophobic surface of the target. It is shown that this
electrochemical printing process may be implemented under a variety of
experimental configurations conducive to the formation of nanometric
electrolyte bridges between stamp and target; however, using plain
liquid water for this purpose is, in general, not satisfactory because
of the high surface tension, volatility, and incompressibility of
water. High-fidelity replication of monolayer patterns with variable
size of hydrophilic features was achieved by replacing water with a
sponge-like hydrogel that is nonvolatile, compressible, and binds
specifically to the hydrophilic features of such patterns. Since any
copy resulting from the CER process can equally perform as stamp in a
subsequent CER step, this methodology offers the rather unique option
of multiple parallel reproduction of an initially fabricated master
pattern.

Nathan McCorkle

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Mar 21, 2009, 5:51:41 PM3/21/09
to diy...@googlegroups.com
what could we use to control the flow rate?
--
Nathan McCorkle
Rochester Institute of Technology
College of Science, Biotechnology/Bioinformatics

Bryan Bishop

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Mar 21, 2009, 6:36:10 PM3/21/09
to diy...@googlegroups.com, kan...@gmail.com
On Sat, Mar 21, 2009 at 4:51 PM, Nathan McCorkle <nmz...@gmail.com> wrote:
> what could we use to control the flow rate?

That's a good question. I have not been able to get significant flow
anyway- except when I apply a perpendicular force to one of the two
surfaces, which decreases the separation between the two pieces of
plastic or two pieces of glass (in either scenario) and the water then
spreads out further. This isn't particularly useful for 'actuation'
(the movement of the water) because it requires human contact, and
even if there was some mechanism to provide that same force, the water
tends to be forced over the sharpie lines unless the force is very
exact.

Another method I've read about is the use of Marangoni forces, for
instance any paper by Banu, who recently published his PhD thesis on
the topic. In particular, he made a 16-by-16 array of tiny resistors
on a PCB that he sent to a job house. Each resistor is individually
addressable. He rests the PCB board a few hundred microns from the
surface of an open-air ambient temperature surface with water
droplets. By activating the resistors in certain patterns through a
computer interface, Banu has been able to move the water droplets just
by Marangoni force effects. This is more promising than sharpie
microfluidics overall since it's similar to FPGAs, but I haven't taken
the time to make the diagrams or PCB files and so on. But I highly
recommend checking out his work.

Another method I've read about is the use of screws. First, holes are
drilled into the microfluidic device (but not through the
microchannels), such that then a screw can be twisted into the hole
and as the screw goes into the hole, the greater the internal pressure
(force over an area) and thus the water can be actuated just by
turning a screw. I don't know if this is interesting or not- do we
want to be able to automate these sharpie microfluidic systems, or are
we okay with human energy inputs, or what? Also, I am fairly sure that
screws-for-actuators would not work well with the laminated laser
printed microfluidic devices method.

Another method I've read about is the use of T-junctions and other
shapes of channels for the water to flow through. Obviously, a funnel
is one way of controlling flow rate. Another way is to look at
resistors in electronic circuits, in particular the parallel circuits,
etc. This, however, requires there to be some sort of input flow.
Maybe if there's a straw that is connected to a hole (much like a hole
made for a screw), and liquids travel down due to gravity, that would
be enough to start the water flowing through the device?

And maybe there's a way to do it just by playing off of
superhydrophobic surfaces, which might be possible with the help of
carbon nanotubes, or something.

So, in the last email I sent I mentioned CD patterning with sharpies.
I don't know if that works or not- I haven't tested it since I've been
away from a microscope for a few days- but in the mean time, at one
point I became very annoyed by my inability to handle scotch tape. You
always get finger prints on it when you're ripping off pieces of tape.
And if you're really terrible, the tape might flutter in the wind and
then stick to your hand, and when you rip it off, you have these small
fine lines in the pattern of your skin or finger print or palm print.
Huh. Wonder what use that could be? You mostly get small parallel
lines.

(To be clear, if you then proceed to stick the tape on top of a
splotch of sharpie, you're able to remove sharpie where no layer of
skin was removed, so it's a way to do fingerprint patterning. It's
probably useless.)

A few other interesting papers that I've been reading recently include
a method for making carbon nanotubes (CNTs) from grass. Yes, grass.
But the method kind of sucks and requires 50 cycles of baking at 600
degrees Celsius. There have also been a few papers about in situ
synthesis of CNTs in microchannels via chemical vapor deposition
processes. And a few other papers on making CNTs and "carbon onions"
via an arc discharge in water, or aqueous sucrose or aqueous salt
solutions with graphite electrodes in the case of water, or copper
electrodes in the case of sucrose, which makes lots of small
nanoshapes. These can be used to make superhydrophobic surfaces, or
with selective laser welding, to build things out of nanotubes, more
or less. (Mostly less.) If anyone is interested in these papers,
there's an archive:

http://heybryan.org/books/papers/2009-03-21_CNTs.zip
(or alternatively go to /books/papers/CNTs/ for an index of the papers)

There's probably a few methods of actuation that I'm forgetting.
Gravity, heat, electric current, conduction in general, capillary
rise, Marangoni surface tension forces, mechanical pressure via
screws, anything else?

Jake

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Mar 22, 2009, 5:05:19 AM3/22/09
to DIYbio
I can see some interesting aplications in biocomputing. I've been
wanting a micro/nano spec for awhile... Anybody have any ideas on how
to use something like this for a nano spec? Would such a tiny path
length work in a spec if you used two glass slides sandwhiched
together or a glass slide with a coverslip with a microdrop under it?

I'm guessing I'd need to know the exact path length of the slide
sandwhich and do some calculations and just hope the spec is sensitive
enough to even register any change.


> My bottle states "Caution: Denatured Alcohol" (Something like that)
> What does it mean for alcohol to be denatured?

In the US denatured alcohol used to be mostly ethanol with 4-15%
methanol added. Now it's ethanol with up to 50% methanol. (methanol
is cheaper)

The main manufacturers for denatured alcohol are "Kleen Strip" and
Parks corp. Kleen Strip is walmart and other big box stores. Parks
corp is Ace, Tru Value, etc. check the label for "Parks corp" or
"Zinsser Company, Inc."

Kleen Strip (S-L-X denatured alcohol) is:
Ethyl alcohol 45.0-50.0%
Methanol 45.0-50.0%
Methyl isobutyl ketone 1.0-4.0%

Parks corp is:
Ethanol 80% (minimum)
Methanol 10% (max)
Methyl Isobutyl Ketone 5% (max)
Ethyl Acetate 5% (max)


-Jake

Bryan Bishop

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Mar 22, 2009, 7:59:09 AM3/22/09
to diy...@googlegroups.com, kan...@gmail.com
On Sun, Mar 22, 2009 at 4:05 AM, Jake <jake...@mail.com> wrote:
> I can see some interesting aplications in biocomputing.  I've been
> wanting a micro/nano spec for awhile... Anybody have any ideas on how
> to use something like this for a nano spec?  Would such a tiny path
> length work in a spec if you used two glass slides sandwhiched
> together or a glass slide with a coverslip with a microdrop under it?
>
> I'm guessing I'd need to know the exact path length of the slide
> sandwhich and do some calculations and just hope the spec is sensitive
> enough to even register any change.

Yes, take a look here for some information on making a mass spec out of this-

http://groups.google.com/group/diybio/msg/d84596be7a2786f5
http://groups.google.com/group/diybio/msg/c6aba2175be59dc9

Here's some literature on the topic-

* Continuous flow separation of particles within an asymmetric
microfluidic device
* Hydrodynamic filtration for on-chip particle concentration and
classification utilizing microfluidics
* Continuous cell partitioning using an aqueous two-phase flow system
in microfluidic devices
* Microfluidic particle sorter employing flow splitting and recombining
* In-channel focusing of flowing microparticles utilizing hydrodynamic
filtration
* Pinched Flow Fractionation - Continuous Size Separation of Particles
Utilizing a Laminar Flow Profile in a Pinched Microchannel
* Characterization of microseparator-classifier with a simple arc microchannel
* High Throughput Membrane-less Water Purification
* Modular microfluidics for gradient generation
* Numerical simulation of multiple species detection using
hydrodynamic and electrokinetic focusing
* Thermocapillary valve for droplet production and sorting
* Controlling drop size and polydispersity using chemically patterned
surfaces - sort drops by size via parallel hydrophilic lines of
varying width
* (maybe) Pressure drops for droplet flows in microfluidic channels
* (maybe) Modeling shapes and dynamics of confined bubbles
* Design and evaluation of a Dean vortex-based micromixer - separations
* High resolution DNA separations using microchip electrophoresis
* Boosting migration of large particles by solute contrasts
* Generation of dynamic temporal and spatial concentration gradients
using microfluidic devices
* Generation of complex concentration profiles in microchannels in a
logarithmically small number of steps
* Systematic modeling of microfluidic concentration gradient generators
* Thermophoresis: moving particles with thermal gradients
* Effects of flow and diffusion on chemotaxis studies in a
microfabricated gradient generator
* Generation of gradients having complex shapes using microfluidic networks
* Generating fixed concentration arrays in a microfluidic device
* Particle Continuous Separation by Evaporation Force on Microfluidic System
* Inertial migration of rigid spherical particles in Poiseuille flow
* Separation enhancement in pinched flow fractionation
* Inertial migration of spherical particles in circular Poiseuille
flow at moderately high Reynolds numbers
* The lateral migration of neutrally-buoyant spheres transported
through square microchannels
* Inertial migration of neutrally buoyant particles in a square duct -
an investigation of multiple equilibrium positions
* Membrane-free microfiltration by asymmetric inertial migration -
spirals - bifurcations
* Enhanced particle filtration in straight microchannels using
shear-modulated inertial migration
* Continuous particle separation in spiral microchannels using dean
flows and differential migration
* Membraneless microseparation by asymmetry in curvilinear laminar flows
* Microvortex for focusing, guiding and sorting of particles
* A Gravity-Driven Microfluidic Particle Sorting Device with
Hydrodynamic Separation Amplification
* Critical particle size for fractionation by deterministic lateral displacement
* Continuous flow separations in microfluidic devices
* Continuous particle separation in a microchannel having
asymmetrically arranged multiple branches
* Continuous Particle Separation Through Deterministic Lateral Displacement
* Hydrodynamic metamaterials: Microfabricated arrays to steer,
refract, and focus streams of biomaterials
* Separation of suspended particles by asymmetric arrays of obstacles
in microfluidic devices
* Accumulating particles at the boundaries of a laminar flow
* Flows of concentrated suspensions through an asymmetric bifurcation

Again, this paper was particularly neat: "Spiral microfluidic
nanoparticle separators".

Jeswin John

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Mar 22, 2009, 2:12:17 PM3/22/09
to diy...@googlegroups.com
Is there an alternative hydrophobic substance for making the channels? Sharpies are fine but its hard to get small channels. I thought about dye-colored Rain X but the fumes give me headaches.

Fumes seem to be a problem as Sharpies give me headaches sometimes. Jake mentioned some substances like Rain X but I'm going to guess they are volatile also.

Bryan Bishop

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Mar 22, 2009, 6:21:46 PM3/22/09
to diy...@googlegroups.com, kan...@gmail.com
On Sun, Mar 22, 2009 at 1:12 PM, Jeswin John <phill...@gmail.com> wrote:
> Is there an alternative hydrophobic substance for making the channels?
> Sharpies are fine but its hard to get small channels. I thought about
> dye-colored Rain X but the fumes give me headaches.

Candle wax is hydrophobic. I don't know about crayola crayon wax.
Grease-proof paper. Paint. Butter. Oil. "The stuff you put your baking
on." Rain X. Maybe it's time I start looking into the "print out a
pattern with an inkjet and gently rub a hot iron across it"- maybe
even heating a metal plate by an open candle flame to the right
temperature since I don't have an iron? Although an iron should be a
simple purchase to make. And anyone with a laser printer and a
lamination machine is encouraged to try the lamination method, as
well.

Jeswin John

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Mar 22, 2009, 6:53:42 PM3/22/09
to diy...@googlegroups.com
you gave me an idea. I know that the people who do the painted pysanka eggs use an instrument to put a fine line of melted wax on the eggs. Maybe something like that would work?

Bryan Bishop

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Mar 22, 2009, 7:03:43 PM3/22/09
to diy...@googlegroups.com, kan...@gmail.com
On Sun, Mar 22, 2009 at 5:53 PM, Jeswin John <phill...@gmail.com> wrote:
> you gave me an idea. I know that the people who do the painted pysanka eggs
> use an instrument to put a fine line of melted wax on the eggs. Maybe
> something like that would work?

http://en.wikipedia.org/wiki/Pysanka

"Pysanky (from писати pysaty, "to write") are raw eggs created with
the wax-resist method (batik). The designs are "written" in hot wax
with a stylus or a pin-head. Wooden eggs and beaded eggs are often
referred to as "pysanky" because they mimic the decorative style of
pysanky in a different medium."

http://en.wikipedia.org/wiki/Batik

"""
Melted wax (Javanese: malam) is applied to cloth before being dipped
in dye. It is common for people to use a mixture of beeswax and
paraffin wax. The beeswax will hold to the fabric and the paraffin wax
will allow cracking, which is a characteristic of batik. Wherever the
wax has seeped through the fabric, the dye will not penetrate.
Sometimes several colours are used, with a series of dyeing, drying
and waxing steps.

Thin wax lines are made with a canting (also spelled tjanting or
tjunting), a wooden handled tool with a tiny metal cup with a tiny
spout, out of which the wax seeps. Other methods of applying the wax
onto the fabric include pouring the liquid wax, painting the wax on
with a brush, and applying the hot wax to pre-carved wooden or metal
wire block (called a tjap) and stamping the fabric.

After the last dyeing, the fabric is hung up to dry. Then it is dipped
in a solvent to dissolve the wax, or ironed between paper towels or
newspapers to absorb the wax and reveal the deep rich colors and the
fine crinkle lines that give batik its character. This traditional
method of batik making is called Batik Tulis (lit: Written Batik).

The invention of the copper block or cap developed by the Javanese in
the 20th century revolutionized batik production. It became possible
to make high quality designs and intricate patterns much faster than
one could possibly do by hand-painting. This method of using copper
block to applied melted wax pattern is called Batik Cap (pronounced
like "chop").
"""

Maybe just going with paraffin wax would be ideal?

http://homecooking.about.com/od/cookingfaqs/f/faqparaffin.htm

"You can find paraffin wax, also sometimes called baker's wax or
canning wax, in your grocery store where canning jars and supplies are
sold. Paraffin is still commonly used (although not recommended) to
seal home-canned jellies and jams. However, some paraffin is not
intended to be ingested, such as that sold for candlemaking, so check
the label."

UV curable wax, anyone?

javagu...@gmail.com

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Mar 22, 2009, 10:11:35 PM3/22/09
to DIYbio
On Mar 22, 4:53 pm, Jeswin John <phillyj...@gmail.com> wrote:
> you gave me an idea. I know that the people who do the painted pysanka eggs
> use an instrument to put a fine line of melted wax on the eggs. Maybe
> something like that would work?
>
The tool to apply the wax is called a kistka.

Nathan McCorkle

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Apr 5, 2009, 12:55:59 AM4/5/09
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So I have been reading a lot of papers that Brian has on his site... I'd like to try to design something that could take cells, lyse them, then separate everything, with a goal of having proteins and RNA separated in two distinct channels (the other stuff can get flushed... or whatev I don't care)

So it seems I could first start by trying to separate some short ethidium stained DNA mixed with a lysed cell solution.

I'm not sure the best way to approach this, I was thinking laser printer, but, it seems that the edges are pretty rough especially dependent on the size of the toner molecules... also I think I need to find a good source for the PDMS overlay, soo, I'm not sure exactly how to start, but in one of the papers it did some tests separating 3um and 5um wide polymers... so maybe DNA would function similarly, and I could borrow from their design.

Input or advice? Please!

-Nate

Bryan Bishop

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Apr 5, 2009, 1:41:10 AM4/5/09
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On Sat, Apr 4, 2009 at 11:55 PM, Nathan McCorkle <nmz...@gmail.com> wrote:
> So I have been reading a lot of papers that Brian has on his site... I'd
> like to try to design something that could take cells, lyse them, then
> separate everything, with a goal of having proteins and RNA separated in two
> distinct channels (the other stuff can get flushed... or whatev I don't
> care)

There is a paper from the biopoets at Berkeley where they lyse
erythrocytes with nanoknives in a microchannel with something like 8%
efficiency. Nanoknives were discussed on Slashdot once--

http://science.slashdot.org/article.pl?sid=06/11/26/1822245

And the main nanoknife-lysis paper is over here:
http://biopoets.berkeley.edu/projects/nanoknives.php

"We are developing reagentless means to conduct sample preparation for
lab-on-chip devices. By modifiying a deep reactive ion etching process
to create enhanced "scallops" one can create sharp tips with can be
used to mechanically disrupt cells flowing in microchannels.
Nanostructured barbs (nano-knives) are created within the lysis filter
by using a modified deep reactive ion etching (DRIE) process. Lysis
filters with nanostructured barbs perform better at extracting protein
from cells for analysis. This has been shown to enhance availability
of proteins of cell lysate by a factor of 2 at 300 microliters/min."

Also, for separating out very small particles, see this paper in
particular- "Spiral microfluidic nanoparticle separators".

> So it seems I could first start by trying to separate some short ethidium
> stained DNA mixed with a lysed cell solution.

Huh? Why that particular mix?

> I'm not sure the best way to approach this, I was thinking laser printer,
> but, it seems that the edges are pretty rough especially dependent on the
> size of the toner molecules... also I think I need to find a good source for
> the PDMS overlay, soo, I'm not sure exactly how to start, but in one of the
> papers it did some tests separating 3um and 5um wide polymers... so maybe
> DNA would function similarly, and I could borrow from their design.

I think that it is a good idea to look into SU-8 or PDMS for
templating molds maybe printed by laser printers. The SU-8 and PDMS
methods are the most common for microfluidics, but it's not as easy as
drawing in sharpie or printing out a design and making a laminated
transparency. Once you make a PDMS microfluidics design, you have to
also consider the interconnects and figure out if you want to use a
syringe pump, or something, to get things moving through it, unless
you're going to go all out and try Maragoni forces or something (but
one experimental variable at a time would be best).

In the mean time, while sorting out the hardware on the other end of
the equation, I have been working on the computational fluid dynamics
of microfluidics. I did a simulation of an electro-osmotic flow of an
analyte through a T-junction and threw up a video:

http://tinyurl.com/cdwpgc

And combined with shape optimization techniques for target density
profiles, things might get interesting, like in the work that this
group did:

http://tinyurl.com/dxgny9

I have been working out the different types of equations that are used
in the different microfluidic separators. Some use inertial
displacement, others use Dean vortices, others use differential
migration, etc. Honestly it shouldn't take me this long to transcribe
the equations from the literature, but the other part of the issue is
figuring out how to write it down in terms of freefem++ or elmer. Once
we get this, we can do some simulations to figure out what various
designs will do to flow profiles, and such.

Nathan McCorkle

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Apr 5, 2009, 6:33:02 AM4/5/09
to diy...@googlegroups.com
>> So it seems I could first start by trying to separate some short ethidium
>> stained DNA mixed with a lysed cell solution.

>Huh? Why that particular mix?

Oh, so I can throw the microfluidic device in the UV visualiser, and use the ethidium stained DNA to see if my separator is working... I figure staining something like a DNA ladder, then mixing it with some lysed cells would simulate things pretty well, I just figure staining the lysis solution could introduce inspecific binding.

As for PDMS, etc... if it is cheap enough, I don't mind throwing a few devices away if need be, for now I was thinking a resevoir would gravity feed and should be enough for separations, at least I think would be a good place to start.

What software are you using to do the CFD (flash isn't working, so I haven't seen your vids yet)? It would be cool for you to share the methods if it is modular, i.e. I have about 5 minutes training using solid works, so, could I make a 3D device, and plug n chug with your components?

-Nate