[ExI] Fwd: Sharpie microfluidics

[Bryan Bishop]

Kicking it up (another) notch. The full discussion is over at the
following link, but of course extropian insight is always neat:

http://groups.google.com/group/diybio/browse_frm/thread/b3bb2d8b8a654fd4/1197606e3c3dc439?#1197606e3c3dc439
general FAQ: http://heybryan.org/mediawiki/index.php/DIYbio_FAQ

---------- Forwarded message ----------
From: Bryan Bishop <kanzure at gmail.com>
Date: Mon, Mar 2, 2009 at 12:05 PM
Subject: Sharpie microfluidics
To: diybio at googlegroups.com, Open Manufacturing
<openmanufacturing at googlegroups.com>, kanzure at 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