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microfabrication
fabricating small patterns or structures in micrometer. (not about the accuracies or tolerances) (upper is 100 microm and lower 100 nm)
microstructure technology
looking at fabrication, mechanics, fluidics and optics.
focus on properties and behavior of materials at microscope scale
understanding and optimizing materials for engineering and manufacturing purposes
involves techniques to modify or observe material properties at microscale—> enhance prop
microsystem technology (MST)
Micropatterns, structures, sensors, actuators, transducers, energy sources and packaging.
focuses on miniatured systems that integrate different functions at micom scale or even smaller
designing and fabricating complex systems that integrate various components (applications such as medical devices)
microfrabriation and integration of small-scale devices
microfabrication
making already existing structures smaller, but also produce meta-materials. Materials with unfound properties in the nature.
pulling at one side and the other side also expending
scale influence on physica
volume shrinks faster than areas, areas shrink faster than lines—> influences the corresponding forces
microfabrication where does it take place
happens in clean room
controlled temp+ humidity
low partile concentration
low vibrations
yellow light
air filtering
—> takes place in vacuum
—> takes place in plasma
ways of air filtering
laminar: parallell smooth flow, no mixing, low velocity, and Re also low, viscous is dominant and flor pattern is predictabe ISO<6 and for high precision
turbulent flow: moves chaotic and irregular flow is highly disordered and irregular fluctations. A high velocity, Re is found and inertia dominates and is unpredicted (higher ISO)
Light is sometimes blocked two zones
low transmission: below 500 nm to ensure high contrast between exposed and non exposed photoresist parts
high transmission: above 550 nm, allows energy-efficient clean room illumination at reasonable visibility
why vacuum need?
due to avoding entrapment of air in molded area/materials. Preventing contamination and enable collusion-free propagation of deposition material towards substrates that need to be coated. Preventing oxidative degredation, and absorption of high radiation.
microfabrication in plasma, what is plasma?
Plasma is a state of matter whereby it is made out of ions and free electrons. They are electrically conductie and made by heating neutral gas or subjecting it to strong electromagnetic fields (plasma etching or depositioning)
plasma etching
process whereby material is removed fro surface typically thin film or substrate by exposing to plasma (used for patterning or etching)
plasma based depositioning
used to deposit thin films or materials onto a substrate, the plasma facillitates a chemreaction between the fases on the surface
different types of microfabrication
etching, photolithography, sputtering, chemical vapor depositioning, atomical depositioning, nanoimprint lithography and electroplating
standard photo-optical/ UV lithography (UVL)
Starting with a wafer that we want to pattern, which gets coated with a photoresist and patterned glass which get lighted. That causes some material to dissolve and some not.
negative photoresist
positive photoresist
—> often nice and flat, and uses one single crystal and how the lattice is orientated is indicated by the miler indices
negative photoresist
solubility in the developer decreases with the exposure
example: SU-8 epoxy which is quite suitable for thick engraved material
positive photoresist
Solubility in developer increses with exposure dose.
example: high-mw PMMA
spin-coating (resist layers)
The waver rotates and spin coating layer is deposited on the rotating waver.
—> higher speed means a thinner film (10 nm-100 microm)
other coatings: resist casting, spray coating and dry film lamination
the photomask
The part that lets through the light. This is most of the time glass, but it depends on the nm. Cronium absorbs a lot of light and therefore has a high optical density.
line glass used for short wave lengths
edge lengths most of the time 4 inch
note: most of the time cronium is made with laser/e-beam lithography.
different lithography techniques
Contact or UV proximity (UVL), X-ray lithography (XRL), electronbeam, digital light processing (DLP), thermal hot embossing and nanoprint lithography (NIL), laser direct writing (LDW), two photon polymerization (2pp)
2 pp laser lithography
layer by layer fashion. An ultrashort pulse laser beam is scanned through a photosenstivie resin. Due to high intensity in the focal point, 2 photons are absorbed and polymerization/ cross-linking happens.
digital light processing (DLP)
Based upon mirrors and how these are positioned to create an ‘on’ or ‘off’ idea. The Light cross-links the materials also in a layer by layer fashion.
nanoimprint lithography (NIL)
Thermal based: A thermal plastic resist is placed, that is heated end pressed at a temp above the Tg. Those are than cooled and seperated.
UV-based: A photopolymer resist is placed and UV-light combined with pressing happens. Than they are seperated
two working principles
substractive: isotrpic wet ething, anisotropic Si wet etching, and dry/plasma etching. A high aspect ratio is created with Deep reactive ion etching (DRIE)
additive: Build on the top of the wafer (electroplating, falvanoforming of metals on the wafer with electrically conductive layer, evaporation, sputtering or lift-off.
DRIE
is a very precise etching method mostly used for deep or narrow structures (micro-electro-mechanical systems)
steps:
plasma generation
ion bombardement (removing or etching the material)
anisotropic etching (etching directional matter)
stop layer deposited for etching
differences between etching, lift off, electroplating and stencil masking
etching removes material
lift off removes unwanted deposited material
electroplating deposits material by electrical reduction
stencil masking deposits material controlled with a mask
physical vapor depositioning (PVD)
the process of physically adding thin filmlayer. Particles land on a substrate.
There are different types: evaporation, laser, sputering, chemical vapor depositioning
e-beam evaporation
Happens in vacuum whereby source material is evaporized by the e-beam and hitted by electrons. Once it is vaporixed it forms a cloud and is guided with a magnetic field. Most of the time the cooling of the wafer is crucible.
shutter prevents contamination
anode+cathode help guide and accelerate
sputtering
a negative cathode with a target material gets striked by plasma and atoms are ejected.
bluk micrmachining vs surface micromachining
bulk: Involves etching deep into silicon wafer to creatae structures and is typically done on a whole wafer and etches through it.
surface: Structures are build up by growing or depositioning layers on the surface instead of etching. Thin films are often later etched. The sacrificial layer, isolation layer, structural layer and micromechanical layer.
laser micromachining
Is used for cutting, engraving or modifying materials (frilling/ milling and has F-theta lense)
steps:
focus of the laser beam
beam expansion and the focus
laser movement
material interaction
post-processing
(macroscopic) thermoplastic injection molding
A moving screw plays an actie part in this process. The screw is moved forwards and the liquid therefore can be injected. The mold itself can be opened and the material can be taken out of it.
small parts weights and shot weights are what is injected in the parts
micomold inserts are attached to an injection molding tool
evacuation of the molding space
A good homogenity of the molding material is need just like a precise dosing and metering and injection.
The mold cavity is heated
A low viscosity of molding material and a high injection pressure is needed
play free guidance tool opening
Hot embossing
it is a bit like NIL, also starting with a plate, mold and subset plate. Those are heated and than pressed together. They stick to the starter plate.
used for thermoplastic plats, films and sheets
Important is to leave space between the plate-type micromold and the substrate
mold space is getting evacuated
polymer is heated in the mold and cooled down in the same variothermal process
adhesion to the substrate is important
sometimes removal of resudal layers or dicing is needed
micro pressure (thermos)forming
Polymer is softened but not liquified for this process, such as in micro blow molding and not such as in micro injection. The film is than pressured and formed. This is done with differential pressure. Hot embossing sometimes goes with a slightly flowing materials, micropressure however the temp is just Tg< depending on the crystallisation.
(macroscopic)blow molding
Looks a lot like glass molding, the parison that is hollow tubed is extruded in the hollow mold that surrounds it due to the steam of the air. The material is pushed in the mold and once it solidifies the mold opens again.
LIGA (lithography, galvanik, und abformung)
made out up of 3 methods:
lithography: the proces where a mask is placed to define a pattern mostly due to x-ray photolithography and due to resist eventually the structure is chemically altered.
electroplating: used to build a micrstructure, often after lithography and to add metal to the structure. Hereby an electric current runs through a solution and metal ions are deposited on the substrate (creating 3D structures)
Making a replica of the made structure for mass production.
adv: high precision, scalability and material versatility.
metrological methods
styllus profilometry for surface and height with a needle that scans parts and is measured 13
atomic force microscopy (AFM) for surface topography works the same as a stylus 13
confocal laser scanning microscopy (CLSM), measures the vertical side walls. IS very precise and looks at the lateral direction. 23
White light interferometry (WLI) mostly used for surface characterization and is a electron modality microscope 2
scanning elecron microscope 23
tactile-contact- mechanical based
not contact based/ optical
scanning based
microfluidics+ adv
the science of systems that process or manipulate small amounts of fluids
adv:
less weight
less space requirements
less material consumption
less energy consumption
smaller sample and waste volumes
faster analysis/ synthesis
increases spatial control
reduced associated costs
Reynolds number
tells us something about the fluidic
Re= inertial forces/ viscous forces
you can hereby identicate laminar (minimal mixing due to layer by layer moving)or turbulent (easy mixing) flow
—> for mixing ofcourse micromixers can also be added. The inlet and outlet flows are the places wehre flow occurs.
Hagen-Poiseuille equation
Is for calculating the flow rate (Q)
Calculation is dependent on whether it is a rectangle or a circular system.
Though only to be used for small systems, because it does not take into account the shear stress. It shows for an incompressable fluid throug a pipe or a channel. In bigger systems those are seen and thus this formula cannot be used.
parallel channels
P= P2=P1
Q=Q1+Q2
R= (R1*R2)/(R1+R2)
series channels
Q1=Q2=Q
P=P1+P2
R=R1+2
inducing flow, different methods
mechanical displacement pumps (syringe or peristaltic)
pressure controllers
micropumps
capillary forces
gravity
centrigugal forces
electroosmotic forces
maintaining a stable flow rate
pressure to fluid in the microchannels
This pressure causes the fluid to be maintained. Creating a feedback loop.
valves (membranes or ball valves) are influenced by external stimuli like pressure, magentism, electricity or temperature.
measuring flow on microscale
a thermometer structure whebery time and distance is measured and thereby the flow can be calculated
flow sensor/ anemometer
Two measure points are taken
measuring pressure
can be done with a strain-gauge based micro pressure measurer. It measures the strain/ deformation.
mixing of microfluidics
passive: Happens due to the geometries of the system and no external powers. (laminations, injection)
active: Involves external forces er energy, pumps. (magnetohydrodynamic, acoustic, waves, thermal and high energy)
Staggered herrinbone mixer (SHM)
A specialised microfluidic mixer that is used in calcification risk. It makes complex fluid flow patterns to efficiently mix fluid in very small channels. Creating more interafce and making it more efficient.
gradient generators
1D chambers: used to create gradient profiles of a substance in a microfluidic devie, studying diffusion and concentration.
2D diffusion chambers: create an orthogonal gradients, channels overlap most of the time and they create these gradients in every direction. Every gradient is created in the perepndicular direction, showing more complex situations.
T-junction: Two different fluids flow into the junction from seperate channels. One fluid enter the horizontally side and the other the vertical siede. Two fluids thereby mix and create a gradient.
dilution network, ‘christmas tree’: A more complex dilution network. Which involves branching of the networks and flow thorugh smaller and smaller channels. Which is more suitable for complex systems.
microTAS
has everything for prepping, chem and biochem analysis and is integrated on a chip. (reaction and detection)
Lab on a chip LOC
is an extentsion of microTAS, with also data analysis, detection and manipulation.
PDMS
often used for microfabrication
adv:
easy and cheap
high flexibility
high gas permeability
high transparency+low autofluorescence
disadv:
slow fabrication
uptake+release small hydrophobic mol
flexbility not suitable for high pressure applications
permanent recovery after surface modifications
different types of microfluidic platforms
minitaturized total chemical analysis system
lab on a chip
lab on a tube
droplet-based microfluidics
paper-based—> suitable low income
digital
organ on a chip
mimics the key aspects of the human physiology (structure and function of human organs)
Instead of 2D structures they control the input and output of toxins.—> so it is more nature relevant
key aspects: being able to do experiments with cells from humans outside of the body, they contain microchannels, control microenvironments and allow real-time observations and can be powerful for physiology and disease models.
—> fill the gap between complex animal models and 2D models which causes it’s relevance
advantages of an organ on a chip model
physiological relevance
controlled microenvironment (compartilization)
multi-organ integration (for system studies)
reduced reliance on animal testing (faster, more ethical and the costs)
predictivve power drug testing
customization and personalized medicine
high-throghput and scalable (automation, AI, multiple screening)
designing a organ on a chip steps
conceptualization + design
materials selection (dependent on functionality)
selection of biological elements
supporting life inside the organ on a chip
read outs
conceptualization+ design
Do you want to recreate one organ (or tissue) or multi-organs (several organs/ body on a chip—> focus on interaction between)
Simplifying where this can be done.
Is it a solid organ or a barrier? Solid organs are; bone, tumour, liver, pancreas, cartilage mostly 3D masses or embedded in the ECM. Barrier organs are; endothelial and epithelial cells (skin/gut), they regulate active transport of molecules and a membrane can seperate environments.
materials selection (dependent on functionality)
For the chose idea a microfabrication strategy should be determined just as the read-outs options and biocompatibility. PDMS is often used in these systems due to its transparency, elasticity( could be used as stretchable membrane or for mechanical tests), gas-permeability and biocompatibility.
But it can also absorb small molecules such as growth factors.
—> compromise between function, acces and fabrication facitilities.
After fabrication sterilization is often required
sterilization methods
autoclaving (pressurised steam)
ethanol
UV
surface treatments (also used for better biocompatibility or cell adhesion—>protein coatings or ecm
→ depends on the used material, for organoids or 3D spheroids we do not want attachment of cells and therefore we use pluronic acid often
selection of biological elements
two approaches
top-down: Using primary tissue (organ slices for example)or engineered tissue in the ooc. Those are very important for personalized medicine and specific cases. The culturing of the cells and isolation of those is done, outside of the chip.
bottom-up: Isolated cells such as primary, immortalized or stem cells are directly cultured on a chip. The microenvironment is crated for the specific tissue.
options for cells in bottom-up
primary cells: retain full function which is seen in vivo but are difficult to isolate, batch-to-batch variables a lot. (dedifferentiation is sometimes needed)
immortalized cells: easy to grow and robust/reproducible. However they are modified to promote themself forever.
IPCS: derived with the minimal invasive procedures—> often very good option
functional time window
period that is required to develop and maintain physiological conditions for cells.
supporting life inside organ on a chip
selection of cell culture medium depending on how many types of cells and may require optimal medium to maintain also the phenotype
perfusion/ delivery of the medium (via microchannel)
—>could be by convective flow, driven by pumps or gravity
one-pass perfusion flow: syringe pumps and stable supply of fresh nutrients and downstream inter-tisue. Most of time with reservoir spent medium.
recirculary flow:peristaltic pump and recirculting signalling molecules with accumulation of waste products
—> important to focus on controlling microenvironment
Damköhler number
tells why change is seen, due to velocity or by things in the chips that are biologically
peclet number
tells whether transport dominated by advection or diffusion
ALI Air liquid interface culture
used for several purpouses:
cell differentiation+ maturation
encouraging cilia formation, mucus production
it is a way of supporting the life inside the device, whereby cells are in the middle and one side with air and the other with medium.
read outs
in situ/real-time: optical imaging, barrier function assays, integrated sensors, molecular and functional read outs
end popint/ after experiment with harvesting cells fixation or media collection: gene expresion, cytokine/protein analysis, structural and morphological analysis, metabolics and lipidomics and functional assays.
mechanical stimulation that cells normally experience
active: direct consequences of organs, tissues that are used to constant stretching (mimicked with vacuum chambers, flexible membranes or mechanical actuators)
passive: indirect experience. Such as endotheial cells in connective tissue cells. This can be done with fluid perfusion in microchannels.
stress/strain—> mechanotransduction—>proliferation,migration,phenotype and differentiation
limitation organ on a chip
variability (batch to batch)
donor to donor variability in genetics for example
line to line variability (patient heterogenity)
standardization—>not easy and done yet
data+ validation gathering
different methods for synthetic porous cell culture membranes
ion tracking, phase speration, solvent casting/particulate leaching, electrospinning of polymers, melt electrowriting, PDMS molding over micropillar (pores), photolithography and etching (depending on membranes)
ion track etching
A technique to creat well-defined narrow pores or channels. The combination of high energy-ion radiation with chemical etching. Membran most of the time s-10 microm thick.
the ions make the holes and the etching deepens the holes.
→ mostly produce cylindrical and perpendicular to the membrane structures which is good for visualization.
phase seperation PSmicroM
can happen 2 ways
NIPS with a polymer solution and solvent
TIPS with temperature
This creates porous or patterned structures
PDMS molding over micropillars
basically pressure while on micropillars will create a porous structure
high costs
membrane could be stretchable (usable for biomimetic cultures:collagen membrane (type 1),collagen IC-laminin basement like membranes, surface-immobalized lipid by layers)
micropatterning of the substrates, different types of patterns
patterns organize and pattern the cels but also influence the cells faith.
subcellular (near cell scale or size of multiple cells)
discrete (high-low, adhesive-non-adhesive, soft-stiff) or smoothened
gradients either discrete or continious—> on feature size and density
synthetic, bioinspired/mimter or nature-derived
how to do topographical screening?
Topochip an be used, which is topographical library for screening cell-surface interactions.
galapagos chip: cell-adhesive library for scree cell-surface interactions
pocket lithography—> choosing a small piece to do lithography on
chemical ways of patterning
photopatterning
micro contact printing
dip pen nanolithography (DPN)
DPN dip pen nanolithography
A pen in the form of an AFM tip that dips into a biomolecule ink and depostits patterns of biomolecules on a substrate in the form of a self-assembled monolayers (SAMs) An increased stiffness causes a higher rigidy.
different curvature engineering processes
mechanical micromachining, lithography, isotropic wet edging, lithography+thermal reflow of photoresist structures, laser micromacining/ ablation. Microtunable mold derived techniques, microthermoforming of thin films, stereolithography and 2 pp laser lithography.
soft lithography
using elastomer stamps, conformable photomasks and molds (soft and moldable ones)
different types of molding +description
replica molding (REM): a mold of PDMS is given and a prepolymer is placed on that cured and peeled of.
microTM, a prepolymer is placed on support. That is cured and the mold is removed and placed on the support. Residual film is left.
MIMIC, a PDMS mold is placed on support and drops of a prepolymer is placed at one end Channels are filed by capillary action and those are cured and the mold is removed.
SAMIM, starts with wetting the liquid (solvent) and PDMS mold. That is placed on a support (film on top of support). The solvent gets evaporated and the mold gets removed, leaving the support, residual layer and softened polymer that is changed due to the mold.
microcontact printing (microCP) is as well inking as stamping. A master is created with lithography and used as a stamp which could be inked. Those cacn habe cehm reaction from transfer of the stamp on the glass. These create a highly spatial controlled space/arrangement of cells. Sometimes pre-conditioning is needed.
A cell culture
growing cells in a controlled environment, outside of their native environment (culture dish), those are controlled in every sense.
Culture environment needs:
nutrients
gases and gas exchange
physiological environment
sterile environments
adhesion for adherent cells
2D cultures
Culturing cells on flat substrates such as tissue culture plastics without or with ecm coatings → monolayers
adv of 2D culture
easy and cost-effective
standardization and established protocols
comparitive studies
easy access to cells for analysis or manipulation
disadv of 2D culture
cell-cell attachments only in corners
adhesions to matrix only on one side
forced apical-bassal polarity due to anisotropic contact
continious layer of the ecm-→ this is not in reality
unconstrained spreading and migration
high stiffness substrate (sandwhich method)
absence of soluble gradient
3D culture
Culturing cells in 3D environment mimicking the 3D in vivo tissue environment
3D advantages
our body is not 2D so more physiological relevance
aggregation of cells, matrix, gel or scaffold
cell-cell contact diff layers
2D cell- matrix interactions (adhesion)
no forced polarity
proper mech cues
soluble gradient→ takes time for molecules and signal to travel
tunable stiffness
miniaturization possibility
compatible to downstream analysis
disadv 3D cultures
high costs but can be made cost-effective
time consuming
more complex to analyse due to more layers
standardization still getting worked upon
3D cultures types/methods
scaffold free:
self assembly into spheroids:
liquid overlay
rotary cultures
spinner flask
hanging drop culture
culture in microwells
embryoid bodies
organoids
matrigel dome culture
microwell clture
organ on a chip
scaffold based:
cells seed onto scaffld
cell laden hydrogels/ bioprinted structures
cells seed onto scaffold
Scaffold provides structural support and mimics the exm, which allows cell attachment, proliferation and tissue formation. Allows nutrients to diffuse.
creates porous, biocompatible, tuned mechanical properties and designed architecture (meso, micro and nano)
cell laden hydrogels/ bioprinted constructs
Are 3D in vitro models weherby living cells are encapsulated or embedded within hydrogel matrix.
Hydrogels are 3D networks of hydrphilic polymer that are formed by crosslinking of the polymer (retain lot of water), they have molecular pores.
cells seeded on microparticles
4 main ideas for why using this
A) cell expansion, looking at giving cues or temporary support
B) direcct filling for creating structural support and anchoring points to the injected cells.
C) 3D tissue/ disease modelling; looking at self assembly of cells with different cues
D) bioinks, need control of rheological properties and mechanical stability
self assembly into spheroids
cells are in a non-adherent environment and come into contact with each-other. They adhere via cahersin forming clusters. The cytoskeletal forces pull the cells thightly together.
layered zones are created→diffusion gradient
outer to inner:proliferating, quiescent, necrotic
Necrotic should be prevented, by making spheroid size withing the diffusion limit or adding microparticles to help create porous environment (making structure less dense). Or vascularization of the spheroid (making a bath of endothelial cells trying to get vascularization)
liquid overlay
Cells are seeded into regular flat-bottom or U-bottom wells which have non-adhesive surfaces. they can’t attach to the surface so they aggregate due to gravity and cell-cell interactions.
adv: simple and inexpensive and works in standard lab equipment.
disadv: less control of the spheroid size/uniformity, cells might form irregular aggregates if density is not optimal and limited scalability for high- throughput needs.
rotary cultures
A microgravity was created with draggging forces and is quite a neat method. A low shear stress was seen and cells were not damaged. It has a slow rotating horizontal cylindrical vessel, filled with medium+cells. The cells constant are in a free fall state where the cells are allowed to float and interact naturally.
adv: low shear stress and fgood uniform spheroid formatio at scale.
spinner flask
A stir bar or impeller is used to agitate the culture medium. Agitation keeps the cells in suspension and prevents them from settlng on the bottom of the flask. The cell-cell interaction is imp and the stirring speed should therefore be optimized.
adv: simple set-up, scaling up, allows diffusion by mixing
hanging drop culture
placing small droplets of cell suspension on the inverted surface. The gravity pulls the cells to the bottom of the droplets where those aggregate and form spheroids. The liquid is often in a well to prevent evaporation of the droplet.
adv: cost-effective, simple, no need for specialized equipment, high reproducibility and control over spheroid size.
disadv: limited scalability, manual handling, build up nutrients/waste in drop and influence on long-term.
culture in microwells
Using microfabricated microwells with non-adherent materials. Cells are trapped and lead them to self-aggregation and form a uniform spheroid.
Controlled→ high univormity
adv: High control spheroid size/shape, scalable and high throughput, allows formation of hundreds to thousand of spehoirds in parallel. the are reproducible and downstream analysis is possible.
disadv: requires specialized plates, fabrication techniques, slightly more complex than liquid overlay is costlier than basic liquid overlay.
embryoid bodies
A 3D cluster of pluripotent stem cells like embryonic stem cells or induced pluripotent stem cells. Thoseorganize and differentiate into varioius cell types when cultured. They are used to study early development processes, observer differntiation into 3 germlayers or test toxicity/ kick-off directed differentiation processes.
→ aggregate just like as in embryogenesis.
organoids
3D self organizing structures derived from stem cells (pluripotent or adult) they mimic the architecture and function of real organs in vitro.
→ miniature/simplified versions of organs.
stem cell derived
3D structure
cellular diversity
tissue/cell organization
functional properties—> functional tissue pieces
top down TE
Cells are seeded onto a pre-formed scaffold, attach, grow, produce matrix and form a tissue
adv:
benefit from the scaffold
various fabrication techniques ( tuned chem compo, porosity and mech prop)
suitable large tissue constructs
disadv:
uniform cell distribution is a challenge
limited spatial control
lack cell guided tissue formation
vascularization= requirement
high cell conc difficult→no control of the cells
scaffold guided tissue form
bottom-up TE
building tissues by creating small functional tissue building blocks which assemble modularly into larger more complex structures.
→ can be made from cells, aggregation cells, microtissues with or withou biomaterial/molecules. Mimics the natural formation.
adv:
precise control of environment+better mimicry of native tissue
cell guided tissue formation and remodelling
control spatial positioning
enabling vascularization due to including vascular building blocks
allow large scale prodution microtissues to larger tissues
→no one actually proved these advantages