Microfluidic chips, molds, and flow cells

Channel networks, soft-lithography molds, printed chips, gaskets, and manifolds.

First: decide what you are actually modelling

This is the error that wastes the most time in microfluidic CAD. Three different objects get called "the chip":

A model that is correct as a chip is exactly wrong as a mold. Put the polarity in the module docstring and in a named parameter, and verify it numerically, not by eye: inverted polarity is invisible in the bounding box, the volume, and the validity check — and at typical channel scale (a 0.3 mm ridge on a 40+ mm part) it is invisible in an outline render too, because raised and recessed features draw the same edges. Declare it as geometry checks instead (references/build123d-patterns.md): a material region where the ridge must stand above the casting surface, and a clear region over the rest of that layer — a groove fails the first, an inverted full-area layer fails the second. For a one-off question, check.py probe <step> --box ... --expect material answers it without editing the model. State the measured relief height in the report. Use the snapshot for visible layout; verify hidden channel connectivity with sections and a connected void/gauge model, then a physical flow/leak test.

polarity = "mold"   # "mold" = raised ridges; "chip" = recessed grooves

If casting PDMS, the mold also needs a surrounding wall or a casting frame to contain the uncured polymer, and enough flat land around the features for the cast part to release.

Channel cross-section and aspect ratio

Channels are usually rectangular because that is what planar fabrication produces. Two failure modes bound the aspect ratio, and both depend on mechanics as well as geometry:

• Roof sag / collapse — a channel much wider than it is tall has an unsupported ceiling. In PDMS the roof bows down and can stick to the floor. Commonly cited guidance keeps width : height below roughly 10 : 1; wide channels need support pillars.
• Sidewall collapse — a mold ridge much taller than it is wide falls over or fails to release. Keep height : width below roughly 10 : 1 on the mold.

Treat both as rules of thumb, not guarantees: the real limits depend on PDMS mixing ratio, cure schedule, and applied pressure. For anything load-bearing or high-pressure, prototype.

Also keep channel-to-channel spacing at least the channel height, so the wall between two channels does not deflect or leak, and leave a flat bonding land — typically 1 mm or more of uninterrupted flat surface around the network perimeter — for plasma or adhesive bonding.

Minimum features by process

Achievable feature size drives the entire design, and the range across processes is three orders of magnitude. Confirm against your specific tool before committing.

Design enclosed printed channels for drainage. Every lumen needs a path for uncured resin to escape, and orientation on the build plate determines whether it drains. If the user is printing, say which way up.

Ports and tubing

The port is where most chips leak. Options, roughly in order of how common they are in a research lab:

• Direct tubing insertion — a bore slightly under the tubing OD so the tubing seals by interference. For 1/16 inch OD tubing (1.5875 mm), a bore around 1.5 mm in PDMS is typical. This works in elastomer and fails in rigid printed parts, which crack instead of gripping.
• Luer taper — the standard syringe interface, a 6% taper (ISO 80369-7:2021 supersedes the legacy ISO 594 series for medical use). Use the selected connector's pressure rating. If you model a Luer taper, get the profile from the standard, not from memory.
• Threaded fittings — flat-bottom 1/4-28 UNF is the common lab standard for low-pressure fluidics; 10-32 coned is used at higher pressures. Obtain the fitting's port drawing: thread, seat angle/depth and ferrule are a matched system. A generic heat-set screw insert is not a fluid seal.
• Barbs — reliable with soft tubing and a clamp, bulky.

Flat-bottom fittings need the specified flat seat; coned fittings and Luer connectors seal on different geometries. Model the actual sealing surface and its finish, not just a thread or a flat external face. Pressure-test the assembly.

Dead volume

Dead volume dominates the response time of any perfusion or gradient device, and it is trivially computable, so compute it rather than estimating:

V = pi * r^2 * L                # round tubing / bore
V = w * h * L                   # rectangular channel

With lengths in mm, these formulas give mm³ = µL. Use diameter/2 for r. Report the volume of every connecting bore alongside the channel network volume. A 20 mm long 1 mm diameter bore holds ~15.7 µL, which is often larger than the entire channel network it feeds.

Flow regime sanity check

Calculate Reynolds number using consistent SI units (kg/m³, m/s, m and Pa·s):

Re = rho * v * D_h / mu
D_h = 2 * w * h / (w + h)       # hydraulic diameter, rectangular channel

For water in a 100 µm channel at 1 mm/s, Re is of order 0.1 — laminar. Transverse transport in a straight channel is mainly diffusive; chaotic advection can enhance laminar mixing. If the design depends on mixing, it needs a mixer geometry (serpentine, herringbone, or split-and-recombine); relying on turbulence will not work at these scales.

For a long, shallow rectangular channel (h << w), steady incompressible Newtonian flow with no-slip walls gives Δp ≈ 12 μ L Q / (w h³). At fixed volumetric flow Q, halving h raises pressure drop about eightfold; at fixed mean velocity the scaling is about fourfold. This approximation does not cover entrance losses, compliant PDMS walls or non-Newtonian fluids. Compare predicted pressure with the pump and weakest connection rating before finalising the cross-section.

Material and optical constraints

• PDMS absorbs small hydrophobic molecules and is gas-permeable. Both are sometimes features (oxygenation in organ-on-chip) and sometimes fatal to an assay (drug studies).
• SLA resins are frequently cytotoxic uncured and often still after a nominal cure. For cell work, require post-cure plus a documented biocompatibility check, or use a different process. See references/fabrication-limits.md.
• Autofluorescence matters for any fluorescence readout. Most printed resins autofluoresce strongly. Image through glass or a thin COC/COP film, not through printed material.
• Optical path: printed and milled surfaces scatter. Any imaging window should be a bonded coverslip or film, and the model must specify its thickness so the objective working distance works out.

Checks to run

python scripts/gen.py chip_model.py --outdir out/
python scripts/check.py facts out/chip.step
python scripts/snapshot.py out/chip.step --out out/chip.png

facts reports solid material volume, not void volume. For a simple blank, compare blank volume minus finished solid volume with the intended removed volume, including ports and reliefs. Equal volumes do not prove connectivity. Check each channel/port with clear gauges or sections and verify connectivity of a separately modelled void.

Then read the snapshot and confirm, explicitly:

1. Visible layout and polarity where resolvable; use measured gauges for small relief.
2. Every port lands on the channel it should, and passes fully through to the surface.
3. The bonding land is continuous around the network.
4. No channel has been closed off or consumed by a fillet.

Sources

• ISO 80369-7:2021, current catalogue record — <https://www.iso.org/standard/79173.html>. The full dimensional/functional standard was not licensed in this review; use a vendor drawing.
• IDEX fittings guide — <https://www.idex-hs.com/docs/default-source/brochures/fittings-101-guide_forweb3.pdf>.
• Rectangular Poiseuille-flow treatment — <https://arxiv.org/abs/physics/0412015>.
• Formlabs process-specific fluidic guidance — <https://formlabs.com/blog/microfluidics-millifluidics-lab-on-a-chip-manufacturing/>. Obtain the taper profile from the standard itself.
• Aspect-ratio and spacing guidance here is standard soft-lithography practice; the numerical limits are rules of thumb and depend on material and process. Prototype before committing.