MINIATURE BIOREACTOR

design & build · mechanical / fluidics / controls · benchtop tissue-culture rig

Exploded CAD assembly of one bioreactor unit — base tube, three scaffold wells, presses, and caps

A benchtop bioreactor that does something most benchtop bioreactors can't: hold a 3D cell scaffold and physically stretch it. It was built to grow skeletal-muscle tissue — C2C12 myoblasts on silk scaffolds — under the cyclic mechanical loading that muscle actually needs to differentiate, while perfusing fresh media past every sample and swapping spent media on a schedule. Every part that touches cells unscrews: swap it, reprint it, or reconfigure the whole array for a different experiment.

What this is. This began as a university course project, and we show it as an engineering design-and-build piece, not a finished product. The biological validation — actually culturing cells in it — was outside the project's scope and was not completed. What was designed, built, and bench-tested is the instrument itself. That is what's documented here.

The whole system. Bioreactor frame with the actuation motor on top, the custom peristaltic pump (left), and the Arduino UNO + CNC-shield electronics that stay outside the incubator. — **The whole system.** Bioreactor frame with the actuation motor on top, the custom peristaltic pump (left), and the Arduino UNO + CNC-shield electronics that stay outside the incubator.

The brief

Before any CAD, the design was pinned to seven hard requirements. Six are mechanical and material; the seventh is software and user experience:

Modular — every component removable and swappable; nothing single-purpose.
Perfusion — media reaches every scaffold with no stagnant dead zones.
Media exchange — spent-for-fresh swaps, continuous or cyclic, unattended.
Mechanical stimulation — repeatable linear actuation on any scaffold in the array, through a connection that isn't permanent.
Separable — the reactor goes into the incubator; the electronics stay outside it.
Sterilizable — every material survives an autoclave or a chemical wipe-down.
Programmable — retunable by someone who doesn't write code.

Modular by design

The system is built up from one atomic part. The Scaffold Well is a small threaded cylinder that holds a single scaffold on a centering base plate, with four lumen cutouts so media flows through it in any orientation. The threads are the quiet win here: rather than tapping every part by hand, the M6 threads were printed directly, with the clearance dialed in empirically to 0.3 mm per side after comparing CAD to real prints. They thread and unthread smoothly, with no backlash or loosening.

3D CAD render of the Scaffold Well showing threaded top and lumen cutouts — **Scaffold Well · 3D**

Wireframe CAD of the Scaffold Well showing the internal base plate and through-lumens — **Scaffold Well · wireframe**

The perfusion channel

Scaffold Wells thread into a Well Base Tube — a rectangular perfusion channel with three chambers, raised inlets and outlets, and mounting holes — and Base Tubes tile side by side into an array as large as the experiment needs. Media enters one chamber, passes through the well's lumens feeding the scaffold, and exits to the next chamber; every corner is smoothed to avoid turbulence and dead zones. Press-fit silicone tubing seats against a small indentation so it can't overshoot and block the bore. A leak test on the assembled channel showed no leakage.

Top view CAD of the Well Base Tube showing the central channel and three chambers — **Well Base Tube · top**

Isometric wireframe CAD of the Well Base Tube showing chambers, inlets and outlets — **Well Base Tube · isometric**

Applying the load

Cells need linear stretch, but almost every affordable actuator makes rotary motion. Three mechanisms convert one to the other — crankshaft, scotch-yoke, and lead screw. Crankshaft and scotch-yoke are simple, but their stroke is capped by a fixed offset; the lead screw has no such limit and gives finer control, at the cost of needing a stronger, precisely driven motor.

Precision and adjustable amplitude mattered most, so the design uses a single NEMA-17 stepper turning an 8 mm lead screw (2 mm pitch — one turn moves the platform 8 mm). One motor drives a shared actuation platform that presses every actuated sample at once, riding on two guide rods with linear bearings for stability. Combining all modules onto one platform was the economical call — the alternative was one precisely controlled motor per module.

Front view. Stepper and lead screw up top drive the actuation platform; the clear biocompatible-resin wells sit in the array below, plumbed with silicone tubing. — **Front view.** Stepper and lead screw up top drive the actuation platform; the clear biocompatible-resin wells sit in the array below, plumbed with silicone tubing.

Keeping it fed

Media exchange runs on a custom peristaltic pump built around another NEMA-17. A PETG cover routes two silicone tubes past ball-bearing rollers — two always clamped — so fresh media is pushed in at one end of the array and spent media leaves the other. Inlets use simple pipe fittings; outlets use 3-way valves for sampling or diverting flow.

An honest result. One NEMA-17 wasn't quite enough to drive both tubes at once — the doubled friction outran its torque. The documented fix is a higher-torque motor (a longer NEMA-17 drops straight into the same housing) or a DC motor; a single tube pumped fine.

Custom pump. One motor, two channels, ball-bearing rollers, and 3-way valves on the outlets — built in-house to save cost and space over two off-the-shelf pumps. — **Custom pump.** One motor, two channels, ball-bearing rollers, and 3-way valves on the outlets — built in-house to save cost and space over two off-the-shelf pumps.

Making the scaffolds

The scaffolds themselves were fabricated from silk: cocoons boiled and degummed, the fibroin dissolved and dialyzed to a ~6.9% solution, cast into a flexible 3D-printed mold, frozen, freeze-dried, and autoclaved. The result is a batch of small porous cylinders (7 mm × 8 mm) that seat into the Scaffold Wells. A practical note logged for next time: wet the scaffolds before demolding — dry ones tended to crack on the way out.

Silk scaffolds. Porous fibroin cylinders, cast and lyophilized in a printed mold, ready to seat into the wells. — **Silk scaffolds.** Porous fibroin cylinders, cast and lyophilized in a printed mold, ready to seat into the wells.

Running the experiment

Everything is controlled by an Arduino UNO with a CNC shield stacked on top — no external libraries, about 84 lines of C. Operating it needs no programming: a handful of named variables at the top of the file set the stroke amplitude, pump volume, and cycle count, and push-buttons start and stop a run. That was enough to lay out the intended study — a 2×2 factorial of media type (regular vs. differentiation) against loading (actuated vs. static), each with an empty control.

Planned study. Two media conditions × three sample roles (empty control, actuated, non-actuated) across the array. — **Planned study.** Two media conditions × three sample roles (empty control, actuated, non-actuated) across the array.

What shipped

A working, leak-tested, fully modular perfusion bioreactor: single-motor lead-screw actuation across a tiled array, a custom dual-channel peristaltic pump, all cell-contact parts printed in biocompatible resin (the rest in PETG on a sterilizable MakerBeam frame), and a controller a non-programmer can retune. The open questions were logged honestly too — a stronger motor for simultaneous dual-channel pumping, and the biological validation the course didn't run.

This is the kind of instrument we build for research labs: the thing your protocol needs that no catalog sells — designed, built, and documented thoroughly enough to hand to the next student.

The build, in detail

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