A high-performance calculator must continuously advance in two critical metrics: speed and accuracy. This is why silicon-based chips continue to push the boundaries of photolithography to achieve smaller transistor scales. Similarly, our biological computing system requires continuous improvement in these areas—which constitutes the main objective of our dry lab research. Our software tools enable the design of numerous high-performance algorithms. The next challenge is to accurately "implement" these algorithms on the petri dish—that is, to precisely control the positioning of AHL molecule droplets. To address this, we designed a hardware device that works in concert with the software, enabling precise spatial control via rods that are mutually perpendicular and parallel to the petri dish.
Hardware
Software-Driven Precision Positioning Device
Overview
Our inspiration stems from a children's toy—the Etch A Sketch. Its working principle involves a glass interface uniformly coated with aluminum powder, beneath which a sharp stylus, controlled by two knobs in a cross-configuration, scrapes away the powder to leave traces. This stylus is manipulated by two rotary knobs located at the bottom. We naturally envisioned replacing the glass screen with a petri dish and repurposing the drawing mechanism into a positioning device. This concept marks the very origin of our hardware design.
Our hardware offers a simple, low-cost, and mechanically feasible solution, highlighting how engineering principles can significantly enhance biological experimentation. We hope that our device will inspire researchers to integrate engineering and biology, paving the way for more precise and novel experimental methodologies.
Hardware List
Our device is built from readily available, cost-effective components. The complete hardware list includes:
| Component | Specification | Quantity | Cost (USD) |
|---|---|---|---|
| Timing pulley | 10 mm inner diameter, 20 teeth | 8 units | $7.00 |
| Timing pulley | 5 mm inner diameter, 15 teeth | 2 units | $1.40 |
| Timing pulley | 10 mm inner diameter, 30 teeth | 6 units | $5.80 |
| Timing belt | 3 mm pitch, 246 mm circumference | 1 unit | $1.40 |
| Timing belt | 3 mm pitch, 375 mm circumference | 4 units | $7.42 |
| Timing belt | 3 mm pitch, 315 mm circumference | 2 units | $3.34 |
| 42 Stepper motor | — | 2 units | $13.30 |
| Arduino UNO controller board | — | 1 unit | $2.50 |
| Rotating shaft | 10 mm inner diameter, 140 mm length | 6 units | $2.78 |
| Dupont wires | — | 10 units | $1.40 |
| 1:1 direction reverse | — | 2 units | $35.60 |
Gear System
The positioning rods are mounted on timing belts, arranged perpendicularly to one another. Their intersection defines the target position. Each rod is secured by two timing pulleys and a timing belt. The base layer of the structure requires eight timing pulleys and four timing belts (see Figure 2).The system is assembled into two sets, each securing one positioning rod. The two gear systems are shown in their respective diagrams, with the overall assembly depicted separately.
To prevent rotation of the rod, the two pulley sets controlling the same rod must move in opposite directions. This is achieved by incorporating a reversal mechanism in one of the two pulley sets (see Figure 3).
An additional fixation component is added to prevent rotation of the reversal mechanism itself. The two transmission sets for each rod are linked to ensure synchronous motion.
Each positioning rod is ultimately driven by a stepper motor connected to one of its pulley sets. This completes the entire gear assembly.
Base Design
For ease of assembly, the device is divided into two layers: the top layer holds the petri dish, and the bottom layer houses the gear shafts and motors. The two layers are detachable, simplifying assembly and maintenance.
The lower layer features several key mounting points:
- Eight orange holes: for mounting timing pulley shafts and reversal mechanisms
- Two blue holes: for installing the reversal mechanism fixtures
- Four corner holes: for attaching to the top layer
- Square recess on the bottom plate: for mounting stepper motors
All components—timing pulley shafts, reversal modules, and motors—are assembled onto the lower base, creating a compact and functional positioning system.
Motor System
Our motor system consists of 42 stepper motors driven by MSPM0G3507-based drivers, all controlled through an Arduino UNO R3 board.
For serial communication on macOS, we used the CH341SER_MAC driver provided by Nanjing Qinheng Microelectronics Co., Ltd. (available at https://www.wch.cn/downloads/category/67.html).
- Six clearly labeled control interfaces for the two motors
- Activated enable interface
- Code implementation for direction and pulse control
- Integration of position values from the software's "move" function into the motor control routine
- Loop implementation in the setup function where the number of steps corresponds directly to the motion distance
The firmware is uploaded to the controller, enabling precise and programmable positioning control.
Assembly and Demonstration Video
Watch our comprehensive assembly guide and device demonstration:
Hardware and Software Integration
We have incorporated a distance display function into the software to link the software and hardware, forming a complete system for biological computer design. This section will demonstrate the usage of the distance display function and important considerations.
Steps for Use:
- 1. Identify the positions requiring location. This display shows the relative position between two points. During initial use, you set the position of the first point.
- 2. Right-click on the point to be positioned and click the "Show Distance" button to display the distance (unit: millimeters).
- 3. After obtaining the distance data, convert it into motor steps. Drive the distance motor via the Arduino control board.
Important Considerations:
- 1. The distance-to-step conversion depends on the tooth count of the timing pulley used in the actual setup. We provide the following formula:\[ C_{step}=k \cdot d\] \[ k=\frac{T_{lower}}{2\pi \cdot \theta_{step}\cdot T_{upper}\cdot T_{moter}\cdot r_{upper}} \]
Among which:
- $C_{step}$ represents the Step Count.
- $d$ represents the Distance.
- $T$ represents the Tooth Count, which includes: Tooth count of the motor gear; Tooth count of the upper gear; Tooth count of the lower gear.
- $r$ represents the diameter of Gear.
- $\theta_{step}$ represents the Step Angle.
- 2. Confirm the rotation direction. Pay attention to the respective directions corresponding to clockwise and counter-clockwise rotation of the stepper motor.
- 3. The single rotational step length should not exceed 32768.
- 4. The dark purple rectangle on the interface represents the 160mm × 90mm dimension and can be used as a distance reference.
Outlook
The invention of cryo-electron microscopy has revolutionized biological observation at the molecular level, while flow cytometry has fundamentally transformed how we manipulate and analyze cells. These examples vividly demonstrate the immense power of integrating engineering with biology. We hope our work will inspire more researchers to build upon our foundation.
Below are the potential development directions for our hardware:
Scalability
Our hardware features a modular architecture comprising gear, base, and motor systems. The gear system is designed to be replicable and can be seamlessly scaled and transplanted to larger culture platforms, enabling computation over broader areas.
Functional Expansion
By equipping the positioner with additional capabilities—such as integrating automated control and automated liquid handling—we can significantly enhance its functionality. A higher degree of automation is crucial for achieving superior sterile conditions, which is paramount for contamination-sensitive biological experiments.