Just like the digestive system!
The standard eVOLVER peristaltic pumps (since ~2020) sourced by Fynch Bio are selected specifically to eVOLVER use. Previous pumps used with eVOLVER during its early development tended to wear out quickly and have variable flow rates, primarily due to the mechanism for rotating the rollers against the tubing to drive pump flow. The motor shaft directly turned the rollers through friction, which led to slippage and abrasion over time. The current pumps do not have drirect contact between the motor shaft and rollers, instead driving roller rotation through a gear reduction system.
This gear system drives a roller casing with fixed roller axles contained in the pump head. In this way, the pump action does not rely on friction and thus much more accurate and durable than previous pumps.
Inside the pump head, the pump tubing can be removed and inspected. The tubing is 2x4mm Pharmed BPT, which has similar chemical compatibility as the silicone tubing for the rest of eVOLVER fluidics, and is rated to over 1000 hours of operating life. Learn more here: https://www.biopharm.saint-gobain.com/components/fluid-transfer/pharmed-bpt-tubing
Because the current pump style has been introduced so recently, very few of them have failed from wear and tear. Based on our experience with other pump styles, the most likely failure mode will be collapse or tear of the tubing inside the pump head, or shearing of the tubing on the barb outside the head. This can be solved by replacing the pump head (contact Fynch Bio) or replacing the tubing.
Pharmed BPT can be purchased from Saint-Gobain suppliers. However, the tubing should be 2mm ID and 4mm OD, and there is not enough tolerance to allow for similar non-metric sizes (like 1/16"x1/8"). 2x4mm Pharmed tubing is difficult to find in the US, and we are working on finding a reputable supplier for it. In the meantime, these alternatives from McMaster-Carr have been tested to seal and pump properly: https://www.mcmaster.com/5102K11/ and https://www.mcmaster.com/7027N11/
The induction motor inside the pump is very unlikely to fail through normal use. If there is a liquid spill on the pump array and some pumps are not spinning, the most likely cause is corroded contacts with the pump array PCB. While the pumps themselves will be fine, they should be removed and replaced to a new PCB, ordered from Fynch or PCBWay. This will require removing solder, which can be tricky.
The pump heads can be rotated 90 degrees in any direction, should your bench setup require changing the direction your pumps face.
The low-flow pumps available through Fynch use an additional gear reduction box to reduce the speed of pump action by a factor of 45. This is useful for addition of inducers, antibiotics, or other media feeds that require a small and precise bolus.
Plenty of other peristaltic pumps are suitable for eVOLVER, so long as they operate at 12V.
The flow rate of eVOLVER pumps (and any pump with an induction motor) is somewhat modifiable through PWM modulation. This effectively reduces the voltage going to the pump, which will slow its rotation, down to the point where the coils can't generate enough torque to consistently turn the shaft. This happens about halfway through the PWM range (around 2000), where you can get the pumps to run at about 1/3 speed. This is rarely necessary for experiments, so it has not been optimized, but is a potential feature for users to explore.
Also known as plumbing
For reference: Inner diameter = ID, Outer diameter = OD. Quotation marks (") indicate inches, single apostrophe (') indicates feet. Most eVOLVER hardware is in US customary units (i.e. not metric) due to wider availability of parts.
The standard eVOLVER package includes 1/16" ID (1/8" OD) soft silicone tubing for all fluid handling operations. For exact specifications, see the part sourcing google sheet, "Fluidics" tab.
Silicone is the tubing of choice for eVOLVER because of its flexibility, durability, cost, and resistance to beach and ethanol. It is also autoclavable, although 30 minutes of 10% bleach sterilization is sufficient to completely sterilize the lines.
Silicone tubing is highly permeable to gasses, including water vapor. If you leave media in the tubing for >1 week, it will likely dry out and cause an obstruction (see obstruction troubleshooting).
The standard eVOLVER package includes 1/16" barb to luer-lok connectors for all pump-to-vial connections. For exact specifications, see the part sourcing google sheet, "Fluidics" tab.
The barb side of the connector is rated for the ID of tubing it is mean to be used with, i.e. 1/16" barb for 1/16" ID tubing, 1/8" barb for 1/8" ID tubing, etc. Barbs are designed to get a tight seal around their widest diameter, with the max pressure and resistance to slippage depending on the softness of the tubing and style of barb (40 psi for standard eVOLVER connectors).
Luer connectors work by pressing a "male" plug into a "female" socket, both tapered at 6%. Because of the smooth surfaces and large contact area, this creates an effective seal without tools, held in place by friction. Syringes and medical equipment commonly make use of luer connections.
To hold luer connections in place more securely, luer-lok connectors use a screw-like "skirt" to prevent luer connectors from simply being pulled apart. eVOLVER tubing connections are luer-lok, allowing for easy but relatively secure connections between most components.
However, luer-lok connections have some common failure modes. Because the threads of the skirt are so coarse, it only takes a 1/4 turn to break the seal at the plug-socket interface, leading to a leak (if positive pressure) or air bubble source (if negative pressure). Loose luer connections easily become disconnected, leading to spills (the major source of electronics failure) and of course, failed experiments. One should always ensure luer connections are snug (hand tight), and tubing free from torsion that might unscrew the luer-lok.
Additionally, because the male connector comes in direct contact with fluid, it becomes your most likely contamination source. Be careful not to bump the tips of the male connectors against contaminated surfaces when setting up your experiment. Doing a final wash with 70% ethanol after bleach sterilizing can prevent some contamination from this route, depending on your media and organism.
For more information on luer connections (and credit for the above images), see here: https://www.apsf.org/article/managing-luer-connections/
Any soft tubing (durometer 40-70A) works well with the barbed connectors. Vinyl (PVC) or tygon tubing might be a suitable alternative for decreased permeability. Opaque tubing may make sense for light-sensitive media or antibiotic feeds that have extended time exposed to light in the tubing due to low flow rates, at the cost of not being able to observe media in your line. Remember that 1/16" ID tubing contains about 0.75 mL per foot.
Separating fluidic control from the motherboard
The fluidics box can be opened by removing the 8 phillips head screws on the sides. Inside the box is the fluidics board (with a SAMD21 and three PWM boards) with RS485 and 5V connections for the SAMD21, and a 12V power supply beneath the board. Should the need arise to update the arduino code on the SAMD21, you'll need to open the box to get to it.
The connections to the pumps are numbered according to their address, i.e. cable 1 connects to pumps 1-8, cable 2 connects to pumps 9-16, etc.
Not many things can go wrong inside the box, but we have dealt with a situation where the 5V power connection was faulty and led to malfunction. This part can be replaced by opening the box and replacing the faulty connector.
The existing pump pox can control up to 16 additional pumps (or any other 12V valve, actuator, etc) with no modifications. Typically this would mean using connections 5 and 6 on the back of the box, which correspond to indices 33-48.
Adding another pump array will of course require changes to custom_script.py, because pump indices 33-48 are not being sent commands during normal eVOLVER operation. The MESSAGE variable holds all information on how long to run each pump, and this is where you should implement your commands in custom_script. See the turbidostat section of the custom_script page for more information.
Two RS485 ports (the telephone jack-looking ports) are available on the back of the fluidics box so that multiple boxes can be linked together on the same RS485 "line". All SAMD21 microcontrollers are receiving the same serial data from the Raspberry Pi, and only responding to commands when the appropriate address for that SAMD21 is in the command, like "temp" or "stir". Additional fluidics boxes can have the same "pump" address with higher pump indices (i.e. pumps 49-96 for a second box), so long as you change the number of expected pump values on the conf.yml file. You will also need to modify the SAMD21 arduino code accordingly. You can also have a different address for the other fluidics box, by adding another parameter in the conf.yml and modifying the arduino code accordingly.
Making culture continuous
For eVOLVER to be more than a 16-well plate reader, there needs to be control of liquid flow through each vial. The most common hardware for this application is the peristaltic pump, used in continuous culture for almost a century. Novel aspects of eVOLVER include the automated, individual control of these pumps, and modularity for different types and numbers of pumps. This is enabled by an auxiliary fluidic board, separate from the motherboard, that controls up to 48 fluidic actuators. For typical eVOLVER use, this is coupled with 32 pumps (16 for influx, 16 for efflux), 64 lines of tubing (to and from each pump), and 128 barbed connectors (for both ends of each line of tubing). This section of the Wiki will go into detail of how each component works, and options for repair, troubleshooting, swapping, and modifying them in the eVOLVER fluidic hardware framework.
