Category Archives: Components

The heated lid

Hi rock stars,

Many thanks to the thoughtful, smart suggestions in Name that component!, from Kyle, David, AdamT, Kyle@otyp, and Ben. All together, we worked through the panini/linkage idea, browsed camera shops to find ball joints, and really set out to get the best design that’s easy to build. That said, it can be impossible to find off the shelf parts to bring a new design to reality. More specifically, I’ll say that my current source for searching (McMasterCarr) has lots of really *big* things, lots of door hinges or refrigerator hinges, but not so much in the *small* side of things. Is there a good source for electronics-sized components that you like? Digikey and Mouser stick to electronics components, what I’m wondering about is a digikey+mcmaster love child. Of course, this will be helped in the near future with the rise of 3D printing and Makerbots, where small batches of custom parts start to make sense. Maybe a Makerbot is in my future.

The best design turned out to be the most simple one, suggested by AdamT — 4 springs pushing down the aluminum plate, the whole assembly floats on 4 bolts. The lid gets locked down into a low position, and the springs/hinge float around as needed. I prototyped it up, showed Josh, and we like it. We’re going to be mounting a heater and really testing it out over the next few weeks.

2 opportunities for improvement are:

  • how to lock the lid in the “down” position (magnets would be great, a bolt with a thumb screw is more realistic).
  • Secondly, the nuts/bolts in the picture are metal and heat up a lot. I’m planning onfinding nylon screws (M3), though their operating temperature is 85C (the lid is heated at 100C to 110C, the melting point of nylon is over double that). Suggestions welcome :)

(Skinny shoulder screws/binding barrels would be nice so that the plate can slide easily up and down except I need 2 nuts on each bolt, one nut to hold the bolt in place at its base, the other nut to keep the aluminum plate/spring on. A bolt with threads at the beginning and end but not the middle would be good.)

Thank you to everyone!


Bottom view of the heated lid. 4 nuts show where the springs are

Took off the front side of the heated lid so you can see the assembly inside. Springs and bolts hold the aluminum plate in place

Re: Treat your machine/pcb/acrylic/laser shop professionally

Update: 9/25/2010 to

Good comment from mo – spread the love around. I want to point out that the relationship with your machine/PCB/acrylic/wood shop can be challenging! It’s important but not necessarily easy!

If you can’t meet in person it’s tougher to build repertoire over email or telephone, no matter how charismatic you are. And though I’m usually close to my email, people in shops are on tools and machines most of the time. A phone call is a lot quicker and more personal, but conversations on the phone often lead to miscommunications and frustration. What’s worked for me is talking on the phone, and then summarizing in a follow-up email immediately afterwards. Other points of friction I’ve found are in file formats (I was in Bangalore, India, bouncing between coffee shops and I just couldn’t get the right program in order) and computer use  (for instance a shop that insists on printed 2D drawings of a nice 3D CAD file you struggled to put together…), and one guy that always returned calls around a week later.

Experience says: lavishly praise shops you come across when everything goes smoothly.

Right now: I’m working with a shop called OharaRP (out of Dayton, Ohio) on a PCB board and they kick ass!


Name that component!

Welcome to an exciting round of “name that component”. Here’s your host, Tito!

Hi everybody,

We are working to design our heated lid so that it can adjust to small differences in the size or height of tubes. In PCR, we’re cycling the temperature of a small aluminum block between 50C and 100C. We place a plastic tube in each well of the aluminum block, which contains a liquid DNA sample. Now, if we simply have this setup, we will heat our samples to 100C and they will evaporate and condense in the lid of the tube. This is a problem, which is commonly solved by something called a “heated lid”. The 100 C lid needs to make contact with the caps of the PCR tubes, to prevent condensation of the sample. At this point, we have a flat aluminum plate with a heater mounted to it, and are able to reach 100 C. The issue is having the plate make flat contact with all 16 (4 x 4) tubes in the OpenPCR. I’m looking for some sort of a ball joint that we can mount the plate to so that it will rotate every so slightly (10 degrees would be enough).

Now, I know I’ve seen a part like this in existence, but we have little idea where to find it or what is it called?

I would describe it simple as 2 flat plates with a ball joint in between. The size of the plates should be smaller than 1.5″ square, with a few holes in each plate for mounting. I’ve drawn up a crude illustration to attempt at describing this, and have searched mcmastercarr (“ball socket”) got me the closest, but no cigar.

Here’s some “similar” products to what I have in mind…but looking in the <$10 price range and much smaller:
(car gps mount)

Hope you have ideas in mind!


Machining aluminum

Another week zooms by! I’ve been working on sourcing for the aluminum heating block. One thing that’s a bit elusive is finding shops to prototype the block out of 1100 aluminum. Most prototype shops stick to 6061, which is a strong material, but we want as high conductivity and low specific heat as we can (reasonably) get, and 1100 is the purest alloy of aluminum.

The material itself is cheap but because it’s a softer (I think) grade of aluminum, it takes more time to machine. CNC machine time adds up very quickly so Josh and I are both putting out requests for quotes to different shops. Chime in if you have experience with this :)

I hate glue (feat. Nodes)

New cases arrived this week, acrylic and wood!

Nodes rock!

That is, when you design them correctly. Working with birch wood, I added 1 simple node on each of the notches for the lid parts. The parts “snap” together, and glue doesn’t even seem necessary.

With 1/4″ acrylic, I used the exact same sized node as with the birch which didn’t work out so well. Acrylic is a lot less flexible than wood. I ended up just sanding off the nodes on the acrylic parts to get them to fit together correctly. (I’ll read up on what size nodes to use with acrylic, or comments are appreciated!)

This was my first time designing a case and immediately having it made with 2 different materials. The design was for birch, and I attempted to change the design for acrylic which is a good bit thicker. I made the holes for the notches wider which was a good first step. What I skipped was making the parts themselves a bit shorter to accommodate for the thicker material.

One other revision to make is 4 sets of holes/T slots don’t line up perfectly. I’m not sure why they got a bit off (Update: the tooth on the bottom edge was a few mm off, which pushed the holes off), but it’s definitely something to fix. I hacked the birch case to get everything to fit.

Down to business, the T-slot design is sturdy, and assembly is straightforward. With the T-slow and notched teeth, glue will no longer be necessary! I also found that rounded corners on laser cut wood make a big difference in durability. In my experience, sharp corners easily chip, wear down, and start to look less than best. Rounded corners are more durable and can take a bit more wear and tear.

Next up is the important step — when the flat aluminum parts arrive from Ponoko NZ we’ll test out the heated lid.

Both the acrylic and birch look great! Thanks Pololu and Ponoko :)

Inspired by:

Cutting flat aluminum parts

If you think I’m making a lot of posts over the past week, it’s true! I took 2 weeks off of my day job and have been able to get a lot done on OpenPCR. Back to my day job on Monday :\

We are prototyping 3 1/8″ flat aluminum parts for OpenPCR:

1. ~ 2″ square plate, with holes for 2 screws for the heated lid. Our prototype heated lid involves a peltier, aluminum plate, and thermal pad

2. ~ 4.25″ square plate for mounting the heat sink and aluminum heat block to one surface. This needs holes for the aluminum block and screw holes for mounting the aluminum block and heat sink.

3. 4 cm square square plate to serve as an “adapter” between smaller heat sinks and the peltier. This might not be necessary if we go with a larger heatsink, though the trade off would be the entire case is about 1″ bigger to accommodate the heatsink.

Designing the part and drawing squares in Illustrator? Easy!

Unlike software, when you want to test a design you get out your wallet. I’m addicted to “Just hit ‘Preview’ or ‘Compile’ and I’ll be done!”. I’m so thankful for the support that we’re receiving from everyone on Kickstarter!

I looked around locally and online  for a shop to make the test pieces. Local prototyping didn’t move as quickly as I had hoped, I still haven’t heard back from the guy I started talking to a week ago. Prototyping shops are pretty pricey, I found rates of about $100 per part. With flat pieces cut from a sheet, Ponoko was the best deal because I could fit a whole slew of parts on one sheet. In about 15 days I expect to receive the flat aluminum parts from Ponoko in New Zealand, hopefully right around the time I receive the new laser cut wooden case. (Ponoko says they’ll have aluminum cutting live in the USA in a month).

Got a lot of things moving over the past 2 weeks! Over and out :)

Laser cutting – Acrylic and Wood

This week I designed and sent off requests for new laser cut cases — one wood sheet from Ponoko, and an acrylic sheet from Pololu.

Material: One surprise for me — I made a slightly bigger case, and adding on 1″ to each dimension roughly doubles the material. For instance, take a 4″ square, that’s 16 square inches of material. A 5″ square is 25 inches of material. This can get out of hand pretty quickly!

Speed: On the recommendation of a friend, I browsed onto, which offers custom laser cutting services. Pololu doesn’t have plywood or bamboo in stock, but they do have 1/4″ acrylic and promise a 3 day turnaround time vs Ponoko’s 11-15 day turn time. Of course, I pay extra for the speed but for prototyping it’s well worth it. I placed my Pololu order on Thursday afternoon and it shipped Friday!

Prototyping: Designing laser cut cases sure can be a pain in the butt. I spent all day on July 4th simply designing a bigger OpenPCR case with bolted edges rather than teethed edges. My workflow goes from the overall design in Google Sketchup, adding features like teeth, bolt holes, nodes, and radii. Then importing that into Illustrator, adding additional teeth, and the submitting it to be cut.

This is fine if you’re putting together a one-off design, but for prototyping, changing, and updating designs I certainly could use some better tools. A good friend of mine has the same issues. If you have any suggestions or experience in converting Sketchup designs to Illustrator for Ponoko/laser cutting, let us know!

Thermal pads

Just received the 2 test thermal pads in the mail from Digikey.

BER165-ND is 3 mm thick and pliable. It runs about about $3.50 per OpenPCR (28 parts fit in a $94 sheet). 3M9601-ND is 2.5 mm thick and very soft, and about $1.20 per OpenPCR (25 parts fit on a $30 sheet)

We’ll want to test these out with our current heated lid to see that they work great and make it easy to maintain the temperature of samples. Once we receive the first set of aluminum and a new wooden case from Ponoko, we’ll be able to test these out even better.

Heat sinks arrived

All right, went and picked up the heatsinks at the UPS office last night. Broken them open while sitting in my car and made a couple quick judgments. Remember, my concerns are:

1. big enough surface area for the peltier
2. cost – $20 to $30
3. overall size and weight

The MassCool, while bigger in all dimensions, just isn’t big enough for the 4 cm square peltier. We would still need an aluminum plate adapter between the heat sink and the peltier.

The Titan on the other hand has the perfect sized surface for the 4 cm square peltier. It’s MASSIVE though.

I’m designing a quick prototype box today to send of to Ponoko. My focus is getting the case made to test out the heated lid. I’ve got a design using a spring hinge + thermal pads that I think will be easy to use and prevent condensation.

I’m also making the overall dimensions a lot bigger so they can fit any components we want to test out. Overall, it’s going to be 7″ tall, 7.25″ long, and 4.7″ wide. Our original case was and 5.7″ tall, 6.7″ long, and 5.4″ wide so this is test is quite a bit bigger. I’m going to test this out with both wood and acrylic, using a bolt design (the same one as the Makerbot) instead of glue. Glue is best for permanent slick looks, but since we’re  this is a hackable kit, bolts are easier to take on and off.

I’m also adding:

  1. Enlarging the hole for the aluminum block (4 cm square) to 4.4 cm square, to accommodate a layer of insulation around the block.
  2. Power port for the MicroATX ATX
  3. Front vents for the MicroATX so that we can test it internally

The heated lid

Now that the heat sink is ordered, on to the heated lid. The lid is a major component of the OpenPCR machine. It eliminates the mineral oil that screws up experiments of newbies and professionals alike. More importantly, it’s the one part of OpenPCR that you’ll interact with *every* time you do PCR. It needs to be done right.

As I’ve shared with a lot of you, our prototype lid is nichrome wire and silicone tape, sandwiched between two plates of aluminum in a wooden lid and it needs a lot of help. A few posts ago, Josh figured out that a peltier device + aluminum plate would fit the bill, and a custom board heater was suggested as something to try out long term.

Getting hot is only half of the story. The hot piece of aluminum needs to make good contact with the top of the tubes (which can have minor variations in size) — which means flat AND compressed. One idea that was suggested was a double hinged lid that would be able to rotate to be flat for a range of tube heights – kind of like the lid on a scanner, which can accommodate paper, thin magazines, and thick books. We also need a good downward force on the tubes, so that good contact is made. After wrangling on it for awhile, I’m going to try a lid on a single springd-hinge to handle compression and a piece of thermal pad (stock image below) to make contact with the tubes. Bought some on Mcmaster (spring hinge) and digikey (thermal pads, various softness, 2.5 – 3 mm, capable of 100-150C+). I think this will be straightforward to use, cheap, and reliable. We will see :)

We’ve got the aluminum parts on hand to test out these components, but we’ll need some better plates to test with. I’ll be working on putting together a design doc for Ponoko to get the flat aluminum parts made, as well as the case (wood or plastic).

If you want detailed specs, sign up as a donor to OpenPCR. For only $32 you get behind the scenes months before anyone else with access to photos, design documents, and software for the OpenPCR project.