Re: Copper beads as thermocycling "block" - Was: [DIYbio] What do open source PCRs need?

The downside to a water based system is that there are more moving parts. I'd imagine that pumps and valves tend to have a shorter lifespan than solid state parts like a peltier device. Water also tends to grow things if it's not changed regularly or the parts are not cleaned.

On Wed, Feb 17, 2016 at 9:16 AM Simon Quellen Field <sfield@scitoys.com> wrote:

Water is best for many reasons.

It has a much higher heat capacity than alcohol.

It is cheap, and the lab has a ready supply of it.

It is non-toxic, and easy to clean up in case of a spill.

It is odorless.

When sprayed into a stream of cold air from a blow dryer, it will be quite cool enough.

All that said, let's first try just the cold air. It will probably be quite enough by itself.

We can add the spray later if it is needed.

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On Tue, Feb 16, 2016 at 11:00 PM, Alex D <alexxxdean@gmail.com> wrote:

induction heater could be built way cheaper, but if something will spray the cold mist over the heat sink would it force the heat sink loose more heat? perhaps something that evaporates in far lower temperature then water even like alcohol , but then it has to be sprayed at very low temperature and cooled after it evaporated?  perhaps something like tosol or engine coolant or freon could be pumped 

On Tue, Feb 16, 2016 at 7:03 PM, Simon Quellen Field <sfield@scitoys.com> wrote:

You said:

> for some reason Ti cools within few seconds

I joke that my job is teaching physics to people with short attention spans.

The effect you noticed is called "heat capacity".

Titanium has low heat capacity. So does air. Water has very high heat capacity.

I think the reason people are using big aluminum blocks in thermocyclers is to even out the heat, so all of the tubes are heated and cooled equally.

An experiment with 96 tubes in a thermocycler would be suspect if the tubes were not all subjected to the same temperatures.

Thermal conductivity is important in evening out the temperatures, and titanium has low conductivity.

Again, I would prefer graphite if we determine that the temperatures are uneven.

Flowing water or flowing air would have to be carefully arranged so that turbulence and thorough mixing occur, so that all tubes are heated and cooled equally.

Peltier junctions are notoriously inefficient. Most of the benefit in computer chip cooling is due to the large heat sinks and air flow, not to the Peltier junction.

Putting electricity into a Peltier junction causes the system as a whole to heat up, as most of that electricity goes into heating the Peltier junction.

A little bit goes into pumping heat from one side to the other, if the hot side is properly cooled, either by a large heat sink and fan, or by a liquid cooling system.

That said, there are situations where we throw energy at the problem without caring a lot about the cost.

In data centers, the chips are not cooled by Peltier junctions. They are water cooled. Power is the main cost in a data center, and more power is spent on cooling than on powering the computers.

There are very few cooling solutions that can drop the temperature faster than dunking the hot thing in cold water.

Cold water is also cheap.

Adding a spray of cold water to the hot air thermocycler is something we have not talked about yet, but it seems easy to accomplish with a cheap water pump and an atomizer nozzle. Blow cold air past the spray and let the phase change from liquid to vapor soak up the heat in a hurry.

The most efficient refrigerators are all designed around a phase change.

The advantage of using the liquid cooling system from a gaming computer is that it is inexpensive, widely available, and pre-made.

We should look into that for the convenient appliance thermocycler.

They are also quiet, which has many advantages in a lab.

On the related subject of inexpensive lab equipment:

I've noticed that single-pot induction burners are inexpensive ($99), and can be set to a particular temperature like an oven, in the range of 160 to 430 Fahrenheit.

While I would not expect the temperature to be all that accurate or precise, many lab tasks don't require high precision or accuracy. Boiling water, for example.

And they are easy to clean. Some have built-in automatic timers.

One for $49 has five heat settings. This one for $60 has ten temperature settings (140 F to 460 F). This one has 52 temperature settings in 10 degree F increments from 100 F to 575 F, and is programmable to 100 hours of heating time or delayed start.

And speaking of titanium, this one has increments of 5 degrees F, and 94 temperature settings. Boils water in 60 seconds.

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On Tue, Feb 16, 2016 at 6:10 PM, Alex D <alexxxdean@gmail.com> wrote:

Hello Simon, 

thanks for the full review)) the reason I have mentioned Ti is from a camping experience. I have also tried Al  cups but they loose to Ti I would say by 20-30% in time for heating, but in cooling for some reason Ti cools within few seconds while Al or Cu takes much longer time. In PCR cooling takes probably the most time as i have noticed I am not sure if there is a relay to switch Peltier's polarity so the hot side turns into cool side but perhaps by placing a second pertier unit right under it will harvest all the heat from the one that is attached to the heat sink perhaps... 

I recently met a guy who works for AUTOCAD he mentioned that they are working on liquid cooling PCR where it is heated the normal way not sure which is it peltier based or by enduction, but he said that they are trying to design a water cooled heat sink similar to the computer liquid  cooling system so as he mentioned times could be cut from 3h to 30min not sure how is it possible if 30 cycles by itself are 30min but thats what I have heard. 

There is another thing GE works on is magnetic cooling which creates magnetic field to align molecules and force them to loose the energy, i believe they already have built the prototype of a new type of refrigerator   not sure how fast that would be but lack of any mechanical parts would definitely have a benefit as well as lack of peltier units which in my experience break quiet often. 

On Mon, Feb 15, 2016 at 8:06 AM, Simon Quellen Field <sfield@scitoys.com> wrote:

Titanium has a heat capacity of 0.125 calories per gram.

It thus sits between aluminum with 0.22 and copper with 0.092.

The thermal conductivity of titanium is about 12, on a scale where copper is 223, and aluminum is 118.

As titanium has a density of 4.43, to copper's 8.96 and aluminum's 2.7, and titanium is stronger than copper, I suspect that a titanium cup weighs less than one made from copper, and perhaps also one made from aluminum.

Boiling water in an aluminum cup might take a tiny amount more time than in a titanium cup, due to the slight difference in heat capacity and mass, but it will be dwarfed by the heat capacity and mass of the water, and any difference may be difficult to measure.

The low thermal conductivity of titanium is a problem, since it will heat unevenly. A copper bottomed pot will heat more evenly (which is why you find copper bottomed pots for sale), and aluminum is not far behind. But you would not want to scramble eggs in a titanium skillet over a fire -- you'd have to be very careful not to scorch them. Cast iron skillets, known for their low thermal conductivity (you can hold the iron handle while the rest of the skillet is in the fire), still have three times the conductivity of titanium, and use their mass to make up for the low conductivity, heating slowly enough that the heat has time to even out.

For a thermocycler, you want something with low heat capacity, low density, and high thermal conductivity. Graphite would be very hard to beat. Aluminum would beat titanium because of the dismal thermal conductivity of the latter.

The price of the titanium used in camping gear has fallen to about $4 a kilogram due to new cheaper manufacturing processes. Aluminum is $1.47 per kilogram, and is easier to machine, and much more thermally conductive, and less dense (2.7 g/cc to titanium's 4.5). These make it much preferable as a heat sink material, and also preferable in a thermocycler.

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On Mon, Feb 15, 2016 at 5:57 AM, Alex D <alexxxdean@gmail.com> wrote:

HI all, 

I dont really understand how Ti is not an option here? I have looked at the tables and Ti is stated 20x less then copper and roughly 10 time less conductive then Al ? I am not a specialist in this area so perhaps someone could clarify or had an experience with Ti? But I do camping sometimes and all of my cooking equipment is Grade A titanium, what I can add is when you boil a water in titanium cup and then pour water out of it, the cup itself goes from ~90C to room temperature in a matter of 3-4 seconds. Also I have used the titanium cups to boil water on the fire and on the induction oven , I havent tried copper cops but it boils water definitely twice faster then any Al cups ive had. 

anyone can clarify on that?

On Fri, Feb 12, 2016 at 5:02 PM, Lee Nelson <technologiclee@gmail.com> wrote:

You could use metal infused filament and 3D print the block.

https://blog.pinshape.com/3d-printing-metal/

You may be able to make a computer model of the heat transfer on a site called SimScale.

https://www.simscale.com/

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