On whizzy things and how they fall apart

Some might say there’s no such thing as centrifugal force.

You spin me right round, baby, right round, in a manner depriving me of an inertial reference frame. Baby.

Such people are probably not molecular biologists, cell biologists, nor any other kind of scientist who has to separate very small things on the basis of size, mass or density; or all three. Because when you spin something round it does tend to move away from the centre of spinnage. That’s spinnage, not spinach. Thank you. And wet-wranglers know that heavier, denser things (quiet at the back, Steel) move faster under this force we call ‘centrifugal’. Even nuclear physicists have worked this out.

Now the thing is, when you’re trying to separate things that are very small, you tend to have to have quite a reasonable centrifugal force for this to work. And the smaller the size differential, the higher this force needs to be if you’re to do it in a reasonable time. So if you’re separating cultured mammalian cells from the trypsin solution, you spin at with a relative centrifugal force equivalent to an acceleration 400 times that due to gravity (or g — not to be confused with Gee), for about two minutes. If you want to separate bacteria from their culture media, you’re looking at about two thousand g for five minutes, or thirteen thousand g for thirty seconds. (It’s not just a matter of real cells being bigger than bacterial cells: if you spin real cells too hard they tend to get a bit upset.) But when you want to separate F-actin from G-actin, it pays to be able to reach one hundred thousand g. You can do it at less, about twenty thousand, but then it takes half an hour to an hour instead of ten minutes. Let’s not forget plasmid DNA from a solution of ethanol and acetate — sixteen thousand g for ten minutes is good, here.

And the point of all this is that you need quite sturdy and expensive equipment. Consider a rotor that is about a foot across, developing thousands of accelerations due to gravity, spinning at say twenty thousand revolutions per minute (this is not uncommon for polymerized actin; or indeed caesium chloride density gradients, which I haven’t done in 15 years because there are much better ways of getting the same result, but anyway). The circumference, or the distance travelled by a single tube in this rotor, is going to be ∏ × 0.3 m = 0.94 m. Call it a meter. It travels this distance 20,000 times a minute. That’s 1,200 kilometers an hour. 745 mph. In other words, Mach 1 (near enough). Which is why laboratory centrifuges — at least, the ones that go at a reasonable lick — are not only big and sturdy, but also evacuated (otherwise they’d be much noisier, and hotter, than they already are).

So when I got an email from a particular ARC Australian Research Fellow saying

Yesterday i discovered a fault with the Sorvall Evolution centrifuge on level 5 (floor-standing model). The “cone” upon which the rotor is seated had become partially dismantled.

This morning, i was alarmed to find that my “out of order” notice had been removed. Tape covering the start button had been removed and the centrifuge had been operated. Foolhardy and potentially dangerous

I too was somewhat ‘alarmed’, if not ‘gibbering’, as well as ‘grateful I’d left the city, indeed the country’. Now, I know the centrifuge in question, and although the lump of metal that makes up the rotor doesn’t travel at Mach 1, it is a heavy lump of metal and goes bloody fast. And you’ll all recall that E = ½ m × v². Which leads directly to this sort of metal fatigue

No Meester Bond, I expect you to die
Flying metal fragments damaged walls, the ceiling and other equipment. The shock wave blew out the laboratory’s windows and shook down shelves.

The email was followed up by the safety officer, who informed us

[ARC fellow] is absolutely correct when he says not to operate an ‘out of order’ centrifuge.This is very dangerous, and also could make an existing problem more serious and more expensive to fix.

which is slightly understating things.

Note also that NO-ONE should use one of these large centrifuges on any of the floors unless they have first been instructed in proper practice by the equipment/room custodian, or a senior member of your lab who knows what they are doing.

That’s the MMB screwed, then.

About rpg

Scientist, poet, gadfly
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41 Responses to On whizzy things and how they fall apart

  1. Åsa Karlström says:

    that pic of the centrifuge is what they showed me when I was an undergrad…. needless to say, I always have been weary of using the BIG centrifuges. After all, they can get loose and do “The Mangler” …. evil things 😉

  2. Richard P. Grant says:

    Fantastic. I have always maintained that the best undergraduate is a scared undergraduate.

  3. Eva Amsen says:

    We weren’t allowed to use the big centrifuge in undergrad! A tech had to help. And then I did my research project and it was allowed, but I could never lift the rotor so I still had to ask male PhD students and lab techs for help. [Cue feminist outrage.]

  4. Richard P. Grant says:

    Hey Eva, you choose to be weak and feeble, don’t you?

  5. Eva Amsen says:

    Oh, yes, right, of course!

  6. Cath Ennis says:

    “I have always maintained that the best undergraduate is a scared undergraduate.”
    I had to do my own scar(r)ing of undergrads during my one and only stint as a TA. This stupid student started running a bench-top microifuge that was obviously unbalanced (as evidenced by the screaming noise coming from it), and walked away. I came running over and told her to stop the spin. She was by this point behind the fuge… so she grabbed it and tipped it backwards towards her while it was spinning at 15,000 rpm to reach the stop button.
    I don’t think I’ve ever given anyone such a bollocking as I did that day. And of course I was “that English bitch” for the rest of the course!

  7. Cath Ennis says:

    need to preview… that’s scar ( r ) ing

  8. Richard P. Grant says:

    Seriously though, it’s interesting being male and being expected to toss aluminum rotors around with gay abandon. Now while I’m quite strong enough to lift them out of the centrifuge, I’m not actually all that tool, so have to stand on an undergraduate in order to be able to reach.

  9. Cath Ennis says:

    “I’m not actually all that tool”
    It’s plane that you are a tool 😉

  10. Richard P. Grant says:

    I did wonder, Cath (and I should type my comments faster).
    One day (“memoirs”:http://network.nature.com/people/UE19877E8/blog/2009/05/11/in-which-i-defend-the-editorial-profession-–-belatedly#comment-36214, again) I’ll tell you about how I made a med student cry.

  11. Richard P. Grant says:

    Bah. ‘tall’.
    And I’ll assume that ‘plane’ was a joke.

  12. Cath Ennis says:

    Yup, it saw was.

  13. Richard P. Grant says:

    Are you shore?

  14. Cath Ennis says:

    “microifuge” was a typo though.

  15. Richard P. Grant says:

    Y’see, I was too gallant to notice that.

  16. Elizabeth Moritz says:

    We’ve had the rotor in our floor centrifuge come off the spindle once due to the lid not being tightened all the way. However,it didn’t really do a dance because our department requires (wisely) that all floor centrifuges be bolted to the floor.
    What was a bit more frightening than a floor centrifuge on the loose was a hemorrhagic microcentrifuge our lab once owned.
    The microcentrifuge oozed a mysterious reddish-brown liquid from most of its joints and openings. We cleaned it multiple times, put protective coating on all the metal parts and still, in the morning, the stains would be back…even in areas where there was only plastic, no metal.
    We sent it back to the manufacturer and had most of the nuts and bolts replaced. However, about a week into its return to our lab, the hemorrhaging began again.
    We eventually just stopped using that centrifuge and relegated it a closet for storage…

  17. Åsa Karlström says:

    cath> I don’t think I would’ve been able to refrain from screaming… as in angry voice… I did however experience an undergrad who, after stating I was stupid to say she needed to have her hair in a ponytail in lab, ended up with parts of the lab bench on fire and almost her hair that flopped out of “under the collar secure” as she claimed… I think the smoke from the banch and the realization that it could have gotten very much worse fast made her quiet the rest of the course.
    Richard> I had night mares and OCD about going back and listening to the rotor not being unbalanced … not to mention how many times I actually did weigh and balanced the tubes. Once a fellow ph student stood by me and stared on how exact I was with the weights. “you don’t have to be that thorough” well… at least I knew that once the rotor was unblanaced it wasn’t my fault 😉

  18. Richard P. Grant says:

    Is it time to start the discussion about 7 tubes in a 12 (or 24)-space rotor?

  19. Kristi Vogel says:

    When I started using ultracentrifuges in the lab where I worked as an undergrad, I was told (possibly apocryphal) tales about Svedberg and the development of analytical ultracentrifugation. Tales of exploding rotors and chunks of scientists metal embedded in the concrete bunkers that housed the prototypes. The most enthusiastic teller of these tales from the Svedberg ultracentrifugation crypt is none other than my father, a biochemist.
    Though according to this article about Svedberg, the tales of exploding rotors are true.

  20. Eva Amsen says:

    Oooh, I just found the sketch I did to figure out 13 tubes in a 24 rotor! It’s on the pile of paper-to-be-recycled.

  21. Richard P. Grant says:

    Balance 9 (3 sets of 3) then four (two pairs). No problems for anyone who can play cribbage.

  22. Cath Ennis says:

    Hee hee @ Åsa! I once went to a party where someone set her hair on fire. Candle + too much hairspray = bad smell and emergency trip to the hairdresser the next day! Luckily there was no more damage than that though.
    I had a hell of a time getting the undergrads to wear labcoats. But then the female students would put on those actual coats that were really popular at the time (~1999) that looked just like labcoats, and quite happily walk down the street in them…

  23. Beta Gal says:

    So how are you still getting our emails bk?

  24. Jennifer Rohn says:

    I always wait on the other side of the door when the Big Nasty Sorvall (BNS) is coming up to speed. Even through the door it sounds like a 747 making final approach.

  25. Richard P. Grant says:

    beta gal — no, they revoked my access. But I have lots of material stored up. Mwah hah hah.
    Jenny, does it wobble particularly noisily around 1,000 rpm?

  26. Åsa Karlström says:

    Richard. doesn’t all the cfg wobble around 1000 rpm? Even our small one does it and my heart flutters. ever. silly. time. And I’m not an undergrad nor a grad student anymore… seems to be one of those things*…
    *a)falling into the large -80 freezer in the basement where you had to fold yourself into them to get the racks and avoid getting the lid in your head
    b)falling into the large autoclave with room for two full adults in each basket… yes, I probably spent too much time with horror and murder books/movies

  27. Eva Amsen says:

    “the large autoclave with room for two full adults in each basket”
    …and how do you know this?

  28. Richard P. Grant says:

    Ah! all of them? That’s what I’m trying to find out. Is it a universal?
    (b) I have often wondered about as a means of … well, anyway. I guess someone must have done the experiment.

  29. Åsa Karlström says:

    Eva> don’t ask 😉 although it is one adult in each basket, i.e. two in total. my mistake.
    Richard> at least all the centrifuges I have used… the wobble around 1000 rpm and then they stabilize. And the other post docs in my lab have noticed the same thing…

  30. Kyrsten Jensen says:

    Centrifuge stories!
    1) I was first taught to use a centrifuge when I was a co-op for a Big Pharma. The first story I was ever told by the PI was how a Sorvall went through a wall because it was unbalanced at 10,000 RPM, which promptly scared me each time I spun down E.coli for plasmid preps. I got over it after a summer of way, way, way too many minipreps.
    2) Learning to use the ultracentrifuge to pellet a protein from a supernatant – now that was fast and I would often have to wait through part of my lunch hour to wait for it to go up to speed and be fine. The PI himself taught me to use it, and fiddled with the weights in the tubes for nearly 15 min and I was told that if I didn’t have things exact, I would be fired immediately (I guess he appreciated the fact that the centrifuge was across the hall from his office, and he would have been in ahem, “direct line of fire” should something go awry)
    3) The centrifuge in the Level 3 biohazard facility I used to use. I would spin down 2 litres of culture at a time, while wearing a respirator to protect from any potential aerosols if it spilled (it never did) because a) the centrifuge was a huge Sorvall that wouldn’t fit in ANY biocontainment hood and b) the pathogen we were working with was a respiratory pathogen. On my centrifuge days, I used to have to ban everyone else from the lab while I was working, because if there was a centrifuge spill, we couldn’t take the chance that someone would be exposed. I tell you, I treated that Sorvall and the bottles in it like a Faberge egg, as no one needs a spill in Level 3.
    4) I taught someone last week that RCF is NOT x g, who had a PhD and uses a centrifuge daily. They are not equivalent, and it’s a fight I have on a nearly weekly basis (though why people still challenge others on basic science, I just don’t understand). I also told this person that the old, outdated RCF to g conversion chart they were using wouldn’t actually be exact for their particular centrifuge because the rotor was older than them, and believe it or not, they do warp after time.

  31. Richard P. Grant says:

    Everyone seems to have a centrifuge story! This from Herbert :

    The [PhD Institution] once had an unbalanced centrifuge walk along a bench and push itself through a stud partition wall and onto the bench in the next lab. With the big machines, I was always very scared of being in the same room as them. The idea of that rotor flying around at the speed of sound was just too scary to contemplate. I HATE centrifuges.

  32. Cath Ennis says:

    g – RCF always reminds me of this:

  33. Richard P. Grant says:

    Angular velocity — the speed of angels in a vacuum.

  34. Surya Setiyaputra says:

    Talking about angular velocity. Our lab (RPG’s old one) had recently purchased a new incushaker http://www.nbsc.com/44_44r.aspx . It was all posh and new. I happened to be the first person to use it (unfortunately).
    It was shaking alright at 37C for 4 hours before it suddenly decided to accelerate super fast after restart (may be more than ~1000rpm normally you would use this machine at 200rpm max?). The instrument started dancing along and making noise, destroying my flasks that were inside it in the process. The flasks got shattered into pieces. By the way, I was just standing next to the instrument when this whole thing happened. My heart stopped beating and I suddenly felt so sick in the stomach. What a horrible Thursday (for a two-day old machine). o.0′
    Something wrong with the powerboard and the software that controlled the instrument somehow. 🙁 Still traumatized….

  35. Richard P. Grant says:

    Yow, Paul — that stinks. And not only do you have to clean up the mess, it sets you back, how long?

  36. Heather Etchevers says:

    I am giggling uncontrollably at the images in this thread. Sorry, Surya – you set me over the edge. I can totally see what happened (not why! but what). It was the “dancing along and making noise” that set me off. And Elizabeth’s centrifugal poltergeist! Ok, xkcd started it.
    “Which is why laboratory centrifuges — at least, the ones that go at a reasonable lick — are not only big and sturdy, but” expensive. Believe you me, I’m taking my refrigerated microcentrifuge (which does go up to 20K g, as I explained to my student this very afternoon) back to Paris with me. I’ll be eloping with a centrifuge.

  37. Richard P. Grant says:

    I’ll be eloping with a centrifuge.
    {steals for future use}

  38. Åsa Karlström says:

    Heather: Priceless. Elope on…..
    Is it because the refrig one is going to last shorter than all the others so you’d rather have it in the fridge at the other place too?!?

  39. Heather Etchevers says:

    Asa: No, the centrifuge refrigerates inside. I want him because I bought him with my own funds and he will be better cared for under my watchful eye. Given that I am going to elope within France where objects have genders, my machine is therefore masculine and not feminine, unlike other bits of kit that have been mentioned earlier. Here are his specs.
    Placing a regular centrifuge in a cold room is a much less satisfactory solution because of condensation issues, as you’ve alluded to. And you have to work in the cold room with it.

  40. Åsa Karlström says:

    Heather: oh I know… we had a sad little centrifuge in my old department. It was small and stuck in the cold room… it was specially sad that time when the glass tubes broke and the phenol spread within it…..
    His specs makes him look like quite the guy….. does he have a brother? 😉

  41. Richard P. Grant says:

    NN just got an email saying the link to the centrifugal force document is broken, and Pierce suggest here http://www.piercenet.com/files/TR0040-Centrifuge-speed.pdf or how to convert between g and RPM instead.
    I’d edit the post that would take far too much time and effort, given the clumsiness of MT4.

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