# 3D printing sterile parts

As a biologist with a 3D printer, one of the questions I get most often about 3D printed parts is, “Can you autoclave these things?” As it turns out, no, not really. There are only a handful of thermoplastics that can survive the autoclave process, and most of them are not very good for 3D printing. With few exceptions, only polypropylene and blends of polypropylene hold up to repeated autoclave cycles, and polypropylene is, unfortunately, very a difficult material to print. It shrinks a lot when it cools, which causes a lot of warping during printing, and it is very difficult to get molten polypropylene to bond strongly to cooler, solid polypropylene.

It turns out that this is all unnecessary. Fused deposition modeling (FDM) 3D printing involves shoving a rod of thermoplastic into a hot nozzle until it melts and squirts out the nozzle. For most popular 3D printing plastics like ABS and PLA, the nozzle temperature is somewhere between 180C and 260C, and the plastic stays at that temperature for around a minute, depending on what the toolpath looks like. It’s actually a lot like Pasteurization, except way overkill. Get it? Overkill?

Anyway, here’s how FDM 3D printing compares to various Pasteurization (in black) and autoclave (in red) protocols :

Earlier this year, I was wondering about this, and my friend Emily Tung convinced me to just try it. So, on her advice, I heated up the nozzle of my 3D printer to 220C and placed a beaker of sterile liquid LB media under it. I then extruded some plastic until the blob fell into the media. I then incubated it, along with a positive an negative control, at 37C until… well, until nothing. Only the positive control (a short length of raw plastic feedstock) grew anything.

I tweeted this little experiment as it went along, and suddenly I had two collaborators, Kaitlin Flynn in Michele Swanson lab at the University of Michigan, and Luis Zaman in Richard Lenski’s lab at Michigan State University. Kaitlin immediately started suggesting different growth conditions I should try, and Luis, who also has a 3D printer, replicated all of my experiments and invented new variations to try. Because Kaitlin didn’t have a 3D printer of her own, Luis and I 3D printed a bunch of little test parts for her to try out, and mailed them to her. In her spare time, Kaitlin tried culturing the parts under all sorts of different conditions, including with mouse macrophages.

The results are detailed in our new paper On the intrinsic sterility of 3D printing, which is now available as a PeerJ PrePrint as of yesterday.

The tl;dr is that yes, 3D prints are sterile after printing. They are not sterile after touching them with your fingers or dropping them on the floor.

#### Posted by Russell Neches

on 17/10/2014 at 00:32 under a Creative Commons Attributuion License.

# Fifth Street, now with less suck!

I’ve been thinking a lot (and writing a little) about road safety for several years. The catalyst for this was an accident that nearly killed my sister while she was riding her bicycle in Norman, Oklahoma. The driver was on the wrong side of the road, but couldn’t tell because of the mind-bendingly poor quality of Norman’s street design. Not long after I came to Davis, I witnessed a pretty nasty accident on Russell Boulevard, and wrote about it here. The response to that blog post got me involved in the long-simmering debate over a proposed re-design of the Fifth Street/Russell Boulevard corridor. To me, the debate seemed to hinge on a factual question regarding the frequency and severity of accidents, and so I did some data analysis of city-wide accident reports to satisfy my own curiosity. Well, maybe more than just my curiosity. It’s pretty damned personal to me.

I suppose my data-centric approach made it possible for me to open a dialog with the Davis Chamber of Commerce. Once the business community and activists were able to communicate their concerns to one another, it turned out that the substantive disagreements were not very disagreeable after all; the Chamber’s biggest concern was that in the original design, as proposed, the left turn pockets were too small. I signaled that the activists wanted a general concept: A two-lane design with bike lanes and left turn pockets. As long as the Chamber was willing to roll with that, the details were mostly a matter of law and necessity. Within the general two-lane concept, whatever variations were legal and physically possible would likely be acceptable to the pro-redesign camp. The preliminary design was approved shortly after, with the support of the Chamber. Later on, this lead to my appointment to the City of Davis Safety and Parking Advisory Commission, and later to the new Transportation Advisory Commission. If only all political fights would boil down to misunderstandings, and if only opposing parties could get what they want by arranging the details just so. Alas!

As a commissioner, I’m proud to have been involved in several modest improvements to the street design in Davis. We’ve scrutinized speed limits and moved lane strips around. We were also among the many quarters that called for the City’s swift re-design and signalization of the Russell/Lake intersection and the similar Pole Line/Moore intersection after the death of UC Davis law student Megan Glanville. In the background, though, the Fifth Street Project has preoccupied us throughout my term as a Commissioner.

Well, if you’ve been downtown in the last few days, you’ve probably seen the new signals, the new lines and crosswalks. Fifth Street is no longer a four lane road on which it is suicidal to bicycle and dangerous to cross. It is now a normal, two lane road with left turn pockets and bike lanes. It’s actually quite wonderful.

Expect traffic to move a little more slowly on the new street, but with fewer and abbreviated complete stops. The time it takes to get from one side of downtown to the other should be a few seconds less, despite the slower speed – even in heavy traffic. You will have to slow down, but you will spend less time waiting. It should feel a little bit less “busy.” Of course, it won’t be perfect. Road designs are always compromises. This new design is simply a compromise that better fits the needs of the people who use it.

I am proud that I can finally say, “Go ahead, ride your bike on the new Fifth Street now.”

#### Posted by Russell Neches

on 11/08/2014 at 23:18 under a Creative Commons Attributuion License.

# Vort.org, now with Erlenmeyer

Welcome to the new Vort.org! After much fussing about, I’m finally migrating away from my old blogging platform and officially re-launched. I’ve built a new blogging tool specifically designed for science. It’s called Erlenmeyer. Erlenmeyer is still a work in progress, but even in its current larval instar it is already quite nice to use, especially if you have something to say like

$\underbrace{\nabla p}_{\cal{O}(\beta)} + \underbrace{\frac{\nabla B^2_{\mathrm{T}}}{2}}_{{\cal O}( 1 )} + \underbrace{\frac{\nabla B^2_{\mathrm{P}}}{2}}_{{\cal O}( \epsilon^2/q^2)} + \underbrace{\frac{B^2_{\mathrm{T}} \nabla R}{R}}_{{\cal O}(\epsilon)} + \underbrace{B_{\mathrm{P}} \cdot \nabla B_{\mathrm{P}}}_{{\cal O}(\epsilon^2/q^2)} = 0$

Erlenmeyer has built-in citation management, so blog posts can seamlessly include a proper bibliography, generated automatically. For example, the equation above comes from a paper I wrote a few years ago. [1] Erlenmeyer also supports a syntax highlighting in a large number of languages.

def findregions( data, N ) :
"""
Return all the regions of an array that exceed N.
"""
pos = filter(lambda(a) : a[1] == abs(a[1]), zip(range(len(data)),data-N) )
if len(pos) == 0 :
return []
pos = numpy.array( zip(*pos)[0] )
regions = []
for k,g in itertools.groupby( enumerate(pos), lambda(i,x):i-x ) :
l = map( operator.itemgetter(1),g )
regions.append( {'start':l[0],'stop':l[-1] } )
return regions

There’s still a lot of work to do, but at this point, the best way to make sure that it gets done is learn to eat my own dogfood.. There have been a lot of things I’ve wanted to blog about, but I was so annoyed with my software that I didn’t bother with it. So, this is both a return to blogging and a return to web development – now with more Science!

### References

1. Neches RY, Cowley SC, Gourdain PA, Leboeuf JN (2008) The convergence of analytic high-β equilibrium in a finite aspect ratio tokamak. Phys Plasmas 15: 122504. Available: http://dx.doi.org/10.1063/1.3008049.

#### Posted by Russell Neches

on 17/06/2014 at 23:50 under a Creative Commons Attributuion License.