Hot-ish off the press

A good portion of my PhD work was trying to understand how reconstituted silk protein assembles into non-fibrous structures. To accomplish this, I used small-angle neutron scattering in collaboration with Katie Weigandt at the National Institute of Standards and Technology Center of Neutron Research.

This work was recently published in the journal Physical Review E, and a copy can be found here: Silk_PRE_2017

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I defended my thesis titled “I celebrate my silk, and shear my silk: assembly and rheology of reconstituted silk protein.” Read some Walt Whitman. Although I have some loose ends to tie up, I’m afraid my silk escapades are on hiatus for now.

I have since started a postdoc at Yale in the Murrell group. More details to come.

APS March Meeting recap

Laissez les bonnes physiques rouler.

March Meeting 2017 was fun not only because it was in New Orleans, but because the sessions were interesting and diverse. When not hearing about the Physics of the Cytoskeleton or Cell and Tissue Mechanics, I was drinking chicory coffee at Cafe du Monde or eating a delicious vegan poboy at Seed.

Talks of particular interest to me were:

Itai Cohen – Once again, Itai makes the list. Not only does he provide an entertaining talk, but he addressed the issue of friction in colloidal systems that I have mentioned previously. More specifically, he discussed how two particles don’t have to come into contact in order to “feel” one another.

Farzan Beroz – The extracellular matrix is a heterogeneous place. Farzan talked about quantifying the spatially varying stiffness of a collagen network by modeling deformations from 3D confocal images. The arXiv paper can be found here.

Margaret Gardel – Among many things, the ability to achieve an active nematic, similar to Zvonomir Dogic’s lab, with a contractile system stood out.

Upcoming Talk: Percolation is not the end of gelation

I will be giving a talk at the American Physical Society March Meeting in New Orleans titled “Percolation is not the end of gelation” on work done with Ben Partlow and David Kaplan at Tufts University. We directly observe how bond formation in a covalently cross linked silk gel correlates to bulk modulus changes in the material.

For anyone that is attending the meeting, my talk is Abstract S9.00008 Thursday, March 16, at 1:03 PM.

Protein phase separation

Remember learning about the parts of a cell in school? In a eukaryotic cell there’s the nucleus, which has a membrane that separates itself from the rest of the cell, and I was okay with that. Then I learned about the nucleolus – a membrane-less part of the nucleus, and I wasn’t a big fan. If it doesn’t have a membrane, how does it stay separated from the rest of the nucleus? No one taught me about phase separation.

Inside of cells, dense droplets of protein (along with DNA and RNA) form and redissolve depending on the conditions of the cell, where these droplets are responsible for useful functions in our bodies. In the case of the nucleolus, the density of pieces presumably helps it with the complicated task of ribosome synthesis. However, the nucleolus must be dynamic during the cell life cycle.

In general, if something goes wrong in a phase separating system (ex: separation stops being reversible) serious conditions like cataract formation or Alzheimers can occur. Therefore, understanding how and why proteins phase separate can lead us towards understanding both how our body works and how to prevent/cure some diseases.

I had a visitor from Lewis Kay‘s group in Toronto come down to do some experiments. He brought with him some samples of protein that are known to phase separate in cells. At high temperatures, the proteins are dispersed but form droplets when cooled. The image below is of droplets forming as the sample temperature is lowered. It can also be found on the Georgetown University Physics’s department twitter account. You can see that the droplets are liquid-like because some coalesce between frames. Enjoy.

ddx4

Fotografiert mit dem iPhone 6

I began my PhD by studying silk electrogels; gels that are made by running a DC current through a solution of silk protein. We published a paper to show that the rheological properties of these gels are pretty impressive – super stretchy, and they get stronger as you pull them.

I finally got around to taking a video of gelation, which I purposefully captured with my iPhone so that I could recreate the Apple catchphrase I saw on a billboard in Munich.

The positive electrode is on the left, and a DC potential of 25 V is held across the ~2 cm sample length. As current flows through the reconstituted silk sample, electrolysis of water at the electrodes creates an acidic domain near the positive electrode, and a gel front propagates while bubbles form at the negative electrode on the right. Images are acquired every 30 seconds for a total of 15 minutes.

The fact that reconstituted silk solutions form a gel in the acidic environment created by electrolysis has led us to investigate the effects of silk solutions in the presence of HCl. It turns out that the effects of HCl alone are not exactly the same as the electric field! The differences between the two systems likely comes from either the migration of ions along the field lines or by reaction kinetics. The paper studying HCl effects will be published soon.

The 2016 Physics Nobel is for … what?

In 2013, the Nobel prize in Physics was awarded to Peter Higgs and Francois Englert for theoretical contributions that explained the origin of mass in subatomic particles: the Higgs boson. Everyone and their mother had likely heard of the Higgs boson by the time of this award, mostly through media exposure/hype of the “Goddamn particle.”

In 2014, the Nobel prize in Physics went to Isamu Akasaki, Hiroshi Amano, and Shuji Nakamura for the invention of the blue LED. LEDs are prevalent in technology all around us.

And in 2015, the Nobel prize in Physics was given to Takaaki Kajita and Arthur McDonald for showing that neutrinos have mass. And after the erroneous result that neutrinos travel faster than the speed of light, the idea of a neutrino became semi-general knowledge.

But when the 2016 Nobel prize in Physics was awarded for “topological phase transitions and topological phases of matter,” I didn’t think that this would resonate with non-physicists. Apparently I am not the only one to think this way, seeing as the Nobel website includes the poll “Have you ever heard of topological materials?”

Luckily, Michael Shirber at the American Physical Society provided a nice overview of the Physics that resulted in David Thouless, Duncan Haldane, and Michael Kosterlitz receiving the award. These three Nobel winners pioneered using topology as a way to explain physical phenomena by finding a way to compare a real physical problem (like the quantum hall effect) to an “easier” problem with equivalent topology.

In topology, a sphere is the same as a bowl, since you can deform one into the other. However, a bowl and a donut are topologically different because you cannot transform a bowl into a donut without creating a hole. A similar argument can be made with a donut and a figure-8, etc, where all of these topological materials differ by integer numbers of holes.

If you are still interested, the Nobel website has a general description and an advanced description of the award.

The first citation

As a scientist, I want my work to be impactful. I don’t want my work to only exist in a dark corner of the internet. I want other people to learn from me and build upon my results. To paraphrase David Bowie in Zoolander, “first scientist researches, second scientist duplicates then elaborates.” The most tangible (but not to be used as a definite marker of success) is through citations. While some papers have thousands of citations, you cannot reach a thousand without first having one. I am happy to announce that I have eclipsed that barrier.

Work done by Chris Holland, Fritz Vollrath, and others shows that the silk fiber from the Bombyx mori silkworm is not fully developed immediately after spinning; as the fiber exits the animal gland, it is still high in water content and minimally crystalline. The fiber becomes stronger, forming more crystalline domains while drying. By changing the relative humidity of the environment during fiber spinning, the researchers were able to control the crystallinity in the fiber.

Here’s where my work comes in. Ben Partlow and I have shown that chemically reconstituting silk from a fiber back into solution is a destructive process. The paper by Chris and Fritz chose to alter the humidity to minimize the amount of crystallinity in the fiber so that reconstituting the fiber could be easier and less destructive. As a result, they created a reconstituted silk that behaves rheologically more similar to the silk inside the gland of the silkworm. Pretty cool stuff, and as always, great silk work coming out of England.

How could I not include this?

Imaging a collagen network under shear

When you stretch a rubber band, all of the parts of the rubber band move in unison. When you stretch a more complicated material, this is not necessarily the case.

Below is a video of a 3D collagen gel (which you cannot see) and the fibers of the gel are decorated with small fluorescent particles (bright dots). The video is a minimally artistic compilation of 4 different parts of the gel. Instead of stretching the gel, I have applied a shear deformation by moving a boundary, causing the network to move. In the video, you can imagine the top edge moving to the right, while the bottom edge moves to the left. During this deformation, I am using confocal microscopy to image inside the network.

While this collagen network is deformed, you can see that the particles attached to the fibers move both along the direction of shear and in bursts; sometimes these even move in and out of the plane. This is very different than what is seen in a rubber band. Hopefully by understanding how these particles move, we can gain insight into how structural changes in collagen affect its strength.

Silk in the News: “Dragon Silk”

Many people ask me, “what is the difference between spider and silkworm silk?” Most commonly my answer involves how spiders have many different kinds of silk (specialized for either web building, egg protection, etc.) while silkworms only have one. I am involved in silkworm silk research mostly because silkworm silk is significantly easier to acquire in bulk, and you don’t need a room full of spiders (Kate already dislikes being in the lab as is). But when people study spider silk, it is often the dragline because its the strongest version of silk created by the spider.

Kraig Biocraft Laboratories has received a US Army contract to use their “dragon silk” to make a bulletproof material.

“Dragon silk,” completely unrelated to dragons, is a genetic insertion of a spider’s dragline silk DNA into the silkworm DNA. So these special silkworms will make cocoons out of a hybrid “dragon silk” that is just as strong as spider silk, but easy to access.

However, I am interested but a bit skeptical about using silk as a replacement for Kevlar. Naively you can draw comparisons between the toughness of silk and Kevlar, but the purpose of Kevlar is to absorb the bullet’s energy in a short amount of time – silk needs to stretch significantly before it can achieve the same energy storage, but it is still possible.

I look forward to seeing how silk does in this next challenge. Maybe American soldiers will be wearing silk in the near future à la 13th century Mongolio.