Tuesday, March 20, 2018


Today, I focused on the physical process of silk synthesis in a laboratory.

The process used in SLU's biomimetic spinning process is as follows:

"Highly concentrated NT2RepCT spinning dope in a syringe is pumped through a pulled-glass capillary with a tip size of 10-30 μm, with the tip submerged into a low-pH aqueous collection bath. Fibers can be taken up from the collection bath and rolled up onto frames."

This method yields fibers 40 μm in diameter (wet; 30 μm capillary). SLU has reported that it has been able to produce strands up to a km in length.

The dope used by SLU (NT2RepCT) is of course a chemical I won't be able to replicate- it is a chimeric protein created by genetically modifying e coli bacteria. However, like in real spiders, they used the dope in a highly concentrated solution, with the concentration interval being 100-500 mg/ml. The low-pH solution that the dope is pumped into should have a pH from 5.5 to 3. That interval supposedly produced the strongest, continuous fibers. pH's lower than 2.5 yielded no fibers, and any pH higher than 6 yielded discontinuous fibers. SLU also varied the diameter of their syringe (which was a custom, pulled-glass capillary), from 10 μm in diameter to 30 μm.

The silk fibers produced in this process are extraordinary, but still not as impressive as nature. "The mechanical characteristics of the fibers were highly reproducible, although the toughness and ultimate tensile strength were lower than native silk. One possible way to increase the toughness could be to spin NT2RepCT fibers with diameters closer to that of native dragline silk, as this apparently has an impact on the mechanical properties of silk fibers."

The SLU report also encouraged that their method can be further developed. It said some examples could be a pH gradient, and an ion composition gradient. This would make their current set-up more like an actual spider, and may result in stronger fibers. I aim to implement such developments in a biomimetic spinning device, along with other things that I may encounter in the future.

The ultimate goal of refining this method is to make artificial spider silk fibers that perform at or above the level of natural spider silk in terms of mechanical properties. And with that, have the process be economically feasible enough that it can be used in an industrial level for mass production of synthetic silk to be used in whatever product/industry necessary.

- Noah

Saturday, March 17, 2018

Last Wednesday (Junior SAT Day)

I missed last Wednesday, not because I didn't want to write (I had a draft in progress), but because I simply forgot.

I've been out of town this entire spring break, so that's why I'm just now rectifying my mistake.

Anyways, here's what I did:

Because silk has low birefrigence, I may not be able to apply it to as much as I thought I could. I suppose there are still uses with optical materials with low birefrigence, I'll just have to keep looking.

My study on the structure of spider silk should only be a small portion of my final paper, but it'll be an important component nonwithstanding. It'll give me a better understanding of how the silk functions structurally, and how those unique structural properties could be applied in developing new materials, whether they are made to duplicate spider silk or not.

My main focus in my paper will be the applications of spider silk. I figure that here forward, as I begin writing, I should concentrate my research on all potential or possible applications. My looking in to birefrigence, for example, shows that even spider silk has its limits, and it's important that I thoroughly investigate every potential before making any conclusions about it being even feasible.

Now that I've wrapped up structure and some resulting properties, I'll look at deconstructing SLU's process step-by-step, so that I can first write about it, but then also apply that to the designing of my "biomimetic silk spinner." I may not even have a physical model finished/prepared, but it'll be an interesting synthesis of what I've learned.

Monday, March 5, 2018

I start my paper...

Today, I really wasn't able to do much research, we just reviewed the guidelines for our final thesis paper and presentation.

I began my final paper. I formatted the title page, made a table of contents, and have all of the topics/subjects I will cover planned out. Hopefully, each week I can finish (mostly) each section, so that I'll be finished in plenty of time to get it reviewed, corrected, etc. Plus, it'll be nice to be done with.

I should also probably start looking for judges.

- Noah

Thursday, March 1, 2018

Today, I looked at the primary and secondary structure of spider silk.

Side note, apparently spider silk has low birefrigence. Now this actually is okay, because you don't want the index of refraction to change much if used in fiber optics. And, because it's already been used/planned to be used in molecule detection, it's been proven to be applicable there.

Okay, now, structure. Primary structure is fairly simple and I discussed it some in my presentation. Primary structure of spider silk is mainly (90%) repetitive amino acid sequences. Most of these amino acids are glycine and alanine. This chart I made shows the molar %. --->

Image result for beta sheet
"Structural analysis revealed that oligopeptides with the sequence (GA)n/(A)n tend to form α-helices in solution and β-sheet structures in assembled fibers." This allows for the elasticity of spider silk. ( A β-sheet looks like a piece of paper that's been creased along the length so it looks like... nevermind, here's a picture: --->) So when stress is applied, the protein will stretch ("straighten out"...?) instead of breaking. The repetitive protein sequences is also crucial to its tensile strength. 

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Object name is prion0204_0154_fig003.jpgHowever, at the terminals (ends) of the protein, there are nonrepetitive proteins. These are crucial for protein assembly because they form intermolecular bonds that stabilize dimers (2+ monomers), etc. during the "assembly." 

At a more macroscopic level, spider silk looks more like a rope that's coated in a protective "skin."  In this diagram, you can see the macroscopic view with a diameter of 1-50𝜇m (1𝜇m = 1x10⁻⁶m). Then there are subunits (diameter of 2nm and average length of 7nm. 1nm = 1x10⁻⁹ m) which are comprised of the repetitive amino acid sequences which form the β-sheet structures (in blue). 

We still don't fully understand the entire structure and functions within the spider silk. It's probably one of the most complicated structures we know of. But it's also fascinating, so I will do all that I can to learn as much as I can about the structure, at least enough to present my thesis, which I think I've surpassed already. (At least I'll have plenty to write about.)

So what I know right now isn't even scratching the surface of the current understanding, and there's no way I will know as much as we know, that would take years. Really, as long as I have a fundamental understanding of how the structure works, how it changes during fiber formation, and how the structure gives silk its properties, I'll be set. Next week, I'll focus on tertiary and quarternary structure, and begin looking at making a step by step journey through silk synthesis in nature, so that I can compare it to laboratory methods later. 

- Noah

Tuesday, February 27, 2018

Birefringence of Spider Silk

As planned last week, today I investigated the birefringence of spider silk and its possible applicability in medical technology, etc.

First off, let me explain birefringence. It's the property of a substance where the index of refraction changes based on the polarization and direction of propagation of light.

Basically, polarization is the orientation of an electromagnetic wave, in this case visible light. See, these transverse waves have their E (electric field vector) and B (magnetic field vector) perpendicular (90°) to the direction that the wave is moving. So, a vertically polarized wave traveling in the z direction would look like this:

Where λ is one wavelength. (Note how E oscillates in the x direction and B in the y.)

Okay, so birefringent substances change their index of refraction as the orientation and direction of light changes.

This means that the speed of light through the substance is no longer constant. And if we wanted to know the index of refraction we'd need some math. (This is really simple, but just to get an idea of what's happening. There's a bunch of del's and multivariable calculus in the actual theory.)

We'll say that the index of refraction (n) is equal to v/c. But this time, v will be a function of x, a function of position of a substance on the x axis.

n = v(x) / c

Now, the index is dependent on where you are in the substance.

So what can you do with a birefringent substance?

Some researchers in EPFL's group for Fibre Optics believe that spider silk could potentially be used in chemical detection. Because of the way it can conduct light, they think it could be useful in medical devices to be implanted in a living body. This is also possible because silk is biodegradable.

Birefringence is also used to diagnose diseases, but silk doesn't have an application there. Next time, I will probably look more at applications, and then move on to the different levels/domains of silk's structure.

Friday, February 23, 2018

Time to catch up

I haven't posted in about a week, so this is to account both for this week (which was really one day because I was absent Wednesday) and last week. 

I been mostly looking at the optical properties of spider silk. As I discussed among the many applications of spider silk was the possibility of using it in place of fiber optic cable (FOC). At the time of my presentation, I had yet to learn more about it since I was looking in to other things. I have now been investigating this. What I have found so far is very promising. 

First let me explain the index of refraction. The index of refraction is defined as:

n ≡ c/v 

where n is the index, c is the speed of light in a vacuum, and v is the speed of light through a particular substance. The index of space is obviously 1, and air is very close to that. Normal FOC typically has an index of about 1.44 which is pretty good. There is only about a 31% decrease in the speed of light, which is still ridiculously fast. (~2.083X10⁸ m/s) 

Now, spider silk has been found to have an index of about 1.55. That's still good, but not as good as FOC. Spider silk reduces the speed of light by ~36%. So, between FOC and spider silk, there's only a 5% difference in speed. While it would take light traveling the distance to the moon 1.85 seconds through FOC, it would take 1.98 seconds through spider silk. So the question I have to answer now is: is it worth it to reduce the speed?

FOC typically has a diameter of 50 microns (50 millionths of a meter) not including the layers of insulation and protection around it. Spider silk has a diameter close to 7 microns. This means that you have more channels to transport information in the same space, ~7 times as much. 

Also I've considered too the production of FOC vs. silk in making it available for common and universal use. FOC can now be made at 50 m/s. Silk likely can't compete with that speed. At best, you can only produce a few meters per second. 

The process of manufacturing FOC is a very complex process that involves chemical vapor deposition, drawing, and coating. The manufacturing of spider silk is also complex, as discussed in my presentation. However, silk has no bi-products and the lab setup is simple.

FOC also has some practical issues. It's glass, so it's not nearly flexible as silk. It also has issues with installation because of its maximum tensile strength. 
Thinking holistically, you have to make the best use of time, resources, money, and space for this to be a feasible option. Spider silk as a product itself would reduce the normal speed by 5% and is manufactured at a slower rate. However, it is smaller in diameter, is cheaper to make, is clean, and more durable. 

Of course I may be biased because this is my thesis and I want silk to be used anywhere possible, but I think silk could be a viable alternative to fiber optic cable despite any cons. I will continue to investigate this one application as I move on to others. 

Next week, I'll look at applications based on its birefringence.

Birefringence is the property of a material where the index of refraction changes based on the polarization and propagation direction of light. Think liquid crystal displays in alarm clocks. The display changes as you angle it away or towards you. This property is made use of in numerous medical instruments etc. 

Should be interesting...

- Noah

Thursday, February 8, 2018

Back in the swing

Today, since we finished all the presentations, I went back to working on my thesis.

the feedback that I got for my presentation was helpful, and I'll use it for next time.

So, today I took a closer look at the quaternary structure of the proteins (in aqueous solution anyway). Apparently it doesn't have any "considerable" secondary or tertiary structure. "Particularly in their repetitive core domains, however, the long repetitive sequences permit weak but numerous intra- and intermolecular interactions between neighboring domains and proteins upon passage through the spinning duct." And it's because of these interactions through the extrusion, that the secondary through tertiary structures emerge as the proteins polymerize.

Cool stuff.

Also, "the high electron density regions comprise crystalline sub-structures with high β-sheet content. These sub-structures are thought to be responsible for the mechanical strength of the silk thread. The elasticity of silk is based on the areas with low electron density, which are characterized by amorphous structures with few defined elements of secondary or supersecondary structure.40, Such arrangement closely resembles that of protein hydrogels. Upon tensile loading, the hydrogel-like areas can partially deform, contributing to the elasticity and flexibility of the thread." 

This gives me a better understanding of the chemical/physical reasons for the rigidity/elasticity.

I'm really enjoying this topic, and I can't wait to present my finished project! I should probably start that paper soon...

All in a day's work,

- Noah