College work day

Today I worked on my ApplyTexas essay, and also updated/edited information in the website for my UT application.

(I also looked at audition music for MIT ensemble/jazz band so I'll be ready for auditions next year. Mainly just for any college, not just MIT. The music was for this year, so I'm not counting chicks before they hatch, I just like to be best prepared for any scenario.)

- Noah

There's a mistake in the math...?

Yesterday, I realized that the equation used in the study to find the energy stored in the silk as it is stretched is odd. The units don't work out, so I'll have to find a solution and fix it. (Dr. J confirmed that it had incorrect units.)

- Noah

After the break

To briefly summarize what I did over the break: I worked on my supplements, my Apply TX essay, and read up on my thesis. (I'm still trying to understand the "lock and trigger" mechanism described by SLU.)

Today I'm working on my mid-term report and my Apply TX essay. I'm hoping to submit my UT app by thursday. After that, really the only one left is Rice, which I'm essentially finished with. I just need to make sure the supplementals are solid. 

Oh! Also I found this neat study of spider silk. It describes how qualities were quantified and has a ton of data. I also found equations used in the study that may be helpful.

- Noah

I'm Back

I got back from the campout yesterday. (It was cold and very windy.) I didn't manage to make a post yesterday, and quite honestly, I didn't work on my thesis. I fell asleep.

This post will be my itinerary for the week, so if I forget to log a day, you'll know what I'm up to.

Monday (today): Work on Rice supplemental essays

Tuesday: Read on thesis

Wednesday: Read on thesis

Thursday: I will be eating copious amounts of turkey, potatoes, cranberry sauce, and pies.

Friday: Work on college applications for Dec. 1/Jan. 1 deadlines.

Saturday: Eagle Scout Court of Honor

Sunday: Update/edit mid-term report


- Noah

Camping this weekend

I will be gone camping this weekend so I will not have an entry tomorrow. Today was fully loaded schedule-wise so I wasn’t able to do anything today. Over the break I plan to make good progress on my research.

- Noah

Thesis day # 1093234001

Jk, there hasn't been that many thesis days.

I worked on my mid-term report more today. I took out some things, added more to it, and made sure my formatting was correct.

- Noah

[original title]

I've been looking into other ways of creating my own protein solution. Nothing I've found would be feasible, due to expenses, availability of materials, etc. The only semi-possible way would be to harvest naturally-occurring spider silk, dissolve it into an aqueous solution, use the lyophilization process to purify it, then resuspend the resulting powder in HFIP solvent to create a usable dope. Now, I can't do this at home. I highly, highly doubt SMU would let me use their labs/chemicals. Even if they did, I wouldn't be able to collect spider silk. Collect silk from webs just hanging around would be mean to the spiders, not to mention dirty, and harvesting them directly from the actual spiders seems inhumane to me (even though it has been done multiple times before).  

I did pretty much finish my mid-term thesis report. It's already three pages just in one sitting. I'll still add to it as I progress and turn it in on the deadline (or maybe earlier to get it out of the way). It's just nice to know that I have a good portion of it finished.

- Noah

Thesis (college) day

Today, I worked on supplementals for Rice. I also began my thesis mid-term paper.

I've also decided that I will try to build something*, but will still write a substantial research paper. Unfortunately, most of it will be conjecture and theory so I'll have to make sure I am very thorough in my research.

- Noah

*- I dunno what something though...

This changes things...

I heard back from SLU this morning. I will not be able to have any of the dope for my project. They only make enough material for their own experiments, and shipping it would be difficult as the solution will aggregate at room temperature.

One thing that she did point out is that the silk is polymerized primarily through being pulled through the spinneret organ, not extruded. My thought was that an air pressure pushing the protein solution through the pH gradient would have the same effect, but sounds like not.(?) She did point out that I was on to something though. It would matter what gas was being used as pressure, because I knew that CO₂ would have an effect on the C-Terminal domain, so it would have to be an inert gas.

So, this changes things:

I won't be able to make a working, tested prototype. I can create a similar setup as SLU, or make a new design for manufacturing based on that. (that won't even do anything! Ugh.)

or

I can look into my original thought more, with the new information, and revise the design. (which STILL won't do anything.)

or

I can abandon the idea of building something and simply write a long research paper (boring).

What to do...?

- Noah

Nov. 9-12

I'm still waiting to hear back from SLU about the protein dope. I think I'll wait a few more days, then try sending it again.

I did some research on calculating a new pressure for a nozzle with a changing diameter (essentially a cone), and I think it'll take awhile. I need to learn some more fluid dynamics first. There's much that I haven't considered. There will be a normal force opposite to the pressure, the force AND area change, and probably some other things I've yet to learn. This week, I'll do more reading on FD so that next week during the break I can maybe calculate. On the other hand, it'd be much easier to just experiment with the pressure and find one suitable. The nice thing is that I can use water to test it with.

If I can't get a hold of the dope from SLU, I may have to just present the device as a proposed, untested prototype (I'm planning to start building during winter break: when I'll know more about fluid dynamics and hydraulics). It'd be a neat water gun, but it won't have the same effect.

Sorry about writing late. I'll really try to do a blog every day, I just need to get into the habit.

- Noah

That's so "dope." Ha! I'm friggin' hilarious. (No. I'm not.)

Senior Thesis #23

Today, I added to my annotated bibliography and began calculations for pressure with a "spinneret" that has a changing radius. This will most likely be closest to the design that I will use. I'll check with Dr. J later.

I guess that's what I spent an entirety of 90 min on today.

All in a day's work

- Noah

Senior Thesis day #22

Today I worked on my annotated bibliography for my thesis. I'm going to have difficulty trying to get to 15 sources. My topic is very new, and done by only one group, so finding many sources will be difficult. I've gotten 4 so far. I haven't heard back from Dr. Rising about my last email.

Annotated Bibliography

A Study of Biomimetically Synthesizing Spider Silk from a Chimeric Minispidroin

Project Description:

My project will be study-based. I’m studying laboratory methods used to artificially synthesize spider silk, and it’s potential uses and applications. I plan to produce a paper and at least a prototype of a “Biomimetic Silk Spinner” that will apply what I have learned in my study in attempts to recreate the process or explore other potential methods. As of now, I am reading up on many papers sent to me by Dr. Anna Rising of SLU (a lead researcher in synthetic production of spider silk), and working on a design for a prototype. My next move will be to carefully request a sample of the “dope” in order to test my device (that I have yet to build). I will likely have the capability to build it, but the actual protein solution used by researchers is something I cannot replicate on my own.

Andersson, Marlene, et al. Biomimetic Spinning of Artificial Spider Silk from a Chimeric Minispidroin. Nature America, Inc, 2017, Biomimetic Spinning of Artificial Spider Silk from a Chimeric Minispidroin, nature.com/naturechemicalbiology.

[This source is from a research team at SLU. They described their experimental setup, the materials and equipment used, and described their results based on changes in pH. There are also pictures of the experiment and the produced strands of silk at varying pH’s. From this source, I know that the optimal pH would be ~5.5, and the concentration of the NT2repCT dope should be ~100-500 mg/ml. Additional specifications for equipment models and sizes is also listed. The procedure for this experiment is essentially this: Pump the dope through the pulled glass capillary into the acidic buffer and then wind produced strands onto a reel for collection. The dope can be stored for extended periods at 20℃.]

Andersson, Marlene, et al. Carbonic Anhydrase Generates CO₂ and H⁺ That Drive Spider Silk Formation Via Opposite Effects in the Terminal Domains. vol. 12, PLOS Biology, 2014, pp. 1–14, Carbonic Anhydrase Generates CO₂ and H⁺ That Drive Spider Silk Formation Via Opposite Effects in the Terminal Domains.

[This source is a scientific report by the SLU research team. It describes the research that went into the experiment, discoveries made, and goes more in-depth into the specific chemical and biological processes the production goes through. The paper details how the team attempted to replicate the processes, reactions, and conditions. This report describes the “lock and trigger” mechanism, and the discovery of the role the pH gradient plays in the synthesis of spider silk. The report contains dozens of graphs, graphics, and images of various tests done to determine conditions, of which they needed to replicate.]

Rising, Anna, and Jan Johnson. Toward Spinning Artificial Spider Silk. Nature America, Inc, 2015, pp. 309–315, Toward Spinning Artificial Spider Silk.

[This is a paper written by Dr. Anna Rising and Dr. Jan Johansson detailing the quantitative and qualitative properties of natural spider silk, and how their synthetic silk compares to it. This also describes their initial approach to synthesizing it. The report also has a schematic of a hypothetical “biomimetic [silk] spinning device.” I plan on making at least one prototype that should operate on the same principle as the theoretical device. It differs slightly from the experimental setup, so I plan to also make one based on the experiment. It also briefly describes future prospects for manufacturing it on a larger scale to be used in a variety of real-world applications.]

Matchar, Emily. “New Artificial Spider Silk: Stronger Than Steel and 98 Percent Water.”Smithsonian.com, Smithsonian Institution, 26 July 2017, www.smithsonianmag.com/innovation/new-artificial-spider-silk-stronger-steel-and-98-percent-water-180964176/.

[This source doesn’t discuss the silk I am studying, but it does talk about the applications for silk based on its tensile strength and ability to absorb energy. One proposed application was for protective clothing in military or bullet-proof armor. Or in sails or parachutes, or helmets. Spider silk is also biocompatible, which means that it can be used in many medical applications including stitches, tendons, skin grafts, etc. The wide range of applications for this material make it well worth researching in attempts to recreate it and produce it en-masse.]

All in a day's work

- Noah

Finally past Nov.1 !

I have finished and submitted all of my early action applications!! I applied to MIT, SMU, and TCU. Today in thesis I worked on my bibliography. I also made a list of materials used by the team at SLU in their method. I won't be doing exactly what they did, 'cause laboratory-grade equipment is $$$$. I may be able to use the same extrusion capillary and the low pH buffer, but otherwise, I'll have to come up with another idea.

So here's what SLU used:

• NT2RepCT solution (dope) 100-500 mg/ml
• NaC₂H₃O₂ 100 mM
• Round Glass Capillaries (G1, Narishige) outer: 1mm; inner: .6mm
• Pulled to diameter of 10-30 𝜇m
• 1ml syringe with Luer Lok tip (BD)
• 27 G steel needle(Braun) outer: .4mm
• connect to capillary via polyethylene tubing 
• neMESYS low pressure (290 N) syringe pump (Cetoni)

What I plan to actually use/need:

• NT2RepCT solution (dope) 100-500 mg/ml
• NaC₂H₃O₂ 100 mM
• Round Glass Capillaries (G1, Narishige) outer: 1mm; inner: .6mm
• Pulled to diameter of 10-30 𝜇m

I will ask Dr. Rising (nicely) for the NT2RepCT solution. I can easily get the sodium acetate solution from a chemical supplier. The capillaries I would have to buy somewhere... I can't find them cheap enough. I can buy them, but they're $142.00 a pop. So, no. I'd probably break it anyway. (for a comparison: the average human hair is 17-181 𝜇m, that capillary is 10-30 𝜇m!) I'll have to find another solution...

If I can't get the dope from SLU, I may try creating a solution of silk dissolved in acid (...?). Or just build a prototype and talk about it.

All in a day's work 

- Noah