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October 8, 2008

The next five years.

Some of you may be wondering when I'm going to grow up and do something with my life. I'm proud to announce my five year plan.

Biofuels biofuels biofuels 'glucose economy' cellulose biofuels.

I've joined Doug Clark's research group in the chemical engineering department at UC Berkeley. I'll be working on the problem of breaking down cellulose into glucose, which can be used as a feed material for microbes producing ethanol, butanol and other fuel products, polymers, chemicals, and all manner of things we need but get from oil. Cells eat up glucose, and we engineer the cells to produce the stuff we want. Here are the steps:

1. Grow plants with lots of cellulose. Plants take carbon from the air (CO2) and produce cellulose via photosynthesis.
2. Dissolve the cellulose
3. Add enzymes to break the cellulose down into sugar molecules.
4. Feed the sugar to microbes which have been engineered to produce the molecule(s) of interest

Cellulose is a long chain of glucose (sugar), all wound up and crystallized, and then stabilized with some other molecules. It's tough stuff; it has to be. Plants use it for structure and protection, so it makes sense that it's hard to break down. The dissolution and enzymatic breakdown of cellulose is widely considered the rate-limiting step in the production of biofuels from cellulose. (The ethanol plants dotting the midwest don't have to deal with cellulose - they feed the microbes using starch from corn plants. That's not very efficient, because it takes a lot of resources to produce corn, and only the kernels are used in the biofuel production. If anyone asks you to invest in a corn-based ethanol plant, tell them you got a bridge for sale...)

Ionic liquids are a special kind of solvent which have unique properties which make them able to dissolve cellulose in very high concentrations. They are essentially salts, or ions, which are liquid at room temperature. They're part organic solvent (think benzene, or methanol) and part salt (think NaCl). Their split personality allows them to wiggle between cellulose chains and pry them apart, dissolving them and breaking down their crystalline structure. This makes them much more susceptible to attack by enzymes converting the cellulose to sugar.

Problem is, these cellulase enzymes evolved in water, not in ionic liquids. In order to use enzymes to break down the cellulose that we dissolve in ionic liquids, we have to precipitate the cellulose out of the ionic liquid solution and put it back in water. My research project will involve trying to understand how the properties of the ionic liquids affect enzyme activity, and to engineer new enzymes that are active in ionic liquids.

Or at least what I think I'm doing. I'll let you know in a year or two if things turn out that way.

January 14, 2009

Facebook prelims

I'm taking my big chemical engineering exams tomorrow and Friday. Oral exams over all aspects of chemical engineering that I should have learned as an undergrad. I didn't start to freak out until I opened facebook and saw this status update:

Josh Wise is wondering if a high of -2 is low enough to physically prevent ice skating.54 minutes ago

And I thought, well shit, we know that the P-V diagram of water is strange because the solid-liquid equilibrium line has a negative slope, so pressure can push us into the liquid regime. But we really need to know how much weight Josh has gained since I last saw him, and his shoe size, then we could figure out whether ice skating is an appropriate activity for a day like today...

And then I passed out in a whirlwind of differential equations.

See ya in 36 hours!

January 17, 2009

In for five.

I guess I should have written a post before I found out that I actually passed my preliminary exams. But as far as I remember, this is how it went:

First test: transport. This was my weakest area, lots of math, lots of funny vector notation that I had a weak grasp on, lots of permutations of the same problems that gave me fits. I bought a copy of the seminal book in transport phenomena, and worked through a good 60% of it in the three weeks leading up to the tests. My first problem was easy - momentum balance on a plate moving up through a pool of water and causing a film to collect on the surface of the plate. Find an expression for the velocity profile of the film.

For the second problem, dbags asked me to draw a bubble at the surface of a pool of water, and then to draw it down some distance below the surface. What happens to the bubble? I fumbled for a while before realizing that the force of the column of water would cause diffusion out of the bubble until the partial pressures were equal. I think I was in denial about the surface tension contribution, because I HATE surface tension. I still don't really get it. But after being harassed about it, I added in the term, realized that the bubble would eventually disappear completely, and waited for the next pitch.

Gravie gets that look on his face that says I'm about to tell you something that will satisfy me greatly. Then he launches into a bunch of facts about a certain beetle - this beetle gathers a bubble from the surface of the water, takes it underwater with him, and uses it to breathe. Some Darwin wannabee decides to do an experiment: give the beetle pure nitrogen, pure oxygen, or a regular air bubble. To his surprise, it turns out the beetle can stay underwater longer on air than pure oxygen, why?

Then Davie whips out another beetle. THIS beetle, he tells me, has evolved a mechanism for keeping his bubble viable indefinitely - this despite the surface tension that's causing a driving force for mass transfer from the bubble into the water. How does he do it??

Then they let me out. I caught a Muller-Graves mutual head nod, which I took to mean "yup that's a pass". I was off to a good start. Thermo was next though, and I've hated thermo since the day I was born.

It started with a softball of a kinetics question about some catalyzed reaction and multiple steady states in a CSTR. The thermo question was about osmotic pressure - sophomore chemistry stuff. As soon as the words came out of the prof's mouth I knew it was going to be a train wreck - I hated osmotic pressure as a sophomore and hadn't given it a thought since. I wrote some equilibrium conditions on the board, and the prof goes, "OK, so that's what you think it is. Continue." And I was like, well that's pretty much all I got. Long awkward silence. I tried to make it into a different problem and began solving that one, but I was reeled back in. Lots of moving from one side of the board to the other, maybe I'll see the answer if I stand here... nope. I bumbled around and got nowhere for another 15 minutes, after which we were out of time (the exam had been running late so I think I only took about 35 minutes. A long 35 minutes though). Thank goodness.

Process was the next morning. I had John Prausnitz, major contributor to the concept of fugacity (still don't understand what that shit means) and elder statesman of the department. The other prof was Rachel Seagalman, admissions chair and a big question mark. I expected her to be bad cop, but she must have felt sorry for me.

I launched into a gripping schpiel about bioprocessing, in lieu of the senior design project that I can't recall a thing about. They loved it, they were intrigued, they wanted to know more. After all the process details that Steve sent me to prepare for the exam, I only got through protein A chromatography, and got cut off. OK, let's talk about some shit you don't know about now. Damn.

So Rachel wanted me to explain how to keep a fishtank clean. Obviously the first thing you do is get some of those sweet suckerfish, an activated carbon filter, and bubble some O2 through there. No problems. How do you reactivate the carbon? Whatever, eventually I got to hot water. Fish=alive!

Then Prau wanted to know about azeotropic distillation, extractive distillation, and all manner of chemE stuff upon which my grasp was quite loose. I was starting to frustrate him, aaah dammit woman why can't you just tell me the answer!! I was supposed to draw a T-x-y diagram for two components crystallizing - I pretty much completely failed to do that, until Prausnitz stomped to the board and drew it for me. This was accompanied by Rachel imploring me to "just count the phases Katie. Count the phases!! Can't you count!?!?" I could not count the phases.

Then we talked about the device that cools your microchip - a copper tube with a drop of water on it. The chip vaporizes the water, cooling the chip, and the water then condenses on the tube and rolls back to the chip to absorb more water. After that discussion, Prausnitz and Seags look at each other, and he says, "let's stop while we're ahead, shall we?" I hung my head, thanked them, and took a lap through campus to calm down before facing my classmates.

Everyone felt like shit, which seems to be the whole point of these exams, remind the smart kids how much smarter their professors are. It's an academic version of a frat hazing. But shit, I did just learn the bulk of 4 years of chemical engineering in 3 weeks. And that's something.

I'll tell you about the rest of the day later. I gotta clean my apartment.

April 23, 2009

Giant leap

Caution: the views expressed on in this blog are the views of Katie, and not necessarily completely thought out, logical, or rational. They have likely been conceived of within the last hour.

I saw Al Gore speak today; he was at the groundbreaking ceremony for the Richard Blum Center for Developing Economies. He was looking good - despite the red face he got each time the UCB Chancellor him "Our 46th President" (three times, corrected more hilariously each time. "Better to call the vice president the president than vice versa!" Maybe not in this case, Mr. Chancellor; I think that's a soft spot...).

Al was talking about how there is a lot of poverty and income disparity, and how we can't solve our environmental problems until the poverty problems are also solved. Then he let out the worst analogy in the whole climate change - you could see it coming from a mile away. "You know, it was just 48 years ago that Kennedy challenged America to land a man on the moon and bring him back safely, within 10 years. 8 years later, blah blah one small step." So obviously we can solve this climate change problem we have, if we just want it bad enough.

He also pointed out that since the industrial revolution, our society had turned much fossil fuel into much atmospheric carbon dioxide. That's true, but it wasn't what I expected him to say. I thought he was going to say that we'd turned all that fuel into knowledge, infrastructure, civilization, and population. Humans have proven themselves exceptionally capable of that - fossil fuels made the industrial revolution possible, which made the scientific advances of the 20th century and the society we live in possible. It made the moon shot possible. We're great at turning fossil fuel into knowledge and stuff and rearranged molecules.

We are not so practiced at taking knowledge and turning it into stuff. We have a society that can support cities and skyscrapers and salads and big populations, and that society is made of fossil fuel. We've learned a lot, but we have not learned to make stuff from nothing, or from orders of magnitude less than we do now.

Do you understand what I'm trying to say here? The moon shot was a simple matter of taking fossil fuel and turning it into a rocket ship and some mathematical equations that could get it to the moon and back. The energy problem is a matter of learning to make all the things our society can't do without, with very little. That is a problem of incomparable magnitude, and suggesting that it's not is irresponsible, naive, or a plain lie.

Who knows though, the moon shot only took 8 years. Maybe if Al had been prez, we'd have this shit figured out by now.


April 29, 2009

What is a chemical engineer?

Prof. Smit:

A mathematician is a person who can turn caffeine into theorems.

A chemical engineer can make excellent coffee in a swimming pool.

June 3, 2009

The next 4 years

Nice to meet you, mr. horseradish peroxidase.

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