"I once had a sparrow alight upon my shoulder for a moment... and I felt that I was more distinguished by that circumstance than I should have been by any epaulet I could have worn." -Thoreau

Friday, April 26, 2013

A Post From the Draft Archives. Incomplete, but Interesting.

Hello Dear Reader,

Well. This is being composed from within the confines of LAX. Somehow, too much time has passed and we find ourselves within the realm of 2013. One more trip, a few more hours of travel, and I complete the return to normalcy.
I'm going home, folks. Back to work.

There is too much to be said about the last semester, and about the year that has so recently come to a close. There are too many defining moments, too many short stories, too many characters to bring to life, too many scenes to sketch out: it is the problem of moving between worlds. Worlds are constructed out of impossibly many tiny details, delicately interwoven so as to avoid attracting the attention of those within their bounds. As a result, it is impossible to convey the rich, subtle structure of our foreign lives.

The remainder of my semester in Budapest was fantastic. It always surprises me how time is capable of shifting and re-shaping structures that appear fixed. But so it goes. New, wonderful, surprising friendships emerged. Lessons were learned. Fun was had.
In terms of travels, I ventured to Prague, Paris, Auschwitz, and Krakow. Each of these was an amazing experience onto itself. I had several nights of staying up to mad hours of the night, even going to bed just as the sun began to rise after a night of laughter, dancing, mangoes, and hot chocolate with friends. I enjoyed many a heartfelt, silly, earnest, intriguing conversation with people who effortlessly stole their way into my heart.
I am usually a bit disappointed and frustrated with myself when it comes to closings or goodbyes. It never feels sufficiently real and adequately heart-wrenching, and I am left feeling altogether too sensible and removed.
Leaving Budapest was not like that. It was hard. It was really hard.

(And that's when I boarded the flight back to Carleton. And life became crazy once more.)

Thursday, December 27, 2012

From a Lady to her Love, Expressing Sincere Regret

Dear Blog Of Mine,

    It is true that I have neglected you awfully. This I cannot deny, and I extend my most heartfelt apologies. When we began this relationship I vowed to treat you with affection and consideration. Yet with the passing of time I have allowed greater and greater distances to come between us. From once every few days to once a week to once every two weeks, it seems I am now down to visiting you once every two months. I am truly sorry.
    But, I plead you, you must not think this means that I do not love you. I have not come to see you, I have not sent word of my love, I have given you no sign of my affection or reason to believe in my devotion to you, but I swear that I have thought of you often.
    Yes, frequently have I found little pieces of life bringing me back to memories of you, despite the great distance between us and my voyages in foreign lands. Many times in the course of the last two months have I contemplated what I would say to you, how I would greet you upon our reunion, how I would devise some brilliant idea and present it to you for your admiration.
    Alas, no brilliant idea ever came. It is true, I was distracted, and I let time slip from my hands. I began to grow ashamed. I knew that I needed to see you, I yearned to return to you, but how could I face you as I was, shamefully tardy and embarrassingly empty-handed?
    However, I could wait no longer. I realize that I have been too far for too long, and despite the fact that I return unworthy of your attention, I wish for you to know that my affections have remained constant.
    I do not expect you to believe hollow words. It is not enough to utter statements of love and devotion, for these are empty if they remain unbacked. What can it mean to tell you that I love you, if that statement is the only reason you have to believe that it is so?
    Therefore, I do not propose to fill your head with empty words. Instead, I seek simply to love you. I hope that, if not your affection or esteem, I may at least earn your forgiveness along the way.

I assure you, I hope to remain yours, &c.
    A. Martin

Monday, November 5, 2012

Still alive. Still in Budapest.

Dear Reader,

Yes, I am still alive. And I am still in Budapest. And it is, mostly, exceedingly wonderful.
I am absolutely ashamed that it has been a long (yet short!) two months since last we met. It is embarrassing. I promise it will not happen again!
But, there's no use in lamentations at this point. We must boldly move forward!

So... How to even describe the last two months?
There is no way I can do it justice.

For one, I have developed two very dear and wonderful friends who I almost regard as sisters. Luckily, I get to take those two girls back "home" with me... at least until they graduate in June! Oh noes! But my two roommates have been crazy-awesome and I have come to love them immensely. Our room seems to be always filled with happiness and laughter, or else some good heart-to-heart. I have been infected by their speech patterns, I have started learning how to cook thanks to them, I have been enlightened through exposure to Riverdance, I have learned how to do a mean air-violin to Call Me Maybe, and much much more! Even had I not gained anything else from this program, befriending these two would have made my Budapestan adventures more than worthwhile.

But that's not all!
I have gotten to meet even more awesome people while in Budapest. Alas, most of these are people that I *don't* get to take back to Carleton with me. But I have thoroughly enjoyed our potluck dinners, crepe adventures,  discussions about connectionist neural networks, forays into Euclidean geometry, disagreements about the value of philosophy, late-night philosophical-movie watching, good-humored teasing, and all the rest of it! I love that I have gotten to know a group of passionate, intelligent, well-read, fun nerds who like to laugh and be silly, as well as to share/discuss/explain/argue about ideas. There are a lot of people I will be sad to leave come December...!
But it's been a good two months, and we still have one more! Huzzah!

I no longer embarrass myself at grocery stores (mostly). I have successfully navigated the Hungarian mailing system. I have befriended a couple of Hungarian students and an absolutely delightful French student. I have gone on two excursions with the program as a whole, which provided lots of good bonding time and pretty Hungarian scenery. I have learned to j-walk like a true Hungarian. I have learned how to put together healthy, delicious, and happy one-pot-wonders. I have come to love Budapest and its glorious river Duna.

I have also gotten to venture outside of Hungary. I went on a weekend trip to Vienna with my roommate Lauren. This was glorious-- not least because I was well-accompanied. I also spent a week in Italy for our break: one day in Pisa and three days in Florence (with my other roommate and another friend), followed by one day in Pompei and three days in Rome (flying solo). Oh my goodness... So, so glorious!

Vienna-- definitely the Albertina, with its jaw-dropping impressionist paintings.

Italy... Oh boy!: Climbing the leaning tower of Pisa. The sculptures at the camposanto at the Field of Miracles in Pisa, as well as the sinopias.  Florence's duomo. Michelangelo's David (!!). Pretty much all of Pompei-- ruins and gorgeous scenery both. Passing myself as a Spanish girl from Barcelona while in Pompei... The Roman frescoes at the National Museum in Rome (particularly the four walls of garden fresco... glorious!). The House of the Vestal Virgins at the Forum, as well as the rostrum, Ceasar's mound, and the temple of Romulus. The Colosseum and the Pantheon. Roman sculpture at both the National Museum and the Capitoline museum. Several of the rooms in the Vatican Museum. The art (especially Bernini's sculptures!!) at the Borghese gallery.

I basically discovered during my trip that 1) Medieval art can be hilariously not-that-great 2) David is a piece of beautiful, artistic perfection 3) Roman frescoes/art blow my mind 3) Gian Lorenzo Bernini is (was...) a freakin god.

As proof of that last claim, just look at this. I stole this from the internet (someone successfully violated the no-photo policy of the gallery...), but it is a close-up of part of Bernini's Rape of Proserpine, whose home is at the Borghese.
It's just like flesh!!
But it's marble!!!
Mind: blown. Life is wonderful.

My only point of displeasure is the fact that a number of these beautiful sculptures are supposed to be depicting rape.
...What? Not cool!
There seems to be a disparity between what it is showing and what it is claiming to show. It's weird and I don't understand. So that whole issue curbs my enthusiasm a bit, but... the artwork... and the sculpture itself... is astoundingly beautiful.

Sooo... Italy was amazing. Basically.

A brief note on academics before I must go to bed... It's already rather later than my bedtime...

Our semester is composed of a series of one-week courses, each taught by a different professor and tackling a different aspect of the very broad field of Cognitive Science. Thus far we have had: Intro to CogSci, Cognitive Neuroscience, Cognitive Ethology, Brain Imaging, Philosophy of Language, Cognitive Informatics, Consciousness, and now we're on Embodied Cognition.

The semester started off roughly, with professors who failed to provide texts or supportive materials, did not give very good conceptual explanations, or assumed a non-existent background in their field... but the semester has more or less steadily progressed, which is wonderful. Also, at the beginning, I was quite frustrated by the very cursory one-week structure of the semester as a whole. However, I think my opinion is starting to soften. I wouldn't say that the different classes *build* upon one another- not exactly. But there are certainly overlaps and interesting connections between different courses, and I am really enjoying the conceptual framework that is starting to build across these various sub-disciplines.

In addition to these classes, I am also taking Theories of Meaning, a philosophy of language seminar, "on the side." Much to my delight, this class has complemented my CogSci coursework and my general interests quite beautifully.

So, generally speaking, life is pretty awesome.
I am in a beautiful place with relatively easy access to other amazing and beautiful places.
I am surrounded by warm, fun, nerdy, wonderful people.
I am making connections between concepts and being introduced to seductive fields of study... What more could I possibly want?

Moreover, I feel as though, albeit very slowly and not at all clearly, I am making some sort of progress in life. I am still highly uncertain as to what I want to do, but it's becoming clear that the path I am on can probably take me to wherever I decide I want to go.

So, for now, I will just enjoy the gorgeous scenery.

Wednesday, September 5, 2012

Language Barriers (and some pictures!)

Hello, hello!

It occurred to me that it would be appropriate to start off this post with a Hungarian greeting.... but, unfortunately, my Hungarian remains virtually non-existent. The only words I know how to pronounce or recognize are köszönöm (thank you) and 205b (my room number).
Yes, this is pathetic.

I have decided that perhaps it should be some sort of requirement for people to venture off to a land where a significant (though certainly not impossible) language barrier exists.
It just so happens that Hungarian is a non-Indo-European language. Of course.
What this translates to is utter impenetrability. Never before have I looked at signs, labels, or any decent-sized body of text and had absolutely no clue- or worse, no hope!- of what its contents is. (Okay- never when looking at a language where I recognize the characters.) It's really rather disconcerting.

I have become more used to navigating the local parts of Buda on foot, and am starting to get a vague idea of the whole transportation thing. So it's gotten to a point where I feel more or less comfortable walking around in Budapest, and it can be easy to forget that I am in a foreign country.
And then I get hungry, and decide to look for food.
And then I realize that I am incapable of ordering food or of communicating my desires to a non-English speaker.
And then stress emerges.

Although my roommates and I are now capable of navigating the grocery store without embarrassment, we have had moments where we decide to not buy something because we're not sure it's what we think we is. Scanning the product description does no good... because Hungarian is not Indo-European!
Life is hard.

It's also startling when I find something written in English or hear English music being played. For a moment it is normal, and then I realize, 'Wait! I understand that!'
It is surprisingly comforting.

So. Yes. I think it might be enlightening for some to experience the sense of hopelessness which can emerge when you are surrounded by incomprehensible words and people who may or may not  1) be able to understand you or help you and 2) be okay with the fact that you do not speak their language.
I think I shall certainly be returning to the states with a greater sense of empathy and understanding.

But anyway, my first Hungarian language class is tomorrow! So hopefully I shall improve my food-procuring abilities and prevent starvation!

Other than exciting language barriers, there has been a lot of... taking care of business (buying transportation passes, applying for a residence permit, purchasing a cell phone, etc) and doing touristy things and enjoying down time. Good stuff, I guess. Class starts tomorrow, though. I'm excited, but a little uncertain what to expect.

As promised, I finally got around to taking a few pictures of my new home!
Here is the front of the building:

These are stairs that lead up to where the dorm is...

And some images from the interior...

The last is the view from my window. It makes me happy :]

Well, classes start tomorrow... I must be up early! It is past my bedtime.
More exciting updates and pictures to come soon!

Au revoir!

Sunday, September 2, 2012

I am in Budapest!

Hello World!


After a long day of travel, I finally arrived in Budapest yesterday!
This is very exciting.

Whilst travelling, I was most impressed by the apparent competency of my foreign travel companions. My flight route was LAX --> OHare -->München (aka Munich, but München is much more fun) --> Budapest.
I felt completely at a disadvantage during the whole international portion of my travels, given that while I, a foolish American, spoke only English (well, and Spanish, but I heard little Spanish), all the foreigners seemed well-versed in a multitude of languages. It was very amusing to have flight attendants look at me and list off a number of languages to figure out how to address me.
If only I were that cool.

Fortunately for me, English is widespread, but I can't help but wish I were cool and European and well-versed in a handful of European tongues. (Adds note to bucket list.) I don't think I've ever felt quite so American.

Eventually, I survived the approximately-20-hours of travel time, and was greeted at the airport by a friendly BSCS representative, only to discover that one of my flight companions was also to accompany me in this whole crazy Budapest thing. He seemed pretty cool and very excited to be in Budapest (which I greatly appreciated), but I was mostly gratified by the fact that his pile of stuff was larger than my pile of stuff.
Ha! Success!

After some taxi travel through this city of seemingly endless pretty buildings, we arrived at our home for the next three months. (Pictures to follow eventually.)
We are dorming in the Eötvös Collegium, which is a pretty building to satisfy my yearning for pretty buildings.

I am rooming in a triple with two other awesome Carleton girls, which I think was a good decision on my part. Friend-making and adventuring! Huzzah!

Last night I had my first Budapest adventure.
My roommates and I decided to venture to a nearby mall for the purposes of procuring dinner, as well as entertainment.
We weren't very impressed by the fast food places inside the mall, so we decided to shop at the grocery store there instead.
Well, that was pretty exciting.

The actual shopping experience was pretty uneventful, because product labeling is pretty excellent and not all that language-dependent. It's not difficult to figure out what things are.

Checking out was an altogether different experience.
Our cashier was not very English speaking, and this led to some fun times.

1) We were supposed to remove our grocery items from their basket.
We did not know this, and his repeated attempts to command us to do this in Hungarian were remarkably unfruitful. And slilghtly mortifying. Eventually, a nearby customer figured out we were clueless English speakers and clued us in.

2) Unlike in the U.S., the scales at grocery markets are apparently useful in Hungary. We did not realize this. Our friendly English-speaking fellow customer had left at this point, and our cashier was now trying to communicate to us that we were to have weighed out our fruit and gotten a price for it in the produce section. Again, he said this many times in Hungarian, and we were left exchanging helpless looks with one another.
Ah, language barriers.
Eventually, he pulled out a piece of paper and managed to write out "measuring bananas," which provided us with instantaneous illumination as to what he wanted.
Again, mortifying, but slightly hilarious.

3) You are supposed to purchase the bag into which you put your groceries. Preferably, this should occur before (or at the same time as) your grocery purchase.
Another embarrassing and hilarious moment for the clueless American girls.
We have finally figured out the whole de-basket groceries and pre-weigh fruit thing, and have apparently successfully completed our first transactions. Woo!
But then we realize a conspicuous lack of bags or bagging, stand around awkwardly, and finally figure out we need to buy our grocery bag.
So we finally do that, bag our groceries, and leave the grocery store in a fit of laughter and many apologies to the poor cashier, who seems glad to have survived this encounter with a group of idiots.

Mind you that this whole process was even more amusing because the failures occurred in two consecutive transactions, since my roommate was bearing the direct embarrassment, and I was following in her shadow (but still attracting attention as fellow clueless American girl.)

All in all, it was an exciting, humbling, and amusing adventure. We've decided to learn key Hungarian phrases like "I'm sorry" (we felt the need for this phrase a lot...), "Thank you," "Please," and especially "I don't speak Hungarian..." (likely to be paired with an "I'm sorry.")

I think this Budapest thing is going to yield some fun times :]

And now I must get ready to do some touristing! Farewell!

P.S. Another amusing thing is how google (and all these other websites) assume that because I am in Hungary, I must speak Hungarian.
Ha! If only, if only.

Sunday, August 26, 2012

Lessons from Computational Chemistry!

Hello, hello!

If anyone could explain to me how there is less than a week left of the long month of August, I would be most grateful.

I find myself back in my SoCal home... somewhat disoriented, excited, distraught, happy, lonely, scared, nostalgic... yearning at turns for comfiness&coziness and for excitement&adventure.
Mostly, I feel very unprepared about the unreal reality that, granted the benevolence of the Fates, I shall be leaving for Budapest in five days(!!).

The last two weeks or so since I last wrote were a little crazy, and quite wonderful.

Research ended nicely- and I shall attempt to provide an explanation of the exciting things I was doing! :]
Brace yourself, dear Reader. We are in for a trip!

So... Our simulations for LTA were failing quite miserably, and we believe the cause (or one major cause, anyway) to be the presence of a dipole in our unit cell structure (we'll talk more about dipoles later).

Backing up a bit. My work was with zeolites. Zeolites are pretty crystals, which means they have repetitive structural units-- aka unit cells. What this means is that you can tile a bunch of unit cells together to get a zeolite-- this not only contributes to the beauty of staring at atom-level pictures of zeolites (which I am fond of doing), but it also means that we can save ourselves time by exploiting the symmetry of the system. Look! A picture!
A unit cell is here boxed in red.

In order to run our simulations, we tile together something like 12 to 36 unit cells (pretending we actually have a 2D system, we can see 4 unit cells in the picture) because 1) we can't afford to try to model a super large system and 2) we can use tricks to make the system seem bigger than it actually is (to get more realistic results).
[For those more mathematically inclined, refer to periodic boundary conditions (we’re mapping onto a torus!!)]

We have essentially two versions of the code that controls our simulations-- one which uses Ewald summation to deal with interactions between charges, and one which does not. For the purposes of this discussion, it doesn’t matter what Ewald does. I’m just using it to differentiate between two different ways of running the simulation. The important thing here is that the version of the code which uses Ewald (which is the version we were interested in) needs the coordinates of the unit cell to be such that the center is (0,0). The other important thing is that using Ewald requires that the unit cell not have a dipole.

For those of us who do not remember what a dipole is, dipoles emerge when you have an imbalance of charge. To use my professor's example from intro chem, think of elephants pulling on a rope tied to a tree. If you have two elephants pulling just as hard in exactly opposite directions, the tree will not fall over. If one is pulling harder than the other, or if they’re pulling in a way that the forces they are exerting on the tree don’t cancel out, the tree will fall over. So having a dipole è the tree falls over.
In this case, we don’t want the tree to fall over.

So we want a structure centered at zero. However, the crystal structure does not start off this way. Instead, it starts off such that the (0,0) point is at the lower left corner.

Original, Uncentered LTA Crystal Structure

Ewald thinks that this is not okay, and so there is a function in the Ewald code that “centers” the structure to make sure that the structure is the way that it likes it.
At least theoretically.

Problem: Somehow or another this function was not working quite properly. The original crystal structure has no dipole (we know this because when we use the non-Ewald version of our code, all is well, and when we use Ewald, things go terribly wrong), but after centering it, it does. This suggests that something funky is going on... and the crystal is not, in fact, being centered properly.

 So, my job for the last few days of summer research was to understand what was going on with the centering process— with the goal of modifying the crystal structure such that it is centered (and dipole-less) to begin with, and undergoes no modification when put through the centering function in the Ewald code.

How things are--
 Crystal structure (no dipole, uncentered) --[Ewald centering function]--> Weird, dipole-carrying structure
How I want things to be--
 Modified, centered structure –[Ewald centering function]--> Still nice and centered structure

Alright, so now the problem-solving part.

First, some terminology. 
Because I can’t look at the structure in 3D very easily, I was looking at projections onto a plane.
So what does this mean?

Imagine you’re looking at a cube. This is 3D. Now imagine you start to push on the top of the cube and the inside of the cube kind of collapses so you can flatten the cube into the ground, and you’re just left with…. 
A square, yes? (Yes.) That square is the projection of the cube onto a plane.

Or, if we started off with a delicious donut and for some reason decided to squash it down instead of eat it, we’d get two concentric circles as the projection onto what I shall arbitrarily term the xy plane:

A torus (or mathematical donut)
Projection of torus onto plane

[Of course, there’s no reason why you must squish your donut down towards the floor. You could also think of squashing it against a wall—what would that look like?]

Now that we have that, the pictures we saw earlier were the projections of the crystal structure onto the xy plane. And, again, here is the original, uncentered structure:

And here is the output of the centering function (again, projection onto the xy plane), which then gets used in the simulation:
Centered structure.
Red = oxygen atoms, blue = silicon atoms

See how we’re now “centered” at zero?

However, there is a problem, and it is one which would clearly give rise to a dipole. Remember, we want things to be nice and symmetric (such that for any elephant pulling in one direction, there is another elephant pulling just as hard in the opposite direction to balance things out)—but they are not!

(The problem is with the O atoms, specifically, so here we're just showing the oxygens)

Essentially, in the orange circles we have little oxygen elephants pulling on an imaginary tree at the origin. The problem is, the other two edges are missing little oxygen elephants-- so the tree is going down! Oh noes! 
If we look back at the uncentered structure, which has both Si and O atoms (they're just both in the same color [we also have these "X" atoms at the center of each "ball," but don't worry about that]), we see that we have elephant oxygens along all four edges (as well as two sets along each axis)-- but once we center it, we lose two edges of elephant oxygens, and the tree comes crashing down. Clearly something is amiss.

This means it is time to understand the behavior of the centering function!

Initially, I started trying to think in 2D, and this led to my being very confused about what was happening, such that I didn’t get the point of how things worked. Bad idea.
Lesson learned: when trying to understand something, it’s not stupid or simple-minded to start off with the simple model. Au contraire! Keeping things basic allows you to see and understand the important behavior, which will help you out when the system becomes more complicated. At any rate, it’s what scientists seem to believe, and it was wisdom that served me well.

So, let’s focus on 1D.

First, the function:
 xnew = xold – ROUND(xold/L)*L    (where L is the length of the unit cell)

So let’s pretend we’re looking at a unit cell (in this case, let’s just look at a line segment) of length 8, and let’s see what happens at each “quarter point” – so what happens to 0, 2, 4, 6, and 8.

For 0:                          
  xnew = 0 – ROUND(0/8)*8
        = 0 – ROUND(0)*8
        = 0 – 0*8
        = 0

For 4:
  xnew = 4 – ROUND(4/8)*8
        = 4 – ROUND(0.5)*8
        = 4 – 1*8
        = -4

For 8:
 xnew = 8 – ROUND(8/8)*8 = 0

For 2:
 xnew = 2 – ROUND(2/8)*8 = 2
For 6:
 xnew = 6 – ROUND(6/8)*8 = -2

To illustrate what happens, we can look at the original line, and see where the original points end up in the centered line:
             Original line:


Transformed line:
The color coding is intended
 to "trace" points.

Now, I will point out the interesting things. The points from 0 to right up to 4 (or more generally, from 0 to right up to L/2) end up being unchanged. The points from 4 to 8 (or L/2 to L) end up becoming the negative half of the line (well, plus 0), with L/2 becoming –L/2. It’s like we have cut the original line at the halfway point and moved what used to be the upper half to the end, so that the last point (L, or 8 in thi case) matches up with zero.  

The problem is, that now we have two points that get transformed to zero, and we have no point mapped onto 4, or L/2.

To look at more pretty pictures of projections of LTA….

Below, I noted how the transformation works. The blue is the original input structure, and the beige is the “centered” structure. Because the unit cell has so many nice lines of symmetry, I considered what happened to each of the four “balls” that make up the unit cell. If you don't get what's going on, don't worry about it, and just admire the pretty picture (at least, I think it's pretty). Or use the discussion about our 1D model to try to make sense of it! :]

Once again, I used color coding to trace things.
The arrows are intended to provide  perspective.

And here we see that the “missing points” in the projection are located at Lx/2 and Ly/2, which is to be expected from our discussion.


In other words... it's like instead of having a set of elephants along each edge, as well as along the axes, we now have relocated the elephants which should be along the edges corresponding to the midpoints (Lx/2, and Ly/2) to the x and y axes (respectively). This means we have two sets of oxygen elephants located along the axes... stacked on top of each other, so to speak. This image, quite properly, is rather ridiculous.

Now I’ll fast forward the story, because I’ve probably already long lost my few readers.
(As always, feel free to ask me about anything I've mentioned. I'd LOVE to talk about it!)

Basically, we have the points at both 0 and L mapping on to the new zero point. So what I did was figure out which points in the centered structure which were located at zero (or rather, along an axis) originally came from a point whose x, y, or z value was equal to L, and then moved that point in the centered structure from 0 to L/2. [Well, actually, I moved it just a teeeeny bit to the left of L/2, because if you’ll remember, a point at L/2 gets moved to –L/2 (4 got moved to -4, in our 1D example above)].
To translate into elephant language, I looked at the silly stack of elephants on the axes and relocated the elephants on top to a more dignified position-- along the empty edges.

At the end of this process I had a centered, dipoleless structure (uh, in theory…). Moreover, because this structure is already centered, upon going through the centering function, nothing changes.

Here is the result of centering my new centered input structure (also, just so you know, the projections onto the yz and xz planes look the same):


Yay! Things appear to be fixed!

BUT WAIT. The problem was the dipole, and now I needed to actually calculate the dipole and make sure it was zero. I’ll spare you the detail, but… THE STRUCTURE STILL HAD  A DIPOLE! Granted, it was a much smaller dipole than it originally had… but still! Not cool, man!

Unfortunately, this realization happened at nearly the end of my last day of research, and there was no real time to do more problem-solving.

What I can say is the following. If you will recall, all these pretty pictures are projections onto a plane—aka, squished donuts. I would argue that squished donuts are not as enjoyable as real donuts, and it is much the same with these projections. You lose information in the flattening process.

To get an idea of this, imagine that cube again. Now imagine giving the side edges of the cube a jagged cut, so when you look at it straight ahead, you see something like:


The problem is, if you squish it toward the ground, you still just see:

This isn’t the best example, but the point is, we can imagine that there was important information being lost in the squishing process, such that while the projection was nicely symmetric (and thus dipole-less), the 3D structure still had rowdy elephants causing problems and knocking over trees.

Unfortunately, my story ends here. I have a bit more detailed information about the remaining problem (ask if interested), but alas, at this point my research time was over, and I needed to get ready to get on a plane to visit a certain Russian-enthusiast close to my heart (if very far away in spacetime). So I still don’t understand exactly what was happening in the 3D structure that I wasn’t seeing in the projections, and I don’t understand at all how that problem came about.

I did learn a few things, though, including:

1) I love staring at pictures of pretty crystals. !
2) Start small when trying to understand tricky things.
3) It’s okay to feel clueless and lost and not good enough. You are good enough. Just take a  deep breath, and start grasping onto whatever you can. Eventually things will start to make   sense.
4) It is good to start small, but don’t be surprised (or traumatized) when you take it up a level, and suddenly things are broken again. You’ve made progress! And you’re that much better at fixing things.

I learned this while getting lost in lines of Fortran and suspecting I was actually stupid and incompetent and while fearing that I would never understand what the hell was going on with these zeolite things…

But I suspect that what I learned this summer will extend far beyond the abstract world of atomistic simulations and impact the way I carry myself in everyday life--  in the same surprising way that playing around with code can extend beyond the virtual world and uncover some truth about reality.

Huzzah for computational chemistry! :D

Monday, August 6, 2012

A Summery Crescendo- And a Happy Belated Blogiversary!

Ah, hello lovely people!

Well. It is strange to say, but my summer is coming to a spectacular crescendo finish.
This image of my dry-erase monthly calendar, as written in on August 1st (more things have since been added) may give you an idea of how spectacular life appears right now:

I am currently in the ninth, and penultimate week of my computational chemistry research, which transitions to a Dylan-reunion in which I get to spend FIVE GLORIOUS DAYS with a most-beloved boyfriend I won't have seen in 5 months (and whom I will almost certainly not see again for another four...), only to arrive home with just enough time to bask in the light of kinship before going to BUDAPEST for a semester.

These super-exciting things are interspersed with smaller but also very exciting things-- like the happy "girls' night" which awaits me in but half an hour, a happy anniversary, a chem talk to be delivered on my research for the last nine weeks, a canoe adventure with the chem department, a celebratory dinner at my professor's house, and my last four remaining Summer Social Dance clubs! If we conveniently ignore the miserable packing process which must occur in the next ten days, the next three weeks promise virtually nonstop happiness and excitement. And, given that I then transition into a voyage to Europe...
Life is so great.
I am happy and excited.

In general, I think this summer has been a happy one. I think I have done well in life since turning twenty. Despite the suggestions of my previous post... (it was not a good day or week, and it is acceptable to have those moments of sadness and weakness) I really have done a much better job of feeling confident, worthy of love, and capable of standing alone.

In the past I have struggled tremendously with giving myself credit for anything. While I highly prize modestly and humility, I still think that it is important to give credit where credit is due-- and I have slowly been able to say, "You know what, self- I am proud of you for that. That was difficult, but you pulled through. Nicely done."

Near the end of my "Spring Quest" I mentioned that, in a way, I would be away from Home for a while. I expected year 20 to be a hard one. It's certainly not over yet, but as I reach the almost-half-point, I would say it is less of a hard one than a challenging one with great opportunity for growth. It is true that I have had moments of insecurity and loneliness and sadness. BUT those days could be counted on a hand! (Maybe two hands...) I expected to feel estranged and alone in a kind-of-exciting-but-mostly-scary foreign land.
Instead, what I see is a large number of new friends and acquaintances-- I have effectively expanded the stretch of metaphorical land that I can call "home."
I have helped create a wonderful summer social dance community filled with people I have grown exceedingly fond of, I have deepened old and developed new friendships, I have learned that I can hold a conversation with people I don't know very well and have a wonderful time without crumbling into crippling awkward-nerd-girl-awkwardness. I have gained a smidgen of culinary experience, explored the natural beauty surrounding my Carletonian home, learned that I actually kind of enjoy running (what?), discovered that piano is awesome and beautiful, become fluent in the language of zeolites, and generally partaken in wonderful growth.

There are challenges ahead, however!
I have about a year before I need to make scary decisions about life post-Carleton.
I have three months to take Europe by storm. (Yeah, life is hard...)
I have to learn to be strong and to actually communicate my thoughts to those around me.
I have to push myself to continue creeping outside my comfort zone.

I thought I wouldn't make it past the level of Slightly Slower Slug... but we're making it to Slow Swan this year!

To my very small handful of Readers, happy belated blogiversary!
Yup, this little blog has been in existence for a little over 365 days (372 to be exact).  I don't know that the blog has grown all that much... but I think that I have grown more than I expected. And I would like to thank you, rare and dear Reader, for sharing in that wonderful process with me.

I hope year two brings even more exciting challenges, adventures, and happiness.

Huzzah! Cheers!