Friday, July 29, 2011


Since it's a busy day, no full blog post. However, I'm curious to know who reads my ramblings. Stats tell me where y'all are from, but not much else. Hence, a poll!

What best describes you?
Undergraduate student
Graduate student
Industry Engineer
Lost and confused Googler
None of the above: I'll explain in comments free polls

Thursday, July 28, 2011

Speculative Abstracts and Golden Children

... are the bane of my existence. Because my advisor wasn't willing to say no to an invited talk, in an area in which no one in my group is actively working, I now have major deadline convergence, between the Project That Won't Die (PTWD) and the Project My Thesis (proposal) is On (PMTpO). Combined with recent server downtime for maintenance, I'm alternating between panicked analysis/coding and thumb twiddling while I wait for something to run.

PTWD is producing the data for his invited talk, while PMTpO needs to have results for the annual funding review (we'll ignore that I'm a fellowship student). I think under normal circumstances, my advisor might have been sane enough to say no to the invited talk, but the invitation was from his perpetual Golden Child, who somehow remains the golden child, despite having left for a professorship position three years ago.

This isn't the first time my advisor submitting abstracts has resulting in non-thesis work for me, requiring generation of fairly substantial amounts of data in short times. However, I've been here for 2+ years now, and I can't recall this happening to other students in my group. I'm chalking it up to egocentric obliviousness, but my code is done for the moment, and it's time to switch from thumb-twiddling to panic.

Tuesday, July 26, 2011

Dealing With Data

When I arrived at GiantU, I got involved in a project to understand how scientists deal with data, how the Information Sciences can help, and how to get scientists to start sharing data. I've learned more about metadata than I ever wanted to, but I've also realized this: dealing with data is largely a personal issue. The knee jerk reaction seems to be to declare that we need standards. However, I feel XKCD describes the issue with standard succinctly:

The project here involves the Information Science people, biologist, and materials scientists. The biologists seem to have it (comparatively) together, especially for gene sequencing. MSE, on the other hand, is a mess. Within a lab group, there may be some standards for how data is organized and formated (behold the power of nested folders and descriptive file names), but there's very little agreement as what is the data, and what is the metadata (i.e., descriptive information). If you're tracking rainfall in the Pacific Northwest basin, there is a fairly discrete list of data/metadata you need to report. Time frame of data collection, geographic coordinates, amount of precipitation, etc.

Materials science can be very process driven (remember the tetrahedron?) and so if you're tracking the density of carbon precipitates in a bar sample, you need the precipitate count and the bar size, but you also need the composition, the specimen manufacturing history, the heat treating history, the sectioning method, the polishing method, the counting technique and microscopy method, just to start with. So while the final data may be density of carbon precipitates, the *main* data is more or less everything else leading up to it. Several years ago, there was a project to develop a markup language for materials science, sponsored by some of the major professional societies. This conservative list still came up with 39 tags, most of which require significant text for any given data point.

There is an increasing push for researchers to share data, but in what format? Who decides what format? Right now, the biggest decider for raw data formats is the software you're using, which can depend on your equipment manufacturer, and may be adjustable. What counts as data?

Many of the Information Science folks feel very passionately about the issue, but seemed to think of it as an issue of building an appropriate database. The overwhelming reaction they've had in working with us has been "We never realized how much metadata you had".

Open data is a nice philosophy, but there are a lot of barriers to be overcome, far beyond where the data will be stored.

Thursday, July 21, 2011


I'd have something witty to say today, but my code is being mysteriously buggy, and there's a heat index of 110 right now, so my brain is out of spare wit.  I'm not meant for warm and muggy...

EDIT: Oh goody, now the warn us that they're going to have to minimize cooling in non-critical areas, because the air conditioners are overstressed.  So fun...

Wednesday, July 20, 2011

Safety Training

Since I am a computationalist at GiantU, I've gotten away with not sitting through OSHA training for two whole years. However, I'm tentatively TAing a lab course this fall, so I had to go sit in a  dark room and listen to a rather quiet man talk about gloves for 30 minutes, plus everything else.

Because it's summer, they only offer the combined safety class, which meant I also got an hour of lecturing about blood-borne pathogens and other biological hazards. Surprisingly, this safety training spent rather little time on scare tactics compared to other training I've done, and almost nothing about espionage (a big feature of both LargeManufacturingCompany and NationalLab trainings).

Even though most of it wasn't personally relevant, it was rather reassuring to know that GiantU has a pretty rigorous lab safety program. They were very keen to reiterate "if it seems unsafe, you can ask us for help". Hopefully people actually do.

Tuesday, July 19, 2011

Conference Presentations

I have finally learned when my presentation at this fall's MS&T conference will be (one of the largest conferences in my field), and boy, is it a crappy time slot. The conference runs Monday through Thursday, and I'm scheduled for one of the last time slots on Thursday. I didn't expect high attendance at my session anyhow, but I may have an audience that consists solely of other people presenting in my session and a few advisers.

Worse, all of the networking events/sessions I want to attend are on Monday. I'm still waiting to hear when the other students in my lab group are scheduled to present, but it's hard to justify the expense of staying the extra nights if they aren't presenting until later either, particularly since my fellowship has no travel support.

When do you find is the worst time to give a conference talk?

Monday, July 18, 2011

How Marching Band Made Me a Better Presenter

One topic that seems to pop up a lot in the academic blogging community is how to give better presentations, or how women can command respect. Many people rather more qualified than I have commented on the rules of Power Point, and Better Posters is a fantastic resource.  However, most often, it's the speaking part that people seem to really struggle with. After four years of marching and 4 years of anti-m******* band, I've learned a few things that help me present more effectively. While I may not be a renowned public speaker, I'm pretty sure I don't suck at it. So here's some of the things that I learned that I think make a difference:

1) How to stand "at ease": Standing up straight conveys confidence to your audience, as well as making you feel more confident. However, many people tend to also become very tense when they try and stand up straight. By standing at ease, with your feet spaced at roughly shoulder width and deliberately relaxing your shoulders, you still look confident, but much less tense.

2) How to breathe properly: Ok, so you aren't fainting from a lack of oxygen, and you've been breathing your whole life. That doesn't mean you're doing it in the most effective way properly. When you take a deep breath, does your chest move first? Then you're doing it WRONG. To fill the lungs fully, you have to start at the bottom. Musicians learn to do this to maximize phrases and support tonal quality. Taking deeper, controlled breaths can slow you heart rate and calm down some of those presentation nerves. It also feed directly into my next point.

3) How to speak loudly (without yelling): Project from the diaphragm. Volume shouldn't come from the throat, it should come from lower. By using air to support your voice, you have a more solid tone that will carry more effectively. For women with higher-pitched voices, thinking about speaking from the gut instead of the head can help shift your tone down a bit, which tends to help you sound a bit more mature.

4) The importance of pauses: Take a few moments and listen to Shenandoah: (it's ok, I'll wait)

It's a very fluid piece, and it seems like there's always something happening. But if you pay attention, there are certain places where everyone seems to stop for a breath, creating more interest in the line that will follow. By pausing, you can subtly emphasize the statement following your pause. Use this as a time to take a proper breath. For a true masterpiece of pausing, Aaron Copland's Fanfare for the Common Man is hard to beat:

Sometimes, just by thinking about little things, like breathing, rather than focusing on what word you are going to say next, you can seem much more confident. And if you ever need to find a marching band geek to help you, just mention how amazing you think John Phillips Sousa and wait for them to come out of the woodwork (warning: there are very few moderate opinions on Sousa, especially amongst brass players).

Friday, July 15, 2011

Reference Lists

I'm in the process of polishing a manuscript, as well as preparing for my preliminary thesis proposal. One thing I've noticed is a lack of standard for how many references a paper is expected to have. In my subfield, there seems to be an average of 30-40, but I've seen from 20 to 120 (neglecting review papers).

What's average in your field?

Thursday, July 14, 2011

Not Everyone Should Go to College

Once upon a time, before I accidentally became a computationalist, I was educated as a classical metallurgist. Consequently, I spent a decent amount of time in machine shops and foundries. I spent a summer working for Large Manufacturing Company, and spent a decent amount of time interacting with guys who didn't have a college degree, but knew more than I ever would about how machines work.  And while my parents are engineers, my mom's family and Mr. ME's family are mostly very blue-collar people. Not all of them have a college education, and several have degrees that have nothing to do with their careers. College wouldn't have gotten them where they wanted to go in life.

College gets more expensive every year (Mike the Mad Biologist has some lovely numbers here). The Chronicle of Higher Education asked the question "Are too many students going to college?" Most of the panelists seem to avoid the main question, but as academics, there's a certain amount they have invested in getting more students in the door. They focus on things like the wage premium. However, that wage premium is relative to all people without degrees. What about the difference between a bachelor's degree and trade school? I think the gap narrows dramatically then.

We need welders. We need plumbers, electricians, car mechanics, glassblowers. But we also need to stop telling every high school student that they should go to college. I had friends in high school, who were academically gifted, but knew that what they really, really wanted to do with their lives was fix things. They were lucky to have parents who supported that, and to live in a school district that had courses that would help them get their technical certification. There are some people who are not suited to a desk job. There are some people, who after 12 years in the US educational system, want to learn something practical, not theoretical. Why are we trying to convince them to go to college, an increasingly expensive proposition? Why is making money more important to our definition of success than being satisfied with your job? When did going into a trade stop being considered a good option?

This is also one of the things I love about the steampunk community. It's very much a maker's movement, with a strong appreciation from craftsmanship. Instead of throwing things away when they broke, building them well, and fixing them.  My college education has taught me a lot about thermodynamics and Newtonian physics, but that won't help me fix my car.

Wednesday, July 13, 2011

Outreach: Why High School Teachers Matter

One of the materials science professional societies, ASM (which used to stand for the American Society of Metals, but now just stands for ASM), runs a series of camps for high school teachers to learn about materials science. It's a multi-year program, and for a week each year, they learn about some of the basics of MSE, and do experiments they can take back into their own classrooms. While the NSF Broader Impact criterion typically seem like they encourage K-12 outreach by working with students, I think working with the teachers can make more sense.

  • Teachers are more enthusiastic and interested learners. If you have a group of 30 teachers, you have a group of 30 people who probably want to be there. If you have a group of 30 high schoolers, you probably have 2-3 who really want to be there, and at least one who would rather be *anywhere* else.

  • One teacher reaches hundreds of students. Teaching 30 teachers about science, and what scientists do, potentially reaches thousands of kids over years. Working directly with students reaches those students, and  some of their peers. 

  • Teachers can tie in new concepts into the curriculum much more effectively, because they know what else is actually covered.
This is not to say that I think we should stop running student-directed outreach in the slightest. Summer science camps are a fantastic thing, and many of my peers went into engineering because of similar experiences. It also gives kids a chance to explore an area that may not be feasible for their school to have a program in, due to demand/budget/classroom space. However, teaching teachers is a great way to reach a wider audience. For a field like MSE, which many students don't even know exists until partway through college (and some not  until they've graduated and gotten a job), having potentially interested kids know the field exists is a pretty good start.

Monday, July 11, 2011

New Kitten!

I totally had meaningful posts about real-world issues lined up, but I got a new kitten! And because this is the internet, kitten pictures trump intellectual content any day.

Rory, aka Mini-Me:

Friday, July 8, 2011

This is the project that never ends....

My advisor was in town briefly yesterday, and managed to stop by the office in the sub-24 hour period he was going to be in the correct time zone. He's finally started reading the manuscript that's been sitting on his desk longer than I'm comfortable admitting. Foolish me, I was hoping this would be a sign that the associated project might wrap up sometime soon.

Despite the fact that the funding for this project ran out over a year ago, and I'm supported by a completely different project (i.e., my alleged thesis topic...), half of our brief meeting time was spent with him talking about all the things he wants to do next for this project. Note that this project was supposed to only be for my first summer, to get me acquainted with molecular dynamics, and help the post-doc working on it wrap up his papers.  So a project that was originally intended to last 3-6 months has now taken two years, and the papers *still* haven't left the building.

I'm reluctant to simply announce that I'm done with this particular branch of work, because I'm sitting on three more manuscript drafts, and I would like them to make it out the door sometime before I manage to. On the other hand, the longer I'm working on this first project, the longer it's going to take me to get fully entrenched in my supposed thesis project. It doesn't help that it takes some serious shoe-horning to try and get both of these projects into a thesis together in any sort of semi-coherent fashion.

Any suggestions for how to tell my advisor that I would like to work on my thesis project full-time?

Wednesday, July 6, 2011

MSE 501: Molecular Dynamics, An Introduction

I've discussed the sheer number of subspecialties in materials science before. I'd like to go into a bit of depth on my personal subspecialty, simulation. My work is in molecular dynamics (MD). The linked Wikipedia article is fairly technical. Fundamentally speaking, molecular dynamics uses Newton's First Law to determine the motion of atoms or particles according to a force equation. Particle interaction forces are described using one of many possible forms of the potential energy equation, and by integrating F=ma over a finite timestep, the motion of each particle can be determined.

Force potentials (mostly just called potentials) come in several basic forms, but typically are strongly repulsive at short distances with a low energy well at the preferential distance between different particle types. These potentials can be empirical or derived from quantum mechanical calculations, and may or may not take into account things like charge interactions or bonding, depending on your system. The majority of work in simulation goes into generating and validating these potentials for your system.

But how do we get started? There has to be an initial configuration from which positions are predicted and integrated. There's several ways, but it typically boils down to either using a crystalline structure, a random generator, or some combination of the two. These systems typically contain 10^4 to 10^6 atoms, with very few facilities capable of reaching millions of atoms(BlueGeneL, Blue Waters, etc). This is because for a number of atoms N, the number of calculations for each time step scales as roughly 3*N^2.

One million atoms isn't very big. One mole is more than 100,000,000,000,000,000 times larger than that. Even if Moore's Law were to continue indefinitely (which it probably can't, but that's another post), the sheer amount of computing time necessary to simulate a mole of material for more than a picosecond will still be staggering. For me, currently, to simulate 100,000 atoms using 8 clusters for one nanosecond would take roughly 20 hours on our fairly fancy schmancy server, or 160 hours of CPU time. To get around this, we use periodic boundary conditions. As long as our simulation box is large enough that atoms can't try and interact with themselves, we can effectively create an infinite solid. If we want to study a surface, we can chose not to implement periodic boundaries in that direction, or add a vacuum layer. However, in amorphous systems especially, periodic boundaries must be used carefully, lest you over-constrain your system.

So what is MD good for? Quantum mechanical methods are more accurate and finite element analysis can simulate much larger systems. Molecular dynamics (and its cousin, Monte Carlo) is one of the best ways to understand biomolecules and predict things like protein folding. It can be used to understand the mechanisms of radiation damage and shock wave damage. It's also growing as a tool to study interfaces, which tend to become surfaces in experimental methods, which changes certain structural details. It can also be used to study molecules which are simply too large for quantum methods (i.e., more than a few hundred atoms). MD can predict crystal structures for pressures and temperatures, which while not achievable in the lab, happen at the center of the Earth, or in space. The ultra-high tensile strength of carbon nanotubes was predicted by MD before it was verified by experiment.

Materials science is far from the only field that uses molecular dynamics as a tool. We may ask different questions of our results, but people from geophysicists to biologists use MD. And I think that's pretty spiffy.

Awkward Questions

Visiting with relatives almost inevitably results in being asked lots of questions, many of which are potentially awkward. You're sitting and eating your half burned hamburger and trying to defend yourself from mosquitos when someone drops the conversational bombshell. Some of these questions I've been asked so many times, I've got a solid canned response for them. Now that Mr. ME and I are hitched, we've suddenly opened the gateway to a whole world of new questions...

"How does it feel to be married?" ... Let's see, we've lived together since before we were engaged and we've been engaged for over half of our relationship. I'm going with... almost exactly the same?

"When are you going to have kids?" When we decide to. Why is this one of the first questions every single heterosexual married couples gets asked? What if we don't want them?

"Are you merging your bank accounts?" Unless you are my banker, or someone I get financial advice from, I find this rather rude.

Then, of course, there's the standard awkward questions grad students get like "When are you going to graduate?" and "What exactly do you do?", or my personal favorite, "But what's your real job?". Because apparently being a barista at Starbucks would be a more real job than research.

What are your favorite (or least favorite) awkward questions? Have any good responses?

Tuesday, July 5, 2011

A Steampunk Wedding

All picture credits go to my sister's boyfriend. Photoediting... can be blamed on me.

Disclaimer: Steampunk is open to interpretation. This is ours.

Rule one of steampunk is to add gears to things. Because our colors were lavender and silver, we didn't have much brass around. My wonderful aunt made our very lovely and very, very chocolate cake. She does the most beautiful sculpted flowers I've seen, so rather than making her do gears and things, we went with a more Victorian inspired cake and used a large gear for a cakestand. We also got our tin-type taken at the local reenactment museum, which is in the picture next to the cake. I now totally understand why everyone looks angry and stoned in those. You need the brightest light possible, and even then you have to hold as still as possible for at least 30 seconds. It's harder than it sounds.

I made the bridesmaids fascinators (look, more gears!). Peacock was an unofficial color. These were surprisingly straightforward to do.

My bouquet was mostly ribbon and lace flowers, with various green leafy bits from whatever herbs looked healthiest that morning, which ended up being a mix of sage, dill, cinnamon basil and mint. Also pictured are my hat and Mr. ME's cane and our card box, which was probably the only brass thing around.

 We did an afternoon tea reception, and sent the guests home with their own teacup to keep. Our caterers were totally fantastic and made everything less stressful. They solved problems before they even happened!

One of our bubble girls. The venue is a botanic garden, and we would have been required to cleanup any flower petals, so they got bubble guns instead. Mr. ME modded them to look extra spiffy, instead of neon green. The garden provided the parasols, which was unexpected by awesome.

Our mutual friend performed the ceremony (based on Bill Nye's vows) with extra nerd references, including multiple Monty Python and Doctor Who references. And of course, The Princess Bride got a nod. The processional music was all from the new Doctor Who. Mr. ME is indeed wearing a Utilikilt. Also, we snuck in some googles on the officiant's head. There are tons of details, especially in his outfit, but I don't have any of those pictures.

And for a better view of my outfit:

We had a lot of fun planning our wedding, but I'm glad that we're at the married bit. Though Facebook pretty much instantly changed ads from "weddings" to "babies"...

Life goes on

I should have the wedding picture post up soon, but there's some picture editing to be done first. I'm almost done with all of the paperwork for my name change, other than finding a fax machine...

We went to visit my now in-laws this weekend. They are strangely exhausting people to be around, given how much they do, because they spend so much time worrying about whether or not they should do something at all. Decisions do not come quickly, so they're often running late (which drives me nuts). It was still fun, since I got to meet more of the extended family (who are way less stressful) and play with the small children. We also went to the park, and for some reason, the mosquitos went straight for my feet. 10 of 11 bites are on my feet...

And with itchy feet, it's time to buckle down and get some data before all of my August deadlines.