Lawrence Berkley Labratory

This last week I was in Berkeley California at the Phenix developer’s workshop. Phenix is a software package whose goal it is to advance the automation of macromolecular structure determination. The workshop was held on the grounds of Lawrence Berkeley National Laboratory, situated on the hillside right above the campus of UC Berkeley. I liked the area a lot. As I showed in my last post, the lab has its own resident turkeys. Further, black-tailed deer can be seen further up the hill. The mornings were awesome, they reminded me of mornings in Utah. I think it is because there was a large hill immediately to the east, thus the direct-sunlight wasn’t seen until later in the morning.

While at the workshop I had the opportunity to work with lots of cool people. I truly enjoyed working with my Phenix friends. My PI had a great idea for a research project that I could tackle to be part of my dissertation project. While there I told a colleague about the project and he suggested a way in which I might accomplish the project, he even had code that advanced my project by several steps! However, this has mad me keenly aware of the fact that I have a ton to learn!! It is good though as this gives me direction whereas before I feel I was lacking a clear direction.

The fight home was my first red-eye. Its very difficult to fly east with the time change. Anyway, we left San Francisco at midnight, Pacific Time, and landed in Durham around 9:30 AM, Eastern Time. I find it hard to sleep in a bed let alone on an airplane. Needless to say, I did not sleep on the plane, one of only a handful on the flight. By the time I got home I was, surprisingly, wide-awake. I didn’t go to bed until 11PM that night making 39 consecutive hours without sleep, a new record for me!

Anyway, it was a great trip and I am looking forward to the next Phenix workshop this fall here at Duke.

LBL

What, may you ask, is LBL? Well, I'm here to not only tell you but show you also. LBL stands for Lawrence Berkeley Laboratory. It is on the campus of the University of California, you know, the one in Berkeley. This happens to be where I am right now, for a collaboration workshop. This workshop, which is held every six months, rotates between here, Duke, and Cambridge. I may have more to say when all is said and done at the end of the week. Until then, enjoy these pictures I managed to get with my phone this morning.

Looking down onto the campus from LBL.

The LBL guest house.

Trees and the overcast sky.

Resident turkeys.

A resident.

A random building.

Look out on the bay.

Opposition in all Things

So, from my last post it looks like I promised to write a new post a few weeks ago. Obviously, this did not happen. I have been quite busy with life in general; taxes, research, class, TA duties, and yard work…you get the idea. Yup, you heard right, I said yard work. It has been warm as of late and I have been turning the soil over in my garden. I meant to get early crops in but time was not to be found. I have been really busy in the lab, learning a new programming language, Java. Programming is quite simple, all you are doing is telling the computer to take input from the user and if that input is some action, such as a right-click, then do thing A. There are really only a very few primitive commands that you need to make a program, quite amazing. I have been busy doing other school activities too, class and TA responsibilities (A.K.A. thermodynamics and grading).

You may ask then, what do I do when I am not in lab or doing the school thing? I do bike but not a lot. When I get done with the day I usually go home trying ever so hard to keep school and lab things behind. One thing I do not do when I get home is sit in front of the TV; I can’t stand TV. Instead I read. Since I am a great believer in opposition in all things, I have chosen to read Stephen Hawking’s ‘A brief History of Time.’ How does this introduce opposition? Quit simply really. You see, as a student of structural biology I am working in a world where measurements are made on the angstrom scale. An angstrom is a whole magnitude of order less than a nanometer! Certainly almost all have heard of a nanometer but that doesn’t mean that you have an intuition of how small that is. Let me try to instill some intuition about the nanometer and then the angstrom.

I will assume you are familiar with the length of a meter. One tenth of a meter is a decimeter (or 0.1 meter) and one tenth of a decimeter (or one one-hundredth of a meter if you’d like) is a centimeter (or 0.01 meter). Approximately 2.5 centimeters is the length of an inch (this will be the only reference I will give to the cockamamie U.S. convention of length measurement). So, a tenth of a tenth of a meter is a centimeter. Are you with me so far? Good. A tenth of a centimeter is a millimeter (or a tenth of a tenth of a tenth of a meter or 0.001 meter). Now think of a human hair, the average size of which is a tenth of a millimeter, pretty small!

This will be the last reference of anything observable to the human eye as anything smaller is fairly difficult, if not impossible, to see with the naked eye. We’ve come a long way but the millimeter is not even half way to the angstrom! Go down three orders of magnitude from a millimeter and you’ll arrive at the micrometer (or 0.000 001 meter). Lets jump down ANOTHER three orders of magnitude, we’ve now arrived at the nanometer (or 0.000 000 001 meter). Recap: three orders of magnitude below meter is millimeter, three more orders down is the micrometer, and three orders down still is the nanometer. Now we go just one order of magnitude below the nanometer and we finally arrive at the angstrom (1 angstrom = 0. 000 000 000 1meter). I hope you followed; my goal was simply to underscore the fact that I am constantly thinking in these small lengths within my research and schoolwork too.

I have yet to answer the question that brought on that rant, why does reading ‘A Brief History of Time’ introduce opposition at all into my life? Well, you see, being a theoretical astrophysicist and all Stephen Hawking tends to write about length scales that are, quite literally, astronomically big. It is nice to come home and peek into another world where people are always thinking about large distances rather than small distances, as I do.

Opposition is like taking a break from a grueling run. It does not only feels amazing but is essential for physical and mental health. Did I just compare my research to a grueling run? Yes, yes I did. I’m ok with that.