I like the sleepy box

[tebtebbert]

Two posts ago talked about minimizing the force field parameters. Turns out, it's been done and used. It's neat that I was able to come up with this solution entirely on my own. It's like doing a derivation from scratch and then finding out that it was correct. On the other hand, if only I was 16 years earlier to this party. I could have had 125+ citations to my name. I would have been the nerdiest 11 year old ever.

[tebtebbert]

My Laundry Machine is Magic

I'm writing a new paper. Here is the abstract:

Spontaneous Chirality Flipping in Toe Socks.

The chiral nature of sock pairs plays an important role in podiatric comfort. While this handedness may be ignored for certain brands of tube socks to varying degrees, proper symmetry is of paramount importance for toe sock pairs. It is well documented that toe socks are known to undergo spontaneous chirality flipping (SCF) during laundry cycles. We present a study describing the experimental procedure of measuring SCF probability. Further, we present a new model describing the underlying thermodynamics of this unfortunate phenomenon.

[tebtebbert]

It's been a while. I haven't been writing like I am supposed to. So I figure I might write something of substance today.

Molecular dynamics is a finicky business. The problem of MD is, at its core, a many body problem. You sum up pairwise electrostatic interactions, toss it into Newton's equations, then watch a bunch of pixels lurch forward in time. This process is repeated ad nauseum.

Pairwise sums of anything scale as O(n^2). Ain't nobody got time for that. So some very smart people get together and figure out all sorts of approximations and tricks to reduce that 2 into something much more manageable. The particular approximation I use is called the General AMBER Force Field (GAFF).

The use of any approximation introduces error. In this case, we can get around them by modifying the two constants associated with the Lennard-Jones potential for each particular atom type. One simply plays around with them, and checks to see if density and some other measurements of your substance match with accepted values.

Now there are no hard and fast rules for doing this sort of thing. It's possible that more than one combination of constants will lead to the correct density. Also, there's often no good indication of how to even go about adjusting these parameters in the first place.

I hate work. My motto is "Automate what can be automated. Make automatable what cannot." So I wasn't about to go and try to figure this out on my own. Instead, I programmed a minimizer to do that biz for me.

I popped open "Numerical Recipes" and implemented the Nelder-Mead simplex algorithm. A simplex is a general name for an n-dimensional polyhedron. The vertices of this shape corresponds to a particular set of parameters. The simplex then navigates through the solution space much the same way an amoeba might crawl through some primordial goop. Eventually, it will happen upon a minimum and the corners of the simplex will cage around the solution.

The gif shown here is the algorithm at work. The contour plot is of Rosenbrock's Banana. With the coefficients that I used, the global minimum exists at (1,1). The red triangle is the simplex reaching and feeling out for the minimum of this function.

[tebtebbert]

Rest

I have been dreaming lately. I love to dream. It lets my sleeping self know that I am alive. It also means that I might actually be getting restful sleep. I hope I can be my normal self again. Lord knows its been a few months. One of these dreams inspired me to write and not let one of my ideas stagnate. I have an idea for a post apocalyptic world where the rending of the earth let loose magic upon the world. I also have a very technical approach to magic for this universe. I also will post something substantial next time.

[tebtebbert]

Return of the rambler

I have missed my entries for a few days, I apologize. I was wiped out by the stomach flu. It was bad enough to land myself in the emergency room, and get hooked up to an IV. I have never been to the ER before. It was kind of exciting and awful at the same time. First you wait for a few hours, they stick you with what is easily a two inch needle, then screw some plumbing into your arm. Mostly I felt like a tax burden. I am still super dehydrated from the ordeal. The most regretable thing from this is that I failed to take a selfie with the RNs. Those cats were great. As a child, I was told to look away whenever I was going to be poked with small sharp bits of metal. Presumably people assumed that I would be squeamish and that I would cry like most children. The habit persists today. I tried, but I couldn't bring myself to watch the catheter insertion. Now I'm not sure if it's just ingrained habits or if I am actually squeamish. Though I did watch the blood draw. Often it's more than a few vacuets worth of blood that is to be filled. It takes time and it's boring. So I watch my own blood shoot into a plastic container.

[tebtebbert]

Sick

Current status: wiped out by stomach flu.

[tebtebbert]

MY FEET HAVE BLISTERS!

I have recently started long distance running again. This time, I am doing it without shoes. When I run, there is nothing between me and the earth. I do these long runs whenever I need to log onto my workstation and hit my simulations with a wrench. Unfortunately, those little berries that many of the trees around here produce are like caltrops. The path is paved with them in places. It stressed my calves and Achilles tendons to high heck the first day I started, but it seems I'm already used to it. Now it's on to conditioning my feet. One day, I hope to run like a hobbit.

[teachingfeelslike]

When I give students extra days to complete missing work in order to possibly save their grade and then they STILL DON’T DO IT.

[tebtebbert]

I've been considering teaching high school science as a backup plan. I went through the rest of this person's blog, and now I'm not sure. Yeah, we're needed and I can be easily appealed to a sense of duty. But I might be allergic to children.

God, I remember being a kid. It was awful. (Though sometimes, I wonder if anything has really changed.) And I wanna deal with that every day? Hnnnggg...

This thing here is something I have personally experienced. It is exactly how I felt.

[tebtebbert]

I had myself quite the adventure today. I went to the California Science Center to look at fish and to finally see the Endeavor. You see, I love fish and space. A better museum does not exist the area. When I laid eyes on that craft, I was overcome with emotion. It must have been an interesting sight to see a lone man tearing quietly at the center of the hangar. I am neither apologetic nor embarrassed for my display, for I understand what this vessel represents for humanity. On my way home, I got on the bus going the wrong way and had a little tour of East LA. Thanks to smart phones, one never gets lost like we used to. Instead, Google tells you things like, cross the 105 to get to the Commerce station. Thanks Google! Industrial parks are vast unique landscapes. The Commerce station is little more than a passenger train sized slab of concrete sitting in the middle of a train yard. The track extends out past the horizon, dipping over the edge of the world on both ends. On the side of the entrance, there are warehouses and factories, both quiet and unmanned. On the other, freight and very literal engines of the economy lay to rest. A distant machine hums its low lullaby. Its colors are a stark juxtaposition to the parks and trails around the area. There is no green save for the odd weeds growing between cement cracks. The scene is dominated by the color of rust and steel. I find it to be beautiful in its own way.

[tebtebbert]

End of the Year, Sounds for the Ear

I've decided that the Tumblr will win. I find it to be fairly minimalist. I can just post things and it's cool. It's also much easier to sign out of my account than in Wordpress.

I won't be divulging many personal things here. Suffice to say that this year has been eventful. May the next be more so and bring success along with it. I wish the same for everyone.

This coming year, I'm hoping to get into music again. I mean deep into music. Some months ago, I purchased a trumpet at a near criminal discount. I should learn to play that.

I have also been spending some time on the piano. It's good to see that restoring the lost ruins of muscle memory will require a housekeeper, not an archeologist.

A dear friend of mine also gave me a trial copy of Ableton. It is taking forever to install. I wish to go to sleep.

Also science. Always science. Science is the no. 1 priority. It's what is going to pay the bills and fulfill my dreams once I'm out of grad school.

I should really be studying instead...

[tebtebbert]

First

So I made one of these because I thought daily writing of some sort would be a good habit for me to start. I also made a Wordpress blog. I'm not sure which one I'm gonna keep. Tumblr has this sort of new age ADD feel to it, but it definitely makes blogging simple. Wordpress lets me narcissistically brood over viewership stats, but operates more like a traditional blogging service.

Either way, I'm going to try to make it a habit of writing something every day.