“I have the stripes, but where is the zebra?”

October 29, 2009

piglickerHi Everyone.  Sorry I haven’t posted anything in the long time.  My apology is a post that even longer and more meandering than usual.

I’m at Indiana University for the Biocomplexity X workshop on Quantitative Tissue Biology and Virtual Tissues.  It’s been great — perhaps because there are many physicists converted to biology.  There have been several talks that touched on non-linear elasticity, though most people’s background is in foams and not granular matter.   Rene Doursat gave an especially good talk today on agent-based models of morphogenesis in which he mentioned another alleged quotation, attributed to Alan Turing, who made either the titular comment or said “The stripes are easy, it’s the horse part that troubles me!” in reference to the ability of certain systems of equations to create seemingly biologically-relevant patterns without necessarily providing biological insight.  Brad has Read the rest of this entry »


Bob in Physics Today

September 25, 2009

Those of you who aren’t current in your APS subscriptions might miss this “Quick Study” article by Bob in this month’s Physics Today.

Good News Everyone

December 4, 2008

I’m happy to say that I was offered and accepted a permanent position with the National Center for Computational Toxicology within the US EPA.  I’ll be primarily working on the Virtual Liver project — an initiative to develop a computer model that can take in vitro toxicological information about an environmentally-relevant compound to determine the likelihood that that compound will cause harm to people.  In particular, I’ll be looking at how to model the spatial extent of the liver by coupling all of the constituent cells appropriately.  Right now it looks like we may be taking a cellular automata or finite state approach.

The cool thing is that my former office mate was also hired into a separate position.  For the first time since 2001 I don’t have an office mate from William and Mary (sorry Brad and Brian), but I’ll try to get by…

Hard to resist…

August 8, 2008

I’ve been in a bit of a funk — my tv and computer broke last month, we don’t have cable/internet in our temporary apartment, and I’ve been swamped with work — but I simply cannot resist posting this video:

[Today’s Big Thing]

One of the things I always liked about our work with force chains was how much they seemed like lightning. Even in slow motion that seems to be the case. Compare, for instance, with the distribution of force during a simulated meteor impact:

Burgers, not just for grillin’

July 28, 2008

In th early 20th century J.M. Burgers’ attempted to model fluid flow by adding a nonlinear term to the linear diffusion equation. The idea never panned out for modeling fluids, but the nonlinear diffusion equation, now known as Burgers’ Equation has been studied quite a bit nonetheless. More recently (1988, 1992, and 2002) a form of the Burgers’ Equation was derived for the twist dynamics of twisted scroll waves. Scroll waves are the 3D analog to spiral waves (think of a scrolled up piece of paper). Scrolls are found in many types of excitable media and a number of experts believe they play a role in cardiac arrhythmia.

Until this week there had not been good experimental evidence published for scroll wave twist behaving according to Burgers’ Equation. But now you can read all about in in Europhysics Letters, “Evidence for Burgers’ equation describing the untwisting of scroll rings” (volume 83, article number 30010).

Oh, and I’m still waiting to hear about Entropy Maximization from one of my esteemed colleagues in blogging. And is each of us publishing in a journal on the other ones current continent of residence something Alanis Morisette would call “ironic”?

What happened to John?

June 24, 2008

Hi everyone. I’m still alive and life has been interesting. Ann and I bought a house that we’ll move into in August, but in the mean time we’re packing up and heading to an apartment in Chapel Hill. The lease on our rental house is up at the end of the month and the crummy owners wanted to get it on the market so as not to miss out on those oh-so-common July renters rather than give us an extension of less than a year.

In addition to that fun, I’ve been to both Huntsville and Jacksonville briefly and watched one of my EPA mentors head off for industry.

Finally, on Sunday night, as we were driving into RTP to get some paperwork for the next morning’s mortgage signing, we got caught in a freak rain storm that caused puddles to form on Martin Luther King Parkway (a newly built, divided four lane road). The first puddle was fine (I was going less than 20 MPH so we didn’t even hydroplane) but the second one was two to three feet deep and as we plunged in my engine cut out and still hasn’t restarted. The water was most of the way up the passenger door and we were stuck for a good fifteen minutes or so before the water drained and we could push the car off the road (with the welcome help of some samaritans).

Fortunately, Andy’s googling and Mary’s dashing rescue allowed us to get out of the lightning and retrieve the needed papers in time for the morning.  Unfortunately, I may have totaled my relatively new, unpaid-off car. Oh, why couldn’t we have hydroplaned over that puddle? (Feel free to discuss the physics of that, or lack thereof, in the comments section.) In the meantime I am driving a rental pick-up truck — you should have seen the rental agent’s draw drop when I asked for one — in order to help with moving. For some reason everyone wants a compact right now. All I know is I’ve already ordered my “W – The President” bumper sticker.

In the meantime, I have a great story on how two ball boys saved Michigan’s undefeated season in 1997 as well as a nominee for the blog roll:


It’s like crack for anyone who likes graphs, statistics or politics (a triple-whammy for me). Also in the intersection of cool graphs and politics is Presidential Watch 08, which has great tools for plotting the political blogosphere as well as trends. Without these very impressive analyses, would we have ever been able to tell that Fox news leans Republican?

Finally, if you can show that playing Minesweeper is NP-complete, you can win a million dollars

The Physics Arxiv Blog

April 6, 2008

Force chains in a granular silo... In the physics community it is common practice to submit “finished,” but not yet peer-reviewed, research papers to a preprint server so that they become time-stamped (useful for establishing credit) and freely available to the public. Often, once a paper is revised in response to peer-review and published, a “preprint” copy of the final version is placed on the server so that copies can easily be obtained without tracking down whatever journal it was published in (something that has gotten vastly easier thanks to Google Scholar). The arXiv preprint server started in 1991 at Los Alamos (where it had the dubious-sounding address of xxx.lanl.gov since the Web was not yet especially World-Wide) and now hosts papers in physics, mathematics, computer science, and quantitative biology. Anyone who wants may subscribe to have a listing of all the new and updated papers on a given topic regularly sent via e-mail. For me, at least, scanning through the daily cond-mat listing is one of the main ways I try to stay current in my field.

The newest addition to our blogroll is a very cool idea — The Physics Arxiv blog. The author combs through the daily update emails and writes about the interesting papers they see and you’ll never guess how I stumbled across it. Sometimes papers on arXiv are kinda crazy and take a long time to get published (if ever). Sometimes research is happening so quickly that entire research groups dictate what they do in response to the latest preprint (right Joe?). No matter what it’s a neat blog and a good way to stay current in physics.