Friday, September 27, 2013


The authors of this paper are now my heroes! Click on the link and read the "Unacknowledgements" section. Wow!

Labyrinths and Ears

A viral labyrinthine infection makes me think of minotaurs holding athletic contests in my ear. (Of course, we're not sure what this is, but the doctor says that all symptoms point to this.)

The doctor prescribes patience, which is of course my best quality. :)

Update (10/1/13): As an alternative visuals to the minotaurs, perhaps David Bowie is dancing the Magic Dance in my ears.

Thursday, September 26, 2013

"Task-Based Core-Periphery Organization of Human Brain Dynamics"

Another of my papers just came out today, though I have to say that putting 12 pieces of supplementary information (8 figures, 3 tables, and supplementary text) as 13 separate files is absolutely ridiculous. It also led to some botching on the part of the journal --- such as in the table numbering in the .pdf versions and a messed-up reference in the caption of a table in the .pdf version --- and we never had the chance to do anything about it because this journal doesn't do page proofs. Sigh... Anyway, here is a combined version of the .pdf files that my postdoc Sang Hoon Lee assembled, and here is the accepted preprint version of the paper.

And now for the details about the paper itself...

Title: Task-Based Core-Periphery Organization of Human Brain Dynamics

Authors: Danielle S. Bassett, Nicholas F. Wymbs, M. Puck Rombach, Mason A. Porter, Peter J. Mucha, and Scott T. Grafton

Abstract: As a person learns a new skill, distinct synapses, brain regions, and circuits are engaged and change over time. In this paper, we develop methods to examine patterns of correlated activity across a large set of brain regions. Our goal is to identify properties that enable robust learning of a motor skill. We measure brain activity during motor sequencing and characterize network properties based on coherent activity between brain regions. Using recently developed algorithms to detect time-evolving communities, we find that the complex reconfiguration patterns of the brain's putative functional modules that control learning can be described parsimoniously by the combined presence of a relatively stiff temporal core that is composed primarily of sensorimotor and visual regions whose connectivity changes little in time and a flexible temporal periphery that is composed primarily of multimodal association regions whose connectivity changes frequently. The separation between temporal core and periphery changes over the course of training and, importantly, is a good predictor of individual differences in learning success. The core of dynamically stiff regions exhibits dense connectivity, which is consistent with notions of core-periphery organization established previously in social networks. Our results demonstrate that core-periphery organization provides an insightful way to understand how putative functional modules are linked. This, in turn, enables the prediction of fundamental human capacities, including the production of complex goal-directed behavior.

Hunter's Hitters

Giants outfielder Hunter Pence is good at comedy. This video is really damn funny! I wonder whose idea it was? (And while you're on this page, you might just want to click on the link that leads to more funny baseball-related clips.)

A Tom Lehrer Recording from 1997!

How awesome! Here is a Tom Lehrer performance from 1997. It includes some songs I have never heard him sing before! (I had never even heard of a couple of these songs before.) Big win!

(The penultimate song takes a really low shot at sociology and the attempt to mathematize it. It's really funny, though, perhaps because I can think of specific examples that it fits very well. Still, the assessment is not even close to fair.)

(Tip of the cap to Marina Chugunova.)

Update: I forgot to mention that I am wearing my "Let ε < 0" shirt today. How appropriate!

Wednesday, September 25, 2013

To Comment or Not To Comment

That is the question.

Popular Science has decided to shut off comments on their new articles (with occasional but rare exceptions). Their online content director eloquently explains why.

If anybody has any thoughts on this, I would be very interested to hear them (well, to read them). On the balance, I think it's the right call on their part, but I make this statement with sadness.

(Tip of the cap to James Fowler.)

"Data is Imaginary. This Burrito is Real."

Hah! I am amused by the latest XKCD.

New to the Blogroll: Easter Eggs in Scientific Papers

There is a new blog called Easter Eggs in Scientific Papers. Most of the good ones that it's discussed so far are incidents I already knew about, but it's still good to collect them in one place, and I'm sure that there are plenty of good ones to come. (I should remove some of the blogs that are never updated from the blogroll, but I just haven't gotten around to it yet.)

(Tip of the cap to Petter Holme.)

Tuesday, September 24, 2013

"Solitary Matter Waves in Combined Linear and Nonlinear Potentials: Detection, Stability, and Dynamics"

One of my papers came out in its final published form today. Here are the details.

Title: Solitary matter waves in combined linear and nonlinear potentials: Detection, stability, and dynamics

Authors: Scott Holmes, Mason A. Porter, Peter Krüger, and Panayotis G. Kevrekidis

Abstract: We study statically homogeneous Bose-Einstein condensates with spatially inhomogeneous interactions and outline an experimental realization of compensating linear and nonlinear potentials that can yield constant-density solutions. We illustrate how the presence of a step in the nonlinearity coefficient can only be revealed dynamically and examine how to reveal it by exploiting the inhomogeneity of the sound speed with a defect-dragging experiment. We conduct computational experiments and observe the spontaneous emergence of dark solitary waves. We use effective-potential theory to perform a detailed analytical investigation of the existence and stability of solitary waves in this setting, and we corroborate these results computationally using a Bogoliubov–de Gennes linear stability analysis. We find that dark solitary waves are unstable for all step widths, whereas bright solitary waves can become stable through a symmetry-breaking bifurcation as one varies the step width. Using phase-plane analysis, we illustrate the scenarios that permit this bifurcation and explore the dynamical outcomes of the interaction between the solitary wave and the step.

As an additional note, there have been a couple of hundred theoretical/computational papers on BECs with spatially inhomogeneous nonlinearities, but (to my knowledge) there has been only a single experimental paper on the topic, and that paper's basic point was essentially just that one can actually make these things in the laboratory. The challenge is thus to do something interesting in the laboratory, and this paper includes some experimental designs to try to do that (and, indeed, it includes an experimentalist as one of the authors). So here's hoping that we'll see some of these things or other phenomena soon in spatially inhomogeneous BECs studied in laboratories...

Saturday, September 21, 2013

Carpet Camouflage and its Unintended Consequences

Perhaps the most awesome costume at Dragon Con this year were from the people who dressed up in camouflage based on the carpet pattern at the Marriott Marquis hotel. I didn't see it in person, but I remember first seeing the picture on Facebook while I was at Dragon Con. It's the best costume from there that I have seen. Unfortunately, the company that made that carpet is being lame: it threatened the cosplayers with legal action after they started selling the costumes online after many people requested that. (You can also see the canonical picture of the carpet camouflage in that article.)

(Tip of the cap to someone who posted on one of the Dragon Con Facebook pages.)

Friday, September 20, 2013

An Aural Poincaré Section

This musical creation seems to essentially amount to an aural representation of a Poincaré section of the dynamics of a triple pendulum (though the description provided with the video is a bit hard to parse, so I am not 100% sure that this is precisely a legitimate Poincaré section).

(Tip of the cap to whoever posts for Physics Today on Facebook.)

Update: Here is a different aural Poincaré section of a triple pendulum.

Thursday, September 19, 2013

Dodgers Win the NL West!!!!!!

The Dodgers just clinched the National League West division title!!!! This is our first division title since 2009, and we have become the first team to clinch a division title in 2013. Yay!!!!! Go Dodgers!

RIP Hiroshi Yamauchi (1927-2013)

Hiroshi Yamauchi, who was the President of Nintendo from 1949 to 2002 (and oversaw Nintendo's transformation into the company we know today), has died.

(Tip of the cap to baseball writer Buster Olney, who wrote about Yamauchi's death in the context of the latter's never having attended a Mariners baseball game even though he was their majority owner.)

Wednesday, September 18, 2013

Long Live the Billiard Simulator!

How exciting! It turns out that this bit of Matlab software --- a simulator for billiard systems along with a graphical user interface --- that my Georgia Tech student Steven Lansel wrote in 2003-04 as part of his undergraduate research project (with Leonid Bunimovich and me) and that my Caltech undergrad student Kris Kazlowski then updated somewhat in 2006 is still being used as a tool for teaching and producing nice graphics in 2013! That is just sweet! The last update of any kind to the software dates to December 2007. (That was an update to get things to work on the then-latest version of Matlab, although we also included code for a couple of new billiard tables from Kris's 2006 summer research project.) This is excellent!

Bohemian Gravity

If you want to listen to some tidbits about string theory and the like to the tune of "Bohemian Rhapsody", then I strongly suggest that you watch the music video by Timothy Blaise called Bohemian Gravity. It's awesome!

(Tip of the cap to Jeff Moehlis.)

Good for the Audience

The following exchange just occurred at ECCS:

After a coughing spasms interrupted what I said to my collaborator Renaud Lambiotte, I said "Sorry. My mind is working much faster than I can talk at the moment."

Marc Timme (matter-of-factly): "Probably this will be good for the audience."

Sunday, September 15, 2013

What Happens in Barcelona Stays in Barcelona

Well, I finally made it to Barcelona. I have been meaning to go for several years, and I even was planning to go to a conference here a few years ago (but I was only given a poster presentation and --- under the circumstances of the initial e-mail response to my abstract when I submitted it --- it felt like a bait-and-switch, so I declined it). Now I am here for the 2013 European Conference on Complex Systems and for its associated satellite meetings. I have never gone to this conference series before, though some of my collaborators have previously presented our joint work at ECCS conferences. I already ran into Alex Vespignani at the hotel check-in desk, so I know I'm in the right place!

I was tempted to introduce this post with a Crystallian (as in Billy) fake European accent as a nod to a certain oral report I did in 7th grade on the city of Barcelona. The school year was 1988-89, and we chose Barcelona as our city on which to report because of the 1992 Summer Olympic Games for a presentation in Andrea Ambler's class. I think it was my idea --- not too creative, I admit. In our oral presentation (and in other presentations on other European cities), every single person used the same fake European accent --- no matter which European city was covered in their report. It was kind of ridiculous. (Is it too late to apologize for this past transgression? Now that I have several European friends, I feel like I owe them a retrospective apology for that oral report.) And for those of you who don't know what that "European" accent sounds like, let's just say that it's simply marvelous. In summary: My group's 7th-grade report on a European city was on Barcelona, our collective notion of a European accent (for all countries) was Billy Crystal, and this series of oral reports must have been extremely painful to watch (and, especially, to listen to) for anybody in the room who had any knowledge at all about Europe. Those were the days.

Update (7/01/14): I think I forgot to post my pictures from Barcelona.

Saturday, September 14, 2013

Sweet Dreams are Made of Granular Packings (and Who am I to Disagree?)

On Friday morning, I had a strange dream dream. It included an ice-cream parlor, which was rumored to be wild and crazy. I backtracked to this parlor after leaving my friends in our hotel. The parlor had two flavors named after one of my Oxford colleagues (though I decided in my dream that it must be a coincidence), and their method of choosing mix-ins --- which were required to come with the ice cream (one couldn't opt out) were based on which part of their large vat with a mixture toppings had the largest local packing density (and one had no choice in the algorithm either). That's right: granular packings are now officially showing up in my dreams.

There were some other parts as well, but that was the most vivid. Clearly, I need to get some ice cream --- though I still don't feel well enough to do that (I've been really sick with the flu for a week). I also need to work on reviewing a paper on granular force chains (which is on my desk) and finishing up a new paper of my own on granular force chains.

As Matt Sullivan reminded me on Facebook, some candies have been used to study granular packings. Given that things like M&Ms and the other things were all mixed together in one container, I think the dream store's idea was that the property of particular items having a higher local packing fraction than others was going to systematically make specific items show up more often among the mix-ins. I also suspect that having seen that project before had an influence on some of the particulars of my dream.

Friday, September 13, 2013

This Happens to Me All the Time

Sometimes, you're in a dark alley, and somebody points a gun to your head and demands the answer to a calculus question. Seriously. This happens to me all the time.

(Tip of the cap to I Fucking Love Science.)

2013 Ig Nobel Prizes

The 2013 Ig Nobel Prizes have now been announced. Sadly, the 2013 Prize in Probability is going to make it just about impossible for my cow project (and, in particular, this paper) to ever get an Ig Nobel. (I think that we should have been awarded a share of that prize.)

I love this year's Peace Prize, by the way. The Safety Engineering Prize is also awesome.

Thursday, September 12, 2013

An Excellent Metaphor

When I get sick, my bedroom sometimes starts to resemble a war room, with crumpled tissues strewn about like discarded battle plans.

(I may have cobwebs in my head and be unable to think many deep scientific thoughts at the moment, but damn I can come up with a fantastic metaphor!)


Rob Neyer got this exactly right. Let's be respectful without going overboard, pandering, diluting things, or being disrespectful of people whose believes are different.

Tuesday, September 10, 2013

Effects of Drugs on Spiderweb Design

Take a look at this article for a primer on the design of spiderwebs by spiders exposed to various drugs. And don't forget to watch the video at the bottom of the page! Wow...

It reminds me of an artist's work on the effect of drugs on his self-portraits.

(Tip of the cap to I Fucking Love Science.)

Monday, September 09, 2013

RIP Cal Worthington (1920-2013)

Cal Worthington, a well-known West Coast used-car salesman who appeared all over the place (and early and often) on television commercials during my childhood---and starting several decades before then---died on Sunday while watching a football game. Worthington's jingle was burned into my head for many years, and I still remember it pretty well. I have no idea where his "dog" Spot is buried.

Update (9/10/13): As I have been reminded by many people, "Go see Cal! Go see Cal! Go see Cal!" sounded like "Pussy cow! Pussy cow! Pussy cow!" to so many of us.

A New Way to Give People the Raspberry

Hopefully, nobody who goes to the market and notices the liquid-droplet remnants from the minor raspberry avalanche will think that those are drops of blood.

Only one person would dare give them the raspberry...

Sunday, September 08, 2013

Oxford's New Mathematical Institute (aka the "Andrew Wiles Building")

I just got back from a two-week trip to the US, and the stuff in my old office in Dartington House got moved into our shiny new building while I was gone.

We are going to have the official opening conference for the new building on 3 October.

The building is a bit of an eyesore from the outside, but the inside is excellent. There is one large visual kluge (where a walkway and an otherwise-nice architectural feature butt heads in a particularly grating manner), but the whole ambiance of an Escher-esque ant farm on the inside just works. (We are, of course, the ants.) There are a bunch of diagonal walkways within the floors and also diagonal vertical stairways and a very open feel. This will increase the chances of random encounters (and I expect many of them will be useful), though I'll need to be careful not to make a Bugs-Bunny-like wrong turn at OxPDE. :)

My office seems about twice as large as my old one, and I have tons more shelf space, a desk to facilitate meetings (finally!). Presumably, I also finally have working windows and blinds, and the Powers That Be could never manage to get either of those truly working properly in my almost 6 years in my old office. My office is also located strategically. For one thing, many of my lab members near it, and a restroom and both grayscale and color printers nearby. Moreover, when using a grayscale printer, I get to choose whether to use a printer that passes the offices of my lab members or one that does not... how very convenient :P ). Arguably even cooler than that is that my office is situated so that its entrance is just above one of the diagonal staircases. This will allow me to rain 'Death From Above' on people as they walk up and down the nearby staircase. (Now where are my red shells when I need them?) Truly, this building's layout would make one truly awesome arena for battle mode in a Mario Kart game. I will simply have to try to resist the urge to drop things on people as they are traversing the nearby staircase.

And, of course, there is the following extremely important fact: Once everybody has moved in, the mathematics department is going to be in one building (though a few stragglers will likely still be using an office elsewhere as their main office), and that is simply awesome! Most recently, we had been split over 4 different buildings (and we had gotten up to 5 at some point), so this consolidation will simplify things like having quick conversations with graph theorists without e-mailing back and forth to schedule something for a month later, etc. It's also very helpful for everybody that all of the support staff are now in the same building. Many of the ones with whom I dealt were in Dartington House (the building I was in) and quite a few things needed to be delivered by hand, and this is a royal pain in the butt when the deliverer and the deliveree are not in the same building (which was often the case for many of our faculty).

Thursday, September 05, 2013

Tuesday, September 03, 2013

Pinky and The Brain Read "Who's On First"

I didn't catch this while I was at Dragon Con, but it turns out that there was a performance of "Who's on First" in the voices of Pinky and The Brain.

(Tip of the cap to somebody who does Facebook postings for Dragon Con.)

Monday, September 02, 2013

What Happens in Troy Stays in Troy

Tonight I am heading over to Troy, NY. Tomorrow and Wednesday, I will be giving seminars in RPI's Department of Mathematical Sciences.