Stochastic Processes in Physics and Biology

My friend Dibyendu Das, who is an associate professor in the physics department of IIT Bombay India will be visiting CSU from May 10-24 2011 as an APS-IUSSTF Professor. Dibyendu is a theoretical physicist who works on non-equilibrium statistical mechanics. As part of the APS-IUSSTF Professorship, he will be delivering a lecture series at CSU titled “Study of stochastic processes in certain physical and biological systems” hosted by the Dept of Chemical and Biological Engineering.

The lectures will be held in Glover 201 on May 16, 18, 20 and 23 The lecture on May 16 will start at 11am and the subsequent ones at 10 am. There will be coffee and refreshments.
The following is a brief outline of the lectures.

May 16 11 am – 1 pm

Lecture 1: Phenomena of collective migration of active matter — birds, bacteria, driven granular matter, cells, and actins — will be introduced. Other phenomena involving stochasticity, namely polymer motion, and microbial evolution will also be discussed. Some statistical models to understand these phenomena will be discussed. Mathematical similarities of some of these models will be mentioned.

May 18 10 am – 1.30 pm
Lecture 2: Basics of statistics. Random variables to stochastic processes. Two simplest linear processes — Random walk problem, and the growth/autocatalytic process. Similar analytical methods to treat more complicated problems — flexible polymers, and mutating bacteria.
Mathematical approaches using Master equation, and Langevin equation.

May 20 10 am – 1pm
Lecture 3: Numerical methods — Kinetic Monte Carlo, Molecular dynamics, Langevin dynamics. It will be demonstrated how the discussed numerical approaches have been used to obtain recent research results on
– (i) collective cell migration, (ii) collective motion of active/granular matter.

May 23 10 am – 1.30 pm
Lecture 4: Analytical Methods — It will be demonstrated how the discussed analytical approaches have been used to obtain recent research results on — (i) polymer motion in flow fields, (ii) microbial population dynamics.

Tribute to New York City

The New York Times just published Tony Judt’s piece on New York a few days ago. This was something he wrote much earlier ( of course since he died in August this year) and is coming out in a book. You can read it here:

http://www.nytimes.com/2010/11/08/opinion/08judt.html

Anyway, the point of this posting is that it inspired me to write my own recollections of the year I and my wife Ramaa lived in New York, since to me too, its so much of a world city in the way Tony Judt talks about.
We lived in Brooklyn amidst the remnants of what once was an Italian street. It still had a working class Italian pastry shop, womanned by a couple of beautiful young sisters and their mom, who had to keep a stern eye on the rather unsuitable suitors that could be found there at any time. Next to it was Johnny’s, in mine and my wife’s opinion, the best pizza in New York..one of his pizzas that we still dream about was called Granny’s pizza .. thin crust with fresh moz and fresh basil, drizzled with olive oil. A pizza completely at home in a Michelin star restaurant if you ask me, served with no fanfare at a hole-in-the-wall Brooklyn pizzeria. A block to the east was the little Brooklyn Chinatown that, we were told, people would refer to as Taiwan to compare it with the mainland across the Hudson! Three meat dinner for 3 dollars flat… the cheapest vegetables you could ever buy overflowing the sidewalks, and bustling with people…who suddenly vanished into the brownstones after 7pm. Our favorite however was a Vietnamese restaurant where the staff were all nieces and nephews, some of who were students at CUNY, with cute accents and blond spikes in their hair, and late at night the whole family ate together, often sending off-menu delicacies to our table.
A block to the north the neighborhood turned distinctly Hispanic, redolent every evening with the smell of baking buns from a hole-in-the wall Mexican bakery, that we noticed only after passing it about a hundred times, that made the most amazing sesame buns. A few more blocks up on 5th avenue there was a little metal shack on one of the cross-streets where a large genial Mexican grandma doled out, from a battered cold case, amazing home made tamales. We loved it .. it was so third world!
If you managed to walk that mile and still have an appetite .. Fifth Avenue Brooklyn was full of vendors with freshly fried empanadas, that became a daily addiction for my wife, and corn roasting on coals, with the occasional meat cart, dripping with links of blood red sausages.
If you walked south however you entered a middle-eastern neighborhood… first a couple of Greek restaurants heralded the hookah bars and the pastry shops including an amazing Lebanese pastry shop where we first tasted mamoul. Coming back stuffed with Zaatar and mamoul, the hookah bars were full of oldish men with large mustaches sucking away in complete silence at the hookah’s while children played all around them!
You could even buy at an oud at a curio shop at one corner!
Finally if you walked west, crossing first the Palestinian grocery store next to the subway station at the first crossing, and the Indian grocery store at the next, you would traverse a couple of blocks of closed warehouses and decaying factories, till you came to the grey industrial waters separating you from Manhattan. But even here, you could take a crowded ferry, probably plying this route for more than a half-a century, and get a sense, till you reached the black-clad Manhattanites on the other side, of being in another world.

The Cellular Cytoskeleton

The first exciting news on the new Prasad lab blog is that the conference on the Cellular Cytoskeleton is finally almost here. This conference has an interesting history. Like many others I enjoyed conferences for a chance to see what people were doing; however you sometimes wanted to be able to just sit down and talk, and throw around ideas. Traditional conference formats are not very good in that, though conferences like the Gordon conference series do achieve that to some extent. One of my favorite experiences was a brain-storming session on the glass transition organized by Bulbul Chakraborty and Jane’ Kondev at Brandeis University, while I was still a starting graduate student. That was what science was supposed to be about … a bunch of smart people collectively trying to solve a problem. That seemed to be the perfect format for quantitative and systems biology, since I sometimes get the impression that biologists and theorists sometimes don’t ‘get’ each other! When I was a postdoc at MIT I was talking about all of that to Dan Needleman, who was a postdoc at Harvard and a friend. Dan was thinking on similar lines and we threw ideas around about what we could do. Dan spoke with Dimitrios Vavylonis, who is in the physics department at Lehigh, and the three of us started imagining a real life conference. Since Dan and Dimitrios both worked on the cytoskeleton (which was something that interested me too) we decided to start with organizing a discussion centered conference on the Cytoskeleton that would bring together modelers from physics and engineering with cytoskeleton biologists and give them a chance to talk with each other in a relaxed and secluded environment. When I came to Colorado State University, James Bamburg, who has done pioneering work on cytoskeletal biology, and Meredith Betterton who, like me, is a theoretical physicist working on biology joined the group. The five of us then started contacting people, and applied for a CSU internal grant from International Programs which we got. That was the seed money which enabled the whole thing to go forward… but till a few months ago I was still worrying!

The conference is going full steam ahead. Join us on June 13 at 12 noon in Fort Collins, Clark A203 on the CSU campus for the first day, an eclectic mix of modelers and experimentalists, who will lay out those aspects of cytoskeletal dynamics which we will be discussing in greater detail in Pingree Park from Monday, June 14th. The conference website is here:

http://athena.physics.lehigh.edu/cytoskeleton/index.html