Computations in Science Seminars

Wednesdays at KPTC 206, unless otherwise specified

The Kersten Physics Teaching Center is on the corner of 57th Street and Ellis Avenue.

Discussion over bag-lunch at 12:15 PM. Talk starts at 12:30 PM.

INFORMATION FOR SPEAKERS

INFORMATION FOR SPEAKER'S HOSTS

Upcoming seminars

Previous seminars

This seminar series is organized by William Irvine, email address, David Biron, email address, Wendy Zhang, email address, and Leo Kadanoff, email address.

 A photo of M51 Galaxy

Whirlpool Galaxy M51
February 15, 2012 (^) Hosted by Margaret Gardel
Fred MacKintosh, Vrije University, Amsterdam
e-mail: email address
Mechanics and dynamics of fiber networks: criticality, mechanical integrity
Much like the bones in our bodies, the cytoskeleton consisting of filamentous proteins largely determines the mechanical response and stability of cells. These biopolymers form fiber networks, whose mechanical stability relies on the fibers' bending resistance, in contrast to rubbers that are governed by entropic stretching of polymer segments.Thus, the elastic and dynamic properties of such semi-flexible polymers are very different from conventional polymeric materials. We show that these networks exhibit both a low-connectivity rigidity threshold governed by fiber bending, as well as a high-connectivity threshold governed by fibre-stretching elasticity. We show that the latter exhibits rich zero-temperature critical behavior, including a crossover between various mechanical regimes along with diverging strain fluctuations and a concomitant diverging correlation length. Inspired by both intra- and extracellular networks, we describe recent theoretical modelling and experiments on simplified fiber networks in vitro. Among the more striking material properties of these networks is their nonlinear elasticity, with a strong stiffening response to stress. Unlike passive materials, however, living cells are kept far out of equilibrium by metabolic processes and energy-consuming molecular motors that generate forces to drive the machinery behind various cellular processes. We show how such internal force generation by motors can lead to dramatic mechanical effects, including a strong stiffening of cytoskeletal networks. Furthermore, stochastic motor activity can give rise to diffusive-like motion in elastic networks, as has been observed in living cells.
February 22, 2012 (^)
Charles Sykes, Tufts University
e-mail: email address, Faculty contact: David Biron, email address
Turning a Single Molecule into an Electric Motor
In stark contrast to nature, current manmade devices, with the exception of liquid crystals, make no use of nanoscale molecular motion. In order for molecules to be used as components in molecular machines, methods are required to couple individual molecules to external energy sources and to selectively excite motion in a given direction. Significant progress has been made in the construction of molecular motors powered by light and by chemical reactions, but electrically-driven motors have not been demonstrated yet, despite a number of theoretical proposals for such motors. Studying the rotation of molecules bound to surfaces offers the advantage that a single layer can be assembled, monitored and manipulated using the tools of surface science. Thioether molecules constitute a simple, robust system with which to study molecular rotation as a function of temperature, electron energy, applied fields, and proximity of neighboring molecules. A butyl methyl sulphide (BuSMe) molecule adsorbed on a copper surface can be operated as a single-molecule electric motor. Electrons from a scanning tunneling microscope are used to drive directional motion of the BuSMe molecule in a two terminal setup. Moreover, the temperature and electron flux can be adjusted to allow each rotational event to be monitored at the molecular-scale in real time. The direction and rate of the rotation are related to the chiralities of the molecule and the tip of the microscope (which serves as the electrode), which illustrates the importance of the symmetry of the metal contacts in atomic-scale electrical devices.
February 29, 2012
Anette (Peko) Hosoi, MIT
e-mail: email address, Faculty contact: Leo Kadanoff, email address
Low temperature solvent annealing in organic thin films
We examine solidification in thin liquid films produced by annealing amorphous films in a solvent vapor. Micrographs captured during annealing reveal the nucleation and growth of single-crystal needles. The needle lengths scale like power laws in time where the growth exponent depends on the thickness of the deposited film. The evolution of the thin film is modeled by a lubrication equation, and an advection-diffusion equation captures the transport of material and solvent within the film. We define a dimensionless transport parameter which describes the relative effects of diffusion and coarsening-driven advection. For large values of this parameter, needle growth matches the theory of 1D, diffusion-driven solidification. For low values, the collapse of droplets -- i.e. coarsening -- drives flow and regulates the growth of needles. Within this regime, we identify and analyze two asymptotic limits: needles that are small compared to the typical drop size, and those that are large. grad: "Niels"
March 7, 2012 (^)
Elisha Moses, Weizmann Institute
e-mail: email address, Faculty contact: David Biron, email address
Computing with living neuronal networks
Neurons explanted from the brain will grow on the bottom of a dish and form a highly connected, electrically active neural network. We show that its computational abilities are determined by collective effects in a new kind of percolation system, and are limited due to random connectivity. Geometrical guidance, along with redundancy and multiplexing, reproduce some minimal yet reliable computation functions of the network.
March 14, 2012
Robert Schroll, University of Massachusetts
e-mail: email address, Faculty contact: Wendy Zhang, email address
The wrinkling behavior of highly bendable thin sheets
The behavior of a thin elastic sheet can be characterized by its 'bendability', a number that compares bending and stretching forces applied to the sheet. Highly bendability sheets are so thin that bending energies are essentially negligible. Because of this, highly bendable sheets wrinkle easily when subject to confinement. Traditionally, such wrinkles have been described by a 'post-buckling analysis' that describes the wrinkled state as a perturbation of the flat, un-buckled state. We argue that this is inappropriate for highly bendable sheets, since wrinkles are able to reduce the compressive stress essentially to zero. Instead, a 'far-from-threshold' analysis, in which wrinkles are treated as a singular perturbarion of a collapsed compressive stress state, must be used. A simple planar problem is used to illustrate this method, which is then used to analyze the behavior of thin sheets on liquid drops. Experiments demonstrate the need for this far-from-threshold analysis, but they reveal additional unexpected behavior.
March 21, 2012
(open date)
March 28, 2012
Michael Rust, University of Chicago
e-mail: email address, Faculty contact: David Biron, email address
It's about Time: A Three-Protein Clock from Photosynthetic Bacteria
Despite being composed of molecular components subject to intense thermal fluctuations, living cells routinely display strikingly precise and coherent behavior. A recently discovered example of this phenomenon is a ~24-hour oscillator found in the photosynthetic cyanobacterium Synechococcus elongatus. In a realistic environment, this oscillator is phase-locked to the daily rhythms of light and dark experienced by the organism, but precise oscillations will continue even if the organism is deprived of rhythmic cues. Thus, it is similar in function to the circadian clocks found in animals and plants, familiar to anyone who has become jet-lagged following a cross-country flight. Surprisingly, three purified protein components from this organism, KaiA, KaiB and KaiC, can be mixed in a test tube with ATP to reconstitute stable biochemical oscillations outside of the cell. Though the phase of this oscillation can be quite responsive to the environment, the period remains close to 24 hours over a broad physiological range of temperatures, protein concentrations and nucleotide conditions. I will describe a combination of biochemical experimental work and dynamical systems analysis in our attempt to understand both the emergence of robust oscillations and phase shifting in this simple system.
April 4, 2012 (^)
(open date)
April 11, 2012
Sonja Schmid, Virginia Tech
e-mail: email address, Faculty contact: Leo Kadanoff, email address
April 18, 2012
(open date)
April 25, 2012
Humphrey Maris, Brown University
e-mail: email address, Faculty contact: Leo Kadanoff, email address
May 2, 2012 (^)
(open date)
May 9, 2012 (^)
(open date)
May 16, 2012
Seth Lloyd, MIT
e-mail: email address, Faculty contact: Leo Kadanoff, email address
May 23, 2012
(open date)
May 30, 2012
Randy Ewoldt, University of Illinois at Urbana-Champaign
e-mail: email address, Faculty contact: Wendy Zhang, email address
A Volume-Expanding Self-Defense Gel: The Non-linear Rheology of Hagfish Slime
June 6, 2012
Allan Drummond, University of Chicago
e-mail: email address, Faculty contact: David Biron, email address
June 13, 2012
(open date)
June 20, 2012
Stephanie Palmer, Princeton
e-mail: email address, Faculty contact: Leo Kadanoff, email address
June 27, 2012
(open date)
July 11, 2012
(open date)
July 18, 2012
(open date)
July 25, 2012
(open date)
August 1, 2012
(open date)
August 8, 2012
(open date)
August 15, 2012
(open date)
August 22, 2012
(open date)
August 29, 2012
(open date)
September 5, 2012
(open date)
September 12, 2012
(open date)
September 19, 2012
(open date)
September 26, 2012
(open date)
October 3, 2012
(open date)
October 10, 2012
(open date)
October 17, 2012
(open date)
October 24, 2012
(open date)

(&) : When Wendy Zhang is unavailable for the seminar.

(^) : When Leo Kadanoff is unavailable for the seminar.

(#) : When David Biron is unavailable for the seminar.

(*) : When William Irvine is unavailable for the seminar.

Back to JFI home page.

Valid XHTML 1.0 Transitional