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
May 16, 2012
Seth Lloyd, MIT
e-mail: email address, Faculty contact: Leo Kadanoff, email address
Physical limits to computation
This talk reviews the fundamental physical limits to computation and shows how they can be approached. Quantum mechanics governs the speed at which elementary logical operations can be performed. Statistical mechanics governs limits to memory space and to dissipation during computation. Special relativity governs speed of communication, and general relativity and quantum mechanics combine to govern the amount of information processing that can be performed in a volume of space and time. Implications for computer design are discussed.
May 23, 2012
Guillaume Blanquart, Caltech
e-mail: email address, Faculty contact: Wendy Zhang, email address
Challenges in modeling soot formation: from laminar to turbulent flames
Understanding and modeling soot particle dynamics in combustion systems is a key issue in the development of low emission engines. In engines, soot particles are formed as a result of complex hydrocarbon chemistry and are subject to a turbulent flow field which controls ultimately the yield of soot particles. In this work, we will detail the strategies used to model the various chemical and physical processes encountered both in laminar and turbulent flames. More precisely, we will consider the impact of the chemistry on the inception of the first soot particles, the geometrical and statistical representation of fractal aggregates, the oxidation and fragmentation of particles under lean conditions, and finally the turbulent transport of soot in complex unsteady flows. For each of these cases, we will compare our results with experimental measurements and discuss the differences. Finally, we will discuss results of a Large Eddy Simulation of a sooting turbulent jet diffusion flame with detailed chemical and soot models. This last simulation highlights the challenges in modeling soot evolution in turbulent flames due to the nonlinear interactions between the particles and the gas-phase turbulent combustion processes.
May 30, 2012
Randy Ewoldt, University of Illinois at Urbana-Champaign
e-mail: email address, Faculty contact: Wendy Zhang, email address
Hagfish Self-Defense: Non-linear Rheology of a Biopolymer Physical Gel
We report the first experimental measurements of nonlinear rheological material properties of hagfish gel, a volume-expanding self-defense material composed of a hydrated biopolymer/biofiber gel network. To explain the observed nonlinear viscoelastic behavior, we develop a microstructural constitutive model that has also proven useful for other biopolymer physical gels with non-covalent crosslinks. The linear elastic modulus of the network is observed to be G' ~ 2 Pa for timescales of 0.1s to 10s, making it one of the softest elastic biomaterials known. Nonlinear rheology is examined via simple shear deformation, and we observe a secant elastic modulus which strain-softens at large input strain while the local tangent elastic modulus strain-stiffens simultaneously. This juxtaposition of simultaneous softening and stiffening suggests a general network structure composed of nonlinear elastic strain-stiffening elements, here modeled as Finite Extensible Nonlinear Elastic (FENE) springs, in which network connections are destroyed as elements are stretched. We simulate the network model in oscillatory shear and creep, including instrument effects which cause inertio-elastic creep ringing. The network model captures the simultaneous softening of the secant modulus and stiffening of tangent modulus as the model enters the nonlinear viscoelastic regime.
June 6, 2012
Allan Drummond, University of Chicago
e-mail: email address, Faculty contact: David Biron, email address
New biology or noisy data? The role of transcription in regulating steady-state protein levels in the world's best-studied eukaryote
Synthesizing multiple global measurements of cellular characteristics into a coherent whole remains an essential aim of the post-genomic era. Yet most syntheses fail to contend with two major issues: inescapable and varying measurement variability between groups, and massive amounts of missing data. Such failures have consequences. For example, it is widely accepted that cells use transcriptional regulation to shape steady-state protein levels, but the modest correlations between mRNA and protein measurements (about 0.6) have been repeatedly interpreted as prima facie evidence for alternate modes of regulation. An unappreciated alternative is that the correlation is actually very high, but the data are noisy. As Spearman noted a century ago, measurement error ensures that the correlation between two unbiased measurements underestimates the true correlation between the measured variables---and, crucially, this attenuation may be corrected. Applying a novel factor-analytical framework to decades's worth of measurements of mRNA levels protein levels during exponential growth of budding yeast in rich medium, we show that the correlation between mRNA level and protein abundance is greater than 0.9, suggesting that previous analyses have argued a larger role for other forms of regulation than the data demand. The general problem addressed here, while underappreciated in biology, is endemic to scientific inquiry and well-known in other fields.
June 13, 2012
John Royer, New York University
e-mail: email address, Faculty contact: Wendy Zhang, email address
Sand settles down: simulations of frictional grains under cyclic shear
We perform molecular dynamics (MD) simulations of spherical grains subjected to cyclic, quasi-static shear in a 3D parallelepiped shear cell. Using a standard routine for MD simulations of frictional grains, we simulate thousands of shear cycles, measuring grain displacements, the local packing density and changes in the contact network. We find that cyclic shear leads to dynamic self-organization into several phases with different spatial and temporal order. We present a phase diagram in strain - friction space which shows chaotic dispersion, crystal formation, vortex patterns and most unusually a disordered phase in which each particle precisely retraces its unique path. Particles remain in these periodic trajectories despite the fact that the contact network reveals a sizable fraction of disconnects in this limit cycle.
June 20, 2012
Stephanie Palmer, Princeton
e-mail: email address, Faculty contact: Leo Kadanoff, email address
June 27, 2012
(open date)
July 11, 2012
Janet Pierrehumbert, Northwestern
e-mail: email address, Faculty contact: Wendy Zhang, email address
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
Elisabeth Moyer, University of Chicago
e-mail: email address, Faculty contact: Wendy Zhang, email address
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
Taylor Perron, MIT
e-mail: email address, Faculty contact: Leo Kadanoff, email address
October 31, 2012
(open date)
November 7, 2012
(open date)
November 14, 2012
(open date)
November 21, 2012
(open date)
November 28, 2012
(open date)
December 5, 2012
(open date)
December 12, 2012
(open date)
December 19, 2012
(open date)
January 2, 2013
(open date)
January 9, 2013
(open date)
January 16, 2013
(open date)
January 23, 2013
(open date)
January 30, 2013
(open date)
March 5, 2013
(open date)
March 12, 2013
(open date)
March 19, 2013
(open date)
March 26, 2013
(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.

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