Computations in Science Seminars

Previous Talks: 2004

December 8, 2004
Herbert Levine, University of California, San Diego

The Surprising Mathematics of Darwinian Evolution Models
The simplest model of Darwinian evolution posits a smooth and unchanging fitness landscape upon which organisms evolve and compete for finite resources. This model has been used to explain several features of laboratory-scale experiments on viruses and bacteria. From a mathematics perspective, evolutionary dynamics translates to front propagation of the leading edge of the population. We show that this front problem is dominated by fluctuations and has no sensible mean-field aka reaction-diffusion limit. The leading order effect of these fluctuations can be treated semi-heuristically via the introduction of a growth-term cutoff, but no full theory exists at present. The implications of all this for the evolution problem are both surprising and interesting.

December 1, 2004
Humphrey J. Maris, Brown University
Experiments with Electrons in Liquid Helium
Quantum mechanics provides an extremely successful method for the calculation of the energy levels and other properties of physical systems. However, from the earliest days of quantum theory there has been controversy about the interpretation of the theory and what happens when a measurement is made. This talk will address these issues through a discussion of experiments that study the strange behavior of electrons in liquid helium. When electrons are injected into liquid helium, they force open a spherical region inside the liquid from which the helium atoms are excluded. The diameter of this bubble is approximately 40 Angstroms. When the electron is excited optically, the bubble changes shape and may break into two parts, possibly each containing a part of the electron wave function. What happens after this is not established. We will describe the experiments that have been performed to study this process and summarize the recent results.

November 17, 2004
Emmanuel Villermaux, IRPHE, Marseille, France

Simple ideas on Mixing and Fragmentation
A dye diffusing in a diluting medium while it is stirred and a set of dispersed droplets in the spray entrained by the wind blowing over a liquid surface are at first sight very dissimilar objects. However, discovering the process by which they are built reveals unexpected analogies. As we will suggest, both the concentration levels in a stirred mixture and the liquid drops in a spray result from a process of random addition which has its counterpart on the shape of the concentration distribution in the mixture, and the drop size distribution in the spray.

November 10, 2004
Andrew Johnson, University of Illinois, Chicago

Visualization Techniques for Big Data on Big Displays
The amount of information that people want to visualize is increasing rapidly. For example the US Geological Survey has 51 Terabytes of imagery from aerial photography of US cities at 1 square foot per pixel resolution. You can't open a 365,000 x 365,000 pixel image in Adobe Photoshop, and even if you could you could only see 1 block at full resolution on a typical display. Building large tile displays solves part of the problem but introduces new issues in interacting with the data. Is a user interface based on a desktop metaphor appropriate when your display is covering all the walls of your office? This talk will describe research currently going on at the Electronic Visualization Laboratory that envisions a future with situation-rooms and research labs in which all the walls are made from seamless ultra-high-resolution displays fed by data streamed over ultra-high-speed networks from distantly located visualization and storage servers, and high definition video cameras.

November 3, 2004
Jointly sponsored by the Institute for Biophysical Dynamics
Gerhard Hummer, National Institute of Health

Bridging the gap between theory and experiment: picosecond x-ray crystallography, membrane translocation, and single-molecule pulling
In my talk, I will show how experiments help validate simulations, how simulations and theory help interpret experiments, and how experiments foster the development of new theory. I will discuss recent time-resolved x-ray crystallography experiments that have allowed us to perform a first detailed comparison of calculated and measured motions of a protein, its ligand, and water on a picosecond time scale. This comparison highlights the remarkable level of accuracy achievable in current molecular dynamics simulations. I will then show how simulation and theory provide new insights into recent single-molecule measurements of polymer translocation through membranes. Finally, I will describe how non-equilibrium single-molecule pulling experiments with optical tweezers and atomic force microscopes lead to the development of new theory. In particular, I will discuss how one can rigorously obtain equilibrium free energies from nonequilibrium pulling, and illustrate the theory with recent experiments of forced RNA unfolding.

October 27, 2004
Dottie Hanck, University of Chicago

A Simple Answer to a BIG Problem: Permeation and Gating in Intercellular Channels
In vertebrate cells, direct communication between cells is achieved through gap junction channels, which provide electrical coupling between cells and are permeable to a wide variety of molecules as large as 1 kDa. Within individual cells, connexins are assembled to form hexameric connexons or hemichannels, with the six subunits arranged symmetrically around a large, central pore and put into the plasma membrane. Hemichannels dock with connexin hemi- channels in neighboring cells to form dodecameric gap junction channels. The large pores must exist at least transiently in the plasma membrane of cells before they pair. Given that they have large single channel conduct- ances and are permeable to large solutes, it is imperative that their opening be tightly regulated. A cell must keep hemichannels closed when they are unpaired, but allow them to open when they are paired so that cytoplasmic coupling may be achieved. A variety of methods to control gating have been described, including block of channels by chemical agents such as protons and divalent cations and voltage, via a poorly understood mechanism. It is possible to combine the idea of voltage dependent gating with that of voltage dependent block to explain at once hemichannel and gap junctional gating. The model builds on elements of voltage- dependent block first characterized in narrow pores in which block is complete and rapid, but with modifications necessary to take into account the case for large pores like those of gap junction hemichannels.

October 20, 2004
L. Mahadevan, Harvard University

Extreme Elastohydrodynamics: Flag Flutter, Joint Lubrication, and Fly Traps
The borderlands between elasticity and hydrodynamics lead naturally to a number of moving boundary problems in elastohydrodynamics. I will discuss some phenomena in this rich area involving extreme geometries: the flutter of a slender flag in a breeze (and its relation to fish swimming), the lift on a soft fluid-lubricated solid sliding/rolling near a wall (and relation to joint lubrication), and the dynamics of fluid-filled tissues (and its relation to rapid movements in some plants).

October 13, 2004
Igal Szleifer, Dept. of Chemistry, Purdue University

Healing of Cell Membranes: Molecular Understanding of Lipid-Poloxamer Interactions and Phase Behavior
Recent experimental observations in the laboratory of Prof. K. Y. Lee at the University of Chicago showed that the spreading of poloxamers (triblock copolymers formed by two symmetric hydrophilic blocks at the ends of a hydrophobic block) into a dilute monolayer of lipids results in a sharp increase of the lateral pressure coupled with a re- arrangement of the lipid molecules into domains that show crystal-like order. In this talk we present a theoretical description aimed at explaining the experimental findings. More specifically, we build a coarse grained model for the lipid-polymer mixture and study the ability of the polymers to induce the formation of lipid clusters and under what conditions the cluster show the same degree of order found in the solid pure lipid layers. We will show how the different aspects of the model system are built and how the different parts of the block copolymer influence the structure of the formed lipid clusters. Our findings demon- strate that both blocks of the polymer are important in inducing the observed behavior. Namely, the hydrophobic block of the polymer should have a size mismatched with the lipid hydrophobic tails and the hydrophilic tails need to have long enough polymer-polymer repulsion. Other type of interactions may induce cluster formation but without the observed ordering. Furthermore, we will show that there is a minimal amount of polymer adsorbed needed to crystallize the clusters. The implications of our studies to tune the structure of two-dimensional clusters of colloidal particles and proteins will be discussed.

TUESDAY, October 12, 2004: 12 p.m., Crerar Library, Lower Level Conference Room
Jointly sponsored by the Institute for Biophysical Dynamics
Chao Tang, NEC Laboratories America, Princeton, NJ

The Yeast Cell Cycle Network Is Robustly Designed
Despite the complex environment in and outside of the cell, various cellular functions are carried out reliably by the underlying biomolecular networks. How is the stability of a cell state achieved? How can a biological pathway take the cell from one state to another reliably? Here we address these questions from a dynamic systems point of view. We study the network regulating the cell cycle of the budding yeast, investigating its global dynamical property and stability. We found that this network is extremely stable and robust for its function. The stationary state of the cell, or the state at a checkpoint in general, corresponds to a global attractor of the dynamics-almost all initial protein states flow to the biological stationary state. Furthermore, the biological pathway of the cell-cycle sequence-which is a particular trajectory in the state space-is a globally stable and attracting trajectory of the dynamics. These dynamic properties, arising from the underlying network connection, are also robust against small perturbations to the network and against parameter changes in the model.

October 6, 2004
David Levin, University of Chicago

Channel-Independent and Sensor-Independent Stimulus Representations
It is a remarkable fact that different individuals perceive similar relationships among stimuli even though they observe those stimuli through different channels and with different sensory organs and sensory cortices. This talk addresses the engineering problem of how to design intelligent sensory devices that represent stimulus relationships in a similarly channel-independent and sensor-independent manner. First, we demonstrate that a device's channel and sensors define a coordinate system that the device imposes on the space of stimulus states. Then, differential geometry is applied to find coordinate-system-independent statistical characteristics of the trajectory of previously-encountered stimuli, and these are used to derive coordinate-system-independent relationships among stimuli. Devices, which are built on these principles but have different channels and sensors, will represent stimulus relationships in the same way, as long as they have statistically similar histories of previously-encountered stimuli. In an intelligent sensory device, this kind of representation "engine" could function as a "front end" that passes invariant stimulus representations to a pattern recognition module. Because the effects of many extraneous observational conditions have been "filtered out" of these representations, it would not be necessary to recalibrate the device's detectors or to retrain its pattern analysis module in order to account for these effects. This talk covers the material in the preprint at, and additional work on this problem is posted at

September 29, 2004
Raghu Parthasarathy, University of California, Berkeley

Protein patterns at inter-membrane junctions
Membrane-bound proteins are a remarkable class of functional, nanometer-scale building blocks whose mobility along cellular membranes contributes to a wide range of organizational and structural applications in cells. Many striking examples of spatial organization of membrane proteins exist, especially at inter- cellular junctions. With the aim of studying the dynamics of mobile, membrane-bound proteins at inter-membrane junctions, we have constructed a simple experimental platform based on supported lipid bilayer technology. With a variety of nanometer-scale imaging techniques, we analyze the structure of patterns formed at inter-membrane junctions, the mechanics behind the pattern formation, and the electrostatic interactions that give rise to further patterns.

September 22, 2004
Lincoln Chayes, University of California, Los Angeles

K-SAT, K-core and, ... , The Jamming. A new phase transition of possible relevance to computer science.
The problem of K-SAT is investigated from the perspective of phase transitions with somewhat surprising results. Not unexpectedly, this problem is related to the so-called K-core problem which, slightly unexpectedly is in turn related to the jamming transition. Lurking behind all of these systems is an apparently novel sort of phase transition which may be of universal interest in the study of problems which take a long time to study.

September 15, 2004
James S. Langer, University of California, Santa Barbara

Dynamics of Large Deformations in Glassy Solids: Why Structural Engineers Need New Ideas in Nonequilibrium Physics
There remain many remarkably fundamental, unsolved puzzles in theories of deformation and failure of solids. For example: What is the basic difference between brittleness and ductility? How do simple solids such as metallic glasses remember --- and forget --- their histories of deformation? I will summarize some recent attempts to find answers to these questions, and will argue that useful progress requires exploration of new concepts in non- equilibrium statistical physics. In particular, I will describe the way in which an effective disorder temperature, not necessarily the same as the ordinary, ambient temperature, may be needed for understanding the behavior of deforming amorphous solids.

September 8, 2004
Peter J. Mucha, School of Mathematics, Georgia Institute of Technology

Diffusivities and Front Propagation in Sedimentation
Continuum models for particles sedimenting in a fluid often assume that the diffusivity is a local function of the particulate volume fraction. Since the hydrodynamically induced diffusivity is a direct consequence of particle velocity fluctuations (for low Reynolds numbers, small concentrations, and large Peclet numbers), the identification [Tee et al., Phys. Rev. Lett. 89, 054501 (2002)] of particle density stratification as a controlling parameter for the velocity fluctuations also extends to the diffusivities. In particular, the stratification strongly affects the diffusivity in the vicinity of the falling sediment front between particle-laden fluid below and clarified fluid above. The resulting scaling for stratification-controlled diffusivities in creeping flow sedimentation is presented and compares favorably with measurements from dilute-limit particle simulations. Steadily-falling concentration profiles with these diffusivities are then presented, leading to a surprising reinterpretation of the common wisdom of self-sharpening. An extension of the model to higher volume fractions is also discussed.

September 1, 2004
Michael Marder, University of Texas

Leaves, Flowers, and Popping Balloons: Numerical Methods for Nonlinear Elastiticy
In many nonlinear problems, uncertainty about convergence of numerical methods is less severe than uncertainty about the equations that ought to be solved. In these cases, it is valuable to have numerical methods that are flexible, stable, and can easily incorporate changing ideas about physical mechanisms. I will discuss methods of this sort, tentatively called Muli-Particle Modeling, for use with nonlinear elastic problems. I will apply these methods to nonuniform metrics that cause flat sheets to deform into leaves and flowers, and to the dynamic rupture of a rubber sheet.


August 11, 2004
Yingjie Liu, Georgia Institute of Technology

New results on a simple method for interface tracking based on level sets.
Level set method uses a level set function, usually an approximate signed distance function, Phi, to represent the interface as the zero set of Phi. When Phi is advanced to the next time level by a transportation equation, its new zero level set will represent the new interface position. We update the level set function Phi forward in time and then backward to get another copy of the level set function, say Phi_1. Phi_1 and Phi should have been equal if there were no numerical error. Therefore Phi-Phi_1 provides us the information of error and this information can be used to compensate Phi before updating Phi forward again in time. One nice property is that it has the convenience of possibly improving the temporal and spatial order of an odd order scheme simultaneously. We found that when applying this idea to semi-Lagrangian schemes, e.g., CIR scheme (which has no CFL restriction, a nice feature for local refinement), the property is still valid (while MacCormack scheme having similar property may not be easily applied here). This technique coupled with a simple yet less diffusive redistancing technique produces a very efficient algorithm even for unstructured triangle meshes. Numerical results for interface movements with level set equation computed by the new methods will be presented in the talk. Also we would like show some interesting theoretical results for applying this idea to a general linear scheme.

August 4, 2004
Maximino Aldana Gonzalez, Centro de Ciencias Fisicas, Universidad Nacional Autonoma de Mexico

Phase transitions in complex neural networks: departure from the mean-field universality class.
I investigate how the topology of a network affects its dynamical properties. To this end, I will study the nature of the phase transition from an ordered to a disordered state that occurs in a family of neural network models with noise. These models are closely related to the Majority Voter Model, where a ferromagnetic-like interaction prevails. Each member of the family is distinguished by the network topology, which is determined by the distribution of the number of incoming links. I will show that for homogeneous random topologies, the phase transition always belongs to the mean-field universality class. However, scale-free networks depart from this universality class in the sense that phase transition exponents ranging from 1/2 to infinity are obtained. Furthermore, the scale-free topology provides the first example of a phase transition at finite temperature in networks with infinite average connectivity.

July 28, 2004
Todd Dupont, University of Chicago
Using Optimal Control to Compare Simulation with Experiment
It is often difficult to decide whether we can reliably model the behavior of a physical system with a particular program. I will discuss some of the possible applications of PDE-constrained optimization in such situations. There are interesting numerical analytic questions to be addressed. I will summarize some new, very positive, results in the thesis of Andrei Draganescu about the amount of work involved. However, it is not at all clear how to cast the questions we want to answer so that optimal control gives us valuable insight.

July 21, 2004
Greg Huber, University of Massachusetts, Boston

Q theory: Complex feedback, functioning designs and informatic turbulence emerging from nested recursion
In 1979, Hofstadter introduced and briefly discussed a chaotic, recursively-defined function which he called Q:
Q(n) = Q(n-Q(n-1)) + Q(n-Q(n-2))
Over the past 25 years, a number of mathematicians have studied this function and a handful of variants of it, and though some statistical details about Q's type of chaos have been observed, no one has managed to prove a single fact about Q -- not even that it -is- a function! In my talk, I'll describe a new avenue of (mostly empirical) which looks at a family of variants of Q, and which borrows some ideas from other disciplines. It turns out that this family of functions, on the collective level, exhibits an amazing degree of regularity, and yet within the framework of that family-level regularity, there are very weird irregular patterns unlike any seen before. I'll discuss what is currently known and unknown about this new family of functions, presenting the ideas mainly through a series of computer-generated graphs which display the tantalizing eccentricities that have been recently uncovered.

July 14, 2004
Moses Hohman, Center for Functional Genomics, Northwestern University

Computations in Science, indeed.
Rather than discuss a particular computation, this talk will look at how the producers and consumers of scientific computation communicate, and how these interactions affect the scientific process, e.g. productivity, the quality of results, etc.

We can roughly divide software used in research efforts into three groups. In the first group, researchers purchase or download software created by programmers with whom they will never communicate. This software may be very general productivity software like Microsoft Excel, or it may be intended for a very specific use, such as supporting instrumentation. In the second group, a single researcher (or possibly a very small group) writes his/her own software, seeking to produce a novel, computational result. The software is not written for anyone but that researcher (although it may come to be used by others). In the third group, the scientific program involves a larger group or community of researchers, and part of the research requires completion of a set of data and/or computation intensive tasks. In this case, the users and the programmers are not the same people, and communication becomes a critical factor for the atmosphere and success of the project.

After completing a physics PhD involving a fair amount of programming at the University of Chicago, my professional background has been in both custom business software development and database bioinformatics in an academic setting. Rather than bore you with endless details about my experiences, however, I hope that this talk will be interactive. I will present a set of ideas and topics, and then will solicit experiences from the audience for discussion, examining as a group the way we all work.

People who write research code for themselves, who write code for others or who have code written for them are encouraged to attend.

July 7, 2004
Eric Isaacs, Argonne National Laboratory & U. of Chicago

New Approaches to Studies of Quantum Critical Behavior

June 30, 2004
Stéphan Fauve, Ecole Normale Superiéure

Talk partially sponsored by the Center for Magnetic Self-organization
Large scale fluctuations in dissipative systems out of equilibrium
Fluctuations of macroscopic quantities in systems at thermal equilibrium have well known properties. Much less is known for dissipative systems out of equilibrium. We first present several experimental or numerical results on a few examples: fluctuations of the total heat flux in turbulent convection, or of the power needed to drive a turbulent flow in a statistically stationnary regime, fluctuations of the kinetic energy or of the injected or dissipated power in a granular gas, etc. We then propose different methods to characterize these fluctuations and show that some of their statistical properties do not depend on the particular system under consideration.

THURSDAY, July 1, 2004, KPTC 206 at 2:00 p.m.
Stéphan Fauve, Ecole Normale Superiéure

Talk partially sponsored by the Center for Magnetic Self-organization
Generation of magnetic fields by turbulent flows of liquid metal
The generation of a magnetic field by a flow of liquid sodium has been observed in recent experiments (Karlsruhe, Riga). We emphasize two very interesting features displayed by these experiments.
  • The observed dynamo threshold is in good agreement with the one computed from the mean flow alone, i. e. neglecting turbulent fluctuations although the kinematic Reynolds number is of order 105 to 106.
  • On the contrary, the mean magnetic field measured above dynamo threshold is 1000 times larger than the one predicted from a laminar weakly nonlinear calculation.
We first understand these two observations and give the expected scaling law for the magnetic energy above dynamo threshold. We then consider magnetic fluctuations above dynamo threshold or in MHD turbulence and report a Kolmogorov type spectrum in the inertial range and 1/f noise at low frequency. Finally, we discuss the effect of turbulence and rotation on dynamo onset and saturation in flows without strong geometrical constraints.

June 23, 2004
Sascha Hilgenfeldt, University of Twente, The Netherlands

The power of bubbles: Biomechanics and Microfluidics
To manipulate suspensions of cells and other micron- sized particles in bioengineering or lab-on-a-chip applications, strong hydrodynamic forces on small scales are necessary. Ideally, these forces should both ensure rapid transport of the particles and be strong enough at well-defined locations to porate or rupture cell membranes in order to achieve transfection of large molecules such as drugs or DNA into the cell. We show that ultrasound is an efficient driving mechanism for such microfluidic flows, if the sound energy is focused onto small scales through oscillating microbubbles. The bubbles excite a streaming flow that can be used to aggregate, deform, and rupture lipid vesicles and cells, making it a promising tool for both membrane studies and drug delivery applications. When combining bubbles with passive flow elements, other modes of streaming are excited, allowing for directional microfluidic transport of cells and particles without microchannels. All observed flows are in quantitative agreement with Stokes flow singularity theory.

June 16, 2004
Rajesh Ravindran, Brandeis University

Plane and solid partitions of an integer
Combinatorial enumeration problems arise naturally in many problems of statistical physics. The number of partitions of an integer is one such enumeration problem with a history dating back to Euler. Partitions of an integer is the number of ways a positive integer can be decomposed into sum of smaller parts. Depending on the dimension of the lattice on which these parts are arranged, the partitions are called linear partitions, plane partitions, solid partitions and so on. Very little is known about solid partitions and higher dimensions. In this talk I will present numerical results for the asymptotic behavior of solid partitions. A simple proof for the MacMahon formula for the plane partitions of an integer will also be discussed.

June 9, 2004
Igor Aronson, Argonne National Laboratory

Self-assembly and patters in electrostatically driven granular media
Large ensembles of small particles display fascinating collective behavior when they acquire an electric charge and respond to competing long-range electromagnetic and short-range contact forces. We conduct experimental and theoretical studies of the dynamics of conducting microparticles in strong electric field in the air or in poorly conducting liquids. We show that granular media consisting of metallic microparticles immersed in a poorly conducting liquid in strong DC electric field self-assemble a rich variety of novel phases. These phases include static precipitate: periodic honeycombs and Wigner crystals; and novel dynamic condensate: toroidal vortices and pulsating rings. The observed structures are explained by the interplay between charged granular gas and electrohydrodynamic convective flows in the liquid. We developed continuum theory of self-assembly and pattern formation in this system. The theory is formulated in terms of two conservation laws for the densities of immobile particles (precipitate) and bouncing particles (granular gas) coupled to the Navier-Stokes equation for the liquid. This theory successfully reproduces correct topology of the phase diagram and primary patterns observed in the experiment: static crystals and honeycombs and dynamic pulsating rings and rotating multi-petal vortices.

April 28, 2004, BSLC 205 starting at 12:00 p.m.
Ron Vale, University of California San Francisco
Talk sponsored by the Burroughs Wellcome Fund Interfaces in Science program
Dissecting the mechanism of the kinesin motor protein using structural and single molecule approaches

The evolution of living organisms required developing special strategies for synthesizing complex molecules and creating order and asymmetrical distributions of molecules within their interior. Many of these operations are performed by nanometer-scale "molecular machines" that use chemical energy to drive unidirectional processes, produce linear motion and/or generate mechanical work. I will discuss the mechanism of kinesins, which are motor proteins that use ATP energy to move along microtubules. In humans, there are 45 different kinesin motor proteins that are involved in a myriad of different biological functions including organelle, protein, mRNA transport, mitosis/meiosis, and control of microtubule dynamics. We have used a combination of single molecule motility assays, cryo-electron microscopy, spectroscopy, x-ray crystallography and mutagenesis to identify a new type of mechanical amplification process for kinesin. Recently, we have tested our model by "watching" changes in the structure of an individual kinesin motor protein as it undergoes motility. This work, which involves a combination of protein engineering and low light level fluorescence microscopy, provides new insight into how chemical energy causes the step-wise motion of kinesin along its track.

A general review on kinesin (as well as another motor- myosin): Vale, R. D. and Milligan, R. A. 2000. The way things move: looking under the hood of molecular motor proteins. Science 288: 88-95.

April 21, 2004, NOTE time and place: RI L-112 at 2 p.m.
Eric Clement, Dept. of Physics, Université Paris VI and ESPCI

Response functions, unjamming, and mobility in dense granular matter

April 14, 2004
Julian Hunt, University College London and TU Delft
Convective and stably stratified turbulence and mean flows generated by the turbulence (*)
A brief review is given of how convective and stably stratified turbulence occurs in geophysical flows, especially boundary layers. General aspects of the steady/unsteady (plume/puff) eddy structure, as a function of thermal/momentum surface boundary conditions are described using results from lab and field experiments, theory and numerical simulations. These results are important for determining the levels of temperature and velocity fluctuations at the surfaces bounding the convection. In stably stratified turbulent shear layers, perturbation theory and DNS results show how the fluctuations are strongly distorted by the buoyancy forces in such a way as to reduce the transfer of energy from the shear to the turbulence-a more universal and different mechanism to the GI Taylor instability or LF Richardson energy damping mechanisms. Because of its local structure, stably stratified turbulence, except when it is very inhomogeneous, has certain general characteristics found in a variety of different types of flow, except in highly inhomogeneous layers when the results are rather unpredictable (with consequences for weather forecasts). Forecasts are also difficult when convective turbulence is perturbed by weak shear; so that the mean flow can be amplified. In the resulting mean profile jets tend to appear.

April 7, 2004
James Shapiro, University of Chicago
How a simple genetic network operates- why there is neither Cartesian nor Turing dualism in the E. coli cell
In 1942, Jacques Monod discovered that E. coli bacteria can discriminate between glucose and lactose and decide to consume the glucose first. The talk will present a standard molecular biology description of how the E. coli cell makes this decision. The computational process involves sequence-specific DNA-binding proteins, protein phosphorylation, action of membrane proteins and soluble cytoplasmic enzymes, protein-protein interactions, small molecule messengers and the construction of highly specific nucleoprotein complexes. Because all compartments of the cell are involved in information processing, there is no Cartesian separation into dedicated "informational" and "operational" molecules. Because the DNA participates as a physical component of the nucleoprotein regulatory and transcriptional complexes, it is not simply a software "tape" in the sense of a Turing machine. Our inability to make basic Cartesian or Turing distinctions indicates that biological (i.e. cellular) computation follows a novel computing paradigm.

TUESDAY, April 6, 2004, KPTC 206, 12 p.m.
Dave Dearborn, Lawrence Livermore National Laboratory
Children of the Sun
By 1572 the last legitimate heir to the Inca crown had been executed, and many of the important shrines had been desecrated, or destroyed. A great deal of information on Inca social structure, ceremonial activity, and belief is lost. Still, through ethnohistoric accounts, and archaeological fieldwork, it is possible to piece together the sky watching practices of the Inca, and understand some of its use in organizing their empire. From such work we know that as children of the sun god, Inti, the Inca ruled their empire, Tawintinsuyu. This elite position was reinforced through ceremonies honoring the sun, and involving a system of solar markers around the horizon of Cuzco. The remains of such solar markers have now been found at Titicaca, giving flesh to early Spanish accounts. However, this archaeological find demonstrated that the system required the support of other observations. Important clues defining these supporting observations were then found at Machu Picchu.

MONDAY, April 5, 2004, LASR Conference (eastside), 3:30 p.m.
ASC Flash Center Special Seminar
Dave Dearborn, Lawrence Livermore National Laboratory

Danger - Asteroid Crossing
Every couple of years, a celestial body impacts the earth with energy near that of the Hiroshima bomb. On much longer timescales, impacts will occur with the potential to destroy regions, or whole civilizations. This lecture will present an overview on efforts to define the impact threat, followed by a systematic development of the requirements to divert an object on an earth-impacting course. We then examine today's technologies for achieving perturbation magnitudes necessary to protect the planet.

March 31, 2004
Roland Netz, Ludwig-Maximilians Universit - Munchen

Stretching and aligning polymers
I will discuss theoretical models which are useful for understanding the properties of single polymer molecules under mechanical, hydrodynamical and electrical stress.

1) If one pulls on a polymer, for example using an atomic-force-microscope (AFM), one obtains a characteristic force-extension profile. For small forces the fluctuation spectrum of the polymer is modified and the response is mostly entropic. For large forces bond lengths and bond angles change which leads to an enthalpic response. The elastic modulus of a wide class of different synthetic and biopolymers can be predicted from ab-initio quantum-chemical calculations and compares well with experimental data at large forces in the nano-Newton range.

2) Motion of a deformable polymer within a viscous medium gives rise to an intricate coupling of shape deformations and hydrodynamic interactions. As a result, uniformly driven polymers will usually align perpendicularly to the direction of the driving force, in agreement with birefringence measurements.

3) Charged polymers are also deformed by applying an electric field, due to their huge polarizability, which is an important factor in understanding the electrophoretic mobility of charged bio molecules. By performing dynamic simulations, the relation between the electrophoretic mobility and the the non-equilibrium perturbation of the polymer structure can be understood.

March 17, 2004
Roman Grigoriev, Georgia Institute of Technology

Chaotic mixing in microdroplets: theory and experiment
Liquids do not mix easily in microfluidic systems, which are being developed into "labs-on-a-chip" that promise revolutionary applications in biotechnology, chemistry and medicine. Recent studies have suggested that microfluidic stirring via chaotic advection can achieve the efficient mixing required in typical uses. For devices based on continuous flow through microchannels, strategies for inducing chaotic mixing by altering device geometries have been proposed. I will describe a general methodology for introducing chaotic mixing in discrete volume (microdroplet) systems, which allow miniaturization of many standard laboratory protocols that are difficult to realize with continuous flow. The mixing properties of the flows in microdroplets are governed by their symmetries, which give rise to invariant surfaces serving as barriers to transport. Complete three- dimensional mixing by chaotic advection requires destruction of all flow invariants. As an illustration of this idea, I will demonstrate that complete mixing can be obtained in a time-dependent flow produced by motion of a microdroplet along a two-dimensional path and describe the experiments that optically manipulate and mix microdroplets.

March 10, 2004
Bulbul Chakraborty, Brandeis University and the University of Chicago
Critical dynamics in a funnel-shaped landscape: a Landau-type theory of the glass transition
Glassy dynamics occur in a large variety of systems, such as supercooled liquids, foams and granular matter. They are characterized by an exponentially rapid increase of relaxation times, as a control parameter such as temperature or density in tuned, and by a non-exponential decay of time-dependent correlation functions indicating a broad distribution of time scales. In this talk, I will present an exact solution of a Landau model of an order-disorder transition with activated critical dynamics. The model describes a funnel-shaped topography of the order parameter space in which the number of energy lowering trajectories rapidly diminishes as the ordered ground state is approached. This leads to an asymmetry in the effective transition rates, which results in a non-exponential relaxation of the order-parameter fluctuations and a Vogel-Fulcher-Tammann divergence of the relaxation times, typical of a glass transition. I will discuss a lattice model where this class of critical dynamics is realized and I will argue that the Landau model provides a general framework for studying glassy dynamics in a variety of systems.

THURSDAY, March 4, 2004: RI 480, 1:30 p.m.
Stephen Smale (*), Toyota Technical Institute of Chicago and the University of California, Berkeley
Shannon Sampling, Learning Theory and Reconstructing Functions from Point Values
Shannon sampling is a special case of the general problem of reconstruction of a function from its values at a discrete set of points. The talk with deal with age-old algorithms for solving this problem and new estimates for their error and efficiency.

March 3, 2004, KPTC 206, 12:15 p.m. (Partially sponsored by the Burroughs-Wellcome Fund)
Eytan Domany, Weizmann Institute
Applications of Gene Expression Analysis to Studies of Cancer and Differentiation
DNA chips are novel experimental tools that have revolutionized research in molecular biology and generated considerable excitement. A single chip allows simultaneous measurement of the level at which thousands of genes are expressed. A typical experiment uses a few tens of such chips, each devoted to one sample - such as material extracted from a tumor. Hence the results of such an experiment consist of a table, of several thousand rows (one for each gene) and 50 - 100 columns (one for each sample). Extracting relevant information from such a large, complex and noisy data set requires development of novel methods of analysis.

In this talk I will briefly explain how gene expression is measured by DNA chips, and demonstrate how we combine standard statistical analysis with these novel unsupervised methods to mine expression data obtained from leukemia samples. If time permits, I will demonstrate how some intriguing design principles can be obtained from recent experiments on stem cells.

TUESDAY, March 2, 2004: IBD Seminar, Crerar Conference Room (Lower Level), 12:00 p.m. (Partially sponsored by the Burroughs-Wellcome Fund)
Eytan Domany, Weizmann Institute
Introduction to Gene Expression Analysis
DNA chips are novel experimental tools that have revolutionized research in molecular biology and generated considerable excitement. A single chip allows simultaneous measurement of the level at which thousands of genes are expressed. A typical experiment uses a few tens of such chips, each devoted to one sample - such as material extracted from a tumor. Hence the results of such an experiment consist of a table, of several thousand rows (one for each gene) and 50 - 100 columns (one for each sample). Extracting relevant information from such a large, complex and noisy data set requires development of novel methods of analysis.

This talk will provide a very basic introduction, with no prior knowledge of any biology assumed. I will explain what genes are, what is gene expression and how it is measured by DNA chips. I will also explain what is meant by clustering and sorting, and demonstrate how standard statistical methods and novel, unsupervised techniques are used to analyse data on various forms of cancer.

February 25, 2004
Wouter Hoff, University of Chicago
Exploring protein structure-function relationships using a photoreceptor protein
A major challenge in structural biology is to derive a quantitative understanding of the relationship between the structure of a protein and its function, and use this to extract general rules on protein structure-function relationships. While thousands of protein crystal structures have been determined, many proteins have been studied using mutagenesis, and computational approaches have been applied to functional aspects of proteins, this remains a central open problem in biochemistry.

I will present work on the use of photoactive yellow protein (PYP) as a model system to identify general principles in protein structure-function relationships. PYP is a photoreceptor protein found in photosynthetic bacteria. Activation of PYP by blue light causes this protein to generate a transient signal within the bacterial cell. This is initiated by the photoisomerization of the covalently attached chromophore buried within PYP. The following findings will be discussed. (i) We have found that photoactivation of PYP results in its transient partial unfolding, challenging the notion that signal transduction only occurs between fully folded proteins. (ii) We have developed a model in which this transient unfolding event is caused by light-triggered proton transfer, which generates a buried charge within PYP that functions as an "electrostatic epicenter" for the "protein quake" that activates PYP. (iii) We found that removal of the chromophore from PYP causes its partial unfolding. This partially unfolded state catalyzed the covalent attachment of the chromophore to itself. This presents the second example in the PYP system of a biological function for a partially unfolded state, challenging the influential notion that only fully folded proteins are functionally active. (iv) We recently initiated a high-throughput biophysics approach to systematically probe structure-function relationships in PYP. Computational methods will be essential in analyzing the experimental data obtained in this project.

February 18, 2004
Ute Ebert, CWI Amsterdam and TU Eindhoven, The Netherlands
Branching sparks --- the dynamics of electric breakdown
The initial phase of sparking is determined by so-called streamers. These are weakly ionized channels during their growth period. The growth is characterized by a self-induced enhancement of the electric field at the tip of the discharge channel. Streamers propagate with velocities of the order of 1000 km/sec; recent ultrafast photography gives a new view on their dynamics. Streamer concepts are also being applied to recently discovered high altitude lightning, so-called red sprites.

I will review recent observations and then explain the state of microscopic modelling, computations and theoretical concepts. Basically, already a single discharge channel has a multiscale structure with a thin ionization front surrounding a rather inert body. I will present computational results with adaptive grids, and I will discuss the properties of ionization fronts, moving boundary approximations for these fronts, and solutions of the moving boundary problem with conformal mapping methods. The result is the prediction that streamers in a sufficiently high potential can branch spontaneously due to a Laplacian instability as is also observed in computations. This quantitative prediction has to be confronted with phenomenological models for spark branching of the type of diffusion limited aggregation.

February 11, 2004
Marko Kleine Berkenbusch, University of Chicago (CANCELLED: Sara A. Solla, Northwestern University)
Discrete charges on a two-dimensional conductor: Energies and Symmetries
We study the placement of charged particles on a two-dimensional conductor. Particularly, we focus on the placement of N equal discrete charges in the asymptotic limit as N goes to infinity, for both the case of a smooth conductor and also the situation in which the conductor contains cusp-like points.

This problem is closely related to diffusion limited aggregation (DLA), and to the two-dimensional motion of viscous fluids (Hele-Shaw). A similar problem has been originally introduced under the notion of "Fekete points". However, in that context, results about the asymptotic placement of the charges as well as the (first order) asymptotic energies have been derived only for domains bounded by analytic curves. In contrast, we are trying to study how non-analyticities of the conductor boundaries affect the charge placements and expansions of equilibrium energies in the number of charges.

Furthermore, systems with an intrinsic symmetry of the conductor show a breaking of this symmetry in the placement of the charges, depending on the number of charges and the local curvature of the boundary.

February 4, 2004
Norbert F. Scherer, University of Chicago
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Insights into folding and unfolding of large biomolecules from single molecule measurements

January 28, 2004: LOCATION: RI L-112
J. Rudi Strickler, University of Wisconsin - Milwaukee
500 Million Years of Evolution made Planktonic Copepods Masters of Applied Fluid Dynamics
Copepods are micro-crustaceans of 1 to 5 mm in length. They create feeding currents to find food, use hydro-dynamical disturbances to distinguish predators from mates, and 1.347x10exp21 of them populate the vast 3D environments of our fresh and marine waters. I will show (in short videos) results of 30 years of detailed observations of the interaction between these animals and their surrounding water.

January 21, 2004
Elise Lorenceau, Harvard University
Air entrainment through viscous liquid
We study the impact of a jet of a viscous fluid in a bath of the same liquid. We measure the radius of curvature of the liquid air-interface where the impact occurs. We show that it decreases exponentially with the capillary number. Above a threshold speed, capillary can not overtake this high confinement and a thin sheet of air is dragged into the bath by the jet, in a trumpet-like form. We measure the threshold speed for which a film of air is dragged into the pool and the thickness of the film.

TUESDAY, January 13, 2004: KPTC 206, 1:30 p.m.
(Partially sponsored by CAMP, MRSEC, and EFI Theory).
John Cardy, University of Oxford
Multiple SLEs, Random Matrices, and Conformal Field Theory
Schramm-Loewner evolution (SLE) describes the statistics of single random curves in 2d critical systems. It relates questions about these curves to simple problems in 1d Brownian motion. Many old and new results can be derived using these methods. I present a generalisation to $N$ curves. The corresponding 1d problem is Dyson's Brownian motion, which describes the statistics of the eigenvalues of random matrices. It is also related to the quantum Calogero-Sutherland hamiltonian. I show that this connection arises also in conformal field theory (and could have been discovered 20 years ago.) The values of bulk critical exponents of 2d systems are given by the spectrum of this hamiltonian.

MONDAY, January 12, 2004: MRSEC Seminar, KPTC 206, 12:30 p.m.
(Partially sponsored by CAMP, MRSEC, and EFI Theory).
John Cardy, University of Oxford
Crossing Probabilities in Percolation
Given a large but finite region, filled with a medium which is a composite of conducting and insulating components, can current flow between two contacts attached to separate parts of the boundary? This is a problem in percolation. Above the percolation threshold $p_c$ current always flows, while below $p_c$ it never does so. But at $p_c$ there is a finite probability, between zero and one, of a connection, and this depends on the shape of the region.

In quantum Hall systems, the value of the quantised conductance depends not just on whether there is a connection, but on the number of independent such ones.

These problems share the property of conformal invariance. In two dimensions, there are exact results for them. I shall present these, and discuss the variety of methods by which they have been obtained.

January 7, 2004
Stanislav Boldyrev, University of Chicago
On magnetic field generation in Kolmogorov turbulence
In a turbulent highly conducting fluid, magnetic fields are amplified since the field lines are generally stretched by randomly moving fluid elements in which these lines are frozen. Such a mechanism of turbulent dynamo is expected to work in a variety of astrophysical systems (galaxy clusters, interstellar medium, stars, planets), is confirmed numerically, and is consistent with simple analytical models.

Recently, there appeared the number of high-resolution numerical simulations of MHD turbulence with small magnetic Prandtl numbers [Pm=fluid viscosity/fluid resistivity], where magnetic fluctuations were not amplified. This revived old claims that dynamo does not exist in the Kolmogorov turbulence with Pm << 1. However, astrophysical observations show that magnetic fields are generated by turbulent motion rather effectively in planets and stars where magnetic Prandtl numbers are small (e.g., in the geo-dynamo, Pm=10^-5, in stars, Pm= 0.01). The talk will address this apparent contradiction.