Computations in Science Seminars

Previous Talks: 2008

Jan 2008
7
Mon 12:30
Nigel Goldenfeld, University of Illinois at Urbana-Champaign
e-mail:
Host: Leo Kadanoff ()
Organizer: Kostya
Biocomplexity in Action: Pattern Formation and Microbial Ecology at Yellowstone's Hot Springs
(12:30 in KPTC 206)

Biocomplexity is the term that is becoming used to describe efforts to understand strongly-interacting dynamical systems with a biological, ecological or even social component. I provide a brief overview of why this field is not only interesting for physicists, but can benefit substantially from their participation. In particular, microbes represent a fascinating opportunity for physicists to contribute to biology, because their strong interactions, via both signalling and exchange of genes, means that the techniques of statistical mechanics are ideally suited to exploring the ecology of microbial communities and even the evolutionary dynamics of microbial genomes.

I describe our work at Yellowstone's Mammoth Hot Springs, to answer the following questions: do heat-loving microbes play a role in the dynamics of landscape evolution? And how can we quantitatively account for the architecture of the landscape in the vicinity of geothermal hot springs?

Sponsors of Nigel Goldenfield's talks include the JFI, the CI, the IBD, and the CIS lecture series.

Jan 2008
8
Tue 12:30
Nigel Goldenfeld, University of Illinois at Urbana-Champaign
e-mail:
Host: Leo Kadanoff ()
Organizer: Kostya
Patterns, Universality and Computational Algorithms
(JFI Colloquium - 4:00 in CIS W301)

Can we use computational algorithms to make accurate predictions of physical phenomena? In this talk, intended for non-experts, I will give examples where complicated space-time phenomena can be exquisitely captured with simple computational algorithms, that not only produce patterns resembling those seen in experiment, but also make accurate predictions about probes of dynamics and spatial organisation, such as correlation functions. In the last part of this talk, I describe how to handle materials pattern formation when structure emerges on multiple length and time scales, from atoms to polycrystalline sample dimensions.

Sponsors of Nigel Goldenfield's talks include the JFI, the CI, the IBD, and the CIS lecture series.

Jan 2008
9
Wed 12:30
Nigel Goldenfeld, University of Illinois at Urbana-Champaign
e-mail:
Host: Leo Kadanoff ()
Organizer: Kostya
Statistical Mechanics of the Genetic Code: a Glimpse of Early Life?

Relics of early life, preceding even the last universal common ancestor of all life on Earth, are present in the structure of the modern day canonical genetic code. In this talk, I will draw attention to these relics, and discuss their interpretation from the perspective of the dynamical system that is evolution. I will argue that this viewpoint, and the quantitative, statistical dynamical calculations that it entails, suggest a natural scenario in which evolution exhibits three distinct dynamical regimes, differentiated respectively by the way in which information flow, genetic novelty and complexity emerge. Possible observational signatures of these predictions are discussed.

Sponsors of Nigel Goldenfield's talks include the JFI, the CI, the IBD, and the CIS lecture series.

Jan 2008
16
Wed 12:30
Hassan Nagib, Illinois Institute of Technology
e-mail:
Host: Wendy Zhang ()
Organizer: Robert
High Reynolds Number Wall-Bounded Turbulence: The Approach to an Asymptotic State and its Universality

Just over one-hundred years ago Prandtl introduced the new concept of "boundary layers" to explain, analyze and model fluid flow behavior near surfaces. Today we can use similar ideas for interfaces where rapid local changes occur in fields including economics, political and social systems, biomedical applications, and even psychology. Since modeling the rapid changes in this boundary layer generally requires more detailed physics than in the slowly varying "outer" regions, special mathematical tools, i.e., singular perturbation analysis, had to be developed to connect the different regions. For example, the method of matched asymptotics has contributed a great deal to our understanding of turbulent boundary layers, starting with the classical two-layer approach of Millikan, which leads to the logarithmic velocity profile in the overlap region between "inner or small scales" and "outer or large scales," and the "von Karman constant". Nearly all currently used commercial codes for computation of flow in applications including aeronautics, energy generating machines and weather prediction rely on such a Karman constant. However, our recent examination of boundary layers with streamwise pressure gradient, and pipe and channel flows indicates that the von Karman coefficient of the log law is not universal, and exhibits dependence on not only the pressure gradient but also the wall-bounded flow geometry, thereby raising fundamental questions regarding turbulence flow theory and modeling for all wall-bounded flows.

Jan 2008
23
Wed 12:30
Andrea Liu, University of Pennsylvania
e-mail:
Host: Wendy Zhang ()
Organizer: Arnab
The Physics of Cell Crawling and Listeria Motility

When a cells crawls, its shape re-organizes via polymerization and depolymerization of a network of actin filaments. The growing ends of the filaments are localized near the outside of the cell, and their polymerization, regulated by a host of proteins, pushes the cell membrane forwards in a biological model known as the dendritic nucleation model. The same dendritic nucleation mechanism comes into play when the bacterial pathogen Listeria monocytogenes infects a cell. The bacterium hijacks the host cell's actin machinery to create an actin network (the actin comet tail) that propels the bacterium through cells and into neighboring cells. I will discuss recent results from Brownian dynamics simulations that suggest a new picture for the physical mechanism underlying this form of motility.

Jan 2008
30
Wed 12:30
Ursula Perez-Salas, Argonne National Laboratory
e-mail:
Host: Wendy Zhang ()
Organizer: Robert
To Wet or Not to Wet: Profile of the Interface Between a Hydrophobic Surface and Water

Aqueous interfaces are ubiquitous and play a fundamental role in biology, chemistry, and geology. The structure of water near interfaces is of the utmost importance, including chemical reactivity and macromolecular function. Theoretical work by Chandler et al. on polar-apolar interfaces predicts that a water depletion layer exists between a hydrophobic surface and bulk water for hydrophobes larger than ~20nm^2 (a ~4A in radius apolar molecule). Until now, what the interface really looks like remains in dispute since recent experiments give conflicting results: from complete wetting (no water depletion layer) to a water depletion layer. Those experiments that have found a water depletion layer report 40-70% water in the depletion zone: 40-70% and a width of ~3A. However, an alternative interpretation to the profiles exists where no depletion layer is required. By studying hydrophobic self assembling monolayer surfaces against several water mixtures of D2O and H2O we obtained the hydrophobic/water profile by phase sensitive neutron reflectivity. With this model independent technique we observe a 2 times wider and drier depletion water layer: 6A thick and 0-25% water. Given the level of disagreement, I will review and discuss the topic of immiscible interfaces.

Feb 2008
4
Mon 12:30
Uri Alon, Weizmann Institute of Science
e-mail:
Host: Leo Kadanoff ()
Organizer: Kostya
Evolution, Optimality and Biological Design
(Special MRSEC Seminar - 12:30 in KPTC 206)

It is clear that evolution tends to optimize fitness if it can. The question for research is what are the constraints under which this optimization is done. A theory of biological design thus must include mathematical formulations of these constraints. This talk will present experimental data that measures the fitness as a function of molecular parameters in E. coli, and laboratory evolution epxeriments that follow the optimization process directly. This is used to suggest the beginnings of a theory for understanding basic design questions: What sets the concentration of as protein in the cell to a specific value? What is the cost and benefit of a regulatory interaction? What is the cost of stochastic noise in the design? The blackboard will be used to hopefully invite audience interaction.

[E. Dekel and U. Alon, Optimality and evolutionary tuning of the expression level of a protein. Nature, 436, 7050, 588-922 (2005).],

Sponsors of Uri Alon's talks include the MRSEC, the IBD, the CI, and the CIS lecture series.

Feb 2008
5
Tue 12:30
Uri Alon, Weizmann Institute of Science
e-mail:
Host: Leo Kadanoff ()
Organizer: Kostya
Design Principles of Biological Circuits
(JFI Colloquium - 4:00 in CIS W301)

Biological networks of interactions are of course very complex. Recently, however, some biological networks, namely those that control gene expression, have been found to display a degree of simplicity: they seem to be built of only a small set of recurring inetraction patterns. These elementary patterns, called network motifs, can each carry out a specific dynamical function in the network. These functions have been studied experimentally using high resolution experiments in living cells. The same network motifs seem to be found across organisms from bacteria to humans. Network motifs are found also in other types of biological networks, including neuronal networks. This raises the hope that the dynamic of complex biological entworks could be understood in terms of elementary circuit patterns.

[Uri Alon, Network motifs: theory and experimental approaches. Nature Reviews Genetics 8, 450-461 (2007).],

Sponsors of Uri Alon's talks include the MRSEC, the IBD, the CI, and the CIS lecture series.

Feb 2008
6
Wed 12:30
Uri Alon, Weizmann Institute of Science
e-mail:
Host: Leo Kadanoff ()
Organizer: Kostya
On the Speed of Evolution

Bats, whales, and cows all evolved from an ancestral mammal in less than 100 million generations. In contrast, computer simulations of evolution need far more generations to solve rather simple computational problems. There may thus be a challenge to understand the speed of natural evolution. This talk will present a computational study of evolution that demonstrates ways to dramatically speed evolution, based on temporally varying goals. It is seen how speedup of evolution is linked with spontaneous emergence of modular structure in the organism.

[N. Kashtan, E. Noor and U. Alon, Varying environments can speed up evolution. PNAS, 104: 13711-13716 (2007).],

Sponsors of Uri Alon's talks include the MRSEC, the IBD, the CI, and the CIS lecture series.

Feb 2008
13
Wed 12:30
Steve Kron, University of Chicago
e-mail:
Host: Leo Kadanoff ()
Your Proteome in an Hour? Experimental and Computational Approaches to High Throughput Protein Mass Spectrometry

Despite the buildup, completing the sequencing of the genome was at best anticlimactic, and the functions of most of the genes remain mysterious to this day. Hopes for systems biology to explain how the genome works rest on the hypothesis that comprehensive and quantitative measurements of gene activities will reveal the fundamental mechanisms that determine cell growth, metabolism, interactions and identity. To date, systems biology's greatest successes have been in understanding gene expression, where comprehensive analysis has become straightforward in the last ten years. The RNAs that derive from transcription of each gene can be reliably isolated from the organism and then individually measured using highly multiplexed tools such as hybridization microarrays. Sophisticated informatics permits the investigator to compare many conditions and recognize patterns of gene activity that correspond to distinct cell states, revealing the logic of the cell.

This happy story is in stark contrast to the state-of-the-art in comprehensive analysis of cellular proteins. Proteins are considerably more diverse than RNA and there seems no future for a generic protein detection technology equivalent to the DNA microarray. Despite a decade of pundits touting mass spectrometry as the enabling technology for analysis of cellular proteins, current tools and methods do not offer the sensitivity, dynamic range or throughput required and there seems no clear path to comprehensive analysis. Our group of experimentalists and informaticists has been working to reinvent mass spectrometry proteomics with high throughput comprehensive analysis in mind. We will present the current state of mass spectrometry experiments and informatics, exploring strengths and weaknesses, and describe an alternative approach that can overcome many of the current limitations. We are developing experimental and computational strategies, hoping to take full advantage of the capabilities of current and future mass spectrometers to identify and measure proteins. Successful implementation would have the potential for significant impact on medicine and industry and provide one of the missing tools for systems biology.

Feb 2008
20
Wed 12:30
Maximino Aldana, Universidad Nacional Autonoma de Mexico
e-mail:
Host: Leo Kadanoff ()
Organizer: Arnab
On the Emergence of Collective Order in Swarming Systems: A Recent Debate

An important characteristic of flocks of birds, schools of fish, and many similar assemblies of self-propelled particles is the emergence of states of collective order in which the particles move in the same direction. When noise is added into the system, the onset of such collective order occurs through a dynamical phase transition controlled by the noise intensity. While originally thought to be continuous, the phase transition has been claimed to be discontinuous on the basis of recently reported numerical evidence. This has originated a (heated) debate about the nature of the phase transition, i.e. whether it is continuous or discontinuous. In this talk I will present evidence showing that the phase transition actually depends crucially on the way in which the noise is introduced into the system. Such a dependence was not taken into account in previous studies of swarms and flocks, which is probably what caused all the confusion about the onset of collective order in these systems.

Feb 2008
27
Wed 12:30
Laura Schmidt, University of Chicago
e-mail:
Non-universality of an Implosion Singularity

Recent experiments show that when an air bubble breaks away from an underwater nozzle, the thin neck that pinches off retains a detailed memory of initial asymmetries in its shape (Keim et al, Phys. Rev. Lett. 97, 144503 (2006)). This is in contrast to other break-up studies (e.g. water falling from a faucet) which reveal universal break-up dynamics. Motivated by these observations, we consider the singularity dynamics of a collapsing 2-D circular hole in water. Upon perturbing the natural circular symmetry, memory is manifested as the conservation of the size of the initial distortion and in vibrations of the shape as the hole closes. As break-up is approached, the vibrations dramatically alter the final stages of the singularity. We show that this ideal implosion is relevant to reality by directly comparing the 2-D model to vibrations induced in experiments by the release of a bubble from a slot-shaped nozzle.

Mar 2008
5
Wed 12:30
Bob Eisenberg, Rush Medical College
e-mail:
Host: Leo Kadanoff ()
Organizer: Robert
Bubbles, Gating, and Anesthetics in Ion Channels

Ion channels are proteins with a hole down their middle that act as the "valves of life". Ion channels control the flow of ions (hard spheres) like Na+ , Ca2+ , K+ , and Cl- across the otherwise insulating membrane of cells. They act much like Field Effect Transistors which control the flow of quasi-particles - holes and electrons - through glass "membranes" (layers).

Channels open and close suddenly ("gate") and different channels control this opening and closing in very different ways. The control and mechanism of gating is studied by hundreds if not thousands of scientists every day because of the clinical and biological importance of these valves of life. If the valves of a car, or your plumbing, get stuck, everything goes wrong. If a transistor sticks open, the computer stops. If a channels sticks open, the patient dies of hyperthermia (for real!).

The mechanism of opening and closing of channels is not known. Here we propose that an empty space - a bubble - is the gate that opens and closes channels. When the empty space fills with ions (and water), current flows and the channel conducts. Ions cannot cross the empty space and so a channel containing a bubble has a closed gate. It cannot conduct current.

Gaseous anesthetics - including xenon - are known to interfere with gating even though they do not bind to receptors and do not fit in the usual receptor paradigm of pharmacology. We propose that xenon acts by modifying and filling bubbles.

Mar 2008
12
Wed 12:30
(During APS March Meeting)
Mar 2008
14
Fri 12:30
Tom Mullin, University of Manchester
e-mail:
Host: Wendy Zhang ()
Organizer: Kostya
Pattern Switching in a Cellular Solid: Potential Applications in Phononic/Photonic Crystals
(Special MRSEC Seminar - 12:30 in CIS E123)

Periodic elastomeric cellular solids are subjected to uniaxial compression, and novel transformations of the patterned structures are found upon reaching a critical value of applied load. The results of a numerical investigation reveal that the pattern switch is triggered by a reversible elastic instability. Excellent quantitative agreement between numerical and experimental results is found and the transformations are found to be remarkably uniform across the samples. Moreover the phenomenon is found to be robust for a range of soft solids including rubber and jelly. Potential applications in phononic and photonic crystals will be discussed.

Mar 2008
18
Tue 12:30
Tom Mullin, University of Manchester
e-mail:
Host: Wendy Zhang ()
Organizer: Kostya
The Enigma of the Transition to Turbulence in a Pipe
(JFI Seminar - 4:00 in KPTC 206)

The puzzle of why fluid motion along a pipe is observed to become turbulent as the flow rate is increased remains the outstanding challenge of hydrodynamic stability theory, despite more than a century of research. The issue is both of deep scientific and engineering interest since most pipe flows are turbulent in practice even at modest flow rates. All theoretical work indicates that the flow is linearly stable i.e. infinitesimal disturbances decay as they propagate along the pipe and the flow will remain laminar. Finite amplitude perturbations are responsible for triggering turbulence and these become more important as the non-dimensionalized flow rate, the Reynolds number Re, increases. Our experimental work has shown that the threshold amplitude scales with Re and this gives new insights into origins of the turbulent motion through connections with recent theoretical and numerical results.

Apr 2008
9
Wed 12:30
Bob Ecke, Los Alamos National Laboratory
e-mail:
Host: Wendy Zhang () *
Granular Flow on a Rough Incline: From Avalanche Dynamics to Layer Evaporation

The flow of granular media on a rough surface has many realizations in nature, from rock slides and avalanches to dense ash flow during volcanic eruptions. I will describe laboratory experiments where precise measurements of such flows can be made with controllable parameters such as inclination angle, volume flow rate, and grain size, shape and composition. I will present a phase diagram of accessible states, from avalanches to uniform flowing states which can be unstable to the formation of lateral patterns, and finally a "liquid-gas" transition from a well defined layer to an "evaporated" low density state. Of particular interest are intermittent avalanches where the size and speed of spatially localized avalanches depend qualitatively and quantitatively on grain size and shape: smooth grains lead to stable shock-like solutions whereas rough grains lead to breaking, overturning fronts.

May 2008
21
Wed 12:30
Gregory Falkovich, Weizmann Institute of Science
e-mail:
Host: Leo Kadanoff ()
Organizer: Arnab
How Does Rain Start?

The brief history of rain theories, from primordial chaos to modern turbulence, will be presented. Recent experimental and theoretical results on fractal distribution of water droplets in clouds will be reviewed. Some unsolved problems of cloud physics will be described along with their relations to problems in field theory and condensed matter physics.

Jun 2008
18
Wed 12:30
Sascha Hilgenfeldt, University of Illinois at Urbana-Champaign
e-mail:
Host: Leo Kadanoff ()
Organizer: Robert
Mechanics of Morphogenesis: The Fly Eye

The complex, highly reproducible shapes of epithelial cells in the Drosophila eye are crucially dependent on the expression of adhesion molecules (cadherins). We show that not only the overall tissue organization, but the shape of each individual cell can be understood through quantitative modeling using minimization of an interfacial energy functional. The model contains only two free parameters, encoding for the adhesion strengths of E- and N-cadherin, and reproduces interfacial angles and lengths to within a few percent accuracy. Characteristic morphological changes in mutant ommatidia can be modeled within this approach, indicating an important role of changing levels of cadherin expression during morphogenesis.

Jun 2008
25
Wed 12:30
Etienne Reyssat, Harvard University
e-mail:
Host: Wendy Zhang ()
Organizer: Kostya
Opening Pine Cones

This talk will deal with the response of pine cones to humidity fluctuations. The scales of the cones are known to close on rainy days, they bend and open up when they dry. This mechanism enables the cones to release seeds and the trees to reproduce. We are interested in understanding the dynamics of these processes. The structure of the pine cone scale may be reproduced in very simple devices. I will show some potential applications of these cheap biomimetic systems.

Jun 2008
27
Fri 12:30
Mathilde Reyssat, Harvard University
e-mail:
Host: Wendy Zhang ()
Organizer: Kostya
Pearl Drops and Imbibition
(MRSEC Baglunch Seminar - 12:30 in CIS E123)

Hydrophobic surfaces can be made superhydrophobic by creating a texture on them. This effect, sometimes referred to as the "lotus effect", is due to air trapping in the structure, which provides a composite surface made of solid and air on which the deposited drop sits.

We will present recent experiments done on such superhydrophobic surfaces, made of forests of micro-pillars. We will see in particular what happens when water drops evaporate on such surfaces or when they impact them. We will also present experiments achieved on surfaces made of density gradient of micropillars, and will discuss the possibility of inducing spontaneous drop motions on such surfaces.

A last part of the talk will be devoted to imbibition phenomena. We will see that contrary to water drops, oil drops prefer to invade micro-textures or micro-channels with kinetics which depend on the local geometry.

Jun 2008
30
Mon 12:30
Frans Spaepen, Harvard University
e-mail:
Host: Tom Witten
Mechanical Properties of Metallic Glasses
(MRSEC Seminar - 12:30 in KPTC 206)

The basics of glass science (structure, formation, thermodynamic stability, relaxation and atomic transport) as they apply to metallic alloys are reviewed. The essential phenomenology of mechanical behavior is presented: stiffness, homogeneous deformation (creep), inhomogeneous deformation (shear bands), and fracture (ductile and brittle). All of these phenomena can be understood based on ordering and disordering processes on the atomic scale. Experiments on colloidal glasses allow a direct look at the atomic scale mechanisms.

Jul 2008
9
Wed 12:30
Dean Astumian, University of Maine
e-mail:
Host: Leo Kadanoff ()
Organizer: Robert
Extended Symmetry Relations for 2-D Brownian Sieves and Other Coupled Transport Processes

A Brownian sieve is a microstructured device that combines the effects of thermal noise, spatial asymmetry, and external forces to separate particles based on their transport properties. The separation characteristics of these systems can be modelled in terms of the motion of Brownian particles on a 2-D periodic potential. By treating the motion of an individual particle as a cyclical process in which the particle fluctuates away from, and then returns to the origin of any unit cell of the periodic potential we derive expressions for the averages and all moments for the number of periodic displacements in the horizontal and vertical directions in each excursion. The average displacements in the x- and y-direction obey symmetry relations for arbitrary values of the external forces, extended reciprocal relations through second order are shown to hold. Using the Onsager-Machlup thermodynamic action theory for the probabilities new symmetry relations for particle trajectories in the presence of magnetic fields. The magnetic effects are very small for colloidal particles in solution but may be significant in other contexts such as electron and spin transport on patterned superconductors.

Jul 2008
23
Wed 12:30
Itamar Procaccia, Weizmann Institute of Science
e-mail:
Host: Leo Kadanoff ()
Organizer: Arnab
How Mysterious Is the Mysterious Glass Transition?

I will briefly review the phenomenology of the glass transition, stressing those issues that are confused in the literature and confusing the interested community. I will present rigorous results regarding some popular models of the glass transition, showing that the common beliefs that glasses lose ergodicity and are "jammed" in some sense are not true. Having ergodicity resurrected, we apply statistical mechanics to shed some new light on the phenomena of interest.

Jul 2008
30
Wed 12:30
Robert Deegan, University of Michigan
e-mail:
Host: Leo Kadanoff ()
Organizer: Kostya
Fingers and Holes in Shear Thickening Fluids

The simplest models of matter posit a linear relationship between the stress and deformation, as for example in Hooke's law. However, many useful and important fluids (such as shampoos, industrial slurries, geophysical fluids, polymeric melts) exhibit a nonlinear response to stress. I will discuss the behavior of shear thickening fluids subjected to vertical vibrations in the context of pattern forming systems. I will show that a mixture of cornstarch/water or glass beads/water vibrated above a critical acceleration (approximately 10 g) is unstable to perturbations. At low accelerations a small indentation of the fluid surface will grow until it reaches the bottom of the container, forming a circular hole. At higher accelerations the rim of the hole becomes unstable and develops an upward growing tongue. At even higher accelerations, the entire layer writhes in a disordered manner. The mechanism for these instabilities is unknown. I will present experimental correlations between these instabilities and the fluid's rheological proprieties and attempts to model this phenomenon.

Aug 2008
6
Wed 12:30
Maximino Aldana Gonzalez, Universidad Nacional Autonoma de Mexico
e-mail:
Host: Leo Kadanoff ()
Organizer: Arnab
Critical Dynamics in Genetic Networks: Examples from Four Kingdoms

The coordinated expression of the different genes in an organism is essential to sustain functionality under the random external perturbations to which the organism might be subjected. To cope with such external variability, the global dynamics of the genetic network must possess two central properties. (a) It must be robust enough as to guarantee stability under a broad range of external conditions, and (b) it must be flexible enough to recognize and integrate specific external signals that may help the organism to change and adapt to different environments. This compromise between robustness and adaptability has been observed in dynamical systems operating at the brink of a phase transition between order and chaos. Such systems are termed critical. Thus, criticality, a precise, measurable, and well characterized property of dynamical systems, makes it possible for robustness and adaptability to coexist in living organisms. In this talk I investigate the dynamical properties of the gene transcription networks reported for S. cerevisiae, E. coli, and B. subtilis, as well as the network of segment polarity genes of D. melanogaster, and the network of flower development of A. thaliana. By analyzing hundreds of microarray experiments to infer the nature of the regulatory interactions among genes, and implementing these data into the Boolean models of the genetic networks, I will show that, to the best of the current experimental data available, the five networks under study indeed operate close to criticality. The generality of this result suggests that criticality at the genetic level might constitute a fundamental evolutionary mechanism that generates the great diversity of dynamically robust living forms that we observe around us.

Aug 2008
13
Wed 12:30
Norman Lebovitz, University of Chicago
e-mail:
Host: Leo Kadanoff ()
Organizer: Arnab
Subcritical Instability in Shear Flows: the Shape of the Basin Boundary

The boundary of the basin of attraction of the stable 'laminar' point is investigated for several of the dynamical systems modeling subcritical instability. In the cases thus far considered, this boundary contains a linearly unstable structure (equilibrium point or periodic orbit). The stable manifold of this unstable structure coincides at least locally with the basin boundary. The unstable structure plays a decisive role in mediating the transition in that transition orbits cluster tightly around its (one-dimensional) unstable manifold, illustrating a scenario proposed by Waleffe. The picture that emerges augments the bypass scenario for transition and reconciles it with Waleffe's scenario.

We consider a model proposed by Waleffe (W97) for which an unstable equilibrium point U lies on the boundary. We find numerically that all orbits staring near U decay toward the origin, whereas 'half' of them should remain permanently bounded away from the origin. We offer an interpretation of this tendency toward decay based on the structure of the basin boundary.

Aug 2008
20
Wed 12:30
OPEN
Aug 2008
27
Wed 12:30
OPEN
Sep 2008
3
Wed 12:30
Osman Basaran, Purdue University
e-mail:
Host: Wendy Zhang ()
Organizer: Robert
Electrohydrodynamic Tip-streaming and Emission of Charged Drops from Liquid Cones
New Location: GCIS EB041

When subjected to strong electric fields, raindrops in thunderclouds, pendant drops in electrospray mass spectrometry, and planar films form conical tips and emit thin jets from their tips. Theoretical analysis of the temporal development of such electrohydrodynamic (EHD) tip-streaming or cone-jetting phenomena has heretofore been elusive given the large disparity in length scales between the macroscopic drops/films and the microscopic jets. Here, simulation and experiment are used to investigate EHD tip-streaming from a liquid film of finite conductivity. In the simulations, the full Taylor-Melcher leaky-dielectric model, which accounts for charge relaxation, is solved to probe the mechanisms of "Taylor" cone formation, jet emission, and breakup of the jet into small drops. Simulations show that tip-streaming does not occur if the liquid is perfectly conducting or perfectly insulating. A scaling law for sizes of micro-(nano-)scale drops produced from the breakup of the thin jets is also developed. The reported advances have implications to a variety of new application areas ranging from microfluidics to printing of flexible electronic circuits.

Sep 2008
10
Wed 12:30
Konstantin Turitsyn, University of Chicago
e-mail:
Vesicle Dynamics in External Flows

Dynamics of vesicles in external flows has been a subject of great experimental and theoretical attention recently. A vesicle can exhibit a variety of different dynamical behaviors when placed in an external flow. At least three qualitative different motions have been observed in recent experiments: tumbling, tank-treading, trembling. I will review these experiments and will present a theoretical analysis of this effect, resulting in a phase-diagram which predicts the type of the vesicle motion. For planar external flows, the character of the vesicle dynamics is determined by two dimensionless parameters, which are formed out of viscosities of inner and outer fluids, external velocity gradient matrix and vesicle excess area. Transitions between different types of motions are analyzed separately. The tank-treading to tumbling transition is described by a saddle-node bifurcation whereas the tank-treading to trembling transition occurs via a Hopf bifurcation. In the vicinity of the transition lines the vesicle experiences critical slowing down, which can be described universal scaling exponents. In the end of the talk I will also discuss the effect of vesicle wrinkling in extensional flows.

Sep 2008
17
Wed 12:30
Michael Marder, University of Texas
e-mail:
Host: Leo Kadanoff ()
Organizer: Arnab
Student Flows in Texas

Texas, like all other states, has been gathering test data on public school students for many years. What can one do with test records from 4 million students? I have been visualizing math test scores using ideas loosely borrowed from statistical mechanics and fluid mechanics. The visual representations give a more complete picture than is obtained by focusing on single numbers. They make it possible to address questions about the relative importance of income levels, race, and other factors in the Texas public K-12 educational system, and about whether testing pressure is improving educational performance. I will also comment on local, state, and national efforts in which I have been involved to better educate science and mathematics teachers.

Sep 2008
24
Wed 12:30
Lee Smolin, Perimeter Institute for Theoretical Physics
e-mail:
Host: Leo Kadanoff ()
Organizer: Kostya
Quantum Gravity as a Problem in Critical Phenomena

Several current approaches to quantum gravity construct or derive models of quantum spacetime as discrete quantum systems on dynamical lattices. The key problem to be resolved in these models is whether and how classical spacetime arises from a discrete quantum system. This problem of the emergence of spacetime in the low energy limit is thus a problem in critical phenomena. I will introduce some of the models of quantum spacetime of current interest and illustrate the progress being made using them towards the problem of the emergence of classical spacetime. I will emphasize an important question, which is currently the subject of experimental probes, which is the symmetry of the ground state: is it Poincare, broken Poincare or quantum deformed Poincare?

Sep 2008
29
Mon 12:30
Itai Cohen, Cornell University
e-mail:
Host: Leo Kadanoff ()
Flight of the Fruit Fly
(Joint seminar with MRSEC: 12:30 in KPTC 206)

There comes a time in each of our lives where we grab a thick section of the morning paper, roll it up and set off to do battle with one of nature's most accomplished aviators - the fly. If however, instead of swatting we could magnify our view and experience the world in slow motion we would be privy to a world-class ballet full of graceful figure-eight wing strokes, effortless pirouettes, and astonishing acrobatics. After watching such a magnificent display, who among us could destroy this virtuoso? How do flies produce acrobatic maneuvers with such precision? Are they flying in the most efficient way possible? What control mechanisms do they need to maneuver? More abstractly, what problem are they solving as they fly? Despite pioneering studies of flight control in tethered insects, robotic wing experiments, and fluid dynamics simulations that have revealed basic mechanisms for unsteady force generation during steady flight, the answers to these questions remain elusive. In this talk I will discuss our strategy for investigating these unanswered questions. I will begin by describing our automated apparatus for recording the free flight of fruit flies and a new technique called Hull Reconstruction Motion Tracking (HRMT) for backing out the wing and body kinematics. I will then show that these techniques can reveal the underlying mechanisms for dodge and strafe flight maneuvers that require lateral force generation. Finally I will describe a new approach for exploring the flight stability and control system of these insects.

Oct 2008
1
Wed 12:30
Doug Smith, University of California, San Diego
e-mail:
Host: Leo Kadanoff ()
Organizer: Robert
Physics of Single DNA Molecules, Proteins, Viruses, and Knots

We use optical tweezers to manipulate single DNA molecules, enabling a wide array of different studies in polymer physics and molecular biology. Here we review several recent projects. In one application, we directly measure the forces confining a single entangled DNA molecule. We directly confirm and quantify for the first time the precise nature of the "tube" constraint postulated in the reptation model of P.G. de Gennes. In another application, relevant to biochemical regulation, we study protein-mediated DNA looping and show that loop size and unbinding force distributions are highly variable and do not depend solely on the mechanical properties of DNA. In another application, we study the packaging of DNA into viruses. We show that this process is driven by a very strong ATP-powered molecular motor that must exert large forces to overcome large forces that resist the dense DNA confinement inside viruses. We show that electrostatic repulsion and ionic screening are major factors governing the resistance forces. We are now investigating the mechanism of three different viral DNA packaging motors using biophysical, biochemical, and genetic methods. Finally, we recently became interested in studying why and how long strings tend to become knotted (DNA molecules, iPod headphone cables, umbilical cords, etc.). We have made some progress towards answering this question by applying concepts from mathematical knot theory.

Oct 2008
8
Wed 12:30
Leo Kadanoff, University of Chicago
e-mail:
Calculating Eigenvalues and Eigenvectors of Large Matrices

Matrices are used to describe the modes of oscillation of physical objects. Generally, N by N matrices describe objects with N modes. Often, when the objects are composed of pieces arrayed in a line, the matrix elements depend only upon the relative position along the line. They are then called Toeplitz matrices. We calculate the eigenvectors of large matrices of this kind by making use of calculations for infinite matrices. Propagation of information over the whole range of spatial indices in these eigenvectors is demonstrated by power law and logarithmic N-dependence of the eigenvalues and eigenvectors. The dependences can be interpreted in terms of the transfer of information along the line of objects described by the matrix.

Hui Dai, Zachary Geary, and Leo Kadanoff

Oct 2008
15
Wed 12:30
Dmitri Talapin, University of Chicago
e-mail:
Self-assembled Multicompenent Nanoparticle Superlattices: Why Do They Form and What Can We Use Them For?

Self-assembly of chemically-synthesized colloidal nanocrystals can yield complex long-range ordered structures. Nanocrystals of different size and functionality (noble metals, semiconductors, oxides, magnetic alloys) can be induced to self-assemble into ordered superlattices. We have built a variety of binary superlattices from monodisperse nanocrystals, mixing and matching these nanoscale building blocks to yield multicomponent assemblies. We have identified superlattices with cubic, hexagonal, tetragonal, and orthorhombic symmetries, isostructural with NaCl, CuAu, AlB2, MgZn2, MgNi2, Cu3Au, Fe4C, CaCu5, CaB6 and NaZn13 compounds emphasizing the parallels between nanoparticle assembly and atomic scale crystal growth. We even demonstrated the formation of nanoparticle superlattices with dodecahedral quasicrystalline ordering.

What brings spherical nanoparticles together and packs them into these sophisticated low-symmetry superlattices? Observed structural diversity has shown that we have very limited understanding of the processes and interactions that govern self-assembly of nanoscale objects, formation of complex structures and their thermodynamic stability. I will discuss the delicate balance of competing inter-nanoparticle interactions that can be responsible for formation of binary nanoparticle superlattices.

I will show that ordered nanocrystal assemblies can be used as model systems for studying transport phenomena in low-dimensional materials. The exchange coupling energy in the nanocrystal assemblies can be tuned by tailoring interparticle spacing; the conductivity of nanocrystal solids can be switched between n- and p-type transports by surface transfer doping. Doping of PbSe and PbTe nanocrystal solids can also occur through the exchange coupling with other semiconductor (Ag2Te) or metal (Au) nanocrystals in binary nanocrystal assemblies.

Oct 2008
22
Wed 12:30
Berni Alder, Lawrence Livermore National Laboratory
e-mail:
Host: Leo Kadanoff ()
Organizer: Arnab
Limitations of the Navier-Stokes Equations

Molecular Dynamics and stochastic collision dynamics (DSMC) particle methods allow testing of the approximations in the Navier-Stokes approach to hydrodynamic flows. The neglect of correlations leads to divergence of transport coefficients in 2 dimensions and the Burnett coefficients in 3 dimensions. From shock simulations, the neglect of nonlinear effects seem relatively small. The use of boundary conditions with amplitude variations, instead of stick boundary conditions, removes the dilemma of no linear instability in pipe flow at any Reynolds number, as well as possibly explaining the drag reduction problem when a small amount of polymer is introduced in the fluid. The neglect of fluctuations in the Rayleigh-Taylor instability leads to an incorrect long time behavior, however, by adding fluctuations to the continuum equations, the correct behavior should be recovered.

The Rayleigh-Taylor instability was simulated in a comparable amount of computer time as the Navier-Stokes calculation for a comparable period of the mixing process, using about 1 billion particles,so as to avoid boundary effects. The short time behavior is shown to be quantitatively given by linear stability analyses, starting from a flat interface, roughened only by natural fluctuations. The merging of the mushrooms leads to a quadratic time dependence for the advance of the mixing front, with a coefficient in agreement with experiment. Subsequently, the front slows to a linear time dependence as drops break off from the stems of the mushrooms, and Stokes law applies. Magnetic levitation experiments confirm these results.

Oct 2008
29
Wed 12:30
Petia Vlahovska, Dartmouth College
e-mail:
Host: Wendy Zhang () *
Organizer: Kostya *
Electrohydrodynamic Deformation of Lipid Bilayer Membranes

I will present an analytical theory that explains the experimentally-observed shapes of vesicles in AC electric fields [1]. The model treats the inner and suspending media as lossy dielectrics, and the membrane as an ion-impermeable flexible incompressible-fluid sheet. The vesicle shape is obtained by balancing electric, hydrodynamic, and bending stresses exerted on the membrane.

The theory predicts that stationary vesicle deformation depends on field frequency and conductivity conditions. If the inner fluid is more conducting than the suspending medium, the vesicle always adopts a prolate shape. In the opposite case, the vesicle undergoes a transition from a prolate to an oblate ellipsoid at a critical frequency, which the theory identifies with the inverse membrane charging time. At frequencies higher than the inverse Maxwell-Wagner polarization time, the electrohydrodynamic stresses become too small to alter the vesicle's quasi-spherical rest shape. The analysis shows that the evolution towards the stationary vesicle shapes strongly depends on membrane properties such as viscosity. The model can be used to rationalize the transient and steady deformation of biological cells in electric fields.

[1] Aranda et al. Biophys. J. 95 L19-21 (2008)

Nov 2008
5
Wed 12:30
Benoit Roman, Ecole Superieure de Physique et de Chimie Industrielles
e-mail:
Host: Tom Witten *
Organizer: Eric *
Elasticity and capillarity : from wet hairs to origami

Capillary forces are responsible for a large range of everyday observations: the shape of rain droplets or the imbibition of a sponge. Although they are weak at macroscopic scale, surface capillary forces may overcome volume forces at small scales and deform compliant micro-structures. Capillary-induced sticking can indeed prevent the actuation of mobile elements in micro-electro-mechanical systems (MEMS), or even cause their collapse. I will present a few experimental situations where capillary forces are able to deform two types of elastic objects: rods, and thin sheets. How many hairs are present in a bundle of wet fur? Can a thin sheet spontaneously wrap around droplet? I will try to describe how these different experiments are connected to the same length scale.

Nov 2008
12
Wed 12:30
Pedro Reis, Massachusetts Institute of Technology
e-mail:
Host: Ka Yee Lee *
Organizer: Arnab *
Thin Sheets Adhered to Solic Interfaces: Localized Folding and Blistering

The study of the elasticity of thin objects (sheets or rods) is a rapidly burgeoning field that is bringing together seemingly separate communities ranging from non-linear and statistical physics through to differential geometry and nanotechnology. Moreover, coupling the elasticity of thin objects with other phenomena - such as fracture, surface tension, and adhesion at a solid or liquid interface - represents a new fundamental challenge.

In this talk I shall explore, mostly through experiments, two problems that involve the elasticity of thin sheets adhered to solid interfaces: 1) Localization through surface folding in solid foams under compression and 2) Blistering of a thin sheet adhered to a soft elastic substrate.

Nov 2008
19
Wed 12:30
Lei Xu, Harvard University
e-mail:
Host: Wendy Zhang ()
Organizer: Eric
Watching the Paint Dry: Dynamics of Drying in Porous Media

What is the dynamics of drying in porous media? It has been difficult to visualize due to the non-transparency of the media. We study this phenomenon in an optical index matched system with confocal microscopy. We observe abrupt air invasions which result from the strong flow from menisci in large pores to menisci in small pores. The size and structure of the air invasions are in accord with 3D invasion percolation. By varying the particle size and contact angle we unambiguously demonstrate that capillary pressure dominates the drying process.

Nov 2008
21
Fri 12:30
Detlef Lohse, University of Twente
e-mail:
Host: Leo Kadanoff ()
Organizer: Eric
Micro- and nanoscale surface bubbles
(Special Seminar: 12:30 in KPTC 206)

Bubble nucleation at surfaces is a poorly understood phenomenon. We did visualization experiments at hydrophobic surfaces structured at the microscale and compared the results with both boundary integral simulations and Rayleigh-Plesset type model calculations, in particular focusing on bubble-bubble interactions. It is demonstrated that in the many bubble case the bubble collapse is delayed due to shielding effects. We succeed in making cavitation totally reproducible in space and time. When reducing the surface structure by a factor of 10 to about 100nm, one reaches the scale of the so-called surface nanobubbles. These are structure seen in atomic force (AFM) microscopy images. We will give evidence that these structure are indeed bubbles and will analyse the conditions under which they form. However, we find them to be stable against massive pressure 'reduction': Surprisingly, their appearance is uncorrelated with bubble nucleation events on the surface.

Surface nanobubbles do not act as bubble nuclei, Bram Borkent, Stephan Dammer, Holger Schoenherr, Julius Vancso, and Detlef Lohse, Phys. Rev. Lett. 98, 204502 (2007).

Controlled multi-bubble surface cavitation, Nicolas Bremond, Manish Arora, Claus-Dieter Ohl, and Detlef Lohse, Phys. Rev. Lett. 96, 224501 (2006).

Dec 2008
3
Wed 12:30
Jaci Conrad, University of Illinois at Urbana
e-mail:
Host: Margaret Gardel
Organizer: Kostya
Structure and flow behavior of colloidal gels during microchannel flow

Colloidal suspensions are excelent model systems for a variety of complex fluids, and moreover are ubiquitous in industrial and technological applications. In particular, the flow properties of attractive colloidal suspensions determine their utility as inks, paints, coatings, and personal care products. We investigate the flow properties of colloidal gels in microchannels and constrictions using confocal microscopy and finite-element modeling. Under shear flow, the suspension contains dense clusters that yield at intercluster boundaries, resulting in network breakup at high shear rates. These structural changes coincide with a transition from pluglike flow at low pressures to fluidlike flow at high pressures.

Dec 2008
15
Mon 12:30
Nicholas Guttenberg, University of Illinois at Urbana
e-mail:
Host: Wendy Zhang ()
Scaling laws and turbulence in a two-dimensional rough pipe
(Special Date)

The foremost observable property of turbulent flows is their spatial and temporal unsteady structure - a scale-free pattern of motions originating from the conservation of momentum and the degree of compressibility of the fluid. However, previous attempts at explaining certain macroscopic properties of these flows ignore their rich structure in favor of treating only the average behavior. I will talk about how the friction drag in a rough pipe and the wall velocity profile depend on the spectrum of turbulence. The roughness and finite Reynolds number act as thermodynamic variables on the approach to a dynamical critical point, as evidenced by an observed data collapse. I test this proposition with direct numerical simulations of 2D turbulence, in which (unlike in 3D flows) the spectrum of fully developed turbulence depends on how it was initiated. I will also present the numerical method used for the simulation, which uses conformal mapping to capture the geometry of the rough pipe walls.