Computations in Science Seminars

Upcoming seminars

January 7, 2008 (12:30 in KPTC 206)
Nigel Goldenfeld, University of Illinois at Urbana-Champaign
e-mail: email address, Faculty contact: Leo Kadanoff, email address
Biocomplexity in Action: Pattern Formation and Microbial Ecology at Yellowstone's Hot Springs
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.
January 8, 2008 (JFI Colloquium - 4:00 in CIS W301)
Nigel Goldenfeld, University of Illinois at Urbana-Champaign
e-mail: email address, Faculty contact: Leo Kadanoff, email address
Patterns, Universality and Computational Algorithms
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.
January 9, 2008
Nigel Goldenfeld, University of Illinois at Urbana-Champaign
e-mail: email address, Faculty contact: Leo Kadanoff, email address
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.
January 16, 2008
Hassan Nagib, Illinois Institute of Technology
e-mail: email address, Faculty contact: Wendy Zhang, email address
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.
January 23, 2008
Andrea Liu, University of Pennsylvania
e-mail: email address, Faculty contact: Wendy Zhang, email address
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.
January 30, 2008
Ursula Perez-Salas, Argonne National Laboratory
e-mail: email address, Faculty contact: Wendy Zhang, email address
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.
February 4, 2008 (Special MRSEC Seminar - 12:30 in KPTC 206)
Uri Alon, Weizmann Institute of Science
e-mail: email address, Faculty contact: Leo Kadanoff, email address
Evolution, Optimality and Biological Design
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.
February 5, 2008 (JFI Colloquium - 4:00 in CIS W301)
Uri Alon, Weizmann Institute of Science
e-mail: email address, Faculty contact: Leo Kadanoff, email address
Design Principles of Biological Circuits
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.
February 6, 2008
Uri Alon, Weizmann Institute of Science
e-mail: email address, Faculty contact: Leo Kadanoff, email address
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.
February 13, 2008
Steve Kron, University of Chicago
e-mail: email address, Faculty contact: Leo Kadanoff, email address
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.
February 20, 2008
Maximino Aldana, Universidad Nacional Autonoma de Mexico
e-mail: email address, Faculty contact: Leo Kadanoff, email address
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.
February 27, 2008 (^)
Laura Schmidt, University of Chicago
e-mail: email address
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.
March 5, 2008
Bob Eisenberg, Rush Medical College
e-mail: email address, Faculty contact: Leo Kadanoff, email address
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.
March 14, 2008 (Special MRSEC Seminar - 12:30 in CIS E123)
Tom Mullin, University of Manchester
e-mail: email address, Faculty contact: Wendy Zhang, email address
Pattern Switching in a Cellular Solid: Potential Applications in Phononic/Photonic Crystals
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.
March 18, 2008 (JFI Seminar - 4:00 in KPTC 206)
Tom Mullin, University of Manchester
e-mail: email address, Faculty contact: Wendy Zhang, email address
The Enigma of the Transition to Turbulence in a Pipe
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.
April 9, 2008 (^)
Bob Ecke, Los Alamos National Laboratory
e-mail: email address, Faculty contact: Wendy Zhang, email address
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 21, 2008
Gregory Falkovich, Weizmann Institute of Science
e-mail: email address, Faculty contact: Leo Kadanoff, email address
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.
June 18, 2008
Sascha Hilgenfeldt, University of Illinois at Urbana-Champaign
e-mail: email address, Faculty contact: Leo Kadanoff, email address
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.
June 25, 2008
Etienne Reyssat, Harvard University
e-mail: email address, Faculty contact: Wendy Zhang, email address
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.
June 27, 2008 (MRSEC Baglunch Seminar - 12:30 in CIS E123)
Mathilde Reyssat, Harvard University
e-mail: email address, Faculty contact: Wendy Zhang, email address
Pearl Drops and Imbibition
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.
June 30, 2008 (MRSEC Seminar - 12:30 in KPTC 206)
Frans Spaepen, Harvard University
e-mail: email address, Faculty contact: Tom Witten, email address
Mechanical Properties of Metallic Glasses
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.
July 9, 2008
Dean Astumian, University of Maine
e-mail: email address, Faculty contact: Leo Kadanoff, email address
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.
July 23, 2008 (&)
Itamar Procaccia, Weizmann Institute of Science
e-mail: email address, Faculty contact: Leo Kadanoff, email address
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.

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

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

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