Computations in Science Seminars
Previous Talks: 2005
January 12, 2005
Vakhtang Putkaradze, Dept. of Mathematics and Statistics, University of New Mexico
Faculty contact:Wendy Zhang, 
Mathematical models of self-aggregation of particles at nano-scales
We derive a non-local evolution equation for self-assembly of particles at the nano-scale. The physical assumptions underpinning the problem are the presence of interaction potential between the particles and the dependence of mobility on averaged local density. We show that for almost any choice of sufficiently smooth potential and averaging functions the evolution is reduced to a finite-dimensional system of ODEs describing the dynamics of particle clumps, and the order of that system is generally very low. We also discuss how our equation can be reduced in some (singular) limits to several well-known models of different physical phenomena, including chemotaxis models, Cahn-Hilliard equation and some crystal growth phenomena.
January 19, 2005
Rho Shin Myong
, Gyeongsang National University
Faculty contact: Timur Linde
Modeling Micro Flows: Surface Chemistry, Boltzmann Equation, and Irreversible Thermodynamics
The interfacial interaction between the gas (or liquid) molecules and the material surface plays a dominant role in the nonlinear transport phenomena associated with micro- and nano-devices. A slip model by Maxwell based on the concept of accommodation coefficient is usually employed to describe this effect. In this talk, an alternative model based on Langmuir°Øs theory of adsorption of gases on solids is presented. It turned out that the new model is capable of providing a physical meaning to the accommodation coefficient in the Maxwell model. In addition, a computational model for micro and rarefied gas flows beyond the Navier-Stokes-Fourier equations is presented. It is derived from the Boltzmann equation by employing the Eu's modified moment method in which a formal mathematical structure of the non-equilibrium entropy compatible with the 2nd law of thermodynamics is developed. Finally, various benchmark problems--internal flows in micro-channels and concentric rotating micro-cylinders, external flow over a micro-sphere, heat transfer in forced laminar flow through a circular micro-tube, and shock-dominated hypersonic flow around a blunt body--will be considered in order to validate the prediction of the new models.
February 2, 2005
Jointly sponsored by the Institute for Biophysical Dynamics
Amit Meller, Harvard University
Faculty contact: Tom Witten
Translocation and unzipping kinetics of DNA molecules using a nanopore
The discovery that a voltage
gradient can be used to drive single-stranded DNA or RNA molecules through the
~1.5 nm a-Hemolysin nanopore, has
opened up the possibility of detecting and characterizing unlabelled individual
polynucleotide molecules. By measuring the ion current flowing through the pore
when the biopolymer is threaded, we detect the passage time of each DNA
molecule. We found that the translocation dynamics is dominated by the DNA-pore
interactions that depend strongly on the DNA sequence as well as on its
direction of entry inside the pore.
Recently we have developed a
method to dynamically set the voltage that drives the polynucleotides. This
method makes it possible to study the unzipping kinetics of individual DNA
molecules under fixed or time-varying forces. In particular, we have
characterized the unzipping kinetics of DNA hairpin molecules under fixed
voltage amplitudes (V) or steady voltage ramps (dV/dt). At high
voltages (V>30mV) or at high voltage ramps
(dV/dt>5 V/s) the unzipping process can be described by a single step kinetics model
width negligible re-zipping probability. But at the low voltage (or voltage
ramp) regime re-zipping probability must be included to account for our data. A
model that includes re-zipping is introduced and is used to fit our data at low
and at high voltages. From the fits we estimate the effective DNA charge inside
the nanopore and the unzipping rate of the hairpins at the limit of zero force.
February 9, 2005
Douglas MacAyeal, University of Chicago
Faculty contact: Leo kadanoff, 
Ice-shelf explosions, iceberg calving and other oddities of the glaciological world
Over the last 4 years, I have been observing the processes by which
large parts of the Antarctic ice sheet have disintegrated (e.g., since
Y2K, a surface area of glacial ice equivalent to all the main New England states has broken into small bits and drifted off to oblivion in the warm waters of the Southern Ocean). Current study involves little computation, so expect a descriptive travelogue-style presentation of the main ideas at play in glaciodyanmics of ice-sheet breakup.
TUESDAY, February 15, 2005: 12 p.m.,
Crerar Library, Lower Level Conference Room
Jointly sponsored by the Institute for Biophysical Dynamics
Mark Goulian, Department of Physics, University of Pennsylvania
Faculty contact: Aaron Dinner, 
Perturbing, imaging, and modeling two-component signaling in bacteria
February 16, 2005
Mary Silber, Northwestern University
Faculty contact: Wendy Zhang,
Controlling Pattern Formation with Multi-Frequency Parametric Forcing
I will describe our work on manipulating the weakly nonlinear interactions
of parametrically-excited standing waves on the surface of a fluid layer.
Our mathematical analysis is motivated by recent experiments on standing
wave patterns, first reported by Michael Faraday in 1831. The surface
waves are generated by subjecting the fluid container to a periodic
vibration in the vertical. It has been demonstrated in the lab that one
can switch between different, exotic nonlinear wave patterns by adjusting
the frequency content of the forcing function. We have focused on
three-wave interactions, as building blocks of more complicated nonlinear
wave interactions. In the weak forcing limit, we use methods of
equivariant bifurcation theory to determine which additional frequency
components to add to a sinusoidal forcing function in order to enhance or
suppress particular resonant triad interaction. We have used our results
to interpret experimental findings, suggest new experiments, and to
explain the results of our companion analysis on impulsively-forced
Faraday waves. In the latter problem, we consider surface waves excited by
a periodic sequence of delta-function impulses, which is an idealization
of smooth periodic forcing that proves analytically tractable in the
linear and weakly nonlinear regimes.
February 23, 2005
Sung Joon Moon, Princeton University
Faculty contact: Wendy Zhang,
Modeling grains and powders: Multiscale methods for multiphase flow problems
Discrete particles are pervasive in nature and industry,
but many industrial processes are far from cost-effectiveness
because of a lack of understanding of particle flow behavior.
Numerical methods for particulate flows have significant
potential for uncovering the underlying physics, cost
savings, and productivity enhancements.
In this talk, two examples that have been investigated with
experiments or that have significant practical importance
will be considered: vertically vibrated shallow granular
layers and vibrated gas fluidized beds of cohesive fine powders.
Oscillating shallow granular layers, where the interparticle
interaction can be modeled as an instantaneous binary, frictional
dissipative collision, exhibit various phenomena including
the spatial pattern formation and the so called "horizontal
Brazil-nut effect".
They will be discussed, together with the issues in modeling.
The second problem examined is the gas fluidized bed of fine
particles, often referred to as the powders, where the
interstitial gas effects and interparticle forces such as
cohesion play an important role.
A particle dynamics-based hybrid model is used to study this
system, and a multiscale computational method is used to
facilitate the efficient computation.
It will be shown how the vibration enables fluidizing highly
cohesive powders, which are unable to get fluidized otherwise.
March 2, 2005
Mohammad Islam, Physics Department, University of Pennsylvania
email:
,
Faculty contact: Sidney Nagel, 
Single-Wall Carbon Nanotube Dispersions: Gels, Liquid Crystalline Phases, Optical and Magnetic Anisotropies
I will describe our explorations of carbon nanotube science and
technology from a soft materials perspective. We first created stable
dispersions of purified single-wall carbon nanotubes (SWNTs) using an
anionic surfactant, sodium dodecyl benzene sulfonate (NaDDBS), and then
studied their structure and rheology in suspension, demonstrating
interconnected networks of stiff filaments. Our attempts to induce
nematic liquid crystalline alignment of SWNTs in suspension did not
succeed, but eventually led us to create a new class of nanocomposite:
nematic nanotube gels. These gels exhibit rich physical properties due
to a coupling between the nematic alignment and the polymer network
elasticity. Finally, these gels and dispersions have been enabling
technologies for fundamental measurements of single tube optical and
magnetic anisotropy.
March 9, 2005
Norbert Schorghofer, Institute for Astronomy, University of Hawaii
e-mail:
,
Faculty contact: Wendy Zhang,
The Stability of Ice on Mars
An extensive reservoir of ground ice has been discovered on Mars
using neutron and gamma spectroscopy from orbit. Atmospheric
water vapor diffuses into the ground and deposits frost and, vice
versa, ground ice sublimes and diffuses upward, while exposed to
temperature cycles and adsorption. The ground ice should rapidly
evolve toward vapor equilibrium, but it is unknown if this
equilibrium solution depends on history. Vapor diffusion on a
small scale determines the distribution of ground ice on a
planetary scale. The theory is used to predict the occurrence of
ice elsewhere on the planet and to explain how the oldest ice on
Earth can survive 20 cm beneath the surface.
March 30, 2005
Snezhana Abarzhi, Center for Turbulence Research, Stanford University
e-mail:
,
Faculty contact: Leo Kadanoff,
Turbulent mixing and beyond
Whenever fluids of different densities are accelerated against the density
gradient we observe the development of the Rayleigh-Taylor instability
(RTI), which causes extensive interfacial mixing of the fluids. The
turbulent mixing plays a key role in preventing the formation of "hot
spot" in inertial confinement fusion, providing proper conditions for the
synthesis of heavy mass elements in thermonuclear flashes on the surface
of compact star, in core-collapse supernovae, and many other applications.
The properties of the Rayleigh-Taylor turbulent mixing flow differs
significantly from those of the classical Kolmogorov turbulence. We study
theoretically the dynamics of the large-scale coherent structures in RTI,
identify the invariants of the flow and show that the instability
evolution has a non-local and multi-scale character. A phenomenological
model is suggested to describe the turbulent mixing of immiscible,
miscible and stratified fluids, and to account for the stochastic
properties of the process. We discuss the applications of the results
obtained in stellar non-Boussinesq convection, supernovae, and reactive
flows.
April 6, 2005
Matthew Hastings, Los Alamos National Laboratory
e-mail:
,
Faculty contact: Wendy Zhang,
Lieb-Schultz-Mattis in Higher Dimensions
In 1961, Lieb, Schultz, and Mattis showed the absence
of a gap in a class of one-dimensional spin chains:
chains with half-integer spin per unit cell and SU(2)-
invariant short-range interactions. This basic result
has guided research on spins chains ever since. For
example, the discovery of the Haldane gap in chains
with integer spin was surprising as it indicated a
fundamental difference between integer and half-
integer spins.
Since then, there has been much work searching for
higher dimensional extensions of this result, in
particular due to possible connections to high-
temperature superconductivity. The clearest
statement of the basic physical reasons to expect
such an extension are due to Misguich et. al, who
argued that any such system would either have long-
range spin order, and hence have gapless spin wave
excitations, or else would have a class of
topological excitations with vanishing gap. Thus,
showing this result in higher dimensions would
connect directly to recent ideas on topological
order in quantum systems. I will sketch my recent
proof of this result, emphasizing connections to
these basic physical ideas. In the process, I will
derive various results about locality of correlation
functions in these systems.
April 13, 2005
Jointly sponsored by the Institute for Biophysical Dynamics
Alexander Van Oudenaarden, MIT
e-mail:
,
Faculty contact: Philippe Cluzel 
Information storage and propagation in genetic networks
The ability of a living cell to grow and divide, and to sense and respond to its environment is determined by a complex web of intracellular, and sometimes intercellular, protein and gene networks. During the last decade new technologies such as high-throughput genome sequencing and gene arrays have enabled a large-scale identification of these interaction networks. Although many of these networks have already been mapped, surprisingly little is known about the function of specific network architectures. Rather than taking a genome-wide approach, our lab focuses on the smaller, recurring network motifs buried in the larger networks. These motifs are built from a handful of genes and proteins and display a network structure that appears over and over again in different networks and different organisms. The underlying idea is that these motifs define autonomous functional modules that are the building blocks for the entire cellular network. In this talk I will focus on two elementary motifs: positive feedback loops that can be used to store information and generate steep switches; and feed-forward loops that are used to propagate signals and the concomitant noise through the network. I will present both theoretical models and experiments on natural and synthetic genetic networks in the bacterium Escherichia coli and the budding yeast Saccharomyces cerevisiae.
April 20, 2005
Pavel M. Lushnikov, University of Notre Dame and Landau
Institute
email:
,
Faculty contact: Paul Wiegmann, 
Singularity formation in hydrodynamics, nonlinear optics and plasma
Many nonlinear systems have a striking phenomenon, an explosive
instability, which occurs if the system is linearly unstable and
nonlinearity does not saturate an exponential growth of small
perturbations, but, on the contrary, results in singularity
formation in a finite time. Near singularity point there is
usually a qualitative change in underlying physical phenomena,
reduced models loose their applicability and other physical
mechanisms become important such as inelastic collisions in the
Bose-Einstein condensate; optical breakdown and dissipation in
nonlinear optical media and plasma, wave breaking in
hydrodynamics. Special focus will be on two examples of explosive
instability. First is the spontaneous breaking of rotational
symmetry and formation of coherent hexagonal pattern in
photorefractive crystals. Second is the wave breaking and foam
formation on crest of sea waves.
TUESDAY, April 26, 2005: 12 p.m.,
Crerar Library, Lower Level Conference Room
Jointly sponsored by the Institute for Biophysical Dynamics
William Gelbart, Department of Chemistry, University of California, Los Angeles
e-mail:
,
Faculty contact: Aaron Dinner,
Physical aspects of viral infection
The sole job of a virus is to get its genome into a host cell. It is
then replicated a large number of times and each new copy in turn infects
neighboring cells. In this talk I outline the essentials of viral life
cycles for the cases of infection by viruses of bacteria, plants, and
animals, highlighting the basic differences between the modes of entry in
these three general situations. In virtually all plant and animal cases,
the entire viral particle enters the host cell, i.e., the (nucleic acid)
genome and the (protein) capsid. In the case of viruses that infect bacteria,
on the other hand, the viral particle remains outside the host cell and
injects its genome by virtue of the high pressure in its capsid.
Experiments are described in which these pressures are measured and in
which it is shown that genome delivery is necessarily incomplete due to
osmotic pressure in the host cell (bacterial) cytoplasm. It is then
conjectured that the remainder of the genome enters the cell via a
ratcheted diffusion mechanism due to nonspecific binding of proteins. We
argue that the translocation process is significantly faster than
predicted by ideal ratcheting, because of an entropic force
associated with particle binding. This speed-up is estimated by both
molecular dynamics simulation and by analytic and numerical solutions to
the equations describing the coupling of chain diffusion and particle
binding. Explicit account is taken of both the driving forces due to
capsid pressure and the resisting forces arising from osmotic pressure in
the host cell cytoplasm. I finish by outlining new experiments, both in
vitro and in vivo, for testing this general theory of the kinetics of
genome delivery by bacterial viruses.
April 27, 2005
Shenda Baker, Harvey Mudd College
e-mail:
,
Faculty contact: Leo Kadanoff,
Pasta science: self-assembling diblock copolymers in two dimensions
We have developed and modeled a means to deposit nanoscopic
structures such as dots or lines of a monolayer of diblock
copolymer at a liquid interface (that can be subsequently
deposited onto a solid) by a very simple preparation. A droplet
of known concentration of polystyrene-polyethylene oxide PS-PEO
with a particular ratio of block sizes is spread on an air-water
interface. A competition between spreading, caused by Marangoni
effects, and solvent evaporation leading to aggregation produces
2-dimensional features that can be controlled by judicious
choice of solution and polymer variables. We have also developed
a fluid hydrodynamic model that captures the details of the
process quantitatively with no free fitting parameters.
If there is time, I shall morph to a brief discussion of
"Strange Matter" --- a traveling museum exhibition that
highlights Materials Science. The exhibit was a partnership of
he Materials Research Society and Industry with funding through
NSF and a contracted museum design team.
May 4, 2005
Constantino Tsallis, Centro Brasileiro de Pesquisas Fisicas
e-mail:
,
Faculty contact: Leo Kadanoff,
Finally, the entropy Sq is extensive or nonextensive?
Boltzmann-Gibbs entropy and associated statistical mechanics constitute
what is well known to be the correct thermostatistical theory to be used
for systems whose microscopic dynamics is strongly chaotic (e.g., positive
Lyapunov exponents for classical systems). For a vast class of the so
called complex systems -- typically nonlinear dynamical systems at some
kind of edge of chaos (e.g., with zero Lyapunov exponents) -- this theory
needs to be generalized. Nonextensive statistical mechanics constitutes a
possible such generalization, introduced in 1988, and addressing non
equilibrium systems. A brief introduction to the theory, as well as to its
dynamical foundations (calculation from first principles of the entropic
index q) will be provided. Some selected applications will be mentioned.
Emphasis will be given to the analysis of the extensivity of the entropy Sq
which generalizes the Boltzmann-Gibbs form. Bibliography: (i)
http://tsallis.cat.cbpf.br/biblio.htm ; (ii) M. Gell-Mann and C. Tsallis,
eds., Nonextensive Entropy - Interdisciplinary Applications (Oxford
University Press, New York, 2004); (iii) C. Tsallis, M. Gell-Mann and Y.
Sato, Special scale-invariant occupancy of phase space makes the entropy Sq
additive, cond-mat/0502274.
May 11, 2005
Jim Sethna, Cornell Center for Materials Research, Cornell University
e-mail:
,
Faculty contact: Wendy Zhang,
Sophisticated Statistical Mechanics of Sloppy Models
Science is filled with multiparameter models that must be
fit to observations. An ecosystem has many interacting
species, a cell has interacting proteins and genes, and
a material has many atoms whose forces are governed by
quantum-mechanical electronic calculations. A key question
for these models is when we can trust their predictions:
usually only wisdom and experience can judge for which
problems a given model will likely be reliable. One source
of unreliability in these models is that they are sloppy:
the parameters are ill-determined by the data, with enormous
ranges giving roughly equivalent fits. These parameters
giving roughly equivalent fits, however, do not yield the
same predictions! By using an ensemble of good parameter sets,
we have been able to produce falsifiable predictions for
regulatory networks in cells with fifty unknown parameters.
We have also used them to generate estimates for the
`sloppy model' component of the systematic `transferability'
errors in interatomic potentials.
June 1, 2005
Thomas Witelski, Dept. of Mathematics, Duke University
e-mail:
,
Faculty contact: Wendy Zhang,
The coarsening dynamics of dewetting fluid films
The study of instabilities of thin fluid films on solid surfaces is of great
importance in understanding coating flows. These instabilities lead to rupture,
the formation of dry spots, and further morphological changes that promote
non-uniformity of coatings; these behaviors in unstable thin films are
generally called dewetting. Following rupture and subsequent transient
behavior, the long-time structure of films takes the form of an array of
droplets. The evolution of this system can be represented in terms of coupled
ODEs for the masses and positions of the droplets. Regimes where droplet
coarsening by each of two mechanisms (collision and collapse) are identified,
and power laws for the statistics of the coarsening processes are explained.
This is joint work with Karl Glasner, University of Arizona.
June 8, 2005
Jointly sponsored by the Institute for Biophysical Dynamics
Michael Brenner, Harvard University
e-mail:
,
Faculty contact: Leo Kadanoff,
Towards models for the structure and evolution of ion channels
This talk summarizes some very preliminary theoretical ideas and
calculations regarding the structure and evolution of ion channels. The
great advantage of ion channels is that they are individual proteins
whose function has long been known and is readily inferred through voltage
measurements. Their evolution can be readily tracked through the growing
data base of sequences. The kinetic schemes of ion channels (regulating
membrane permeability to ions) have been studied for more than 50 years,
and in general can be quite complex. We will describe our endeavors to ask
a somewhat dangerous question: Why are they this way?
Examples of questions we would like to answer include: to what extent do
design principles dictate the details of the kinetic schemes of ion
channels, such as (a) the symmetry of the sodium and potassium channels
(or lack thereof), as reflected in their kinetic schemes ; (b) the
coupling of sodium channel kinetics to potassium channel kinetics; or (c)
activation/inactivation of the channels themselves.
The talk will combine a description of what is known and not know about
ion channels, and their evolution; a description and some analysis of
models; and some preliminary analysis of using data for the evolution of
the sequences of voltage gated sodium and potassium channels in
conjunction with the models. The great hope is to be able to draw
conclusions that are not 'just so' stories.
June 15, 2005
Adriana Pesci, University of Arizona
e-mail:
,
Faculty contact: Leo Kadanoff, .
Connections between classical statistics and the Schroedinger
and Pauli equations.
In the year 1926 Madelung found a transformation that connected the
Schroedinger operator of quantum mechanics with the continuity
and Euler equations of fluid mechanics in which the ``pressure" is
proportional to the Laplacian of the density of the fluid. Later on,
Bohm and Takabayasi found a similar transformation connecting the Pauli
and the ideal fluid equations where the new ``pressure" term
involved the same Madelung term plus a vortical component.
We know that the Euler and continuity equations can be derived from
statistical descriptions of fluids. Correspondingly we might ask: What
statistical description, if any, stands behind the Madelung and Bohm-Takabayasi
equations?
Here we suggest a possible answer to such question in the form of an irreversible
mapping in Fourier space with a single free parameter. We find a particular
class of probability functions that give rise to the Schroedinger and
Pauli equations for which the averages of physical quantities read like the
postulates of quantum mechanics. This procedure seems to provide a statistical
representation of quantum mechanics.
June 22, 2005
Jointly sponsored by the Institute for Biophysical Dynamics
John Bechhoefer, Simon Fraser University
e-mail:
,
Faculty contact: Leo Kadanoff, .
Kinetic model of DNA replication in higher organisms
Higher organisms contain about three billion DNA base pairs.
Although the genome is replicated in times as short as fifteen
minutes, individual base pairs are copied at only ten bases/second.
The apparent paradox is resolved by having many "origins" of
replication distributed along the genome and initiating stochastically.
New experimental and theoretical techniques are beginning to shed light
on the organization of replication -- giving, for example, the rate of
initiation
of origins at different moments during the replication cycle. We discuss
evidence that the looping of chromatin -- the DNA-protein complex that
makes up chromosomes -- plays an important biological role in organizing
DNA replication.
June 29, 2005
Anette Hosoi, Department of Mechanical Engineering, MIT
e-mail:
,
Faculty contact: Leo Kadanoff,
Building a better snail: lubrication and adhesive locomotion
Many gastropods, such as slugs and snails, crawl via an unusual
mechanism known as
adhesive locomotion. We investigate this method of propulsion using
two mathematical
models, one for direct waves and one for retrograde waves.
We then test the effectiveness of both proposed mechanisms by
constructing
two mechanical crawlers. Each crawler uses a different mechanical
strategy to move on a thin layer of viscous fluid. The first uses a
flexible flapping sheet to generate lubrication pressures in a
Newtonian fluid which in turn propel the mechanical snail. The second
generates a
wave of compression on a layer of Laponite, a non-Newtonian,
finite-yield stress fluid with characteristics similar to those of
snail mucus. This second design can climb smooth
vertical walls and perform an inverted traverse.
July 6, 2005 (&)
Uri Hershberg, Yale University School of Medicine
e-mail:
Finding rules of immune selection dynamics by analyzing their genetic starting point.
Selection, whether in evolution or in the process of immune reaction to pathogen takes place on two landscapes. Mutation occurs at the level of the genotype while selection occurs at the level of the phenotype. In the immune reaction to invading pathogens B cells undergo high levels of mutation of the DNA encoding their antigen receptors. In parallel they undergo rapid proliferation and death in a pattern dependent on the affinity of their receptors to antigens exhibited by the patogen. The relationship between the genotypic and phenotypic landscapes is complex. Movement in one does not imply movement in the other. For a given phenotype there may be multiple states in the genotype landscape. This implies that two individuals with the same phenotype can nonetheless differ in the potential for change that the genotype encodes i.e. what they can mutate to. Ultimately this potential is determined by the codons and the amino acids they specify.
We have developed a network view of the amino acid table in which every codon is a node and every edge is a mutation. We have used the measures this view generates to analyze the DNA sequences that start the process of affinity maturation in the immune reaction. The results of our analysis suggest three new ideas about selection: First, the traits of amino acids and the potential to change them are a meaningful signal for selection. Second, we found that while the DNA encoding B cell receptors has evolved to generate variable progeny under high rates of mutation, the different gene families differ in the extent to which they will risk their potential viability. Finally, the existence of a transition bias in mutations means that not all movements on the amino acid network are equal. Codons tend to mutate to codons that are a Transiton mutation away from them, dividing the amino acid network into Transition Neighborhoods.
July 13, 2005
Eric Isaac Corwin, University of Chicago
e-mail:
,
Faculty contact:Wendy Zhang,
Structural signature of jamming in granular media
Glasses are rigid but flow when the temperature is increased.
Likewise, granular materials are rigid but become unjammed and flow
if sufficient shear stress is applied. The rigid and flowing phases
are strikingly different, yet measurements of the structure in
glasses and liquids are virtually indistinguishable. Is there a
structural signature of the jammed state that distinguishes it from
its unjammed counterpart? We address this question with a novel
experiment that accesses the contact-force distribution measured
during shearing. Because forces are sensitive to minute variations
in particle position, the distribution of forces can serve as a
microscope with which to observe nearest-neighbor position
correlations. We find a qualitative change in the force distribution
at the onset of jamming. If, as has been proposed, the jamming and
glass transitions are related, this observation of a structural
signature at jamming hints at a similar structural difference, too
subtle for conventional scattering techniques to uncover, at the
glass transition. Our measurements also provide a determination of
a new granular temperature that would be the counterpart in granular
systems to the glass-transition temperature in liquids.
July 20, 2005
Marko Kleine Berkenbusch, University of Chicago
e-mail:
, Faculty contact: Wendy Zhang,
Numerical studies of the selective withdrawal transition
Emulsification studies show that droplets immersed in an external straining
flow are easily pulled apart. In situations of comparable viscosity of the
inner and outer liquid, the only stable steady state shapes are slightly
deformed drops with rounded edges.
In selective withdrawal experiments, two immiscible fluids form a layered
system with a horizontal interface. Fluid is withdrawn from the top layer
through a straw suspended closely above the interface. Cohen et al. found in
their setup that steady state interfaces with sharp tips could be produced
even when the two fluid viscosities were almost matched. This is
surprising since the stress balancing mechanisms in the breakup and withdrawal
situation are closely related. Furthemore, at a certain flow rate the tips
undergo a topological transition into a steady spout state in which both
liquids are entrained simultaneously. We investigate the mechanisms of this
transition numerically in a simplified boundary integral model. In the tip
state, two lengthscales emerge naturally, the deflection of the interface and
the radius of the tip. We study the dependencies of these two lengthscales on
each other and on external flow parameters and on boundary conditions.
August 10, 2005
Francois Blanchette, University of Chicago
e-mail:
Simulations of interfacial flows: from multiple coalescence
to air bubble pinch off
In this talk, I will present highly accurate simulations of
fluid flows in which surface tension is dominant. The position
of the interface is modelled using markers, which allows to
determine its location very precisely and thus greatly reduces
numerical errors near the interface. Simple topological changes
such as drop or bubble pinch off and coalescence may also be handled
by our method. Applications to the problem of multiple coalescence
of a drop coming into contact with horizontal surface will be presented.
The mechanism allowing multiple coalescence is described in details
for the first time and the conditions in which multiple coalescence
may occur are determined. I will also present a second application of
my simulations to air bubble pinching off from a nozzle and discuss
how such computations may help understand ongoing experiments.
September 7, 2005 (&)
Thierry Emonet, University of Chicago
e-mail:
,
Faculty contact: Leo Kadanoff, .
Towards a digital bacterium
In recent years, single-cell biology has focused on the relationship between the stochastic nature of molecular interactions and variability of cellular processes. In addressing this problem, most efforts in computational biology have isolated one particular scale of interest, concentrating on either intracellular, cellular or population dynamics.
Our long-term goal is to develop a modular computational framework able to cross scales and relate stochastic events at the intracellular level to the behavior of a single cell and ultimately to the dynamics of a population of cells. In this talk I will relate our first steps towards that goal.
As a test-bed for our approach we are using bacterial chemotaxis. /E.
coli /bacteria can sense their environment and use that information to control their flagellar motors and move closer to sources of nutrients.
To understand how a single /E. coli/ processes information we decomposed the chemotaxis pathway into simpler information processing units. We then modeled each unit analytically and/or numerically, and when possible tested model predictions with data obtained from measurements in single cells. Finally, we constructed a digital bacterium equipped with the necessary modules to perform chemotaxis: receptors, adaptation module, intracellular signal carriers (response regulator), motors and flagella. Digital chemotaxis assays consisting of more than 1000 independent digital cells swimming in a 3D environment reproduced experimental data from both single cells and bacterial populations.
September 21, 2005 (^)
Predrag Cvitanovic, Georgia Institute of Technology
e-mail:
,
Faculty contact: Wendy Zhang,
Recurrent Coherent States in Turbulent Flows
Elucidating the onset and nature of turbulence in flows such as channel
and pipe flows is arguably one of the longest-standing and most
fundamental questions in fluid dynamics.
Experimental and computational studies point to the existence and
importance of coherent structures. Waleffe's `Self-Sustaining Process'
theory together with recent full Navier-Stokes computations of unstable
traveling waves in plane Couette, Poiseuille, and pipe flows captures
remarkably well qualitatively and quantitatively the turbulent structures
recently observed in great detail in several 3-d PVI experiments.
However, turbulence itself does not occur on the steady solutions, but on
nearby ergodic attractors. We test the ``recurrent coherrent states''
description of turbulence on a Kuramoto-Sivashinsky model, deploying a new
variational method that yields a large number of numerical unstable
spatiotemporally periodic solutions. For a small but turbulent system, the
attracting set appears surprisingly thin. Its backbone are several Smale
horseshoe repellers, well approximated by local return maps, each with
good symbolic dynamics.
September 28, 2005
Tobin Sosnick, University of Chicago
e-mail:
,
Faculty contact: Leo Kadanoff,
Integrating multiple length scales in protein folding
One of the central problems in structural biology is the prediction of a protein's 3D structure from its 1D amino acid sequence. The refolding polypeptide chain and its surrounding solvent generally are too computationally expensive to simulate at the atomic level. However, folding is sensitive to properties of individual atoms. Hence, a major hurdle is the development of a reduced representation of the system which retains the information necessary to accurately specify a proteinís fold. We propose a representation that includes realistic chain conformations along with a potential that depends on detailed chemical properties throughout the chain. In our computational approach, backbone dihedral rotations are the only allowed motions and each side-chain is represented by a single pseudo-atom. Rotation probabilities are obtained from a rotamer library that is built from 1000's of known crystal structures by combining joint information about amino acid sequence and Ramachandran basin occupancies. A statistical potential of mean force for backbone heavy atoms and the side-chain pseudo-atom is obtained from the crystal structures. These two facets are combined to predict native structures of small proteins. Successes, failures, and needed improvements to the model will be discussed.
October 5 , 2006
Wolfgang Losert, University of Maryland
e-mail:
,
Faculty contact: Wendy Zhang,
Cell motility: Dynamic networks and flexible membranes
Motion of cells in response to external signals is crucial for many biological processes, from wound healing to the spread of cancer.
Experimental studies of two physical processes involved in cell motion will be described:
(1) the continusously breaking, rearranging and growing actin scaffolding that gives a cell mechanical strength while it moves.
Our work focuses on gradients in actin network properties that play an important role at the leading edge of a moving cell.
(2) the deformations of a model cell membrane to local forcing. Shape
instabilities and phase separation characterize the membrane response.
October 12, 2005
Maximino Aldana Gonzalez, Universidad Nacional Autónoma de México
e-mail:
,
Faculty contact: Leo Kadanoff,
Robustness and Evolvability in Genetic Regulatory Networks.
Living organisms are robust to a myriad of random perturbations.
At the same time, they are evolvable, which means that internal perturbations can eventually make the organism acquire new functions and adapt to new environments. It is still an open problem to determine how robustness and evolvability blend together to produce stable organisms that yet can change and evolve. In this talk I will address this problem by studying the dynamical stability of genetic regulatory network models under the process of gene duplication and functional divergence. I will show that an intrinsic property of this kind of networks is that, after the divergence of the parent and duplicate genes, with a high probability the previous functions of the network are preserved and new ones might appear. Furthermore, the robustness observed in the network dynamics is not associated with any kind of gene redundancy. Rather, it seems to be a distributed robustness produced by the collective behavior of the entire network.
October 19, 2005(^)
Sanjay Sampath ,State University of New York Stony Brook
e-mail:
,
Faculty contact: Wendy Zhang,
The Science and Technology of Thermal Sprays and Droplet based Deposition
Thermal spray, a generic term used to describe a family of deposition processes involving heating/melting of powdered materials in either combustion flame or thermal plasmas, providing momentum transfer and acceleration, and finally impinging the droplets onto prepared surfaces. The resulting impacted and solidified droplets (splats) are the building block of a consolidated thick film coating offering wide ranging opportunities for tailored surface engineering.
An important advantage of thermal spray is the flexibility with respect to feed materials (most metals and ceramics), a single step material consolidation, limited substrate heating, and ability to process under ambient conditions. These benefits have resulted in a highly versatile and flexible process which has translated to a rapidly growing industry (estimated $4B worldwide). However, complexities associated with far-from- equilibrium treatment of materials involving two rapid phase change operations (melting and solidification) have challenged the fundamental understanding of the process. In the same vein, the extremes that the materials are subjected also offer exciting opportunities for exploratory materials research.
This presentation will provide a brief overview of the process and experimental measurements for splat formation on cold and "warm"
surfaces, under low pressure conditions, and at various impact velocities.
FIG. CAPTION: Top view micrograph of Zirconia splats formed on cold (A) and warm (B) stainless steel substrates displaying elimination of fragmentation in the latter case. Both were processed under identical process conditions under ambient environments. Similar phenonmena has been observed for wide ranging combinations of droplets and substrates.
October 26, 2005 (^)
Stephen Berry, University of Chicago
e-mail:
,
Faculty contact: Leo Kadanoff,
The strange ways small systems differ from bulk but tell us about it anyway
While thermodynamics is perfectly valid for very small systems, the behavior of such systems, e.g. atomic and molecular clusters, sometimes seems to be in sharp disagreement with our traditional concepts. The phases and phase changes of small systems, and properties such as their heat capacities (under appropriate conditions) seem very unlike what we have come to expect. However by analyzing such behavior suitably, we not only learn why the small systems seem strange and "badly behaved"; we also get new insights into the behavior of bulk matter. This discussion will concentrate on the ways phase behavior of small systems violates the Gibbs phase rule and our entire notion of sharp phase transitions, yet is really in harmony with fundamental thermodynamics.
November 2, 2005
Ian Foster, Argonne National Laboratory
e-mail:
,
Faculty contact: Leo Kadanoff,
Service-Oriented Science
My work is frequently motivated by the information technology concerns
of "big science", a frequently fascinating source of problems for the
computer scientist due to the broad scope and ambitious goals of many
scientific communities. I speak here about work that seeks to rethink
science's information technology foundations in terms of
service-oriented architecture. In principle, service-oriented
approaches can have a transformative effect on scientific communities,
allowing tools formerly accessible only to the specialist to be made
available to all, and permitting previously manual data-processing and
analysis tasks to be automated. However, while the potential of such
"service-oriented science" has been demonstrated, its routine
application across many disciplines raises challenging technical
problems. One important requirement is to achieve a separation of
concerns between discipline-specific content and domain-independent
infrastructure; another is to streamline the formation and evolution
of the "virtual organizations" that create and access content. I
describe the architectural principles, software, and deployments that
I am and my colleagues have produced as we tackle these problems, and
point to future technical challenges and scientific opportunities.
November 9, 2005 (^)
Michael Tabor, University of Arizona
email:
,
Faculty contact: Wendy Zhang,
Modeling the growth, form and function of micro-organisms
Bacterial and fungal microorganisms are everywhere and play many important roles in our environment and health. For example, they can produce antibiotics, bore through concrete, and destroy crops. Many of their functions involve very interesting mechanical processes, often involving the equivalent of enormous forces. This talk will describe the modeling of: (i) actinomycetes, which are a type of filamentary bacteria that produces antibiotics; and (ii) the rice blast fungus, which destroys rice crops. Despite the many biological and functional differences of these two microorganisms, there are certain common modeling approaches at the biomechanical level, and we show how the use of exact, nonlinear, elasticity theory can be used successfully to explain the growth and form of both of them. Further aspects of the function of the rice blast fungus, such as its strong adhesive properties and powerful mechanism to penetrate biological and inert media will be discussed.
November 16, 2005 (^)
Detlef Lohse, Dept. of Applied Physics, University of Twente, Netherlands
e-mail:
,
Faculty contact: Wendy Zhang,
Bubbles in micro- and nanofluidics
I will flash several of our activities in micro- and nanofluidics.
(i) Ink jet printing
Ink-jet printing is considered as the hitherto most successful application of microfluidics.
A notorious problem in piezo-acoustic ink-jet systems is the formation of air bubbles during operation.
They seriously disturb the
acoustics and can cause the droplet formation to stop.
We could show that the air-bubbles are entrained at the nozzle and then grow by rectified diffusion. Both high-speed bubble visualizations and numerical results are presented.
(ii) Bubble nucleation
Bubble nucleation at surfaces is a poorly understood phenomenon.
We did visualization experiments at structured hydrophobic surfaces and compared the results with 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.
(iii) Surface nanobubbles
It is a more than 200 year old dogma
that fluid flowing along a solid wall does not ``slip'', i.e., it sticks to the boundary.
On a macroscale this assumption seems to work extremely well.
However, recently, a number of micro- and nano-fluidics experiments and simulations have shed increasing doubts on the dogma, because they show strong indications of partial slip.
It has been suggested by de Gennes and others that the observed slip could be explained by the presence of surface nanobubbles.
We performed controlled
surface force atomic force microscope (AFM) studies for different surface materials and liquid conditions, in order to clarify whether the structures seen in the AFM experiments are indeed consistent with an interpretation as ``nanobubbles''.
We have also performed molecular dynamics simulations in order to find out why nanobubbles do not dissolve.
The work is done in collaboration with Jos de Jong, Michel Versluis, Hans Reinten and colleagues from Oce (ink-jet printing), Nicolas Bremond, Manish Arora, and C.D. Ohl (cavitation), Stephan Dammer, S. Yang, and Harald Zandvliet and colleagues (surface nanobubbles).
November 30, 2005 (^)
Alex Barnett, Courant Institute of Mathematical Sciences,
New York University
email:
, Faculty contact: Wendy Zhang,
High-frequency cavity modes: efficient algorithms, and quantum chaos
The `drum problem' - finding the modes (eigenfunctions) of the Laplacian in a cavity - has a 150-year history including acoustics, quantum mechanics and electromagnetics. Modern applications, such as modeling dielectric micro-cavity lasers, can involve complex geometries and high frequencies: a challenging multiscale problem. I present efficient numerical methods which rely on global basis representations and boundary matching. I will overview the exciting recent convergence of methods developed independently by physicists and numerical analysts. A long-standing question in the field of `quantum chaos' is: To what, if anything, do eigenmodes tend in the high-frequency limit? Do they become spatially uniform, if so, how fast? Can `scars' persist? Using the above tools, I will present numerical evidence towards some answers in planar chaotic cavities.
December 7, 2005
Bernard Derrida, Laboratoire de Physique Statistique, Département de Physique,Ecole Normale Supérieure
e-mail:
,
Faculty contact: Leo Kadanoff,
Effect of noise on travelling waves (such as in the Fisher Equation)
Travelling wave equations such as the Fisher equation appear as the mean-field limit in a number of problems: reaction-diffusion, evolution in presence of selection, growth,etc. .
The main effect of noise at the microscopic scale is to shift the velocity of the travelling waves by an amount which can be predicted by a simple cut-off theory.
Other characteristics of the position of the front, such as the diffusion constant, can be predicted by a simple phenomenological theory.
In the case of evolution models, the structure of the genealogical trees in presence of selection looks numerically universal and very close to those found for an exactly soluble case.
Brunet E, Derrida B
Shift in the velocity of a front due to a cutoff Phys. Rev. E 56, 2597 (1997) Effect of microscopic noise on front propagation J. Stat. Phys. 103, 269 (2001)
Brunet E., Derrida B., A.H. Mueller Munier S.
A phenomenological theory giving the full statistics of the position of fluctuating pulled fronts preprint 2005
)
)
)
)
)
)
)