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Past Colloquia

September 9, 2008
Eugene Shakhnovich
Harvard University
"Bridging scales in biological evolution: from atoms to organisms"
Host: Michael Hagan

Abstract:
One of the key unsolved problems in Biology today is understanding impact of  classical evolution, on organismal and population level on molecular evolution of genes and proteins. In this lecture I will present a microscopic physical model of early, biological evolution, where phenotype - organism life expectancy - is directly related to genotype – the stability of its proteins and interactions between them which can be determined exactly in the model. Simulating the model on a computer, we consistently observe the ‘’Big Bang’’ scenario whereby exponential population growth ensues as favorable sequence-structure combinations (precursors of stable proteins) are discovered. After that, random diversity of the structural space abruptly collapses into a small set of preferred proteins. The key feature of evolved proteins is their remarkable robustness with respect to point mutations.  Further, we noted that evolution of populations of organisms each carrying M genes  is isomorphic to the problem of M-dimensional random walkers in space of protein sequences with two adsorbing boundary conditions: at high energies of protein native conformations where proteins become unviable and organisms carrying their genes die and at lower energies where proteins are depleted of possible stable sequences. This problem can be solved exactly and we obtained the relation between mutation rates, duplication rate and stability range of the proteins at which populations remain viable. This formula predicts the universal speed limit on molecular evolution at 6 mutations per genome per replication. It provides important insights into genomic organization and evolution of viruses and simple organisms. Further analysis highlights relationship between selection and mutations – an exact solution of the selection-mutation equation provides insights into evolution of bacteria viruses and immune response.

September 16, 2008
Albion Lawrence
Brandeis University
"(De)construcing spacetime in string theory"
Host: Michael Hagan

Abstract:
The famous difficulty of combining Einstein's theory of gravity with quantum mechanics teaches us that the degrees of freedom of nature should change drastically at short distances and high energies.  String theory provides such a change of perspective by positing that the fundamental constituents of nature are extended objects.  In this scenario, there is no operational notion of a "point" in space or in time.  To probe this new description of spacetime, we will describe explicit examples of "stringy" spacetimes which have features that are very different from those that we are used to (these generalizations also have applications to particle physics and cosmology).  We will then discuss how two familiar concepts--time, and the dimension of space--arise in string theory.  We will close by discussing current work on recovering the physics of black holes.

Tuesday, September 23, 2008
James Bensinger
Brandeis University
"A precision muon detector for the ATLAS experiment at the LHC"

Abstract:
The muon detector, the outermost part of the ATLAS experiment at the LHC, was built to an unprecedented size and with unprecedented precision.  The muon system occupies a volum 40 meters long and 25 meters in diameter.  It contains aproximately 300,000 wires and the position of each one has to be known to 40 mm.  This sytem is expected to measure the momentum of muons up to 1 TeV/c with 10% accuracy.  As muons and electrons are expected to be significant signatures of new phenomenon, this is a critical part of the ATLAS experiment.  I will describe the experiment and in particular the muon system and discuss the technological developments and advances that enabled us to build this system with emphasis on those developments achieved at Brandeis.

Tuesday, October 7, 2008
Paul Miller
Brandeis University
"Learning associations while retaining specificity: competing demands on network plasticity rules"

Abstract:
Many cognitive tasks require behavioral responses to specific pairings or combinations of stimuli (A with B or X with Y) that differ from responses to the same individual stimuli, but in alternative combinations (A with Y or X with B). Such pair-specific responses can require logic equivalent to XOR, and can not be solved with a single layer neural network.  Generation of a neurons with responses to specific pairs of stimuli becomes essential.  We assess how various plasticity rules, which describe how connections between neurons alter as a function of neural activity, can assist or detract from the necessary generation of neurons with responses to specific associations. We find that standard rules for spike-timing dependent plasticity tends to produce over-association (so that any cell responding to the pair "A and B" would also respond to "A and Y" or to "X and B". However, the more recently discovered long-term potentiation of inhibitory connections counters such over-association by generating cross-inhibition, which suppresses the unwanted responses. We show how such association-specific neurons can arise in an initially random network. We also address which types of network structure can generate stimulus-specific memory activity, which is needed when pairs of stimuli are separated in time. Some of these memory networks can retain information about the order of stimuli as well as the specific pairing.

Tuesday, October 28, 2008
Rudi Podgornik
Josef Stefan Institute and NIH
"The Nature and Characterization of Order in High Density DNA Mesophases"
Host: Jane' Kondev

Abstract:
I will describe the nature of known mesophases of DNA at high densities (cholesteric, line hexatic, hexagonal colunar, hexagonal and orthorhombic) and invoke some recent advances in their understanding.  Concerted rotations and translations of long helical molecules around their long axes in bulk samples lead to a new mesophase with a screw-like order.  This screw-like order actually expels the cholesteric twist from a line hexatic phase and allows it to show a typical sixfold lhexatic scattering intensity.  Next I will describe a partially constrained system like DNA fibers where the molecules are allowed to rotate but are not allowed to fluctuate translationally.  In this case, general considerations based on angular dependence of the DNA-DNA interaction potential, lead to new phases with non-hexagonal symmetry as already seen in classical DNA X-ray scattering studies in the '50s.  I will also show how the azimutal interactions lead to crystallization of the fiber with an orthorhombic unit cell which can be observed in DNA at high density.

Tuesday, November 4, 2008
Martin Zwierlein
MIT
"Ultracold Fermi gases of atoms: Strongly interacting model matter"
Host: Albion Lawrence

Abstract:
Ultracold atomic gases allow us to study fermions, the building blocks of matter, in a highly controllable environment. The interactions between atoms can be varied at will over an enormous range via Feshbach scattering resonances. In an equal mixture of spin up and spin down fermions with attractive interactions, the gas forms a superfluid of fermion pairs. By varying the interaction strength, we can study the crossover from a Bose-Einstein condensate of tightly bound molecules to a Bardeen-Cooper-Schrieffer superfluid of long-range Cooper pairs. Superfluidity in this crossover regime is demonstrated by setting the gas under rotation and observing ordered lattices of quantized vortices. Thanks to its strong interactions, the gas is a high-temperature superfluid: Scaled to the density of electrons in a metal, superfluidity would occur already far above room temperature. A new regime is entered when the number of spin up versus spin down atoms is imbalanced. In this case, not every spin up atom can find a spin down partner. The ground state of such a system has been under debate for over 40 years. We observe the breakdown of the superfluid at a critical imbalance, giving way to an intriguing, strongly interacting Fermi gas with unequal spin populations.

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Tuesday, November 11, 2008
Cristina Marchetti
Syracuse University
"Soft Active Matter"
Host: Bulbul Chakraborty

Abstract:
Assemblies of interacting self-driven units form a new type of active soft matter with intriguing collective behavior and mechanical properties. Active systems exhibit novel nonequilibrium phase transitions, can  generate forces and adapt their structure and mechanical properties in response to stimuli. Examples include extracts of cytoskeletal filaments and motor proteins, bacterial colonies, migrating cells, and vibrated layers of granular rods. The most remarkable realization is perhaps the cell cytoskeleton, a viscoelastic polymer gel that controls cell shape, motility and division. In this talk I will review our work on using nonequilibrium statistical physics to derive a continuum description of active matter from specific models of single particle dynamics. Using a simple hydrodynamic model, I will demonstrate the surprising properties of active matter in specific geometries that may have relevance to some of the mechanical properties of living cells. 

Tuesday, November 18, 2008
Alexander Grosberg
NYU
"To Knot or Not to Knot"
Host: Jane' Kondev

Abstract:
The mathematics and physics of knots has a long and fascinating history, starting from a model of an atom suggested by W.Thompson (Lord Kelvin) and enthusiastically supported by Maxwell.  Knots in DNA are abundant and important. Recently, we surveyed the protein data bank and found that evolution for some as yet unknown reason strongly preferred unknotted proteins.  In theoretical aspect, the field was long dominated by either highly abstract mathematics or computer simulations.  Recently, some progress was made in the direction of physical understanding of knots.  One fruit of it is the prediction that knots under certain circumstances behave like a material with negative Poisson ratio.  In the talk, all these various aspects will be reviewed in some mixture.

Tuesday, November 25, 2008
Dr. Stefi Baum
Director, Center for Imaging Science, RIT
"The Universe Unveiled"
Host: John Wardle

Abstract:
This talk will review the remarkable history of imaging and its impact on discovery and modern society. Through technology, many things our eyes could never see--from images of earth from space to atoms and molecules at the smallest scale—are revealed with amazing resolution and detail. The images we form today use not only the visible light our eyes can see, but the full range of the electromagnetic spectrum, from gamma rays through infrared and on down to the lowest radio frequencies; while modern ultrasound and electron micoroscope imaging techniques transcend the realm of electromagnetic waves. To increase the physical information and diagnostic power of images, we employ a range of imaging techniques, such as spectroscopy, radar and polarimetry. We utilize in situ sensors to provide calibration for remotely sensed images. We manipulate particle beams, as well as electromagnetic radiation, to probe on nano scales at the highest energies. We create databases of the images so obtained, computer algorithms that fuse information from multiple imaging modalities, and visualization products that allow humans, aided by computers, to obtain the answers to fundamental questions critical to human knowledge, health, and security.

Tuesday, December 2, 2008
Priya Natarajan
Yale University and Harvard University
"Mapping dark energy and dark matter using cluster lensing"
Host: Albion Lawrence

Abstract:
Gravitational lensing has emerged as a powerful technique to map dark matter in the Universe. I will present the status of our current understanding of some key dark matter properties inferred from cluster lensing studies. I will also present new results on the feasibility of using cluster strong lensing to probe dark energy.

Tuesday, December 9, 2008
co-sponsored by MRSEC
Erik Luijten
University of Illinois, Urbana-Champaign
“Self-assembly of rod-like polyelectrolytes: from materials to cystic fibrosis”
Host: Michael Hagan

Abstract:
Electrostatic interactions play an important role in many biological problems and can lead to counterintuitive phenomena. I will highlight a number of problems in this area that we have addressed by means of computational methods.  Specifically, we have used Monte Carlo and molecular dynamics simulations to better understand the self-assembly of stiff polyelectrolytes (charged polymers).  Such molecules, e.g. filamentous actin, form close-packed bundles in the presence of multivalent ions or proteins.  We elucidate the mechanism of this self-assembly process and are able to make direct comparison to experimental results obtained via small-angle x-ray scattering. I will also demonstrate how these findings pertain to fighting bacterial infections in cystic fibrosis patients. 

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Thursday, February 5, 2009
4:00 p.m.
Abelson 131
Gregg Lois, Yale University
"Frustrated phenomena in physics and biology:  From supercooled liquids and glasses to protein folding dynamics."
Host: Seth Fraden

Abstract:
Frustration occurs when competing interactions between many degrees of freedom give rise to a large number of metastable states.  Although some frustrated systems are able to equilibrate on experimental time-scales, others never equilibrate and their dynamics remain far from equilibrium on all accessible timescales. Frustrated systems far from equilibrium are typically termed glasses, and most materials will become a glass if quenched quickly from high to low temperature.  Near the glass transition structural relaxation becomes sluggish, with relaxation times growing by many orders of magnitude over a relatively small temperature range.  This slowdown is not accompanied by an obvious change in structure, and thus its origin has been the subject of intense study and debate.  In the first half of the talk, I will discuss my recent work on the correspondence between the glass transition and mean-field percolation, as well as introduce a new simulation model for glass-forming materials that is inspired by this correspondence and yields an orders-of-magnitude reduction in computing time. In the second half of the talk, I will focus on my theoretical and computational studies of proteins.  Proteins fold to a unique native state at room temperature despite being highly frustrated.  How this occurs on timescales accessible to experiment, and relevant to biological function, is an open question that has intrigued scientists for decades.  I will outline the Free Energy Reaction Path theory, a framework I developed for understanding the near-equilibrium dynamics of frustrated proteins, and discuss my recent protein folding simulations that validate its predictions.  Results from both theory and simulation suggest a new non-equilibrium mechanism for reliable folding that could also be used to target metastable states in "structure-seeking" materials.

Tuesday, February 10, 2009
4:00pm
Abelson 131
Ali Khademhosseini, HST
"Microengineered hydrogels for stem cell bioengineering and tissue regeneration"
Host: Azadeh Samadani

Abstract:
Micro-and nanoscale technologies are emerging as powerful tools for controlling the interaction between cells and their surroundings for biological studies, tissue engineering, and cell-based screening.  In addition, hydrogel biomaterials have been increasingly used in various tissue engineering applications since they provide cells with a hydrated 3D microenvironment that mimics the native extracellular matrix. In this talk, I will outline our lab's work in controlling the cell-microenvironment interactions by using patterned hydrogels to direct the differentiation of stem cells.   In addition, I will describe the fabrication and the use of microscale hydrogels for tissue engineering by using a ‘bottom-up’ and a ‘top-down’ approach.  Top-down approaches for fabricating complex engineered tissues involve the use of miniaturization techniques to control cell-cell interactions or to recreate biomimetic microvascular networks within mesoscale hydrogels.  Our group has also pioneered bottom-up approaches to generate tissues by the assembly of shape-controlled cell-laden microgels (i.e. tissue building blocks), that resemble functional tissue units.  In this approach, microgels were fabricated and seeded with different cell types and induced to self assemble to generate 3D tissue structures with controlled microarchitecture and cell-cell interactions.

Thursday, February 12, 2009
4:00 p.m.
Henry Fu, Brown University
"Swimming in viscoelastic fluids and gels"
Host: Seth Fraden

Abstract:
The swimming of microorganisms in Newtonian fluids has been, and still remains, an active area of research.  However, in many cases the natural environments which microorganisms navigate are non- Newtonian fluids or even gels.  For example, mammalian sperm swim through mucus in the female reproductive tract. In this talk I focus on swimming through polymeric viscoelastic fluids and gels.  First, the forces exerted by a viscoelastic medium are different from those exerted by a Newtonian fluid.  I address how this affects swimming shapes and speeds of flexible swimmers such as sperm.  Second, the kinematic reversibility of the zero-Reynolds-number Stokes flow constrains what types of swimming motions are effective in Newtonian fluids (Purcell's "Scallop theorem").  I discuss how this is altered in nonlinearly viscoelastic fluids, and whether any new swimming strategies become available to swimmers in viscoelastic media.  Finally, I describe issues that arise for swimmers moving through viscoelastic gels, which are solids rather than fluids.

Tuesday, February 24, 2009
4:00 p.m.
Abelson 131
Aparna Baskaran, Syracuse University
"Bacteria as a fluid: Applying the materials physics paradigm to biology"
Host: Bulbul Chakraborty

Abstract:
The advent of advanced imaging and other experimental techniques as applied to in vivo and in vitro biology experiments have brought many new systems under the purview of soft materials theorists. In this talk, I will give a flavor for the contributions that can be made by materials physicists to systems of biological relevance by describing recent work in the context of self-propelled particles. Self propelled particles are active units that live in a medium and exert forces on it and actively move through it.  I will consider two simple theoretical models for this class of systems :
1) self propelled hard rods on a substrate
2) a stroke averaged swimmer in a viscous fluid.
I will use these to illustrate the interplay between self propulsion and physical interactions such as excluded volume interactions and hydrodynamic interactions on the large scale collective behavior of these systems

Thursday, February 26, 2009
4:00
Abelson 131
Vincenzo Vitelli, University of Pennsylvania
"Vibrational dynamics and heat conduction in amorphous solids"
Host: Seth Fraden

Abstract:
The development of a theoretical framework that encompasses the dynamical properties of amorphous solids stands as one of the lasting challenges of material science and mayunveil further technological potential for a vast class of soft materials such as emulsions, gels, colloidal suspensions as well as granular media and covalent glasses.

In recent years, an intriguing route to studying amorphous materials has emerged from investigating the random geometry of packings comprised of soft spheres interacting with finite-ranged repulsions. The central tenet of this approach is the existence of a zerotemperature jamming transition that occurs at a critical packing fraction, point J, at which the average number of contacts between particles barely satisfies the constraints of mechanical equilibrium.

At point J, the effect of disorder becomes overwhelming and the physics remarkably simple: we find that both the density of states and the thermal diffusivity of the vibrational modes exhibit a plateau extending to zero frequency. This talk focuses on the thermal conductivity of amorphous materials under pressure, which unlike crystals, increases monotonically with temperature. I will show that this distinct property emerges from the vibrational modes at Point J which controls energy transport in a manner akin to a critical point.

Tuesday, March 3, 2009
4:00 pm
Abelson 131
Andy Lau, Florida Atlantic University
"Response and Fluctuations in Active Systems"
Host: Zvomimir Dogic

Abstract: Active complex fluid systems like living cells, assemblies of motors and filaments, flocks of birds, and vibrated granular material are nonequilibrium systems that consume and dissipate energy. These active systems exhibit phenomena that can be quite distinct from those of conventional equilibrium soft materials.  Nevertheless, their long-wavelength properties can at times be described by hydrodynamic-like stochastic equations similar to those of equilibrium systems but with additional terms that break Onsager reciprocity and noise sources that violate
the fluctuation dissipation theorem.  In this talk, we focus on a model active system, namely, a bacterial bath, which consists of a population of rod-like motile or self-propelled bacteria suspended in a fluid environment. We discuss results of recent microrheological experiments in terms of a dynamical model for nematic liquid crystals in the isotropic state,appropriately modified to reflect the activity of bacteria. We show, in particular,that the non-equilibrium contributions to the stress arising from the swimming of the bacteria lead to a Ω scaling in the power spectrum of the active stress fluctuations, as observed experimentally.

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Tuesday, March 24, 2009
4:00 pm
Abelson 131
Aravi Samuel, Harvard University
"How worms and maggots navigate temperature gradients"
Host: Azadeh Samadani

Abstract:
Animals are intrinsically computational. We acquire sensory information about our environments, transform this information into neural representations and memories, and calculate and execute decisions based on recent and past experiences. Our own brains are staggeringly complex, with billions of neurons networked by trillions of synapses. But the basic "stuff" of our brains -- molecular and cellular structures and interactions -- is shared with our simplest animal relatives. Thus simple and well-chosen model organisms can be accessible vantage points with perspective over general biological principles. We study brain and behavior in the roundworm C. elegans and in the larval fruit fly. We focus specifically on navigational behaviors responding to physical sensory inputs. These inputs (e.g., temperature) can be delivered both reliably and quantifiably. Navigation of worms and maggots itself can be reduced to a quantified pattern as an alternating sequence of forward movements, turns, and reversals. From the systematic analysis of outward motile behavior we can infer the inner workings of neural algorithms. Applying recent advances in microscopy and optics, we are also able to manipulate and monitor the workings o-f these neural circuits in the intact animal. In this way, we strive to link brain and behavior in these simple but fascinating creatures.
 

Tuesday, March 31, 2009
4:00 p.m.
Abelson 131
"Expectations for the Large Hadron Collider"
Matthew Schwartz
Harvard University
Host: Matthew Headrick

Abstract: The Large Hadron Collider is the largest scientific instrument ever built. It had its first beam of protons last fall and plans to have the first collisions this summer. But what is it looking for? What are we hoping to find? There are many possibilities, including supersymmetry and the elusive Higgs boson. These concepts will be discussed through an exploration of the the theoretical motivation and historical context of this fantastic machine.

Tuesday, April 21
4:00pm
Abelson 131
Lecture I:  "Making a Splash, Breaking a Neck: The Development of Complexity in Fluids"
Question: Have fluids been touched by Intelligent Design?
Eisenbud Lecture Series in Mathematics and Physics
Leo P. Kadanoff, University of Chicago
Host: Albion Lawrence

Wednesday, April 22
4:00pm
Abelson 131
Lecture II: "The Good the Bad and the Awful-- Scientific Simulation and Prediction"
Question:   How far can you trust a computer simulation?
Eisenbud Lecture Series in Mathematics and Physics
Leo P. Kadanoff, University of Chicago
Host: Albion Lawrence

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Tuesday, April 28, 2009
4:00 pm
Abelson 131
speaker: John Wardle, Brandeis University

Understanding Black Hole X-ray Binary Systems: Clues from Radio Polarization Imaging of the Microquasar GRS 1915+105

Abstract:

Black hole x-ray binary systems are superb laboratories for studying general relativity, special relativity, relativistic hydrodynamics and all the processes of high energy astrophysics. They consist of a several solar mass black hole and a normal star in orbit about their center of mass. Matter streams from the atmosphere of the normal star (often a giant filling its Roche lobe) and spirals down towards the black hole, forming a hot accretion disk around it. The inner disk is a source of intense thermal x-rays. Rapid fluctuations in the x-ray intensity reveal physical processes near the “innermost stable orbit” close to the event horizon. The 6.4 keV iron K alpha line shows directly the Doppler velocities in the disk and the depth of the gravitational potential well.

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Tuesday, September 22, 2009

Intrinsic Alignments of Galaxies: Effects of Large-Scale Structure on Galaxy Formation
Tereasa Brainerd, Boston University

How the Hippies Saved Physics
David Kaiser, MIT

Watching Worlds Collide
Matthew Kleban, NYU