Seminars
are held on Tuesdays from 4:00 p.m. at 114 Dana Research Center,
with refreshments served beforehand at 3:45. All are welcome to
attend!
June 10th, 2004
THURSDAY Special Colloquium/CIRCS Talk
TITLE: "Biopolymer
translocation through membrane nanopores "
By:
Dr. Tobias Ambjörnsson
Nordic Institute for Theoretical Physics (NORDITA),
Copenhagen Denmark
ABSTRACT: The passage (translocation) of a biopolymer through a narrow membrane
pore has received considerable attention in recent years. In
particular, single molecule translocation experiments allow detailed
investigations of such translocation processes, which now has to be
understood from a theoretical point of view. Two fundamentally
different transport mechanisms are distinguished: (i) For (highly)
charged biopolymers, like DNA, electric fields is used to induce the
translocation. Experiments reveal a threshold-like behaviour of the
flux (number of DNAs passing through the pore per unit time) of
single-stranded DNA molecules through the pore as a function of
applied voltage. Above the threshold the flux depends exponentially on
voltage. A theoretical model of the process is developed, in which it
is shown (see ref. 1 below) that the behaviour above is essentially
caused by entropic confinement effects in the nanopore. (ii) For less
charged polymers, such as proteins, the translocation is guided by
chaperones (binding proteins) which due to their binding to the
biopolymer drive the passage. It is shown (see ref. 2 below) how the
interaction between chaperones and the translocating biopolymer act to
drive the translocation dynamics, and in detail how the rate of
translocation depend on the different types and concentrations of
chaperones on both sides of the membrane.
March 9th,
2004 TUESDAY Colloquium/CIRCS Talk
TITLE: "Statistical physics and neuronal connectivity"
By:
Dr. Armen Stepanyants
Cold Spring Harbor Laboratory, NY
ABSTRACT: Understanding connectivity principles in the human brain is one of the oldest and most important problems in neuroscience. This problem is complicated
in part by the fact that the human brain presents a highly interconnected network of about a hundred billion neurons. The geometry of neuronal arbors can provide valuable clues to the solution of the connectivity problem. By analyzing shapes of cortical neurons we attempt to answer a number of
important questions: 1. Is there a potential for reorganization of neuronal circuits in the adult brain? 2. What is the upper bound for the information storage capacity associated with this reorganization? 3. Is the cortical neuropil optimally designed to store information in neuronal connectivity patterns? The answers to these basic questions will improve our understanding of essential brain functions, such as learning and memory.
March 4th,
2004 THURSDAY Colloquium/CIRCS Talk
TITLE: "Minimal Paths and Signal Propagation in a Model Cortex"
By:
Dr. Rava da Silveira
Harvard University
ABSTRACT: The cortex is the outer shell
of the brain largely responsible for sensory and higher
faculties, each of which relies on collective processing
by a large number of neurons. Given the complexity of
cortical function, a natural first step in a theoretical
approach consists in delineating the constraints imposed
upon 'macroscopic' processing, and in particular upon
'macroscopic' length and time scales, by 'microscopic'
parameters such as local wiring and single-neuron dynamics.
Experimental data imply the existence
of cortex-spanning paths of synaptically connected neurons
with no more than about ten synapses. At the same time,
only few long axons are available for the construction
of such paths. Is then a delicate 'design' needed? Based
on experimental data, we introduce a simple model of
random ('non-designed') wiring, in which the probability
of a synapse between two neurons decreases algebraically
with the distance separating the two neurons. We then
show that the number of synapses needed in a path spanning
a distance r grows very slowly with r
, as a power of ln(r). Thus, according to this
model, paths that crisscross the cortex with a few synapses
are present even in the absence of any 'design.'
Beyond purely structural questions, we
turn to dynamics and ask how neural activity propagates
in the (model) cortex, a question for which precise
experimental data are again available. Here, the central
conceptual difficulty lies in the requirement that the
dynamics be at the same time sensitive to weak stimuli
and stable with respect to stronger ones. We present
preliminary results on the mechanisms of signal propagation
and on its dependence upon 'microscopic' parameters.
To conclude, we mention a number of interesting questions
that follow from this first attempt at the problem.
February 26th,
2004 THURSDAY Colloquium/CIRCS Talk
TITLE: "The
Quantum Physics of Photosynthesis"
By:
Dr. Ana Damjanovic
John Hopkins University
ABSTRACT: Photosynthetic organisms utilize
sunlight to drive their cellular reactions. Through
natural selection, the light harvesting apparatii of
various life forms were optimized for high efficiency
in particular habitats. For several organisms, x-ray
crystallography has revealed the arrangement of photo-active
molecules, chlorophylls and carotenoids in light-harvesting
proteins. Through structure based molecular dynamics
and quantum calculations we reveal the design principles
underlying efficient absorption and energy transfer,
and how these molecules cope with physiological temperatures,
where thermal disorder is significant. Thus, the natural
photo cell, as engineered and optimized by evolution,
provides clues invaluable for design of efficient artificial
nano-scale light harvesting antennae and photo cells.
February 24th,
2004 Colloquium/CIRCS Talk
TITLE: "Membrane
Elasticity - Computational Modeling and Theoretical
Study"
By:
Dr. Oded Farago
Materials Research Laboratory
University of CA, Santa Barbara
ABSTRACT: One of the factors limiting the
size of membranes in computer simulations is the large
number of solvent molecules which fill the simulation
cell. We have recently developed a novel computer model
of bilayer membranes in which the membranes are simulated
without the embedding solvent as if they were in vacuum.
Using this new model we have been able to investigate
the behavior of large membranes containing 1000 lipids.
In the talk I will present the results of computer simulations
demonstrating the efficiency of the model and its ability
to mimic the physical behavior of bilayer membranes.
I will explain some of the numerical results using theoretical
arguments.
February 19th,
2004 THURSDAY Colloquium/CIRCS Talk
TITLE: "Microrheology
and Stress Fluctuations in Living Cells"
By:
Dr. Andy W.C. Lau
Department of Physics and Astronomy
University of Pennsylvania
ABSTRACT: One of the major challenges for
modern biology is to understand how cells sense and
produce force to respond to their environment in a directed
manner. As a prerequisite, an accurate physical picture
of the viscoelasticity and active behaviors of the cytoplasm
requires powerful experimental techniques and theoretical
modelling. Recently, microrheology has emerged as a
new experimental tool to probe active cytoskeleton dynamics.
In this talk, we provide a theoretical framework for
interpreting passive microrheology experiments on non-equilibrium
active systems such as living cells, demonstrate that
microrheology can be used to sensibly quantify the power
spectrum of cytoskeletal stress fluctuations due to
molecular motor activity in vivo, and propose a plausible
microscopic model that explains the observed 1/f2
spectrum.
February 12th,
2004 Colloquium/CIRCS Talk
TITLE: "Cortical
Circuits, Finite State Automata, and Decoding of Spatiotemporal
Sequences of Spikes"
By:
Dr. Dezhe Z. Jin
Howard Hughes Medical Institute
Department of Brain and Cognitive Sciences
Massachusetts Institute of Technology
ABSTRACT: How does the brain recognize time
dependent signals such as speech? Recent experiments
demonstrated that neurons in the primary sensory brain
areas detect temporal features in short time intervals
(tens of milliseconds). Furthermore, different sensory
neurons prefer different features. A complex temporal
signal lasting over several seconds thus drives sensory
neurons to spike at different moments, creating a spatiotemporal
spike sequence code that is sent to higher areas of
the brain to decipher. In this talk, I will discuss
a mechanism for neurons in cortex to decode such spatiotemporal
spike sequences. The mechanism is based on the observation
that spatiotemporal spike sequences are analogous to
strings of symbols such as text; thus, they can be decoded
in the same way as the strings of symbols recognized
by finite state automata. Indeed, any finite state automata
can be implemented with cortical neural networks. The
implementation utilizes the morphological and biophysical
properties of the cortical neurons, as well as the connection
patterns from the sensory neurons to the cortical neurons
and those among the cortical neurons. Specifically,
cortical neurons transit between bistable membrane potentials
(the UP and DOWN states) when spikes from the sensory
neurons arrive. The UP states of some cortical neurons
can be realized if and only if particular spike sequences
are present in the input spikes, signaling recognition
of the specific spike sequence code. Finite state automata
are an important part of the Turing machine. It appears,
therefore, that the way the brain recognizes time dependent
signals may be quite similar to how a digital computer
understands a program.
January 27th,
2004 CIRCS Talk
TITLE: "Coupling of flux quantum bits"
By:
Dr. Johannes Majer
Department of Applied Physics
Yale University
ABSTRACT: Quantum computers are machines that store their information in quantum
variables, so-called quantum bits (qubits). Qubits have been
implemented in various systems. However, the requirement for upscaling
makes solid state implementations highly attractive. Several single
flux qubits have been realized using superconducting Josephson junction
circuits. I will present spectroscopy measurements on two coupled flux
qubits. The qubits are coupled inductively. The interaction is of Ising
form. By applying microwave radiation, we observe resonances due to
transitions from the ground state to the first two excited states. From
the position of these resonances as a function of the magnetic field
applied, we observe the coupling of the qubits.
January 13th,
2004 CIRCS Talk
TITLE: "Targeted
delivery of pharmaceutical agents: Challenges and
solutions"
By:
Professor and Chair, Vladimir Torchilin
Department of Pharmaceutical Sciences
Northestern University
ABSTRACT: The main problems associated currently with systemic drug administration
are: even biodistribution of pharmaceuticals throughout the body; the lack
of drug specific affinity towards a pathological site; the necessity of a
large total dose of a drug to achieve high local concentration;
non-specific toxicity and other adverse side-effects due to high drug
doses. Drug targeting, i.e. predominant drug accumulation in the target
zone independently on the method and route of drug administration, may
resolve many of these problems. Currently, the principal schemes of drug
targeting include direct application of a drug into the affected zone,
passive drug targeting (spontaneous drug accumulation in the areas with
leaky vasculature), "physical" targeting (based on abnormal pH value and/or
temperature in the pathological zone), magnetic targeting (or targeting of
a drug immobilized on paramagnetic materials under the action of an
external magnetic field), and targeting using a specific "vector" molecules
(ligands having an increased affinity towards the area of interest). The
last approach provides the widest opportunities. Such pharmaceutical
carriers as soluble polymers, microcapsules, microparticles, cells, cell
ghosts, liposomes, and micelles have been successfully used for targeted
drug delivery in vivo. Though the direct conjugation of a drug molecule
with a targeted moiety is also possible (immunotoxin), the use of
microreservoir-type systems provides clear advantages, such as high loading
capacity, possibility to control size and permeability of drug carrier
systems and use relatively small number of vector molecules to deliver
substantial quantities of a drug to the target. Intracellular targeting
allows for a still further increase in the efficiency of pharmaceutical
agents.
Special CIRCS
Seminar
Tuesday January 13th, 2004 CIRCS Talk
TITLE: "Fractal
Escape Times and the Chaotic Ionization of Hydrogen"
By:
Professor John Delos
William and Mary
ABSTRACT:
CIRCS seminar
Tuesday January 6th, 2004
TITLE:
"Impenetrable bosons and topological quantum computing"
By:
Professor Maxim Olshanii
University of Southern California
ABSTRACT: Following the striking analogy between the Quantum Hall Effect and
fermionization in the harmonically trapped Tonks-Girardeau gas of
impenetrable bosons we propose a one-dimensional scheme for generating of
topologically robust anyon-like excitations, thought to be the root to
implementation of the topologically protected quantum computing protocols.
We discuss the technological advantages of the scheme based on well
developed atom-waveguide techniques.
Special
Joint Biology Department/CIRCS seminar
Monday December 1st, 2003
Snell Library at Noon
TITLE:
"Beyond Hebb: Optimizing with Synapses"
By:
Professor Sebastian Seung
Department of Brain and Cognitive Sciences
M.I.T.
ABSTRACT:
Special Seminar
Monday November 24th, 2003 CIRCS Talk
TITLE: "Rheology
of Composite Actin Networks"
By:
David Weitz
Physics Department Harvard University
ABSTRACT:
November 18th, 2003
CIRCS Talk
TITLE: "A 'budding'
problem: the design principles in the establishment of cell polarity.
"
By:
Rong Li
Harvard Medical School
ABSTRACT: The establishment of cell polarity is required for fundamental
cellular processes such as directional growth, asymmetric cell
division, and cell migration. Studies of different biological systems
have revealed highly regulated chains of events that lead to cell
polarization in specific orientations but also that polarization can
occur in random directions in the absence of any spatial cues. To
investigate the mechanism for spontaneous cell polarization, we used
an assay in budding yeast where expression of an activated form of
the small GTPase Cdc42 can generate its own polar distribution
without pre-existing asymmetry. In this assay, both the establishment
and maintenance of a polar Cdc42 distribution required targeted
secretion directed by filamentous actin. A mathematical simulation
demonstrated how such a symmetry breaking process could be achieved
through a positive feedback circuit involving the actin cytoskeleton.
We further investigated the relevance of such a feedback loop under
normal growth conditions. We used GFP fusion proteins to follow Cdc42
and its GEF, Cdc24, upon release from G1 arrest. Polar localization
of both proteins was partially dependent on actin-based transport, as
polarization efficiency was reduced in cells with disrupted actin and
cells lacking tropomyosin or a type V myosin. This result together
with additional experiments further suggested the existence of an
actin-independent mechanism that is also sufficient for spontaneous
symmetry breaking, and that rapid polarization requires a coupling of
above two mechanisms. Finally, we are investigating, through
experimental and modelling work, how above spontaneous mechanisms are
coordinated with a GTPase cascade to generate a polarity axis in a
physiologically relevant orientation.
November 4th, 2003
CIRCS Talk
TITLE: "Moving through
fluids: experimental hydrodynamics of locomotion in fishes"
By:
George Lauder
Professor of Organismic and Evolutionary Biology
Harvard
University
ABSTRACT: Fishes comprise almost 25,000 species and a hallmark of their diversity is
the ability to effectively move through the aquatic medium, exert force on
the water, and control their body position in a turbulent environment.
Attempts to study aquatic locomotion over the past 20 years have met with
many difficulties, including visualizing the motion of moving and
deformable fins, and the quantifying the forces exerted by fish fins on
the water. In this talk I will discuss recent experimental advances in
quantifying both fin and fluid motion, and describe new results
demonstrating the function of fish fins as force-generating control
surfaces. Fish fins exert force on the water by generating vortex rings,
and these vortex rings change shape as swimming speed increases. Vortex
rings shed by fins also can differ in shape among species. A key challenge
for the future will be incorporating detailed three-dimensional kinematic
descriptions of fin motion into computational fluid dynamic models and
validating these models with experimental data from freely-swimming fishes.
October 28th, 2003
CIRCS Talk
TITLE: "Waiting for the Bus"
By:
Dr. Scott A Hill
CIRCS and Department of Physics
Northeastern Universit
ABSTRACT: In this talk we will consider a simple model for buses on a bus
route. Using numerical simulation and linear analysis, we enumerate
the stable and unstable modes of a homogeneous system, and explain why
buses tend to clump together. We show that strict stability of a
homogeneous bus route requires careful collaboration among bus
drivers, but that in many practical cases (particularly in rural
areas) the time it takes for instabilities to appear is longer than a
bus would normally spend en route.
September 30th, 2003 CIRCS Talk
TITLE: "
Quantum Entanglement as a Resource for Communication"
By:
William Wootters
Williams College
ABSTRACT: Quantum mechanical objects can exhibit
correlations with one another that are fundamentally at
odds with the paradigm of classical physics; one says that
the objects are "entangled." In the past decade, entanglement
has come to be studied not only as a marvel of nature but
also as a potential resource, particularly as a resource
for certain unusual kinds of communication. This talk reviews
three proposed communication schemes based on entanglement:
(i)
dense coding, which is the effective doubling of the information-carrying
capacity of a quantum particle through prior entanglement
with a particle at the receiving end;
(ii) teleportation,
in which a quantum state is transferred from one particle
to another over a distance, apparently without traversing
the intervening space; and
(iii) the efficient pooling of
classical data, in which separated participants arrive at
a conclusion faster because they share entanglement. These
three schemes highlight three distinct ways in which entanglement
can enhance communication.
September 23th,
2003
TITLE:
"The Fermi-Pasta-Ulam Problem:
A Watershed in Computational and Nonlinear Physics
"
By: Professor David K. Campbell
Departments of Physics and Electrical Engineering,
Dean, College of Engineering
ABSTRACT: The Fermi-Pasta-Ulam (FPU) "problem," which began in Los Alamos in
the early 1950s and produced results characterized by Fermi as "a suprising little
discovery," was a in fact a defining event in computational and nonlinear physics.
It marked the first systematic study of a nonlinear system by digital computers
("experimental mathematics") and led directly to the development of the concept of "solitons"
and indirectly to the modern understanding of "deterministic chaos." With the approach of the
50th anniversary of this pioneering study, it seems timely to review the origins, examine the
present descendants, and predict the future implications of this watershed problem.
Beginning with a discussion of the nature of the FPU problem and the results of
the original simulations, including the remarkable "FPU recurrences," I show how
a continuum limit analysis clarifies the nature of these recurrences and leads directly
to the equations to which the concept of solitons was first applied. I next establish
the existence of deterministic chaos in the FPU problem and discuss briefly recent
attempts to clarify the transition between the solitonic and chaotic regimes. I close
by discussing the consequences of the interplay between solitons and chaos for
several outstanding problems in physics, including anomalous heat transport in FPU-like
model systems and real low-dimensional materials and the origins of statistical
mechanics.
