Spin Structure of the Nucleon and QCD.

Abstract:

In the last 20 years the investigation of the spin structure of the nucleon spawned a very productive experimental and theoretical activity with exciting results and new challenges. This investigation has included a variety of aspects, such as testing Quantum Chromo Dynamics (QCD), the theory of strong interactions in its perturbative regime via spin sum rules (like the Bjorken sum rule) and understanding how the spin of the nucleon is build from the intrinsic degrees of freedom of the theory, namely quarks and gluons. Results from a new generation of experiments performed at Jefferson Lab seeking to address key issues in the nucleon spin structure and QCD will be presented. The extension of this spin physics program using the 12 GeV upgrade of Jefferson Lab will be also discussed.

See

http://indico.cern.ch/materialDisplay.py?contribId=7&sessionId=2&materialId=slides&confId=9499

Cosmic Voids and Void Galaxies

Abstract:

Wide-angle, moderately deep redshift surveys such as that conducted as part of the Sloan Digital Sky Survey (SDSS) allow study of the relationship between the structural elements of the large-scale distribution of galaxies - including groups, cluster, superclusters, and voids - and the dependence of galaxy formation and evolution on these environments. In this talk I will focus on the identification of voids as dynamically distinct large-scale structures and examine their properties. Then I will discuss the properties of galaxies in voids, from normal galaxies to merging galaxies and active galactic nuclei.

Simulations of Functional Magnetic

Nano-particles on Supercomputers

Using Numerical Simulations to Study the Formation and Evolution of Galaxies

Abstract:

The past decade has produced an amazingly robust picture for the universe we live in. This picture predicts that structure forms hierarchically, i.e., small objects collapse at early times and grow via mergers and gravity. The prevailing idea for the formation of galaxies is that the morphology and structure that we observe is a direct byproduct of this hierarchical merger history; however, a detailed mapping between specific merger histories, and the wide variety of galaxy types, is still uncertain. By using a comprehensive set of state-of-the-art numerical simulations, we show how this process is being studied, and what some of the common scenarios might be. For example, we show that a single disk-disk merger, such as that which will occur in 5 Gyr between our own Milky Way and our nearest neighbor Andromeda, is a plausible mechanism to form many elliptical galaxies provided that dissipation is involved. We also show were this picture fails, and outline how current and future work will address these shortcomings and yield testable predictions of the model.

References:

"The collision between the Milky Way and Andromeda", T.J. Cox & Avi Loeb, 2008, MNRAS, 386, 461 (arXiv:0705:1170)

"Our Galaxy's date with destruction", Avi Loeb & T.J. Cox, 2008, Astronomy, Vol. 36, No. 6, p. 28

From Classical Resonators to Novel Artificial Atoms

Abstract:

When two superconductors are interrupted by a weak link, the behavior of the resulting physical system can be described as a tunable classical resonator which can be excited by microwaves. When sufficiently cooled and isolated from the environment, this classical resonator behaves like an artificial atom with distinct quantum energy states. In this talk, I will discuss the results of our transport and microwave experiments carried out at temperatures between 4K and 0.010 K showing classical and quantum behavior in these systems. I will discuss results involving conventional Nb junctions, new data involving microwave resonant activation in magnesium diboride (MgB2) junctions and work involving graphene-based junctions.

Simulations of Protein Aggregation

Abstract:

A number of diseases, known as amyloid diseases, are associated with pathological protein folding. In the case of Alzheimer’s disease, incorrectly folded Amyloid-beta (Aβ) proteins self-assemble into a variety of neurotoxic aggregate species, ranging from small soluble oligomers to amyloid fibrils. An attractive therapeutic approach to combat amyloid diseases lies in the development of strategies to inhibit or reverse aggregation. In the first part of my talk, I will present fully atomistic molecular dynamics simulations of the interaction of aggregation inhibiting peptides with Aβ amyloid fibrils. In the second part, I will introduce a novel off-lattice coarse-grained model for the Aβ protein and discuss the kinetics and thermodynamics of aggregation and fibrillogenesis inhibition.

Gelation of stomach mucus and its relevance to motility of the ulcer causing bacterium

Abstract:

In this talk, I will describe the underlying biophysical mechanisms involved in the remarkable ability of the mucus lining of the stomach for protecting the stomach from being digested by the acidic gastric juices that it secretes. These remarkable physical properties can be attributed to the presence of a high molecular weight glycoprotein found in mucus, called mucin, which forms a gel under acidic pH preventing the acid from diffusing back. A model of gelation based on the interplay of hydrophobic and electrostatic interactions will be discussed. Molecular Dynamics simulation studies of folding and aggregation of mucin domains provide further support for this model.

In the second part of the talk I will address the question, “How does H. Pylori, the bacterium that causes ulcers, move across the mucus layer”. Stay tuned for the surprising answer.

Super-massive Black Holes: Rulers of the Universe?

Abstract:

Once the realm of philosophers, black holes have now been shown to

exist. Indeed, black holes as massive as 1 million to 1 billion Suns

populate the cores of essentially all massive galaxies. Contrary to

popular thought, these super-massive black holes are messy eaters,

spewing out nearly as much (in the form of mass and energy) as they

consume. This "feedback" process has been postulated to be the

valve that controls the growth and evolution of their host galaxies,

shaping the very evolution of our Universe. I will discuss how

statistical analyses of active galactic nuclei and quasars from the

Sloan Digital Sky Survey (SDSS) can be used to test the hypothesis

that super-massive black holes are so all-powerful. We'll find that

the answer requires pushing even the currently most expansive dataset

to its limits, providing an important argument for the next generation

of astronomical surveys, including the LSST project.

Raman Scattering from Nanocarbon

Abstract:

Carbon is one of the earliest materials known to human civilization. In its most stable forms, namely graphite and diamond, it exhibits varied properties arising from their distinct structures. More recently three other stable forms of carbon have been discovered, namely the Fullerenes, the Carbon Nanotubes and the Graphene. All these different forms of carbon can be grouped together as nanocarbon, because their sizes in some dimensions are of nanometer scale. These too, possess exotic properties with potentiality for technological innovations. A brief review [1] of the properties of of all the stable forms of carbon will be presented. One of the most effective tools for characterizing the material carbon is to take recourse to Raman spectroscopy. With a quick introduction to Raman scattering in solids the Raman spectra from different forms of nanocarbon will be presented. Some anomalous features in the observed Raman spectra in all the three forms of naocarbon will be pointed out. In conclusion our attempts [2,3] to understand these anomalies will be outlined.

References:

1. ´Carbon: the material and its characterization by Raman Spectroscopy´ S. N. Behera in AIP Conference Proceedings 1063 (2008) p61, Mesescopic Nanoscopic and Macroscopic Materials: Proceedings of the International Workshop IWMNMM-2008, Bhubaneswar Eds. S. M. Bose, S. N. Behera and B. K. Roul.

2. ´Raman spectra of unfilled and filled carbon nanotubes: Theory´ S. Gayen, S. N. Behera and S. M. Bose, Phys. Rev. B 76 ,165433 (2007).

3. ´Theory of tangential G-band feature in the Raman spectra of metallic carbon nanotubes´ S. M. Bose, S. Gayen and S. N. Behera, Phys. Rev. B 72, 153402 (2005).

Superconductivity Without Pairing?

Abstract:

Do we really understand the physical basis for superconductivity? Electrical current can flow around a superconducting loop forever, with zero electrical resistance. This phenomenon, which represents a quantum coherent state on the macroscopic scale, was explained by Bardeen, Cooper, and Schrieffer (BCS) in 1957 as due to the formation of bound pairs of electrons known as “Cooper pairs”, held together by a “virtual phonon”. Such Cooper pairs are effectively bosons with zero spin, and condense into a quantum ground state with a coherent wavefunction at low temperatures. While this theory is well accepted, at least for conventional superconductors, the fundamental physical interpretation remains unclear. In this talk, a novel alternative explanation for superconductivity without Cooper pairs is proposed. Instead, superconducting electrons form a band of localized states in a “virtual phonon lattice”. This coupled structure can move with respect to the crystalline lattice, carrying lossless current. Surprisingly, this picture reproduces the same macroscopic quantum coherence, corresponding to flux quantization in units of h/2e, as that from the BCS theory. But this picture also predicts distinct structures on the microscopic and mesoscopic scales that are accessible to experimental observation. Implications of this novel theory for high-temperature superconductors will be discussed.

References:

A.M. Kadin, “Spatial structure of the Cooper pair”, J. Supercond. & Novel Magn. 20, 285 (2007); also on ArXiv http://arxiv.org/abs/cond-mat/0510279

A.M. Kadin, “Coherent lattice vibrations in superconductors”, Physica C: Supercond. 468, 255 (2008); also on ArXiv http://arxiv.org/abs/0706.0338

A.M. Kadin, Introduction to Superconducting Circuits (Wiley, New York, 1999). http://www.amazon.com/Introduction-Superconducting-Circuits-Alan-Kadin/dp/0471314323

Kinetics of Peptide Folding and Aggregation in Crowded and Confined Environments

Abstract:

I will discuss our recent efforts in the study of how macromolecular crowding, confinement, as well as dehydration might affect the folding and aggregation dynamics of various small peptides and proteins.

Evidence-Based Reform in Education

Abstract:

Evidence-based reform is the field of education’s greatest hope for genuine, sustained progress. Its core principle is simple. Use what works. Who could oppose this? The adoption of solutions that have been rigorously evaluated is what caused rapid advances in medicine, agriculture, technology, and other fields in the 20th century. In those fields, evidence-based reform drives an ongoing process of research, development, and dissemination of constantly improving methods. Education has long resisted evidence-based reform, partly because of a lack of agreement on desired outcomes. However, with the worldwide movement toward test-based accountability, there are now clear goals for at least some outcomes of education, and evidence of effectiveness in achieving these goals could be of great importance in policy and practice.

This presentation will focus on how education research, practice, and policy must change to focus on research-proven programs and practices, as well as the potential and pitfalls of expanding research and development on programs that work.

The Success for All Foundation works to develop and evaluate new programs, recruit and support pilot schools, and broadly disseminate the resulting program to the students in most need of high-quality instruction. SFA partner schools serve a population of students that is approximately 75% economically disadvantaged, compared to a nationwide average population of 40% economically disadvantaged students, yet a greater percentage of SFA partner schools made adequate yearly progress (AYP) on high stakes state tests than all schools nationally. During the last 20 years, more than 50 high-quality research studies, conducted by researchers at more than 30 universities have documented the impact of SFA programs on student achievement. Examples from current research projects in adolescent literacy and STEM education will provide a real-world view of school reform efforts.

Are We Through with Solar Neutrinos?

Abstract:

The sun is powered by a series of nuclear reactions that produce neutrinos. Our picture of the physics of the neutrino has come into focus thanks to the results of the SNO, Super Kamiokande, and KamLAND experiments. Together, their results show that neutrinos undergo flavor oscillation, and this is the solution to the long standing Solar Neutrino Problem. In the mean time, a new solar model problem has developed, and we are waiting for a definitive observation of the transition from matter to vacuum dominated oscillation in solar neutrinos. I will present the current status of the field, paying particular attention to the KamLAND experiment’s current and future contributions to the study of solar neutrinos.

Quantum Computation and Quantum Optics with Circuit QED

Abstract:

Electrical circuits, when composed of superconducting material and cooled to temperatures close to absolute zero, can behave quantum mechanically. Similar to regular atoms, superconducting circuits possess discrete energy level spectra. The idea of employing superconducting circuits as artificial atoms and coupling them to on-chip microwave resonators is termed circuit quantum electrodynamics (cQED).

In the last few years, cQED has established itself as a promising candidate for solid-state quantum computation. It has been successfully employed in a number of experiments probing fundamental aspects of quantum mechanics and quantum optics, including generation of single microwave photons, coherent coupling between distant qubits, and most recently, the demonstration of simple quantum algorithms. For the theorist, cQED constitutes an appealing testbed for the theoretical understanding and modeling of driven open quantum systems.

In my talk, I will give an introduction to cQED and highlight recent results obtained with the transmon qubit, an improved Cooper pair box immune to 1/f charge noise. As an outlook, I will present the fluxonium device -- the newest member of the superconducting circuit family, currently being measured in Michel Devoret’s lab.

Literature:

[1] John Clarke & Frank K. Wilhelm: Superconducting quantum bits, Nature 453, 1031-1042

[2] R. J. Schoelkopf & S. M. Girvin: Wiring up quantum systens, Nature 451, 664-669

Quantum Computing with Superconduncting Electronics: Qubits, Coherence, Correlations, and Noise

Abstract:

A century ago, quantum mechanics ushered in a revolution in how we think about the very small length scales characteristic of atoms. Today, another revolution is taking place but at the much larger scale of man made quantum systems built from superconducting circuits and Josephson junctions. These devices behave as one dimensional atoms—but atoms with many of their parameters freely adjustable at the designer’s whim. In this talk, I will discuss recent progress in using superconducting quantum systems as quantum bits (qubits), mostly focusing on a device called the “phase qubit” which consists of a single current biased Josephson junction. Our hope is that these devices will form the building blocks for a quantum computer. I will discuss coherent effects in single and coupled quantum devices. I will also discuss some of the limitations of these devices which, in the end, confirm their quantum behavior.

References:

For those who wish to review some of the quantum mechanics, I would suggest looking at David Griffith’s book, “Introduction to Quantum Mechanics” particularly the Afterward, section A.2 Bell’s Theorem.

Michael Tinkhams book: “Introduction to Superconductivity” (Chap. 6) is a good place to learn about Josephson Junctions.

Coupled phase qubits:

A. J. Berkley et al., Science 300, 1548 (2003).

R. McDermott et al., Science 307, Issue 5713, 1299-1302 (2005).

Interferometry, cooling, and amplitude spectroscopy with a superconducting artificial atom

Abstract:

Superconducting persistent-current qubits are quantum-coherent artificial atoms with multiple energy levels. In the presence of large-amplitude harmonic excitation, the qubit state can be driven through one or more of the energy-level avoided crossings. The resulting Landau-Zener transitions mediate a rich array of quantum-coherent phenomena as a function of the driving amplitude and frequency.

In this talk, we present three demonstrations of Landau-Zener-mediated quantum coherence in a strongly-driven niobium persistent-current qubit. The first is Mach-Zehnder-type interferometry [1], with which we observed quantum interference fringes in the transition rates for n-photon transitions, with n = 1…50. The second is microwave-induced cooling [2], by which we achieved effective qubit temperatures < 3 mK, a factor 10x-100x lower than the dilution refrigerator ambient temperature. The third is amplitude spectroscopy [3], a spectroscopy approach that monitors the system response to amplitude rather than frequency. This allowed us to probe the energy spectra of our artificial atom from 0.01 – 120 GHz, while driving it at a fixed frequency 0.16 GHz.

These experiments exhibit a remarkable agreement with theory, and are extensible to other solid-state qubit modalities. In addition to our interest in these techniques for fundamental studies of quantum coherence in strongly-driven solid-state systems, we anticipate they will find application to nonadiabatic qubit control and state-preparation methods for quantum information science and technology.

[1] W.D. Oliver, et al., Science 310, 1653 (2005)

[2] S.O. Valenzuela, et al., Science (2006)

[3] D.M. Berns et al., Nature 455, 51 (2008)

The work at Lincoln Laboratory was sponsored by the Air Force under Air Force Contract FA8721-05-C-0002. Opinions, interpretations, conclusions, and recommendations are those of the author(s) and are not necessarily endorsed by the United States Government.

Cosmology from the Cosmic Microwave Background

Abstract:

I will present cosmological results from NASA's WMAP satellite. WMAP measures the temperature and polarization of the Cosmic Microwave Background, relic light from the early universe. The data, collected since 2001, gives us strong evidence for a simple cosmological model: a universe with a flat geometry, filled with ‘normal’ baryonic matter, dark matter, and dark energy as a cosmological constant. I will describe the observations, and discuss implications for cosmic inflation in the very early universe, and for the lighting up of the universe by the first stars. I will also discuss future prospects for upcoming CMB experiments, from telescopes on the ground in Chile and the South Pole, to the next satellite missions.

See

http://map.gsfc.nasa.gov/

and

http://arxiv.org/abs/0803.0586

Science Writers: Ink-Stained Wretches or Descendants of Prometheus?

Abstract:

If you're a scientist, sooner or later you're probably going to run into a science writer, bugging you with phone calls and emails, wanting to ask you lots of silly questions. Who are these people? Where do they come from? What qualifies them to write about your research? I'll provide some answers, try to persuade you that science writers can be your best allies in a culture in which the public often doesn't understand or realize the importance of your work, and point out that science writing might even provide an alternate career path for scientists weary of the academic or corporate grind.

http://www.markwolverton.com

Algorithms for Machine Learning on Astronomically-Large Datasets

Abstract:

I'll describe algorithms and data structures for allowing the most

powerful machine learning methods, which often scale quadratically or

even cubically with the number of data points, to be performed many

orders of magnitude faster than naive implementations. Such

techniques can make previously impossible statistical analyses

tractable on the scale of entire sky surveys. I will discuss

scalable algorithms we have developed for n-point correlations,

friends-of-friends, nearest-neighbors, kernel density estimation,

nonparametric Bayes classification, principal component analysis,

local linear regression, isometric non-negative matrix factorization,

hidden Markov models, k-means, support vector machine-like

classifiers, Gaussian process regression, and Gaussian graphical

model inference, among others. In addition to techniques inspired by

computational geometry, fast multipole methods, and Monte Carlo

integration, we employ a distributed framework which can be thought

of as a higher-order version of Google's MapReduce. Our algorithms

have enabled several first-of-a-kind large-scale cosmological

analyses.

Dielectric studies for superconducting qubit circuits

Abstract:

In superconducting qubits dielectric films are used for Josephson

junction tunnel barriers and interlayer insulators. These dielectrics

are lossy at rf frequencies, which leads to decoherence in the qubits.

As a result, there are a number of efforts in the qubit community to

improve dielectric quality. Lately we have been studying a-Si and SiNx

films for interlayer capacitors and wiring crossovers. To do so, we use

superconducting LC resonators, where the capacitor (C) contains the

dielectric under study. At milliKelvin temperatures and low resonator

photon numbers, the dielectric loss is believed to be limited by

two-level system defects. This is confirmed in our data on a-Si. We have

also tested SiNx films near x=4/3 with different growth conditions, and

found different values of intrinsic loss that are related to a different

effective density of these defects. Incredibly, the temperature

dependent data on the best SiNx film indicates that an independent

two-level system model for the lossy defects is not sufficient.

References:

http://link.aip.org/link/?APPLAB/92/112903/1

http://prola.aps.org/abstract/PRL/v95/i21/e210503

Imaging Pathological Synchronization in the Brain

Abstract:

The electrical activity of neurons in the brain is a highly nonlinear phenomenon. Synchronized activity in the brain – which has been implicated in everything from pathological processes such as epilepsy to fundamental cognitive processes such as attention itself – can be approached using the tools of nonlinear dynamics. Specifically, I will discuss how nonlinear dynamics can be used to investigate brain activity during epileptic seizures. The "conventional wisdom" is that seizures result from an excess of synchronization in the brain. However, some recent studies suggest that this may not be the case. I will show how experimental bio-imaging techniques can be combined with nonlinear dynamics analysis tools in order to investigate synchronization (or lack of it) in the brain during seizures. As to whether our results indicate synchronization or not ... you'll have to attend the talk to find out!

See http://www.umsl.edu/~neurodyn/

Planning for a Business Career with a Physics Degree- the basics to succeed that an MBA may not teach you.

Abstract:

I will describe my personal migration path -- from working towards a Physics degree at Drexel to CEO of a public company- what I learned along the way and what you should know to maximize your talent, discipline, and goals for a career outside of pure science research.

Structure and Interactions of Biomembranes: Results obtained from X-ray scattering using a non-crystallographic method

Abstract:

Most natural biomembranes are too fluid and flexible to have traditional crystallographic structures. My group has developed a method based on liquid crystal physics that provides appropriately detailed information from diffuse x-ray synchrotron scattering. Selected results from recent work will be presented. See http://lipid.phys.cmu.edu

Regularities in Galaxy Rotation Curves

Abstract:

Individual galaxies, and groups and clusters of galaxies, have dynamically-estimated masses that greatly exceed any reasonable estimates of their normal (baryonic) masses. The standard explanation is that these objects also contain large quantities of dark matter, which has to be in a form that has thus far defied all experimental detection aside from its gravitational influence. It is therefore reasonable to question whether the supposed existence of this mysterious material is no more than an artifact of the breakdown of Newton's law of gravity in extremely weak fields. Milgrom's phenomenologically motivated ad hoc rule, known as MOND, is extraordinarily successful at accounting for rotation curves of galaxies, but is looking increasingly beleaguered in other contexts; dark matter seems the more likely explanation. However, the predictive power of the MOND rule suggests underlying systematics that constitute a serious fine-tuning problem for conventional Cold Dark Matter cosmology.

Massless and Massive Electrons in Atomically-thin Carbon

Abstract:

Graphene, a single atom-thick plane of graphite, has recently been isolated

and studied experimentally. In this two-dimensional hexagonal lattice of

carbon atoms, the electrons obey the Dirac equation for massless particles,

complete with a two-component spinor degree of freedom that mimics the spin

of a relativistic particle. Graphene thus represents a unique opportunity

to study ultra-relativistic Dirac Fermions in the laboratory. In addition,

the extraordinary materials parameters of graphene are attractive for a

range of applications from high-speed electronic devices to flexible,

transparent conducting coatings. I will first discuss the electronic

structure of graphene, and its implications for electronic properties. I

will then describe diffusive electron transport in graphene, and the unique

consequences of its massless electronic dispersion relation. Finally, I

will discuss experiments on mesoscopic graphene samples which provide a

direct probe of the massless Fermion particle-in-a-box states in graphene,

as well as the massive Fermion particle-in-a-box states in its bilayer

counterpart.

http://www.sciam.com/article.cfm?id=carbon-wonderland

http://www.physics.umd.edu/condmat/mfuhrer/

Rhythmic patterns of activity in purely electrically-coupled neuronal networks. Role of dendrite diameter

Abstract:

The generation of rhythmic activity in the nervous system has been known to be based on either pacemaking activity of individual, or groups of, neurons or to be due to chemical synaptic interactions. However, gap junctions (i.e. electrical or resistive coupling) are known to be important for many network functions such as synchronization of activity and also the generation of waves and oscillations. Furthermore, slow rhythmic patterns of activity can be recorded in the mouse embryonic spinal cord before the appearance of chemical synapses, but at a time when gap junctions are known to be expressed. In this presentation I will show computational and analytical results that prove that: 1) Network rhythmic activity patterns can be generated in a manner that exclusively depends on electrical coupling through gap junctions and no chemical synaptic interactions; 2) The amplitude of a signal transmitted across a gap junction between passive cable-like structures (such as axons and dendrites) is maximized at a unique diameter. This suggests that threshold-dependent signals may propagate through gap junctions for a finite range of diameters around this optimal value.

The frequency of the rhythmic activity generated in gap junction-coupled networks depends on the length of the path traveled by the signal and on the cable diameter. For large networks of randomly coupled neurons, we find that the architecture of the network that underlies rhythmic activity also depends on dendrite diameter. These results underline the potential importance of dendrite diameter as a determinant of network activity in gap-junctionally coupled networks, such as network rhythms that are observed during early nervous system development.

Finally, I propose that gap junction communication between spinal cord neurons is responsible for the generation of embryonic spinal cord rhythmic patterns of activity.

Results of MiniBooNE Neutrino Oscillation Experiment

Abstract:

Neutrinos are, along with the photons, most abundant particles in the Universe. Although detected more than fifty years ago, many of their fundamental properties remain a mystery. We perform experiments to deduce the behavior of neutrinos, but learning new things often comes with surprises. I will describe the latest results from the MiniBooNE experiment and discuss potential new stories neutrinos could tell us.

Reaching for the sky with SDSS and LSST

Abstract

Despite a several thousand years long history, sky surveying

is experiencing a bonanza as detectors, telescopes and computers

become ever more powerful. I will discuss how the unprecedentedly

accurate and diverse data from the optical Sloan Digital Sky Survey

(SDSS) have recently enabled numerous exciting discoveries. I will

use three specific examples (asteroids, quasar variability, and

mapping of the Milky Way stellar distribution) to give a preview of

what to expect from the upcoming next-generation surveys, such as

the Large Synoptic Survey Telescope (LSST). I will also describe

how LSST data will be used to measure the properties of dark matter

and dark energy.

Probing anomalous two-level systems with a Cooper-pair box

Abstract:

The interaction of superconducting quantum bits (qubits) with

anomalous "two-level" systems can lead to decoherence, dissipation,

inhomogeneous broadening and a loss of measurement fidelity for the

qubit. Typically, it is difficult to observe individual two-level

systems and extract detailed microscopic information about them. We have

used an Al/AlOx/Al Cooper-pair box (CPB) qubit to detect coupling to

discrete anomalous two-level quantum systems. Our CPB operates at 40 mK,

can detect changes in charge that are much smaller than the charge of a

single electron, and it has a resonance frequency that can be tuned from

15 GHz to 50 GHz at a temperature of 40 mK. By measuring the excitation

spectrum and lifetime of the first excited state of the CPB, we can

identify avoided level crossings that arise when the CPB couples to

anomalous two-level systems. We find that the frequency of the crossings

depends on gate voltage applied to the CPB and the size of the splitting

depends on the effective Josephson energy of the CPB. This behavior is

exactly what one would expect for two-level systems formed by point

charges that can tunnel between two positions in the oxide of the

Josephson junction. By fitting a model Hamiltonian to our data, we are

able to extract microscopic information about each charge fluctuator

such as the well asymmetry, tunneling rate, and the minimum hopping

distance.

References:

1. J. Q. You & Franco Nori, "Superconducting Circuits and Quantum

Information," Physics Today, (November 2005) p. 42.

2. M. H. Devoret, A. Wallraff, and J. M. Martinis, "Superconducting

Qubits: A Short Review," arXiv:cond-mat/0411174

(http://lanl.arxiv.org/abs/cond-mat/0411174).

Biophysics of Insulin

Abstract:

In this talk, I will discuss two ongoing projects devoted to using molecular dynamics simulations to understand better the structural bases for several important aspects of the molecular biology of insulin. I first discuss our novel simulations aimed at identifying binding and unbinding mechanisms of phenol from insulin hexamers. We discuss the combined use of random acceleration molecular dynamics (RAMD) and non‐equilibrium work relation free energy calculations to identify and quantify various exit pathways of phenol from hexameric insulin. We find that, in addition to the canonical pathway involving “gate‐keeper” residues at the dimer interfaces, phenol readily exits through the hexamer interface as well as by several other distinct pathways. Interestingly, two of these newly discovered pathways involve aromatic ring flips previously hinted at by NMR experiments. In the second part of this talk I will describe our recent efforts aimed at building a three‐dimensional model of the insulin receptor (IR). IR is an unusual hormone receptor in that it is expressed as a disulfide‐linked homodimer, which, upon high‐affinity (pM) binding of insulin undergoes a poorly understood structural change that results in trans‐phosphorylation of its cytosolic tyrosine kinase modules. The structure of IR is unknown; however, a crystal structure of the dimeric ectodomain fragment (IRΔβ) was recently published by the Ward group. Using a novel method combining Monte Carlo and molecular dynamics simulations, we propose a docking of insulin on the IRΔβ structure. Because the binding domain involves a large number of residues from each monomer, it is important that the inherent large‐scale flexibility of the entire dimer be taken into account. We find that, in an optimal orientation, bound insulin places much of its exposed B‐chain hydrophobic residues along the surface of the L1 domain, as previously predicted, but in doing so, generates never‐before‐seen A‐chain contacts with the FnIII‐2 domain of the second monomer. We also discuss the flexibility of IRΔβ in terms of the monomer‐monomer interfaces, and speculate on the structural changes associated with receptor activation.