http://ilp-www.mit.edu/ List of 40 most recently entered publications, as compiled by the Industrial Liaison Office. en-us Copyright 2008 MIT ILP Fri, 4 Jul 2008 23:29:14 GMT http://ilp-www.mit.edu/favicon.ico http://ilp-www.mit.edu/display_page.a4d?key=P5d http://ilp-www.mit.edu/display_paper.a4d?paperId=83240 We show that open strings living on a D-brane which lies outside an AdS black hole can tunnel into the black hole through worldsheet instantons. These instantons have a simple interpretation in terms of thermal quarks in the dual Yang-Mills (YM) theory. As an application we calculate the width of a meson in a strongly coupled quark-gluon plasma which is described holographically as a massless mode on a D7 brane in AdS5°—S5. While the width of the meson is zero to all orders in the 1/p£f expansion with £f the ’t Hooft coupling, it receives non-perturbative contributions in 1/p£f from worldsheet instantons. We find that the width increases quadratically with momentum at large momentum and comment on potential phenomenological implications of this enhancement for heavy ion collisions. We also comment on how this non-perturbative effect has important consequences for the phase structure of the YM theory obtained in the classical gravity limit. 07/02/08 Hong Liu http://ilp-www.mit.edu/display_paper.a4d?paperId=83239 We investigate scenarios in which a charged, long-lived scalar particle decouples from the primordial plasma in the Early Universe. We compute the number density at time of freeze-out considering both the cases of abelian and non-abelian interactions and including the effect of Sommerfeld enhancement at low initial velocity. We also discuss as extreme case the maximal cross section that fulfils the unitarity bound. We then compare these number densities to the exotic nuclei searches for stable relics and to the BBN bounds on unstable relics and draw conclusions for the cases of a stau or stop NLSP in supersymmetric models with a gravitino or axino LSP. 07/02/08 Carola Berger http://ilp-www.mit.edu/display_paper.a4d?paperId=83237 Implosions of spherical and cone-in-shell targets in direct-drive inertial confinement fusion (ICF) are studied with proton radiography. Time-gated, 15-MeV proton images provide a unique and comprehensive picture of ICF implosions that cover all the implosion phases from acceleration, through coasting, deceleration, to stagnation. Observation and study have resulted in the discovery and characterization of self-generated internal radial electric fields, and the direction reversal of such fields during the course of implosions. Monte-Carlo simulations quantitatively confirm the observations of the electric field and its evolution. For further elucidation of these implosions, data is also contrasted using both self-emitted x rays and hydrodynamic simulations. 06/30/08 Fredrick Seguin http://ilp-www.mit.edu/display_paper.a4d?paperId=83236 We present a calculation of the light-hadron spectrum in full QCD using two plus one flavor Asqtad sea quarks and domain wall valence quarks. Calculations of meson and baryon masses are performed on a lattice of spatial size L . 2.5 fm, and a lattice spacing of a . 0.124 fm, for pion masses as light as m Å` 300 MeV. Extrapolation of baryon masses to the physical pion mass is studied using continuum and mixed action heavy baryon chiral perturbation theory for two and three flavors. The successes and limitations of chiral perturbation theory with these extrapolations are discussed. 06/30/08 John Negele http://ilp-www.mit.edu/display_paper.a4d?paperId=83235 Wolfgang Kummer was a pioneer of two-dimensional gravity and a strong advocate of the first order formulation in terms of Cartan variables. In the present work we apply Wolfgang Kummer’s philosophy, the ‘Vienna School approach’, to a specific three-dimensional model of gravity, cosmological topologically massive gravity at the chiral point. Exploiting a new Chern–Simons representation we perform a canonical analysis. The dimension of the physical phase space is two per point, and thus the theory exhibits a local physical degree of freedom, the topologically massive graviton. 06/30/08 Daniel Grumiller http://ilp-www.mit.edu/display_paper.a4d?paperId=83234 It is puzzling today to explain diversity and imperfection of actual transmission monopoly designs in competitive electricity markets. We argue that transmission monopoly in competitive electricity markets has to be analysed within a Wilson (2002) modular framework. Applied to the management of electricity flows, at least three modules make the core of transmission design: 10 the short run management of network externalities; 2° the long run management of network investment; and 30 the coordination of neighboring Transmission System Operators for cross border trade. In order to tackle this diversity of designs of TSOs, we show that for each of these modules, three different basic ways of managing them are possible. Among the identified twenty seven options of organisation, we define an Ideal TSO. Second, we demonstrate that l *monopoly design differs from this Ideal TSO and cannot handle these three modules irrespective of the "institutional" definition and allocation of property rights on transmission; while 2°definition and allocation of property rights on transmission cannot ignore the existing electrical industry and transmission network structure: they have to complement each other to be efficient. Some conclusions for regulatory issues of transmission systems operators are derived from this analysis of network monopoly organisation. 06/30/08 Vincent Rious http://ilp-www.mit.edu/display_paper.a4d?paperId=83233 In the absence of a federal policy to cap carbon emissions many states are moving forward with their own initiatives, which currently range from announcements of commitments to reduce greenhouse gases to a regional multi-state cap-and-trade program slated to begin in 2009. While federal legislation is expected in the next few years, it is unclear how such legislation will define the relationship between a federal cap and trade program and other state regulations. Assuming the introduction of a cap-and- trade program at the federal level, this paper analyzes the economic and environmental impacts of the range of possible interactions between the federal program and state programs. We find that the impacts of interaction depend on relative stringency of the federal and state program and overlap in source coverage. Where state programs are both duplicative of and more demanding than the federal cap, the effect is entirely redistributive of costs and emissions, with in-state sources facing higher marginal abatement costs. Also, differing marginal abatement costs among states create economic inefficiencies that make achievement of the climate goal more costly than it need be. These redistributive effects and the associated economic inefficiency are avoided under either federal preemption of duplicative state programs or a 'carve out' of state programs from the federal cap with linkage to the federal allowance market. 06/30/08 A Ellerman http://ilp-www.mit.edu/display_paper.a4d?paperId=83232 Graphical models fuse probability theory and graph theory in such a way as to permit efficient representation and computation with probability distributions. They intuitively capture statistical relationships among random variables and provide a succinct formalism that allows for the development of tractable algorithms for statistical inference. In recent years, certain types of graphical models, particularly Bayesian networks and dynamic Bayesian networks (DBNs), have been applied to various problems in missile defense that involve decision making under uncertainty and estimation in dynamic systems, such as data association, multitarget tracking, and classification. While the set of problems addressed in the missile defense arena is quite diverse, all require mathematically sound machinery for dealing with uncertainty. The graphical model regime provides a robust, flexible framework for representing and computationally handling uncertainty in real-world problems. While the graphical model regime is relatively new, it has deep roots in many fields, as the formalism generalizes many commonly used stochastic models, including Kalman filters and hidden Markov models. In this report, we describe the mathematical foundations of graphical models and statistical inference, focusing on the concepts and techniques that are most useful to the problem of decision making in dynamic systems under uncertainty. In general, statistical inference on a graphical model is an NP-Hard problem, so there have been large research efforts that involve developing algorithms for performing inference efficiently for certain classes of models, or obtaining approximations for quantities of interest using algorithms for approximate inference. Due to the breadth of problems addressed, a broad class of algorithms has been of interest to researchers over the past several years. As such, the need arose early on for an extensible and efficient software library for performing statistical inference on graphical models. The Bayesian Network Evaluation Tool (BNET), a Java software product spearheaded by MIT Lincoln Laboratory as part of our research effort program, fills this need. BNET features a rich collection of both exact and approximate statistical inference algorithms, which we describe in detail in this report. In general, graphical models and statistical inference are rich subjects, so an exhaustive treatment is well beyond the scope of this report. We will direct our coverage of these topics according to the particular algorithms that we have used and those that are currently subjects of ongoing research. Forthcoming reports will discuss the details of particular algorithms that build upon the mathematical machinery that developed in this report. 06/30/08 Eric Evans http://ilp-www.mit.edu/display_paper.a4d?paperId=83231 By fielding several, compact proton spectrometers at various locations around an ignition-capsule implosion at the National Ignition facility (NIF), pR and pR modulations of the ablator for a failed implosion can be obtained through absolute measurements of knock-on proton (KO-P) spectra. For ignition capsules with a Cu-doped beryllium (Be) ablator, 50:50 mixture of deuterium-tritium (DT) fuel and ~1% residual hydrogen (H) by atom, failed implosions can be diagnosed for neutron yields ranging from ~10(11) to ~5 x10(16) and local pRs up to ~240 mg/cm2. For capsules with an ablator of Ge-doped CH, which contains large amounts of H, failed implosions can be diagnosed for neutron yields ranging from ~1010 to ~3° x10(16) and local pRs up to ~200 mg/cm2. Prior to the first ignition experiments, capsules with a Cu-doped Be ablator (or Ge-doped CH ablator), more deuterium-lean fuel mixture and H-dopant levels up to 25% in the fuel will be imploded to primarily reduce the neutron yield. The HDT-filled Be capsule implosion, which can be diagnosed for neutron yields ranging from ~5 x10(9) to ~5 x10(16) and local £lRs up to ~240 mg/cm2, is more suitable to diagnose using KO-P’s as the signal-tobackground ratio is significantly higher than for an ignition-capsule implosion. In addition, analysis of CH-ablator data obtained from analogous OMEGA experiments indicate that the shape of the KO-P spectrum is affected mainly by the ablator pR. Other effects such as ablator-density-profile variations, time evolution of the ablator pR, fuel-ablator mix and electron temperature variations typically predicted for the ablator play minor roles. 06/30/08 Johan Frenje http://ilp-www.mit.edu/display_paper.a4d?paperId=83230 A neutron spectrometer, called a Magnetic Recoil Spectrometer (MRS), has been built and implemented at the OMEGA laser facility [T. R. Boehly. D. L. Brown, R. S. Craxton et al., Opt. Commun. 133, 495 (1997)] for absolute measurements of the neutron spectrum in the range 6 to 30 MeV, from which fuel areal density (ÉœR), ion temperature (Ti) and yield (Yn) can be determined. The results from the first MRS measurements of the absolute neutron spectrum are presented. In addition, measuring ÉœR at the National Ignition Facility (NIF) [G.H. Miller, E.I. Moses and C.R. Wuest, Nucl. Fusion 44, S228 (2004)] will be essential for assessing implosion performance during all stages of development from surrogate implosions to cryogenic fizzles to ignited implosions. To accomplish this, we are also developing an MRS for the NIF. As much of the R&D and instrument optimization of the MRS at OMEGA is directly applicable to the MRS at the NIF, a description of the MRS design and characterization on the NIF is discussed as well. 06/30/08 Johan Frenje http://ilp-www.mit.edu/display_paper.a4d?paperId=83229 A fusion product source, utilizing a 150 kV Cockraft-Walton linear accelerator, has been refurbished to provide a reliable nuclear diagnostic development tool to the national Inertial Confinement Fusion (ICF) research program. The accelerator is capable of routinely generating DD reaction rates at ~107 per second when using a 150 kV, 150 £gA deuterium (D) beam onto an erbium (Er) or titanium (Ti) target doped with D, and D3He reaction rates at ~5°—105 per second when using a using a 120 kV, ~100 £gA D beam onto a Er or Ti target doped with 3He. The new accelerator is currently being used in a number of projects related to the national ICF program at the OMEGA Laser Fusion Facility, which includes the Wedge Range Filter charged-particle spectrometry program and the Magnetic Recoil neutron Spectrometer. 06/30/08 C K Li http://ilp-www.mit.edu/display_paper.a4d?paperId=83227 We report the results of operation of Alcator C-Mod with all high-Z molybdenum Plasma Facing Component (PFC) surfaces. Without boron-coated PFCs energy confinement was poor (HJTER,89 1) due to high core molybdenum (nMo/neSO. 1%) and radiation. After applying boron coatings, nMJn was reduced by a factor of 10-20 with H1TERJ9 approaching 2. Results of between-discharge boronization, localized at various major radii, point towards important molybdenum source regions being small, outside the divertor, and due to RF- sheath-rectification. Boronization also has a significant effect on the plasma startup phase lowering Zcff, radiation, and lowering the runaway electron damage. The requirement of low- Z coatings over at least a fraction of the Mo PFCs in C-Mod for best performance together with the larger than expected D retention in Mo, give impetus for further high-Z PFC investigations to better predict the performance of uncoated tungsten surfaces in ITER and beyond. 06/30/08 Bruce Lipschultz http://ilp-www.mit.edu/display_paper.a4d?paperId=83226 A malleable coding scheme considers not only compression efficiency but also the ease of alteration, thus encouraging some form of recycling of an old compressed version in the formation of a new one. Malleability cost is the difficulty of synchronizing compressed versions, and malleable codes are of particular interest when representing information and modifying the representation are both expensive. We examine the trade-off between compression efficiency and malleability cost under a malleability metric defined with respect to a string edit distance. This problem introduces a metric topology to the compressed domain. We characterize the achievable rates and malleability as the solution of a subgraph isomorphism problem. This can be used to argue that allowing conditional entropy of the edited message given the original message to grow linearly with block length creates an exponential increase in code length. 06/30/08 Vivek Goyal http://ilp-www.mit.edu/display_paper.a4d?paperId=83225 We have recently described the use of chiral nickel complexes to achieve catalytic asymmetric cross-couplings of organozinc,1,2 -silicon,3 and -boron4 reagents with racemic secondary alkyl electrophiles, specifically, £\-halocarbonyl compounds and allylic, benzylic, and homobenzylic halides.5 In order to fully exploit the tremendous potential of enantioselective cross-couplings, it is necessary to expand the scope to other families of reaction partners. With respect to electrophiles, propargylic halides are attractive substrates, since an alkyne is an extremely versatile functional group.6 In this report, we establish that, in the presence of a chiral Ni/pybox complex, a wide array of racemic propargylic bromides can be cross-coupled with arylzinc reagents in a stereoconvergent process (eq 1). 06/30/08 Sean Smith http://ilp-www.mit.edu/display_paper.a4d?paperId=83224 Block copolymers can self-assemble to generate patterns with nanoscale periodicity, which may be useful in lithographic applications. Block copolymers in which one block is organic and the other contains Si are appealing for self-assembled lithography because of the high etch contrast between the blocks, the high etch-resistance of the Si-containing block, and the high Flory- Huggins interaction parameter, which is expected to minimise line edge roughness. The locations and long-range order of the microdomains can be controlled using shallow topographical features. Pattern generation from polystyrene-polyferrocenyldimethylsilane and polystyrenepolydimethylsiloxane block copolymers, and the subsequent pattern transfer into metal, oxide and polymer films, is described. 06/30/08 Caroline Ross http://ilp-www.mit.edu/display_paper.a4d?paperId=83219 This paper documents a forward looking multi-regional general equilibrium model developed from the latest version of the recursive-dynamic MIT Emissions Prediction and Policy Analysis (EPPA) model. The model represents full inter-temporal optimization (perfect foresight), which makes it possible to better address economic and policy issues such as borrowing and banking of GHG allowances, efficiency implications of environmental tax recycling, endogenous depletion of fossil resources, international capital flows, and optimal emissions abatement paths among others. It was designed with the flexibility to represent different aggregations of countries and regions, different horizon lengths, as well as the ability to accommodate different assumptions about the economy, in terms of economic growth, foreign trade closure, labor leisure choice, taxes on primary factors, vintaging of capital and data calibration. The forward-looking dynamic model provides a complementary tool for policy analyses, to assess the robustness of results from the recursive EPPA model, and to illustrate important differences in results that are driven by the perfect foresight behavior. We present some applications of the model that include the reference case and its comparison with the recursive EPPA version, as well as some greenhouse gas mitigation cases where we explore economic impacts with and without inter-temporal trade of permits. 06/26/08 Mustafa Babiker http://ilp-www.mit.edu/display_paper.a4d?paperId=83218 We describe in this report an effort using the MJT/NCAR three-dimensional aerosol-climate model to study the impact of ship emissions on chemical composition and radiative forcing of aerosols. Our results indicate that international shipping can be a non-negligible factor in determining the radiative forcing of aerosols over specific regions with intensive ship activities. These places include the European, eastern Asian, and American coastal regions. The global mean aerosol radiative forcing caused by the ship emissions ranges from -12.5 to -23 mW/m2, depending on whether the mixing between black carbon and sulfate is included in the model. However, over the aforementioned places, the radiative forcing resulting from ship emissions can be much more important in the total regional aerosol forcing. 06/26/08 Chien Wang http://ilp-www.mit.edu/display_paper.a4d?paperId=83217 We present revised probability density functions for climate model parameters (effective climate sensitivity, the rate of deep-ocean heat uptake, and the strength of the net aerosol forcing) that are based on climate change observations from the 20th century First, we compare observed changes in surface, upper-air, and deep-ocean temperature changes against simulations of 20th century climate in which the climate model parameters were systematically varied. The estimated 90% range of climate sensitivity is 2. to 5. K. The net aerosol forcing strength for the 1980s has 90% bounds of -0.70 to -0.27 W/m2. The rate of deep-ocean heat uptake corresponds to an effective diffusivity, Ku, with a 90% range of 0.04 to 4.1 cm2/s. Second, we estimate the effective climate sensitivity and rate of deep-ocean heat uptake for 11 of the IPCC AR4 AOGCMs. By comparing against the acceptable combinations inferred by the observations, we conclude that the rate of deep-ocean heat uptake for the majority of AOGCMs lie above the observationally based median value. This implies a bias in the pre- dictions inferred from the IPCC models alone. This bias can be seen in the range of transient climate response from the AOGCMs as compared to that from the observational constraints. 06/26/08 Chris Forest http://ilp-www.mit.edu/display_paper.a4d?paperId=83216 The US. Congress is considering a set of bills designed to limit the nation's greenhouse gas (GHG) emissions. Several of these proposals call for a cap-and-trade system; others propose an emissions tax. This paper complements the analysis by Paltsev et al. (2007) of cap-and-trade bills and applies the MIT Emissions Prediction and Policy Analysis ('EPP4) model to carry out an analysis of the tax proposals. Several lessons emerge from this analysis. First, a low starting tax rate combined with a low rate of growth in the tax rate will not reduce emissions significantly. Second, the costs of GHG reductions are reduced with the inclusion of non-CO2 gases in the carbon tax scheme. The costs of the Larson plan, for example, fall by 20% with inclusion of the other GHGs. Third, welfare costs of the policies can be affected by the rate of growth of the tax, even after controlling for cumulative emissions. Fourth, a carbon tax - like any form of carbon pricing - is regressive. However, general equilibrium considerations suggest that the short-run measured regressivity may be overstated. A portion of the carbon tax is passed back to workers, owners of equity, and resource owners. To the extent that relatively wealthy resource and equity owners bear some fraction of the tax burden, the regressivity will be reduced. Additionally, the regressivity can be offset with a carefully designed rebate of some or all of the revenue. Finally, the carbon tax bills that have been proposed or submitted are for the most part comparable to many of the carbon cap-and-trade proposals that have been suggested. Thus the choice between a carbon tax and cap-and-trade system can be made on the basis of considerations other than their effectiveness at reducing emissions over some control period. Either approach (or some hybrid of the two approaches) can be equally effective at reducing GHG emissions in the United States. 06/26/08 Gilbert Metcalf http://ilp-www.mit.edu/display_paper.a4d?paperId=83215 Following our previous work (Ring and Plumb, 2007) where we found the annular modes to be a preferred response of a simplified general circulation model atmosphere to a number of mechanical forcings, we explore the quantitative relationship between forcing and response. In particular, we investigate the applicability of the fluctuation-dissipation theorem (Leith, 1975) to this problem. We first expand our set of model trials by including runs where the applied forcings are thermal rather than mechanical. For thermal forcings confined to the extratropics, we find annular mode-like responses reminiscent of those in our earlier paper. As in our earlier paper and in other studies (e.g. Son and Lee, 2006), the response is less annular mode-like when the forcing has significant amplitude in the tropics. Assuming small departures from the control climatology, and making a few further assumptions, we derive a theoretical relationship between forcing and response. This relationship is a statement of the fluctuation-dissipation theorem for this problem. We find the response of the model is qualitatively consistent with the theoretical predictions. However, several aspects of the response diverge quantitatively from the theoretical expectation. 06/26/08 Raymond Plumb http://ilp-www.mit.edu/display_paper.a4d?paperId=83214 We document a new stylized fact regarding the term-structure of futures volatility. We show that the relationship between the volatility of futures prices and the slope of the term structure of prices is non-monotone and has a "V-shape". This aspect of the data cannot be generated by basic models that emphasize storage while this fact is consistent with models that emphasize investment constraints or, more generally, time-varying supply-elasticity. We develop an equilibrium model in which futures prices are determined endogenously in a production economy in which investment is both irreversible and is capacity constrained. Investment constraints affect firms' investment decisions, which in turn determine the dynamic properties of their output and consequently imply that the supply-elasticity of the commodity changes over time. Since demand shocks must be absorbed either by changes in prices, or by changes in supply, time-varying supply-elasticity results in time-varying volatility of futures prices. Estimating this model, we show it is quantitatively consistent with the aforementioned "V-shape" relationship between the volatility of futures prices and the slope of the term-structure. 06/26/08 Leonid Kogan http://ilp-www.mit.edu/display_paper.a4d?paperId=83212 Our laboratory is investigating the in vitro and in vivo metabolic processing of endogenously formed DNA adducts as a means of evaluating candidate urinary biomarkers. In particular, we have focused our studies on the metabolism and disposition of the peroxidalion-derived pyrimidopurinone deoxyguanosine (dG) adduct. 3-(2-deoxy-fi-D-erylhro-pentofuranosyl)pyrimido[ I ,2-aJpurin- I 0(3H)-one (M dG). and its principal metabolite, 6-oxo-M1dG. We now report the metabolic processing of M,dG at concentrations 4-8 orders of magnitude lower in concentration than previously analyzed, by the use of accelerator mass spectrometry analysis. Administration of 2.0 nCi/kg j'4C]M,dG resulted in 49% of the '4C recovered in urine, whereas 51% was recovered in feces. In urine samples, approximately 40% of the '4C corresponded to the metabolite, 6-oxo-M dG. Following iv administration of 0.5 and 54 pCi/kg I '4C IM 1d6, approximately 25% of the urinary recovery corresponded to the metabolite, 6-oxo-M1dG. Thus, upon administration of trace amounts of MIX, a significant percentage of 6-oxo-M1dG was produced, suggesting that 6-oxo-M ,dG maybe a useful urinary marker of exposure to endogenous oxidative damage. 06/26/08 Paul Skipper http://ilp-www.mit.edu/display_paper.a4d?paperId=83211 We present Chandra X-ray Observatory ACIS-S3 X-ray imaging observations and VLTIFORS2 and Hobble Space Telescope optical observations of two low-density Galactic globular clusters; NGC 6366 and M55. We detect 16 X-ray sources with O.$-6.OkeV lumi- nosities above Lx = 4 x 1031 erg s within the half-mass radius of M55, of which 8 or 9 are expected to be background sources, and 5 within the half-mass radius of NGC 6366, of which 4 are expected to be background sources. Optical counterparts are identified for several X-ray sources in both clusters and from these we conclude that 3 of the X-ray sources in M55 and 2 or 3 of the X-ray sources in NGC 6366 are probably related to the cluster. Combining these results with those for other clusters, we find the best fit for a predicted number of X-ray sources in a globular cluster Pc = 1.21' + I - l M, where 1' is the collision number and Mb is (half of) the cluster mass, both normalized to the values for the globular cluster M4. Some sources tentatively classified as magnetically active binaries are more luminous in X-rays than the upper limit of Lx = 0.001 Lt., of such binaries in the solar neighbourhood. Comparison with XMM and ROSAT observations lead us to conclude that the brightest X-ray source in M55, a dwarf nova, becomes fainter in X-rays during the optical outburst, in accordance with other dwarf novae. The brightest X-ray source in NGC 6366 is a point source surrounded by a slightly offset extended source. The absence of galaxies and Hat emission in our optical observations argues against a cluster of galaxies and against a planetary nebula, and we suggest that the source may be an old nova. 06/26/08 David Pooley http://ilp-www.mit.edu/display_paper.a4d?paperId=83210 The metalloneurochemistry of Zn(II) is of substantial current interest. Zinc is the second most abundant d-block metal ion in the human brain and its distribution varies with relatively high concentrations found in the hippocampus. Brain zinc is generally divided into two types, protein-bound and loosely bound, the latter also being termed histochemically observable, chelatable, labile, or mobile zinc. The neurophysiological and neuropathological significance of mobile Zn(lJ) remains enigmatic. Studies of mobile Zn(II) distribution, translocation, and function in vivo require tools for its detection. Because Zn(II) has a closed-shell d'° configuration and no convenient spectroscopic signature, fluorescence is a well-suited method for monitoring Zn(II) in biological contexts. This Account summarizes and unifies work by our laboratory addressing the design, preparation, characterization, and use of small-molecule fluorescent sensors for imaging Zn(II) in living cells and samples of brain tissue. These sensors provide "turn- on" or ratiometric Zn(II) detection in aqueous solution at neutral pH. By making alterations to the Zn(H)-binding unit and fluorophore platform, we have devised sensors with varied photophysical and metal-binding properties. Several of these probes have been applied to image Zn(II) distribution, uptake and mobilization in a variety of cell types, including neuronal cultures. 06/25/08 Elizabeth Nolan http://ilp-www.mit.edu/display_paper.a4d?paperId=83209 Nitric oxide is an important molecule in biology and modulates a variety of physiological and pathophysiological processes. Some of its regulatory functions are exerted through interactions with redox active elements, including iron, nickel, cobalt and sulfur. Metalloenzymes containing [nFe-nS] (n = 2 or 4) clusters can be activated or inactivated by reaction with NO, affording dinitrosyl iron complexes. Studies of the NO chemistry of small molecule iron thiolate complexes have provided insight into these biological processes and suggested probable intermediates. To explore this chemistry from a different perspective, we prepared nickel and cobalt thiolate complexes and investigated their reactions with NO and related compounds. We report here the first examples of anionic complexes containing {Ni(NO)}'° and {Co(NO)2}1° units, the reactivity of which suggests possible intermediates in the interconversion of iron thiolate nitrosyl compounds. Our results demonstrate new chemistry involving NO and simple complexes of nickel and cobalt supported by thiolates, which have been known for more than 30 years. The use of mass balance methodology was key to their discovery. Among the novel complexes reported are (Et4N)2[Ni(NO)(SPh)3] (2), from (Et4N)2[Ni(SPh)4J (1) and NO, (Et4N)2[Ni2(NO)2Qx-SPh)2(SPh)2], from 1 and NO or 2 and Me3O, (Et4N)[Co(NO)2(SPh)2] (5), from (Et4N)2[Co(SPh)4] (4) and NO, and [Co3(NO)6(ji-SPh)3] (6), from 5 and Me3O. In the syntheses of 2 and 5, NO could be replaced by the convenient solid Ph3CSNO. 06/25/08 Stephen Lippard http://ilp-www.mit.edu/display_paper.a4d?paperId=83208 We calculate the thermal Euclidean correlators and the spectral functions of the energymomentum tensor for pure gauge theories, including at non-zero spatial momentum, at leading order in perturbation theory. Our goal is to improve the extraction of transport properties from Euclidean correlators that are computable in lattice QCD. Based on our results and the predictions of hydrodynamics for the structure of the spectral functions at low frequencies, we show that the shear and bulk viscosities can advantageously be extracted from the Euclidean correlators of the conserved charges, energy and momentum, at small but non-vanishing spatial momentum. The spectral functions in these channels are free of the ultraviolet É÷4 term which represents a large background to the thermal physics encoded in the correlators of the fluxes. 06/25/08 Edward Farhi http://ilp-www.mit.edu/display_paper.a4d?paperId=83207 As a good multi-tasking modern, I finished reading this cornucopian volume while watching the Bob Dylan film I’m Not There. I was struck by their parallels and the clarity of the haze surrounding both. The topics are enigmatic and rich in contradiction and paradox, resisting efforts at didactic, fixed and linear interpretation. At the same time there are abundant re-occurring social patterns and processes. Therein lays (and at time lies as well) their appeal and challenge. 06/24/08 Gary Marx http://ilp-www.mit.edu/display_paper.a4d?paperId=83205 Analysis of the jaws of the Humboldt squid (Dosidicus gigas) and Nautilus belauensis using mass spectrometric techniques revealed a chitin-protein composition, confirmed by analysis of chitin and amino acid model compounds. Analysis of comparable fossil material from several cephalopod taxa (Placenticeras, Nanaimoteuthis jeletzkyi, Anagaudryceras limatum, and Hoploscaphites) from Upper Cretaceous (Campanian and Maastrichtian) localities from North America and Japan detected nocompounds from the chitin-protein biopolymer complex but showed the presence of aromatic compounds, including alkyl benzene derivatives, alkyl phenols, naphthalenes, and phenanthrene. An n-alkyl component, ranging in carbon chain length up to C24,was also detected. There was no evidence of the presence of these compounds in the host sediment. Cleavage of ester bonds in the fossil macromolecules (including fossils with both predominantly aromatic and aliphatic compounds) using thermally assisted methylation (THM) revealed a carboxylic acid distribution from C6 to C18. Additionally, methyl ketones were detected in the fossils, in which the n-alkyl (aliphatic) component was significant. Methyl ketones (alkan-2-ones) have been reported in fossil algae and kerogen and are indicative of ether functional groups in macromolecules, which are probably crosslinked via oxidative reticulation. Thus, the aliphatic component is likely derived from in situ incorporation and polymerisation of labile lipid precursors, in part crosslinked via ether and ester bonds. This is the first demonstration of ether linkages and of oxidative crosslinking in animal fossils, suggesting that such a process may be important in the long term preservation of both animal and plant derived organic matter. 06/24/08 Roger Summons http://ilp-www.mit.edu/display_paper.a4d?paperId=83204 Chemical analysis of leaves of modern Metasequoia revealed the presence of the structural polyester cutin, guaiacyl lignin units and polysaccharides but non hydrolysable aliphatic constituents (cutan) were absent. Analysis of environmentally decayed Metasequoia leaves revealed that guaiacyl lignin units and cellulose were degraded relative to the cutin, suggesting that cutin is more stable than lignin and cellulose during decay. This is paralleled by changes in the cellular structure of the modern, decayed and fossil Metasequoia leaves. To investigate the contribution of cutin to the preservation of plant fossils and to sedimentary organic matter, modern pine needle was heated experimentally in confined conditions. This generated a composition with a long chain aliphatic polymer up to C30 and additional phenolic compounds similar to those present in the fossils. However, earlier experimental maturation of cutin demonstrated that it generates an aliphatic polymer < C20; the n-alkyl component > C20 generated in pine needle may be a diagenetic product of longer chain plant waxes. Analysis of Tertiary fossil Metasequoia and Pinus from the Eocene of Republic (Washington State) showed a significant aliphatic component up to C23 with ester linkages in the macromolecule; biopolymeric lignin and polysaccharides were absent. The resistant nature of cutin compared to lignin and polysaccharides explains the ubiquitous presence of n-alkyl component (<C20) in fossil leaves even when lignin is absent and polysaccharides have decayed; cutin may also contribute to the presence of aliphatic components in sedimentary organic matter. 06/24/08 Roger Summons http://ilp-www.mit.edu/display_paper.a4d?paperId=83203 We evaluated the structure of planktonic communities and paleoenvironmental conditions throughout the Cenomanian-Turonian Oceanic Anoxic Event (OAE2) by studying bulk geochemical properties and the molecular-isotopic composition of sourcespecific hydrocarbons from organic-rich sediments deposited in an intra-shelf basin at the Levant Platform, Central Jordan. High concentrations of desmethyl and 4-methyl steranes as well as dinosteranes indicate that marine algae including dinoflagellates were the main primary producing organisms. The presence of 2-methyl hopanes and low delta-15N values, in addition to isotopically enriched aryl isoprenoids, evidenced the contribution of N-fixing cyanobacteria and green-sulfur bacteria, respectively. Changes in the relative contribution of biomarkers revealed successions in planktonic communities associated with sea level changes and water column stratification. The OAE2 interval was characterized by a strong stratification of the water column, anoxic bottom waters, and a deep chemocline, as evidenced by high gammacerane and homohopane indices, and the absence of photic zone euxinia markers, respectively. However, the presence of isorenieratane and its derivatives in post-OAE black shales point to a shoaling of the chemocline and protracted euxinic conditions that extended into the photic zone. These sediments were also characterized by an exceptionally high abundance of chlorophyll-derived pristane and phytane (up to 2 mg g-1 TOC) likely as a result of high primary production and organic matter preservation. Our results provide further evidence for the importance of cyanobacteria and nitrogen fixation fueling primary production during the deposition of black shales, not only in open ocean settings but also in stratified/anoxic continental platforms during OAE2. 06/24/08 Roger Summons http://ilp-www.mit.edu/display_paper.a4d?paperId=83202 Understanding the nature and origin of the asteroid population in Earth’s vicinity (near-Earth asteroids, and its subset of potentially hazardous asteroids) is a matter of both scientific interest and practical importance1. It is generally expected that the compositions of the asteroids that are most likely to hit Earth should reflect those of the most common meteorites. Here we report that most near-Earth asteroids (including the potentially hazardous subset) have spectral properties quantitatively similar to the class of meteorites known as LL chondrites. The prominent Flora family in the inner part of the asteroid belt shares the same spectral properties, suggesting that it is a dominant source of near-Earth asteroids. The observed similarity of near-Earth asteroids to LL chondrites is, however, surprising, as this meteorite class is relatively rare ( 8 per cent of all meteorite falls). One possible explanation is the role of a size dependent process, such as the Yarkovsky effect, in transporting material from the main belt. 06/24/08 Richard Binzel http://ilp-www.mit.edu/display_paper.a4d?paperId=83201 Observations of the predicted occultation between the satellites Miranda and Oberon were performed on 2007 July 30. Data analysis reveals that the predicted magnitude drop for this phenomenon was overestimated and we establish an upper limit of 0.m 05 for the phenomenon, perhaps due to a non-lambertian limb scattering. The new astrometry obtained from this run is in good agreement with the LA06 numerical model and these new data will improve the dynamical models of the Uranus system. The paper concludes with an uncertainty analysis on the parameters for the event, determined by the uncertainty of the magnitude drop of about 0.04 mag, and the difficulty to observe mutual phenomena between satellites in the Uranian system. 06/24/08 Richard Binzel http://ilp-www.mit.edu/display_paper.a4d?paperId=83200 This paper presents the results of an experimental study on nucleate pool boiling. Experiments were performed using vapor-deposited thin films which were electrically heated. High-speed infrared and visible cameras simultaneously observed bubble growth from the heater surface. Possible experimental confirmation of microlayer dynamics is presented. 06/23/08 Jacopo Buongiorno http://ilp-www.mit.edu/display_paper.a4d?paperId=83199 The objective of this research is to systematically investigate the boiling heat transfer characteristics of nanofluids during quenching experiments with a hot sphere. The experiments are carried out with a small (9.5 mm) stainless steel sphere with initial temperatures near 1000 °C. Alumina nanofluids and deionized water are tested at low volume concentrations (less than 0.1 % by volume) and saturated conditions (100 °C). The results show that the quenching behavior in nanofluids is nearly identical to that in pure water. Moreover it is found that some nanoparticles accumulate on the sphere surface during the quenching process. Such accumulation of nanoparticles on the surface promotes the destabilization of the vapor film in subsequent quenching experiments, thus accelerating the return to nucleate boiling at higher temperature than that in the clean surface case. 06/23/08 Jacopo Buongiorno http://ilp-www.mit.edu/display_paper.a4d?paperId=83198 We have developed a new unnatural amino acid based on the solvatochromic fluorophore 4-N,N-dimethylamino-1,8-naphthalimide (4-DMN) for application in the study of protein-protein interactions. The fluorescence quantum yield of this chromophore is highly sensitive to changes in the local solvent environment, demonstrating “switch-like” emission properties characteristic of the dimethylaminophthalimide family of fluorophores. In particular, this new species possesses a number of significant advantages over related fluorophores including greater chemical stability under a wide range of conditions, a longer wavelength of excitation (408 nm), and improved synthetic accessibility. This amino acid has been prepared as an Fmoc-protected building block and may readily be incorporated into peptides via standard solid-phase peptide synthesis (SPPS). A series of comparative studies are presented to demonstrate the advantageous properties of the 4-DMN amino acid relative to that of the previously reported 4-N,N-dimethylaminophthalimidoalanine (4-DAPA) and 6-N,N-dimethylamino-2,3-naphthalimidoalanine (6-DMNA) amino acids. Other commercially available solvatochromic fluorophores are also include in these studies. The potential of this new probe as a tool for the study of protein-protein interactions is demonstrated by introducing it into a peptide that is recognized by calcium-activated calmodulin. The binding interaction between these two components yields an increase in fluorescence emission greater than 900-fold. 06/23/08 Barbara Imperiali http://ilp-www.mit.edu/display_paper.a4d?paperId=83197 Catalyzed by kinases, serine/threonine and tyrosine phosphorylation is a vital mechanism of intracellular regulation. Thus, assays that easily monitor kinase activity are critical in both academic and pharmaceutical settings. We previously developed sulfonamido-oxine (Sox)-based fluorescent peptides following a £]-turn focused (BTF) design for the continuous assay of kinase activity in vitro and in cell lysates. Upon phosphorylation of the Sox-containing peptide, the chromophore binds Mg2+ and undergoes chelation-enhanced fluorescence (CHEF). While the design was applied successfully to the development of several kinase sensors, an intrinsic limitation was that only residues C- or N-terminal to the phosphorylated residue could be used to derive specificity for the target kinase. To address this limitation, a new, recognition-domain focused (RDF) strategy has been developed that also relies on CHEF. In this approach, the requirement for the constrained £]-turn motif is obviated by alkylation of a cysteine residue with a Sox-based derivative to afford an amino acid termed C-Sox. The RDF design allows inclusion of extended binding determinants to maximize recognition by the cognate kinase, which has now permitted the construction of chemosensors for a variety of representative Ser/Thr, as well as receptor (IRK) and non-receptor (Src, Abl) Tyr kinases with greatly enhanced selectivity. The new sensors have up to 28-fold improved catalytic efficiency and up to 66-fold lower KM when compared to the corresponding BTF probes. The improved generality of the strategy is exemplified with the synthesis and analysis of Sox-based probes, which were previously unattainable using the BTF approach. 06/20/08 Barbara Imperiali http://ilp-www.mit.edu/display_paper.a4d?paperId=83196 We report on the fabrication of 200 nm-period blazed transmission gratings on silicon-on- insulator (SOI) wafers. These critical angle transmission (CAT) gratings require 3-5 1m tall free-standing grating bars with a very high aspect ratio (>100) and smooth sidewalls. In or- der to meet the challenging geometrical requirements, we modi¯ed and improved our previously reported process for the fabrication of a CAT grating prototype with 574 nm period. We have used potassium hydroxide (KOH) solutions to fabricate high aspect ratio gratings on h110i SOI wafers. The KOH etching process was improved to minimize the lateral undercut through precise grating alignment to h111i planes within §0.05± and a room temperature etch process with 50 wt% KOH. In addition, an image reversal technique with a high silicon content spin-on polymer was applied to increase process latitude with a high duty cycle nitride mask. A surfactant was also added to the KOH solution to promote hydrogen bubble release. With the improved process, we achieved a high etch anisotropy of above 300 on a h110i silicon wafer. We successfully fabricated 200 nm-period CAT gratings with support mesh periods of 25 and 40 1m in a 9 mm2 area of 4 1m-thick silicon membranes on h110i SOI wafers. 06/20/08 Ralf Heilmann http://ilp-www.mit.edu/display_paper.a4d?paperId=83195 Amyloid and prion proteins are clinically and biologically important !-structures, whose supersecondary structures are difficult to determine by standard experimental or computational means. In addition, significant conformational heterogeneity is known or suspected to exist in many prion fibrils. Recent work has indicated the utility of pairwise probabilistic statistics in !-structure prediction. We develop here a new strategy for !- structure prediction, emphasizing the determination of !-strands and pairs of !-strands as fundamental units of !-structure. Our program, BETASCAN, calculates likelihood scores for potential !-strands and strand-pairs based on correlations observed in parallel !- sheets. The program then determines the strands and pairs with the greatest local likelihood for all of the sequence’s potential !-structures. BETASCAN suggests multiple alternate folding patterns and assigns relative a priori probabilities based solely on amino acid sequence, probability tables, and pre-chosen parameters. The algorithm improves upon the results of previous algorithms (BETAPRO, PASTA, and SALSA) in !-structure prediction and amyloid propensity prediction. Accurate prediction is demonstrated for both experimentally determined amyloid !-structures and the parallel !-strands of !- helices, amyloid-like globular proteins. BETASCAN is able to both detect !-strands with higher sensitivity and to detect the edges of !-strands in a richly !-like sequence. In two cases (A! and Het-s), differing experimental results are predicted as potential alternate folds. The ability to correlate multiple alternate !-structures to experiment opens the possibility of computational investigation of prion strains and amyloid structural heterogeneity. 06/19/08 Lenore Cowen http://ilp-www.mit.edu/display_paper.a4d?paperId=83194 Prion diseases are fatal, transmissible neurodegenerative diseases caused by the misfolding of the prion protein (PrP). At present, the molecular pathways underlying prion-mediated neurotoxicity are almost completely unknown. We hypothesized that the transcriptional regulator of the stress response, heat shock factor 1 (HSF1), would play an important role in prion disease. The HSF1 knockout (KO) mice used in our study do not show signs of neurodegeneration as assessed by survival, motor performance, or pathology. When inoculated with RML prions HSF1 KO mice showed a dramatically shortened lifespan, succumbing to disease approximately 20% faster than controls. Surprisingly, both the onset of home cage behavioral symptoms and the pathological alterations occurred at a similar time in HSF1 KOs and controls. The accumulation of proteinase K-resistant PrP also occurred with similar kinetics in the HSF1 KOs and prion infectivity accrued at an equal or slower rate. Thus, HSF1 provides a critically important protective function during the clinical phase of prion disease. 06/19/08 Susan Lindquist http://ilp-www.mit.edu/display_paper.a4d?paperId=83193 The “misfolding” and assembly of proteins into £]-sheet rich, amyloid fibers is important in both disease1 and normal biological function. Although many proteins form amyloid fibers in vitro, understanding the biological relevance and consequence of this process in vivo is difficult. Given that we can genetically manipulate the yeast S. cerevisiae better than any other organism, analysis of protein misfolding in yeast is especially attractive. Prions are one class of naturally occurring, amyloid-forming proteins in yeast that have received much attention. The first prion protein, PrP, was initially identified in mammals and conversion to its beta-sheet rich, aggregated conformation is associated with several related infectious, neurodegenerative diseases known collectively as the spongiform encephalopathies. More recently, several prions have been identified in yeast and other fungi that are unrelated to their mammalian counterpart in terms of primary sequence and can be beneficial biologically. Although fungal and mammalian prions are unrelated in terms of sequence, they display many functional similarities. Most importantly, both prions perform functions previously reserved for nucleic acids. In the case of PrP the protein functions as an infectious agent that causes neurodegenerative disease. In the case of yeast the prion reveals hidden genetic variation and encodes complex heritable phenotypes. At the molecular level, both types of prions form not just one prion conformation, but a collection of structurally related yet distinct conformations (known as prion strains). Moreover, both fungal and mammalian prions display barriers to prion transmission between different species.18-29 Further, particular prion strains can overcome species barriers for both types of prions. To decipher the complexities of these problems in vivo, it is necessary to analyze the biochemical properties of these proteins in vitro. Unfortunately, it has been difficult to form highly infectious mammalian prion conformers in vitro from recombinant protein. In contrast, bona fide highly infectious prion conformers can be readily formed in vitro for fungal prions. This has prompted many biochemical studies of these prions using diverse probes of prion assembly and prion amyloid structure, leading to many important findings and some controversy. Herein, we review the recent biochemical analysis of fungal prions and highlight potential future areas of investigation. 06/19/08 Susan Lindquist