Slow-light and evanescent modes at interfaces in photonic crystal waveguides: optimal extraction from experimental near-field measurements

We develop a systematic approach for simultaneous extraction of the dispersion relations and profiles of multiple modes in periodic waveguides though a special global optimization procedure applied to near-field electric field measurements in the waveguide plane. We apply this method to perform in-depth analysis of experimental data on wave propagation close to an interface between waveguide sections with different dispersion characteristics, and we successfully identify several modes contributing to the experimentally measured fields. We find clear evidence that when the group velocity is reduced across the interface, evanescent modes that facilitate the excitation of propagating slow-light waves appear, confirming previous theoretical predictions. (C) 2011 Optical Society of AmericaPublisher PDFPeer reviewe

Sequence-based design of a peptide probe for the APC tumor suppressor protein

AbstractBackground: Proteins form specific associations, but predictive rules for protein pairing are generally unknown. Here, we describe amino-acid sequence patterns capable of mediating specific pairing of a widespread protein motif: the parallel, dimeric, α-helical coiled coil. The pairing rules were tested by designing a 54-residue peptide (anti-APCp1) that is predicted to dimerize preferentially with a coiled-coil sequence from the adenomatous polyposis coli (APC) tumor suppressor protein.Results: As judged by circular dichroism, ultracentrifugation and native gel electrophoresis, anti-APCp1 formed a specific, helical, dimeric complex with the target APC coiled coil. On western blots of APC fragments expressed in Escherichia coli, the designed peptide detected a pattern of bands identical to the pattern detected by an antibody directed against the APC coiled coil. Peptide-mediated precipitation experiments showed that anti-APCp1 bound and sequestered wild-type and mutant APC proteins in extracts of human colon cancer cell lines. In addition, binding of the designed peptide preserved native APC–β-catenin complexes.Conclusions: These biochemical experiments demonstrate that the anti-APC peptide preferentially forms a heterodimeric coiled coil with mutant and full-length APC proteins. The specificity of the designed peptide is sufficient to support several applications that commonly use antibodies. The observed specificity of anti-APCp1 validates the pairing rules used as the basis for the probe design, and it suggests that residues in the core positions of coiled coils help impart pairing selectivity

Resolving the Formation of Protogalaxies. III. Feedback from the First Stars

The first stars form in dark matter halos of masses ~10^6 M_sun as suggested by an increasing number of numerical simulations. Radiation feedback from these stars expels most of the gas from their shallow potential well of their surrounding dark matter halos. We use cosmological adaptive mesh refinement simulations that include self-consistent Population III star formation and feedback to examine the properties of assembling early dwarf galaxies. Accurate radiative transport is modeled with adaptive ray tracing. We include supernova explosions and follow the metal enrichment of the intergalactic medium. The calculations focus on the formation of several dwarf galaxies and their progenitors. In these halos, baryon fractions in 10^8 solar mass halos decrease by a factor of 2 with stellar feedback and by a factor of 3 with supernova explosions. We find that radiation feedback and supernova explosions increase gaseous spin parameters up to a factor of 4 and vary with time. Stellar feedback, supernova explosions, and H_2 cooling create a complex, multi-phase interstellar medium whose densities and temperatures can span up to 6 orders of magnitude at a given radius. The pair-instability supernovae of Population III stars alone enrich the halos with virial temperatures of 10^4 K to approximately 10^{-3} of solar metallicity. We find that 40% of the heavy elements resides in the intergalactic medium (IGM) at the end of our calculations. The highest metallicity gas exists in supernova remnants and very dilute regions of the IGM.Comment: 15 pages, 16 figures, accepted to ApJ. Many changes, including estimates of metal line cooling. High resolution images and movies available at http://www.slac.stanford.edu/~jwise/research/PGalaxies3

Resolving the Formation of Protogalaxies. I. Virialization

(Abridged) Galaxies form in hierarchically assembling dark matter halos. With cosmological three dimensional adaptive mesh refinement simulations, we explore in detail the virialization of baryons in the concordance cosmology, including optically thin primordial gas cooling. We focus on early protogalaxies with virial temperatures of 10^4 K and their progenitors. Without cooling, virial heating occurs in shocks close to the virial radius for material falling in from voids. Material in dense filaments penetrates deeper to about half that radius. With cooling the virial shock position shrinks and also the filaments reach scales as small as a third the virial radius. The temperatures in protogalaxies found in adiabatic simulations decrease by a factor of two from the center and show flat entropy cores. In cooling halos the gas reaches virial equilibrium with the dark matter potential through its turbulent velocities. We observe turbulent Mach numbers ranging from one to three in the cooling cases. This turbulence is driven by the large scale merging and interestingly remains supersonic in the centers of these early galaxies even in the absence of any feedback processes. The virial theorem is shown to approximately hold over 3 orders of magnitude in length scale with the turbulent pressure prevailing over the thermal energy. The turbulent velocity distributions are Maxwellian and by far dominate the small rotation velocities associated with the total angular momentum of the galaxies. Decomposing the velocity field using the Cauchy-Stokes theorem, we show that ample amounts of vorticity are present around shocks even at the very centers of these objects.Comment: 13 pages, 6 figures. Submitted to ApJ on 8 March 2007. Revised manuscript. Comments welcom

When cheating is an honest mistake

Dishonesty is an intriguing phenomenon, studied extensively across various disciplines due to its impact on people’s lives as well as society in general. To examine dishonesty in a controlled setting, researchers have developed a number of experimental paradigms. One of the most popular approaches in this regard, is the matrix task, in which participants receive matrices wherein they have to find two numbers that sum to 10 (e.g., 4.81 and 5.19), under time pressure. In a next phase, participants need to report how many matrices they had solved correctly, allowing them the opportunity to cheat by exaggerating their performance in order to get a larger reward. Here, we argue, both on theoretical and empirical grounds, that the matrix task is ill-suited to study dishonest behavior, primarily because it conflates cheating with honest mistakes. We therefore recommend researchers to use different paradigms to examine dishonesty, and treat (previous) findings based on the matrix task with due caution

Should NICE reconsider the 2016 UK guidelines on TB contact tracing? A cost-effectiveness analysis of contact investigations in London.

BACKGROUND: In January 2016, clinical TB guidance in the UK changed to no longer recommend screening contacts of non-pulmonary, non-laryngeal (ETB) index cases. However, no new evidence was cited for this change, and there is evidence that screening these contacts may be worthwhile. The objective of this study was to estimate the cost-effectiveness of screening contacts of adult ETB cases and adult pulmonary or laryngeal TB (PTB) cases in London, UK. METHODS: We carried out a cross-sectional analysis of data collected on TB index cases and contacts in the London TB register and an economic evaluation using a static model describing contact tracing outcomes. Incremental cost-effectiveness ratios (ICERs) were calculated using no screening as the baseline comparator. All adult TB cases (≥15 years old) in London from 2012 to 2015, and their contacts, were eligible (2465/5084 PTB and 2559/6090 ETB index cases were included). RESULTS: Assuming each contact with PTB infects one person/month, the ICER of screening contacts of ETB cases was £78 000/quality-adjusted life-years (QALY) (95% CI 39 000 to 140 000), and screening contacts of PTB cases was £30 000/QALY (95% CI 18 000 to 50 000). The ICER of screening contacts of ETB cases was £30 000/QALY if each contact with PTB infects 3.4 people/month. Limitations of this study include the use of self-reported symptomatic periods and lack of knowledge about onward transmission from PTB contacts. CONCLUSIONS: Screening contacts of ETB cases in London was almost certainly not cost-effective at any conventional willingness-to-pay threshold in England, supporting recent changes to National Institute for Health and Care Excellence national guidelines

Seismicity of the Askja and Bárðarbunga volcanic systems of Iceland, 2009–2015,

A large seismic network deployed in the Icelandic highlands recorded >100,000 earthquakes from 2009 to 2015. We develop a local magnitude scale, appropriate for use in central Iceland, which is similar to the scale used by the Iceland Meteorological Office. Using this large catalogue of earthquakes, we analyze the spatial and temporal changes in seismicity rates and b-values. In microearthquakes recorded from the usually ductile lower crust we find that b-values are high, reflecting the presence of high thermal gradients and low stresses driving seismicity associated with the movement of melt. In contrast, b-values in the upper crust are variable. Low b-values, indicative of a high stress environment, are observed during seismic swarms such as those around Mt. Herðubreið and around Bárðarbunga caldera. A persistently seismically active area around a geothermal area within Askja caldera has a b-value around 1 but has a strong annual cycle of seismicity. We attribute the annual cycle to varying load from the snow cover modulating the seismicity. Seismicity driven by the intrusion of a large dyke has a b-value well above 1, driven by the high pore fluid pressures and thermal gradients around the dyke

Evolution of a lateral dike intrusion revealed by relatively-relocated dike-induced earthquakes: the 2014-15 Bárðarbunga-Holuhraun rifting event, Iceland

Understanding dikes is vital as they serve both as bodies that build the crust and as conduits that feed eruptions, and must be monitored to evaluate volcanic hazard. During the 2014–15 Bárðarbunga rifting event, Iceland, intense seismicity accompanied the intrusion of a ∼50 km lateral dike which culminated in a 6 month long eruption. We here present relocations of earthquakes induced by the lateral dike intrusion, using cross-correlated, sub-sample relative travel times. The ∼100 m spatial resolution achieved reveals the complexity of the dike propagation pathway and dynamics (jerky, segmented), and allows us to address the precise relationship between the dike and seismicity, with direct implications for hazard monitoring. The spatio-temporal characteristics of the induced seismicity can be directly linked in the first instance to propagation of the tip and opening of the dike, and following this – after dike opening – indicate a relationship with magma pressure changes (i.e. dike inflation/deflation), followed by a general ‘post-opening’ decay. Seismicity occurs only at the base of the dike, where dike-imposed stresses – combined with the background tectonic stress (from regional extension over >200 yr since last rifting) – are sufficient to induce failure of pre-existing weaknesses in the crust, while the greatest opening is at shallower depths. Emplacement oblique to the spreading ridge resulted in left-lateral shear motion along the distal dike section (studied here), and a prevalence of left-lateral shear failure. Fault plane strikes are predominately independent of the orientation of lineations delineated by the hypocenters, indicating that they are controlled by the underlying host rock fabric. This high-resolution study provides unprecedented opportunity for comparison with both geodetic and field (frozen dike) observations, and development and consolidation of analytical and analogue models, with implications for rifting processes and real-time monitoring of magma intrusion

Resolving the Formation of Protogalaxies. II. Central Gravitational Collapse

Numerous cosmological hydrodynamic studies have addressed the formation of galaxies. Here we choose to study the first stages of galaxy formation, including non-equilibrium atomic primordial gas cooling, gravity and hydrodynamics. Using initial conditions appropriate for the concordance cosmological model of structure formation, we perform two adaptive mesh refinement simulations of ~10^8 M_sun galaxies at high redshift. The calculations resolve the Jeans length at all times with more than 16 cells and capture over 14 orders of magnitude in length scales. In both cases, the dense, 10^5 solar mass, one parsec central regions are found to contract rapidly and have turbulent Mach numbers up to 4. Despite the ever decreasing Jeans length of the isothermal gas, we only find one site of fragmentation during the collapse. However, rotational secular bar instabilities transport angular momentum outwards in the central parsec as the gas continues to collapse and lead to multiple nested unstable fragments with decreasing masses down to sub-Jupiter mass scales. Although these numerical experiments neglect star formation and feedback, they clearly highlight the physics of turbulence in gravitationally collapsing gas. The angular momentum segregation seen in our calculations plays an important role in theories that form supermassive black holes from gaseous collapse.Comment: Replaced with accepted version. To appear in ApJ v681 (July 1

Simulations of Early Structure Formation: Primordial Gas Clouds

(abridged) We use large cosmological simulations to study the origin of primordial star-forming clouds in a Lambda CDM universe, by following the formation of dark matter halos and the cooling of gas within them. To model the physics of chemically pristine gas, we employ a non-equilibrium treatment of the chemistry of 9 species and include cooling by molecular hydrogen. We explore the hierarchical growth of bound structures forming at redshifts z = 25 - 30 with total masses in the range 10^5 - 10^6 Msun. The complex interplay between the gravitational formation of dark halos and the thermodynamic and chemical evolution of the gas clouds compromises analytic estimates of the critical H2 fraction. Dynamical heating from mass accretion and mergers opposes relatively inefficient cooling by molecular hydrogen, delaying the production of star-forming clouds in rapidly growing halos. We also investigate the impact of photo-dissociating ultra-violet (UV) radiation on the formation of primordial gas clouds. We consider two extreme cases by first including a uniform radiation field in the optically thin limit and secondly by accounting for the maximum effect of gas self-shielding in virialized regions. In both the cases we consider, the overall impact can be described by computing an equilibrium H2 abundance for the radiation flux and defining an effective shielding factor. Based on our numerical results, we develop a semi-analytic model of the formation of the first stars, and demonstrate how it can be coupled with large N-body simulations to predict the star formation rate in the early universe.Comment: Revised version accepted by ApJ. Description of semi-analytic models extende