Perfect Sampling with Unitary Tensor Networks

Tensor network states are powerful variational ans\"atze for many-body ground states of quantum lattice models. The use of Monte Carlo sampling techniques in tensor network approaches significantly reduces the cost of tensor contractions, potentially leading to a substantial increase in computational efficiency. Previous proposals are based on a Markov chain Monte Carlo scheme generated by locally updating configurations and, as such, must deal with equilibration and autocorrelation times, which result in a reduction of efficiency. Here we propose a perfect sampling scheme, with vanishing equilibration and autocorrelation times, for unitary tensor networks -- namely tensor networks based on efficiently contractible, unitary quantum circuits, such as unitary versions of the matrix product state (MPS) and tree tensor network (TTN), and the multi-scale entanglement renormalization ansatz (MERA). Configurations are directly sampled according to their probabilities in the wavefunction, without resorting to a Markov chain process. We also describe a partial sampling scheme that can result in a dramatic (basis-dependent) reduction of sampling error.Comment: 11 pages, 9 figures, renamed partial sampling to incomplete sampling for clarity, extra references, plus a variety of minor change

Characterization of the ZFX family of transcription factors that bind downstream of the start site of CpG island promoters

Our study focuses on a family of ubiquitously expressed human C₂H₂ zinc finger proteins comprised of ZFX, ZFY and ZNF711. Although their protein structure suggests that ZFX, ZFY and ZNF711 are transcriptional regulators, the mechanisms by which they influence transcription have not yet been elucidated. We used CRISPR-mediated deletion to create bi-allelic knockouts of ZFX and/or ZNF711 in female HEK293T cells (which naturally lack ZFY). We found that loss of either ZFX or ZNF711 reduced cell growth and that the double knockout cells have major defects in proliferation. RNA-seq analysis revealed that thousands of genes showed altered expression in the double knockout clones, suggesting that these TFs are critical regulators of the transcriptome. To gain insight into how these TFs regulate transcription, we created mutant ZFX proteins and analyzed them for DNA binding and transactivation capability. We found that zinc fingers 11–13 are necessary and sufficient for DNA binding and, in combination with the N terminal region, constitute a functional transactivator. Our functional analyses of the ZFX family provides important new insights into transcriptional regulation in human cells by members of the large, but under-studied family of C₂H₂ zinc finger proteins

Stratospheric dynamics and midlatitude jets under geoengineering with space mirrors, and sulfate and titania aerosols

Copyright © 2015 The AuthorsThe impact on the dynamics of the stratosphere of three approaches to geoengineering by solar radiation management is investigated using idealized simulations of a global climate model. The approaches are geoengineering with sulfate aerosols, titania aerosols, and reduction in total solar irradiance (representing mirrors placed in space). If it were possible to use stratospheric aerosols to counterbalance the surface warming produced by a quadrupling of atmospheric carbon dioxide concentrations, tropical lower stratospheric radiative heating would drive a thermal wind response which would intensify the stratospheric polar vortices. In the Northern Hemisphere this intensification results in strong dynamical cooling of the polar stratosphere. Northern Hemisphere stratospheric sudden warming events become rare (one and two in 65 years for sulfate and titania, respectively). The intensification of the polar vortices results in a poleward shift of the tropospheric midlatitude jets in winter. The aerosol radiative heating enhances the tropical upwelling in the lower stratosphere, influencing the strength of the Brewer-Dobson circulation. In contrast, solar dimming does not produce heating of the tropical lower stratosphere, and so there is little intensification of the polar vortex and no enhanced tropical upwelling. The dynamical response to titania aerosol is qualitatively similar to the response to sulfate.Natural Environment Research Counci

Verification of European subseasonal wind speed forecasts

Analysis of the forecasts and hindcasts from the ECMWF 32-day forecast model reveals that there is statistically significant skill in predicting weekly mean wind speeds over areas of Europe at lead times of at least 14–20 days. Previous research on wind speed predictability has focused on the short- to medium-range time scales, typically finding that forecasts lose all skill by the later part of the medium-range forecast. To the authors’ knowledge, this research is the first to look beyond the medium-range time scale by taking weekly mean wind speeds, instead of averages at hourly or daily resolution, for the ECMWF monthly forecasting system. It is shown that the operational forecasts have high levels of correlation (~0.6) between the forecasts and observations over the winters of 2008–12 for some areas of Europe. Hindcasts covering 20 winters show a more modest level of correlation but are still skillful. Additional analysis examines the probabilistic skill for the United Kingdom with the application of wind power forecasting in mind. It is also shown that there is forecast “value” for end users (operating in a simple cost/loss ratio decision-making framework). End users that are sensitive to winter wind speed variability over the United Kingdom, Germany, and some other areas of Europe should therefore consider forecasts beyond the medium-range time scale as it is clear there is useful information contained within the forecast

Stratospheric dynamics and midlatitude jets under geoengineering with space mirrors and sulfate and titania aerosols

The impact on the dynamics of the stratosphere of three approaches to geoengineering by solar radiation management is investigated using idealized simulations of a global climate model. The approaches are geoengineering with sulfate aerosols, titania aerosols, and reduction in total solar irradiance (representing mirrors placed in space). If it were possible to use stratospheric aerosols to counterbalance the surface warming produced by a quadrupling of atmospheric carbon dioxide concentrations, tropical lower stratospheric radiative heating would drive a thermal wind response which would intensify the stratospheric polar vortices. In the Northern Hemisphere this intensification results in strong dynamical cooling of the polar stratosphere. Northern Hemisphere stratospheric sudden warming events become rare (one and two in 65 years for sulfate and titania, respectively). The intensification of the polar vortices results in a poleward shift of the tropospheric midlatitude jets in winter. The aerosol radiative heating enhances the tropical upwelling in the lower stratosphere, influencing the strength of the Brewer-Dobson circulation. In contrast, solar dimming does not produce heating of the tropical lower stratosphere, and so there is little intensification of the polar vortex and no enhanced tropical upwelling. The dynamical response to titania aerosol is qualitatively similar to the response to sulfate

The influence of the stratospheric state on North Atlantic weather regimes

Stratosphere-troposphere coupling is often viewed from the perspective of the annular modes and their dynamics. Despite the obvious benefits of this approach, recent work has emphasised the greater tropospheric sensitivity to stratospheric variability in the Atlantic basin than in the Pacific basin. In this study, a new approach to understanding stratosphere-troposphere coupling is proposed, with a focus on the influence of the stratospheric state on North Atlantic weather regimes (during extended winter, November to March). The influence of the strength of the lower stratospheric vortex on four commonly used tropospheric weather regimes is quantified. The negative phase of the North Atlantic Oscillation is most sensitive to the stratospheric state, occurring on 33% of days following weak vortex conditions but on only 5% of days following strong vortex conditions. An opposite and slightly weaker sensitivity is found for the positive phase of the North Atlantic Oscillation and the Atlantic Ridge regime. For the North Atlantic Oscillation regimes, stratospheric conditions change both the probability of remaining in each regime and the probability of transitioning to that regime from others. A logistic regression model is developed to further quantify the sensitivity of tropospheric weather regimes to the lower stratospheric state. The logistic regression model predicts an increase of 40-60% in the probability of transition to the negative phase of the North Atlantic Oscillation for a one standard deviation reduction in the strength of the stratospheric vortex. Similarly it predicts a 10-30% increase in the probability of transition to the positive phase of the North Atlantic Oscillation for a one standard deviation increase in the strength of the stratospheric vortex. The stratosphere-troposphere coupling in the European Centre for Medium Range Weather Forecasts, Integrated Forecasting System model is found to be consistent with the re- analysis data by fitting the same logistic regression model

Storm naming and forecast communication: A case study of Storm Doris

On the 23rd February 2017, a significant low-pressure system named Storm Doris crossed the Republic of Ireland and the UK causing widespread disruption. As an early example of a storm named through the Met Office and Met Eireann ‘Name our Storms’ project, this provided an excellent opportunity to study how information about extreme weather in the UK spread through the media. In traditional media, the forecast of Storm Doris was widely reported upon on the 21st and 22nd February. On the 23rd February, newspaper coverage of the event rapidly switched to reporting the impact of the storm. Around three times the number of words and twice the number of articles were published about the impacts of Storm Doris in comparison to its forecast. Storm Doris rapidly became a broader cultural topic with an imprint on political news because of two by-elections that occurred by coincidence on the 23rd February. In the social media, rapid growth of the number of tweets about Storm Doris closely mirrored the growth of newspaper articles about the impacts of the storm. The network structure of the tweets associated with Storm Doris revealed the importance of both the Met Office official twitter account and newspaper and rail company accounts in disseminating information about the storm. Storm names, in addition to their benefit for forecast communication, also provide researchers with a useful and easily collected target to study the development and evolution of public understanding of extreme weather events

dCas9-based epigenome editing suggests acquisition of histone methylation is not sufficient for target gene repression.

Distinct epigenomic profiles of histone marks have been associated with gene expression, but questions regarding the causal relationship remain. Here we investigated the activity of a broad collection of genomically targeted epigenetic regulators that could write epigenetic marks associated with a repressed chromatin state (G9A, SUV39H1, Krüppel-associated box (KRAB), DNMT3A as well as the first targetable versions of Ezh2 and Friend of GATA-1 (FOG1)). dCas9 fusions produced target gene repression over a range of 0- to 10-fold that varied by locus and cell type. dCpf1 fusions were unable to repress gene expression. The most persistent gene repression required the action of several effector domains; however, KRAB-dCas9 did not contribute to persistence in contrast to previous reports. A 'direct tethering' strategy attaching the Ezh2 methyltransferase enzyme to dCas9, as well as a 'recruitment' strategy attaching the N-terminal 45 residues of FOG1 to dCas9 to recruit the endogenous nucleosome remodeling and deacetylase complex, were both successful in targeted deposition of H3K27me3. Surprisingly, however, repression was not correlated with deposition of either H3K9me3 or H3K27me3. Our results suggest that so-called repressive histone modifications are not sufficient for gene repression. The easily programmable dCas9 toolkit allowed precise control of epigenetic information and dissection of the relationship between the epigenome and gene regulation

Nuclear spirals as feeding channels to the Supermassive Black Hole: the case of the galaxy NGC 6951

We report the discovery of gas streaming motions along nuclear spiral arms towards the LINER nucleus of the galaxy NGC 6951. The observations, obtained using the GMOS integral field spectrograph on the Gemini North telescope, yielded maps of the flux distributions and gas kinematics in the Halpha, [NII]6584 and [SII]6717,31 emission lines of the inner 7x5 arcsec^2 of the galaxy. This region includes a circumnuclear star-forming ring with radius 500pc, a nuclear spiral inside the ring and the LINER nucleus. The kinematics of the ionized gas is dominated by rotation, but subtraction of a kinematic model of a rotating exponential disk reveals deviations from circular rotation within the nuclear ring which can be attributed to (1) streaming motions along the nuclear spiral arms and (2) a bipolar outflow which seems to be associated to a nuclear jet. On the basis of the observed streaming velocities and geometry of the spiral arms we estimate a mass inflow rate of ionized gas of 3x10^(-4) Msun/yr, which is of the order of the accretion rate necessary to power the LINER nucleus of NGC 6951. Similar streaming motions towards the nucleus of another galaxy with LINER nucleus -- NGC 1097 -- have been reported by our group in a previous paper. Taken together, these results support a scenario in which nuclear spirals are channels through which matter is transferred from galactic scales to the nuclear region to feed the supermassive black hole.Comment: 25 pages, 6 eps figures, accepted for publication in Ap

Hollow-fiber membrane technology: Characterization and proposed use as a potential mimic of skin vascularization towards the development of a novel skin absorption <i>in vitro</i> model

Dermal bioavailability is currently estimated through skin penetration studies using ex vivo models, which lack any measure of capillary bed function, and thus do not fully reproduce physiological conditions. We propose a novel strategy to mimic skin vascularization using newly fabricated hollow fibers made from a biocompatible membrane material, polystyrene, which is hydrophobic if left untreated, or hydrophilic when its surface polarity is modified through plasma-treatment. Caffeine has been well studied in skin penetration assays and was used here to determine the permeation properties of the hollow fibers in a novel jacketed glass bioreactor. For hydrophobic fibers, approximately 87.2 % of the caffeine dose did not penetrate the porous surface; 0.2 % of the dose was collected after 24 h (permeated through the pores), and therefore 12.6 % of the initial dose was suspected to block the membrane. For hydrophilic fibers, both the percentage of the initial dose that permeated and that of blocking caffeine increased to 1.2 % and 35.2 % respectively. It was concluded that caffeine permeated the hollow fibers at similar times of clearance to those observed in vivo, and therefore shows that this new model could provide a surrogate for capillary-based clearance in in vitro skin absorption studies.<br/