Physical realization of coupled Hilbert-space mirrors for quantum-state engineering

Manipulation of superpositions of discrete quantum states has a mathematical counterpart in the motion of a unit-length statevector in an N-dimensional Hilbert space. Any such statevector motion can be regarded as a succession of two-dimensional rotations. But the desired statevector change can also be treated as a succession of reflections, the generalization of Householder transformations. In multidimensional Hilbert space such reflection sequences offer more efficient procedures for statevector manipulation than do sequences of rotations. We here show how such reflections can be designed for a system with two degenerate levels - a generalization of the traditional two-state atom - that allows the construction of propagators for angular momentum states. We use the Morris-Shore transformation to express the propagator in terms of Morris-Shore basis states and Cayley-Klein parameters, which allows us to connect properties of laser pulses to Hilbert-space motion. Under suitable conditions on the couplings and the common detuning, the propagators within each set of degenerate states represent products of generalized Householder reflections, with orthogonal vectors. We propose physical realizations of this novel geometrical object with resonant, near-resonant and far-off-resonant laser pulses. We give several examples of implementations in real atoms or molecules.Comment: 15 pages, 6 figure

Two-color QCD via dimensional reduction

We study the thermodynamics of two-color QCD at high temperature and/or density using a dimensionally reduced superrenormalizable effective theory, formulated in terms of a coarse grained Wilson line. In the absence of quarks, the theory is required to respect the Z(2) center symmetry, while the effects of quarks of arbitrary masses and chemical potentials are introduced via soft Z(2) breaking operators. Perturbative matching of the effective theory parameters to the full theory is carried out explicitly, and it is argued how the new theory can be used to explore the phase diagram of two-color QCD.Comment: 17 pages, 1 eps figure, jheppub style; v2: minor update, references added, published versio

Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method

<p>Abstract</p> <p>Background</p> <p>Antigen presenting cells (APCs) sample the extra cellular space and present peptides from here to T helper cells, which can be activated if the peptides are of foreign origin. The peptides are presented on the surface of the cells in complex with major histocompatibility class II (MHC II) molecules. Identification of peptides that bind MHC II molecules is thus a key step in rational vaccine design and developing methods for accurate prediction of the peptide:MHC interactions play a central role in epitope discovery. The MHC class II binding groove is open at both ends making the correct alignment of a peptide in the binding groove a crucial part of identifying the core of an MHC class II binding motif. Here, we present a novel stabilization matrix alignment method, SMM-align, that allows for direct prediction of peptide:MHC binding affinities. The predictive performance of the method is validated on a large MHC class II benchmark data set covering 14 HLA-DR (human MHC) and three mouse H2-IA alleles.</p> <p>Results</p> <p>The predictive performance of the SMM-align method was demonstrated to be superior to that of the Gibbs sampler, TEPITOPE, SVRMHC, and MHCpred methods. Cross validation between peptide data set obtained from different sources demonstrated that direct incorporation of peptide length potentially results in over-fitting of the binding prediction method. Focusing on amino terminal peptide flanking residues (PFR), we demonstrate a consistent gain in predictive performance by favoring binding registers with a minimum PFR length of two amino acids. Visualizing the binding motif as obtained by the SMM-align and TEPITOPE methods highlights a series of fundamental discrepancies between the two predicted motifs. For the DRB1*1302 allele for instance, the TEPITOPE method favors basic amino acids at most anchor positions, whereas the SMM-align method identifies a preference for hydrophobic or neutral amino acids at the anchors.</p> <p>Conclusion</p> <p>The SMM-align method was shown to outperform other state of the art MHC class II prediction methods. The method predicts quantitative peptide:MHC binding affinity values, making it ideally suited for rational epitope discovery. The method has been trained and evaluated on the, to our knowledge, largest benchmark data set publicly available and covers the nine HLA-DR supertypes suggested as well as three mouse H2-IA allele. Both the peptide benchmark data set, and SMM-align prediction method (<it>NetMHCII</it>) are made publicly available.</p

The influence of soil communities on the temperature sensitivity of soil respiration

Soil respiration represents a major carbon flux between terrestrial ecosystems and the atmosphere, and is expected to accelerate under climate warming. Despite its importance in climate change forecasts, however, our understanding of the effects of temperature on soil respiration (RS) is incomplete. Using a metabolic ecology approach we link soil biota metabolism, community composition and heterotrophic activity, to predict RS rates across five biomes. We find that accounting for the ecological mechanisms underpinning decomposition processes predicts climatological RS variations observed in an independent dataset (n = 312). The importance of community composition is evident because without it RS is substantially underestimated. With increasing temperature, we predict a latitudinal increase in RS temperature sensitivity, with Q10 values ranging between 2.33 ±0.01 in tropical forests to 2.72 ±0.03 in tundra. This global trend has been widely observed, but has not previously been linked to soil communities

Maxwell-Chern-Simons Vortices and Holographic Superconductors

We investigate probe limit vortex solutions of a charged scalar field in Einstein-Maxwell theory in 3+1 dimensions, for an asymptotically AdS Schwarzschild black hole metric with the addition of an axionic coupling to the Maxwell field. We show that the inclusion of such a term, together with a suitable potential for the axion field, can induce an effective Chern-Simons term on the 2+1 dimensional boundary. We obtain numerical solutions of the equations of motion and find Maxwell-Chern-Simons like magnetic vortex configurations, where the magnetic field profile varies with the size of the effective Chern-Simons coupling. The axion field has a non-trivial profile inside the AdS bulk but does not condense at spatial infinity.Comment: 17 pages, 5 figures, version accepted for publication in JHE

Genomic hotspots for adaptation: the population genetics of Müllerian mimicry in Heliconius erato

This is the final version of the article. Available from the publisher via the DOI in this record.Wing pattern evolution in Heliconius butterflies provides some of the most striking examples of adaptation by natural selection. The genes controlling pattern variation are classic examples of Mendelian loci of large effect, where allelic variation causes large and discrete phenotypic changes and is responsible for both convergent and highly divergent wing pattern evolution across the genus. We characterize nucleotide variation, genotype-by-phenotype associations, linkage disequilibrium (LD), and candidate gene expression patterns across two unlinked genomic intervals that control yellow and red wing pattern variation among mimetic forms of Heliconius erato. Despite very strong natural selection on color pattern, we see neither a strong reduction in genetic diversity nor evidence for extended LD across either patterning interval. This observation highlights the extent that recombination can erase the signature of selection in natural populations and is consistent with the hypothesis that either the adaptive radiation or the alleles controlling it are quite old. However, across both patterning intervals we identified SNPs clustered in several coding regions that were strongly associated with color pattern phenotype. Interestingly, coding regions with associated SNPs were widely separated, suggesting that color pattern alleles may be composed of multiple functional sites, conforming to previous descriptions of these loci as "supergenes." Examination of gene expression levels of genes flanking these regions in both H. erato and its co-mimic, H. melpomene, implicate a gene with high sequence similarity to a kinesin as playing a key role in modulating pattern and provides convincing evidence for parallel changes in gene regulation across co-mimetic lineages. The complex genetic architecture at these color pattern loci stands in marked contrast to the single casual mutations often identified in genetic studies of adaptation, but may be more indicative of the type of genetic changes responsible for much of the adaptive variation found in natural populations.Funding: Funding for this study was provided by National Science Foundation grants to WOM (DEB-0715096 and IBN-0344705) and BAC (DEB-0513424). Funding for work on H. melpomene came from a BBSRC grant to CDJ and RHf-C (011845). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Plasma and Muscle Myostatin in Relation to Type 2 Diabetes

OBJECTIVE: Myostatin is a secreted growth factor expressed in skeletal muscle tissue, which negatively regulates skeletal muscle mass. Recent animal studies suggest a role for myostatin in insulin resistance. We evaluated the possible metabolic role of myostatin in patients with type 2 diabetes and healthy controls. DESIGN: 76 patients with type 2 diabetes and 92 control subjects were included in the study. They were matched for age, gender and BMI. Plasma samples and biopsies from the vastus lateralis muscle were obtained to assess plasma myostatin and expression of myostatin in skeletal muscle. RESULTS: Patients with type 2 diabetes had higher fasting glucose (8.9 versus 5.1 mmol/L, P<0.001), plasma insulin (68.2 versus 47.2 pmol/L, P<0.002) and HOMA2-IR (1.6 versus 0.9, P<0.0001) when compared to controls. Patients with type 2 diabetes had 1.4 (P<0.01) higher levels of muscle myostatin mRNA content than the control subjects. Plasma myostatin concentrations did not differ between patients with type 2 diabetes and controls. In healthy controls, muscle myostatin mRNA correlated with HOMA2-IR (r = 0.30, P<0.01), plasma IL-6 (r = 0.34, P<0.05) and VO2 max (r = -0.26, P<0.05), however, no correlations were observed in patients with type 2 diabetes. CONCLUSIONS: This study supports the idea that myostatin may have a negative effect on metabolism. However, the metabolic effect of myostatin appears to be overruled by other factors in patients with type 2 diabetes

Measures used to assess interventions for increasing patient involvement in Danish healthcare setting: a rapid review

Objective: To identify measures used within Denmark evaluating any type of intervention designed to facilitate patient involvement in healthcare. Design: Environmental scan employing rapid review methods. Data sources: MEDLINE, PsycInfo and CINAHL were searched from 6–9 April 2021 from database inception up to the date of the search. Eligibility criteria: Quantitative, observational and mixed methods studies with empirical data on outcomes used to assess any type of intervention aiming to increase patient involvement with their healthcare. Language limitations were Danish and English. Data extraction and synthesis: Two independent reviewers extracted data from 10% of the included studies and, due to their agreement, the data from the rest were extracted by first author. Data were analysed with reference to existing categories of measuring person-centred care; findings were synthesised using narrative summaries. Adapted Preferred Reporting Items for Systematic Reviews and Meta-Analyses 2020 guidelines were used to guide reporting. Results: Among 3767 records, 43 studies met the inclusion criteria, including 74 different measures used to evaluate interventions aimed at increasing patient involvement within healthcare in Danish hospital and community settings. Generic measures assessed: patient engagement (n=3); supporting self-management (n=8); supporting shared decision-making (n=9); patient satisfaction and experiences of care (n=11); health-related patient-reported outcome (n=20). Conclusions: Across Denmark, complex interventions designed to improve patient involvement with healthcare vary in their goals and content. Some targeting healthcare professionals, some patient health literacy and some service infrastructure. A plethora of measures assess the impact of these interventions on patient, professional and service delivery outcomes. Few measures assessed patient involvement directly, and it is unclear which proxy measures capture indicators of perceived involvement. Lack of conceptual clarity between intervention goals, the components of change and measures makes it difficult to see what types of intervention can best support change in services to ensure patients are more effectively involved in their healthcare

Efimov effect in quantum magnets

Physics is said to be universal when it emerges regardless of the underlying microscopic details. A prominent example is the Efimov effect, which predicts the emergence of an infinite tower of three-body bound states obeying discrete scale invariance when the particles interact resonantly. Because of its universality and peculiarity, the Efimov effect has been the subject of extensive research in chemical, atomic, nuclear and particle physics for decades. Here we employ an anisotropic Heisenberg model to show that collective excitations in quantum magnets (magnons) also exhibit the Efimov effect. We locate anisotropy-induced two-magnon resonances, compute binding energies of three magnons and find that they fit into the universal scaling law. We propose several approaches to experimentally realize the Efimov effect in quantum magnets, where the emergent Efimov states of magnons can be observed with commonly used spectroscopic measurements. Our study thus opens up new avenues for universal few-body physics in condensed matter systems.Comment: 7 pages, 5 figures; published versio