3,568 research outputs found
Spin swap gate in the presence of qubit inhomogeneity in a double quantum dot
We study theoretically the effects of qubit inhomogeneity on the quantum
logic gate of qubit swap, which is an integral part of the operations of a
quantum computer. Our focus here is to construct a robust pulse sequence for
swap operation in the simultaneous presence of Zeeman inhomogeneity for quantum
dot trapped electron spins and the finite-time ramp-up of exchange coupling in
a double dot. We first present a geometric explanation of spin swap operation,
mapping the two-qubit operation onto a single-qubit rotation. We then show that
in this geometric picture a square-pulse-sequence can be easily designed to
perform swap in the presence of Zeeman inhomogeneity. Finally, we investigate
how finite ramp-up times for the exchange coupling negatively affect the
performance of the swap gate sequence, and show how to correct the problems
numerically.Comment: published versio
Identification of specificity determining residues in peptide recognition domains using an information theoretic approach applied to large-scale binding maps
<p>Abstract</p> <p>Background</p> <p>Peptide Recognition Domains (PRDs) are commonly found in signaling proteins. They mediate protein-protein interactions by recognizing and binding short motifs in their ligands. Although a great deal is known about PRDs and their interactions, prediction of PRD specificities remains largely an unsolved problem.</p> <p>Results</p> <p>We present a novel approach to identifying these Specificity Determining Residues (SDRs). Our algorithm generalizes earlier information theoretic approaches to coevolution analysis, to become applicable to this problem. It leverages the growing wealth of binding data between PRDs and large numbers of random peptides, and searches for PRD residues that exhibit strong evolutionary covariation with some positions of the statistical profiles of bound peptides. The calculations involve only information from sequences, and thus can be applied to PRDs without crystal structures. We applied the approach to PDZ, SH3 and kinase domains, and evaluated the results using both residue proximity in co-crystal structures and verified binding specificity maps from mutagenesis studies.</p> <p>Discussion</p> <p>Our predictions were found to be strongly correlated with the physical proximity of residues, demonstrating the ability of our approach to detect physical interactions of the binding partners. Some high-scoring pairs were further confirmed to affect binding specificity using previous experimental results. Combining the covariation results also allowed us to predict binding profiles with higher reliability than two other methods that do not explicitly take residue covariation into account.</p> <p>Conclusions</p> <p>The general applicability of our approach to the three different domain families demonstrated in this paper suggests its potential in predicting binding targets and assisting the exploration of binding mechanisms.</p
Quantum cellular automata quantum computing with endohedral fullerenes
We present a scheme to perform universal quantum computation using global
addressing techniques as applied to a physical system of endohedrally doped
fullerenes. The system consists of an ABAB linear array of Group V endohedrally
doped fullerenes. Each molecule spin site consists of a nuclear spin coupled
via a Hyperfine interaction to an electron spin. The electron spin of each
molecule is in a quartet ground state . Neighboring molecular electron
spins are coupled via a magnetic dipole interaction. We find that an
all-electron construction of a quantum cellular automata is frustrated due to
the degeneracy of the electronic transitions. However, we can construct a
quantum celluar automata quantum computing architecture using these molecules
by encoding the quantum information on the nuclear spins while using the
electron spins as a local bus. We deduce the NMR and ESR pulses required to
execute the basic cellular automata operation and obtain a rough figure of
merit for the the number of gate operations per decoherence time. We find that
this figure of merit compares well with other physical quantum computer
proposals. We argue that the proposed architecture meets well the first four
DiVincenzo criteria and we outline various routes towards meeting the fifth
criteria: qubit readout.Comment: 16 pages, Latex, 5 figures, See http://planck.thphys.may.ie/QIPDDF/
submitted to Phys. Rev.
Symmetry and Topology in Superconductors - Odd-frequency pairing and edge states -
Superconductivity is a phenomenon where the macroscopic quantum coherence
appears due to the pairing of electrons. This offers a fascinating arena to
study the physics of broken gauge symmetry. However, the important symmetries
in superconductors are not only the gauge invariance. Especially, the symmetry
properties of the pairing, i.e., the parity and spin-singlet/spin-triplet,
determine the physical properties of the superconducting state. Recently it has
been recognized that there is the important third symmetry of the pair
amplitude, i.e., even or odd parity with respect to the frequency. The
conventional uniform superconducting states correspond to the even-frequency
pairing, but the recent finding is that the odd-frequency pair amplitude arises
in the spatially non-uniform situation quite ubiquitously. Especially, this is
the case in the Andreev bound state (ABS) appearing at the surface/interface of
the sample. The other important recent development is on the nontrivial
topological aspects of superconductors. As the band insulators are classified
by topological indices into (i) conventional insulator, (ii) quantum Hall
insulator, and (iii) topological insulator, also are the gapped
superconductors. The influence of the nontrivial topology of the bulk states
appears as the edge or surface of the sample. In the superconductors, this
leads to the formation of zero energy ABS (ZEABS). Therefore, the ABSs of the
superconductors are the place where the symmetry and topology meet each other
which offer the stage of rich physics. In this review, we discuss the physics
of ABS from the viewpoint of the odd-frequency pairing, the topological
bulk-edge correspondence, and the interplay of these two issues. It is
described how the symmetry of the pairing and topological indices determines
the absence/presence of the ZEABS, its energy dispersion, and properties as the
Majorana fermions.Comment: 91 pages, 38 figures, Review article, references adde
CDK-dependent nuclear localization of B-Cyclin Clb1 promotes FEAR activation during meiosis I in budding yeast
Cyclin-dependent kinases (CDK) are master regulators of the cell cycle in eukaryotes. CDK activity is regulated by the presence, post-translational modification and spatial localization of its regulatory subunit cyclin. In budding yeast, the B-cyclin Clb1 is phosphorylated and localizes to the nucleus during meiosis I. However the functional significance of Clb1's phosphorylation and nuclear localization and their mutual dependency is unknown. In this paper, we demonstrate that meiosis-specific phosphorylation of Clb1 requires its import to the nucleus but not vice versa. While Clb1 phosphorylation is dependent on activity of both CDK and polo-like kinase Cdc5, its nuclear localization requires CDK but not Cdc5 activity. Furthermore we show that increased nuclear localization of Clb1 during meiosis enhances activation of FEAR (Cdc Fourteen Early Anaphase Release) pathway. We discuss the significance of our results in relation to regulation of exit from meiosis I
Evidence for the accelerated expansion of the Universe from weak lensing tomography with COSMOS
We present a tomographic cosmological weak lensing analysis of the HST COSMOS
Survey. Applying our lensing-optimized data reduction, principal component
interpolation for the ACS PSF, and improved modelling of charge-transfer
inefficiency, we measure a lensing signal which is consistent with pure
gravitational modes and no significant shape systematics. We carefully estimate
the statistical uncertainty from simulated COSMOS-like fields obtained from
ray-tracing through the Millennium Simulation. We test our pipeline on
simulated space-based data, recalibrate non-linear power spectrum corrections
using the ray-tracing, employ photometric redshifts to reduce potential
contamination by intrinsic galaxy alignments, and marginalize over systematic
uncertainties. We find that the lensing signal scales with redshift as expected
from General Relativity for a concordance LCDM cosmology, including the full
cross-correlations between different redshift bins. For a flat LCDM cosmology,
we measure sigma_8(Omega_m/0.3)^0.51=0.75+-0.08 from lensing, in perfect
agreement with WMAP-5, yielding joint constraints Omega_m=0.266+0.025-0.023,
sigma_8=0.802+0.028-0.029 (all 68% conf.). Dropping the assumption of flatness
and using HST Key Project and BBN priors only, we find a negative deceleration
parameter q_0 at 94.3% conf. from the tomographic lensing analysis, providing
independent evidence for the accelerated expansion of the Universe. For a flat
wCDM cosmology and prior w in [-2,0], we obtain w<-0.41 (90% conf.). Our dark
energy constraints are still relatively weak solely due to the limited area of
COSMOS. However, they provide an important demonstration for the usefulness of
tomographic weak lensing measurements from space. (abridged)Comment: 26 pages, 25 figures, matches version accepted for publication by
Astronomy and Astrophysic
Comparison of Standard Ruler and Standard Candle constraints on Dark Energy Models
We compare the dark energy model constraints obtained by using recent
standard ruler data (Baryon Acoustic Oscillations (BAO) at z=0.2 and z=0.35 and
Cosmic Microwave Background (CMB) shift parameters R and l_a) with the
corresponding constraints obtained by using recent Type Ia Supernovae (SnIa)
standard candle data (ESSENCE+SNLS+HST from Davis et. al.). We find that, even
though both classes of data are consistent with LCDM at the 2\sigma level,
there is a systematic difference between the two classes of data. In
particular, we find that for practically all values of the parameters
(\Omega_0m,\Omega_b) in the 2\sigma range of the the 3-year WMAP data (WMAP3)
best fit, LCDM is significantly more consistent with the SnIa data than with
the CMB+BAO data. For example for (\Omega_0m,\Omega_b)=(0.24,0.042)
corresponding to the best fit values of WMAP3, the dark energy equation of
state parametrization w(z)=w_0 + w_1 (z/(1+z)) best fit is at a 0.5\sigma
distance from LCDM (w_0=-1,w_1=0) using the SnIa data and 1.7\sigma away from
LCDM using the CMB+BAO data. There is a similar trend in the earlier data (SNLS
vs CMB+BAO at z=0.35). This trend is such that the standard ruler CMB+BAO data
show a mild preference for crossing of the phantom divide line w=-1, while the
recent SnIa data favor LCDM. Despite of this mild difference in trends, we find
no statistically significant evidence for violation of the cosmic distance
duality relation \eta \equiv d_L(z)/(d_A(z) (1+z)^2)=1. For example, using a
prior of \Omega_0m=0.24, we find \eta=0.95 \pm 0.025 in the redshift range
0<z<2, which is consistent with distance duality at the 2\sigma level.Comment: References added. 9 pages, 7 figures. The Mathematica files with the
numerical analysis of the paper can be found at
http://leandros.physics.uoi.gr/rulcand/rulcand.ht
The Endogenous Th17 Response in NO<inf>2</inf>-Promoted Allergic Airway Disease Is Dispensable for Airway Hyperresponsiveness and Distinct from Th17 Adoptive Transfer
Severe, glucocorticoid-resistant asthma comprises 5-7% of patients with asthma. IL-17 is a biomarker of severe asthma, and the adoptive transfer of Th17 cells in mice is sufficient to induce glucocorticoid-resistant allergic airway disease. Nitrogen dioxide (NO2) is an environmental toxin that correlates with asthma severity, exacerbation, and risk of adverse outcomes. Mice that are allergically sensitized to the antigen ovalbumin by exposure to NO2 exhibit a mixed Th2/Th17 adaptive immune response and eosinophil and neutrophil recruitment to the airway following antigen challenge, a phenotype reminiscent of severe clinical asthma. Because IL-1 receptor (IL-1R) signaling is critical in the generation of the Th17 response in vivo, we hypothesized that the IL-1R/Th17 axis contributes to pulmonary inflammation and airway hyperresponsiveness (AHR) in NO2-promoted allergic airway disease and manifests in glucocorticoid-resistant cytokine production. IL-17A neutralization at the time of antigen challenge or genetic deficiency in IL-1R resulted in decreased neutrophil recruitment to the airway following antigen challenge but did not protect against the development of AHR. Instead, IL-1R-/- mice developed exacerbated AHR compared to WT mice. Lung cells from NO2-allergically inflamed mice that were treated in vitro with dexamethasone (Dex) during antigen restimulation exhibited reduced Th17 cytokine production, whereas Th17 cytokine production by lung cells from recipient mice of in vitro Th17-polarized OTII T-cells was resistant to Dex. These results demonstrate that the IL-1R/Th17 axis does not contribute to AHR development in NO2-promoted allergic airway disease, that Th17 adoptive transfer does not necessarily reflect an endogenously-generated Th17 response, and that functions of Th17 responses are contingent on the experimental conditions in which they are generated. © 2013 Martin et al
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Outcomes in patients with gunshot wounds to the brain.
Introduction:Gunshot wounds to the brain (GSWB) confer high lethality and uncertain recovery. It is unclear which patients benefit from aggressive resuscitation, and furthermore whether patients with GSWB undergoing cardiopulmonary resuscitation (CPR) have potential for survival or organ donation. Therefore, we sought to determine the rates of survival and organ donation, as well as identify factors associated with both outcomes in patients with GSWB undergoing CPR. Methods:We performed a retrospective, multicenter study at 25 US trauma centers including dates between June 1, 2011 and December 31, 2017. Patients were included if they suffered isolated GSWB and required CPR at a referring hospital, in the field, or in the trauma resuscitation room. Patients were excluded for significant torso or extremity injuries, or if pregnant. Binomial regression models were used to determine predictors of survival/organ donation. Results:825 patients met study criteria; the majority were male (87.6%) with a mean age of 36.5 years. Most (67%) underwent CPR in the field and 2.1% (n=17) survived to discharge. Of the non-survivors, 17.5% (n=141) were considered eligible donors, with a donation rate of 58.9% (n=83) in this group. Regression models found several predictors of survival. Hormone replacement was predictive of both survival and organ donation. Conclusion:We found that GSWB requiring CPR during trauma resuscitation was associated with a 2.1% survival rate and overall organ donation rate of 10.3%. Several factors appear to be favorably associated with survival, although predictions are uncertain due to the low number of survivors in this patient population. Hormone replacement was predictive of both survival and organ donation. These results are a starting point for determining appropriate treatment algorithms for this devastating clinical condition. Level of evidence:Level II
Mechanism of selective benzene hydroxylation catalyzed by iron-containing zeolites
A direct, catalytic conversion of benzene to phenol would have wide-reaching economic impacts. Fe zeolites exhibit a remarkable combination of high activity and selectivity in this conversion, leading to their past implementation at the pilot plant level. There were, however, issues related to catalyst deactivation for this process. Mechanistic insight could resolve these issues, and also provide a blueprint for achieving high performance in selective oxidation catalysis. Recently, we demonstrated that the active site of selective hydrocarbon oxidation in Fe zeolites, named α-O, is an unusually reactive Fe(IV)=O species. Here, we apply advanced spectroscopic techniques to determine that the reaction of this Fe(IV)=O intermediate with benzene in fact regenerates the reduced Fe(II) active site, enabling catalytic turnover. At the same time, a small fraction of Fe(III)-phenolate poisoned active sites form, defining a mechanism for catalyst deactivation. Density-functional theory calculations provide further insight into the experimentally defined mechanism. The extreme reactivity of α-O significantly tunes down (eliminates) the rate-limiting barrier for aromatic hydroxylation, leading to a diffusion-limited reaction coordinate. This favors hydroxylation of the rapidly diffusing benzene substrate over the slowly diffusing (but more reactive) oxygenated product, thereby enhancing selectivity. This defines a mechanism to simultaneously attain high activity (conversion) and selectivity, enabling the efficient oxidative upgrading of inert hydrocarbon substrates
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