231 research outputs found
A trapped single ion inside a Bose-Einstein condensate
Improved control of the motional and internal quantum states of ultracold
neutral atoms and ions has opened intriguing possibilities for quantum
simulation and quantum computation. Many-body effects have been explored with
hundreds of thousands of quantum-degenerate neutral atoms and coherent
light-matter interfaces have been built. Systems of single or a few trapped
ions have been used to demonstrate universal quantum computing algorithms and
to detect variations of fundamental constants in precision atomic clocks. Until
now, atomic quantum gases and single trapped ions have been treated separately
in experiments. Here we investigate whether they can be advantageously combined
into one hybrid system, by exploring the immersion of a single trapped ion into
a Bose-Einstein condensate of neutral atoms. We demonstrate independent control
over the two components within the hybrid system, study the fundamental
interaction processes and observe sympathetic cooling of the single ion by the
condensate. Our experiment calls for further research into the possibility of
using this technique for the continuous cooling of quantum computers. We also
anticipate that it will lead to explorations of entanglement in hybrid quantum
systems and to fundamental studies of the decoherence of a single, locally
controlled impurity particle coupled to a quantum environment
Quantum critical states and phase transitions in the presence of non equilibrium noise
Quantum critical points are characterized by scale invariant correlations and
correspondingly long ranged entanglement. As such, they present fascinating
examples of quantum states of matter, the study of which has been an important
theme in modern physics. Nevertheless very little is known about the fate of
quantum criticality under non equilibrium conditions. In this paper we
investigate the effect of external noise sources on quantum critical points. It
is natural to expect that noise will have a similar effect to finite
temperature, destroying the subtle correlations underlying the quantum critical
behavior. Surprisingly we find that in many interesting situations the
ubiquitous 1/f noise preserves the critical correlations. The emergent states
show intriguing interplay of intrinsic quantum critical and external noise
driven fluctuations. We demonstrate this general phenomenon with specific
examples in solid state and ultracold atomic systems. Moreover our approach
shows that genuine quantum phase transitions can exist even under non
equilibrium conditions.Comment: 9 pages, 2 figure
Towards a large-scale quantum simulator on diamond surface at room temperature
Strongly-correlated quantum many-body systems exhibits a variety of exotic
phases with long-range quantum correlations, such as spin liquids and
supersolids. Despite the rapid increase in computational power of modern
computers, the numerical simulation of these complex systems becomes
intractable even for a few dozens of particles. Feynman's idea of quantum
simulators offers an innovative way to bypass this computational barrier.
However, the proposed realizations of such devices either require very low
temperatures (ultracold gases in optical lattices, trapped ions,
superconducting devices) and considerable technological effort, or are
extremely hard to scale in practice (NMR, linear optics). In this work, we
propose a new architecture for a scalable quantum simulator that can operate at
room temperature. It consists of strongly-interacting nuclear spins attached to
the diamond surface by its direct chemical treatment, or by means of a
functionalized graphene sheet. The initialization, control and read-out of this
quantum simulator can be accomplished with nitrogen-vacancy centers implanted
in diamond. The system can be engineered to simulate a wide variety of
interesting strongly-correlated models with long-range dipole-dipole
interactions. Due to the superior coherence time of nuclear spins and
nitrogen-vacancy centers in diamond, our proposal offers new opportunities
towards large-scale quantum simulation at room temperatures
Out-of-equilibrium physics in driven dissipative coupled resonator arrays
Coupled resonator arrays have been shown to exhibit interesting many- body
physics including Mott and Fractional Hall states of photons. One of the main
differences between these photonic quantum simulators and their cold atoms
coun- terparts is in the dissipative nature of their photonic excitations. The
natural equi- librium state is where there are no photons left in the cavity.
Pumping the system with external drives is therefore necessary to compensate
for the losses and realise non-trivial states. The external driving here can
easily be tuned to be incoherent, coherent or fully quantum, opening the road
for exploration of many body regimes beyond the reach of other approaches. In
this chapter, we review some of the physics arising in driven dissipative
coupled resonator arrays including photon fermionisa- tion, crystallisation, as
well as photonic quantum Hall physics out of equilibrium. We start by briefly
describing possible experimental candidates to realise coupled resonator arrays
along with the two theoretical models that capture their physics, the
Jaynes-Cummings-Hubbard and Bose-Hubbard Hamiltonians. A brief review of the
analytical and sophisticated numerical methods required to tackle these systems
is included.Comment: Chapter that appeared in "Quantum Simulations with Photons and
Polaritons: Merging Quantum Optics with Condensed Matter Physics" edited by
D.G.Angelakis, Quantum Science and Technology Series, Springer 201
An improved method for constructing and selectively silanizing double-barreled, neutral liquid-carrier, ion-selective microelectrodes
We describe an improved, efficient and reliable method for the vapour-phase silanization of multi-barreled, ion-selective microelectrodes of which the silanized barrel(s) are to be filled with neutral liquid ion-exchanger (LIX). The technique employs a metal manifold to exclusively and simultaneously deliver dimethyldichlorosilane to only the ion-selective barrels of several multi-barreled microelectrodes. Compared to previously published methods the technique requires fewer procedural steps, less handling of individual microelectrodes, improved reproducibility of silanization of the selected microelectrode barrels and employs standard borosilicate tubing rather than the less-conventional theta-type glass. The electrodes remain stable for up to 3 weeks after the silanization procedure. The efficacy of a double-barreled electrode containing a proton ionophore in the ion-selective barrel is demonstrated in situ in the leaf apoplasm of pea (Pisum) and sunflower (Helianthus). Individual leaves were penetrated to depth of ~150 Ī¼m through the abaxial surface. Microelectrode readings remained stable after multiple impalements without the need for a stabilizing PVC matrix
clusterMaker: a multi-algorithm clustering plugin for Cytoscape
<p>Abstract</p> <p>Background</p> <p>In the post-genomic era, the rapid increase in high-throughput data calls for computational tools capable of integrating data of diverse types and facilitating recognition of biologically meaningful patterns within them. For example, protein-protein interaction data sets have been clustered to identify stable complexes, but scientists lack easily accessible tools to facilitate combined analyses of multiple data sets from different types of experiments. Here we present <it>clusterMaker</it>, a Cytoscape plugin that implements several clustering algorithms and provides network, dendrogram, and heat map views of the results. The Cytoscape network is linked to all of the other views, so that a selection in one is immediately reflected in the others. <it>clusterMaker </it>is the first Cytoscape plugin to implement such a wide variety of clustering algorithms and visualizations, including the only implementations of hierarchical clustering, dendrogram plus heat map visualization (tree view), k-means, k-medoid, SCPS, AutoSOME, and native (Java) MCL.</p> <p>Results</p> <p>Results are presented in the form of three scenarios of use: analysis of protein expression data using a recently published mouse interactome and a mouse microarray data set of nearly one hundred diverse cell/tissue types; the identification of protein complexes in the yeast <it>Saccharomyces cerevisiae</it>; and the cluster analysis of the vicinal oxygen chelate (VOC) enzyme superfamily. For scenario one, we explore functionally enriched mouse interactomes specific to particular cellular phenotypes and apply fuzzy clustering. For scenario two, we explore the prefoldin complex in detail using both physical and genetic interaction clusters. For scenario three, we explore the possible annotation of a protein as a methylmalonyl-CoA epimerase within the VOC superfamily. Cytoscape session files for all three scenarios are provided in the Additional Files section.</p> <p>Conclusions</p> <p>The Cytoscape plugin <it>clusterMaker </it>provides a number of clustering algorithms and visualizations that can be used independently or in combination for analysis and visualization of biological data sets, and for confirming or generating hypotheses about biological function. Several of these visualizations and algorithms are only available to Cytoscape users through the <it>clusterMaker </it>plugin. <it>clusterMaker </it>is available via the Cytoscape plugin manager.</p
Managing patients with ICD shocks and programming tachycardia therapies during acute heart failure syndromes
We review the pharmacologic, interventional and device programming treatment options for patients with implantable cardioverter-defibrillators who present with acute heart failure and implantable cardioverter-defibrillator shocks
Evaluation of clustering algorithms for protein-protein interaction networks
BACKGROUND: Protein interactions are crucial components of all cellular processes. Recently, high-throughput methods have been developed to obtain a global description of the interactome (the whole network of protein interactions for a given organism). In 2002, the yeast interactome was estimated to contain up to 80,000 potential interactions. This estimate is based on the integration of data sets obtained by various methods (mass spectrometry, two-hybrid methods, genetic studies). High-throughput methods are known, however, to yield a non-negligible rate of false positives, and to miss a fraction of existing interactions. The interactome can be represented as a graph where nodes correspond with proteins and edges with pairwise interactions. In recent years clustering methods have been developed and applied in order to extract relevant modules from such graphs. These algorithms require the specification of parameters that may drastically affect the results. In this paper we present a comparative assessment of four algorithms: Markov Clustering (MCL), Restricted Neighborhood Search Clustering (RNSC), Super Paramagnetic Clustering (SPC), and Molecular Complex Detection (MCODE). RESULTS: A test graph was built on the basis of 220 complexes annotated in the MIPS database. To evaluate the robustness to false positives and false negatives, we derived 41 altered graphs by randomly removing edges from or adding edges to the test graph in various proportions. Each clustering algorithm was applied to these graphs with various parameter settings, and the clusters were compared with the annotated complexes. We analyzed the sensitivity of the algorithms to the parameters and determined their optimal parameter values. We also evaluated their robustness to alterations of the test graph. We then applied the four algorithms to six graphs obtained from high-throughput experiments and compared the resulting clusters with the annotated complexes. CONCLUSION: This analysis shows that MCL is remarkably robust to graph alterations. In the tests of robustness, RNSC is more sensitive to edge deletion but less sensitive to the use of suboptimal parameter values. The other two algorithms are clearly weaker under most conditions. The analysis of high-throughput data supports the superiority of MCL for the extraction of complexes from interaction networks
Temporal changes in HCV genotype distribution in three different high risk populations in San Francisco, California
Abstract Background Hepatitis C virus (HCV) genotype (GT) has become an important measure in the diagnosis and monitoring of HCV infection treatment. In the United States (U.S.) HCV GT 1 is reported as the most common infecting GT among chronically infected patients. In Europe, however, recent studies have suggested that the epidemiology of HCV GTs is changing. Methods We assessed HCV GT distribution in 460 patients from three HCV-infected high risk populations in San Francisco, and examined patterns by birth cohort to assess temporal trends. Multiple logistic regression was used to assess factors independently associated with GT 1 infection compared to other GTs (2, 3, and 4). Results Overall, GT 1 was predominant (72.4%), however younger injection drug users (IDU) had a lower proportion of GT 1 infections (54.7%) compared to older IDU and HIV-infected patients (80.5% and 76.6%, respectively). Analysis by birth cohort showed increasing proportions of non-GT 1 infections associated with year of birth: birth before 1970 was independently associated with higher adjusted odds of GT 1: AOR 2.03 (95% CI: 1.23, 3.34). African-Americans as compared to whites also had higher adjusted odds of GT 1 infection (AOR: 3.37; 95% CI: 1.89, 5.99). Conclusions Although, HCV GT 1 remains the most prevalent GT, especially among older groups, changes in GT distribution could have significant implications for how HCV might be controlled on a population level and treated on an individual level
GWAS meta-analysis of over 29,000 people with epilepsy identifies 26 risk loci and subtype-specific genetic architecture
Epilepsy is a highly heritable disorder affecting over 50 million people worldwide, of which about one-third are resistant to current treatments. Here we report a multi-ancestry genome-wide association study including 29,944 cases, stratified into three broad categories and seven subtypes of epilepsy, and 52,538 controls. We identify 26 genome-wide significant loci, 19 of which are specific to genetic generalized epilepsy (GGE). We implicate 29 likely causal genes underlying these 26 loci. SNP-based heritability analyses show that common variants explain between 39.6% and 90% of genetic risk for GGE and its subtypes. Subtype analysis revealed markedly different genetic architectures between focal and generalized epilepsies. Gene-set analyses of GGE signals implicate synaptic processes in both excitatory and inhibitory neurons in the brain. Prioritized candidate genes overlap with monogenic epilepsy genes and with targets of current antiseizure medications. Finally, we leverage our results to identify alternate drugs with predicted efficacy if repurposed for epilepsy treatment
- ā¦