579 research outputs found
High fidelity readout scheme for rare-earth solid state quantum computing
We propose and analyze a high fidelity readout scheme for a single instance
approach to quantum computing in rare-earth-ion-doped crystals. The scheme is
based on using different species of qubit and readout ions, and it is shown
that by allowing the closest qubit ion to act as a readout buffer, the readout
error can be reduced by more than an order of magnitude. The scheme is shown to
be robust against certain experimental variations, such as varying detection
efficiencies, and we use the scheme to predict the expected quantum fidelity of
a CNOT gate in these solid state systems. In addition, we discuss the potential
scalability of the protocol to larger qubit systems. The results are based on
parameters which we believed are experimentally feasible with current
technology, and which can be simultaneously realized.Comment: 7 pages, 5 figure
Statistical-mechanical lattice models for protein-DNA binding in chromatin
Statistical-mechanical lattice models for protein-DNA binding are well
established as a method to describe complex ligand binding equilibriums
measured in vitro with purified DNA and protein components. Recently, a new
field of applications has opened up for this approach since it has become
possible to experimentally quantify genome-wide protein occupancies in relation
to the DNA sequence. In particular, the organization of the eukaryotic genome
by histone proteins into a nucleoprotein complex termed chromatin has been
recognized as a key parameter that controls the access of transcription factors
to the DNA sequence. New approaches have to be developed to derive statistical
mechanical lattice descriptions of chromatin-associated protein-DNA
interactions. Here, we present the theoretical framework for lattice models of
histone-DNA interactions in chromatin and investigate the (competitive) DNA
binding of other chromosomal proteins and transcription factors. The results
have a number of applications for quantitative models for the regulation of
gene expression.Comment: 19 pages, 7 figures, accepted author manuscript, to appear in J.
Phys.: Cond. Mat
Sub-kHz-level relative stabilization of an intracavity doubled continuous wave optical parametric oscillator using Pound-Drever-Hall scheme
We report the relative frequency stabilization of an intracavity frequency
doubled singly resonant optical parametric oscillator on a Fabry-Perot\'etalon.
The red/orange radiation produced by the frequency doubling of the intracavity
resonant idler is stabilized using the Pound-Drever-Hall locking technique. The
relative frequency noise of this orange light, when integrated from 1 Hz to 50
kHz, corresponds to a standard deviation of 700 Hz. The frequency noise of the
pump laser is shown experimentally to be transferred to the non resonant signal
beam
Population structure and connectivity of the mountainous star coral, Orbicella faveolata , throughout the wider Caribbean region
As coral reefs continue to decline worldwide, it becomes ever more necessary to understand the connectivity between coral populations to develop efficient management strategies facilitating survival and adaptation of coral reefs in the future. Orbicella faveolata is one of the most important reef-building corals in the Caribbean and has recently experienced severe population reductions. Here, we utilize a panel of nine microsatellite loci to evaluate the genetic structure of O. faveolata and to infer connectivity across ten sites spanning the wider Caribbean region. Populations are generally well-mixed throughout the basin (FST = 0.038), although notable patterns of substructure arise at local and regional scales. Eastern and western populations appear segregated with a genetic break around the Mona Passage in the north, as has been shown previously in other species; however, we find evidence for significant connectivity between Curaçao and Mexico, suggesting that the southern margin of this barrier is permeable to dispersal. Our results also identify a strong genetic break within the Mesoamerican Barrier Reef System associated with complex oceanographic patterns that promote larval retention in southern Belize. Additionally, the diverse genetic signature at Flower Garden Banks suggests its possible function as a downstream genetic sink. The findings reported here are relevant to the ongoing conservation efforts for this important and threatened species, and contribute to the growing understanding of large-scale coral reef connectivity throughout the wider Caribbean
Population structure and connectivity of the mountainous star coral, Orbicella faveolata , throughout the wider Caribbean region
As coral reefs continue to decline worldwide, it becomes ever more necessary to understand the connectivity between coral populations to develop efficient management strategies facilitating survival and adaptation of coral reefs in the future. Orbicella faveolata is one of the most important reef-building corals in the Caribbean and has recently experienced severe population reductions. Here, we utilize a panel of nine microsatellite loci to evaluate the genetic structure of O. faveolata and to infer connectivity across ten sites spanning the wider Caribbean region. Populations are generally well-mixed throughout the basin (FST = 0.038), although notable patterns of substructure arise at local and regional scales. Eastern and western populations appear segregated with a genetic break around the Mona Passage in the north, as has been shown previously in other species; however, we find evidence for significant connectivity between Curaçao and Mexico, suggesting that the southern margin of this barrier is permeable to dispersal. Our results also identify a strong genetic break within the Mesoamerican Barrier Reef System associated with complex oceanographic patterns that promote larval retention in southern Belize. Additionally, the diverse genetic signature at Flower Garden Banks suggests its possible function as a downstream genetic sink. The findings reported here are relevant to the ongoing conservation efforts for this important and threatened species, and contribute to the growing understanding of large-scale coral reef connectivity throughout the wider Caribbean
Src kinase participates in LPS-induced activation of NADPH oxidase
The production of superoxide from NADPH oxidase by macrophages in response to endotoxin (LPS) is an important innate immune response, yet it is not clear how LPS signals the activation of NADPH oxidase. The hypothesis is that LPS-induced src kinase and PI3 kinase (PI3K) facilitates the activation of p47phox, the regulatory subunit of NADPH oxidase. In mouse macrophage RAW264.7 cells, inhibition of src tyrosine family kinases inhibited LPS-induced activation of NADPH oxidase, phosphorylation of p47phox, activation of PI3K and phosphorylation of the TLR4. Moreover, inhibition of LPS-induced increases in intracellular calcium blunted src kinase activation, PI3K association with TLR4, as well as PI3 kinase activation. These data suggest that both src kinase and PI3 kinase are involved in LPS-induced NADPH oxidase activation. Importantly, these data suggest that LPS-induced src kinase activation is critical for PI3 kinase activation as well as TLR4 phosphorylation and is dependent upon LPS-induced increase in intracellular calcium. These signaling events fill critical gaps in our understanding of LPS-induced free radical production as well as may potentially responsible for the mechanism of innate immune tolerance or desensitization caused by steroids or ethanol
Protein Localization with Flexible DNA or RNA
Localization of activity is ubiquitous in life, and also within sub-cellular compartments. Localization provides potential advantages as different proteins involved in the same cellular process may supplement each other on a fast timescale. It might also prevent proteins from being active in other regions of the cell. However localization is at odds with the spreading of unbound molecules by diffusion. We model the cost and gain for specific enzyme activity using localization strategies based on binding to sites of intermediate specificity. While such bindings in themselves decrease the activity of the protein on its target site, they may increase protein activity if stochastic motion allows the acting protein to touch both the intermediate binding site and the specific site simultaneously. We discuss this strategy in view of recent suggestions on long non-coding RNA as a facilitator of localized activity of chromatin modifiers
Role of AP-1 in the Coordinate Induction of Rat Glutamate-cysteine Ligase and Glutathione Synthetase by tert -Butylhydroquinone
GSH synthesis occurs via two enzymatic steps catalyzed by glutamate-cysteine ligase (GCL, made up of two subunits) and GSH synthetase (GS). Recently, we described coordinate induction of GCL subunits and GS. To study GS transcriptional regulation, we have cloned and characterized a 2.2-kb 5'-flanking region of the rat GS (GenBank accession number AF333982). One transcriptional start site is located at 51 nucleotides upstream of the translational start site. The rat GS promoter drove efficiently luciferase expression in H4IIE cells. Sequential deletion analysis revealed DNA regions that are involved in positive and negative regulation. One repressor identified was NF1. tert-Butylhydroquinone (TBH) exerted a dose- and time-dependent increase in the mRNA level and promoter activity of both GCL subunits and GS. TBH increased protein binding to several regions of the GS promoter, c-jun expression, and activator protein 1 (AP-1) binding activity to several of the putative AP-1-binding sites of the GS promoter. Blocking AP-1 binding with dominant-negative c-jun led to decreased basal expression and significantly blocked the TBH-induced increase in promoter activity and mRNA level of all three genes. In conclusion, AP-1 is required for basal expression of GCL and GS; while NF1 serves as a repressor of GS, increased AP-1 transactivation is the predominant mechanism for coordinate induction of GCL and GS expression by TBH
Quantum Computing
Quantum mechanics---the theory describing the fundamental workings of
nature---is famously counterintuitive: it predicts that a particle can be in
two places at the same time, and that two remote particles can be inextricably
and instantaneously linked. These predictions have been the topic of intense
metaphysical debate ever since the theory's inception early last century.
However, supreme predictive power combined with direct experimental observation
of some of these unusual phenomena leave little doubt as to its fundamental
correctness. In fact, without quantum mechanics we could not explain the
workings of a laser, nor indeed how a fridge magnet operates. Over the last
several decades quantum information science has emerged to seek answers to the
question: can we gain some advantage by storing, transmitting and processing
information encoded in systems that exhibit these unique quantum properties?
Today it is understood that the answer is yes. Many research groups around the
world are working towards one of the most ambitious goals humankind has ever
embarked upon: a quantum computer that promises to exponentially improve
computational power for particular tasks. A number of physical systems,
spanning much of modern physics, are being developed for this task---ranging
from single particles of light to superconducting circuits---and it is not yet
clear which, if any, will ultimately prove successful. Here we describe the
latest developments for each of the leading approaches and explain what the
major challenges are for the future.Comment: 26 pages, 7 figures, 291 references. Early draft of Nature 464, 45-53
(4 March 2010). Published version is more up-to-date and has several
corrections, but is half the length with far fewer reference
Visualization of Genomic Changes by Segmented Smoothing Using an L0 Penalty
Copy number variations (CNV) and allelic imbalance in tumor tissue can show strong segmentation. Their graphical presentation can be enhanced by appropriate smoothing. Existing signal and scatterplot smoothers do not respect segmentation well. We present novel algorithms that use a penalty on the norm of differences of neighboring values. Visualization is our main goal, but we compare classification performance to that of VEGA
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