For atomic frequency standards in which fluctuations of the local oscillator (LO) frequency are the dominant noise source, we examine the role of the servo algorithm that predicts and corrects these frequency fluctuations. We derive the optimal linear prediction algorithm, showing how to measure the relevant spectral properties of the noise and optimise servo parameters while the standard is running, using only the atomic error signal. We find that, for realistic LO noise spectra, a conventional integrating servo with a properly chosen gain performs nearly as well as the optimal linear predictor. Using simple analytical models and numerical simulations, we establish optimum probe times as a function of clock atom number and of the dominant noise type in the local oscillator. We calculate the resulting LO-dependent scaling of achievable clock stability with atom number for product states as well as for maximally-correlated states.The instability of frequency standards limits the total uncertainty achievable in a measurement of finite duration [1,2]. This limit can be practically relevant even when performing measurements of static frequency ratios, since many-month-long measurement campaigns place stringent demands on the reliability of all components in an experiment. Instability becomes a fundamental concern when attempting to measure time-varying frequency ratios. For instance, in the emerging field of chronometric leveling [3][4][5], direct observation of tidal fluctuations expected in the gravitational red shift [6] requires frequency ratio measurements with a fractional uncertainty at the level of 10 −18 to be completed in a matter of hours. Physics beyond the Standard Model might be detectable in clock frequency ratio measurements as postulated transient shifts associated with dark-matter domain walls [7] or ultralight scalar darkmatter candidates [8,9]. Searches for such signals require the highest possible measurement resolution at timescales where the statistical uncertainty due to instability plays a far greater role than long-term systematic uncertainty.Of the noise processes contributing to the instability of atomic frequency standards, the most fundamental one is quantum projection noise [10], which arises from the discreteness in the measurement results obtainable from a finite number of atoms. For an ensemble of N uncorrelated two-level atoms, this noise imposes a minimum statistical uncertaintyon any measurement of the phase accumulated in an atomic superposition state. For a standard operating at a frequency ω and in the ideal case of Ramsey interrogation without technical noise, this leads to a long-term fractional * Ian.Leroux@nrc-cnrc.gc.ca; Current Address: National Research Council Canada, Ottawa, Ontario, Canada K1A 0R6 instability [11]where T is the duration of a single Ramsey interrogation and T c is the length of the frequency standard's operating cycle, such that τ/T c measurements can be performed in an averaging time τ. This quantum projection noise limit (QPN) 1 for clocks using unco...
With the advent of optical clocks featuring fractional frequency uncertainties on the order of 10 −17 and below, new applications such as chronometric levelling with few-cm height resolution emerge. We are developing a transportable optical clock based on a single trapped aluminium ion, which is interrogated via quantum logic spectroscopy. We employ singlycharged calcium as the logic ion for sympathetic cooling, state preparation and readout.Here we present a simple and compact physics and laser package for manipulation of 40 Ca + . Important features are a segmented multi-layer trap with separate loading and probing zones, a compact titanium vacuum chamber, a near-diffraction-limited imaging system with high numerical aperture based on a single biaspheric lens, and an all-in-fiber 40 Ca + repump laser system. We present preliminary estimates of the trap-induced frequency shifts on 27 Al + , derived from measurements with a single calcium ion. The micromotion-induced secondorder Doppler shift for 27 Al + has been determined to be δνEMM ν = −0.4 +0.4 −0.3 × 10 −18 and the black-body radiation shift is δν BBR /ν = (−4.0±0.4)×10 −18 . Moreover, heating rates of 30 (7) quanta per second at trap frequencies of ω rad,Ca+ ≈ 2π × 2.5 MHz (ω ax,Ca+ ≈ 2π × 1.5 MHz) in radial (axial) direction have been measured, enabling interrogation times of a few hundreds of milliseconds.
F-values and real TFBS occurrences calculated for human, chimp, mouse, rat, zebrafish and fugu genomes are available for free download at http://www.gmu.edu/departments/mmb/baranova/pages/bioinformatics
Some specialized transcription factors recognize specific DNA sequences arranged in inverted and direct repeats with a short nucleotide spacer in between. Identification of these motifs has been challenging due to their high divergence. In this paper, we describe a novel computational approach that can greatly improve the efficiency and accuracy in prediction of these DNA binding sites. A Hopfield neural classifier was designed with the flexibility of internal structure being adapted recurrently for the target motif structure. An FPGA implementation of this recurrent neural network is presented. It contains 60 neurons, and is described by the Verilog HDL modules. The circuitry was mapped onto an Alpha Data Virtex-4LX160 FPGA board. A set of 600 experimentally verified steroid hormone binding sites was used as the training set, and the developed Hopfield neural classifier has been used to identify and classify actual Hormone Response Elements. The program has been proven to be an effective tool in studying hormone-regulated gene networks.
Background: An important step in understanding the conditions that specify gene expression is the recognition of gene regulatory elements. Due to high diversity of different types of transcription factors and their DNA binding preferences, it is a challenging problem to establish an accurate model for recognition of functional regulatory elements in promoters of eukaryotic genes.
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