2016-01-01
Over recent years, several alternative relaxed clock models have been proposed in the context of Bayesian dating. These models fall in two distinct categories: uncorrelated and autocorrelated across branches. The choice between these two classes of relaxed clocks is still an open question. More fundamentally, the true process of rate variation may have both long-term trends and short-term fluctuations, suggesting that more sophisticated clock models unfolding over multiple time scales should ultimately be developed. Here, a mixed relaxed clock model is introduced, which can be mechanistically interpreted as a rate variation process undergoing short-term fluctuations on the top of Brownian long-term trends. Statistically, this mixed clock represents an alternative solution to the problem of choosing between autocorrelated and uncorrelated relaxed clocks, by proposing instead to combine their respective merits. Fitting this model on a dataset of 105 placental mammals, using both node-dating and tip-dating approaches, suggests that the two pure clocks, Brownian and white noise, are rejected in favour of a mixed model with approximately equal contributions for its uncorrelated and autocorrelated components. The tip-dating analysis is particularly sensitive to the choice of the relaxed clock model. In this context, the classical pure Brownian relaxed clock appears to be overly rigid, leading to biases in divergence time estimation. By contrast, the use of a mixed clock leads to more recent and more reasonable estimates for the crown ages of placental orders and superorders. Altogether, the mixed clock introduced here represents a first step towards empirically more adequate models of the patterns of rate variation across phylogenetic trees. This article is part of the themed issue ‘Dating species divergences using rocks and clocks’. PMID:27325829
Accurate model selection of relaxed molecular clocks in bayesian phylogenetics.
Baele, Guy; Li, Wai Lok Sibon; Drummond, Alexei J; Suchard, Marc A; Lemey, Philippe
2013-02-01
Recent implementations of path sampling (PS) and stepping-stone sampling (SS) have been shown to outperform the harmonic mean estimator (HME) and a posterior simulation-based analog of Akaike's information criterion through Markov chain Monte Carlo (AICM), in bayesian model selection of demographic and molecular clock models. Almost simultaneously, a bayesian model averaging approach was developed that avoids conditioning on a single model but averages over a set of relaxed clock models. This approach returns estimates of the posterior probability of each clock model through which one can estimate the Bayes factor in favor of the maximum a posteriori (MAP) clock model; however, this Bayes factor estimate may suffer when the posterior probability of the MAP model approaches 1. Here, we compare these two recent developments with the HME, stabilized/smoothed HME (sHME), and AICM, using both synthetic and empirical data. Our comparison shows reassuringly that MAP identification and its Bayes factor provide similar performance to PS and SS and that these approaches considerably outperform HME, sHME, and AICM in selecting the correct underlying clock model. We also illustrate the importance of using proper priors on a large set of empirical data sets.
Zhu, Tianqi; Dos Reis, Mario; Yang, Ziheng
2015-03-01
Genetic sequence data provide information about the distances between species or branch lengths in a phylogeny, but not about the absolute divergence times or the evolutionary rates directly. Bayesian methods for dating species divergences estimate times and rates by assigning priors on them. In particular, the prior on times (node ages on the phylogeny) incorporates information in the fossil record to calibrate the molecular tree. Because times and rates are confounded, our posterior time estimates will not approach point values even if an infinite amount of sequence data are used in the analysis. In a previous study we developed a finite-sites theory to characterize the uncertainty in Bayesian divergence time estimation in analysis of large but finite sequence data sets under a strict molecular clock. As most modern clock dating analyses use more than one locus and are conducted under relaxed clock models, here we extend the theory to the case of relaxed clock analysis of data from multiple loci (site partitions). Uncertainty in posterior time estimates is partitioned into three sources: Sampling errors in the estimates of branch lengths in the tree for each locus due to limited sequence length, variation of substitution rates among lineages and among loci, and uncertainty in fossil calibrations. Using a simple but analogous estimation problem involving the multivariate normal distribution, we predict that as the number of loci ([Formula: see text]) goes to infinity, the variance in posterior time estimates decreases and approaches the infinite-data limit at the rate of 1/[Formula: see text], and the limit is independent of the number of sites in the sequence alignment. We then confirmed the predictions by using computer simulation on phylogenies of two or three species, and by analyzing a real genomic data set for six primate species. Our results suggest that with the fossil calibrations fixed, analyzing multiple loci or site partitions is the most effective way
Stochastic models for atomic clocks
Barnes, J. A.; Jones, R. H.; Tryon, P. V.; Allan, D. W.
1983-01-01
For the atomic clocks used in the National Bureau of Standards Time Scales, an adequate model is the superposition of white FM, random walk FM, and linear frequency drift for times longer than about one minute. The model was tested on several clocks using maximum likelihood techniques for parameter estimation and the residuals were acceptably random. Conventional diagnostics indicate that additional model elements contribute no significant improvement to the model even at the expense of the added model complexity.
Modeling circadian clocks: From equations to oscillations
Gonze, Didier
2011-01-01
... (such as light and temperature) is greatly helped by mathematical modeling. In the present paper we review some mathematical models for circadian clocks, ranging from abstract, phenomenological models to the most detailed molecular models...
Dornburg, Alex; Brandley, Matthew C; McGowen, Michael R; Near, Thomas J
2012-02-01
Various nucleotide substitution models have been developed to accommodate among lineage rate heterogeneity, thereby relaxing the assumptions of the strict molecular clock. Recently developed "uncorrelated relaxed clock" and "random local clock" (RLC) models allow decoupling of nucleotide substitution rates between descendant lineages and are thus predicted to perform better in the presence of lineage-specific rate heterogeneity. However, it is uncertain how these models perform in the presence of punctuated shifts in substitution rate, especially between closely related clades. Using cetaceans (whales and dolphins) as a case study, we test the performance of these two substitution models in estimating both molecular rates and divergence times in the presence of substantial lineage-specific rate heterogeneity. Our RLC analyses of whole mitochondrial genome alignments find evidence for up to ten clade-specific nucleotide substitution rate shifts in cetaceans. We provide evidence that in the uncorrelated relaxed clock framework, a punctuated shift in the rate of molecular evolution within a subclade results in posterior rate estimates that are either misled or intermediate between the disparate rate classes present in baleen and toothed whales. Using simulations, we demonstrate abrupt changes in rate isolated to one or a few lineages in the phylogeny can mislead rate and age estimation, even when the node of interest is calibrated. We further demonstrate how increasing prior age uncertainty can bias rate and age estimates, even while the 95% highest posterior density around age estimates decreases; in other words, increased precision for an inaccurate estimate. We interpret the use of external calibrations in divergence time studies in light of these results, suggesting that rate shifts at deep time scales may mislead inferences of absolute molecular rates and ages.
Temperature influences in receiver clock modelling
Wang, Kan; Meindl, Michael; Rothacher, Markus; Schoenemann, Erik; Enderle, Werner
2016-04-01
In Precise Point Positioning (PPP), hardware delays at the receiver site (receiver, cables, antenna, …) are always difficult to be separated from the estimated receiver clock parameters. As a result, they are partially or fully contained in the estimated "apparent" clocks and will influence the deterministic and stochastic modelling of the receiver clock behaviour. In this contribution, using three years of data, the receiver clock corrections of a set of high-precision Hydrogen Masers (H-Masers) connected to stations of the ESA/ESOC network and the International GNSS Service (IGS) are firstly characterized concerning clock offsets, drifts, modified Allan deviations and stochastic parameters. In a second step, the apparent behaviour of the clocks is modelled with the help of a low-order polynomial and a known temperature coefficient (Weinbach, 2013). The correlations between the temperature and the hardware delays generated by different types of antennae are then analysed looking at daily, 3-day and weekly time intervals. The outcome of these analyses is crucial, if we intend to model the receiver clocks in the ground station network to improve the estimation of station-related parameters like coordinates, troposphere zenith delays and ambiguities. References: Weinbach, U. (2013) Feasibility and impact of receiver clock modeling in precise GPS data analysis. Dissertation, Leibniz Universität Hannover, Germany.
Simultaneous Buffer-sizing and Wire-sizing for Clock Trees Based on Lagrangian Relaxation
Yu-Min Lee
2002-01-01
Full Text Available Delay, power, skew, area and sensitivity are the most important concerns in current clock-tree design. We present in this paper an algorithm for simultaneously optimizing the above objectives by sizing wires and buffers in clock trees. Our algorithm, based on Lagrangian relaxation method, can optimally minimize delay, power and area simultaneously with very low skew and sensitivity. With linear storage overall and linear runtime per iteration, our algorithm is extremely economical, fast and accurate; for example, our algorithm can solve a 6201-wire-segment clock-tree problem using about 1-minute runtime and 1.3-MB memory and still achieve pico-second precision on an IBM RS/6000 workstation.
Aurore Woller; Hélène Duez; Bart Staels; Marc Lefranc
2016-01-01
To maintain energy homeostasis despite variable energy supply and consumption along the diurnal cycle, the liver relies on a circadian clock synchronized to food timing. Perturbed feeding and fasting cycles have been associated with clock disruption and metabolic diseases; however, the mechanisms are unclear. To address this question, we have constructed a mathematical model of the mammalian circadian clock, incorporating the metabolic sensors SIRT1 and AMPK. The clock response to various tem...
Pérez, María Encarnación; Pol, Diego
2012-01-01
Background Caviidae is a diverse group of caviomorph rodents that is broadly distributed in South America and is divided into three highly divergent extant lineages: Caviinae (cavies), Dolichotinae (maras), and Hydrochoerinae (capybaras). The fossil record of Caviidae is only abundant and diverse since the late Miocene. Caviids belongs to Cavioidea sensu stricto (Cavioidea s.s.) that also includes a diverse assemblage of extinct taxa recorded from the late Oligocene to the middle Miocene of South America (“eocardiids”). Results A phylogenetic analysis combining morphological and molecular data is presented here, evaluating the time of diversification of selected nodes based on the calibration of phylogenetic trees with fossil taxa and the use of relaxed molecular clocks. This analysis reveals three major phases of diversification in the evolutionary history of Cavioidea s.s. The first two phases involve two successive radiations of extinct lineages that occurred during the late Oligocene and the early Miocene. The third phase consists of the diversification of Caviidae. The initial split of caviids is dated as middle Miocene by the fossil record. This date falls within the 95% higher probability distribution estimated by the relaxed Bayesian molecular clock, although the mean age estimate ages are 3.5 to 7 Myr older. The initial split of caviids is followed by an obscure period of poor fossil record (refered here as the Mayoan gap) and then by the appearance of highly differentiated modern lineages of caviids, which evidentially occurred at the late Miocene as indicated by both the fossil record and molecular clock estimates. Conclusions The integrated approach used here allowed us identifying the agreements and discrepancies of the fossil record and molecular clock estimates on the timing of the major events in cavioid evolution, revealing evolutionary patterns that would not have been possible to gather using only molecular or paleontological data alone. PMID
Aurore Woller
2016-10-01
Full Text Available To maintain energy homeostasis despite variable energy supply and consumption along the diurnal cycle, the liver relies on a circadian clock synchronized to food timing. Perturbed feeding and fasting cycles have been associated with clock disruption and metabolic diseases; however, the mechanisms are unclear. To address this question, we have constructed a mathematical model of the mammalian circadian clock, incorporating the metabolic sensors SIRT1 and AMPK. The clock response to various temporal patterns of AMPK activation was simulated numerically, mimicking the effects of a normal diet, fasting, and a high-fat diet. The model reproduces the dampened clock gene expression and NAD+ rhythms reported for mice on a high-fat diet and predicts that this effect may be pharmacologically rescued by timed REV-ERB agonist administration. Our model thus identifies altered AMPK signaling as a mechanism leading to clock disruption and its associated metabolic effects and suggests a pharmacological approach to resetting the clock in obesity.
Woller, Aurore; Duez, Hélène; Staels, Bart; Lefranc, Marc
2016-10-18
To maintain energy homeostasis despite variable energy supply and consumption along the diurnal cycle, the liver relies on a circadian clock synchronized to food timing. Perturbed feeding and fasting cycles have been associated with clock disruption and metabolic diseases; however, the mechanisms are unclear. To address this question, we have constructed a mathematical model of the mammalian circadian clock, incorporating the metabolic sensors SIRT1 and AMPK. The clock response to various temporal patterns of AMPK activation was simulated numerically, mimicking the effects of a normal diet, fasting, and a high-fat diet. The model reproduces the dampened clock gene expression and NAD(+) rhythms reported for mice on a high-fat diet and predicts that this effect may be pharmacologically rescued by timed REV-ERB agonist administration. Our model thus identifies altered AMPK signaling as a mechanism leading to clock disruption and its associated metabolic effects and suggests a pharmacological approach to resetting the clock in obesity.
Models of the Primordial Standard Clock
Chen, Xingang; Wang, Yi
2014-01-01
Oscillating massive fields in the primordial universe can be used as Standard Clocks. The ticks of these oscillations induce features in the density perturbations, which directly record the time evolution of the scale factor of the primordial universe, thus if detected, provide a direct evidence for the inflation scenario or the alternatives. In this paper, we construct a full inflationary model of primordial Standard Clock and study its predictions on the density perturbations. This model provides a full realization of several key features proposed previously. We compare the theoretical predictions from inflation and alternative scenarios with the Planck 2013 temperature data on Cosmic Microwave Background (CMB), and identify a statistically marginal but interesting candidate. We discuss how future CMB temperature and polarization data, non-Gaussianity analysis and Large Scale Structure data may be used to further test or constrain the Standard Clock signals.
A compact model for the complex plant circadian clock
Didier eGonze
2016-02-01
Full Text Available The circadian clock is an endogenous timekeeper that allows organisms to anticipate and adapt to the daily variations of their environment. The plant clock is an intricate network of interlocked feedback loops, in which transcription factors regulate each other to generate oscillations with expression peaks at specific times of the day. Over the last decade, mathematical modeling approaches have been used to understand the inner workings of the clock in the model plant Arabidopsis thaliana. Those efforts have produced a number of models of ever increasing complexity. Here, we present an alternative model that combines a low number of equations and parameters, similar to the very earliest models, with the complex network structure found in more recent ones. This simple model describes the temporal evolution of the abundance of eight clock genes and captures key features of the clock on a qualitative level, namely the entrained and free-running behaviors of the wild type clock, as well as the defects found in knockout mutants (such as altered free-running periods, lack of entrainment, or changes in the expression of other clock genes. Additionally, our model produces complex responses to various light cues, such as extreme photoperiods and non-24h environmental cycles, and can describe the control of hypocotyl growth by the clock. Our model constitutes a useful tool to probe dynamical properties of the clock as well as model more clock-dependent processes.
Relaxed molecular clock provides evidence for long-distance dispersal of Nothofagus (southern beech.
Michael Knapp
2005-01-01
Full Text Available Nothofagus (southern beech, with an 80-million-year-old fossil record, has become iconic as a plant genus whose ancient Gondwanan relationships reach back into the Cretaceous era. Closely associated with Wegener's theory of "Kontinentaldrift", Nothofagus has been regarded as the "key genus in plant biogeography". This paradigm has the New Zealand species as passengers on a Moa's Ark that rafted away from other landmasses following the breakup of Gondwana. An alternative explanation for the current transoceanic distribution of species seems almost inconceivable given that Nothofagus seeds are generally thought to be poorly suited for dispersal across large distances or oceans. Here we test the Moa's Ark hypothesis using relaxed molecular clock methods in the analysis of a 7.2-kb fragment of the chloroplast genome. Our analyses provide the first unequivocal molecular clock evidence that, whilst some Nothofagus transoceanic distributions are consistent with vicariance, trans-Tasman Sea distributions can only be explained by long-distance dispersal. Thus, our analyses support the interpretation of an absence of Lophozonia and Fuscospora pollen types in the New Zealand Cretaceous fossil record as evidence for Tertiary dispersals of Nothofagus to New Zealand. Our findings contradict those from recent cladistic analyses of biogeographic data that have concluded transoceanic Nothofagus distributions can only be explained by vicariance events and subsequent extinction. They indicate that the biogeographic history of Nothofagus is more complex than envisaged under opposing polarised views expressed in the ongoing controversy over the relevance of dispersal and vicariance for explaining plant biodiversity. They provide motivation and justification for developing more complex hypotheses that seek to explain the origins of Southern Hemisphere biota.
Vďačný, Peter
2015-08-01
The class Litostomatea comprises a diverse assemblage of free-living and endosymbiotic ciliates. To understand diversification dynamic of litostomateans, divergence times of their main groups were estimated with the Bayesian molecular dating, a technique allowing relaxation of molecular clock and incorporation of flexible calibration points. The class Litostomatea very likely emerged during the Cryogenian around 680 Mya. The origin of the subclass Rhynchostomatia is dated to about 415 Mya, while that of the subclass Haptoria to about 654 Mya. The order Pleurostomatida, emerging about 556 Mya, was recognized as the oldest group within the subclass Haptoria. The order Spathidiida appeared in the Paleozoic about 442 Mya. The three remaining haptorian orders evolved in the Paleozoic/Mesozoic periods: Didiniida about 419 Mya, Lacrymariida about 269 Mya, and Haptorida about 194 Mya. The subclass Trichostomatia originated from a spathidiid ancestor in the Mesozoic about 260 Mya. A further goal of this study was to investigate the impact of various settings on posterior divergence time estimates. The root placement and tree topology as well as the priors of the rate-drift model, birth-death process and nucleotide substitution rate, had no significant effect on calculation of posterior divergence time estimates. However, removal of calibration points could significantly change time estimates at some nodes.
Vizcaíno Sergio F
2004-04-01
Full Text Available Abstract Background Comparative genomic data among organisms allow the reconstruction of their phylogenies and evolutionary time scales. Molecular timings have been recently used to suggest that environmental global change have shaped the evolutionary history of diverse terrestrial organisms. Living xenarthrans (armadillos, anteaters and sloths constitute an ideal model for studying the influence of past environmental changes on species diversification. Indeed, extant xenarthran species are relicts from an evolutionary radiation enhanced by their isolation in South America during the Tertiary era, a period for which major climate variations and tectonic events are relatively well documented. Results We applied a Bayesian approach to three nuclear genes in order to relax the molecular clock assumption while accounting for differences in evolutionary dynamics among genes and incorporating paleontological uncertainties. We obtained a molecular time scale for the evolution of extant xenarthrans and other placental mammals. Divergence time estimates provide substantial evidence for contemporaneous diversification events among independent xenarthran lineages. This correlated pattern of diversification might possibly relate to major environmental changes that occurred in South America during the Cenozoic. Conclusions The observed synchronicity between planetary and biological events suggests that global change played a crucial role in shaping the evolutionary history of extant xenarthrans. Our findings open ways to test this hypothesis further in other South American mammalian endemics like hystricognath rodents, platyrrhine primates, and didelphid marsupials.
Relaxing the Molecular Clock to Different Degrees for Different Substitution Types.
Lee, Hui-Jie; Rodrigue, Nicolas; Thorne, Jeffrey L
2015-08-01
Rates of molecular evolution can vary over time. Diverse statistical techniques for divergence time estimation have been developed to accommodate this variation. These typically require that all sequence (or codon) positions at a locus change independently of one another. They also generally assume that the rates of different types of nucleotide substitutions vary across a phylogeny in the same way. This permits divergence time estimation procedures to employ an instantaneous rate matrix with relative rates that do not differ among branches. However, previous studies have suggested that some substitution types (e.g., CpG to TpG changes in mammals) are more clock-like than others. As has been previously noted, this is biologically plausible given the mutational mechanism of CpG to TpG changes. Through stochastic mapping of sequence histories from context-independent substitution models, our approach allows for context-dependent nucleotide substitutions to change their relative rates over time. We apply our approach to the analysis of a 0.15 Mb intergenic region from eight primates. In accord with previous findings, we find comparatively little rate variation over time for CpG to TpG substitutions but we find more for other substitution types. We conclude by discussing the limitations and prospects of our approach.
Stefanie M. ICKERT-BOND; Catarina RYDIN; Susanne S. RENNER
2009-01-01
Ephedra comprises approximately 50 species, which are roughly equally distributed between the Old and New World deserts, but not in the intervening regions (amphitropical range). Great heterogeneity in the substitution rates of Gnetales (Ephedra, Gnetum, and Welwitschia) has made it difficult to infer the ages of the major divergence events in Ephedra, such as the timing of the Beringian disjunction in the genus and the entry into South America. Here, we use data from as many Gnetales species and genes as available from GenBank and from a recent study to investigate the timing of the major divergence events. Because of the tradeoff between the amount of missing data and taxon/gene sampling, we reduced the initial matrix of 265 accessions and 12 loci to 95 accessions and 10 loci, and further to 42 species (and 7736 aligned nucleotides) to achieve stationary distributions in the Bayesian molecular clock runs. Results from a relaxed clock with an uncorrelated rates model and fossil-based calibration reveal that New World species are monophyletic and diverged from their mostly Asian sister clade some 30 mya, fitting with many other Beringian disjunctions. The split between the single North American and the single South American clade occurred approximately 25 mya, well before the closure of the Panamanian Isthmus. Overall, the biogeographic history of Ephedra appears dominated by long-distance dispersal, but finer-scale studies are needed to test this hypothesis.
Enhanced Phenotyping of Complex Traits with a Circadian Clock Model
Merrow, Martha; Roenneberg, Till
2005-01-01
Models of biological systems are increasingly used to generate and test predictions in silico. This article explores the basic workings of a multifeedback network model of a circadian clock. In a series of in silico experiments, we investigated the influence of the number of feedbacks by adding and
Digital clocks: simple Boolean models can quantitatively describe circadian systems.
Akman, Ozgur E; Watterson, Steven; Parton, Andrew; Binns, Nigel; Millar, Andrew J; Ghazal, Peter
2012-09-07
The gene networks that comprise the circadian clock modulate biological function across a range of scales, from gene expression to performance and adaptive behaviour. The clock functions by generating endogenous rhythms that can be entrained to the external 24-h day-night cycle, enabling organisms to optimally time biochemical processes relative to dawn and dusk. In recent years, computational models based on differential equations have become useful tools for dissecting and quantifying the complex regulatory relationships underlying the clock's oscillatory dynamics. However, optimizing the large parameter sets characteristic of these models places intense demands on both computational and experimental resources, limiting the scope of in silico studies. Here, we develop an approach based on Boolean logic that dramatically reduces the parametrization, making the state and parameter spaces finite and tractable. We introduce efficient methods for fitting Boolean models to molecular data, successfully demonstrating their application to synthetic time courses generated by a number of established clock models, as well as experimental expression levels measured using luciferase imaging. Our results indicate that despite their relative simplicity, logic models can (i) simulate circadian oscillations with the correct, experimentally observed phase relationships among genes and (ii) flexibly entrain to light stimuli, reproducing the complex responses to variations in daylength generated by more detailed differential equation formulations. Our work also demonstrates that logic models have sufficient predictive power to identify optimal regulatory structures from experimental data. By presenting the first Boolean models of circadian circuits together with general techniques for their optimization, we hope to establish a new framework for the systematic modelling of more complex clocks, as well as other circuits with different qualitative dynamics. In particular, we anticipate
The precision of the hominid timescale estimated by relaxed clock methods.
Schrago, C G; Voloch, C M
2013-04-01
The chronological scenario of the evolution of hominoid primates has been thoroughly investigated since the advent of the molecular clock hypothesis. With the availability of genomic sequences for all hominid genera and other anthropoids, we may have reached the point at which the information from sequence data alone will not provide further evidence for the inference of the hominid evolution timescale. To verify this conjecture, we have compiled a genomic data set for all of the anthropoid genera. Our estimate places the Homo/Pan divergence at approximately 7.4 Ma, the Gorilla lineage divergence at approximately 9.7 Ma, the basal Hominidae divergence at 18.1 Ma and the basal Hominoidea divergence at 20.6 Ma. By inferring the theoretical limit distribution of posterior densities under a Bayesian framework, we show that it is unlikely that lengthier alignments or the availability of new genomic sequences will provide additional information to reduce the uncertainty associated with the divergence time estimates of the four hominid genera. A reduction of this uncertainty will be achieved only by the inclusion of more informative calibration priors. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.
Nonlinear Model of non-Debye Relaxation
Zon, Boris A
2010-01-01
We present a simple nonlinear relaxation equation which contains the Debye equation as a particular case. The suggested relaxation equation results in power-law decay of fluctuations. This equation contains a parameter defining the frequency dependence of the dielectric permittivity similarly to the well-known one-parameter phenomenological equations of Cole-Cole, Davidson-Cole and Kohlrausch-Williams-Watts. Unlike these models, the obtained dielectric permittivity (i) obeys to the Kramers-Kronig relation; (ii) has proper behaviour at large frequency; (iii) its imaginary part, conductivity, shows a power-law frequency dependence \\sigma ~ \\omega^n where n1 is also observed in several experiments. The nonlinear equation proposed may be useful in various fields of relaxation theory.
Modeling aftershocks as a stretched exponential relaxation
Mignan, A.
2015-11-01
The decay rate of aftershocks has been modeled as a power law since the pioneering work of Omori in the late nineteenth century. Although other expressions have been proposed in recent decades to describe the temporal behavior of aftershocks, the number of model comparisons remains limited. After reviewing the aftershock models published from the late nineteenth century until today, I solely compare the power law, pure exponential and stretched exponential expressions defined in their simplest forms. By applying statistical methods recommended recently in applied mathematics, I show that all aftershock sequences tested in three regional earthquake catalogs (Southern and Northern California, Taiwan) and with three declustering techniques (nearest-neighbor, second-order moment, window methods) follow a stretched exponential instead of a power law. These results infer that aftershocks are due to a simple relaxation process, in accordance with most other relaxation processes observed in Nature.
Maltsev, Victor A; Lakatta, Edward G
2009-03-01
Recent experimental studies have demonstrated that sinoatrial node cells (SANC) generate spontaneous, rhythmic, local subsarcolemmal Ca(2+) releases (Ca(2+) clock), which occur during late diastolic depolarization (DD) and interact with the classic sarcolemmal voltage oscillator (membrane clock) by activating Na(+)-Ca(2+) exchanger current (I(NCX)). This and other interactions between clocks, however, are not captured by existing essentially membrane-delimited cardiac pacemaker cell numerical models. Using wide-scale parametric analysis of classic formulations of membrane clock and Ca(2+) cycling, we have constructed and initially explored a prototype rabbit SANC model featuring both clocks. Our coupled oscillator system exhibits greater robustness and flexibility than membrane clock operating alone. Rhythmic spontaneous Ca(2+) releases of sarcoplasmic reticulum (SR)-based Ca(2+) clock ignite rhythmic action potentials via late DD I(NCX) over much broader ranges of membrane clock parameters [e.g., L-type Ca(2+) current (I(CaL)) and/or hyperpolarization-activated ("funny") current (I(f)) conductances]. The system Ca(2+) clock includes SR and sarcolemmal Ca(2+) fluxes, which optimize cell Ca(2+) balance to increase amplitudes of both SR Ca(2+) release and late DD I(NCX) as SR Ca(2+) pumping rate increases, resulting in a broad pacemaker rate modulation (1.8-4.6 Hz). In contrast, the rate modulation range via membrane clock parameters is substantially smaller when Ca(2+) clock is unchanged or lacking. When Ca(2+) clock is disabled, the system parametric space for fail-safe SANC operation considerably shrinks: without rhythmic late DD I(NCX) ignition signals membrane clock substantially slows, becomes dysrhythmic, or halts. In conclusion, the Ca(2+) clock is a new critical dimension in SANC function. A synergism of the coupled function of Ca(2+) and membrane clocks confers fail-safe SANC operation at greatly varying rates.
Modeling Aftershocks as a Stretched Exponential Relaxation
Mignan, Arnaud
2015-01-01
The decay rate of aftershocks has been modeled as a power law since the pioneering work of Omori in the late nineteenth century. Considered the second most fundamental empirical law after the Gutenberg-Richter relationship, the power law paradigm has rarely been challenged by the seismological community. By taking a view of aftershock research not biased by prior conceptions of Omori power law decay and by applying statistical methods recommended in applied mathematics, I show that all aftershock sequences tested in three regional earthquake catalogs (Southern and Northern California, Taiwan) and with three declustering techniques (nearest-neighbor, second-order moment, window methods) follow a stretched exponential instead of a power law. These results infer that aftershocks are due to a simpler relaxation process than originally thought, in accordance with most other relaxation processes observed in Nature.
Khosla, Kiran
2016-01-01
The notion of time is given a different footing in Quantum Mechanics and General Relativity, treated as a parameter in the former and being an observer dependent property in the later. From a operational point of view time is simply the correlation between a system and a clock, where an idealized clock can be modelled as a two level systems. We investigate the dynamics of clocks interacting gravitationally by treating the gravitational interaction as a classical information channel. In particular, we focus on the decoherence rates and temporal resolution of arrays of $N$ clocks showing how the minimum dephasing rate scales with $N$, and the spatial configuration. Furthermore, we consider the gravitational redshift between a clock and massive particle and show that a classical channel model of gravity predicts a finite dephasing rate from the non-local interaction. In our model we obtain a fundamental limitation in time accuracy that is intrinsic to each clock.
RELAXATION TIME LIMITS PROBLEM FOR HYDRODYNAMIC MODELS IN SEMICONDUCTOR SCIENCE
无
2007-01-01
In this article, two relaxation time limits, namely, the momentum relaxation time limit and the energy relaxation time limit are considered. By the compactness argument, it is obtained that the smooth solutions of the multidimensional nonisentropic Euler-Poisson problem converge to the solutions of an energy transport model or a drift diffusion model, respectively, with respect to different time scales.
Critical behavior of the random-bond clock model
Wu, Raymond P. H.; Lo, Veng-cheong; Huang, Haitao
2012-09-01
The critical behavior of the clock model in two-dimensional square lattice is studied numerically using Monte Carlo method with Wolff algorithm. The Kosterlitz-Thouless (KT) transition is observed in the 8-state clock model, where an intermediate phase exists between the low-temperature ordered phase and the high-temperature disordered phase. The bond randomness is introduced to the system by assuming a Gaussian distribution for the coupling coefficients with the mean μ = 1 and different values of variance: from σ2 = 0.1 to σ2 = 3.0. An abrupt jump in the helicity modulus at the transition, which is the key characteristic of the KT transition, is verified with a stability argument. Our results show that, a small amount of disorder (small σ) reduces the critical temperature of the system, without altering the nature of transition. However, a larger amount of disorder changes the transition from the KT-type into that of non-KT-type.
Integrating Biosystem Models Using Waveform Relaxation
Stephen Baigent
2008-12-01
Full Text Available Modelling in systems biology often involves the integration of component models into larger composite models. How to do this systematically and efficiently is a significant challenge: coupling of components can be unidirectional or bidirectional, and of variable strengths. We adapt the waveform relaxation (WR method for parallel computation of ODEs as a general methodology for computing systems of linked submodels. Four test cases are presented: (i a cascade of unidirectionally and bidirectionally coupled harmonic oscillators, (ii deterministic and stochastic simulations of calcium oscillations, (iii single cell calcium oscillations showing complex behaviour such as periodic and chaotic bursting, and (iv a multicellular calcium model for a cell plate of hepatocytes. We conclude that WR provides a flexible means to deal with multitime-scale computation and model heterogeneity. Global solutions over time can be captured independently of the solution techniques for the individual components, which may be distributed in different computing environments.
Modelling the widespread effects of TOC1 signalling on the plant circadian clock and its outputs.
Pokhilko, Alexandra; Mas, Paloma; Millar, Andrew J
2013-03-19
24-hour biological clocks are intimately connected to the cellular signalling network, which complicates the analysis of clock mechanisms. The transcriptional regulator TOC1 (TIMING OF CAB EXPRESSION 1) is a founding component of the gene circuit in the plant circadian clock. Recent results show that TOC1 suppresses transcription of multiple target genes within the clock circuit, far beyond its previously-described regulation of the morning transcription factors LHY (LATE ELONGATED HYPOCOTYL) and CCA1 (CIRCADIAN CLOCK ASSOCIATED 1). It is unclear how this pervasive effect of TOC1 affects the dynamics of the clock and its outputs. TOC1 also appears to function in a nested feedback loop that includes signalling by the plant hormone Abscisic Acid (ABA), which is upregulated by abiotic stresses, such as drought. ABA treatments both alter TOC1 levels and affect the clock's timing behaviour. Conversely, the clock rhythmically modulates physiological processes induced by ABA, such as the closing of stomata in the leaf epidermis. In order to understand the dynamics of the clock and its outputs under changing environmental conditions, the reciprocal interactions between the clock and other signalling pathways must be integrated. We extended the mathematical model of the plant clock gene circuit by incorporating the repression of multiple clock genes by TOC1, observed experimentally. The revised model more accurately matches the data on the clock's molecular profiles and timing behaviour, explaining the clock's responses in TOC1 over-expression and toc1 mutant plants. A simplified representation of ABA signalling allowed us to investigate the interactions of ABA and circadian pathways. Increased ABA levels lengthen the free-running period of the clock, consistent with the experimental data. Adding stomatal closure to the model, as a key ABA- and clock-regulated downstream process allowed to describe TOC1 effects on the rhythmic gating of stomatal closure. The integrated
Clock genes in hypertension: novel insights from rodent models.
Richards, Jacob; Diaz, Alexander N; Gumz, Michelle L
2014-10-01
The circadian clock plays an integral role in the regulation of physiological processes, including the regulation of blood pressure. However, deregulation of the clock can lead to pathophysiological states including hypertension. Recent work has implicated the circadian clock genes in the regulation of processes in the heart, kidney, vasculature, and the metabolic organs, which are all critical in the regulation of the blood pressure. The goal of this review is to provide an introduction and general overview into the role of circadian clock genes in the regulation of blood pressure with a focus on their deregulation in the etiology of hypertension. This review will focus on the core circadian clock genes CLOCK, BMAL1, Per, and Cry.
Time of relaxation in dusty plasma model
Timofeev, A. V.
2015-11-01
Dust particles in plasma may have different values of average kinetic energy for vertical and horizontal motion. The partial equilibrium of the subsystems and the relaxation processes leading to this asymmetry are under consideration. A method for the relaxation time estimation in nonideal dusty plasma is suggested. The characteristic relaxation times of vertical and horizontal motion of dust particles in gas discharge are estimated by analytical approach and by analysis of simulation results. These relaxation times for vertical and horizontal subsystems appear to be different. A single hierarchy of relaxation times is proposed.
Immersed boundary lattice Boltzmann model based on multiple relaxation times.
Lu, Jianhua; Han, Haifeng; Shi, Baochang; Guo, Zhaoli
2012-01-01
As an alterative version of the lattice Boltzmann models, the multiple relaxation time (MRT) lattice Boltzmann model introduces much less numerical boundary slip than the single relaxation time (SRT) lattice Boltzmann model if some special relationship between the relaxation time parameters is chosen. On the other hand, most current versions of the immersed boundary lattice Boltzmann method, which was first introduced by Feng and improved by many other authors, suffer from numerical boundary slip as has been investigated by Le and Zhang. To reduce such a numerical boundary slip, an immerse boundary lattice Boltzmann model based on multiple relaxation times is proposed in this paper. A special formula is given between two relaxation time parameters in the model. A rigorous analysis and the numerical experiments carried out show that the numerical boundary slip reduces dramatically by using the present model compared to the single-relaxation-time-based model.
Molecular-clock methods for estimating evolutionary rates and timescales.
Ho, Simon Y W; Duchêne, Sebastián
2014-12-01
The molecular clock presents a means of estimating evolutionary rates and timescales using genetic data. These estimates can lead to important insights into evolutionary processes and mechanisms, as well as providing a framework for further biological analyses. To deal with rate variation among genes and among lineages, a diverse range of molecular-clock methods have been developed. These methods have been implemented in various software packages and differ in their statistical properties, ability to handle different models of rate variation, capacity to incorporate various forms of calibrating information and tractability for analysing large data sets. Choosing a suitable molecular-clock model can be a challenging exercise, but a number of model-selection techniques are available. In this review, we describe the different forms of evolutionary rate heterogeneity and explain how they can be accommodated in molecular-clock analyses. We provide an outline of the various clock methods and models that are available, including the strict clock, local clocks, discrete clocks and relaxed clocks. Techniques for calibration and clock-model selection are also described, along with methods for handling multilocus data sets. We conclude our review with some comments about the future of molecular clocks.
GPS/GLONASS Combined Precise Point Positioning with Receiver Clock Modeling.
Wang, Fuhong; Chen, Xinghan; Guo, Fei
2015-06-30
Research has demonstrated that receiver clock modeling can reduce the correlation coefficients among the parameters of receiver clock bias, station height and zenith tropospheric delay. This paper introduces the receiver clock modeling to GPS/GLONASS combined precise point positioning (PPP), aiming to better separate the receiver clock bias and station coordinates and therefore improve positioning accuracy. Firstly, the basic mathematic models including the GPS/GLONASS observation equations, stochastic model, and receiver clock model are briefly introduced. Then datasets from several IGS stations equipped with high-stability atomic clocks are used for kinematic PPP tests. To investigate the performance of PPP, including the positioning accuracy and convergence time, a week of (1-7 January 2014) GPS/GLONASS data retrieved from these IGS stations are processed with different schemes. The results indicate that the positioning accuracy as well as convergence time can benefit from the receiver clock modeling. This is particularly pronounced for the vertical component. Statistic RMSs show that the average improvement of three-dimensional positioning accuracy reaches up to 30%-40%. Sometimes, it even reaches over 60% for specific stations. Compared to the GPS-only PPP, solutions of the GPS/GLONASS combined PPP are much better no matter if the receiver clock offsets are modeled or not, indicating that the positioning accuracy and reliability are significantly improved with the additional GLONASS satellites in the case of insufficient number of GPS satellites or poor geometry conditions. In addition to the receiver clock modeling, the impacts of different inter-system timing bias (ISB) models are investigated. For the case of a sufficient number of satellites with fairly good geometry, the PPP performances are not seriously affected by the ISB model due to the low correlation between the ISB and the other parameters. However, the refinement of ISB model weakens the
Evaluating the Adequacy of Molecular Clock Models Using Posterior Predictive Simulations.
Duchêne, David A; Duchêne, Sebastian; Holmes, Edward C; Ho, Simon Y W
2015-11-01
Molecular clock models are commonly used to estimate evolutionary rates and timescales from nucleotide sequences. The goal of these models is to account for rate variation among lineages, such that they are assumed to be adequate descriptions of the processes that generated the data. A common approach for selecting a clock model for a data set of interest is to examine a set of candidates and to select the model that provides the best statistical fit. However, this can lead to unreliable estimates if all the candidate models are actually inadequate. For this reason, a method of evaluating absolute model performance is critical. We describe a method that uses posterior predictive simulations to assess the adequacy of clock models. We test the power of this approach using simulated data and find that the method is sensitive to bias in the estimates of branch lengths, which tends to occur when using underparameterized clock models. We also compare the performance of the multinomial test statistic, originally developed to assess the adequacy of substitution models, but find that it has low power in identifying the adequacy of clock models. We illustrate the performance of our method using empirical data sets from coronaviruses, simian immunodeficiency virus, killer whales, and marine turtles. Our results indicate that methods of investigating model adequacy, including the one proposed here, should be routinely used in combination with traditional model selection in evolutionary studies. This will reveal whether a broader range of clock models to be considered in phylogenetic analysis.
Beyond Arabidopsis: the circadian clock in non-model plant species.
McClung, C Robertson
2013-05-01
Circadian clocks allow plants to temporally coordinate many aspects of their biology with the diurnal cycle derived from the rotation of Earth on its axis. Although there is a rich history of the study of clocks in many plant species, in recent years much progress in elucidating the architecture and function of the plant clock has emerged from studies of the model plant, Arabidopsis thaliana. There is considerable interest in extending this knowledge of the circadian clock into diverse plant species in order to address its role in topics as varied as agricultural productivity and the responses of individual species and plant communities to global climate change and environmental degradation. The analysis of circadian clocks in the green lineage provides insight into evolutionary processes in plants and throughout the eukaryotes. Copyright © 2013 Elsevier Ltd. All rights reserved.
A model of guarded recursion with clock synchronisation
Bizjak, Aleš; Møgelberg, Rasmus Ejlers
2015-01-01
productivity to be captured in types. The calculus uses clocks representing time streams and clock quantifiers which allow limited and controlled elimination of modalities. The calculus has since been extended to dependent types by Møgelberg. Both works give denotational semantics but no rewrite semantics...... by removing freshness restrictions from typing rules, and is a necessary step towards defining rewrite semantics, and ultimately implementing the calculus....
ZHOU Peiyuan
2016-03-01
Full Text Available Yaw attitude model switching of navigation satellites have great impact on its orbit and clock products derived from precise orbit determination. Firstly, the yaw attitude and solar radiation model of QZSS is given briefly. Then, using QZSS precise orbit and clock products provided by IGS MGEX analysis center, precision of orbit and clock is analyzed by satellite laser ranging residuals and polynomial fit residuals respectively. Finally, spectral analysis and modified Allan variance is carried out on clock products to reveal its periodic variations. Research on QZSS satellite orbit and clock products of 2014 shows that there are two eclipse seasons of 20 days and the beta angle is fluctuating with a period of half-year. And there is significant correlation between the precision of orbit and clock products and beta angle. Moreover, the satellite clock offset has periodic variations similar to orbit periods and its amplitude is changing with the beta angle which indicates problems of current orbit determination strategies. In view of similarities between QZSS and BeiDou IGSO and MEO satellites in yaw attitude model, the conclusion is beneficial to improve BeiDou precise orbit determination.
State resolved vibrational relaxation modeling for strongly nonequilibrium flows
Boyd, Iain D.; Josyula, Eswar
2011-05-01
Vibrational relaxation is an important physical process in hypersonic flows. Activation of the vibrational mode affects the fundamental thermodynamic properties and finite rate relaxation can reduce the degree of dissociation of a gas. Low fidelity models of vibrational activation employ a relaxation time to capture the process at a macroscopic level. High fidelity, state-resolved models have been developed for use in continuum gas dynamics simulations based on computational fluid dynamics (CFD). By comparison, such models are not as common for use with the direct simulation Monte Carlo (DSMC) method. In this study, a high fidelity, state-resolved vibrational relaxation model is developed for the DSMC technique. The model is based on the forced harmonic oscillator approach in which multi-quantum transitions may become dominant at high temperature. Results obtained for integrated rate coefficients from the DSMC model are consistent with the corresponding CFD model. Comparison of relaxation results obtained with the high-fidelity DSMC model shows significantly less excitation of upper vibrational levels in comparison to the standard, lower fidelity DSMC vibrational relaxation model. Application of the new DSMC model to a Mach 7 normal shock wave in carbon monoxide provides better agreement with experimental measurements than the standard DSMC relaxation model.
Theoretical model of intravascular paramagnetic tracers effect on tissue relaxation
Kjølby, Birgitte Fuglsang; Østergaard, Leif; Kiselev, Valerij G
2006-01-01
that the relaxivity of intravascular contrast agents depends significantly on the host tissue. This agrees with experimental data by Johnson et al. (Magn Reson Med 2000;44:909). In particular, the present results suggest a several-fold increase in the relaxivity of Gd-based contrast agents in brain tissue compared...... with bulk blood. The enhancement of relaxation in tissue is due to the contrast in magnetic susceptibility between blood vessels and parenchyma induced by the presence of paramagnetic tracer. Beyond the perfusion measurements, the results can be applied to quantitation of functional MRI and to vessel size......The concentration of MRI tracers cannot be measured directly by MRI and is commonly evaluated indirectly using their relaxation effect. This study develops a comprehensive theoretical model to describe the transverse relaxation in perfused tissue caused by intravascular tracers. The model takes...
Modeling and simulation for a new virtual-clock-based collision resolution algorithm
Yin rupo; Cai yunze; He xing; Zhang weidong; Xu xiaoming
2006-01-01
Virtual time Ethernet is a multiple access protocol proposed to provide FCFS transmission service over the predominant Ethernet bus. It incorporates a novel message-rescheduling algorithm based on the virtual clock mechanism. By manipulating virtual clocks back up over a common virtual time axis and performing timely collision resolution, the algorithm guarantees the system's queuing strictness. The protocol is particularly modeled as a finite state machine and implemented using OPNET tools. Simulation studies prove its correctness and effectiveness.
Approximating the XY model on a random graph with a q -state clock model
Lupo, Cosimo; Ricci-Tersenghi, Federico
2017-02-01
Numerical simulations of spin glass models with continuous variables set the problem of a reliable but efficient discretization of such variables. In particular, the main question is how fast physical observables computed in the discretized model converge toward the ones of the continuous model when the number of states of the discretized model increases. We answer this question for the XY model and its discretization, the q -state clock model, in the mean-field setting provided by random graphs. It is found that the convergence of physical observables is exponentially fast in the number q of states of the clock model, so allowing a very reliable approximation of the XY model by using a rather small number of states. Furthermore, such an exponential convergence is found to be independent from the disorder distribution used. Only at T =0 , the convergence is slightly slower (stretched exponential). Thanks to the analytical solution to the q -state clock model, we compute accurate phase diagrams in the temperature versus disorder strength plane. We find that, at zero temperature, spontaneous replica symmetry breaking takes place for any amount of disorder, even an infinitesimal one. We also study the one step of replica symmetry breaking (1RSB) solution in the low-temperature spin glass phase.
Gérard, Claude; Goldbeter, Albert
2012-05-01
The cell division cycle and the circadian clock represent two major cellular rhythms. These two periodic processes are coupled in multiple ways, given that several molecular components of the cell cycle network are controlled in a circadian manner. For example, in the network of cyclin-dependent kinases (Cdks) that governs progression along the successive phases of the cell cycle, the synthesis of the kinase Wee1, which inhibits the G2/M transition, is enhanced by the complex CLOCK-BMAL1 that plays a central role in the circadian clock network. Another component of the latter network, REV-ERBα, inhibits the synthesis of the Cdk inhibitor p21. Moreover, the synthesis of the oncogene c-Myc, which promotes G1 cyclin synthesis, is repressed by CLOCK-BMAL1. Using detailed computational models for the two networks we investigate the conditions in which the mammalian cell cycle can be entrained by the circadian clock. We show that the cell cycle can be brought to oscillate at a period of 24 h or 48 h when its autonomous period prior to coupling is in an appropriate range. The model indicates that the combination of multiple modes of coupling does not necessarily facilitate entrainment of the cell cycle by the circadian clock. Entrainment can also occur as a result of circadian variations in the level of a growth factor controlling entry into G1. Outside the range of entrainment, the coupling to the circadian clock may lead to disconnected oscillations in the cell cycle and the circadian system, or to complex oscillatory dynamics of the cell cycle in the form of endoreplication, complex periodic oscillations or chaos. The model predicts that the transition from entrainment to 24 h or 48 h might occur when the strength of coupling to the circadian clock or the level of growth factor decrease below critical values.
Baele, Guy; Lemey, Philippe; Bedford, Trevor; Rambaut, Andrew; Suchard, Marc A; Alekseyenko, Alexander V
2012-09-01
Recent developments in marginal likelihood estimation for model selection in the field of Bayesian phylogenetics and molecular evolution have emphasized the poor performance of the harmonic mean estimator (HME). Although these studies have shown the merits of new approaches applied to standard normally distributed examples and small real-world data sets, not much is currently known concerning the performance and computational issues of these methods when fitting complex evolutionary and population genetic models to empirical real-world data sets. Further, these approaches have not yet seen widespread application in the field due to the lack of implementations of these computationally demanding techniques in commonly used phylogenetic packages. We here investigate the performance of some of these new marginal likelihood estimators, specifically, path sampling (PS) and stepping-stone (SS) sampling for comparing models of demographic change and relaxed molecular clocks, using synthetic data and real-world examples for which unexpected inferences were made using the HME. Given the drastically increased computational demands of PS and SS sampling, we also investigate a posterior simulation-based analogue of Akaike's information criterion (AIC) through Markov chain Monte Carlo (MCMC), a model comparison approach that shares with the HME the appealing feature of having a low computational overhead over the original MCMC analysis. We confirm that the HME systematically overestimates the marginal likelihood and fails to yield reliable model classification and show that the AICM performs better and may be a useful initial evaluation of model choice but that it is also, to a lesser degree, unreliable. We show that PS and SS sampling substantially outperform these estimators and adjust the conclusions made concerning previous analyses for the three real-world data sets that we reanalyzed. The methods used in this article are now available in BEAST, a powerful user
Impaired light detection of the circadian clock in a zebrafish melanoma model.
Hamilton, Noémie; Diaz-de-Cerio, Natalia; Whitmore, David
2015-01-01
The circadian clock controls the timing of the cell cycle in healthy tissues and clock disruption is known to increase tumourigenesis. Melanoma is one of the most rapidly increasing forms of cancer and the precise molecular circadian changes that occur in a melanoma tumor are unknown. Using a melanoma zebrafish model, we have explored the molecular changes that occur to the circadian clock within tumors. We have found disruptions in melanoma clock gene expression due to a major impairment to the light input pathway, with a parallel loss of light-dependent activation of DNA repair genes. Furthermore, the timing of mitosis in tumors is perturbed, as well as the regulation of certain key cell cycle regulators, such that cells divide arhythmically. The inability to co-ordinate DNA damage repair and cell division is likely to promote further tumourigenesis and accelerate melanoma development.
Microscopic origin of shear relaxation in a model viscoelastic liquid.
Ashwin, J; Sen, Abhijit
2015-02-01
An atomistic description of shear stress relaxation in a viscoelastic liquid is developed from first principles through accurate molecular dynamic simulations in a model Yukawa system. It is shown that the relaxation time τ(M)(ex) of the excess part of the shear stress autocorrelation function provides a correct measure of the relaxation process. Below a certain critical value Γ(c) of the Coulomb coupling strength, the lifetime of local atomic connectivity τ(LC) converges to τ(M)(ex) and is the microscopic origin of the relaxation. At Γ≫Γ(c), i.e., in the potential energy dominated regime, τ(M)(ex)→τ(M) (the Maxwell relaxation time) and can, therefore, fully account for the elastic or "solidlike" behavior. Our results can help provide a better fundamental understanding of viscoelastic behavior in a variety of strongly coupled systems such as dusty plasmas, colloids, and non-Newtonian fluids.
Microscopic Origin of Shear Relaxation in a Model Viscoelastic Liquid
Ashwin, J.; Sen, Abhijit
2015-02-01
An atomistic description of shear stress relaxation in a viscoelastic liquid is developed from first principles through accurate molecular dynamic simulations in a model Yukawa system. It is shown that the relaxation time τMex of the excess part of the shear stress autocorrelation function provides a correct measure of the relaxation process. Below a certain critical value Γc of the Coulomb coupling strength, the lifetime of local atomic connectivity τLC converges to τMex and is the microscopic origin of the relaxation. At Γ ≫Γc, i.e., in the potential energy dominated regime, τMex→τM (the Maxwell relaxation time) and can, therefore, fully account for the elastic or "solidlike" behavior. Our results can help provide a better fundamental understanding of viscoelastic behavior in a variety of strongly coupled systems such as dusty plasmas, colloids, and non-Newtonian fluids.
Modeling multi-clocked data-flow programs using the Generic Modeling Environment
Brunette, Christian; Talpin, Jean-Pierre; Besnard, Loïc; Gautier, Thierry
2006-01-01
International audience; This paper presents Signal-Meta, the metamodel designed for the synchronous data-flow language Signal. It relies on the Generic Modeling Environment (GME), a configurable object-oriented toolkit that supports the creation of domain-specific modeling and program synthesis environments. The graphical description constitutes the base to build multi-clock environments, and a good front-end for the Polychrony platform. To complete this frontend, we develop a tool that trans...
Models of Flux Tubes from Constrained Relaxation
Α. Mangalam; V. Krishan
2000-09-01
We study the relaxation of a compressible plasma to an equilibrium with flow. The constraints of conservation of mass, energy, angular momentum, cross-helicity and relative magnetic helicity are imposed. Equilibria corresponding to the energy extrema while conserving these invariants for parallel flows yield three classes of solutions and one of them with an increasing radial density profile, relevant to solar flux tubes is presented.
Extended MHD Modeling of Tearing-Driven Magnetic Relaxation
Sauppe, Joshua
2016-10-01
Driven plasma pinch configurations are characterized by the gradual accumulation and episodic release of free energy in discrete relaxation events. The hallmark of this relaxation in a reversed-field pinch (RFP) plasma is flattening of the parallel current density profile effected by a fluctuation-induced dynamo emf in Ohm's law. Nonlinear two-fluid modeling of macroscopic RFP dynamics has shown appreciable coupling of magnetic relaxation and the evolution of plasma flow. Accurate modeling of RFP dynamics requires the Hall effect in Ohm's law as well as first order ion finite Larmor radius (FLR) effects, represented by the Braginskii ion gyroviscous stress tensor. New results find that the Hall dynamo effect from / ne can counter the MHD effect from - in some of the relaxation events. The MHD effect dominates these events and relaxes the current profile toward the Taylor state, but the opposition of the two dynamos generates plasma flow in the direction of equilibrium current density, consistent with experimental measurements. Detailed experimental measurements of the MHD and Hall emf terms are compared to these extended MHD predictions. Tracking the evolution of magnetic energy, helicity, and hybrid helicity during relaxation identifies the most important contributions in single-fluid and two-fluid models. Magnetic helicity is well conserved relative to the magnetic energy during relaxation. The hybrid helicity is dominated by magnetic helicity in realistic low-beta pinch conditions and is also well conserved. Differences of less than 1 % between magnetic helicity and hybrid helicity are observed with two-fluid modeling and result from cross helicity evolution through ion FLR effects, which have not been included in contemporary relaxation theories. The kinetic energy driven by relaxation in the computations is dominated by velocity components perpendicular to the magnetic field, an effect that had not been predicted. Work performed at University of Wisconsin
Modeling circadian clock-cell cycle interaction effects on cell population growth rates.
El Cheikh, R; Bernard, S; El Khatib, N
2014-12-21
The circadian clock and the cell cycle are two tightly coupled oscillators. Recent analytical studies have shown counter-intuitive effects of circadian gating of the cell cycle on growth rates of proliferating cells which cannot be explained by a molecular model or a population model alone. In this work, we present a combined molecular-population model that studies how coupling the circadian clock to the cell cycle, through the protein WEE1, affects a proliferating cell population. We show that the cell cycle can entrain to the circadian clock with different rational period ratios and characterize multiple domains of entrainment. We show that coupling increases the growth rate for autonomous periods of the cell cycle around 24 h and above 48 h. We study the effect of mutation of circadian genes on the growth rate of cells and show that disruption of the circadian clock can lead to abnormal proliferation. Particularly, we show that Cry 1, Cry 2 mutations decrease the growth rate of cells, Per 2 mutation enhances it and Bmal 1 knockout increases it for autonomous periods of the cell cycle less than 21 h and decreases it elsewhere. Combining a molecular model to a population model offers new insight on the influence of the circadian clock on the growth of a cell population. This can help chronotherapy which takes benefits of physiological rhythms to improve anti-cancer efficacy and tolerance to drugs by administering treatments at a specific time of the day.
A Stable Clock Error Model Using Coupled First and Second Order Gauss-Markov Processes
Carpenter, Russell; Lee, Taesul
2008-01-01
Long data outages may occur in applications of global navigation satellite system technology to orbit determination for missions that spend significant fractions of their orbits above the navigation satellite constellation(s). Current clock error models based on the random walk idealization may not be suitable in these circumstances, since the covariance of the clock errors may become large enough to overflow flight computer arithmetic. A model that is stable, but which approximates the existing models over short time horizons is desirable. A coupled first- and second-order Gauss-Markov process is such a model.
Effects of different per translational kinetics on the dynamics of a core circadian clock model.
Paula S Nieto
Full Text Available Living beings display self-sustained daily rhythms in multiple biological processes, which persist in the absence of external cues since they are generated by endogenous circadian clocks. The period (per gene is a central player within the core molecular mechanism for keeping circadian time in most animals. Recently, the modulation PER translation has been reported, both in mammals and flies, suggesting that translational regulation of clock components is important for the proper clock gene expression and molecular clock performance. Because translational regulation ultimately implies changes in the kinetics of translation and, therefore, in the circadian clock dynamics, we sought to study how and to what extent the molecular clock dynamics is affected by the kinetics of PER translation. With this objective, we used a minimal mathematical model of the molecular circadian clock to qualitatively characterize the dynamical changes derived from kinetically different PER translational mechanisms. We found that the emergence of self-sustained oscillations with characteristic period, amplitude, and phase lag (time delays between per mRNA and protein expression depends on the kinetic parameters related to PER translation. Interestingly, under certain conditions, a PER translation mechanism with saturable kinetics introduces longer time delays than a mechanism ruled by a first-order kinetics. In addition, the kinetic laws of PER translation significantly changed the sensitivity of our model to parameters related to the synthesis and degradation of per mRNA and PER degradation. Lastly, we found a set of parameters, with realistic values, for which our model reproduces some experimental results reported recently for Drosophila melanogaster and we present some predictions derived from our analysis.
Relaxation Oscillations in New IS-LM Model
Volná, Barbora
2012-01-01
In this paper, we create new version of IS-LM model. The original IS-LM model has two main deficiencies: assumptions of constant price level and of strictly exogenous money supply. New IS-LM model eliminates these deficiencies. In the second section, we prove the existence of relaxation oscillations in this new IS-LM model.
Treenut Saithong
Full Text Available BACKGROUND: Sensitivity and robustness are essential properties of circadian clock systems, enabling them to respond to the environment but resist noisy variations. These properties should be recapitulated in computational models of the circadian clock. Highly nonlinear kinetics and multiple loops are often incorporated into models to match experimental time-series data, but these also impact on model properties for clock models. METHODOLOGY/PRINCIPAL FINDINGS: Here, we study the consequences of complicated structure and nonlinearity using simple Goodwin-type oscillators and the complex Arabidopsis circadian clock models. Sensitivity analysis of the simple oscillators implies that an interlocked multi-loop structure reinforces sensitivity/robustness properties, enhancing the response to external and internal variations. Furthermore, we found that reducing the degree of nonlinearity could sometimes enhance the robustness of models, implying that ad hoc incorporation of nonlinearity could be detrimental to a model's perceived credibility. CONCLUSION: The correct multi-loop structure and degree of nonlinearity are therefore critical in contributing to the desired properties of a model as well as its capacity to match experimental data.
Predictability of the large relaxations in a cellular automaton model
Tejedor, Alejandro; Ambroj, Samuel; Gomez, Javier B; Pacheco, Amalio F [Faculty of Sciences, University of Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza (Spain)
2008-09-19
A simple one-dimensional cellular automaton model with threshold dynamics is introduced. It is loaded at a uniform rate and unloaded by abrupt relaxations. The cumulative distribution of the size of the relaxations is analytically computed and behaves as a power law with an exponent equal to -1. This coincides with the phenomenological Gutenberg-Richter behavior observed in seismology for the cumulative statistics of earthquakes at the regional or global scale. The key point of the model is the zero-load state of the system after the occurrence of any relaxation, no matter what its size. This leads to an equipartition of probability between all possible load configurations in the system during the successive loading cycles. Each cycle ends with the occurrence of the greatest-or characteristic-relaxation in the system. The duration of the cycles in the model is statistically distributed with a coefficient of variation ranging from 0.5 to 1. The predictability of the characteristic relaxations is evaluated by means of error diagrams. This model illustrates the value taking into account the refractory periods to obtain a considerable gain in the quality of the predictions.
A disruption mechanism of the molecular clock in a MPTP mouse model of Parkinson's disease.
Hayashi, Akane; Matsunaga, Naoya; Okazaki, Hiroyuki; Kakimoto, Keisuke; Kimura, Yoshinori; Azuma, Hiroki; Ikeda, Eriko; Shiba, Takeshi; Yamato, Mayumi; Yamada, Ken-Ichi; Koyanagi, Satoru; Ohdo, Shigehiro
2013-06-01
Parkinson's disease (PD) is a common neurodegenerative disorder that is characterized by the degeneration of dopaminergic neurons in the substantia nigra and dopamine depletion in the striatum. Although the motor symptoms are still regarded as the main problem, non-motor symptoms in PD also markedly impair the quality of life. Several non-motor symptoms, such as sleep disturbances and depression, are suggested to be implicated in the alteration in circadian clock function. In this study, we investigated circadian disruption and the mechanism in a 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) mouse model of PD. MPTP-treated mice exhibited altered 24-h rhythms in body temperature and locomotor activity. In addition, MPTP treatment also affected the circadian clock system at the genetic level. The exposure of human neuroblastoma cells (SH-SY5Y) to 1-metyl-4-phenylpyridinium (MPP(+)) increased or decreased the mRNA levels of several clock genes in a dose-dependent manner. MPP(+)-induced changes in clock genes expression were reversed by Compound C, an inhibitor of AMP-activated protein kinase (AMPK). Most importantly, addition of ATP to the drinking water of MPTP-treated mice attenuated neurodegeneration in dopaminergic neurons, suppressed AMPK activation and prevented circadian disruption. The present findings suggest that the activation of AMPK caused circadian dysfunction, and ATP may be a novel therapeutic strategy based on the molecular clock in PD.
Simultaneous single epoch satellite clock modelling in Global Navigation Satellite Systems
Thongtan, Thayathip
In order to obtain high quality positions from navigation satellites, range errors have to be identified and either modelled or estimated. This thesis focuses on satellite clock errors, which are needed to be known because satellite clocks are not perfectly synchronised with navigation system time. A new approach, invented at UCL, for the simultaneous estimation, in a single epoch, of all satellite clock offsets within a Global Navigation Satellite System (GNSS) from range data collected at a large number of globally distributed ground stations is presented. The method was originally tested using only data from a limited number of GPS satellites and ground stations. In this work a total of 50 globally distributed stations and the whole GPS constellation are used in order to investigate more fully the capabilities of the method, in terms of both accuracy and reliability. A number of different estimation models have been tested. These include those with different weighting schemes, those with and without tropospheric bias parameters and those that include assumptions regarding prior knowledge of satellite orbits. In all cases conclusions have been drawn based on formal error propagation theory. Accuracy has been assessed largely through the sizes of the predicted satellite clock standard deviations and, in the case of simultaneously estimating satellite positions, their error ellipsoids. Both internal and external reliability have been assessed as these are important contributors to integrity, something that is essential for many practical applications. It has been found that the accuracy and reliability of satellite clock offsets are functions of the number of known ground station clocks and distance from them, quality of orbits and quality of range measurement. Also the introduction of tropospheric zenith delay parameters into the model reduces both accuracy and reliability by amounts depending on satellite elevation angles. (Abstract shortened by UMI.)
High fidelity modeling of thermal relaxation and dissociation of oxygen
Andrienko, Daniil A., E-mail: daniila@umich.edu; Boyd, Iain D. [Department of Aerospace Engineering, University of Michigan, 1320 Beal Ave., Ann Arbor, Michigan 48108 (United States)
2015-11-15
A master equation study of vibrational relaxation and dissociation of oxygen is conducted using state-specific O{sub 2}–O transition rates, generated by extensive trajectory simulations. Both O{sub 2}–O and O{sub 2}–O{sub 2} collisions are concurrently simulated in the evolving nonequilibrium gas system under constant heat bath conditions. The forced harmonic oscillator model is incorporated to simulate the state-to-state relaxation of oxygen in O{sub 2}–O{sub 2} collisions. The system of master equations is solved to simulate heating and cooling flows. The present study demonstrates the importance of atom-diatom collisions due to the extremely efficient energy randomization in the intermediate O{sub 3} complex. It is shown that the presence of atomic oxygen has a significant impact on vibrational relaxation time at temperatures observed in hypersonic flow. The population of highly-excited O{sub 2} vibrational states is affected by the amount of atomic oxygen when modeling the relaxation under constant heat bath conditions. A model of coupled state-to-state vibrational relaxation and dissociation of oxygen is also discussed.
Chidambaram Ramanathan
2014-04-01
Full Text Available In animals, circadian rhythms in physiology and behavior result from coherent rhythmic interactions between clocks in the brain and those throughout the body. Despite the many tissue specific clocks, most understanding of the molecular core clock mechanism comes from studies of the suprachiasmatic nuclei (SCN of the hypothalamus and a few other cell types. Here we report establishment and genetic characterization of three cell-autonomous mouse clock models: 3T3 fibroblasts, 3T3-L1 adipocytes, and MMH-D3 hepatocytes. Each model is genetically tractable and has an integrated luciferase reporter that allows for longitudinal luminescence recording of rhythmic clock gene expression using an inexpensive off-the-shelf microplate reader. To test these cellular models, we generated a library of short hairpin RNAs (shRNAs against a panel of known clock genes and evaluated their impact on circadian rhythms. Knockdown of Bmal1, Clock, Cry1, and Cry2 each resulted in similar phenotypes in all three models, consistent with previous studies. However, we observed cell type-specific knockdown phenotypes for the Period and Rev-Erb families of clock genes. In particular, Per1 and Per2, which have strong behavioral effects in knockout mice, appear to play different roles in regulating period length and amplitude in these peripheral systems. Per3, which has relatively modest behavioral effects in knockout mice, substantially affects period length in the three cellular models and in dissociated SCN neurons. In summary, this study establishes new cell-autonomous clock models that are of particular relevance to metabolism and suitable for screening for clock modifiers, and reveals previously under-appreciated cell type-specific functions of clock genes.
Optimizing passive quantum clocks
Mullan, Michael; Knill, Emanuel
2014-10-01
We describe protocols for passive atomic clocks based on quantum interrogation of the atoms. Unlike previous techniques, our protocols are adaptive and take advantage of prior information about the clock's state. To reduce deviations from an ideal clock, each interrogation is optimized by means of a semidefinite program for atomic state preparation and measurement whose objective function depends on the prior information. Our knowledge of the clock's state is maintained according to a Bayesian model that accounts for noise and measurement results. We implement a full simulation of a running clock with power-law noise models and find significant improvements by applying our techniques.
A model for the generic alpha relaxation in viscous liquids
Dyre, Jeppe
2005-01-01
. Rev. Lett., 86 (2001) 1271]. Assuming that long-wavelength fluctuations dominate the dynamics, a model for the dielectric alpha relaxation based on the simplest coupling between the density and dipole density fields is proposed here. The model, which is solved in second-order perturbation theory......Dielectric measurements on molecular liquids just above the glass transition indicate that alpha relaxation is characterized by a generic high-frequency loss varying as one over square root of frequency, whereas deviations from this come from one or more low-lying beta processes [Olsen et al., Phys...
Relaxation of polymers modeled by generalized Husimi cacti
Galiceanu, M.
2010-07-01
We focus on the generalized Husimi cacti, which are dual structures to the dendrimers but, distinct from the latter, contain loops. We determine their complete spectra by making use of the normal mode analysis. These spectra have been used in computing some physical quantities, such as the averaged monomer displacement and the mechanical relaxation moduli with its two components: the storage and the loss modulus. We also study the dynamics of Husimi cacti in solutions, introducing the hydrodynamic interactions in a preaveraged Oseen fashion, the so-called Zimm model. We observe that the relaxation quantities mentioned above do not scale, in the presence or in the absence of the hydrodynamic interactions. Our results show that all the relaxation forms depend on the number of monomers in the networks in the absence of the hydrodynamic interactions (Rouse model), while by taking into account the hydrodynamic interactions the results do not vary too much.
Relaxation of polymers modeled by generalized Husimi cacti
Galiceanu, M, E-mail: mircea@fisica.ufpr.b [Departamento de Fisica, Universidade Federal do Parana, 81531-990 Curitiba (Brazil)
2010-07-30
We focus on the generalized Husimi cacti, which are dual structures to the dendrimers but, distinct from the latter, contain loops. We determine their complete spectra by making use of the normal mode analysis. These spectra have been used in computing some physical quantities, such as the averaged monomer displacement and the mechanical relaxation moduli with its two components: the storage and the loss modulus. We also study the dynamics of Husimi cacti in solutions, introducing the hydrodynamic interactions in a preaveraged Oseen fashion, the so-called Zimm model. We observe that the relaxation quantities mentioned above do not scale, in the presence or in the absence of the hydrodynamic interactions. Our results show that all the relaxation forms depend on the number of monomers in the networks in the absence of the hydrodynamic interactions (Rouse model), while by taking into account the hydrodynamic interactions the results do not vary too much.
Lego clocks: building a clock from parts.
Brunner, Michael; Simons, Mirre J P; Merrow, Martha
2008-06-01
A new finding opens up speculation that the molecular mechanism of circadian clocks in Synechococcus elongatus is composed of multiple oscillator systems (Kitayama and colleagues, this issue, pp. 1513-1521), as has been described in many eukaryotic clock model systems. However, an alternative intepretation is that the pacemaker mechanism-as previously suggested-lies primarily in the rate of ATP hydrolysis by the clock protein KaiC.
Relaxation and diffusion models with non-singular kernels
Sun, HongGuang; Hao, Xiaoxiao; Zhang, Yong; Baleanu, Dumitru
2017-02-01
Anomalous relaxation and diffusion processes have been widely quantified by fractional derivative models, where the definition of the fractional-order derivative remains a historical debate due to its limitation in describing different kinds of non-exponential decays (e.g. stretched exponential decay). Meanwhile, many efforts by mathematicians and engineers have been made to overcome the singularity of power function kernel in its definition. This study first explores physical properties of relaxation and diffusion models where the temporal derivative was defined recently using an exponential kernel. Analytical analysis shows that the Caputo type derivative model with an exponential kernel cannot characterize non-exponential dynamics well-documented in anomalous relaxation and diffusion. A legitimate extension of the previous derivative is then proposed by replacing the exponential kernel with a stretched exponential kernel. Numerical tests show that the Caputo type derivative model with the stretched exponential kernel can describe a much wider range of anomalous diffusion than the exponential kernel, implying the potential applicability of the new derivative in quantifying real-world, anomalous relaxation and diffusion processes.
Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution
2017-01-01
Molecular sequence data provide information about relative times only, and fossil-based age constraints are the ultimate source of information about absolute times in molecular clock dating analyses. Thus, fossil calibrations are critical to molecular clock dating, but competing methods are difficult to evaluate empirically because the true evolutionary time scale is never known. Here, we combine mechanistic models of fossil preservation and sequence evolution in simulations to evaluate different approaches to constructing fossil calibrations and their impact on Bayesian molecular clock dating, and the relative impact of fossil versus molecular sampling. We show that divergence time estimation is impacted by the model of fossil preservation, sampling intensity and tree shape. The addition of sequence data may improve molecular clock estimates, but accuracy and precision is dominated by the quality of the fossil calibrations. Posterior means and medians are poor representatives of true divergence times; posterior intervals provide a much more accurate estimate of divergence times, though they may be wide and often do not have high coverage probability. Our results highlight the importance of increased fossil sampling and improved statistical approaches to generating calibrations, which should incorporate the non-uniform nature of ecological and temporal fossil species distributions. PMID:28637852
Kinetic theories for spin models for cooperative relaxation dynamics
Pitts, Steven Jerome
The facilitated kinetic Ising models with asymmetric spin flip constraints introduced by Jackle and co-workers [J. Jackle, S. Eisinger, Z. Phys. B 84, 115 (1991); J. Reiter, F. Mauch, J. Jackle, Physica A 184, 458 (1992)] exhibit complex relaxation behavior in their associated spin density time correlation functions. This includes the growth of relaxation times over many orders of magnitude when the thermodynamic control parameter is varied, and, in some cases, ergodic-nonergodic transitions. Relaxation equations for the time dependence of the spin density autocorrelation function for a set of these models are developed that relate this autocorrelation function to the irreducible memory function of Kawasaki [K. Kawasaki, Physica A 215, 61 (1995)] using a novel diagrammatic series approach. It is shown that the irreducible memory function in a theory of the relaxation of an autocorrelation function in a Markov model with detailed balance plays the same role as the part of the memory function approximated by a polynomial function of the autocorrelation function with positive coefficients in schematic simple mode coupling theories for supercooled liquids [W. Gotze, in Liquids, Freezing and the Glass Transition, D. Levesque, J. P. Hansen, J. Zinn-Justin eds., 287 (North Holland, New York, 1991)]. Sets of diagrams in the series for the irreducible memory function are summed which lead to approximations of this type. The behavior of these approximations is compared with known results from previous analytical calculations and from numerical simulations. For the simplest one dimensional model, relaxation equations that are closely related to schematic extended mode coupling theories [W. Gotze, ibid] are also derived using the diagrammatic series. Comparison of the results of these approximate theories with simulation data shows that these theories improve significantly on the results of the theories of the simple schematic mode coupling theory type. The potential
Kunichika Tsumoto
Full Text Available Periods of biological clocks are close to but often different from the rotation period of the earth. Thus, the clocks of organisms must be adjusted to synchronize with day-night cycles. The primary signal that adjusts the clocks is light. In Neurospora, light transiently up-regulates the expression of specific clock genes. This molecular response to light is called light adaptation. Does light adaptation occur in other organisms? Using published experimental data, we first estimated the time course of the up-regulation rate of gene expression by light. Intriguingly, the estimated up-regulation rate was transient during light period in mice as well as Neurospora. Next, we constructed a computational model to consider how light adaptation had an effect on the entrainment of circadian oscillation to 24-h light-dark cycles. We found that cellular oscillations are more likely to be destabilized without light adaption especially when light intensity is very high. From the present results, we predict that the instability of circadian oscillations under 24-h light-dark cycles can be experimentally observed if light adaptation is altered. We conclude that the functional consequence of light adaptation is to increase the adjustability to 24-h light-dark cycles and then adapt to fluctuating environments in nature.
Tsumoto, Kunichika; Kurosawa, Gen; Yoshinaga, Tetsuya; Aihara, Kazuyuki
2011-01-01
Periods of biological clocks are close to but often different from the rotation period of the earth. Thus, the clocks of organisms must be adjusted to synchronize with day-night cycles. The primary signal that adjusts the clocks is light. In Neurospora, light transiently up-regulates the expression of specific clock genes. This molecular response to light is called light adaptation. Does light adaptation occur in other organisms? Using published experimental data, we first estimated the time course of the up-regulation rate of gene expression by light. Intriguingly, the estimated up-regulation rate was transient during light period in mice as well as Neurospora. Next, we constructed a computational model to consider how light adaptation had an effect on the entrainment of circadian oscillation to 24-h light-dark cycles. We found that cellular oscillations are more likely to be destabilized without light adaption especially when light intensity is very high. From the present results, we predict that the instability of circadian oscillations under 24-h light-dark cycles can be experimentally observed if light adaptation is altered. We conclude that the functional consequence of light adaptation is to increase the adjustability to 24-h light-dark cycles and then adapt to fluctuating environments in nature.
Characterization and modeling of intermittent locomotor dynamics in clock gene-deficient mice.
Toru Nakamura
Full Text Available The scale-invariant and intermittent dynamics of animal behavior are attracting scientific interest. Recent findings concerning the statistical laws of behavioral organization shared between healthy humans and wild-type mice (WT and their alterations in human depression patients and circadian clock gene (Period 2; Per2 mutant mice indicate that clock genes play functional roles in intermittent, ultradian locomotor dynamics. They also claim the clinical and biological importance of the laws as objective biobehavioral measures or endophenotypes for psychiatric disorders. In this study, to elucidate the roles of breakdown of the broader circadian regulatory circuit in intermittent behavioral dynamics, we studied the statistical properties and rhythmicity of locomotor activity in Per2 mutants and mice deficient in other clock genes (Bmal1, Clock. We performed wavelet analysis to examine circadian and ultradian rhythms and estimated the cumulative distributions of resting period durations during which locomotor activity levels are continuously lower than a predefined threshold value. The wavelet analysis revealed significant amplification of ultradian rhythms in the BMAL1-deficient mice, and instability in the Per2 mutants. The resting period distributions followed a power-law form in all mice. While the distributions for the BMAL1-deficient and Clock mutant mice were almost identical to those for the WT mice, with no significant differences in their parameter (power-law scaling exponent, only the Per2 mutant mice showed consistently and significantly lower values of the scaling exponent, indicating the increased intermittency in ultradian locomotor dynamics. Furthermore, based on a stochastic priority queuing model, we explained the power-law nature of resting period distributions, as well as its alterations shared with human depressive patients and Per2 mutant mice. Our findings lead to the development of a novel mathematical model for abnormal
Minimal model for beta relaxation in viscous liquids
Dyre, Jeppe; Olsen, Niels Boye
2003-01-01
Contrasts between beta relaxation in equilibrium viscous liquids and glasses are rationalized in terms of a double-well potential model with structure-dependent asymmetry, assuming structure is described by a single order parameter. The model is tested for tripropylene glycol where it accounts...... for the hysteresis of the dielectric beta loss peak frequency and magnitude during cooling and reheating through the glass transition....
A study of temporal estimation from the perspective of the Mental Clock Model.
Carmeci, Floriana; Misuraca, Raffaella; Cardaci, Maurizio
2009-04-01
M. Cardaci's (2000) Mental Clock Model maintains that a task requiring a low mental workload is associated with an acceleration of perceived time, whereas a task requiring a high mental workload is associated with a deceleration. The authors examined the predictions of this model in a musical listening condition in which musical pieces were audible in several structural complexities. To measure the effects of musical complexity on time estimation, the authors used retrospective and prospective time-estimation paradigms. For the retrospective paradigm, the authors invited participants to listen to a musical piece and then estimate its duration. For the prospective paradigm, the authors invited participants to stop the musical reproduction after a certain interval of time. Results show that the variations of musical complexity yielded the empirical effects that the Mental Clock Model predicted for both paradigms.
Creep and stress relaxation modeling of polycrystalline ceramic fibers
Dicarlo, James A.; Morscher, Gregory N.
1994-01-01
A variety of high performance polycrystalline ceramic fibers are currently being considered as reinforcement for high temperature ceramic matrix composites. However, under mechanical loading about 800 C, these fibers display creep related instabilities which can result in detrimental changes in composite dimensions, strength, and internal stress distributions. As a first step toward understanding these effects, this study examines the validity of a mechanism-based empirical model which describes primary stage tensile creep and stress relaxation of polycrystalline ceramic fibers as independent functions of time, temperature, and applied stress or strain. To verify these functional dependencies, a simple bend test is used to measure stress relaxation for four types of commercial ceramic fibers for which direct tensile creep data are available. These fibers include both nonoxide (SCS-6, Nicalon) and oxide (PRD-166, FP) compositions. The results of the Bend Stress Relaxation (BSR) test not only confirm the stress, time, and temperature dependencies predicted by the model, but also allow measurement of model empirical parameters for the four fiber types. In addition, comparison of model tensile creep predictions based on the BSR test results with the literature data show good agreement, supporting both the predictive capability of the model and the use of the BSR text as a simple method for parameter determination for other fibers.
An application-semantics-based relaxed transaction model for internetware
HUANG Tao; DING Xiaoning; WEI Jun
2006-01-01
An internetware application is composed by existing individual services, while transaction processing is a key mechanism to make the composition reliable. The existing research of transactional composite service (TCS) depends on the analysis to composition structure and exception handling mechanism in order to guarantee the relaxed atomicity.However, this approach cannot handle some application-specific requirements and causes lots of unnecessary failure recoveries or even aborts. In this paper, we propose a relaxed transaction model, including system mode, relaxed atomicity criterion, static checking algorithm and dynamic enforcement algorithm. Users are able to define different relaxed atomicity constraint for different TCS according to application-specific requirements, including acceptable configurations and the preference order. The checking algorithm determines whether the constraint can be guaranteed to be satisfied. The enforcement algorithm monitors the execution and performs transaction management work according to the constraint. Compared to the existing work, our approach can handle complex application requirements, avoid unnecessary failure recoveries and perform the transaction management work automatically.
Modelling of diffusion and conductivity relaxation of oxide ceramics
Preis, Wolfgang
2016-12-01
A two-dimensional square grain model has been applied to simulate simultaneously the diffusion process and relaxation of the dc conduction of polycrystalline oxide materials due to a sudden change of the oxygen partial pressure of the surrounding gas phase. The numerical calculations are performed by employing the finite element approach. The grains are squares of equal side length (average grain size) and the grain boundaries may consist of thin slabs of uniform thickness. An additional (space charge) layer adjacent to the grain boundary cores (thin slabs) either blocking (depletion layer) or highly conductive for electronic charge carriers may surround the grains. The electronic transport number of the mixed ionic-electronic conducting oxide ceramics may be close to unity (predominant electronic conduction). If the chemical diffusion coefficient of the neutral mobile component (oxygen) of the grain boundary core regions is assumed to be higher by many orders of magnitude than that in the bulk, the simulated relaxation curves for mass transport (diffusion) and dc conduction can deviate remarkably from each other. Deviations between the relaxation of mass transport and dc conduction are found in the case of considerably different electronic conductivities of grain boundary core regions, space charge layers, and bulk. On the contrary, the relaxation curves of mass transport and electronic conductivity are in perfect coincidence, when either effective medium diffusion occurs or the effective conductivity is unaffected by the individual conductivities of core regions and possible space charge layers, i.e. the grain boundary resistivity is negligible.
Lezhnin Sergey
2017-01-01
Full Text Available The two-temperature model of the outflow from a vessel with initial supercritical parameters of medium has been realized. The model uses thermodynamic non-equilibrium relaxation approach to describe phase transitions. Based on a new asymptotic model for computing the relaxation time, the outflow of water with supercritical initial pressure and super- and subcritical temperatures has been calculated.
Pokhilko, Alexandra; Hodge, Sarah K; Stratford, Kevin; Knox, Kirsten; Edwards, Kieron D; Thomson, Adrian W; Mizuno, Takeshi; Millar, Andrew J
2010-01-01
Circadian clocks generate 24-h rhythms that are entrained by the day/night cycle. Clock circuits include several light inputs and interlocked feedback loops, with complex dynamics. Multiple biological components can contribute to each part of the circuit in higher organisms. Mechanistic models with morning, evening and central feedback loops have provided a heuristic framework for the clock in plants, but were based on transcriptional control. Here, we model observed, post-transcriptional and post-translational regulation and constrain many parameter values based on experimental data. The model's feedback circuit is revised and now includes PSEUDO-RESPONSE REGULATOR 7 (PRR7) and ZEITLUPE. The revised model matches data in varying environments and mutants, and gains robustness to parameter variation. Our results suggest that the activation of important morning-expressed genes follows their release from a night inhibitor (NI). Experiments inspired by the new model support the predicted NI function and show that the PRR5 gene contributes to the NI. The multiple PRR genes of Arabidopsis uncouple events in the late night from light-driven responses in the day, increasing the flexibility of rhythmic regulation. PMID:20865009
Multiple-relaxation-time model for the correct thermohydrodynamic equations.
Zheng, Lin; Shi, Baochang; Guo, Zhaoli
2008-08-01
A coupling lattice Boltzmann equation (LBE) model with multiple relaxation times is proposed for thermal flows with viscous heat dissipation and compression work. In this model the fixed Prandtl number and the viscous dissipation problems in the energy equation, which exist in most of the LBE models, are successfully overcome. The model is validated by simulating the two-dimensional Couette flow, thermal Poiseuille flow, and the natural convection flow in a square cavity. It is found that the numerical results agree well with the analytical solutions and/or other numerical results.
More relaxed conditions for model predictive control with guaranteed stability
Bin LIU; Yugeng XI
2005-01-01
For the model predictive controller,terminal state satisfying a certain inequality can guarantee the stability but it is somewhat conservative.In this paper,we give a more relaxed stability condition by considering the effect of the initial state.Based on that we propose an algorithm to guarantee that the closed loop system is asymptotically stable.Finally,the conclusions are verified by a simulation.
Numerical modeling of bubble dynamics in viscoelastic media with relaxation
Warnez, M. T.; Johnsen, E.
2015-06-01
Cavitation occurs in a variety of non-Newtonian fluids and viscoelastic materials. The large-amplitude volumetric oscillations of cavitation bubbles give rise to high temperatures and pressures at collapse, as well as induce large and rapid deformation of the surroundings. In this work, we develop a comprehensive numerical framework for spherical bubble dynamics in isotropic media obeying a wide range of viscoelastic constitutive relationships. Our numerical approach solves the compressible Keller-Miksis equation with full thermal effects (inside and outside the bubble) when coupled to a highly generalized constitutive relationship (which allows Newtonian, Kelvin-Voigt, Zener, linear Maxwell, upper-convected Maxwell, Jeffreys, Oldroyd-B, Giesekus, and Phan-Thien-Tanner models). For the latter two models, partial differential equations (PDEs) must be solved in the surrounding medium; for the remaining models, we show that the PDEs can be reduced to ordinary differential equations. To solve the general constitutive PDEs, we present a Chebyshev spectral collocation method, which is robust even for violent collapse. Combining this numerical approach with theoretical analysis, we simulate bubble dynamics in various viscoelastic media to determine the impact of relaxation time, a constitutive parameter, on the associated physics. Relaxation time is found to increase bubble growth and permit rebounds driven purely by residual stresses in the surroundings. Different regimes of oscillations occur depending on the relaxation time.
Modeling the emergence of circadian rhythms in a clock neuron network.
Luis Diambra
Full Text Available Circadian rhythms in pacemaker cells persist for weeks in constant darkness, while in other types of cells the molecular oscillations that underlie circadian rhythms damp rapidly under the same conditions. Although much progress has been made in understanding the biochemical and cellular basis of circadian rhythms, the mechanisms leading to damped or self-sustained oscillations remain largely unknown. There exist many mathematical models that reproduce the circadian rhythms in the case of a single cell of the Drosophila fly. However, not much is known about the mechanisms leading to coherent circadian oscillation in clock neuron networks. In this work we have implemented a model for a network of interacting clock neurons to describe the emergence (or damping of circadian rhythms in Drosophila fly, in the absence of zeitgebers. Our model consists of an array of pacemakers that interact through the modulation of some parameters by a network feedback. The individual pacemakers are described by a well-known biochemical model for circadian oscillation, to which we have added degradation of PER protein by light and multiplicative noise. The network feedback is the PER protein level averaged over the whole network. In particular, we have investigated the effect of modulation of the parameters associated with (i the control of net entrance of PER into the nucleus and (ii the non-photic degradation of PER. Our results indicate that the modulation of PER entrance into the nucleus allows the synchronization of clock neurons, leading to coherent circadian oscillations under constant dark condition. On the other hand, the modulation of non-photic degradation cannot reset the phases of individual clocks subjected to intrinsic biochemical noise.
A thermodynamically consistent model of the post-translational Kai circadian clock
Lubensky, David K.; ten Wolde, Pieter Rein
2017-01-01
The principal pacemaker of the circadian clock of the cyanobacterium S. elongatus is a protein phosphorylation cycle consisting of three proteins, KaiA, KaiB and KaiC. KaiC forms a homohexamer, with each monomer consisting of two domains, CI and CII. Both domains can bind and hydrolyze ATP, but only the CII domain can be phosphorylated, at two residues, in a well-defined sequence. While this system has been studied extensively, how the clock is driven thermodynamically has remained elusive. Inspired by recent experimental observations and building on ideas from previous mathematical models, we present a new, thermodynamically consistent, statistical-mechanical model of the clock. At its heart are two main ideas: i) ATP hydrolysis in the CI domain provides the thermodynamic driving force for the clock, switching KaiC between an active conformational state in which its phosphorylation level tends to rise and an inactive one in which it tends to fall; ii) phosphorylation of the CII domain provides the timer for the hydrolysis in the CI domain. The model also naturally explains how KaiA, by acting as a nucleotide exchange factor, can stimulate phosphorylation of KaiC, and how the differential affinity of KaiA for the different KaiC phosphoforms generates the characteristic temporal order of KaiC phosphorylation. As the phosphorylation level in the CII domain rises, the release of ADP from CI slows down, making the inactive conformational state of KaiC more stable. In the inactive state, KaiC binds KaiB, which not only stabilizes this state further, but also leads to the sequestration of KaiA, and hence to KaiC dephosphorylation. Using a dedicated kinetic Monte Carlo algorithm, which makes it possible to efficiently simulate this system consisting of more than a billion reactions, we show that the model can describe a wealth of experimental data. PMID:28296888
Two-Temperature Model of Nonequilibrium Electron Relaxation:. a Review
Singh, Navinder
The present paper is a review of the phenomena related to nonequilibrium electron relaxation in bulk and nano-scale metallic samples. The workable Two-Temperature Model (TTM) based on Boltzmann-Bloch-Peierls kinetic equation has been applied to study the ultra-fast (femto-second) electronic relaxation in various metallic systems. The advent of new ultra-fast (femto-second) laser technology and pump-probe spectroscopy has produced wealth of new results for micro- and nano-scale electronic technology. The aim of this paper is to clarify the TTM, conditions of its validity and nonvalidity, its modifications for nano-systems, to sum-up the progress, and to point out open problems in this field. We also give a phenomenological integro-differential equation for the kinetics of nondegenerate electrons that goes beyond the TTM.
Theoretical Modeling and Simulation of Phase-Locked Loop (PLL) for Clock Data Recovery (CDR)
Ashari, Zainab
2012-01-01
Modern communication and computer systems require rapid (Gbps), efficient and large bandwidth data transfers. Agressive scaling of digital integrated systems allow buses and communication controller circuits to be integrated with the microprocessor on the same chip. The Peripheral Component Interconnect Express (PCIe) protocol handles all communcation between the central processing unit (CPU) and hardware devices. PCIe buses require efficient clock data recovery circuits (CDR) to recover clock signals embedded in data during transmission. This paper describes the theoretical modeling and simulation of a phase-locked loop (PLL) used in a CDR circuit. A simple PLL architecture for a 5 GHz CDR circuit is proposed and elaborated in this work. Simulations were carried out using a Hardware Description Language, Verilog- AMS. The effect of jitter on the proposed design is also simulated and evaluated in this work. It was found that the proposed design is robust against both input and VCO jitter.
Convergence of clock processes in random environments and ageing in the p-spin SK model
Bovier, Anton
2010-01-01
We derive a general criterion for the convergence of clock processes in random dynamics in random environments that is applicable in cases when correlations are not negligible, extending recent results by Gayrard [15,16], based on general criterion for convergence of sums of dependent random variables due to Durrett and Resnick [13]. We demonstrate the power of this criterion by applying it to the case of random hopping time dynamics of the p-spin SK model. We prove that on a wide range of time scales, the clock process converges to a stable subordinator almost surely with respect to the environment. We also show that a time-time correlation function converges to the arcsine law for this subordinator, almost surely. This improves recent results of Ben Arous et al. [1] that obtained similar convergence result in law with respect to the random environment.
Stochastic delay models for molecular clocks and somite formation
Burrage, Kevin; Burrage, Pamela; Leier, André; Marquez-Lago, Tatiana T.
2007-12-01
Delays are an important feature in temporal models of genetic regulation due to slow biochemical processes such as transcription and translation. In this paper we show how to model intrinsic noise effects in a delayed setting by either using a delay stochastic simulation algorithm (DSSA) or, for larger and more complex systems, a generalized Binomial tau-leap method (Bt-DSSA). As a particular application we apply these ideas to modeling somite segmentation in zebrafish across a number of cells in which two linked oscillatory genes her1 and her7 are synchronized via Notch signaling between the cells.
CHEN Liang
2016-09-01
Full Text Available Real-time high-precise satellite orbit and clock products are needed in real-time GNSS precise point positioning (PPP. In this paper, Estimation model and strategy of multi-GNSS precise satellite clock integrated resolving are researched and BeiDou/GPS real-time precise clock integrated estimation algorithm is realized by filter. Real-time simulation test results show: the STD accuracy of BeiDou/GPS real-time clock estimated in this paper compared to GFZ multi-GNSS precise clock(GBM is about 0.15ns; horizontal accuracy after convergence of GPS kinematic PPP using simulation real-time clock products estimated in this paper is better than 5cm and vertical accuracy is better than 10cm, respectively; in BeiDou kinematic PPP test, horizontal and vertical accuracy results are same as the results using GFZ multi-GNSS precise clock(GBM products, and the decimeter positioning can be realized.
Bayesian random local clocks, or one rate to rule them all
Drummond Alexei J
2010-08-01
Full Text Available Abstract Background Relaxed molecular clock models allow divergence time dating and "relaxed phylogenetic" inference, in which a time tree is estimated in the face of unequal rates across lineages. We present a new method for relaxing the assumption of a strict molecular clock using Markov chain Monte Carlo to implement Bayesian modeling averaging over random local molecular clocks. The new method approaches the problem of rate variation among lineages by proposing a series of local molecular clocks, each extending over a subregion of the full phylogeny. Each branch in a phylogeny (subtending a clade is a possible location for a change of rate from one local clock to a new one. Thus, including both the global molecular clock and the unconstrained model results, there are a total of 22n-2 possible rate models available for averaging with 1, 2, ..., 2n - 2 different rate categories. Results We propose an efficient method to sample this model space while simultaneously estimating the phylogeny. The new method conveniently allows a direct test of the strict molecular clock, in which one rate rules them all, against a large array of alternative local molecular clock models. We illustrate the method's utility on three example data sets involving mammal, primate and influenza evolution. Finally, we explore methods to visualize the complex posterior distribution that results from inference under such models. Conclusions The examples suggest that large sequence datasets may only require a small number of local molecular clocks to reconcile their branch lengths with a time scale. All of the analyses described here are implemented in the open access software package BEAST 1.5.4 (http://beast-mcmc.googlecode.com/.
A model of asynchronous left ventricular relaxation predicting the bi-exponential pressure decay
R.W. Brower (Ronald); S. Meij (Simon); P.W.J.C. Serruys (Patrick)
1983-01-01
textabstractA new model for the pressure relaxation of the left ventricle is proposed. The model presumes that the myocardium relaxes asynchronously, but that when regions begin to relax, after a delay, the local wall stress decays as a mono-exponential process. This formulation results in an appare
Thommen, Quentin; Pfeuty, Benjamin; Schatt, Philippe; Bijoux, Amandine; Bouget, François-Yves; Lefranc, Marc
2015-01-01
Most organisms anticipate daily environmental variations and orchestrate cellular functions thanks to a circadian clock which entrains robustly to the day/night cycle, despite fluctuations in light intensity due to weather or seasonal variations. Marine organisms are also subjected to fluctuations in light spectral composition as their depth varies, due to differential absorption of different wavelengths by sea water. Studying how light input pathways contribute to circadian clock robustness is therefore important. Ostreococcus tauri, a unicellular picoplanktonic marine green alga with low genomic complexity and simple cellular organization, has become a promising model organism for systems biology. Functional and modeling approaches have shown that a core circadian oscillator based on orthologs of Arabidopsis TOC1 and CCA1 clock genes accounts for most experimental data acquired under a wide range of conditions. Some evidence points at putative light input pathway(s) consisting of a two-component signaling system (TCS) controlled by the only two histidine kinases (HK) of O. tauri. LOV-HK is a blue light photoreceptor under circadian control, that is required for circadian clock function. An involvement of Rhodopsin-HK (Rhod-HK) is also conceivable since rhodopsin photoreceptors mediate blue to green light input in animal circadian clocks. Here, we probe the role of LOV-HK and Rhod-HK in mediating light input to the TOC1-CCA1 oscillator using a mathematical model incorporating the TCS hypothesis. This model agrees with clock gene expression time series representative of multiple environmental conditions in blue or green light, characterizing entrainment by light/dark cycles, free-running in constant light, and resetting. Experimental and theoretical results indicate that both blue and green light can reset O. tauri circadian clock. Moreover, our mathematical analysis suggests that Rhod-HK is a blue-green light receptor and drives the clock together with LOV-HK.
Modelling of intercellular synchronization in the Drosophila circadian clock
Wang Jun-Wei; Chen Ai-Min; Zhang Jia-Jun; Yuan Zhan-Jiang; Zhou Tian-Shou
2009-01-01
In circadian rhythm generation, intercellular signaling factors are shown to play a crucial role in both sustaining intrinsic cellular rhythmicity and acquiring collective behaviours across a population of circadian neurons. However, the physical mechanism behind their role remains to be fully understood. In this paper, we propose an indirectly coupled multicellular model for the synchronization of Drosophila circadian oscillators combining both intracellular and intercellular dynamics. By simulating different experimental conditions, we find that such an indirect coupling way can synchronize both heterogeneous self-sustained circadian neurons and heterogeneous mutational damped circadian neurons. Moreover, they can also be entrained to ambient light-dark (LD) cycles depending on intercellular signaling.
Maria Luisa eGuerriero
2014-10-01
Full Text Available Rhythmic behavior is essential for plants; for example, daily (circadian rhythms control photosynthesis and seasonal rhythms regulate their life cycle. The core of the circadian clock is a genetic network that coordinates the expression of specific clock genes in a circadian rhythm reflecting the 24-hour day/night cycle.Circadian clocks exhibit stochastic noise due to the low copy numbers of clock genes and the consequent cell-to-cell variation: this intrinsic noise plays a major role in circadian clocks by inducing more robust oscillatory behavior. Another source of noise is the environment, which causes variation in temperature and light intensity: this extrinsic noise is part of the requirement for the structural complexity of clock networks.Advances in experimental techniques now permit single-cell measurements and the development of single-cell models. Here we present some modeling studies showing the importance of considering both types of noise in understanding how plants adapt to regular and irregular light variations. Stochastic models have proven useful for understanding the effect of regular variations. By contrast, the impact of irregular variations and the interaction of different noise sources are less studied.
Relaxation oscillation model of hemodynamic parameters in the cerebral vessels
Cherevko, A. A.; Mikhaylova, A. V.; Chupakhin, A. P.; Ufimtseva, I. V.; Krivoshapkin, A. L.; Orlov, K. Yu
2016-06-01
Simulation of a blood flow under normality as well as under pathology is extremely complex problem of great current interest both from the point of view of fundamental hydrodynamics, and for medical applications. This paper proposes a model of Van der Pol - Duffing nonlinear oscillator equation describing relaxation oscillations of a blood flow in the cerebral vessels. The model is based on the patient-specific clinical experimental data flow obtained during the neurosurgical operations in Meshalkin Novosibirsk Research Institute of Circulation Pathology. The stability of the model is demonstrated through the variations of initial data and coefficients. It is universal and describes pressure and velocity fluctuations in different cerebral vessels (arteries, veins, sinuses), as well as in a laboratory model of carotid bifurcation. Derived equation describes the rheology of the ”blood stream - elastic vessel wall gelatinous brain environment” composite system and represents the state equation of this complex environment.
A Sequence of Relaxations Constraining Hidden Variable Models
Steeg, Greg Ver
2011-01-01
Many widely studied graphical models with latent variables lead to nontrivial constraints on the distribution of the observed variables. Inspired by the Bell inequalities in quantum mechanics, we refer to any linear inequality whose violation rules out some latent variable model as a "hidden variable test" for that model. Our main contribution is to introduce a sequence of relaxations which provides progressively tighter hidden variable tests. We demonstrate applicability to mixtures of sequences of i.i.d. variables, Bell inequalities, and homophily models in social networks. For the last, we demonstrate that our method provides a test that is able to rule out latent homophily as the sole explanation for correlations on a real social network that are known to be due to influence.
Homogeneous gas phase models of relaxation kinetics in neon afterglow
Marković Vidosav Lj.
2007-01-01
Full Text Available The homogeneous gas phase models of relaxation kinetics (application of the gas phase effective coefficients to represent surface losses are applied for the study of charged and neutral active particles decay in neon afterglow. The experimental data obtained by the breakdown time delay measurements as a function of the relaxation time td (τ (memory curve is modeled in early, as well as in late afterglow. The number density decay of metastable states can explain neither the early, nor the late afterglow kinetics (memory effect, because their effective lifetimes are of the order of milliseconds and are determined by numerous collision quenching processes. The afterglow kinetics up to hundreds of milliseconds is dominated by the decay of molecular neon Ne2 + and nitrogen ions N2 + (present as impurities and the approximate value of N2 + ambipolar diffusion coefficient is determined. After the charged particle decay, the secondary emitted electrons from the surface catalyzed excitation of nitrogen atoms on the cathode determine the breakdown time delay down to the cosmic rays and natural radioactivity level. Due to the neglecting of number density spatial profiles, the homogeneous gas phase models give only the approximate values of the corresponding coefficients, but reproduce correctly other characteristics of afterglow kinetics from simple fits to the experimental data.
Altered expression pattern of clock genes in a rat model of depression
Christiansen, Sofie; Bouzinova, Elena; Fahrenkrug, Jan;
2016-01-01
quantified expression of clock genes on brain sections in the prefrontal cortex, nucleus accumbens, pineal gland, suprachiasmatic nucleus, substantia nigra, amygdala, ventral tegmental area, subfields of the hippocampus, and the lateral habenula using in situ hybridization histochemistry. Expression of clock...
Keily, Jack; MacGregor, Dana R; Smith, Robert W; Millar, Andrew J; Halliday, Karen J; Penfield, Steven
2013-10-01
Circadian clocks confer advantages by restricting biological processes to certain times of day through the control of specific phased outputs. Control of temperature signalling is an important function of the plant oscillator, but the architecture of the gene network controlling cold signalling by the clock is not well understood. Here we use a model ensemble fitted to time-series data and a corrected Akaike Information Criterion (AICc) analysis to extend a dynamic model to include the control of the key cold-regulated transcription factors C-REPEAT BINDING FACTORs 1-3 (CBF1, CBF2, CBF3). AICc was combined with in silico analysis of genetic perturbations in the model ensemble, and selected a model that predicted mutant phenotypes and connections between evening-phased circadian clock components and CBF3 transcriptional control, but these connections were not shared by CBF1 and CBF2. In addition, our model predicted the correct gating of CBF transcription by cold only when the cold signal originated from the clock mechanism itself, suggesting that the clock has an important role in temperature signal transduction. Our data shows that model selection could be a useful method for the expansion of gene network models. © 2013 The Authors The Plant Journal © 2013 John Wiley & Sons Ltd.
Modeling charge relaxation in graphene quantum dots induced by electron-phonon interaction
Reichardt, Sven; Stampfer, Christoph
2016-06-01
We study and compare two analytic models of graphene quantum dots for calculating charge relaxation times due to electron-phonon interaction. Recently, charge relaxation processes in graphene quantum dots have been probed experimentally and here we provide a theoretical estimate of relaxation times. By comparing a model with pure edge confinement to a model with electrostatic confinement, we find that the latter features much larger relaxation times. Interestingly, relaxation times in electrostatically defined quantum dots are predicted to exceed the experimentally observed lower bound of ˜100 ns.
A Catapult (Slingshot) Current Sheet Relaxation Model for Substorm Triggering
Machida, S.; Miyashita, Y.; Ieda, A.
2010-12-01
Based on the results of our superposed epoch analysis of Geotail data, we have proposed a catapult (slingshot) current sheet relaxation model in which earthward flows are produced in the central plasma sheet (CPS) due to the catapult (slingshot) current sheet relaxation, together with the rapid enhancement of Poynting flux toward the CPS in the lobe around X ~ -15 Re about 4 min before the substrom onset. These earthward flows are characterized by plasma pressure decrease and large amplitude magnetic field fluctuations. When these flows reach X ~ 12Re in the magnetotail, they give significant disturbances to the inner magnetosphere to initiate some instability such as a ballooning instability or other instabilities, and the substorm starts in the inner magnetosphere. The occurrence of the magnetic reconnection is a natural consequence of the initial convective earthward flows, because the relaxation of a highly stretched catapult current sheet produces a very thin current at its tailward edge being surrounded by intense magnetic fields which were formerly the off-equatorial lobe magnetic fields. Recently, Nishimura et al. [2010] reported that the substorm onset begins when faint poleward discrete arcs collide with equatorward quiet arcs. The region of earthward convective flows correlatively moves earthward prior to the onset. Thus, this region of the earthward convective flows seems to correspond to the faint poleward discrete arcs. Interestingly, our statistical analysis shows that the earthward convective flows are not produced by the magnetic reconnection, but they are attributed to the dominance of the earthward JxB force over the tailward pressure associated with the progress of the plasma sheet thinning.
Upper D region chemical kinetic modeling of LORE relaxation times
Gordillo-Vázquez, F. J.; Luque, A.; Haldoupis, C.
2016-04-01
The recovery times of upper D region electron density elevations, caused by lightning-induced electromagnetic pulses (EMP), are modeled. The work was motivated from the need to understand a recently identified narrowband VLF perturbation named LOREs, an acronym for LOng Recovery Early VLF events. LOREs associate with long-living electron density perturbations in the upper D region ionosphere; they are generated by strong EMP radiated from large peak current intensities of ±CG (cloud to ground) lightning discharges, known also to be capable of producing elves. Relaxation model scenarios are considered first for a weak enhancement in electron density and then for a much stronger one caused by an intense lightning EMP acting as an impulsive ionization source. The full nonequilibrium kinetic modeling of the perturbed mesosphere in the 76 to 92 km range during LORE-occurring conditions predicts that the electron density relaxation time is controlled by electron attachment at lower altitudes, whereas above 79 km attachment is balanced totally by associative electron detachment so that electron loss at these higher altitudes is controlled mainly by electron recombination with hydrated positive clusters H+(H2O)n and secondarily by dissociative recombination with NO+ ions, a process which gradually dominates at altitudes >88 km. The calculated recovery times agree fairly well with LORE observations. In addition, a simplified (quasi-analytic) model build for the key charged species and chemical reactions is applied, which arrives at similar results with those of the full kinetic model. Finally, the modeled recovery estimates for lower altitudes, that is <79 km, are in good agreement with the observed short recovery times of typical early VLF events, which are known to be associated with sprites.
Clock face model applied to tibial intraneural ganglia in the popliteal fossa
Spinner, Robert J. [Mayo Clinic, Department of Neurologic Surgery, Rochester, MN (United States); Mayo Clinic, Department of Orthopedics, Rochester, MN (United States); Mayo Clinic, Rochester, MN (United States); Hebert-Blouin, Marie-Noelle [Mayo Clinic, Department of Neurologic Surgery, Rochester, MN (United States); Maniker, Allen H. [Beth Israel Hospital, Department of Neurosurgery, New York, NY (United States); Amrami, Kimberly K. [Mayo Clinic, Department of Neurologic Surgery, Rochester, MN (United States); Mayo Clinic, Department of Radiology, Rochester, MN (United States)
2009-07-15
Tibial intraneural ganglia occurring in the popliteal fossa are often misdiagnosed because of their relative rarity. Their joint connection is typically not recognized and therefore not treated, leading to recurrence. This is a retrospective clinical study. Magnetic resonance images (MRIs) of six patients with confirmed tibial intraneural ganglia arising from the superior tibiofibular joint were analyzed and were compared to ten individuals with normal tibial nerves who were imaged with MRI. All studies were interpreted as left-sided. A previously designed clock face model introduced for peroneal intraneural ganglia was used to describe the superior tibiofibular joint connection (tail sign). A single axial image was sought to determine the normal anatomic and pathologic relationships of the tibial nerve and tibial articular branch to the superior tibiofibular joint. In all patients with intraneural ganglia, a single conventional axial image at the mid-fibular head level could reliably demonstrate: (1) intraneural cyst within the articular branch at the superior tibiofibular joint connection (tail sign) between 8 and 9 o'clock and intraneural cyst within the tibial nerve, (2) the central location of the tibial nerve posterior to the tibia, and (3) popliteus muscle denervation changes and atrophy (popliteus sign). This technique can provide radiologists and surgeons with rapid and reproducible information for diagnosis and treatment planning of tibial intraneural ganglia. Similar to its use with the clock face model in peroneal intraneural ganglia, a standard axial image at the mid-fibular head level can be used to interpret key features of tibial intraneural ganglia and identify the joint connection. Improved identification of the presence of a joint connection will change the therapeutic approach of this pathology and reduce cyst recurrences. (orig.)
Donner, L.
2009-12-01
The certainty of climate change projected under various scenarios of emissions using general circulation models is an issue of vast societal importance. Unlike numerical weather prediction, a problem to which general circulation models are also applied, projected climate changes usually lie outside of the range of external forcings for which the models generating these changes have been directly evaluated. This presentation views climate models as complex scientific hypotheses and thereby frames these models within a well-defined process of both advancing scientific knowledge and recognizing its limitations. Karl Popper's Logik der Forschung (The Logic of Scientific Discovery, 1934) and 1965 essay “On Clocks and Clouds” capture well the methodologies and challenges associated with constructing climate models. Indeed, the process of a problem situation generating tentative theories, refined by error elimination, characterizes aptly the routine of general circulation model development. Limitations on certainty arise from the distinction Popper perceived in types of natural processes, which he exemplified by clocks, capable of exact measurement, and clouds, subject only to statistical approximation. Remarkably, the representation of clouds in general circulation models remains the key uncertainty in understanding atmospheric aspects of climate change. The asymmetry of hypothesis falsification by negation and much vaguer development of confidence in hypotheses consistent with some of their implications is an important practical challenge to confirming climate models. The presentation will discuss the ways in which predictions made by climate models for observable aspects of the present and past climate can be regarded as falsifiable hypotheses. The presentation will also include reasons why “passing” these tests does not provide complete confidence in predictions about the future by climate models. Finally, I will suggest that a “reductionist” view, in
Convex Relaxations for a Generalized Chan-Vese Model
Bae, Egil
2013-01-01
We revisit the Chan-Vese model of image segmentation with a focus on the encoding with several integer-valued labeling functions. We relate several representations with varying amount of complexity and demonstrate the connection to recent relaxations for product sets and to dual maxflow-based formulations. For some special cases, it can be shown that it is possible to guarantee binary minimizers. While this is not true in general, we show how to derive a convex approximation of the combinatorial problem for more than 4 phases. We also provide a method to avoid overcounting of boundaries in the original Chan-Vese model without departing from the efficient product-set representation. Finally, we derive an algorithm to solve the associated discretized problem, and demonstrate that it allows to obtain good approximations for the segmentation problem with various number of regions. © 2013 Springer-Verlag.
A relaxation-based approach to damage modeling
Junker, Philipp; Schwarz, Stephan; Makowski, Jerzy; Hackl, Klaus
2017-01-01
Material models, including softening effects due to, for example, damage and localizations, share the problem of ill-posed boundary value problems that yield mesh-dependent finite element results. It is thus necessary to apply regularization techniques that couple local behavior described, for example, by internal variables, at a spatial level. This can take account of the gradient of the internal variable to yield mesh-independent finite element results. In this paper, we present a new approach to damage modeling that does not use common field functions, inclusion of gradients or complex integration techniques: Appropriate modifications of the relaxed (condensed) energy hold the same advantage as other methods, but with much less numerical effort. We start with the theoretical derivation and then discuss the numerical treatment. Finally, we present finite element results that prove empirically how the new approach works.
Mechanical Relaxation of Metallic Glasses: An Overview of Experimental Data and Theoretical Models
Chaoren Liu
2015-06-01
Full Text Available Relaxation phenomena in glasses are a subject of utmost interest, as they are deeply connected with their structure and dynamics. From a theoretical point of view, mechanical relaxation allows one to get insight into the different atomic-scale processes taking place in the glassy state. Focusing on their possible applications, relaxation behavior influences the mechanical properties of metallic glasses. This paper reviews the present knowledge on mechanical relaxation of metallic glasses. The features of primary and secondary relaxations are reviewed. Experimental data in the time and frequency domain is presented, as well as the different models used to describe the measured relaxation spectra. Extended attention is paid to dynamic mechanical analysis, as it is the most important technique allowing one to access the mechanical relaxation behavior. Finally, the relevance of the relaxation behavior in the mechanical properties of metallic glasses is discussed.
Probability-changing cluster algorithm for two-dimensional XY and clock models
Tomita, Yusuke; Okabe, Yutaka
2002-05-01
We extend the newly proposed probability-changing cluster (PCC) Monte Carlo algorithm to the study of systems with the vector order parameter. Wolff's idea of the embedded cluster formalism is used for assigning clusters. The Kosterlitz-Thouless (KT) transitions for the two-dimensional (2D) XY and q-state clock models are studied by using the PCC algorithm. Combined with the finite-size scaling analysis based on the KT form of the correlation length, ξ~exp(c/(T/TKT-1)), we determine the KT transition temperature and the decay exponent η as TKT=0.8933(6) and η=0.243(4) for the 2D XY model. We investigate two transitions of the KT type for the 2D q-state clock models with q=6,8,12 and confirm the prediction of η=4/q2 at T1, the low-temperature critical point between the ordered and XY-like phases, systematically.
Wang, Junwei; Zhou, Tianshou
2010-06-01
Previous studies showed that a single negative feedback structure should be sufficient for robust circadian oscillations. It is thus pertinent to ask why current cellular clock models almost universally have interlocked negative feedback loop (NFL) and positive feedback loop (PFL). Here, we propose a molecular model that reflects the essential features of the Drosophila circadian clock to clarify the different roles of negative and positive feedback loops. In agreement with experimental observations, the model can simulate circadian oscillations in constant darkness, entrainment by light-dark cycles, as well as phenotypes of per and clk mutants. Moreover, sustained oscillations persist when the PFL is removed, implying the crucial role of NFL for rhythm generation. Through parameter sensitivity analysis, it is revealed that incorporation of PFL increases the robustness of the system to regulatory processes in PFL itself. Such reduced models can aid understanding of the design principles of circadian clocks in Drosophila and other organisms with complex transcriptional feedback structures.
Model-independent estimations for the curvature from standard candles and clocks
Li, Zhengxiang; Liao, Kai; Zhu, Zong-Hong
2016-01-01
Model-independent estimations for the spatial curvature not only provide a test for the fundamental Copernican principle assumption, but also can effectively break the degeneracy between curvature and dark energy properties. In this paper, we propose to achieve model-independent constraints on the spatial curvature from observations of standard candles and standard clocks, without assuming any fiducial cosmology and other priors. We find that, for the popular Union2.1 type Ia supernovae (SNe Ia ) observations, the spatial curvature is constrained to be $\\Omega_K=-0.045_{-0.172}^{+0.176}$. For the latest joint light-curve analysis (JLA) of SNe Ia observations, we obtain $\\Omega_K=-0.140_{-0.158}^{+0.161}$. It is suggested that these results are in excellent agreement with the spatially flat Universe. Moreover, compared to other approaches aiming for model-independent estimations of spatial curvature, this method also achieves constraints with competitive precision.
Byrne, Mark
2014-01-01
The KaiABC circadian clock from cyanobacteria is the only known three-protein oscillatory system which can be reconstituted outside the cell and which displays sustained periodic dynamics in various molecular state variables. Despite many recent experimental and theoretical studies there are several open questions regarding the central mechanism(s) responsible for creating this ~24 hour clock in terms of molecular assembly/disassembly of the proteins and site-dependent phosphorylation and dephosphorylation of KaiC monomers. Simulations of protein-protein interactions and phosphorylation reactions constrained by analytical fits to partial reaction experimental data support the central mechanism of oscillation as KaiB-induced KaiA sequestration in KaiABC complexes associated with the extent of Ser431 phosphorylation in KaiC hexamers. A simple two-state deterministic model in terms of the degree of phosphorylation of Ser431 and Thr432 sites alone can reproduce the previously observed circadian oscillation in the...
Trung Dung Nguyen
2014-01-01
Full Text Available Based on atomic force microscopytechnique, we found that the chondrocytes exhibits stress relaxation behavior. We explored the mechanism of this stress relaxation behavior and concluded that the intracellular fluid exuding out from the cells during deformation plays the most important role in the stress relaxation. We applied the inverse finite element analysis technique to determine necessary material parameters for porohyperelastic (PHE model to simulate stress relaxation behavior as this model is proven capable of capturing the non-linear behavior and the fluid-solid interaction during the stress relaxation of the single chondrocytes. It is observed that PHE model can precisely capture the stress relaxation behavior of single chondrocytes and would be a suitable model for cell biomechanics.
Zámborszky, Judit; Csikász-Nagy, Attila; Hong, Christian I
2014-10-01
Budding and fission yeast pioneered uncovering molecular mechanisms of eukaryotic cell division cycles. However, they do not possess canonical circadian clock machinery that regulates physiological processes with a period of about 24h. On the other hand, Neurospora crassa played a critical role in elucidating molecular mechanisms of circadian rhythms, but have not been utilized frequently for cell cycle studies. Recent findings demonstrate that there exists a conserved coupling between the cell cycle and the circadian clock from N.crassa to Mus musculus, which poses Neurospora as an ideal model organism to investigate molecular mechanisms and emerging behavior of the coupled network of the cell cycle and circadian rhythms. In this review, we briefly describe generic eukaryotic cell cycle regulation focusing on G1/S and G2/M transitions, and highlight that these transitions may be targeted for the circadian clock to influence timing of cell division cycles.
Casado, J M
2015-01-01
Rhythms in electrical activity in the membrane of cells in the suprachiasmatic nucleus (SCN) are crucial for the function of the circadian timing system, which is characterized by the expression of the so-called clock genes. Intracellular Ca$^{2+}$ ions seem to connect, at least in part, the electrical activity of SCN neurons with the expression of clock genes. In this paper, we introduce a simple mathematical model describing the linking of membrane activity to the transcription of one gene by means of a feedback mechanism based on the dynamics of intracellular calcium ions.
Nonequilibrium relaxation study of Ising spin glass models
Ozeki, Yukiyasu; Ito, Nobuyasu
2001-07-01
As an analysis of equilibrium phase transitions, the nonequilibrium relaxation method is extended to the spin glass (SG) transition. The +/-J Ising SG model is analyzed for three-dimensional (cubic) lattices up to the linear size of L=127 and for four-dimensional (hypercubic) lattice up to L=41. These sizes of systems are quite large as compared with those calculated, so far, by equilibrium simulations. As a dynamical order parameter, we calculate the clone correlation function (CCF) Q(t,tw)≡[F], which is a spin correlation of two replicas produced after the waiting time tw from a simple starting state. It is found that the CCF shows an exponential decay in the paramagnetic phase, and a power-law decay after aginglike development (t>>tw) in the SG phase. This provides a reliable upper bound of the transition temperature Tg. It is also found that a scaling relation, Q(t,tw)=t-λqwq¯(t/tw), holds just around the transition point providing the lower bound of Tg. Together with these two bounds, we propose a new dynamical way for the estimation of Tg from much larger systems. In the SG phase, the power-law behavior of the CCF for t>>tw suggests that the SG phase in short-range Ising models has a rugged phase space.
Multiple-relaxation-time lattice Boltzmann kinetic model for combustion.
Xu, Aiguo; Lin, Chuandong; Zhang, Guangcai; Li, Yingjun
2015-04-01
To probe both the hydrodynamic nonequilibrium (HNE) and thermodynamic nonequilibrium (TNE) in the combustion process, a two-dimensional multiple-relaxation-time (MRT) version of lattice Boltzmann kinetic model (LBKM) for combustion phenomena is presented. The chemical energy released in the progress of combustion is dynamically coupled into the system by adding a chemical term to the LB kinetic equation. Aside from describing the evolutions of the conserved quantities, the density, momentum, and energy, which are what the Navier-Stokes model describes, the MRT-LBKM presents also a coarse-grained description on the evolutions of some nonconserved quantities. The current model works for both subsonic and supersonic flows with or without chemical reaction. In this model, both the specific-heat ratio and the Prandtl number are flexible, the TNE effects are naturally presented in each simulation step. The model is verified and validated via well-known benchmark tests. As an initial application, various nonequilibrium behaviors, including the complex interplays between various HNEs, between various TNEs, and between the HNE and TNE, around the detonation wave in the unsteady and steady one-dimensional detonation processes are preliminarily probed. It is found that the system viscosity (or heat conductivity) decreases the local TNE, but increases the global TNE around the detonation wave, that even locally, the system viscosity (or heat conductivity) results in two kinds of competing trends, to increase and to decrease the TNE effects. The physical reason is that the viscosity (or heat conductivity) takes part in both the thermodynamic and hydrodynamic responses.
A Simple Electromagnetic Model for the Light Clock of Special Relativity
Smith, Glenn S.
2011-01-01
Thought experiments involving a light clock are common in introductory treatments of special relativity, because they provide a simple way of demonstrating the non-intuitive phenomenon of time dilation. The properties of the ray or pulse of light that is continuously reflected between the parallel mirrors of the clock are often stated vaguely and…
Catapult current sheet relaxation model confirmed by THEMIS observations
Machida, S.; Miyashita, Y.; Ieda, A.; Nose, M.; Angelopoulos, V.; McFadden, J. P.
2014-12-01
In this study, we show the result of superposed epoch analysis on the THEMIS probe data during the period from November, 2007 to April, 2009 by setting the origin of time axis to the substorm onset determined by Nishimura with THEMIS all sky imager (THEMS/ASI) data (http://www.atmos.ucla.edu/~toshi/files/paper/Toshi_THEMIS_GBO_list_distribution.xls). We confirmed the presence of earthward flows which can be associated with north-south auroral streamers during the substorm growth phase. At around X = -12 Earth radii (Re), the northward magnetic field and its elevation angle decreased markedly approximately 4 min before substorm onset. A northward magnetic-field increase associated with pre-onset earthward flows was found at around X = -17Re. This variation indicates the occurrence of the local depolarization. Interestingly, in the region earthwards of X = -18Re, earthward flows in the central plasma sheet (CPS) reduced significantly about 3min before substorm onset. However, the earthward flows enhanced again at t = -60 sec in the region around X = -14 Re, and they moved toward the Earth. At t = 0, the dipolarization of the magnetic field started at X ~ -10 Re, and simultaneously the magnetic reconnection started at X ~ -20 Re. Synthesizing these results, we can confirm the validity of our catapult current sheet relaxation model.
Phase transitions and relaxation dynamics of Ising models exchanging particles
Goh, Segun; Fortin, Jean-Yves; Choi, M. Y.
2017-01-01
A variety of systems in nature and in society are open and subject to exchanging their constituents with other systems (e.g., environments). For instance, in biological systems, cells collect necessary energy and material by exchange of molecules or ions. Similarly, countries, cities or research institutes evolve as their constituents move in or out. To probe the corresponding particle exchange dynamics in such systems, we consider two Ising models exchanging particles and establish a master equation describing the equilibrium phases as well as the non-equilibrium dynamics of the system. It is found that an additional stable phase emerges as a consequence of the particle exchange process. Furthermore, we formulate the Ginzburg-Landau theory which allows to probe correlation effects. Accordingly, critical slowing down is manifested and the associated dynamic exponent is computed in the linear relaxation regime. In particular, this approach is relevant for investigating the grand canonical description of the system plus environment, with particle exchange and state transitions taken into account explicitly.
Entanglement, decoherence and thermal relaxation in exactly solvable models
Lychkovskiy, Oleg
2011-01-01
Exactly solvable models provide an opportunity to study different aspects of reduced quantum dynamics in detail. We consider the reduced dynamics of a single spin in finite XX and XY spin 1/2 chains. First we introduce a general expression describing the evolution of the reduced density matrix. This expression proves to be tractable when the combined closed system (i.e. open system plus environment) is integrable. Then we focus on comparing decoherence and thermalization timescales in the XX chain. We find that for a single spin these timescales are comparable, in contrast to what should be expected for a macroscopic body. This indicates that the process of quantum relaxation of a system with few accessible states can not be separated in two distinct stages - decoherence and thermalization. Finally, we turn to finite-size effects in the time evolution of a single spin in the XY chain. We observe three consecutive stages of the evolution: regular evolution, partial revivals, irregular (apparently chaotic) evol...
A remark on the GNSS single difference model with common clock scheme for attitude determination
Chen, Wantong
2016-09-01
GNSS-based attitude determination technique is an important field of study, in which two schemes can be used to construct the actual system: the common clock scheme and the non-common clock scheme. Compared with the non-common clock scheme, the common clock scheme can strongly improve both the reliability and the accuracy. However, in order to gain these advantages, specific care must be taken in the implementation. The cares are thus discussed, based on the generating technique of carrier phase measurement in GNSS receivers. A qualitative assessment of potential phase bias contributes is also carried out. Possible technical difficulties are pointed out for the development of single-board multi-antenna GNSS attitude systems with a common clock.
Scribner, Elizabeth Y; Fathallah-Shaykh, Hassan M
2011-01-01
Biological networks can be very complex. Mathematical modeling and simulation of regulatory networks can assist in resolving unanswered questions about these complex systems, which are often impossible to explore experimentally. The network regulating the Drosophila circadian clock is particularly amenable to such modeling given its complexity and what we call the clockwork orange (CWO) anomaly. CWO is a protein whose function in the network as an indirect activator of genes per, tim, vri, and pdp1 is counterintuitive--in isolated experiments, CWO inhibits transcription of these genes. Although many different types of modeling frameworks have recently been applied to the Drosophila circadian network, this chapter focuses on the application of continuous deterministic dynamic modeling to this network. In particular, we present three unique systems of ordinary differential equations that have been used to successfully model different aspects of the circadian network. The last model incorporates the newly identified protein CWO, and we explain how this model's unique mathematical equations can be used to explore and resolve the CWO anomaly. Finally, analysis of these equations gives rise to a new network regulatory rule, which clarifies the unusual role of CWO in this dynamical system.
Theoretical Modeling and Simulation of Phase-Locked Loop (PLL for Clock Data Recovery (CDR
Zainab Mohamad Ashari
2012-01-01
Full Text Available Modern communication and computer systems require rapid (Gbps, efficient and large bandwidth data transfers. Agressive scaling of digital integrated systems allow buses and communication controller circuits to be integrated with the microprocessor on the same chip. The Peripheral Component Interconnect Express (PCIe protocol handles all communcation between the central processing unit (CPU and hardware devices. PCIe buses require efficient clock data recovery circuits (CDR to recover clock signals embedded in data during transmission. This paper describes the theoretical modeling and simulation of a phase-locked loop (PLL used in a CDR circuit. A simple PLL architecture for a 5 GHz CDR circuit is proposed and elaborated in this work. Simulations were carried out using a Hardware Description Language, Verilog-AMS. The effect of jitter on the proposed design is also simulated and evaluated in this work. It was found that the proposed design is robust against both input and VCO jitter.ABSTRAK: Sistem komunikasi dan komputer moden memerlukan pemindahan data yang cekap (Gbps, dan bandwidth yang besar. Pengecilan agresif menggunakan teknik sistem digital bersepadu membenarkan bas dan litar pengawal komunikasi disatukan dengan mikroprocessor dalam cip yang sama. Protokol persisian komponen sambung tara ekspres (PCIe mengendalikan semua komunikasi antara unit pemprosesan pusat (CPU dan peranti perkakasan. Bas PCIe memerlukan litar jam pemulihan data (CDR yang cekap untuk mendapatkan kembali isyarat jam yang tertanam dalam data semasa transmisi. Karya ini menerangkan teori pemodelan dan simulasi gelung fasa terkunci (PLL untuk CDR. Rekabentuk 5 GHz PLL yang mudah telah dicadangkan dalm kertas kerja ini. Simulasi telah dijalankan menggunakan perisian verilog-AMS. Simulasi mengunnakan kesan ketar dalam reka bentuk yang dicadangkan telah dinilai. Reka bentuk yang dicadangkan terbukti teguh mengatasi ganguan ketar di input dan VCO.KEY WORDS
Wang Ting
2014-01-01
Full Text Available Motivated by the importance of the clock synchronization in wireless sensor networks (WSNs, this paper proposes a new research approach and model approach, which quantitatively analyzes clock synchronization from the perspective of modern control theory. Two kinds of control strategies are used as examples to analyze the effect of the control strategy on clock synchronization from different perspectives, namely, the single-step optimal control and the LQG global optimal control. The proposed method establishes a state space model for clock relationship, thus making dimension extension and parameter identification easier, and is robust to changes under the condition of node failures and new nodes. And through the design of different control strategies and performance index functions, the method can satisfy various requirements of the synchronization precision, convergence speed, energy consumption and the computational complexity, and so on. Finally, the simulations show that the synchronization accuracy of the proposed method is higher than that of the existing protocol, and the former convergence speed of the synchronization error is faster.
Souillard-Mandar, William; Davis, Randall; Rudin, Cynthia; Au, Rhoda; Libon, David J.; Swenson, Rodney; Price, Catherine C.; Lamar, Melissa; Penney, Dana L.
2015-01-01
The Clock Drawing Test – a simple pencil and paper test – has been used for more than 50 years as a screening tool to differentiate normal individuals from those with cognitive impairment, and has proven useful in helping to diagnose cognitive dysfunction associated with neurological disorders such as Alzheimer’s disease, Parkinson’s disease, and other dementias and conditions. We have been administering the test using a digitizing ballpoint pen that reports its position with considerable spatial and temporal precision, making available far more detailed data about the subject’s performance. Using pen stroke data from these drawings categorized by our software, we designed and computed a large collection of features, then explored the tradeoffs in performance and interpretability in classifiers built using a number of different subsets of these features and a variety of different machine learning techniques. We used traditional machine learning methods to build prediction models that achieve high accuracy. We operationalized widely used manual scoring systems so that we could use them as benchmarks for our models. We worked with clinicians to define guidelines for model interpretability, and constructed sparse linear models and rule lists designed to be as easy to use as scoring systems currently used by clinicians, but more accurate. While our models will require additional testing for validation, they offer the possibility of substantial improvement in detecting cognitive impairment earlier than currently possible, a development with considerable potential impact in practice. PMID:27057085
Effect of the initial stage of annealing on modeling of enthalpy relaxation in a hyperquenched glass
Zhang, Yanfei; Guo, Xiaoju; Yue, Yuanzheng
2013-01-01
relaxation in both HQG and AHQG during the initial stage of both the sub-Tg and above-Tg annealing cannot be captured by the existing models. In this Letter we show that the combination of a modified stretched exponential equation [M. Peyron, et al., J. Magn. Reson, Series A 118 (1996) 214] and the recently......One of the major challenges in glass relaxation study is to establish a universal model describing the enthalpy relaxation in both the hyperquenched glass (HQG) (i.e., far from equilibrium) and the partially annealed hyperquenched glass(AHQG). In particular, the detailed features of the enthalpy...... proposed composite relaxation function [L. Hornboell, et al., Chem. Phys. Lett. 1-3 (2010) 37] is a reasonable approach for describing those features. In addition, our modeling results imply that the structural heterogeneity plays a crucial role in relaxation of HQG....
Active open boundary forcing using dual relaxation time-scales in downscaled ocean models
Herzfeld, M.; Gillibrand, P. A.
2015-05-01
Regional models actively forced with data from larger scale models at their open boundaries often contain motion at different time-scales (e.g. tidal and low frequency). These motions are not always individually well specified in the forcing data, and one may require a more active boundary forcing while the other exert less influence on the model interior. If a single relaxation time-scale is used to relax toward these data in the boundary equation, then this may be difficult. The method of fractional steps is used to introduce dual relaxation time-scales in an open boundary local flux adjustment scheme. This allows tidal and low frequency oscillations to be relaxed independently, resulting in a better overall solution than if a single relaxation parameter is optimized for tidal (short relaxation) or low frequency (long relaxation) boundary forcing. The dual method is compared to the single relaxation method for an idealized test case where a tidal signal is superimposed on a steady state low frequency solution, and a real application where the low frequency boundary forcing component is derived from a global circulation model for a region extending over the whole Great Barrier Reef, and a tidal signal subsequently superimposed.
A synaptic input portal for a mapped clock oscillator model of neuronal electrical rhythmic activity
Zariffa, José; Ebden, Mark; Bardakjian, Berj L.
2004-09-01
Neuronal electrical oscillations play a central role in a variety of situations, such as epilepsy and learning. The mapped clock oscillator (MCO) model is a general model of transmembrane voltage oscillations in excitable cells. In order to be able to investigate the behaviour of neuronal oscillator populations, we present a neuronal version of the model. The neuronal MCO includes an extra input portal, the synaptic portal, which can reflect the biological relationships in a chemical synapse between the frequency of the presynaptic action potentials and the postsynaptic resting level, which in turn affects the frequency of the postsynaptic potentials. We propose that the synaptic input-output relationship must include a power function in order to be able to reproduce physiological behaviour such as resting level saturation. One linear and two power functions (Butterworth and sigmoidal) are investigated, using the case of an inhibitory synapse. The linear relation was not able to produce physiologically plausible behaviour, whereas both the power function examples were appropriate. The resulting neuronal MCO model can be tailored to a variety of neuronal cell types, and can be used to investigate complex population behaviour, such as the influence of network topology and stochastic resonance.
Dai, Yan-Wei; Cho, Sam Young; Batchelor, Murray T.; Zhou, Huan-Qiang
2017-01-01
The von Neumann entanglement entropy is used to estimate the critical point hc/J ≃0.143 (3 ) of the mixed ferro-antiferromagnetic three-state quantum Potts model H =∑i[J (XiXi+1 2+Xi2Xi +1) -h Ri] , where Xi and Ri are standard three-state Potts spin operators and J >0 is the antiferromagnetic coupling parameter. This critical point value gives improved estimates for two Kosterlitz-Thouless transition points in the antiferromagnetic (β model, where Δ and β are, respectively, the chirality and coupling parameters in the clock model. These are the transition points βc≃-0.143 (3 ) at Δ =1/2 between incommensurate and commensurate phases and βc≃-7.0 (1 ) at Δ =0 between disordered and incommensurate phases. The von Neumann entropy is also used to calculate the central charge c of the underlying conformal field theory in the massless phase h ≤hc . The estimate c ≃1 in this phase is consistent with the known exact value at the particular point h /J =-1 corresponding to the purely antiferromagnetic three-state quantum Potts model. The algebraic decay of the Potts spin-spin correlation in the massless phase is used to estimate the continuously varying critical exponent η .
Channel Modeling and Time Delay Estimation for Clock Synchronization Among Seaweb Nodes
Gagnon, P; Rice, J; Clark, G A
2012-07-08
From simulations, tracking of the impulse response is feasible. Potential to benefit other functions such as ranging between two nodes. Potential to combine the features of different protocols to create a new and more realistic clock-synchronization protocol.
Determination of a high spatial resolution geopotential model using atomic clock comparisons
Lion, Guillaume; Panet, Isabelle; Wolf, Peter; Guerlin, Christine; Bize, Sébastien; Delva, Pacôme
2016-01-01
Recent technological advances in optical atomic clocks are opening new perspectives for the direct determination of geopotential differences between any two points at a centimeter-level accuracy in geoid height. However, so far detailed quantitative estimates of the possible improvement in geoid determination when adding such clock measurements to existing data are lacking. We present a first step in that direction with the aim and hope of triggering further work and efforts in this emerging ...
Lock, Maximilian P E
2016-01-01
The conflict between quantum theory and the theory of relativity is exemplified in their treatment of time. We examine the ways in which their conceptions differ, and describe a semiclassical clock model combining elements of both theories. The results obtained with this clock model in flat spacetime are reviewed, and the problem of generalizing the model to curved spacetime is discussed, before briefly describing an experimental setup which could be used to test of the model. Taking an operationalist view, where time is that which is measured by a clock, we discuss the conclusions that can be drawn from these results, and what clues they contain for a full quantum relativistic theory of time.
Revealing spatially heterogeneous relaxation in a model nanocomposite
Cheng, Shiwang; Carrillo, Jan-Michael Y; Bocharova, Vera; Sumpter, Bobby G; Schweizer, Kenneth S; Sokolov, Alexei P
2015-01-01
The detailed nature of spatially heterogeneous dynamics of glycerol-silica nanocomposites is unraveled by combining dielectric spectroscopy with atomistic simulation and statistical mechanical theory. Analysis of the spatial mobility gradient shows no 'glassy' layer, but the alpha relaxation time near the nanoparticle grows with cooling faster than the alpha relaxation time in the bulk, and is ~ 20 times longer at low temperatures. The interfacial layer thickness increases from ~ 1.8 nm at higher temperatures to ~ 3.5 nm upon cooling to near Tg. A real space microscopic description of the mobility gradient is constructed by synergistically combining high temperature atomistic simulation with theory. Our analysis suggests that the interfacial slowing down arises mainly due to an increase of the local cage scale barrier for activated hopping induced by enhanced packing and densification near the nanoparticle surface. The theory is employed to predict how local surface densification can be manipulated to control...
Wang Junwei, E-mail: wangjunweilj@yahoo.com.c [Cisco School of Informatics, Guangdong University of Foreign Studies, Guangzhou 510006 (China); Zhou Tianshou [School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou 510275 (China)
2010-06-14
Previous studies showed that a single negative feedback structure should be sufficient for robust circadian oscillations. It is thus pertinent to ask why current cellular clock models almost universally have interlocked negative feedback loop (NFL) and positive feedback loop (PFL). Here, we propose a molecular model that reflects the essential features of the Drosophila circadian clock to clarify the different roles of negative and positive feedback loops. In agreement with experimental observations, the model can simulate circadian oscillations in constant darkness, entrainment by light-dark cycles, as well as phenotypes of per{sup 01} and clk{sup Jrk} mutants. Moreover, sustained oscillations persist when the PFL is removed, implying the crucial role of NFL for rhythm generation. Through parameter sensitivity analysis, it is revealed that incorporation of PFL increases the robustness of the system to regulatory processes in PFL itself. Such reduced models can aid understanding of the design principles of circadian clocks in Drosophila and other organisms with complex transcriptional feedback structures.
Comparison of Vibrational Relaxation Modeling for Strongly Non-Equilibrium Flows
2014-01-01
145 .98 4396 V. Summary and Conclusions The form of two vibrational relaxation models that are commonly used in DSMC and CFD simula- tions have been...Technical Paper 3. DATES COVERED (From - To) Dec 2013 – Jan 2014 4. TITLE AND SUBTITLE Comparison of Vibrational Relaxation Modeling for Strongly Non...including experimental gas measurement techniques , shock layer vibration-dissociation coupling, and vibrational energy freezing in strong expansions
Modeling and Estimation of Stationary and Non-stationary Noises of Rubidium Atomic Clock
Deepak Mishra,
2014-07-01
Full Text Available Noise estimation of atomic clock is one of the important research areas in the field of atomic clock development and application. Most of the atomic clocks are having random-stochastic noises and periodic noises due to temperature variation. Random-stochastic noises have a well identified signature in time domain but periodic noises are difficult to analyze in time domain. However, in this paper, an effort is made to identify and analyze the deterministic trends of both random-stochastic noises and periodic noises due to variation in temperature using an alternate approach of least-squares normalized-error (LSNE regression algorithm. A MATLAB based application with graphical user interface (GUI is developed to estimate and analyze random-stochastic noises and periodic noises and re-estimate the stability of rubidium atomic clock after removing these noises from the raw phase data. The estimation of stationary noises are done using Allan variance from time domain data and noise profile is calculated using curve fit method. The estimation of periodic noises due to temperature variation is carried in frequency domain through spurious analysis of the frequency data of atomic clock.
曹国辉; 胡佳星; 张锴
2016-01-01
The calculation model for the relaxation loss of concrete mentioned in the Code for Design of Highway Reinforced Concrete and Prestressed Concrete Bridges and Culverts(JTG D62—2004) wasmodified according to experimental data. Time-varying relaxation loss was considered in the new model. Moreover, prestressed reinforcement with varying lengths (caused by the shrinkage and creep of concrete) might influence the final values and the time-varying function of the forecast relaxation loss. Hence, the effects of concrete shrinkage and creep were considered when calculating prestress loss, which reflected the coupling relation between these effects and relaxation loss in concrete. Hence, the forecast relaxation loss of prestressed reinforcement under the effects of different initial stress levels at any time point can be calculated using the modified model. To simplify the calculation, the integral expression of the model can be changed into an algebraic equation. The accuracy of the result is related to the division of the periods within the ending time of deriving the final value of the relaxation loss of prestressed reinforcement. When the time division is reasonable, result accuracy is high. The modified model works excellently according to the comparison of the test results. The calculation result of the modified model mainly reflects the prestress loss values of prestressed reinforcement at each time point, which confirms that adopting the finding in practical applications is reasonable.
Carroll, Matthew R J; Woodward, Robert C; House, Michael J; St Pierre, Timothy G [Centre for Strategic Nanofabrication, School of Physics, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 (Australia); Teoh, Wey Yang; Amal, Rose [ARC Centre of Excellence for Functional Nanomaterials, School of Chemical Engineering and Industrial Chemistry, University of New South Wales, Sydney, NSW 2052 (Australia); Hanley, Tracey L, E-mail: stpierre@physics.uwa.edu.au [Bragg Institute, Australian Nuclear Science and Technology Organization, New Illawarra Road, Lucas Heights, NSW 2234 (Australia)
2010-01-22
Analytical models of proton transverse relaxation rate enhancement by magnetic nanoparticles were tested by making measurements on model experimental systems in a field of 1.4 T. Proton relaxivities were measured for five aqueous suspensions of iron oxide (maghemite) nanoparticles with nominal mean particle sizes of 6, 8, 10, 11, and 13 nm. Proton relaxivity increased with mean particle size ranging from 13 s{sup -1} mM Fe{sup -1} for the 6 nm sample, up to 254 s{sup -1} mM Fe{sup -1} for the 13 nm sample. A strong correlation between the measured and predicted values of the relaxivity was observed, with the predicted values being consistently higher than the measured values. The results indicate that the models give a reasonable agreement with experimental results and hence can be used as the basis for the design of new magnetic resonance imaging contrast and labelling agents.
Mechanical relaxation in a Zr-based bulk metallic glass: Analysis based on physical models
Qiao, J. C.; Pelletier, J. M.
2012-08-01
The mechanical relaxation behavior in a Zr55Cu30Ni5Al10 bulk metallic glass is investigated by dynamic mechanical analysis in both temperature and frequency domains. Master curves can be obtained for the storage modulus G' and for the loss modulus G'', confirming the validity of the time-temperature superposition principle. Different models are discussed to describe the main (α) relaxation, e.g., Debye model, Havriliak-Negami (HN) model, Kohlrausch-Williams-Watt (KWW) model, and quasi-point defects (QPDs) model. The main relaxation in bulk metallic glass cannot be described using a single relaxation time. The HN model, the KWW model, and the QPD theory can be used to fit the data of mechanical spectroscopy experiments. However, unlike the HN model and the KWW model, some physical parameters are introduced in QPD model, i.e., atomic mobility and correlation factor, giving, therefore, a new physical approach to understand the mechanical relaxation in bulk metallic glasses.
Revealing spatially heterogeneous relaxation in a model nanocomposite
Cheng, Shiwang; Bocharova, Vera [Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 (United States); Mirigian, Stephen; Schweizer, Kenneth S. [Department of Materials Science and Chemistry, Frederick Seitz Materials Research Laboratory, University of Illinois, Urbana, Illinois 61801 (United States); Carrillo, Jan-Michael Y.; Sumpter, Bobby G. [Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 (United States); Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 (United States); Sokolov, Alexei P., E-mail: sokolov@utk.edu [Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 (United States); Department of Chemistry, Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996 (United States)
2015-11-21
The detailed nature of spatially heterogeneous dynamics of glycerol-silica nanocomposites is unraveled by combining dielectric spectroscopy with atomistic simulation and statistical mechanical theory. Analysis of the spatial mobility gradient shows no “glassy” layer, but the α-relaxation time near the nanoparticle grows with cooling faster than the α-relaxation time in the bulk and is ∼20 times longer at low temperatures. The interfacial layer thickness increases from ∼1.8 nm at higher temperatures to ∼3.5 nm upon cooling to near bulk T{sub g}. A real space microscopic description of the mobility gradient is constructed by synergistically combining high temperature atomistic simulation with theory. Our analysis suggests that the interfacial slowing down arises mainly due to an increase of the local cage scale barrier for activated hopping induced by enhanced packing and densification near the nanoparticle surface. The theory is employed to predict how local surface densification can be manipulated to control layer dynamics and shear rigidity over a wide temperature range.
Post-seismic relaxation theory on laterally heterogeneous viscoelastic model
Pollitz, F.F.
2003-01-01
Investigation was carried out into the problem of relaxation of a laterally heterogeneous viscoelastic Earth following an impulsive moment release event. The formal solution utilizes a semi-analytic solution for post-seismic deformation on a laterally homogeneous Earth constructed from viscoelastic normal modes, followed by application of mode coupling theory to derive the response on the aspherical Earth. The solution is constructed in the Laplace transform domain using the correspondence principle and is valid for any linear constitutive relationship between stress and strain. The specific implementation described in this paper is a semi-analytic discretization method which assumes isotropic elastic structure and a Maxwell constitutive relation. It accounts for viscoelastic-gravitational coupling under lateral variations in elastic parameters and viscosity. For a given viscoelastic structure and minimum wavelength scale, the computational effort involved with the numerical algorithm is proportional to the volume of the laterally heterogeneous region. Examples are presented of the calculation of post-seismic relaxation with a shallow, laterally heterogeneous volume following synthetic impulsive seismic events, and they illustrate the potentially large effect of regional 3-D heterogeneities on regional deformation patterns.
Immiscible multicomponent lattice Boltzmann model for fluids with high relaxation time ratio
Tao Jiang; Qiwei Gong; Ruofan Qiu; Anlin Wang
2014-10-01
An immiscible multicomponent lattice Boltzmann model is developed for fluids with high relaxation time ratios, which is based on the model proposed by Shan and Chen (SC). In the SC model, an interaction potential between particles is incorporated into the discrete lattice Boltzmann equation through the equilibrium velocity. Compared to the SC model, external forces in our model are discretized directly into the discrete lattice Boltzmann equation, as proposed by Guo et al. We develop it into a new multicomponent lattice Boltzmann (LB) model which has the ability to simulate immiscible multicomponent fluids with relaxation time ratio as large as 29.0 and to reduce `spurious velocity’. In this work, the improved model is validated and studied using the central bubble case and the rising bubble case. It finds good applications in both static and dynamic cases for multicomponent simulations with different relaxation time ratios.
Minelli, Matteo; Doghieri, Ferruccio [Dipartimento di Ingegneria Civile, Chimica, Ambientale e dei Materiali (DICAM), Centro Interdipartimentale per la Ricerca Industriale - Meccanica Avanzata e Materiali (CIRI-MAM), Alma Mater Studiorum - Università di Bologna, via Terracini 28 - (Italy)
2014-05-15
Data for kinetics of mass uptake from vapor sorption experiments in thin glassy polymer samples are here interpreted in terms of relaxation times for volume dilation. To this result, both models from non-equilibrium thermodynamics and from mechanics of volume relaxation contribute. Different kind of sorption experiments have been considered in order to facilitate the direct comparison between kinetics of solute induced volume dilation and corresponding data from process driven by pressure or temperature jumps.
When the clock strikes: Modeling the relation between circadian rhythms and cardiac arrhythmias
Seenivasan, Pavithraa; Menon, Shakti N.; Sridhar, S.; Sinha, Sitabhra
2016-10-01
It has recently been observed that the occurrence of sudden cardiac death has a close statistical relationship with the time of day, viz., ventricular fibrillation is most likely to occur between 12am-6am, with 6pm-12am being the next most likely period. Consequently there has been significant interest in understanding how cardiac activity is influenced by the circadian clock, i.e., temporal oscillations in physiological activity with a period close to 24 hours and synchronized with the day-night cycle. Although studies have identified the genetic basis of circadian rhythm at the intracellular level, the mechanisms by which they influence cardiac pathologies are not yet fully understood. Evidence has suggested that diurnal variations in the conductance properties of ion channel proteins that govern the excitation dynamics of cardiac cells may provide the crucial link. In this paper, we investigate the relationship between the circadian rhythm as manifested in modulations of ion channel properties and the susceptibility to cardiac arrhythmias by using a mathematical model that describes the electrical activity in ventricular tissue. We show that changes in the channel conductance that lead to extreme values for the duration of action potentials in cardiac cells can result either in abnormally high-frequency reentrant activity or spontaneous conduction block of excitation waves. Both phenomena increase the likelihood of wavebreaks that are known to initiate potentially life- threatening arrhythmias. Thus, disruptive cardiac excitation dynamics are most likely to occur in time-intervals of the day-night cycle during which the channel properties are closest to these extreme values, providing an intriguing relation between circadian rhythms and cardiac pathologies.
Grzegorczyk, Marco; Aderhold, Andrej; Husmeier, Dirk
2015-01-01
There has been much interest in reconstructing bi-directional regulatory networks linking the circadian clock to metabolism in plants. A variety of reverse engineering methods from machine learning and computational statistics have been proposed and evaluated. The emphasis of the present paper is on
Lookman, Turab [Los Alamos National Laboratory; Vasseur, Romain [ECOLE NORMALE SUPERIEURE
2009-01-01
We obtain the microstructure of ferroelastic transitions in two and three dimensions from the solution of their corresponding discrete pseudo-spin models. In two dimensions we consider two transitions each from the high symmetry square and triangle symmetries: square-to-rectangle (SR), square-to-oblique (SO), triangle-to-centered rectangle (TR) and triangle-to-oblique (TO). In three dimensions we study the corresponding spin model for the cubic to tetragonal transition. The Landau free energies for these transitions result in N+ I states clock models (Z{sub N}) with long range interactions and we derive mean-field self-consistency equations for the clock model Hamiltonians. The microstructures from the mean-field solutions of the models are very similar to those obtained from the original continuum models or Monte Carlo simulations on the spin models (in the SR case), illustrating that these discrete models capture the salient physics. The models, in the presence of disorder, provide the basis for the study of the strain glass phase observed in martensitic alloys.
Xiong, Q. L.; Tian, X. G.; Lu, T. J.
2012-07-01
The thermoelastic response of thin gold films induced by femtosecond laser irradiation is numerically simulated using a modified combined two-temperature model (TTM) and molecular dynamics (MD) method, with focus placed upon the influence of the electron relaxation effect. The validity of the numerical approach is checked against existing experimental results. While the electron relaxation effect is found negligible when the laser duration is much longer than the electron thermal relaxation time, it becomes significant if the laser duration matches the electron relaxation time, especially when the former is much shorter than the latter. The characteristics of thermo-mechanical interaction in the thin film are analyzed, and the influence of temperature-dependent material properties upon the thermoelastic response of the film quantified.
刘洪毓
2000-01-01
“Body clocks” are biological methods of controling body activities.Every living thing has one. In humans, a body clock controls normal periods of sleeping and waking. It controls the time swhen you are most likely to feel pain.Eating, sleeping and exercising at about the same time each day will help keep body activities normal. But changes in your life, a new job, for example, destroy the balance and thus cause health problems.
Direct simulation Monte Carlo modeling of relaxation processes in polyatomic gases
Pfeiffer, M.; Nizenkov, P.; Mirza, A.; Fasoulas, S.
2016-02-01
Relaxation processes of polyatomic molecules are modeled and implemented in an in-house Direct Simulation Monte Carlo code in order to enable the simulation of atmospheric entry maneuvers at Mars and Saturn's Titan. The description of rotational and vibrational relaxation processes is derived from basic quantum-mechanics using a rigid rotator and a simple harmonic oscillator, respectively. Strategies regarding the vibrational relaxation process are investigated, where good agreement for the relaxation time according to the Landau-Teller expression is found for both methods, the established prohibiting double relaxation method and the new proposed multi-mode relaxation. Differences and applications areas of these two methods are discussed. Consequently, two numerical methods used for sampling of energy values from multi-dimensional distribution functions are compared. The proposed random-walk Metropolis algorithm enables the efficient treatment of multiple vibrational modes within a time step with reasonable computational effort. The implemented model is verified and validated by means of simple reservoir simulations and the comparison to experimental measurements of a hypersonic, carbon-dioxide flow around a flat-faced cylinder.
Direct simulation Monte Carlo modeling of relaxation processes in polyatomic gases
Pfeiffer, M., E-mail: mpfeiffer@irs.uni-stuttgart.de; Nizenkov, P., E-mail: nizenkov@irs.uni-stuttgart.de; Mirza, A., E-mail: mirza@irs.uni-stuttgart.de; Fasoulas, S., E-mail: fasoulas@irs.uni-stuttgart.de [Institute of Space Systems, University of Stuttgart, Pfaffenwaldring 29, D-70569 Stuttgart (Germany)
2016-02-15
Relaxation processes of polyatomic molecules are modeled and implemented in an in-house Direct Simulation Monte Carlo code in order to enable the simulation of atmospheric entry maneuvers at Mars and Saturn’s Titan. The description of rotational and vibrational relaxation processes is derived from basic quantum-mechanics using a rigid rotator and a simple harmonic oscillator, respectively. Strategies regarding the vibrational relaxation process are investigated, where good agreement for the relaxation time according to the Landau-Teller expression is found for both methods, the established prohibiting double relaxation method and the new proposed multi-mode relaxation. Differences and applications areas of these two methods are discussed. Consequently, two numerical methods used for sampling of energy values from multi-dimensional distribution functions are compared. The proposed random-walk Metropolis algorithm enables the efficient treatment of multiple vibrational modes within a time step with reasonable computational effort. The implemented model is verified and validated by means of simple reservoir simulations and the comparison to experimental measurements of a hypersonic, carbon-dioxide flow around a flat-faced cylinder.
Elastic models for the non-Arrhenius relaxation time of glass-forming liquids
Dyre, Jeppe
We first review the phenomenology of viscous liquids and the standard models used for explaining the non-Arrhenius average relaxation time. Then the focus is turned to the so-called elastic models, arguing that these models are all equivalent in the Einstein approximation (where the short...
Elastic models for the Non-Arrhenius Relaxation Time of Glass-Forming Liquids
Dyre, J. C.
2006-01-01
We first review the phenomenology of viscous liquids and the standard models used for explaining the non-Arrhenius average relaxation time. Then the focus is turned to the so-called elastic models, arguing that these models are all equivalent in the Einstein approximation (where the short...
O. H. Kapitonov
2010-05-01
Full Text Available A mathematical model of coulostatic relaxation of the potential for solid metallic electrode was presented. The solution in the case of limiting diffusion current was obtained. On the basis of this model the technique of concentration measurements for heavy metal ions in diluted solutions was suggested. The model adequacy was proved by experimental data.
Competitive growth model involving random deposition and random deposition with surface relaxation
Horowitz, Claudio M.; Monetti, Roberto A.; Albano, Ezequiel V.
2001-06-01
A deposition model that considers a mixture of random deposition with surface relaxation and a pure random deposition is proposed and studied. As the system evolves, random deposition with surface relaxation (pure random deposition) take place with probability p and (1{minus}p), respectively. The discrete (microscopic) approach to the model is studied by means of extensive numerical simulations, while continuous equations are used in order to investigate the mesoscopic properties of the model. A dynamic scaling ansatz for the interface width W(L,t,p) as a function of the lattice side L, the time t and p is formulated and tested. Three exponents, which can be linked to the standard growth exponent of random deposition with surface relaxation by means of a scaling relation, are identified. In the continuous limit, the model can be well described by means of a phenomenological stochastic growth equation with a p-dependent effective surface tension.
Heiland, Ines; Bodenstein, Christian; Hinze, Thomas; Weisheit, Olga; Ebenhoeh, Oliver; Mittag, Maria; Schuster, Stefan
2012-06-01
Endogenous circadian rhythms allow living organisms to anticipate daily variations in their natural environment. Temperature regulation and entrainment mechanisms of circadian clocks are still poorly understood. To better understand the molecular basis of these processes, we built a mathematical model based on experimental data examining temperature regulation of the circadian RNA-binding protein CHLAMY1 from the unicellular green alga Chlamydomonas reinhardtii, simulating the effect of temperature on the rates by applying the Arrhenius equation. Using numerical simulations, we demonstrate that our model is temperature-compensated and can be entrained to temperature cycles of various length and amplitude. The range of periods that allow entrainment of the model depends on the shape of the temperature cycles and is larger for sinusoidal compared to rectangular temperature curves. We show that the response to temperature of protein (de)phosphorylation rates play a key role in facilitating temperature entrainment of the oscillator in Chlamydomonas reinhardtii. We systematically investigated the response of our model to single temperature pulses to explain experimentally observed phase response curves.
Statistics of avalanches with relaxation and Barkhausen noise: A solvable model
Dobrinevski, Alexander; Le Doussal, Pierre; Wiese, Kay Jörg
2013-09-01
We study a generalization of the Alessandro-Beatrice-Bertotti-Montorsi (ABBM) model of a particle in a Brownian force landscape, including retardation effects. We show that under monotonous driving the particle moves forward at all times, as it does in absence of retardation (Middleton's theorem). This remarkable property allows us to develop an analytical treatment. The model with an exponentially decaying memory kernel is realized in Barkhausen experiments with eddy-current relaxation and has previously been shown numerically to account for the experimentally observed asymmetry of Barkhausen pulse shapes. We elucidate another qualitatively new feature: the breakup of each avalanche of the standard ABBM model into a cluster of subavalanches, sharply delimited for slow relaxation under quasistatic driving. These conditions are typical for earthquake dynamics. With relaxation and aftershock clustering, the present model includes important ingredients for an effective description of earthquakes. We analyze quantitatively the limits of slow and fast relaxation for stationary driving with velocity v>0. The v-dependent power-law exponent for small velocities, and the critical driving velocity at which the particle velocity never vanishes, are modified. We also analyze nonstationary avalanches following a step in the driving magnetic field. Analytically, we obtain the mean avalanche shape at fixed size, the duration distribution of the first subavalanche, and the time dependence of the mean velocity. We propose to study these observables in experiments, allowing a direct measurement of the shape of the memory kernel and tracing eddy current relaxation in Barkhausen noise.
A study of internal energy relaxation in shocks using molecular dynamics based models
Li, Zheng, E-mail: zul107@psu.edu; Parsons, Neal, E-mail: neal.parsons@cd-adapco.com [Department of Aerospace Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802 (United States); Levin, Deborah A., E-mail: deblevin@illinois.edu [Department of Aerospace Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801-2935 (United States)
2015-10-14
Recent potential energy surfaces (PESs) for the N{sub 2} + N and N{sub 2} + N{sub 2} systems are used in molecular dynamics (MD) to simulate rates of vibrational and rotational relaxations for conditions that occur in hypersonic flows. For both chemical systems, it is found that the rotational relaxation number increases with the translational temperature and decreases as the rotational temperature approaches the translational temperature. The vibrational relaxation number is observed to decrease with translational temperature and approaches the rotational relaxation number in the high temperature region. The rotational and vibrational relaxation numbers are generally larger in the N{sub 2} + N{sub 2} system. MD-quasi-classical trajectory (QCT) with the PESs is also used to calculate the V-T transition cross sections, the collision cross section, and the dissociation cross section for each collision pair. Direct simulation Monte Carlo (DSMC) results for hypersonic flow over a blunt body with the total collision cross section from MD/QCT simulations, Larsen-Borgnakke with new relaxation numbers, and the N{sub 2} dissociation rate from MD/QCT show a profile with a decreased translational temperature and a rotational temperature close to vibrational temperature. The results demonstrate that many of the physical models employed in DSMC should be revised as fundamental potential energy surfaces suitable for high temperature conditions become available.
Yan, Wan; Fang, Liang; Heuchel, Matthias; Kratz, Karl; Lendlein, Andreas
2015-01-01
Stress relaxation can strongly influence the shape-memory capability of polymers. Recently a modified Maxwell-Wiechert model comprising two Maxwell units and a single spring unit in parallel has been introduced to successfully describe the shape recovery characteristics of amorphous polyether urethanes. In this work we explored whether such a modified Maxwell-Wiechert model is capable to describe the stress relaxation behavior of a semi-crystalline multiblock copolymer named PCL-PIBMD, which consists of crystallizable poly(ɛ-caprolactone) (PCL) segments and crystallizable poly(3S-isobutylmorpholine-2,5-dione) (PIBMD) segments. The stress relaxation behavior of PCL-PIBMD was explored after uniaxial deformation to different strains ranging from 50 to 900% with various strain rates of 1 or 10 or 50 mm·min -1. The modeling results indicated that under the assumption that in PCL-PIBMD both PCL and PIBMD blocks have narrow molecular weight distributions and are arranged in sequence, the two relaxation processes can be related to the amorphous PCL and PIBMD domains and the spring element can be associated to the PIBMD crystalline domains. The first Maxwell unit representing the faster relaxation process characterized by the modulus E1 and the relaxation time τ1 is related to the amorphous PCL domains (which are in the rubbery state), while the second Maxwell unit (E2 ; τ2) represents the behavior of the amorphous PIBMD domains, which are in the glassy state at 50 °C. Increasing strain rates resulted in an increase of E1 and a significant reduction in τ1, whereas the elastic modulus as well as the relaxation time related to the amorphous PIBMD domains remained almost constant. When a higher deformation was applied (ɛ ≥ 200% ) lower values for the elastic moduli of the three model elements were obtained. In general the applied model was also capable to describe the relaxation behavior of PCL-PIBMD at a deformation temperature of 20 °C, where additional crystalline
Theoretical Modeling and Simulation of Phase-Locked Loop (PLL) for Clock Data Recovery (CDR)
Zainab Mohamad Ashari; Anis Nurashikin Nordin
2012-01-01
Modern communication and computer systems require rapid (Gbps), efficient and large bandwidth data transfers. Agressive scaling of digital integrated systems allow buses and communication controller circuits to be integrated with the microprocessor on the same chip. The Peripheral Component Interconnect Express (PCIe) protocol handles all communcation between the central processing unit (CPU) and hardware devices. PCIe buses require efficient clock data recovery circuits (CD...
Determination of a high spatial resolution geopotential model using atomic clock comparisons
Lion, G.; Panet, I.; Wolf, P.; Guerlin, C.; Bize, S.; Delva, P.
2017-01-01
Recent technological advances in optical atomic clocks are opening new perspectives for the direct determination of geopotential differences between any two points at a centimeter-level accuracy in geoid height. However, so far detailed quantitative estimates of the possible improvement in geoid determination when adding such clock measurements to existing data are lacking. We present a first step in that direction with the aim and hope of triggering further work and efforts in this emerging field of chronometric geodesy and geophysics. We specifically focus on evaluating the contribution of this new kind of direct measurements in determining the geopotential at high spatial resolution (≈ 10 km). We studied two test areas, both located in France and corresponding to a middle (Massif Central) and high (Alps) mountainous terrain. These regions are interesting because the gravitational field strength varies greatly from place to place at high spatial resolution due to the complex topography. Our method consists in first generating a synthetic high-resolution geopotential map, then drawing synthetic measurement data (gravimetry and clock data) from it, and finally reconstructing the geopotential map from that data using least squares collocation. The quality of the reconstructed map is then assessed by comparing it to the original one used to generate the data. We show that adding only a few clock data points (less than 1% of the gravimetry data) reduces the bias significantly and improves the standard deviation by a factor 3. The effect of the data coverage and data quality on the results is investigated, and the trade-off between the measurement noise level and the number of data points is discussed.
Determination of a high spatial resolution geopotential model using atomic clock comparisons
Lion, G.; Panet, I.; Wolf, P.; Guerlin, C.; Bize, S.; Delva, P.
2017-06-01
Recent technological advances in optical atomic clocks are opening new perspectives for the direct determination of geopotential differences between any two points at a centimeter-level accuracy in geoid height. However, so far detailed quantitative estimates of the possible improvement in geoid determination when adding such clock measurements to existing data are lacking. We present a first step in that direction with the aim and hope of triggering further work and efforts in this emerging field of chronometric geodesy and geophysics. We specifically focus on evaluating the contribution of this new kind of direct measurements in determining the geopotential at high spatial resolution (≈ 10 km). We studied two test areas, both located in France and corresponding to a middle (Massif Central) and high (Alps) mountainous terrain. These regions are interesting because the gravitational field strength varies greatly from place to place at high spatial resolution due to the complex topography. Our method consists in first generating a synthetic high-resolution geopotential map, then drawing synthetic measurement data (gravimetry and clock data) from it, and finally reconstructing the geopotential map from that data using least squares collocation. The quality of the reconstructed map is then assessed by comparing it to the original one used to generate the data. We show that adding only a few clock data points (less than 1% of the gravimetry data) reduces the bias significantly and improves the standard deviation by a factor 3. The effect of the data coverage and data quality on the results is investigated, and the trade-off between the measurement noise level and the number of data points is discussed.
Maillard, Pierre
The purpose of this PhD work has been to investigate, model, test, develop and provide hardening techniques and guidelines for the mitigation of single event transients (SETs) in analog mixed-signal (AMS) delay locked loops (DLLs) for radiation-hardened applications. Delay-locked-loops (DLLs) are circuit substructures that are present in complex ASIC and system-on-a-chip designs. These circuits are widely used in on-chip clock distribution systems to reduce clock skew, to reduce jitter noise, and to recover clock signals at regional points within a global clock distribution system. DLLs are critical to the performance of many clock distribution systems, and in turn, the overall performance of the associated integrated system; as such, complex systems often employ multiple DLLs for clock deskew and distribution tasks. In radiation environments such as on-orbit, these critical circuits represent at-risk points of malfunction for large sections of integrated circuits due to vulnerabilities to radiation-generated transients (i.e. single event transients) that fan out across the system. The analysis of single event effects in analog DLLs has shown that each DLL sub-circuit primitive is vulnerable to single event transients. However, we have identified the voltage controlled delay line (VCDL) sub-circuit as the most sensitive to radiation-induced single event effects generating missing clock pulses that increase with the operating frequency of the circuit. This vulnerability increases with multiple instantiation of DLLs as clock distribution nodes throughout an integrated system on a chip. To our knowledge, no complete work in the rad-hard community regarding the hardening of mixed-signal DLLs against single event effects (missing pulses) has been developed. Most of the work present in the literature applies the "brute force" and well-established digital technique of triple modular redundancy (TMR) to the digital subcomponents. We have developed two novel design
Mesta, M.; Schaefer, C.; de Groot, J.; Cottaar, J.; Coehoorn, R.; Bobbert, P. A.
2013-11-01
Understanding of stationary charge transport in disordered organic semiconductors has matured during recent years. However, charge-carrier relaxation in nonstationary situations is still poorly understood. Such relaxation can be studied in dark injection experiments, in which the bias applied over an unilluminated organic semiconductor device is abruptly increased. The resulting transient current reveals both charge-carrier transport and relaxation characteristics. We performed such experiments on hole-only devices of a polyfluorene-based organic semiconductor. Modeling the dark injection by solving a one-dimensional master equation using the equilibrium carrier mobility leads to a too-slow current transient, since this approach does not account for carrier relaxation. Modeling by solving a three-dimensional time-dependent master equation does take into account all carrier transport and relaxation effects. With this modeling, the time scale of the current transient is found to be in agreement with experiment. With a disorder strength somewhat smaller than extracted from the temperature-dependent stationary current-voltage characteristics, also the shape of the experimental transients is well described.
Self-consistent tight-binding atomic-relaxation model of titanium dioxide
Schelling, P.K.; Yu, N.; Halley, J.W. [School of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota 55455 (United States)
1998-07-01
We report a self-consistent tight-binding atomic-relaxation model for titanium dioxide. We fit the parameters of the model to first-principles electronic structure calculations of the band structure and energy as a function of lattice parameters in bulk rutile. We report the method and results for the surface structures and energies of relaxed (110), (100), and (001) surfaces of rutile TiO{sub 2} as well as work functions for these surfaces. Good agreement with first-principles calculations and experiments, where available, is found for these surfaces. We find significant charge transfer (increased covalency) at the surfaces. {copyright} {ital 1998} {ital The American Physical Society}
Model Of Relaxation Of Residual Stresses In Hot-Rolled Strips
Milenin A.
2015-09-01
Full Text Available Residual stresses in hot-rolled strips are of practical importance when the laser cutting of these strip is applied. The factors influencing the residual stresses include the non uniform distribution of elastic-plastic deformations, phase transformation occurring during cooling and stress relaxation during rolling and cooling. The latter factor, despite its significant effect on the residual stress, is scarcely considered in the scientific literature. The goal of the present study was development of a model of residual stresses in hot-rolled strips based on the elastic-plastic material model, taking into account the stress relaxation.
Can We Efficiently Check Concurrent Programs Under Relaxed Memory Models in Maude?
Arrahman, Yehia Abd; Andric, Marina; Beggiato, Alessandro
2014-01-01
to the state space explosion. Several techniques have been proposed to mitigate those problems so to make verification under relaxed memory models feasible. We discuss how to adopt some of those techniques in a Maude-based approach to language prototyping, and suggest the use of other techniques that have been......Relaxed memory models offer suitable abstractions of the actual optimizations offered by multi-core architectures and by compilers of concurrent programming languages. Using such abstractions for verification purposes is challenging in part due to their inherent non-determinism which contributes...
Convex relaxation for a 3D spatiotemporal segmentation model using the primal-dual method
Shi-yan WANG; Hui-min YU
2012-01-01
A method based on 3D videos is proposed for multi-target segmentation and tracking with a moving viewing system.A spatiotemporal energy functional is built up to perform motion segmentation and estimation simultaneously.To overcome the limitation of the local minimum problem with the level set method,a convex relaxation method is applied to the 3D spatiotemporal segmentation model.The relaxed convex model is independent of the initial condition.A primal-dual algorithm is used to improve computational efficiency.Several indoor experiments show the validity of the proposed method.
Comparison between phenomenological and ab-initio reaction and relaxation models in DSMC
Sebastião, Israel B.; Kulakhmetov, Marat; Alexeenko, Alina
2016-11-01
New state-specific vibrational-translational energy exchange and dissociation models, based on ab-initio data, are implemented in direct simulation Monte Carlo (DSMC) method and compared to the established Larsen-Borgnakke (LB) and total collision energy (TCE) phenomenological models. For consistency, both the LB and TCE models are calibrated with QCT-calculated O2+O data. The model comparison test cases include 0-D thermochemical relaxation under adiabatic conditions and 1-D normal shockwave calculations. The results show that both the ME-QCT-VT and LB models can reproduce vibrational relaxation accurately but the TCE model is unable to reproduce nonequilibrium rates even when it is calibrated to accurate equilibrium rates. The new reaction model does capture QCT-calculated nonequilibrium rates. For all investigated cases, we discuss the prediction differences based on the new model features.
Phase Noise Analysis of Clock Recovery Based on an Optoelectronic Phase-Locked Loop
Zibar, Darko; Mørk, Jesper; Katsuo Oxenløwe, Leif; Clausen, Anders T.
2007-03-01
A detailed theoretical analysis of a clock-recovery (CR) scheme based on an optoelectronic phase-locked loop is presented. The analysis emphasizes the phase noise performance, taking into account the noise of the input data signal, the local voltage-controlled oscillator (VCO), and the laser employed in the loop. The effects of loop time delay and the laser transfer function are included in the stochastic differential equations describing the system, and a detailed timing jitter analysis of this type of optoelectronic CR for high-speed optical-time-division-multiplexing systems is performed. It is shown that a large loop length results in a higher timing jitter of the recovered clock signal. The impact of the loop length on the clock signal jitter can be reduced by using a low-noise VCO and a low loop filter bandwidth. Using the model, the timing jitter of the recovered optical and electrical clock signal can be evaluated. We numerically investigate the timing jitter requirements for combined electrical/optical local oscillators, in order for the recovered clock signal to have less jitter than that of the input signal. The timing jitter requirements for the free-running laser and the VCO are more relaxed for the extracted optical clock (lasers's output) signal.
A nonlinear constitutive model for stress relaxation in ligaments and tendons.
Davis, Frances M; De Vita, Raffaella
2012-12-01
A novel constitutive model that describes stress relaxation in transversely isotropic soft collagenous tissues such as ligaments and tendons is presented. The model is formulated within the nonlinear integral representation framework proposed by Pipkin and Rogers (J. Mech. Phys. Solids. 16:59-72, 1968). It represents a departure from existing models in biomechanics since it describes not only the strain dependent stress relaxation behavior of collagenous tissues but also their finite strains and transverse isotropy. Axial stress-stretch data and stress relaxation data at different axial stretches are collected on rat tail tendon fascicles in order to compute the model parameters. Toward this end, the rat tail tendon fascicles are assumed to be incompressible and undergo an isochoric axisymmetric deformation. A comparison with the experimental data proves that, unlike the quasi-linear viscoelastic model (Fung, Biomechanics: Mechanics of Living Tissues. Springer, New York, 1993) the constitutive law can capture the observed nonlinearities in the stress relaxation response of rat tail tendon fascicles.
Critical behavior of two-dimensional spin systems under the random-bond six-state clock model
Wu, Raymond P. H.; Lo, Veng-cheong; Huang, Haitao
2012-09-01
The critical behavior of the clock model in two-dimensional square lattice is studied numerically using Monte Carlo method with Wolff algorithm. The Kosterlitz-Thouless (KT) transition is observed in the six-state clock model, where an intermediate phase exists between the low-temperature ordered phase and the high-temperature disordered phase. The bond randomness is introduced to the system by assuming a Gaussian distribution for the coupling coefficients with the mean μ =1 and different values of variance, from σ2=0.1 to σ2=3.0. An abrupt jump in the helicity modulus at the transition, which is the key characteristic of the KT transition, is verified with a stability argument. The critical temperature Tc for both pure and disordered systems is determined from the critical exponent η(Tc)=1/4. The results showed that a small amount of disorder (small σ) reduces the critical temperature of the system, without altering the nature of transition. However, a larger amount of disorder changes the transition from the KT-type into that of non-KT-type.
Traynard, Pauline; Feillet, Céline; Soliman, Sylvain; Delaunay, Franck; Fages, François
2016-11-01
Experimental observations have put in evidence autonomous self-sustained circadian oscillators in most mammalian cells, and proved the existence of molecular links between the circadian clock and the cell cycle. Some mathematical models have also been built to assess conditions of control of the cell cycle by the circadian clock. However, recent studies in individual NIH3T3 fibroblasts have shown an unexpected acceleration of the circadian clock together with the cell cycle when the culture medium is enriched with growth factors, and the absence of such acceleration in confluent cells. In order to explain these observations, we study a possible entrainment of the circadian clock by the cell cycle through a regulation of clock genes around the mitosis phase. We develop a computational model and a formal specification of the observed behavior to investigate the conditions of entrainment in period and phase. We show that either the selective activation of RevErb-α or the selective inhibition of Bmal1 transcription during the mitosis phase, allow us to fit the experimental data on both period and phase, while a uniform inhibition of transcription during mitosis seems incompatible with the phase data. We conclude on the arguments favoring the RevErb-α up-regulation hypothesis and on some further predictions of the model.
On a Random Matrix Models of Quantum Relaxation
Lebowitz, J L; Pastur, L
2007-01-01
Earlier two of us (J.L. and L.P.) considered a matrix model for a two-level system interacting with a $n\\times n$ reservoir and assuming that the interaction is modelled by a random matrix. We presented there a formula for the reduced density matrix in the limit $n\\to \\infty $ as well as several its properties and asymptotic forms in various regimes. In this paper we give the proofs of the assertions, and present also a new fact about the model.
Model analysis of edge relaxation phenomena in Tokamak plasmas
Matsukawa, Shogo [Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, Kasuga, Fukuoka (Japan); Itoh, Sanae I.; Yagi, Masatoshi [Kyushu Univ., Fukuoka (Japan). Research Inst. for Applied Mechanics
2000-09-01
From the view point of the oscillatory characteristics, the heat transport in the plasma edge region is investigated based on a transition transport model with hysteresis nature. A hysteresis type flux-force relation is incorporated into the model by introducing a transition model of the heat diffusivity. For a given influx from the upstream side, the one dimensional heat transport equitation is solved numerically. The time evolution of the heat flux oscillation due to the hysteresis nature and the parameter dependences of its amplitude and frequency are examined. The non-monotonous relation between the frequency of the flux oscillation and the influx is obtained. The critical behavior of the transition between transport mechanisms, i.e., the hysteresis type and the discontinuous one, is expressed as power law relations of them. The self-organized criticality like behavior, i.e., power spectrum obeying power law, is found in a limiting case of the model. (author)
Lazado, Carlo C; Kumaratunga, Hiruni P S; Nagasawa, Kazue; Babiak, Igor; Caipang, Christopher Marlowe A; Fernandes, Jorge M O
2014-10-01
The notion that the circadian rhythm is exclusively regulated by a central clock has been challenged by the discovery of peripheral oscillators. These peripheral clocks are known to have a direct influence on the biological processes in a tissue or cell. In fish, several peripheral clocks respond directly to light, thus raising the hypothesis of autonomous regulation. Several clock genes are expressed with daily rhythmicity in Atlantic cod (Gadus morhua) fast skeletal muscle. In the present study, myosatellite cell culture and short-term cultured fast skeletal muscle explant models were developed and characterized, in order to investigate the autonomy of the clock system in skeletal muscle of Atlantic cod. Myosatellite cells proliferated and differentiated in vitro, as shown by the changes in cellular and myogenic gene markers. The high expression of myogenic differentiation 1 during the early days post-isolation implied the commitment to myogenic lineage and the increasing mRNA levels of proliferating cell nuclear antigen (pcna) indicated the proliferation of the cells in vitro. Transcript levels of myogenic marker genes such as pcna and myogenin increased during 5 days in culture of skeletal muscle explants, indicating that the muscle cells were proliferating and differentiating under ex vivo conditions. Transcript levels of the clock gene aryl hydrocarbon receptor nuclear translocator-like 2 (arntl2) in myosatellite cells showed no daily oscillation regardless of photoperiod manipulation. On the other hand, mRNA levels of the clock gene circadian locomotor output cycles kaput (clock) showed circadian rhythmicity in 5-day-old skeletal muscle explant under different photoperiod regimes. The expression of arntl2, cryptochrome2 (cry2), period 2a (per2a) and nuclear receptor subfamily 1, group D, member 1 was not rhythmic in muscle explants but photoperiod manipulation had a significant effect on mRNA levels of cry2 and per2a. Taken together, the lack of rhythmicity
Two-Temperature Model of non-equilibrium electron relaxation: A Review
Singh, Navinder
2007-01-01
The present paper is a review of the phenomena related to non-equilibrium electron relaxation in bulk and nano-scale metallic samples. The workable Two-Temperature Model (TTM) based on Boltzmann-Bloch-Peierls (BBP) kinetic equation has been applied to study the ultra-fast(femto-second) electronic relaxation in various metallic systems. The advent of new ultra-fast (femto-second) laser technology and pump-probe spectroscopy has produced wealth of new results for micro and nano-scale electronic...
Two-Temperature Model of non-equilibrium electron relaxation: A Review
Singh, Navinder
2007-01-01
The present paper is a review of the phenomena related to non-equilibrium electron relaxation in bulk and nano-scale metallic samples. The workable Two-Temperature Model (TTM) based on Boltzmann-Bloch-Peierls (BBP) kinetic equation has been applied to study the ultra-fast(femto-second) electronic relaxation in various metallic systems. The advent of new ultra-fast (femto-second) laser technology and pump-probe spectroscopy has produced wealth of new results for micro and nano-scale electronic...
Conductivity analysis of epoxy/carbon nanotubes composites by dipole relaxation and hopping models
Ramos, Airton; Pezzin, Sergio H.; Farias, Heric Denis; Becker, Daniela; Bello, Roger H.; Coelho, Luiz A. F.
2016-10-01
In this study it was used a numerical technique of successive approximations to estimate parameters of a conductivity model that includes the hopping process and the dipole relaxation for the purpose of describing the behavior of the conductivity measured on nanocomposites with carbon nanotubes in epoxy resin in the range of frequency of 100 Hz to 40 MHz. Two relaxation bands were detected, one with a response below 10 kHz and one above 10 MHz. For the first band, it was observed that the nanocomposites become more conductive, and its conductivity less temperature dependent, as the nanotube content increases. The second band is characterized by a large spread in relaxation time. The results show that the percolation threshold is below 0.15 vol% and that 'ac' hopping is the main transport process above 100 kHz, becoming dominant with respect to percolation at higher temperatures (>340 K).
Application to Rat Lung of the Extended Rorschach-Hazlewood Model of Spin-Lattice Relaxation
Hackmann, Andreas; Ailion, David C.; Ganesan, Krishnamurthy; Goodrich, K. Craig; Chen, Songhua; Laicher, Gernot; Cutillo, Antonio G.
1996-02-01
The spin-lattice relaxation timeT1was measured in excised degassed (airless) rat lungs over the frequency range 6.7 to 80.5 MHz. The observed frequency dependence was fitted successfully to the water-biopolymer cross-relaxation theory proposed by H. E. Rorschach and C. F. Hazlewood (RH) [J. Magn. Reson.70,79 (1986)]. The rotating frame spin-lattice relaxation timeT1ρwas also measured in rat lung fragments over the frequency range 0.56 to 5.6 kHz, and the observed frequency dependence was explained with an extension of the RH model. The agreement between the theory and the experimental data in both cases is good.
Ruban, Andrei; Simak, S.I.; Shallcross, S.;
2003-01-01
We present a simple effective tetrahedron model for local lattice relaxation effects in random metallic alloys on simple primitive lattices. A comparison with direct ab initio calculations for supercells representing random Ni0.50Pt0.50 and Cu0.25Au0.75 alloys as well as the dilute limit of Au...
Akindele, Abidemi J; Ajao, Mutiu Y; Aigbe, Flora R; Enumah, Uchenna S
2013-09-01
Telfairia occidentalis (Cucurbitaceae) is a leafy vegetable used in soup and folk medicine in southern Nigeria. Ethnobotanical survey revealed that preparations of the plant are used in the treatment of central nervous system-related disorders including convulsion. This study was conducted to investigate the effect of the hydroethanolic leaf extract of T. occidentalis in mouse models of convulsion, muscle relaxation, and depression. The strychnine and isoniazid convulsion, traction and climbing muscle relaxation, and forced swim and tail suspension depression tests were used in this study. The extract was administered orally (p.o.) at dose range of 25-800 mg/kg while distilled water (10 mL/kg p.o.) served as negative control. Diazepam (5 mg/kg p.o.) was used as positive control in the convulsion and muscle relaxation models while imipramine (64 mg/kg p.o.) served the same purpose in the depression tests. T. occidentalis significantly increased the onset (Pconvulsion (P<.05, .01) in the strychnine test and increased the time to death (P<.05, .01, .001) in the isoniazid model. The extract insignificantly increased the reaction time in the traction test while it significantly increased the time in the climbing test (P<.001). In the forced swim and tail suspension models, T. occidentalis significantly (P<.001) and dose-dependently increased the duration of immobility. The results obtained in this study suggest that the hydroethanolic leaf extract of T. occidentalis possesses anticonvulsant and muscle relaxant properties, thus justifying its folkloric use.
Small velocity and finite temperature variations in kinetic relaxation models
Markowich, Peter
2010-01-01
A small Knuden number analysis of a kinetic equation in the diffusive scaling is performed. The collision kernel is of BGK type with a general local Gibbs state. Assuming that the flow velocity is of the order of the Knudsen number, a Hilbert expansion yields a macroscopic model with finite temperature variations, whose complexity lies in between the hydrodynamic and the energy-transport equations. Its mathematical structure is explored and macroscopic models for specific examples of the global Gibbs state are presented. © American Institute of Mathematical Sciences.
Maltsev, Victor A; Lakatta, Edward G
2013-06-01
Recent evidence supports the idea that robust and, importantly, FLEXIBLE automaticity of cardiac pacemaker cells is conferred by a coupled system of membrane ion currents (an "M-clock") and a sarcoplasmic reticulum (SR)-based Ca(2+) oscillator ("Ca(2+)clock") that generates spontaneous diastolic Ca(2+) releases. This study identified numerical models of a human biological pacemaker that features robust and flexible automaticity generated by a minimal set of electrogenic proteins and a Ca(2+)clock. Following the Occam's razor principle (principle of parsimony), M-clock components of unknown molecular origin were excluded from Maltsev-Lakatta pacemaker cell model and thirteen different model types of only 4 or 5 components were derived and explored by a parametric sensitivity analysis. The extended ranges of SR Ca(2+) pumping (i.e. Ca(2+)clock performance) and conductance of ion currents were sampled, yielding a large variety of parameter combination, i.e. specific model sets. We tested each set's ability to simulate autonomic modulation of human heart rate (minimum rate of 50 to 70bpm; maximum rate of 140 to 210bpm) in response to stimulation of cholinergic and β-adrenergic receptors. We found that only those models that include a Ca(2+)clock (including the minimal 4-parameter model "ICaL+IKr+INCX+Ca(2+)clock") were able to reproduce the full range of autonomic modulation. Inclusion of If or ICaT decreased the flexibility, but increased the robustness of the models (a relatively larger number of sets did not fail during testing). The new models comprised of components with clear molecular identity (i.e. lacking IbNa & Ist) portray a more realistic pacemaking: A smaller Na(+) influx is expected to demand less energy for Na(+) extrusion. The new large database of the reduced coupled-clock numerical models may serve as a useful tool for the design of biological pacemakers. It will also provide a conceptual basis for a general theory of robust, flexible, and energy
Ilker, Efe; Berker, A Nihat
2014-12-01
Distinctive orderings and phase diagram structures are found, from renormalization-group theory, for odd q-state clock spin-glass models in d=3 dimensions. These models exhibit asymmetric phase diagrams, as is also the case for quantum Heisenberg spin-glass models. No finite-temperature spin-glass phase occurs. For all odd q≥5, algebraically ordered antiferromagnetic phases occur. One such phase is dominant and occurs for all q≥5. Other such phases occupy small low-temperature portions of the phase diagrams and occur for 5≤q≤15. All algebraically ordered phases have the same structure, determined by an attractive finite-temperature sink fixed point where a dominant and a subdominant pair states have the only nonzero Boltzmann weights. The phase transition critical exponents quickly saturate to the high q value.
江冰; 方岱宁; 黄克智
1999-01-01
Based on micromechanics and Laplace transformation, a constitutive model of ferroelectric composites with a linear elastic and linear dielectric matrix is developed and extended to the ferroelectric composites with a viscoelastic and dielectric relaxation matrix. Thus, a constitutive model for ferroelectric composites with a viscoelastic and dielectric relaxation matrix has been set up.
Modelling anelastic contribution to nuclear fuel cladding creep and stress relaxation
Tulkki, Ville, E-mail: ville.tulkki@vtt.fi; Ikonen, Timo
2015-10-15
In fuel behaviour modelling accurate description of the cladding mechanical response is important for both operational and safety considerations. While accuracy is desired, a certain level of simplicity is needed as both computational resources and detailed information on properties of particular cladding may be limited. Most models currently used in the integral codes divide the mechanical response into elastic and viscoplastic contributions. These have difficulties in describing both creep and stress relaxation, and often separate models for the two phenomena are used. In this paper we implement anelastic contribution to the cladding mechanical model, thus enabling consistent modelling of both creep and stress relaxation. We show that the model based on assumption of viscoelastic behaviour can be used to explain several experimental observations in transient situations and compare the model to published set of creep and stress relaxation experiments performed on similar samples. Based on the analysis presented we argue that the inclusion of anelastic contribution to the cladding mechanical models provides a way to improve the simulation of cladding behaviour during operational transients.
Non-Arrhenius relaxation of the Heisenberg model with dipolar and anisotropic interactions
Diaz-Mendez, Rogelio, E-mail: rogelio@electrica.cujae.edu.cu [Nanophysics Group, Department of Physics, Electric Engineering Faculty, CUJAE, ave 114 final, La Habana (Cuba); ' Henri Poincare' Group of Complex Systems, Physics Faculty, University of Havana, La Habana, CP 10400 (Cuba); Mulet, Roberto [' Henri Poincare' Group of Complex Systems, Physics Faculty, University of Havana, La Habana, CP 10400 (Cuba); Department of Theoretical Physics, Physics Faculty, University of Havana, La Habana, CP 10400 (Cuba)
2012-01-15
The dynamical properties of a 2D Heisenberg model with dipolar interactions and perpendicular anisotropy are studied using Monte Carlo simulations in two different ordered regions of the equilibrium phase diagram. We find a temperature defining a dynamical transition below which the relaxation suddenly slows down and the system apart from the typical Arrhenius relaxation to a Vogel-Fulcher-Tamann law. This anomalous behavior is observed in the scaling of the magnetic relaxation and may eventually lead to a freezing of the system. Through the analysis of the domain structures we explain this behavior in terms of the domains dynamics. Moreover, we calculate the energy barriers distribution obtained from the data of the magnetic viscosity. Its shape supports our comprehension of both, the Vogel-Fulcher-Tamann dynamical slowing down and the freezing mechanism. - Highlights: > We make Monte Carlo simulations in a dipolar Heisenberg model with anisotropy. > We find a dynamical transition temperature below which the relaxation is VFT-like. > An interpretation is done by analyzing the domains structure and energy barriers.
The influence of dimension on the relaxation process of East-like models: Rigorous results
Chleboun, P.; Faggionato, A.; Martinelli, F.
2014-08-01
We study facilitated models which extend to arbitrary dimensions the one-dimensional East process and which are supposed to catch some of the main features of the complex dynamics of fragile glasses. We focus on the low-temperature regime (small density c\\approx e^{-\\beta} of the facilitating sites). In the literature the relaxation process has been assumed to be quasi-one-dimensional and the equilibration time has been computed using the relaxation time of the East model (d=1) on the equilibrium length scale L_c=(1/c)^{1/d} in d-dimension. This led to a super-Arrhenius scaling for the relaxation time of the form T_{\\text{rel}}\\asymp \\exp(\\beta^2/dlog 2) . In a companion paper, using renormalization group ideas and electrical networks methods, we rigorously establish that instead T_{\\text{rel}}\\asymp \\exp(\\beta^2/2dlog 2) , contradicting the quasi-one-dimensional assumption. The above scaling confirms previous MCAMC simulations. Next we compute the relaxation time at finite and mesoscopic length scales, and show a dramatic dependence on the boundary conditions. Our final result is related to the out-of-equilibrium dynamics. Starting with a single facilitating site at the origin we show that, up to length scales L=O(L_c) , its influence propagates much faster (on a logarithmic scale) along the diagonal direction than along the axes directions.
Kawai, Masamichi; Kazama, Takeshi; Masuko, Yoichi; Tsuda, Hiroshi; Takahashi, Jun; Kemmochi, Kiyoshi
Off-axis stress relaxation behavior of unidirectional T800H/3631 carbon/epoxy composite exposed to high temperature is examined at relatively high tensile strain levels, and a phenomenological viscoplasticity model is tested on the capability to describe the time-dependent response observed. First, stress relaxation tests are performed at 100°C on plain coupon specimens with different fiber orientations, θ=0, 10, 30, 45, and 90°. For each of the fiber orientations, in principle, stress relaxation tests are carried out at three different strain levels. The relaxation of axial stress in the unidirectional composite is clearly observed, regardless of the fiber orientation. Just after the total strain hold, the axial stress quickly relaxes with time in a short period. The stress relaxation rate of the composite tends to become zero, irrespective of the fiber orientation. The associated relaxation modulus depends on the level of strain. The entire process of the prior instantaneous tensile response and the subsequent off-axis stress relaxation behavior is simulated using a macromechanical viscoplasticity model based on an overstress concept. It is demonstrated that the model succeeds in adequately reproducing the off-axis stress relaxation behavior of the unidirectional composite laminate.
When the clock strikes: Modeling the relation between circadian rhythms and cardiac arrhythmias
Seenivasan, Pavithraa; Sridhar, S; Sinha, Sitabhra
2016-01-01
It has recently been observed that the occurrence of sudden cardiac death has a close statistical relationship with the time of day, viz., ventricular fibrillation is most likely to occur between 12 am-6 am, with 6 pm-12 am being the next most likely period. Consequently there has been significant interest in understanding how cardiac activity is influenced by the circadian clock, i.e., temporal oscillations in physiological activity with a period close to 24 hours and synchronized with the day-night cycle. Although studies have identified the genetic basis of circadian rhythms at the intracellular level, the mechanisms by which they influence cardiac pathologies are not yet fully understood. Evidence has suggested that diurnal variations in the conductance properties of ion channel proteins that govern the excitation dynamics of cardiac cells may provide the crucial link. In this paper, we investigate the relationship between the circadian rhythm as manifested in modulations of ion channel properties and the...
Shan, Ming-Lei; Zhu, Chang-Ping; Yao, Cheng; Yin, Cheng; Jiang, Xiao-Yan
2016-10-01
The dynamics of the cavitation bubble collapse is a fundamental issue for the bubble collapse application and prevention. In the present work, the modified forcing scheme for the pseudopotential multi-relaxation-time lattice Boltzmann model developed by Li Q et al. [Li Q, Luo K H and Li X J 2013 Phys. Rev. E 87 053301] is adopted to develop a cavitation bubble collapse model. In the respects of coexistence curves and Laplace law verification, the improved pseudopotential multi-relaxation-time lattice Boltzmann model is investigated. It is found that the thermodynamic consistency and surface tension are independent of kinematic viscosity. By homogeneous and heterogeneous cavitation simulation, the ability of the present model to describe the cavitation bubble development as well as the cavitation inception is verified. The bubble collapse between two parallel walls is simulated. The dynamic process of a collapsing bubble is consistent with the results from experiments and simulations by other numerical methods. It is demonstrated that the present pseudopotential multi-relaxation-time lattice Boltzmann model is applicable and efficient, and the lattice Boltzmann method is an alternative tool for collapsing bubble modeling. Project supported by the National Natural Science Foundation of China (Grant Nos. 11274092 and 1140040119) and the Natural Science Foundation of Jiangsu Province, China (Grant No. SBK2014043338).
Dong, Y.
2014-07-26
Si-Ge interdiffusion and strain relaxation were studied in a metastable SiGe epitaxial structure. With Ge concentration profiling and ex-situ strain analysis, it was shown that during thermal anneals, both Si-Ge interdiffusion and strain relaxation occurred. Furthermore, the time evolutions of both strain relaxation and interdiffusion were characterized. It showed that during the ramp-up stage of thermal anneals at higher temperatures (800°C and 840°C), the degree of relaxation, R, reached a “plateau”, while interdiffusion was negligible. With the approximation that the R value is constant after the ramp-up stage, a quantitative interdiffusivity model was built to account for both the effect of strain relaxation and the impact of the relaxation induced dislocations, which gave good agreement with the experiment data.
Relaxation and self-sustained oscillations in the time elapsed neuron network model
Pakdaman, Khashayar; Salort, Delphine
2011-01-01
The time elapsed model describes the firing activity of an homogeneous assembly of neurons thanks to the distribution of times elapsed since the last discharge. It gives a mathematical description of the probability density of neurons structured by this time. In an earlier work, based on generalized relative entropy methods, it is proved that for highly or weakly connected networks the model exhibits relaxation to the steady state and for moderately connected networks it is obtained numerical evidence of appearance of self-sustained periodic solutions. Here, we go further and, using the particular form of the model, we quantify the regime where relaxation to a stationary state occurs in terms of the network connectivity. To introduce our methodology, we first consider the case where the neurons are not connected and we give a new statement showing that total asynchronous firing of neurons appears asymptotically. In a second step, we consider the case with connections and give a low connectivity condition that...
Schmidt, Thomas; Balzani, Daniel
2016-05-01
In this paper, a three-dimensional relaxed incremental variational damage model is proposed, which enables the description of complex softening hysteresis as observed in supra-physiologically loaded arterial tissues, and which thereby avoids a loss of convexity of the underlying formulation. The proposed model extends the relaxed formulation of Balzani and Ortiz [2012. Relaxed incremental variational formulation for damage at large strains with application to fiber-reinforced materials and materials with truss-like microstructures. Int. J. Numer. Methods Eng. 92, 551-570], such that the typical stress-hysteresis observed in arterial tissues under cyclic loading can be described. This is mainly achieved by constructing a modified one-dimensional model accounting for cyclic loading in the individual fiber direction and numerically homogenizing the response taking into account a fiber orientation distribution function. A new solution strategy for the identification of the convexified stress potential is proposed based on an evolutionary algorithm which leads to an improved robustness compared to solely Newton-based optimization schemes. In order to enable an efficient adjustment of the new model to experimentally observed softening hysteresis, an adjustment scheme using a surrogate model is proposed. Therewith, the relaxed formulation is adjusted to experimental data in the supra-physiological domain of the media and adventitia of a human carotid artery. The performance of the model is then demonstrated in a finite element example of an overstretched artery. Although here three-dimensional thick-walled atherosclerotic arteries are considered, it is emphasized that the formulation can also directly be applied to thin-walled simulations of arteries using shell elements or other fiber-reinforced biomembranes.
Ancient dates or accelerated rates? Morphological clocks and the antiquity of placental mammals.
Beck, Robin M D; Lee, Michael S Y
2014-10-22
Analyses of a comprehensive morphological character matrix of mammals using 'relaxed' clock models (which simultaneously estimate topology, divergence dates and evolutionary rates), either alone or in combination with an 8.5 kb nuclear sequence dataset, retrieve implausibly ancient, Late Jurassic-Early Cretaceous estimates for the initial diversification of Placentalia (crown-group Eutheria). These dates are much older than all recent molecular and palaeontological estimates. They are recovered using two very different clock models, and regardless of whether the tree topology is freely estimated or constrained using scaffolds to match the current consensus placental phylogeny. This raises the possibility that divergence dates have been overestimated in previous analyses that have applied such clock models to morphological and total evidence datasets. Enforcing additional age constraints on selected internal divergences results in only a slight reduction of the age of Placentalia. Constraining Placentalia to less than 93.8 Ma, congruent with recent molecular estimates, does not require major changes in morphological or molecular evolutionary rates. Even constraining Placentalia to less than 66 Ma to match the 'explosive' palaeontological model results in only a 10- to 20-fold increase in maximum evolutionary rate for morphology, and fivefold for molecules. The large discrepancies between clock- and fossil-based estimates for divergence dates might therefore be attributable to relatively small changes in evolutionary rates through time, although other explanations (such as overly simplistic models of morphological evolution) need to be investigated. Conversely, dates inferred using relaxed clock models (especially with discrete morphological data and MrBayes) should be treated cautiously, as relatively minor deviations in rate patterns can generate large effects on estimated divergence dates.
Cellular circadian clocks in mood disorders.
McCarthy, Michael J; Welsh, David K
2012-10-01
Bipolar disorder (BD) and major depressive disorder (MDD) are heritable neuropsychiatric disorders associated with disrupted circadian rhythms. The hypothesis that circadian clock dysfunction plays a causal role in these disorders has endured for decades but has been difficult to test and remains controversial. In the meantime, the discovery of clock genes and cellular clocks has revolutionized our understanding of circadian timing. Cellular circadian clocks are located in the suprachiasmatic nucleus (SCN), the brain's primary circadian pacemaker, but also throughout the brain and peripheral tissues. In BD and MDD patients, defects have been found in SCN-dependent rhythms of body temperature and melatonin release. However, these are imperfect and indirect indicators of SCN function. Moreover, the SCN may not be particularly relevant to mood regulation, whereas the lateral habenula, ventral tegmentum, and hippocampus, which also contain cellular clocks, have established roles in this regard. Dysfunction in these non-SCN clocks could contribute directly to the pathophysiology of BD/MDD. We hypothesize that circadian clock dysfunction in non-SCN clocks is a trait marker of mood disorders, encoded by pathological genetic variants. Because network features of the SCN render it uniquely resistant to perturbation, previous studies of SCN outputs in mood disorders patients may have failed to detect genetic defects affecting non-SCN clocks, which include not only mood-regulating neurons in the brain but also peripheral cells accessible in human subjects. Therefore, reporters of rhythmic clock gene expression in cells from patients or mouse models could provide a direct assay of the molecular gears of the clock, in cellular clocks that are likely to be more representative than the SCN of mood-regulating neurons in patients. This approach, informed by the new insights and tools of modern chronobiology, will allow a more definitive test of the role of cellular circadian clocks
IRT models with relaxed assumptions in eRm: A manual-like instruction
REINHOLD HATZINGER
2009-03-01
Full Text Available Linear logistic models with relaxed assumptions (LLRA as introduced by Fischer (1974 are a flexible tool for the measurement of change for dichotomous or polytomous responses. As opposed to the Rasch model, assumptions on dimensionality of items, their mutual dependencies and the distribution of the latent trait in the population of subjects are relaxed. Conditional maximum likelihood estimation allows for inference about treatment, covariate or trend effect parameters without taking the subjects' latent trait values into account. In this paper we will show how LLRAs based on the LLTM, LRSM and LPCM can be used to answer various questions about the measurement of change and how they can be fitted in R using the eRm package. A number of small didactic examples is provided that can easily be used as templates for real data sets. All datafiles used in this paper are available from http://eRm.R-Forge.R-project.org/
Elastic models for the non-Arrhenius relaxation time of glass-forming liquids
Dyre, Jeppe
We first review the phenomenology of viscous liquids and the standard models used for explaining the non-Arrhenius average relaxation time. Then the focus is turned to the so-called elastic models, arguing that these models are all equivalent in the Einstein approximation (where the short......-time elastic properties are all determined by just one effective, temperature-dependent force constant). We finally discuss the connection between the elastic models and two well-established research fields of condensed-matter physics: point defects in crystals and solid-state diffusion....
Elastic models for the Non-Arrhenius Relaxation Time of Glass-Forming Liquids
Dyre, J. C.
2006-01-01
We first review the phenomenology of viscous liquids and the standard models used for explaining the non-Arrhenius average relaxation time. Then the focus is turned to the so-called elastic models, arguing that these models are all equivalent in the Einstein approximation (where the short......-time elastic properties are all determined by just one effective, temperature-dependent force constant). We finally discuss the connection between the elastic models and two well-established research fields of condensed-matter physics: point defects in crystals and solid-state diffusion....
Elastic Models for the Non-Arrhenius Relaxation Time of Glass-Forming Liquids
Dyre, Jeppe C.
2006-05-01
We first review the phenomenology of viscous liquids and the standard models used for explaining the non-Arrhenius average relaxation time. Then the focus is turned to the so-called elastic models, arguing that these models are all equivalent in the Einstein approximation (where the short-time elastic properties are all determined by just one effective, temperature-dependent force constant). We finally discuss the connection between the elastic models and two well-established research fields of condensed-matter physics: point defects in crystals and solid-state diffusion.
Modelling of the Relaxation Least Squares-Based Neural Networks and Its Application
无
2002-01-01
A relaxation least squares-based learning algorithm for neural networks is proposed. Not only does it have a fast convergence rate, but it involves less computation quantity. Therefore, it is suitable to deal with the case when a network has a large scale but the number of training data is very limited. It has been used in converting furnace process modelling, and impressive result has been obtained.
CONVERGENCE RATES TO TRAVELLING WAVES FOR A RELAXATION MODEL WITH LARGE INITIAL DISTURBANCE
张辉; 赵引川
2004-01-01
This paper is concerned with the convergence rates to travelling waves for a relaxation model with general flux functions. Compared with former results in this direction, the main novelty in this paper lies in the fact that the initial disturbance can be chosen large in suitable norm. Our analysis is based on the L1-stability results obtained by C. Mascia and R. Natalini in [12].
FOI-PERFECT code: 3D relaxation MHD modeling and Applications
Wang, Gang-Hua; Duan, Shu-Chao; Comutational Physics Team Team
2016-10-01
One of the challenges in numerical simulations of electromagnetically driven high energy density (HED) systems is the existence of vacuum region. FOI-PERFECT code adopts a full relaxation magnetohydrodynamic (MHD) model. The electromagnetic part of the conventional model adopts the magnetic diffusion approximation. The vacuum region is approximated by artificially increasing the resistivity. On one hand the phase/group velocity is superluminal and hence non-physical in the vacuum region, on the other hand a diffusion equation with large diffusion coefficient can only be solved by implicit scheme which is difficult to be parallelized and converge. A better alternative is to solve the full electromagnetic equations. Maxwell's equations coupled with the constitutive equation, generalized Ohm's law, constitute a relaxation model. The dispersion relation is given to show its transition from electromagnetic propagation in vacuum to resistive MHD in plasma in a natural way. The phase and group velocities are finite for this system. A better time stepping is adopted to give a 3rd full order convergence in time domain without the stiff relaxation term restriction. Therefore it is convenient for explicit & parallel computations. Some numerical results of FOI-PERFECT code are also given. Project supported by the National Natural Science Foundation of China (Grant No. 11571293) And Foundation of China Academy of Engineering Physics (Grant No. 2015B0201023).
Viscosity, relaxation time, and dynamics within a model asphalt of larger molecules
Li, Derek D.; Greenfield, Michael L.
2014-01-01
The dynamics properties of a new "next generation" model asphalt system that represents SHRP AAA-1 asphalt using larger molecules than past models is studied using molecular simulation. The system contains 72 molecules distributed over 12 molecule types that range from nonpolar branched alkanes to polar resins and asphaltenes. Molecular weights range from 290 to 890 g/mol. All-atom molecular dynamics simulations conducted at six temperatures from 298.15 to 533.15 K provide a wealth of correlation data. The modified Kohlrausch-Williams-Watts equation was regressed to reorientation time correlation functions and extrapolated to calculate average rotational relaxation times for individual molecules. The rotational relaxation rate of molecules decreased significantly with increasing size and decreasing temperature. Translational self-diffusion coefficients followed an Arrhenius dependence. Similar activation energies of ˜42 kJ/mol were found for all 12 molecules in the model system, while diffusion prefactors spanned an order of magnitude. Viscosities calculated directly at 533.15 K and estimated at lower temperatures using the Debye-Stokes-Einstein relationship were consistent with experimental data for asphalts. The product of diffusion coefficient and rotational relaxation time showed only small changes with temperature above 358.15 K, indicating rotation and translation that couple self-consistently with viscosity. At lower temperatures, rotation slowed more than diffusion.
Viscosity, relaxation time, and dynamics within a model asphalt of larger molecules
Li, Derek D.; Greenfield, Michael L., E-mail: greenfield@egr.uri.edu [Department of Chemical Engineering, University of Rhode Island, Kingston, Rhode Island 02881 (United States)
2014-01-21
The dynamics properties of a new “next generation” model asphalt system that represents SHRP AAA-1 asphalt using larger molecules than past models is studied using molecular simulation. The system contains 72 molecules distributed over 12 molecule types that range from nonpolar branched alkanes to polar resins and asphaltenes. Molecular weights range from 290 to 890 g/mol. All-atom molecular dynamics simulations conducted at six temperatures from 298.15 to 533.15 K provide a wealth of correlation data. The modified Kohlrausch-Williams-Watts equation was regressed to reorientation time correlation functions and extrapolated to calculate average rotational relaxation times for individual molecules. The rotational relaxation rate of molecules decreased significantly with increasing size and decreasing temperature. Translational self-diffusion coefficients followed an Arrhenius dependence. Similar activation energies of ∼42 kJ/mol were found for all 12 molecules in the model system, while diffusion prefactors spanned an order of magnitude. Viscosities calculated directly at 533.15 K and estimated at lower temperatures using the Debye-Stokes-Einstein relationship were consistent with experimental data for asphalts. The product of diffusion coefficient and rotational relaxation time showed only small changes with temperature above 358.15 K, indicating rotation and translation that couple self-consistently with viscosity. At lower temperatures, rotation slowed more than diffusion.
Relaxation limit of a compressible gas-liquid model with well-reservoir interaction
Solem, Susanne; Evje, Steinar
2017-02-01
This paper deals with the relaxation limit of a two-phase compressible gas-liquid model which contains a pressure-dependent well-reservoir interaction term of the form q (P_r - P) where q>0 is the rate of the pressure-dependent influx/efflux of gas, P is the (unknown) wellbore pressure, and P_r is the (known) surrounding reservoir pressure. The model can be used to study gas-kick flow scenarios relevant for various wellbore operations. One extreme case is when the wellbore pressure P is largely dictated by the surrounding reservoir pressure P_r. Formally, this model is obtained by deriving the limiting system as the relaxation parameter q in the full model tends to infinity. The main purpose of this work is to understand to what extent this case can be represented by a well-defined mathematical model for a fixed global time T>0. Well-posedness of the full model has been obtained in Evje (SIAM J Math Anal 45(2):518-546, 2013). However, as the estimates for the full model are dependent on the relaxation parameter q, new estimates must be obtained for the equilibrium model to ensure existence of solutions. By means of appropriate a priori assumptions and some restrictions on the model parameters, necessary estimates (low order and higher order) are obtained. These estimates that depend on the global time T together with smallness assumptions on the initial data are then used to obtain existence of solutions in suitable Sobolev spaces.
Clock genes, pancreatic function, and diabetes.
Vieira, Elaine; Burris, Thomas P; Quesada, Ivan
2014-12-01
Circadian physiology is responsible for the temporal regulation of metabolism to optimize energy homeostasis throughout the day. Disturbances in the light/dark cycle, sleep/wake schedule, or feeding/activity behavior can affect the circadian function of the clocks located in the brain and peripheral tissues. These alterations have been associated with impaired glucose tolerance and type 2 diabetes. Animal models with molecular manipulation of clock genes and genetic studies in humans also support these links. It has been demonstrated that the endocrine pancreas has an intrinsic self-sustained clock, and recent studies have revealed an important role of clock genes in pancreatic β cells, glucose homeostasis, and diabetes.
Alekseenko, Alexander; Euler, Craig
2016-05-01
We propose a Bhatnagar-Gross-Krook (BGK) kinetic model in which the collision frequency is a linear combination of polynomials in the velocity variable. The coefficients of the linear combination are determined so as to enforce proper relaxation rates for a selected group of moments. The relaxation rates are obtained by a direct numerical evaluation of the full Boltzmann collision operator. The model is conservative by construction. Simulations of the problem of spatially homogeneous relaxation of hard spheres gas show improvement in accuracy of controlled moments as compared to solutions obtained by the classical BGK, ellipsoidal-statistical BGK and the Shakhov models in cases of strong deviations from continuum.
Zhang Jin-Lu; Wang Li-Na; Zhao Xing-Yu; Zhang Li-Li; Zhou Heng-Wei; Wei Lai; Huang Yi-Neng
2011-01-01
The string model for the glass transition can quantitatively describe the universal α-relaxation in glassformers. The string relaxation equation (SRE) of the model simplifies the well-known Debye and Rouse-Zimm relaxation equations at high and low enough temperatures, respectively. However, its initial condition, necessary to the further model predictions of glassy dynamics, has not been solved. In this paper, the general initial condition of the SRE for stochastically spatially configurative strings is solved exactly based on the obtained special initial condition of the SRE for straight strings in a previous paper (J. L. Zhang et al. 2010 Chin. Phya. B 19, 056403).
Davies, H. C.; Turner, R. E.
1977-01-01
A dynamical relaxation technique for updating prediction models is analyzed with the help of the linear and nonlinear barotropic primitive equations. It is assumed that a complete four-dimensional time history of some prescribed subset of the meteorological variables is known. The rate of adaptation of the flow variables toward the true state is determined for a linearized f-model, and for mid-latitude and equatorial beta-plane models. The results of the analysis are corroborated by numerical experiments with the nonlinear shallow-water equations.
Mathematical model for blood flow autoregulation by endothelium-derived relaxing factor
Chernyavsky, I L; Chernyavsky, Igor L.; Kudryashov, Nikolai A.
2006-01-01
The fluid shear stress is an important regulator of the cardiovascular system via the endothelium-derived relaxing factor (EDRF) that is Nitric Oxide. This mechanism involves biochemical reactions in an arterial wall. The autoregulation process is managed by the vascular tonus and gives the negative feedback for the shear stress changing. A new mathematical model for the autoregulation of a blood flow through arteria under the constant transmural pressure is presented. Endothelium-derived relaxing factor Nitric Oxide, the multi-layer structure of an arterial wall, and kinetic-diffusion processes are taken into consideration. The limit case of the thin-wall artery is analytically studied. The stability condition for a stationary point of the linearized system is given. The exact stationary solutions of the origin system are found. The numerical simulation for the autoregulation system is presented. It is shown the arteria adaptation to an initial radial perturbation and the transition of the system to new equi...
Relaxation dynamics of a polymer network modeled by a multihierarchical structure.
Jurjiu, A; Volta, A; Beu, T
2011-07-01
We numerically analyze the scaling behavior of experimentally accessible dynamical relaxation forms for polymer networks modeled by a finite multihierarchical structure. In the framework of generalized Gaussian structures, by making use of the eigenvalue spectrum of the connectivity matrix, we determine the averaged monomer displacement under local external forces as well as the mechanical relaxation quantities (storage and loss moduli). Hence we generalize the known analysis for both classes of fractals to the case of multihierarchical structure, for which even though we have a mixed growth algorithm, the above cited observables still give information about the two different underlying topologies. For very large lattices, reached via an algebraic procedure that avoids the numerical diagonalizations of the corresponding connectivity matrices, we depict the scaling of both component fractals in the intermediate time (frequency) domain, which manifests two different slopes.
Schiller, S; Nevsky, A; Koelemeij, J C J; Wicht, A; Gill, P; Klein, H A; Margolis, H S; Mileti, G; Sterr, U; Riehle, F; Peik, E; Tamm, C; Ertmer, W; Rasel, E; Klein, V; Salomon, C; Tino, G M; Lemonde, P; Holzwarth, R; Hänsch, T W; Tamm, Chr.
2007-01-01
The performance of optical clocks has strongly progressed in recent years, and accuracies and instabilities of 1 part in 10^18 are expected in the near future. The operation of optical clocks in space provides new scientific and technological opportunities. In particular, an earth-orbiting satellite containing an ensemble of optical clocks would allow a precision measurement of the gravitational redshift, navigation with improved precision, mapping of the earth's gravitational potential by relativistic geodesy, and comparisons between ground clocks.
江冰; 方岱宁; 黄克智
2000-01-01
Experimental analysis of ferroelectric composites with a viscoelastic and dieiectric relax-ation matrix is carried out, and the electromechanical coupling behavior of the ferroelectric composites is calculated by means of the constitutive model proposed in this paper. Comparisons between the ex-perimental results and the calculations show that the constitutive model can reflect the electromechanical coupling behavior of the ferroelectric composites. The analysis indicates that the effect of viscoelas-ticity and dieiectric relaxation of the matrix on the electromechanical coupling behavior of ferroelectric composites cannot be neglected.
Localization model description of diffusion and structural relaxation in glass-forming Cu-Zr alloys
Douglas, Jack F.; Pazmino Betancourt, Beatriz A.; Tong, Xuhang; Zhang, Hao
2016-05-01
We test the localization model (LM) prediction of a parameter-free relationship between the α-structural relaxation time τ α and the Debye-Waller factor for a series of simulated glass-forming Cu-Zr metallic liquids having a range of alloy compositions. After validating this relationship between the picosecond (‘fast’) and long-time relaxation dynamics over the full range of temperatures and alloy compositions investigated in our simulations, we show that it is also possible to estimate the self-diffusion coefficients of the individual atomic species (D Cu, D Zr) and the average diffusion coefficient D using the LM, in conjunction with the empirical fractional Stokes-Einstein (FSE) relation linking these diffusion coefficients to τ α . We further observe that the fragility and extent of decoupling between D and τ α strongly correlate with at the onset temperature of glass-formation T A where particle caging and the breakdown of Arrhenius relaxation first emerge.
Bennati, L.; Calais, E.; Freed, A. M.; Hamling, I. J.; Wright, T. J.; Lewi, E.; Nooner, S. L.; Buck, W. R.
2009-12-01
In September 2005, a 60km-long dike intrusion took place at the Dabbahu rift, Afar, Ethiopia, at the boundary between the Nubian and Danakil plates. Since this major event, 12 new intrusions have affected the central and southern parts of the 2005 dike. Time series from continuous GPS stations outside of volcanoes show a combination of discrete diking events and quasi constant velocity displacement at rates up to 10 times faster than the secular divergence rate between Nubia and Arabia. Survey GPS sites in the far-field show rates twice as fast as the secular Nubia/Arabia divergence. Similar observations after the 1975-1985 Krafla events in Iceland and the 1978 Asal-Ghoubbet events in Afar have been interpreted as the result of stress relaxation in a viscoelastic lithospheric mantle and/or continued magma injection. Nooner et al. (submitted) showed that horizontal GPS displacements are well explained by the relaxation, in a viscoelastic upper mantle, of the stresses imparted by the dike intrusions. The best fit is obtained for a 13.2km-thick crust overlying a mantle with a viscosity of 5.2x10^18Pa.s. We improve upon this approach with a model accounting for dike intrusions, viscoelastic stress relaxation in a power-law rheology upper mantle, laterally varying crustal thicknesses, and pressure changes in magma reservoirs. Preliminary results indicate that 3-dimensional velocity field from GPS and InSAR requires a combination of viscoelastic relaxation and magma transport at depth.
On the Rate of Relaxation for the Landau Kinetic Equation and Related Models
Bobylev, Alexander; Gamba, Irene M.; Zhang, Chenglong
2017-08-01
We study the rate of relaxation to equilibrium for Landau kinetic equation and some related models by considering the relatively simple case of radial solutions of the linear Landau-type equations. The well-known difficulty is that the evolution operator has no spectral gap, i.e. its spectrum is not separated from zero. Hence we do not expect purely exponential relaxation for large values of time t>0. One of the main goals of our work is to numerically identify the large time asymptotics for the relaxation to equilibrium. We recall the work of Strain and Guo (Arch Rat Mech Anal 187:287-339 2008, Commun Partial Differ Equ 31:17-429 2006), who rigorously show that the expected law of relaxation is \\exp (-ct^{2/3}) with some c > 0. In this manuscript, we find an heuristic way, performed by asymptotic methods, that finds this "law of two thirds", and then study this question numerically. More specifically, the linear Landau equation is approximated by a set of ODEs based on expansions in generalized Laguerre polynomials. We analyze the corresponding quadratic form and the solution of these ODEs in detail. It is shown that the solution has two different asymptotic stages for large values of time t and maximal order of polynomials N: the first one focus on intermediate asymptotics which agrees with the "law of two thirds" for moderately large values of time t and then the second one on absolute, purely exponential asymptotics for very large t, as expected for linear ODEs. We believe that appearance of intermediate asymptotics in finite dimensional approximations must be a generic behavior for different classes of equations in functional spaces (some PDEs, Boltzmann equations for soft potentials, etc.) and that our methods can be applied to related problems.
Mavroudis, Panteleimon D; Corbett, Siobhan A; Calvano, Steven E; Androulakis, Ioannis P
2014-10-15
In this work we propose a semimechanistic model that describes the photic signal transduction to the hypothalamic-pituitary-adrenal (HPA) axis that ultimately regulates the synchronization of peripheral clock genes (PCGs). Our HPA axis model predicts that photic stimulation induces a type-1 phase response curve to cortisol's profile with increased cortisol sensitivity to light exposure in its rising phase, as well as the shortening of cortisol's period as constant light increases (Aschoff's first rule). Furthermore, our model provides insight into cortisol's phase and amplitude dependence on photoperiods and reveals that cortisol maintains highest amplitude variability when it is entrained by a balanced schedule of light and dark periods. Importantly, by incorporating the links between HPA axis and PCGs we were able to investigate how cortisol secretion impacts the entrainment of a population of peripheral cells and show that disrupted light schedules, leading to blunted cortisol secretion, fail to synchronize a population of PCGs which further signifies the loss of circadian rhythmicity in the periphery of the body.
On the age of eukaryotes: evaluating evidence from fossils and molecular clocks.
Eme, Laura; Sharpe, Susan C; Brown, Matthew W; Roger, Andrew J
2014-08-01
Our understanding of the phylogenetic relationships among eukaryotic lineages has improved dramatically over the few past decades thanks to the development of sophisticated phylogenetic methods and models of evolution, in combination with the increasing availability of sequence data for a variety of eukaryotic lineages. Concurrently, efforts have been made to infer the age of major evolutionary events along the tree of eukaryotes using fossil-calibrated molecular clock-based methods. Here, we review the progress and pitfalls in estimating the age of the last eukaryotic common ancestor (LECA) and major lineages. After reviewing previous attempts to date deep eukaryote divergences, we present the results of a Bayesian relaxed-molecular clock analysis of a large dataset (159 proteins, 85 taxa) using 19 fossil calibrations. We show that for major eukaryote groups estimated dates of divergence, as well as their credible intervals, are heavily influenced by the relaxed molecular clock models and methods used, and by the nature and treatment of fossil calibrations. Whereas the estimated age of LECA varied widely, ranging from 1007 (943-1102) Ma to 1898 (1655-2094) Ma, all analyses suggested that the eukaryotic supergroups subsequently diverged rapidly (i.e., within 300 Ma of LECA). The extreme variability of these and previously published analyses preclude definitive conclusions regarding the age of major eukaryote clades at this time. As more reliable fossil data on eukaryotes from the Proterozoic become available and improvements are made in relaxed molecular clock modeling, we may be able to date the age of extant eukaryotes more precisely.
2008-09-01
McLean, M. “Tension- Compression creep asymmetry in a turbine disc superalloy : roles of internal stress and thermal ageing,” Acta Materialia, 52, 2004...AFRL-RX-WP-TP-2009-4156 A COUPLED CREEP PLASTICITY MODEL FOR RESIDUAL STRESS RELAXATION OF A SHOT PEENED NICKEL-BASE SUPERALLOY (POSTPRINT...SUBTITLE A COUPLED CREEP PLASTICITY MODEL FOR RESIDUAL STRESS RELAXATION OF A SHOT PEENED NICKEL-BASE SUPERALLOY (POSTPRINT) 5a. CONTRACT NUMBER
Chen, Ko-Fan; Possidente, Bernard; Lomas, David A; Crowther, Damian C
2014-04-01
Circadian behavioural deficits, including sleep irregularity and restlessness in the evening, are a distressing early feature of Alzheimer's disease (AD). We have investigated these phenomena by studying the circadian behaviour of transgenic Drosophila expressing the amyloid beta peptide (Aβ). We find that Aβ expression results in an age-related loss of circadian behavioural rhythms despite ongoing normal molecular oscillations in the central clock neurons. Even in the absence of any behavioural correlate, the synchronised activity of the central clock remains protective, prolonging lifespan, in Aβ flies just as it does in control flies. Confocal microscopy and bioluminescence measurements point to processes downstream of the molecular clock as the main site of Aβ toxicity. In addition, there seems to be significant non-cell-autonomous Aβ toxicity resulting in morphological and probably functional signalling deficits in central clock neurons.
Jung, Kwan-Jin
2009-09-01
A mathematical model to regress the nonlinear blood oxygen level-dependent (BOLD) fMRI signal has been developed by incorporating the refractory effect into the linear BOLD model of the biphasic gamma variate function. The refractory effect was modeled as a relaxation of two separate BOLD capacities corresponding to the biphasic components of the BOLD signal in analogy with longitudinal relaxation of magnetization in NMR. When tested with the published fMRI data of finger tapping, the nonlinear BOLD model with the refractory effect reproduced the nonlinear BOLD effects such as reduced poststimulus undershoot and saddle pattern in a prolonged stimulation as well as the reduced BOLD signal for repetitive stimulation.
Study on Short-Term Prediction for Satellite Clock Bias Based on ARIMA Model%基于 ARIMA 模型的卫星钟差短期预报研究
范旭亮; 王晓红; 张显云; 王阳; 潘绍林; 冯富寿
2015-01-01
The precision of satellite clock bias has a significant impact on the capacity of navigation and positioning system .Based on the space atomic clocks from different types , this paper used the ARIMA time series model to predict the short -term (6h and one day) satellite clock error by adopting IGS 5min and 30s -interval precise satellite clock products on one day .Results show that, the prediction accuracy of rubidium clock can reach sub nanosecond level ;caesium clock is at the nanosecond level .Moreover, the sam-ple interval of original satellite clock products has effect on the precision of satellite clock error prediction .%卫星钟差的精度直接影响导航定位的性能。本文针对不同类型的星载原子钟，采用ARIMA时间序列模型分别对1 d的IGS 5 min、30 s采样间隔的精密卫星钟差产品进行建模，并作6 h、一天的短期预报。结果表明，铷钟的预报精度达到了亚纳秒级，铯钟的预报精度处于纳秒级，并且原始钟差产品的采样间隔对卫星钟差预报精度有一定的影响。
Remme, Espen W; Opdahl, Anders; Smiseth, Otto A
2011-05-01
We investigated the determinants of ventricular early diastolic lengthening and mechanics of suction using a mathematical model of the left ventricle (LV). The model was based on a force balance between the force represented by LV pressure (LVP) and active and passive myocardial forces. The predicted lengthening velocity (e') from the model agreed well with measurements from 10 dogs during 5 different interventions (R = 0.69, P relaxation rate and systolic shortening increased, when passive stiffness was decreased, and when the rate of fall of LVP during early filling was decreased relative to the rate of fall of active stress. We first defined suction as the work the myocardium performed to pull blood into the ventricle. This occurred when contractile active forces decayed below and became weaker than restoring forces, producing a negative LVP. An alternative definition of suction is filling during falling pressure, commonly believed to be caused by release of restoring forces. However, the model showed that this phenomenon also occurred when there had been no systolic compression below unstressed length and therefore in the absence of restoring forces. In conclusion, relaxation rate, LVP, systolic shortening, and passive stiffness were all independent determinants of e'. The model generated a suction effect seen as lengthening occurring during falling pressure. However, this was not equivalent with the myocardium performing pulling work on the blood, which was performed only when restoring forces were higher than remaining active fiber force, corresponding to a negative transmural pressure.
Qin, Bing; Deng, Yunlong
2015-01-01
Disturbance of the circadian clock by sleep deprivation has been proposed to be involved in the regulation of inflammation. However, the underlying mechanism of circadian oscillator components in regulating the pro-inflammatory process during sleep deprivation remains poorly understood. Using a sleep deprivation mouse model, we showed here that sleep deprivation increased the expression of pro-inflammatory cytokines expression and decreased the expression of cryptochrome 1 (CRY1) in vascular endothelial cells. Furthermore, the adhesion molecules including intercellular adhesion molecule-1, vascular cell adhesion molecule-1 and E-selectin were elevated in vascular endothelial cells and the monocytes binding to vascular endothelial cells were also increased by sleep deprivation. Interestingly, overexpression of CRY1 in a mouse model by adenovirus vector significantly inhibited the expression of inflammatory cytokines and adhesion molecules, and NF-κB signal pathway activation, as well as the binding of monocytes to vascular endothelial cells. Using a luciferase reporter assay, we found that CRY1 could repress the transcriptional activity of nuclear factor (NF)-κB in vitro. Subsequently, we demonstrated that overexpression of CRY1 inhibited the basal concentration of cyclic adenosine monophosphate (cAMP), leading to decreased protein kinase A activity, which resulted in decreased phosphorylation of p65. Taken together, these results suggested that the overexpression of CRY1 inhibited sleep deprivation-induced vascular inflammation that might be associated with NF-κB and cAMP/PKA pathways.
Self-consistent models of quasi-relaxed rotating stellar systems
Varri, A L
2012-01-01
Two new families of self-consistent axisymmetric truncated equilibrium models for the description of quasi-relaxed rotating stellar systems are presented. The first extends the spherical King models to the case of solid-body rotation. The second is characterized by differential rotation, designed to be rigid in the central regions and to vanish in the outer parts, where the energy truncation becomes effective. The models are constructed by solving the nonlinear Poisson equation for the self-consistent mean-field potential. For rigidly rotating configurations, the solutions are obtained by an asymptotic expansion on the rotation strength parameter. The differentially rotating models are constructed by means of an iterative approach based on a Legendre series expansion of the density and the potential. The two classes of models exhibit complementary properties. The rigidly rotating configurations are flattened toward the equatorial plane, with deviations from spherical symmetry that increase with the distance f...
Riehle, Fritz
2017-01-01
Within the last decade, optical atomic clocks have surpassed the best cesium clocks, which are used to realize the unit of time and frequency, in terms of accuracy and stability by about two orders of magnitude. When remote optical atomic clocks are connected by links without degradation in the clock signals, an optical clock network is formed, with distinct advantages for the dissemination of time, geodesy, astronomy and basic and applied research. Different approaches for time and frequency transfer in the microwave and optical regime, via satellites and free-space links, optical fibre links, or transportable optical atomic clocks, can be used to form a hybrid clock network that may allow a future redefinition of the unit of time based on an optical reference transition.
Wei-Cheng Wang
2002-06-01
Full Text Available We study the asymptotic equivalence of the Jin-Xin relaxation model and its formal limit for genuinely nonlinear $2imes 2$ conservation laws. The initial data is allowed to have jump discontinuities corresponding to centered rarefaction waves, which includes Riemann data connected by rarefaction curves. We show that, as long as the initial data is a small perturbation of a constant state, the solution for the relaxation system exists globally in time and converges, in the zero relaxation limit, to the solution of the corresponding conservation law uniformly except for an initial layer.
Simple Model for the Deformation-Induced Relaxation of Glassy Polymers
Fielding, S. M.; Larson, R. G.; Cates, M. E.
2012-01-01
Glassy polymers show “strain hardening”: at constant extensional load, their flow first accelerates, then arrests. Recent experiments have found this to be accompanied by a striking and unexplained dip in the segmental relaxation time. Here we explain such behavior by combining a minimal model of flow-induced liquefaction of a glass with a description of the stress carried by strained polymers, creating a nonfactorable interplay between aging and strain-induced rejuvenation. Under constant load, liquefaction of segmental motion permits strong flow that creates polymer-borne stress. This slows the deformation enough for the segmental modes to revitrify, causing strain hardening.
ZHU Ping; CHEN Shi-Bo; MEI Dong-Cheng
2006-01-01
We investigate the intensity correlation function C(s) and its associated relaxation time Tc for a saturation model of single-mode laser with correlated noises.The expressions of C(s) and Tc are derived by means of the projection operator method,and effects of correlations between an additive noise and a multiplicative noise are discussed by numerical calculation.Based on the calculated results,it is found that the correlation strength λ between the additive noise and the multiplicative noise can enhance the fluctuation decay of the laser intensity.
A new multiple-relaxation-time lattice Boltzmann model for incompressible flows in porous media
Liu, Qing; He, Chao
2013-01-01
In this paper, a two-dimensional eight-velocity (D2Q8) multiple-relaxation-time (MRT) lattice Boltzmann (LB) model is proposed for incompressible porous flows at the representative elementary volume scale based on the Brinkman-Forchheimer-extended Darcy formulation. In the MRT-LB model, newly defined equilibrium moments are employed to account for the porosity of the porous media, and the linear and nonlinear drag forces of the media are incorporated into the model by adding a forcing term to the MRT-LB equation in the moment space. The model is validated by simulating the 2D Poiseuille flow, Couette flow and lid-driven cavity flow in porous media. The numerical results are in excellent agreement with the analytical solutions and/or the well-documented data available in the literature.
Heinz, Sebastian; Mielke, Alexander
2016-04-28
We revisit the model for a two-well phase transformation in a linearly elastic body that was introduced and studied in Mielke et al. (2002 Arch. Ration. Mech. Anal. 162: , 137-177). This energetic rate-independent system is posed in terms of the elastic displacement and an internal variable that gives the phase portion of the second phase. We use a new approach based on mutual recovery sequences, which are adjusted to a suitable energy increment plus the associated dissipated energy and, thus, enable us to pass to the limit in the construction of energetic solutions. We give three distinct constructions of mutual recovery sequences which allow us (i) to generalize the existence result in Mielke et al. (2002), (ii) to establish the convergence of suitable numerical approximations via space-time discretization and (iii) to perform the evolutionary relaxation from the pure-state model to the relaxed-mixture model. All these results rely on weak converge and involve the H-measure as an essential tool.
Van Loocke, M; Lyons, C G; Simms, C K
2008-01-01
The compressive properties of skeletal muscle are important in impact biomechanics, rehabilitation engineering and surgical simulation. However, the mechanical behaviour of muscle tissue in compression remains poorly characterised. In this paper, the time-dependent properties of passive skeletal muscle were investigated using a combined experimental and theoretical approach. Uniaxial ramp and hold compression tests were performed in vitro on fresh porcine skeletal muscle at various rates and orientations of the tissue fibres. Results show that above a very small compression rate, the viscoelastic component plays a significant role in muscle mechanical properties; it represents approximately 50% of the total stress reached at a compression rate of 0.5% s(-1). A stiffening effect with compression rate is observed especially in directions closer to the muscle fibres. Skeletal muscle viscoelastic behaviour is thus dependent on compression rate and fibre orientation. A model is proposed to represent the observed experimental behaviour, which is based on the quasi-linear viscoelasticity framework. A previously developed strain-dependent Young's Moduli formulation was extended with Prony series to account for the tissue viscoelastic properties. Parameters of the model were obtained by fitting to stress-relaxation data obtained in the muscle fibre, cross-fibre and 45 degrees directions. The model then successfully predicted stress-relaxation behaviour at 60 degrees from the fibre direction (errors muscle behaviour at rates of 0.05% s(-1) and 5% s(-1) (errors <25%).
Maltsev, Victor A.; Lakatta, Edward G.
2015-01-01
Recent evidence supports the idea that robust and, importantly, FLEXIBLE automaticity of cardiac pacemaker cells is conferred by a coupled system of membrane ion currents (an “M-clock”) and a sarcoplasmic reticulum (SR)-based Ca2+ oscillator (“Ca2+clock”) that generates spontaneous diastolic Ca2+ releases. This study identified numerical models of a human biological pacemaker that features robust and flexible automaticity generated by a minimal set of electrogenic proteins and a Ca2+clock. Following the Occam’s razor principle (principle of parsimony), M-clock components of unknown molecular origin were excluded from Maltsev-Lakatta pacemaker cell model and thirteen different model types of only 4 or 5 components were derived and explored by a parametric sensitivity analysis. The extended ranges of SR Ca2+ pumping (i.e. Ca2+clock performance) and conductance of ion currents were sampled, yielding a large variety of parameter combination, i.e. specific model sets. We tested each set’s ability to simulate autonomic modulation of human heart rate (minimum rate of 50 to 70 bpm; maximum rate of 140 to 210 bpm) in response to stimulation of cholinergic and β-adrenergic receptors. We found that only those models that include a Ca2+clock (including the minimal 4-parameter model “ICaL+IKr+INCX+Ca2+clock”) were able to reproduce the full range of autonomic modulation. Inclusion of If or ICaT decreased the flexibility, but increased the robustness of the models (a relatively larger number of sets did not fail during testing). The new models comprised of components with clear molecular identity (i.e. lacking IbNa & Ist) portray a more realistic pacemaking: A smaller Na+ influx is expected to demand less energy for Na+ extrusion. The new large database of the reduced coupled-clock numerical models may serve as a useful tool for the design of biological pacemakers. It will also provide a conceptual basis for a general theory of robust, flexible, and energy
The Physics of Miniature Atomic Clocks: 0-0 Versus "End" Transitions
Post, Amber; Jau, Yuan-Yu; Kuzma, Nicholas; Happer, William
2003-05-01
The majority of traditional atomic-clock designs are based on the 0-0 hyperfine transition of a Cs 133 atom. We are currently investigating the advantages of operating a miniature optical atomic clock using the "end" transitions, e.g. connecting states |f=1, mf =+/-1> and |f=2, mf=+/-2> in 87Rb. In our paper we present extensive new measurements of relevant relaxation rates, such as those due to spin-exchange collisions, buffer-gas pressure shifts, Carver Rates and others, which ultimately determine the choices of an operating regime for the miniature optical atomic clock. The relationship between these rates is non-trivial: for example, using higher laser power will increase polarization and reduce the spin-exchange rate [1], but it can simultaneously increase the linewidth due to the optical pumping rate. The dependence of these and other relaxation rates on the cell size, temperature, pressure, a choice of buffer gas, and other parameters will be reported. Based on these measured rates, our modeling can be used to predict the transition linewidths, signal-to-noise ratios and thus the stability of the clock in different operating regimes. The trade-off between the stability of the clock and the desired small cell size and low power consumption needs to be carefully considered in order to optimize our design. In our experiments we used optical, microwave, and radio-frequency excitation to study hyperfine and Zeeman resonance lines in heated glass cells containing pure-isotope alkali-metal vapor and buffer gasses (N2, Ar, He, etc.) at low (0 - 10 G) magnetic fields. Simultaneous use of light, microwave and radio-frequency fields allowed us to calibrate surrounding magnetic fields by observing the corresponding shifts of the resonance, thus leading us to a quantitative understanding of our system. [1] S. Appelt, A. B. Baranga, A. R. Young, W. Happer, Phys. Rev. A 59, 2078 (1999).
Coarse-grained model for N2-N relaxation in hypersonic shock conditions using two-dimensional bins
Zhu, Tong; Li, Zheng; Levin, Deborah A.
2016-11-01
A high fidelity internal energy relaxation model for N2-N suitable for use in direct simulation Monte Carlo (DSMC) modeling of chemically reacting flows is proposed. A novel two-dimensional binning approach with variable bin energy resolutions in the rotational and vibrational modes is developed for treating the internal mode of N2. Both bin-to-bin and state-specific relaxation cross sections are obtained using the molecular dynamics/quasi-classical trajectory (MD/QCT) method with two potential energy surfaces as well as the state-specific database of Jaffe et al. The 99 bin model is used in homogeneous DSMC relaxation simulations and is found to be able to recover the state-specific master equation results of Panesi et al. when the Jaffe state-specific cross sections are used. Rotational relaxation energy profiles and relaxation times obtained using the ReaxFF and Jaffe potential energy surfaces (PESs) are in general agreement but there are larger differences between the vibrational relaxation times. These differences become smaller as the translational temperature increases because the difference in the PES energy barrier becomes less important.
Development of a two-dimensional binning model for N2-N relaxation in hypersonic shock conditions
Zhu, Tong; Li, Zheng; Levin, Deborah A.
2016-08-01
A high fidelity internal energy relaxation model for N2-N suitable for use in direct simulation Monte Carlo (DSMC) modeling of chemically reacting flows is proposed. A novel two-dimensional binning approach with variable bin energy resolutions in the rotational and vibrational modes is developed for treating the internal mode of N2. Both bin-to-bin and state-specific relaxation cross sections are obtained using the molecular dynamics/quasi-classical trajectory (MD/QCT) method with two potential energy surfaces as well as the state-specific database of Jaffe et al. The MD/QCT simulations of inelastic energy exchange between N2 and N show that there is a strong forward-preferential scattering behavior at high collision velocities. The 99 bin model is used in homogeneous DSMC relaxation simulations and is found to be able to recover the state-specific master equation results of Panesi et al. when the Jaffe state-specific cross sections are used. Rotational relaxation energy profiles and relaxation times obtained using the ReaxFF and Jaffe potential energy surfaces (PESs) are in general agreement but there are larger differences between the vibrational relaxation times. These differences become smaller as the translational temperature increases because the difference in the PES energy barrier becomes less important.
Extending the EGP constitutive model for polymer glasses to multiple relaxation times
van Breemen, L. C. A.; Klompen, E. T. J.; Govaert, L. E.; Meijer, H. E. H.
2011-10-01
The one-mode EGP (Eindhoven glassy polymer) model captures the plastic flow at yield and post-yield quantitatively, but behaves poor in the non-linear viscoelastic pre-yield region. Since a proper description here is important in cases of complex loading and unloading situations, such as e.g. in indentation and scratching, an extension to non-linear modeling is required using a spectrum of relaxation times. It is shown that such a reference spectrum can be obtained from simple tensile tests. It shifts to shorter times under the influence of stress and is independent of the two important time-dependent processes in polymers: the strain rate applied during testing and the aging time during storage and use. The multi-mode model is critically tested and proves quantitative in describing the intrinsic polymer response and, based thereupon, in predicting the correct response in tensile testing, including necking, in flat tip indentation and in notched loading.
The construction of non-spherical models of quasi-relaxed stellar systems
Bertin, G
2008-01-01
Spherical models of collisionless but quasi-relaxed stellar systems have long been studied as a natural framework for the description of globular clusters. Here we consider the construction of self-consistent models under the same physical conditions, but including explicitly the ingredients that lead to departures from spherical symmetry. In particular, we focus on the effects of the tidal field associated with the hosting galaxy. We then take a stellar system on a circular orbit inside a galaxy represented as a "frozen" external field. The equilibrium distribution function is obtained from the one describing the spherical case by replacing the energy integral with the relevant Jacobi integral in the presence of the external tidal field. Then the construction of the model requires the investigation of a singular perturbation problem for an elliptic partial differential equation with a free boundary, for which we provide a method of solution to any desired order, with explicit solutions to two orders. We outl...
McClung, C. Robertson; Gutiérrez, Rodrigo A.
2011-01-01
Summary Whole-transcriptome analyses have established that the plant circadian clock regulates virtually every plant biological process and most prominently hormonal and stress response pathways. Systems biology efforts have successfully modeled the plant central clock machinery and an iterative process of model refinement and experimental validation has contributed significantly to the current view of the central clock machinery. The challenge now is to connect this central clock to the output pathways for understanding how the plant circadian clock contributes to plant growth and fitness in a changing environment. Undoubtedly, systems approaches will be needed to integrate and model the vastly increased volume of experimental data in order to extract meaningful biological information. Thus, we have entered an era of systems modeling, experimental testing, and refinement. This approach, coupled with advances from the genetic and biochemical analyses of clock function, is accelerating our progress towards a comprehensive understanding of the plant circadian clock network. PMID:20889330
CronoClock: A Multiagent Mobile Model to Assist Drivers in Park Zones
María NAVARRO
2014-10-01
Full Text Available We present a model based on multiagent environment to help users of park zones. A multiagent system is built to communicate the different roles and devices belonging to the system. The result is a model that assists the different users in their payments and identifies the vehicle plate by image recognition and NFC (Near Field Communication technology. An evaluation of the system is provided to know the efficiency of the model.
Wright, James R.
2008-01-01
The GPS composite clock defines GPS time, the timescale used today in GPS operations. GPS time is illuminated by examination of its role in the complete estimation and control problem relative to UTC/TAI. The phase of each GPS clock is unobservable from GPS pseudorange measurements, and the mean phase of the GPS clock ensemble (GPS time) is unobservable. A new and useful observability definition is presented, together with new observability theorems, to demonstrate explicitly that GPS time is...
Angélil, Raymond
2014-01-01
The S stars near the Galactic centre and any pulsars that may be on similar orbits, can be modelled in a unified way as clocks orbiting a black hole, and hence are potential probes of relativistic effects, including block-hole spin. The high eccentricities of many S stars mean that relativistic effects peak strongly around pericentre; for example, orbit precession is not a smooth effect but almost a kick at pericentre. We argue that concentration around pericentre will be an advantage when analysing redshift or pulse-arrival data to measure relativistic effects, because cumulative precession will be drowned out by Newtonian perturbations from other mass in the Galactic-centre region. Wavelet decomposition may be a way to disentangle relativistic effects from Newton perturbations. Assuming a plausible model for Newtonian perturbations on S2, relativity appears to be strongest in a two-year interval around pericentre, in wavelet modes of timescale approximately 6 months.
Performance analysis of successive over relaxation method for solving glioma growth model
Hussain, Abida; Faye, Ibrahima; Muthuvalu, Mohana Sundaram
2016-11-01
Brain tumor is one of the prevalent cancers in the world that lead to death. In light of the present information of the properties of gliomas, mathematical models have been developed by scientists to quantify the proliferation and invasion dynamics of glioma. In this study, one-dimensional glioma growth model is considered, and finite difference method is used to discretize the problem. Then, two stationary methods, namely Gauss-Seidel (GS) and Successive Over Relaxation (SOR) are used to solve the governing algebraic system. The performance of the methods are evaluated in terms of number of iteration and computational time. On the basis of performance analysis, SOR method is shown to be more superior compared to GS method.
An Analysis of Surface Relaxation in the Surface Cauchy--Born Model
Jayawardana, K; Ortner, C; Park, H S
2011-01-01
The Surface Cauchy-Born (SCB) method is a computational multi-scale method for the simulation of surface-dominated crystalline materials. We present an error analysis of the SCB method, focused on the role of surface relaxation. In a linearized 1D model we show that the error committed by the SCB method is O(1) in the mesh size; however, we are able to identify an alternative "approximation parameter" - the stiffness of the interaction potential - with respect to which the error in the mean strain is exponentially small. Our analysis naturally suggests an improvement of the SCB model by enforcing atomistic mesh spacing in the normal direction at the free boundary.
Bhatt, Shashi B; Amann, Anton; Nigrovic, Vladimir
2006-08-01
Nondepolarizing muscle relaxants (MRs) diminish the indirectly evoked single twitch due to their binding to the postsynaptic receptors. Additionally, the MRs produce progressive diminution of successive twitches upon repetitive stimulation (fade). Our study addresses the generation of fade as observed under clinical situation. The study was conducted in two phases. In the clinical part, we have evaluated the time course of twitch depression and fade following the administration of several doses of three MRs (rocuronium, pancuronium, and cisatracurium). In the second part, we have modified our model of neuromuscular transmission to simulate the time course of twitch depression and fade. The MR was assumed to bind to a single site on the presynaptic receptor to produce fade. The rates of interaction with the presynaptic receptors were characterized in terms of the arbitrarily assigned equilibrium dissociation constant and the half-life for dissociation of the presynaptic complex. A method was developed to relate the release of acetylcholine to the occupancy of the presynaptic receptors. The strength of the first and the fourth twitch was calculated from the peak concentration of the activated postsynaptic receptors, i.e., of those receptors with both sites occupied by acetylcholine. Our results indicate that, while the affinity of the MR for the presynaptic receptor plays little role in the time course of fade, the rate of dissociation of the complex between the presynaptic receptors and the muscle relaxant may be critical in determining the time course of fade. Tentative estimates of this parameter are offered.
Non-equilibrium relaxation in a two-dimensional stochastic lattice Lotka-Volterra model
Chen, Sheng; Täuber, Uwe C.
We employ Monte Carlo simulations to study a stochastic Lotka-Volterra model on a two-dimensional square lattice with periodic boundary conditions. There are stable states when the predators and prey coexist. If the local prey carrying capacity is finite, there emerges an extinction threshold for the predator population at a critical value of the predation rate. We investigate the non-equilibrium relaxation of the predator density in the vicinity of this critical point. The expected power law dependence between the relaxation time and predation rate is observed (critical slowing down). The numerically determined associated critical exponents are in accord with the directed percolation universality class. Following a sudden predation rate change to its critical value, one observes critical aging for the predator density autocorrelation function with a universal scaling exponent. This aging scaling signature of the absorbing state phase transition emerges at significantly earlier times than stationary critical power laws, and could thus serve as an advanced indicator of the population's proximity to its extinction threshold. This research is supported by the U. S. Department of Energy, Office of Basic Energy Sciences, Division of Materials Science and Engineering under Award DE-FG02-09ER46613.
Non-equilibrium relaxation in a stochastic lattice Lotka-Volterra model
Chen, Sheng; Täuber, Uwe C.
2016-04-01
We employ Monte Carlo simulations to study a stochastic Lotka-Volterra model on a two-dimensional square lattice with periodic boundary conditions. If the (local) prey carrying capacity is finite, there exists an extinction threshold for the predator population that separates a stable active two-species coexistence phase from an inactive state wherein only prey survive. Holding all other rates fixed, we investigate the non-equilibrium relaxation of the predator density in the vicinity of the critical predation rate. As expected, we observe critical slowing-down, i.e., a power law dependence of the relaxation time on the predation rate, and algebraic decay of the predator density at the extinction critical point. The numerically determined critical exponents are in accord with the established values of the directed percolation universality class. Following a sudden predation rate change to its critical value, one finds critical aging for the predator density autocorrelation function that is also governed by universal scaling exponents. This aging scaling signature of the active-to-absorbing state phase transition emerges at significantly earlier times than the stationary critical power laws, and could thus serve as an advanced indicator of the (predator) population’s proximity to its extinction threshold.
Non-equilibrium relaxation in a stochastic lattice Lotka-Volterra model.
Chen, Sheng; Täuber, Uwe C
2016-04-19
We employ Monte Carlo simulations to study a stochastic Lotka-Volterra model on a two-dimensional square lattice with periodic boundary conditions. If the (local) prey carrying capacity is finite, there exists an extinction threshold for the predator population that separates a stable active two-species coexistence phase from an inactive state wherein only prey survive. Holding all other rates fixed, we investigate the non-equilibrium relaxation of the predator density in the vicinity of the critical predation rate. As expected, we observe critical slowing-down, i.e., a power law dependence of the relaxation time on the predation rate, and algebraic decay of the predator density at the extinction critical point. The numerically determined critical exponents are in accord with the established values of the directed percolation universality class. Following a sudden predation rate change to its critical value, one finds critical aging for the predator density autocorrelation function that is also governed by universal scaling exponents. This aging scaling signature of the active-to-absorbing state phase transition emerges at significantly earlier times than the stationary critical power laws, and could thus serve as an advanced indicator of the (predator) population's proximity to its extinction threshold.
Precision Clock Evaluation Facility
Federal Laboratory Consortium — FUNCTION: Tests and evaluates high-precision atomic clocks for spacecraft, ground, and mobile applications. Supports performance evaluation, environmental testing,...
An analytic technique for statistically modeling random atomic clock errors in estimation
Fell, P. J.
1981-01-01
Minimum variance estimation requires that the statistics of random observation errors be modeled properly. If measurements are derived through the use of atomic frequency standards, then one source of error affecting the observable is random fluctuation in frequency. This is the case, for example, with range and integrated Doppler measurements from satellites of the Global Positioning and baseline determination for geodynamic applications. An analytic method is presented which approximates the statistics of this random process. The procedure starts with a model of the Allan variance for a particular oscillator and develops the statistics of range and integrated Doppler measurements. A series of five first order Markov processes is used to approximate the power spectral density obtained from the Allan variance.
Kendall, William L.; Hines, James E.; Nichols, James D.; Grant, Evan H. Campbell
2013-01-01
Occupancy statistical models that account for imperfect detection have proved very useful in several areas of ecology, including species distribution and spatial dynamics, disease ecology, and ecological responses to climate change. These models are based on the collection of multiple samples at each of a number of sites within a given season, during which it is assumed the species is either absent or present and available for detection while each sample is taken. However, for some species, individuals are only present or available for detection seasonally. We present a statistical model that relaxes the closure assumption within a season by permitting staggered entry and exit times for the species of interest at each site. Based on simulation, our open model eliminates bias in occupancy estimators and in some cases increases precision. The power to detect the violation of closure is high if detection probability is reasonably high. In addition to providing more robust estimation of occupancy, this model permits comparison of phenology across sites, species, or years, by modeling variation in arrival or departure probabilities. In a comparison of four species of amphibians in Maryland we found that two toad species arrived at breeding sites later in the season than a salamander and frog species, and departed from sites earlier.
Kim, Won-Wook; McMahan, Kevin Weston; Srinivasan, Shiva Kumar
2017-01-17
The present application provides a clocked combustor can array for coherence reduction in a gas turbine engine. The clocked combustor can array may include a number of combustor cans positioned in a circumferential array. A first set of the combustor cans may have a first orientation and a second set of the combustor cans may have a second orientation.
Kim, Won-Wook; McMahan, Kevin Weston; Srinivasan, Shiva Kumar
2017-01-17
The present application provides a clocked combustor can array for coherence reduction in a gas turbine engine. The clocked combustor can array may include a number of combustor cans positioned in a circumferential array. A first set of the combustor cans may have a first orientation and a second set of the combustor cans may have a second orientation.
Modig, Kristofer; Poulsen, Flemming
2008-01-01
We have investigated the acid-unfolded state of acyl-coenzyme A binding protein (ACBP) using (15)N laboratory frame nuclear magnetic resonance (NMR) relaxation experiments at three magnetic field strengths. The data have been analyzed using standard model-free fitting and models involving....... The analysis also shows that the relaxation data are consistent with and complementary to information obtained from other parameters, especially secondary chemical shifts and residual dipolar couplings, and strengthens the conclusions of previous observations that three out of the four regions that form...
Govind, Chinju; Karunakaran, Venugopal
2017-04-13
Hemin is a unique model compound of heme proteins carrying out variable biological functions. Here, the excited state relaxation dynamics of heme model compounds in the ferric form are systematically investigated by changing the axial ligand (Cl/Br), the peripheral substituent (vinyl/ethyl-meso), and the solvent (methanol/DMSO) using femtosecond pump-probe spectroscopy upon excitation at 380 nm. The relaxation time constants of these model compounds are obtained by global analysis. Excited state deactivation pathway of the model compounds comprising the decay of the porphyrin excited state (S*) to ligand to metal charge transfer state (LMCT, τ1), back electron transfer from metal to ligand (MLCT, τ2), and relaxation to the ground state through different electronic spin states of iron (τ3 and τ4) are proposed along with the vibrational cooling processes. This is based on the excited state absorption spectral evolution, similarities between the transient absorption spectra of the ferric form and steady state absorption spectra of the low-spin ferrous form, and the data analysis. The observation of an increase of all the relaxation time constants in DMSO compared to the methanol reflects the stabilization of intermediate states involved in the electronic relaxation. The transient absorption spectra of met-myoglobin are also measured for comparison. Thus, the transient absorption spectra of these model compounds reveal the involvement of multiple iron spin states in the electronic relaxation dynamics, which could be an alternative pathway to the ground state beside the vibrational cooling processes and associated with the inherent features of the heme b type.
CHEN JingBiao
2009-01-01
This article presents the principles and techniques of active optical clock, a special laser combining the laser physics of one-atom laser, bad-cavity gas laser, super-cavity stabilized laser and optical atomic clock together. As a simple example, an active optical clock based on thermal strontium atomic beam shows a quantum-limited linewidth of 0.51 Hz, which is insensitive to laser cavity-length noise, and may surpass the recorded narrowest 6.7 Hz of Hg ion optical clock and 1.5 Hz of very recent optical lattice clock. The estimated 0.1 Hz one-second instability and 0.27 Hz uncertainty are limited only by the rela-tivistic Doppler effect, and can be improved by cold atoms.
Tarrío-Saavedra, Javier; González, Cécilia Galindo; Naya, Salvador; López-Beceiro, Jorge
2017-01-01
This study investigated a methodology based on image processing and statistics to characterize and model the deformation upon controlled and uniform magnetic field and the relaxation under zero field of droplets observed in aqueous solutions of sodium alginate incorporating magnetic maghemite nanoparticles stabilized by adsorption of citrate ions. The changes of droplet geometry were statistically analyzed using a new approach based on the data obtained from optical microscopy, image processing, nonlinear regression, evolutionary optimization, analysis of variance and resampling. Image enhancement and then image segmentation (Gaussian mixture modeling) processes were applied to extract features with reliable information of droplets dimensions from optical micrographs. The droplets deformation and relaxation trends were accurately adjusted by the Kohlrausch-Williams-Watts (KWW) function and a mean relaxation time was obtained by fitting the time evolution of geometry parameters. It was found to be proportional to the initial radius of the spherical droplets and was associated to interfacial tension. PMID:28081239
Oates, Chris
2012-06-01
Since they were first proposed in 2003 [1], optical lattice clocks have become one of the leading technologies for the next generation of atomic clocks, which will be used for advanced timing applications and in tests of fundamental physics [2]. These clocks are based on stabilized lasers whose frequency is ultimately referenced to an ultra-narrow neutral atom transition (natural linewidths magic'' value so as to yield a vanishing net AC Stark shift for the clock transition. As a result lattice clocks have demonstrated the capability of generating high stability clock signals with small absolute uncertainties (˜ 1 part in 10^16). In this presentation I will first give an overview of the field, which now includes three different atomic species. I will then use experiments with Yb performed in our laboratory to illustrate the key features of a lattice clock. Our research has included the development of state-of-the-art optical cavities enabling ultra-high-resolution optical spectroscopy (1 Hz linewidth). Together with the large atom number in the optical lattice, we are able to achieve very low clock instability (< 0.3 Hz in 1 s) [3]. Furthermore, I will show results from some of our recent investigations of key shifts for the Yb lattice clock, including high precision measurements of ultracold atom-atom interactions in the lattice and the dc Stark effect for the Yb clock transition (necessary for the evaluation of blackbody radiation shifts). [4pt] [1] H. Katori, M. Takamoto, V. G. Pal'chikov, and V. D. Ovsiannikov, Phys. Rev. Lett. 91, 173005 (2003). [0pt] [2] Andrei Derevianko and Hidetoshi Katori, Rev. Mod. Phys. 83, 331 (2011). [0pt] [3] Y. Y. Jiang, A. D. Ludlow, N. D. Lemke, R. W. Fox, J. A. Sherman, L.-S. Ma, and C. W. Oates, Nature Photonics 5, 158 (2011).
Competition between surface relaxation and ballistic deposition models in scale free networks
La Rocca, Cristian E; Braunstein, Lidia A
2012-01-01
In this paper we study the scaling behavior of the fluctuations in the steady state $W_S$ with the system size $N$ for a surface growth process given by the competition between the surface relaxation (SRM) and the Ballistic Deposition (BD) models on degree uncorrelated Scale Free networks (SF), characterized by a degree distribution $P(k)\\sim k^{-\\lambda}$, where $k$ is the degree of a node. It is known that the fluctuations of the SRM model above the critical dimension ($d_c=2$) scales logarithmically with $N$ on euclidean lattices. However, Pastore y Piontti {\\it et. al.} [A. L. Pastore y Piontti {\\it et. al.}, Phys. Rev. E {\\bf 76}, 046117 (2007)] found that the fluctuations of the SRM model in SF networks scale logarithmically with $N$ for $\\lambda <3$ and as a constant for $\\lambda \\geq 3$. In this letter we found that for a pure ballistic deposition model on SF networks $W_S$ scales as a power law with an exponent that depends on $\\lambda$. On the other hand when both processes are in competition, we...
Towards Relaxing the Spherical Solar Radiation Pressure Model for Accurate Orbit Predictions
Lachut, M.; Bennett, J.
2016-09-01
The well-known cannonball model has been used ubiquitously to capture the effects of atmospheric drag and solar radiation pressure on satellites and/or space debris for decades. While it lends itself naturally to spherical objects, its validity in the case of non-spherical objects has been debated heavily for years throughout the space situational awareness community. One of the leading motivations to improve orbit predictions by relaxing the spherical assumption, is the ongoing demand for more robust and reliable conjunction assessments. In this study, we explore the orbit propagation of a flat plate in a near-GEO orbit under the influence of solar radiation pressure, using a Lambertian BRDF model. Consequently, this approach will account for the spin rate and orientation of the object, which is typically determined in practice using a light curve analysis. Here, simulations will be performed which systematically reduces the spin rate to demonstrate the point at which the spherical model no longer describes the orbital elements of the spinning plate. Further understanding of this threshold would provide insight into when a higher fidelity model should be used, thus resulting in improved orbit propagations. Therefore, the work presented here is of particular interest to organizations and researchers that maintain their own catalog, and/or perform conjunction analyses.
The spectral relaxation model of the scalar dissipation rate in homogeneous turbulence
Fox, R. O.
1995-05-01
A model for the effect of scalar spectral relaxation on the scalar dissipation rate of an inert, passive scalar (Sc≥1) in fully developed homogeneous turbulence is presented. In the model, wave-number space is divided into a finite number [the total number depending on the turbulence Reynolds number Reλ and the Schmidt number (Sc)] of intermediate stages whose time constants are determined from the velocity spectrum. The model accounts for the evolution of the scalar spectrum from an arbitrary initial shape to its fully developed form and its effect on the scalar dissipation rate for finite Reλ and Sc≥1. Corrsin's result [AIChE J. 10, 870 (1964)] for the scalar mixing time is attained for large Reλ in the presence of a constant mean scalar gradient and a stationary, isotropic turbulence field. Comparisons with DNS results for stationary, isotropic turbulence and experimental data for decaying, homogeneous grid turbulence demonstrate the satisfactory performance of the model.
Bennati, L.; Calais, E.; Wright, T.; Hamling, I.; Lewi, E.; Nooner, S.; Buck, R.; Ebinger, C.
2008-12-01
Accelerated deformation after major dike intrusion events such the 1975-1985 Krafla events in Iceland and the 1978 Asal-Ghoubbet events in Afar have been interpreted as the result of stress relaxation in a viscoelastic lithospheric mantle and/or continued magma injection. Separating these contributions, estimating mantle viscosity and quantifying the interaction with long-term stretching has however proven difficult in the absence of geodetic measurements early on after the main dike intrusion. In September 2005, a 60km-long dike intrusion took place at the Dabbahu rift, Afar, Ethiopia, at the boundary between the Nubian and Arabian (Danakil) plates. Since this major event, 8 new intrusions have affected the central and southern parts of the 2005 dike. In order to measure post-diking deformation, we installed 19 continuous stations in the near-field of the 2005 intrusion and 20 survey sites in the mid- and far-field. Time series from continuous GPS stations outside of volcanoes show a combination of discrete diking events and quasi-constant velocity displacements. Continuous GPS stations on volcanoes show non-linear behaviour related to the feeding of shallow magma chambers. Survey GPS sites in the far-field (up to 150km from the rift) show current extension rates twice as fast as the secular divergence rate between Nubia and Arabia. We present the GPS results and, with some constraints from seismicity, propose a preliminary model that accounts for the combination of dike intrusions and viscoelastic stress relaxation in the upper mantle below Afar.
Clock Technology Development in the Laser Cooling and Atomic Physics (LCAP) Program
Seidel, Dave; Thompson, R. J.; Klipstein, W. M.; Kohel, J.; Maleki, L.
2000-01-01
This paper presents the Laser Cooling and Atomic Physics (LCAP) program. It focuses on clock technology development. The topics include: 1) Overview of LCAP Flight Projects; 2) Space Clock 101; 3) Physics with Clocks in microgravity; 4) Space Clock Challenges; 5) LCAP Timeline; 6) International Space Station (ISS) Science Platforms; 7) ISS Express Rack; 8) Space Qualification of Components; 9) Laser Configuration; 10) Clock Rate Comparisons: GPS Carrier Phase Frequency Transfer; and 11) ISS Model Views. This paper is presented in viewgraph form.
Stretched Exponential Relaxation in Disordered Complex Systems: Fractal Time Random Walk Model
Ekrem Aydmer
2007-01-01
We have analytically derived the relaxation function for one-dimensional disordered complex systems in terms of autocorrelation function of fractal time random walk by using operator formalism. We have shown that the relaxation function has stretched exponential, i.e. the Kohlrausch-Williams-Watts character for a fractal time random walk process.
Dielectric Relaxation of Lanthanide-Based Ternary Oxides: Physical and Mathematical Models
Chun Zhao
2012-01-01
Full Text Available Cerium-doped hafnium oxides (CexHf1−xO2 and lanthanum-doped zirconium oxides (LaxZr1−xO2 were investigated. The highest dielectric constants, k, were obtained from lightly doped oxides with an La content of x=0.09 and a Ce content of x=0.1, for which k-values of 33~40 were obtained. The dielectric relaxation appears to be related to the size of crystal grains formed during annealing, which was dependent on the doping level. The physical and mathematical models were used to analyze the relationship between k-values and frequencies. The variations in the k-values up to megahertz frequencies for both CexHf1−xO2 and LaxZr1−xO2 are simulated based on the Curie-von Schweidler (CS or Havriliak-Negami (HN relationships. Concerning the lightly doped CexHf1−xO2 and LaxZr1−xO2, the data extracted are best modeled by the HN law, while LaxZr1−xO2 with doping level from x=0.22 to 0.63 are best modelled based on the CS law.
Vignes, Ryan M. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). National Ignition Facility and Photon Sciences; Soules, Thomas F. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). National Ignition Facility and Photon Sciences; Stolken, James S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). National Ignition Facility and Photon Sciences; Settgast, Randolph R. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). National Ignition Facility and Photon Sciences; Elhadj, Selim [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). National Ignition Facility and Photon Sciences; Matthews, Manyalibo J. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). National Ignition Facility and Photon Sciences; Mauro, J.
2012-12-17
In a fully coupled thermomechanical model of the nanoscale deformation in amorphous SiO_{2} due to laser heating is presented. Direct measurement of the transient, nonuniform temperature profiles was used to first validate a nonlinear thermal transport model. Densification due to structural relaxation above the glass transition point was modeled using the Tool-Narayanaswamy (TN) formulation for the evolution of structural relaxation times and fictive temperature. TN relaxation parameters were derived from spatially resolved confocal Raman scattering measurements of Si–O–Si stretching mode frequencies. These thermal and microstructural data were used to simulate fictive temperatures which are shown to scale nearly linearly with density, consistent with previous measurements from Shelby et al. Volumetric relaxation coupled with thermal expansion occurring in the liquid-like and solid-like glassy states lead to residual stresses and permanent deformation which could be quantified. But, experimental surface deformation profiles between 1700 and 2000 K could only be reconciled with our simulation by assuming a roughly 2 × larger liquid thermal expansion for a-SiO_{2} with a temperature of maximum density ~150 K higher than previously estimated by Bruckner et al. Calculated stress fields agreed well with recent laser-induced critical fracture measurements, demonstrating accurate material response prediction under processing conditions of practical interest.
Hackmann, Andreas; Ailion, David C.; Ganesan, Krishnamurthy; Laicher, Gernot; Goodrich, K. Craig; Cutillo, Antonio G.
1996-02-01
The water-biopolymer cross-relaxation model, proposed by H. E. Rorschach and C. F. Hazlewood (RH) [J. Magn. Reson.70,79 (1986)], explains the Larmor frequency dependence ofT1in many biological systems. However, the RH theory fails at low Larmor frequencies. In this paper, a more general version of the RH theory has been developed. This theory is valid at all frequencies. Use of the new expression for the spin-lattice relaxation rate (1/T1), earlier published experimental data in H2O/D2O bovine serum albumin, which had been measured over a wide frequency range (10 kHz to 100 MHz), were fitted over the entire frequency range. The agreement between theory and the experimental data is excellent. Theoretical expressions for the rotating-frame spin-lattice relaxation rate (1/T1ρ) were also obtained.
Chou, C. W.; Hume, D. B.; Rosenband, T.; Wineland, D. J.
2010-09-01
Observers in relative motion or at different gravitational potentials measure disparate clock rates. These predictions of relativity have previously been observed with atomic clocks at high velocities and with large changes in elevation. We observed time dilation from relative speeds of less than 10 meters per second by comparing two optical atomic clocks connected by a 75-meter length of optical fiber. We can now also detect time dilation due to a change in height near Earth’s surface of less than 1 meter. This technique may be extended to the field of geodesy, with applications in geophysics and hydrology as well as in space-based tests of fundamental physics.
Madeo, Angela; Miniaci, Marco; Billon, Kévin; Ouisse, Morvan; Neff, Patrizio
2016-01-01
In this paper the relaxed micromorphic continuum model with weighted free and gradient micro-inertia is used to describe the dynamical behavior of a real two-dimensional phononic crystal for a wide range of wavelengths. In particular, a periodic structure with specific micro-structural topology and mechanical properties, capable of opening a phononic band-gap, is chosen with the criterion of showing a low degree of anisotropy (the band-gap is almost independent of the direction of propagation of the traveling wave). A Bloch wave analysis is performed to obtain the dispersion curves and the corresponding vibrational modes of the periodic structure. A linear-elastic, isotropic, relaxed micromorphic model including both a free micro-inertia (related to free vibrations of the microstructures) and a gradient micro-inertia (related to the motions of the microstructure which are coupled to the macro-deformation of the unit cell) is introduced and particularized to the case of plane wave propagation. The parameters o...
Modeling the relaxation of polymer glasses under shear and elongational loads
Fielding, S. M.; Moorcroft, R. L.; Larson, R. G.; Cates, M. E.
2013-03-01
Glassy polymers show "strain hardening": at constant extensional load, their flow first accelerates, then arrests. Recent experiments under such loading have found this to be accompanied by a striking dip in the segmental relaxation time. This can be explained by a minimal nonfactorable model combining flow-induced melting of a glass with the buildup of stress carried by strained polymers. Within this model, liquefaction of segmental motion permits strong flow that creates polymer-borne stress, slowing the deformation enough for the segmental (or solvent) modes then to re-vitrify. Here, we present new results for the corresponding behavior under step-stress shear loading, to which very similar physics applies. To explain the unloading behavior in the extensional case requires introduction of a "crinkle factor" describing a rapid loss of segmental ordering. We discuss in more detail here the physics of this, which we argue involves non-entropic contributions to the polymer stress, and which might lead to some important differences between shear and elongation. We also discuss some fundamental and possibly testable issues concerning the physical meaning of entropic elasticity in vitrified polymers. Finally, we present new results for the startup of steady shear flow, addressing the possible role of transient shear banding.
Grünwald-Letnikov operators for fractional relaxation in Havriliak-Negami models
Garrappa, Roberto
2016-09-01
Several classes of differential and integral operators of non integer order have been proposed in the past to model systems exhibiting anomalous and hereditary properties. A wide range of complex and heterogeneous systems are described in terms of laws of Havriliak-Negami type involving a special fractional relaxation whose behavior in the time-domain can not be represented by any of the existing operators. In this work we introduce new integral and differential operators for the description of Havriliak-Negami models in the time-domain. In particular we propose a formulation of Grünwald-Letnikov type which turns out to be effective not only to provide a theoretical characterization of the operators associated to Havriliak-Negami systems but also for computational purposes. We study some properties of the new operators and, by means of some numerical experiments, we present their use in practical computation and we show the superiority with respect to the few other approaches previously proposed in literature.
The Mechanics of Mechanical Watches and Clocks
Du, Ruxu
2013-01-01
"The Mechanics of Mechanical Watches and Clocks" presents historical views and mathematical models of mechanical watches and clocks. Although now over six hundred years old, mechanical watches and clocks are still popular luxury items that fascinate many people around the world. However few have examined the theory of how they work as presented in this book. The illustrations and computer animations are unique and have never been published before. It will be of significant interest to researchers in mechanical engineering, watchmakers and clockmakers, as well as people who have an engineering background and are interested in mechanical watches and clocks. It will also inspire people in other fields of science and technology, such as mechanical engineering and electronics engineering, to advance their designs. Professor Ruxu Du works at the Chinese University of Hong Kong, China. Assistant Professor Longhan Xie works at the South China University of Technology, China.
Marzola, Luca; Raidal, Martti
2016-11-01
Motivated by natural inflation, we propose a relaxation mechanism consistent with inflationary cosmology that explains the hierarchy between the electroweak scale and Planck scale. This scenario is based on a selection mechanism that identifies the low-scale dynamics as the one that is screened from UV physics. The scenario also predicts the near-criticality and metastability of the Standard Model (SM) vacuum state, explaining the Higgs boson mass observed at the Large Hadron Collider (LHC). Once Majorana right-handed neutrinos are introduced to provide a viable reheating channel, our framework yields a corresponding mass scale that allows for the seesaw mechanism as well as for standard thermal leptogenesis. We argue that considering singlet scalar dark matter extensions of the proposed scenario could solve the vacuum stability problem and discuss how the cosmological constant problem is possibly addressed.
Stable clocks and general relativity
Will, C M
1995-01-01
We survey the role of stable clocks in general relativity. Clock comparisons have provided important tests of the Einstein Equivalence Principle, which underlies metric gravity. These include tests of the isotropy of clock comparisons (verification of local Lorentz invariance) and tests of the homogeneity of clock comparisons (verification of local position invariance). Comparisons of atomic clocks with gravitational clocks test the Strong Equivalence Principle by bounding cosmological variations in Newton's constant. Stable clocks also play a role in the search for gravitational radiation: comparision of atomic clocks with the binary pulsar's orbital clock has verified gravitational-wave damping, and phase-sensitive detection of waves from inspiralling compact binaries using laser interferometric gravitational observatories will facilitate extraction of useful source information from the data. Stable clocks together with general relativity have found important practical applications in navigational systems s...
Liu, Qing; He, Ya-Ling
2015-11-01
In this paper, a double multiple-relaxation-time lattice Boltzmann model is developed for simulating transient solid-liquid phase change problems in porous media at the representative elementary volume scale. The model uses two different multiple-relaxation-time lattice Boltzmann equations, one for the flow field and the other for the temperature field with nonlinear latent heat source term. The model is based on the generalized non-Darcy formulation, and the solid-liquid interface is traced through the liquid fraction which is determined by the enthalpy-based method. The present model is validated by numerical simulations of conduction melting in a semi-infinite space, solidification in a semi-infinite corner, and convection melting in a square cavity filled with porous media. The numerical results demonstrate the efficiency and accuracy of the present model for simulating transient solid-liquid phase change problems in porous media.
Liu, Qing
2015-01-01
In this paper, a double multiple-relaxation-time lattice Boltzmann model is developed for simulating transient solid-liquid phase change problems in porous media at the representative elementary volume scale. The model uses two different multiple-relaxation-time lattice Boltzmann equations, one for the flow field and the other for the temperature field with nonlinear latent heat source term. The model is based on the generalized non-Darcy formulation, and the solid-liquid phase change interface is traced through the liquid fraction which is determined by the enthalpy method. The model is validated by numerical simulations of conduction melting in a semi-infinite space, solidification in a semi-infinite corner, and convection melting in a square cavity filled with porous media. The numerical results demonstrate the efficiency and accuracy of the present model for simulating transient solid-liquid phase change problems in porous media.
Line-Mixing Relaxation Matrix model for spectroscopic and radiative transfer studies
Mendaza, Teresa; Martin-Torres, Javier
2016-04-01
We present a generic model to compute the Relaxation Matrix easily adaptable to any molecule and type of spectroscopic lines or bands in non-reactive molecule collisions regimes. It also provides the dipole moment of every transition and level population of the selected molecule. The model is based on the Energy-Corrected Sudden (ECS) approximation/theory introduced by DePristo (1980), and on previous Relaxation Matrix studies for the interaction between molecular ro-vibrational levels (Ben-Rueven, 1966), atoms (Rosenkranz, 1975), linear molecules (Strow and Reuter, 1994; Niro, Boulet and Hartmann, 2004), and symmetric but not linear molecules (Tran et al., 2006). The model is open source, and it is user-friendly. To the point that the user only has to select the wished molecule and vibrational band to perform the calculations. It reads the needed spectroscopic data from the HIgh-resolution TRANsmission molecular absorption (HITRAN) (Rothman et al., 2013) and ExoMol (Tennyson and Yurchenko, 2012). In this work we present an example of the calculations with our model for the case of the 2ν3 band of methane (CH4), and a comparison with a previous work (Tran et al., 2010). The data produced by our model can be used to characterise the line-mixing effects on ro-vibrational lines of the infrared emitters of any atmosphere, to calculate accurate absorption spectra, that are needed in the interpretation of atmospheric spectra, radiative transfer modelling and General Circulation Models (GCM). References [1] A.E. DePristo, Collisional influence on vibration-rotation spectral line shapes: A scaling theoretical analysis and simplification, J. Chem. Phys. 73(5), 1980. [2] A. Ben-Reuven, Impact broadening of microwave spectra, Phys. Rev. 145(1), 7-22, 1966. [3] P.W. Rosenkranz, Shape of the 5 mm Oxygen Band in the Atmosphere, IEEE Transactions on Antennas and Propagation, vol. AP-23, no. 4, pp. 498-506, 1975. [4] Strow, L.L., D.D. Tobin, and S.E. Hannon, A compilation of
Winfree, Arthur T.
1975-01-01
Reports on experiments conducted on two biological clocks, in organisms in the plant and animal kingdoms, which indicate that biological oscillation can be arrested by a single stimulus of a definite strength delivered at the proper time. (GS)
Winfree, Arthur T.
1975-01-01
Reports on experiments conducted on two biological clocks, in organisms in the plant and animal kingdoms, which indicate that biological oscillation can be arrested by a single stimulus of a definite strength delivered at the proper time. (GS)
O'Brien, L.; Spivak, D.; Krueger, N.; Peterson, T. A.; Erickson, M. J.; Bolon, B.; Geppert, C. C.; Leighton, C.; Crowell, P. A.
2016-09-01
In the nonlocal spin valve (NLSV) geometry, four-terminal electrical Hanle effect measurements have the potential to provide a particularly simple determination of the lifetime (τs) and diffusion length (λN) of spins injected into nonmagnetic (N) materials. Recent papers, however, have demonstrated that traditional models typically used to fit such data provide an inaccurate measurement of τs in ferromagnet (FM)/N metal devices with low interface resistance, particularly when the separation of the source and detector contacts is small. In the transparent limit, this shortcoming is due to the back diffusion and subsequent relaxation of spins within the FM contacts, which is not properly accounted for in standard models of the Hanle effect. Here we have used the separation dependence of the spin accumulation signal in NLSVs with multiple FM/N combinations, and interfaces in the diffusive limit, to determine λN in traditional spin valve measurements. We then compare these results to Hanle measurements as analyzed using models that either include or exclude spin sinking. We demonstrate that differences between the spin valve and Hanle measurements of λN can be quantitatively modelled provided that both the FM contact-induced isotropic spin sinking and the full three-dimensional geometry of the devices, which is particularly important at small contact separations, are accounted for. We find, however, that considerable difficulties persist, in particular due to the sensitivity of fitting to the contact interface resistance and the FM contact magnetization rotation, in precisely determining λN with the Hanle technique alone, particularly at small contact separations.
无
2007-01-01
There was a slow-relaxing tail of skeletal muscles in vitro upon the inhibition of Ca2+-pump by cyclopiazonic acid (CPA). Herein, a new linearly-combined bi-exponential model to resolve this slow-relaxing tail from the fast-relaxing phase was investigated for kinetic analysis of the isometric relaxation process of Bufo gastrocnemius in vitro, in comparison to the single exponential model and the classical bi-exponential model. During repetitive stimulations at a 2-s interval by square pulses of a 2-ms duration at 12 V direct currency (DC), the isometric tension of Bufo gastrocnemius was recorded at 100 Hz. The relaxation curve with tensions falling from 90% of the peak to the 15th datum before next stimulation was analyzed by three exponential models using a program in MATLAB 6.5. Both the goodness of fit and the distribution of the residuals for the best fitting supported the comparable validity of this new bi-exponential model for kinetic analysis of the relaxation process of the control muscles. After CPA treatment, however, this new bi-exponential model showed an obvious statistical superiority for kinetic analysis of the muscle relaxation process, and it gave the estimated rest tension consistent to that by experimentation, whereas both the classical bi-exponential model and the single exponential model gave biased rest tensions. Moreover, after the treatment of muscles by CPA, both the single exponential model and the classical bi-exponential model yielded lowered relaxation rates,nevertheless, this new bi-exponential model had relaxation rates of negligible changes except much higher rest tensions. These results suggest that this novel linearly-combined bi-exponential model is desirable for kinetic analysis of the relaxation process of muscles with altered Ca2+-pumping activity.
Andrea Sorzia
2016-01-01
Full Text Available A tensile test until breakage and a creep and relaxation test on a polypropylene fibre are carried out and the resulting creep and stress relaxation curves are fit by a model adopting a fraction-exponential kernel in the viscoelastic operator. The models using fraction-exponential functions are simpler than the complex ones obtained from combination of dashpots and springs and, furthermore, are suitable for fitting experimental data with good approximation allowing, at the same time, obtaining inverse Laplace transform in closed form. Therefore, the viscoelastic response of polypropylene fibres can be modelled straightforwardly through analytical methods. Addition of polypropylene fibres greatly improves the tensile strength of composite materials with concrete matrix. The proposed analytical model can be employed for simulating the mechanical behaviour of composite materials with embedded viscoelastic fibres.
Lemaître Class Dark Energy Model for Relaxing Cosmological Constant
Irina Dymnikova
2017-05-01
Full Text Available Cosmological constant corresponds to the maximally symmetric cosmological term with the equation of state p = − ρ . Introducing a cosmological term with the reduced symmetry, p r = − ρ in the spherically symmetric case, makes cosmological constant intrinsically variable component of a variable cosmological term which describes time-dependent and spatially inhomogeneous vacuum dark energy. Relaxation of the cosmological constant from the big initial value to the presently observed value can be then described in general setting by the spherically symmetric cosmology of the Lemaître class. We outline in detail the cosmological model with the global structure of the de Sitter spacetime distinguished by the holographic principle as the only stable product of quantum evaporation of the cosmological horizon entirely determined by its quantum dynamics. Density of the vacuum dark energy is presented by semiclassical description of vacuum polarization in the spherically symmetric gravitational field, and its initial value is chosen at the GUT scale. The final non-zero value of the cosmological constant is tightly fixed by the quantum dynamics of evaporation and appears in the reasonable agreement with its observational value.
Cellular Imaging Using Equivalent Cross-Relaxation Rate Technique in Rabbit VX-2 Tumor Model.
Nishiofuku, Hideyuki; Matsushima, Shigeru; Taguchi, Osamu; Inaba, Yoshitaka; Yamaura, Hidekazu; Sato, Yozo; Tanaka, Toshihiro; Kichikawa, Kimihiko
2011-01-01
Equivalent cross-relaxation rate (ECR) imaging (ECRI) is a measurement technique that can be used to quantitatively evaluate changes in structural organization and cellular density by MRI. The aim of this study was to evaluate the correlation between the ECR value and cellular density in the rabbit VX2 tumor model. Five rabbits implanted with 10 VX2 tumors in the femur muscles were included in this study. We adopted the off-resonance technique with a single saturation transfer pulse frequency of 7 ppm downfield from water resonance. The ECR value was defined as the percentage of signal loss between the unsaturated and saturated images. ECR images were constructed based on the percentage of the ECR value. Pathological specimens were divided into 34 areas and classified into two groups: the viable group and the necrotic group. ECR values were measured and compared between groups. The correlation between the ECR value and cellular density was then determined. The mean ECR value was significantly higher in the viable group than in the necrotic group (61.2% vs. 35.8%). The area under the curve that calculated by receiver operating characteristic curve was 0.991 at 7 ppm. The regression graph showed a linear relationship between the ECR value and cellular density; the correlation coefficient (r) was 0.858. There is a strong association between the ECR value and cellular density in VX2 tumors and so ECRI could be a potentially useful technique for accurately depicting viable and necrotic areas.
Chen, Sheng; Täuber, Uwe C.
2015-03-01
Spatially extended stochastic models for predator-prey competition and coexistence display complex, correlated spatio-temporal structures and are governed by remarkably large fluctuations. Both populations are characterized by damped erratic oscillations whose properties are governed by the reaction rates. Here, we specifically study a stochastic lattice Lotka-Volterra model by means of Monte Carlo simulations that impose spatial restrictions on the number of occupants per site. The system tends to relax into a quasi-stationary state, independent of the imposed initial conditions. We investigate the non-equilibrium relaxation between two such quasi-stationary states, following an instantaneous change of the predation rate. The ensuing relaxation times are measured via the peak width of the population density Fourier transforms. As expected, we find that the initial state only influences the oscillations for the duration of this relaxation time, implying that the system quickly loses any memory of the initial configuration. Research supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering under Award DE-FG02-09ER46613.
Self-Adaptive Clock Synchronization for Computational Grid
ZHAO Ying(赵英); ZHOU WanLei(周万雷); HUANG JiuMei(黄九梅); YU Shui(余水); E.J.Lanham
2003-01-01
This paper presents an innovative method to synchronize physical clocks for a computational grid, in particular for a computational grid linked through the asynchronous Intranet or Internet environments. The method discussed is an asynchronous self-adaptive clock synchronization mechanism. Two strategies for clock synchronisation are introduced. (1) Use continuous time intervals to calculate the precision of clocks, which can reduce the effect of network delay efficiently. (2) Every node synchronizes its clock with its leader actively. In addition, a node self-adaptive model is presented, and the relationship between the clock precision and synchronization time is induced, hence a node can predict when it should begin the synchronization process.Detailed simulation and extension of this issue are provided at the end of the paper. The presented model is both practical and feasible.
Pattanayek, Rekha; Williams, Dewight R; Pattanayek, Sabuj; Mori, Tetsuya; Johnson, Carl H; Stewart, Phoebe L; Egli, Martin [Vanderbilt
2010-03-08
The circadian clock of the cyanobacterium Synechococcus elongatus can be reconstituted in vitro by the KaiA, KaiB and KaiC proteins in the presence of ATP. The principal clock component, KaiC, undergoes regular cycles between hyper- and hypo-phosphorylated states with a period of ca. 24 h that is temperature compensated. KaiA enhances KaiC phosphorylation and this enhancement is antagonized by KaiB. Throughout the cycle Kai proteins interact in a dynamic manner to form complexes of different composition. We present a three-dimensional model of the S. elongatus KaiB-KaiC complex based on X-ray crystallography, negative-stain and cryo-electron microscopy, native gel electrophoresis and modelling techniques. We provide experimental evidence that KaiB dimers interact with KaiC from the same side as KaiA and for a conformational rearrangement of the C-terminal regions of KaiC subunits. The enlarged central channel and thus KaiC subunit separation in the C-terminal ring of the hexamer is consistent with KaiC subunit exchange during the dephosphorylation phase. The proposed binding mode of KaiB explains the observation of simultaneous binding of KaiA and KaiB to KaiC, and provides insight into the mechanism of KaiB's antagonism of KaiA.
A clock network for geodesy and fundamental science
Lisdat, C; Quintin, N; Shi, C; Raupach, S M F; Grebing, C; Nicolodi, D; Stefani, F; Al-Masoudi, A; Dörscher, S; Häfner, S; Robyr, J -L; Chiodo, N; Bilicki, S; Bookjans, E; Koczwara, A; Koke, S; Kuhl, A; Wiotte, F; Meynadier, F; Camisard, E; Abgrall, M; Lours, M; Legero, T; Schnatz, H; Sterr, U; Denker, H; Chardonnet, C; Coq, Y Le; Santarelli, G; Amy-Klein, A; Targat, R Le; Lodewyck, J; Lopez, O; Pottie, P -E
2015-01-01
Leveraging the unrivaled performance of optical clocks in applications in fundamental physics beyond the standard model, in geo-sciences, and in astronomy requires comparing the frequency of distant optical clocks truthfully. Meeting this requirement, we report on the first comparison and agreement of fully independent optical clocks separated by 700 km being only limited by the uncertainties of the clocks themselves. This is achieved by a phase-coherent optical frequency transfer via a 1415 km long telecom fiber link that enables substantially better precision than classical means of frequency transfer. The fractional precision in comparing the optical clocks of three parts in $10^{17}$ was reached after only 1000 s averaging time, which is already 10 times better and more than four orders of magnitude faster than with any other existing frequency transfer method. The capability of performing high resolution international clock comparisons paves the way for a redefinition of the unit of time and an all-optic...
A Tropical Atmosphere Model with Moisture: Global Well-posedness and Relaxation Limit
Li, Jinkai
2015-01-01
In this paper, we consider a nonlinear interaction system between the barotropic mode and the first baroclinic mode of the tropical atmosphere with moisture; that was derived in [Frierson, D.M.W.; Majda, A.J.; Pauluis, O.M.: Dynamics of precipitation fronts in the tropical atmosphere: a novel relaxation limit, Commum. Math. Sci., 2 (2004), 591-626.] We establish the global existence and uniqueness of strong solutions to this system, with initial data in $H^1$, for each fixed convective adjustment relaxation time parameter $\\varepsilon>0$. Moreover, if the initial data enjoy slightly more regularity than $H^1$, then the unique strong solution depends continuously on the initial data. Furthermore, by establishing several appropriate $\\varepsilon$-independent estimates, we prove that the system converges to a limiting system, as the relaxation time parameter $\\varepsilon$ tends to zero, with convergence rate of the order $O(\\sqrt\\varepsilon)$. Moreover, the limiting system has a unique global strong solution, fo...
M. K. Witte
2013-09-01
Full Text Available Cumulus clouds exhibit a life cycle that consists of: (a the growth phase (increasing size, most notably in the vertical direction; (b the mature phase (growth ceases; any precipitation that develops is strongest during this period; and (c the dissipation phase (cloud dissipates because of precipitation and/or entrainment; no more dynamical support. Although radar can track clouds over time and give some sense of the age of a cloud, most aircraft in situ measurements lack temporal context. We use large eddy simulations of trade wind cumulus cloud fields from cases during the Barbados Oceanographic and Meteorological Experiment (BOMEX and Rain In Cumulus over the Ocean (RICO campaigns to demonstrate a potential cumulus cloud "clock". We find that the volume-averaged total water mixing ratio rt is a useful cloud clock for the 12 clouds studied. A cloud's initial rt is set by the subcloud mixed-layer mean rt and decreases monotonically from the initial value due primarily to entrainment. The clock is insensitive to aerosol loading, environmental sounding and extrinsic cloud properties such as lifetime and volume. In some cases (more commonly for larger clouds, multiple pulses of buoyancy occur, which complicate the cumulus clock by replenishing rt. The clock is most effectively used to classify clouds by life phase.
Buffer Gas Experiments in Mercury (Hg+) Ion Clock
Chung, Sang K.; Prestage, John D.; Tjoelker, Robert L.; Maleki, Lute
2004-01-01
We describe the results of the frequency shifts measured from various buffer gases that might be used as a buffer gas to increase the loading efficiency and cooling of ions trapped in a small mercury ion clock. The small mass, volume and power requirement of space clock precludes the use of turbo pumps. Hence, a hermetically sealed vacuum system, incorporating a suitable getter material with a fixed amount of inert buffer gas may be a practical alternative to the groundbased system. The collision shifts of 40,507,347.996xx Hz clock transition for helium, neon and argon buffer gases were measured in the ambient earth magnetic field. In addition to the above non-getterable inert gases we also measured the frequency shifts due to getterable, molecular hydrogen and nitrogen gases which may be used as buffer gases when incorporated with a miniature ion pump. We also examined the frequency shift due to the low methane gas partial pressure in a fixed higher pressure neon buffer gas environment. Methane gas interacted with mercury ions in a peculiar way as to preserve the ion number but to relax the population difference in the two hyperfine clock states and thereby reducing the clock resonance signal. The same population relaxation was also observed for other molecular buffer gases (N H,) but at much reduced rate.
Buffer Gas Experiments in Mercury (Hg+) Ion Clock
Chung, Sang K.; Prestage, John D.; Tjoelker, Robert L.; Maleki, Lute
2004-01-01
We describe the results of the frequency shifts measured from various buffer gases that might be used as a buffer gas to increase the loading efficiency and cooling of ions trapped in a small mercury ion clock. The small mass, volume and power requirement of space clock precludes the use of turbo pumps. Hence, a hermetically sealed vacuum system, incorporating a suitable getter material with a fixed amount of inert buffer gas may be a practical alternative to the groundbased system. The collision shifts of 40,507,347.996xx Hz clock transition for helium, neon and argon buffer gases were measured in the ambient earth magnetic field. In addition to the above non-getterable inert gases we also measured the frequency shifts due to getterable, molecular hydrogen and nitrogen gases which may be used as buffer gases when incorporated with a miniature ion pump. We also examined the frequency shift due to the low methane gas partial pressure in a fixed higher pressure neon buffer gas environment. Methane gas interacted with mercury ions in a peculiar way as to preserve the ion number but to relax the population difference in the two hyperfine clock states and thereby reducing the clock resonance signal. The same population relaxation was also observed for other molecular buffer gases (N H,) but at much reduced rate.
Poli, N; Gill, P; Tino, G M
2014-01-01
In the last ten years extraordinary results in time and frequency metrology have been demonstrated. Frequency-stabilization techniques for continuous-wave lasers and femto-second optical frequency combs have enabled a rapid development of frequency standards based on optical transitions in ultra-cold neutral atoms and trapped ions. As a result, today's best performing atomic clocks tick at an optical rate and allow scientists to perform high-resolution measurements with a precision approaching a few parts in $10^{18}$. This paper reviews the history and the state of the art in optical-clock research and addresses the implementation of optical clocks in a possible future redefinition of the SI second as well as in tests of fundamental physics.
Serafini, L.; Viganò, W.; Donati, A.; Porciani, M.; Zolesi, V.; Schulze-Varnholt, D.; Manieri, P.; El-Din Sallam, A.; Schmäh, M.; Horn, E. R.
2007-02-01
The study of internal clock systems of scorpions in weightless conditions is the goal of the SCORPI experiment. SCORPI was selected for flight on the International Space Station (ISS) and will be mounted in the European facility BIOLAB, the European Space Agency (ESA) laboratory designed to support biological experiments on micro-organisms, cells, tissue, cultures, small plants and small invertebrates. This paper outlines the main features of a breadboard designed and developed in order to allow the analysis of critical aspects of the experiment. It is a complete tool to simulate the experiment mission on ground and it can be customised, adapted and tuned to the scientific requirements. The paper introduces the SCORPI-T experiment which represents an important precursor for the success of the SCORPI on BIOLAB. The capabilities of the hardware developed show its potential use for future similar experiments in space.
Chan, Woan-Yi; Figus, Andrea; Ekwobi, Chidi; Srinivasan, Jeyaram R; Ramakrishnan, Venkat V
2010-08-01
Microsurgery is an essential technique in free flap reconstructions today. The technical skills involved require a learning curve, which may be affected by the current issues of limited training resources and patient safety. We describe a study on the value of a microsurgery training device as an assessment and warm up tool in basic microsurgery skills. Forty volunteers with different levels of microsurgery experience performed a microsurgical 'round-the-clock' exercise on the training device three consecutive times. Video-recordings of these performances were rated by two blinded independent assessors using a modified Global Rating Scale to assess basic microsurgery skills on the following parameters: steadiness, instruments handling and speed. Time to complete a round was also recorded objectively. The Kruskal-Wallis test was used to analyse the construct validity of the parameters assessed between the groups of level of microsurgery experience. Crohnbach's coefficient alpha was used to determine the reliability index of the independent assessors. All participants improved their time on consecutive rounds of the exercise. A median of 82 s (range 6-583 s) improvement in time between the first and third round was observed. Different mean performance time could be identified between the groups, but individual speed did not correlate significantly with microsurgery experience. Assessment of microsurgery skills using the modified Global Rating Scale demonstrated statistically significant differences for instruments handling (p=0.03) and speed (p=0.01) between the groups with regard to microsurgery experience, and improvement in the parameters assessed for all groups. Difference in steadiness (p=0.07) was not significant amongst the juniors. Consultants performed better than juniors but, at all levels of experience, significant improvement in skills was demonstrated after practice. The 'round-the-clock' microsurgery training device is an inexpensive and readily
The circadian clock goes genomic.
Staiger, Dorothee; Shin, Jieun; Johansson, Mikael; Davis, Seth J
2013-06-24
Large-scale biology among plant species, as well as comparative genomics of circadian clock architecture and clock-regulated output processes, have greatly advanced our understanding of the endogenous timing system in plants.
Kasim, Shahreen; Hafit, Hanayanti; Leong, Tan Hua; Hashim, Rathiah; Ruslai, Husni; Jahidin, Kamaruzzaman; Syafwan Arshad, Mohammad
2016-11-01
Nowadays, some people facing the problem to wake up in the morning. This was result to absence of the classes, meetings, and even exams. The aim of this project is to develop an android application that can force the user to wake up. The method used in this application are pedometer and Short Message Service (SMS) function. This application need the user to take their smartphone and walk about 10 steps to disable it, when the alarm clock is activated. After that, when the alarm clock was rang, this alarm application has automatically send a message to the users’ friends or parents phone to wake them up.
Gravitomagnetism, clocks and geometry
Tartaglia, A
2001-01-01
New techniques to evaluate the clock effect using light are described. These are based on the flatness of the cylindrical surface containing the world lines of the rays constrained to move on circular trajectories about a spinning mass. The effect of the angular momentum of the source is manifested in the fact that inertial observers must be replaced by local non rotating observers. Starting from this an exact formula for circular trajectories is found. Numerical estimates for the Earth environment show that light would be a better probe than actual clocks to evidence the angular momentum influence. The advantages of light in connection with some principle experiments are shortly reviewed.
Labois, M
2008-10-15
This thesis deals with hyperbolic models for the simulation of compressible two-phase flows, to find alternatives to the classical bi-fluid model. We first establish a hierarchy of two-phase flow models, obtained according to equilibrium hypothesis between the physical variables of each phase. The use of Chapman-Enskog expansions enables us to link the different existing models to each other. Moreover, models that take into account small physical unbalances are obtained by means of expansion to the order one. The second part of this thesis focuses on the simulation of flows featuring velocity unbalances and pressure balances, in two different ways. First, a two-velocity two-pressure model is used, where non-instantaneous velocity and pressure relaxations are applied so that a balancing of these variables is obtained. A new one-velocity one-pressure dissipative model is then proposed, where the arising of second-order terms enables us to take into account unbalances between the phase velocities. We develop a numerical method based on a fractional step approach for this model. (author)
Temperature regulates transcription in the zebrafish circadian clock.
Kajori Lahiri
2005-11-01
Full Text Available It has been well-documented that temperature influences key aspects of the circadian clock. Temperature cycles entrain the clock, while the period length of the circadian cycle is adjusted so that it remains relatively constant over a wide range of temperatures (temperature compensation. In vertebrates, the molecular basis of these properties is poorly understood. Here, using the zebrafish as an ectothermic model, we demonstrate first that in the absence of light, exposure of embryos and primary cell lines to temperature cycles entrains circadian rhythms of clock gene expression. Temperature steps drive changes in the basal expression of certain clock genes in a gene-specific manner, a mechanism potentially contributing to entrainment. In the case of the per4 gene, while E-box promoter elements mediate circadian clock regulation, they do not direct the temperature-driven changes in transcription. Second, by studying E-box-regulated transcription as a reporter of the core clock mechanism, we reveal that the zebrafish clock is temperature-compensated. In addition, temperature strongly influences the amplitude of circadian transcriptional rhythms during and following entrainment by light-dark cycles, a property that could confer temperature compensation. Finally, we show temperature-dependent changes in the expression levels, phosphorylation, and function of the clock protein, CLK. This suggests a mechanism that could account for changes in the amplitude of the E-box-directed rhythm. Together, our results imply that several key transcriptional regulatory elements at the core of the zebrafish clock respond to temperature.
Zoback, M. D.; Xu, S.; Rassouli, F.; Ma, X.
2016-12-01
In this paper we extend the viscoplastic stress relaxation model of Sone and Zoback (Jour. Petrol. Sci. and Eng., 2014) for predicting variations of least principal stress with stress and its impact on the vertical propagation of hydraulic fractures. Viscoplastic stress relaxation in clay-rich (or diagenetically immature) sedimentary rocks makes the stress field more isotropic. In normal faulting and strike-slip faulting environments, this causes the least principal stress to increase making such formations likely barriers to vertical hydraulic fracture growth. In order to predict the magnitude of viscoplastic stress relaxation in different unconventional formations, we generalize a constitutive law developed from a wide range of creep experiments in our lab over the past several years and apply it to areas of stacked pay in Oklahoma and Texas. Using frac gradients were measured from minifrac and DFIT (Diagnostic Fracture Injection Test) experiments. The viscoplastic model does a good job of explaining vertical hydraulic fracture propagation, as indicated by the distribution of microseismic events recorded during stimulation.
Perturbations and quantum relaxation
Kandhadai, Adithya
2016-01-01
We investigate whether small perturbations can cause relaxation to quantum equilibrium over very long timescales. We consider in particular a two-dimensional harmonic oscillator, which can serve as a model of a field mode on expanding space. We assume an initial wave function with small perturbations to the ground state. We present evidence that the trajectories are highly confined so as to preclude relaxation to equilibrium even over very long timescales. Cosmological implications are briefly discussed.
Biogeographic calibrations for the molecular clock.
Ho, Simon Y W; Tong, K Jun; Foster, Charles S P; Ritchie, Andrew M; Lo, Nathan; Crisp, Michael D
2015-09-01
Molecular estimates of evolutionary timescales have an important role in a range of biological studies. Such estimates can be made using methods based on molecular clocks, including models that are able to account for rate variation across lineages. All clock models share a dependence on calibrations, which enable estimates to be given in absolute time units. There are many available methods for incorporating fossil calibrations, but geological and climatic data can also provide useful calibrations for molecular clocks. However, a number of strong assumptions need to be made when using these biogeographic calibrations, leading to wide variation in their reliability and precision. In this review, we describe the nature of biogeographic calibrations and the assumptions that they involve. We present an overview of the different geological and climatic events that can provide informative calibrations, and explain how such temporal information can be incorporated into dating analyses.
Vicente, J. de; Castilla, J.; Martinez, G.
2007-09-27
Decamp (Dark Energy Survey Camera) is a new instrument designed to explore the universe aiming to reveal the nature of Dark Energy. The camera consists of 72 CCDs and 520 Mpixels. The readout electronics of DECam is based on the Monsoon system. Monsoon is a new image acquisition system developed by the NOAO (National Optical Astronomical Observatory) for the new generation of astronomical cameras. The Monsoon system uses three types of boards inserted in a Eurocard format based crate: master control board, acquisition board and clock board. The direct use of the Monsoon system for DECam readout electronics requires nine crates mainly due to the high number of clock boards needed. Unfortunately, the available space for DECam electronics is constrained to four crates at maximum. The major drawback to achieve such desired compaction degree resides in the clock board signal density. This document describes the changes performed at CIEMAT on the programmable logic of the Monsoon clock board aiming to meet such restricted space constraints. (Author) 5 refs.
Rosu, H C
2003-01-01
In the wake of our recent work on cyclotomic effects in quantum phase locking [M. Planat and H. C. Rosu, Phys. Lett. A 315, 1 (2003)], we briefly discuss here a cyclotomic extension of the Salecker and Wigner quantum clock. We also hint on a possible cyclotomic structure of time at the Planck scales
Mutual information reveals multiple structural relaxation mechanisms in a model glass former.
Dunleavy, Andrew J; Wiesner, Karoline; Yamamoto, Ryoichi; Royall, C Patrick
2015-01-22
Among the key challenges to our understanding of solidification in the glass transition is that it is accompanied by little apparent change in structure. Recently, geometric motifs have been identified in glassy liquids, but a causal link between these motifs and solidification remains elusive. One 'smoking gun' for such a link would be identical scaling of structural and dynamic lengthscales on approaching the glass transition, but this is highly controversial. Here we introduce an information theoretic approach to determine correlations in displacement for particle relaxation encoded in the initial configuration of a glass-forming liquid. We uncover two populations of particles, one inclined to relax quickly, the other slowly. Each population is correlated with local density and geometric motifs. Our analysis further reveals a dynamic lengthscale similar to that associated with structural properties, which may resolve the discrepancy between structural and dynamic lengthscales.
Relaxed Arakawa-Schubert - A parameterization of moist convection for general circulation models
Moorthi, Shrinivas; Suarez, Max J.
1992-01-01
A simple implementation of the Arakawa and Schubert (1974) cumulus parameterization is presented. The major simplification made is to 'relax' the state toward equilibrium each time the parameterization is invoked, rather than requiring that the final state be balanced, as in the original Arakawa-Schubert implementation. This relaxed Arakawa-Schubert (RAS) scheme is evaluated in off-line tests using the Global Atmospheric Research Program (GARP) Atlantic Tropical Experiment (GATE) Phase III data. The results show that RAS is equivalent to the standard implementation of Arakawa-Schubert but is more economical and simpler to code. RAS also avoids the ill-posed problem that occurs in Arakawa-Schubert as a result of having to solve for a balanced state.
Yugang YU; Feng CHU; Haoxun CHEN
2006-01-01
In this paper, we propose a new model for improving the lot size obtained with the model of Woo, Hsu, and Wu (2001) proposed in their paper "An integrated inventory model for a single vendor and multiple buyers with ordering cost reduction" (Int. J. Production Economics 73 203-215). The new model can provide a lower or equal joint total cost as compared to Woo, Hsu, and Wu's model due to the relaxation of their integral multiple material ordering cycle policy to a fractional-integral multiple material ordering cycle policy. The proposed model is analyzed and an algorithm for calculating the optimal lot size of the model is developed. A numerical study based on the example used by Woo, Hsu, and Wu is presented.
Michael J McCarthy
Full Text Available Circadian rhythm abnormalities in bipolar disorder (BD have led to a search for genetic abnormalities in circadian "clock genes" associated with BD. However, no significant clock gene findings have emerged from genome-wide association studies (GWAS. At least three factors could account for this discrepancy: complex traits are polygenic, the organization of the clock is more complex than previously recognized, and/or genetic risk for BD may be shared across multiple illnesses. To investigate these issues, we considered the clock gene network at three levels: essential "core" clock genes, upstream circadian clock modulators, and downstream clock controlled genes. Using relaxed thresholds for GWAS statistical significance, we determined the rates of clock vs. control genetic associations with BD, and four additional illnesses that share clinical features and/or genetic risk with BD (major depression, schizophrenia, attention deficit/hyperactivity. Then we compared the results to a set of lithium-responsive genes. Associations with BD-spectrum illnesses and lithium-responsiveness were both enriched among core clock genes but not among upstream clock modulators. Associations with BD-spectrum illnesses and lithium-responsiveness were also enriched among pervasively rhythmic clock-controlled genes but not among genes that were less pervasively rhythmic or non-rhythmic. Our analysis reveals previously unrecognized associations between clock genes and BD-spectrum illnesses, partly reconciling previously discordant results from past GWAS and candidate gene studies.
Dunlap, Jay C.; Loros, Jennifer J.; Aronson, Benjamin D.; Merrow, Martha; Crosthwaite, Susan; Bell-Pedersen, Deborah; Johnson, Keith; Lindgren, Kristin; Garceau, Norman Y.
1995-01-01
Genetic approaches to the identification of clock components have succeeded in two model systems, Neurospora and Drosophila. In each organism, genes identified through screens for clock-affecting mutations (frq in Neurospora, per in Drosophila) have subsequently been shown to have characteristics of
Orbitography for next generation space clocks
Duchayne, Loïc; Wolf, Peter
2007-01-01
Over the last decade of the 20th century and the first few years of the 21st, the uncertainty of atomic clocks has decreased by about two orders of magnitude, passing from the low 10^-14 to below 10^-16, in relative frequency . Space applications in fundamental physics, geodesy, time/frequency metrology, navigation etc... are among the most promising for this new generation of clocks. Onboard terrestrial or solar system satellites, their exceptional frequency stability and accuracy makes them a prime tool to test the fundamental laws of nature, and to study gravitational potentials and their evolution. In this paper, we study in more detail the requirements on orbitography compatible with operation of next generation space clocks at the required uncertainty based on a completely relativistic model. Using the ACES (Atomic Clock Ensemble in Space) mission as an example, we show that the required accuracy goal can be reached with relatively modest constraints on the orbitography of the space clock, much less str...
Feng, Xiao-Li; Li, Yu-Xiao; Gu, Jian-Zhong; Zhuo, Yi-Zhong
2009-10-01
The relaxation property of both Eigen model and Crow-Kimura model with a single peak fitness landscape is studied from phase transition point of view. We first analyze the eigenvalue spectra of the replication mutation matrices. For sufficiently long sequences, the almost crossing point between the largest and second-largest eigenvalues locates the error threshold at which critical slowing down behavior appears. We calculate the critical exponent in the limit of infinite sequence lengths and compare it with the result from numerical curve fittings at sufficiently long sequences. We find that for both models the relaxation time diverges with exponent 1 at the error (mutation) threshold point. Results obtained from both methods agree quite well. From the unlimited correlation length feature, the first order phase transition is further confirmed. Finally with linear stability theory, we show that the two model systems are stable for all ranges of mutation rate. The Eigen model is asymptotically stable in terms of mutant classes, and the Crow-Kimura model is completely stable.
Indentation load relaxation test
Hannula, S.P.; Stone, D.; Li, C.Y. (Cornell Univ., Ithaca, NY (USA))
Most of the models that are used to describe the nonelastic behavior of materials utilize stress-strain rate relations which can be obtained by a load relaxation test. The conventional load relaxation test, however, cannot be performed if the volume of the material to be tested is very small. For such applications the indentation type of test offers an attractive means of obtaining data necessary for materials characterization. In this work the feasibility of the indentation load relaxation test is studied. Experimental techniques are described together with results on Al, Cu and 316 SS. These results are compared to those of conventional uniaxial load relaxation tests, and the conversion of the load-indentation rate data into the stress-strain rate data is discussed.
2017-01-01
resonance (NMR) Spectral density functions Spin - spin relaxation Molecular dynamics Nuclear Overhauser effect Symmetric top rotor Spin -lattice relaxation...SYMMETRIC TOP ROTOR MODELS AND THE FLEXIBLE SYMMETRIC TOP ROTOR MODEL ECBC-TR-1428 Terry J. Henderson RESEARCH AND TECHNOLOGY DIRECTORATE...Symmetric Top Rotor Models and the Flexible Symmetric Top Rotor Model 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR
Relativity and Al^+ Optical Clocks
Chou, Chin-Wen; Hume, David B.; Wineland, David J.; Rosenband, Till
2010-03-01
We have constructed an optical clock based on quantum logic spectroscopy of an Al+ ion that has a fractional frequency inaccuracy of 8.6x10-18. The frequency of the ^1S0^3P0 clock transition is compared to that of a previously constructed Al^+ optical clock with a statistical measurement uncertainty of 7.0x10-18. The two clocks exhibit a relative stability of 2.8x10-15&-1/2circ;, and a fractional frequency difference of -1.8x10-17, consistent with the accuracy limit of the older clock. By comparing the frequencies of the clocks, we have observed relativistic effects, such as time dilation due to velocities less than 10 m/s and the gravitational red shift from a 0.33 m height change of one of the clocks.
Niss, K.; Jakobsen, B.; Olsen, N.B.
2005-01-01
The Gemant-DiMarzio-Bishop model, which connects the frequency-dependent shear modulus to the frequency-dependent dielectric constant, is reviewed and a new consistent macroscopic formulation is derived. It is moreover shown that this version of the model can be tested without fitting parameters...... that the Gemant-DiMarzio-Bishop model is correct on a qualitative level. The quantitative agreement between the model and the data is on the other hand moderate to poor. It is discussed if a model-free comparison between the dielectric and shear mechanical relaxations is relevant, and it is concluded...... that the shear modulus should be compared with the rotational dielectric modulus, 1/(epsilon(omega)–n^2), which is extracted from the Gemant-DiMarzio-Bishop model, rather than to the dielectric susceptibility or the conventional dielectric modulus M=1/epsilon(omega)...
Noise in state of the art clocks and their impact for fundamental physics
Maleki, L.
2001-01-01
In this paper a review of the use of advanced atomic clocks in testing the fundamental physical laws will be presented. Noise sources of clocks will be discussed, together with an outline their characterization based on current models. The paper will conclude with a discussion of recent attempts to reduce the fundamental, as well as technical noise in atomic clocks.
Genome-wide identification of CCA1 targets uncovers an expanded clock network in Arabidopsis
Nagel, Dawn H.; Doherty, Colleen J.; Pruneda-Paz, Jose L.; Schmitz, Robert J; Ecker, Joseph R.; Kay, Steve A.
2015-01-01
The circadian clock, an endogenous time-keeping mechanism common to most species, allows organisms to coordinate biological processes with specific times of day. In plants, the role of the clock extends to almost every aspect of growth and development, including responses to biotic and abiotic stresses. The core molecular components and circuits of the clock have been well studied in the model organism Arabidopsis thaliana; however, how this mechanism connects to clock-controlled outputs rema...
Using Integer Clocks to Verify the Timing-Sync Sensor Network Protocol
Huang, Xiaowan; Singh, Anu; Smolka, Scott A.
2010-01-01
We use the UPPAAL model checker for Timed Automata to verify the Timing-Sync time-synchronization protocol for sensor networks (TPSN). The TPSN protocol seeks to provide network-wide synchronization of the distributed clocks in a sensor network. Clock-synchronization algorithms for sensor networks such as TPSN must be able to perform arithmetic on clock values to calculate clock drift and network propagation delays. They must be able to read the value of a local clock and assign it to another local clock. Such operations are not directly supported by the theory of Timed Automata. To overcome this formal-modeling obstacle, we augment the UPPAAL specification language with the integer clock derived type. Integer clocks, which are essentially integer variables that are periodically incremented by a global pulse generator, greatly facilitate the encoding of the operations required to synchronize clocks as in the TPSN protocol. With this integer-clock-based model of TPSN in hand, we use UPPAAL to verify that the protocol achieves network-wide time synchronization and is devoid of deadlock. We also use the UPPAAL Tracer tool to illustrate how integer clocks can be used to capture clock drift and resynchronization during protocol execution
Saxena, Vikrant, E-mail: vikrant.saxena@desy.de [Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg (Germany); Hamburg Center for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg (Germany); Ziaja, Beata, E-mail: ziaja@mail.desy.de [Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg (Germany); Hamburg Center for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg (Germany); Institute of Nuclear Physics, Polish Academy of Sciences, Radzikowskiego 152, 31-342 Kraków (Poland)
2016-01-15
The irradiation of an atomic cluster with a femtosecond x-ray free-electron laser pulse results in a nanoplasma formation. This typically occurs within a few hundred femtoseconds. By this time the x-ray pulse is over, and the direct photoinduced processes no longer contributing. All created electrons within the nanoplasma are thermalized. The nanoplasma thus formed is a mixture of atoms, electrons, and ions of various charges. While expanding, it is undergoing electron impact ionization and three-body recombination. Below we present a hydrodynamic model to describe the dynamics of such multi-component nanoplasmas. The model equations are derived by taking the moments of the corresponding Boltzmann kinetic equations. We include the equations obtained, together with the source terms due to electron impact ionization and three-body recombination, in our hydrodynamic solver. Model predictions for a test case, expanding spherical Ar nanoplasma, are obtained. With this model, we complete the two-step approach to simulate x-ray created nanoplasmas, enabling computationally efficient simulations of their picosecond dynamics. Moreover, the hydrodynamic framework including collisional processes can be easily extended for other source terms and then applied to follow relaxation of any finite non-isothermal multi-component nanoplasma with its components relaxed into local thermodynamic equilibrium.
Yi Ting
2012-11-01
Full Text Available Abstract It has been reported previously that diabetic cardiomyopathy can be inhibited or reverted with chronic zinc supplementation. In the current study, we hypothesized that total cardiac calcium and zinc content is altered in early onset diabetes mellitus characterized in part as hyperglycemia (HG and that exposure of zinc ion (Zn2+ to isolated cardiomyocytes would enhance contraction-relaxation function in HG more so than in nonHG controls. To better control for differential cardiac myosin isoform expression as occurs in rodents after β-islet cell necrosis, hypothyroidism was induced in 16 rats resulting in 100% β-myosin heavy chain expression in the heart. β-Islet cell necrosis was induced in half of the rats by streptozocin administration. After 6 wks of HG, both HG and nonHG controls rats demonstrated similar myofilament performance measured as thin filament calcium sensitivity, native thin filament velocity in the myosin motility assay and contractile velocity and power. Extracellular Zn2+ reduced cardiomyocyte contractile function in both groups, but enhanced relaxation function significantly in the HG group compared to controls. Most notably, a reduction in diastolic sarcomere length with increasing pacing frequencies, i.e., incomplete relaxation, was more pronounced in the HG compared to controls, but was normalized with extracellular Zn2+ application. This is a novel finding implicating that the detrimental effect of HG on cardiomyocyte Ca2+ regulation can be amelioration by Zn2+. Among the many post-translational modifications examined, only phosphorylation of ryanodine receptor (RyR at S-2808 was significantly higher in HG compared to nonHG. We did not find in our hypothyroid rats any differentiating effects of HG on myofibrillar protein phosphorylation, lysine acetylation, O-linked N-acetylglucosamine and advanced glycated end-products, which are often implicated as complicating factors in cardiac performance due to HG. Our
Yi, Ting; Cheema, Yaser; Tremble, Sarah M; Bell, Stephen P; Chen, Zengyi; Subramanian, Meenakumari; LeWinter, Martin M; VanBuren, Peter; Palmer, Bradley M
2012-11-02
It has been reported previously that diabetic cardiomyopathy can be inhibited or reverted with chronic zinc supplementation. In the current study, we hypothesized that total cardiac calcium and zinc content is altered in early onset diabetes mellitus characterized in part as hyperglycemia (HG) and that exposure of zinc ion (Zn2+) to isolated cardiomyocytes would enhance contraction-relaxation function in HG more so than in nonHG controls. To better control for differential cardiac myosin isoform expression as occurs in rodents after β-islet cell necrosis, hypothyroidism was induced in 16 rats resulting in 100% β-myosin heavy chain expression in the heart. β-Islet cell necrosis was induced in half of the rats by streptozocin administration. After 6 wks of HG, both HG and nonHG controls rats demonstrated similar myofilament performance measured as thin filament calcium sensitivity, native thin filament velocity in the myosin motility assay and contractile velocity and power. Extracellular Zn2+ reduced cardiomyocyte contractile function in both groups, but enhanced relaxation function significantly in the HG group compared to controls. Most notably, a reduction in diastolic sarcomere length with increasing pacing frequencies, i.e., incomplete relaxation, was more pronounced in the HG compared to controls, but was normalized with extracellular Zn2+ application. This is a novel finding implicating that the detrimental effect of HG on cardiomyocyte Ca2+ regulation can be amelioration by Zn2+. Among the many post-translational modifications examined, only phosphorylation of ryanodine receptor (RyR) at S-2808 was significantly higher in HG compared to nonHG. We did not find in our hypothyroid rats any differentiating effects of HG on myofibrillar protein phosphorylation, lysine acetylation, O-linked N-acetylglucosamine and advanced glycated end-products, which are often implicated as complicating factors in cardiac performance due to HG. Our results suggest that the
数学建模在昼夜节律生物钟中的应用%APPLICATION OF MATHEMATICAL MODEL IN CIRCADIAN CLOCK
李莹; 郑明银; 刘曾荣
2015-01-01
Circadian rhythms are endogenous oscillations characterized by a period of about 24h.The abundance of genetic information and the complexity of the molecular circuitry make circadian clocks a system of choice for theoretical studies.Mathematical model can help us understand the molecular regulatory mechanisms that under-lie these circadian oscillations and account for their dynamic properties.By numerical simulations,mathematical models can highlight the role of key parameters and can be used to predict the behavior of the system in condi-tions not yet tested by experiments.Mathematical models can also be used to provide possible explanations to un-intuitive observations or to unravel the design principles of the circadian molecular oscillator.In this paper,we summarized the mathematical models used in circadian clock.The building and analysis of mathematical model, as well as its advantages and limitations,were highlighted.All of these will provide scientific basis for further studying on circadian clock,and even for understanding the functions of mathematical model in life system.%昼夜节律生物钟是在分子水平上产生的以24小时为周期的内在节律振子，大量的遗传信息和复杂的分子环路使得人们能在系统的角度对昼夜节律生物钟进行理论研究。数学模型有助于我们理解产生生物钟振子的分子调控机制及其动力学特性。通过数值模拟，数学模型可以分析关键参数在系统中的作用、预测新的行为以供实验进一步验证，也可以为实验中的直观发现提供合理的解释，或者揭示生物钟分子机制的设计原理。本文总结了一些昼夜节律生物钟的数学模型，讨论并阐述了数学模型的建立和分析以及数学模型的优势及局限性。这个论述将为研究昼夜节律生物钟提供广泛的参考，同时为进一步了解数学模型在生命系统研究中的作用提供借鉴。
1995-01-01
The concept of Round the Clock Librarianship (ROCLOLIB) is one such opportunity of terminal and critical importance to librarians, which helps people (clients) in general and reassures them about the professional commitment and devotedness of librarians. Although the concept is old, it is an exercise here to analyse its importance for the overall image and status of the practice/occupation. The chapter discusses the proposal of opening Libraries for 24 Hours. It also points out the reasons fo...
A tropical atmosphere model with moisture: global well-posedness and relaxation limit
Li, Jinkai; Titi, Edriss S.
2016-09-01
In this paper, we consider a nonlinear interaction system between the barotropic mode and the first baroclinic mode of the tropical atmosphere with moisture, which was derived in Frierson et al (2004 Commum. Math. Sci. 2 591-626). We establish the global existence and uniqueness of strong solutions to this system, with initial data in H 1, for each fixed convective adjustment relaxation time parameter \\varepsilon >0 . Moreover, if the initial data possess slightly more regularity than H 1, then the unique strong solution depends continuously on the initial data. Furthermore, by establishing several appropriate ɛ-independent estimates, we prove that the system converges to a limiting system as the relaxation time parameter ɛ tends to zero, with a convergence rate of the order O≤ft(\\sqrt{\\varepsilon}\\right) . Moreover, the limiting system has a unique global strong solution for any initial data in H 1 and such a unique strong solution depends continuously on the initial data if the initial data posses slightly more regularity than H 1. Notably, this solves the viscous version of an open problem proposed in the above mentioned paper of Frierson, Majda and Pauluis.
Hunting for topological dark matter with atomic clocks
Derevianko, A
2013-01-01
The cosmological applications of atomic clocks so far have been limited to searches of the uniform-in-time drift of fundamental constants. In this paper, we point out that a transient in time change of fundamental constants can be induced by dark matter objects that have large spatial extent, and are built from light non-Standard Model fields. The stability of this type of dark matter can be dictated by the topological reasons. We point out that correlated networks of atomic clocks, some of them already in existence, can be used as a powerful tool to search for the topological defect dark matter, thus providing another important fundamental physics application to the ever-improving accuracy of atomic clocks. During the encounter with a topological defect, as it sweeps through the network, initially synchronized clocks will become desynchronized. Time discrepancies between spatially-separated clocks are expected to exhibit a distinct signature, encoding defect's space structure and its interaction strength wit...
Network news: prime time for systems biology of the plant circadian clock.
McClung, C Robertson; Gutiérrez, Rodrigo A
2010-12-01
Whole-transcriptome analyses have established that the plant circadian clock regulates virtually every plant biological process and most prominently hormonal and stress response pathways. Systems biology efforts have successfully modeled the plant central clock machinery and an iterative process of model refinement and experimental validation has contributed significantly to the current view of the central clock machinery. The challenge now is to connect this central clock to the output pathways for understanding how the plant circadian clock contributes to plant growth and fitness in a changing environment. Undoubtedly, systems approaches will be needed to integrate and model the vastly increased volume of experimental data in order to extract meaningful biological information. Thus, we have entered an era of systems modeling, experimental testing, and refinement. This approach, coupled with advances from the genetic and biochemical analyses of clock function, is accelerating our progress towards a comprehensive understanding of the plant circadian clock network. Copyright © 2010 Elsevier Ltd. All rights reserved.
García, M. F.; Restrepo-Parra, E.; Riaño-Rojas, J. C.
2015-05-01
This work develops a model that mimics the growth of diatomic, polycrystalline thin films by artificially splitting the growth into deposition and relaxation processes including two stages: (1) a grain-based stochastic method (grains orientation randomly chosen) is considered and by means of the Kinetic Monte Carlo method employing a non-standard version, known as Constant Time Stepping, the deposition is simulated. The adsorption of adatoms is accepted or rejected depending on the neighborhood conditions; furthermore, the desorption process is not included in the simulation and (2) the Monte Carlo method combined with the metropolis algorithm is used to simulate the diffusion. The model was developed by accounting for parameters that determine the morphology of the film, such as the growth temperature, the interacting atomic species, the binding energy and the material crystal structure. The modeled samples exhibited an FCC structure with grain formation with orientations in the family planes of , and . The grain size and film roughness were analyzed. By construction, the grain size decreased, and the roughness increased, as the growth temperature increased. Although, during the growth process of real materials, the deposition and relaxation occurs simultaneously, this method may perhaps be valid to build realistic polycrystalline samples.
Nonlinear fractional relaxation
A Tofighi
2012-04-01
We deﬁne a nonlinear model for fractional relaxation phenomena. We use -expansion method to analyse this model. By studying the fundamental solutions of this model we ﬁnd that when → 0 the model exhibits a fast decay rate and when → ∞ the model exhibits a power-law decay. By analysing the frequency response we ﬁnd a logarithmic enhancement for the relative ratio of susceptibility.
Renner, S S; Grimm, Guido W; Kapli, Paschalia; Denk, Thomas
2016-07-19
The fossilized birth-death (FBD) model can make use of information contained in multiple fossils representing the same clade, and we here apply this model to infer divergence times in beeches (genus Fagus), using 53 fossils and nuclear sequences for all nine species. We also apply FBD dating to the fern clade Osmundaceae, with about 12 living species and 36 fossils. Fagus nuclear sequences cannot be aligned with those of other Fagaceae, and we therefore use Bayes factors to choose among alternative root positions. The crown group of Fagus is dated to 53 (62-43) Ma; divergence of the sole American species to 44 (51-39) Ma and divergence between Central European F. sylvatica and Eastern Mediterranean F. orientalis to 8.7 (20-1.8) Ma, unexpectedly old. The FBD model can accommodate fossils as sampled ancestors or as extinct or unobserved lineages; however, this makes its raw output, which shows all fossils on short or long branches, problematic to interpret. We use hand-drawn depictions and a bipartition network to illustrate the uncertain placements of fossils. Inferred speciation and extinction rates imply approximately 5× higher evolutionary turnover in Fagus than in Osmundaceae, fitting a hypothesized low turnover in plants adapted to low-nutrient conditions.This article is part of the themed issue 'Dating species divergences using rocks and clocks'. © 2016 The Author(s).
Ko-Fan Chen
2014-04-01
Full Text Available Circadian behavioural deficits, including sleep irregularity and restlessness in the evening, are a distressing early feature of Alzheimer’s disease (AD. We have investigated these phenomena by studying the circadian behaviour of transgenic Drosophila expressing the amyloid beta peptide (Aβ. We find that Aβ expression results in an age-related loss of circadian behavioural rhythms despite ongoing normal molecular oscillations in the central clock neurons. Even in the absence of any behavioural correlate, the synchronised activity of the central clock remains protective, prolonging lifespan, in Aβ flies just as it does in control flies. Confocal microscopy and bioluminescence measurements point to processes downstream of the molecular clock as the main site of Aβ toxicity. In addition, there seems to be significant non-cell-autonomous Aβ toxicity resulting in morphological and probably functional signalling deficits in central clock neurons.
Microchip-Based Trapped-Atom Clocks
Vuletic, Vladan; Schleier-Smith, Monika H
2011-01-01
This is a chapter of a recently published book entitled Atom Chips, edited by Jakob Reichel and Vladan Vuletic. The contents of this chapter include: Basic Principles; Atomic-Fountain versus Trapped-Atom Clocks; Optical-Transition Clocks versus Microwave Clocks; Clocks with Magnetically Trapped Atoms--Fundamental Limits and Experimental Demonstrations; Readout in Trapped-Atom Clocks; and Spin Squeezing.
Coffey, W. T.; Déjardin, P. M.; Walsh, M. E.
1999-03-01
Exact solutions obtained by Gross [J. Chem. Phys. 23, 1415 (1955)] and Sack [Proc. Phys. Soc. London, Sect. B 70, 402 (1957)] for the complex polarizability of assemblies of nonelectrically interacting rotators subjected to a variety of collisions and various approximations to that quantity, specifically the Rocard equation are reappraised in view of recent attempts to use a variety of forms of that equation for the interpretation of far infrared resonance absorption spectra. It is shown that for small values of the inertial parameter (heavy damping) the Rocard equation yields a really good approximation for the complex polarizability only for the small collision model considered by Gross and Sack. In the case of large inertial parameter values it is emphasized by means of plots of the complex polarizability that such an approximation always exhibits behavior characteristic of a sharply resonant system, i.e., a pronounced absorption peak well in excess of the Debye peak and a strongly negative real part, while the exact complex polarizability spectrum for the same parameter values merely displays inertia corrected Debye relaxation. Therefore, an explanation of the resonant term other than that based on a Rocard equation with a large inertial parameter must be sought as that equation strictly applies to inertia corrected Debye (heavily damped) relaxation only. The application of the itinerant oscillator model and the three variable Mori theory to the problem is discussed in view of this conclusion.
Müller, Andreas; Hochrath, Katrin; Stroeder, Jonas; Hittatiya, Kanishka; Schneider, Günther; Lammert, Frank; Buecker, Arno; Fries, Peter
2017-01-01
Recently, clinical studies demonstrated that magnetic resonance relaxometry with determination of relaxation times T1 and T2(⁎) may aid in staging and management of liver fibrosis in patients suffering from viral hepatitis and steatohepatitis. In the present study we investigated T1 and T2(⁎) in different models of liver fibrosis to compare alternate pathophysiologies in their effects on relaxation times and to further develop noninvasive quantification methods of liver fibrosis. MRI was performed with a fast spin echo sequence for measurement of T1 and a multigradient echo sequence for determination of T2(⁎). Toxic liver fibrosis was induced by injections of carbon tetrachloride (1.4 mL CCl4 per kg bodyweight and week, for 3 or 6 weeks) in BALB/cJ mice. Chronic sclerosing cholangitis was mimicked using the ATP-binding cassette transporter B4 knockout (Abcb4 (-/-)) mouse model. Untreated BALB/cJ mice served as controls. To assess hepatic fibrosis, we ascertained collagen contents and fibrosis scores after Sirius red staining. T1 and T2(⁎) correlate differently to disease severity and etiology of liver fibrosis. T2(⁎) shows significant decrease correlating with fibrosis in CCl4 treated animals, while demonstrating significant increase with disease severity in Abcb4 (-/-) mice. Measurements of T1 and T2(⁎) may therefore facilitate discrimination between different stages and causes of liver fibrosis.
Müller, Andreas; Hochrath, Katrin; Stroeder, Jonas; Hittatiya, Kanishka; Schneider, Günther; Lammert, Frank; Buecker, Arno
2017-01-01
Recently, clinical studies demonstrated that magnetic resonance relaxometry with determination of relaxation times T1 and T2⁎ may aid in staging and management of liver fibrosis in patients suffering from viral hepatitis and steatohepatitis. In the present study we investigated T1 and T2⁎ in different models of liver fibrosis to compare alternate pathophysiologies in their effects on relaxation times and to further develop noninvasive quantification methods of liver fibrosis. MRI was performed with a fast spin echo sequence for measurement of T1 and a multigradient echo sequence for determination of T2⁎. Toxic liver fibrosis was induced by injections of carbon tetrachloride (1.4 mL CCl4 per kg bodyweight and week, for 3 or 6 weeks) in BALB/cJ mice. Chronic sclerosing cholangitis was mimicked using the ATP-binding cassette transporter B4 knockout (Abcb4 −/−) mouse model. Untreated BALB/cJ mice served as controls. To assess hepatic fibrosis, we ascertained collagen contents and fibrosis scores after Sirius red staining. T1 and T2⁎ correlate differently to disease severity and etiology of liver fibrosis. T2⁎ shows significant decrease correlating with fibrosis in CCl4 treated animals, while demonstrating significant increase with disease severity in Abcb4 −/− mice. Measurements of T1 and T2⁎ may therefore facilitate discrimination between different stages and causes of liver fibrosis. PMID:28194423
Andreas Müller
2017-01-01
Full Text Available Recently, clinical studies demonstrated that magnetic resonance relaxometry with determination of relaxation times T1 and T2⁎ may aid in staging and management of liver fibrosis in patients suffering from viral hepatitis and steatohepatitis. In the present study we investigated T1 and T2⁎ in different models of liver fibrosis to compare alternate pathophysiologies in their effects on relaxation times and to further develop noninvasive quantification methods of liver fibrosis. MRI was performed with a fast spin echo sequence for measurement of T1 and a multigradient echo sequence for determination of T2⁎. Toxic liver fibrosis was induced by injections of carbon tetrachloride (1.4 mL CCl4 per kg bodyweight and week, for 3 or 6 weeks in BALB/cJ mice. Chronic sclerosing cholangitis was mimicked using the ATP-binding cassette transporter B4 knockout (Abcb4 -/- mouse model. Untreated BALB/cJ mice served as controls. To assess hepatic fibrosis, we ascertained collagen contents and fibrosis scores after Sirius red staining. T1 and T2⁎ correlate differently to disease severity and etiology of liver fibrosis. T2⁎ shows significant decrease correlating with fibrosis in CCl4 treated animals, while demonstrating significant increase with disease severity in Abcb4 -/- mice. Measurements of T1 and T2⁎ may therefore facilitate discrimination between different stages and causes of liver fibrosis.
Modeling the pulse shape of Q-switched lasers to account for terminal-level relaxation
Zeng Qin-Yong; Wan Yong; Xiong Ji-Chuan; Zhu Da-Yong
2011-01-01
To account for the effect of lower-level relaxation, we have derived a characteristic equation for describing the laser pulse from the modified rate equations for Q-switched lasers. The pulse temporal profile is related to the ratio of the lower-level lifetime to the cavity lifetime and the number of times the population inversion density is above the threshold. By solving the coupled rate equations numerically, the effect of terminal-level lifetime on pulse temporal behaviour is analysed. The mode is applied to the case of a diode-pumped Nd:YAG laser that is passively Q-switched by a Cr4+:YAG absorber. Theoretical results show good agreement with the experiments.
Vibrational relaxation of NO stretching modes in ferrous NO and ferric NO in model heme
Park, Jaeheung; Lee, Taegon; Lim, Manho
2013-08-01
Femtosecond IR-pump-IR-probe spectroscopy was used to measure the vibrational lifetimes (T1) of NO stretching modes of ferrous NO near 1600 cm-1 and ferric NO near 1900 cm-1 at room temperature. The T1 of NO bound to the heme, ranging from 3.5 to 34 ps, is much shorter in ferrous NO. The vibrational relaxation (VR) of NO was independent of solvent used and excess imidazole concentration, suggesting that intramolecular VR into the internal vibrational modes of the probed molecule may be the dominant pathway for VR of the bound NO. With estimated T1 of the bound NO, we simulated transient spectra of NO bound to ferrous hemoglobin (HbII) after photodeligation of HbIINO and discussed the influence of the hot band on the determination of the dynamics of geminate rebinding of NO to HbII using the change in the magnitude of the fundamental band.
Folk, R; Holovatch, Yu; Moser, G
2009-03-01
We calculate the relaxational dynamical critical behavior of systems of O(n_{ parallel}) plus sign in circleO(n_{ perpendicular}) symmetry including conservation of magnetization by renormalization group theory within the minimal subtraction scheme in two-loop order. Within the stability region of the Heisenberg fixed point and the biconical fixed point, strong dynamical scaling holds, with the asymptotic dynamical critical exponent z=2varphinu-1 , where varphi is the crossover exponent and nu the exponent of the correlation length. The critical dynamics at n_{ parallel}=1 and n_{ perpendicular}=2 is governed by a small dynamical transient exponent leading to nonuniversal nonasymptotic dynamical behavior. This may be seen, e.g., in the temperature dependence of the magnetic transport coefficients.
Circadian clocks and breast cancer
Blakeman, Victoria; Jack L. Williams; Meng, Qing-Jun; Streuli, Charles H
2016-01-01
Circadian clocks respond to environmental time cues to coordinate 24-hour oscillations in almost every tissue of the body. In the breast, circadian clocks regulate the rhythmic expression of numerous genes. Disrupted expression of circadian genes can alter breast biology and may promote cancer. Here we overview circadian mechanisms, and the connection between the molecular clock and breast biology. We describe how disruption of circadian genes contributes to cancer via multiple mechanisms, an...
Circadian clocks are designed optimally
Hasegawa, Yoshihiko
2014-01-01
Circadian rhythms are acquired through evolution to increase the chances for survival by synchronizing to the daylight cycle. Reliable synchronization is realized through two trade-off properties: regularity to keep time precisely, and entrainability to synchronize the internal time with daylight. Since both properties have been tuned through natural selection, their adaptation can be formalized in the framework of mathematical optimization. By using a succinct model, we found that simultaneous optimization of regularity and entrainability entails inherent features of the circadian mechanism irrespective of model details. At the behavioral level we discovered the existence of a dead zone, a time during which light pulses neither advance nor delay the clock. At the molecular level we demonstrate the role-sharing of two light inputs, phase advance and delay, as is well observed in mammals. We also reproduce the results of phase-controlling experiments and predict molecular elements responsible for the clockwork...
Marshall, David C; Hill, Kathy B R; Moulds, Max; Vanderpool, Dan; Cooley, John R; Mohagan, Alma B; Simon, Chris
2016-01-01
Dated phylogenetic trees are important for studying mechanisms of diversification, and molecular clocks are important tools for studies of organisms lacking good fossil records. However, studies have begun to identify problems in molecular clock dates caused by uncertainty of the modeled molecular substitution process. Here we explore Bayesian relaxed-clock molecular dating while studying the biogeography of ca. 200 species from the global cicada tribe Cicadettini. Because the available fossils are few and uninformative, we calibrate our trees in part with a cytochrome oxidase I (COI) clock prior encompassing a range of literature estimates for arthropods. We show that tribe-level analyses calibrated solely with the COI clock recover extremely old dates that conflict with published estimates for two well-studied New Zealand subclades within Cicadettini. Additional subclade analyses suggest that COI relaxed-clock rates and maximum-likelihood branch lengths become inflated relative to EF-1[Formula: see text] intron and exon rates and branch lengths as clade age increases. We present corrected estimates derived from: (i) an extrapolated EF-1[Formula: see text] exon clock derived from COI-calibrated analysis within the largest New Zealand subclade; (ii) post hoc scaling of the tribe-level chronogram using results from subclade analyses; and (iii) exploitation of a geological calibration point associated with New Caledonia. We caution that considerable uncertainty is generated due to dependence of substitution estimates on both the taxon sample and the choice of model, including gamma category number and the choice of empirical versus estimated base frequencies. Our results suggest that diversification of the tribe Cicadettini commenced in the early- to mid-Cenozoic and continued with the development of open, arid habitats in Australia and worldwide. We find that Cicadettini is a rare example of a global terrestrial animal group with an Australasian origin, with all non
Clock measurements to improve the geopotential determination
Lion, Guillaume; Panet, Isabelle; Delva, Pacôme; Wolf, Peter; Bize, Sébastien; Guerlin, Christine
2017-04-01
Comparisons between optical clocks with an accuracy and stability approaching the 10-18 in term of relative frequency shift are opening new perspectives for the direct determination of geopotential at a centimeter-level accuracy in geoid height. However, so far detailed quantitative estimates of the possible improvement in geoid determination when adding such clock measurements to existing data are lacking. In this context, the present work aims at evaluating the contribution of this new kind of direct measurements in determining the geopotential at high spatial resolution (10 km). We consider the Massif Central area, marked by smooth, moderate altitude mountains and volcanic plateaus leading to variations of the gravitational field over a range of spatial scales. In such type of region, the scarcity of gravity data is an important limitation in deriving accurate high resolution geopotential models. We summarize our methodology to assess the contribution of clock data in the geopotential recovery, in combination with ground gravity measurements. We sample synthetic gravity and disturbing potential data from a spherical harmonics geopotential model, and a topography model, up to 10 km resolution; we also build a potential control grid. From the synthetic data, we estimate the disturbing potential by least-squares collocation. Finally, we assess the quality of the reconstructed potential by comparing it to that of the control grid. We show that adding only a few clock data reduces the reconstruction bias significantly and improves the standard deviation by a factor 3. We discuss the role of different parameters, such as the effect of the data coverage and data quality on these results, the trade-off between the measurement noise level and the number of data, and the optimization of the clock data network.
Cellular Clocks : Coupled Circadian Dispatch and Cell Division Cycles
Merrow, Martha; Roenneberg, Till
2004-01-01
Gating of cell division by the circadian clock is well known, yet its mechanism is little understood. Genetically tractable model systems have led to new hypotheses and questions concerning the coupling of these two cellular cycles.
Cellular Clocks : Coupled Circadian Dispatch and Cell Division Cycles
Merrow, Martha; Roenneberg, Till
2004-01-01
Gating of cell division by the circadian clock is well known, yet its mechanism is little understood. Genetically tractable model systems have led to new hypotheses and questions concerning the coupling of these two cellular cycles.
Complementary approaches to understanding the plant circadian clock
Akman, Ozgur E; Loewe, Laurence; Troein, Carl; 10.4204/EPTCS.19.1
2010-01-01
Circadian clocks are oscillatory genetic networks that help organisms adapt to the 24-hour day/night cycle. The clock of the green alga Ostreococcus tauri is the simplest plant clock discovered so far. Its many advantages as an experimental system facilitate the testing of computational predictions. We present a model of the Ostreococcus clock in the stochastic process algebra Bio-PEPA and exploit its mapping to different analysis techniques, such as ordinary differential equations, stochastic simulation algorithms and model-checking. The small number of molecules reported for this system tests the limits of the continuous approximation underlying differential equations. We investigate the difference between continuous-deterministic and discrete-stochastic approaches. Stochastic simulation and model-checking allow us to formulate new hypotheses on the system behaviour, such as the presence of self-sustained oscillations in single cells under constant light conditions. We investigate how to model the timing of...
A Light Clock Satisfying the Clock Hypothesis of Special Relativity
West, Joseph
2007-01-01
The design of the FMEL, a floor-mirrored Einstein-Langevin "light clock", is introduced. The clock provides a physically intuitive manner to calculate and visualize the time dilation effects for a spatially extended set of observers (an accelerated "frame") undergoing unidirectional acceleration or observers on a rotating cylinder of constant…
Clocks and cardiovascular function
McLoughlin, Sarah C.; Haines, Philip; FitzGerald, Garret A.
2016-01-01
Circadian clocks in central and peripheral tissues enable the temporal synchronization and organization of molecular and physiological processes of rhythmic animals, allowing optimum functioning of cells and organisms at the most appropriate time of day. Disruption of circadian rhythms, from external or internal forces, leads to widespread biological disruption and is postulated to underlie many human conditions, such as the incidence and timing of cardiovascular disease. Here, we describe in vivo and in vitro methodology relevant to studying the role of circadian rhythms in cardiovascular function and dysfunction PMID:25707279
Cryptochrome mediates light-dependent magnetosensitivity of Drosophila's circadian clock.
Taishi Yoshii
2009-04-01
Full Text Available Since 1960, magnetic fields have been discussed as Zeitgebers for circadian clocks, but the mechanism by which clocks perceive and process magnetic information has remained unknown. Recently, the radical-pair model involving light-activated photoreceptors as magnetic field sensors has gained considerable support, and the blue-light photoreceptor cryptochrome (CRY has been proposed as a suitable molecule to mediate such magnetosensitivity. Since CRY is expressed in the circadian clock neurons and acts as a critical photoreceptor of Drosophila's clock, we aimed to test the role of CRY in magnetosensitivity of the circadian clock. In response to light, CRY causes slowing of the clock, ultimately leading to arrhythmic behavior. We expected that in the presence of applied magnetic fields, the impact of CRY on clock rhythmicity should be altered. Furthermore, according to the radical-pair hypothesis this response should be dependent on wavelength and on the field strength applied. We tested the effect of applied static magnetic fields on the circadian clock and found that flies exposed to these fields indeed showed enhanced slowing of clock rhythms. This effect was maximal at 300 muT, and reduced at both higher and lower field strengths. Clock response to magnetic fields was present in blue light, but absent under red-light illumination, which does not activate CRY. Furthermore, cry(b and cry(OUT mutants did not show any response, and flies overexpressing CRY in the clock neurons exhibited an enhanced response to the field. We conclude that Drosophila's circadian clock is sensitive to magnetic fields and that this sensitivity depends on light activation of CRY and on the applied field strength, consistent with the radical pair mechanism. CRY is widespread throughout biological systems and has been suggested as receptor for magnetic compass orientation in migratory birds. The present data establish the circadian clock of Drosophila as a model system
Use of Very Stable Clocks in Satellite Geodesy
Hugentobler, Urs; Romanyuk, Tetyana
2016-07-01
Time and frequency play an essential role in satellite geodesy and navigation. Global Navigation Satellite Systems (GNSS) rely on precise measurements of signal travel times. The satellite and receiver clocks involved in measuring this time interval need to be synchronized at the picosecond level. The concept of GNSS allows for an epoch-wise synchronization of space and ground clocks, a feature which is consequently used in satellite geodesy by estimating epoch-wise clock corrections for all clocks in the system, either explicitly or implicitly by forming double differences. Ultra-stable clocks allow to estimate only few parameters for each clock, e.g., offset and drift. The much reduced number of parameters should stabilize GNSS solutions, e.g., tracking network station coordinates. On the other hand systematic errors, e.g., from troposphere or orbit modeling deficiencies or temperature induced hardware delay variations may systematically affect the solutions. The presentation shows trade-offs of modelling higly stable clocks and negative impact of error sources based on simulations.
Kummer, E. E.; Siegel, Edward Carl-Ludwig
2011-03-01
Clock-model Archimedes [http://linkage.rockeller.edu/ wli/moved.8.04/ 1fnoise/ index. ru.html] HYPERBOLICITY inevitability throughout physics/pure-maths: Newton-law F=ma, Heisenberg and classical uncertainty-principle=Parseval/Plancherel-theorems causes FUZZYICS definition: (so miscalled) "complexity" = UTTER-SIMPLICITY!!! Watkins[www.secamlocal.ex.ac.uk/people/staff/mrwatkin/]-Hubbard[World According to Wavelets (96)-p.14!]-Franklin[1795]-Fourier[1795;1822]-Brillouin[1922] dual/inverse-space(k,w) analysis key to Fourier-unification in Archimedes hyperbolicity inevitability progress up Siegel cognition hierarchy-of-thinking (HoT): data-info.-know.-understand.-meaning-...-unity-simplicity = FUZZYICS!!! Frohlich-Mossbauer-Goldanskii-del Guidice [Nucl.Phys.B:251,375(85);275,185 (86)]-Young [arXiv-0705.4678y2, (5/31/07] theory of health/life=aqueous-electret/ ferroelectric protoplasm BEC = Archimedes-Siegel [Schrodinger Cent.Symp.(87); Symp.Fractals, MRS Fall Mtg.(89)-5-pprs] 1/w-"noise" Zipf-law power-spectrum hyperbolicity INEVITABILITY= Chi; Dirac delta-function limit w=0 concentration= BEC = Chi-Quong.
Cuesta, Ines H; Lahiri, Kajori; Lopez-Olmeda, Jose Fernando; Loosli, Felix; Foulkes, Nicholas S; Vallone, Daniela
2014-05-01
One key challenge for the field of chronobiology is to identify how circadian clock function emerges during early embryonic development. Teleosts such as the zebrafish are ideal models for studying circadian clock ontogeny since the entire process of development occurs ex utero in an optically transparent chorion. Medaka (Oryzias latipes) represents another powerful fish model for exploring early clock function with, like the zebrafish, many tools available for detailed genetic analysis. However, to date there have been no reports documenting circadian clock gene expression during medaka development. Here we have characterized the expression of key clock genes in various developmental stages and in adult tissues of medaka. As previously reported for other fish, light dark cycles are required for the emergence of clock gene expression rhythms in this species. While rhythmic expression of per and cry genes is detected very early during development and seems to be light driven, rhythmic clock and bmal expression appears much later around hatching time. Furthermore, the maturation of clock function seems to correlate with the appearance of rhythmic expression of these positive elements of the clock feedback loop. By accelerating development through elevated temperatures or by artificially removing the chorion, we show an earlier onset of rhythmicity in clock and bmal expression. Thus, differential maturation of key elements of the medaka clock mechanism depends on the developmental stage and the presence of the chorion.
Differential clock comparisons with phase-locked local oscillators
Hume, David B
2015-01-01
We develop protocols that circumvent the laser noise limit in the stability of optical clock comparisons by synchronous probing of two clocks using phase-locked local oscillators. This allows for probe times longer than the laser coherence time, avoids the Dick effect, and supports Heisenberg-limited scaling of measurement precision. We present a model for such frequency comparisons and develop numerical simulations of the protocol with realistic noise sources. This provides a route to reduce frequency ratio measurement durations by more than an order of magnitude as clock inaccuracies reach 1x10^-18.
Standard Clock in Primordial Density Perturbations and Cosmic Microwave Background
Chen, Xingang
2014-01-01
Standard Clocks in the primordial epoch leave a special type of features in the primordial perturbations, which can be used to directly measure the scale factor of the primordial universe as a function of time a(t), thus discriminating between inflation and alternatives. We have started to search for such signals in the Planck 2013 data using the key predictions of the Standard Clock. In this Letter, we present an interesting candidate with the inflation fingerprint. Motivated by this candidate, we construct and compute full Standard Clock models and use the more complete prediction to make more extensive comparison with data.
Rethinking transcriptional activation in the Arabidopsis circadian clock.
Fogelmark, Karl; Troein, Carl
2014-07-01
Circadian clocks are biological timekeepers that allow living cells to time their activity in anticipation of predictable daily changes in light and other environmental factors. The complexity of the circadian clock in higher plants makes it difficult to understand the role of individual genes or molecular interactions, and mathematical modelling has been useful in guiding clock research in model organisms such as Arabidopsis thaliana. We present a model of the circadian clock in Arabidopsis, based on a large corpus of published time course data. It appears from experimental evidence in the literature that most interactions in the clock are repressive. Hence, we remove all transcriptional activation found in previous models of this system, and instead extend the system by including two new components, the morning-expressed activator RVE8 and the nightly repressor/activator NOX. Our modelling results demonstrate that the clock does not need a large number of activators in order to reproduce the observed gene expression patterns. For example, the sequential expression of the PRR genes does not require the genes to be connected as a series of activators. In the presented model, transcriptional activation is exclusively the task of RVE8. Predictions of how strongly RVE8 affects its targets are found to agree with earlier interpretations of the experimental data, but generally we find that the many negative feedbacks in the system should discourage intuitive interpretations of mutant phenotypes. The dynamics of the clock are difficult to predict without mathematical modelling, and the clock is better viewed as a tangled web than as a series of loops.
Rethinking transcriptional activation in the Arabidopsis circadian clock.
Karl Fogelmark
2014-07-01
Full Text Available Circadian clocks are biological timekeepers that allow living cells to time their activity in anticipation of predictable daily changes in light and other environmental factors. The complexity of the circadian clock in higher plants makes it difficult to understand the role of individual genes or molecular interactions, and mathematical modelling has been useful in guiding clock research in model organisms such as Arabidopsis thaliana. We present a model of the circadian clock in Arabidopsis, based on a large corpus of published time course data. It appears from experimental evidence in the literature that most interactions in the clock are repressive. Hence, we remove all transcriptional activation found in previous models of this system, and instead extend the system by including two new components, the morning-expressed activator RVE8 and the nightly repressor/activator NOX. Our modelling results demonstrate that the clock does not need a large number of activators in order to reproduce the observed gene expression patterns. For example, the sequential expression of the PRR genes does not require the genes to be connected as a series of activators. In the presented model, transcriptional activation is exclusively the task of RVE8. Predictions of how strongly RVE8 affects its targets are found to agree with earlier interpretations of the experimental data, but generally we find that the many negative feedbacks in the system should discourage intuitive interpretations of mutant phenotypes. The dynamics of the clock are difficult to predict without mathematical modelling, and the clock is better viewed as a tangled web than as a series of loops.
Equivalent Relaxations of Optimal Power Flow
Bose, S; Low, SH; Teeraratkul, T; Hassibi, B
2015-03-01
Several convex relaxations of the optimal power flow (OPF) problem have recently been developed using both bus injection models and branch flow models. In this paper, we prove relations among three convex relaxations: a semidefinite relaxation that computes a full matrix, a chordal relaxation based on a chordal extension of the network graph, and a second-order cone relaxation that computes the smallest partial matrix. We prove a bijection between the feasible sets of the OPF in the bus injection model and the branch flow model, establishing the equivalence of these two models and their second-order cone relaxations. Our results imply that, for radial networks, all these relaxations are equivalent and one should always solve the second-order cone relaxation. For mesh networks, the semidefinite relaxation and the chordal relaxation are equally tight and both are strictly tighter than the second-order cone relaxation. Therefore, for mesh networks, one should either solve the chordal relaxation or the SOCP relaxation, trading off tightness and the required computational effort. Simulations are used to illustrate these results.
Kamm, James R [Los Alamos National Laboratory; Shashkov, Mikhail J [Los Alamos National Laboratory
2009-01-01
Despite decades of development, Lagrangian hydrodynamics of strengthfree materials presents numerous open issues, even in one dimension. We focus on the problem of closing a system of equations for a two-material cell under the assumption of a single velocity model. There are several existing models and approaches, each possessing different levels of fidelity to the underlying physics and each exhibiting unique features in the computed solutions. We consider the case in which the change in heat in the constituent materials in the mixed cell is assumed equal. An instantaneous pressure equilibration model for a mixed cell can be cast as four equations in four unknowns, comprised of the updated values of the specific internal energy and the specific volume for each of the two materials in the mixed cell. The unique contribution of our approach is a physics-inspired, geometry-based model in which the updated values of the sub-cell, relaxing-toward-equilibrium constituent pressures are related to a local Riemann problem through an optimization principle. This approach couples the modeling problem of assigning sub-cell pressures to the physics associated with the local, dynamic evolution. We package our approach in the framework of a standard predictor-corrector time integration scheme. We evaluate our model using idealized, two material problems using either ideal-gas or stiffened-gas equations of state and compare these results to those computed with the method of Tipton and with corresponding pure-material calculations.
Ammar, Sami; Pernaudat, Guillaume; Trépanier, Jean-Yves
2017-08-01
The interdependence of surface tension and density ratio is a weakness of pseudo-potential based lattice Boltzmann models (LB). In this paper, we propose a 3D multi-relaxation time (MRT) model for multiphase flows at large density ratios. The proposed model is capable of adjusting the surface tension independently of the density ratio. We also present the 3D macroscopic equations recovered by the proposed forcing scheme. A high order of isotropy for the interaction force is used to reduce the amplitude of spurious currents. The proposed 3D-MRT model is validated by verifying Laplace's law and by analyzing its thermodynamic consistency and the oscillation period of a deformed droplet. The model is then applied to the simulation of the impact of a droplet on a dry surface. Impact dynamics are determined and the maximum spread factor calculated for different Reynolds and Weber numbers. The numerical results are in agreement with data published in the literature. The influence of surface wettability on the spread factor is also investigated. Finally, our 3D-MRT model is applied to the simulation of the impact of a droplet on a wet surface. The propagation of transverse waves is observed on the liquid surface.
Crosstalk of clock gene expression and autophagy in aging
Kalfalah, Faiza; Janke, Linda; Schiavi, Alfonso; Tigges, Julia; Ix, Alexander; Ventura, Natascia; Boege, Fritz; Reinke, Hans
2016-01-01
Autophagy and the circadian clock counteract tissue degeneration and support longevity in many organisms. Accumulating evidence indicates that aging compromises both the circadian clock and autophagy but the mechanisms involved are unknown. Here we show that the expression levels of transcriptional repressor components of the circadian oscillator, most prominently the human Period homologue PER2, are strongly reduced in primary dermal fibroblasts from aged humans, while raising the expression of PER2 in the same cells partially restores diminished autophagy levels. The link between clock gene expression and autophagy is corroborated by the finding that the circadian clock drives cell-autonomous, rhythmic autophagy levels in immortalized murine fibroblasts, and that siRNA-mediated downregulation of PER2 decreases autophagy levels while leaving core clock oscillations intact. Moreover, the Period homologue lin-42 regulates autophagy and life span in the nematode Caenorhabditis elegans, suggesting an evolutionarily conserved role for Period proteins in autophagy control and aging. Taken together, this study identifies circadian clock proteins as set-point regulators of autophagy and puts forward a model, in which age-related changes of clock gene expression promote declining autophagy levels. PMID:27574892
Diurnal oscillations of soybean circadian clock and drought responsive genes.
Juliana Marcolino-Gomes
Full Text Available Rhythms produced by the endogenous circadian clock play a critical role in allowing plants to respond and adapt to the environment. While there is a well-established regulatory link between the circadian clock and responses to abiotic stress in model plants, little is known of the circadian system in crop species like soybean. This study examines how drought impacts diurnal oscillation of both drought responsive and circadian clock genes in soybean. Drought stress induced marked changes in gene expression of several circadian clock-like components, such as LCL1-, GmELF4- and PRR-like genes, which had reduced expression in stressed plants. The same conditions produced a phase advance of expression for the GmTOC1-like, GmLUX-like and GmPRR7-like genes. Similarly, the rhythmic expression pattern of the soybean drought-responsive genes DREB-, bZIP-, GOLS-, RAB18- and Remorin-like changed significantly after plant exposure to drought. In silico analysis of promoter regions of these genes revealed the presence of cis-elements associated both with stress and circadian clock regulation. Furthermore, some soybean genes with upstream ABRE elements were responsive to abscisic acid treatment. Our results indicate that some connection between the drought response and the circadian clock may exist in soybean since (i drought stress affects gene expression of circadian clock components and (ii several stress responsive genes display diurnal oscillation in soybeans.
Hunting for dark matter with GPS and atomic clocks
Derevianko, Andrei
2015-05-01
Atomic clocks are arguably the most accurate scientific instruments ever build. Modern clocks are astonishing timepieces guaranteed to keep time within a second over the age of the Universe. The cosmological applications of atomic clocks so far have been limited to searches of the uniform-in-time drift of fundamental constants. We point out that a transient in time change of fundamental constants (translating into clocks being sped up or slowed down) can be induced by dark matter objects that have large spatial extent, and are built from light non-Standard Model fields. The stability of this type of dark matter can be dictated by the topological reasons. We argue that correlated networks of atomic clocks, such as atomic clocks onboard satellites of the GPS constellation, can be used as a powerful tool to search for the topological defect dark matter. In other words, one could envision using GPS as a 50,000 km-aperture dark-matter detector. Similar arguments apply to terrestrial networks of atomic clocks. Details:
Redox rhythm reinforces the circadian clock to gate immune response.
Zhou, Mian; Wang, Wei; Karapetyan, Sargis; Mwimba, Musoki; Marqués, Jorge; Buchler, Nicolas E; Dong, Xinnian
2015-07-23
Recent studies have shown that in addition to the transcriptional circadian clock, many organisms, including Arabidopsis, have a circadian redox rhythm driven by the organism's metabolic activities. It has been hypothesized that the redox rhythm is linked to the circadian clock, but the mechanism and the biological significance of this link have only begun to be investigated. Here we report that the master immune regulator NPR1 (non-expressor of pathogenesis-related gene 1) of Arabidopsis is a sensor of the plant's redox state and regulates transcription of core circadian clock genes even in the absence of pathogen challenge. Surprisingly, acute perturbation in the redox status triggered by the immune signal salicylic acid does not compromise the circadian clock but rather leads to its reinforcement. Mathematical modelling and subsequent experiments show that NPR1 reinforces the circadian clock without changing the period by regulating both the morning and the evening clock genes. This balanced network architecture helps plants gate their immune responses towards the morning and minimize costs on growth at night. Our study demonstrates how a sensitive redox rhythm interacts with a robust circadian clock to ensure proper responsiveness to environmental stimuli without compromising fitness of the organism.
Maximum likelihood molecular clock comb: analytic solutions.
Chor, Benny; Khetan, Amit; Snir, Sagi
2006-04-01
Maximum likelihood (ML) is increasingly used as an optimality criterion for selecting evolutionary trees, but finding the global optimum is a hard computational task. Because no general analytic solution is known, numeric techniques such as hill climbing or expectation maximization (EM), are used in order to find optimal parameters for a given tree. So far, analytic solutions were derived only for the simplest model--three taxa, two state characters, under a molecular clock. Four taxa rooted trees have two topologies--the fork (two subtrees with two leaves each) and the comb (one subtree with three leaves, the other with a single leaf). In a previous work, we devised a closed form analytic solution for the ML molecular clock fork. In this work, we extend the state of the art in the area of analytic solutions ML trees to the family of all four taxa trees under the molecular clock assumption. The change from the fork topology to the comb incurs a major increase in the complexity of the underlying algebraic system and requires novel techniques and approaches. We combine the ultrametric properties of molecular clock trees with the Hadamard conjugation to derive a number of topology dependent identities. Employing these identities, we substantially simplify the system of polynomial equations. We finally use tools from algebraic geometry (e.g., Gröbner bases, ideal saturation, resultants) and employ symbolic algebra software to obtain analytic solutions for the comb. We show that in contrast to the fork, the comb has no closed form solutions (expressed by radicals in the input data). In general, four taxa trees can have multiple ML points. In contrast, we can now prove that under the molecular clock assumption, the comb has a unique (local and global) ML point. (Such uniqueness was previously shown for the fork.).
Setting the clock--by nature: circadian rhythm in the fruitfly Drosophila melanogaster.
Peschel, Nicolai; Helfrich-Förster, Charlotte
2011-05-20
Nowadays humans mainly rely on external, unnatural clocks such as of cell phones and alarm clocks--driven by circuit boards and electricity. Nevertheless, our body is under the control of another timer firmly anchored in our genes. This evolutionary very old biological clock drives most of our physiology and behavior. The genes that control our internal clock are conserved among most living beings. One organism that shares this ancient clock mechanism with us humans is the fruitfly Drosophila melanogaster. Since it turned out that Drosophila is an excellent model, it is no surprise that its clock is very well and intensely investigated. In the following review we want to display an overview of the current understanding of Drosophila's circadian clock. Copyright © 2011 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.
CSAC Characterization and Its Impact on GNSS Clock Augmentation Performance
Fernández, Enric; Calero, David; Parés, M. Eulàlia
2017-01-01
Chip Scale Atomic Clocks (CSAC) are recently-developed electronic instruments that, when used together with a Global Navigation Satellite Systems (GNSS) receiver, help improve the performance of GNSS navigation solutions in certain conditions (i.e., low satellite visibility). Current GNSS receivers include a Temperature Compensated Cristal Oscillator (TCXO) clock characterized by a short-term stability (τ = 1 s) of 10−9 s that leads to an error of 0.3 m in pseudorange measurements. The CSAC can achieve a short-term stability of 2.5 × 10−12 s, which implies a range error of 0.075 m, making for an 87.5% improvement over TCXO. Replacing the internal TCXO clock of GNSS receivers with a higher frequency stability clock such as a CSAC oscillator improves the navigation solution in terms of low satellite visibility positioning accuracy, solution availability, signal recovery (holdover), multipath and jamming mitigation and spoofing attack detection. However, CSAC suffers from internal systematic instabilities and errors that should be minimized if optimal performance is desired. Hence, for operating CSAC at its best, the deterministic errors from the CSAC need to be properly modelled. Currently, this modelling is done by determining and predicting the clock frequency stability (i.e., clock bias and bias rate) within the positioning estimation process. The research presented in this paper aims to go a step further, analysing the correlation between temperature and clock stability noise and the impact of its proper modelling in the holdover recovery time and in the positioning performance. Moreover, it shows the potential of fine clock coasting modelling. With the proposed model, an improvement in vertical positioning precision of around 50% with only three satellites can be achieved. Moreover, an increase in the navigation solution availability is also observed, a reduction of holdover recovery time from dozens of seconds to only a few can be achieved. PMID:28216600
CSAC Characterization and Its Impact on GNSS Clock Augmentation Performance
Enric Fernández
2017-02-01
Full Text Available Chip Scale Atomic Clocks (CSAC are recently-developed electronic instruments that, when used together with a Global Navigation Satellite Systems (GNSS receiver, help improve the performance of GNSS navigation solutions in certain conditions (i.e., low satellite visibility. Current GNSS receivers include a Temperature Compensated Cristal Oscillator (TCXO clock characterized by a short-term stability (τ = 1 s of 10−9 s that leads to an error of 0.3 m in pseudorange measurements. The CSAC can achieve a short-term stability of 2.5 × 10−12 s, which implies a range error of 0.075 m, making for an 87.5% improvement over TCXO. Replacing the internal TCXO clock of GNSS receivers with a higher frequency stability clock such as a CSAC oscillator improves the navigation solution in terms of low satellite visibility positioning accuracy, solution availability, signal recovery (holdover, multipath and jamming mitigation and spoofing attack detection. However, CSAC suffers from internal systematic instabilities and errors that should be minimized if optimal performance is desired. Hence, for operating CSAC at its best, the deterministic errors from the CSAC need to be properly modelled. Currently, this modelling is done by determining and predicting the clock frequency stability (i.e., clock bias and bias rate within the positioning estimation process. The research presented in this paper aims to go a step further, analysing the correlation between temperature and clock stability noise and the impact of its proper modelling in the holdover recovery time and in the positioning performance. Moreover, it shows the potential of fine clock coasting modelling. With the proposed model, an improvement in vertical positioning precision of around 50% with only three satellites can be achieved. Moreover, an increase in the navigation solution availability is also observed, a reduction of holdover recovery time from dozens of seconds to only a few can be achieved.
Using a transportable optical clock for chronometric levelling
Lisdat, Christian; Sterr, Uwe; Koller, Silvio; Grotti, Jacopo; Vogt, Stefan; Häfner, Sebastian; Herbers, Sofia; Al-Masoudi, Ali
2016-07-01
With their supreme accuracy and precision, optical clocks in combination with new methods of long-distance frequency transfer can be used to determine height differences by measuring the gravitational red shift between two clocks without accumulation of measurement errors, as in classical levelling. We are developing transportable optical clocks for this purpose that will also serve for the technology development regarding optical clocks in Space and for international comparisons between optical clocks that cannot be linked with sufficient accuracy otherwise. In this talk we will focus on the transportable strontium lattice clock that we are developing and its first evaluation. Presently, we achieve a fractional frequency instability of 3 × 10^{-17} after 1000 s averaging time, which is equivalent to a height resolution of 30 cm. The first uncertainty evaluation of the system yielded 7 × 10^{-17}. We expect rapid improvements to an uncertainty of a few parts in 10^{17}. The clock is now located within a car trailer, which requires compact and rugged lasers systems and physics package. Special care has been taken in the design of the ultra-frequency stable interrogation laser that has to achieve fractional frequency instabilities of considerably below 10^{-15}. Typical laboratory constructions of the reference resonator system used to pre-stabilize the laser frequency are not compatible with the requirement of transportability. In an actual levelling campaign, this clock will be connected via a stabilized optical fibre link with another, stationary frequency standard. The measured gravitational red shift will be compared with the ones calculated from potential differences derived with state of the art geodetic data and models. We will discuss the status of measurements of geodetic relevance with optical clocks and give an outlook on our next steps. This work is supported by QUEST, DFG (RTG 1729, CRC 1128), EU-FP7 (FACT) and EMRP (ITOC). The EMRP is jointly funded
Machine learning helps identify CHRONO as a circadian clock component.
Ron C Anafi
2014-04-01
Full Text Available Over the last decades, researchers have characterized a set of "clock genes" that drive daily rhythms in physiology and behavior. This arduous work has yielded results with far-reaching consequences in metabolic, psychiatric, and neoplastic disorders. Recent attempts to expand our understanding of circadian regulation have moved beyond the mutagenesis screens that identified the first clock components, employing higher throughput genomic and proteomic techniques. In order to further accelerate clock gene discovery, we utilized a computer-assisted approach to identify and prioritize candidate clock components. We used a simple form of probabilistic machine learning to integrate biologically relevant, genome-scale data and ranked genes on their similarity to known clock components. We then used a secondary experimental screen to characterize the top candidates. We found that several physically interact with known clock components in a mammalian two-hybrid screen and modulate in vitro cellular rhythms in an immortalized mouse fibroblast line (NIH 3T3. One candidate, Gene Model 129, interacts with BMAL1 and functionally represses the key driver of molecular rhythms, the BMAL1/CLOCK transcriptional complex. Given these results, we have renamed the gene CHRONO (computationally highlighted repressor of the network oscillator. Bi-molecular fluorescence complementation and co-immunoprecipitation demonstrate that CHRONO represses by abrogating the binding of BMAL1 to its transcriptional co-activator CBP. Most importantly, CHRONO knockout mice display a prolonged free-running circadian period similar to, or more drastic than, six other clock components. We conclude that CHRONO is a functional clock component providing a new layer of control on circadian molecular dynamics.
Zhen-Hua Chai; Tian-Shou Zhao
2012-01-01
In this paper,a pseudopotential-based multiplerelaxation-time lattice Boltzmann model is proposed for multicomponent/multiphase flow systems.Unlike previous models in the literature,the present model not only enables the study of multicomponent flows with different molecular weights,different viscosities and different Schmidt numbers,but also ensures that the distribution function of each component evolves on the same square lattice without invoking additional interpolations.Furthermore,the Chapman-Enskog analysis shows that the present model results in the correct hydrodynamic equations,and satisfies the indifferentiability principle.The numerical validation exercises further demonstrate that the favorable performance of the present model.
Nouh, M.R., E-mail: mragab73@yahoo.com [Department of Radiodiagnosis and Diagnostic Imaging, Faculty of Medicine, Alexandria University, 1 Kolya-El Teb St., Mahata El-Ramel, Alexandria (Egypt); Schweitzer, M.E., E-mail: mschweitzer@toh.on.ca [501 Smyth Module S-1, University of Ottawa, Ottawa, ON K1H 8L6 (Canada); Ragatte, Ravinder R., E-mail: Ravinder.regatte@nyumc.org [301 E17th Street, Department of Radiology, Hospital for Joint Disease, New York University, New York, NY 10003 (United States)
2011-11-15
. Gadoteridol is suggested on 3 T field indirect MR arthrograms. Protein had no positive effect on either SI or relaxivities in any joint model.
Chi-Castañeda, Donají
2016-01-01
Circadian rhythms are periodic patterns in biological processes that allow the organisms to anticipate changes in the environment. These rhythms are driven by the suprachiasmatic nucleus (SCN), the master circadian clock in vertebrates. At a molecular level, circadian rhythms are regulated by the so-called clock genes, which oscillate in a periodic manner. The protein products of clock genes are transcription factors that control their own and other genes’ transcription, collectively known as “clock-controlled genes.” Several brain regions other than the SCN express circadian rhythms of clock genes, including the amygdala, the olfactory bulb, the retina, and the cerebellum. Glia cells in these structures are expected to participate in rhythmicity. However, only certain types of glia cells may be called “glial clocks,” since they express PER-based circadian oscillators, which depend of the SCN for their synchronization. This contribution summarizes the current information about clock genes in glia cells, their plausible role as oscillators and their medical implications. PMID:27666286
Evans, Phillip G.; Dapino, Marcelo J.
2008-03-01
A general framework is developed to model the nonlinear magnetization and strain response of cubic magnetostrictive materials to 3-D dynamic magnetic fields and 3-D stresses. Dynamic eddy current losses and inertial stresses are modeled by coupling Maxwell's equations to Newton's second law through a nonlinear constitutive model. The constitutive model is derived from continuum thermodynamics and incorporates rate-dependent thermal effects. The framework is implemented in 1-D to describe a Tonpilz transducer in both dynamic actuation and sensing modes. The model is shown to qualitatively describe the effect of increase in magnetic hysteresis with increasing frequency, the shearing of the magnetization loops with increasing stress, and the decrease in the magnetostriction with increasing load stiffness.
Simulating Future GPS Clock Scenarios with Two Composite Clock Algorithms
2010-11-01
Alexandria, Virginia), pp. 223-242. [8] C. A. Greenhall, 2007, “A Kalman filter clock ensemble algorithm that admits measurement noise,” Metrologia ...43, S311-S321. [9] J. A. Davis, C. A. Greenhall, and P. W. Stacey, 2005, “A Kalman filter clock algorithm for use in the presence of flicker frequency modulation noise,” Metrologia , 42, 1-10.
Circadian clock components in the rat neocortex
Rath, Martin Fredensborg; Rohde, Kristian; Fahrenkrug, Jan
2013-01-01
The circadian master clock of the mammalian brain resides in the suprachiasmatic nucleus (SCN) of the hypothalamus. At the molecular level, the clock of the SCN is driven by a transcriptional/posttranslational autoregulatory network with clock gene products as core elements. Recent investigations...... have shown the presence of peripheral clocks in extra-hypothalamic areas of the central nervous system. However, knowledge on the clock gene network in the cerebral cortex is limited. We here show that the mammalian clock genes Per1, Per2, Per3, Cry1, Cry2, Bmal1, Clock, Nr1d1 and Dbp are expressed...
A new pressure relaxation closure model for one-dimensional two-material Lagrangian hydrodynamics
Rider W.J.
2011-01-01
Full Text Available We present a new model for closing a system of Lagrangian hydrodynamics equations for a two-material cell with a single velocity model. We describe a new approach that is motivated by earlier work of Delov and Sadchikov and of Goncharov and Yanilkin. Using a linearized Riemann problem to initialize volume fraction changes, we require that each material satisfy its own p dV equation, which breaks the overall energy balance in the mixed cell. To enforce this balance, we redistribute the energy discrepancy by assuming that the corresponding pressure change in each material is equal. This multiple-material model is packaged as part of a two-step time integration scheme. We compare results of our approach with other models and with corresponding pure-material calculations, on two-material test problems with ideal-gas or stiffened-gas equations of state.
Wang, Jun-Wei; Chen, Ai-Min; Zhang, Jia-Jun; Yuan, Zhan-Jiang; Zhou, Tian-Shou
2009-03-01
In circadian rhythm generation, intercellular signaling factors are shown to play a crucial role in both sustaining intrinsic cellular rhythmicity and acquiring collective behaviours across a population of circadian neurons. However, the physical mechanism behind their role remains to be fully understood. In this paper, we propose an indirectly coupled multicellular model for the synchronization of Drosophila circadian oscillators combining both intracellular and intercellular dynamics. By simulating different experimental conditions, we find that such an indirect coupling way can synchronize both heterogeneous self-sustained circadian neurons and heterogeneous mutational damped circadian neurons. Moreover, they can also be entrained to ambient light-dark (LD) cycles depending on intercellular signaling.
Simulations of Bingham plastic flows with the multiple-relaxation-time lattice Boltzmann model
Chen, SongGui; Sun, QiCheng; Jin, Feng; Liu, JianGuo
2014-03-01
Fresh cement mortar is a type of workable paste, which can be well approximated as a Bingham plastic and whose flow behavior is of major concern in engineering. In this paper, Papanastasiou's model for Bingham fluids is solved by using the multiplerelaxation-time lattice Boltzmann model (MRT-LB). Analysis of the stress growth exponent m in Bingham fluid flow simulations shows that Papanastasiou's model provides a good approximation of realistic Bingham plastics for values of m > 108. For lower values of m, Papanastasiou's model is valid for fluids between Bingham and Newtonian fluids. The MRT-LB model is validated by two benchmark problems: 2D steady Poiseuille flows and lid-driven cavity flows. Comparing the numerical results of the velocity distributions with corresponding analytical solutions shows that the MRT-LB model is appropriate for studying Bingham fluids while also providing better numerical stability. We further apply the MRT-LB model to simulate flow through a sudden expansion channel and the flow surrounding a round particle. Besides the rich flow structures obtained in this work, the dynamics fluid force on the round particle is calculated. Results show that both the Reynolds number Re and the Bingham number Bn affect the drag coefficients C D , and a drag coefficient with Re and Bn being taken into account is proposed. The relationship of Bn and the ratio of unyielded zone thickness to particle diameter is also analyzed. Finally, the Bingham fluid flowing around a set of randomly dispersed particles is simulated to obtain the apparent viscosity and velocity fields. These results help simulation of fresh concrete flowing in porous media.
Optimal Implementations for Reliable Circadian Clocks
Hasegawa, Yoshihiko; Arita, Masanori
2014-09-01
Circadian rhythms are acquired through evolution to increase the chances for survival through synchronizing with the daylight cycle. Reliable synchronization is realized through two trade-off properties: regularity to keep time precisely, and entrainability to synchronize the internal time with daylight. We find by using a phase model with multiple inputs that achieving the maximal limit of regularity and entrainability entails many inherent features of the circadian mechanism. At the molecular level, we demonstrate the role sharing of two light inputs, phase advance and delay, as is well observed in mammals. At the behavioral level, the optimal phase-response curve inevitably contains a dead zone, a time during which light pulses neither advance nor delay the clock. We reproduce the results of phase-controlling experiments entrained by two types of periodic light pulses. Our results indicate that circadian clocks are designed optimally for reliable clockwork through evolution.
Sagnac interferometry with a single atomic clock
Stevenson, R; Bishop, T; Lesanovsky, I; Fernholz, T
2015-01-01
We theoretically discuss an implementation of a Sagnac interferometer with cold atoms. In contrast to currently existing schemes our protocol does not rely on any free propagation of atoms. Instead it is based on superpositions of fully confined atoms and state-dependent transport along a closed path. Using Ramsey sequences for an atomic clock, the accumulated Sagnac phase is encoded in the resulting population imbalance between two internal (clock) states. Using minimal models for the above protocol we analytically quantify limitations arising from atomic dynamics and finite temperature. We discuss an actual implementation of the interferometer with adiabatic radio-frequency potentials that is inherently robust against common mode noise as well as phase noise from the reference oscillator.
Einstein's Clocks and Langevin's Twins
Weinstein, Galina
2012-01-01
In 1905 Einstein presented the Clock Paradox and in 1911 Paul Langevin expanded Einstein's result to human observers, the "Twin Paradox." I will explain the crucial difference between Einstein and Langevin. Einstein did not present the so-called "Twin Paradox." Later Einstein continued to speak about the clock paradox. Einstein might not have been interested in the question: what happens to the observers themselves. The reason for this could be the following; Einstein dealt with measurement procedures, clocks and measuring rods. Einstein's observers were measuring time with these clocks and measuring rods. Einstein might not have been interested in so-called biology of the observers, whether these observers were getting older, younger, or whether they have gone any other changes; these changes appeared to be out of the scope of his "Principle of relativity" or kinematics. The processes and changes occurring within observers seemed to be good for philosophical discussions. Later writers criticized Einstein's c...
History of early atomic clocks
Ramsey, N.F. [Harvard Univ., Cambridge, MA (United States). Lyman Lab. of Physics
2005-06-01
This review of the history of early atomic clocks includes early atomic beam magnetic resonance, methods of separated and successive oscillatory fields, microwave absorption, optical pumping and atomic masers. (author)
Kómár, P.; Kessler, E. M.; Bishof, M.; Jiang, L.; Sørensen, A. S.; Ye, J.; Lukin, M. D.
2014-08-01
The development of precise atomic clocks plays an increasingly important role in modern society. Shared timing information constitutes a key resource for navigation with a direct correspondence between timing accuracy and precision in applications such as the Global Positioning System. By combining precision metrology and quantum networks, we propose a quantum, cooperative protocol for operating a network of geographically remote optical atomic clocks. Using nonlocal entangled states, we demonstrate an optimal utilization of global resources, and show that such a network can be operated near the fundamental precision limit set by quantum theory. Furthermore, the internal structure of the network, combined with quantum communication techniques, guarantees security both from internal and external threats. Realization of such a global quantum network of clocks may allow construction of a real-time single international time scale (world clock) with unprecedented stability and accuracy.
Identification of relaxation parameter of a physical model of vein from fluid transient experiment
Hromádka David
2014-03-01
Full Text Available This paper presents a new fluid transient inflation experiment applied on a physical model of vein (short latex tube, 5mm diameter. Aim of experiments is assessment of wall viscous behaviour from attenuated pulsation of the tested sample. Experimental data obtained from dynamic test are compared with numerical simulation and a viscoelastic parameter of Haslach constitutive model is identified. It is verified that the viscoelasticity of wall has a greater impact to the damping of pulsation than the viscosity of water filling the sample and the attached capillary. Volume of sample depends on internal pressure measured by a pressure transducer. The maximum dissipation constitutive model of viscoelastic wall sample was employed for description of viscoelastic behaviour. Frequency of natural oscillation of pressure is determined by inertia of water column within the tested sample and attached capillary and by the tested specimen stiffness. The pressure pulsations are initiated by a sudden pressure drop at water surface.
User-Defined Clocks in the Real-Time Specification for Java
Wellings, Andy; Schoeberl, Martin
2011-01-01
This paper analyses the new user-defined clock model that is to be supported in Version 1.1 of the Real-Time Specification for Java (RTSJ). The model is a compromise between the current position, where there is no support for user-defined clocks, and a fully integrated model. The paper investigat...
The Long-term Performance Analysis for On-board Atomic Clocks of BDS
WANG Yupu
2017-02-01
Full Text Available BeiDou Navigation Satellite System (BDS has begun to provide regional services since the end of 2012. It plays an important role in analyzing the long-term performance of BDS satellite clocks in evaluating the performance of the whole system, determining and predicting satellite clock bias (SCB etc. Precise satellite clock data products derived from multi-satellite orbit determination are used to conduct the performance analysis of BDS satellite clocks. Specifically, the characteristics of SCB data are discussed by using a proposed modified median absolute deviation (MAD to preprocess original SCB data. Long-term variations of satellite clocks' phase, frequency, frequency drift and model noise level are analyzed based on the quadratic polynomial SCB model. Frequency stability of BDS satellite clocks is calculated and discussed based on Overlapping Hadamard Variance. Periodicity of BDS SCB is analyzed by using spectral analysis method. Integrating the above mentioned discussions and corresponding experiment results, the long-term performance of BDS satellite clocks is relatively comprehensively evaluated and analyzed. In addition, some valuable conclusions are obtained. For example, in the aspects of noise characteristics and clock drift, the performance of MEO satellite clocks is the best, followed by the IGSO satellite clocks, and the GEO satellite clocks' performance is the worst. The average values of noise level and frequency drift of BDS satellite clocks are respectively 0.677 ns and 1.922×10-18. There are also obvious periodic terms in BDS SCB data derived from multi-satellite orbit determination and their primary periods are approximate equal or one-half to the corresponding satellite orbit periods. The average value of frequency stability of BDS satellite clocks is 1.484×10-13.
Reconstructing ATLAS SU3 in the CMSSM and relaxed phenomenological supersymmetry models
Fowlie, Andrew
2011-01-01
Assuming that the LHC makes a positive end-point measurement indicative of low-energy supersymmetry, we examine the prospects of reconstructing the parameter values of a typical low-mass point in the framework of the Constrained MSSM and in several other supersymmetry models that have more free parameters and fewer assumptions than the CMSSM. As a case study, we consider the ATLAS SU3 benchmark point with a Bayesian approach and with a Gaussian approximation to the likelihood for the measured masses and mass differences. First we investigate the impact of the hypothetical ATLAS measurement alone and show that it significantly narrows the confidence intervals of relevant, otherwise fairly unrestricted, model parameters. Next we add information about the relic density of neutralino dark matter to the likelihood and show that this further narrows the confidence intervals. We confirm that the CMSSM has the best prospects for parameter reconstruction; its results had little dependence on our choice of prior, in co...
Maciejewski, Michał; Schöps, Sebastian; Auchmann, Bernhard; Bortot, Lorenzo; Prioli, Marco; Verweij, Arjan P.
In this paper we present the co-simulation of a PID class power converter controller and an electrical circuit by means of the waveform relaxation technique. The simulation of the controller model is characterized by a fixed-time stepping scheme reflecting its digital implementation, whereas a circuit simulation usually employs an adaptive time stepping scheme in order to account for a wide range of time constants within the circuit model. In order to maintain the characteristic of both models as well as to facilitate model replacement, we treat them separately by means of input/output relations and propose an application of a waveform relaxation algorithm. Furthermore, the maximum and minimum number of iterations of the proposed algorithm are mathematically analyzed. The concept of controller/circuit coupling is illustrated by an example of the co-simulation of a PI power converter controller and a model of the main dipole circuit of the Large Hadron Collider.
Systems biology of the clock in Neurospora crassa.
Wubei Dong
Full Text Available A model-driven discovery process, Computing Life, is used to identify an ensemble of genetic networks that describe the biological clock. A clock mechanism involving the genes white-collar-1 and white-collar-2 (wc-1 and wc-2 that encode a transcriptional activator (as well as a blue-light receptor and an oscillator frequency (frq that encodes a cyclin that deactivates the activator is used to guide this discovery process through three cycles of microarray experiments. Central to this discovery process is a new methodology for the rational design of a Maximally Informative Next Experiment (MINE, based on the genetic network ensemble. In each experimentation cycle, the MINE approach is used to select the most informative new experiment in order to mine for clock-controlled genes, the outputs of the clock. As much as 25% of the N. crassa transcriptome appears to be under clock-control. Clock outputs include genes with products in DNA metabolism, ribosome biogenesis in RNA metabolism, cell cycle, protein metabolism, transport, carbon metabolism, isoprenoid (including carotenoid biosynthesis, development, and varied signaling processes. Genes under the transcription factor complex WCC ( = WC-1/WC-2 control were resolved into four classes, circadian only (612 genes, light-responsive only (396, both circadian and light-responsive (328, and neither circadian nor light-responsive (987. In each of three cycles of microarray experiments data support that wc-1 and wc-2 are auto-regulated by WCC. Among 11,000 N. crassa genes a total of 295 genes, including a large fraction of phosphatases/kinases, appear to be under the immediate control of the FRQ oscillator as validated by 4 independent microarray experiments. Ribosomal RNA processing and assembly rather than its transcription appears to be under clock control, suggesting a new mechanism for the post-transcriptional control of clock-controlled genes.
Tissue-intrinsic dysfunction of circadian clock confers transplant arteriosclerosis.
Cheng, Bo; Anea, Ciprian B; Yao, Lin; Chen, Feng; Patel, Vijay; Merloiu, Ana; Pati, Paramita; Caldwell, R William; Fulton, David J; Rudic, R Daniel
2011-10-11
The suprachiasmatic nucleus of the brain is the circadian center, relaying rhythmic environmental and behavioral information to peripheral tissues to control circadian physiology. As such, central clock dysfunction can alter systemic homeostasis to consequently impair peripheral physiology in a manner that is secondary to circadian malfunction. To determine the impact of circadian clock function in organ transplantation and dissect the influence of intrinsic tissue clocks versus extrinsic clocks, we implemented a blood vessel grafting approach to surgically assemble a chimeric mouse that was part wild-type (WT) and part circadian clock mutant. Arterial isografts from donor WT mice that had been anastamosed to common carotid arteries of recipient WT mice (WT:WT) exhibited no pathology in this syngeneic transplant strategy. Similarly, when WT grafts were anastamosed to mice with disrupted circadian clocks, the structural features of the WT grafts immersed in the milieu of circadian malfunction were normal and absent of lesions, comparable to WT:WT grafts. In contrast, aortic grafts from Bmal1 knockout (KO) or Period-2,3 double-KO mice transplanted into littermate control WT mice developed robust arteriosclerotic disease. These lesions observed in donor grafts of Bmal1-KO were associated with up-regulation in T-cell receptors, macrophages, and infiltrating cells in the vascular grafts, but were independent of hemodynamics and B and T cell-mediated immunity. These data demonstrate the significance of intrinsic tissue clocks as an autonomous influence in experimental models of arteriosclerotic disease, which may have implications with regard to the influence of circadian clock function in organ transplantation.
Fluctuations of a surface relaxation model in interacting scale free networks
Torres, M. F.; La Rocca, C. E.; Braunstein, L. A.
2016-12-01
Isolated complex networks have been studied deeply in the last decades due to the fact that many real systems can be modeled using these types of structures. However, it is well known that the behavior of a system not only depends on itself, but usually also depends on the dynamics of other structures. For this reason, interacting complex networks and the processes developed on them have been the focus of study of many researches in the last years. One of the most studied subjects in this type of structures is the Synchronization problem, which is important in a wide variety of processes in real systems. In this manuscript we study the synchronization of two interacting scale-free networks, in which each node has ke dependency links with different nodes in the other network. We map the synchronization problem with an interface growth, by studying the fluctuations in the steady state of a scalar field defined in both networks. We find that as ke slightly increases from ke = 0, there is a really significant decreasing in the fluctuations of the system. However, this considerable improvement takes place mainly for small values of ke, when the interaction between networks becomes stronger there is only a slight change in the fluctuations. We characterize how the dispersion of the scalar field depends on the internal degree, and we show that a combination between the decreasing of this dispersion and the integer nature of our growth model are the responsible for the behavior of the fluctuations with ke.
Taichenachev, A V; Yudin, V I; Oates, C W; Hoyt, C W; Barber, Z W; Hollberg, L
2006-03-01
We develop a method of spectroscopy that uses a weak static magnetic field to enable direct optical excitation of forbidden electric-dipole transitions that are otherwise prohibitively weak. The power of this scheme is demonstrated using the important application of optical atomic clocks based on neutral atoms confined to an optical lattice. The simple experimental implementation of this method--a single clock laser combined with a dc magnetic field--relaxes stringent requirements in current lattice-based clocks (e.g., magnetic field shielding and light polarization), and could therefore expedite the realization of the extraordinary performance level predicted for these clocks. We estimate that a clock using alkaline-earth-like atoms such as Yb could achieve a fractional frequency uncertainty of well below 10(-17) for the metrologically preferred even isotopes.
A clock network for geodesy and fundamental science
Lisdat, C.; Grosche, G.; Quintin, N.; Shi, C.; Raupach, S. M. F.; Grebing, C.; Nicolodi, D.; Stefani, F.; Al-Masoudi, A.; Dörscher, S.; Häfner, S.; Robyr, J.-L.; Chiodo, N.; Bilicki, S.; Bookjans, E.; Koczwara, A.; Koke, S.; Kuhl, A.; Wiotte, F.; Meynadier, F.; Camisard, E.; Abgrall, M.; Lours, M.; Legero, T.; Schnatz, H.; Sterr, U.; Denker, H.; Chardonnet, C.; Le Coq, Y.; Santarelli, G.; Amy-Klein, A.; Le Targat, R.; Lodewyck, J.; Lopez, O.; Pottie, P.-E.
2016-08-01
Leveraging the unrivalled performance of optical clocks as key tools for geo-science, for astronomy and for fundamental physics beyond the standard model requires comparing the frequency of distant optical clocks faithfully. Here, we report on the comparison and agreement of two strontium optical clocks at an uncertainty of 5 × 10-17 via a newly established phase-coherent frequency link connecting Paris and Braunschweig using 1,415 km of telecom fibre. The remote comparison is limited only by the instability and uncertainty of the strontium lattice clocks themselves, with negligible contributions from the optical frequency transfer. A fractional precision of 3 × 10-17 is reached after only 1,000 s averaging time, which is already 10 times better and more than four orders of magnitude faster than any previous long-distance clock comparison. The capability of performing high resolution international clock comparisons paves the way for a redefinition of the unit of time and an all-optical dissemination of the SI-second.
Onboard clock correction for SS/TDMA and baseband processing satellites
Inukai, T.; Campanella, S. J.
1981-05-01
A clock correction scheme is presented that employs a predictor to achieve stability. A linear discrete model is used to analyze the worst-case timing error, clock correction rate, and buffer size requirements for traffic stations. The effects of secondary factors such as Doppler shift, range measurement error, quantization error of correction data, and delay incurred in transferring correction data to the satellite are also discussed. Special consideration is given to a sidereal day clock correction.
Djouani-Tahri, El Batoul; Motta*, Jean-Paul; Bouget, François-Yves; Corellou, Florence
2010-01-01
Living organisms such as plants and animals have evolved endogenous clocks in order to anticipate the environmental changes associated with the earth’s rotation and to orchestrate biological processes in the course of the 24 hour daily cycle. We have recently identified clock components in the primitive green picoalga Ostreococcus tauri, a promising minimal cellular and genomic model for systems biology approaches. A homologue of the Arabidopsis core clock gene Time of CAB expression-1 (TOC1)...
Stopper, Daniel; Roth, Roland; Hansen-Goos, Hendrik
2016-11-01
Within the Asakura-Oosawa model, we study structural relaxation in mixtures of colloids and polymers subject to Brownian motion in the overdamped limit. We obtain the time evolution of the self and distinct parts of the van Hove distribution function G(r,t) by means of dynamical density functional theory (DDFT) using an accurate free-energy functional based on Rosenfeld’s fundamental measure theory. In order to remove unphysical interactions within the self part, we extend the recently proposed quenched functional framework (Stopper et al 2015 J. Chem. Phys. 143 181105) toward mixtures. In addition, we obtain results for the long-time self diffusion coefficients of colloids and polymers from dynamic Monte Carlo simulations, which we incorporate into the DDFT. From the resulting DDFT equations we calculate G(r, t), which we find to agree very well with our simulations. In particular, we examine the influence of polymers which are slow relative to the colloids—a scenario for which both DDFT and simulation show a significant peak forming at r = 0 in the colloid-colloid distribution function, akin to experimental findings involving gelation of colloidal suspensions. Moreover, we observe that, in the presence of slow polymers, the long-time self diffusivity of the colloids displays a maximum at an intermediate colloid packing fraction. This behavior is captured by a simple semi-empirical formula, which provides an excellent description of the data.
Fluctuations of a surface relaxation model in interacting scale free networks
Torres, Marcos F; Braunstein, Lidia A
2016-01-01
Isolated complex networks has been studied deeply in the last decades due to the fact that many real systems can be modeled using these type of structures. However, it is well known that the behavior of a system not only depends on itself, but usually also depends on the dynamics of other structures. For this reason, interacting complex networks and the processes developed on them have been the focus of study of many researches in the last years. One of the most studied subjects in this type of structures is the Synchronization problem, which is important in a wide variety of processes in real systems. In this manuscript we study the synchronization of two interacting scale-free networks, in which each node has $ke$ dependency links with different nodes in the other network. We map the synchronization problem with an interface growth, by studying the fluctuations in the steady state of a scalar field defined in both networks. We find that as $ke$ slightly increases from $ke=0$, there is a really significant d...
Negative magnetic relaxation in superconductors
Krasnoperov E.P.
2013-01-01
Full Text Available It was observed that the trapped magnetic moment of HTS tablets or annuli increases in time (negative relaxation if they are not completely magnetized by a pulsed magnetic field. It is shown, in the framework of the Bean critical-state model, that the radial temperature gradient appearing in tablets or annuli during a pulsed field magnetization can explain the negative magnetic relaxation in the superconductor.
Simulation of the clock framework of Gaia
Castaneda, J; Portell, J; García-Berro, E; Luri, X; Castaneda, Javier; Gordo, Jose P.; Portell, Jordi; Garcia-Berro, Enrique; Luri, Xavier
2005-01-01
Gaia will perform astrometric measurements with an unprecedented resolution. Consequently, the electronics of the Astro instrument must time tag every measurement with a precision of a few nanoseconds. Hence, it requires a high stability clock signal, for which a Rb-type spacecraft master clock has been baselined. The distribution of its signal and the generation of clock subproducts must maintain these high accuracy requirements. We have developed a software application to simulate generic clock frameworks. The most critical clock structures for Gaia have also been identified, and its master clock has been parameterised.
Molecular mechanisms underlying the Arabidopsis circadian clock.
Nakamichi, Norihito
2011-10-01
A wide range of biological processes exhibit circadian rhythm, enabling plants to adapt to the environmental day-night cycle. This rhythm is generated by the so-called 'circadian clock'. Although a number of genetic approaches have identified >25 clock-associated genes involved in the Arabidopsis clock mechanism, the molecular functions of a large part of these genes are not known. Recent comprehensive studies have revealed the molecular functions of several key clock-associated proteins. This progress has provided mechanistic insights into how key clock-associated proteins are integrated, and may help in understanding the essence of the clock's molecular mechanisms.
Maulik, Romit
2016-01-01
In this paper, we introduce a relaxation filtering closure approach to account for subgrid scale effects in explicitly filtered large eddy simulations using the concept of anisotropic diffusion. We utilize the Perona-Malik diffusion model and demonstrate its shock capturing ability and spectral performance for solving the Burgers turbulence problem, which is a simplified prototype for more realistic turbulent flows showing the same quadratic nonlinearity. Our numerical assessments present the behavior of various diffusivity functions in conjunction with a detailed sensitivity analysis with respect to the free modeling parameters. In comparison to direct numerical simulation (DNS) and under-resolved DNS results, we find that the proposed closure model is efficient in the prevention of energy accumulation at grid cut-off and is also adept at preventing any possible spurious numerical oscillations due to shock formation under the optimal parameter choices. In contrast to other relaxation filtering approaches, it...
Wang, Ruizhi; Hu, Yong; Yang, Yuchan; Xu, Wei; Yao, Mingrong; Gao, Dongmei; Zhao, Yan; Zhan, Songhua; Shi, Xiangyang; Wang, Xiaolin
2017-02-01
Hepatocellular carcinoma (HCC) is the most common type of liver malignant tumor, which is often diagnosed in advanced stages, resulting in low survival rate. The sensitive diagnosis of early HCC presents a great interest. Herein, a novel superparamagnetic contrast agent composed of iron oxide nanoparticles is reported. Firstly, polyethyleneimine-coated iron oxide (Fe3O4@PEI) nanoparticles (NPs) were synthesized via a mild reduction route, followed by their modification of polyethylene glycol monomethyl ether ( mPEG-COOH) via 1-ethyl-3-(3-(dimethylamino)propyl) carbodiimide hydrochloride coupling chemistry. After acetylation of the remaining PEI amines, the PEGylated Fe3O4 (Fe3O4@PEI.Ac- mPEG-COOH) NPs were successively characterized via different techniques. The Fe3O4@PEI.Ac- mPEG-COOH probes with an Fe3O4 NP size of 9 nm are water dispersible and cytocompatible within the given concentration range. The percentages of PEI and m-PEG-COOH on the particles surface are calculated to be 15.5 and 7.2%, respectively. Prior to the administration of Fe3O4@PEI.Ac- mPEG-COOH NPs of ultrahigh r 2 relaxivity (461.29 mM-1 s-1) via tail intravenous injection for MR imaging of HCC, the orthotopic model of HCC was established in the nude mice by surgical transplantation with HCCLM3 cells. The analysis of MR signal intensity (SI) in the orthotopic tumor model demonstrated that the developed Fe3O4@PEI.Ac- mPEG-COOH NPs were able to infiltrate into the tumor area through the enhanced permeability and retention (EPR) effect reaching the bottom at 2 h postinjection. The developed Fe3O4@PEI.Ac- mPEG-COOH NPs may be further applied for theranostics of different diseases through combing various therapeutic agents.
Circadian clocks, epigenetics, and cancer
Masri, Selma
2015-01-01
The interplay between circadian rhythm and cancer has been suggested for more than a decade based on the observations that shift work and cancer incidence are linked. Accumulating evidence implicates the circadian clock in cancer survival and proliferation pathways. At the molecular level, multiple control mechanisms have been proposed to link circadian transcription and cell-cycle control to tumorigenesis.The circadian gating of the cell cycle and subsequent control of cell proliferation is an area of active investigation. Moreover, the circadian clock is a transcriptional system that is intricately regulated at the epigenetic level. Interestingly, the epigenetic landscape at the level of histone modifications, DNA methylation, and small regulatory RNAs are differentially controlled in cancer cells. This concept raises the possibility that epigenetic control is a common thread linking the clock with cancer, though little scientific evidence is known to date.This review focuses on the link between circadian clock and cancer, and speculates on the possible connections at the epigenetic level that could further link the circadian clock to tumor initiation or progression.
Circadian clock proteins and immunity.
Curtis, Anne M; Bellet, Marina M; Sassone-Corsi, Paolo; O'Neill, Luke A J
2014-02-20
Immune parameters change with time of day and disruption of circadian rhythms has been linked to inflammatory pathologies. A circadian-clock-controlled immune system might allow an organism to anticipate daily changes in activity and feeding and the associated risk of infection or tissue damage to the host. Responses to bacteria have been shown to vary depending on time of infection, with mice being more at risk of sepsis when challenged ahead of their activity phase. Studies highlight the extent to which the molecular clock, most notably the core clock proteins BMAL1, CLOCK, and REV-ERBα, control fundamental aspects of the immune response. Examples include the BMAL1:CLOCK heterodimer regulating toll-like receptor 9 (TLR9) expression and repressing expression of the inflammatory monocyte chemokine ligand (CCL2) as well as REV-ERBα suppressing the induction of interleukin-6. Understanding the daily rhythm of the immune system could have implications for vaccinations and how we manage infectious and inflammatory diseases. Copyright © 2014 Elsevier Inc. All rights reserved.
Mark Campanelli
2010-04-01
Full Text Available Somitogenesis is a process common to all vertebrate embryos in which repeated blocks of cells arise from the presomitic mesoderm (PSM to lay a foundational pattern for trunk and tail development. Somites form in the wake of passing waves of periodic gene expression that originate in the tailbud and sweep posteriorly across the PSM. Previous work has suggested that the waves result from a spatiotemporally graded control protein that affects the oscillation rate of clock-gene expression. With a minimally constructed mathematical model, we study the contribution of two control mechanisms to the initial formation of this gene-expression wave. We test four biologically motivated model scenarios with either one or two clock protein transcription binding sites, and with or without differential decay rates for clock protein monomers and dimers. We examine the sensitivity of wave formation with respect to multiple model parameters and robustness to heterogeneity in cell population. We find that only a model with both multiple binding sites and differential decay rates is able to reproduce experimentally observed waveforms. Our results show that the experimentally observed characteristics of somitogenesis wave initiation constrain the underlying genetic control mechanisms.
Metabolic regulation of circadian clocks.
Haydon, Michael J; Hearn, Timothy J; Bell, Laura J; Hannah, Matthew A; Webb, Alex A R
2013-05-01
Circadian clocks are 24-h timekeeping mechanisms, which have evolved in plants, animals, fungi and bacteria to anticipate changes in light and temperature associated with the rotation of the Earth. The current paradigm to explain how biological clocks provide timing information is based on multiple interlocking transcription-translation negative feedback loops (TTFL), which drive rhythmic gene expression and circadian behaviour of growth and physiology. Metabolism is an important circadian output, which in plants includes photosynthesis, starch metabolism, nutrient assimilation and redox homeostasis. There is increasing evidence in a range of organisms that these metabolic outputs can also contribute to circadian timing and might also comprise independent circadian oscillators. In this review, we summarise the mechanisms of circadian regulation of metabolism by TTFL and consider increasing evidence that rhythmic metabolism contributes to the circadian network. We highlight how this might be relevant to plant circadian clock function.
Francisco Martins
2011-10-01
Full Text Available X10 is a modern language built from the ground up to handle future parallel systems, from multicore machines to cluster configurations. We take a closer look at a pair of synchronisation mechanisms: finish and clocks. The former waits for the termination of parallel computations, the latter allow multiple concurrent activities to wait for each other at certain points in time. In order to better understand these concepts we study a type system for a stripped down version of X10. The main result assures that well typed programs do not run into the errors identified in the X10 language reference, namely the ClockUseException. The study will open, we hope, doors to a more flexible utilisation of clocks in the X10 language.
Synchronous clock stopper for microprocessor
Kitchin, David A. (Inventor)
1985-01-01
A synchronous clock stopper circuit for inhibiting clock pulses to a microprocessor in response to a stop request signal, and for reinstating the clock pulses in response to a start request signal thereby to conserve power consumption of the microprocessor when used in an environment of limited power. The stopping and starting of the microprocessor is synchronized, by a phase tracker, with the occurrences of a predetermined phase in the instruction cycle of the microprocessor in which the I/O data and address lines of the microprocessor are of high impedance so that a shared memory connected to the I/O lines may be accessed by other peripheral devices. The starting and stopping occur when the microprocessor initiates and completes, respectively, an instruction, as well as before and after transferring data with a memory. Also, the phase tracker transmits phase information signals over a bus to other peripheral devices which signals identify the current operational phase of the microprocessor.
Novel concepts on pregnancy clocks and alarms: redundancy and synergy in human parturition
Menon, Ramkumar; Bonney, Elizabeth A.; Condon, Jennifer; Mesiano, Sam; Taylor, Robert N.
2016-01-01
The signals and mechanisms that synchronize the timing of human parturition remain a mystery and a better understanding of these processes is essential to avert adverse pregnancy outcomes. Although our insights into human labor initiation have been informed by studies in animal models, the timing of parturition relative to fetal maturation varies among viviparous species, indicative of phylogenetically different clocks and alarms; but what is clear is that important common pathways must converge to control the birth process. For example, in all species, parturition involves the transition of the myometrium from a relaxed to a highly excitable state, where the muscle rhythmically and forcefully contracts, softening the cervical extracellular matrix to allow distensibility and dilatation and thus a shearing of the fetal membranes to facilitate their rupture. We review a number of theories promulgated to explain how a variety of different timing mechanisms, including fetal membrane cell senescence, circadian endocrine clocks, and inflammatory and mechanical factors, are coordinated as initiators and effectors of parturition. Many of these factors have been independently described with a focus on specific tissue compartments. In this review, we put forth the core hypothesis that fetal membrane (amnion and chorion) senescence is the initiator of a coordinated, redundant signal cascade leading to parturition. Whether modified by oxidative stress or other factors, this process constitutes a counting device, i.e. a clock, that measures maturation of the fetal organ systems and the production of hormones and other soluble mediators (including alarmins) and that promotes inflammation and orchestrates an immune cascade to propagate signals across different uterine compartments. This mechanism in turn sensitizes decidual responsiveness and eventually promotes functional progesterone withdrawal in the myometrium, leading to increased myometrial cell contraction and the
Novel concepts on pregnancy clocks and alarms: redundancy and synergy in human parturition.
Menon, Ramkumar; Bonney, Elizabeth A; Condon, Jennifer; Mesiano, Sam; Taylor, Robert N
2016-09-01
The signals and mechanisms that synchronize the timing of human parturition remain a mystery and a better understanding of these processes is essential to avert adverse pregnancy outcomes. Although our insights into human labor initiation have been informed by studies in animal models, the timing of parturition relative to fetal maturation varies among viviparous species, indicative of phylogenetically different clocks and alarms; but what is clear is that important common pathways must converge to control the birth process. For example, in all species, parturition involves the transition of the myometrium from a relaxed to a highly excitable state, where the muscle rhythmically and forcefully contracts, softening the cervical extracellular matrix to allow distensibility and dilatation and thus a shearing of the fetal membranes to facilitate their rupture. We review a number of theories promulgated to explain how a variety of different timing mechanisms, including fetal membrane cell senescence, circadian endocrine clocks, and inflammatory and mechanical factors, are coordinated as initiators and effectors of parturition. Many of these factors have been independently described with a focus on specific tissue compartments.In this review, we put forth the core hypothesis that fetal membrane (amnion and chorion) senescence is the initiator of a coordinated, redundant signal cascade leading to parturition. Whether modified by oxidative stress or other factors, this process constitutes a counting device, i.e. a clock, that measures maturation of the fetal organ systems and the production of hormones and other soluble mediators (including alarmins) and that promotes inflammation and orchestrates an immune cascade to propagate signals across different uterine compartments. This mechanism in turn sensitizes decidual responsiveness and eventually promotes functional progesterone withdrawal in the myometrium, leading to increased myometrial cell contraction and the
Zhuo, Congshan; Sagaut, Pierre
2017-06-01
In this paper, a variant of the acoustic multipole source (AMS) method is proposed within the framework of the lattice Boltzmann method. A quadrupole term is directly included in the stress system (equilibrium momentum flux), and the dependency of the quadrupole source in the inviscid limit upon the fortuitous discretization error reported in the works of E. M. Viggen [Phys. Rev. E 87, 023306 (2013)PLEEE81539-375510.1103/PhysRevE.87.023306] is removed. The regularized lattice Boltzmann (RLB) method with this variant AMS method is presented for the 2D and 3D acoustic problems in the inviscid limit, and without loss of generality, the D3Q19 model is considered in this work. To assess the accuracy and the advantage of the RLB scheme with this AMS for acoustic point sources, the numerical investigations and comparisons with the multiple-relaxation-time (MRT) models and the analytical solutions are performed on the 2D and 3D acoustic multipole point sources in the inviscid limit, including monopoles, x dipoles, and xx quadrupoles. From the present results, the good precision of this AMS method is validated, and the RLB scheme exhibits some superconvergence properties for the monopole sources compared with the MRT models, and both the RLB and MRT models have the same accuracy for the simulations of acoustic dipole and quadrupole sources. To further validate the capability of the RLB scheme with AMS, another basic acoustic problem, the acoustic scattering from a solid cylinder presented at the Second Computational Aeroacoustics Workshop on Benchmark Problems, is numerically considered. The directivity pattern of the acoustic field is computed at r=7.5; the present results agree well with the exact solutions. Also, the effects of slip and no-slip wall treatments within the regularized boundary condition on this pure acoustic scattering problem are tested, and compared with the exact solution, the slip wall treatment can present a better result. All simulations demonstrate
Colloquium: Physics of optical lattice clocks
Derevianko, Andrei
2010-01-01
Recently invented and demonstrated, optical lattice clocks hold great promise for improving the precision of modern timekeeping. These clocks aim at the 10^-18 fractional accuracy, which translates into a clock that would neither lose or gain a fraction of a second over an estimated age of the Universe. In these clocks, millions of atoms are trapped and interrogated simultaneously, dramatically improving clock stability. Here we discuss the principles of operation of these clocks and, in particular, a novel concept of "magic" trapping of atoms in optical lattices. We also highlight recently proposed microwave lattice clocks and several applications that employ the optical lattice clocks as a platform for precision measurements and quantum information processing.
A circadian clock in Saccharomyces cerevisiae
Eelderink-Chen, Zheng; Mazzotta, Gabriella; Sturre, Marcel; Bosman, Jasper; Roenneberg, Till; Merrow, Martha
2010-01-01
Circadian timing is a fundamental biological process, underlying cellular physiology in animals, plants, fungi, and cyanobacteria. Circadian clocks organize gene expression, metabolism, and behavior such that they occur at specific times of day. The biological clocks that orchestrate these daily
Pasko, V. P.
2009-12-01
Thomas et al. [JGR, A12306, 2008] has reported lightning-driven electric (E) field pulses at 75-130 km altitude recorded during rocket experiment in 1995 from Wallops Island, Virginia. The measurements were compared to a 2D electromagnetic model of Cho and Rycroft [JASTP, 60,871,1998]. Thomas et al.[2008] indicated that the observed field magnitudes were an order of magnitude lower than predicted by the model and questioned validity of the electromagnetic pulse mechanism of elves. The goal of the present work, which utilizes Monte Carlo and FDTD electromagnetic modeling, is to emphasize range of validity of the local field approximation (LFA) employed in the Cho and Rycroft's [1998] model and other similar models for the cases when weak (~10 mV/m as reported in [Thomas et al., 2008]) E field pulses are considered. Glukhov et al. [GRL, 23, 2193, 1996] and Sukhorukov et al. [GRL, 23, 2911, 1996] performed Monte Carlo simulations for large E fields ~10V/m at typical altitudes of elves, which fully confirmed validity of models of elves based on LFA [Taranenko et al., GRL, 20, 2675, 1993; Inan et al., GRL, 23, 133, 1996]. We demonstrate that the time of relaxation of the momentum of the electron distributions subjected to the external E field scales approximately as 1/E and exceeds 10s of microseconds for E1 V/m when fast (10 kHz) processes are considered. The models of elves relying on LFA [e.g., Taranenko et al., 1993; Inan et al., 1996] generally require E>1 V/m for production of observable optical emissions at lower ionospheric altitudes and therefore remain valid, in agreement with original conclusions reached by Glukhov et al. [1996] and Sukhorukov et al. [1996]. Two additional factors may have contributed to the low field magnitudes reported in [Thomas et al., 2008]: 1) The measurements were conducted on September 2, 1995 around evening hours (9:22 PM local time) at which the lower ionosphere likely exhibited enhancement of electron density in comparison with
Clock Estimation for Long-Term Synchronization in Wireless Sensor Networks with Exponential Delays
Erchin Serpedin
2007-12-01
Full Text Available Although the existing time synchronization protocols in wireless sensor networks (WSNs are efficient for short periods, many applications require long-term synchronization among the nodes, for example, coordinated sleep and wakeup modes, and synchronized sampling. In such applications, experiments have shown that even clock skew correction cannot maintain long-term clock synchronization and a quadratic model of clock variations can better capture the dynamics of the actual clock model involved, hence increasing the resynchronization period and conserving significant energy. This paper derives the maximum likelihood (ML estimator for all the clock parameters in a two-way timing exchange model with exponential delays. The same estimation procedure can be applied to one-way timing exchange models with little modification.
Lefkidis, G.; Sold, S.; Hübner, W.
2017-06-01
We study an s-p model magnetic system with a triplet ground state coupled to two temperature baths. By varying the temperatures we both generate non-thermal electronic distributions and create additional coherences in the density matrix of the system. Thus the thermally-induced magnetic response goes beyond the simple picture of majority-minority population dynamics. Furthermore, we discuss the influence of temperature induced relaxation effects on the dynamics induced by an optical perturbation for this quantum system.
Single-transistor-clocked flip-flop
Zhao, Peiyi; Darwish, Tarek; Bayoumi, Magdy
2005-08-30
The invention provides a low power, high performance flip-flop. The flip-flop uses only one clocked transistor. The single clocked transistor is shared by the first and second branches of the device. A pulse generator produces a clock pulse to trigger the flip-flop. In one preferred embodiment the device can be made as a static explicit pulsed flip-flop which employs only two clocked transistors.
Meng, Xuhui; Guo, Zhaoli
2015-10-01
A lattice Boltzmann model with a multiple-relaxation-time (MRT) collision operator is proposed for incompressible miscible flow with a large viscosity ratio as well as a high Péclet number in this paper. The equilibria in the present model are motivated by the lattice kinetic scheme previously developed by Inamuro et al. [Philos. Trans. R. Soc. London, Ser. A 360, 477 (2002), 10.1098/rsta.2001.0942]. The fluid viscosity and diffusion coefficient depend on both the corresponding relaxation times and additional adjustable parameters in this model. As a result, the corresponding relaxation times can be adjusted in proper ranges to enhance the performance of the model. Numerical validations of the Poiseuille flow and a diffusion-reaction problem demonstrate that the proposed model has second-order accuracy in space. Thereafter, the model is used to simulate flow through a porous medium, and the results show that the proposed model has the advantage to obtain a viscosity-independent permeability, which makes it a robust method for simulating flow in porous media. Finally, a set of simulations are conducted on the viscous miscible displacement between two parallel plates. The results reveal that the present model can be used to simulate, to a high level of accuracy, flows with large viscosity ratios and/or high Péclet numbers. Moreover, the present model is shown to provide superior stability in the limit of high kinematic viscosity. In summary, the numerical results indicate that the present lattice Boltzmann model is an ideal numerical tool for simulating flow with a large viscosity ratio and/or a high Péclet number.
R Daniel Rudic
2004-11-01
Full Text Available Circadian timing is generated through a unique series of autoregulatory interactions termed the molecular clock. Behavioral rhythms subject to the molecular clock are well characterized. We demonstrate a role for Bmal1 and Clock in the regulation of glucose homeostasis. Inactivation of the known clock components Bmal1 (Mop3 and Clock suppress the diurnal variation in glucose and triglycerides. Gluconeogenesis is abolished by deletion of Bmal1 and is depressed in Clock mutants, but the counterregulatory response of corticosterone and glucagon to insulin-induced hypoglycaemia is retained. Furthermore, a high-fat diet modulates carbohydrate metabolism by amplifying circadian variation in glucose tolerance and insulin sensitivity, and mutation of Clock restores the chow-fed phenotype. Bmal1 and Clock, genes that function in the core molecular clock, exert profound control over recovery from insulin-induced hypoglycaemia. Furthermore, asynchronous dietary cues may modify glucose homeostasis via their interactions with peripheral molecular clocks.
THE STOCHASTIC ESTIMATION OF SATELLITE CLOCK CORRECTION INFORMATION IN WADGPS
无
2000-01-01
Using autocorrelation information of the pseudorange errors generated by se lective availability (SA) frequency dithering, we have constructed a simple first order stochas tic model for SA effects. This model has been used in a Kalman filter to account for the stochastic behavior of SA dithering in estimating satellite clock information in wide area dif ferential GPS. We have obtained fifteen percent improvement in the user positioning using the correlation information on the satellite clock information in a Kalman filter, when comparing the results obtained using a regular least square estimation.
Light and the human circadian clock
Roenneberg, Till; Kantermann, Thomas; Juda, Myriam; Vetter, Céline; Allebrandt, Karla V
2013-01-01
The circadian clock can only reliably fulfil its function if it is stably entrained. Most clocks use the light-dark cycle as environmental signal (zeitgeber) for this active synchronisation. How we think about clock function and entrainment has been strongly influenced by the early concepts of the
Light and the human circadian clock
Roenneberg, Till; Kantermann, Thomas; Juda, Myriam; Vetter, Céline; Allebrandt, Karla V
2013-01-01
The circadian clock can only reliably fulfil its function if it is stably entrained. Most clocks use the light-dark cycle as environmental signal (zeitgeber) for this active synchronisation. How we think about clock function and entrainment has been strongly influenced by the early concepts of the f
Wójcik, Beata; Jabłoński, Mirosław; Gębala, Edyta; Drelich, Małgorzata
2012-01-01
Degenerative joint disease usually leads to functional failure and pain in the affected parts of the musculoskeletal system. The aim of this study was to evaluate the effectiveness of fascial relaxation for tense muscles in the affected hip joint by comparing this method and classic physiotherapeutic rehabilitation in patients after hip arthroplasty with regard to the range of motion, presence of pain and quality of life. The study involved 35 females qualified for hip arthroplasty. A control group consisted of 10 patients aged 47 to 77 years who received classic kinesiotherapy, including antithrombotic prophylaxis and isometric muscle exercises for the operated lower limb followed by active exercises for supported flexion in the hip and knee joints, active decompression exercises, assuming the upright position, and gait training. The experimental group consisted of 25 women aged 45 to 75 years who, along with conventional therapeutic exercises, were treated by fascial relaxation of the affected hip joint. The arthroplasty procedure was carried out from a posterior approach in all patients, in accordance with the technique recommended by Swanson. The results indicate that the group of patients who additionally received fascial relaxation demonstrated a significantly increased range of motion in the operated hip joint. The experimental group also reported considerable pain reduction and improved daily activity in comparison to the control group. The techniques of fascial relaxation significantly reduced recovery time and liminated muscle tensing in the operated hip joint, thus contributing to improving the range of motion.
A Method for Estimating BeiDou Inter-frequency Satellite Clock Bias
LI Haojun
2016-02-01
Full Text Available A new method for estimating the BeiDou inter-frequency satellite clock bias is proposed, considering the shortage of the current methods. The constant and variable parts of the inter-frequency satellite clock bias are considered in the new method. The data from 10 observation stations are processed to validate the new method. The characterizations of the BeiDou inter-frequency satellite clock bias are also analyzed using the computed results. The results of the BeiDou inter-frequency satellite clock bias indicate that it is stable in the short term. The estimated BeiDou inter-frequency satellite clock bias results are molded. The model results show that the 10 parameters of model for each satellite can express the BeiDou inter-frequency satellite clock bias well and the accuracy reaches cm level. When the model parameters of the first day are used to compute the BeiDou inter-frequency satellite clock bias of the second day, the accuracy also reaches cm level. Based on the stability and modeling, a strategy for the BeiDou satellite clock service is presented to provide the reference of our BeiDou.
Flip-Flops for accurate multiphase clocking: transmission gate versus current mode logic
Dutta, R.; Klumperink, Eric A.M.; Gao, X.; Ru, Z.; van der Zee, Ronan A.R.; Nauta, Bram
2013-01-01
Dynamic transmission gate (DTG) flip-flops (FFs) (DTG-FFs) and current mode logic (CML) FFs (CML-FFs) are compared targeting power efficient multiphase clock generation with low phase error. The effect of component mismatches on multiphase clock timing inaccuracies is modeled and compared, using the
Flip-Flops for accurate multiphase clocking: transmission gate versus current mode logic
Dutta, R.; Klumperink, E.A.M.; Gao, X.; Ru, Z.; Zee, van der R.A.R.; Nauta, B.
2013-01-01
Dynamic transmission gate (DTG) flip-flops (FFs) (DTG-FFs) and current mode logic (CML) FFs (CML-FFs) are compared targeting power efficient multiphase clock generation with low phase error. The effect of component mismatches on multiphase clock timing inaccuracies is modeled and compared, using the
Biological clocks: riding the tides.
de la Iglesia, Horacio O; Johnson, Carl Hirschie
2013-10-21
Animals with habitats in the intertidal zone often display biological rhythms that coordinate with both the tidal and the daily environmental cycles. Two recent studies show that the molecular components of the biological clocks mediating tidal rhythms are likely different from the phylogenetically conserved components that mediate circadian (daily) rhythms.
A generalized gravitomagnetic clock effect
Hackmann, Eva
2014-01-01
In General Relativity the rotation of a gravitating body like the Earth influences the motion of orbiting test particles or satellites in a non-Newtonian way. This causes e.g. a precession of the orbital plane, known as the Lense-Thirring effect, and a precession of the spin of a gyroscope, known as the Schiff effect. Here we discuss a third effect, first introduced by Cohen and Mashhoon, called the gravitomagnetic clock effect. It describes the difference in proper time of counter revolving clocks after a revolution of $2\\pi$. For two clocks on counter rotating equatorial circular orbits around the Earth the effect is about $10^{-7}$ seconds per revolution, which is quite large. We introduce a general relativistic definition of the gravitomagnetic clock effect which is valid for arbitrary pairs of orbits. This includes rotations in the same direction and different initial conditions, which is crucial if the effect can be detected with existing satellites or with payloads on non-dedicated missions. We also de...
Collevatti, Rosane G; Terribile, Levi C; Rabelo, Suelen G; Lima-Ribeiro, Matheus S
2015-01-01
Understanding the dispersal routes of Neotropical savanna tree species is an essential step to unravel the effects of past climate change on genetic patterns, species distribution and population demography. Here we reconstruct the demographic history and dispersal dynamics of the Neotropical savanna tree species Tabebuia aurea to understand the effects of Quaternary climate change on its current spatial patterns of genetic diversity. We sampled 285 individuals from 21 populations throughout Brazilian savannas and sequenced all individuals for three chloroplast intergenic spacers and ITS nrDNA. We analyzed data using a multi-model inference framework by coupling the relaxed random walk model (RRW), ecological niche modeling (ENM) and statistical phylogeography. The most recent common ancestor of T. aurea lineages dated from ~4.0 ± 2.5 Ma. T. aurea lineages cyclically dispersed from the West toward the Central-West Brazil, and from the Southeast toward the East and Northeast Brazil, following the paleodistribution dynamics shown by the ENMs through the last glacial cycle. A historical refugium through time may have allowed dispersal of lineages among populations of Central Brazil, overlapping with population expansion during interglacial periods and the diversification of new lineages. Range and population expansion through the Quaternary were, respectively, the most frequent prediction from ENMs and the most likely demographic scenario from coalescent simulations. Consistent phylogeographic patterns among multiple modeling inferences indicate a promising approach, allowing us to understand how cyclical climate changes through the Quaternary drove complex population dynamics and the current patterns of species distribution and genetic diversity.
Relaxation Techniques for Health
... R S T U V W X Y Z Relaxation Techniques for Health Share: On This Page What’s the ... Bottom Line? How much do we know about relaxation techniques? A substantial amount of research has been done ...
Atomic clocks as a tool to monitor vertical surface motion
Bondarescu, Ruxandra; Lundgren, Andrew; Hetényi, György; Houlié, Nicolas; Jetzer, Philippe; Bondarescu, Mihai
2015-01-01
Atomic clock technology is advancing rapidly, now reaching stabilities of $\\Delta f/f \\sim 10^{-18}$, which corresponds to resolving $1$ cm in equivalent geoid height over an integration timescale of about 7 hours. At this level of performance, ground-based atomic clock networks emerge as a tool for monitoring a variety of geophysical processes by directly measuring changes in the gravitational potential. Vertical changes of the clock's position due to magmatic, volcanic, post-seismic or tidal deformations can result in measurable variations in the clock tick rate. As an example, we discuss the geopotential change arising due to an inflating point source (Mogi model), and apply it to the Etna volcano. Its effect on an observer on the Earth's surface can be divided into two different terms: one purely due to uplift and one due to the redistribution of matter. Thus, with the centimetre-level precision of current clocks it is already possible to monitor volcanoes. The matter redistribution term is estimated to b...
The circadian molecular clock creates epidermal stem cell heterogeneity.
Janich, Peggy; Pascual, Gloria; Merlos-Suárez, Anna; Batlle, Eduard; Ripperger, Jürgen; Albrecht, Urs; Cheng, Hai-Ying M; Obrietan, Karl; Di Croce, Luciano; Benitah, Salvador Aznar
2011-11-09
Murine epidermal stem cells undergo alternate cycles of dormancy and activation, fuelling tissue renewal. However, only a subset of stem cells becomes active during each round of morphogenesis, indicating that stem cells coexist in heterogeneous responsive states. Using a circadian-clock reporter-mouse model, here we show that the dormant hair-follicle stem cell niche contains coexisting populations of cells at opposite phases of the clock, which are differentially predisposed to respond to homeostatic cues. The core clock protein Bmal1 modulates the expression of stem cell regulatory genes in an oscillatory manner, to create populations that are either predisposed, or less prone, to activation. Disrupting this clock equilibrium, through deletion of Bmal1 (also known as Arntl) or Per1/2, resulted in a progressive accumulation or depletion of dormant stem cells, respectively. Stem cell arrhythmia also led to premature epidermal ageing, and a reduction in the development of squamous tumours. Our results indicate that the circadian clock fine-tunes the temporal behaviour of epidermal stem cells, and that its perturbation affects homeostasis and the predisposition to tumorigenesis.
Suarez, Max J. (Editor); Yang, Wei-Yu; Todling, Ricardo; Navon, I. Michael
1997-01-01
A detailed description of the development of the tangent linear model (TLM) and its adjoint model of the Relaxed Arakawa-Schubert moisture parameterization package used in the NASA GEOS-1 C-Grid GCM (Version 5.2) is presented. The notational conventions used in the TLM and its adjoint codes are described in detail.
Temperature relaxation in dense plasma mixtures
Faussurier, Gérald; Blancard, Christophe
2016-09-01
We present a model to calculate temperature-relaxation rates in dense plasma mixtures. The electron-ion relaxation rates are calculated using an average-atom model and the ion-ion relaxation rates by the Landau-Spitzer approach. This method allows the study of the temperature relaxation in many-temperature electron-ion and ion-ion systems such as those encountered in inertial confinement fusion simulations. It is of interest for general nonequilibrium thermodynamics dealing with energy flows between various systems and should find broad use in present high energy density experiments.
Nima Toosizadeh
Full Text Available Experimental studies suggest that prolonged trunk flexion reduces passive support of the spine. To understand alterations of the synergy between active and passive tissues following such loadings, several studies have assessed the time-dependent behavior of passive tissues including those within spinal motion segments and muscles. Yet, there remain limitations regarding load-relaxation of the lumbar spine in response to flexion exposures and the influence of different flexion angles. Ten healthy participants were exposed for 16 min to each of five magnitudes of lumbar flexion specified relative to individual flexion-relaxation angles (i.e., 30, 40, 60, 80, and 100%, during which lumbar flexion angle and trunk moment were recorded. Outcome measures were initial trunk moment, moment drop, parameters of four viscoelastic models (i.e., Standard Linear Solid model, the Prony Series, Schapery's Theory, and the Modified Superposition Method, and changes in neutral zone and viscoelastic state following exposure. There were significant effects of flexion angle on initial moment, moment drop, changes in normalized neutral zone, and some parameters of the Standard Linear Solid model. Initial moment, moment drop, and changes in normalized neutral zone increased exponentially with flexion angle. Kelvin-solid models produced better predictions of temporal behaviors. Observed responses to trunk flexion suggest nonlinearity in viscoelastic properties, and which likely reflected viscoelastic behaviors of spinal (lumbar motion segments. Flexion-induced changes in viscous properties and neutral zone imply an increase in internal loads and perhaps increased risk of low back disorders. Kelvin-solid models, especially the Prony Series model appeared to be more effective at modeling load-relaxation of the trunk.
Ras-mediated deregulation of the circadian clock in cancer.
Angela Relógio
Full Text Available Circadian rhythms are essential to the temporal regulation of molecular processes in living systems and as such to life itself. Deregulation of these rhythms leads to failures in biological processes and eventually to the manifestation of pathological phenotypes including cancer. To address the questions as to what are the elicitors of a disrupted clock in cancer, we applied a systems biology approach to correlate experimental, bioinformatics and modelling data from several cell line models for colorectal and skin cancer. We found strong and weak circadian oscillators within the same type of cancer and identified a set of genes, which allows the discrimination between the two oscillator-types. Among those genes are IFNGR2, PITX2, RFWD2, PPARγ, LOXL2, Rab6 and SPARC, all involved in cancer-related pathways. Using a bioinformatics approach, we extended the core-clock network and present its interconnection to the discriminative set of genes. Interestingly, such gene signatures link the clock to oncogenic pathways like the RAS/MAPK pathway. To investigate the potential impact of the RAS/MAPK pathway - a major driver of colorectal carcinogenesis - on the circadian clock, we used a computational model which predicted that perturbation of BMAL1-mediated transcription can generate the circadian phenotypes similar to those observed in metastatic cell lines. Using an inducible RAS expression system, we show that overexpression of RAS disrupts the circadian clock and leads to an increase of the circadian period while RAS inhibition causes a shortening of period length, as predicted by our mathematical simulations. Together, our data demonstrate that perturbations induced by a single oncogene are sufficient to deregulate the mammalian circadian clock.
Kobayashi, M; Irisawa, H
1961-10-27
The latent period of relaxation of molluscan myocardium due to anodal current is much longer than that of contraction. Although the rate and the grade of relaxation are intimately related to both the stimulus condition and the muscle tension, the latent period of relaxation remains constant, except when the temperature of the bathing fluid is changed.
Unraveling the circadian clock in Arabidopsis.
Wang, Xiaoxue; Ma, Ligeng
2013-02-01
The circadian clock is an endogenous timing system responsible for coordinating an organism's biological processes with its environment. Interlocked transcriptional feedback loops constitute the fundamental architecture of the circadian clock. In Arabidopsis, three feedback loops, the core loop, morning loop and evening loop, comprise a network that is the basis of the circadian clock. The components of these three loops are regulated in distinct ways, including transcriptional, post-transcriptional and posttranslational mechanisms. The discovery of the DNA-binding and repressive activities of TOC1 has overturned our initial concept of its function in the circadian clock. The alternative splicing of circadian clock-related genes plays an essential role in normal functioning of the clock and enables organisms to sense environmental changes. In this review, we describe the regulatory mechanisms of the circadian clock that have been identified in Arabidopsis.
Circadian clock, cell cycle and cancer
Cansu Özbayer
2011-12-01
Full Text Available There are a few rhythms of our daily lives that we are under the influence. One of them is characterized by predictable changes over a 24-hour timescale called circadian clock. This cellular clock is coordinated by the suprachiasmatic nucleus in the anterior hypothalamus. The clock consist of an autoregulatory transcription-translation feedback loop compose of four genes/proteins; BMAL1, Clock, Cyrptochrome, and Period. BMAL 1 and Clock are transcriptional factors and Period and Cyrptochrome are their targets. Period and Cyrptochrome dimerize in the cytoplasm to enter the nucleus where they inhibit Clock/BMAL activity.It has been demonstrate that circadian clock plays an important role cellular proliferation, DNA damage and repair mechanisms, checkpoints, apoptosis and cancer.
Evaluating and Minimizing Distributed Cavity Phase Errors in Atomic Clocks
Li, Ruoxin
2010-01-01
We perform 3D finite element calculations of the fields in microwave cavities and analyze the distributed cavity phase errors of atomic clocks that they produce. The fields of cylindrical cavities are treated as an azimuthal Fourier series. Each of the lowest components produces clock errors with unique characteristics that must be assessed to establish a clock's accuracy. We describe the errors and how to evaluate them. We prove that sharp structures in the cavity do not produce large frequency errors, even at moderately high powers, provided the atomic density varies slowly. We model the amplitude and phase imbalances of the feeds. For larger couplings, these can lead to increased phase errors. We show that phase imbalances produce a novel distributed cavity phase error that depends on the cavity detuning. We also design improved cavities by optimizing the geometry and tuning the mode spectrum so that there are negligible phase variations, allowing this source of systematic error to be dramatically reduced.
Circadian clocks optimally adapt to sunlight for reliable synchronization
Hasegawa, Yoshihiko
2014-01-01
Circadian oscillation provides selection advantages through synchronization to the daylight cycle. However, a reliable clock must be designed through two conflicting properties: entrainability to properly respond to external stimuli such as sunlight, and regularity to oscillate with a precise period. These two aspects do not easily coexist because better entrainability favors higher sensitivity, which may sacrifice the regularity. To investigate conditions for satisfying the two properties, we analytically calculated the optimal phase-response curve with a variational method. Our result indicates an existence of a dead zone, i.e., a time during which external stimuli neither advance nor delay the clock. This result is independent of model details and a dead zone appears only when the input stimuli obey the time course of actual insolation. Our calculation demonstrates that every circadian clock with a dead zone is optimally adapted to the daylight cycle. Our result also explains the lack of a dead zone in osc...
Clock Synchronization and Navigation in the Vicinity of the Earth
Bahder, T B
2004-01-01
Clock synchronization is the backbone of applications such as high-accuracy satellite navigation, geolocation, space-based interferometry, and cryptographic communication systems. The high accuracy of synchronization needed over satellite-to-ground and satellite-to-satellite distances requires the use of general relativistic concepts. The role of geometrical optics and antenna phase center approximations are discussed in high accuracy work. The clock synchronization problem is explored from a general relativistic point of view, with emphasis on the local measurement process and the use of the tetrad formalism as the correct model of relativistic measurements. The treatment makes use of J. L. Synge's world function of space-time as a basic coordinate independent geometric concept. A metric is used for space-time in the vicinity of the Earth, where coordinate time is proper time on the geoid. The problem of satellite clock syntonization is analyzed by numerically integrating the geodesic equations of motion for...
Methods to study the mechanism of the Neurospora Circadian Clock
Cha, Joonseok; Zhou, Mian; Liu, Yi
2015-01-01
Eukaryotic circadian clocks are comprised of interlocked auto-regulatory feedback loops that control gene expression at the levels of transcription and translation. The filamentous fungus Neurospora crassa is an excellent model for the complex molecular network of regulatory mechanisms that are common to all eukaryotes. In the heart of the network, post-translational regulations and functions of the core clock elements are of major interest. This chapter will discuss the methods that were recently used to study the Neurospora circadian oscillator mechanisms at the molecular level. PMID:25662455
Liu, Y H; Hawk, R M; Ramaprasad, S
1995-01-01
RIF tumors implanted on mice feet were investigated for changes in relaxation times (T1 and T2) after photodynamic therapy (PDT). Photodynamic therapy was performed using Photofrin II as the photosensitizer and laser light at 630 nm. A home-built proton solenoid coil in the balanced configuration was used to accommodate the tumors, and the relaxation times were measured before, immediately after, and up to several hours after therapy. Several control experiments were performed untreated tumors, tumors treated with Photofrin II alone, or tumors treated with laser light alone. Significant increases in T1s of water protons were observed after PDT treatment. In all experiments, 31P spectra were recorded before and after the therapy to study the tumor status and to confirm the onset of PDT. These studies show significant prolongation of T1s after the PDT treatment. The spin-spin relaxation measurements, on the other hand, did not show such prolongation in T2 values after PDT treatment.
Madeo, Angela; Neff, Patrizio; Ghiba, Ionel-Dumitrel; Rosi, Giuseppe
2016-10-01
In this paper we derive, by means of a suitable least action principle, the duality jump conditions to be imposed at surfaces of discontinuity of the material properties in non-dissipative, linear-elastic, isotropic, Mindlin's and relaxed micromorphic media, respectively. The introduced theoretical framework allows the transparent set-up of different types of micro-macro connections which are intrinsically compatible with the governing bulk equations. To illustrate the interest of the many introduced jump conditions, we focus on the case of an interface between a classical Cauchy continuum on one side and a relaxed micromorphic one on the other side. As expected, we find a complete reflection in the frequency intervals for which band-gaps are known to occur in the relaxed micromorphic continuum and precise microstructure-related reflective patterns are identified. We repeat a similar study for analogous connections between a classical Cauchy continuum and a Mindlin's micromorphic one and we show that the reflective properties of the considered interfaces are drastically modified due to the fact that band-gaps are not allowed in standard Mindlin's micromorphic media. The present work opens the way towards the possibility of conceiving complex metastructures in which band-gap metamaterials and classical materials are coupled together to produce structures with completely new and unorthodox properties with respect to wave propagation, transmission and reflection. Last, but not least, indirect measurements of the material coefficients of the relaxed micromorphic model based upon real experiments of reflection and transmission in band-gap metamaterials are uncovered by the present work which makes them finally realizable in the short term.
Baryogenesis via Elementary Goldstone Higgs Relaxation
Gertov, Helene; Pearce, Lauren; Yang, Louis
2016-01-01
We extend the relaxation mechanism to the Elementary Goldstone Higgs frame- work. Besides studying the allowed parameter space of the theory we add the minimal ingredients needed for the framework to be phenomenologically viable. The very nature of the extended Higgs sector allows to consider very flat scalar potential directions along which the relaxation mechanism can be implemented. This fact translates into wider regions of applicability of the relaxation mechanism when compared to the Standard Model Higgs case. Our results show that, if the electroweak scale is not fundamental but radiatively generated, it is possible to generate the observed matter-antimatter asymmetry via the relaxation mechanism.
Entanglement of quantum clocks through gravity.
Castro Ruiz, Esteban; Giacomini, Flaminia; Brukner, Časlav
2017-03-21
In general relativity, the picture of space-time assigns an ideal clock to each world line. Being ideal, gravitational effects due to these clocks are ignored and the flow of time according to one clock is not affected by the presence of clocks along nearby world lines. However, if time is defined operationally, as a pointer position of a physical clock that obeys the principles of general relativity and quantum mechanics, such a picture is, at most, a convenient fiction. Specifically, we show that the general relativistic mass-energy equivalence implies gravitational interaction between the clocks, whereas the quantum mechanical superposition of energy eigenstates leads to a nonfixed metric background. Based only on the assumption that both principles hold in this situation, we show that the clocks necessarily get entangled through time dilation effect, which eventually leads to a loss of coherence of a single clock. Hence, the time as measured by a single clock is not well defined. However, the general relativistic notion of time is recovered in the classical limit of clocks.
Physical Layer Ethernet Clock Synchronization
2010-11-01
42 nd Annual Precise Time and Time Interval (PTTI) Meeting 77 PHYSICAL LAYER ETHERNET CLOCK SYNCHRONIZATION Reinhard Exel , Georg...5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES...Austrian Academy of Sciences Viktor Kaplan StraÃe 2, A-2700 Wiener Neustadt, Austria 8. PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING
Inertial Frames and Clock Rates
Kak, Subhash
2012-01-01
This article revisits the historiography of the problem of inertial frames. Specifically, the case of the twins in the clock paradox is considered to see that some resolutions implicitly assume inertiality for the non-accelerating twin. If inertial frames are explicitly identified by motion with respect to the large scale structure of the universe, it makes it possible to consider the relative inertiality of different frames.
Researchers Discover Plants Biological Clock
王全良
1996-01-01
Scientists who created glow-in-the-dark plants by shooting up seedlingswith firefly DNA have identified the first biological clock gene in plants. Discovery of the timepiece gene, which controls such biological rhythmsas daily leaf movements and proe openings, flower-blooming schedules andphotosynthesis cycles, could lead to a host of applications in ornamental horti-culture, agriculture and even human health. Many researchers believe that
Microresonator Frequency Comb Optical Clock
2014-07-22
Number Microresonator frequency comb optical clock Block 13: Supplementary Note © 2014 . Published in Optica , Vol. Ed. 0 1, (1) (2014), (, (1). DoD...Oscillators. http://dx.doi.org/10.1364/ OPTICA .1.000010 1. INTRODUCTION Optical frequency combs enable extraordinary measurement precision and accuracy...1, No. 1 / July 2014 / Optica 10 deviation for 1 s averaging is completely dominated by the Rb reference, and the microcomb contribution is only ɚ
Hanle Detection for Optical Clocks
Xiaogang Zhang
2015-01-01
Full Text Available Considering the strong inhomogeneous spatial polarization and intensity distribution of spontaneous decay fluorescence due to the Hanle effect, we propose and demonstrate a universe Hanle detection configuration of electron-shelving method for optical clocks. Experimental results from Ca atomic beam optical frequency standard with electron-shelving method show that a designed Hanle detection geometry with optimized magnetic field direction, detection laser beam propagation and polarization direction, and detector position can improve the fluorescence collection rate by more than one order of magnitude comparing with that of inefficient geometry. With the fixed 423 nm fluorescence, the improved 657 nm optical frequency standard signal intensity is presented. The potential application of the Hanle detection geometry designed for facilitating the fluorescence collection for optical lattice clock with a limited solid angle of the fluorescence collection has been discussed. The Hanle detection geometry is also effective for ion detection in ion optical clock and quantum information experiments. Besides, a cylinder fluorescence collection structure is designed to increase the solid angle of the fluorescence collection in Ca atomic beam optical frequency standard.
Effect of light on expression of clock genes in Xenopus laevis melanophores.
Magalhães Moraes, Maria Nathália de Carvalho; de Oliveira Poletini, Maristela; Ribeiro Ramos, Bruno Cesar; de Lima, Leonardo Henrique Ribeiro Graciani; de Lauro Castrucci, Ana Maria
2014-01-01
Light-dark cycles are considered important cues to entrain biological clocks. A feedback loop of clock gene transcription and translation is the molecular basis underlying the mechanism of both central and peripheral clocks. Xenopus laevis embryonic melanophores respond to light with melanin granule dispersion, response possibly mediated by the photopigment melanopsin. To test whether light modulates clock gene expression in Xenopus melanophores, we used qPCR to evaluate the relative mRNA levels of Per1, Per2, Clock and Bmal1 in cultured melanophores exposed to light-dark (LD) cycle or constant darkness (DD). LD cycles elicited temporal changes in the expression of Per1, Per2 and Bmal1. A 10-min pulse of blue light was able to increases the expression of Per1 and Per2. Red light had no effect on the expression of these clock genes. These data suggest the participation of a blue-wavelength sensitive pigment in the light-dark cycle-mediated oscillation of the endogenous clock. Our results add an important contribution to the emerging field of peripheral clocks, which in nonmammalian vertebrates have been mostly studied in Drosophila and Danio rerio. Within this context, we show that X. laevis melanophores, which have already led to melanopsin discovery, represent an ideal model to understanding circadian rhythms.
Rosane Garcia Collevatti
2015-08-01
Full Text Available Understanding the dispersal routes of Neotropical savanna tree species is an essential step to unravel the effects of past climate change on genetic patterns, species distribution and population demography. Here we reconstruct the demographic history and dispersal dynamics of the Neotropical savanna tree species Tabebuia aurea to understand the effects of Quaternary climate change on its current spatial patterns of genetic diversity. We sampled 285 individuals from 21 populations throughout Brazilian savannas and sequenced all individuals for three chloroplast intergenic spacers and ITS nrDNA. We analyzed data using a multi-model inference framework by coupling the relaxed random walk model, ecological niche modeling (ENM and statistical phylogeography. The most recent common ancestor of T. aurea lineages dated from ~4.0 ± 2.5 Ma. Tabebuia aurea lineages cyclically dispersed from the West towards the Central-West Brazil, and from the Southeast towards the East and Northeast Brazil, following the paleodistribution dynamics shown by the ENMs through the last glacial cycle. A historical refugium through time may have allowed dispersal of lineages among populations of Central Brazil, overlapping with population expansion during interglacial periods and the diversification of new lineages. Range and population expansion through the Quaternary were, respectively, the most frequent prediction from ENMs and the most likely demographic scenario from coalescent simulations. Consistent phylogeographic patterns among multiple modeling inferences indicate a promising approach, allowing us to understand how cyclical climate changes through the Quaternary drove complex population dynamics and the current patterns of species distribution and genetic diversity.
Maltsev, Victor A; Lakatta, Edward G
2008-01-15
For almost half a century it has been thought that the initiation of each heartbeat is driven by surface membrane voltage-gated ion channels (M clocks) within sinoatrial nodal cells. It has also been assumed that pacemaker cell automaticity is initiated at the maximum diastolic potential (MDP). Recent experimental evidence based on confocal cell imaging and supported by numerical modelling, however, shows that initiation of cardiac impulse is a more complex phenomenon and involves yet another clock that resides under the sarcolemma. This clock is the sarcoplasmic reticulum (SR): it generates spontaneous, but precisely timed, rhythmic, submembrane, local Ca(2+) releases (LCR) that appear not at the MDP but during the late, diastolic depolarization (DD). The Ca(2+) clock and M clock dynamically interact, defining a novel paradigm of robust cardiac pacemaker function and regulation. Rhythmic LCRs during the late DD activate inward Na(+)/Ca(2+) exchanger currents and ignite action potentials, which in turn induceCa(2+) transients and SR depletions, resetting the Ca(2+) clock. Both basal and reserve protein kinaseA-dependent phosphorylation of Ca(2+) cycling proteins control the speed and amplitude of SR Ca(2+) cycling to regulate the beating rate by strongly coupled Ca(2+) and M clocks.
Lin, Zhiyue; Kahrilas, P J; Roman, S; Boris, L; Carlson, D; Pandolfino, J E
2012-08-01
The Integrated Relaxation Pressure (IRP) is the esophageal pressure topography (EPT) metric used for assessing the adequacy of esophagogastric junction (EGJ) relaxation in the Chicago Classification of motility disorders. However, because the IRP value is also influenced by distal esophageal contractility, we hypothesized that its normal limits should vary with different patterns of contractility. Five hundred and twenty two selected EPT studies were used to compare the accuracy of alternative analysis paradigms to that of a motility expert (the 'gold standard'). Chicago Classification metrics were scored manually and used as inputs for MATLAB™ programs that utilized either strict algorithm-based interpretation (fixed abnormal IRP threshold of 15 mmHg) or a classification and regression tree (CART) model that selected variable IRP thresholds depending on the associated esophageal contractility. The sensitivity of the CART model for achalasia (93%) was better than that of the algorithm-based approach (85%) on account of using variable IRP thresholds that ranged from a low value of >10 mmHg to distinguish type I achalasia from absent peristalsis to a high value of >17 mmHg to distinguish type III achalasia from distal esophageal spasm. Additionally, type II achalasia was diagnosed solely by panesophageal pressurization without the IRP entering the algorithm. Automated interpretation of EPT studies more closely mimics that of a motility expert when IRP thresholds for impaired EGJ relaxation are adjusted depending on the pattern of associated esophageal contractility. The range of IRP cutoffs suggested by the CART model ranged from 10 to 17 mmHg. © 2012 Blackwell Publishing Ltd.
Lyulin, Alexey V; Michels, M A J
2007-08-24
Molecular-dynamics simulation is used to explore the influence of thermal and mechanical history of typical glassy polymers on their deformation. Polymer stress-strain and energy-strain developments have been followed for different deformation velocities, also in closed extension-recompression loops. The latter simulate for the first time the experimentally observed mechanical rejuvenation and overaging of polymers, and energy partitioning reveals essential differences between mechanical and thermal rejuvenation. All results can be qualitatively interpreted by considering the ratios of the relevant time scales: for cooling down, for deformation, and for segmental relaxation.
Glowacki, David R., E-mail: drglowacki@gmail.com [School of Chemistry, University of Bristol, Bristol BS8 1TS (United Kingdom); Department of Computer Science, University of Bristol, Bristol BS8 1UB (United Kingdom); PULSE Institute and Department of Chemistry, Stanford University, Stanford, California 94305 (United States); SLAC National Accelerator Laboratory, Menlo Park, California 94025 (United States); Orr-Ewing, Andrew J. [School of Chemistry, University of Bristol, Bristol BS8 1TS (United Kingdom); Harvey, Jeremy N. [Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Heverlee (Belgium)
2015-07-28
We describe a parallelized linear-scaling computational framework developed to implement arbitrarily large multi-state empirical valence bond (MS-EVB) calculations within CHARMM and TINKER. Forces are obtained using the Hellmann-Feynman relationship, giving continuous gradients, and good energy conservation. Utilizing multi-dimensional Gaussian coupling elements fit to explicitly correlated coupled cluster theory, we built a 64-state MS-EVB model designed to study the F + CD{sub 3}CN → DF + CD{sub 2}CN reaction in CD{sub 3}CN solvent (recently reported in Dunning et al. [Science 347(6221), 530 (2015)]). This approach allows us to build a reactive potential energy surface whose balanced accuracy and efficiency considerably surpass what we could achieve otherwise. We ran molecular dynamics simulations to examine a range of observables which follow in the wake of the reactive event: energy deposition in the nascent reaction products, vibrational relaxation rates of excited DF in CD{sub 3}CN solvent, equilibrium power spectra of DF in CD{sub 3}CN, and time dependent spectral shifts associated with relaxation of the nascent DF. Many of our results are in good agreement with time-resolved experimental observations, providing evidence for the accuracy of our MS-EVB framework in treating both the solute and solute/solvent interactions. The simulations provide additional insight into the dynamics at sub-picosecond time scales that are difficult to resolve experimentally. In particular, the simulations show that (immediately following deuterium abstraction) the nascent DF finds itself in a non-equilibrium regime in two different respects: (1) it is highly vibrationally excited, with ∼23 kcal mol{sup −1} localized in the stretch and (2) its post-reaction solvation environment, in which it is not yet hydrogen-bonded to CD{sub 3}CN solvent molecules, is intermediate between the non-interacting gas-phase limit and the solution-phase equilibrium limit. Vibrational
Ye H
2015-06-01
Full Text Available Hua Ye, Kai Yang, Xue-Mei Tan, Xiao-Juan Fu, Han-Xue LiDepartment of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of ChinaBackground: Recent studies have demonstrated that the clock gene PER1 regulates various tumor-related genes. Abnormal expressions and circadian rhythm alterations of PER1 are closely related to carcinogenesis. However, the dynamic circadian variations of PER1 and tumor-related genes at different stages of carcinogenesis remain unknown. This study was conducted to investigate the daily rhythm variation of PER1 and expression of tumor-related genes VEGF, KI67, C-MYC, and P53 in different stages of carcinogenesis.Materials and methods: Dimethylbenzanthracene was used to establish a golden hamster model of buccal mucosa carcinogenesis. Hamsters with normal buccal mucosa, precancerous lesion, and cancerous lesion were sacrificed at six different time points during a 24-hour period of a day. Pathological examination was conducted using routine hematoxylin and eosin staining. PER1, VEGF, KI67, C-MYC, and P53 mRNAs were detected by real-time reverse transcriptase polymerase chain reaction, and a cosinor analysis was applied to analyze the daily rhythm.Results: PER1, VEGF, C-MYC, and P53 mRNA exhibited daily rhythmic expression in three carcinogenesis stages, and KI67 mRNA exhibited daily rhythmic expression in the normal and precancerous stages. The daily rhythmic expression of KI67 was not observed in cancerous stages. The mesor and amplitude of PER1 and P53 mRNA expression decreased upon the development of cancer (P<0.05, whereas the mesor and amplitude of VEGF, KI67, and C-MYC mRNA increased upon the development of cancer (P<0.05. Compared with the normal tissues, the acrophases of PER1, VEGF, and C-MYC mRNA occurred earlier, whereas the acrophases of P53 and KI67 mRNA lagged remarkably in the precancerous lesions. In the cancer stage, the acrophases
The Implementation of E1 Clock Recovery
Wang Ziyu
2016-01-01
Full Text Available Clock transform and recovery is of significant importance in microwave TDM service, and it is always extracted from the E1 line data stream in most cases. However, intrinsically uncertain delay and jitter caused by packet transmission of E1 data information, may lead to the indexes of the data recovery clock exceed the clock performance template. Through analysis of the E1 clock indexes and measuring methods, this paper proposes a new clock recovery method. The method employs two buffers, the first RAM is used as a buffer to deduct excess information, and the second FIFO is used as a buffer to recovery the clock and data. The first buffer has a feedback from the second one, and is able to actively respond to changes in the data link and requests from the second one. The test results validate the effectiveness of the method, and the corresponding scheme is also valuable for the other communication systems.
The circadian clock coordinates ribosome biogenesis.
Céline Jouffe
Full Text Available Biological rhythms play a fundamental role in the physiology and behavior of most living organisms. Rhythmic circadian expression of clock-controlled genes is orchestrated by a molecular clock that relies on interconnected negative feedback loops of transcription regulators. Here we show that the circadian clock exerts its function also through the regulation of mRNA translation. Namely, the circadian clock influences the temporal translation of a subset of mRNAs involved in ribosome biogenesis by controlling the transcription of translation initiation factors as well as the clock-dependent rhythmic activation of signaling pathways involved in their regulation. Moreover, the circadian oscillator directly regulates the transcription of ribosomal protein mRNAs and ribosomal RNAs. Thus the circadian clock exerts a major role in coordinating transcription and translation steps underlying ribosome biogenesis.
Optical to microwave clock frequency ratios with a nearly continuous strontium optical lattice clock
Lodewyck, Jérôme; Bookjans, Eva; Robyr, Jean-Luc; Shi, Chunyan; Vallet, Grégoire; Targat, Rodolphe Le; Nicolodi, Daniele; Coq, Yann Le; Guéna, Jocelyne; Abgrall, Michel; Rosenbusch, Peter; Bize, Sébastien
2016-01-01
Optical lattice clocks are at the forefront of frequency metrology. Both the instability and systematic uncertainty of these clocks have been reported to be two orders of magnitude smaller than the best microwave clocks. For this reason, a redefinition of the SI second based on optical clocks seems possible in the near future. However, the operation of optical lattice clocks has not yet reached the reliability that microwave clocks have achieved so far. In this paper, we report on the operation of a strontium optical lattice clock that spans several weeks, with more than 80% uptime. We make use of this long integration time to demonstrate a reproducible measurement of frequency ratios between the strontium clock transition and microwave Cs primary and Rb secondary frequency standards.
Collisionally induced atomic clock shifts and correlations
Band, Y. B.; Osherov, I. [Departments of Chemistry and Electro-Optics and the Ilse Katz Center for Nano-Science, Ben-Gurion University, Beer-Sheva 84105 (Israel)
2011-07-15
We develop a formalism to incorporate exchange symmetry considerations into the calculation of collisional frequency shifts for atomic clocks using a density-matrix formalism. The formalism is developed for both fermionic and bosonic atomic clocks. Numerical results for a finite-temperature {sup 87}Sr {sup 1}S{sub 0} (F=9/2) atomic clock in a magic wavelength optical lattice are presented.
Molecular Mechanisms Underlying the Arabidopsis Circadian Clock
Nakamichi, Norihito
2011-01-01
A wide range of biological processes exhibit circadian rhythm, enabling plants to adapt to the environmental day–night cycle. This rhythm is generated by the so-called ‘circadian clock’. Although a number of genetic approaches have identified >25 clock-associated genes involved in the Arabidopsis clock mechanism, the molecular functions of a large part of these genes are not known. Recent comprehensive studies have revealed the molecular functions of several key clock-associated proteins. Thi...
The Square Light Clock and Special Relativity
Galli, J. Ronald; Amiri, Farhang
2012-01-01
A thought experiment that includes a square light clock is similar to the traditional vertical light beam and mirror clock, except it is made up of four mirrors placed at a 45[degree] angle at each corner of a square of length L[subscript 0], shown in Fig. 1. Here we have shown the events as measured in the rest frame of the square light clock. By…
Modes Of The Spiral Clock Gong
Perrin, R.; Charnley, T.; Swallowe, G. M.; Banu, H.
1993-03-01
The modal frequencies of a spiral clock gong have been measured. The mode numbers and forms of vibrations have been identified by finite element modelling and photographic techniques; very good agreement between modelling and experiment was achieved. All modes were found to be either purely in-plane or out-of-plane. In both cases plots of log (2 n - 1) vs. log ƒ yielded curves with two distinct regions, the transition occurring where the wavelength corresponded to one turn of the spiral. Both sets of lower modes were very complex but the modal frequencies above n = 11 were found to fit a modified form of Chladni's law. It is suggested that the modified Chladni law may form the basis of many musical sounds.
Distinction between Clock and Time, and a Suggested Experiment with Different Types of Clocks in GPS
Smarandache, Florentin
2013-03-01
The clock is an instrument for measuring the time, instrument that may not run perfectly (accurately) under certain conditions (like, say, in strong electromagnetic field, in strong gravitational field, in extremely high or low temperature, pressure, etc.), but this does not mean that time itself runs slower or faster as Einstein's Theory of Relativity asserts. We are referring to an absolute time, i.e. time measured not with respect to ether or non-ether, but with respect to an absolute mathematical reference frame. Several types of clocks could run at a more slowly rate in a moving frame of reference than other types of clocks; it depends on the construction material and functioning principle of each type of clock. Relativists say that ``gravity slows time''. This is incorrect, since actually gravity slows today's types of clocks. And one type of clock is slowed more or less than another type of clock. Not only gravity but other (electric, magnetic, etc.) fields or various medium composition elements or structures may slow or accelerate clocks that are in that medium. The clocks used today in the satellites for the GPS necessitate a correction with respect to the Earth clocks. But in the future, when new types of clocks will be built based on different construction material and functioning principle, the correction of the GPS clocks would be different. In order to make the distinction between ``clock'' and ``time'', we suggest a Experiment # 1 with different types of clocks for the GPS clocks, in order to prove that the resulted dilation and contraction factors are different from those obtained with today's cesium atomic clock.
Influences of clock resolution of bandwidth measurement on packet pair algorithm
Wu Weiguo; Zhang Wenjie; Qian Depei; Liu Yi
2007-01-01
Influences of the clock resolution of bandwidth estimator on the accuracy and stability of the packet pair algorithm was analyzed. A mathematic model has been established to reveal the relationship between the result deviation coefficient and the packet size, clock resolution and real bandwidth(value)of the measured route. A bandwidth self-adapting packet pair algorithm was presented based on the mathematic model to reduce the estimation error resulting from the clock resolution and to improve the accuracy and stability of measurement by adjusting the deviation coefficient. Experimental results have verified the validity and stability of the algorithm.
Improved Short-Term Clock Prediction Method for Real-Time Positioning
Yifei Lv
2017-06-01
Full Text Available The application of real-time precise point positioning (PPP requires real-time precise orbit and clock products that should be predicted within a short time to compensate for the communication delay or data gap. Unlike orbit correction, clock correction is difficult to model and predict. The widely used linear model hardly fits long periodic trends with a small data set and exhibits significant accuracy degradation in real-time prediction when a large data set is used. This study proposes a new prediction model for maintaining short-term satellite clocks to meet the high-precision requirements of real-time clocks and provide clock extrapolation without interrupting the real-time data stream. Fast Fourier transform (FFT is used to analyze the linear prediction residuals of real-time clocks. The periodic terms obtained through FFT are adopted in the sliding window prediction to achieve a significant improvement in short-term prediction accuracy. This study also analyzes and compares the accuracy of short-term forecasts (less than 3 h by using different length observations. Experimental results obtained from International GNSS Service (IGS final products and our own real-time clocks show that the 3-h prediction accuracy is better than 0.85 ns. The new model can replace IGS ultra-rapid products in the application of real-time PPP. It is also found that there is a positive correlation between the prediction accuracy and the short-term stability of on-board clocks. Compared with the accuracy of the traditional linear model, the accuracy of the static PPP using the new model of the 2-h prediction clock in N, E, and U directions is improved by about 50%. Furthermore, the static PPP accuracy of 2-h clock products is better than 0.1 m. When an interruption occurs in the real-time model, the accuracy of the kinematic PPP solution using 1-h clock prediction product is better than 0.2 m, without significant accuracy degradation. This model is of practical
Song I-Yeong's Armillary Clock
Kim, Sang Hyuk; Lee, Yong Sam
In 1669 (the 10th year of the reign of King Hyeonjong), Song I-Yeong (宋以穎, 1619-1692), who was a professor of astronomy at Gwansanggam (Bureau of Astronomy), developed the armillary clock which uses the weight power system of an alarm clock. The armillary clock is a unique astronomical clock that combines the traditional armillary sphere of Joseon and the principle of a Western alarm clock. Song I-Yeong's armillary clock was repaired in 1687-1688 according to the records, and since then not much is known about the history of the armillary clock. After many years, in the early 1930s which was the Japanese colonial era, Inchon (仁村) Kim Seong-Su (金性洙, 1891-1955) purchased the armillary clock at the Insa-dong antique street and donated to the Korea University Museum of the present time (designated as National Treasure No. 230 in 1985). Currently, the armillary clock is not in operation because some of the parts are damaged or lost.
Human intestinal circadian clock: expression of clock genes in colonocytes lining the crypt.
Pardini, L; Kaeffer, B; Trubuil, A; Bourreille, A; Galmiche, J-P
2005-01-01
Biological clock components have been detected in many epithelial tissues of the digestive tract of mammals (oral mucosa, pancreas, and liver), suggesting the existence of peripheral circadian clocks that may be entrainable by food. Our aim was to investigate the expression of main peripheral clock genes in colonocytes of healthy humans and in human colon carcinoma cell lines. The presence of clock components was investigated in single intact colonic crypts isolated by chelation from the biopsies of 25 patients (free of any sign of colonic lesions) undergoing routine colonoscopy and in cell lines of human colon carcinoma (Caco2 and HT29 clone 19A). Per-1, per-2, and clock mRNA were detected by real-time RT-PCR. The three-dimensional distributions of PER-1, PER-2, CLOCK, and BMAL1 proteins were recorded along colonic crypts by immunofluorescent confocal imaging. We demonstrate the presence of per-1, per-2, and clock mRNA in samples prepared from colonic crypts of 5 patients and in all cell lines. We also demonstrate the presence of two circadian clock proteins, PER-1 and CLOCK, in human colonocytes on crypts isolated from 20 patients (15 patients for PER-1 and 6 for CLOCK) and in colon carcinoma cells. Establishing the presence of clock proteins in human colonic crypts is the first step toward the study of the regulation of the intestinal circadian clock by nutrients and feeding rhythms.
Loss of circadian clock gene expression is associated with tumor progression in breast cancer.
Cadenas, Cristina; van de Sandt, Leonie; Edlund, Karolina; Lohr, Miriam; Hellwig, Birte; Marchan, Rosemarie; Schmidt, Marcus; Rahnenführer, Jörg; Oster, Henrik; Hengstler, Jan G
2014-01-01
Several studies suggest a link between circadian rhythm disturbances and tumorigenesis. However, the association between circadian clock genes and prognosis in breast cancer has not been systematically studied. Therefore, we examined the expression of 17 clock components in tumors from 766 node-negative breast cancer patients that were untreated in both neoadjuvant and adjuvant settings. In addition, their association with metastasis-free survival (MFS) and correlation to clinicopathological parameters were investigated. Aiming to estimate functionality of the clockwork, we studied clock gene expression relationships by correlation analysis. Higher expression of several clock genes (e.g., CLOCK, PER1, PER2, PER3, CRY2, NPAS2 and RORC) was found to be associated with longer MFS in univariate Cox regression analyses (HR<1 and FDR-adjusted P < 0.05). Stratification according to molecular subtype revealed prognostic relevance for PER1, PER3, CRY2 and NFIL3 in the ER+/HER2- subgroup, CLOCK and NPAS2 in the ER-/HER2- subtype, and ARNTL2 in HER2+ breast cancer. In the multivariate Cox model, only PER3 (HR = 0.66; P = 0.016) and RORC (HR = 0.42; P = 0.003) were found to be associated with survival outcome independent of established clinicopathological parameters. Pairwise correlations between functionally-related clock genes (e.g., PER2-PER3 and CRY2-PER3) were stronger in ER+, HER2- and low-grade carcinomas; whereas, weaker correlation coefficients were observed in ER- and HER2+ tumors, high-grade tumors and tumors that progressed to metastatic disease. In conclusion, loss of clock genes is associated with worse prognosis in breast cancer. Coordinated co-expression of clock genes, indicative of a functional circadian clock, is maintained in ER+, HER2-, low grade and non-metastasizing tumors but is compromised in more aggressive carcinomas.
Flagg, Thomas P; Cazorla, Olivier; Remedi, Maria S; Haim, Todd E; Tones, Michael A; Bahinski, Anthony; Numann, Randal E; Kovacs, Attila; Schaffer, Jean E; Nichols, Colin G; Nerbonne, Jeanne M
2009-01-02
Previous studies demonstrated increased fatty acid uptake and metabolism in MHC-FATP transgenic mice that overexpress fatty acid transport protein (FATP)1 in the heart under the control of the alpha-myosin heavy chain (alpha-MHC) promoter. Doppler tissue imaging and hemodynamic measurements revealed diastolic dysfunction, in the absence of changes in systolic function. The experiments here directly test the hypothesis that the diastolic dysfunction in MHC-FATP mice reflects impaired ventricular myocyte contractile function. In vitro imaging of isolated adult MHC-FATP ventricular myocytes revealed that mean diastolic sarcomere length is significantly (P<0.01) shorter than in wild-type (WT) cells (1.79+/-0.01 versus 1.84+/-0.01 microm). In addition, the relaxation rate (dL/dt) is significantly (P<0.05) slower in MHC-FATP than WT myocytes (1.58+/-0.09 versus 1.92+/-0.13 microm/s), whereas both fractional shortening and contraction rates are not different. Application of 40 mmol/L 2,3-butadionemonoxime (a nonspecific ATPase inhibitor that relaxes actin-myosin interactions) increased diastolic sarcomere length in both WT and MHC-FATP myocytes to the same length, suggesting that MHC-FATP myocytes are partially activated at rest. Direct measurements of intracellular Ca(2+) revealed that diastolic [Ca(2+)](i) is unchanged in MHC-FATP myocytes and the rate of calcium removal is unexpectedly faster in MHC-FATP than WT myocytes. Moreover, diastolic sarcomere length in MHC-FATP and WT myocytes was unaffected by removal of extracellular Ca(2+) or by buffering of intracellular Ca(2+) with the Ca(2+) chelator BAPTA (100 micromol/L), indicating that elevated intracellular Ca(2+) does not underlie impaired diastolic function in MHC-FATP ventricular myocytes. Functional assessment of skinned myocytes, however, revealed that myofilament Ca(2+) sensitivity is markedly increased in MHC-FATP, compared with WT, ventricular cells. In addition, biochemical experiments demonstrated
Yan, Zhifeng; Hilpert, Markus
2014-10-01
Bacterial chemotaxis can enhance the bioremediation of contaminants in aqueous and subsurface environments if the contaminant is a chemoattractant that the bacteria degrade. The process can be promoted by traveling bands of chemotactic bacteria that form due to metabolism-generated gradients in chemoattractant concentration. We developed a multiple-relaxation-time (MRT) lattice-Boltzmann method (LBM) to model chemotaxis, because LBMs are well suited to model reactive transport in the complex geometries that are typical for subsurface porous media. This MRT-LBM can attain a better numerical stability than its corresponding single-relaxation-time LBM. We performed simulations to investigate the effects of substrate diffusion, initial bacterial concentration, and hydrodynamic dispersion on the formation, shape, and propagation of bacterial bands. Band formation requires a sufficiently high initial number of bacteria and a small substrate diffusion coefficient. Uniform flow does not affect the bands while shear flow does. Bacterial bands can move both upstream and downstream when the flow velocity is small. However, the bands disappear once the velocity becomes too large due to hydrodynamic dispersion. Generally bands can only be observed if the dimensionless ratio between the chemotactic sensitivity coefficient and the effective diffusion coefficient of the bacteria exceeds a critical value, that is, when the biased movement due to chemotaxis overcomes the diffusion-like movement due to the random motility and hydrodynamic dispersion.
Hales, Patrick W; Kirkham, Fenella J; Clark, Christopher A
2016-02-01
Many MRI techniques require prior knowledge of the T1-relaxation time of blood (T1bl). An assumed/fixed value is often used; however, T1bl is sensitive to magnetic field (B0), haematocrit (Hct), and oxygen saturation (Y). We aimed to combine data from previous in vitro measurements into a mathematical model, to estimate T1bl as a function of B0, Hct, and Y. The model was shown to predict T1bl from in vivo studies with a good accuracy (± 87 ms). This model allows for improved estimation of T1bl between 1.5-7.0 T while accounting for variations in Hct and Y, leading to improved accuracy of MRI-derived perfusion measurements.
Mischenko, I.; Chuev, M.
2016-12-01
Principal difference of magnetic nanoparticles from the bulk matter which cannot be ignored when constructing upon them combined metamaterials and modern devices is the essential influence on their behavior thermal fluctuations of the environment. These disturbances lead to specific distributions of the particles characteristics and to stochastic reorientations of their magnetic moments. On the basis of quantum-mechanical representation of the particle possessing intrinsic magnetic anisotropy and being placed onto the external magnetic field we developed general approach to describe equilibrium magnetization curves and relaxation Mössbauer spectra of magnetic nanoparticles for diagnostics of magnetic nanomaterials in the whole temperature or external field ranges. This approach has universal character and may be applied not only to the systems under thermal equilibrium, but may in principle describe macroscopic dynamical phenomena such as magnetization reversal.
Nemati Hasan
2011-01-01
Full Text Available A numerical investigation of the two-dimensional laminar flow and heat transfer a rotating circular cylinder with uniform planar shear, where the free-stream velocity varies linearly across the cylinder using Multi-Relaxation-Time Lattice Boltzmann method is conducted. The effects of variation of Reynolds number, rotational speed ratio at shear rate 0.1, blockage ratio 0.1 and Prandtl number 0.71 are studied. The Reynolds number changing from 50 to 160 for three rotational speed ratios of 0, 0.5, 1 is investigated. Results show that flow and heat transfer depends significantly on the rotational speed ratio as well as the Reynolds number. The effect of Reynolds number on the vortex-shedding frequency and period-surface Nusselt numbers is overall very strong compared with rotational speed ratio. Flow and heat conditions characteristics such as lift and drag coefficients, Strouhal number and Nusselt numbers are studied.
Md. Noor-E-Alam
2012-01-01
Full Text Available p-cycle networks have attracted a considerable interest in the network survivability literature in recent years. However, most of the existing work assumes a known network topology upon which to apply p-cycle restoration. In the present work, we develop an incremental topology optimization ILP for p-cycle network design, where a known topology can be amended with new fibre links selected from a set of eligible spans. The ILP proves to be relatively easy to solve for small test case instances but becomes computationally intensive on larger networks. We then follow with a relaxation-based decomposition approach to overcome this challenge. The decomposition approach significantly reduces computational complexity of the problem, allowing the ILP to be solved in reasonable time with no statistically significant impact on solution optimality.
Uncertainty principle in larmor clock
QIAO Chuan; REN Zhong-Zhou
2011-01-01
It is well known that the spin operators of a quantum particle must obey uncertainty relations.We use the uncertainty principle to study the Larmor clock.To avoid breaking the uncertainty principle,Larmor time can be defined as the ratio of the phase difference between a spin-up particle and a spin-down particle to the corresponding Larmor frequency.The connection between the dwell time and the Larmor time has also been confirmed.Moreover,the results show that the behavior of the Larmor time depends on the height and width of the barrier.
Clock genes, chronotypes and diseases
Bogdan I. Voinescu
2009-08-01
Full Text Available Many common diseases in humans (such as cancer, heart disease, diabetes mellitus orpsychiatric disorders, such as depression seem to be linked to disruptions of circadian cycles and toclock genes variation. It is unlikely that such diseases to be caused by a genetic variation within a singlegene. They must be influenced by complex interactions among multiple genes, as well as environmentaland lifestyle factors. Therefore, it is important to understand how the resulting perturbations in ourcircadian biology could affect our physiological processes and susceptibility to disease. Associationsbetween the polymorphisms of the main components of the circadian molecular clock, circadian type(also known as diurnal preference or chronotype and diseases are presented.
Magnetization Transfer Induced Biexponential Longitudinal Relaxation
Prantner, Andrew M.; Bretthorst, G. Larry; Neil, Jeffrey J.; Garbow, Joel R.; Ackerman, Joseph J.H.
2009-01-01
Longitudinal relaxation of brain water 1H magnetization in mammalian brain in vivo is typically analyzed on a per voxel basis using a monoexponential model, thereby assigning a single relaxation time constant to all 1H magnetization within a given voxel. This approach was tested by obtaining inversion recovery data from grey matter of rats at 64 exponentially-spaced recovery times. Using Bayesian probability for model selection, brain water data were best represented by a biexponential function characterized by fast and slow relaxation components. At 4.7 T, the amplitude fraction of the rapidly relaxing component is 3.4 ± 0.7 % with a rate constant of 44 ± 12 s-1 (mean ± SD; 174 voxels from 4 rats). The rate constant of the slow relaxing component is 0.66 ± 0.04 s-1. At 11.7 T, the corresponding values are 6.9 ± 0.9 %, 19 ± 5 s-1, and 0.48 ± 0.02 s-1 (151 voxels from 4 rats). Several putative mechanisms for biexponential relaxation behavior were evaluated, and magnetization transfer between bulk water protons and non-aqueous protons was determined to be the source of biexponential longitudinal relaxation. MR methods requiring accurate quantification of longitudinal relaxation may need to take this effect explicitly into account. PMID:18759367
Gigabit Ethernet Asynchronous Clock Compensation FIFO
Duhachek, Jeff
2012-01-01
Clock compensation for Gigabit Ethernet is necessary because the clock recovered from the 1.25 Gb/s serial data stream has the potential to be 200 ppm slower or faster than the system clock. The serial data is converted to 10-bit parallel data at a 125 MHz rate on a clock recovered from the serial data stream. This recovered data needs to be processed by a system clock that is also running at a nominal rate of 125 MHz, but not synchronous to the recovered clock. To cross clock domains, an asynchronous FIFO (first-in-first-out) is used, with the write pointer (wprt) in the recovered clock domain and the read pointer (rptr) in the system clock domain. Because the clocks are generated from separate sources, there is potential for FIFO overflow or underflow. Clock compensation in Gigabit Ethernet is possible by taking advantage of the protocol data stream features. There are two distinct data streams that occur in Gigabit Ethernet where identical data is transmitted for a period of time. The first is configuration, which happens during auto-negotiation. The second is idle, which occurs at the end of auto-negotiation and between every packet. The identical data in the FIFO can be repeated by decrementing the read pointer, thus compensating for a FIFO that is draining too fast. The identical data in the FIFO can also be skipped by incrementing the read pointer, which compensates for a FIFO draining too slowly. The unique and novel features of this FIFO are that it works in both the idle stream and the configuration streams. The increment or decrement of the read pointer is different in the idle and compensation streams to preserve disparity. Another unique feature is that the read pointer to write pointer difference range changes between compensation and idle to minimize FIFO latency during packet transmission.
Circadian molecular clock in lung pathophysiology.
Sundar, Isaac K; Yao, Hongwei; Sellix, Michael T; Rahman, Irfan
2015-11-15
Disrupted daily or circadian rhythms of lung function and inflammatory responses are common features of chronic airway diseases. At the molecular level these circadian rhythms depend on the activity of an autoregulatory feedback loop oscillator of clock gene transcription factors, including the BMAL1:CLOCK activator complex and the repressors PERIOD and CRYPTOCHROME. The key nuclear receptors and transcription factors REV-ERBα and RORα regulate Bmal1 expression and provide stability to the oscillator. Circadian clock dysfunction is implicated in both immune and inflammatory responses to environmental, inflammatory, and infectious agents. Molecular clock function is altered by exposomes, tobacco smoke, lipopolysaccharide, hyperoxia, allergens, bleomycin, as well as bacterial and viral infections. The deacetylase Sirtuin 1 (SIRT1) regulates the timing of the clock through acetylation of BMAL1 and PER2 and controls the clock-dependent functions, which can also be affected by environmental stressors. Environmental agents and redox modulation may alter the levels of REV-ERBα and RORα in lung tissue in association with a heightened DNA damage response, cellular senescence, and inflammation. A reciprocal relationship exists between the molecular clock and immune/inflammatory responses in the lungs. Molecular clock function in lung cells may be used as a biomarker of disease severity and exacerbations or for assessing the efficacy of chronotherapy for disease management. Here, we provide a comprehensive overview of clock-controlled cellular and molecular functions in the lungs and highlight the repercussions of clock disruption on the pathophysiology of chronic airway diseases and their exacerbations. Furthermore, we highlight the potential for the molecular clock as a novel chronopharmacological target for the management of lung pathophysiology.
Plikus, Maksim V; Van Spyk, Elyse N; Pham, Kim; Geyfman, Mikhail; Kumar, Vivek; Takahashi, Joseph S; Andersen, Bogi
2015-06-01
Historically, work on peripheral circadian clocks has been focused on organs and tissues that have prominent metabolic functions, such as the liver, fat, and muscle. In recent years, skin has emerged as a model for studying circadian clock regulation of cell proliferation, stem cell functions, tissue regeneration, aging, and carcinogenesis. Morphologically, skin is complex, containing multiple cell types and structures, and there is evidence for a functional circadian clock in most, if not all, of its cell types. Despite the complexity, skin stem cell populations are well defined, experimentally tractable, and exhibit prominent daily cell proliferation cycles. Hair follicle stem cells also participate in recurrent, long-lasting cycles of regeneration: the hair growth cycles. Among other advantages of skin is a broad repertoire of available genetic tools enabling the creation of cell type-specific circadian mutants. Also, due to the accessibility of skin, in vivo imaging techniques can be readily applied to study the circadian clock and its outputs in real time, even at the single-cell level. Skin provides the first line of defense against many environmental and stress factors that exhibit dramatic diurnal variations such as solar ultraviolet (UV) radiation and temperature. Studies have already linked the circadian clock to the control of UVB-induced DNA damage and skin cancers. Due to the important role that skin plays in the defense against microorganisms, it also represents a promising model system to further explore the role of the clock in the regulation of the body's immune functions. To that end, recent studies have already linked the circadian clock to psoriasis, one of the most common immune-mediated skin disorders. Skin also provides opportunities to interrogate the clock regulation of tissue metabolism in the context of stem cells and regeneration. Furthermore, many animal species feature prominent seasonal hair molt cycles, offering an attractive model
Arabidopsis circadian clock and photoperiodism: time to think about location
Imaizumi, Takato
2009-01-01
Plants possess a circadian clock that enables them to coordinate internal biological events with external daily changes. Recent studies in Arabidopsis revealed that tissue specific clock components exist and that the clock network architecture also varies within different organs. These findings indicate that the makeup of circadian clock(s) within a plant is quite variable. Plants utilize the circadian clock to measure day-length changes for regulating seasonal responses, such as flowering. T...
1H relaxation dispersion in solutions of nitroxide radicals: Influence of electron spin relaxation
Kruk, D.; Korpała, A.; Kubica, A.; Kowalewski, J.; Rössler, E. A.; Moscicki, J.
2013-03-01
The work presents a theory of nuclear (1H) spin-lattice relaxation dispersion for solutions of 15N and 14N radicals, including electron spin relaxation effects. The theory is a generalization of the approach presented by Kruk et al. [J. Chem. Phys. 137, 044512 (2012)], 10.1063/1.4736854. The electron spin relaxation is attributed to the anisotropic part of the electron spin-nitrogen spin hyperfine interaction modulated by rotational dynamics of the paramagnetic molecule, and described by means of Redfield relaxation theory. The 1H relaxation is caused by electron spin-proton spin dipole-dipole interactions which are modulated by relative translational motion of the solvent and solute molecules. The spectral density characterizing the translational dynamics is described by the force-free-hard-sphere model. The electronic relaxation influences the 1H relaxation by contributing to the fluctuations of the inter-molecular dipolar interactions. The developed theory is tested against 1H spin-lattice relaxation dispersion data for glycerol solutions of 4-oxo-TEMPO-d16-15N and 4-oxo-TEMPO-d16-14N covering the frequency range of 10 kHz-20 MHz. The studies are carried out as a function of temperature starting at 328 K and going down to 290 K. The theory gives a consistent overall interpretation of the experimental data for both 14N and 15N systems and explains the features of 1H relaxation dispersion resulting from the electron spin relaxation.
Global synchronization of parallel processors using clock pulse width modulation
Chen, Dong; Ellavsky, Matthew R.; Franke, Ross L.; Gara, Alan; Gooding, Thomas M.; Haring, Rudolf A.; Jeanson, Mark J.; Kopcsay, Gerard V.; Liebsch, Thomas A.; Littrell, Daniel; Ohmacht, Martin; Reed, Don D.; Schenck, Brandon E.; Swetz, Richard A.
2013-04-02
A circuit generates a global clock signal with a pulse width modification to synchronize processors in a parallel computing system. The circuit may include a hardware module and a clock splitter. The hardware module may generate a clock signal and performs a pulse width modification on the clock signal. The pulse width modification changes a pulse width within a clock period in the clock signal. The clock splitter may distribute the pulse width modified clock signal to a plurality of processors in the parallel computing system.
Fast Clock Recovery for Digital Communications
Tell, R. G.
1985-01-01
Circuit extracts clock signal from random non-return-to-zero data stream, locking onto clock within one bit period at 1-gigabitper-second data rate. Circuit used for synchronization in opticalfiber communications. Derives speed from very short response time of gallium arsenide metal/semiconductor field-effect transistors (MESFET's).
Could Atomic clocks be affected by neutrinos?
Hanafi, Hanaa
2016-01-01
An atomic clock is a clock device that uses an electronic transition frequency of the electromagnetic spectrum of atoms as a frequency standard in order to derive a time standard since time is the reciprocal of frequency. If the electronic transition frequencies are in an "optical region", we are talking in this case about optical atomic clocks. If they are in an "microwave region" these atomic clocks are made of the metallic element cesium so they are called Cesium atomic clocks. Atomic clocks are the most accurate time and frequency standards known despite the different perturbations that can affect them, a lot of researches were made in this domain to show how the transitions can be different for different type of perturbations..Since atomic clocks are very sensitive devices, based on coherent states (A coherent state tends to loose coherence after interacting). One question can arise (from a lot of questions) which is why cosmic neutrinos are not aﬀecting these clocks? The answer to this question requir...
Internal Clock Drift Estimation in Computer Clusters
Hicham Marouani
2008-01-01
Full Text Available Most computers have several high-resolution timing sources, from the programmable interrupt timer to the cycle counter. Yet, even at a precision of one cycle in ten millions, clocks may drift significantly in a single second at a clock frequency of several GHz. When tracing the low-level system events in computer clusters, such as packet sending or reception, each computer system records its own events using an internal clock. In order to properly understand the global system behavior and performance, as reported by the events recorded on each computer, it is important to estimate precisely the clock differences and drift between the different computers in the system. This article studies the clock precision and stability of several computer systems, with different architectures. It also studies the typical network delay characteristics, since time synchronization algorithms rely on the exchange of network packets and are dependent on the symmetry of the delays. A very precise clock, based on the atomic time provided by the GPS satellite network, was used as a reference to measure clock drifts and network delays. The results obtained are of immediate use to all applications which depend on computer clocks or network time synchronization accuracy.
Atomic clocks with suppressed blackbody radiation shift
Yudin, V I; Okhapkin, M V; Bagayev, S N; Tamm, Chr; Peik, E; Huntemann, N; Mehlstaubler, T E; Riehle, F
2011-01-01
We develop a nonstandard concept of atomic clocks where the blackbody radiation shift (BBRS) and its temperature fluctuations can be dramatically suppressed (by one to three orders of magnitude) independent of the environmental temperature. The suppression is based on the fact that in a system with two accessible clock transitions (with frequencies $\
A circadian clock in Saccharomyces cerevisiae
Eelderink-Chen, Zheng; Mazzotta, Gabriella; Sturre, Marcel; Bosman, Jasper; Roenneberg, Till; Merrow, Martha
2010-01-01
Circadian timing is a fundamental biological process, underlying cellular physiology in animals, plants, fungi, and cyanobacteria. Circadian clocks organize gene expression, metabolism, and behavior such that they occur at specific times of day. The biological clocks that orchestrate these daily cha
A clock synchronization skeleton based on RTAI
Huang, Y.; Visser, P.M.; Broenink, Johannes F.
2006-01-01
This paper presents a clock synchronization skeleton based on RTAI (Real Time Application Interface). The skeleton is a thin layer that provides unified but extendible interfaces to the underlying operating system, the synchronization algorithms and the upper level applications in need of clock
"Molecular Clock" Analogs: A Relative Rates Exercise
Wares, John P.
2008-01-01
Although molecular clock theory is a commonly discussed facet of evolutionary biology, undergraduates are rarely presented with the underlying information of how this theory is examined relative to empirical data. Here a simple contextual exercise is presented that not only provides insight into molecular clocks, but is also a useful exercise for…
Progress of the ~(87)Rb Fountain Clock
ZHOU Zi-Chao; WEI Rong; SHI Chun-Yan; LV De-Sheng; LI Tang; WANG Yu-Zhu
2009-01-01
A fountain atomic clock based on cold ~(87)Rb atoms has been in operation in our laboratory for several months.We therefore report the design of the rubidium fountain clock including its physical package,optical system and daily operation.Ramsey fringes have been attained with the signal to noise ratio of about 100.
High accuracy correction of blackbody radiation shift in an optical lattice clock
Middelmann, Thomas; Lisdat, Christian; Sterr, Uwe
2012-01-01
We have determined the frequency shift that blackbody radiation is inducing on the $5s^2$ $^1$S$_0$ -- $5s5p$ $^3$P$_0$ clock transition in strontium. Previously its uncertainty limited the uncertainty of strontium lattice clocks to $1\\times10^{-16}$. Now the uncertainty associated to the black body radiation shift correction translates to $5\\times 10^{-18}$ relative frequency uncertainty at room temperature. Our evaluation is based on a measurement of the differential dc-polarizability of the two clock states and on a modeling of the dynamic contribution using this value and experimental data for other atomic properties.
Phase noise analysis of clock recovery based on an optoelectronic phase-locked loop
Zibar, Darko; Mørk, Jesper; Oxenløwe, Leif Katsuo
2007-01-01
A detailed theoretical analysis of a clock-recovery (CR) scheme based on an optoelectronic phase-locked loop is presented. The analysis emphasizes the phase noise performance, taking into account the noise of the input data signal, the local voltage-controlled oscillator (VCO), and the laser....... It is shown that a large loop length results in a higher timing jitter of the recovered clock signal. The impact of the loop length on the clock signal jitter can be reduced by using a low-noise VCO and a low loop filter bandwidth. Using the model, the timing jitter of the recovered optical and electrical...
Single electron relativistic clock interferometer
Bushev, P. A.; Cole, J. H.; Sholokhov, D.; Kukharchyk, N.; Zych, M.
2016-09-01
Although time is one of the fundamental notions in physics, it does not have a unique description. In quantum theory time is a parameter ordering the succession of the probability amplitudes of a quantum system, while according to relativity theory each system experiences in general a different proper time, depending on the system's world line, due to time dilation. It is therefore of fundamental interest to test the notion of time in the regime where both quantum and relativistic effects play a role, for example, when different amplitudes of a single quantum clock experience different magnitudes of time dilation. Here we propose a realization of such an experiment with a single electron in a Penning trap. The clock can be implemented in the electronic spin precession and its time dilation then depends on the radial (cyclotron) state of the electron. We show that coherent manipulation and detection of the electron can be achieved already with present day technology. A single electron in a Penning trap is a technologically ready platform where the notion of time can be probed in a hitherto untested regime, where it requires a relativistic as well as quantum description.