Time Scale Of Transition Research Articles

Longitudinal variability of organic nutrients in the North Atlantic subtropical gyre

We combine modelled timescales of ocean circulation with satellite-retrieved and in situ biogeochemical observations collected in spring along 24.5°N in the subtropical North Atlantic. Longitudinal gradients in the distribution of dissolved organic nitrogen (DON) and dissolved organic phosphorus (DOP) and in other biogeochemical parameters are associated with the longitudinal variability in physical forcing and in the eastward increase of the timescale of advective transport. The western (West of 70°W) and eastern (East of 30°W) margins of the subtropical gyre appear influenced by the productive regions of the Gulf Stream and upwelling zones off Africa, respectively. Within the oligotrophic zone between 70 and 31°W, at approximately 46°W there is a change in the nutrient-controlling factors from the western ultraoligotrophic with barely any seasonal cycle to an eastern oligotrophic environment with a more intense mixed layer dynamics. The allochthonous supply of semilabile-DOP may be important in the western sector of the oligotrophic gyre (approx. 70–46°W) where, together with the combination of shallow mixed layers, almost permanent stratification and high water temperatures create a niche for the growth of diazotrophs, which we detect from space. Turnover estimates exceeding 3yr suggest that even reactive fractions of DON are unlikely to be a significant N source. In the eastern sector of the oligotrophic gyre (46–31°W), transit timescales longer than 3 years suggest that the allochthonous supply of the semilabile DOP is negligible due to its exhaustion. Here, an intense mixed layer dynamics favours nutrient supply from below the mixed layer. We speculate that longitudinal variability in physical forcing and gradients in the timescale of advection, combined with distinct turnover timescales of reactive fractions of DON and DOP, drive diverse phytoplankton assemblages and surface nitrogen fixation gradients across our region of investigation.

Physical Modeling of Stress Communication between Chromosome Loci

The organizational dynamics of chromosomal DNA are critical to many biological processes including genetic regulation, recombination, condensation, and segregation. The physical understanding of such processes would be greatly improved by predictive, quantitative modeling that can be directly compared to experimental measurements. Previous work has examined or modeled either single locus dynamics or the organization of multiple loci through static or ensemble measurements. New tools in fluorescence microscopy now enable the real-time tracking of several loci simultaneously, requiring additional physical model development to interpret the observed behaviors. Toward this end, we employ a polymer dynamics framework to predict the correlation in the velocities of two loci connected by chromatin. This predictive theory uses a minimal number of fitting parameters and reveals that the signature of correlated motion between loci can be identified by varying the lag time between locus position measurements. Our results predict that as the lag time interval increases, the dual-loci dynamic behavior changes from being uncorrelated to behaving as an effective single locus. This transition is determined by the timescale of the stress communication between loci through the intervening segments. We show that this single transition timescale is the only fit parameter needed to make direct quantitative comparisons to the in vivo motion of fluorescently labeled chromosome loci. We further show that our predictions are qualitatively consistent with recently published experimental measurements of the motion of sets of two loci on a single chromosome in budding yeast during interphase. Furthermore, this theoretical framework enables the detection of dynamically coupled chromosome regions from the signature of their correlated motion.

VARIABILITY OF KEPLER SOLAR-LIKE STARS HARBORING SMALL EXOPLANETS

ABSTRACT We examine Kepler light-curve variability on habitable zone transit timescales for a large uniform sample of spectroscopically studied Kepler exoplanet host stars. The stars, taken from Everett et al., are solar-like in their properties and each harbors at least one exoplanet (or candidate) of radius ≤2.5 R e ?> . The variability timescale examined is typical for habitable zone planets orbiting solar-like stars and we note that the discovery of the smallest exoplanets (≤1.2 R e ?> ) with corresponding transit depths of less than ∼0.18 mmag occur for the brightest and photometrically quietest stars. Thus, these detections are quite rare in Kepler observations. Some brighter and more evolved stars (subgiants), the latter of which often show large radial velocity jitter, are found to be among the photometrically quietest solar-like stars in our sample and the most likely small planet transit hunting grounds. The Sun is discussed as a solar-like star proxy to provide insight into the nature and cause of photometric variability. It is shown that Kepler’s broad, visible light observations are insensitive to variability caused by chromospheric activity that may be present in the observed stars.

How long will it take? Conceptualizing the temporal dynamics of energy transitions

Transitioning away from our current global energy system is of paramount importance. The speed at which a transition can take place—its timing, or temporal dynamics—is a critical element of consideration. This study therefore investigates the issue of time in global and national energy transitions by asking: What does the mainstream academic literature suggest about the time scale of energy transitions? Additionally, what does some of the more recent empirical data related to transitions say, or challenge, about conventional views? In answering these questions, the article presents a “mainstream” view of energy transitions as long, protracted affairs, often taking decades to centuries to occur. However, the article then offers some empirical evidence that the predominant view of timing may not always be supported by the evidence. With this in mind, the final part of the article argues for more transparent conceptions and definitions of energy transitions, and it asks for analysis that recognizes the causal complexity underlying them.

Discovery of an eclipsing dwarf nova in the ancient nova shell Te 11

We report on the discovery of an eclipsing dwarf nova (DN) inside the peculiar, bilobed nebula Te 11. Modelling of high-speed photometry of the eclipse finds the accreting white dwarf to have a mass 1.18 M$_\odot$ and temperature 13 kK. The donor spectral type of M2.5 results in a distance of 330 pc, colocated with Barnard's loop at the edge of the Orion-Eridanus superbubble. The perplexing morphology and observed bow shock of the slowly-expanding nebula may be explained by strong interactions with the dense interstellar medium in this region. We match the DN to the historic nova of 483 CE in Orion and postulate that the nebula is the remnant of this eruption. This connection supports the millennia time scale of the post-nova transition from high to low mass-transfer rates. Te 11 constitutes an important benchmark system for CV and nova studies as the only eclipsing binary out of just three DNe with nova shells.

KEPLERMISSION STELLAR AND INSTRUMENT NOISE PROPERTIES REVISITED

An earlier study of the Kepler Mission noise properties on time scales of primary relevance to detection of exoplanet transits found that higher than expected noise followed to a large extent from the stars, rather than instrument or data analysis performance. The earlier study over the first six quarters of Kepler data is extended to the full four years ultimately comprising the mission. Efforts to improve the pipeline data analysis have been successful in reducing noise levels modestly as evidenced by smaller values derived from the current data products. The new analyses of noise properties on transit time scales show significant changes in the component attributed to instrument and data analysis, with essentially no change in the inferred stellar noise. We also extend the analyses to time scales of several days, instead of several hours to better sample stellar noise that follows from magnetic activity. On the longer time scale there is a shift in stellar noise for solar-type stars to smaller values in comparison to solar values.

Interfacial dynamics of polydimethylsiloxane adsorbed on fumed metal oxide particles of a wide range of specific surface area

Interfacial dynamics of polydimethylsiloxane adsorbed on silica and titania nanoparticles of a wide range of specific surface area (S, 25–342 m2/g) and size (8–80 nm in diameter for primary particles) was studied employing differential scanning calorimetry (DSC) and broadband dielectric spectroscopy (BDS). Both techniques revealed an increase of the interfacial polymer fraction with increasing of surface roughness S, accompanied with an enhancement of dynamics and cooperativity of the corresponding segmental relaxation (interfacial relaxation, αint). At the same time, bulk dynamics (glass transition temperature, Tg, and time scale of α relaxation) was not significantly affected. The results are discussed in terms of bimodal conformations of polymers adsorbed on solid surfaces and in terms of an increase of the apparent thickness of the interfacial layer with increasing of surface roughness.

Modeling river dune development and dune transition to upper stage plane bed

AbstractLarge asymmetric bedforms known as dunes commonly dominate the bed of sand rivers. Due to the turbulence generation over their stoss and lee sides, dunes are of central importance in predicting hydraulic roughness and water levels. During floods in steep alluvial rivers, dunes are observed to grow rapidly as flow strength increases, undergoing an unstable transition regime, after which they are washed out in what is called upper stage plane bed. This transition of dunes to upper stage plane bed is associated with high transport of bed sediment in suspension and large decrease in bedform roughness. In the present study, we aim to improve the prediction of dune development and dune transition to upper stage plane bed by introducing the transport of suspended sediment in an existing dune evolution model. In addition, flume experiments are carried out to investigate dune development under bed load and suspended load dominated transport regimes, and to get insight in the time scales related to the transition of dunes to upper stage plane bed. Simulations with the extended model including the transport of suspended sediment show significant improvement in the prediction of equilibrium dune parameters (e.g. dune height, dune length, dune steepness, dune migration rate, dune lee side slope) both under bed load dominant and suspended load dominant transport regimes. The chosen modeling approach also allows us to model the transition of dunes to upper stage plane bed which was not possible with the original dune evolution model. The extended model predicts change in the dune shapes as was observed in the flume experiments with decreasing dune heights and dune lee slopes. Furthermore, the time scale of dune transition to upper stage plane bed was quite well predicted by the extended model. Copyright © 2015 John Wiley & Sons, Ltd.

A Geographic Mosaic of Climate Change Impacts on Terrestrial Vegetation: Which Areas Are Most at Risk?

Changes in climate projected for the 21st century are expected to trigger widespread and pervasive biotic impacts. Forecasting these changes and their implications for ecosystem services is a major research goal. Much of the research on biotic responses to climate change has focused on either projected shifts in individual species distributions or broad-scale changes in biome distributions. Here, we introduce a novel application of multinomial logistic regression as a powerful approach to model vegetation distributions and potential responses to 21st century climate change. We modeled the distribution of 22 major vegetation types, most defined by a single dominant woody species, across the San Francisco Bay Area. Predictor variables included climate and topographic variables. The novel aspect of our model is the output: a vector of relative probabilities for each vegetation type in each location within the study domain. The model was then projected for 54 future climate scenarios, spanning a representative range of temperature and precipitation projections from the CMIP3 and CMIP5 ensembles. We found that sensitivity of vegetation to climate change is highly heterogeneous across the region. Surprisingly, sensitivity to climate change is higher closer to the coast, on lower insolation, north-facing slopes and in areas of higher precipitation. While such sites may provide refugia for mesic and cool-adapted vegetation in the face of a warming climate, the model suggests they will still be highly dynamic and relatively sensitive to climate-driven vegetation transitions. The greater sensitivity of moist and low insolation sites is an unexpected outcome that challenges views on the location and stability of climate refugia. Projections provide a foundation for conservation planning and land management, and highlight the need for a greater understanding of the mechanisms and time scales of potential climate-driven vegetation transitions.

Opening mechanism of adenylate kinase can vary according to selected molecular dynamics force field.

Adenylate kinase is a widely used test case for many conformational transition studies. It performs a large conformational transition between closed and open conformations while performing its catalytic function. To understand conformational transition mechanism and impact of force field choice on E. Coli adenylate kinase, we performed all-atom explicit solvent classical molecular dynamics simulations starting from the closed conformation with four commonly used force fields, namely, Amber99, Charmm27, Gromos53a6, Opls-aa. We carried out 40 simulations, each one 200ns. We analyzed completely 12 of them that show full conformational transition from the closed state to the open one. Our study shows that different force fields can have a bias toward different transition pathways. Transition time scales, frequency of conformational transitions, order of domain motions and free energy landscapes of each force field may also vary. In general, Amber99 and Charmm27 behave similarly while Gromos53a6 results have a resemblance to the Opls-aa force field results.

Rainfall hotspots over the southern tropical Andes: Spatial distribution, rainfall intensity, and relations with large‐scale atmospheric circulation

AbstractThe Andes/Amazon transition is among the rainiest regions of the world and the interactions between large‐scale circulation and the topography that determine its complex rainfall distribution remain poorly known. This work provides an in‐depth analysis of the spatial distribution, variability, and intensity of rainfall in the southern Andes/Amazon transition, at seasonal and intraseasonal time scales. The analysis is based on comprehensive daily rainfall data sets from meteorological stations in Peru and Bolivia. We compare our results with high‐resolution rainfall TRMM‐PR 2A25 estimations. Hotspot regions are identified at low elevations in the Andean foothills (400–700 masl) and in windward conditions at Quincemil and Chipiriri, where more than 4000 mm rainfall per year are recorded. Orographic effects and exposure to easterly winds produce a strong annual rainfall gradient between the lowlands and the Andes that can reach 190 mm/km. Although TRMM‐PR reproduces the spatial distribution satisfactorily, it underestimates rainfall by 35% in the hotspot regions. In the Peruvian hotspot, exceptional rainfall occurs during the austral dry season (around 1000 mm in June–July–August; JJA), but not in the Bolivian hotspot. The direction of the low‐level winds over the Andean foothills partly explains this difference in the seasonal rainfall cycle. At intraseasonal scales in JJA, we found that, during northerly wind regimes, positive rainfall anomalies predominate over the lowland and the eastern flank of the Andes, whereas less rain falls at higher altitudes. On the other hand, during southerly regimes, rainfall anomalies are negative in the hotspot regions. The influence of cross‐equatorial winds is particularly clear below 2000 masl.

Precise time series photometry for the Kepler-2.0 mission

The recently approved NASA K2 mission has the potential to multiply by an order of magnitude the number of short-period transiting planets found by Kepler around bright and low-mass stars, and to revolutionise our understanding of stellar variability in open clusters. However, the data processing is made more challenging by the reduced pointing accuracy of the satellite, which has only two functioning reaction wheels. We present a new method to extract precise light curves from K2 data, combining list-driven, soft-edged aperture photometry with a star-by-star correction of systematic effects associated with the drift in the roll-angle of the satellite about its boresight. The systematics are modelled simultaneously with the stars' intrinsic variability using a semi-parametric Gaussian process model. We test this method on a week of data collected during an engineering test in January 2014, perform checks to verify that our method does not alter intrinsic variability signals, and compute the precision as a function of magnitude on long-cadence (30-min) and planetary transit (2.5-hour) timescales. In both cases, we reach photometric precisions close to the precision reached during the nominal Kepler mission for stars fainter than 12th magnitude, and between 40 and 80 parts per million for brighter stars. These results confirm the bright prospects for planet detection and characterisation, asteroseismology and stellar variability studies with K2. Finally, we perform a basic transit search on the light curves, detecting 2 bona fide transit-like events, 7 detached eclipsing binaries and 13 classical variables.

Measurement and Observation of Elementary Transition Boiling Process after Sudden Contact of Liquid with Hot Surface

A Fast response surface temperature measurement technique has been developed to investigate transient transition boiling phenomena after ethanol droplet impact on a nickel hot surface. Our motivation is to make clear the mechanism of boiling transition between nucleate and film boiling which is closely related the recovery of wetting on the hot surface being higher than the Leidenfrost temperature. In this study transient boiling phenomena during sudden contact of an ethanol sessile droplet on a hot solid surface has been investigated to understand what governs whether the solid surface keeps wet or not. The droplet impact boiling system is very simple and easier to observe but it includes the elementary transition boiling process. Since the transient transition took place within a couple ten milliseconds, observation with high speed video system and fast response surface temperature measurement technique are essential for better understanding of the transition boiling phenomena.The experiments were conducted for single and multiple droplet impacts. The multiple droplet impacts simulates liquid and solid contact situations on a hot surface during spray or laminar jet quench. The nickel disk of 50mm in diameter and 5mm in thickness was used as the hot surface. The hot surface was inclined from 0 deg (horizontal) to 40 deg. The fast-response film thermocouple with a typical minimum response time of 80 microseconds was developed and fabricated on the nickel disk at the depth of 3 micrometers from the surface. The temperature histories just beneath the surface were recorded at the sampling frequency of 200kHz. The boiling phenomena beneath a sessile droplet impacted on the hot surface were observed by using a microscope equipped with the high speed video camera at the maximum frame rate of 22.5 kfps. The surface temperature and surface heat flux were estimated with 1D inverse heat conduction analysis. Histories of local surface temperature and local heat flux were compared with the boiling video image. The experiments were done for different initial wall temperatures up to 250°C, different liquid subcoolings from 33 to 53K. The multiple impact frequency was changed from 280 to 840Hz.In case of the single droplet impact tests, the observation results showed that wetting situation was maintained for very short time even though the surface temperature was beyond the liquid superheat limit temperature. We defined the vapor film generation time as the characteristic boiling transition time scale from wetted nucleation boiling regime to dry film boiling regime. The film generation time were measured for the extensive initial surface temperature range, different subcoolings and different impact velocities. As the initial surface temperature increased, the film generation time decreased to order of microsecond and film boiling situation seemed to be established via spontaneous nucleation (vapor explosion) process. In case of the multiple droplets impact tests, film generation times were evaluated every droplet impact during continuous cooling from the initial solid temperature. As long as the generation time was less than 1 millisecond and much shorter than the impact period, stable film boiling was observed. Then the film generation time increased with the droplet impact times and approached to the droplet impact period as the cooling time elapsed. This region was recognized as the transition boiling region. After the generation time reached to the droplet impact period and then stable wetted situation, namely nucleate boiling was observed. As compared with the single impact tests, the generation time for the multiple impact became shorter than that for the single droplet impact at same initial surface temperature and the lower limit surface temperature observed vapor film generation was reduced. This fact may imply the effect of transient heat conduction on the wetting temperature shifts to higher wall superheat temperature beyond liquid superheat limit temperature during quenching with jets or sprays.

Coronal mass ejections: a driver of severe space weather

Coronal mass ejections: a driver of severe space weather

Variation in propagule and colonization pressures following rapid human‐mediated transport: Implications for a universal assemblage‐based management model

Recent studies have recognized the importance of propagule pressure (number of individuals) and colonization pressure (number of species) for explaining establishment success of nonindigenous species. However, the International Ballast Water Management Convention, when ratified, will require ships to satisfy a numeric discharge standard that focuses only on cumulative propagule pressure of all individuals released. Because of practical constraints, the standard does not differentiate between discharges of single vs. multiple species. The assemblage‐based approach, which uses rank‐abundance gradients to quantify and manage introduction risk, may compensate for this limitation (e.g., even gradient [relatively consistent propagule pressures among n transported species] or uneven gradient [uneven propagule pressures among n transported species]). Here we explore species abundance distributions of zooplankton during transportation in ballast water to assess variability in the structure of assemblages, with implications for the potential development of an assemblage‐based management model. Specifically, we explored species abundance distributions for voyages that lasted < 24 h, those from 24 to 48 h, and those from 48 to 72 h (i.e., three time scales). Species abundance distributions within and across transit time scales were highly variable. As transport time increased, we observed a shift from uneven to even rank‐abundance gradients. Owing to variation in assemblage structure, the number of organisms necessary to quantify colonization pressure exhibited similarly strong variation within and across time scales. Our study indicates that assemblage‐based approaches to estimate introduction risk are warranted, yet the variation inherent in transported assemblages will induce substantial uncertainty within management models.

Adrift.org.au — A free, quick and easy tool to quantitatively study planktonic surface drift in the global ocean

Almost all organisms in the ocean are impacted by ocean currents. Hence, there is growing interest by marine ecologists in using objective methods to assess current drift and its implications for marine connectivity. Here, an online tool – hosted at adrift.org.au – is introduced that allows for a simple, quantitative assessment of drift patterns and transit time scales on the global scale. The tool is based on a statistical transition matrix representation of the observed trajectories of more than 15 thousand surface drifters. Users can select any point in the ocean and obtain the evolution of the probability density distribution for a tracer released at that point, both forward and backward in time, for a maximum interval of 10years. It is envisioned that this tool will be used in research and teaching, especially where estimates of drift patterns and transit times are required quickly.

Transient coherence of media under strong phase modulation exploiting electromagnetically induced transparency

When quantum systems are shifted faster than their transition and coupling time scales, their susceptibility is dramatically modified. We measure the optical susceptibility of a strongly modulated electromagnetically induced transparency system. Time vs detuning plots for different pump modulation frequencies reveal a transition between an adiabatic regime where a series of smooth pulses are created and a nonadiabatic regime where a strong transient oscillating response is added. Applying a magnetic field lifts the hyperfine level degeneracy, revealing an interference effect between the different magnetic level transients. We explore the dynamics of the magnetic and nonmagnetic cases and discuss their coherent nature. We finally combine the global phase of the transmitted pulses with the transient interference to achieve broadband magnetic sensing without losing the sensitivity of a single electromagnetically induced transparency line.

Assessing the Accuracy of Two Enhanced Sampling Methods Using EGFR Kinase Transition Pathways: The Influence of Collective Variable Choice

Structurally elucidating transition pathways between protein conformations gives deep mechanistic insight into protein behavior but is typically difficult. Unbiased molecular dynamics (MD) simulations provide one solution, but their computational expense is often prohibitive, motivating the development of enhanced sampling methods that accelerate conformational changes in a given direction, embodied in a collective variable. The accuracy of such methods is unclear for complex protein transitions, because obtaining unbiased MD data for comparison is difficult. Here, we use long-time scale, unbiased MD simulations of epidermal growth factor receptor kinase deactivation as a complex biological test case for two widely used methods-steered molecular dynamics (SMD) and the string method. We found that common collective variable choices, based on the root-mean-square deviation (RMSD) of the entire protein, prevented the methods from producing accurate paths, even in SMD simulations on the time scale of the unbiased transition. Using collective variables based on the RMSD of the region of the protein known to be important for the conformational change, however, enabled both methods to provide a more accurate description of the pathway in a fraction of the simulation time required to observe the unbiased transition.

The length and time scales of water's glass transitions.

Using a general model for the equilibrium dynamics of supercooled liquids, I compute from molecular properties the emergent length and time scales that govern the nonequilibrium relaxation behavior of amorphous ice prepared by rapid cooling. Upon cooling, the liquid water falls out of equilibrium whereby the temperature dependence of its relaxation time is predicted to change from super-Arrhenius to Arrhenius. A consequence of this crossover is that the location of the apparent glass transition temperature depends logarithmically on cooling rate. Accompanying vitrification is the emergence of a dynamical length-scale, the size of which depends on the cooling rate and varies between angstroms and tens of nanometers. While this protocol dependence clarifies a number of previous experimental observations for amorphous ice, the arguments are general and can be extended to other glass forming liquids.

Unknown Unknowns: the Challenge of Systematic and Statistical Error in Molecular Dynamics Simulations

Unknown Unknowns: the Challenge of Systematic and Statistical Error in Molecular Dynamics Simulations