439 research outputs found
Fractal properties of relaxation clusters and phase transition in a stochastic sandpile automaton
We study numerically the spatial properties of relaxation clusters in a two
dimensional sandpile automaton with dynamic rules depending stochastically on a
parameter p, which models the effects of static friction. In the limiting cases
p=1 and p=0 the model reduces to the critical height model and critical slope
model, respectively. At p=p_c, a continuous phase transition occurs to the
state characterized by a nonzero average slope. Our analysis reveals that the
loss of finite average slope at the transition is accompanied by the loss of
fractal properties of the relaxation clusters.Comment: 11 page
Integration of metabolite with transcript and enzyme activity profiling during diurnal cycles in Arabidopsis rosettes
ABSTRACT: BACKGROUND: Genome-wide transcript profiling and analyses of enzyme activities from central carbon and nitrogen metabolism has shown that transcript levels undergo marked and rapid changes during diurnal cycles and after transfer to darkness, whereas changes of enzyme activities are smaller and delayed. In the starchless pgm mutant, where sugars are depleted every night, there are accentuated diurnal changes of transcript levels. Enzyme activities do not show larger diurnal changes; instead they shift towards the levels found in wild-type after several days of darkness. These results indicate that enzyme activities change slowly, integrating the changes of transcript levels over several diurnal cycles. RESULTS: To generalize this conclusion, 137 metabolites were profiled using GC-MS and LC-MS. Amplitudes of the diurnal changes of metabolites in pgm were (with the exception of sugars) similar or smaller than in wild-type. The average levels shifted towards those found after several days of darkness in wild-type. Examples include increased levels of many amino acids due to protein degradation, decreased levels of many fatty acids, increased tocopherol and decreased myo-inositol. Many metabolite-transcript correlations were found and the proportion of transcripts correlated with sugars increased dramatically in the starchless pgm mutant. CONCLUSION: Rapid diurnal changes of transcripts are integrated over time to generate quasi-stable changes across large sectors of metabolism. The slow response of enzyme activities and metabolites implies that correlations between metabolites and transcripts are due to regulation of gene expression by metabolites, rather than metabolites being changed as a consequence of a change in gene expression
Global transcript levels respond to small changes of the carbon status during progressive exhaustion of carbohydrates in Arabidopsis rosettes
The balance between the supply and utilization of carbon (C) changes continually. It has been proposed that plants respond in an acclimatory manner, modifying C utilization to minimize harmful periods of C depletion. This hypothesis predicts that signaling events are initiated by small changes in C status. We analyzed the global transcriptional response to a gradual depletion of C during the night and an extension of the night, where C becomes severely limiting from 4 h onward. The response was interpreted using published datasets for sugar, light, and circadian responses. Hundreds of C-responsive genes respond during the night and others very early in the extended night. Pathway analysis reveals that biosynthesis and cellular growth genes are repressed during the night and genes involved in catabolism are induced during the first hours of the extended night. The C response is amplified by an antagonistic interaction with the clock. Light signaling is attenuated during the 24-h light/dark cycle. A model was developed that uses the response of 22K genes during a circadian cycle and their responses to C and light to predict global transcriptional responses during diurnal cycles of wild-type and starchless pgm mutant plants and an extended night in wild-type plants. By identifying sets of genes that respond at different speeds and times during C depletion, our extended dataset and model aid the analysis of candidates for C signaling. This is illustrated for AKIN10 and four bZIP transcription factors, and sets of genes involved in trehalose signaling, protein turnover, and starch breakdown
Field Theory of Mesoscopic Fluctuations in Superconductor/Normal-Metal Systems
Thermodynamic and transport properties of normal disordered conductors are
strongly influenced by the proximity of a superconductor. A cooperation between
mesoscopic coherence and Andreev scattering of particles from the
superconductor generates new types of interference phenomena. We introduce a
field theoretic approach capable of exploring both averaged properties and
mesoscopic fluctuations of superconductor/normal-metal systems.
As an example the method is applied to the study of the level statistics of a
SNS-junction.Comment: 4 pages, REVTEX, two eps-figures included; submitted to JETP letter
Critical behavior of a traffic flow model
The Nagel-Schreckenberg traffic flow model shows a transition from a free
flow regime to a jammed regime for increasing car density. The measurement of
the dynamical structure factor offers the chance to observe the evolution of
jams without the necessity to define a car to be jammed or not. Above the
jamming transition the dynamical structure factor exhibits for a given k-value
two maxima corresponding to the separation of the system into the free flow
phase and jammed phase. We obtain from a finite-size scaling analysis of the
smallest jam mode that approaching the transition long range correlations of
the jams occur.Comment: 5 pages, 7 figures, accepted for publication in Physical Review
Reorientation transition of ultrathin ferromagnetic films
We demonstrate that the reorientation transition from out-of-plane to
in-plane magnetization with decreasing temperature as observed experimentally
in Ni-films on Cu(001) can be explained on a microscopic basis. Using a
combination of mean field theory and perturbation theory, we derive an analytic
expression for the temperature dependent anisotropy. The reduced magnetization
in the film surface at finite temperatures plays a crucial role for this
transition as with increasing temperature the influence of the uniaxial
anisotropies is reduced at the surface and is enhanced inside the film.Comment: 4 pages(RevTeX), 3 figures (EPS
Proximity-induced superconductivity in graphene
We propose a way of making graphene superconductive by putting on it small
superconductive islands which cover a tiny fraction of graphene area. We show
that the critical temperature, T_c, can reach several Kelvins at the
experimentally accessible range of parameters. At low temperatures, T<<T_c, and
zero magnetic field, the density of states is characterized by a small gap
E_g<T_c resulting from the collective proximity effect. Transverse magnetic
field H_g(T) E_g is expected to destroy the spectral gap driving graphene layer
to a kind of a superconductive glass state. Melting of the glass state into a
metal occurs at a higher field H_{g2}(T).Comment: 4 pages, 3 figure
The potential of integrative phenomics to harness underutilized crops for improving stress resilience
The current agricultural and food system faces diverse and increasing challenges. These
include feeding an ever-growing human population, expected to reach about 10 billion by
2050 combined with societal disruption, and the need to cope with the impact of climate
change (FAO, 2022). Given that future environmental conditions will limit crop
productivity (Zhao et al., 2017; Cooper et al., 2021) and the limited potential to
continually increase the performance of staple crops by conventional breeding (Hickey
et al., 2019), there is an urgent need to transform agricultural systems. Central to this
transformation is the application of alternative, accelerated, and sustainable approaches for
the improvement and development of underutilized crops (Hickey et al., 2019). Modern
breeding strategies for major crops have widely integrated novel technologies, such as
advanced phenotyping or genome-wide interactions, and even epigenomics within
“beyond the gene” strategies (Crisp et al., 2022) to speed up crop/genotype selection
(Hickey et al., 2019; Kumar et al., 2023). Deploying phenotyping at different scales has the
potential to identify novel trait(s) components that can be targeted to accelerate crop
improvement (Araus and Cairns, 2014; GroĂźkinsky et al., 2015b; Zhao et al., 2019;
Varshney et al., 2021). There is even greater potential for these technologies when used
to improve underutilized crops and support the agricultural transformation, as
underutilized crops typically lack a biased breeding/selection history, i.e., they often
exhibit a high genetic diversity and potential, and are usually better adapted to challenging environments (Kumar et al., 2021; Kumar et al., 2023).
To illustrate the application of an integrative phenomics approach
we discuss how combining multi-omics and advanced phenotyping
is being applied to the underutilized oilseed crop Camelina sativa
(camelina, gold-of-pleasure, false flax) to facilitate the generation of
climate-smart crops for future agricultural systems
Gap Fluctuations in Inhomogeneous Superconductors
Spatial fluctuations of the effective pairing interaction between electrons
in a superconductor induce variations of the order parameter which in turn lead
to significant changes in the density of states. In addition to an overall
reduction of the quasi-particle energy gap, theory suggests that mesoscopic
fluctuations of the impurity potential induce localised tail states below the
mean-field gap edge. Using a field theoretic approach, we elucidate the nature
of the states in the `sub-gap' region. Specifically, we show that these states
are associated with replica symmetry broken instanton solutions of the
mean-field equations.Comment: 11 pages, 3 figures included. To be published in PRB (Sept. 2001
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