30,458 research outputs found
The role of type 4 phosphodiesterases in generating microdomains of cAMP: Large scale stochastic simulations
Cyclic AMP (cAMP) and its main effector Protein Kinase A (PKA) are critical for several aspects of neuronal function including synaptic plasticity. Specificity of synaptic plasticity requires that cAMP activates PKA in a highly localized manner despite the speed with which cAMP diffuses. Two mechanisms have been proposed to produce localized elevations in cAMP, known as microdomains: impeded diffusion, and high phosphodiesterase (PDE) activity. This paper investigates the mechanism of localized cAMP signaling using a computational model of the biochemical network in the HEK293 cell, which is a subset of pathways involved in PKA-dependent synaptic plasticity. This biochemical network includes cAMP production, PKA activation, and cAMP degradation by PDE activity. The model is implemented in NeuroRD: novel, computationally efficient, stochastic reaction-diffusion software, and is constrained by intracellular cAMP dynamics that were determined experimentally by real-time imaging using an Epac-based FRET sensor (H30). The model reproduces the high concentration cAMP microdomain in the submembrane region, distinct from the lower concentration of cAMP in the cytosol. Simulations further demonstrate that generation of the cAMP microdomain requires a pool of PDE4D anchored in the cytosol and also requires PKA-mediated phosphorylation of PDE4D which increases its activity. The microdomain does not require impeded diffusion of cAMP, confirming that barriers are not required for microdomains. The simulations reported here further demonstrate the utility of the new stochastic reaction-diffusion algorithm for exploring signaling pathways in spatially complex structures such as neurons
Running Gluon Mass from Landau Gauge Lattice QCD Propagator
The interpretation of the Landau gauge lattice gluon propagator as a massive
type bosonic propagator is investigated. Three different scenarios are
discussed: i) an infrared constant gluon mass; ii) an ultraviolet constant
gluon mass; iii) a momentum dependent mass. We find that the infrared data can
be associated with a massive propagator up to momenta MeV, with a
constant gluon mass of 723(11) MeV, if one excludes the zero momentum gluon
propagator from the analysis, or 648(7) MeV, if the zero momentum gluon
propagator is included in the data sets. The ultraviolet lattice data is not
compatible with a massive type propagator with a constant mass. The scenario of
a momentum dependent gluon mass gives a decreasing mass with the momentum,
which vanishes in the deep ultraviolet region. Furthermore, we show that the
functional forms used to describe the decoupling like solution of the
Dyson-Schwinger equations are compatible with the lattice data with similar
mass scales.Comment: Version to appear in J. Phys. G. New version include some rewriting
and new analysis. In particular, the section on the running mass is ne
Operational Classification and Quantification of Multipartite Entangled States
We formalize and extend an operational multipartite entanglement measure
introduced by T. R. Oliveira, G. Rigolin, and M. C. de Oliveira, Phys. Rev. A
73, 010305(R) (2006), through the generalization of global entanglement (GE)
[D. A. Meyer and N. R. Wallach, J. Math. Phys. 43, 4273 (2002)]. Contrarily to
GE the main feature of this measure lies in the fact that we study the mean
linear entropy of all possible partitions of a multipartite system. This allows
the construction of an operational multipartite entanglement measure which is
able to distinguish among different multipartite entangled states that GE
failed to discriminate. Furthermore, it is also maximum at the critical point
of the Ising chain in a transverse magnetic field, being thus able to detect a
quantum phase transition.Comment: 14 pages, RevTex4, published versio
Effect of hydrogen bond cooperativity on the behavior of water
Four scenarios have been proposed for the low--temperature phase behavior of
liquid water, each predicting different thermodynamics. The physical mechanism
which leads to each is debated. Moreover, it is still unclear which of the
scenarios best describes water, as there is no definitive experimental test.
Here we address both open issues within the framework of a microscopic cell
model by performing a study combining mean field calculations and Monte Carlo
simulations. We show that a common physical mechanism underlies each of the
four scenarios, and that two key physical quantities determine which of the
four scenarios describes water: (i) the strength of the directional component
of the hydrogen bond and (ii) the strength of the cooperative component of the
hydrogen bond. The four scenarios may be mapped in the space of these two
quantities. We argue that our conclusions are model-independent. Using
estimates from experimental data for H bond properties the model predicts that
the low-temperature phase diagram of water exhibits a liquid--liquid critical
point at positive pressure.Comment: 18 pages, 3 figure
Rendimento de milho e braquiaria com diferentes doses de nitrogênio em cobertura em sistema agrossilvipastoril no Acre.
O objetivo deste trabalho foi avaliar o rendimento produtivo das culturas do milho e Brachiaria brizantha cv. Xaraés consorciadas, cultivadas a diferentes distâncias de árvores nativas de mulateiro (Calycophyllum spruceanum Benth) e com aplicação de diferentes doses de nitrogênio em cobertura, em um sistema agrossilvipastoril no Acre. O delineamento experimental utilizado foi de blocos ao acaso, arranjado em parcelas subdivididas, com duas posições de amostragem (Perto da Linha e Distante da Linha do mulateiro) nas parcelas e cinco doses de adubação nitrogenada em cobertura (0; 50; 100; 150; 200 kg ha) nas subparcelas, totalizando dez tratamentos. Foram avaliados na cultura do milho a altura de plantas, teor de clorofila foliar e a produtividade de grãos e para forragem o acúmulo de matéria seca. Constatou-se que a produtividade do milho não é afetada pelo mulateiro aos quatro anos de idade e a adubação nitrogenada em cobertura até a dose de 200 Kg ha de N aumenta linearmente a produtividade de grãos. A pastagem formada apresentou acúmulo de matéria seca da forragem estatisticamente igual para todos os tratamentos, aos 90 dias após a colheita do milho
Diffusion in the Continuous-Imaginary-Time Quantum World-Line Monte Carlo Simulations with Extended Ensembles
The dynamics of samples in the continuous-imaginary-time quantum world-line
Monte Carlo simulations with extended ensembles are investigated. In the case
of a conventional flat ensemble on the one-dimensional quantum S=1 bi-quadratic
model, the asymmetric behavior of Monte Carlo samples appears in the diffusion
process in the space of the number of vertices. We prove that a local
diffusivity is asymptotically proportional to the number of vertices, and we
demonstrate the asymmetric behavior in the flat ensemble case. On the basis of
the asymptotic form, we propose the weight of an optimal ensemble as
, where denotes the number of vertices in a sample. It is shown
that the asymmetric behavior completely vanishes in the case of the proposed
ensemble on the one-dimensional quantum S=1 bi-quadratic model.Comment: 4 pages, 2 figures, update a referenc
Symmetry breaking effects upon bipartite and multipartite entanglement in the XY model
We analyze the bipartite and multipartite entanglement for the ground state
of the one-dimensional XY model in a transverse magnetic field in the
thermodynamical limit. We explicitly take into account the spontaneous symmetry
breaking in order to explore the relation between entanglement and quantum
phase transitions. As a result we show that while both bipartite and
multipartite entanglement can be enhanced by spontaneous symmetry breaking deep
into the ferromagnetic phase, only the latter is affected by it in the vicinity
of the critical point. This result adds to the evidence that multipartite, and
not bipartite, entanglement is the fundamental indicator of long range
correlations in quantum phase transitions.Comment: 13 pages, 19 figures, comments welcome. V2: small changes, published
versio
Optimized cross-slot flow geometry for microfluidic extension rheometry
A precision-machined cross-slot flow geometry with a shape that has been optimized by numerical simulation of the fluid kinematics is fabricated and used to measure the extensional viscosity of a dilute polymer solution. Full-field birefringence microscopy is used to monitor the evolution and growth of macromolecular anisotropy along the stagnation point streamline, and we observe the formation of a strong and uniform birefringent strand when the dimensionless flow strength exceeds a critical Weissenberg number Wicrit 0:5. Birefringence and bulk pressure drop measurements provide self consistent estimates of the planar extensional viscosity of the fluid over a wide range of deformation rates (26 s1 "_ 435 s1) and are also in close agreement with numerical simulations performed by using a finitely extensible nonlinear elastic dumbbell model
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