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 $\sim 500$ 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

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

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 $1/\sqrt{n}$, where $n$ 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

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