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

Physical properties of the Schur complement of local covariance matrices

General properties of global covariance matrices representing bipartite Gaussian states can be decomposed into properties of local covariance matrices and their Schur complements. We demonstrate that given a bipartite Gaussian state $\rho_{12}$ described by a $4\times 4$ covariance matrix \textbf{V}, the Schur complement of a local covariance submatrix $\textbf{V}_1$ of it can be interpreted as a new covariance matrix representing a Gaussian operator of party 1 conditioned to local parity measurements on party 2. The connection with a partial parity measurement over a bipartite quantum state and the determination of the reduced Wigner function is given and an operational process of parity measurement is developed. Generalization of this procedure to a $n$-partite Gaussian state is given and it is demonstrated that the $n-1$ system state conditioned to a partial parity projection is given by a covariance matrix such as its $2 \times 2$ block elements are Schur complements of special local matrices.Comment: 10 pages. Replaced with final published versio

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

A comparison of extremal optimization with flat-histogram dynamics for finding spin-glass ground states

We compare the performance of extremal optimization (EO), flat-histogram and equal-hit algorithms for finding spin-glass ground states. The first-passage-times to a ground state are computed. At optimal parameter of tau=1.15, EO outperforms other methods for small system sizes, but equal-hit algorithm is competitive to EO, particularly for large systems. Flat-histogram and equal-hit algorithms offer additional advantage that they can be used for equilibrium thermodynamic calculations. We also propose a method to turn EO into a useful algorithm for equilibrium calculations. Keywords: extremal optimization. flat-histogram algorithm, equal-hit algorithm, spin-glass model, ground state.Comment: 10 LaTeX pages, 2 figure

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

Density-functionals not based on the electron gas: Local-density approximation for a Luttinger liquid

By shifting the reference system for the local-density approximation (LDA) from the electron gas to other model systems one obtains a new class of density functionals, which by design account for the correlations present in the chosen reference system. This strategy is illustrated by constructing an explicit LDA for the one-dimensional Hubbard model. While the traditional {\it ab initio} LDA is based on a Fermi liquid (the electron gas), this one is based on a Luttinger liquid. First applications to inhomogeneous Hubbard models, including one containing a localized impurity, are reported.Comment: 4 pages, 4 figures (final version, contains additional applications and discussion; accepted by Phys. Rev. Lett.

Photoassociative ionization of Na inside a storage ring

Motivated by recent interest in low dimensional arrays of atoms, we experimentally investigated the way cold collisional processes are affected by the geometry of the considered atomic sample. More specifically, we studied the case of photoassociative ionization (PAI) both in a storage ring where collision is more unidirectional in character and in a trap with clear undefinition of collision axis. First, creating a ring shaped trap (atomotron) we investigated two-color PAI dependence with intensity and polarization of a probing laser. The intensity dependence of the PAI rate was also measured in a magneto-optical trap presenting equivalent temperature and density conditions. Indeed, the results show that in the ring trap, the value of the PAI rate constant is much lower and does not show evidences of saturation, unlike in the case of the 3D-MOT. Cold atomic collisions in storage ring may represent new possibilities for study.Comment: 5 pages, 5 figures; Accepted by Optics Communicatio