Modeling reaction-diffusion of molecules on surface and in volume spaces with the E-Cell System

The-Cell System is an advanced open-source simulation platform to model and analyze biochemical reaction networks. The present algorithm modules of the system assume that the reacting molecules are all homogeneously distributed in the reaction compartments, which is not the case in some cellular processes. The MinCDE system in Escherichia coli, for example, relies on intricately controlled reaction, diffusion and localization of Min proteins on the membrane and in the cytoplasm compartments to inhibit cell division at the poles of the rod-shaped cell. To model such processes, we have extended the E-Cell System to support reaction-diffusion and dynamic localization of molecules in volume and surface compartments. We evaluated our method by modeling the in vivo dynamics of MinD and MinE and comparing their simulated localization patterns to the observations in experiments and previous computational work. In both cases, our simulation results are in good agreement

Long wavelength iteration of Einstein's equations near a spacetime singularity

We clarify the links between a recently developped long wavelength iteration scheme of Einstein's equations, the Belinski Khalatnikov Lifchitz (BKL) general solution near a singularity and the antinewtonian scheme of Tomita's. We determine the regimes when the long wavelength or antinewtonian scheme is directly applicable and show how it can otherwise be implemented to yield the BKL oscillatory approach to a spacetime singularity. When directly applicable we obtain the generic solution of the scheme at first iteration (third order in the gradients) for matter a perfect fluid. Specializing to spherical symmetry for simplicity and to clarify gauge issues, we then show how the metric behaves near a singularity when gradient effects are taken into account.Comment: 35 pages, revtex, no figure

Second-order power spectra of CMB anisotropies due to primordial random perturbations in flat cosmological models

Second-order power spectra of Cosmic Microwave Background (CMB) anisotropies due to random primordial perturbations at the matter dominant stage are studied, based on the relativistic second-order theory of perturbations in flat cosmological models and on the second-order formula of CMB anisotropies derived by Mollerach and Matarrese. So far the second-order integrated Sachs-Wolfe effect has been analyzed using the three-point correlation or bispectrum. In this paper we derive the second-order term of power spectra given using the two-point correlation of temperature fluctuations. The second-order density perturbations are small, compared with the first-order ones. The second-order power spectra of CMB anisotropies, however, are not small at all, compared with the first-order power spectra, because at the early stage the first-order integrated Sachs-Wolfe effect is very small and the second-order integrated Sachs-Wolfe effect may be dominant over the first-order ones. So their characteristic behaviors may be measured through the future precise observation and bring useful informations on the structure and evolution of our universe in the future.Comment: 11 page

Changes of variables in modulation and Wiener amalgam spaces

In this paper various properties of global and local changes of variables as well as properties of canonical transforms are investigated on modulation and Wiener amalgam spaces. We establish several relations among localisations of such spaces and, as a consequence, we obtain several versions of local and global Beurling–Helson type theorems. We also establish a number of positive results such as local boundedness of canonical transforms on modulation spaces, properties of homogeneous changes of variables, and local continuity of Fourier integral operators on equation image. Finally, counterparts of these results are discussed for spaces on the torus

Probing violation of the Copernican principle via the integrated Sachs-Wolfe effect

Recent observational data of supernovae indicate that we may live in an underdense region, which challenges the Copernican principle. We show that the integrated Sachs-Wolfe (ISW) effect is an excellent discriminator between anti-Copernican inhomogeneous models and the standard Copernican models. As a reference model, we consider an anti-Copernican inhomogeneous model that consists of two inner negatively curved underdense regions and an outer flat Einstein-de Sitter region. We assume that these regions are connected by two thin-walls at redshifts z = 0.067 and z=0.45. In the inner two regions, the first-order ISW effect is dominant and comparable to that in the concordant flat-Lambda models. In the outer Einstein-de Sitter region, the first-order ISW effect vanishes but the second-order ISW effect plays a dominant role, while the first-order ISW effect is dominant in the flat-Lambda models at moderate redshifts. This difference can discrimate the anti-Copernican models from the concordant flat-Lambda model. At high redshits, the second-order ISW effect is dominant both in our inhomogeneous model and the concordant model. In the outer region, moreover, the ISW effect due to large-scale density perturbations with a present matter density contrast much less than 0.37 is negligible, while the effect due to small-scale density perturbations (such as clusters of galaxies, superclusters and voids) with matter density contrast much larger than 0.37 would generate anisotropies which are larger than those generated by the ISW effect in the concordant model.Comment: 9 pages, 2 figure