Propagating chain-free normal forms for EOL systems

We establish two types of normal forms for EOL systems. We first show that each ε-free EOL language can be generated by a propagating EOL system in which each derivation tree is chain-free. By this we mean that it contains at least one path from the root to the grandfather of a leaf in which each node has more than one son. We use this result to prove that each ε-free EOL language can be generated by a propagating EOL system in which each production has a right side of length at most two and which does not contain nonterminal chainproductions, i.e., productions A → B for nonterminals A and B. As applications of our results we give a simple proof for the decidability of the finiteness problem for EOL systems and solve an open problem concerning completeness of EOL forms

Metabolic flux from the chloroplast provides signals controlling photosynthetic acclimation to cold in Arabidopsis thaliana

Photosynthesis is especially sensitive to environmental conditions, and the composition of the photosynthetic apparatus can be modulated in response to environmental change, a process termed photosynthetic acclimation. Previously, we identified a role for a cytosolic fumarase, FUM2 in acclimation to low temperature in Arabidopsis thaliana. Mutant lines lacking FUM2 were unable to acclimate their photosynthetic apparatus to cold. Here, using gas exchange measurements and metabolite assays of acclimating and non‐acclimating plants, we show that acclimation to low temperature results in a change in the distribution of photosynthetically fixed carbon to different storage pools during the day. Proteomic analysis of wild‐type Col‐0 Arabidopsis and of a fum2 mutant, which was unable to acclimate to cold, indicates that extensive changes occurring in response to cold are affected in the mutant. Metabolic and proteomic data were used to parameterize metabolic models. Using an approach called flux sampling, we show how the relative export of triose phosphate and 3‐phosphoglycerate provides a signal of the chloroplast redox state that could underlie photosynthetic acclimation to cold

Flux sampling is a powerful tool to study metabolism under changing environmental conditions

The development of high-throughput ‘omic techniques has sparked a rising interest in genome-scale metabolic models, with applications ranging from disease diagnostics to crop adaptation. Efficient and accurate methods are required to analyze large metabolic networks. Flux sampling can be used to explore the feasible flux solutions in metabolic networks by generating probability distributions of steady-state reaction fluxes. Unlike other methods, flux sampling can be used without assuming a particular cellular objective. We have undertaken a rigorous comparison of several sampling algorithms and concluded that the coordinate hit-and-run with rounding (CHRR) algorithm is the most efficient based on both run-time and multiple convergence diagnostics. We demonstrate the power of CHRR by using it to study the metabolic changes that underlie photosynthetic acclimation to cold of Arabidopsis thaliana plant leaves. In combination with experimental measurements, we show how the regulated interplay between diurnal starch and organic acid accumulation defines the plant acclimation process. We confirm fumarate accumulation as a requirement for cold acclimation and further predict γ–aminobutyric acid to have a key role in metabolic signaling under cold conditions. These results demonstrate how flux sampling can be used to analyze the feasible flux solutions across changing environmental conditions, whereas eliminating the need to make assumptions which introduce observer bias

Unstable particles in matter at a finite temperature: the rho and omega mesons

Unstable particles (such as the vector mesons) have an important role to play in low mass dilepton production resulting from heavy ion collisions and this has been a subject of several investigations. Yet subtleties, such as the implications of the generalization of the Breit-Wigner formula for nonzero temperature and density, e.g. the question of collisional broadening, the role of Bose enhancement, etc., the possibility of the kinematic opening (or closing) of decay channels due to environmental effects, the problem of double counting through resonant and direct contributions, are often given insufficient emphasis. The present study attempts to point out these features using the rho and omega mesons as illustrative examples. The difference between the two versions of the Vector Meson Dominance Model in the present context is also presented. Effects of non-zero temperature and density, through vector meson masses and decay widths, on dilepton spectra are studied, for concreteness within the framework of a Walecka-type model, though most of the basic issues highlighted apply to other scenarios as well.Comment: text and figures modifie

Strength Reduction in Electrical and Elastic Networks

Particular aspects of problems ranging from dielectric breakdown to metal insu- lator transition can be studied using electrical o elastic networks. We present an expression for the mean breakdown strength of such networks.First, we intro- duce a method to evaluate the redistribution of current due to the removal of a finite number of elements from a hyper-cubic network of conducatances.It is used to determine the reduction of breakdown strength due to a fracture of size $\kappa$.Numerical analysis is used to show that the analogous reduction due to random removal of elements from electrical and elastic networks follow a similar form.One possible application, namely the use of bone density as a diagnostic tools for osteorosporosis,is discussed.Comment: one compressed file includes: 9 PostScrpt figures and a text fil

Passing to the Limit in a Wasserstein Gradient Flow: From Diffusion to Reaction

We study a singular-limit problem arising in the modelling of chemical reactions. At finite {\epsilon} > 0, the system is described by a Fokker-Planck convection-diffusion equation with a double-well convection potential. This potential is scaled by 1/{\epsilon}, and in the limit {\epsilon} -> 0, the solution concentrates onto the two wells, resulting into a limiting system that is a pair of ordinary differential equations for the density at the two wells. This convergence has been proved in Peletier, Savar\'e, and Veneroni, SIAM Journal on Mathematical Analysis, 42(4):1805-1825, 2010, using the linear structure of the equation. In this paper we re-prove the result by using solely the Wasserstein gradient-flow structure of the system. In particular we make no use of the linearity, nor of the fact that it is a second-order system. The first key step in this approach is a reformulation of the equation as the minimization of an action functional that captures the property of being a curve of maximal slope in an integrated form. The second important step is a rescaling of space. Using only the Wasserstein gradient-flow structure, we prove that the sequence of rescaled solutions is pre-compact in an appropriate topology. We then prove a Gamma-convergence result for the functional in this topology, and we identify the limiting functional and the differential equation that it represents. A consequence of these results is that solutions of the {\epsilon}-problem converge to a solution of the limiting problem.Comment: Added two sections, corrected minor typos, updated reference

Simultaneous Softening of sigma and rho Mesons associated with Chiral Restoration

Complex poles of the unitarized pi-pi scattering amplitude in nuclear matter are studied. Partial restoration of chiral symmetry is modeled by the decrease of in-medium pion decay constant f*_{pi}. For large chiral restoration (f*_{pi}/f_{pi} << 1), 2nd sheet poles in the scalar (sigma) and the vector (rho) mesons are both dictated by the Lambert W function and show universal softening as f*_{pi} decreases. In-medium pi-pi cross section receives substantial contribution from the soft mode and exhibits a large enhancement in low-energy region. Fate of this universality for small chiral restoration (f*_{pi}/f_{pi} ~ 1) is also discussed.Comment: 5 pages, 4-eps figures, version accepted by Phys. Rev. C (R) with minor modification

Closed-Time Path Integral Formalism and Medium Effects of Non-Equilibrium QCD Matter

We apply the closed-time path integral formalism to study the medium effects of non-equilibrium gluon matter. We derive the medium modified resummed gluon propagator to the one loop level in non-equilibrium in the covariant gauge. The gluon propagator we derive can be used to remove the infrared divergences in the secondary parton collisions to study thermalization of minijet parton plasma at RHIC and LHC.Comment: Final version, To appear in Physical Review D, Minor modification, reference adde

Directed flow in Au+Au, Xe+CsI and Ni+Ni collisions and the nuclear equation of state

We present new experimental data on directed flow in collisions of Au+Au, Xe+CsI and Ni+Ni at incident energies from 90 to 400A MeV. We study the centrality and system dependence of integral and differential directed flow for particles selected according to charge. All the features of the experimental data are compared with Isospin Quantum Molecular Dynamics (IQMD) model calculations in an attempt to extract information about the nuclear matter equation of state (EoS). We show that the combination of rapidity and transverse momentum analysis of directed flow allow to disentangle various parametrizations in the model. At 400A MeV, a soft EoS with momentum dependent interactions is best suited to explain the experimental data in Au+Au and Xe+CsI, but in case of Ni+Ni the model underpredicts flow for any EoS. At 90A MeV incident beam energy, none of the IQMD parametrizations studied here is able to consistently explain the experimental data.Comment: RevTeX, 20 pages, 30 eps figures, accepted for publication in Phys. Rev. C. Data files available at http://www.gsi.de/~fopiwww/pub

Infrared Behaviour of The Gluon Propagator in Non-Equilibrium Situations

The infrared behaviour of the medium modified gluon propagator in non-equilibrium situations is studied in the covariant gauge using the Schwinger-Keldysh closed-time path formalism. It is shown that the magnetic screening mass is non-zero at the one loop level whenever the initial gluon distribution function is non isotropic with the assumption that the distribution function of the gluon is not divergent at zero transverse momentum. For isotropic gluon distribution functions, such as those describing local equilibrium, the magnetic mass at one loop level is zero which is consistent with finite temperature field theory results. Assuming that a reasonable initial gluon distribution function can be obtained from a perturbative QCD calculation of minijets, we determine these out of equilibrium values for the initial magnetic and Debye screening masses at energy densities appropriate to RHIC and LHC. We also compare the magnetic masses obtained here with those obtained using finite temperature lattice QCD methods at similar temperatures at RHIC and LHC.Comment: 21 pages latex, 4 figures, final version to be published in Phys. Rev.