Control Words of String Rewriting P Systems

P systems with controlled computations have been introduced and investigated in the recent past, by assigning labels to the rules in the regions of the P system and guiding the computations by control words. Here we consider string rewriting cell-like transition P system with label assigned rules working in acceptor mode and compare the obtained family of languages of control words over the rule labels with certain well-known language families. An application to chain code picture generation is also pointed out

The Geometrodynamics of Sine-Gordon Solitons

The relationship between N-soliton solutions to the Euclidean sine-Gordon equation and Lorentzian black holes in Jackiw-Teitelboim dilaton gravity is investigated, with emphasis on the important role played by the dilaton in determining the black hole geometry. We show how an N-soliton solution can be used to construct ``sine-Gordon'' coordinates for a black hole of mass M, and construct the transformation to more standard ``Schwarzchild-like'' coordinates. For N=1 and 2, we find explicit closed form solutions to the dilaton equations of motion in soliton coordinates, and find the relationship between the soliton parameters and the black hole mass. Remarkably, the black hole mass is non-negative for arbitrary soliton parameters. In the one-soliton case the coordinates are shown to cover smoothly a region containing the whole interior of the black hole as well as a finite neighbourhood outside the horizon. A Hamiltonian analysis is performed for slicings that approach the soliton coordinates on the interior, and it is shown that there is no boundary contribution from the interior. Finally we speculate on the sine-Gordon solitonic origin of black hole statistical mechanics.Comment: Latex, uses epsf, 30 pages, 6 figures include

The Statistical Mechanics of the (2+1)-Dimensional Black Hole

The presence of a horizon breaks the gauge invariance of (2+1)-dimensional general relativity, leading to the appearance of new physical states at the horizon. I show that the entropy of the (2+1)-dimensional black hole can be obtained as the logarithm of the number of these microscopic states.Comment: 12 pages, UCD-94-32 and NI-9401

Fluctuations of elastic interfaces in fluids: Theory and simulation

We study the dynamics of elastic interfaces-membranes-immersed in thermally excited fluids. The work contains three components: the development of a numerical method, a purely theoretical approach, and numerical simulation. In developing a numerical method, we first discuss the dynamical coupling between the interface and the surrounding fluids. An argument is then presented that generalizes the single-relaxation time lattice-Boltzmann method for the simulation of hydrodynamic interfaces to include the elastic properties of the boundary. The implementation of the new method is outlined and it is tested by simulating the static behavior of spherical bubbles and the dynamics of bending waves. By means of the fluctuation-dissipation theorem we recover analytically the equilibrium frequency power spectrum of thermally fluctuating membranes and the correlation function of the excitations. Also, the non-equilibrium scaling properties of the membrane roughening are deduced, leading us to formulate a scaling law describing the interface growth, W^2(L,T)=L^3 g[t/L^(5/2)], where W, L and T are the width of the interface, the linear size of the system and the temperature respectively, and g is a scaling function. Finally, the phenomenology of thermally fluctuating membranes is simulated and the frequency power spectrum is recovered, confirming the decay of the correlation function of the fluctuations. As a further numerical study of fluctuating elastic interfaces, the non-equilibrium regime is reproduced by initializing the system as an interface immersed in thermally pre-excited fluids.Comment: 15 pages, 11 figure

Beyond series expansions: mathematical structures for the susceptibility of the square lattice Ising model

We first study the properties of the Fuchsian ordinary differential equations for the three and four-particle contributions $\chi^{(3)}$ and $\chi^{(4)}$ of the square lattice Ising model susceptibility. An analysis of some mathematical properties of these Fuchsian differential equations is sketched. For instance, we study the factorization properties of the corresponding linear differential operators, and consider the singularities of the three and four-particle contributions $\chi^{(3)}$ and $\chi^{(4)}$, versus the singularities of the associated Fuchsian ordinary differential equations, which actually exhibit new ``Landau-like'' singularities. We sketch the analysis of the corresponding differential Galois groups. In particular we provide a simple, but efficient, method to calculate the so-called ``connection matrices'' (between two neighboring singularities) and deduce the singular behaviors of $\chi^{(3)}$ and $\chi^{(4)}$. We provide a set of comments and speculations on the Fuchsian ordinary differential equations associated with the $n$-particle contributions $\chi^{(n)}$ and address the problem of the apparent discrepancy between such a holonomic approach and some scaling results deduced from a Painlev\'e oriented approach.Comment: 21 pages Proceedings of the Counting Complexity conferenc

Prayers to Kāli: practicing radical numinosity

Prayers to Kāli is an invocation of the radical-sacred as a way into decolonization, liberation, and healing. The radical-sacred, as I conceive of it, is broadly to do with the work of retrieving our spiritual dimensions as an inextricable part of queer, and decolonial futurities. The construction and performance of decolonial, queer-feminist theory, and knowledge discourses as fundamentally located in communities of coalition, new modes of resistance and cosmologies, form the theoretical foil of this paper. The broader aim of the paper is to highlight the significance of spiritual, corporeal, and emotional knowledges in the work of decoloniality and dismantling systems of oppression. I locate this exploration within the narrative specifics of contemporary spirit- poetry from Tamil Nadu; a radical, border site where these connections and dimensions of decoloniality, gender, desire, and resistance play out

On the asymptotics of higher-dimensional partitions

We conjecture that the asymptotic behavior of the numbers of solid (three-dimensional) partitions is identical to the asymptotics of the three-dimensional MacMahon numbers. Evidence is provided by an exact enumeration of solid partitions of all integers <=68 whose numbers are reproduced with surprising accuracy using the asymptotic formula (with one free parameter) and better accuracy on increasing the number of free parameters. We also conjecture that similar behavior holds for higher-dimensional partitions and provide some preliminary evidence for four and five-dimensional partitions.Comment: 30 pages, 8 tables, 4 figures (v2) New data (63-68) for solid partitions added; (v3) published version, new subsection providing an unbiased estimate of the leading for the leading coefficient added, some tables delete

Domain Organization of Long Signal Peptides of Single-Pass Integral Membrane Proteins Reveals Multiple Functional Capacity

Targeting signals direct proteins to their extra - or intracellular destination such as the plasma membrane or cellular organelles. Here we investigated the structure and function of exceptionally long signal peptides encompassing at least 40 amino acid residues. We discovered a two-domain organization (“NtraC model”) in many long signals from vertebrate precursor proteins. Accordingly, long signal peptides may contain an N-terminal domain (N-domain) and a C-terminal domain (C-domain) with different signal or targeting capabilities, separable by a presumably turn-rich transition area (tra). Individual domain functions were probed by cellular targeting experiments with fusion proteins containing parts of the long signal peptide of human membrane protein shrew-1 and secreted alkaline phosphatase as a reporter protein. As predicted, the N-domain of the fusion protein alone was shown to act as a mitochondrial targeting signal, whereas the C-domain alone functions as an export signal. Selective disruption of the transition area in the signal peptide impairs the export efficiency of the reporter protein. Altogether, the results of cellular targeting studies provide a proof-of-principle for our NtraC model and highlight the particular functional importance of the predicted transition area, which critically affects the rate of protein export. In conclusion, the NtraC approach enables the systematic detection and prediction of cryptic targeting signals present in one coherent sequence, and provides a structurally motivated basis for decoding the functional complexity of long protein targeting signals

Phylogeny of the tropical tree family Dipterocarpaceae based on nucleotide sequences of the chloroplast RBCL gene

The Dipterocarpaceae, well-known trees of the Asian rain forests, have been variously assigned to Malvales and Theales. The family, if the Monotoideae of Africa (30 species) and South America and the Pakaraimoideae of South America (one species) are included, comprises over 500 species. Despite the high diversity and ecological dominance of the Dipterocarpaceae, phylogenetic relationships within the family as well as between dipterocarps and other angiosperm families remain poorly defined. We conducted parsimony analyses on rbcL sequences from 35 species to reconstruct the phylogeny of the Dipterocarpaceae. The consensus tree resulting from these analyses shows that the members of Dipterocarpaceae, including Monotes and Pakaraimaea, form a monophyletic group closely related to the family Sarcolaenaceae and are allied to Malvales. The present generic and higher taxon circumscriptions of Dipterocarpaceae are mostly in agreement with this molecular phylogeny with the exception of the genus Hopea, which forms a clade with Shorea sections Anthoshorea and Doona. Phylogenetic placement of Dipterocarpus and Dryobalanops remains unresolved. Further studies involving representative taxa from Cistaceae, Elaeocarpaceae, Hopea, Shorea, Dipterocarpus, and Dryobalanops will be necessary for a comprehensive understanding of the phylogeny and generic limits of the Dipterocarpaceae

Global Self-Organization of the Cellular Metabolic Structure

Background: Over many years, it has been assumed that enzymes work either in an isolated way, or organized in small catalytic groups. Several studies performed using "metabolic networks models'' are helping to understand the degree of functional complexity that characterizes enzymatic dynamic systems. In a previous work, we used "dissipative metabolic networks'' (DMNs) to show that enzymes can present a self-organized global functional structure, in which several sets of enzymes are always in an active state, whereas the rest of molecular catalytic sets exhibit dynamics of on-off changing states. We suggested that this kind of global metabolic dynamics might be a genuine and universal functional configuration of the cellular metabolic structure, common to all living cells. Later, a different group has shown experimentally that this kind of functional structure does, indeed, exist in several microorganisms. Methodology/Principal Findings: Here we have analyzed around 2.500.000 different DMNs in order to investigate the underlying mechanism of this dynamic global configuration. The numerical analyses that we have performed show that this global configuration is an emergent property inherent to the cellular metabolic dynamics. Concretely, we have found that the existence of a high number of enzymatic subsystems belonging to the DMNs is the fundamental element for the spontaneous emergence of a functional reactive structure characterized by a metabolic core formed by several sets of enzymes always in an active state. Conclusions/Significance: This self-organized dynamic structure seems to be an intrinsic characteristic of metabolism, common to all living cellular organisms. To better understand cellular functionality, it will be crucial to structurally characterize these enzymatic self-organized global structures.Supported by the Spanish Ministry of Science and Education Grants MTM2005-01504, MTM2004-04665, partly with FEDER funds, and by the Basque Government, Grant IT252-07