Ultrasensitivity in phosphorylation-dephosphorylation cycles with little substrate

Cellular decision-making is driven by dynamic behaviours, such as the preparations for sunrise enabled by circadian rhythms and the choice of cell fates enabled by positive feedback. Such behaviours are often built upon ultrasensitive responses where a linear change in input generates a sigmoidal change in output. Phosphorylation-dephosphorylation cycles are one means to generate ultrasensitivity. Using bioinformatics, we show that in vivo levels of kinases and phosphatases frequently exceed the levels of their corresponding substrates in budding yeast. This result is in contrast to the conditions often required by zero-order ultrasensitivity, perhaps the most well known means for how such cycles become ultrasensitive. We therefore introduce a mechanism to generate ultrasensitivity when numbers of enzymes are higher than numbers of substrates. Our model combines distributive and non-distributive actions of the enzymes with two-stage binding and concerted allosteric transitions of the substrate. We use analytical and numerical methods to calculate the Hill number of the response. For a substrate with [Formula: see text] phosphosites, we find an upper bound of the Hill number of [Formula: see text], and so even systems with a single phosphosite can be ultrasensitive. Two-stage binding, where an enzyme must first bind to a binding site on the substrate before it can access the substrate's phosphosites, allows the enzymes to sequester the substrate. Such sequestration combined with competition for each phosphosite provides an intuitive explanation for the sigmoidal shifts in levels of phosphorylated substrate. Additionally, we find cases for which the response is not monotonic, but shows instead a peak at intermediate levels of input. Given its generality, we expect the mechanism described by our model to often underlay decision-making circuits in eukaryotic cells

Causal sites as quantum geometry

We propose a structure called a causal site to use as a setting for quantum geometry, replacing the underlying point set. The structure has an interesting categorical form, and a natural "tangent 2-bundle," analogous to the tangent bundle of a smooth manifold. Examples with reasonable finiteness conditions have an intrinsic geometry, which can approximate classical solutions to general relativity. We propose an approach to quantization of causal sites as well.Comment: 21 pages, 3 eps figures; v2: added references; to appear in JM

Endomorphisms and automorphisms of locally covariant quantum field theories

In the framework of locally covariant quantum field theory, a theory is described as a functor from a category of spacetimes to a category of *-algebras. It is proposed that the global gauge group of such a theory can be identified as the group of automorphisms of the defining functor. Consequently, multiplets of fields may be identified at the functorial level. It is shown that locally covariant theories that obey standard assumptions in Minkowski space, including energy compactness, have no proper endomorphisms (i.e., all endomorphisms are automorphisms) and have a compact automorphism group. Further, it is shown how the endomorphisms and automorphisms of a locally covariant theory may, in principle, be classified in any single spacetime. As an example, the endomorphisms and automorphisms of a system of finitely many free scalar fields are completely classified.Comment: v2 45pp, expanded to include additional results; presentation improved and an error corrected. To appear in Rev Math Phy

The Influence of Metallicity on Star Formation in Protogalaxies

In cold dark matter cosmological models, the first stars to form are believed to do so within small protogalaxies. We wish to understand how the evolution of these early protogalaxies changes once the gas forming them has been enriched with small quantities of heavy elements, which are produced and dispersed into the intergalactic medium by the first supernovae. Our initial conditions represent protogalaxies forming within a fossil H II region, a previously ionized region that has not yet had time to cool and recombine. We study the influence of low levels of metal enrichment on the cooling and collapse of ionized gas in small protogalactic halos using three-dimensional, smoothed particle hydrodynamics (SPH) simulations that incorporate the effects of the appropriate chemical and thermal processes. Our previous simulations demonstrated that for metallicities Z < 0.001 Z_sun, metal line cooling alters the density and temperature evolution of the gas by less than 1% compared to the metal-free case at densities below 1 cm-3) and temperatures above 2000 K. Here, we present the results of high-resolution simulations using particle splitting to improve resolution in regions of interest. These simulations allow us to address the question of whether there is a critical metallicity above which fine structure cooling from metals allows efficient fragmentation to occur, producing an initial mass function (IMF) resembling the local Salpeter IMF, rather than only high-mass stars.Comment: 3 pages, 2 figures, First Stars III conference proceeding

Solenoidal versus compressive turbulence forcing

We analyze the statistics and star formation rate obtained in high-resolution numerical experiments of forced supersonic turbulence, and compare with observations. We concentrate on a systematic comparison of solenoidal (divergence-free) and compressive (curl-free) forcing, which are two limiting cases of turbulence driving. Our results show that for the same RMS Mach number, compressive forcing produces a three times larger standard deviation of the density probability distribution. When self-gravity is included in the models, the star formation rate is more than one order of magnitude higher for compressive forcing than for solenoidal forcing.Comment: 1 page, to appear in the proceedings of the IAU General Assembly Joint Discussion 14 "FIR2009: The ISM of Galaxies in the Far-Infrared and Sub-Millimetre", ed. M. Cunningha

Abstract Tensor Systems as Monoidal Categories

The primary contribution of this paper is to give a formal, categorical treatment to Penrose's abstract tensor notation, in the context of traced symmetric monoidal categories. To do so, we introduce a typed, sum-free version of an abstract tensor system and demonstrate the construction of its associated category. We then show that the associated category of the free abstract tensor system is in fact the free traced symmetric monoidal category on a monoidal signature. A notable consequence of this result is a simple proof for the soundness and completeness of the diagrammatic language for traced symmetric monoidal categories.Comment: Dedicated to Joachim Lambek on the occasion of his 90th birthda

Kedudukan Kejaksaan dalam Menyelesaikan Kasus Tindak Pidana Korupsi Pasca Terbentuknya Komisi Pemberantasan Korupsi

Prostitusi dikategorikan sebagai penyakit masyarakat, yang sulit di tumpas, sulit diobati, demikianlah penenpatan Korupsi yang di-ibaratkan sebagai penyakit yang sudah menyebar sangat luar biasa. Fenomena korupsi ini adalah sebuah hal yang perlu mendapat perhatian serius dalam penangannya. Tindak pidana korupsi merugikan keuangan negara karena merongrong dan menggerogoti keuangan negara sebagai sumber daya pembangunan, membahayakan stabilitas ekonomi, dan politik negara yang akan menghambat pembangunan dan merampas hak rakyat. Oleh sebab itu pemerintah sebagai penyelenggara negara harus se-segera mungkin menuntaskan masalah korupsi dengan mengedepankan kepentingan masyarakat dan bangsa. Dari hasil paparan di atas, yang menjadi permasalahan yakni bagaimanakah dasar pengaturan hukum mengenai kewenangan Kejaksaan dalam menangani Tindak Pidana Korupsi di Indonesia dan bagaimana kedudukan Kejaksaan dalam pemberantasan Tindak Pidana Korupsi setelah terbentuknya Komisi Pemberantasan Korupsi. Metode penelitian yang digunakan adalah penelitian kepustakaan, yaitu menggali dari sumber-sumber bahan penelitian dalam penulisan yaitu bahan hukum primer, sekunder dan tertier. Hasil penelitian menunjukkan bahwa tugas dan kewenangan Kejaksaan diatur dalam hukum acara pidana, yaitu Undang-undang No. 08 Tahun 1981 tentang KUHAP sementara dalam kaitannya dengan kelembagaannya sendiri diatur dalam Undang-undang No. 05 Tahun 1991 sebagaimana telah diubah dengan Undang-undang No. 16 Tahun 2004 sebagai produk reformasi telah memberi nuansa baru bagi kemandirian lembaga kejaksaan ini.Dalam sistem peradilan pidana Indonesia, kedudukan Kejaksaan memiliki peran sentral. Hal ini tidak terlepas dari kewenangan yang dimiliki kejaksaan dalam hal menentukan apakah suatu perkara dapat atau tidak diajukan kemuka persidangan. Kekuasaan untuk menentukan apakah suatu perkara dapat diteruskan atau tidak kepersidangan berdasarkan alat bukti yang sah. Berdasarkan hal tersebut sejatinya kejaksaan dalam proses penyelidikan dan penyidikan suatu perkara sudah harus terlibat, jadi tidak hanya sebatas berkas perkara yang dikirimkan oleh penyidik Polri untuk diteliti oleh Jaksa. Dari hasil penelitian dapat ditarik kesimpulan bahwa Kejaksaan memiliki kewenangan dalam menangani Tindak Pidana Korupsi di Indonesia berdasarkan Pasal 26 Undang-Undang Nomor 31 tahun 1999 Jo. Undang-Undang Nomor 20 tahun 2001 penyidikan, penuntutan dan pemeriksaandisidang pengadilan terhadap tindak pidana korupsi dilakukan berdasarkanhukum Acara Pidana (KUHAP). Bahwa setelah terbentuknya Komisi Pemberantasan Korupsi, Kejaksaan tetap memiliki yurisdiksi dalam pemberantasan Tindak Pidana Korupsi, dalam hal ini didasarkan pada posisi sentral dari kejaksaan dalam hal menentukan apakah suatu perkara dapat atau tidakdiajukan kemuka persidangan

Wolf-Rayet and LBV Nebulae as the Result of Variable and Non-Spherical Stellar Winds

The physical basis for interpreting observations of nebular morphology around massive stars in terms of the evolution of the central stars is reviewed, and examples are discussed, including NGC 6888, OMC-1, and eta Carinae.Comment: To be published in the Proceedings of IAU Colloquium 169 on Variable and Non-Spherical Stellar Winds in Luminous Hot Stars, ed. B. Wolf (Springer-Verlag, Berlin, Heidelberg). 7 pages, including 5 figures. A full-resolution version of fig 4 is available in the version at http://www.mpia-hd.mpg.de/theory/preprints.html#maclo

Modification of Projected Velocity Power Spectra by Density Inhomogeneities in Compressible Supersonic Turbulence

(Modified) The scaling of velocity fluctuation, dv, as a function of spatial scale L in molecular clouds can be measured from size-linewidth relations, principal component analysis, or line centroid variation. Differing values of the power law index of the scaling relation dv = L^(g3D) in 3D are given by these different methods: the first two give g3D=0.5, while line centroid analysis gives g3D=0. This discrepancy has previously not been fully appreciated, as the variation of projected velocity line centroid fluctuations (dv_{lc} = L^(g2D)) is indeed described, in 2D, by g2D=0.5. However, if projection smoothing is accounted for, this implies that g3D=0. We suggest that a resolution of this discrepancy can be achieved by accounting for the effect of density inhomogeneity on the observed g2D obtained from velocity line centroid analysis. Numerical simulations of compressible turbulence are used to show that the effect of density inhomogeneity statistically reverses the effect of projection smoothing in the case of driven turbulence so that velocity line centroid analysis does indeed predict that g2D=g3D=0.5. Using our numerical results we can restore consistency between line centroid analysis, principal component analysis and size-linewidth relations, and we derive g3D=0.5, corresponding to shock-dominated (Burgers) turbulence. We find that this consistency requires that molecular clouds are continually driven on large scales or are only recently formed.Comment: 28 pages total, 20 figures, accepted for publication in Ap