Spontaneous Breaking of Translational Invariance in One-Dimensional Stationary States on a Ring

We consider a model in which positive and negative particles diffuse in an asymmetric, CP-invariant way on a ring. The positive particles hop clockwise, the negative counterclockwise and oppositely-charged adjacent particles may swap positions. Monte-Carlo simulations and analytic calculations suggest that the model has three phases; a "pure" phase in which one has three pinned blocks of only positive, negative particles and vacancies, and in which translational invariance is spontaneously broken, a "mixed" phase with a non-vanishing current in which the three blocks are positive, negative and neutral, and a disordered phase without blocks.Comment: 7 pages, LaTeX, needs epsf.st

Twisted signatures of GC-biased gene conversion embedded in an evolutionary stable karyotype

The genomes of many vertebrates show a characteristic heterogeneous distribution of GC content, the so-called GC isochore structure. The origin of isochores has been explained via the mechanism of GC-biased gene conversion (gBGC). However, although the isochore structure is declining in many mammalian genomes, the heterogeneity in GC content is being reinforced in the avian genome. Despite this discrepancy, which remains unexplained, examinations of individual substitution frequencies in mammals and birds are both consistent with the gBGC model of isochore evolution. On the other hand, a negative correlation between substitution and recombination rate found in the chicken genome is inconsistent with the gBGC model. It should therefore be important to consider along with gBGC other consequences of recombination on the origin and fate of mutations, as well as to account for relationships between recombination rate and other genomic features. We therefore developed an analytical model to describe the substitution patterns found in the chicken genome, and further investigated the relationships between substitution patterns and several genomic features in a rigorous statistical framework. Our analysis indicates that GC content itself, either directly or indirectly via interrelations to other genomic features, has an impact on the substitution pattern. Further, we suggest that this phenomenon is particularly visible in avian genomes due to their unusually low rate of chromosomal evolution. Because of this, interrelations between GC content and other genomic features are being reinforced, and are as such more pronounced in avian genomes as compared with other vertebrate genomes with a less stable karyotype

Universality of Long-Range Correlations in Expansion-Randomization Systems

We study the stochastic dynamics of sequences evolving by single site mutations, segmental duplications, deletions, and random insertions. These processes are relevant for the evolution of genomic DNA. They define a universality class of non-equilibrium 1D expansion-randomization systems with generic stationary long-range correlations in a regime of growing sequence length. We obtain explicitly the two-point correlation function of the sequence composition and the distribution function of the composition bias in sequences of finite length. The characteristic exponent $\chi$ of these quantities is determined by the ratio of two effective rates, which are explicitly calculated for several specific sequence evolution dynamics of the universality class. Depending on the value of $\chi$, we find two different scaling regimes, which are distinguished by the detectability of the initial composition bias. All analytic results are accurately verified by numerical simulations. We also discuss the non-stationary build-up and decay of correlations, as well as more complex evolutionary scenarios, where the rates of the processes vary in time. Our findings provide a possible example for the emergence of universality in molecular biology.Comment: 23 pages, 15 figure

Influence of molecular temperature on the coherence of fullerenes in a near-field interferometer

We study C70 fullerene matter waves in a Talbot-Lau interferometer as a function of their temperature. While the ideal fringe visibility is observed at moderate molecular temperatures, we find a gradual degradation of the interference contrast if the molecules are heated before entering the interferometer. A method is developed to assess the distribution of the micro-canonical temperatures of the molecules in free flight. This way the heating-dependent reduction of interference contrast can be compared with the predictions of quantum theory. We find that the observed loss of coherence agrees quantitatively with the expected decoherence rate due to the thermal radiation emitted by the hot molecules.Comment: 11 pages, 9 figure

Cueva Ein neues Kupferfungizid auf Basis von Kupfersalzen

Cueva ist ein von der Firma Neudorff neu entwickeltes Kupferfungizid, dass mit einer sehr geringen Kupfermenge eine Vielzahl von Pflanzenkrankheiten kontrollieren kann. Cueva ist als Suspensionskonzentrat mit 18 g reinen Kupfer pro Liter formuliert

Symmetry breaking and phase coexistence in a driven diffusive two-channel system

We consider classical hard-core particles moving on two parallel chains in the same direction. An interaction between the channels is included via the hopping rates. For a ring, the stationary state has a product form. For the case of coupling to two reservoirs, it is investigated analytically and numerically. In addition to the known one-channel phases, two new regions are found, in particular the one, where the total density is fixed, but the filling of the individual chains changes back and forth, with a preference for strongly different densities. The corresponding probability distribution is determined and shown to have an universal form. The phase diagram and general aspects of the problem are discussed.Comment: 12 pages, 10 figures, to appear in Phys.Rev.

One-Dimensional Partially Asymmetric Simple Exclusion Process on a Ring with a Defect Particle

The effect of a moving defect particle for the one-dimensional partially asymmetric simple exclusion process on a ring is considered. The current of the ordinary particles, the speed of the defect particle and the density profile of the ordinary particles are calculated exactly. The phase diagram for the correlation length is identified. As a byproduct, the average and the variance of the particle density of the one-dimensional partially asymmetric simple exclusion process with open boundaries are also computed.Comment: 23 pages, 1 figur

The distribution of Polycomb-group proteins during cell division and development in Drosophila embryos: impact on models for silencing

The subcellular three-dimensional distribution of three polycomb-group (PcG) proteins-polycomb, polyhomeotic and posterior sex combs-in fixed whole-mount Drosophila embryos was analyzed by multicolor confocal fluorescence microscopy. All three proteins are localized in complex patterns of 100 or more loci throughout most of the interphase nuclear volume. The rather narrow distribution of the protein intensities in the vast majority of loci argues against a PcG-mediated sequestration of repressed target genes by aggregation into subnuclear domains. In contrast to the case for PEV repression (Csink, A.K., and S. Henikoff. 1996. Nature. 381:529-531), there is a lack of correlation between the occurrence of PcG proteins and high concentrations of DNA, demonstrating that the silenced genes are not targeted to heterochromatic regions within the nucleus. There is a clear distinction between sites of transcription in the nucleus and sites of PcG binding, supporting the assumption that most PcG binding loci are sites of repressive complexes. Although the PcG proteins maintain tissue-specific repression for up to 14 cell generations, the proteins studied here visibly dissociate from the chromatin during mitosis, and disperse into the cytoplasm in a differential manner. Quantitation of the fluorescence intensities in the whole mount embryos demonstrate that the dissociated proteins are present in the cytoplasm. We determined that <2% of PH remains attached to late metaphase and anaphase chromosomes. Each of the three proteins that were studied has a different rate and extent of dissociation at prophase and reassociation at telophase. These observations have important implications for models of the mechanism and maintenance of PcG-mediated gene repression

The distribution of polycomb-group proteins during cell division and development in Drosophila embryos: Impact on models for silencing

The subcellular three-dimensional distribution of three polycomb-group (PcG) proteins—polycomb, polyhomeotic and posterior sex combs—in fixed whole-mount Drosophila embryos was analyzed by multicolor confocal fluorescence microscopy. All three proteins are localized in complex patterns of 100 or more loci throughout most of the interphase nuclear volume. The rather narrow distribution of the protein intensities in the vast majority of loci argues against a PcG-mediated sequestration of repressed target genes by aggregation into subnuclear domains. In contrast to the case for PEV repression (Csink, A.K., and S. Henikoff. 1996. Nature. 381:529–531), there is a lack of correlation between the occurrence of PcG proteins and high concentrations of DNA, demonstrating that the silenced genes are not targeted to heterochromatic regions within the nucleus. There is a clear distinction between sites of transcription in the nucleus and sites of PcG binding, supporting the assumption that most PcG binding loci are sites of repressive complexes. Although the PcG proteins maintain tissue-specific repression for up to 14 cell generations, the proteins studied here visibly dissociate from the chromatin during mitosis, and disperse into the cytoplasm in a differential manner. Quantitation of the fluorescence intensities in the whole mount embryos demonstrate that the dissociated proteins are present in the cytoplasm. We determined that <2% of PH remains attached to late metaphase and anaphase chromosomes. Each of the three proteins that were studied has a different rate and extent of dissociation at prophase and reassociation at telophase. These observations have important implications for models of the mechanism and maintenance of PcG- mediated gene repression

Exact Solution of an Exclusion Model in the Presence of a moving Impurity

We study a recently introduced model which consists of positive and negative particles on a ring. The positive (negative) particles hop clockwise (counter-clockwise) with rate 1 and oppositely charged particles may swap their positions with asymmetric rates q and 1. In this paper we assume that a finite density of positively charged particles $\rho$ and only one negative particle (which plays the role of an impurity) exist on the ring. It turns out that the canonical partition function of this model can be calculated exactly using Matrix Product Ansatz (MPA) formalism. In the limit of infinite system size and infinite number of positive particles, we can also derive exact expressions for the speed of the positive and negative particles which show a second order phase transition at $q_c=2\rho$. The density profile of the positive particles on the ring has a shock structure for $q \leq q_c$ and an exponential behaviour with correlation length $\xi$ for $q \geq q_c$. It will be shown that the mean-field results become exact at q=3 and no phase transition occurs for q>2.Comment: 9 pages,4 EPS figures. To be appear in JP