409,049 research outputs found

    Stepwise bending of DNA by a single TATA-box Binding Protein

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    The TATA-box Binding Protein (TBP) is required by all three eukaryotic RNA polymerases for the initiation of transcription from most promoters. TBP recognizes, binds to, and bends promoter sequences called ``TATA-boxes'' in the DNA. We present results from the study of individual Saccharomyces cerevisia TBPs interacting with single DNA molecules containing a TATA-box. Using video microscopy, we observed the Brownian motion of beads tethered by short surface-bound DNA. When TBP binds to and bends the DNA, the conformation of the DNA changes and the amplitude of Brownian motion of the tethered bead is reduced compared to that of unbent DNA. We detected individual binding and dissociation events and derived kinetic parameters for the process. Dissociation was induced by increasing the salt concentration or by directly pulling on the tethered bead using optical tweezers. In addition to the well-defined free and bound classes of Brownian motion, we observed another two classes of motion. These extra classes were identified with intermediate states on a three-step, linear binding pathway. Biological implications of the intermediate states are discussed.Comment: Accepted for publication in: Biophysical Journa

    Optimal correlations in many-body quantum systems

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    Information and correlations in a quantum system are closely related through the process of measurement. We explore such relation in a many-body quantum setting, effectively bridging between quantum metrology and condensed matter physics. To this aim we adopt the information-theory view of correlations, and study the amount of correlations after certain classes of Positive-Operator-Valued Measurements are locally performed. As many-body system we consider a one-dimensional array of interacting two-level systems (a spin chain) at zero temperature, where quantum effects are most pronounced. We demonstrate how the optimal strategy to extract the correlations depends on the quantum phase through a subtle interplay between local interactions and coherence.Comment: 5 pages, 5 figures + supplementary material. To be published in PR

    Quantum field inspired model of decision making: Asymptotic stabilization of belief state via interaction with surrounding mental environment

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    This paper is devoted to justification of the quantum-like model of the process of decision making based on theory of open quantum systems: decision making as decoher- ence. This process is modeled as interaction of a decision maker, Alice, with a mental (information) environment R surrounding her. Such an interaction generates “dissipation of uncertainty” from Alice’s belief-state ρ ( t ) into R and asymptotic stabilization of ρ ( t ) to a steady belief-state. The latter is treated as the decision state. Mathematically the problem under study is about finding constraints on R guaranteeing such stabilization. We found a partial solution of this problem (in the form of sufficient conditions). We present the corresponding decision making analysis for one class of mental environments, so-called “almost homogeneous environments”, with the illustrative examples: a) behavior of electorate interacting with the mass-media “reservoir”; b) consumers’ persuasion. We also comment on other classes of mental environments

    Modelling Food Webs

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    We review theoretical approaches to the understanding of food webs. After an overview of the available food web data, we discuss three different classes of models. The first class comprise static models, which assign links between species according to some simple rule. The second class are dynamical models, which include the population dynamics of several interacting species. We focus on the question of the stability of such webs. The third class are species assembly models and evolutionary models, which build webs starting from a few species by adding new species through a process of "invasion" (assembly models) or "speciation" (evolutionary models). Evolutionary models are found to be capable of building large stable webs.Comment: 34 pages, 2 figures. To be published in "Handbook of graphs and networks" S. Bornholdt and H. G. Schuster (eds) (Wiley-VCH, Berlin

    Constructing Auxiliary Dynamics for Nonequilibrium Stationary States by Variance Minimization

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    We present a strategy to construct guiding distribution functions (GDFs) based on variance minimization. Auxiliary dynamics via GDFs mitigates the exponential growth of variance as a function of bias in Monte Carlo estimators of large deviation functions. The variance minimization technique exploits the exact properties of eigenstates of the tilted operator that defines the biased dynamics in the nonequilibrium system. We demonstrate our techniques in two classes of problems. In the continuum, we show that GDFs can be optimized to study the interacting driven diffusive systems where the efficiency is systematically improved by incorporating higher correlations into the GDF. On the lattice, we use a correlator product state ansatz to study the 1D weakly asymmetric simple exclusion process. We show that with modest resources, we can capture the features of the susceptibility in large systems that mark the phase transition from uniform transport to a traveling wave state. Our work extends the repertoire of tools available to study nonequilibrium properties in realistic systems

    Observations of multiple nucleus galaxies

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    Disturbed galaxies with two nuclei display the final state of the interaction process of two galaxies (Kollatschny et al., 1986; Fricke and Kollatschny, 1989). A few of these double nucleus galaxies contain Seyfert nuclei. Making the assumption that the Seyfert galaxies Mkn 231 and Mkn 273 are galaxies in the final state of merging, having strong tidal arms but unresolved nuclei, one can estimate that 4 percent of all Seyfert galaxies are in the merging process. The luminosities of multiple nucleus Seyfert galaxies are extremely high in comparison to morphologically undisturbed Seyfert galaxies. In a table, mean values of the visual and blue luminosities and of the far-infrared and radio (6 cm) luminosities as well as the H alpha fluxes are listed for both classes are shown. In addition, the authors have separated Seyfert 1 and Seyfert 2 galaxies. In all cases the luminosities of double nucleus Seyfert galaxies are higher by a factor of more than two with respect to undisturbed Seyfert galaxies. This result might be explained by higher luminosities in the early phases of a Seyfert's life-under the assumption that the nonthermal activity is triggered by tidal interaction-and/or additional strong starburst phenomena. Due to strong nuclear absorption, the UV spectra of these Seyfert nuclei are unusually weak. Corresponding to the Seyfert survey, the authors obtained the H alpha and far infrared radiation (FIR) luminosities as well as the (0III)5007/H beta line ratios of a small sample of non-Seyfert nuclei in double nucleus galaxies. The direct image and the velocity field of the double starburst galaxy Mkn 788 (Kollatschny et al., 1986) are shown. The authors compared their measurements with those of normal interacting galaxies of Keel et al. (1985) and Bushouse (1987). The mean FIR luminosity per nucleus in multiple systems is the same as that of interacting galaxies. But the mean H alpha luminosities as well as the (OIII)/H beta line ratios are higher by a factor of 1.5-2 than those of normal interacting galaxies

    Mathematical Theory of Exchange-driven Growth

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    Exchange-driven growth is a process in which pairs of clusters interact and exchange a single unit of mass. The rate of exchange is given by an interaction kernel K(j,k)K(j,k) which depends on the masses of the two interacting clusters. In this paper we establish the fundamental mathematical properties of the mean field kinetic equations of this process for the first time. We find two different classes of behaviour depending on whether K(j,k)K(j,k) is symmetric or not. For the non-symmetric case, we prove global existence and uniqueness of solutions for kernels satisfying K(j,k)CjkK(j,k)\leq Cjk. This result is optimal in the sense that we show for a large class of initial conditions with kernels satisfying K(j,k)CjβK(j,k)\geq Cj^{\beta} (β>1)\beta>1) the solutions cannot exist. On the other hand, for symmetric kernels, we prove global existence of solutions for K(j,k)C(jμkν+jνkμ)K(j,k)\leq C(j^{\mu}k^{\nu}+j^{\nu}k^{\mu}) (μ,ν2,\mu,\nu\leq2, μ+ν3),\mu+\nu\leq3), while existence is lost for K(j,k)CjβK(j,k)\geq Cj^{\beta} (β>2).\beta>2). In the intermediate regime 3<μ+ν4,3<\mu+\nu\leq4, we can only show local existence. We conjecture that the intermediate regime exhibits finite-time gelation in accordance with the heuristic results obtained for particular kernels.Comment: Mistakes in the uniqueness proofs are fixed. Some typos are corrected. Some references are adde
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