409,049 research outputs found
Stepwise bending of DNA by a single TATA-box Binding Protein
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
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
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
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
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
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
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 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 is symmetric or
not. For the non-symmetric case, we prove global existence and uniqueness of
solutions for kernels satisfying . This result is optimal in
the sense that we show for a large class of initial conditions with kernels
satisfying ( the solutions cannot exist. On
the other hand, for symmetric kernels, we prove global existence of solutions
for (
while existence is lost for
( In the intermediate regime 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
- …