Mechanical response of plectonemic DNA: an analytical solution

We consider an elastic rod model for twisted DNA in the plectonemic regime. The molecule is treated as an impenetrable tube with an effective, adjustable radius. The model is solved analytically and we derive formulas for the contact pressure, twisting moment and geometrical parameters of the supercoiled region. We apply our model to magnetic tweezer experiments of a DNA molecule subjected to a tensile force and a torque, and extract mechanical and geometrical quantities from the linear part of the experimental response curve. These reconstructed values are derived in a self-contained manner, and are found to be consistent with those available in the literature.Comment: 14 pages, 4 figure

Constraints, Histones, and the 30 Nanometer Spiral

We investigate the mechanical stability of a segment of DNA wrapped around a histone in the nucleosome configuration. The assumption underlying this investigation is that the proper model for this packaging arrangement is that of an elastic rod that is free to twist and that writhes subject to mechanical constraints. We find that the number of constraints required to stabilize the nuclesome configuration is determined by the length of the segment, the number of times the DNA wraps around the histone spool, and the specific constraints utilized. While it can be shown that four constraints suffice, in principle, to insure stability of the nucleosome, a proper choice must be made to guarantee the effectiveness of this minimal number. The optimal choice of constraints appears to bear a relation to the existence of a spiral ridge on the surface of the histone octamer. The particular configuration that we investigate is related to the 30 nanometer spiral, a higher-order organization of DNA in chromatin.Comment: ReVTeX, 15 pages, 18 figure

Loitering with intent: dealing with human-intensive systems

This paper discusses the professional roles of information systems analysts and users, focusing on a perspective of human intensive, rather than software intensive information systems. The concept of ‘meaningful use’ is discussed in re-lation to measures of success/failure in IS development. The authors consider how a number of different aspects of reductionism may distort analyses, so that processes of inquiry cannot support organizational actors to explore and shape their requirements in relation to meaningful use. Approaches which attempt to simplify complex problem spaces, to render them more susceptible to ‘solution’ are problematized. Alternative perspectives which attempt a systematic, holistic complexification, by supporting contextual dependencies to emerge, are advocated as a way forward

Enhancement of Magneto-Optic Effects via Large Atomic Coherence

We utilize the generation of large atomic coherence to enhance the resonant nonlinear magneto-optic effect by several orders of magnitude, thereby eliminating power broadening and improving the fundamental signal-to-noise ratio. A proof-of-principle experiment is carried out in a dense vapor of Rb atoms. Detailed numerical calculations are in good agreement with the experimental results. Applications such as optical magnetometry or the search for violations of parity and time reversal symmetry are feasible

Chromatin: a tunable spring at work inside chromosomes

This paper focuses on mechanical aspects of chromatin biological functioning. Within a basic geometric modeling of the chromatin assembly, we give for the first time the complete set of elastic constants (twist and bend persistence lengths, stretch modulus and twist-stretch coupling constant) of the so-called 30-nm chromatin fiber, in terms of DNA elastic properties and geometric properties of the fiber assembly. The computation naturally embeds the fiber within a current analytical model known as the ``extensible worm-like rope'', allowing a straightforward prediction of the force-extension curves. We show that these elastic constants are strongly sensitive to the linker length, up to 1 bp, or equivalently to its twist, and might locally reach very low values, yielding a highly flexible and extensible domain in the fiber. In particular, the twist-stretch coupling constant, reflecting the chirality of the chromatin fiber, exhibits steep variations and sign changes when the linker length is varied. We argue that this tunable elasticity might be a key feature for chromatin function, for instance in the initiation and regulation of transcription.Comment: 38 pages 15 figure

Governments, decentralisation, and the risk of electoral defeat

<p>In the last three decades several countries around the world have transferred authority from their national to their regional governments. However, not all their regions have been empowered to the same degree and important differences can be observed between and within countries. Why do some regions obtain more power than others? Current literature argues that variation in the redistribution of power and resources between regions is introduced by demand. Yet these explanations are conditional on the presence of strong regionalist parties or territorial cleavages. This article proposes instead a theory that links the government’s risk of future electoral defeat with heterogeneous decentralisation, and tests its effects using data from 15 European countries and 141 regions. The results provide evidence that parties in government protect themselves against the risk of electoral defeat by selectively targeting decentralisation towards regions in which they are politically strong. The findings challenge previous research that overestimates the importance of regionalist parties while overlooking differences between regions.</p

Familiarization: A theory of repetition suppression predicts interference between overlapping cortical representations

Repetition suppression refers to a reduction in the cortical response to a novel stimulus that results from repeated presentation of the stimulus. We demonstrate repetition suppression in a well established computational model of cortical plasticity, according to which the relative strengths of lateral inhibitory interactions are modified by Hebbian learning. We present the model as an extension to the traditional account of repetition suppression offered by sharpening theory, which emphasises the contribution of afferent plasticity, by instead attributing the effect primarily to plasticity of intra-cortical circuitry. In support, repetition suppression is shown to emerge in simulations with plasticity enabled only in intra-cortical connections. We show in simulation how an extended ‘inhibitory sharpening theory’ can explain the disruption of repetition suppression reported in studies that include an intermediate phase of exposure to additional novel stimuli composed of features similar to those of the original stimulus. The model suggests a re-interpretation of repetition suppression as a manifestation of the process by which an initially distributed representation of a novel object becomes a more localist representation. Thus, inhibitory sharpening may constitute a more general process by which representation emerges from cortical re-organisation

Search for the Higgs boson in events with missing transverse energy and b quark jets produced in proton-antiproton collisions at s**(1/2)=1.96 TeV

We search for the standard model Higgs boson produced in association with an electroweak vector boson in events with no identified charged leptons, large imbalance in transverse momentum, and two jets where at least one contains a secondary vertex consistent with the decay of b hadrons. We use ~1 fb-1 integrated luminosity of proton-antiproton collisions at s**(1/2)=1.96 TeV recorded by the CDF II experiment at the Tevatron. We find 268 (16) single (double) b-tagged candidate events, where 248 +/- 43 (14.4 +/- 2.7) are expected from standard model background processes. We place 95% confidence level upper limits on the Higgs boson production cross section for several Higgs boson masses ranging from 110 GeV/c2 to 140 GeV/c2. For a mass of 115 GeV/c2 the observed (expected) limit is 20.4 (14.2) times the standard model prediction.Comment: 8 pages, 2 figures, submitted to Phys. Rev. Let

Measurement of Ratios of Fragmentation Fractions for Bottom Hadrons in p-pbar Collisions at sqrt{s}=1.96 TeV

This paper describes the first measurement of b-quark fragmentation fractions into bottom hadrons in Run II of the Tevatron Collider at Fermilab. The result is based on a 360 pb-1 sample of data collected with the CDF II detector in p-pbar collisions at sqrt{s}=1.96 TeV. Semileptonic decays of B0, B+, and B_s mesons, as well as Lambda_b baryons, are reconstructed. For an effective bottom hadron p_T threshold of 7 GeV/c, the fragmentation fractions are measured to be f_u/f_d=1.054 +/- 0.018 (stat) +0.025-0.045(sys) +/- 0.058 (Br), f_s/(f_u+f_d)=0.160 +/- 0.005 (stat) +0.011-0.010 (sys) +0.057-0.034 (Br), and f_{Lambda_b}/(f_u+f_d)=0.281\pm0.012 (stat) +0.058-0.056 (sys) +0.128-0.086 (Br), where the uncertainty (Br) is due to uncertainties on measured branching ratios. The value of f_s/(f_u+f_d) agrees within one standard deviation with previous CDF measurements and the world average of this quantity, which is dominated by LEP measurements. However, the ratio f_{Lambda_b}/(f_u+f_d) is approximately twice the value previously measured at LEP. The approximately 2 sigma discrepancy is examined in terms of kinematic differences between the two production environments.Comment: Submitted to PRD, 54 pages, 53 plot

Two-Particle Momentum Correlations in Jets Produced in ppbar Collisions at s**(1/2) = 1.96-TeV

We present the first measurement of two-particle momentum correlations in jets produced in $p\bar p$ collisions at $\sqrt{s}=1.96$ TeV. Results are obtained for charged particles within a restricted cone with an opening angle of 0.5 radians around the jet axis and for events with dijet masses between 66 and 563 GeV/c$^{2}$. A comparison of the experimental data to theoretical predictions obtained for partons within the framework of resummed perturbative QCD in the next-to-leading log approximation (NLLA) shows that the parton momentum correlations survive the hadronization stage of jet fragmentation, giving further support to the hypothesis of local parton-hadron duality. The extracted value of the NLLA parton shower cutoff scale $Q_\mathit{eff}$ set equal to $\Lambda_\mathit{QCD}$ is found to be $(1.4^{+0.9}_{-0.7})\times 100$ MeV.Comment: Submitted to Phys.Rev.