Deconvolution of dynamic mechanical networks

Time-resolved single-molecule biophysical experiments yield data that contain a wealth of dynamic information, in addition to the equilibrium distributions derived from histograms of the time series. In typical force spectroscopic setups the molecule is connected via linkers to a read-out device, forming a mechanically coupled dynamic network. Deconvolution of equilibrium distributions, filtering out the influence of the linkers, is a straightforward and common practice. We have developed an analogous dynamic deconvolution theory for the more challenging task of extracting kinetic properties of individual components in networks of arbitrary complexity and topology. Our method determines the intrinsic linear response functions of a given molecule in the network, describing the power spectrum of conformational fluctuations. The practicality of our approach is demonstrated for the particular case of a protein linked via DNA handles to two optically trapped beads at constant stretching force, which we mimic through Brownian dynamics simulations. Each well in the protein free energy landscape (corresponding to folded, unfolded, or possibly intermediate states) will have its own characteristic equilibrium fluctuations. The associated linear response function is rich in physical content, since it depends both on the shape of the well and its diffusivity---a measure of the internal friction arising from such processes like the transient breaking and reformation of bonds in the protein structure. Starting from the autocorrelation functions of the equilibrium bead fluctuations measured in this force clamp setup, we show how an experimentalist can accurately extract the state-dependent protein diffusivity using a straightforward two-step procedure.Comment: 9 pages, 3 figures + supplementary material 14 pages, 4 figure

Random walk with barriers: Diffusion restricted by permeable membranes

Restrictions to molecular motion by barriers (membranes) are ubiquitous in biological tissues, porous media and composite materials. A major challenge is to characterize the microstructure of a material or an organism nondestructively using a bulk transport measurement. Here we demonstrate how the long-range structural correlations introduced by permeable membranes give rise to distinct features of transport. We consider Brownian motion restricted by randomly placed and oriented permeable membranes and focus on the disorder-averaged diffusion propagator using a scattering approach. The renormalization group solution reveals a scaling behavior of the diffusion coefficient for large times, with a characteristically slow inverse square root time dependence. The predicted time dependence of the diffusion coefficient agrees well with Monte Carlo simulations in two dimensions. Our results can be used to identify permeable membranes as restrictions to transport in disordered materials and in biological tissues, and to quantify their permeability and surface area.Comment: 8 pages, 3 figures; origin of dispersion clarified, refs adde

New Data on the Distribution of Southern Forests for the West Siberian Plain during the Late Pleistocene: A Paleoentomological Approach

Subfossil remains of insects and branchiopod crustaceans (Cladocera and Notostraca) found in three late Pleistocene deposits in the Novosibirsk region in the vicinity of the village of Suzun have been described. The calibrated radiocarbon dates for these deposits were 24,893-25,966 cal BP (Suzun-1), 20,379-20,699 cal BP (Suzun-2), and 27,693-28,126 cal BP (Nizhny Suzun), which correspond to the onset of marine isotope stage 2 (MIS 2). The insect assemblages of these deposits are mainly represented by Coleoptera, which are noteworthy for high taxonomic and ecological diversity. At least 194 beetle species from 21 families have been found altogether. Of them, 74 species were found in the Pleistocene deposits of Western Siberia for the first time. All deposits were similar in species composition of beetles; Carabidae and Curculionidae prevailed everywhere. The ecological composition was dominated by steppe and tundra-steppe species; aquatic and riparian groups were also well represented. The Cladoceran and notostracan taxa revealed in Suzun-1 and Suzun-2 are characteristic of recent steppes rather than the forest zone of Western Siberia. The studied entomocomplexes are congruent with the periglacial Otiorhynchus-type fauna that inhabited the southern part of the West Siberian Plain at the end of the Pleistocene and had no close contemporary analogues. Cold and dry conditions, as well as the prevailing open landscapes of the tundra-steppe type, were the reconstructed conditions for this fauna. At the same time, the Suzun-1 and Suzun-2 entomocomplexes had a distinctive feature, namely a high proportion of forest species associated with both coniferous and deciduous trees. According to these data, at the beginning of MIS 2 in the Upper Ob region, spruce forests with the participation of small-leaved species (birch) were present. They were probably confined to river valleys and were not widely distributed

Insects and molluscs of the Late Pleistocene at the Gornovo site (Southern Ural foreland, Russia): New data on palaeoenvironment reconstructions

The paper presents new data on the subfossil insects and molluscs, as well a new radiocarbon date for the Gornovo site in the Southern Fore-Urals. As a result, the stratigraphic interpretation of the sediments of the lower part of the first above floodplain terrace of the Belaya River is corrected and they are assigned to the Tabulda Horizon (MIS 3) of the Upper Pleistocene in the regional scheme of the Fore-Urals Quaternary. The malacofauna of the locality is represented by 27 species of terrestrial and freshwater molluscs. The composition of molluscs in the deposits of MIS 3 indicates the succession of deposit accumulation in the river valley from the stage of reservoirs that periodically connecting with the river to the stage of the overgrown oxbow lake. Single occurrence of mollusc shells in the loams of MIS 2 is a result of sharp climate change. New insect material includes 136 species of Coleoptera from 17 families, as well as Heteroptera and Hymenoptera representatives. 29 species of beetles (Carabidae, Histeridae, Scarabaeidae, Elateridae, Tenebrionidae, Chrysomelidae, Brentidae and Curculionidae) are recorded for the Pleistocene for the first time. The insect assemblages from Gornovo site are assigned to periglacial and humid boreal faunal types. The entomofauna of the periglacial type has no analogues in the recent fauna; it corresponds to the deposits assigned to the middle of MIS 3. This entomofauna is characteristic to the MIS 2 and MIS 3 insect assemblages from the south of West Siberian Plain. Based on entomological data, the climate of the middle of MIS 3 of the Southern Fore-Urals is reconstructed as dry and cold, extracontinental, with mean July temperature not exceeding +15 °C. Steppe landscapes likely prevailed in open areas and coniferous forests were restricted to river valleys. Beetles from deposits dated to end of MIS 3 are assigned to the fauna of the boreal humid type. These insect assemblages are significantly poorer in diversity than periglacial type assemblages and are represented mainly by near water and forest Coleoptera. Based on these species, meadow and forest landscapes were reconstructed. The reconstructed mean air temperature of July ranged from +16 to +19 °C. This suggests a trend towards more mild conditions in the region connected to the climate warming at the end of MIS 3. It is likely that humidification during this period was regional, determined by the proximity of the site to the Southern Urals Mountains. © 2021 Elsevier Ltd and INQU

Journal Staff

We present the first measurements of the differential cross section d sigma/dp(T)(gamma) for the production of an isolated photon in association with at least two b-quark jets. The measurements consider photons with rapidities vertical bar y(gamma)vertical bar < 1.0 and transverse momenta 30 < p(T)(gamma) < 200 GeV. The b-quark jets are required to have p(T)(jet) > 15 GeVand vertical bar y(jet)vertical bar < 1.5. The ratio of differential production cross sections for gamma + 2 b-jets to gamma + b-jet as a function of p(T)(gamma) is also presented. The results are based on the proton-antiproton collision data at root s = 1.96 TeV collected with the D0 detector at the Fermilab Tevatron Collider. The measured cross sections and their ratios are compared to the next- to- leading order perturbative QCD calculations as well as predictions based on the k(T)- factorization approach and those from the sherpa and pythia Monte Carlo event generators

Search for bottom squarks in pbarp collisions at sqrt(s)=1.8 TeV

We report on a search for bottom squarks produced in pbarp collisions at sqrt(s) = 1.8 TeV using the D0 detector at Fermilab. Bottom squarks are assumed to be produced in pairs and to decay to the lightest supersymmetric particle (LSP) and a b quark with branching fraction of 100%. The LSP is assumed to be the lightest neutralino and stable. We set limits on the production cross section as a function of bottom squark mass and LSP mass.Comment: 5 pages, Latex. submitted 3-12-1999 to PRD - Rapid Communicatio

Measurement of the WW Boson Mass

A measurement of the mass of the $W$ boson is presented based on a sample of 5982 $W \rightarrow e \nu$ decays observed in $p\overline{p}$ collisions at $\sqrt{s}$ = 1.8~TeV with the D\O\ detector during the 1992--1993 run. From a fit to the transverse mass spectrum, combined with measurements of the $Z$ boson mass, the $W$ boson mass is measured to be $M_W = 80.350 \pm 0.140 (stat.) \pm 0.165 (syst.) \pm 0.160 (scale) GeV/c^2$.Comment: 12 pages, LaTex, style Revtex, including 3 postscript figures (submitted to PRL

Measurement of Leptonic Asymmetries and Top Quark Polarization in ttbar Production

We present measurements of lepton (l) angular distributions in ttbar -> W+ b W- b -> l+ nu b l- nubar bbar decays produced in ppbar collisions at a center-of-mass energy of sqrt(s)=1.96TeV, where l is an electron or muon. Using data corresponding to an integrated luminosity of 5.4fb^-1, collected with the D0 detector at the Fermilab Collider, we find that the angular distributions of l- relative to anti-protons and l+ relative to protons are in agreement with each other. Combining the two distributions and correcting for detector acceptance we obtain the forward-backward asymmetry A^l_FB = (5.8 +- 5.1(stat) +- 1.3(syst))%, compared to the standard model prediction of A^l_FB (predicted) = (4.7 +- 0.1)%. This result is further combined with the measurement based on the analysis of the l+jets final state to obtain A^l_FB = (11.8 +- 3.2)%. Furthermore, we present a first study of the top-quark polarization.Comment: submitted versio

Measurement of the semileptonic charge asymmetry in B0 meson mixing with the D0 detector

We present a measurement of the semileptonic mixing asymmetry for B0 mesons, a^d_{sl}, using two independent decay channels: B0 -> mu+D-X, with D- -> K+pi-pi-; and B0 -> mu+D*-X, with D*- -> antiD0 pi-, antiD0 -> K+pi- (and charge conjugate processes). We use a data sample corresponding to 10.4 fb^{-1} of ppbar collisions at sqrt(s) = 1.96 TeV, collected with the D0 experiment at the Fermilab Tevatron collider. We extract the charge asymmetries in these two channels as a function of the visible proper decay length (VPDL) of the B0 meson, correct for detector-related asymmetries using data-driven methods, and account for dilution from charge-symmetric processes using Monte Carlo simulation. The final measurement combines four signal VPDL regions for each channel, yielding a^d_{sl} = [0.68 \pm 0.45 \text{(stat.)} \pm 0.14 \text{(syst.)}]%. This is the single most precise measurement of this parameter, with uncertainties smaller than the current world average of B factory measurements.Comment: Version includes minor textual changes following peer review by journal, most notably the updating of Ref. [21] to reflect the most recent publicatio

Search for B0→π0π0B^{0}\to \pi^{0}\pi^{0} Decay

We have searched for the charmless hadronic decay of B0 mesons into two neutral pions. Using 9.13fb^-1 taken at the Upsilon(4S) with the CLEO detector, we obtain an improved upper limit for the branching fraction BR(B0-->pi0pi0) < 5.7*10^-6 at the 90% confidence level.Comment: pages postscript, also available through http://w4.lns.cornell.edu/public/CLN