Counting solutions from finite samplings

We formulate the solution counting problem within the framework of inverse Ising problem and use fast belief propagation equations to estimate the entropy whose value provides an estimate on the true one. We test this idea on both diluted models (random 2-SAT and 3-SAT problems) and fully-connected model (binary perceptron), and show that when the constraint density is small, this estimate can be very close to the true value. The information stored by the salamander retina under the natural movie stimuli can also be estimated and our result is consistent with that obtained by Monte Carlo method. Of particular significance is sizes of other metastable states for this real neuronal network are predicted.Comment: 9 pages, 4 figures and 1 table, further discussions adde

The PELskin project—part I: fluid–structure interaction for a row of flexible flaps: a reference study in oscillating channel flow

Previous studies of flexible flaps attached to the aft part of a cylinder have demonstrated a favourable effect on the drag and lift force fluctuation. This observation is thought to be linked to the excitation of travelling waves along the flaps and as a consequence of that, periodic shedding of the von Kármán vortices is altered in phase. A more general case of such interaction is studied herein for a limited row of flaps in an oscillating flow; representative of the cylinder case since the transversal flow in the wake-region shows oscillating character. This reference case is chosen to qualify recently developed numerical methods for the simulation of fluid–structure interaction in the context of the EU funded ‘PELskin’ project. The simulation of the two-way coupled dynamics of the flexible elements is achieved via a structure model for the flap motion, which was implemented and coupled to two different fluid solvers via the immersed boundary method. The results show the waving behaviour observed at the tips of the flexible elements in interaction with the fluid flow and the formation of vortices in the gaps between the flaps. In addition, formation of vortices upstream of the leading and downstream of the trailing flap is seen, which interact with the formation of the shear-layer on top of the row. This leads to a phase shift in the wave-type motion along the row that resembles the observation in the cylinder case

The PELskin project: part II—investigating the physical coupling between flexible filaments in an oscillating flow

The fluid-structure interaction mechanisms of a coating composed of flexible flaps immersed in a periodically oscillating channel flow is here studied by means of numerical simulation, employing the Euler-Bernoulli equations to account for the flexibility of the structures. A set of passively actuated flaps have previously been demonstrated to deliver favourable aerodynamic impact when attached to a bluff body undergoing periodic vortex shedding. As such, the present configuration is identified to provide a useful test-bed to better understand this mechanism, thought to be linked to experimentally observed travelling waves. Having previously validated and elucidated the flow mechanism in Paper 1 of this series, we hereby undertake a more detailed analysis of spectra obtained for different natural frequency of structures and different configurations, in order to better characterize the mechanisms involved in the organized motion of the structures. Herein, this wave-like behaviour, observed at the tips of flexible structures via interaction with the fluid flow, is characterized by examining the time history of the filaments motion and the corresponding effects on the fluid flow, in terms of dynamics and frequency of the fluid velocity. Results indicate that the wave motion behaviour is associated with the formation of vortices in the gaps between the flaps, which itself are a function of the structural resistance to the cross flow. In addition, formation of vortices upstream of the leading and downstream of the trailing flap is seen, which interact with the formation of the shear-layer on top of the row. This leads to a phase shift in the wave-type motion along the row that resembles the observation in the cylinder case

Central African biomes and forest succession stages derived from modern pollen data and plant functional types

New detailed vegetation reconstructions are proposed in Atlantic Central Africa from a modern pollen data set derived from 199 sites (Cameroon, Gabon and Congo) including 131 new sites. In this study, the concept of plant functional classification is improved with new and more detailed plant functional types (PFTs) and new aggregations of pollen taxa. Using the biomisation method, we reconstructed (1) modern potential biomes and (2) potential succession stages of forest regeneration, a new approach in Atlantic Central African vegetation dynamics and ecosystem functioning reconstruction. When compared to local vegetation, potential biomes are correctly reconstructed (97.5% of the sites) and tropical rain forest (TRFO biome) is well identified from tropical seasonal forest (TSFO biome). When the potential biomes are superimposed on the White's vegetation map, only 76.4% of the sites are correctly reconstructed. But using botanical data, correspondence and cluster analyses, the 43 sites from Congo (Mayombe) evidence more affinities with those of central Gabon and so they can also be considered as correctly reconstructed as TRFO biome and White's map should be revised. In terms of potential succession stages of forest regeneration, the mature forest (TMFO) is well differentiated from the secondary forest (TSFE), but inside this latter group, the young and the pioneer stages are not clearly identified due probably to their low sampling representation. Moreover, linked to their progressive and mosaic character, the boundaries between two forest biomes or two forest stages are not clearly detected and need also a more intensive sampling in such transitions

Demonstration of Ramsey-Comb Precision Spectroscopy in Xenon at Vacuum Ultraviolet Wavelengths Produced with High-Harmonic Generation

The remarkable progress in the field of laser spectroscopy induced by the invention of the frequency-comb laser has enabled many new high-precision tests of fundamental theory and searches for new physics. Extending frequency-comb based spectroscopy techniques to the vacuum (VUV) and extreme ultraviolet (XUV) spectral range would enable measurements in e.g. heavier hydrogen-like systems and open up new possibilities for tests of quantum electrodynamics and measurements of fundamental constants. The main approaches rely on high-harmonic generation (HHG), which is known to induce spurious phase shifts from plasma formation. After our initial report (Physical Review Letters 123, 143001 (2019)), we give a detailed account of how the Ramsey-comb technique is used to probe the plasma dynamics with high precision, and enables accurate spectroscopy in the VUV. A series of Ramsey fringes is recorded to track the phase evolution of a superposition state in xenon atoms, excited by two up-converted frequency-comb pulses. Phase shifts of up to 1 rad induced by HHG were observed at ns timescales and with mrad-level accuracy at $110$ nm. Such phase shifts could be reduced to a negligible level, enabling us to measure the $5p^6 \rightarrow 5p^5 8s~^2[3/2]_1$ transition frequency in $^{132}Xe$ at 110 nm (seventh harmonic) with sub-MHz accuracy. The obtained value is $10^4$ times more precise than the previous determination and the fractional accuracy of $2.3 \times 10^{-10}$ is $3.6$ times better than the previous best spectroscopic measurement using HHG. The isotope shifts between $^{132}Xe$ and two other isotopes were determined with an accuracy of $420$ kHz. The method can be readily extended to achieve kHz-level accuracy, e.g. to measure the $1S-2S$ transition in $He^+$. Therefore, the Ramsey-comb method shows great promise for high-precision spectroscopy of targets requiring VUV and XUV wavelengths

Western equatorial African forest-savanna mosaics: a legacy of late Holocene climatic change?

Past vegetation and climate changes reconstructed using two pollen records from Lakes Maridor and Nguène, located in the coastal savannas and inland rainforest of Gabon, respectively, provide new insights into the environmental history of western equatorial African rainforests during the last 4500 cal yr BP. These pollen records indicate that the coastal savannas of western equatorial Africa did not exist during the mid-Holocene and instead the region was covered by evergreen rainforests. From ca. 4000 cal yr BP a progressive decline of inland evergreen rainforest, accompanied by the expansion of semi-deciduous rainforest, occurred synchronously with grassland colonisation in the coastal region of Gabon. The contraction of moist evergreen rainforest and the establishment of coastal savannas in Gabon suggest decreasing humidity from ca. 4000 cal yr BP. The marked reduction in evergreen rainforest and subsequent savanna expansion was followed from 2700 cal yr BP by the colonization of secondary forests dominated by the palm, <i>Elaeis guineensis</i>, and the shrub, <i>Alchornea cordifolia</i> (Euphorbiaceae). A return to wetter climatic conditions from about 1400 cal yr BP led to the renewed spread of evergreen rainforest inland, whereas a forest-savanna mosaic still persists in the coastal region. There is no evidence to suggest that the major environmental changes observed were driven by human impact

Quasi-static magnetohydrodynamic turbulence at high Reynolds number

We analyse the anisotropy of homogeneous turbulence in an electrically conducting fluid submitted to a uniform magnetic field, for low magnetic Reynolds number, in the quasi- static approximation. We interpret disagreeing previous predictions between linearized theory and simulations: in the linear limit, the kinetic energy of transverse velocity components, normal to the magnetic field, decays faster than the kinetic energy of the axial component, along the magnetic field (Moffatt (1967)); whereas many numerical studies predict a final state characterised by dominant energy of transverse velocity components. We investigate the corresponding nonlinear phenomenon using Direct Numerical Simulations of freely-decaying turbulence, and a two-point statistical spectral closure based on the Eddy Damped Quasi-Normal Markovian model. The transition from the three-dimensional turbulent flow to a "two-and-a-half-dimensional" flow (Montgomery & Turner (1982)) is a result of the combined effects of short-time linear Joule dissipation and longer time nonlinear creation of polarisation anisotropy. It is this combination of linear and nonlinear effects which explains the disagreement between predictions from linearized theory and results from numerical simulations. The transition is characterized by the elongation of turbulent structures along the applied magnetic field, and by the strong anisotropy of directional two-point correlation spectra, in agreement with experimental evidence. Inertial equatorial transfers in both DNS and the model are presented to describe in detail the most important equilibrium dynamics. Spectral scalings are maintained in high Reynolds number turbulence attainable only with the EDQNM model, which also provides simplified modelling of the asymptotic state of quasi-static MHD turbulence.Comment: Journal of Fluid Mechanics, 201

Back to the future: Using long-term observational and paleo-proxy reconstructions to improve model projections of antarctic climate

Quantitative estimates of future Antarctic climate change are derived from numerical global climate models. Evaluation of the reliability of climate model projections involves many lines of evidence on past performance combined with knowledge of the processes that need to be represented. Routine model evaluation is mainly based on the modern observational period, which started with the establishment of a network of Antarctic weather stations in 1957/58. This period is too short to evaluate many fundamental aspects of the Antarctic and Southern Ocean climate system, such as decadal-to-century time-scale climate variability and trends. To help address this gap, we present a new evaluation of potential ways in which long-term observational and paleo-proxy reconstructions may be used, with a particular focus on improving projections. A wide range of data sources and time periods is included, ranging from ship observations of the early 20th century to ice core records spanning hundreds to hundreds of thousands of years to sediment records dating back 34 million years. We conclude that paleo-proxy records and long-term observational datasets are an underused resource in terms of strategies for improving Antarctic climate projections for the 21st century and beyond. We identify priorities and suggest next steps to addressing this.The Antarctic Climate Change in the 21st Century (AntClim21) Scientific Research Programme of the Scientific Committee on Antarctic Research are thanked for supporting the international scientific workshop at which the writing of this manuscript was initiated. This is a contribution to the PAGES 2k Network (through the CLIVASH 2k project). NJA acknowledges support by the Australian Research Council through a Future Fellowship (FT160100029) and the Centre of Excellence for Climate Extremes (CE170100023). SJP was supported under the Australian Research Council’s Special Research Initiative for the Antarctic Gateway Partnership (Project ID SR140300001). JMJ acknowledges support from the Leverhulme Trust through a Research Fellowship (RF-2018-183). FC acknowledges support from the PNRA national Italian projects PNRA16_00016, “WHISPERS” and project PNRA_00002, “ANTIPODE”. TJB, LS, and ERT were supported by the Natural Environment Research Council (NERC) as part of the British Antarctic Survey Polar Science for Planet Earth Programme. TJB additionally acknowledges support for this work as a contribution to the NERC grant NE/N01829X/1. IW thanks FAPESP 2015/50686-1, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES) Finance Code 001 and CNPq 300970/2018-8, CNPq INCT Criosfera 704222/200

A gp41 MPER-specific llama VHH requires a hydrophobic CDR3 for neutralization but not for antigen recognition

The membrane proximal external region (MPER) of the HIV-1 glycoprotein gp41 is targeted by the broadly neutralizing antibodies 2F5 and 4E10. To date, no immunization regimen in animals or humans has produced HIV-1 neutralizing MPER-specific antibodies. We immunized llamas with gp41-MPER proteoliposomes and selected a MPER-specific single chain antibody (VHH), 2H10, whose epitope overlaps with that of mAb 2F5. Bi-2H10, a bivalent form of 2H10, which displayed an approximately 20-fold increased affinity compared to the monovalent 2H10, neutralized various sensitive and resistant HIV-1 strains, as well as SHIV strains in TZM-bl cells. X-ray and NMR analyses combined with mutagenesis and modeling revealed that 2H10 recognizes its gp41 epitope in a helical conformation. Notably, tryptophan 100 at the tip of the long CDR3 is not required for gp41 interaction but essential for neutralization. Thus bi-2H10 is an anti-MPER antibody generated by immunization that requires hydrophobic CDR3 determinants in addition to epitope recognition for neutralization similar to the mode of neutralization employed by mAbs 2F5 and 4E10