Inclusion of ionic interactions in force field calculations of charged biomolecules – DNA structural transitions.

The potential of mean force (PMF) approach for treating polyion–diffuse ionic cloud interactions [D. M. Soumpasis (1984) Proceedings of the National Academy of Sciences USA81, 5116–5120] has been combined with the AMBER force field describing intramolecular interactions. The resultant generalized AMBER-PMF force field enables one to treat the conformational stabilities and structural transitions of charged biomolecules in aqueous electrolytes more realistically. For example, we have used it to calculate the relative stabilities of the B and Z conformations of d(C-G)6, and the B and heteronomous (H) conformations of dA12 · dT12, as a function of salt concentration. In the case of d(C-G)6, the predicted B–ZI transition occurs at 2.4M and is essentially driven by the phosphate-diffuse ionic cloud interactions alone as suggested by the results of earlier PMF calculations. The ZII conformer is less stable than the B form under all conditions. It is found that the helical parameters of the refined B and Z structures change with salt concentration. For example, the helical rise of B-DNA increases about 10% and the twist angle decreases by the same amount above 1M NaCl. In the range of 0.01–0.3M NaCl, the H form of dA12 · dT12 is found to be more stable than the B form and its stability increases with increasing salt concentration. The computed greater relative stability of the H conformation is likely due to noninclusion of the free energy contribution from the spine of hydration, a feature presumed to stabilize the B form of this sequence

Multitechnique testing of the viscous decretion disk model I. The stable and tenuous disk of the late-type Be star β\beta CMi

The viscous decretion disk (VDD) model is able to explain most of the currently observable properties of the circumstellar disks of Be stars. However, more stringent tests, focusing on reproducing multitechnique observations of individual targets via physical modeling, are needed to study the predictions of the VDD model under specific circumstances. In the case of nearby, bright Be star $\beta$ CMi, these circumstances are a very stable low-density disk and a late-type (B8Ve) central star. The aim is to test the VDD model thoroughly, exploiting the full diagnostic potential of individual types of observations, in particular, to constrain the poorly known structure of the outer disk if possible, and to test truncation effects caused by a possible binary companion using radio observations. We use the Monte Carlo radiative transfer code HDUST to produce model observables, which we compare with a very large set of multitechnique and multiwavelength observations that include ultraviolet and optical spectra, photometry covering the interval between optical and radio wavelengths, optical polarimetry, and optical and near-IR (spectro)interferometry. Due to the absence of large scale variability, data from different epochs can be combined into a single dataset. A parametric VDD model with radial density exponent of $n$ = 3.5, which is the canonical value for isothermal flaring disks, is found to explain observables typically formed in the inner disk, while observables originating in the more extended parts favor a shallower, $n$ = 3.0, density falloff. Modeling of radio observations allowed for the first determination of the physical extent of a Be disk (35$^{+10}_{-5}$ stellar radii), which might be caused by a binary companion. Finally, polarization data allowed for an indirect measurement of the rotation rate of the star, which was found to be $W \gtrsim 0.98$, i.e., very close to critical.Comment: 19 pages (35 including online material), 17 figures, 2 online figures, 2 online tables with dat

Preassociative aggregation functions

The classical property of associativity is very often considered in aggregation function theory and fuzzy logic. In this paper we provide axiomatizations of various classes of preassociative functions, where preassociativity is a generalization of associativity recently introduced by the authors. These axiomatizations are based on existing characterizations of some noteworthy classes of associative operations, such as the class of Acz\'elian semigroups and the class of t-norms.Comment: arXiv admin note: text overlap with arXiv:1309.730

Revealing the structure of the outer disks of Be stars

Context. The structure of the inner parts of Be star disks (20 stellar radii) is well explained by the viscous decretion disk (VDD) model, which is able to reproduce the observable properties of most of the objects studied so far. The outer parts, on the ther hand, are not observationally well-explored, as they are observable only at radio wavelengths. A steepening of the spectral slope somewhere between infrared and radio wavelengths was reported for several Be stars that were previously detected in the radio, but a convincing physical explanation for this trend has not yet been provided. Aims. We test the VDD model predictions for the extended parts of a sample of six Be disks that have been observed in the radio to address the question of whether the observed turndown in the spectral energy distribution (SED) can be explained in the framework of the VDD model, including recent theoretical development for truncated Be disks in binary systems. Methods. We combine new multi-wavelength radio observations from the Karl. G. Jansky Very Large Array (JVLA) and Atacama Pathfinder Experiment (APEX) with previously published radio data and archival SED measurements at ultraviolet, visual, and infrared wavelengths. The density structure of the disks, including their outer parts, is constrained by radiative transfer modeling of the observed spectrum using VDD model predictions. In the VDD model we include the presumed effects of possible tidal influence from faint binary companions. Results. For 5 out of 6 studied stars, the observed SED shows strong signs of SED turndown between far-IR and radio wavelengths. A VDD model that extends to large distances closely reproduces the observed SEDs up to far IR wavelengths, but fails to reproduce the radio SED. ... (abstract continues but did not fit here)Comment: 20 pages, 8 figure

Interactions between diurnal winds and floodplain mosaics control the insect boundary layer in a river corridor

Insect flight along river corridors is a fundamental process that facilitates sustainable succession and diversity of aquatic and terrestrial insect communities in highly dynamic fluvial environments. This study examines variations in the thickness of the insect boundary layer (i.e., the pre-surface atmosphere layer in which air velocity does not exceed the sustained speed of flying insects) caused by interactions between diurnal winds and the heterogenous habitat mosaics in the floodplain of a braided river. Based on advective–diffusive theory, we develop and test a semi-empirical model that relates vertical flux of flying insects to vertical profiles of diurnal winds. Our model suggests that, in the logarithmic layer of wind, the density of insect fluxes decreases exponentially with the altitude due to the strong physical forcing. Inside the insect boundary layer, the insect fluxes can increase with the altitude while the winds speed remains nearly constant. We suggest a hypothesis that there is a close correspondence between the height of discontinuity points in the insect profiles (e.g. points with abrupt changes of the insect flux) and the displacement heights of the wind profiles (e.g. points above which the wind profile is logarithmic). Vertical profiles were sampled during three time-intervals at three different habitat locations in the river corridor: a bare gravel bar, a gravel bar with shrubs, and an island with trees and shrubs. Insects and wind speed were sampled and measured simultaneously over each location at 1.5-m intervals up to approximately 17 m elevation. The results support our working hypothesis on close correspondence between discontinuity and displacement points. The thickness of the insect boundary layer matches the height of the discontinuity points and was about 5 m above the bare gravel bar and the gravel bar with shrubs. Above the island, the structure of the insect boundary layer was more complex and consisted of two discontinuity points, one at the mean height of the trees’ crowns (ca. 15 m), and a second, internal boundary layer at the top of the shrubs (ca. 5 m). Our findings improve the understanding of how vegetation can influence longitudinal and lateral dispersal patterns of flying insects in river corridors and floodplain systems. It also highlights the importance of preserving terrestrial habitat diversity in river floodplains as an important driver of both biotic and abiotic (i.e., morphology and airscape) heterogeneity

Interactions between diurnal winds and floodplain mosaics control the insect boundary layer in a river corridor

Insect flight along river corridors is a fundamental process that facilitates sustainable succession and diversity of aquatic and terrestrial insect communities in highly dynamic fluvial environments. This study examines variations in the thickness of the insect boundary layer (i.e., the pre-surface atmosphere layer in which air velocity does not exceed the sustained speed of flying insects) caused by interactions between diurnal winds and the heterogenous habitat mosaics in the floodplain of a braided river. Based on advective–diffusive theory, we develop and test a semi-empirical model that relates vertical flux of flying insects to vertical profiles of diurnal winds. Our model suggests that, in the logarithmic layer of wind, the density of insect fluxes decreases exponentially with the altitude due to the strong physical forcing. Inside the insect boundary layer, the insect fluxes can increase with the altitude while the winds speed remains nearly constant. We suggest a hypothesis that there is a close correspondence between the height of discontinuity points in the insect profiles (e.g. points with abrupt changes of the insect flux) and the displacement heights of the wind profiles (e.g. points above which the wind profile is logarithmic). Vertical profiles were sampled during three time-intervals at three different habitat locations in the river corridor: a bare gravel bar, a gravel bar with shrubs, and an island with trees and shrubs. Insects and wind speed were sampled and measured simultaneously over each location at 1.5-m intervals up to approximately 17 m elevation. The results support our working hypothesis on close correspondence between discontinuity and displacement points. The thickness of the insect boundary layer matches the height of the discontinuity points and was about 5 m above the bare gravel bar and the gravel bar with shrubs. Above the island, the structure of the insect boundary layer was more complex and consisted of two discontinuity points, one at the mean height of the trees’ crowns (ca. 15 m), and a second, internal boundary layer at the top of the shrubs (ca. 5 m). Our findings improve the understanding of how vegetation can influence longitudinal and lateral dispersal patterns of flying insects in river corridors and floodplain systems. It also highlights the importance of preserving terrestrial habitat diversity in river floodplains as an important driver of both biotic and abiotic (i.e., morphology and airscape) heterogeneit