Sequence correlations shape protein promiscuity

We predict analytically that diagonal correlations of amino acid positions within protein sequences statistically enhance protein propensity for nonspecific binding. We use the term 'promiscuity' to describe such nonspecific binding. Diagonal correlations represent statistically significant repeats of sequence patterns where amino acids of the same type are clustered together. The predicted effect is qualitatively robust with respect to the form of the microscopic interaction potentials and the average amino acid composition. Our analytical results provide an explanation for the enhanced diagonal correlations observed in hubs of eukaryotic organismal proteomes [J. Mol. Biol. 409, 439 (2011)]. We suggest experiments that will allow direct testing of the predicted effect

Orbital magnetoelectric coupling in band insulators

Magnetoelectric responses are a fundamental characteristic of materials that break time-reversal and inversion symmetries (notably multiferroics) and, remarkably, of "topological insulators" in which those symmetries are unbroken. Previous work has shown how to compute spin and lattice contributions to the magnetoelectric tensor. Here we solve the problem of orbital contributions by computing the frozen-lattice electronic polarization induced by a magnetic field. One part of this response (the "Chern-Simons term") can appear even in time-reversal-symmetric materials and has been previously shown to be quantized in topological insulators. In general materials there are additional orbital contributions to all parts of the magnetoelectric tensor; these vanish in topological insulators by symmetry and also vanish in several simplified models without time-reversal and inversion those magnetoelectric couplings were studied before. We give two derivations of the response formula, one based on a uniform magnetic field and one based on extrapolation of a long-wavelength magnetic field, and discuss some of the consequences of this formula.Comment: 13 page

Strong Stability Preserving Two-Step Runge-Kutta Methods

We investigate the strong stability preserving (SSP) property of two-step Runge– Kutta (TSRK) methods. We prove that all SSP TSRK methods belong to a particularly simple\ud subclass of TSRK methods, in which stages from the previous step are not used. We derive simple order conditions for this subclass. Whereas explicit SSP Runge–Kutta methods have order at most four, we prove that explicit SSP TSRK methods have order at most eight. We present TSRK methods of up to eighth order that were found by numerical search. These methods have larger SSP coefficients than any known methods of the same order of accuracy, and may be implemented in a form with relatively modest storage requirements. The usefulness of the TSRK methods is demonstrated through numerical examples, including integration of very high order WENO discretizations

Spatial variability of climate and past atmospheric circulation patterns from central West Antarctic glaciochemistry

Atmospheric circulation patterns and the spatial variability of atmospheric chemistry and moisture transport in central West Antarctica are investigated using new 40 year long (1954–1994 A.D.) glaciochemical and accumulation rate records developed from four firn cores from this region. The core sites lie on a 200 km traverse from 82° 22′ S, 119° 17′ W to 81° 22′ S, 107° 17′ W. The glaciochemical records represent the major ionic species present in Antarctic snow: Na+, K+, Mg2+, Ca2+, Cl−, NO3−, and SO42−. High spatial variability appears in comparisons of full record averages and poor intersite linear correlation results. Accumulation rates show 50–100% changes over distances of 50–100 km and sea‐salt concentrations drop by 50% between the middle two sites. One likely contributor to the high variability seen at this spatial scale is variability in synoptic‐ and finer‐scale meteorology. Empirical orthogonal function (EOF) analysis shows that 80% or more of the variance in site chemistry can be attributed to two types of air masses: winter season air (50–70% of site variance) with a strong marine signature (heavy loading of sea‐salt species) and summer season air (21% of the variance), marked by marine biogenic non‐sea‐salt SO4 plus NO3. This pattern of winter and summer regimes appears at other West Antarctic sites suggesting it may apply to the entire region. We show that a general picture of the patterns of variability in West Antarctica can best be drawn by using an analysis technique that fully exploits high resolution, multiparameter, multisite data sets

Cognitive consequences of clumsy automation on high workload, high consequence human performance

The growth of computational power has fueled attempts to automate more of the human role in complex problem solving domains, especially those where system faults have high consequences and where periods of high workload may saturate the performance capacity of human operators. Examples of these domains include flightdecks, space stations, air traffic control, nuclear power operation, ground satellite control rooms, and surgical operating rooms. Automation efforts may have unanticipated effects on human performance, particularly if they increase the workload at peak workload times or change the practitioners' strategies for coping with workload. Smooth and effective changes in automation requires detailed understanding of the congnitive tasks confronting the user: it has been called user centered automation. The introduction of a new computerized technology in a group of hospital operating rooms used for heart surgery was observed. The study revealed how automation, especially 'clumsy automation', effects practitioner work patterns and suggest that clumsy automation constrains users in specific and significant ways. Users tailor both the new system and their tasks in order to accommodate the needs of process and production. The study of this tailoring may prove a powerful tool for exposing previously hidden patterns of user data processing, integration, and decision making which may, in turn, be useful in the design of more effective human-machine systems

EPR spectroscopy of iron- and nickel-doped [ZnAl]-layered double hydroxides: modeling active sites in heterogeneous water oxidation catalysts

Iron-doped nickel layered double hydroxides (LDHs) are among the most active heterogeneous water oxidation catalysts. Due to inter-spin interactions, however, the high density of magnetic centers results in line-broadening in magnetic resonance spectra. As a result, gaining atomic-level insight into the catalytic mechanism via electron paramagnetic resonance (EPR) is not generally possible. To circumvent spin-spin broadening, iron and nickel atoms were doped into non-magnetic [ZnAl]-LDH materials and the coordination environments of the isolated Fe(III) and Ni(II) sites were characterized. Multifrequency EPR spectroscopy identified two distinct Fe(III) sites (S = 5/2) in [Fe:ZnAl]-LDH. Changes in zero field splitting (ZFS) were induced by dehydration of the material, revealing that one of the Fe(III) sites is solvent-exposed (i.e. at an edge, corner, or defect site). These solvent-exposed sites feature an axial ZFS of 0.21 cm⁻¹ when hydrated. The ZFS increases dramatically upon dehydration (to -1.5 cm⁻¹), owing to lower symmetry and a decrease in the coordination number of iron. The ZFS of the other (“inert”) Fe(III) site maintains an axial ZFS of 0.19-0.20 cm⁻¹ under both hydrated and dehydrated conditions. We observed a similar effect in [Ni:ZnAl]-LDH materials; notably, Ni(II) (S = 1) atoms displayed a single, small ZFS (±0.30 cm⁻¹) in hydrated material, whereas two distinct Ni(II) ZFS values (±0.30 and ±1.1 cm⁻¹) were observed in the dehydrated samples. Although the magnetically-dilute materials were not active catalysts, the identification of model sites in which the coordination environments of iron and nickel were particularly labile (e.g. by simple vacuum drying) is an important step towards identifying sites in which the coordination number may drop spontaneously in water, a probable mechanism of water oxidation in functional materials

Direct Evidence for the Source of Reported Magnetic Behavior in "CoTe"

In order to unambiguously identify the source of magnetism reported in recent studies of the Co-Te system, two sets of high-quality, epitaxial CoTe$_x$ films (thickness $\simeq$ 300 nm) were prepared by pulse laser deposition (PLD). X-ray diffraction (XRD) shows that all of the films are epitaxial along the [001] direction and have the hexagonal NiAs structure. There is no indication of any second phase metallic Co peaks (either $fcc$ or $hcp$) in the XRD patterns. The two sets of CoTe$_x$ films were grown on various substrates with PLD targets having Co:Te in the atomic ratio of 50:50 and 35:65. From the measured lattice parameters $c = 5.396 \AA$ for the former and $c = 5.402\AA$ for the latter, the compositions CoTe$_{1.71}$ (63.1% Te) and CoTe$_{1.76}$ (63.8% Te), respectively, are assigned to the principal phase. Although XRD shows no trace of metallic Co second phase, the magnetic measurements do show a ferromagnetic contribution for both sets of films with the saturation magnetization values for the CoTe$_{1.71}$ films being approximately four times the values for the CoTe$_{1.76}$ films. $^{59}$Co spin-echo nuclear magnetic resonance (NMR) clearly shows the existence of metallic Co inclusions in the films. The source of weak ferromagnetism reported in several recent studies is due to the presence of metallic Co, since the stoichiometric composition "CoTe" does not exist.Comment: 19 pages, 7 figure