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At least 1,567 records · Page 87

Kinetic Growth of Multicomponent Microcompartment Shells

An important goal of systems and synthetic biology is to produce high value chemical species in large quantities. Microcompartments, which are protein nanoshells encapsulating catalytic enzyme cargo, could potentially function as tunable nanobioreactors inside and outside cells to generate these high value species. Modifying the morphology of microcompartments through genetic engineering of shell proteins is one viable strategy to tune cofactor and metabolite access to encapsulated enzymes. However, this is a difficult task without understanding how changing interactions between the many different types of shell proteins and enzymes affect microcompartment assembly and shape. Here, we use multiscale molecular dynamics and experimental data to describe assembly pathways available to microcompartments composed of multiple types of shell proteins with varied interactions. As the average interaction between the enzyme cargo and the multiple types of shell proteins is weakened, the shell assembly pathway transitions from (i) nucleating on the enzyme cargo to (ii) nucleating in the bulk and then binding the cargo as it grows to (iii) an empty shell. Atomistic simulations and experiments using the 1,2-propanediol utilization microcompartment system demonstrate that shell protein interactions are highly varied and consistent with our multicomponent, coarse-grained model. Furthermore, our results suggest that intrinsic bending angles control the size of these microcompartments. Altogether, our simulations and experiments provide guidance to control microcomparmtent size and assembly by modulating the interactions between shell proteins.

defects↗

A calculation of the Rosseland mean opacity of dust grains in primordial solar system nebulae

The Rosseland mean opacity owing to grains was calculated as a function of temperature and density for nebulae having solar elemental abundances. The values of the mean opacity were evaluated with a generalized formulation allowing for anisotropic scattering. The values of the mean opacity do not depend sensitively on the choice of the particle size distribution function, provided that there are few particles having sizes in excess of several tens of microns. The results indicate that thermal convection in primordial nebulae occurs over broader ranges of altitudes at low temperatures than at high temperatures, and for size distributions for which extensive aggregation has not yet occurred.

Pollack, J. B.↗

Optimization of motion control laws for tether crawler or elevator systems

Based on the proposal of a motion control law by Lorenzini (1987), a method is developed for optimizing motion control laws for tether crawler or elevator systems in terms of the performance measures of travel time, the smoothness of acceleration and deceleration, and the maximum values of velocity and acceleration. The Lorenzini motion control law, based on powers of the hyperbolic tangent function, is modified by the addition of a constant-velocity section, and this modified function is then optimized by parameter selections to minimize the peak acceleration value for a selected travel time or to minimize travel time for the selected peak values of velocity and acceleration. It is shown that the addition of a constant-velocity segment permits further optimization of the motion control law performance.

Swenson, Frank R.↗

Yb Substitution and Ultralow Thermal Conductivity of the Ca 3– x Yb x AlSb 3 (0 ≤ x ≤ 0.81(1)) System

Here, a series of Yb-substituted Zintl phases in the Ca 3–x Yb x AlSb 3 (0 ≤ x ≤ 0.81(1)) system has been synthesized by initial arc melting and post-heat treatment, and their isotypic crystal structures were characterized by both powder and single crystal X-ray diffraction analysis. All four title compounds adopted the Ca 3 AlAs 3 -type structure (space group Pnma, Pearson code oP28, Z = 4). The overall structure can be described as a combination of the 1-dimensional (1D) infinite chain of ∞ 1 [Al(Sb 2 Sb 2/2 )] formed by two vertices sharing [AlSb 4 ] tetrahedral moieties and three Ca 2+ /Yb 2+ mixed sites located in between these 1D chains. The charge balance and the resultant independency of the 1D chains in the title system were explained by the Zintl-Klemm formalism [Ca 2+ /Yb 2+ ] 3 [(4b-Al 1– )(1b-Sb 2– ) 2 (2b-Sb 1– ) 2/2 ]. A series of DFT calculations proved that (1) the band overlap between the d-orbital states from two types of cations and the p-orbital states from Sb at the high symmetry Γ point implied a heavily doped degenerate semiconducting behavior of the quaternary Ca 2 YbAlSb 3 model and (2) the site preference of Yb for the M1 site was due to the electronic-factor criterion based on the Q values of each atomic site. The electron localization function calculations also proved that the two different shapes of lone pairs of the Sb atoms—the “umbrella-shape” and the “C-shape”—are determined by local geometry and the coordination environment on the anionic frameworks. Thermoelectric measurements of the quaternary title compound Ca 2.19(1) Yb 0.81 AlSb 3 showed an approximately two times larger ZT value than that of ternary Ca 3 AlSb 3 at 623 K due to increased electrical conductivity and ultralow thermal conductivity originated from Yb substitution for Ca.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A method of calculating the total flow from a given sea surface topography

Using a simple dynamical model of a wind-driven ocean circulation of the Stommel type, and an analytical basis developed to objectively analyze the sea surface height residuals from an altimeter and, in the process, to determine the total flow instead of just the near surface geostrophic component associated with the given sea surface topography. The method is based on first deriving the solution to the forced problem for a given wind stress required to develop a hypothetical true or perfect data field and to establishing the basis for the objective analysis. The stream function and the surface height field for the forced problem are developed in terms of certain characteristic functions with the same expansion coefficients for both fields. These characteristic functions are simply the solutions for a homogeneous elliptic equation for the stream function and the solutions of an inhomogeneous balance equation for the height field. For the objective analysis, using a sample of randomly selected height values from the true data field, the height field characteristic functions are used to fit the given topography in a least squares sense. The resulting expansion coefficients then permit the synthesis of the total flow field via the stream function characteristic modes and the solution is perfectly well behaved even along the equator. The method of solution is easily adaptable to realistic ocean basis by straight forward numerical methods. The analytical basis of the theory and the results for an ideal rectangular basin on a beta plane are described.

Rao, Desiraju B.↗

Paraburkholderia solitsugae sp. nov. and Paraburkholderia elongata sp. nov., phenolic acid-degrading bacteria isolated from forest soil and emended description of Paraburkholderia madseniana

Two bacterial strains, 1N T and 5N T , were isolated from hemlock forest soil using a soluble organic matter enrichment. Cells of 1N T (0.65×1.85 µm) and 5N T (0.6×1.85 µm) are Gram-stain-negative, aerobic, motile, non-sporulating and exist as single rods, diplobacilli or in chains of varying length. During growth in dilute media (≤0.1× tryptic soy broth; TSB), cells are primarily motile with flagella. At higher concentrations (≥0.3× TSB), cells of both strains increasingly form non-motile chains, and cells of 5N T elongate (0.57×~7 µm) and form especially long filaments. Optimum growth of 1N T and 5N T occurred at 25–30 °C, pH 6.5–7.0 and <0.5% salinity. Results of comparative chemotaxonomic, genomic and phylogenetic analyses revealed that 1N T and 5N T were distinct from one another and their closest related type strains: Paraburkholderia madseniana RP11 T , Paraburkholderia aspalathi LMG 27731 T and Paraburkholderia caffeinilytica CF1 T . The genomes of 1N T and 5N T had an average nucleotide identity (91.6 and 91.3%) and in silico DNA–DNA hybridization values (45.8%±2.6 and 45.5%±2.5) and differed in functional gene content from their closest related type strains. The composition of fatty acids and patterns of substrate use, including the catabolism of phenolic acids, also differentiated strains 1N T and 5N T from each other and their closest relatives. The only ubiquinone present in strains 1N T and 5N T was Q-8. The major cellular fatty acids were C 16 : 0 , 3OH-C 16 : 0 , C 17 : 0 cyclo, C 19 : 0 cyclo ω8 c and summed features 2 (3OH-C 14 : 0 / C 16 : 1 iso I), 3 (C 16 : 1 ω6 c /ω7 c ) and 8 (C 18 : 1 ω7 c /ω6 c ). A third bacterium, strain RL16-012-BIC-B, was isolated from soil associated with shallow roots and was determined to be a strain of P. madseniana (ANI, 98.8%; 16S rRNA gene similarity, 100%). Characterizations of strain RL16-012-BIC-B (DSM 110723=LMG 31706) led to proposed emendments to the species description of P. madseniana . Our polyphasic approach demonstrated that strains 1N T and 5N T represent novel species from the genus Paraburkholderia for which the names Paraburkholderia solitsugae sp. nov. (type strain 1N T =DSM 110721 T =LMG 31704 T ) and Paraburkholderia elongata sp. nov. (type strain 5N T =DSM 110722 T =LMG 31705 T ) are proposed.

Microbiology↗

Spectral and dynamical analysis of a single vortex ring in anisotropic harmonically trapped three-dimensional Bose-Einstein condensates

Here in the present work, motivated by numerous recent experimental developments we revisit the dynamics of a single vortex ring in anisotropic harmonic traps. At the theoretical level, we start from a general Lagrangian dynamically capturing the evolution of a vortex ring and not only consider its spectrum of linearized excitations, but also explore the full nonlinear dynamical evolution of the ring as a vortical filament. The theory predicts that the ring is stable for 1 ≤ λ ≤ 2, where λ = ω z /ω r is the ratio of the trapping frequencies along the z and r axes, i.e., for spherical to slightly oblate condensates. We compare this prediction with direct numerical simulations of the full three-dimensional Gross-Pitaevskii equation (GPE) capturing the linearization spectrum of the ring for different values of the chemical potential and as a function of the anisotropy parameter λ . We identify this result as being only asymptotically valid as the chemical potential μ → ∞, revealing how the stability interval narrows and, in particular, its upper bound decreases for finite μ. Finally, we compare at the dynamical level the results of the GPE with the ones effectively capturing the ring dynamics, revealing the unstable evolution for different values of λ, as well as the good agreement between the two.

74 ATOMIC AND MOLECULAR PHYSICS↗

Mathematical Simulation of Humidification of Earth on a Slope and Calculation of Its Safety Factor

This paper presents a mathematical model of the simultaneous processes of moisture, heat, and salt transfer in a porous medium, as well as a pattern of calculation of earth stability on a slope depending on the above factors and nonlinear dependences on them of the strength characteristics of the earth. The corresponding boundary-value problem has been solved by the method of radial basis functions. A comparison has been made between the results of numerical experiments showing the relationship between the change in the value of the safety factor and the position of the slip curve depending on the heat, salt, and moisture transfer.

42 ENGINEERING↗

Theoretical aspects of photoclinometric terrain profiling on the Galilean satellites

For large parts of the surfaces of the Galilean satellites there is no stereoscopic high resolution imagery, and so for shadow-free regions far from the terminator, the only method of obtaining topograpic information is photoclinometry, the technique of converting brightness variations into local surface tilts and hence into topographic profiles and contour maps. The conversion from brightness changes to slopes require knowledge of the angular photometric function for the type of planetary surface terrain being analyzed, i.e., the relationship describing the brightness of the surface as a function of the angles of incidence (I) and emergence (E) of light at a surface element. In order to investigate the effects of these changes on the shapes of topographic profiles deduced from the functions, an area of grooved terrain (lines 500-505, samples 550-650 on frame 20640.27 0060J2) using wide ranges of values of all the adjustable parameters in Hapke's new photometric function were analyzed.

Wilson, L.↗

Convective Instability in Ice I with Non-Newtonian Rheology: Application to the Galilean Satellites

At the temperatures and stresses associated with the onset of convection in an ice I shell of the Galilean satellites, ice behaves as a non-Newtonian fluid with a viscosity that depends on both temperature and strain rate. The convective stability of a non-Newtonian ice shell can be judged by comparing the Rayleigh number of the shell to a critical value. Previous studies suggest that the critical Rayleigh number for a non-Newtonian fluid depends on the initial conditions in the fluid layer, in addition to the thermal, rheological, and physical properties of the fluid. We seek to extend the existing definition of the critical Rayleigh number for a non-Newtonian, basally heated fluid by quantifying the conditions required to initiate convection in an ice I layer initially in conductive equilibrium. We find that the critical Rayleigh number for the onset of convection in ice I varies as a power (-0.6 to -0.5) of the amplitude of the initial temperature perturbation issued to the layer, when the amplitude of perturbation is less than the rheological temperature scale. For larger-amplitude perturbations, the critical Rayleigh number achieves a constant value. We characterize the critical Rayleigh number as a function of surface temperature of the satellite, melting temperature of ice, and rheological parameters so that our results may be extrapolated for use with other rheologies and for a generic large icy satellite. The values of critical Rayleigh number imply that triggering convection from a conductive equilibrium in a pure ice shell less than 100 km thick in Europa, Ganymede, or Callisto requires a large, localized temperature perturbation of a few kelvins to tens of kelvins to soften the ice and therefore may require tidal dissipation in the ice shell.

Barr, A. C.↗

First-principles calculations of the electronic and structural properties of GaSb

In this paper, we carried out first-principles calculations in order to investigate the structural and electronic properties of the binary compound gallium antimonide (GaSb). This theoretical study was carried out using the Density Functional Theory within the plane-wave pseudopotential method. The effects of exchange and correlation (XC) were treated using the functional Local Density Approximation (LDA), generalized gradient approximation (GGA): Perdew–Burke–Ernzerhof (PBE), Perdew-Burke-Ernzerhof revised for solids (PBEsol), Perdew-Wang91 (PW91), revised Perdew–Burke–Ernzerhof (rPBE), Armiento–Mattson 2005 (AM05) and meta-generalized gradient approximation (meta-GGA): Tao–Perdew–Staroverov–Scuseria (TPSS) and revised Tao–Perdew–Staroverov–Scuseria (RTPSS) and modified Becke-Johnson (MBJ). We calculated the densities of state (DOS) and band structure with different XC potentials identified and compared them with the theoretical and experimental results reported in the literature. It was discovered that functional: LDA, PBEsol, AM05 and RTPSS provide the best results to calculate the lattice parameters (a) and bulk modulus (B{sub 0}); while for the cohesive energy (E{sub coh}), functional: AM05, RTPSS and PW91 are closer to the values obtained experimentally. The MBJ, Rtpss and AM05 values found for the band gap energy is slightly underestimated with those values reported experimentally.

36 MATERIALS SCIENCE↗

The mixing length parameter alpha

The standard mixing length theory, MLT, treats turbulent eddies as if they were isotropic, while the largest eddies that carry most of the flux are highly anisotropic. Recently, an anisotropic MLT was constructed, and the relevant equations derived. It is shown that these new equations can actually be cast in a form that is formally identical to that of the standard isotropic MLT, provided the mixing length parameter, derived from stellar structure calculations, is interpreted as an intermediate, auxiliary function alpha(x), where x, the degree of anisotropy is given as a function of the thermodynamic variables of the problem. The relation between alpha(x) and the physically relevant alpha(l = Hp) is also given. Once the value alpha is deduced, it is found to be a function of the local thermodynamic quantities, as expected.

Canuto, V. M.↗

Moessbauer Spectroscopy of Mineral Separates from SNC Meteorites

Numerous workers have recently focused attention on the issue of the oxygen fugacity (f(sub O2)) of martian samples. Estimates of fO2 based on Fe-Ti oxides and D(sub Eu)/D(sub Gd) and D(sub Eu)/D(sub Sm) ratios suggest a range of fO2 values for SNC meteorites from IW+2.5 - IW+3.5 for Shergotty to IW- 2.0 - IW+0.2 for QUE94201. Fe(3+)/Fe(2+) is also a function of f(sub O2), and synchrotron micro-XANES values for olivine, pyroxene, and feldspar Fe(3+) have been reported. However, the relationship between the reported Fe(3+) values and the other methods for estimating f(sub O2) is not clear, and further measurements of Fe(3+)/Fe(2+) by a more conventional technique have been needed. Accordingly, in this project, new Mossbauer spectroscopy data on mineral separates handpicked from 10 SNC meteorites are reported.

Dyar, M. D.↗

An approach to rescheduling activities based on determination of priority and disruptivity

A constraint-based scheduling system called SPIKE is being used to create long term schedules for the Hubble Space Telescope. Feedback for the spacecraft or from other ground support systems may invalidate some scheduling decisions and those activities concerned must be reconsidered. A function rescheduling priority is defined which for a given activity performs a heuristic analysis and produces a relative numerical value which is used to rank all such entities in the order that they should be rescheduled. A function disruptivity is also defined that is used to place a relative numeric value on how much a pre-existing schedule would be changed in order to reschedule an activity. Using these functions, two algorithms (a stochastic neural network approach and an exhaustive search approach) are proposed to find the best place to reschedule an activity. Prototypes were implemented and preliminary testing reveals that the exhaustive technique produces only marginally better results at much greater computational cost.

Sponsler, Jeffrey L.↗

tSFM 1.0: tRNA Structure–Function Mapper

Structure-conditioned information statistics have proven useful to predict and visualize tRNA Class-Informative Features (CIFs) and their evolutionary divergences. Although permutation P-values can quantify the significance of CIF divergences between two taxa, their naive Monte Carlo approximation is slow and inaccurate. The Peaks-over-Threshold approach of Knijnenburg et al. (2009) promises improvements to both speed and accuracy of permutation P-values, but has no publicly available API. Here, we present tRNA Structure–Function Mapper (tSFM) v1.0, an open-source, multi-threaded application that efficiently computes, visualizes and assesses significance of single- and paired-site CIFs and their evolutionary divergences for any RNA, protein, gene or genomic element sequence family. Multiple estimators of permutation P-values for CIF evolutionary divergences are provided along with confidence intervals. tSFM is implemented in Python 3 with compiled C extensions and is freely available through GitHub (https://github.com/tlawrence3/tSFM) and PyPI.

59 BASIC BIOLOGICAL SCIENCES↗

The annoyance of multiple noisy events

A total of 24 subjects (17 M, 7 F) was tested in an experimental study of annoyance rating of multiple noisy events (30 sets of noise bursts). The scaling technique known as functional measurement was used to determine whether annoyance integrates additively over events and if so, to measure the power law exponent which relates the levels of the events to the additive scale values. To this end, groups of three noises were presented at three levels in a factorial arrangement to check the additivity hypothesis and to estimate the scaling function. Also, a series of sets of noises of constant level but varying in set size were considered. The functional measurement of annoyance ratings of sets of three simulated flyovers showed that the integration of annoyance can be represented as an additive process in terms of scale values that are power functions of the sound power with a power-law exponent near 0.7.

Ahumada, A., Jr.↗

Partition function corrections

The vibration-rotation interaction coupling in diatomic molecules is analyzed and first-order expressions for the energy levels are deduced. Corrections to the partition function to account for this coupling are derived. The effects of long-range intermolecular forces due to induced dipole-induced dipole interactions, dipole-induced dipole interactions, charge-dipole interactions, and charge-charge interactions are considered. London's quantized oscillator model of the induced dipole-induced dipole interaction is developed. The partition function including effects of such dispersion forces is derived and is shown to lead to the virial equation of state. For a model combining the hard sphere and long-range attractive type potentials, this is found to lead to the van der Waals equation of state. The equation of state near the critical point is presented in reduced form (thermodynamic variables expressed in units of critical point values). Finally, approximate corrections to the electronic partition functions are derived to account for perturbations of excited electronic states induced by neighboring neutral particles, heavy ions, and fast electron collisions.

Source record↗