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At least 37 records · Page 2

Dual incorporation of non-canonical amino acids enables production of post-translationally modified selenoproteins

Post-translational modifications (PTMs) can occur on almost all amino acids in eukaryotes as a key mechanism for regulating protein function. The ability to study the role of these modifications in various biological processes requires techniques to modify proteins site-specifically. One strategy for this is genetic code expansion (GCE) in bacteria. The low frequency of post-translational modifications in bacteria makes it a preferred host to study whether the presence of a post-translational modification influences a protein’s function. Genetic code expansion employs orthogonal translation systems engineered to incorporate a modified amino acid at a designated protein position. Selenoproteins, proteins containing selenocysteine, are also known to be post-translationally modified. Selenoproteins have essential roles in oxidative stress, immune response, cell maintenance, and skeletal muscle regeneration. Their complicated biosynthesis mechanism has been a hurdle in our understanding of selenoprotein functions. As technologies for selenocysteine insertion have recently improved, we wanted to create a genetic system that would allow the study of post-translational modifications in selenoproteins. By combining genetic code expansion techniques and selenocysteine insertion technologies, we were able to recode stop codons for insertion of N ε -acetyl- l -lysine and selenocysteine, respectively, into multiple proteins. The specificity of these amino acids for their assigned position and the simplicity of reverting the modified amino acid via mutagenesis of the codon sequence demonstrates the capacity of this method to study selenoproteins and the role of their post-translational modifications. Moreover, the evidence that Sec insertion technology can be combined with genetic code expansion tools further expands the chemical biology applications.

59 BASIC BIOLOGICAL SCIENCES↗

Modeling Intercalation Chemistry with Multiredox Reactions by Sparse Lattice Models in Disordered Rocksalt Cathodes

Modern battery materials can contain many elements with substantial site disorder, and their configurational state has been shown to be critical for their performance. The intercalation voltage profile is a critical parameter to evaluate the performance of energy storage. The application of commonly used cluster expansion techniques to model the intercalation thermodynamics of such systems ab initio is challenged by the combinatorial increase in configurational degrees of freedom as the number of species grows. Such challenges necessitate the efficient generation of lattice models without overfitting and proper sampling of the configurational space under the requirement of charge balance in ionic systems. In this work, we introduce a combined approach that addresses these challenges by (1) constructing a robust cluster expansion Hamiltonian using the sparse regression technique, including -norm regularization and structural hierarchy; and (2) implementing semigrand-canonical Monte Carlo to sample charge-balanced ionic configurations using the table-exchange method and an ensemble average approach. These techniques are applied to a disordered rocksalt oxyfluoride (LMNOF) that is part of a family of promising earth-abundant cathode materials. The simulated voltage profile is found to be in good agreement with experimental data and particularly provides a clear demonstration of the and oxygen contributions to the redox potential as a function of content.

25 ENERGY STORAGE↗

Analytic solution for low thrust out of ecliptic mission design

Description of an analytic trajectory solution for low thrust out of ecliptic mission design based on the two-variable asymptotic expansion technique. A practical steering program utilizing normal thrusting symmetrical about the nodes is assumed. A two-term expansion yields an essentially exact solution of the problem which is in a form suitable for evaluation on small desk-top computers. It is shown that for a circular base orbit at 1 AU, a 15-kw solar electric system with a specific impulse of 3000 sec is capable of delivering an 1100-kg net payload to a heliographic latitude of about 63 deg.

Flandro, G. A.↗

A new numerical method for the simulation of three dimensional flow in a pipe

A new numerical technique for simulating three dimensional, unsteady, incompressible pipe flows is presented and its utility and accuracy is shown. Each vector function in the expansion of the velocity field is divergence free and satisfies the boundary conditions for viscous flow. Some of the benefits of the expansion technique are that pressure is eliminated from the dynamics, only two unknowns per mesh point are required, implicit treatment of the viscous terms is provided at no extra computational cost, and no fractional time steps are required. The method uses spectral expansions: Fourier series in the azimuthal and streamwise directions, and Jacobi polynominals in the radial direction.

Leonard, A.↗

A new numerical method for the simulation of three-dimensional flow in a pipe

A new numerical technique for simulating three dimensional, unsteady, incompressible pipe flows is presented and its utility and accuracy is shown. Each vector function in the expansion of the velocity field is divergence free and satisfies the boundary conditions for viscous flow. Some of the benefits of the expansion technique are that pressure is eliminated from the dynamics, only two unknowns per mesh point are required, implicit treatment of the viscous terms is provided at no extra computational cost, and no fractional time steps are required. The method uses spectral expansions: Fourier series in the azimuthal and streamwise directions, and Jacobi polynominals in the radial direction. Previously announced in STAR as N82-31644

Leonard, A.↗

Simultaneous expansion and orthogonalization of measured modes for structure identification

Tests of large structures on-orbit will be performed with measurements at a relatively few structure points. Values for the unmeasured degrees of freedom (dofs) can be estimated based on measured dofs and analytical model dynamic information. These 'expanded' mode shapes are useful for optimal-update identification and damage location as well as test/analysis correlation. A new method of expansion for test mode shape vectors is developed from the orthogonal Procrustes problem from computational linear algebra. A subspace defined by the set of measured dofs is compared to a subspace defined by mode shapes from an analytical model of the structure. The method simultaneously expands and orthogonalizes the mode shape vectors. Two demonstration problems are used to compare the new method to current expansion techniques. One demonstration uses test data from a laboratory scale-model truss structure. Performance of the new method is comparable or superior to that of the previous expansion methods which require separate orthogonalization.

Smith, Suzanne Weaver↗

Parametrized ion-distribution model for extended x-ray absorption fine-structure analysis at high-energy-density conditions

Experiments today can compress solids near isentropically to pressures approaching 100 × 106 atmospheres; however, determining the temperature of such matter remains a major challenge. Extended x-ray absorption fine-structure (EXAFS) spectroscopy is one of the few techniques sensitive to the bulk temperature of highly compressed solid matter, and the validity of this temperature measurement relies on constraining the local ion structure from the EXAFS spectrum. At high-energy-density (HED) conditions, the local ion structure often becomes distorted, which must be accounted for during the EXAFS analysis. Described here is a technique, using a parametrized ion-distribution model to directly analyze EXAFS spectra that provides a better constraint on the local structure than traditional second- or third-order cumulant expansion techniques at HED conditions. The parametrized ion-distribution model is benchmarked by analyzing EXAFS spectra from nickel molecular-dynamics simulations at ∼100 GPa and shown to provide a 10%–20% improvement in constraining the cumulants of the true ion distribution.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Ideal Resampling Of Discrete Sequences

Spectral information preserved to extent possible. Technique developed to shrink or expand discrete input sequence of numbers into output sequence in manner preserving input spectrum up to Nyquist limit of smaller of two sequences. In case of expansion, technique also prevents introduction of spurious frequencies not present in input. While applicable to many kinds of data sampled at regular interval, particularly useful in processing and enhancement of images, where discrete sequences spatially ordered sets of picture-element brightness values. Image coarsened by resampling to reduce number of picture elements while preserving as much as possible of original image information. Used to generate intermediate images at small intervals between frames, thereby suppressing appearance of jerky motion caused by sudden jumps between frames at low frame rate.

Watson, Andrew B.↗

Topology optimization of 3D photonic crystals with complete bandgaps

The design of photonic crystals with complete bandgaps has recently received considerable research focus for numerous reasons. This work leverages well-known nonlinear programming techniques to alleviate the non-smoothness caused by degenerate eigenvalues such that topology optimization problems can be solved with the open-source IPOPT software. A fully-vectorial plane wave expansion technique is used with an iterative eigensolver to efficiently predict dispersion properties of candidate structures. Nonlinear programming is employed to solve the inverse problem of designing three-dimensional periodic structures that exhibit complete two-dimensional (2D) and three-dimensional (3D) photonic bandgaps. Mesh refinement is performed to alleviate the large computational burden of designing and analyzing photonic crystals, and a periodic density filter is implemented to impose a minimum feature size for manufacturability considerations.

97 MATHEMATICS AND COMPUTING↗

Three-dimensional Navier-Stokes calculations of multiple interacting vortex rings

Results from a finite-difference Navier-Stokes code for three-dimensional, unsteady, vortical flows in unbounded domains are presented and analyzed in this paper. The vortical flows presented are representative of vortex rings and other closed vortical tubes or structures in fluid mechanics. Such structures are important elements in fluid flows such as jets, atmospheric turbulence, and the far-field wakes of aircraft, and studies of their interaction may aid in an understanding of complex fluid flows. The paper demonstrates that computational methods can be used as a viable alternative or supplement to experimental techniques for studying the physics of vortex flows. The separate visualization of vortex stretching, convection, and diffusion is presented in this paper for a single elliptical vortex ring.The calculations employ a truncated series expansion technique to simulate the unbounded nature of the fluid flow with a finite computational domain, which is a more accurate technique than the conventional freestream boundary specification. The numerical divergence of the three-dimensional vorticity field is considered as a useful estimate of truncation error, and the use of a kinetic energy decay law as a calculation check is demonstrated. Results from the Navier-Stokes code are presented for the unsteady motion of two and four vortex rings along parallel axes, and the results agree qualitatively with experimental flow visualization.

Chamberlain, J. P.↗

Predicting 3D Motions from Single-Camera Optical Test Data

In a typical optical test, a stereo camera pair is required to measure the three-dimensional motion of a test article; one camera typically only measures motions in the image plane of the camera, and measurements in the out-of-plane direction are missing. Finite element expansion techniques provide a path to estimate responses from a test at unmeasured degrees of freedom. Treating the case of a single camera as a measurement with unmeasured degrees of freedom, a finite element model is used to expand to the missing third dimension of the image data, allowing a full-field, three-dimensional measurement to be obtained from a set of images from a single camera. The key to this technique relies on the mapping of finite element deformations to image deformations, creating a set of mode shape images that are used to filter the response in the image into modal responses. These modal responses are then applied to the finite element model to estimate physical responses at all finite element model degrees of freedom. The mapping from finite element model to image is achieved using synthetic images produced by a rendering software. Finally, the technique is applied first to a synthetic deformation image, and then is validated using an experimental set of images.

47 OTHER INSTRUMENTATION↗

Computational methods for studying acoustic propagation in nonuniform waveguides.

A variational technique is used to model sound transmission through a nonuniform duct segment consisting of an axial variation in wall admittance or cross sectional area. The method involves the Ritz minimization of functionals which have the governing equations as stationary conditions. The variational method is verified by application to segments of variables-separable geometry for which eigenfunction expansion techniques offer an alternative solution procedure, and by comparison with the results of stepped duct approximations to the nonuniformity. Quantitative data are presented which indicate the boundary condition matching to be a suitable measure of the accuracy of the transmitted field.

Beckemeyer, R. J.↗

Modal sensitivity for structural systems with repeated frequencies

Repeated or closely packed modal frequencies are common physical occurrences for vibrating structures which are complex or possess multi-planes of symmetry. The computation of the sensitivity to structural modifications for these frequencies and mode shapes is made difficult by the fact that the mode shapes are not unique, since any linear combination of eigenvectors corresponding to a repeated eigenvalue is also an eigenvector. The work of Chen and Pan is extended, who used modal expansion techniques for accommodating the sensitivity analysis of structures with repeated eigenvalues. Starting with a discussion of the physical significance of sensitivity analysis for repeated frequency modes, a derivation is presented of the governing equations for the derivatives of a repeated eigenvalue. This is followed with a small example to illustrate the results. An efficient computation procedure, based upon an expansion of Nelson's ideas for large banded systems, is then proposed for systems with repeated or closely spaced eigenvalues.

Ojalvo, I. U.↗

Spherical disharmonics in the Earth sciences and the spatial solution: Ridges, hotspots, slabs, geochemistry and tomography correlations

There is increasing use of statistical correlations between geophysical fields and between geochemical and geophysical fields in attempts to understand how the Earth works. Typically, such correlations have been based on spherical harmonic expansions. The expression of functions on the sphere as spherical harmonic series has many pitfalls, especially if the data are nonuniformly and/or sparsely sampled. Many of the difficulties involved in the use of spherical harmonic expansion techniques can be avoided through the use of spatial domain correlations, but this introduces other complications, such as the choice of a sampling lattice. Additionally, many geophysical and geochemical fields fail to satisfy the assumptions of standard statistical significance tests. This is especially problematic when the data values to be correlated with a geophysical field were collected at sample locations which themselves correlate with that field. This paper examines many correlations which have been claimed in the past between geochemistry and mantle tomography and between hotspot, ridge, and slab locations and tomography using both spherical harmonic coefficient correlations and spatial domain correlations. No conclusively significant correlations are found between isotopic geochemistry and mantle tomography. The Crough and Jurdy (short) hotspot location list shows statistically significant correlation with lowermost mantle tomography for degree 2 of the spherical harmonic expansion, but there are no statistically significant correlations in the spatial case. The Vogt (long) hotspot location list does not correlate with tomography anywhere in the mantle using either technique. Both hotspot lists show a strong correlation between hotspot locations and geoid highs when spatially correlated, but no correlations are revealed by spherical harmonic techniques. Ridge locations do not show any statistically significant correlations with tomography, slab locations, or the geoid; the strongest correlation is with lowermost mantle tomography, which is probably spurious. The most striking correlations are between mantle tomography and post-Pangean subducted slabs. The integrated locations of slabs correlate strongly with fast areas near the transition zone and the core-mantle boundary and with slow regions from 1022-1248 km depth. This seems to be consistent with the 'avalanching' downwellings which have been indicated by models of the mantle which include an endothermic phase transition at the 670-km discontinuity, although this is not a unique interpretation. Taken as a whole, these results suggest that slabs and associated cold downwellings are the dominant feature of mantle convection. Hotspot locations are no better correlated with lower mantle tomography than are ridge locations.

Ray, Terrill W.↗

Quantification of Deformation-Induced Concentration Fluctuations in Polymeric Liquids by Small-Angle Neutron Scattering

This study demonstrates how the large concentration fluctuations of polymeric liquids under deformation and flow can be quantitatively studied by applying the spherical harmonic expansion technique to small-angle neutron scattering. Using a series of binary polymer blends, it is shown that the emergence of the so-called butterfly patterns is caused by the change of sign in the leading anisotropic component of the small-angle spectrum, when the scattering is dominated by intermolecular correlation associated with flow-induced demixing. The increasing spatial fluctuations of concentration are evidenced by the enhancement of the isotropic component of the scattering spectrum in the zero-angle limit and peak shift of the leading anisotropic coefficients toward low Q. Additionally, the spherical harmonic expansion framework permits real-space analysis of anisotropic scattering length density correlation in a convenient form. The methodology described in this work provides a concrete venue for quantitative studies of phase behavior of fluids under deformation and flow via small-angle scattering techniques, where mainly qualitative approaches were previously employed.

Chemical structure↗

Metal-insulator transition and magnetism of SU(3) fermions in the square lattice

We study the SU(3) symmetric Fermi-Hubbard model (FHM) in the square lattice at 1/3-filling using numerically exact determinant quantum Monte Carlo and numerical linked-cluster expansion techniques. We present the different regimes of the model in the T–U plane, which are characterized by local and short-range correlations, and capture signatures of the metal-insulator transition and magnetic crossovers. These signatures are detected as the temperature scales characterizing the rise of the compressibility, and an interaction-dependent change in the sign of the diagonal spin-spin correlation function. The analysis of the compressibility estimates the location of the metal-insulator quantum critical point at U c /t ~ 6, and provides a temperature scale for observing Mott physics at finite T. Furthermore, from the analysis of the spin-spin correlation function we observe that for U/t ≳ 6 and T ~ J = 4⁢t 2 /U there is a development of a short-range two-sublattice (2SL) antiferromagnetic structure, as well as an emerging three-sublattice (3SL) antiferromagnetic structure as the temperature is lowered below T/J ≲ 0.57. This crossover from 2SL to 3SL magnetic ordering agrees with Heisenberg limit predictions, and has observable effects on the density of on-site pairs. Finally, we describe how the features of the regimes in the T–U plane can be explored with alkaline-earth-like atoms in optical lattices with currently achieved experimental techniques and temperatures. Furthermore, the results discussed in this paper provide a starting point for the exploration of the SU(3) FHM upon doping.

74 ATOMIC AND MOLECULAR PHYSICS↗

Discrete control of linear distributed systems with application to the deformable primary mirror of a large orbiting telescope

One of the more significant technological problems associated with the orbital operation of large astronomical telescope's is the fabrication and maintenance of the primary mirror surface to the tolerance required for diffraction-limited performance. An interesting approach to the solution of this problem involves continuously measuring and automatically correcting the optical surface of a thin deformable mirror by means of discrete actuators located on its rear surface: The realization of diffraction-limited performance from a telescope in space by this method rests on the ability of the designer to achieve extremely accurate control of a highly complex, interacting, multivariable system. This paper presents the results of a detailed study of the discrete control of linear distributed systems with specific application to the design of a practical controller for a plant representative of a telescope primary mirror for an orbiting astronomical observatory. The problem of controlling the distributed plant is treated by employing modal techniques to represent variations in the optical figure. Distortion of the mirror surface, which arises primarily from thermal gradients, is countered by actuators working against a backing structure to apply a corrective force distribution to the controlled surface. Each displacement actuator is in series with a spring attached to the mirror by means of a pad intentionally introduced to restrict the excitation of high-order modes. Control is then exerted over a finite number (equal.to the number of actuators) of the most significant modes. Through the application of the modal expansion technique the mirror equation of motion is transformed tb a set of uncoupled, linear, time-invariant, ordinary differential equations. The desired dynamic response and static accuracy may then be achieved by the application of classical single-variable design techniques. The formulation of a quadratic performance index which incorporates a measure of image quality permits determination of the trade-off between the-number of actuators and optical purity. A criterion for defining actuator placement and pad size is presented which minimizes the tendency of the controller to excite the unmonitored modes.

Jeremiah F Creedon↗

Functional methods for Heavy Quark Effective Theory

We use functional methods to compute one-loop effects in Heavy Quark Effective Theory. The covariant derivative expansion technique facilitates the efficient extraction of matching coefficients and renormalization group evolution equations. This paper pro- vides the first demonstration that such calculations can be performed through the algebraic evaluation of the path integral for the class of effective field theories that are (i) constructed using a non-trivial one-to-many mode decomposition of the UV theory, and (ii) valid for non-relativistic kinematics. We discuss the interplay between operators that appear at intermediate steps and the constraints imposed by the residual Lorentz symmetry that is encoded as reparameterization invariance within the effective description. The tools presented here provide a systematic approach for computing corrections to higher order in the heavy mass expansion; precision applications include predictions for experimental data and connections to theoretical tests via lattice QCD. A set of pedagogical appendices comprehensively reviews modern approaches to performing functional calculations algebraically, and derives contributions from a term with open covariant derivatives for the first time.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗