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At least 739 records · Page 41

Global Structure of a Three-Way Junction in a Phi29 Packaging RNA Dimer Determined Using Site-Directed Spin Labeling

The condensation of bacteriophage phi29 genomic DNA into its preformed procapsid requires the DNA packaging motor, which is the strongest known biological motor. The packaging motor is an intricate ring-shaped protein/RNA complex, and its function requires an RNA component called packaging RNA (pRNA). Current structural information on pRNA is limited, which hinders studies of motor function. Here, we used site-directed spin labeling to map the conformation of a pRNA three-way junction that bridges binding sites for the motor ATPase and the procapsid. The studies were carried out on a pRNA dimer, which is the simplest ring-shaped pRNA complex and serves as a functional intermediate during motor assembly. Using a nucleotide-independent labeling scheme, stable nitroxide radicals were attached to eight specific pRNA sites without perturbing RNA folding and dimer formation, and a total of 17 internitroxide distances spanning the three-way junction were measured using Double Electron-Electron Resonance spectroscopy. The measured distances, together with steric chemical constraints, were used to select 3662 viable three-way junction models from a pool of 65 billion. The results reveal a similar conformation among the viable models, with two of the helices (HT and HL) adopting an acute bend. This is in contrast to a recently reported pRNA tetramer crystal structure, in which HT and HL stack onto each other linearly. The studies establish a new method for mapping global structures of complex RNA molecules, and provide information on pRNA conformation that aids investigations of phi29 packaging motor and developments of pRNA-based nanomedicine and nanomaterial.

59 BASIC BIOLOGICAL SCIENCES↗

Deterministic direct aperture optimization using multiphase piecewise constant segmentation

Purpose Direct aperture optimization (DAO) attempts to incorporate machine constraints in the inverse optimization to eliminate the post‐processing steps in fluence map optimization (FMO) that degrade plan quality. Current commercial DAO methods utilize a stochastic or greedy approach to search a small aperture solution space. In this study, we propose a novel deterministic direct aperture optimization that integrates the segmentation of fluence map in the optimization problem using the multiphase piecewise constant Mumford‐Shah formulation. Methods The Mumford‐Shah based direct aperture optimization problem was formulated to include an L2‐norm dose fidelity term to penalize differences between the projected dose and the prescribed dose, an anisotropic total variation term to promote piecewise continuity in the fluence maps, and the multiphase piecewise constant Mumford‐Shah function to partition the fluence into pairwise discrete segments. A proximal‐class, first‐order primal‐dual solver was implemented to solve the large scale optimization problem, and an alternating module strategy was implemented to update fluence and delivery segments. Three patients of varying complexity—one glioblastoma multiforme (GBM) patient, one lung (LNG) patient, and one bilateral head and neck (H&N) patient with 3 PTVs—were selected to test the new DAO method. For each patient, 20 non‐coplanar beams were first selected using column generation, followed by the Mumford‐Shah based DAO (DAO MS ). For comparison, a popular and successful approach to DAO known as simulated annealing—a stochastic approach—was replicated. The simulated annealing DAO (DAO SA ) plans were then created using the same beam angles and maximum number of segments per beam. PTV coverage, PTV homogeneity , and OAR sparing were assessed for each plan. In addition, high dose spillage, defined as the 50% isodose volume divided by the tumor volume, as well as conformity, defined as the van't Riet conformation number, were evaluated. Results DAO MS achieved essentially the same OAR doses compared with the DAO SA plans for the GBM case. The average difference of OAR D max and D mean between the two plans were within 0.05% of the plan prescription dose. The lung case showed slightly improved critical structure sparing using the DAO MS approach, where the average OAR D max and D mean were reduced by 3.67% and 1.08%, respectively, of the prescription dose. The DAO MS plan substantially improved OAR dose sparing for the H&N patient, where the average OAR D max and D mean were reduced by over 10% of the prescription dose. The DAO MS and DAO SA plans were comparable for the GBM and LNG PTV coverage, while the DAO MS plan substantially improved the H&N PTV coverage, increasing D99 by 6.98% of the prescription dose. For the GBM and LNG patients, the DAO MS and DAO SA plans had comparable high dose spillage but slightly worse conformity with the DAO MS approach. For the H&N plan, DAO MS was considerably superior in high dose spillage and conformity to the DAO SA . The deterministic approach is able to solve the DAO problem substantially faster than the simulated annealing approach, with a 9.5‐ to 40‐fold decrease in total solve time, depending on the patient case. Conclusions A novel deterministic direct aperture optimization formulation was developed and evaluated. It combines fluence map optimization and the multiphase piecewise constant Mumford‐Shah segmentation into a unified framework, and the resulting optimization problem can be solved efficiently. Compared to the widely and commercially used simulated annealing DAO approach, it showed comparable dosimetry behavior for simple plans, and substantially improved OAR sparing, PTV coverage, PTV homogeneity, high dose spillage, and conformity for the more complex head and neck plan.

Nguyen, Dan↗

Microstructure prediction for Ti-22Al-25Nb in laser powder bed fusion

This work presents a physics-informed framework for predicting solidification morphology and defect susceptibility in additively manufactured Ti–22Al–25Nb across a broad processing space. The framework integrates solidification microstructure selection (SMS) analysis with a single-track defect-based printability map to establish a unified methodology linking processing parameters to both interfacial morphology and manufacturability. Thermal gradients G and solidification rates R are first computed using the Thermo-Calc Additive Manufacturing (TC-AM) module, a finite-interface-dissipation (FID) phase-field (PF) model coupled with CALPHAD method is then employed to systematically distinguish planar and dendritic regimes as functions of $G$ and $R$. By superimposing the printability map onto the morphology projections, a comprehensive process–structure framework is obtained. Across most processing conditions, the predicted microstructure is predominantly dendritic, while planar growth emerges only under selected laser power $P$ and scan speed $v$ combinations. In addition to morphology classification, the framework quantifies the dendritic area fraction and introduces a width-based morphology descriptor to characterize the spatial extent of planar/dendritic regions within the melt pool. It provides mechanistic insight into the interplay between solidification physics and defect formation, offering practical guidance for parameter selection and microstructural control in Ti–22Al–25Nb additive manufacturing (AM).

36 MATERIALS SCIENCE↗

Radiation Mapping for an Unmanned Aerial Vehicle: Development and Simulated Testing of Algorithms for Source Mapping and Navigation Path Generation

Image reconstruction algorithms were developed for radiation source mapping and used for generating the search path of a moving radiation detector, such as one onboard an unmanned aerial vehicle. Simulations consisted of first assuming radioactive sources of varying complexity and estimating the radiation fields that would then be produced by that source distribution. Next, the "measurements" that would result from a pair of adjacent spatial locations were computed. A crude estimate of the source distribution likely to have produced such "measurements" was reconstructed based upon the limited measurements. Location of the next "measurement" was then determined as halfway between the location of the estimated source and the current "measurement." With each additional sample, improved source distribution reconstructions were made and used to inform the immediate direction of detector motion. Source reconstruction or mapping was formulated as an inverse problem solved with either maximum a posteriori or least squares (LS) regression deconvolution methods. Different amounts of noise were added to the simulated "measurements," allowing evaluation of the methods' performances as functions of signal-to-noise ratio of the measured map. As expected, methods that promote sparsity were better suited in reconstructing point sources. Reliable prior information of the source distribution also improved the reconstruction results, especially with distributed sources. With a non-negative least square algorithm and the suggested paths it generated, location of sources was successfully estimated to an accuracy of 0.014 m within nine iterations in a single-source scenario and 12 iterations in a two-source scenario, given a 10% error on the integrated counts and a Poisson distribution of the noise associated with the measured counts.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

Mapping topological order in coordinate space

The organization of the electrons in the ground state is classified by means of topological invariants, defined as global properties of the wave function. Here we address the Chern number of a two-dimensional insulator and we show that the corresponding topological order can be mapped by means of a ''topological marker'', defined in r space, and which may vary in different regions of the same sample. Notably, this applies equally well to periodic and open boundary conditions. Simulations over a model Hamiltonian validate our theory.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Lyman-tomography of cosmic infrared background fluctuations with euclid : probing emissions and baryonic acoustic oscillations at z ≳ 1

The Euclid space mission, designed to probe evolution of the Dark Energy (DE), will map a large area of the sky at three adjacent near-IR filters, Y, J, and H. This coverage will also enable mapping source-subtracted cosmic infrared background (CIB) fluctuations with unprecedented accuracy on sub-degree angular scales. Here, we propose methodology, using the Lyman-break tomography applied to the Euclid -based CIB maps, to accurately isolate the history of CIB emissions as a function of redshift from 10 ≲ z ≲ 20 and to identify the baryonic acoustic oscillations (BAOs) at those epochs. To identify the BAO signature, we would assemble individual CIB maps over conservatively large contiguous areas of ≳400 deg{sup 2}. The method can isolate the CIB spatial spectrum by z to sub-percent statistical accuracy. We illustrate this with a specific model of CIB production at high z normalized to reproduce the measured Spitzer -based CIB fluctuation. We show that even if the latter contains only a small component from high- z sources, the amplitude of that component can be accurately isolated with the methodology proposed here and the BAO signatures at z ≳ 10 are recovered well from the CIB fluctuation spatial spectrum. Probing the BAO at those redshifts will be an important test of the underlying cosmological paradigm and would narrow the overall uncertainties on the evolution of cosmological parameters, including the DE. Similar methodology is applicable to the planned WFIRST mission, where we show that a possible fourth near-IR channel at ≥2 μ m would be beneficial.

79 ASTRONOMY AND ASTROPHYSICS↗

Conservative velocity mappings for discontinuous Galerkin kinetics

Continuum computational kinetic plasma models evolve the distribution function of a plasma species f s on a phase-space grid over time. In many problems of interest the distribution function has limited extent in velocity space; hence, using a uniform, highly refined mesh would be costly and slow. Nonuniform velocity grids can reduce the computational cost by placing more degrees of freedom where f s is appreciable and fewer where it is not. In this work we introduce a first-of-its kind discontinuous Galerkin approach to nonuniform velocity-space discretization using mapped velocity coordinates. This new method is presented in the context of a gyrokinetic model used to study magnetized plasmas. We create discretizations of collisionless and collisional terms using mappings in a way that exactly conserves particles and energy. Numerical tests of such properties are presented, and we show that this new discretization can reproduce earlier gyrokinetic simulations using grids with up to 6–60 times fewer cells and 22X-60X speed-ups depending on dimensionality, geometry and plasma parameters.

Discontinuous Galerkin↗

Reducing the Strain Required for Ambient‐Pressure Superconductivity in Ruddlesden‐Popper Bilayer Nickelates

ABSTRACT The discovery of high‐temperature superconductivity in pressurized bulk Ruddlesden‐Popper (RP) bilayer nickelates has prompted the conjecture that epitaxial compressive strain might mimic essential aspects of hydrostatic pressure. The realization of superconductivity in films on SrLaAlO 4 (001) (SLAO) supports this correspondence, yet it remains unclear whether the pressure–temperature phase diagram of RP bilayer nickelates can be systematically mapped (and studied at ambient pressure) as a function of epitaxial strain. To this end, experimental access near the elusive edge of the superconducting phase boundary would provide invaluable insight into the nature of the superconducting state and the ground state from which it emerges. Here we report superconducting RP bilayer nickelates grown on LaAlO 3 (001) (LAO), where the compressive strain required for ambient‐pressure superconductivity is nearly halved to −1.2%. These films exhibit a superconducting onset above 10 K and reach zero resistance at 3 K, with normal‐state transport properties differing from those of films grown on SLAO. Our comparative study shows that strain–rather than interfacial structure is the primary factor governing the superconductivity and normal‐state properties. This work offers a new opportunity to probe emergent phenomena near the superconducting phase boundary in the strain–temperature phase diagram of RP bilayer nickelates.

Tarn, Yaoju [Department of Applied Physics Stanfor↗

Organizing thermodynamic data obtained from multicomponent polymer electrolytes: Salt-containing polymer blends and block copolymers

The objective of this review is to organize literature data on the thermodynamic properties of salt-containing polystyrene/poly(ethylene oxide) (PS/PEO) blends and polystyrene-b-poly(ethylene oxide) (SEO) diblock copolymers. These systems are of interest due to their potential to serve as electrolytes in all-solid rechargeable lithium batteries. Mean-field theories, developed for pure polymer blends and block copolymers, are used to describe phenomenon seen in salt-containing systems. An effective Flory–Huggins interaction parameter, χ eff , that increases linearly with salt concentration is used to describe the effect of salt addition for both blends and block copolymers. Segregation strength, χ eff N, where N is the chain length of the homopolymers or block copolymers, is used to map phase behavior of salty systems as a function of composition. Domain spacing of salt-containing block copolymers is normalized to account for the effect of copolymer composition using an expression obtained in the weak segregation limit. The phase behavior of salty blends, salty block copolymers, and domain spacings of the latter systems, are presented as a function of chain length, composition and salt concentration on universal plots. Finally, while the proposed framework has limitations, the universal plots should serve as a starting point for organizing data from other salt-containing polymer mixtures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Spatially Quasi-Periodic Water Waves of Infinite Depth

Abstract We formulate the two-dimensional gravity-capillary water wave equations in a spatially quasi-periodic setting and present a numerical study of solutions of the initial value problem. We propose a Fourier pseudo-spectral discretization of the equations of motion in which one-dimensional quasi-periodic functions are represented by two-dimensional periodic functions on a torus. We adopt a conformal mapping formulation and employ a quasi-periodic version of the Hilbert transform to determine the normal velocity of the free surface. Two methods of time-stepping the initial value problem are proposed, an explicit Runge–Kutta (ERK) method and an exponential time-differencing (ETD) scheme. The ETD approach makes use of the small-scale decomposition to eliminate stiffness due to surface tension. We perform a convergence study to compare the accuracy and efficiency of the methods on a traveling wave test problem. We also present an example of a periodic wave profile containing vertical tangent lines that is set in motion with a quasi-periodic velocity potential. As time evolves, each wave peak evolves differently, and only some of them overturn. Beyond water waves, we argue that spatial quasi-periodicity is a natural setting to study the dynamics of linear and nonlinear waves, offering a third option to the usual modeling assumption that solutions either evolve on a periodic domain or decay at infinity.

Wilkening, Jon (ORCID:0000000327827596)↗

Identification of phases, symmetries and defects through local crystallography

Here we report that advances in electron and probe microscopies allow 10 pm or higher precision in measurements of atomic positions. This level of fidelity is sufficient to correlate the length (and hence energy) of bonds, as well as bond angles to functional properties of materials. Traditionally, this relied on mapping locally measured parameters to macroscopic variables, for example, average unit cell. This description effectively ignores the information contained in the microscopic degrees of freedom available in a high-resolution image. Here we introduce an approach for local analysis of material structure based on statistical analysis of individual atomic neighbourhoods. Clustering and multivariate algorithms such as principal component analysis explore the connectivity of lattice and bond structure, as well as identify minute structural distortions, thus allowing for chemical description and identification of phases. This analysis lays the framework for building image genomes and structure–property libraries, based on conjoining structural and spectral realms through local atomic behaviour.

36 MATERIALS SCIENCE↗

Missing microbial eukaryotes and misleading meta-omic conclusions

Meta-omics is commonly used for large-scale analyses of microbial eukaryotes, including species or taxonomic group distribution mapping, gene catalog construction, and inference on the functional roles and activities of microbial eukaryotes in situ. Here, we explore the potential pitfalls of common approaches to taxonomic annotation of protistan meta-omic datasets. We re-analyze three environmental datasets at three levels of taxonomic hierarchy in order to illustrate the crucial importance of database completeness and curation in enabling accurate environmental interpretation. We show that taxonomic membership of sequence clusters estimates community composition more accurately than returning exact sequence labels, and overlap between clusters can address database shortcomings. Clustering approaches can be applied to diverse environments while continuing to exploit the wealth of annotation data collated in databases, and selecting and evaluating these databases is a critical part of correctly annotating protistan taxonomy in environmental datasets. We argue that ongoing curation of genetic resources is crucial in accurately annotating protists in in situ meta-omic datasets. Moreover, we propose that precise taxonomic annotation of meta-omic data is a clustering problem rather than a feasible alignment problem.

59 BASIC BIOLOGICAL SCIENCES↗

Visualization of structural evolution and phase distribution of a lithium vanadium oxide (Li 1.1 V 3 O 8 ) electrode via an operando and in situ energy dispersive X-ray diffraction technique

We present Li 1+n V 3 O 8 (n = 0–0.2) has been extensively investigated as a cathode material for Li ion batteries because of its superior electrochemical properties including high specific energy and good rate capability. In this paper, a synchrotron based energy dispersive X-ray diffraction (EDXRD) technique was employed to profile the phase transitions and the spatial phase distribution of a Li 1.1 V 3 O 8 electrode during electrochemical (de)lithiation in situ and operando. As annealing temperature during the preparation of the Li 1.1 V 3 O 8 material has a strong influence on the morphology and crystallinity, and consequently influences the electrochemical outcomes of the material, Li 1.1 V 3 O 8 materials prepared at two different temperatures, 500 and 300°C (LVO500 and LVO300), were employed in this study. The EDXRD spectra of LVO500 and LVO300 cells pre-discharged at C/18, C/40 and C/150 were recorded in situ, and phase localization and relative intensity of the peaks were compared. For cells discharged at the C/18 rate, although α and β phases were distributed uniformly within the LVO500 electrode, they were localized on two sides of the LVO300 electrode. Discharging rates of C/40 and C/150 led to homogeneous β phase formation in both LVO500 and LVO300 electrodes. Furthermore, the phase distribution as a function of position and (de)lithiation extent was mapped operando as the LVO500 cell was (de)lithiated. In conclusion, the operando data indicate that (1) the lithiation reaction initiated from the side of the electrode facing the Li anode and proceeded towards the side facing the steel can, (2) during discharge the phase transformation from a Li-poor to a Li-rich α phase and the formation of a β phase can proceed simultaneously in the electrode after the first formation of a β phase, and (3) the structural evolution occurring during charging is not the reverse of that during discharge and takes place homogenously throughout the electrode.

25 ENERGY STORAGE↗

A road map to cosmological parameter analysis with third-order shear statistics: III. Efficient estimation of third-order shear correlation functions and an application to the KiDS-1000 data

Context. Third-order lensing statistics contain a wealth of cosmological information that is not captured by second-order statistics. However, the computational effort it takes to estimate such statistics in forthcoming stage IV surveys is prohibitively expensive. Aims. We derive and validate an efficient estimation procedure for the three-point correlation function (3PCF) of polar fields such as weak lensing shear. We then use our approach to measure the shear 3PCF and the third-order aperture mass statistics on the KiDS-1000 survey. Methods We constructed an efficient estimator for third-order shear statistics that builds on the multipole decomposition of the 3PCF. We then validated our estimator on mock ellipticity catalogs obtained from N -body simulations. Finally, we applied our estimator to the KiDS-1000 data and presented a measurement of the third-order aperture statistics in a tomographic setup. Results. Our estimator provides a speedup of a factor of ∼100–1000 compared to the state-of-the-art estimation procedures. It is also able to provide accurate measurements for squeezed and folded triangle configurations without additional computational effort. We report a significant detection of tomographic third-order aperture mass statistics in the KiDS-1000 data (S/N = 6.69). Conclusions. Our estimator will make it computationally feasible to measure third-order shear statistics in forthcoming stage IV surveys. Furthermore, it can be used to construct empirical covariance matrices for such statistics.

Astronomy & Astrophysics↗

Ergodic theory and visualization. II. Fourier mesochronic plots visualize (quasi)periodic sets

We present an application and analysis of a visualization method for measure-preserving dynamical systems introduced by I. Mezić and A. Banaszuk [Physica D 197, 101 (2004)], based on frequency analysis and Koopman operator theory. This extends our earlier work on visualization of ergodic partition [Z. Levnajić and I. Mezić, Chaos 20, 033114 (2010)]. Our method employs the concept of Fourier time average [I. Mezić and A. Banaszuk, Physica D 197, 101 (2004)], and is realized as a computational algorithms for visualization of periodic and quasi-periodic sets in the phase space. The complement of periodic phase space partition contains chaotic zone, and we show how to identify it. The range of method's applicability is illustrated using well-known Chirikov standard map, while its potential in illuminating higher-dimensional dynamics is presented by studying the Froeschlé map and the Extended Standard Map.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Dewetting and spreading transitions for active matter on random pinning substrates

Here, we show that sterically interacting self-propelled disks in the presence of random pinning substrates exhibit transitions among a variety of different states. In particular, from a phase separated cluster state, the disks can spread out and homogeneously cover the substrate in what can be viewed as an example of an active matter wetting transition. We map the location of this transition as a function of activity, disk density, and substrate strength, and we also identify other phases including a cluster state, coexistence between a cluster and a labyrinth wetted phase, and a pinned liquid. Convenient measures of these phases include the cluster size, which dips at the wetting-dewetting transition, and the fraction of sixfold coordinated particles, which drops when dewetting occurs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗