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At least 127 records · Page 7

Homologous recombination shapes the architecture and evolution of bacterial genomes

Homologous recombination is a key evolutionary force that varies considerably across bacterial species. However, how the landscape of homologous recombination varies across genes and within individual genomes has only been studied in a few species. Here, we used Approximate Bayesian Computation to estimate the recombination rate along the genomes of 145 bacterial species. Our results show that homologous recombination varies greatly along bacterial genomes and shapes many aspects of genome architecture and evolution. The genomic landscape of recombination presents several key signatures: rates are highest near the origin of replication in most species, patterns of recombination generally appear symmetrical in both replichores (i.e. replicational halves of circular chromosomes) and most species have genomic hotspots of recombination. Furthermore, many closely related species share conserved landscapes of recombination across orthologs indicating that recombination landscapes are conserved over significant evolutionary distances. We show evidence that recombination drives the evolution of GC-content through increasing the effectiveness of selection and not through biased gene conversion, thereby contributing to an ongoing debate. Finally, we demonstrate that the rate of recombination varies across gene function and that many hotspots of recombination are associated with adaptive and mobile regions often encoding genes involved in pathogenicity.

Torrance, Ellis L [University of North Carolina, G↗

Mixing bispectrum multipoles under geometric distortions

We derive general expressions for how the Alcock–Paczynski distortions affect the power spectrum and the bispectrum of cosmological fields. We compute explicit formulas for the mixing coefficients of bispectrum multipoles in the linear approximation. The leading-order effect for the bispectrum is the uniform dilation of all three wavevectors. The mixing coefficients depend on the shape of the bispectrum triplet. Our results for the bispectrum multipoles are framed in terms of the ‘natural’ basis of the lengths of three wavevectors but can be easily generalized for other bases and reduction schemes. Our validation tests confirm that the linear approximation is extremely accurate for all power spectrum multipoles. The linear approximation is accurate for the bispectrum monopole but results in sub-per cent level inaccuracies for the bispectrum quadrupole and fails for the bispectrum hexadecapole. Our results can be used to simplify the analysis of the bispectrum from galaxy surveys, especially the measurement of the baryon acoustic oscillation peak position. They can be used to replace numeric schemes with exact analytical formulae.

79 ASTRONOMY AND ASTROPHYSICS↗

Comparing Measured Driver Behavior Distributions to Results from Car-Following Models using SUMO and Real-World Vehicle Trajectories from Radar: SUMO Default vs. Radar-Measured CF model Parameters

In this study, the physical principles governing car-following (CF) behavior and their impact on traffic flow at signalized intersections are investigated. High temporal-resolution radar data is used to provide valuable insights into actual CF behavior, including acceleration, deceleration, and time headway distribution. Demand-calibrated SUMO simulations are run using empirical CF parameter distributions, and three CF models are evaluated: IDM, EIDM, and Krauss. By emulating radar data in SUMO and processing simulated vehicle traces, discrepancies between empirical and simulated parameter distributions are identified. Further analysis includes comparisons with default SUMO CF model parameters. The findings reveal that measured accelerations differ from CF model parameter accelerations and using the empirical value ($\mu = 0.89m/s^2$) leads to unrealistic simulations that fail volume-based calibration. Default parameters for all three models reasonably approximate the mean and median of measured parameters, but fail to capture the true distribution shape, partly due to homogeneity when using default parameters. The results show that it is more effective to simulate with the default parameters provided by SUMO rather than using measurements of real-world distributions without additional calibration. Future work will investigate closing the loop between the measured real-world and SUMO distributions using traditional calibration tactics, as well as assess the impact of calibrated vs. default CF parameters on simulation outputs like fuel consumption.

Schrader, Max (ORCID:0000000336737672)↗

Stable Element Doping of Sol-gel Toward Simulating Environmental Matrix in Surrogate Explosive Nuclear Debris

Training nuclear forensic analysis personnel in post-detonation scenarios is of critical importance to nuclear threat response capabilities. Thus, realistic nuclear debris simulants which resemble the size, color, elemental composition, and radionuclide content of actual nuclear fallout from a recent detonation would be valuable for training nuclear first responders in realistic scenarios. As nuclear fallout types vary significantly in each of these parameters based on detonation environment (rural, urban, maritime etc.) and collection location, the ability to tailor each of these parameters accurately in simulated debris would be of immense benefit to the post-detonation analysis community for training both in-field collections and triage and the validation of laboratory level nuclear forensic techniques. Sol-gel synthesis techniques can provide the tunability of size, shape and composition required for producing surrogate nuclear debris of a wide variety. The sol-gel process consists of forming a metal oxide material, often silica, through polymerization of a metal-alkoxy precursor. In this work, we characterize the ability to load the sol-gel particles with secondary elemental components such as iron, aluminum, and calcium toward approximating the elemental composition of debris from various detonation environments and demonstrate the ability to produce particles with controllable size, shape, and color. We also demonstrate quantitative radionuclide encapsulation toward reproducing the radionuclide content of actual fallout from a recent detonation. Finally, we then employ these techniques in producing simulated aerodynamic debris samples with realistic elemental matrix composition and radionuclide content simulating a recent uranium-fueled detonation taking place in a rural desert environment and compare it to historic fallout from the Nevada Nuclear Security Site.

36 MATERIALS SCIENCE↗

Stable Element Doping of Sol-gel Toward Simulating Environmental Matrix in Surrogate Explosive Nuclear Debris

Training nuclear forensic analysis personnel in post-detonation scenarios is of critical importance to nuclear threat response capabilities. Thus, realistic nuclear debris simulants which resemble the size, color, elemental composition, and radionuclide content of actual nuclear fallout from a recent detonation would be valuable for training nuclear first responders in realistic scenarios. As nuclear fallout types vary significantly in each of these parameters based on detonation environment (rural, urban, maritime etc.) and collection location, the ability to tailor each of these parameters accurately in simulated debris would be of immense benefit to the post-detonation analysis community for training both in-field collections and triage and the validation of laboratory level nuclear forensic techniques. Sol-gel synthesis techniques can provide the tunability of size, shape and composition required for producing surrogate nuclear debris of a wide variety. The sol-gel process consists of forming a metal oxide material, often silica, through polymerization of a metal-alkoxy precursor. In this work, we characterize the ability to load the sol-gel particles with secondary elemental components such as iron, aluminum, and calcium toward approximating the elemental composition of debris from various detonation environments and demonstrate the ability to produce particles with controllable size, shape, and color. We also demonstrate quantitative radionuclide encapsulation toward reproducing the radionuclide content of actual fallout from a recent detonation. Finally, we then employ these techniques in producing simulated aerodynamic debris samples with realistic elemental matrix composition and radionuclide content simulating a recent uranium-fueled detonation taking place in a rural desert environment and compare it to historic fallout from the Nevada Nuclear Security Site.

36 MATERIALS SCIENCE↗

Nonideal mixing effects in warm dense matter studied with first-principles computer simulations

Here, we study nonideal mixing effects in the regime of warm dense matter (WDM) by computing the shock Hugoniot curves of BN, MgO, and MgSiO 3 . First, we derive these curves from the equations of state (EOS) of the fully interacting systems, which were obtained using a combination of path integral Monte Carlo calculations at high temperature and density functional molecular dynamics simulations at lower temperatures. We then use the ideal mixing approximation at constant pressure and temperature to rederive these Hugoniot curves from the EOS tables of the individual elements. We find that the linear mixing approximation works remarkably well at temperatures above ~2 × 10 5 K, where the shock compression ratio exceeds ~3.2. The shape of the Hugoniot curve of each compound is well reproduced. Regions of increased shock compression, which emerge because of the ionization of L and K shell electrons, are well represented, and the maximum compression ratio of the Hugoniot curves is reproduced with high precision. Some deviations are seen near the onset of the L shell ionization regime, where ionization equilibrium in the fully interacting system cannot be well reproduced by the ideal mixing approximation. This approximation also breaks down at lower temperatures, where chemical bonds play an increasingly important role. However, the results imply that the equilibrium properties of binary and ternary mixtures in the regime of WDM can be derived from the EOS tables of the individual elements. This significantly simplifies the characterization of binary and ternary mixtures in the WDM and plasma phases, which otherwise requires large numbers of more computationally expensive first-principles computer simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Multiscale Shear Properties and Flow Performance of Milled Woody Biomass

One dominant challenge facing the development of biorefineries is achieving consistent system throughput with highly variant biomass feedstock quality and handling performance. Current handling unit operations are adapted from other sectors (primarily agriculture), where some simplifying assumptions about granular mechanics and flow performance do not translate well to a highly compressible and anisotropic material with nonlinear time- and stress-dependent properties. This work explores the shear and frictional properties of loblolly pine at multiple experimental test apparatus and particle scales to elucidate a property window that defines the shear behavior over a range of material attributes (particle size, size distribution, moisture content, etc.). In general, it was observed that the bulk internal friction and apparent cohesion depend strongly on both the stress state of the sample in granular shear testers and the overall particle size and distribution span. For equipment designed to characterize the quasi-static shear stress failure of bulk materials ranging from 50 to 1,000 ml in test volume, similar test results were observed for finely milled particles (50% passing size of 1.4 mm) with a narrow size distribution (span between 10 and 90% passing size of 0.9 mm), while stress chaining and over-torque issues persisted for the bench-scale test apparatus for larger particle sizes or widely dispersed sample sizes. Measurement of the anisotropic particle–particle friction ranged from coefficients of approximately 0.20 to 0.45 and resulted in significantly higher and more variable friction measurements for larger particle sizes and in perpendicular alignment orientations. To supplement these laboratory-scale properties, this work explores the flow of loblolly pine and Douglas fir through a pilot-scale wedge-shaped hopper and a screw feeder. For the gravity-driven hopper flow, the critical arching distance and mass discharge rate ranged from approximately 10 to 30 mm and 2 to 16 tons/hour, respectively, for both materials, where the arching distance depends strongly on the overall particle size and depends less on the hopper inclination angle. Comparatively, the auger feeder was found to be much more impacted by the size of the particles, where smaller particles had a more consistent and stable flow while consuming less power.

09 BIOMASS FUELS↗

Localised electromagnetic waves in a rhombic waveguide array with competing nonlinearities

We consider a model of a discrete photonic system representing a quasi-one-dimensional rhombic array of waveguides, where, in addition to the positive cubic nonlinearity, the negative quintic nonlinearity is taken into account for the material of which the central chain of the waveguides is made. The other two waveguide chains are made of an optically linear material. A continual approximation is used to obtain a solution for a system of coupled waves, which describes a wave localised in the transverse direction. In a certain special case, the competition of nonlinearities leads to the formation of a step-shaped distribution of the field intensities over the waveguides. (integrated optics)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

A level set approach for the computational study of a yield stress fluid filling a thin mold

Many important engineering and scientific applications such as cement slurries, foams, crude oil, and granular avalanches involve the concept of yield stress. Therefore, modeling yield stress fluids in different flow configurations, including the accurate prediction of the yield surface, is important. In this paper, we present a computational model based on the finite element method to study the flow of yield stress fluids in a thin mold and compare the results with data from flow visualization experiments. Here, we use the level set method to describe the interface between the filling fluid and air. We use polypropylene glycol as a model Newtonian fluid and Carbopol for the model yield stress fluid, as the Carbopol solution demonstrates yielding without thixotropy. To describe the yielding and shear-thinning behavior, we use a generalized Newtonian constitutive equation with a Bingham–Carreau–Yasuda form. We compare the results obtained from the mold filling experiments with the results from the three-dimensional (3D) model and from a reduced-order Hele-Shaw (HS) model that is two-dimensional, including the effect of shear-thinning along the thin direction only approximately. We show that both the 3D and the HS model can capture the experimental meniscus shape reasonably well for all the fluids considered at three different flow rates. This indicates that the shape evolution is insensitive to the dimensionality of the model. However, the viscosity and yield surfaces predicted by the 3D and HS models are different. The HS model underestimates the high viscosity and unyielded regions compared to the estimation by the 3D model.

42 ENGINEERING↗

Data-driven modeling and control of an X-ray bimorph adaptive mirror

Adaptive X-ray mirrors are being adopted on high-coherent-flux synchrotron and X-ray free-electron laser beamlines where dynamic phase control and aberration compensation are necessary to preserve wavefront quality from source to sample, yet challenging to achieve. Additional difficulties arise from the inability to continuously probe the wavefront in this context, which demands methods of control that require little to no feedback. In this work, a data-driven approach to the control of adaptive X-ray optics with piezo-bimorph actuators is demonstrated. This approach approximates the non-linear system dynamics with a discrete-time model using random mirror shapes and interferometric measurements as training data. For mirrors of this type, prior states and voltage inputs affect the shape-change trajectory, and therefore must be included in the model. Without the need for assumed physical models of the mirror's behavior, the generality of the neural network structure accommodates drift, creep and hysteresis, and enables a control algorithm that achieves shape control and stability below 2 nm RMS. Using a prototype mirror and ex situ metrology, it is shown that the accuracy of our trained model enables open-loop shape control across a diverse set of states and that the control algorithm achieves shape error magnitudes that fall within diffraction-limited performance.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Advanced sorbents for modular oxygen production for REMS gasifiers

Under a DOE funded effort, Thermosolv LLC has been developing a sorbent-based oxygen production technology for gasification and oxy-combustion applications. The sorbents utilize oxygen-storage properties of certain perovskites to (1) selectively adsorb oxygen at moderate temperature from compressed air and (2) release the adsorbed oxygen into a vacuum or a sweep gas such as CO2 and/or steam. Through cyclic operations of multiple sorbent beds such a process can be made continuous. Pressure drop across the sorbent bed and other similar design considerations dictate that the sorbent be in the form of a high surface-area-to-volume pellet and yet still possess sufficient crush strength and integrity. Process efficiency is determined by the sorption and desorption kinetics and sorbent capacity. Typical process involves cycle times in the order of 100 seconds, a time too short to fully utilize the full volume of the sorbent and the sorption capacity of the sorbent pellets. As a part of this project, Thermosolv LLC undertook the development of oxygen sorbents as a high-surface area supported sorbent on a light-weight inert support to (1) reduce the cost, (2) increase the productivity, and (3) reduce the overall weight of the reactor. Using a previously developed perovskite (LSCF 1991) with its well-characterized performance, composite sorbent pellets each consisting of an inert core coated by a thin layer of the functional perovskite material were produced. Several low-density, inexpensive inert solids supports in the 1/8”-1/4” size were selected to keep the pressure drop across the sorbent bed in the acceptable range. A number of commercial technologies including spray coating, dip coating, incipient impregnation of porous substrate followed by thermal annealing at various temperatures and duration were employed and tested to produce robust composite supported sorbent pellets. A sense of optimum coating thickness was developed by testing sorbent pellets of various increasing diameter pellets. LSCF-1991extrudates ranging in size from 1/32” to 3/16” were tested in a TGA and in a fixed-bed pressure swing test set-up for sorption/desorption cycles of interest. The data show that for the operational conditions of interest the coating thickness for a supported sorbent pellet needs to be approximately 1/32” (about 0.8 mm). Subsequent work thereby concentrated on developing composite pellets of various substrates, shapes and sizes with coating layer of about this size range. Candidate support materials were chosen based on cost, inertness, mechanical strength, thermal expansion and chemical stability with sorbent material, and in a size range to give an acceptable pressure drop in fixed-bad reactor configurations. Coating application methods used for application of the sorbent onto the support included precipitation, spray coating and dip coating from sorbent slurries and sol gels. For all coated supports where we could successfully apply a uniform coating of desired thickness with an acceptable handling performance in terms of exfoliation, TGA-based cyclic sorption/desorption testing was performed to determine cycling capacity of oxygen. Among nearly twenty different support materials tested, best adhesion performance was obtained from stainless saddle supports. In the bench-scale fixed-bad tests stainless steel saddle support composite pellets with a coating thickness in the 0.6 mm or so range, the composite sorbent pellet performance approached up to 95% of that of the 2 mm parent material pellets. In a parallel approach to reducing the cost of the sorbent, alternate sorbent formulations replacing/reducing the amount of cobalt in the LSCF family were also investigated. Successful formulations that could match the performance of LSCF 1991 were identified based on TGA cyclic tests as LSCF 1919 and LSF 1910. In the range of operational envelop of cycle times and other relevant process operating conditions, the reduced Co formulations showed comparable performance in the bench-scale fixed-bad cyclic operations. As a part of this project, we also attempted substitution of La and Sr with Ca and Ba, and Co with Mn, Ni and Cu with little success, but the overall project goal of reducing sorbent cost in terms of raw material and manufacturing expenses was successful.

01 COAL, LIGNITE, AND PEAT↗

Simulating the optical properties of soot using a stochastic soot model

KL extinction measurements are common in literature concerning soot producing sprays because of their nonintrusiveness. Unfortunately, these measurements often rely on bold assumptions of uniform and monodisperse spherical particles. In this work, a Spray A case is simulated using a highly detailed 3D stochastic soot model and the measured and simulated soot volume fraction are compared. Although the simulated volume fraction magnitude is approximately correct, features are much sharper than in the measured data. Optical models based on particle shape are applied to the simulated soot particles to nd the local optical thickness. The modeled optical thickness aligns with the measured volume fraction much more closely than the simulated volume fraction indicating KL extinction measurements are not simply related to soot volume fraction.

Strickland, Tyler↗

A deformation-dependent coupled Lagrangian/semi-Lagrangian meshfree hydromechanical formulation for landslide modeling

Abstract The numerical modelling of natural disasters such as landslides presents several challenges for conventional mesh-based methods such as the finite element method (FEM) due to the presence of numerically challenging phenomena such as severe material deformation and fragmentation. In contrast, meshfree methods such as the reproducing kernel particle method (RKPM) possess unique features conducive to modelling extreme events such as the absence of a structured mesh and the ease of adaptive refinement, among others. While the semi-Lagrangian reproducing kernel (SL-RK) shape functions of RKPM defined in the current configuration have proven to be effective in extreme event modelling, the computational cost for the re-evaluation of the shape functions at every time step is costly. In this work, a deformation-dependent coupling of the Lagrangian reproducing kernel (L-RK) and SL-RK approximations is proposed for the solution of a hydro-mechanical formulation for effective simulations of landslides. The ramp function is constructed based on an equivalent plastic strain as a deformation-dependent transition from L-RK shape functions to SL-RK ones as the deformation progresses. The particular focus of the paper will be on modelling seepage-induced landslides with a mixed $$u$$ u – $$p$$ p formulation to couple the solid and fluid phases. Examples are presented to examine the effectiveness of this coupled Lagrangian/semi-Lagrangian reproducing kernel (L–SL RK) formulation and to highlight its performance in landslide modelling.

Baek, Jonghyuk↗

Impact of penetrating collisions of plasma ions on spectral line shapes

Spectral-line-broadening models have been moving towards including full Coulomb interactions between the atom and plasma, replacing the commonly used dipole approximation. The effects of the full Coulomb interaction have been thoroughly explored for plasma electrons, resulting in redshifts of spectral lines in high-energy-density plasmas. We explore the impact of a full Coulomb treatment on ion broadening. Penetrating collisions due to ions do not significantly impact the linewidths. The most significant aspect is the appearance of quasimolecular resonances in the far line wings, such as those previously observed in white-dwarf spectra. We identify several problems with the existing models. The most direct implementation causes the quasimolecular features to appear at the wrong photon energies. It is possible to include the detailed molecular structure, but this currently requires the Anderson-Talman approximation, which ignores the N-body properties of the plasma. We find that N-body effects can substantially broaden these quasimolecular features and even shift them, depending on the plasma conditions. We conclude that penetration of ions into the spatial extent of the radiator wave function does not strongly affect the usual diagnostics and may have a moderate to weak effect on opacity. Furthermore, the Rosseland mean opacity is weighted towards low-opacity regions of a spectrum, where these quasimolecular features are found.

79 ASTRONOMY AND ASTROPHYSICS↗

Precision pulse shape simulation for proton detection at the Nab experiment

The Nab experiment at Oak Ridge National Laboratory, USA, aims to measure the beta-antineutrino angular correlation following neutron β decay to an anticipated precision of approximately 0.1%. The proton momentum is reconstructed through proton time-of-flight measurements, and potential systematic biases in the timing reconstruction due to detector effects must be controlled at the nanosecond level. In conclusion, we present a thorough and detailed semiconductor and quasiparticle transport simulation effort to provide precise pulse shapes, and report on relevant systematic effects and potential measurement schemes.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Reshaped Weyl fermionic dispersions driven by Coulomb interactions in MoTe 2

In this work, we report the direct evidence of impacts of the Coulomb interaction in a prototypical Weyl semimetal, MoTe 2 , that alter its bare bands in a wide range of energy and momentum. Our quasiparticle interference patterns measured using scanning tunneling microscopy are shown to match the joint density of states of quasiparticle energy bands including momentum-dependent self-energy corrections, while electronic energy bands based on the other simpler local approximations of the Coulomb interaction fail to explain neither the correct number of quasiparticle pockets nor the shape of their dispersions observed in our spectrum. With this, we predict a transition between type-I and type-II Weyl fermions with doping and resolve its disparate quantum oscillation experiments, thus highlighting the critical roles of Coulomb interactions in layered Weyl semimetals.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Electron-Nanobunch-Width-Dominated Spectral Power Law for Relativistic Harmonic Generation from Ultrathin Foils

Relativistic high-order harmonic generation from solid-density plasma offers a compact source of coherent ultraviolet and x-ray light. For solid targets much thinner than the laser wavelength, the plasma thickness can be tuned to increase conversion efficiency; a reduction in total charge allows for balancing the laser and plasma driving forces, producing the most effective interaction. Unlike for semi-infinite plasma surfaces, in this study we find that for ultrathin foil targets the dominant factor in the emission spectral shape is the finite width of the electron nanobunches, leading to a power-law exponent of approximately 10/3. Ultrathin foils produce higher-efficiency frequency conversion than solid targets for moderately relativistic (1 0 <40) interactions and also provide unique insight into how the trajectories of individual electrons combine and interfere to generate reflected attosecond pulses.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Space to Air High-Altitude Region Adjoint Neutron Transport

Neutrons from an atmospheric nuclear explosion can be detected by sensors in orbit. Current tools for characterizing the neutron energy spectrum assume a known source and use forward transport to recreate the detector response. In realistic scenarios the true source is unknown, making this an inefficient, iterative approach. In contrast, the adjoint approach directly solves for the source spectrum, enabling source reconstruction. The time–energy fluence at the satellite and adjoint transport equation allow a Monte Carlo method to characterize the neutron source’s energy spectrum directly in a new model: the Space to High-Altitude Region Adjoint (SAHARA) model. A new adjoint source event estimator was developed in SAHARA to find feasible solutions to the neutron transport problem given the constraints of the adjoint environment. This work explores SAHARA’s development and performance for mono-energetic and continuous neutron energy sources. In general, the identified spectra were shifted towards energies approximately 5% lower than the true source spectra, but SAHARA was able to capture the correct spectral shapes. Continuous energy sources, including real-world sources Fat Man and Little Boy, resulted in identifiable spectra that could have been produced by the same distribution as the true sources as demonstrated by two-dimensional (2D) Kolmogorov–Smirnov tests.

LaMere, Zachary W.↗