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At least 253 records · Page 14

Evolution_and_engineering_of_pathways_for_aromatic_O-demethylation_in_Pseudomonas_putida_KT2440

Biological conversion of lignin from biomass offers a promising strategy for sustainable production of fuels and chemicals. However,aromatic compoundsderived from lignin commonly contain methoxy groups, andO-demethylation of these substrates is often a rate-limiting reaction that influences catabolic efficiency. Severalenzymefamilies catalyze aromaticO-demethylation, but they are rarely comparedin vivoto determine an optimal biocatalytic strategy. Here, two pathways for aromaticO-demethylation were compared inPseudomonas putidaKT2440. The native Rieske non-heme ironmonooxygenase(VanAB) and, separately, a heterologous tetrahydrofolate-dependentdemethylase(LigM) were constitutively expressed inP. putida, and the strains were optimized via adaptive laboratory evolution (ALE) withvanillateas a model substrate. All evolved strains displayed improved growth phenotypes, with the evolved strains harboring the native VanAB pathway exhibiting growth rates ∼1.8x faster than those harboring the heterologous LigM pathway.Enzyme kineticsandtranscriptomicsstudies investigated the contribution of selected mutations toward enhanced utilization of vanillate. The VanAB-overexpressing strains contained the most impactful mutations, including those in VanB, thereductasefor vanillateO-demethylase, PP_3494, a global regulator of vanillate catabolism, andfghA, involved in formaldehydedetoxification. These three mutations were combined into a single strain, which exhibited approximately 5x faster vanillate consumption than the wild-type strain in the first 8 h of cultivation. Overall, this study illuminates the details of vanillate catabolism in the context of two distinct enzymatic mechanisms,yielding a platform strain for efficientO-demethylation of lignin-related aromatic compounds to value-added products. This DOI contains supplementary material associated with the published manuscript.

CBI↗

StructuredFuzzer: Fuzzing Structured Text-Based Control Logic Applications

Rigorous testing methods are essential for ensuring the security and reliability of industrial controller software. Fuzzing, a technique that automatically discovers software bugs, has also proven effective in finding software vulnerabilities. Unsurprisingly, fuzzing has been applied to a wide range of platforms, including programmable logic controllers (PLCs). However, current approaches, such as coverage-guided evolutionary fuzzing implemented in the popular fuzzer American Fuzzy Lop Plus Plus (AFL++), are often inadequate for finding logical errors and bugs in PLC control logic applications. They primarily target generic programming languages like C/C++, Java, and Python, and do not consider the unique characteristics and behaviors of PLCs, which are often programmed using specialized programming languages like Structured Text (ST). Furthermore, these fuzzers are ill suited to deal with complex input structures encapsulated in ST, as they are not specifically designed to generate appropriate input sequences. This renders the application of traditional fuzzing techniques less efficient on these platforms. To address this issue, this paper presents a fuzzing framework designed explicitly for PLC software to discover logic bugs in applications written in ST specified by the IEC 61131-3 standard. The proposed framework incorporates a custom-tailored PLC runtime and a fuzzer designed for the purpose. We demonstrate its effectiveness by fuzzing a collection of ST programs that were crafted for evaluation purposes. We compare the performance against a popular fuzzer, namely, AFL++. The proposed fuzzing framework demonstrated its capabilities in our experiments, successfully detecting logic bugs in the tested PLC control logic applications written in ST. On average, it was at least 83 times faster than AFL++, and in certain cases, for example, it was more than 23,000 times faster.

47 OTHER INSTRUMENTATION↗

Inter-Oligomer Interaction Influence on Photoluminescence in Cis-Polyacetylene Semiconductor Materials

Semiconducting conjugated polymers (CPs) are pivotal in advancing organic electronics, offering tunable properties for solar cells and field-effect transistors. Here, we carry out first-principle calculations to study individual cis-polyacetylene (cis-PA) oligomers and their ensembles. The ground electronic structures are obtained using density functional theory (DFT), and excited state dynamics are explored by computing nonadiabatic couplings (NACs) between electronic and nuclear degrees of freedom. We compute the nonradiative relaxation of charge carriers and photoluminescence (PL) using the Redfield theory. Our findings show that electrons relax faster than holes. The ensemble of oligomers shows faster relaxation compared to the single oligomer. The calculated PL spectra show features from both interband and intraband transitions. The ensemble shows broader line widths, redshift of transition energies, and lower intensities compared to the single oligomer. This comparative study suggests that the dispersion forces and orbital hybridizations between chains are the leading contributors to the variation in PL. It provides insights into the fundamental behaviors of CPs and the molecular-level understanding for the design of more efficient optoelectronic devices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Runaway Eccentricity Growth: A Pathway for Binary Black Hole Mergers in AGN Disks

Binary black holes (BBHs) embedded within the accretion disks that fuel active galactic nuclei (AGN) are promising progenitors for the source of gravitational wave (GW) events detected by LIGO/VIRGO. Several recent studies have shown that when these binaries form, they are likely to be highly eccentric and retrograde. However, many uncertainties remain concerning the orbital evolution of these binaries as they either inspiral toward merger or disassociate. Previous hydrodynamical simulations exploring their orbital evolution have been predominantly two-dimensional or have been restricted to binaries on nearly circular orbits. We present the first high-resolution, three-dimensional local shearing-box simulations of both prograde and retrograde eccentric BBHs embedded in AGN disks. We find that retrograde binaries shrink several times faster than their prograde counterparts and exhibit significant orbital eccentricity growth, the rate of which monotonically increases with binary eccentricity. Our results suggest that retrograde binaries may experience runaway orbital eccentricity growth, which may bring them close enough together at pericenter for GW emission to drive them to coalescence. Although their eccentricity is damped, prograde binaries shrink much faster than their orbital eccentricity decays, suggesting they should remain modestly eccentric as they contract toward merger. Finally, binary precession driven by the AGN disk may dominate over precession induced by the supermassive black hole depending on the binary accretion rate and its location in the AGN disk, which can subdue the evection resonance and von Ziepel–Lidov–Kozai cycles.

79 ASTRONOMY AND ASTROPHYSICS↗

Mapping the Outcomes of Stellar Evolution in the Disks of Active Galactic Nuclei

The disks of active galactic nuclei (AGNs) are expected to be populated by numerous stars, either formed in the outer regions of the disk via gravitational instability or captured from the nearby nuclear star cluster. Regardless of their formation mechanism, these stars experience altered evolutionary paths, mostly shaped by the accretion of dense disk material. In this study, through the comparison of different timescales, we chart the evolutionary outcomes of these AGN stars as a function of disk radius and across a range of supermassive black hole masses, spanning from 10 6 to 10 9 M ⊙ , for two popular AGN disk models. We find that in the outer regions of the disk, stars evolve similarly to those in the interstellar medium, but in the inner and denser regions, accretion quickly turns low-mass stars into massive stars, and their fate depends on just how quickly they accrete. If accretion occurs at a faster rate than nuclear burning, they can reach a quasi-steady "immortal" state. If stars accrete faster than they can thermally adjust, runaway accretion occurs, potentially preventing a quasi-steady state and altering the disk structure. During the AGN lifetime, in the regions of the disk that produce massive stars, supernovae (SNe) and gamma-ray bursts (GRBs) may occur within the disk over a wide range of optical depths and ambient densities. Subsequently, in the final phase of the AGN, as the disk becomes depleted, formerly immortal stars will be unable to replenish their fuel, leading to additional SNe and GRBs.

79 ASTRONOMY AND ASTROPHYSICS↗

On the Properties of Cosmological Ionization Fronts

We investigate the properties of cosmological ionization fronts during the epoch of reionization using the Cosmic Reionization on Computers simulations. By analyzing reionization timing maps, we characterize ionization front velocities and curvatures and their dependence on the density structure of the intergalactic medium (IGM). The velocity distribution of ionization fronts in the simulations indicates that while the barrier-crossing analytical model captures the overall shape in high-velocity regions, it fails to reproduce the low-velocity tail, highlighting the non-Gaussian nature of the IGM’s density field. Ionization front velocities are inversely correlated with local density, propagating faster in underdense regions and more slowly in overdense environments. Faster ionization fronts also lead to higher postionization temperatures, reaching a plateau at ∼2 × 10$^{4}$ K for velocities exceeding 3000 km s$^{−1}$. Examining curvature statistics further establishes a connection between ionization front structure and the normalized density contrast ν, with trends in overdense regions aligning well with barrier-crossing model predictions, while deviations appear in underdense environments due to model limitations. These results provide a detailed characterization of ionization front dynamics and their interaction with the underlying density field, bridging small-scale reionization physics with large-scale observables such as the 21 cm signal and the IGM’s thermal history.

79 ASTRONOMY AND ASTROPHYSICS↗

Performance Analysis of an Optimization Algorithm for Metamaterial Design on the Integrated High-Performance Computing and Quantum Systems

Optimizing metamaterials with complex geometries is a big challenge. Although an active learning algorithm, combining machine learning (ML), quantum computing, and optical simulation, has emerged as an efficient optimization tool, it still faces difficulties in optimizing complex structures that have potentially high performance. In this work, we comprehensively analyze the performance of an optimization algorithm for metamaterial design on the integrated HPC and quantum systems. We demonstrate significant time advantages through message-passing interface (MPI) parallelization on the high-performance computing (HPC) system showing approximately 54% faster ML tasks and 67 times faster optical simulation against serial workloads. Furthermore, we analyze the performance of a quantum algorithm designed for optimization, which runs with various quantum simulators on a local computer or HPC-quantum system. Results showcase ~24 times speedup when executing the optimization algorithm on the HPC-quantum hybrid system. This study paves a way to optimize complex metamaterials using the integrated HPC-quantum system.

Kim, Seongmin↗

Comparison of Ion and Neutron Irradiations to 3 dpa at 500C in Ferritic-Martensitic Alloys

The growing global demand for energy will increasingly call upon advanced nuclear fission reactors to supply safe and reliable electricity. The structural and fuel cladding components of these reactors will be subject to extreme conditions of irradiation damage up to several hundred displacements per atom (dpa) at temperatures as high as 700°C. Ferritic-martensitic (F-M) steels are leading candidates for these challenging conditions due to their strength and dimensional stability under irradiation. In order to accelerate the process for evaluating F-M alloys, charged particles are increasingly being used to emulate neutron irradiations. Charged particle irradiations allow the possibility of conducting irradiation experiments within a shorter time period (i.e. at a rate up to 4 orders of magnitude faster) and with minimal radioactivation of the material, enabling lower cost and faster turnaround of post irradiation examination and analysis. However, the irradiation dose rate, damage cascade morphologies, and irradiation damage depth profiles all differ widely between protons, heavier ions, and neutrons. Currently, there is limited understanding of the significance of these physical differences and how they manifest in the irradiated microstructure and mechanical properties of F-M steels. The objective of this study is to evaluate charged particles as a surrogate for neutron irradiations in F-M alloys by assessing common irradiation conditions using Fe++ ions, protons, and neutrons. Keeping the temperature and dose consistent enables isolation of the effects of each irradiating particle and their respective dose rates and cascade morphologies.

Swenson, M.J.↗

The effect of injection angle on the interaction between sonic secondary jets and a supersonic free stream

An experimental investigation, as part of a research program on the development of technology for the design of supersonic combustion ramjets, has been conducted to determine the effect of injection angle on the jet penetration, mixing rate, and airstream total-pressure recovery downstream of five laterally spaced sonic hydrogen jets flush mounted on a flat plate. Results of this investigation indicated that at lower injection angles less free-stream momentum loss was required to turn and accelerate the injected gas downstream and, thereby, less flow disturbance and total-pressure loss were produced. In addition, lower injection angles resulted in improved fuel distribution and faster mixing of the injected gas with the free stream. A correlating parameter, developed from considerations of the effective-momentum-flux differences between the injected gas and the free-stream air, predicted greater penetration and faster mixing for the lower injection angles.

Mcclinton, C. R.↗

Analysis of ATS photographs using a specially designed electronic console

Measurements of cloud motion, cloud size, and growth rate were made on four days in the vicinity of rawin stations in the BOMEX network. These measurements were compared with the rawins and levels of best fit ranging from 980 to 250 mb were found. No correlation was found between cloud size and level of best fit. The magnitude of the vector difference between the cloud motion and wind at the level of best fit was as high as 15 knots for clouds with levels of best fit below the 500-mb level and 8 knots for clouds with levels of best fit above the 500-mb level. When cloud motion vectors with levels of best fit at or above the 500-mb level were compared with winds at the 300-mb level, the vector difference increased to as much as 16 knots or double the greatest minimum vector difference. A comparison between cloud motions and winds at the level of best fit showed that the clouds tended to move slightly faster than the observed winds and to move slightly to the left of the wind direction. Rate of growth appeared to influence whether clouds moved faster or slower than the wind. No relationship between cloud size and amount of deviation from the wind direction was observed.

Blackmer, R. H., Jr.↗

Chilldown study of the single stage inducer test rig

Of the six chilldown tests, data from only one could be used for evaluation. During the rest of the chilldown tests, there was leakage hydrogen flow into the pump cavity prior to the initiation of the chilldown test. In all of the tests the hydrogen condition into the pump was probably 100% vapor. The data from this one test, therefore, can be used to compare only the single phase fluid correlation in the analytical pump chilldown model. In general, the actual pump chilled down much faster than predicted by the analytical pump model. There were insufficient data from the test to measure the pump flow rate and pump inlet fluid condition; therefore, these parameters were extrapolated based on related data which were available. However, even with the highest probable flow rate, the pump chilled faster than predicted.

Kimura, L. A.↗

The use of the modified Cholesky decomposition in divergence and classification calculations

The use of the Cholesky decomposition technique is analyzed as applied to the feature selection and classification algorithms used in the analysis of remote sensing data (e.g. as in LARSYS). This technique is approximately 30% faster in classification and a factor of 2-3 faster in divergence, as compared with LARSYS. Also numerical stability and accuracy are slightly improved. Other methods necessary to deal with numerical stablity problems are briefly discussed.

Vanroony, D. L.↗

The use of the modified Cholesky decomposition in divergence and classification calculations

This report analyzes the use of the modified Cholesky decomposition technique as applied to the feature selection and classification algorithms used in the analysis of remote sensing data (e.g., as in LARSYS). This technique is approximately 30% faster in classification and a factor of 2-3 faster in divergence, as compared with LARSYS. Also numerical stability and accuracy are slightly improved. Other methods necessary to deal with numerical stability problems are briefly discussed.

Van Rooy, D. L.↗

The dynamic response of visual accommodation over a seven-day period

Four college students, ranging in age from 18 to 21 years, were tested on their dynamic, monocular accommodation responses to a square wave stimulus and sine waves of two frequencies. The tests were conducted over a period of seven days in a controlled environment, each subject being tested once every three hours. Latency, magnitude, velocity, gain and phase lag of the responses were measured, and means and standard deviations were computed. The latency of response was stable throughout and agreed fairly well with previous studies. The response magnitude was relatively stable. Three of the subjects had higher velocities on receding targets; one was faster on approaching targets. The group mean velocity increased over the seven days of the study. In keeping with the trend to faster dynamics over the seven days, both gain and phase lag improved.

Randle, R. J.↗

Analysis of multiloop, multirate sampled-data systems

Based upon new identities between z-transforms at a basis rate, z-transforms at faster rates, and modified z-transforms, the equivalence between the frequency decomposition method and the switch decomposition method is precisely presented so that results of one method are easily obtained from results of the other. Next, a method is developed for determining the closed loop transfer function of multiloop, multirate sampled-data systems with noninteger ratio sampling rates. Previously, this process involved solving a complex system of equations with rational polynomial coefficients. Herein, this is avoided by introducing a systematic decomposition of matrix operators which naturally arise from the switch decomposition method. The matrix operators are simplified by introducing the shifted transforms of signals sampled at one of the faster rates.

Boykin, W. H.↗

Rotational excitation of molecular ions in interstellar clouds

Rate constants for rotational excitation of N2H(+) by low-energy collisions with He have been obtained from accurate quantum-mechanical calculations. Rates for excitation of HCO(+) and rates for excitation by collisions with H2 are expected to be qualitatively similar. The excitation rate for molecular ions is found to be only slightly faster than that for similar neutral species, and not much faster as had been previously suggested. The implications of this for interpreting microwave observations of interstellar N2H(+) and HCO(+) are discussed.

Green, S.↗

The relative merits of several numerical techniques for solving the compressible Navier-Stokes equations

Four explicit finite difference techniques designed to solve the time-dependent, compressible Navier Stokes equations are compared. These techniques are: (1) MacCormack, (2) modified Du Fort-Frankel, (3) modified hopscotch, and (4) Brailovskaya. The comparison was made numerically by solving the quasi-one dimensional Navier Stokes equations for the flow in a converging-diverging nozzle. Solutions with and without standing normal shock waves were computed for unit Reynolds numbers (based on total conditions) ranging from 45374 to 2269. The results indicate that all four techniques are comparable in accuracy; however, the modified hopscotch scheme is two to three times faster than the Brailovskaya and MacCormack schemes and three to six times faster than the modified Du Fort-Frankel scheme.

Holst, T. L.↗

An improved algorithm for the isolation of polynomial real zeros

THe Collins-Loos algorithm for computing isolating intervals for the zeros of an integer polynomial requires the evaluation of polynomials at rational points. This implies the use of arbitrary precision integer arithmetic. It is shown how careful use of single precision, floating point arithmetic within the context of a slightly modified algorithm can make the calculation considerably faster and no less exact. Typically, 95% or more of the evaluations can be done without exact arithmetic. The precise speedup depends on the relative costs of the arithmetic in a given implementation. The implementation on DEC KL-10 computer is some 5 to 10 times faster than the original Univac 1110 implementation in SAC-I.

Fateman, R. J.↗