Statistical Analysis of a 1:7 Scale Field Test Wave Energy Converter Using WEC-Sim.
Abstract not provided.
So, Ratanak↗
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Feature-Based Statistical Analysis of Combustion Simulation Data
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97 MATHEMATICS AND COMPUTING↗
CoDDA: A Flexible Copula-based Distribution Driven Analysis Framework for Large-Scale Multivariate Data
Not provided.
Computer Science↗
Climate variables explain neutral and adaptive variation within salmonid metapopulations: the importance of replication in landscape genetics
Abstract Understanding how environmental variation influences population genetic structure is important for conservation management because it can reveal how human stressors influence population connectivity, genetic diversity and persistence. We used riverscape genetics modelling to assess whether climatic and habitat variables were related to neutral and adaptive patterns of genetic differentiation (population‐specific and pairwise F ST ) within five metapopulations (79 populations, 4583 individuals) of steelhead trout ( Oncorhynchus mykiss ) in the Columbia River Basin, USA . Using 151 putatively neutral and 29 candidate adaptive SNP loci, we found that climate‐related variables (winter precipitation, summer maximum temperature, winter highest 5% flow events and summer mean flow) best explained neutral and adaptive patterns of genetic differentiation within metapopulations, suggesting that climatic variation likely influences both demography (neutral variation) and local adaptation (adaptive variation). However, we did not observe consistent relationships between climate variables and F ST across all metapopulations, underscoring the need for replication when extrapolating results from one scale to another (e.g. basin‐wide to the metapopulation scale). Sensitivity analysis (leave‐one‐population‐out) revealed consistent relationships between climate variables and F ST within three metapopulations; however, these patterns were not consistent in two metapopulations likely due to small sample sizes ( N = 10). These results provide correlative evidence that climatic variation has shaped the genetic structure of steelhead populations and highlight the need for replication and sensitivity analyses in land and riverscape genetics.
Hand, Brian K.↗
Complex interactions between day length and diurnal patterns of gene expression drive photoperiodic responses in a perennial C 4 grass
Abstract Photoperiod is a key environmental cue affecting flowering and biomass traits in plants. Key components of the photoperiodic flowering pathway have been identified in many species, but surprisingly few studies have globally examined the diurnal rhythm of gene expression with changes in day length. Using a cost‐effective 3′‐Tag RNA sequencing strategy, we characterize 9,010 photoperiod responsive genes with strict statistical testing across a diurnal time series in the C 4 perennial grass, Panicum hallii . We show that the vast majority of photoperiod responses are driven by complex interactions between day length and sampling periods. A fine‐scale contrast analysis at each sampling time revealed a detailed picture of the temporal reprogramming of cis ‐regulatory elements and biological processes under short‐ and long‐day conditions. Phase shift analysis reveals quantitative variation among genes with photoperiod‐dependent diurnal patterns. In addition, we identify three photoperiod enriched transcription factor families with key genes involved in photoperiod flowering regulatory networks. Finally, coexpression networks analysis of GIGANTEA homolog predicted 1,668 potential coincidence partners, including five well‐known GI‐interacting proteins. Our results not only provide a resource for understanding the mechanisms of photoperiod regulation in perennial grasses but also lay a foundation to increase biomass yield in biofuel crops.
Weng, Xiaoyu↗
Consideration of Nonideal Detonation Regimes Influenced by Wave Modes in a Water-Cooled Rotating Detonation Engine Using OH* Chemiluminescence
Although inherently unstable, existing research in rotating detonation combustion supports its application in notionally steady processes resulting in greater availability compared to conventional, constant pressure combustion. Further improvements rely on a more in-depth understanding of system losses and identifying conditions which optimize device performance. Within this study, the presence and proportion of ideal and nonideal combustion regimes are compared across a variety of process conditions and wave modes. Here, large-scale data analysis seeks to summarize proportional heat release associated with commensal, parasitic, and detonative combustion averaged across individual traces of OH* chemiluminescent data acquired at the detonation plane. Means of regime partitioning based on the anatomy of the time-resolved OH* signal are proposed to ensure consistent analysis throughout the current and future studies concerning combustion regimes. Of particular interest is the possible influence of wave on the nonideal combustion in relative proportion to the desired detonation. Results showed improved percent detonation with increasing significance for the following trends: decreasing equivalence ratio, increasing wave count, decreasing wave velocity, and increasing detonation time. Increased wave number, brought on by decreased equivalence ratios and wave velocities, is thought to decrease fill region surface area, and therefore, decrease nonideal contact burning. Additional analysis is performed to consider possible trend variation due to the presence of stable galloping waves, which were found to have minimal influence on relative percent detonation values. The outcome of this study suggests operational states, which correspond to increased wave quantities for increased proportions of reactants consumed by the targeted detonative combustion regime.
42 ENGINEERING↗
EXPERIMENTAL AND MODELLING ANALYSIS OF A LARGE-SCALE TWO-PHASE LOOP THERMOSYPHON
Liquid pumping requires large quantities of electrical energy, including about 7% of the energy of building heating, ventilation, and air conditioning (HVAC) systems. To replace pumped condenser-cooling tower water loops with a passive alternative system, we implemented a commercial-scale two-phase loop thermosyphon (TPLT). The unit consists of a 13 m riser integrated with a commercially available cooling tower and circulation water heater that simulates heat loads up to 25 kW. In addition to providing passive cooling capabilities, the cooling tower unit is also maintenance free, reliable, and can operate in both dry and wet modes. This study characterizes the performance (temperature difference between the evaporator and condenser) and the two-phase flow behavior of the loop under various refrigerant charges. Sight glasses installed throughout the loop are used to identify the operating flow regimes in the riser and downcomer. Over the range of operating conditions, we identified that there is an optimal refrigerant charge range for a specific heat load at which near-isothermal operation can be achieved. We further developed a model to predict the operating flow rate and gravitational height in the downcomer and compared it with the experimental data. The results show that the model agrees with the experimental data, in particular the threshold gravitational head height at which there will be subcooled liquid at the condenser exit, indicating that it can be used as a predictive tool for identifying the optimal loop charge for a given heat load.
Loop thermosyphon, passive two phase↗
Pulsed radio frequency power modulation for profile control in cryogenic reactive ion etching of silicon gratings
Cryogenic silicon etching with SF 6 /O 2 plasmas enables vertical sidewalls and smooth surfaces for high–aspect-ratio structures, yet precise control of etched profiles (sidewall angle, lateral etching, and linewidth retention) remains challenging under continuous-wave excitation due to coupling among radical fluxes, ion energy distributions, and in situ passivation dynamics. In this work, we investigated pulsed radio frequency bias delivery as a process knob for profile control during cryogenic silicon etching. Systematic experiments on 500 nm-wide, 1 μm-pitch gratings etched to 0.8–1.1 μm depth at 0.5–2 kHz pulsing frequency and 25%–75% duty cycle revealed strong dependencies of etch rate, linewidth, and sidewall angle on modulation conditions. We proposed a conceptual kinetic picture combined with feature-scale electrostatic analysis to understand the alternation of ion-driven etching and passivation recovery between on/off segments and local electric field shaping and modulation of ion trajectories within the trench. Moderate duty cycles (50%–75%) near 1 kHz achieved a balance between anisotropy and etch rate. These results demonstrate pulsed-bias modulation can be utilized to tune directionality and sidewall preservation in cryogenic SF 6 /O 2 etching, which are relevant to photonic, metrology, and quantum device fabrication.
36 MATERIALS SCIENCE↗
Multi-sensor anomalous change detection in remote sensing imagery
Combining multiple satellite remote sensing sources provides a far richer, more frequent view of the earth than that of any single source; the challenge is in distilling these petabytes of heterogeneous sensor imagery into meaningful characterizations of the imaged areas. Meeting this challenge requires effective algorithms for combining multi-modal imagery over time to identify subtle but real changes among the intrinsic data variation. Here, we implement a joint-distribution framework for multi-sensor anomalous change detection (MSACD) that can effectively account for these differences in modality, and does not require any signal resampling of the pixel measurements. This flexibility enables the use of satellite imagery from different sensor platforms and modalities. We use multi-year construction of the SoFi Stadium in California as our testbed, and exploit synthetic aperture radar imagery from Sentinel-1 and multispectral imagery from both Sentinel-2 and Landsat 8. We show results for MSACD using real imagery with implanted, measurable changes, as well as real imagery with real, observable changes, including scaling our analysis over multiple years.
47 OTHER INSTRUMENTATION↗
Experimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota Fungus
Recent genomic analyses have revealed that anaerobic gut fungi possess both the largest number and highest diversity of lignocellulolytic enzymes of all sequenced fungi, explaining their ability to decompose lignocellulosic substrates, e.g., agricultural waste, into fermentable sugars. Despite their potential, the development of engineering methods for these organisms has been slow due to their complex life cycle, understudied metabolism, and challenging anaerobic culture requirements.
59 BASIC BIOLOGICAL SCIENCES↗
Nonlinear equation for Farley–Buneman waves in multispecies plasma
The nonlinear equation describing the Farley–Buneman (FB) waves in multispecies collisional plasmas is derived by employing the multiple-scale reduction analysis. It is shown that the presence of several ion species with different collisionalities and different ion masses removes the degeneracy of the nonlinear equation and generates the nonlinear terms resulting in wave steepening and wave breaking. This effect may be responsible for formation of one-dimensional coherent FB waves of a finite amplitude.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Evaluation of Methods to Integrate Analysis into a Large-Scale Shock Physics Code.
Abstract not provided.
Oldfield, Ron A.↗
Characterization of Fatty Acids in Crenarchaeota by GC-MS and NMR
Lipids composed of condensed isoprenyl units connected to glycerol backbones by ether linkages are a distinguishing feature of Archaea. Data suggesting that fatty acids with linear hydrocarbon chains are present in some Archaea have been available for decades. However, lack of genomic and biochemical evidence for the metabolic machinery required to synthesize and degrade fatty acids has left the field unclear on this potentially significant biochemical aspect. Because lipids are energy currency and cell signaling molecules, their presence in Archaea is significant for understanding archaeal biology. A recent large-scale bioinformatics analysis reignited the debate as to the importance of fatty acids in Archaea by presenting genetic evidence for the presence of enzymes required for anabolic and catabolic fatty acid metabolism across the archaeal domain. Here, we present direct biochemical evidence from gas chromatography-mass spectrometry (GC-MS) and nuclear magnetic resonance (NMR) spectroscopy for the presence of fatty acids in two members of the Crenarchaeota, Sulfolobus solfataricus and Ignicoccus hospitalis . This is the first report providing biochemical data for the existence of fatty acids in these Crenarchaeota, opening new discussions on energy balance and the potential for the discovery of new thermostable enzymes for industry.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
ECoG Cluster Flow v1.0
ECoG ClusterFlow is a novel multi-scale visual analysis system for the detailed exploration of dynamic functional connectivity graphs obtained through electrocorticography.
MURUGESAN, SUGEERTH↗
Performance of Convection-Permitting and Convection-Parameterized Models in Reproducing the Extreme Precipitation Intensity Relationship with Surface Conditions
Here, this study investigates the warm-season extreme precipitation–temperature scaling relationship in CONUS404, a convection-permitting (4 km) Weather Research and Forecasting (WRF) Model simulation over the conterminous United States for the past four decades, and compares it with the WRF-Thermodynamic Global Warming (WRF-TGW) historical simulation at a coarser resolution (12 km) using parameterized convection. We also analyze the NCEP stage IV and NASA Integrated Multi-satellitE Retrievals for the Global Precipitation Measurement (IMERG) datasets as observational benchmarks. We examine how extreme precipitation intensity (EPI) varies with temperature and saturation deficit over representative regions based on hourly data. The stage IV and IMERG data show a similar pattern of EPI variation with temperature and saturation deficit, except that the EPI peak is lower in IMERG than in stage IV. Under dry and hot conditions, EPI decreases too rapidly with elevated saturation deficit in both CONUS404 and WRF-TGW compared to observations, but the performance of CONUS404 is superior to WRF-TGW. When the near-surface atmosphere is saturated or close to saturated, both CONUS404 and WRF-TGW produce higher peak values of EPI relative to the observational references; IMERG exhibits scaling rates close to the Clausius–Clapeyron (C–C) relationship, while CONUS404, WRF-TGW, and stage IV all demonstrate super-C–C scaling behaviors. Despite marked warming over the past four decades, in both CONUS404 and WRF-TGW, the scaling relationship between EPI and temperature in a saturated atmosphere remains stable and robust. This indicates a strong potential for the EPI–temperature scaling rate under saturation to be used as an emergent constraint in reducing uncertainties of future extreme precipitation projection.
Atmosphere↗
Reconstruction and analysis of the genome-scale metabolic model of schizochytrium limacinum SR21 for docosahexaenoic acid production
Schizochytrium limacinum SR21 is a potential industrial strain for docosahexaenoic acid (DHA) production that contains more than 30–40 % DHA among its total fatty acids. To resolve the DHA biosynthesis mechanism and improve DHA production at a systematic level, a genomescale metabolic model (GSMM), named iCY1170_DHA, which contains 1769 reactions, 1659 metabolites, and 1170 genes, was reconstructed. Results: Based on genome annotation results and literature reports, a new DHA synthesis pathway based on a polyketide synthase (PKS) system was detected in S. limacinum. Similarly to conventional fatty acid synthesis, the biosynthesis of DHA via PKS requires abundant acetyl-CoA and NADPH. The in silico addition of malate and citrate led to increases of 24.5 % and 37.1 % in DHA production, respectively. Moreover, based on the results predicted by the model, six amino acids were shown to improve DHA production by experiment. Finally, 30 genes were identified as potential targets for DHA over-production using a Minimization of Metabolic Adjustment algorithm. The reconstructed GSMM, iCY1170_DHA, could be used to elucidate the mechanism by which DHA is synthesized in S. limacinum and predict the requirements of abundant acetyl-CoA and NADPH for DHA production as well as the enhanced yields achieved via supplementation with six amino acids, malate, and citrate.
59 BASIC BIOLOGICAL SCIENCES↗
Microbial life in 25-m-deep boreholes in ancient permafrost illuminated by metagenomics
This study describes the composition and potential metabolic adaptation of microbial communities in northeastern Siberia, a repository of the oldest permafrost in the Northern Hemisphere. Samples of contrasting depth (1.75 to 25.1 m below surface), age (from ~ 10 kyr to 1.1 Myr) and salinity (from low 0.1–0.2 ppt and brackish 0.3–1.3 ppt to saline 6.1 ppt) were collected from freshwater permafrost (FP) of borehole AL1_15 on the Alazeya River, and coastal brackish permafrost (BP) overlying marine permafrost (MP) of borehole CH1_17 on the East Siberian Sea coast. To avoid the limited view provided with culturing work, we used 16S rRNA gene sequencing to show that the biodiversity decreased dramatically with permafrost age. Nonmetric multidimensional scaling (NMDS) analysis placed the samples into three groups: FP and BP together (10–100 kyr old), MP (105–120 kyr old), and FP (> 900 kyr old). Younger FP/BP deposits were distinguished by the presence of Acidobacteriota, Bacteroidota, Chloroflexota_A, and Gemmatimonadota, older FP deposits had a higher proportion of Gammaproteobacteria, and older MP deposits had much more uncultured groups within Asgardarchaeota, Crenarchaeota, Chloroflexota, Patescibacteria, and unassigned archaea. The 60 recovered metagenome-assembled genomes and un-binned metagenomic assemblies suggested that despite the large taxonomic differences between samples, they all had a wide range of taxa capable of fermentation coupled to nitrate utilization, with the exception of sulfur reduction present only in old MP deposits.
54 ENVIRONMENTAL SCIENCES↗
Exposing hidden alternative backbone conformations in X-ray crystallography using qFit
Proteins must move between different conformations of their native ensemble to perform their functions. Crystal structures obtained from high-resolution X-ray diffraction data reflect this heterogeneity as a spatial and temporal conformational average. Although movement between natively populated alternative conformations can be critical for characterizing molecular mechanisms, it is challenging to identify these conformations within electron density maps. Alternative side chain conformations are generally well separated into distinct rotameric conformations, but alternative backbone conformations can overlap at several atomic positions. Our model building program qFit uses mixed integer quadratic programming (MIQP) to evaluate an extremely large number of combinations of sidechain conformers and backbone fragments to locally explain the electron density. Here, we describe two major modeling enhancements to qFit: peptide flips and alternative glycine conformations. We find that peptide flips fall into four stereotypical clusters and are enriched in glycine residues at the n+1 position. The potential for insights uncovered by new peptide flips and glycine conformations is exemplified by HIV protease, where different inhibitors are associated with peptide flips in the “flap” regions adjacent to the inhibitor binding site. Our results paint a picture of peptide flips as conformational switches, often enabled by glycine flexibility, that result in dramatic local rearrangements. Our results furthermore demonstrate the power of large-scale computational analysis to provide new insights into conformational heterogeneity. Furthermore, improved modeling of backbone heterogeneity with high-resolution X-ray data will connect dynamics to the structure-function relationship and help drive new design strategies for inhibitors of biomedically important systems.
59 BASIC BIOLOGICAL SCIENCES↗