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At least 1,099 records · Page 61

Paths and patterns: the biology and physics of swimming bacterial populations

The velocity distribution of swimming micro-organisms depends on directional cues supplied by the environment. Directional swimming within a bounded space results in the accumulation of organisms near one or more surfaces. Gravity, gradients of chemical concentration and illumination affect the motile behaviour of individual swimmers. Concentrated populations of organisms scatter and absorb light or consume molecules, such as oxygen. When supply is one-sided, consumption creates gradients; the presence of the population alters the intensity and the symmetry of the environmental cues. Patterns of cues interact dynamically with patterns of the consumer population. In suspensions, spatial variations in the concentration of organisms are equivalent to variations of mean mass density of the fluid. When organisms accumulate in one region whilst moving away from another region, the force of gravity causes convection that translocates both organisms and dissolved substances. The geometry of the resulting concentration-convection patterns has features that are remarkably reproducible. Of interest for biology are (1) the long-range organisation achieved by organisms that do not communicate, and (2) that the entire system, consisting of fluid, cells, directional supply of consumables, boundaries and gravity, generates a dynamic that improves the organisms' habitat by enhancing transport and mixing. Velocity distributions of the bacterium Bacillus subtilis have been measured within the milieu of the spatially and temporally varying oxygen concentration which they themselves create. These distributions of swimming speed and direction are the fundamental ingredients required for a quantitative mathematical treatment of the patterns. The quantitative measurement of swimming behaviour also contributes to our understanding of aerotaxis of individual cells.

Non-NASA Center↗

CICE on a C-grid: new momentum, stress, and transport schemes for CICEv6.5

Abstract. This article presents the C-grid implementation of the CICE sea ice model, including the C-grid discretization of the momentum equation, the boundary conditions (BCs), and the modifications to the code required to use the incremental remapping transport scheme. To validate the new C-grid implementation, many numerical experiments were conducted and compared to the B-grid solutions. In idealized experiments, the standard advection method (incremental remapping with C-grid velocities interpolated to the cell corners) leads to a checkerboard pattern. A modal analysis demonstrates that this computational noise originates from the spatial averaging of C-grid velocities at corners. The checkerboard pattern can be eliminated by adjusting the departure regions to match the divergence obtained from the solution of the momentum equation. We refer to this novel approach as the edge flux adjustment (EFA) method. The C-grid discretization with edge flux adjustment allows for transport in channels that are one grid cell wide – a capability that is not possible with the B-grid discretization nor with the C-grid and standard remapping advection. Simulation results match the predicted values of a novel analytical solution for one-grid-cell-wide channels.

Lemieux, Jean-François (ORCID:0000000320845759)↗

Magnetic Helicity Condensation and the Solar Cycle

Solar filaments exhibit a global chirality pattern where dextral/sinistral filaments, corresponding to negative/ positive magnetic helicity, are dominant in the northern/southern hemisphere. This pattern is opposite to the sign of magnetic helicity injected by differential rotation along east–west oriented polarity inversion lines, posing a major conundrum for solar physics. A resolution of this problem is offered by the magnetic helicity-condensation model of Antiochos. To investigate the global consequences of helicity condensation for the hemispheric chirality pattern, we apply a temporally and spatially averaged statistical approximation of helicity condensation. Realistic magnetic field configurations in both the rising and declining phases of the solar cycle are simulated. For the helicity-condensation process, we assume convective cells consisting of positive/negative vorticities in the northern/southern hemisphere that inject negative/positive helicity. The magnitude of the vorticity is varied as a free parameter, corresponding to different rates of helicity injection. To reproduce the observed percentages of dominant and minority filament chiralities, we find that a vorticity of magnitude 2.5 x 10(exp −6)/s is required. This rate, however, is insufficient to produce the observed unimodal profile of chirality with latitude. To achieve this, a vorticity of at least 5 x 10(exp −6)/s is needed. Our results place a lower limit on the small-scale helicity injection required to dominate differential rotation and reproduce the observed hemispheric pattern. Future studies should aim to establish whether the helicity injection rate due to convective flows and/or flux emergence across all latitudes of the Sun is consistent with our results.

Mackay, Duncan H.↗

Ground Ice at the Phoenix Landing Site: A Preflight Assessment

One of the objectives of the Mars Scout mission, Phoenix, is to characterize the present state of water in the martian environment, in a location where water may play a significant role in the present and past habitability of Mars. Given the generally dry and cold climate of Mars today any substantial amount of water is expected to occur in the form of ground ice (subsurface ice) within the regolith. The Mars Odyssey Gamma Ray Spectrometer has indicated abundant subsurface hydrogen and inferred ground ice at high latitudes. Therefore, the Phoenix mission will be targeted to land in the northern high latitudes (approximately 65 degrees N - 75 degrees N) where ground ice is expected to be abundantly available for analysis. The lander will be capable of excavating, sampling, and analyzing, dry and water-rich/icy soils. The location and depth of excavation necessary to achieve the goals of sampling and analysis of icy material become important parameters to assess. In the present work we ask two key questions: 1) At what depth within the regolith do we expect to find ice? 2) How might this depth vary over the region of potential landing sites? Numerous lines of evidence can be employed to provide an indication of the presence or absence of shallow ground ice at the potential landing sites. For example geomorphology, neutrons, gamma rays, and theory each contribute clues to an overall understanding of the distribution of ice. Orbital observations provide information on a variety of spatial scales, typically 10 s of meters (patterned ground) to 100 s of kilometers (gamma rays). While information on all of these scales are important, of particular interest is how the presence and depth of ground ice might vary on spatial scales comparable to the lander and its work area. While ground ice may be stable (and present) on a regional scale, local-scale slopes and changes in the physical characteristics of soils can result in significant variations in the distribution of ice.

Mellon, M. T.↗

Color camera computed tomography imaging spectrometer for improved spatial-spectral image accuracy

Computed tomography imaging spectrometers ("CTIS"s) having color focal plane array detectors are provided. The color FPA detector may comprise a digital color camera including a digital image sensor, such as a Foveon X3.RTM. digital image sensor or a Bayer color filter mosaic. In another embodiment, the CTIS includes a pattern imposed either directly on the object scene being imaged or at the field stop aperture. The use of a color FPA detector and the pattern improves the accuracy of the captured spatial and spectral information.

Wilson, Daniel W.↗

Spatial and Spatial Frequency Spreads of Masking: Measurements and A Contrast-Gain-Control Model

Masked pattern detection is affected by the mask's proximity to the target in both the spatial and the spatial frequency domains. We measured contrast thresholds for detection of a Gabor patch centered in a sample of static band-pass noise with a central noise-free aperture. To examine spatial spread, target and mask frequency were identical, at either 2, 4, or 8 cycles/degree (cpd), and the radius of the aperture was 0, 1/2 or 1 cycle of the noise band's center frequency. The results suggest that the spatial spread of masking is scale invariant, with the largest radius producing little masking. To examine spatial frequency spread, a radius of 0 (no aperture) was used with all pairings of 2, 4, and 8 cpd for target and mask. The results suggest that masking is asymmetrical over log frequency: 8 z 0 cpd noise masks a 2 cpd target, but 2 cpd noise does not mask an 8 cpd target. We have used these results to calibrate a model of contrast-gain-control.

Solomon, Joshua A.↗

Spatial and Spatial Frequency Spreads Of Masking: Measurements and a Contrast-Gain-Control Model

Masked pattern detection is affected by the mask's proximity to the target in both the spatial and the spatial frequency domains. We measured contrast thresholds for detection of a Gabor patch centered in a sample of static band-pass noise with a central noise-free aperture. To examine spatial spread, target and mask frequency were identical, at either 2, 4, or 8 cycles/degree (cpd), and the radius of the aperture was 0, 1/2 or 1 cycle of the noise band's center frequency. The results suggest that the spatial spread of masking is scale invariant, with the largest radius producing little masking. To examine spatial frequency spread, a radius of 0 (no aperture) was used with all pairings of 2,4, and 8 cpd for target and mask. The results suggest that masking is asymmetrical over log frequency: 8 cpd noise masks a 2 cpd target, but 2 cpd noise does not mask an 8 cpd target. We have used these results to calibrate a model of contrast-gain-control.

Solomon, J. A.↗

Transforming our understanding of chloroplast-associated genes through comprehensive characterization of protein localizations and protein-protein interactions

Bioenergy crops are a renewable source of fuels and are a critical base for building a carbon-neutral economy. Rational engineering of bioenergy crops has the potential to enhance the yields. However, our ability to engineer plants is limited because the functions of most genes remain unknown. Systematic characterization of gene function in plants thus has the potential to greatly accelerate bioenergy research. Here, we focus on the chloroplast, an underexplored energy-producing organelle that is a hallmark of plants. The chloroplast is one of the promising targets of biofuel crop engineering efforts because of its central role in photosynthesis, metabolism, and intracellular signaling. However, the protein composition of the chloroplast and the functions of most of its proteins remain poorly characterized. At the core of this project, we sought to comprehensively determine the localization of chloroplast-associated proteins and generate a spatially defined protein-protein interaction network for chloroplast. For this purpose, we used the leading model alga Chlamydomonas reinhardtii, which greatly increased experimental speed and throughput. We illustrated the value of our findings to land plants by determining the localization of Arabidopsis thaliana land plant homologs of the Chlamydomonas proteins. Altogether, we were successful in determining the localization of 1,034 chloroplast-associated proteins in Chlamydomonas. The localizations provide numerous insights into the spatial organization of chloroplasts and how they function to support photosynthesis. The localization patterns of distinct proteins revealed new chloroplast structures and revealed new spatial organization inside the chloroplast. We also identified new components of known chloroplast structures, such as the chloroplast envelope, nucleoid, plastoglobuli, and pyrenoid. We identified these new components by investigating the interacting partners of known proteins. Many proteins localized in both the chloroplast and other cellular structures, thereby hinting at new functions and communication between cellular structures. We also applied machine learning on the atlas to generate predictions for the location of all of the proteins in Chlamydomonas. This enabled us to assign putative functions to many uncharacterized proteins based on their cellular location. Altogether, this research establishes a rich resource that opens new avenues of investigation and guides future work in deciphering and manipulating chloroplast function. Next, we developed an extensive protein-protein interaction network for the chloroplast by performing affinity purification-mass spectrometry on ~1,150 tagged chloroplast-associated proteins, the first such large-scale study in any photosynthetic organism. This dataset reveals 4,694 high-confidence protein-protein interactions, offering insights into the functions of thousands of conserved poorly-characterized chloroplast proteins. This systematic identification of protein-protein interactions in the chloroplast also provides multiple exciting new research directions and a detailed blueprint of the chloroplast's operation. This research lays the groundwork to decipher the inner workings of the chloroplast, the cell structure at the heart of photosynthesis. The spatial atlas and protein-protein interactions reveal chloroplast organizational features that would not have been accessible with traditional approaches. The localization mapping, insights into the function, and research materials generated further provide a rich resource for the research community to advance the understanding of how the chloroplast is organized to enable engineering of enhanced photosynthetic organisms.

59 BASIC BIOLOGICAL SCIENCES↗

Optical data processing analysis of stream patterns exhibited on ERTS-1 imagery

The purpose of the investigation described in this paper has been the analysis of large-scale geologic ground patterns in Kansas using ERTS-1 imagery and optical data processing techniques. Optical spatial frequency data provide a repeatable quantitative means of specifying ground pattern characteristics.

Egbert, D.↗

Interference dislocations adjacent to emission spot

We studied interference dislocations (forks) adjacent to an emission spot in an interference pattern. We observed the adjacent interference dislocations in emission of excitons in a monolayer transition metal dichalcogenide and in emission of spatially indirect excitons, also known as interlayer excitons, in a van der Waals heterostructure. Our simulations show that the adjacent interference dislocations appear due to the moiré effect in combined interference patterns produced by constituent parts of the emission spot. In contrast to interference dislocations in coherent states, such as interference dislocations due to quantized vortices in condensates, the appearance of adjacent interference dislocations does not require coherence between the parts of the emission spot, indicating that interference dislocations can be observed in a classical system. Finally, we show that the interference dislocations in classical systems can appear in interference images for various spatially modulated emission patterns.

Leonard, J. R. [Univ. of California, San Diego, CA↗

Greater committed warming after accounting for the pattern effect

Our planet’s energy balance is sensitive to spatial inhomogeneities in sea surface temperature and sea ice changes, but this is typically ignored in climate projections. Here, we show the energy budget during recent decades can be closed by combining changes in effective radiative forcing, linear radiative damping and this pattern effect. The pattern effect is of comparable magnitude but opposite sign to Earth’s net energy imbalance in the 2000s, indicating its importance when predicting the future climate on the basis of observations. Additionally, after the pattern effect is accounted for, the best-estimate value of committed global warming at present-day forcing rises from 1.31 K (0.99–2.33 K, 5th–95th percentile) to over 2 K, and committed warming in 2100 with constant long-lived forcing increases from 1.32 K (0.94–2.03 K) to over 1.5 K, although the magnitude is sensitive to sea surface temperature dataset. Further constraints on the pattern effect are needed to reduce climate projection uncertainty.

58 GEOSCIENCES↗

Designing artificial two-dimensional landscapes via atomic-layer substitution

Significance Manipulating materials with atomic-scale precision is essential for the development of a next-generation material design toolbox. Tremendous efforts have been made to advance the compositional, structural, and spatial accuracy of material deposition and patterning. Here, we presented a new reaction pathway to implement the conversions of two-dimensional materials within the atomic-layer thickness at room temperature for electrical dipole manipulation. Not only could various Janus monolayer transition metal dichalcogenides with vertical dipole be realized, but also some heterostructures, including the dipole-nondipole heterostructures (MoS 2 -MoSSe) and multiheterostructures (MoS 2 -MoSSe-MoSeS-MoSe 2 ) within the same monolayer host structure are developed, in which the dipoles can be selectively patterned to be zero (MoS 2 , MoSe 2 ), positive (MoSSe), and negative (MoSeS).

Guo, Yunfan↗

Comparing multi-source urban flood indicators: satellite, simulation, and citizen-reported data

Urban flooding arises from complex mechanisms, making it challenging to capture accurately with a single detection method. This study evaluates three complementary approaches to detect flooding across three Chicago neighborhoods: (i) Sentinel-1 synthetic aperture radar (SAR), offering weather-independent, high-resolution (10 m) imagery of surface inundation; (ii) the storm water management model (SWMM), simulating combined sewer overflow and drainage performance; and (iii) citizen-generated 311 service requests, capturing observed flooding impacts. By analyzing six storms ranging from severe to mild, we examine how each source uniquely contributes to identifying urban flood events. SAR imagery effectively identifies standing water but can miss brief flooding due to satellite revisit constraints. SWMM provides detailed insights into system-wide drainage behavior yet may underestimate localized street-level flooding. Meanwhile, 311 calls reflect real-world flooding impacts but are vulnerable to underreporting. Statistical overlap analysis highlights chronic flood hotspots repeatedly identified across multiple detection methods, indicating persistent infrastructure and topographic vulnerabilities. Temporal analysis further reveals that while SWMM flooding aligns closely with rainfall peaks, 311 calls typically precede or persist beyond these peaks. Our findings emphasize the value of using satellite observations, hydrological modeling, and resident-reported data in a complementary manner to better interpret patterns in flood timing, severity, and spatial distribution—providing insights that can inform targeted infrastructure improvements and contribute to urban flood resilience planning.

311↗

An Analysis of Postharvest Fungal Pathogens Reveals Temporal–Spatial and Host–Pathogen Associations with Fungicide Resistance-Related Mutations

Fungicides are the primary tools to control a wide range of postharvest fungal pathogens. Fungicide resistance is a widespread problem that has reduced the efficacy of fungicides. Resistance to FRAC-1 (Fungicide Resistance Action Committee-1) chemistries is associated with mutations in amino acid position 198 in the β-tubulin gene. In our study, we conducted a meta-analysis of β-tubulin sequences to infer temporal, spatial, plant host, and pathogen genus patterns of fungicide resistance in postharvest fungal pathogens. In total, data were acquired from 2,647 specimens from 12 genera of fungal phytopathogens residing in 53 countries on >200 hosts collected between 1926 and 2020. The specimens containing a position 198 mutation were globally distributed in a variety of pathosystems. Analyses showed that there are associations among the mutation and the year an isolate was collected, the pathogen genus, the pathogen host, and the collection region. Interestingly, fungicide-resistant β-tubulin genotypes have been in a decline since their peak between 2005 and 2009. FRAC-1 fungicide usage data followed a similar pattern in that applications have been in a decline since their peak between 1997 and 2003. The data show that, with the reduction of selection pressure, FRAC-1 fungicide resistance in fungal populations will decline within 5 to 10 years. Based on this line of evidence, we contend that a β-tubulin position 198 mutation has uncharacterized fitness cost(s) on fungi in nature. The compiled dataset can inform end users on the regions and hosts that are most prone to contain resistant pathogens and assist decisions concerning fungicide resistance management strategies.

Plant Sciences↗

Stroboscopic x-ray diffraction microscopy of dynamic strain in diamond thin-film bulk acoustic resonators for quantum control of nitrogen-vacancy centers

Bulk-mode acoustic waves in a crystalline material exert lattice strain through the thickness of the sample, which couples to the spin Hamiltonian of defect-based qubits such as the nitrogen-vacancy (N-V) center defect in diamond. This mechanism has previously been harnessed for unconventional quantum spin control, spin decoherence protection, and quantum sensing. Bulk-mode acoustic wave devices are also important in the microelectronics industry as microwave filters. A key challenge in both applications is a lack of appropriate operando microscopy tools for quantifying and visualizing gigahertz-frequency dynamic strain. Here, in this work, we directly image acoustic strain within N-V center-coupled diamond thin-film bulk acoustic wave resonators using stroboscopic scanning hard x-ray diffraction microscopy at the Advanced Photon Source. The far-field scattering patterns of the nanofocused x-ray diffraction encode strain information entirely through the illuminated thickness of the resonator. These patterns have a real-space spatial variation that is consistent with the bulk strain’s expected modal distribution and a momentum-space angular variation from which the strain amplitude can be quantitatively deduced. We also perform optical measurements of strain-driven Rabi precession of of the N-V center spin ensemble, providing an additional quantitative measurement of the strain amplitude. As a result, we directly measure one of the six N-V spin-stress coupling parameters, 𝑏 =2.73⁢(2) MHz/GPa, by correlating these measurements at the same spatial position and applied microwave power. Our results demonstrate a unique technique for directly imaging ac lattice strain in micromechanical structures and provide a direct measurement of a fundamental constant for the N-V center defect spin Hamiltonian.

acoustic techniques↗

Phase-resolved terahertz nanoimaging of W Te 2 microcrystals

The terahertz (THz) electrodynamics of few-layer W⁢Te 2 is dominated by the plasmon response. However, THz surface plasmons (SPs) with long wavelengths in two-dimensional exfoliated crystals are typically confined by the lateral geometry. Direct visualization of the plasmonic standing wave patterns is challenging due to the spatial confinement and low quality factor of the SP, especially for samples that are only a few monolayers thick. Here, we resolve subtle real-space features of the plasmonic response of W⁢Te 2 by augmenting more common scattering amplitude experiments with the phase contrast accomplished within the time-domain version of THz nanoimaging. Amplitude and phase images allow us to quantitatively evaluate the evolution of the plasmonic response at cryogenic temperatures in samples with variable thickness from 3 to 12 monolayers. Further, the proposed imaging modality is universally applicable to the THz near-field nanoscopy of low-dimensional materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

The detection of mesogranulation on the sun

Time averages of velocity measurements at disk center on the quiet sun reveal the presence of a fairly stationary pattern of cellular flow with a spatial scale of 5-10 Mm. Such mesogranulation has a spatial rms vertical velocity amplitude of about 60 m/s superposed on the larger scale supergranular flows. The lifetimes of mesogranules appear to be at least 2 hr.

November, L. J.↗

Development of the phase/Doppler spray analyzer for liquid drop size and velocity characterizations

The present novel method for spray drop size and velocity measurement is analogous to a laser Doppler velocimeter, obtaining data from the spatial frequency of the interference fringe pattern produced by light scattering. Monodisperse droplet streams were used as a basic test of the theory, as well as of the susceptibility of the method to effects involved in actual application. Either beam intersection angle or detector spacing can be changed to achieve the same result. Polydispersed sprays were also measured.

Bachalo, W. D.↗