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At least 325 records · Page 18

Insights into the dynamics between viruses and their hosts in a hot spring microbial mat

Abstract Our current knowledge of host–virus interactions in biofilms is limited to computational predictions based on laboratory experiments with a small number of cultured bacteria. However, natural biofilms are diverse and chiefly composed of uncultured bacteria and archaea with no viral infection patterns and lifestyle predictions described to date. Herein, we predict the first DNA sequence-based host–virus interactions in a natural biofilm. Using single-cell genomics and metagenomics applied to a hot spring mat of the Cone Pool in Mono County, California, we provide insights into virus–host range, lifestyle and distribution across different mat layers. Thirty-four out of 130 single cells contained at least one viral contig (26%), which, together with the metagenome-assembled genomes, resulted in detection of 59 viruses linked to 34 host species. Analysis of single-cell amplification kinetics revealed a lack of active viral replication on the single-cell level. These findings were further supported by mapping metagenomic reads from different mat layers to the obtained host–virus pairs, which indicated a low copy number of viral genomes compared to their hosts. Lastly, the metagenomic data revealed high layer specificity of viruses, suggesting limited diffusion to other mat layers. Taken together, these observations indicate that in low mobility environments with high microbial abundance, lysogeny is the predominant viral lifestyle, in line with the previously proposed “Piggyback-the-Winner” theory.

59 BASIC BIOLOGICAL SCIENCES↗

A proposed group management scheme for XTP multicast

The purpose of a group management scheme is to enable its associated transfer layer protocol to be responsive to user determined reliability requirements for multicasting. Group management (GM) must assist the client process in coordinating multicast group membership, allow the user to express the subset of the multicast group that a particular multicast distribution must reach in order to be successful (reliable), and provide the transfer layer protocol with the group membership information necessary to guarantee delivery to this subset. GM provides services and mechanisms that respond to the need of the client process or process level management protocols to coordinate, modify, and determine attributes of the multicast group, especially membership. XTP GM provides a link between process groups and their multicast groups by maintaining a group membership database that identifies members in a name space understood by the underlying transfer layer protocol. Other attributes of the multicast group useful to both the client process and the data transfer protocol may be stored in the database. Examples include the relative dispersion, most recent update, and default delivery parameters of a group.

Dempsey, Bert J.↗

Atomic-Scale Characterization and Electronic Properties of Gold-Capped Niobium Films for Superconducting Qubits

Niobium thin films are central to superconducting qubits, but their complex native oxides contribute significantly to microwave losses. A promising mitigation strategy is to suppress oxide formation using engineered thin-film encapsulation layers. Recent experiments have shown that ∼10 nm metallic overlayers on Nb capacitor films can improve the energy relaxation time T1 of transmon qubits. Here, we present a comparative study of Au-capped Nb films fabricated in situ by molecular beam epitaxy and ex situ by sequential deposition benchmarked against bare Nb films. Using complementary structural, chemical, and spectroscopic techniques, we correlate the interface quality with superconducting electronic properties of the Au surface. Low-temperature scanning tunneling spectroscopy (STS) provides spatially resolved quasiparticle density-of-states maps. While both Au-capped Nb samples exhibit large areas with uniform, fully gapped density of states, clear differences emerge between the two interfaces. Compared to in situ Nb-Au, ex situ Nb-Au exhibits a reduced induced superconducting gap, broadened coherence peak, and localized in-gap states, consistent with a residual NbxOy layer at the interface. Supported by complementary structural and chemical analyses, these findings demonstrate that STS directly links nanoscale superconducting properties to interface preparation, highlighting the importance of controlled in situ encapsulation for minimizing dissipation and improving quantum coherence.

Makita, Junki [MIT; Temple U.] (ORCID:000000026889↗

Using Radiative Convective Equilibrium to Explore Clouds and Climate in the Community Atmosphere Model

Abstract Characteristics of, and fundamental differences between, the radiative‐convective equilibrium (RCE) climate states following the Radiative‐Convective Equilibrium Model Intercomparison Project (RCEMIP) protocols in the Community Atmosphere Model version 5 (CAM5) and version 6 (CAM6) are presented. This paper explores the characteristics of clouds, moisture, precipitation and circulation in the RCE state, as well as the tropical response to surface warming, in CAM5 and CAM6 with different parameterizations. Overall, CAM5 simulates higher precipitation rates that result in larger global average precipitation, despite lower outgoing longwave radiation compared to CAM6. Differences in the structure of clouds, particularly the amount and vertical location of cloud liquid, exist between the CAM versions and can, in part, be related to distinct representations of shallow convection and boundary layer processes. Both CAM5 and CAM6 simulate similar peaks in cloud fraction, relative humidity, and cloud ice, linked to the usage of a similar deep convection parameterization. These anvil clouds rise and decrease in extent in response to surface warming. More generally, extreme precipitation, aggregation of convection, and climate sensitivity increase with warming in both CAM5 and CAM6. This analysis provides a benchmark for future studies that explore clouds, convection, and climate in CAM with the RCEMIP protocols now available in the Community Earth System Model. These results are discussed within the context of realistic climate simulations using CAM5 and CAM6, highlighting the usefulness of a hierarchical modeling approach to understanding model and parameterization sensitivities to inform model development efforts.

Reed, Kevin A.↗

First principles modeling of polymer encapsulant degradation in Si photovoltaic modules

An outstanding issue in the longevity of photovoltaic (PV) modules is the accelerated degradation caused by the presence of moisture. Moisture leads to interfacial instability, de-adhesion, encapsulant decomposition, and contact corrosion. However, experimental characterization of moisture in PV modules is not trivial and its impacts can take years or decades to establish in the field, presenting a major obstacle to designing high-reliability modules. First principles calculations provide an alternative way to study the ingress of water and its detrimental effect on the structure and decomposition of the polymer encapsulant and interfaces between the encapsulant and the semiconductor, the metal contacts, or the dielectric layer. Here, we use density functional theory (DFT) computations to model single chain, crystalline and cross-linked structures, infrared (IR) signatures, and degradation mechanisms of ethylene vinyl acetate (EVA), the most common polymer encapsulant used in Si PV modules. IR-active modes computed for low energy EVA structures and possible decomposition products match well with reported experiments. The EVA decomposition energy barriers computed using the Nudged Elastic Band (NEB) method show a preference for acetic acid formation as compared to acetaldehyde, are lowered in the presence of a water solvent or hydroxyl ion catalyst, and match well with reported experimental activation energies. This systematic study leads to a clear picture of the hydrolysis-driven decomposition of EVA in terms of energetically favorable mechanisms, possible intermediate structures, and IR signatures of reactants and products.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Machine Learning Correction Model of the Winter Clear-Sky Temperature Bias over the Arctic Sea Ice in Atmospheric Reanalyses

Atmospheric reanalyses are widely used to estimate the past atmospheric near-surface state over sea ice. They provide boundary conditions for sea ice and ocean numerical simulations and relevant information for studying polar variability and anthropogenic climate change. Previous research revealed the existence of large near-surface temperature biases (mostly warm) over the Arctic sea ice in the current generation of atmospheric reanalyses, which is linked to a poor representation of the snow over the sea ice and the stably stratified boundary layer in the forecast models used to produce the reanalyses. These errors can compromise the employment of reanalysis products in support of polar research. Here, we train a fully connected neural network that learns from remote sensing infrared temperature observations to correct the existing generation of uncoupled atmospheric reanalyses (ERA5, JRA-55) based on a set of sea ice and atmospheric predictors, which are themselves reanalysis products. The advantages of the proposed correction scheme over previous calibration attempts are the consideration of the synoptic weather and cloud state, compatibility of the predictors with the mechanism responsible for the bias, and a self-emerging seasonality and multidecadal trend consistent with the declining sea ice state in the Arctic. The correction leads on average to a 27% temperature bias reduction for ERA5 and 7% for JRA-55 if compared to independent in situ observations from the MOSAiC campaign (respectively, 32% and 10% under clear-sky conditions). These improvements can be beneficial for forced sea ice and ocean simulations, which rely on reanalyses surface fields as boundary conditions.

54 ENVIRONMENTAL SCIENCES↗

Study and Simulation of Enhancements for TCP (Transmission Control Protocol) Performance Over Noisy, High-Latency Links

The designers of the TCP/IP protocol suite explicitly included support of satellites in their design goals. The goal of the Internet Project was to design a protocol which could be layered over different networking technologies to allow them to be concatenated into an internet. The results of this project included two protocols, IP and TCP. IP is the protocol used by all elements in the network and it defines the standard packet format for IP datagrams. TCP is the end-to-end transport protocol commonly used between end systems on the Internet to derive a reliable bi-directional byte-pipe service from the underlying unreliable IP datagram service. Satellite links are explicitly mentioned in Vint Cerf's 2-page article which appeared in 1980 in CCR [2] to introduce the specifications for IP and TCP. In the past fifteen years, TCP has been demonstrated to work over many differing networking technologies, including over paths including satellites links. So if satellite links were in the minds of the designers from the beginning, what is the problem? The problem is that the performance of TCP has in some cases been disappointing. A goal of the authors of the original specification of TCP was to specify only enough behavior to ensure interoperability. The specification left a number of important decisions, in particular how much data is to be sent when, to the implementor. This was deliberately' done. By leaving performance-related decisions to the implementor, this would allow the protocol TCP to be tuned and adapted to different networks and situations in the future without the need to revise the specification of the protocol, or break interoperability. Interoperability would continue while future implementations would be allowed flexibility to adapt to needs which could not be anticipated at the time of the original protocol design.

Shepard, Timothy J.↗

The Azospirillum brasilense Core Chemotaxis Proteins CheA1 and CheA4 Link Chemotaxis Signaling with Nitrogen Metabolism

Bacterial chemotaxis affords motile bacteria the ability to navigate the environment to locate niches for growth and survival. At the molecular level, chemotaxis depends on chemoreceptor signaling arrays that interact with cytoplasmic proteins to control the direction of movement. In Azospirillum brasilense , chemotaxis is mediated by two distinct chemotaxis pathways: Che1 and Che4. Both Che1 and Che4 are critical in the A. brasilense free-living and plant-associated lifestyles. Here, we use whole-cell proteomics and metabolomics to characterize the role of chemotaxis in A. brasilense physiology. We found that mutants lacking CheA1 or CheA4 or both are affected in nonchemotaxis functions, including major changes in transcription, signaling transport, and cell metabolism. We identify specific effects of CheA1 and CheA4 on nitrogen metabolism, including nitrate assimilation and nitrogen fixation, that may depend, at least, on the transcriptional control of rpoN , which encodes RpoN, a global regulator of metabolism, including nitrogen. Consistent with proteomics, the abundance of several nitrogenous compounds (purines, pyrimidines, and amino acids) changed in the metabolomes of the chemotaxis mutants relative to the parental strain. Further, we uncover novel, and yet uncharacterized, layers of transcriptional and posttranscriptional control of nitrogen metabolism regulators. Together, our data reveal roles for CheA1 and CheA4 in linking chemotaxis and nitrogen metabolism, likely through control of global regulatory networks.

59 BASIC BIOLOGICAL SCIENCES↗

Infrared triggered dwell and active cooling thermal control effects on microstructural uniformity in DED

Directed Energy Deposition (DED) offers rapid large scale fabrication, but difficulty in delivering consistent microstructures and properties hinders the use of DED fabricated components in safety or performance critical applications. Variability stems from the complex thermal cycles generated by the toolpath used to print the required geometry. Several practical methods have become established in DED to regulate overheating, such as active cooling of the baseplate structure or the use of an infrared camera to inject interlayer pauses to ensure the top layer of the component cools to a set temperature, which have been shown to affect microstructure. However, no critical assessment has been performed as to how effective these controls are in promoting microstructural uniformity in the context of complex layer timing commonly generated by non-prismatic geometries. Here we show how controls influence the thermal field, phase transformations, and dynamic annealing of a low-temperature transformation steel using infrared imaging and operando neutron diffraction. Counterintuitively, common thermal homogenization process controls can reduce microstructural uniformity because these approaches stabilize peak temperature while overlooking temperatures near the solid-state phase transformation fronts. Instead, the cyclic reheating induces spatially-variant dynamically annealed regions which can be modulated via control parameters. We show that these controls have spatially linked effects centimeters away from the active weld, which implies that microstructure control must co-optimize thermal input across many subsequent layers. In conclusion, our results demonstrate the pressing need for higher order controls that integrate predictive elements of simulation data to stabilize printed properties for future qualification of DED components.

Directed energy deposition↗

Dynamics of multilayer Rayleigh–Taylor instability at moderately high Atwood numbers

This paper investigates the multilayer Rayleigh–Taylor instability (RTI) using statistically stationary experiments conducted in a gas tunnel. Employing diagnostics such as particle image velocimetry (PIV) and planar laser induced fluorescence (PLIF), we make simultaneous velocity–density measurements to study how dynamics and mixing are linked in this variable density flow. Experiments are conducted in a newly built, blow-down three-layer gas tunnel facility. Mixing between three gas streams is studied, where the top and bottom streams are comprised of air, and the middle stream is an air–helium mixture. Shear is minimized between these streams by matching their inlet velocities. The four experimental conditions investigated here consist of two different density ratios (Atwood numbers 0.3 and 0.6), each investigated at two instability development times (or equivalently, two streamwise locations), and all experiments are with the same middle stream thickness of 3 cm. The growth of the middle layer is measured using laser-based planar Mie scattering visualization. The mixing width is found to grow linearly with time at late times. Various quantitative measures of molecular mixing indicate a very high degree of molecular mixing at late times in the multilayer RTI flow. The vertical turbulent mass flux $a_y$ is calculated. In addition to mostly negative values of $a_y$ , typical of buoyancy-dominated flows due to negative correlation between velocity and density fluctuations, positive regions are also observed in profiles of $a_y$ due to entrainment and erosion at the lower edge of the mixing region. Global energy budgets are calculated for the multilayer RTI flow at late times and it is found that the majority of potential energy released has been dissipated due to viscous effects, and a large value of mixing efficiency ( $\sim$ 60 %) is observed.

Mechanics↗

Shuttle Payload Ground Command and Control: An Experiment Implementation Combustion Module-2 Software Development, STS-107

This presentation covers the design of a command and control architecture developed by the author for the Combustion Module-2 microgravity experiment, which flew aboard the STS-107 Shuttle mission, The design was implemented to satisfy a hybrid network that utilized TCP/IP for both the onboard segment and ground segment, with an intermediary unreliable transport for the space to ground segment. With the infusion of Internet networking technologies into Space Shuttle, Space Station, and spacecraft avionics systems, comes the need for robust methodologies for ground command and control. Considerations of high bit error links, and unreliable transport over intermittent links must be considered in such systems. Internet protocols applied to these systems, coupled with the appropriate application layer protections, can provide adequate communication architectures for command and control. However, there are inherent limitations and additional complexities added by the use of Internet protocols that must be considered during the design. This presentation will discuss the rationale for the: framework and protocol algorithms developed by the author. A summary of design considerations, implantation issues, and learned lessons will be will be presented. A summary of mission results using this communications architecture will be presented. Additionally, areas of further needed investigation will be identified.

Carek, David Andrew↗

3D Realistic Modeling of the Interaction of Quiet-Sun Magnetic Fields with the Chromosphere

High-resolution observations and 3D simulations suggest that a local dynamo operates near the surface and produces ubiquitous small-scale magnetic elements, thus contributing to the magnetic carpet in the photosphere and to the magnetic structure and dynamics of the solar atmosphere. It appears that the traditional mechanisms of chromospheric energy and mass transport by acoustic waves and shocks are likely to play a secondary role; instead, the primary drivers in the energetics and dynamics of the chromosphere and transition region are small-scale, previously unresolved, quiet-Sun magnetic fields. These fields appear as ubiquitous, rapidly changing (on the scale of a few seconds), tiny magnetic loops and magnetized vortex tubes. Questions then arise about their origin and dynamics in the chromosphere, their links to magnetic fields in the photosphere, and their role in the energy storage and exchange between subsurface layers and the chromosphere. In the talk we will present results of 3D radiative MHD simulations obtained with the StellarBox code and discuss the energetics and dynamical interlinks between the subphotospheric layers and low chromosphere, their effects on the structure of the chromosphere, and signatures of the fine-scale magnetic features in high-resolution spectro-polarimetric observations.

Quie-Sun↗

Ionospheric Mapping with the GPS/MET

The GPS/MET experiment, which placed a GPS receiver in a low-Earth orbit tracking the GPS in an occultation geometry, has collected thousands of occultations since its launch in April of 1995. Each occultation can be inverted to give an electron density profile in the ionosphere, temperature and pressure profiles in the lower mesosphere, stratosphere and upper troposphere, and water vapor density profiles in the lower troposphere. This paper gives a summary of the ionospheric effects on the GPS/MET signal and examines some of the retrieved electron density profiles. We examine the bending induced by the ionosphere on the occulting signal and the resulting separation of the two GPS links corresponding to the L1 and L2 phase signals. We also examine the amplitude scintillation caused by sharp layers at the bottom of the ionosphere. We briefly describe the Abel inversion method for obtaining the index of refraction and show several examples of electron density profiles and comparisons derived from the Parameterized Ionospheric Model (PIM) and to incoherent scatter radar measurements.

GPS↗

Zero-Copy Objects System

Zero-Copy Objects System software enables application data to be encapsulated in layers of communication protocol without being copied. Indirect referencing enables application source data, either in memory or in a file, to be encapsulated in place within an unlimited number of protocol headers and/or trailers. Zero-copy objects (ZCOs) are abstract data access representations designed to minimize I/O (input/output) in the encapsulation of application source data within one or more layers of communication protocol structure. They are constructed within the heap space of a Simple Data Recorder (SDR) data store to which all participating layers of the stack must have access. Each ZCO contains general information enabling access to the core source data object (an item of application data), together with (a) a linked list of zero or more specific extents that reference portions of this source data object, and (b) linked lists of protocol header and trailer capsules. The concatenation of the headers (in ascending stack sequence), the source data object extents, and the trailers (in descending stack sequence) constitute the transmitted data object constructed from the ZCO. This scheme enables a source data object to be encapsulated in a succession of protocol layers without ever having to be copied from a buffer at one layer of the protocol stack to an encapsulating buffer at a lower layer of the stack. For large source data objects, the savings in copy time and reduction in memory consumption may be considerable.

Burleigh, Scott C.↗

Ultrathin-film composite (uTFC) membranes based on amorphous perfluoropolymers for liquid separations

Thin-film composite membranes based on ~100nm cross-linked polyamides (PAs) are state-of-the-art membranes for liquid separations such as desalination. However, the PA layer shows poor antifouling properties and instability in chlorine solutions. Herein, we show for the first time that glassy amorphous perfluoropolymers (PFPs, such as Teflon AF and Hyflon AD) can be fabricated into ultrathin film composite (uTFC) membranes with a selective layer of <20nm for desalination. Increasing the polymer concentration in the coating solutions from 0.05 mass% to 0.3 mass% increases the selective layer thickness from 9 to 25nm. When Teflon AF2400 was fabricated into 16-nm selective layers on various porous supports, the water permeance decreases from 0.37 LMH/bar for PES10k to 0.07 LMH/bar for PES1k, and the Na 2 SO 4 rejection increases from 86.6% to 95.2%. While the water permeance is lower than the commercial PA-based NF membranes, the rejection in these PFP-based membranes is comparable. Furthr, the effect of the porous support on the water permeance can be ascribed to the geometric restriction and satisfactorily described using an empirical model. Interestingly, the membranes also exhibit good Na + /Li + separation performance and stable performance for organic solvent nanofiltration, showcasing the versatility of the PFP-based uTFC membranes for various liquid separations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Energy Assets Transformation Web Mapping Application

This submission contains the link and geospatial materials used in the Energy Assets Transformation Web Mapping Application. The zip file contains 19 geospatial layers in a file geodatabase called EAT.gdb to be grouped in the following categories. 1. Industrial Assets: Coal Generation Units Retirements 2012-2040 (EIA); Examples of Repurposing Projects (32 projects in total); Abandoned Coal Mines (CORD, SkyTruth); Abandoned or Orphaned Wells (for ten states only). 2. Energy Transition Communities: 48C (e) Tax Credits - Designated Energy Communities (IRA); Index of Deep Disadvantage; Local Energy Action Program (LEAP); EJ Index for Proximity to Hazardous Waste (EPA). 3. Regional Landscape: State-Level Funding Programs (relevant to repurposing projects, for 2022 and 2023 only); Coal Flows from Mine to Plant 2021 (EIA), Variable Renewable Energy Shares (Wind and Solar, 2021, EIA). 4. Supporting Infrastructure: Railroads (HIFLD), Electric Power Transmission Lines (HIFLD), Major Highways (NHPN, DOT), Major Ports (National Atlas of the U.S.); Independent System Operators (HIFLD), NERC Regions and Subregions (HIFLD).

abandoned coal mines↗

African smoke particles act as cloud condensation nuclei in the wintertime tropical North Atlantic boundary layer over Barbados

Abstract. The number concentration and properties of aerosol particles serving as cloud condensation nuclei (CCN) are important for understanding cloud properties, including in the tropical Atlantic marine boundary layer (MBL), where marine cumulus clouds reflect incoming solar radiation and obscure the low-albedo ocean surface. Studies linking aerosol source, composition, and water uptake properties in this region have been conducted primarily during the summertime dust transport season, despite the region receiving a variety of aerosol particle types throughout the year. In this study, we compare size-resolved aerosol chemical composition data to the hygroscopicity parameter κ derived from size-resolved CCN measurements made during the Elucidating the Role of Clouds–Circulation Coupling in Climate (EUREC4A) and Atlantic Tradewind Ocean-Atmosphere Mesoscale Interaction Campaign (ATOMIC) campaigns from January to February 2020. We observed unexpected periods of wintertime long-range transport of African smoke and dust to Barbados. During these periods, the accumulation-mode aerosol particle and CCN number concentrations as well as the proportions of dust and smoke particles increased, whereas the average κ slightly decreased (κ=0.46±0.10) from marine background conditions (κ=0.52±0.09) when the submicron particles were mostly composed of marine organics and sulfate. Size-resolved chemical analysis shows that smoke particles were the major contributor to the accumulation mode during long-range transport events, indicating that smoke is mainly responsible for the observed increase in CCN number concentrations. Earlier studies conducted at Barbados have mostly focused on the role of dust on CCN, but our results show that aerosol hygroscopicity and CCN number concentrations during wintertime long-range transport events over the tropical North Atlantic are also affected by African smoke. Our findings highlight the importance of African smoke for atmospheric processes and cloud formation over the Caribbean.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗