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This final report describes accomplishments of the project, divided into three sections: 1) Progress in the first year; 2) Progress in the second year; 3) Progress in the third and fourth year.
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The boreal zone of Alaska is dominated by interactions between disturbances, vegetation, and soils. These interactions are likely to change in the future through increasing permafrost thaw, more frequent and intense wildfires, and vegetation change from drought and competition. We utilize an individual tree-based vegetation model, the University of Virginia Forest Model Enhanced (UVAFME), to estimate current and future forest conditions across sites within interior Alaska. We updated UVAFME for application within interior Alaska, including improved simulation of permafrost dynamics, litter decay, nutrient dynamics, fire mortality, and post-fire regrowth. Following these updates, UVAFME output on species-specific biomass and stem density was comparable to inventory measurements at various forest types within interior Alaska. We then simulated forest response to climate change at specific inventory locations and across the Tanana Valley River Basin on a 2 × 2 km2 grid. We derived projected temperature and precipitation from a five-model average taken from the CMIP5 archive under the RCP 4.5 and 8.5 scenarios. Results suggest that climate change and the concomitant impacts on wildfire and permafrost dynamics will result in overall decreases in biomass (particularly for spruce (Picea spp.)) within the interior Tanana Valley, despite increases in quaking aspen (Populus tremuloides) biomass, and a resulting shift towards higher deciduous fraction. Simulation results also predict increases in biomass at cold, wet locations and at high elevations, and decreases in biomass in dry locations, under both moderate (RCP 4.5) and extreme (RCP 8.5) climate change scenarios. These simulations demonstrate that a highly detailed, species interactive model can be used across a large region within Alaska to investigate interactions between vegetation, climate, wildfire, and permafrost. The vegetation changes predicted here have the capacity to feed back to broader scale climate-forest interactions in the North American boreal forest, a region which contributes significantly to the global carbon and energy budgets.
In contrast to bulk FeSe, which exhibits nematic order and low temperature superconductivity, highly doped FeSe reverses the situation, having high temperature superconductivity appearing alongside a suppression of nematic order. To investigate this phenomenon, we study a minimal electronic model of FeSe, with interactions that enhance nematic fluctuations. This model is sign problem free, and is simulated using determinant quantum Monte Carlo (DQMC). We developed a DQMC algorithm with parallel tempering, which proves to be an efficient source of global updates and allows us to access the region of strong interactions. Over a wide range of intermediate couplings, we observe superconductivity with an extended s-wave order parameter, along with enhanced, but short-ranged, q=(0,0) ferro-orbital (nematic) order. These results are consistent with approximate weak-coupling treatments that predict that nematic fluctuations lead to superconducting pairing. Surprisingly, in the parameter range under study, we do not observe nematic long-range order. Furthermore, at stronger coupling an unusual insulating phase with q=(π,π) antiferro -orbital order appears, which is missed by weak-coupling approximations.
Large high-voltage space power systems proposed for future applications in both low earth orbit and geosynchronous altitudes must operate in the space charged-particle environment with possible interactions between this environment and the high-voltage surfaces. The paper reviews the ground experimental work to provide indicators for the interactions that could exist in the space power system. A preliminary analytical model of a large space power system is constructed using the existing NASA Charging Analyzer Program, and its performance in geosynchronous orbit is evaluated. The analytical results are used to illustrate the regions where detrimental interactions could exist and to establish areas where future technology is required.
Photolyases (PLs) reverse UV-induced DNA damage using blue light as an energy source. Of these PLs, (6-4) PLs repair (6-4)-lesioned photoproducts. We recently identified a gene from Vibrio cholerae (Vc) encoding a (6-4) PL, but structural characterization is needed to elucidate specific interactions with the chromophore cofactors. Here, we determined the crystal structure of Vc (6-4) PL at 2.5 Å resolution. Our high-resolution structure revealed that the two well-known cofactors, flavin adenine dinucleotide and the photoantenna 6,7-dimethyl 8-ribityl-lumazin (DMRL), stably interact with an α-helical and an α/β domain, respectively. Additionally, the structure has a third cofactor with distinct electron clouds corresponding to a [4Fe-4S] cluster. Moreover, we identified that Asp106 makes a hydrogen bond with water and DMRL, which indicates further stabilization of the photoantenna DMRL within Vc (6-4) PL. Further analysis of the Vc (6-4) PL structure revealed a possible region responsible for DNA binding. The region located between residues 478 to 484 may bind the lesioned DNA, with Arg483 potentially forming a salt bridge with DNA to stabilize further the interaction of Vc (6-4) PL with its substrate. Our comparative analysis revealed that the DNA lesion could not bind to the Vc (6-4) PL in a similar fashion to the Drosophila melanogaster (Dm, (6-4)) PL without a significant conformational change of the protein. The 23rd helix of the bacterial (6-4) PLs seems to have remarkable plasticity, and conformational changes facilitate DNA binding. In conclusion, our structure provides further insight into DNA repair by a (6-4) PL containing three cofactors.
Recent computational studies of helicopter flowfields for acoustic applications has led to the development of exceptionally efficient analysis methods for carrying out Lagrangian simulations of the vortex wake. The capabilities of these methods are demonstrated here through calculations involving a variety of wake/rotor interactions associated with both main rotor and tail rotor flowfields. These methods incorporate a flowfield reconstruction approach efficiently to compute vortex wake interactions within arbitrary regions located near the main rotor. This paper summarizes the development of the reconstruction approach and outlines some of its potential uses, while focusing primarily on its application to rotor noise calculations. The development of the nearfield velocity corrections used in the analysis of close vortex interactions is described, and the overall structure of the current reconstruction approach is discussed.
The ASR-supported Surface Atmosphere Integrated field Laboratory (SAIL) in the East River Watershed (ERW) of the Upper Colorado River Basin in southwestern Colorado ran from fall 2021 to spring 2023. Two monitoring sites were deployed in the East River Watershed as part of SAIL. The two sites were the Aerosol Observation System (AOS) located on Crested Butte Ski Mountain, and the ARM Mobile Facility (AMF-2), located at the Rocky Mountain Biological Laboratory in Gothic, Colorado. To gain a more comprehensive understanding of aerosols in complex, mountainous terrain, Handix Scientific deployed SAIL-Net, a distributed network of six measurement nodes spanning the domain of the SAIL research area from October 2021 to July 2023. Each node measured aerosol particles between 140 nm and 3.4 μm in diameter using a small particle counter (POPS, (Gao et al., 2016)), CNN using a miniature CCN counter (CloudPuck), and INP using the Time-Resolved Aerosol Filter Sampler (TRAPS, Creamean et al. (2018)). Our approach was similar to other studies that aimed to better characterize and understand aerosols and gas-phase pollutants using networks of lower-cost sensors (Caubel et al., 2019; Kelly et al., 2021; Asher et al., 2022). Such studies have identified neighborhood-level variations in pollutant concentrations (Schneider et al., 2017; Popoola et al., 2018; Caubel et al., 2019). Small-scale variations such as this are poorly represented in models and poorly measured by a single monitoring system (Caubel et al., 2019). Previous work has shown the representation error (the ability of measurements to represent a larger area) increases with complex orography, leading to decreases in model accuracy (Schutgens et al., 2017). The overall goal of SAIL-Net was to improve our understanding of the variability of aerosol in ERW, thus increasing our knowledge of aerosol-cloud interactions in this region and informing the usefulness of distributed networks of measurements for future studies.
Transient radiation of a charged particle in a waveguide with modulated anisotropic magnetodielectric filling is considered. It is assumed that the particle moves with a constant velocity perpendicularly to the axis of the waveguide the filling of which is periodically modulated by the harmonic law. Wave equations for the transverse electric (TE) and transverse magnetic (TM) fields in the waveguide have been obtained. Analytical expressions have been obtained for fields in the waveguide in the first approximation by small modulation indices of waveguide filling. Energies of transient radiation of a charged particle have been calculated in the region of weak (nonresonance) interaction between the radiation and modulation waves, in particular, in the case of a rectangular waveguide. It has been shown that radiation energies at the zero harmonic in the region of weak interaction do not depend on the modulation indices and are proportional to the modulation indices in the first power at the plus and minus first harmonics. The mechanism of the appearance of Cherenkov radiation has been analyzed.
Three-dimensional hybrid particle simulations of the dayside portion of the Mars/solar wind interaction have been performed. These simulations are compared with the in situ measurements taken during the elliptical orbits of Phobos 2. The comparisons show considerable agreement between the magnetic field data and the simulations results. The results of the simulations bring into question the type of structures created in the subsolar region of Mars. It appears that the large larmor radius of the solar wind ions prevents the formation of a traditional collisionless shock in the subsolar region of the interaction.
Propagation of coronal mass ejections (CMEs) from the Sun far into interplanetary space is not well understood, due to limited observations. In this study we examine the propagation characteristics of two geo-effective CMEs, which occurred on 2005 May 6 and 13, respectively. Significant heliospheric consequences associated with the two CMEs are observed, including interplanetary CMEs (ICMEs) at the Earth and Ulysses , interplanetary shocks, a long-duration type II radio burst, and intense geomagnetic storms. We use coronagraph observations from SOHO /LASCO, frequency drift of the long-duration type II burst, in situ measurements at the Earth and Ulysses , and magnetohydrodynamic propagation of the observed solar wind disturbances at 1 au to track the CMEs from the Sun far into interplanetary space. We find that both of the CMEs underwent a major deceleration within 1 au and thereafter a gradual deceleration when they propagated from the Earth to deep interplanetary space, due to interactions with the ambient solar wind. The results also reveal that the two CMEs interacted with each other in the distant interplanetary space even though their launch times on the Sun were well separated. The intense geomagnetic storm for each case was caused by the southward magnetic fields ahead of the CME, stressing the critical role of the sheath region in geomagnetic storm generation, although for the first case there is a corotating interaction region involved.
The impact of global tropical climate to perturbations in land surface processes (LSP) are evaluated using perturbations given by different LSP representations of continental-scale in a global climate model that includes atmosphere-ocean interactions. One representation is a simple land scheme, which specifies climatological albedos and soil moisture availability. The other representation is the more comprehensive Simplified Simple Biosphere Model, which allows for interactive soil moisture and vegetation biophysical processes. The results demonstrate that LSP processes such as interactive soil moisture and vegetation biophysical processes have strong impacts on the seasonal mean states and seasonal cycles of global precipitation, clouds, and surface air temperature. The impact is especially significant over the tropical Pacific. To explore the mechanisms for such impact, different LSP representations are confined to selected continental-scale regions where strong interactions of climate-vegetation biophysical processes are present. We find that the largest impact is mainly from LSP perturbations over the tropical African continent. The impact is through anomalous convective heating in tropical Africa due to changes in the surface heat fluxes, which in turn affect basinwide teleconnections in the Pacific through equatorial wave dynamics. The modifications in the equatorial Pacific climate are further enhanced by strong air-sea coupling between surface wind stress and upwelling, as well as effect of ocean memory. Our results further suggest that correct representations of land surface processes, land use change and the associated changes in the deep convection over tropical Africa are crucial to reducing the uncertainty when performing future climate projections under different climate change scenarios.
A Regional Land-Atmosphere Climate Simulation System (RELACS) project is being developed at NASA Goddard Space Flight Center. One of the major goals of RELACS is to use a regional scale model with improved physical processes and in particular land-related processes, to understand the role of the land surface and its interaction with convection and radiation as well as the water/energy cycles in the IndoChina/South China Sea (SCS) region. The Penn State/NCAR MM5 atmospheric modeling system, a state of the art atmospheric numerical model designed to simulate regional weather and climate, has been successfully coupled to the Parameterization for Land-Atmosphere-Cloud Exchange (PLACE) land surface model. The original MM5 model (without PLACE) includes the option for either a simple slab soil model or a five-layer soil model (MRF) in which the soil moisture availability evolves over time. However, the MM5 soil models do not include the effects of vegetation, and thus important physical processes such as evapotranspiration and interception are precluded. The PLACE model incorporates vegetation type and has been shown in international comparisons to accurately predict evapotranspiration and runoff over a wide variety of land surfaces. The coupling of MM5 and PLACE creates a numerical modeling system with the potential to more realistically simulate atmosphere and land surface processes including land-sea interaction, regional circulations such as monsoons, and flash flood events. In addition, the Penn State/NCAR MM5 atmospheric modeling system has been: (1) coupled to the Goddard Ice Microphysical scheme; (2) coupled to a turbulent kinetic energy (TKE) scheme; (3) modified to ensure cloud budget balance; and (4) incorporated initialization with the Goddard EOS data sets at NASA/Goddard Laboratory for Atmospheres. The improved MM5 with two nested domains (60 and 20 km horizontal resolution) was used to simulate convective activity over IndoChina and the South China Sea, during the monsoon season, from May 6 to May 20, 1986. The model results captured several dominant observed features, such as twin cyclones, a depression system over the Bay of Bengal, strong south-westerly winds over IndoChina before and during the on-set of convection over the SCS, and a vortex over the SCS. Two additional MM5 runs with different land process models, Blackadar and MRF, were performed, and their results are compared to the run with PLACE. The preliminary results indicate that the MM5 results using PLACE and Blackadar are in very good agreement, but the results using MRF do not contain the south-westerly wind over IndoChina prior to the on-set of convection over the SCS.
NOX1 (NADPH oxidase) similar to phagocyte NADPH oxidase, is expressed mainly in the colon epithelium and it is responsible for host defense against microbial infections by generating ROS (reactive oxygen species). NOX1 is activated by two regulatory cytosolic proteins that form a hetero-dimer, Noxo1 (NOX organizer 1) and Noxa1 (NOX activator 1). The interaction between Noxa1 and Noxo1 is critical for activating NOX1. However no structural studies for interaction between Noxa1 and Noxo1 has not been reported till date. Here, we studied the inter-molecular interaction between the SH3 domain of Noxa1 and Noxo1 using pull-down assay and NMR spectroscopy. {sup 15}N/{sup 13}C-labeled SH3 domain of Noxa1 has been purified for hetero-nuclear NMR experiments (HNCACB, CBCACONH, HNCA, HNCO, and HSQC). TALOS analysis using backbone assignment data of the Noxa1 SH3 domain showed that the structure primarily consists of β-sheets. Data from pull-down assay between the Noxo1 and Noxa1 showed that the SH3 domains (Noxa1) is responsible for interaction with Noxo1 C-terminal tail harboring proline rich region (PRR). The concentration-dependent titration of the Noxo1 C-terminal tail to Noxa1 shows that Noxo1 particularly in the RT loop: Q407*, H408, S409, A412*, G414*, E416, D417, L418, and F420; n-Src loop: C430, E431*, V432*, A435, W436, and L437; and terminal region: I447; F448*, F452* and V454 interact with Noxa1. Our results will provide a detailed understanding for interaction between Noxa1 and Noxo1 at the molecular level, providing insights into their cytoplasmic activity-mediated functioning as well as regulatory role of C-terminal tail of Noxo1 in the NOX1 complex. - Highlights: • C-terminal of Noxo1 harboring PRR motif is important for Noxa1 interaction. • Noxa1 SH3 binds C-terminal region of Noxo1with K{sub d} of 8.2 ± 1.41 μM. • Data from NMR experiments determined secondary structures of Noxa1 SH3. • Noxa1 interacts with PRR region of Noxo1, however, binding affinity is weaker than C-terminal tail of Noxo1. • Our results provide insights into regulatory role of C-terminal tail of Noxo1 in the NOX1 complex.
This paper evaluates multi-decadal simulations of the UCLA version of Climate Forecast System version 2 (CFSv2), in which the default Noah land surface model has been replaced with the Simplified Simple Biosphere Model version-2 (SSiB2). To examine the influence of the atmosphere-ocean (AO) interaction on the variability, two different simulations were conducted: one with interactive ocean component, and the other constrained by the prescribed sea surface temperature. We evaluate the mean seasonal climatology of precipitation and temperature, along with the model’s ability to reproduce atmospheric variability at different scales over the globe, including extratropical modes of atmospheric variability, and long-term trends of global and hemispheric temperature and regional precipitation. Here, we particularly selected two monsoon regions, East Asia and West Africa, where the simulation of multi-decadal variations which has heretofore been a challenging task, to examine decadal variation of monsoon precipitation. In general, temperature anomaly trends were better captured than those of precipitation in both simulations. Results suggest that the AO interaction, represented as latent heat flux, contributes to improve reproducibility of global-wide climatology, extratropical modes of atmospheric variability, and variability in the multi-decadal climate simulation, as well as for inter decadal variability of the East Asian summer monsoon.
PUF proteins are characterized by globular RNA-binding domains. They also interact with partner proteins that modulate their RNA-binding activities. Caenorhabditis elegans PUF protein fem-3 binding factor-2 (FBF-2) partners with intrinsically disordered Lateral Signaling Target-1 (LST-1) to regulate target mRNAs in germline stem cells. Here, we report that an intrinsically disordered region (IDR) at the C-terminus of FBF-2 autoinhibits its RNA-binding affinity by increasing the off rate for RNA binding. Moreover, the FBF-2 C-terminal region interacts with its globular RNA-binding domain at the same site where LST-1 binds. This intramolecular interaction restrains an electronegative cluster of amino acid residues near the 5' end of the bound RNA to inhibit RNA binding. LST-1 binding in place of the FBF-2 C-terminus therefore releases autoinhibition and increases RNA-binding affinity. This regulatory mechanism, driven by IDRs, provides a biochemical and biophysical explanation for the interdependence of FBF-2 and LST-1 in germline stem cell self-renewal.
A DNA double strand break (DSB) is one of the most cytotoxic DNA lesions, but it can be repaired by non-homologous end joining (NHEJ) or by homologous recombination. The choice between these two repair pathways depends on the cell cycle stage. Although NHEJ constitutes a simple re-ligation reaction, the regulatory mechanism(s) controlling its activity has not been fully characterized. Lif1 is a regulatory subunit of the NHEJ-specific DNA ligase IV and interacts with Xrs2 of the MRX complex which is a key factor in DSB repair. Specifically, the C-terminal region of Lif1, which contains a CK2-specific phosphorylation motif, interacts with the FHA domain of Xrs2 during canonical- NHEJ (C-NHEJ). Herein, we show that Lif1 and Cka2, a catalytic subunit of yeast CK2, interact and that the C-terminal phosphorylation consensus motif in Lif1 is phosphorylated by recombinant CK2. These observations suggest that phosphorylation of Lif1 by CK2 at a DSB site promotes the Lif1-Xrs2 interaction and facilitates C-NHEJ.
The near-wall region of a turbulent flow is investigated in the limit of large Reynolds numbers. When low-speed streaks are present, the governing equations are shown to be of the boundary-layer type. Physical processes leading to local breakdown and a strong interaction with the outer region are considered. It is argued that convected vortices, predominantly of the hairpin type, will provoke eruptions and regenerative interactions with the outer region.