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Introduction: Man and his total environment

Environmental changes and the utilization of finite resources are analyzed. Beyond the satisfaction of basic physical needs, the advancement of civilization toward an ever-improving quality of like is likewise dependent upon mans' interaction with his entire environment. This larger system is controlled externally by electromagnetic and particle energy from the sun and internally by the dynamic interchange of energy between the solid earth, oceans, the atmosphere, and the magnetosphere. This exchange of energy that determines the structure of the earth's environemental system is evaluated.

Source record↗

The effects on the earth's magnetotail from shocks in the solar wind

A new, minimally diffusive MHD computer code has been used to simulate the time-dependent, 2D interaction of the solar wind with the earth's magnetosphere. The equilibrium with a simulated unmagnetized solar wind shows the basic features of the magnetosphere: bow shock, magnetopause, and long magnetotail. A simulated shock in the solar wind shows the presence of shock focussing in the midplane of the magnetotail. This focussing can be important in the energy budget of the plasma sheet and may have an important role in the initiation of substorms.

Lyon, J.↗

Interacting binary stars - Freaks or rosetta stones

Attention is given to semidetached binaries of the Algol type and to related interacting systems, such as Beta Lyrae and the W Serpentis stars. A brief description is given of observational problems. The basic properties of the Algol variables are satisfactorily explained by means of evolutionary models that assume considerable mass transfer between the components. It is pointed out that ultraviolet spectra obtained with the IUE satellite corroborate the view that the present subgiant secondary component was initially the more massive star and that it has been stripped of a large fraction of its mass so that the deep layers affected by CNO processing are now denuded. It is believed that the present-day 'classical' Algols must have undergone a phase of rapid mass transfer in the past and that Beta Lyrae and the W Serpentis stars are probably closer to that stage than ordinary Algols. Around the accreting star a complex structure is formed, and an induced stellar wind may blow a large part of the transferred matter out of the system.

Plavec, M. J.↗

Measurement of reach envelopes with a four-camera Selective Spot Recognition (SELSPOT) system

The basic Selective Spot Recognition (SELSPOT) system is essentially a system which uses infrared LEDs and a 'camera' with an infrared-sensitive photodetector, a focusing lens, and some A/D electronics to produce a digital output representing an X and Y coordinate for each LED for each camera. When the data are synthesized across all cameras with appropriate calibrations, an XYZ set of coordinates is obtained for each LED at a given point in time. Attention is given to the operating modes, a system checkout, and reach envelopes and software. The Video Recording Adapter (VRA) represents the main addition to the basic SELSPOT system. The VRA contains a microprocessor and other electronics which permit user selection of several options and some interaction with the system.

Stramler, J. H., Jr.↗

Atmospheric and Science Complexity Effects on Surface Bidirectional Reflectance

Among the tools used in passive remote sensing of Earth resources in the visible and near-infrared spectral regions are measurements of spectral signature and bidirectional reflectance functions (BDRFs). Determination of surface properties using these observables is complicated by a number of factors, including: (1) mixing of surface components, such as soil and vegetation, (2) multiple reflections of radiation due to complex geometry, such as in crop canopies, and (3) atmospheric effects. In order to bridge the diversity in these different approaches, there is a need for a fundamental physical understanding of the influence of the various effects and a quantiative measure of their relative importance. In particular, we consider scene complexity effects using the example of reflection by vegetative surfaces. The interaction of sunlight with a crop canopy and interpretation of the spectral and angular dependence of the emergent radiation is basically a multidimensional radiative transfer problem. The complex canopy geometry, underlying soil cover, and presence of diffuse as well as collimated illumination will modify the reflectance characteristics of the canopy relative to those of the individual elements.

Diner, D. J.↗

The probability of detecting absorption features in gamma-ray burst spectra

It has recently been suggested that several mechanisms for the primary release of energy in gamma-ray bursts may result in the excitation of magnetospheric plasma oscillations (MPO) above the polar cap of a neutron star. The basic MPO idea is refined by determining the soft photon source (which damps the particle motion via inverse Compton scattering interactions) self-consistently by means of a Monte Carlo simulation for the deposition of back-scattered gamma-ray energy below the stellar photosphere. The observed fraction of bursts displaying low-energy absorption features may be understood in the context of a model wherein the overall spectrum changes with inclination angle due to the superposition of several components with different angular distributions. GRB spectra should display these cyclotron lines about 18 percent of the time, which is consistent with the KONUS and Ginga sets of data.

Melia, F.↗

Parallel Grid Manipulations in Earth Science Calculations

The National Aeronautics and Space Administration (NASA) Data Assimilation Office (DAO) at the Goddard Space Flight Center is moving its data assimilation system to massively parallel computing platforms. This parallel implementation of GEOS DAS will be used in the DAO's normal activities, which include reanalysis of data, and operational support for flight missions. Key components of GEOS DAS, including the gridpoint-based general circulation model and a data analysis system, are currently being parallelized. The parallelization of GEOS DAS is also one of the HPCC Grand Challenge Projects. The GEOS-DAS software employs several distinct grids. Some examples are: an observation grid- an unstructured grid of points at which observed or measured physical quantities from instruments or satellites are associated- a highly-structured latitude-longitude grid of points spanning the earth at given latitude-longitude coordinates at which prognostic quantities are determined, and a computational lat-lon grid in which the pole has been moved to a different location to avoid computational instabilities. Each of these grids has a different structure and number of constituent points. In spite of that, there are numerous interactions between the grids, e.g., values on one grid must be interpolated to another, or, in other cases, grids need to be redistributed on the underlying parallel platform. The DAO has designed a parallel integrated library for grid manipulations (PILGRIM) to support the needed grid interactions with maximum efficiency. It offers a flexible interface to generate new grids, define transformations between grids and apply them. Basic communication is currently MPI, however the interfaces defined here could conceivably be implemented with other message-passing libraries, e.g., Cray SHMEM, or with shared-memory constructs. The library is written in Fortran 90. First performance results indicate that even difficult problems, such as above-mentioned pole rotation- a sparse interpolation with little data locality between the physical lat-lon grid and a pole rotated computational grid- can be solved efficiently and at the GFlop/s rates needed to solve tomorrow's high resolution earth science models. In the subsequent presentation we will discuss the design and implementation of PILGRIM as well as a number of the problems it is required to solve. Some conclusions will be drawn about the potential performance of the overall earth science models on the supercomputer platforms foreseen for these problems.

Sawyer, W.↗

Decomposition by ectomycorrhizal fungi alters soil carbon storage in a simulation model

Carbon cycle models often lack explicit belowground organism activity, yet belowground organisms regulate carbon storage and release in soil. Ectomycorrhizal fungi are important players in the carbon cycle because they are a conduit into soil for carbon assimilated by the plant. It is hypothesized that ectomycorrhizal fungi can also be active decomposers when plant carbon allocation to fungi is low. Here, we reviewed the literature on ectomycorrhizal decomposition and we developed a simulation model of the plant-mycorrhizae interaction where a reduction in plant productivity stimulates ectomycorrhizal fungi to decompose soil organic matter. Our review highlights evidence demonstrating the potential for ectomycorrhizal fungi to decompose soil organic matter. Our model output suggests that ectomycorrhizal activity accounts for a portion of carbon decomposed in soil, but this portion varied with plant productivity and the mycorrhizal carbon uptake strategy simulated. Lower organic matter inputs to soil were largely responsible for reduced soil carbon storage. Using mathematical theory, we demonstrated that biotic interactions affect predictions of ecosystem functions. Specifically, we developed a simple function to model the mycorrhizal switch in function from plant symbiont to decomposer. In conclusion, we show that including mycorrhizal fungi with the flexibility of mutualistic and saprotrophic lifestyles alters predictions of ecosystem function.

59 BASIC BIOLOGICAL SCIENCES↗

Molecular basis for activation of G protein-coupled receptor kinases

G protein-coupled receptor (GPCR) kinases (GRKs) selectively recognize and are allosterically regulated by activated GPCRs, but the molecular basis for this interaction is not understood. Herein, we report crystal structures of GRK6 in which regions known to be critical for receptor phosphorylation have coalesced to stabilize the kinase domain in a closed state and to form a likely receptor docking site. The crux of this docking site is an extended N-terminal helix that bridges the large and small lobes of the kinase domain and lies adjacent to a basic surface of the protein proposed to bind anionic phospholipids. Mutation of exposed, hydrophobic residues in the N-terminal helix selectively inhibits receptor, but not peptide phosphorylation, suggesting that these residues interact directly with GPCRs. Our structural and biochemical results thus provide an explanation for how receptor recognition, phospholipid binding, and kinase activation are intimately coupled in GRKs.

59 BASIC BIOLOGICAL SCIENCES↗

Bacterial microcompartment assembly: The key role of encapsulation peptides

Bacterial microcompartments (BMCs) are proteinaceous organelles used by a broad range of bacteria to segregate and optimize metabolic reactions. Their functions are diverse, and can be divided into anabolic (carboxysome) and catabolic (metabolosomes) processes, depending on their cargo enzymes. The assembly pathway for the β-carboxysome has been characterized, revealing that biogenesis proceeds from the inside out. The enzymes coalesce into a procarboxysome, followed by encapsulation in a protein shell that is recruited to the procarboxysome by a short (~17 amino acids) extension on the C-terminus of one of the encapsulated proteins. A similar extension is also found on the N- or C-termini of a subset of metabolosome core enzymes. These encapsulation peptides (EPs) are characterized by a primary structure predicted to form an amphipathic α-helix that interacts with shell proteins. In this study, we review the features, function and widespread occurrence of EPs among metabolosomes, and propose an expanded role for EPs in the assembly of diverse BMCs.

59 BASIC BIOLOGICAL SCIENCES↗

14-3-3 protein mediates plant seed oil biosynthesis through interaction with AtWRI1

Plant 14-3-3 proteins are phosphopeptide-binding proteins, belonging to a large family of proteins involved in numerous physiological processes including primary metabolism, although knowledge about the function of 14-3-3s in plant lipid metabolism is sparse. WRINKLED1 (WRI1) is a key transcription factor that governs plant oil biosynthesis. At present, AtWRI1-interacting partners remain largely unknown. Here in this work, we show that 14-3-3 proteins are able to interact with AtWRI1, both in yeast and plant cells. Transient co-expression of 14-3-3- and AtWRI1-encoding cDNAs led to increased oil biosynthesis in Nicotiana benthamiana leaves. Stable transgenic plants overproducing a 14-3-3 protein also displayed increased seed oil content. Co-production of a 14-3-3 protein with AtWRI1 enhanced the transcriptional activity of AtWRI1. The 14-3-3 protein was found to increase the stability of AtWRI1. A possible 14-3-3 binding motif was identified in one of the two AP2 domains of AtWRI1, which was also found to be critical for the interaction of AtWRI1 with an E3 ligase linker protein. Thus, we hypothesize a regulatory mechanism by which the binding of 14-3-3 to AtWRI1 interferes with the interaction of AtWRI1 and the E3 ligase, thereby protecting AtWRI1 from degradation. In conclusion, our studies identified AtWRI1 as a client of 14-3-3 proteins and provide insights into a role of 14-3-3 in mediating plant oil biosynthesis.

14-3-3↗

Neutron Scattering Studies of the Interplay of Amyloid β Peptide(1–40) and An Anionic Lipid 1,2-dimyristoyl-sn-glycero-3-phosphoglycerol

The interaction between lipid bilayers and Amyloid β peptide (Aβ) plays a critical role in proliferation of Alzheimer’s disease (AD). AD is expected to affect one in every 85 humans by 2050, and therefore, deciphering the interplay of Aβ and lipid bilayers at the molecular level is of profound importance. In this work, we applied an array of neutron scattering methods to study the structure and dynamics of Aβ(1–40) interacting 1,2-dimyristoyl-sn-glycero-3-phosphoglycerol (DMPG) bilayers. In the structural investigations of lipid bilayer’s response to Aβ binding, Small Angle Neutron Scattering and Neutron Membrane Diffraction revealed that the Aβ anchors firmly to the highly charged DMPG bilayers in the interfacial region between water and hydrocarbon chain, and it doesn’t penetrate deeply into the bilayer. This association mode is substantiated by the dynamics studies with high resolution Quasi-Elastic Neutron Scattering experiments, showing that the addition of Aβ mainly affects the slower lateral motion of lipid molecules, especially in the fluid phase, but not the faster internal motion. The results revealed that Aβ associates with the highly charged membrane in surface with limited impact on the structure, but the altered membrane dynamics could have more influence on other membrane processes.

59 BASIC BIOLOGICAL SCIENCES↗

EMSL Community Science Campaign Meeting: Critical Minerals and Materials - Rhizo Critical Campaign Breakout Session Report Summary

The “Critical Minerals Biogeochemistry in the Rhizosphere – Ultramafic Soils (Rhizo Critical)” campaign breakout (BO) session was organized to identify major knowledge gaps and fundamental research needs in rhizosphere microbiology and geochemistry that, if addressed, could transform our ability to recover critical minerals from ultramafic soil systems. We sought to identify significant challenges that must be surmounted in the pursuit of deeper science knowledge. Our ultimate goal is to understand this landscape well enough to identify and prioritize opportunities for EMSL to make the greatest impact with Environmental Transformations and Interactions (ETI) science area research campaigns focused on the biogeochemical processes controlling the behavior of critical minerals and materials in the rhizosphere. The increasing demand for critical materials and minerals (CMM) in the U.S. has heightened interest in low-grade ores with much attention on ultramafic soils, which contain valuable metals such as nickel (Ni), chromium (Cr), manganese, cobalt (Co), and copper (Lee et al., 2025; DOE CMM Report, 2023) used in advanced battery, magnet, wiring and wind turbines, and stainless steel technologies. Metal hyperaccumulating plants grown in ultramafic soils can extract economically valuable concentrations of CMMs through the process of phytomining. This technology has evolved from phytoremediation, which involves using plants to cleanse contaminated environments by removing, detoxifying, or stabilizing pollutants like metals and organic compounds. Hyperaccumulator plants are capable of storing metals in their living tissues at concentrations hundreds to thousands of times higher than those found in 'normal' plants. For instance, while the average concentration of Ni in the dry matter of plants growing in typical soils is usually less than 5 µg g?¹, Ni hyperaccumulation is defined by concentrations exceeding 1,000 µg g?¹ (Corzo Remigio et al., 2020; Reeves et al., 2018). Phytomining research has primarily focused on Ni (Rylott and van der Ent, 2025), for which the U.S. has very limited conventional mines in operation. Most soils typically contain Ni concentrations ranging from 7 to 50 mg kg-1, whereas serpentine soils exhibit significantly higher levels, with Ni content often ranging between 700 and 8,000 mg kg-1 (Sobczyk et al., 2017). While more than 500 plant species in over 50 different families have been identified as Ni hyperaccumulators (Kidd et al., 2018), Ni phytomining (and phytominng in general) remains largely untested because most studies are short-term, small-scale, and conducted under simplified or artificially enriched conditions, so they fail to capture the low metal concentrations, environmental variability, and management constraints that would be needed for a field-scale demonstration. Few hyperaccumulator species have been validated as true “metal crops,” and their biomass production, stress tolerance, and rooting characteristics are usually too poor to yield economically meaningful metal outputs. Critically, the basic mechanisms of metal uptake, transport, and sequestration, especially as shaped by belowground processes such as root exudation, rhizosphere chemistry, and root–microbe interactions that control metal mobility and bioavailability (Montreemuk et al., 2023; Kidd et al., 2018; Durand et al., 2023; Alford et al., 2010), are still only partially understood, and downstream metal recovery from biomass is rarely optimized. Because these limitations stem from gaps in fundamental knowledge rather than from a failure of the concept itself (Rylott and van der Ent, 2025; van der Ent et al., 2015), there is a strong need for basic science that dissects plant metal homeostasis, rhizosphere and microbial processes, and their integration with soil chemistry and process engineering to design more robust, scalable phytomining systems.

Ahkami, Amirhossein↗

Atomic Force Microscopy and Infrared Nanospectroscopy of COVID-19 Spike Protein for the Quantification of Adhesion to Common Surfaces

The COVID-19 pandemic has claimed millions of lives worldwide, sickened many more, and has resulted in severe socio-economic consequences. As society returns to normal, understanding the spread and persistence of SARS CoV-2 on commonplace surfaces can help to mitigate future outbreaks of coronaviruses and other pathogens. We hypothesize that such an understanding can be aided from studying the binding and interaction of viral proteins with non-biological surfaces. Here, we propose a methodology for investigating the adhesion of the SARS CoV-2 spike glycoprotein on common inorganic surfaces such as aluminum-, copper-, iron-, silica-, and ceria-oxides as well as metallic gold. Quantitative adhesion was obtained from the analysis of measured forces at the nanoscale using an atomic force microscope operated under ambient conditions. Without imposing further constraints on the measurement conditions, our preliminary findings suggest that spike glycoproteins interact with similar adhesion forces across the majority of the metal oxides tested with the exception to gold, for which attraction forces ~10 times stronger than all other materials studied were observed. Ferritin, which was used as a reference protein, was found to exhibit similar adhesion forces as SARS CoV-2 spike protein. Further, this study results show that glycoprotein adhesion forces for similar ambient humidity, tip shape, and contact surface are non-specific to the properties of metal oxide surfaces, which are expected to be covered by a thin water film. The findings suggest that at ambient conditions glycoprotein adhesion to metal oxides is primarily controlled by the water capillary forces and they depend on the surface tension of the liquid (water). We discuss further strategies warranted to decipher the intricate nanoscale forces for improved quantification of the adhesion.

59 BASIC BIOLOGICAL SCIENCES↗

Enzyme Complexes of Ptr4CL and PtrHCT Modulate Co-enzyme A Ligation of Hydroxycinnamic Acids for Monolignol Biosynthesis in Populus trichocarpa

Co-enzyme A (CoA) ligation of hydroxycinnamic acids by 4-coumaric acid:CoA ligase (4CL) is a critical step in the biosynthesis of monolignols. Perturbation of 4CL activity significantly impacts the lignin content of diverse plant species. In Populus trichocarpa, two well-studied xylem-specific Ptr4CLs (Ptr4CL3 and Ptr4CL5) catalyze the CoA ligation of 4-coumaric acid to 4-coumaroyl-CoA and caffeic acid to caffeoyl-CoA. Subsequently, two 4-hydroxycinnamoyl-CoA:shikimic acid hydroxycinnamoyl transferases (PtrHCT1 and PtrHCT6) mediate the conversion of 4-coumaroyl-CoA to caffeoyl-CoA. Here, we show that the CoA ligation of 4-coumaric and caffeic acids is modulated by Ptr4CL/PtrHCT protein complexes. Downregulation of PtrHCTs reduced Ptr4CL activities in the stem-differentiating xylem (SDX) of transgenic P. trichocarpa. The Ptr4CL/PtrHCT interactions were then validated in vivo using biomolecular fluorescence complementation (BiFC) and protein pull-down assays in P. trichocarpa SDX extracts. Enzyme activity assays using recombinant proteins of Ptr4CL and PtrHCT showed elevated CoA ligation activity for Ptr4CL when supplemented with PtrHCT. Numerical analyses based on an evolutionary computation of the CoA ligation activity estimated the stoichiometry of the protein complex to consist of one Ptr4CL and two PtrHCTs, which was experimentally confirmed by chemical cross-linking using SDX plant protein extracts and recombinant proteins. Based on these results, we propose that Ptr4CL/PtrHCT complexes modulate the metabolic flux of CoA ligation for monolignol biosynthesis during wood formation in P. trichocarpa.

59 BASIC BIOLOGICAL SCIENCES↗

Framework for idealized climate simulations with spatiotemporal stochastic clouds and planetary-scale circulations

In climate predictions, clouds are the leading source of uncertainty. This is partly because, to simulate the fluid dynamics of climate over the entire globe, a large grid spacing must be used, so clouds are a subgrid-scale parametrization rather than a resolved feature. Here, a framework is investigated with finer grid spacing of O(1) or O(10)km so that some clouds are not subgrid-scale; instead, clouds evolve on the numerical grid. This cloud evolution is achieved using stochastic modeling. Hence, the framework is idealized in the sense that the full fluid dynamics of cloud circulations is still not resolved, and simplified vertical structures are used. Nevertheless, the fluid dynamics model includes evolving clouds that interactively adjust in size, shape, lifetime, and regional coverage. In addition, different cloud types are included with different roles in the climate system, including deep convective clouds and also boundary-layer clouds such as shallow cumulus and stratocumulus clouds. Other basic aspects of the idealized climate system are planetary-scale circulations (e.g., Walker circulation) and radiation. With these ingredients (evolving clouds, planetary-scale circulations, and radiation), the framework has the potential for idealized investigations of climate change with interactive cloud–radiative feedback of individual clouds. Here, the formulation of the model equations is presented, and numerical simulations are shown to illustrate the model dynamics and climate change.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Signatures of an energetic charged body streaming in a plasma

A charged body moving in a plasma can excite a variety of linear and nonlinear waves in the form of trailing wakes, fore-wake shocks, and precursor solitons. These structures can further interact with the background plasma to create secondary effects that can serve as signatures of the passage of the charged body. Using particle-in-cell simulations, we carry out a basic investigation of the dynamics of a plasma system that is being traversed by an energetic charged body. Using two different shapes of this charged source, namely, an idealized infinite length planar source and a two-dimensional thin rectangular source, we examine the differences in the nature of the excited wave structures and their consequent impact on the background plasma. Our simulations reveal interesting features such as the dependence of the precursor speeds on the total charge on the driving source, local particle trapping, and energization of the trapped particles in various regions along the traversal path leading to the formation of energetic charged beamlets. So our basic findings could find practical applications such as in analyzing the trajectories of charged objects like space debris orbiting in the ionosphere.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Research in interactive scene analysis

The recovery of information about the three dimensional structure and physical characteristics of surfaces depicted in an image was studied focusing on two complementary problems: (1) basic techniques for inferring three dimensional surface shape from two dimensional images and (2) means for integrating the results of different techniques to obtain a globally consistent surface description. A technique was developed for constraining surface orientation along image contours that correspond to surface boundaries. A means for interpolating surface orientation estimates from a variety of sources into smooth surfaces--a major integration problem--was also developed. A computational model, based on these techniques, was proposed for inferring the three dimensional surface structure depicted in a line drawing.

Tenenbaum, J. M.↗