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At least 163 records · Page 9

A functional microbiome catalogue crowdsourced from North American rivers

Predicting elemental cycles and maintaining water quality under increasing anthropogenic influence requires knowledge of the spatial drivers of river microbiomes. However, understanding of the core microbial processes governing river biogeochemistry is hindered by a lack of genome-resolved functional insights and sampling across multiple rivers. Here we used a community science effort to accelerate the sampling, sequencing and genome-resolved analyses of river microbiomes to create the Genome Resolved Open Watersheds database (GROWdb). GROWdb profiles the identity, distribution, function and expression of microbial genomes across river surface waters covering 90% of United States watersheds. Specifically, GROWdb encompasses microbial lineages from 27 phyla, including novel members from 10 families and 128 genera, and defines the core river microbiome at the genome level. GROWdb analyses coupled to extensive geospatial information reveals local and regional drivers of microbial community structuring, while also presenting foundational hypotheses about ecosystem function. Building on the previously conceived River Continuum Concept, we layer on microbial functional trait expression, which suggests that the structure and function of river microbiomes is predictable. We make GROWdb available through various collaborative cyberinfrastructures, so that it can be widely accessed across disciplines for watershed predictive modelling and microbiome-based management practices.

59 BASIC BIOLOGICAL SCIENCES↗

The many-body expansion for aqueous systems revisited: 1. Water-water interactions

We revisit the Many-Body Expansion (MBE) for water-water interactions by examining the effects of the basis set, including those resulting from the Basis Set Superposition Error (BSSE) correction, on the various terms for selected sizes of water clusters up to n = 21. The analysis is performed at the second order Møller-Plesset (MP2) perturbation theory with the family of augmented correlation consistent basis sets up to five zeta quality for the (H2O)n, n = 7, 10, 13, 16 and 21 clusters, for which we report either the complete MBE (n = 7, 10) or the one through the 6-body (n = 13) and the 5-body terms (n = 16, 21). Our results suggest that any sizeable contributions to the total cluster binding energy arising from the 5-body and larger terms are solely an artifact of the size of the basis set. Indeed, all terms above the 4-body converge monotonically to practically zero at the Complete Basis Set (CBS) limit. The magnitudes of the 5-body and above terms are accurately reproduced even with the smaller basis set of the series (aug-cc-pVDZ) once the BSSE correction is taken into account. The same level of theory (MP2/aug-cc-pVDZ, BSSEcorrected) also accurately reproduces the MP2/CBS values of the 3- and 4-body terms. The contribution of electron correlation to the 3- and 4-body terms is quite small, so that neglecting the correlation contribution in all terms above the 3-body results in an error of ??(0.1%). The BSSE correction to the largest 2-body term in the MBE was accurately estimated from the function ?? [1 + erf(-?? ??)], which is proportional to the common (overlapping) area between two Gaussian distributions whose centers are separated by R, with the constants ??, ?? fitted to the calculated BSSE corrections for the individual 2-body terms of the clusters with each basis set. Our results unquestionably demonstrate that the MBE for water-water interactions converges to the 4-body term, since any finite terms above the 4-body are artifacts of the size of the basis set and can be safely truncated at the 4-body term when either a very large basis set is used or BSSE corrections are taken into account even with the aug-cc-pVDZ basis set. We expect these findings to have important consequences in the pursuit of accurate many-body molecular dynamics simulations for aqueous systems.

Heindel, Joseph↗

Catalyzing the Mass Adoption of High Efficiency Technologies in the Multifamily Housing Market

ICAST’s objective was to catalyze the adoption of very-high-efficiency (VHE) heat pump HVAC (mini-splits) and water heaters (HPWH) in multifamily (MF), especially affordable housing (MFAH). Nationally, the market penetration of ENERGY STAR-certified ASHPs is estimated at 43%, and for HPWHs it’s 3% (ENERGY STAR, 2022). Note that mini-splits are a much more practical choice for MF units than ducted systems and their adoption is only a portion of the number provided above, but isolating the market penetration data for mini-split systems is difficult. Both the heat pump-based HVAC and water heater systems can be approx. three times more efficient than their conventional counterparts for space and water heating. While awareness and adoption of VHE heat pumps has been growing nationally, and electric heat pump systems have outsold gas furnaces for two years in a row, the MF segment continues to lag behind single-family. MF constitutes almost a third of the housing in the U.S., so scaling up VHE adoption in this segment can assist in achieving critical climate change goals, while preserving housing affordability for the low-to-moderate income (LMI) population (historically, 85% of residents of MF are LMI).

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Feasibility Study of NSLS-II Sextupole BBA Measurement

In storage ring light sources, beam-based alignment (BBA) which adjusts the BPM centers to the quadrupole magnet centers is a common practice to maintain the machine performance. For more reliable and convenient BBA process, in the design of the storage ring, BPMs are located as close as possible to the quadrupoles. The most common method is scanning the position of the beam at the BPM (equivalently at the adjacent quadrupole) and find the position where the quadrupole strength change does not give change in the closed orbit. In the simulation of the feasibility test, we choose parameters, tune, orbit and phase advance and measure their variations depending on the sextupole offsets. Also, together with the real configuration of family, we simulate the individual power supply case for the comparisons. In this note, the simulation processes and the results are presented.

43 PARTICLE ACCELERATORS↗

The CFL condition for spectral approximations to hyperbolic initial-boundary value problems

The stability of spectral approximations to scalar hyperbolic initial-boundary value problems with variable coefficients are studied. Time is discretized by explicit multi-level or Runge-Kutta methods of order less than or equal to 3 (forward Euler time differencing is included), and spatial discretizations are studied by spectral and pseudospectral approximations associated with the general family of Jacobi polynomials. It is proved that these fully explicit spectral approximations are stable provided their time-step, delta t, is restricted by the CFL-like condition, delta t less than Const. N(exp-2), where N equals the spatial number of degrees of freedom. We give two independent proofs of this result, depending on two different choices of approximate L(exp 2)-weighted norms. In both approaches, the proofs hinge on a certain inverse inequality interesting for its own sake. The result confirms the commonly held belief that the above CFL stability restriction, which is extensively used in practical implementations, guarantees the stability (and hence the convergence) of fully-explicit spectral approximations in the nonperiodic case.

Gottlieb, David↗

Superconductivity in the Sn-Ba-Sr-Y-Cu-O system

Since Bednorz and Muller discovered high-T(sub c) superconductivity in the La-Ba-Cu-O compound, several families of superconducting oxides have been synthesized. Here, researchers report the results of search for superconductivity in the compounds based on tin, which has a lone electron pair like Bi, Tl, Pb. The following compounds were synthesized: Sn1Ba1Sr1Cu3Ox, Sn1Ba1Ca1Cu3Ox, Sn1Ba1Mg1Cu3Ox, Sn1Sr1Ca1Cu3Ox, Sn1Sr1Mg1Cu3Ox, Sn1Ca1Mg1Cu3Ox. The initial components were oxides and carbonates of the appropriate elements. Standard firing-grinding procedure was used. Final heating was carried out at 960 C during 12 hours. Then the samples were cooled inside the furnace. All the synthesis cycles were carried out in air atmosphere. Among the synthesized compounds only Sn1Ba1Sr1Cu3Ox showed remarkable conductivity. Other compounds were practically dielectrics. Presence of a possible superconductivity in Sn1Ba1Sr1Cu3Ox was defined by using the Meissner effect. At low temperature a deviation from paramagnetic behavior is observed. The hysteresis loops obtained at lower temperatures undoubtly testify to the presence of a superconductive phase in the sample. However, the part of the superconductive phase in the Sn1Ba1Sr1Cu3Ox ceramic turned out to be small, less than 2 percent, which agrees with the estimation from magnetic data. In order to increase the content of the superconductive phase two-valent cations Ba, Sr were partially substituted by univalent (K) and three-valent ones (Y).

Aleksandrov, K. S.↗

The CFL condition for spectral approximations to hyperbolic initial-boundary value problems

The stability of spectral approximations to scalar hyperbolic initial-boundary value problems with variable coefficients are studied. Time is discretized by explicit multi-level or Runge-Kutta methods of order less than or equal to 3 (forward Euler time differencing is included), and spatial discretizations are studied by spectral and pseudospectral approximations associated with the general family of Jacobi polynomials. It is proved that these fully explicit spectral approximations are stable provided their time-step, delta t, is restricted by the CFL-like condition, delta t less than Const. N(exp-2), where N equals the spatial number of degrees of freedom. We give two independent proofs of this result, depending on two different choices of approximate L(exp 2)-weighted norms. In both approaches, the proofs hinge on a certain inverse inequality interesting for its own sake. The result confirms the commonly held belief that the above CFL stability restriction, which is extensively used in practical implementations, guarantees the stability (and hence the convergence) of fully-explicit spectral approximations in the nonperiodic case.

Gottlieb, David↗

Learning Robust Marking Policies for Adaptive Mesh Refinement

Here in this work, we revisit the marking decisions made in the standard adaptive finite element method (AFEM). Experience shows that a naïve marking policy leads to inefficient use of computational resources for adaptive mesh refinement (AMR). Consequently, using AMR in practice often involves ad-hoc or time-consuming offline parameter tuning to set appropriate parameters for the marking subroutine. To address these practical concerns, we recast AMR as a Markov decision process in which refinement parameters can be selected on-the-fly at run time, without the need for pre-tuning by expert users. In this new paradigm, the refinement parameters are also chosen adaptively via a marking policy that can be optimized using methods from reinforcement learning. We use the Poisson equation to demonstrate our techniques on h- and hp-refinement benchmark problems, and our experiments suggest that superior marking policies remain undiscovered for many classical AFEM applications. Furthermore, an unexpected observation from this work is that marking policies trained on one family of PDEs are sometimes robust enough to perform well on problems far outside the training family. For illustration, we show that a simple hp-refinement policy trained on 2D domains with only a single re-entrant corner can be deployed on far more complicated 2D domains, and even 3D domains, without significant performance loss. For reproduction and broader adoption, we accompany this work with an open-source implementation of our methods.

97 MATHEMATICS AND COMPUTING↗

Better Proton-Conducting Polymers for Fuel-Cell Membranes

Polyoxyphenylene triazole sulfonic acid has been proposed as a basis for development of improved proton-conducting polymeric materials for solid-electrolyte membranes in hydrogen/air fuel cells. Heretofore, the proton-conducting membrane materials of choice have been exemplified by a family of perfluorosulfonic acid-based polymers (Nafion7 or equivalent). These materials are suitable for operation in the temperature of 75 to 85 C, but in order to reduce the sizes and/or increase the energy-conversion efficiencies of fuel-cell systems, it would be desirable to increase temperatures to as high as 120 C for transportation applications, and to as high as 180 C for stationary applications. However, at 120 C and at relative humidity values below 50 percent, the loss of water from perfluorosulfonic acid-based polymer membranes results in fuel-cell power densities too low to be of practical value. Therefore, membrane electrolyte materials that have usefully high proton conductivity in the temperature range of 180 C at low relative humidity and that do not rely on water for proton conduction at 180 C would be desirable. The proposed polyoxyphenylene triazole sulfonic acid-based materials have been conjectured to have these desirable properties. These materials would be free of volatile or mobile acid constituents. The generic molecular structure of these materials is intended to exploit the fact, demonstrated in previous research, that materials that contain ionizable acid and base groups covalently attached to thermally stable polymer backbones exhibit proton conduction even in the anhydrous state.

Narayan, Sri↗

Ground and excited state gradients with end-to-end differentiable semiempirical quantum chemistry

Accurate and efficient gradients of molecular energy with respect to nuclear degrees of freedom are essential for geometry optimization and molecular dynamics, including simulations that go beyond the Born–Oppenheimer regime. A common approach involves deriving analytical formulas for new electronic structure methods, which is often conceptually difficult and requires tedious coding. Here, we implement analytical, semi-numerical, and automatic differentiation (AD)-based gradient pathways for semiempirical Hamiltonian models in the PYSEQM software package, leveraging both graphics processing unit (GPU) and central processing unit (CPU) architectures. We further extend these capabilities to excited states calculated using the configuration interaction singles and time-dependent Hartree–Fock ansätze. We benchmark wall time, peak memory usage, and accuracy across three molecular families of varying chemical complexity, including systems of up to a thousand atoms. For ground-state simulations, analytical and AD gradients achieve near-identical GPU runtimes, while semi-numerical gradients are slower on GPU but remain competitive on CPU. For excited states, both analytical and custom AD approaches using implicit differentiation show similar performance and low memory requirements, whereas gradients with full AD are memory-limited. AD gradients match analytical ones in accuracy across all tested systems, aided by a quaternion-based diatomic frame rotation for two-center quantities that ensures smooth energy surfaces. Overall, automatic differentiation emerges as a practical alternative to analytical gradients in semiempirical quantum chemistry, offering high accuracy while allowing seamless integration in AI-driven workflows and popular packages, such as PyTorch and JAX. Our results provide actionable guidance for selecting optimal gradient strategies in large-scale ground- and excited-state molecular dynamics simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

CAHS: Context-Aware Homology Search

Protein homology search is foundational to bioinformatics: it supports annotation transfer, structure/function inference, and evolutionary analysis over rapidly expanding sequence repositories (e.g., UniProtKB). Profile hidden Markov models (pHMMs), as implemented in HMMER, remain the most widely trusted approach because they provide statistically calibrated E-values; however, their gap behavior is fixed once a profile is trained, despite biological evidence that insertion/deletion tolerance varies across flexible loops and intrinsically disordered regions. We present CAHS (Context-Aware Homology Search), a lightweight query-time adapter for pHMM search that incorporates learned and biologically motivated signals without changing HMMER's downstream search pipeline or its calibrated E-value reporting. Given a query sequence, CAHS computes per-residue representations from a protein language model and a disorder predictor, maps these to profile coordinates, and modulates only match-state transition rows (gap-open and gap-extension probabilities) while preserving Plan7 constraints. We comprehensively evaluate CAHS across six structurally diverse protein families and multi-domain architectures against a 570k-sequence target corpus. CAHS expands detection capability, retrieving thousands of additional remote homologs at relaxed thresholds by maintaining alignment quality through flexible regions. For multi-domain proteins, context-aware modulation resolves 94% of fragmented alignments. Crucially, CAHS preserves hit-set invariance at stringent operating points (E<10-10), demonstrating increased statistical confidence without inflating false positives. Furthermore, sharper statistical distinction between homologs and background noise during early filter stages yields up to a 3.87× acceleration in end-to-end wall-clock time on high-performance computing clusters. Overall, CAHS illustrates a practical AI-for-science design pattern: augmenting a trusted probabilistic model with query-specific learned signals to improve interpretable, reproducible inference in data-rich biology.

Bhattaram, Swethasree [Georgia Institute of Techno↗

Gradient-based constrained optimization using a database of linear reduced-order models

A methodology grounded in model reduction is presented for accelerating the gradient-based solution of a family of linear or nonlinear constrained optimization problems where the constraints include at least one linear Partial Differential Equation (PDE). A key component of this methodology is the construction, during an offline phase, of a database of pointwise, linear, Projection-based Reduced-Order Models (PROM)s associated with a design parameter space and the linear PDE(s). A parameter sampling procedure based on an appropriate saturation assumption is proposed to maximize the efficiency of such a database of PROMs. A real-time method is also presented for interpolating at any queried but unsampled parameter vector in the design parameter space the relevant sensitivities of a PROM. The practical feasibility, computational advantages, and performance of the proposed methodology are demonstrated for several realistic, nonlinear, aerodynamic shape optimization problems governed by linear aeroelastic constraints.

97 MATHEMATICS AND COMPUTING↗

Elastic depths for detecting shape anomalies in functional data

This this paper, we propose a new family of depth measures called the elastic depths that can be used to greatly improve shape anomaly detection in functional data. Shape anomalies are functions that have considerably different geometric forms or features from the rest of the data. Identifying them is generally more difficult than identifying magnitude anomalies because shape anomalies are often not distinguishable from the bulk of the data with visualization methods. The proposed elastic depths use the recently developed elastic distances to directly measure the centrality of functions in the amplitude and phase spaces. Measuring shape outlyingness in these spaces provides a rigorous quantification of shape which, in turn, gives the elastic depths a strong theoretical and practical advantage over other methods in detecting shape anomalies. A simple boxplot and thresholding method are introduced to identify shape anomalies using the elastic depths. We assess the elastic depth's detection skill on simulated shape outlier scenarios and compare them against popular shape anomaly detectors. Finally, bond yields, image outlines, and hurricane trajectories are used to demonstrate our method's applicability to functional data observed on three different manifolds.

97 MATHEMATICS AND COMPUTING↗

Strainrange partitioning: A total strain range version

Procedures are presented for expressing the Strainrange Partitioning (SRP) method for creep fatigue life prediction in terms of total strain range. Inelastic and elastic strain-range - life relations are summed to give total strain-range - life relations. The life components due to inelastic strains are dealt with using conventional SRP procedures while the life components due to elastic strains are expressed as families of time-dependent terms for each type of SRP cycle. Cyclic constitutive material behavior plays an important role in establishing the elastic strain-range - life relations as well as the partitioning of the inelastic strains. To apply the approach, however, it is not necessary to have to determine the magnitude of the inelastic strain range. The total strain SRP approach is evaluated and verified using two nickel base superalloys, AF2-1DA and Rene 95. Excellent agreement is demonstrated between observed and predicted cyclic lifetimes with 70 to 80 percent of the predicted lives falling within factors of two of the observed lives. The total strain-range SRP approach should be of considerable practical value to designers who are faced with creep-fatigue problems for which the inelastic strains cannot be calculated with sufficient accuracy to make reliable life predictions by the conventional inelastic strain range SRP approach.

Halford, G. R.↗

Strainrange partitioning - A total strain range version

Procedures are presented for expressing the Strainrange Partitioning (SRP) method for creep fatigue life prediction in terms of total strain range. Inelastic and elastic strain-range - life relations are summed to give total strain-range - life relations. The life components due to inelastic strains are dealt with using conventional SRP procedures while the life components due to elastic strains are expressed as families of time-dependent terms for each type of SRP cycle. Cyclic constitutive material behavior plays an important role in establishing the elastic strain-range life relations as well as the partitioning of the inelastic strains. To apply the approach, however, it is not necessary to have to determine the magnitude of the inelastic strain range. The total strain SRP approach is evaluated and verified using two nickel base superalloys, AF2-1DA and Rene 95. Excellent agreement is demonstrated between observed and predicted cyclic lifetimes with 70 to 80 percent of the predicted lives falling within factors of two of the observed lives. The total strain-range SRP approach should be of considerable practical value to designers who are faced with creep-fatigue problems for which the inelastic strains cannot be calculated with sufficient accuracy to make reliable life predictions by the conventional inelastic strain range SRP approach.

Halford, G. R.↗

Superconductivity in the Sn-Ba-Sr-Y-Cu-O system

After the discovery of high-T(sub c) superconductivity in the La-Ba-Cu-O compound, several families of superconducting oxides were synthesized. Here, researchers report the results of the search for superconductivity in the compounds based on tin which has a lone electron pair like Bi, Tl, and Pb. The following compounds were synthesized: Sn1Ba1Sr1Cu3O(sub x), Sn1Ba1Ca1Cu3O(sub x), Sn1Ba1Mg1Cu3O(sub x), Sn1Sr1Ca1Cu3O(sub x), Sn1Sr1Mg1Cu3O(sub x), and Sn1Ca1Mg1Cu3O(sub x). The initial components were oxides and carbonates of the appropriate elements. A standard firing-grinding procedure was used. Final heating was carried out at 960 C during 12 hours. Then the samples were cooled inside the furnace. All the synthesis cycles were carried out in air atmosphere. Among the synthesized compounds only Sn1Ba1Sr1Cu3O(sub x) showed remarkable conductivity. Other compounds were practically dielectrics. Presence of a possible superconductivity in Sn1Ba1Sr1Cu3O(sub x) was defined by using the Meissner effect. At low temperature a deviation from paramagnetic behavior is observed. The hysteresis loops obtained at lower temperature undoubtly testify to the presence of a superconductive phase in the sample. However, the part of the superconductive phase in the Sn1Ba1Sr1Cu3O(sub x) ceramic turned out to be small, less than 2 percent, which agrees with the estimation from magnetic data. In order to increase the content of the superconductive phase, two-valent cations Ba and Sr were partially substituted by univalent (K) and three-valent ones (Y).

Aleksandrov, K. S.↗

Numerical Simulation of Fluidic Actuators for Flow Control Applications

Active flow control technology is finding increasing use in aerospace applications to control flow separation and improve aerodynamic performance. In this paper we examine the characteristics of a class of fluidic actuators that are being considered for active flow control applications for a variety of practical problems. Based on recent experimental work, such actuators have been found to be more efficient for controlling flow separation in terms of mass flow requirements compared to constant blowing and suction or even synthetic jet actuators. The fluidic actuators produce spanwise oscillating jets, and therefore are also known as sweeping jets. The frequency and spanwise sweeping extent depend on the geometric parameters and mass flow rate entering the actuators through the inlet section. The flow physics associated with these actuators is quite complex and not fully understood at this time. The unsteady flow generated by such actuators is simulated using the lattice Boltzmann based solver PowerFLOW R . Computed mean and standard deviation of velocity profiles generated by a family of fluidic actuators in quiescent air are compared with experimental data. Simulated results replicate the experimentally observed trends with parametric variation of geometry and inflow conditions.

Vasta, Veer N.↗