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At least 145 records · Page 8

Synthetic microbial communities: Bridging research and application in second-generation bioenergy feedstock microbiomes

The sustainable production of purpose-grown bioenergy feedstocks is essential in transitioning away from fossil fuels. Synthetic communities (SynComs) are consortia of microorganisms that can be used as biological interventions to support objectives like plant growth and stress tolerance. This review examines the state of knowledge regarding microbiomes and SynComs of second-generation bioenergy feedstocks, focusing on the rhizosphere. We first provide an overview of second-generation feedstocks, including switchgrass (Panicum virgatum), miscanthus (Miscanthus × giganteus), sorghum (Sorghum spp.), sugarcane (Saccharum spp.), and poplar (Populus spp.), and summarize our current understanding of their plant-soil-microbiome ecology. We next discuss considerations in the objectives, design, and evaluation of SynComs to enhance feedstock production, and then critically review the literature around their use. Our literature analysis revealed that SynCom performance varied substantially between controlled pilot experiments and field trials, possibly due to system complexity that could not be fully considered in their design and pilot evaluation. We identified a gap in the use of SynComs to support the unique sustainability objectives of biofuel feedstock agriculture, presenting an opportunity to leverage these additional microbial traits in SynCom designs. Finally, we emphasize the importance of targeted research to identify the ecological principles that govern the assembly, activation, and persistence of microbes in the feedstock rhizosphere, thereby enhancing our capacity to manage microbiomes under diverse environmental conditions and ensure their functionality. Beyond biofuels, SynComs are a promising microbiome management strategy for crop production; however, an ecologically informed design and evaluation of SynComs are advised.

SynCom↗

Autonomous anomaly detection of proliferation in the AGN-201 nuclear reactor digital twin

The expansion of global nuclear power necessitates advanced methods for analyzing proliferation indicators. This study introduces a novel application of the Isolation Forest Machine Learning (IFML) algorithm within a digital twin (DT) of the AGN-201 nuclear reactor to autonomously detect anomalies. Leveraging real-time operational data from the AGN-201 DT, the IFML algorithm identifies outliers without prior data labeling and operates as a lightweight, complementary approach to traditional physics-based anomaly detection methods for nuclear safeguards. In a simulated Red vs. Blue team exercise, the IFML algorithm successfully detected six significant unseen anomalies related to reactivity changes, achieving an accuracy of 99% for identifying operational deviationxs. These anomalies, caused by deliberate perturbations, were detected alongside known physics-based models, underscoring the potential of IFML to enhance real-time monitoring without displacing traditional methods. Further, this study highlights the applicability of IFML in nuclear environments by providing an additional, redundant layer of anomaly detection to improve safeguards and operational safety in complex systems.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

High-throughput validation of phase formability and simulation accuracy of Cantor alloys

High-throughput methods enable accelerated discovery of novel materials in complex systems such as high-entropy alloys, which exhibit intricate phase stability across vast compositional spaces. Computational approaches, including Density Functional Theory (DFT) and calculation of phase diagrams (CALPHAD), facilitate screening of phase formability as a function of composition and temperature. However, the integration of computational predictions with experimental validation remains challenging in high-throughput studies. In this work, we introduce a quantitative confidence metric to assess the agreement between predictions and experimental observations, providing a quantitative measure of the confidence of machine learning models trained on either DFT or CALPHAD input in accounting for experimental evidence. The experimental dataset was generated via high-throughput in-situ synchrotron X-ray diffraction on compositionally varied FeNiMnCr alloy libraries, heated from room temperature to ~1000 °C. Agreement between the observed and predicted phases was evaluated using either temperature-independent phase classification or a model that incorporates a temperature-dependent probability of phase formation. This integrated approach demonstrates where strong overall agreement between computation and experiment exists, while also identifying key discrepancies, particularly in FCC/BCC predictions at Mn-rich regions to inform future model refinement.

36 - MATERIALS SCIENCE↗

Accelerating multicanonical sampling with irreversibility

Flat-histogram Monte Carlo simulations are well-established, robust methods to perform random walks in a physical observable or parameter space, making them suitable for finding ground states or studying phase transitions in complex systems in statistical physics. However, their efficiency can be limited by the time to attain the desired flat distribution, which is generally unknown prior to the simulations. In particular, they might suffer from slowing down towards the end of a simulation due to the diffusive nature of random walks. In this work we apply irreversibility to the multicanonical Monte Carlo method via the lifting approach to alleviate this behavior. We achieve a 2–4 times speedup in ground-state search for a two-dimensional (2D) Ising model, and up to an order of magnitude of speedup for finding the ground-state energy in an Edwards–Anderson spin glass, compared to traditional multicanonical sampling. In conclusion, the round-trip times between ground states show a narrower distribution and are significantly shorter compared to the reversible counterpart, suggesting that a lower convergence time with a smaller time variance is feasible.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Regional surrogates for predictive control of digital twins

Digital twins of complex systems must involve a model that is fast, generalizable, and usable for real-time control. For example, high-fidelity nonlinear multiphysics simulations can capture laser-material interactions, but are too slow for optimization or model predictive control (MPC). Reduced-order models, used to accelerate such computation, frequently fail to generalize to unseen inputs or control states. We show theoretically that this failure is intrinsic, i.e., that a learned model is non-unique outside the sampled subspace when its low-rank structure arises from limited excitation and clustered eigenvalues, rather than from a user-imposed truncation alone. Motivated by this result, we propose a control-ready regional surrogate-construction framework for both autonomous and nonautonomous dynamics; it employs Koopman lifting to represent nonlinearities, while preserving spatial locality. We illustrate our approach by constructing a control-ready surrogate for the digital twin of a thermal component of additive-manufacturing process. Our surrogate, localized in space through a von Neumann stencil, is learned from noisy high-fidelity simulations that emulate thermal-camera images collected during the manufacturing. It is linear in thermo-physically augmented states so that MPC reduces to a convex quadratic program. The surrogate requires no online correction, generalizes to unseen scan paths and power profiles of the laser, and is more than three orders of magnitude faster than a finite-difference solver. Furthermore, when the MPC sequence computed on the digital twin is applied to this solver, closed-loop temperature regulation is recovered, showing that the surrogate preserves control-relevant input-output behavior.

Data-driven model↗

Single and Dual-Solute Transport in Quaternary Ammonium-Functionalized Anion Exchange Membranes: Isolating the Impact of Water Volume Fraction

Membranes are essential components of photoelectrochemical CO 2 reduction cells (PEC-CRC), as they regulate solute transport and impact device efficiency. These cells are a promising approach for converting carbon dioxide into valuable chemicals. However, electrochemical reactions involve not just a single electrolyte; membrane transport typically includes multiple electrolytes. When a mixture of solutes is present, the presence of one solute in the membrane can impact the diffusion and sorption of other solutes. In complex systems where multiple solutes are diffusing simultaneously through a hydrated, dense polymer membrane, the resulting transport behavior is poorly understood. This study highlights the individual and two solute transport behavior of potassium formate, acetate, and bicarbonate ions in neutral membranes and quaternary ammonium-functionalized anion exchange membranes (AEMs) based on phenyl acrylate polymer backbones. By isolating the effect of water content, we emphasize how fixed charge density and solute-membrane interactions influence transport behavior. In neutral membranes, the diffusivity follows the order of potassium formate > potassium acetate > potassium bicarbonate. However, in AEMs, the order shifts due to changes in ion-membrane interactions, with potassium bicarbonate diffusivity surpassing that of potassium acetate. These results underscore the importance of ion exchange membranes and ion-membrane interaction in modulating transport properties, providing valuable insights for optimizing membranes in electrochemical applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Lowering entry barriers to developing custom simulators of distributed applications and platforms with SimGrid

Researchers in parallel and distributed computing (PDC) often resort to simulation because experiments conducted using a simulator can be for arbitrary experimental scenarios, are less resource-, labor-, and time-consuming than their real-world counterparts, and are perfectly repeatable and observable. Many frameworks have been developed to ease the development of PDC simulators, and these frameworks provide different levels of accuracy, scalability, versatility, extensibility, and usability. Further, the SimGrid framework has been used by many PDC researchers to produce a wide range of simulators for over two decades. Its popularity is due to a large emphasis placed on accuracy, scalability, and versatility, and is in spite of shortcomings in terms of extensibility and usability. Although SimGrid provides sensible simulation models for the common case, it was difficult for users to extend these models to meet domain-specific needs. Furthermore, SimGrid only provided relatively low-level simulation abstractions, making the implementation of a simulator of a complex system a labor-intensive undertaking. In this work we describe developments in the last decade that have contributed to vastly improving extensibility and usability, thus lowering or removing entry barriers for users to develop custom SimGrid simulators.

97 MATHEMATICS AND COMPUTING↗

Regeneration of anion-exchange resins for cyclic selenium removal from industrial wastewaters

Application of ion exchange for the removal of selenium (Se) oxyanions from industrial wastewaters is often limited by ineffective regeneration of the ion-exchange resins, particularly in complex systems containing competing ions, such as coal-ash leachate containing high-sulfate concentrations and heavy metal ions. Here, in this study, it was first demonstrated that while conventional regeneration with sodium chloride (NaCl) is effective for simulated wastewater, with ∼80% efficiency, NaCl fails to regenerate resin loaded with real industrial wastewater, achieving less than 20% efficiency. To overcome this challenge, a two-step regeneration process was investigated using a sodium carbonate (Na 2 CO 3 ) solution for elution, followed by a NaCl solution for restoration. Compared to the one-step NaCl regeneration, this integrated process restored more than 80% of the resin's capacity with real industrial wastewaters. Beyond demonstrating regeneration performance, this research emphasizes fundamental mechanistic interpretations of the observed regeneration behavior across different water matrices and experimental conditions. Particularly, accounting for pH-dependent carbonate speciation, it is proposed that the elution step exploits the resin's strong affinity for divalent carbonate ions to displace strongly bound contaminants, while the subsequent restoration step relies mainly on the mass action effects of chloride ions to regenerate the resin sites. The protocol was optimized to achieve rapid regeneration (<10 min) using moderate chemical concentrations (0.5 M) in treating real leachate. In batch cyclic experiments, Se regeneration reached nearly complete recovery after five consecutive sorption and desorption cycles, while in the fixed-bed system, the regeneration efficiency remained at approximately 80% after five cycles.

Anion-exchange resin↗

Density Functional Tight-Binding Models for Band Structures of Transition-Metal Alloys and Surfaces across the d -Block

First-principles electronic structure simulations are an invaluable tool for understanding chemical bonding and reactions. While machine-learning models such as interatomic potentials significantly accelerate the exploration of potential energy surfaces, electronic structure information is generally lost. Particularly in the field of heterogeneous catalysis, simulated electron band structures provide fundamental insights into catalytic reactivity. This ab initio knowledge is preserved in semiempirical methods such as density functional tight binding (DFTB), which extend the accessible computational length and time scales beyond first-principles approaches. In this paper here we present Shell-Optimized Atomic Confinement (SOAC) DFTB electronic-part-only parametrizations for bulk and surface band structures of all d-block transition metals that enable efficient predictions of electronic descriptors for large structures or high-throughput studies on complex systems outside the computational reach of density functional theory.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Static Subspace Approximation for Random Phase Approximation Correlation Energies: Implementation and Performance

Developing theoretical understanding of complex reactions and processes at interfaces requires using methods that go beyond semilocal density functional theory to accurately describe the interactions between solvent, reactants and substrates. Methods based on many-body perturbation theory, such as the random phase approximation (RPA), have previously been limited due to their computational complexity. However, this is now a surmountable barrier due to the advances in computational power available, in particular through modern GPU-based supercomputers. In this work, we describe the implementation of RPA calculations within BerkeleyGW and show its favorable computational performance on large complex systems relevant for catalysis and electrochemistry applications. Our implementation builds off of the static subspace approximation which, by employing a compressed representation of the frequency dependent polarizability, enables the evaluation of the RPA correlation energy with significant acceleration and systematically controllable accuracy. We find that the computational cost of calculating the RPA correlation energy scales only linearly with system size for systems containing up to 50 thousand bands, and is expected to scale quadratically thereafter. We also show excellent strong scaling results across several supercomputers, demonstrating the performance and portability of this implementation.

algorithmic development↗

The Interplay of Pauli Repulsion, Electrostatics, and Field Inhomogeneity for Blueshifting and Redshifting Vibrational Probe Molecules

Many molecules' vibrational frequencies are sensitive to intermolecular electric fields, enabling them to probe the field in complex molecular environments. However, it is often unclear whether the probe is responding to the local electric field or other types of intermolecular interactions, inhibiting interpretation of the frequency and effectiveness as probes. This is especially true for molecules whose vibrational frequencies blueshift instead of the more typical redshift in hydrogen bonding configurations. In this work, we computationally investigate the causes of redshifting versus blueshifting over a range of vibrational reporters. First, we apply adiabatic energy decomposition analysis to a paradigmatic set of probes, finding that redshifting only occurs when electrostatic interactions are strong enough to overcome the dominant and large blueshifting contribution of Pauli repulsion. Furthermore, we demonstrate that field inhomogeneity can further shift the frequency of many probes substantially to either reinforce or counteract the shift expected from a homogeneous field. We find that redshifting is reinforced by electric field inhomogeneity, otherwise field inhomogeneity further weakens the electrostatic contribution relative to Pauli repulsion, leading to blueshifting. Further calculations indicate that the probe's response to field inhomogeneity can be understood by considering the mass of the atoms involved in the stretching mode and sign of the electric field. In explaining the interplay of different intermolecular interactions and field inhomogeneity for many probes, our results should enable the use and interpretation of spectroscopic probes and their connection to electric fields in more complex systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Capturing Surface Coverage Effects in Heterogeneous Catalysis

Adsorbate–adsorbate lateral interactions at relevant surface coverages have a significant effect on chemical kinetics, thereby influencing the activity of a heterogeneous catalyst. Coverage-dependent kinetic and thermodynamic parameters therefore must be included in studies of such complex systems to properly predict the turnover frequencies and kinetic trends. Thus, it becomes extremely important to accurately capture the strength of lateral interactions between neighboring species under realistic reaction conditions. In this Perspective, we discuss the various existing computational and experimental methods for determining adspecies coverage and configurational effects. The choice of the tools and methods employed in such studies depends on factors such as time, length scales, computational cost, the presence of solvents, and reaction conditions. The applications of each method and the respective challenges are also discussed here. As a result, we discuss the recent developments and future of the state-of-the-art for inclusion of surface coverage and configuration into a holistic picture for accurate predictions of catalytic behavior.

09 BIOMASS FUELS↗

Incorporating Coverage-Dependent Reaction Barriers into First-Principles-Based Microkinetic Models: Approaches and Challenges

Mean-field microkinetic models (MKMs) are appealing for their relatively facile construction, computational tractability, and high-throughput catalyst screening capabilities. As such, they will continue to be a valuable tool for materials design in heterogeneous catalysis even as the field aims to describe more complex systems. Numerous prior reports have provided the groundwork for constructing first-principles-based MKMs, including the analysis of strategies for incorporating lateral interactions into thermodynamic parameters (e.g., adsorption energies). Yet, there remains a need for concerted dialogue on methods for calculating and incorporating coverage-dependent kinetic parameters into MKMs. In this Perspective, we assess strategies for doing so, including the corresponding key physical implications and computational challenges. Here, we emphasize that decoupling thermodynamic and kinetic parameters within MKMs can violate thermodynamic consistency and risk unphysical solutions. For some reactions and catalyst materials, scaling relationships can predict coverage-dependent activation energies, but there are several exceptions evident in the literature, indicating that this approach is not universally applicable and that the field could benefit from research aimed at elucidating the limitations. Conducting high-coverage transition state searches is a rigorous but computationally costly strategy, and the effects of various methods for mitigating this cost on resulting energetics have yet to be broadly explored and validated. The goal of this Perspective is to generate discussion on and inspire focused research into the physical relevance of approaches for describing coverage-dependent reaction barriers in MKMs, including the development of computationally tractable methodologies, to advance the applicability of MKMs across diverse reaction chemistries and conditions.

36 MATERIALS SCIENCE↗

Short-Wave Infrared Upconverting Nanoparticles

Optical technologies enable real-time, noninvasive analysis of complex systems but are limited to discrete regions of the optical spectrum. While wavelengths in the short-wave infrared (SWIR) window (typically, 1700-3000 nm) should enable deep subsurface penetration and reduced photodamage, there are few luminescent probes that can be excited in this region. Here, we report the discovery of lanthanide-based upconverting nanoparticles (UCNPs) that efficiently convert 1740 or 1950 nm excitation to wavelengths compatible with conventional silicon detectors. Screening of Ln3+ ion combinations by differential rate equation modeling identifies Ho3+/Tm3+ or Tm3+ dopants with strong visible or NIR-I emission following SWIR excitation. Experimental upconverted photoluminescence excitation (U-PLE) spectra find that 10% Tm3+-doped NaYF4 core/shell UCNPs have the strongest 800 nm emission from SWIR wavelengths, while UCNPs with an added 2% or 10% Ho3+ show the strongest red emission when excited at 1740 or 1950 nm. Mechanistic modeling shows that addition of a low percentage of Ho3+ to Tm3+-doped UCNPs shifts their emission from 800 to 652 nm by acting as a hub of efficient SWIR energy acceptance and redistribution up to visible emission manifolds. Parallel experimental and computational analysis shows rate equation models are able to predict compositions for specific wavelengths of both excitation and emission. These SWIR-responsive probes open a new IR bioimaging window, and are responsive at wavelengths important for vision technologies.

Qi, Xiao↗

Highest fusion performance without harmful edge energy bursts in tokamak

The path of tokamak fusion and International thermonuclear experimental reactor (ITER) is maintaining high-performance plasma to produce sufficient fusion power. This effort is hindered by the transient energy burst arising from the instabilities at the boundary of plasmas. Conventional 3D magnetic perturbations used to suppress these instabilities often degrade fusion performance and increase the risk of other instabilities. This study presents an innovative 3D field optimization approach that leverages machine learning and real-time adaptability to overcome these challenges. Implemented in the DIII-D and KSTAR tokamaks, this method has consistently achieved reactor-relevant core confinement and the highest fusion performance without triggering damaging bursts. This is enabled by advances in the physics understanding of self-organized transport in the plasma edge and machine learning techniques to optimize the 3D field spectrum. The success of automated, real-time adaptive control of such complex systems paves the way for maximizing fusion efficiency in ITER and beyond while minimizing damage to device components.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Multicationic interactions mitigating lattice strain in sodium layered cathodes

Transition-metal (TM) layered oxides have emerged as the primary cathode choice for sodium-ion batteries (SIBs) due to their high energy density and sustainable chemistry using non-critical elements. However, their anisotropic lattice strain and stress accumulation during (de)sodiation lead to severe structural degradation, yet an intrinsic strain-depressant approach remains elusive. Herein, we propose entropy regulation with zero Li/Co usage to mitigate harmful lattice displacements and enhance the electrochemical performance of sodium layered cathodes. Our findings demonstrate that high entropy design effectively inhibits TMO 6 octahedra distortions upon cycling, as evidenced by hard X-ray absorption spectroscopy, greatly reducing near-surface structural deconstruction and interface side reactions. Furthermore, multicationic interactions driven by configurational entropy thermodynamically mitigate the formation of oxygen defects and strengthen ligand-to-metal coordination. The complementarity inherent in charge compensation within complex systems is unveiled and the restrained lattice parameters deviations without interior volume residuals are successfully achieved. As a result, the multicationic cathode exhibits improved cycling stability and Na + diffusion kinetics in both half and full cells. The cathode chemistries outlined here broaden the prospects for lattice engineering to alleviate bulk fatigue and open up the possibility to develop an economically viable layered oxides with long durability.

Wang, Haoji [Central South University, Changsha (C↗

Crystallization of nanopore-confined imidazolium ionic liquids probed by temperature-resolved in situ grazing-incidence wide angle X-ray scattering (GIWAXS)

The crystallization behavior of ionic liquids (ILs) 1-butyl-3-methylimidazolium [BMIM] hexafluorophosphate [PF 6 ] and chloride [Cl] is investigated upon confinement in 2.3 or 8.2 nm diameter silica nanopore arrays, along with the effects of covalently modifying the pore walls with 1-(3-trimethoxysilylpropyl)3-methylimidazolium [TMS-MIM] + groups. In situ grazing-incidence wide angle x-ray scattering (GIWAXS) is performed during heating from as low as -110 °C to room temperature. Partially ordered “nanodomains” are observed in both ILs in the bulk molten state, but they are disrupted by nanoconfinement. Melting point depression consistent with capillary effects is observed for [BMIM][PF 6 ] in 2.3 nm pores. However, the melting point is elevated for [BMIM][PF 6 ] in 8.2 nm pores, which provide sufficient space to stabilize the crystalline phase. For [BMIM][Cl], crystallization is observed only in 8.2 nm bare silica pores, but the melting point is severely depressed. Tethering with IL-like [TMS-MIM + ] also promotes the crystallization of [BMIM][PF 6 ], resulting in elevated melting points. The combined effects of a larger pore size and pore surface tethering on [BMIM][PF 6 ] result in a single stable crystal phase that persists from -140 °C to 25 °C (vs. the bulk melting point of -11 °C). These results show that when ILs are used in confined systems, complex crystallization behavior can emerge depending on the counterion, pore size, and surface modification that require consideration of ion layering in the confined space in addition to surface free energy effects.

He, Yuxin [University of Kentucky, Lexington, KY (↗

Filling data analysis gaps in time-resolved crystallography by machine learning

There is a growing understanding of the structural dynamics of biological molecules fueled by x-ray crystallography experiments. Time-resolved serial femtosecond crystallography (TR-SFX) with x-ray Free Electron Lasers allows the measurement of ultrafast structural changes in proteins. Nevertheless, this technique comes with some limitations. One major challenge is the quality of data from TR-SFX measurements, which often faces issues like data sparsity, partial recording of Bragg reflections, timing errors, and pixel noise. To overcome these difficulties, conventionally, large volumes of data are collected and grouped into a few temporal bins. The data in each bin are then averaged and paired with the mean of their corresponding jittered timestamps. This procedure provides one structure per bin, resulting in a limited number of averaged structures for the entire time interval spanned by the experiment. Therefore, the information on ultrafast structural dynamics at high temporal resolution is lost. This has initiated research for advanced methods of analyzing experimental TR-SFX data beyond the standard binning and averaging method. To address this problem, we use a machine learning algorithm called Nonlinear Laplacian Spectral Analysis (NLSA), which has emerged as a promising technique for studying the dynamics of complex systems. In this work, we demonstrate the power of this algorithm using synthetic x-ray diffraction snapshots from a protein with significant data incompleteness, timing uncertainties, and noise. Our study confirms that NLSA is a suitable approach that effectively mitigates the effects of these artifacts in TR-SFX data and recovers accurate structural dynamics information hidden in such data.

Trujillo, Justin (ORCID:0000000285505360)↗