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At least 19 records

Artificial intelligence tools for enzyme engineering and metabolic engineering

Enzyme engineering and metabolic engineering drive innovation in energy biotechnology. In recent years, artificial intelligence (AI) has supported successful applications in designing effective enzymes and productive microbial cell factories. This review summarizes recent advances in enzyme redesign using protein language models, de novo enzyme design with generative models, and AI tools for engineering metabolism and related cellular phenotypes. Across these areas, AI models are shifting from single modality inputs to integrated representations of protein function, metabolic pathways, and cell states. We emphasize that unifying the diverse data representations across scales will be necessary for advancements in energy biotechnology.

Volk, Michael [Univ. of Illinois at Urbana-Champai↗

Sustainable Triacetic Acid Lactone Production from Sugarcane by Fermentation and Crystallization

Triacetic acid lactone (TAL) has the potential to serve as a bioderived platform chemical for commercial products including sorbic acid and recyclable polydiketoenamine plastics. In this study, we leveraged BioSTEAM to design, simulate, and evaluate (via techno-economic analysis, TEA, and life cycle assessment, LCA) TAL production from sugarcane. We experimentally characterized TAL solubility, calibrated solubility models, and designed a process to separate TAL from fermentation broths by crystallization. The biorefinery could produce TAL at a minimum product selling price (MPSP) of $\$3.73$–5.86·kg –1 (5th–95th percentiles; baseline at $\$4.60$·kg –1 ) and a carbon intensity (CI) of 5.31 [2.60–8.71] kg CO 2 -eq·kg –1 , which could enable financially viable, low-CI production of sorbic acid and polydiketoenamines. To drive down costs and CI, we explored the theoretical fermentation space (titer, yield, productivity combinations), operation scheduling and capacity expansion strategies (e.g., integrated sorghum processing), and potential separation improvements (mitigating TAL loss through pH control). Advancements in key design and technological parameters could further reduce MPSP by 51% to $\$2.26$·kg –1 [$\$1.97$–2.80·kg –1 ] and CI by 43% to 3.05 [1.91–4.15] kg CO 2 -eq·kg –1 . This research highlights the ability of agile TEA-LCA to screen promising designs, navigate sustainability trade-offs, prioritize research needs, and chart quantitative roadmaps to advance bioproducts and biofuels.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

How Does Metal Spin State Affect Electronic Communication in Mixed-Valence Dimers? Insights from Ultrafast Near-Infrared and Soft X-ray Transient Absorption Spectroscopy

Recent advancements in photocatalysis, photovoltaics, and quantum information science take advantage of electron spin, and determining how spin multiplicity affects electron transfer is key to understanding these phenomena. Here, in this study, we examine how metal spin state affects electronic communication in an organometallic mixed-valence dimer, ferrocenyl cobaltocenium ([Fe II Cp 2 Co III Cp 2 ] + ). This complex can be photoexcited from its low-spin singlet Fe II ground state to form intermediate-spin triplet Fe II and high-spin quintet Fe II excited states. Using femtosecond optical transient absorption (OTA) spectroscopy with visible (vis), near-infrared (NIR), and short-wave IR (SWIR) probes, supported by time-dependent density functional theory (TD-DFT) calculations, we measure Fe II Co III →Fe III Co II intervalence charge transfer (IVCT) bands in each of the Fe II spin states. Mulliken–Hush analysis of the excited-state IVCT bands was used to compute the electronic coupling between the metal centers in all three spin states, which increased as quintet < triplet < singlet. Meanwhile, the peak energy of the bands, and thus the ΔG of the IVCT transition, increased as triplet < quintet < singlet. Then, to directly probe the electronic structure at each metal center, we employed picosecond soft X-ray transient absorption (XTA) spectroscopy at the Fe and Co L 3 edges. Our results show that the low-spin and high-spin states of [Fe II Cp 2 Co III Cp 2 ] + are valence-localized, while the intermediate-spin state is partially delocalized. The differences in charge delocalization are attributed to differences in orbital occupation and geometry that affect the free energy and superexchange coupling.

Burke, John H. [Univ. of Illinois at Urbana-Champa↗

Data-Driven Discovery and Experimental Validation of Solvent Polarity Effects on Conjugated Polymer Solution-to-Film Assembly Pathways

Understanding how solvent properties influence the solution-to-film assembly of conjugated polymers remains a critical challenge due to the complex and intertwined nature of polymer–solvent interactions. In this study, we integrate a data-driven framework with experimental validation to identify key parameters influencing the assembly and performance of poly[2,5-(2-octyldodecyl)-3,6-diketopyrrolopyrrole-alt-5,5-(2,5-di(thien-2-yl)thieno[3,2-b]thiophene)] (DPP-DTT) in organic field-effect transistors (OFETs). A machine learning (ML) approach identified the normalized Reichardt polarity parameter (E T N ) as a significant descriptor correlated with DPP-DTT hole mobility (μ). Systematic DPP-DTT devices fabricated using solvents across a wide E T N range revealed that higher E T N solvents yield enhanced μ. To elucidate the structural origins of high μ, we conducted comprehensive analyses using UV–vis–NIR spectroscopy and grazing incidence wide angle X-ray scattering (GIWAXS) measurements. The results revealed that films processed from high E T N solvents exhibit reduced paracrystallinity. By analyzing the solution-state behavior using optical microscopy and solution WAXS, we revealed polymer solubility differences in the various solvents and associated distinct polymer assembly pathways, elucidating why the high E T N solvent produces long-range ordered films. Notably, the high E T N solvent shows a pronounced preference for liquid-crystal (LC)-mediated assembly, providing a mechanistic explanation for the enhanced structural order. Therefore, these results demonstrate that solvent polarity, as evaluated by E T N , serves as an important parameter that plays a significant role in the DPP-DTT assembly pathway and resultant solid-state morphology. This work provides a strategy for integrating data science with experiments to identify critical parameters associated with complex polymer systems and helps guide rational process design for high-performance organic electronics.

36 MATERIALS SCIENCE↗

Egg yolk as a model for gelation: From rheometry to flow physics

Egg yolks are an excellent model for studying sol-gel transitions, particularly the power law viscoelasticity that defines the critical point of gelation. However, prior studies lack comprehensive datasets and fail to visualize flow behavior linked to temperature and time-dependent linear and nonlinear rheology. Here, we present a detailed dataset characterizing egg yolk viscoelasticity across temperature, time, and forcing amplitude using oscillatory shear, step strain, step stress, and constant high strain rate. Novel protorheology visualizations link rheological properties with observable flow behavior. Our findings highlight the nuanced determination of the critical gel point, emphasizing observation timescale dependencies. We compare methods to identify critical temperatures for gelation, including power law viscoelasticity, moduli crossover, diverging zero-shear viscosity, and emerging equilibrium elastic modulus, while visualizing flow consequences near these transitions. Egg yolk is an accessible, realistic, and nontoxic material relevant to the physicist and the chef alike, making it ideal for understanding the rheology of critical gels. By integrating protorheology photos and videos with rigorous rheometric data, we deepen the understanding of critical gels, with broader impacts for studying other materials with sol-gel transitions.

Marsh, Maxwell C. [Department of Mechanical Scienc↗

The SPT-deep Cluster Catalog: Sunyaev–Zel’dovich Selected Clusters from Combined SPT-3G and SPTpol Measurements over 100 Square Degrees

We present a catalog of 500 galaxy cluster candidates in the SPT-Deep field: a 100 deg$^{2}$ field that combines data from the SPT-3G and SPTpol surveys to reach noise levels of 3.0, 2.2, and 9.0 μK-arcmin at 95, 150, and 220 GHz, respectively. Candidates are selected via the thermal Sunyaev–Zel’dovich (SZ) effect with a minimum significance of ξ = 4.0, resulting in a catalog of purity ∼89%. Optical data from the Dark Energy Survey and infrared data from the Spitzer Space Telescope are used to confirm 442 cluster candidates. The clusters span 0.12 < z ≲ 1.8 and 1.0 × 10$^{14}$M$_{⊙}$/h$_{70}$ < M$_{500c}$ < 8.7 × 10$^{14}$M$_{⊙}$/h$_{70}$. The sample’s median redshift is 0.74, and the median mass is 1.7 × 10$^{14}$M$_{⊙}$/h$_{70}$; these are the lowest median mass and highest median redshift of any SZ-selected sample to date. We assess the effect of infrared emission from cluster member galaxies on cluster selection by performing a joint fit to the infrared dust and tSZ signals by combining measurements from SPT and overlapping submillimeter data from Herschel/SPIRE. We find that at high redshift (z > 1), the tSZ signal is reduced by $17.9_{−3.2}^{+3.8}$%$(3.8_{−0.7}^{+0.9}$%$)$ at 150 GHz (95 GHz) due to dust contamination. We repeat our cluster finding method on dust-nulled SPT maps and find the resulting catalog is consistent with the nominal SPT-Deep catalog, suggesting dust contamination does not significantly impact the SPT-Deep selection function; we attribute this lack of bias to the inclusion of the SPT 220 GHz band.

79 ASTRONOMY AND ASTROPHYSICS↗

Physical Modeling and Design of a Nonvolatile Optically Gated High‐Power Diamond Transistor

In this work, we present the theory and modeling framework of a diamond optically gated junction field‐effect transistor (DOGFET). The device utilizes nitrogen substitutional centers in type‐1b diamond to optically modulate a p‐ boron doped diamond channel. Using sub‐gap lasers with intensities as low as 100 W/cm 2 , electrons are optically excited from substitutional nitrogen sites to the conduction band of the diamond substrate, thus enabling the optical gate to exercise control on modulating the space‐charge region at the junction and therefore the channel conductivity. We show that the device can deliver a current of 7 μA/μm, or equivalently 1750 A/cm 2 , while switching at a frequency greater than 100 kHz, in a form factor of 5 μm 2 . The breakdown voltage is found to be greater than 1850 V, with a breakdown field strength of ~13 MV/cm. Moreover, the device supports nonvolatile operation with a “memory effect” enabling single transistor state retention. The presented simulation framework provides a physically grounded insight into the limits and opportunities of optoelectronic diamond systems.

Engineering - Electronic and electrical engineerin↗

NanoPSD: A software for automatic detection of Nano-Particle Shape Distribution in electron microscopy images

Accurate quantification of the size and morphology of nanoparticles from electron microscopy (EM) images is essential to understand growth mechanisms, surface reactivity, and functional behavior in nanoscale materials. Manual analysis remains slow, subjective, and difficult to reproduce in large datasets. We introduce NanoPSD (Nano-Particle Shape Distribution), an open-source and fully automated framework for quantitative particle detection and morphology analysis from EM images. NanoPSD integrates adaptive contrast enhancement, polarity-agnostic scale-bar detection, Optical Character Recognition (OCR)-based calibration, and classical segmentation via Otsu thresholding with morphological refinement. Particle contours are used to extract geometric descriptors, including equivalent circular diameter, aspect ratio, circularity, and solidity, enabling automated classification into spherical, rod-like, and aggregate morphologies. The framework supports both single-image and batch processing, generating publication-quality visualizations, LaTeX-ready tables, and structured comma-separated values (CSV) datasets. As a demonstration, we applied NanoPSD to plasma-synthesized nanoparticle samples diagnosed via transmission electron microscopy (TEM). The code produced statistically robust size and morphology distributions spanning a few to tens of nanometers with minimal user supervision. The pipeline demonstrates high reproducibility and scalability, processing large image collections with consistent calibration and output formatting. Its modular design enables seamless integration of future deep-learning-based segmentation models, providing a pathway toward intelligent, data-driven electron microscopy analysis.

36 MATERIALS SCIENCE↗

Mesoscale Magnetostructural Phase Separation in Fe‐deficient Fe 5 GeTe 2

Two-dimensional van der Waals ferromagnet Fe 5-x GeTe 2 (F5GT) is promising for spintronic applications due to its high Curie temperature, layered structure, and ability to host complex magnetic textures. However, the origin of its sample-dependent magnetic anisotropy remains unclear, hindering control of its magnetic behavior. Here, we use spatially resolved cryogenic scanning transmission electron microscopy (STEM) to correlatively map magnetism, lattice structure, and chemistry across atomic-to-micron scales. We reveal that only mesoscale, not nanoscale, inclusions of a Fe-deficient secondary phase significantly modify magnetic behavior, establishing a previously unrecognized critical length scale. This phase separation, induced by quenching, leads to in-plane magnetic anisotropy, while slow cooling confines separation to a few nanometers and preserves out-of-plane anisotropy. These findings reconcile prior inconsistencies and establish a predictive framework for tuning magnetism in F5GT through thermal processing, with broader implications for controlling anisotropy in other two-dimensional magnetic materials.

2D ferromagnets↗

A topological superconductor tuned by electronic correlations

A topological superconductor, characterized by either a chiral order parameter or a topological surface state in proximity to bulk superconductivity, is foundational to topological quantum computing. A key open challenge is whether electron-electron interactions can tune such topological superconducting phases. Here, we provide experimental signatures of a unique topological superconducting phase in competition with electronic correlations in 10-unit-cell thick FeTe x Se 1-x films grown on SrTiO 3 substrates. When the Te content x exceeds 0.7, we observe a topological transition marked by the emergence of a superconducting surface state. Near the FeTe limit, the system undergoes another transition where the surface state disappears, and superconductivity is suppressed. Theory suggests that electron-electron interactions in the odd-parity xy− band drives this second topological transition. The flattening and eventual decoherence of d xy -derived bands track the superconducting dome, linking correlation effects directly to superconducting coherent transport. Our work establishes many-body electronic correlations as a sensitive knob for tuning topology and superconductivity, offering a pathway to engineer new topological phases in correlated materials.

36 MATERIALS SCIENCE↗

A parametric study of slow dynamic nonlinear elasticity with comparisons to models

Several phenomenological models that aspire to quantitative description of anomalous nonlinear mesoscopic elasticity are reviewed and compared with laboratory measurements. This class of nonlinearity, best known perhaps for slow dynamics and aging, is seen widely in imperfectly consolidated granular solids but is not well understood. Typical slow dynamic tests show that a modest conditioning oscillatory "pump" strain depresses material stiffness, which then recovers like the logarithm of time after conditioning ceases. Several phenomenological models based on physical arguments have been proposed that predict the material stiffness response to arbitrary pump strain histories during conditioning and recovery. Approximate closed form and numerical solutions to the models are presented that predict the quantitative influence of three key pump parameters: the pump's strain amplitude, the pump's strain rate, and the pump’s duration. Laboratory measurements on Berea sandstone, concrete and a confined single aluminum bead find that slow dynamic responses are linear in pump strain and independent of pump frequency. Measurements also show that, after pump-off, stiffness recovers over times far longer than the pump duration. These observations and others are compared to model predictions. One of the considered models, based on a picture of fast brittle damage and slow healing, successfully matches all these behaviors.

36 MATERIALS SCIENCE↗

Dirac Fermions and Flat Bands in Phosphorus Carbide Nanotubes: Structural and Quantum Phase Transitions in a Quasi-One-Dimensional Material

Chemically realistic quasi-one-dimensional (1D) materials in which Dirac Fermions and highly degenerate flat bands coexist intrinsically at the Fermi level are exceedingly rare, while representing a highly desirable platform for correlated and topological quantum phenomena. Here, in this work, using specialized symmetry-adapted first-principles calculations we predict a new class of nanomaterials─phosphorus carbide nanotubes (P 2 C 3 NTs)─obtained by rolling monolayer P 2 C 3 , a two-dimensional material shown in a previous letter to host “double Kagome bands”. Both armchair and zigzag P 2 C 3 NTs are stable at room temperature and feature the rare coexistence of Dirac crossings and multiple flat bands at the Fermi level inherited from the underlying honeycomb–Kagome lattice, with the flat bands resilient to elastic deformations. Under large strain, the structure transforms from honeycomb–Kagome to “brick-wall”, accompanied by multiple coupled structural and quantum phase transitions. We also uncover localized edge states, spin splitting from vacancies and dopants, and strain-tunable magnetism. Together, these results establish P 2 C 3 NTs as a chemically specific and mechanically tunable 1D material platform with potential applications in quantum hardware and spintronics.

carbon nanotubes↗

Gaunt and Breit two-electron contributions to mean-field transformations and fine structure splitting

Materials utilized by novel energy systems are often studied using weakly correlated mean-field theories. However, if these systems incorporate heavy elements, relativistic effects must be included. Therefore, a Kramers unrestricted coupled cluster with singles and doubles excitation formalism within a molecular mean-field exact two-component framework (X2C mmf ) using a four-component Dirac–Hartree–Fock (DHF) reference state is presented. The exact X2C mmf transformed normal-order Hamiltonian incorporates all one-electron and two-electron (2e) contributions from the Coulomb, Gaunt, and Breit operators and is used with the equation of motion method to calculate the excitation energies of the alkali group of elements. Using this framework, the effects of 2e Gaunt and Breit integrals are studied. Results demonstrate growing contributions from these integrals to the generated X2C mmf mean-fields and electronic fine structure calculations with increasing atomic number. Overall, this paper outlines the method, its effect within the X2C mmf approach, and lays the foundation for future theoretical development of relativistic calculations within this framework.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Enhanced matter power spectrum from axion kination after Big Bang nucleosynthesis

Despite stringent constraints from Big Bang Nucleosynthesis (BBN) and cosmic microwave background (CMB) observations, it is still possible for well-motivated particle physics models to substantially alter the cosmic expansion history between BBN and recombination. In this work we consider two different axion models that can realize a period of first matter domination, then kination, in this epoch. We perform fits to both primordial element abundances as well as CMB data and determine that up to a decade of late axion domination is allowed by these probes of the early universe. We establish the implications of late axion domination for the matter power spectrum on the scales 1/Mpc ≲ k ≲ 10 3 /Mpc. Our 'log' model predicts a relatively modest bump-like feature together with a small suppression relative to the standard ΛCDM predictions on either side of the enhancement. Our 'two-field' model predicts a larger, plateau-like feature that realizes enhancements to the matter power spectrum of up to two orders of magnitude. These features have interesting implications for structure formation at the forefront of current detection capabilities.

79 ASTRONOMY AND ASTROPHYSICS↗

Future Projection of Tropical Upper-Tropospheric Troughs and Implications for Tropical Cyclone Activity

Summertime tropical upper-tropospheric troughs (TUTTs) provide a unified framework to better understand how extratropical and tropical forcings jointly modulate basin-scale tropical cyclone (TC) activity. In this study, we examine future changes in TUTTs and their implications for TC activity. Multimodel ensemble-mean projections from 45 Coupled Model Intercomparison Project phase 6 (CMIP6) models suggest a contraction of the Pacific TUTT and an expansion of the Atlantic TUTT as the climate warms. Consistently, future changes in environment-based TC indices indicate that the large-scale conditions will become more favorable for TC genesis and intensification over the central North Pacific but less favorable over the tropical North Atlantic and Gulf of Mexico. Utilizing a TC-permitting large-ensemble dataset [i.e., the Database for Policy Decision-Making for Future Climate Change (d4PDF)] that adequately captures the observed interannual TUTT–TC relationships, we further confirm the impacts of projected TUTT changes on the TC activity in a warmer climate. In contrast, the TUTT–TC relationship is poorly represented in most CMIP6 High-Resolution Model Intercomparison Project (HighResMIP) models; such deficiencies call for caution when assessing future TC risk based on explicitly tracked TCs in these models. Additionally, CMIP6 projections show large intermodel spread in TUTT changes, implying uncertainty in projected TC activity, especially over the central-to-eastern Pacific and the North Atlantic. This intermodel spread is associated with interhemispheric sea surface temperature warming asymmetry, which leads to a meridional shift of the intertropical convergence zone (ITCZ) and the simultaneous weakening or strengthening of TUTTs in the North Pacific and North Atlantic. The potential contributions of anthropogenic aerosol forcing and oceanic circulation to this interhemispheric warming asymmetry are briefly examined.

Climate Change↗

Role of Fluid and Temperature in Fracture Mechanics and Coupled THMC Processes for Enhanced Geothermal Systems

The ability to sustain high energy extraction efficiency from Enhanced Geothermal Systems (EGS) is affected by the ability to measure, characterize, and predict the effect of different perturbations that arise from fluid injection rates, fluid temperature, and shut-in conditions on existing and stimulated fracture systems throughout a subsurface reservoir’s lifecycle. The difficulty arises from limited knowledge of the interaction of fluid and temperature driven fractures with frictional interfaces that govern local deformation and frictional behavior in the surrounding rock. Thermo-poro-mechanical coupled processes tend to dominate this interaction and strongly affect the permeability and local stress distributions that impact efficiency and prevent optimal stimulation conditions over multi-decadal time frames.

Pyrak-Nolte, Laura [Purdue Univ., West Lafayette, ↗

Data for: A hybrid biophysical-machine learning framework for diurnal surface energy flux estimation using proximal sensing

Thermal-based remote sensing of surface energy fluxes has traditionally relied on high spatial resolution satellite data with revisit frequencies on the order of weeks. In this study, we evaluate a biophysics-based analytical surface energy balance model for predicting latent energy (LE) and sensible heat (H) fluxes using proximal sensing observations. The Surface Temperature Initiated Closure (STIC1.2) model has been extensively validated across a wide range of spatial and temporal scales using various satellite-derived thermal datasets. Here we extend this validation by applying STIC at sub-hourly temporal resolution over multiple growing seasons for four distinct agricultural systems. We further develop and evaluate novel STIC variants that incorporate machine learning (ML) techniques to eliminate the need for specific surface energy balance observations, specifically net radiation and soil heat flux, thereby enhancing model applicability in data-sparse settings. The integration of an ML component to estimate surface available energy is shown to have strong predictive performance for both LE (R2 = 0.81-0.94) and H (R2 = 0.46-0.72) across all agricultural systems examined here, demonstrating the potential of hybrid biophysical – machine learning approaches for surface energy balance modeling with minimal data requirements. This study concludes with a novel application of explainable machine learning (exML) to diagnose sources of model error. This exML framework attributes residual prediction errors to both model input variables and environmental drivers not explicitly included in the simulation experiments. This approach provides a new pathway for improving model design and integrating previously overlooked yet influential variables into future model iterations.

Agricultural Sciences↗