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At least 181 records · Page 10

An approach to learn regulation to maximize growth and entropy production rates in metabolism

Elucidating cell regulation remains a challenging task due to the complexity of metabolism and the difficulty of experimental measurements. Here we present a method for prediction of cell regulation to maximize cell growth rate while maintaining the solvent capacity of the cell. Prediction is formulated as an optimization problem using a thermodynamic framework that can leverage experimental data. We develop a formulation and variable initialization procedure that allows for computing solutions of the optimization with an interior point method. The approach is applied to photoheterotrophic growth of Rhodospirilium rubrum using ethanol as a carbon source, which has applications to biosynthesis of ethylene production. Growth is captured as the rate of synthesis of amino acids into proteins, and synthesis of nucleotide triphoshaptes into RNA and DNA. The method predicts regulation that produces a high rate of protein and RNA synthesis while DNA synthesis is reduced close to zero in agreement with production of DNA being turned off for much of the cell cycle.

59 BASIC BIOLOGICAL SCIENCES↗

Data-driven computational prediction and experimental realization of exotic perovskite-related polar magnets

Rational design of technologically important exotic perovskites is hampered by the insufficient geometrical descriptors and costly and extremely high-pressure synthesis, while the big-data driven compositional identification and precise prediction entangles full understanding of the possible polymorphs and complicated multidimensional calculations of the chemical and thermodynamic parameter space. Here we present a rapid systematic data-mining-driven approach to design exotic perovskites in a high-throughput and discovery speed of the A 2 BB ’O 6 family as exemplified in A 3 TeO 6 . The magnetoelectric polar magnet Co 3 TeO 6 , which is theoretically recognized and experimentally realized at 5 GPa from the six possible polymorphs, undergoes two magnetic transitions at 24 and 58 K and exhibits helical spin structure accompanied by magnetoelastic and magnetoelectric coupling. We expect the applied approach will accelerate the systematic and rapid discovery of new exotic perovskites in a high-throughput manner and can be extended to arbitrary applications in other families.

36 MATERIALS SCIENCE↗

Mechanistically Guided Materials Chemistry: Synthesis of Ternary Nitrides, CaZrN 2 and CaHfN 2

Recent computational studies have predicted many new ternary nitrides, revealing synthetic opportunities in this underexplored phase space. However, synthesizing new ternary nitrides is difficult, in part because intermediate and product phases often have high cohesive energies that inhibit diffusion. Here, we report the synthesis of two new phases, calcium zirconium nitride (CaZrN 2 ) and calcium hafnium nitride (CaHfN 2 ), by solid state metathesis reactions between Ca 3 N2 and MCl 4 (M = Zr, Hf). Although the reaction nominally proceeds to the target phases in a 1:1 ratio of the precursors via Ca 3 N 2 + MCl4 → CaMN 2 + 2 CaCl 2 , reactions prepared this way result in Ca-poor materials (Ca x M 2–x N2, x < 1). A small excess of Ca 3 N 2 (ca. 20 mol %) is needed to yield stoichiometric CaMN 2 , as confirmed by high-resolution synchrotron powder X-ray diffraction. In situ synchrotron X-ray diffraction studies reveal that nominally stoichiometric reactions produce Zr 3+ intermediates early in the reaction pathway, and the excess Ca 3 N 2 is needed to reoxidize Zr 3+ intermediates back to the Zr 4+ oxidation state of CaZrN 2 . Analysis of computationally derived chemical potential diagrams rationalizes this synthetic approach and its contrast from the synthesis of MgZrN 2 . These findings additionally highlight the utility of in situ diffraction studies and computational thermochemistry to provide mechanistic guidance for synthesis.

36 MATERIALS SCIENCE↗

Design Principles for the Synthesis of Self-Pillared ZSM-5 Zeolite Nanosheets

The design of next-generation materials for emerging energy and environmental applications heavily relies on empirical approaches to direct nonclassical nucleation and crystal growth pathways, polymorphism, intercrystalline transformations, and seed-assisted growth processes. A long-standing obstacle to nanoporous materials design is the complexity of their crystallization, which hinders the development of predictive models and/or physical descriptors that can guide their synthesis. In this study, we use a combination of state-of-the-art synthesis, characterization, and computational design to prepare hierarchical MFI-type zeolites, which we couple with benchmark catalytic testing to assess structure-property-performance relationships. These hierarchical materials are intergrowths of two commercially relevant zeolite frameworks, MFI and MEL, prepared as self-pillared pentasil (SPP) zeolites through seed-assisted, organic-free syntheses for which little theoretical guidance existed. Here, by comparing a large library of zeolite seeds with different pore sizes, dimensions, and structural composite building units, we determined the relative impact of seed and silica source selection, among other synthesis variables. Combined experimental and computational studies are used to test several hypotheses in literature to rationalize the choice of seed structure and establish a more robust selection criteria for seed-assisted synthesis of zeolites. Specifically, we show that a data-driven approach to develop structural descriptors correlates to new, facile routes to rationally design SPP zeolites, addressing knowledge gaps in the fundamental understanding of (non)classical crystal growth mechanisms that are characteristic of nanoporous aluminosilicates.

36 MATERIALS SCIENCE↗

From Serendipity to Exploration: Synthesis and Properties of PtSiSb

PtSiSb is a compound with covalent Si–Sb bonds, which are relatively rare instances in solid-state materials. The original report on PtSiSb indicates synthetic challenges for the isolation of single-phase samples, as well as potential discrepancies in the predicted electronic structure and experimental transport properties. In this work, we considered PtSiSb as a case study with the objective of demonstrating the importance of synthesis as a bridge between theoretical predictions and experimental properties. Using guidance from in situ powder X-ray diffraction, the synthesis of single-phase polycrystalline samples was developed, allowing further experimental characterization of transport and catalytic properties. Thermal conductivity and heat capacity demonstrated anomalous behavior, indicating an unconventional phonon scattering mechanism in PtSiSb. Charge transport measurements indicated semimetallic behavior. Hydrogen evolution reaction (HER) tests in acidic electrolyte revealed that the PtSiSb cathode needs an overpotential η 10 = 120 mV to achieve a current density j = −10 mA/cm 2 . This is lower activity than elemental Pt but comparable to known and active transition-metal phosphide HER catalysts, such as CoP, with η 10 = 93 mV when measured at identical conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Deep Neural Network for Accurate and Robust Prediction of the Glass Transition Temperature of Polyhydroxyalkanoate Homo- and Copolymers

The purpose of this study was to develop a data-driven machine learning model to predict the performance properties of polyhydroxyalkanoates (PHAs), a group of biosourced polyesters featuring excellent performance, to guide future design and synthesis experiments. A deep neural network (DNN) machine learning model was built for predicting the glass transition temperature, Tg, of PHA homo- and copolymers. Molecular fingerprints were used to capture the structural and atomic information of PHA monomers. The other input variables included the molecular weight, the polydispersity index, and the percentage of each monomer in the homo- and copolymers. The results indicate that the DNN model achieves high accuracy in estimation of the glass transition temperature of PHAs. In addition, the symmetry of the DNN model is ensured by incorporating symmetry data in the training process. The DNN model achieved better performance than the support vector machine (SVD), a nonlinear ML model and least absolute shrinkage and selection operator (LASSO), a sparse linear regression model. The relative importance of factors affecting the DNN model prediction were analyzed. Sensitivity of the DNN model, including strategies to deal with missing data, were also investigated. Compared with commonly used machine learning models incorporating quantitative structure–property (QSPR) relationships, it does not require an explicit descriptor selection step but shows a comparable performance. The machine learning model framework can be readily extended to predict other properties.

quantitative structure–property relationship (QSPR↗

Predicting Energetics Materials’ Crystalline Density from Chemical Structure by Machine Learning

To expedite new molecular compound development, a long-sought goal within the chemistry community has been to predict molecules’ bulk properties of interest a priori to synthesis from a chemical structure alone. In this work, we demonstrate that machine learning methods can indeed be used to directly learn the relationship between chemical structures and bulk crystalline properties of molecules, even in the absence of any crystal structure information or quantum mechanical calculations. We focus specifically on a class of organic compounds categorized as energetic materials called high explosives (HE) and predicting their crystalline density. An ongoing challenge within the chemistry machine learning community is deciding how best to featurize molecules as inputs into machine learning models—whether expert handcrafted features or learned molecular representations via graph-based neural network models—yield better results and why. We evaluate both types of representations in combination with a number of machine learning models to predict the crystalline densities of HE-like molecules curated from the Cambridge Structural Database, and we report the performance and pros and cons of our methods. Our message passing neural network (MPNN) based models with learned molecular representations generally perform best, outperforming current state-of-the-art methods at predicting crystalline density and performing well even when testing on a data set not representative of the training data. However, these models are traditionally considered black boxes and less easily interpretable. Here, to address this common challenge, we also provide a comparison analysis between our MPNN-based model and models with fixed feature representations that provides insights as to what features are learned by the MPNN to accurately predict density.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Cellular Automaton Simulation for Predicting Phase Evolution in Solid-State Reactions

New computational tools for solid-state synthesis recipe design are needed in order to accelerate the experimental realization of novel functional materials proposed by high-throughput materials discovery workflows. This work contributes a cellular automaton simulation framework for predicting the time-dependent evolution of intermediate and product phases during solid-state reactions as a function of precursor choice and amount, reaction atmosphere, and heating profile. The simulation captures the effects of reactant particle spatial distribution, particle melting, and reaction atmosphere. Reaction rates based on rudimentary kinetics are estimated using density functional theory data from the Materials Project and machine learning estimators for the melting point and the vibrational entropy component of the Gibbs free energy. The resulting simulation framework allows for the prediction of the likely outcome of a reaction recipe before any experiments are performed. We analyze five experimental solid-state recipes for BaTiO 3 , CaZrN 2 , and YMnO 3 found in the literature to illustrate the performance of the model in capturing reaction selectivity and reaction pathways as a function of temperature and precursor choice. This simulation framework offers an easier way to optimize existing recipes, aid in the identification of intermediates, and design effective recipes for yet unrealized inorganic solids in silico .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Elusive Double Perovskite Iodides: Structural, Optical, and Magnetic Properties

Halide double perovskites [A 2 M I M III X 6 ] are an important class of materials that have garnered substantial interest as non-toxic alternatives to conventional lead iodide perovskites for optoelectronic applications. While numerous studies have examined chloride and bromide double perovskites, reports of iodide double perovskites are rare, and their definitive structural characterization has not been reported. Predictive models have aided us here in the synthesis and characterization of five iodide double perovskites of general formula Cs 2 NaLnI 6 (Ln=Ce, Nd, Gd, Tb, Dy). Finally, the complete crystal structures, structural phase transitions, optical, photoluminescent, and magnetic properties of these compounds are reported.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Computational Fermi Level Engineering and Doping-Type Conversion of Mg:Ga 2 O 3 via Three-Step Synthesis Process

Gallium oxide (Ga 2 O 3 ) is being actively explored for electronics that can operate at high power, temperature, and frequency as well as for deep-ultraviolet optoelectronics and other applications due to its ultra-wide bandgap (UWBG) and low projected fabrication cost of large-size and high-quality crystals. Efficient n-type doping of monoclinic beta-phase of Ga 2 O 3 has been achieved, but p-type doping faces fundamental obstacles due to compensation, deep acceptor levels, and the polaron transport mechanism of free holes. However, aside from the challenges of achieving p-type conductivity, plenty of opportunity exists to engineer the position of the Fermi level for improved design of Ga 2 O 3 -based devices. We use first-principles defect theory and defect equilibrium calculations to simulate a three-step growth-annealing-quench synthesis protocol for hydrogen-assisted Mg doping in ß-Ga 2 O 3 . The simulations take into account the gas phase equilibrium between H 2 , O 2 , and H 2 O, which determines the H chemical potential. We predict Ga 2 O 3 doping-type conversion to a net p-type regime after growth under reducing conditions in the presence of H2 followed by O-rich annealing, which is a similar process to Mg acceptor activation by H removal in GaN. For equilibrium annealing with re-equilibration of compensating O vacancies, there is an optimal temperature that maximizes the Ga 2 O 3 net acceptor density for a given Mg doping level; the acceptor density is further increased in the non-equilibrium annealing scenario without re-equilibration. After quenching to operating temperature, the Ga 2 O 3 Fermi level drops below mid-gap down to about 1.5 eV above the valence band maximum, creating a significant number of uncompensated neutral Mg Ga 0 acceptors. The resulting free hole concentration in Ga 2 O 3 is very low even at elevated operating temperature (~10 8 cm -3 at 400°C) due to the deep energy level of these Mg acceptors, and hole conductivity is further impeded by the polaron hopping mechanism. However, the Fermi-level reduction and suppression of free electron density in this doping-type converted (NA>ND) Ga 2 O 3 material are important for improved designs of Ga 2 O 3 electronic devices. These results illustrate the power of computational predictions not only for new materials but also for their synthesis science.

36 MATERIALS SCIENCE↗

Heterostructural interface engineering for ultrawide-gap nitrides from first principles: Ta C / Al N and Ta C / Ga N rocksalt-wurtzite interfaces

Epitaxial lattice matching is an important condition for the formation of coherent interfaces with low defect densities. However, lattice-matched substrates with the same crystal structure as the active layer are often not available, suggesting opportunities for utilizing heterostructural interfaces. For example, at high Al contents that are interesting for ultrawide-gap applications in power electronics, Al x ⁢Ga 1-x ⁢N semiconductor alloys in the (0001) orientation of the wurtzite (wz) structure become lattice-matched to (111)-oriented rocksalt (rs) Ta⁢C substrates. To predict the expected interface atomic structures under different synthesis conditions, we perform high-throughput density-functional-theory calculations, using an algorithm for systematic sampling of the possible stacking sequences of the atomic layers on the in-plane hexagonal lattice. The approach considers octahedral, tetrahedral, and prismatic coordination motifs, and is generally applicable for the modeling of commensurate rs/wz heterostructural interfaces. Our results provide guidance for synthesis control of substrate-film bonding and the polarity of ultrawide-gap Al x⁢ Ga 1-x⁢ N alloys on Ta⁢C substrates.

36 MATERIALS SCIENCE↗

Predictive Engineering of Interfaces and Cathodes for High-Performance All Solid-State Lithium-Sulfur Batteries

The primary goal of this project is to leverage data-driven methods and machine learning strategies to develop accurate multi-physics models for all-solid-state Li-S battery (ASLSB) materials that can capture electrochemical and transport phenomena over atomic to mesoscopic length/timescales. These models will be rigorously validated by synthesis and advanced characterization experiments. The team will leverage the predictive power of these models, alongside synthesis/characterization experiments and battery fabrication to address longstanding issues at the electrode/electrolyte interfaces in ASLSBs. The project’s proposed technology involves the following: (1) halide-doped solid sulfide electrolytes that can concurrently provide high Li + ion conductivity and suppress dendrite growth; (2) novel mesoporous cathode composed of super-P and carbon nanotubes co-infiltrated with sulfur and sulfide electrolyte, which hold potential to allow high sulfur loading and optimal ion/electron pathways; and (3) functionalization of sulfide electrolyte with ionic liquids to improve physical contact and minimize impedance at the cathode/electrolyte interface. Successful development of proposed predictive models (at multiple scales) will bridge this knowledge gap and will advance fundamental understanding of reaction chemistry, kinetics, charge transfer, and dendrite growth at electrified SSIs. This will enable predictive design of effective strategies to mitigate interfacial problems in ASSLSBs, including poor interfacial contact, interfacial impedance to Li + ion transport, and poor electron/ion conduction within cathodes. Ultimately, the fundamental knowledge gained will lead to development of high-performance ASSLSBs.

25 ENERGY STORAGE↗

Step Catalysis to Synthesize Fossil-Free Ammonia at Atmospheric Pressure (Final Technical Report)

Affordable fossil-free ammonia synthesis will enable high-yield sustainable crop production for a growing world population while preserving the planet and making the best use of water and land. Simple technology amenable to intermittent operation using renewable energy will be made available through step catalysis activating dinitrogen at atmospheric pressure by nitride formation. Project objectives: (1) At the single particle level, quantify and analyze N2 activation by doped or alloyed manganese macroscopic- and nano particles at atmospheric pressure, (2) Quantify and analyze ammonia synthesis from doped or alloyed metal nitride particles when contacting them with hydrogen at atmospheric pressure, and (3) Integrate experimental data and atomic-level computational models to predict the behavior of metal alloys in nitrogen activation and subsequent ammonia synthesis.

10 SYNTHETIC FUELS↗

Synthesis of Antiperovskite Solid Electrolytes: Comparing Li 3 SI, Na 3 SI, and Ag 3 SI

Prior calculations have predicted that chalcohalide anti-perovskites may exhibit enhanced ionic mobility compared to oxyhalide anti-perovskites as solid-state electrolytes. Herein, the synthesis of Ag-, Li- and Na-based chalcohalide anti-perovskites is investigated using first-principle calculations and in situ synchrotron X-ray diffraction. These techniques demonstrate that the formation of Ag 3 SI is facilitated by the adoption of a common body centered cubic packing of S 2– and I – in the reactants and products at elevated temperatures, with additional stabilization achieved by the formation of a solid solution of the anions. Further, the absence of these two features appears to hinder the formation of the analogous Li and Na anti-perovskites.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Extending High-Level Synthesis with AI/ML Methods

Artificial Intelligence (AI) and Machine Learning (ML) methods provide significant opportunities of improving quality of results when performing high-level synthesis (HLS). For example, they can be used to model and predict metrics of the final design (e.g., area, considering aspects such as interconnect overhead for different device technologies), facilitating exploration when searching for the best design trade-offs. They can also enable identifying hidden correlations across the various phases of the synthesis and the various optimizations performed, identifying the most effective pipelines. Finally, in more general terms, bio-inspired heuristic algorithms can improve the design space exploration for the synthesis process in terms of time and quality of the result. This paper discusses opportunities and challenges to augment HLS with AI/ML using as example flow the SODA Synthesizer, an open-source hardware generation toolchain which includes SODA-OPT, a hardware/software partitioning and pre-optimization tool developed with the MLIR framework, and PandA-Bambu, a state-of-the art HLS tool. SODA interfaces with OpenROAD to provide a complete end-to-end toolchain.

artificial intelligence↗

Structural stability, elemental ordering, and transport properties of layered ScTaN 2

Ternary transition metal (TM) nitrides have gained significant attention in thin film research due to their promising properties for a broad range of applications. Particularly, some of the ternary TM nitrides have been predicted to adopt layered structures that make them interesting for thermoelectric conversion and quantum materials applications. Unfortunately, synthesis of TM ternary nitride films by physical vapor deposition often favors disordered 3D structures rather than the predicted 2D-like layered structure. In this study, we investigate the structural interplay in the Sc-Ta-N ternary system using a combinatorial approach. Combinatorial libraries S⁢c 𝑥 ⁢T⁢a 1−𝑥 ⁢N are synthesized following a two-step method: First, deposit film precursors by cosputtering and then process the resulting 3D-structured samples with rapid thermal annealing. Synchrotron grazing-incidence wide-angle x-ray scattering on films annealed at 1200 ⁢°⁢C for 20 min leads to the nucleation of ScTaN 2 layered structure (𝑃⁢6 3 /𝑚⁢𝑚⁢𝑐) near stoichiometry. We find that the layered structure can accommodate large off-stoichiometry in the Ta-rich region (𝑥 < 0.5), facilitated by the alloying with quasi-isostructural Ta 5 ⁢N 6 compound that exists on a composition tie line at 𝑥 = 0. While focusing on ScTaN 2 , we estimate the long-range order parameter in near-stoichiometric films to be 0.86, corresponding to a fraction of Sc/Ta antisites of 7%. Transport measurements on ScTaN 2 reveal a nearly temperature-independent high carrier density (10 21 c⁢m −3 ), suggesting a heavily doped semiconductor or semimetallic character, consistent with a small positive Seebeck coefficient of +19 µV/K. The carrier mobility at 2 K is relatively small (9.5c⁢m 2 V −1 s −1 ) and the residual-resistivity ratio is minor, suggesting that electrical conduction is dominated by defects or disorder. Measured magnetoresistance suggests possible weak antilocalization at 2 K. This paper highlights the interplay between ScTaN 2 and Ta 5 ⁢N 6 crystal structures in stabilizing layered materials, emphasizes the importance of cation order/disorder for potential tunable alloys, and suggests that ScTaN 2 is a promising platform for exploring electronic properties.

36 MATERIALS SCIENCE↗

Bioinformatic and Mechanistic Analysis of the Palmerolide PKS-NRPS Biosynthetic Pathway From the Microbiome of an Antarctic Ascidian

Complex interactions exist between microbiomes and their hosts. Increasingly, defensive metabolites that have been attributed to host biosynthetic capability are now being recognized as products of host-associated microbes. These unique metabolites often have bioactivity targets in human disease and can be purposed as pharmaceuticals. Polyketides are a complex family of natural products that often serve as defensive metabolites for competitive or pro-survival purposes for the producing organism, while demonstrating bioactivity in human diseases as cholesterol lowering agents, anti-infectives, and anti-tumor agents. Marine invertebrates and microbes are a rich source of polyketides. Palmerolide A, a polyketide isolated from the Antarctic ascidian Synoicum adareanum, is a vacuolar-ATPase inhibitor with potent bioactivity against melanoma cell lines. The biosynthetic gene clusters (BGCs) responsible for production of secondary metabolites are encoded in the genomes of the producers as discrete genomic elements. A candidate palmerolide BGC was identified from a S. adareanum microbiome-metagenome based on a high degree of congruence with a chemical structure-based retrobiosynthetic prediction. Protein family homology analysis, conserved domain searches, active site and motif identification were used to identify and propose the function of the ~75 kbp trans-acyltransferase (AT) polyketide synthase-non-ribosomal synthase (PKS-NRPS) domains responsible for the stepwise synthesis of palmerolide A. Though PKS systems often act in a predictable co-linear sequence, this BGC includes multiple trans-acting enzymatic domains, a non-canonical condensation termination domain, a bacterial luciferase-like monooxygenase (LLM), and is found in multiple copies within the metagenome-assembled genome (MAG). Detailed inspection of the five highly similar pal BGC copies suggests the potential for biosynthesis of other members of the palmerolide chemical family. This is the first delineation of a biosynthetic gene cluster from an Antarctic microbial species, recently proposed as Candidatus Synoicihabitans palmerolidicus. These findings have relevance for fundamental knowledge of PKS combinatorial biosynthesis and could enhance drug development efforts of palmerolide A through heterologous gene expression.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Subtle metastability of the layered magnetic topological insulator MnBi 2 Te 4 from weak interactions

Abstract Layered quantum materials can host interesting properties, including magnetic and topological, for which enormous computational predictions have been done. Their thermodynamic stability is much less visited computationally, which however determines the existence of materials and can be used to guide experimental synthesis. MnBi 2 Te 4 is one of such layered quantum materials that was predicted to be an intrinsic antiferromagnetic topological insulator, and later experimentally realized but in a thermodynamically metastable state. Here, using a combined first-principles-based approach that considers lattice, charge, and spin degrees of freedom, we investigate the metastability of MnBi 2 Te 4 by calculating the Helmholtz free energy for the reaction Bi 2 Te 3 + MnTe → MnBi 2 Te 4 . We identify a temperature range (~500–873 K) in which the compound is stable with respect to the competing binary phases, consistent with experimental observation. We validate the predictions by comparing the calculated specific heats contributed from different degrees of freedom with experimental results. Our findings indicate that the degrees of freedom responsible for the van der Waals interaction, lattice vibration, magnetic coupling, and nontrivial band topology in MnBi 2 Te 4 not only enable emergent phenomena but also play a crucial role in determining its thermodynamic stability. This conclusion lays the foundation for the future computational material synthesis of novel layered systems.

36 MATERIALS SCIENCE↗