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At least 379 records · Page 21

iNovo479: Metabolic Modeling Provides a Roadmap to Optimize Bioproduct Yield from Deconstructed Lignin Aromatics by Novosphingobium aromaticivorans

Lignin is an abundant renewable source of aromatics and precursors for the production of other organic chemicals. However, lignin is a heterogeneous polymer, so the mixture of aromatics released during its depolymerization can make its conversion to chemicals challenging. Microbes are a potential solution to this challenge, as some can catabolize multiple aromatic substrates into one product. Novosphingobium aromaticivorans has this ability, and its use as a bacterial chassis for lignin valorization could be improved by the ability to predict product yields based on thermodynamic and metabolic inputs. In this work, we built a genome-scale metabolic model of N. aromaticivorans, iNovo479, to guide the engineering of strains for aromatic conversion into products. iNovo479 predicted product yields from single or multiple aromatics, and the impact of combinations of aromatic and non-aromatic substrates on product yields. We show that enzyme reactions from other organisms can be added to iNovo479 to predict the feasibility and profitability of producing additional products by engineered strains. Thus, we conclude that iNovo479 can help guide the design of bacteria to convert lignin aromatics into valuable chemicals.

59 BASIC BIOLOGICAL SCIENCES↗

Chemistry of atmosphere-surface interactions on Venus and Mars

Earth-based, earth-orbital, and spacecraft observational data are used in the present evaluation of Venus atmosphere-surface interactions to quantitatively characterize the reactions between C, H, S, Cl, F, and N gases and plausible surface minerals. Calculation results are used to predict stable minerals and mineral assemblages on the Venus surface, in order to ascertain which (if any) of the atmospheric gases are buffeted by mineral assemblages. Chemical equilibrium calculations using extant thermodynamic data on scapolite minerals predict that carbonate-bearing scapolite and sulfate meionite are unstable on the surface of Venus, while chloride-bearing scapolite is stable.

Fegley, Bruce, Jr.↗

Development and assessment of hierarchical multi-reward reinforcement learning based potential for silicene with state-of-the-art models

We develop a new interatomic force field for Silicene, a 2D material with a buckled hexagonal lattice structure with high polymorphism. We introduce new parameterizations of a Tersoff model using a hierarchical multi-reward reinforcement learning (RL) methodology coupled with a continuous Monte Carlo Tree Search optimization. Our model significantly outperforms existing methods by enhancing the accuracy of predictions for the structural and thermodynamic properties of seven silicene polymorphs-including structure, energy, equation of state, elasticity, and phonon dispersion-when compared to established models. We further make a comprehensive comparison of the various models in predicting the mechanical and thermal properties of silicene. We trace the origin of the improved performance to the description of the angular dependence in the bond-order term, suggesting that modifying the angular terms in short-range models is essential to capture the structural diversity in low dimensional systems.

2D materials↗

Prediction of Combustion Gas Deposit Compositions

Demonstrated procedure used to predict accurately chemical compositions of complicated deposit mixtures. NASA Lewis Research Center's Computer Program for Calculation of Complex Chemical Equilibrium Compositions (CEC) used in conjunction with Computer Program for Calculation of Ideal Gas Thermodynamic Data (PAC) and resulting Thermodynamic Data Base (THDATA) to predict deposit compositions from metal or mineral-seeded combustion processes.

Kohl, F. J.↗

Ising model of cardiac thin filament activation with nearest-neighbor cooperative interactions

We have developed a model of cardiac thin filament activation using an Ising model approach from equilibrium statistical physics. This model explicitly represents nearest-neighbor interactions between 26 troponin/tropomyosin units along a one-dimensional array that represents the cardiac thin filament. With transition rates chosen to match experimental data, the results show that the resulting force-pCa (F-pCa) relations are similar to Hill functions with asymmetries, as seen in experimental data. Specifically, Hill plots showing (log(F/(1-F)) vs. log [Ca]) reveal a steeper slope below the half activation point (Ca(50)) compared with above. Parameter variation studies show interplay of parameters that affect the apparent cooperativity and asymmetry in the F-pCa relations. The model also predicts that Ca binding is uncooperative for low [Ca], becomes steeper near Ca(50), and becomes uncooperative again at higher [Ca]. The steepness near Ca(50) mirrors the steep F-pCa as a result of thermodynamic considerations. The model also predicts that the correlation between troponin/tropomyosin units along the one-dimensional array quickly decays at high and low [Ca], but near Ca(50), high correlation occurs across the whole array. This work provides a simple model that can account for the steepness and shape of F-pCa relations that other models fail to reproduce.

Evaluation Studies↗

Interfacial tension and vapor-liquid equilibria in the critical region of mixtures

In the critical region, the concept of two-scale-factor universality can be used to accurately predict the surface tension between near-critical vapor and liquid phases from the singularity in the thermodynamic properties of the bulk fluid. In the present work, this idea is generalized to binary mixtures and is illustrated using the data of Hsu et al. (1985) for CO2 + n-butane. The pressure-temperature-composition-density data for coexisting, near-critical phases of the mixtures are fitted with a thermodynamic potential comprised of a sum of a singular term and nonsingular terms. The nonuniversal amplitudes characterizing the singular term for the mixtures are obtained from the amplitudes for the pure components by interpolation in a space of thermodynamic 'field' variables. The interfacial tensions predicted for the mixtures from the singular term are within 10 percent of the data on three isotherms in the pressure range (Pc - P)/Pc of less than 0.5. This difference is comparable to the combined experimental and model errors.

Moldover, Michael R.↗

Chemistry Informed Machine Learning-Based Heat Capacity Prediction of Solid Mixed Oxides

Knowing heat capacity is crucial for modeling temperature changes with the absorption and release of heat and for calculating the thermal energy storage capacity of oxide mixtures with energy applications. The current prediction methods (ab initio simulations, computational thermodynamics, and the Neumann–Kopp rule) are computationally expensive, not fully generalizable, or inaccurate. Machine learning has the potential of being fast, accurate, and generalizable, but it has been scarcely used to predict mixture properties, particularly for mixed oxides. Here, we demonstrate a method for the generalizable prediction of heat capacity of solid oxide pseudobinary mixtures using heat capacity data obtained from computational thermodynamics and descriptors from ab initio databases. Further, models trained through this workflow achieved an error (mean absolute error of 0.43 J mol –1 K –1 ) lower than the uncertainty in differential scanning calorimetry measurements, and the workflow can be extended to predict other properties derived from the Gibbs free energy and for higher-order oxide mixtures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

High pressure/high temperature multiphase simulations of dodecane injection to nitrogen: Application on ECN Spray-A

The present work investigates the complex phenomena associated with pressure/high temperature dodecane injection for the Engine Combustion Network (ECN) Spray-A case, employing more elaborate thermodynamic closures, to avoid well known deficiencies concerning density and speed of sound prediction using traditional cubic models. A tabulated thermodynamic approach is proposed here, based on log 10 (p)-T tables, providing very high accuracy across a large range of pressures, spanning from 0 to 2500 bar, with only a small number of interpolation points. The tabulation approach is directly extensible to any thermodynamic model, existing or to be developed in the future. Here NIST REFPROP properties are used, combined with PC-SAFT Vapor-Liquid-Equilibrium to identify the liquid in mixtures penetration, hence avoiding the use of an arbitrary threshold for mass fraction. Identified liquid and vapour penetration are compared against experimental data from the ECN database showing a good agreement, within approximately 3–8% for axial penetration of liquid, 2% for vapor axial penetration and within experimental uncertainty for radial distribution of mass fraction. Analysis of the vortex evolution indicates that driving mechanisms behind the jet break-up are vortex tilting/stretching, then baroclinic torque, leading to Rayleigh-Taylor instabilities, closely followed by vortex dilation and finally viscous effects.

42 ENGINEERING↗

Sensitivity of Short-Term Weather Forecasts to Assimilated AIRS Data: Implications for NPOESS Applications

The Atmospheric Infrared Sounder (AIRS) is acting as a heritage and risk reduction instrument for the Cross-track lnfrared Sounder (CrIS) to be flown aboard the NPP and NPOESS satellites. The hyperspectral nature of AIRS and CrIS provides high-quality soundings that, along with their asynoptic observation time over North America, make them attractive sources to fill the spatial and temporal data voids in upper air temperature and moisture measurements for use in data assimilation and numerical weather prediction. Observations from AlRS can be assimilated either as direct radiances or retrieved thermodynamic profiles, and the Short-Term Prediction Research and Transition (SPORT) Center at NASA's Marshall Space Flight Center has used both data types to improve short-term (0-48h), regional forecasts. The purpose of this paper is to share SPORT'S experiences using AlRS radiances and retrieved profiles in regional data assimilation activities by showing that proper handling of issues-including cloud contamination and land emissivity characterization-are necessary to produce optimal analyses and forecasts.

Zavodsky, Bradley↗

Scaling dynamics in low-salt-rejection reverse osmosis for high-salinity produced water desalination: Mechanistic modeling and membrane autopsy

Membrane scaling remains a critical barrier to the reliable operation of desalination systems, particularly for hypersaline produced water (PW) treatment. This study fills the knowledge gap of autopsy-based model validation for PW desalination by elucidating scaling mechanisms in a Low-Salt-Rejection Reverse Osmosis (LSRRO) system through the integration of pilot-scale experimentation and complementary modeling approaches. A semi-empirical modeling framework was developed and applied to a multistage pilot LSRRO system equipped with nanofiltration and RO membranes treating high-salinity PW from the Permian Basin. Water quality analysis showed that total dissolved solids decreased from ~130,000 mg/L to ~1900 mg/L in the permeate, then further reduced to ~300 mg/L by a second-pass RO. Two different thermodynamic modeling approaches were evaluated: the first extends the LSRRO framework by incorporating system complexity and scaling phenomena, whereas the second method explicitly captures concentration polarization in localized supersaturation. Both methods illustrate the tendency for carbonate and sulfate scaling throughout the stages. Membrane autopsies revealed a silica-dominated deposit matrix, localized CaSO 4 at Stage 2, and minor barite/celestite despite their prominence in model predictions. Quantum-chemical calculations indicated silica scaling can be rationalized by favorable adsorption of H 4 SiO 4 on Fe-oxide surfaces (ΔG ≈ −44 kJ/mol), providing a kinetic pathway for interfacial inorganic polymerization even when bulk equilibrium predictions are conservative. Overall, the thermodynamic scaling modeling and membrane autopsy revealed heterogeneous, localized deposits with limited impact on LSRRO performance, while quantum analysis rationalized the thermodynamically unfavorable precipitation formation under bulk equilibrium, reconciling model–autopsy discrepancies. These insights support targeted pretreatment and silica-specific antiscalants to extend membrane lifetime and increase recovery, providing a transferable framework for hypersaline water desalination systems. The combined experimental–computational approach provides new mechanistic insight into scaling in hypersaline membrane systems and establishes a transferable framework for predicting and mitigating scaling in next-generation desalination technologies.

Low-salt-rejection reverse osmosis↗

Theory of the effect of external stress on the activated dynamics and transport of dilute penetrants in supercooled liquids and glasses

We generalize the self-consistent cooperative hopping theory for a dilute spherical penetrant or tracer activated dynamics in dense metastable hard sphere fluids and glasses to address the effect of external stress, the consequences of which are systematically established as a function of matrix packing fraction and penetrant-to-matrix size ratio. All relaxation processes speed up under stress, but the difference between the penetrant and matrix hopping (alpha relaxation) times decreases significantly with stress corresponding to less time scale decoupling. A dynamic crossover occurs at a critical “slaving onset” stress beyond which the matrix activated hopping relaxation time controls the penetrant hopping time. This characteristic stress increases (decreases) exponentially with packing fraction (size ratio) and can be well below the absolute yield stress of the matrix. Below the slaving onset, the penetrant hopping time is predicted to vary exponentially with stress, differing from the power law dependence of the pure matrix alpha time due to system-specificity of the stress-induced changes in the penetrant local cage and elastic barriers. An exponential growth of the penetrant alpha relaxation time with size ratio under stress is predicted, and at a fixed matrix packing fraction, the exponential relation between penetrant hopping time and stress for different size ratios can be collapsed onto a master curve. Direct connections between the short- and long-time activated penetrant dynamics and between the penetrant (or matrix) alpha relaxation time and matrix thermodynamic dimensionless compressibility are also predicted. The presented results should be testable in future experiments and simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Dynamic Modeling of Solar Dynamic Components and Systems

The purpose of this grant was to support NASA in modeling efforts to predict the transient dynamic and thermodynamic response of the space station solar dynamic power generation system. In order to meet the initial schedule requirement of providing results in time to support installation of the system as part of the initial phase of space station, early efforts were executed with alacrity and often in parallel. Initially, methods to predict the transient response of a Rankine as well as a Brayton cycle were developed. Review of preliminary design concepts led NASA to select a regenerative gas-turbine cycle using a helium-xenon mixture as the working fluid and, from that point forward, the modeling effort focused exclusively on that system. Although initial project planning called for a three year period of performance, revised NASA schedules moved system installation to later and later phases of station deployment. Eventually, NASA selected to halt development of the solar dynamic power generation system for space station and to reduce support for this project to two-thirds of the original level.

Hochstein, John I.↗

Machine-learning informed prediction of high-entropy solid solution formation: Beyond the Hume-Rothery rules

The empirical rules for the prediction of solid solution formation proposed so far in the literature usually have very compromised predictability. Some rules with seemingly good predictability were, however, tested using small data sets. Based on an unprecedented large dataset containing 1252 multicomponent alloys, machine-learning methods showed that the formation of solid solutions can be very accurately predicted (93%). The machine-learning results help identify the most important features, such as molar volume, bulk modulus, and melting temperature. As such a new thermodynamics-based rule was developed to predict solid–solution alloys. The new rule is nonetheless slightly less accurate (73%) but has roots in the physical nature of the problem. The new rule is employed to predict solid solutions existing in the three blocks, each of which consists of 9 elements. The predictions encompass face-centered cubic (FCC), body-centered cubic (BCC), and hexagonal closest packed (HCP) structures in a high throughput manner. The validity of the prediction is further confirmed by CALculations of PHAse Diagram (CALPHAD) calculations with high consistency (94%). Since the new thermodynamics-based rule employs only elemental properties, applicability in screening for solid solution high-entropy alloys is straightforward and efficient.

36 MATERIALS SCIENCE↗

Computational methods in solution-based plastics purification

Plastic waste can be recycled into resins with near-virgin properties by solution-based purification processes that selectively dissolve polymers, remove contaminants, or detach printing residues. Here, in this review, we examine computational methods for predicting the behavior governing solution-based plastic purification, motivated by the vast polymer–solvent–contaminant compositional space. We discuss thermodynamic and machine learning methods for predicting polymer–solvent and polymer–contaminant interaction and review physics-based molecular dynamics simulations that resolve molecular-scale phenomena within polymer matrices inaccessible to screening methods. We highlight how these methods have informed experimental design for dissolution-based recycling and solvent-based contaminant removal. Finally, we discuss the prospective role of agentic AI in integrating these computational tools with real-time sorting data to adapt purification conditions to the compositional variability of real post-consumer feedstocks. This review charts a path toward computationally guided solution-based purification workflows that can respond to the complexity inherent in plastic waste streams.

Altamimi, Ali [Univ. of Wisconsin, Madison, WI (Un↗

Enzyme activities predicted by metabolite concentrations and solvent capacity in the cell

Experimental measurements or computational model predictions of the post-translational regulation of enzymes needed in a metabolic pathway is a difficult problem. Consequently, regulation is mostly known only for well-studied reactions of central metabolism in various model organisms. In this study, we use two approaches to predict enzyme regulation policies and investigate the hypothesis that regulation is driven by the need to maintain the solvent capacity in the cell. The first predictive method uses a statistical thermodynamics and metabolic control theory framework while the second method is performed using a hybrid optimization–reinforcement learning approach. Efficient regulation schemes were learned from experimental data that either agree with theoretical calculations or result in a higher cell fitness using maximum useful work as a metric. As previously hypothesized, regulation is herein shown to control the concentrations of both immediate and downstream product concentrations at physiological levels. Model predictions provide the following two novel general principles: (1) the regulation itself causes the reactions to be much further from equilibrium instead of the common assumption that highly non-equilibrium reactions are the targets for regulation; and (2) the minimal regulation needed to maintain metabolite levels at physiological concentrations maximizes the free energy dissipation rate instead of preserving a specific energy charge. The resulting energy dissipation rate is an emergent property of regulation which may be represented by a high value of the adenylate energy charge. In addition, the predictions demonstrate that the amount of regulation needed can be minimized if it is applied at the beginning or branch point of a pathway, in agreement with common notions. The approach is demonstrated for three pathways in the central metabolism of E. coli (gluconeogenesis, glycolysis-tricarboxylic acid (TCA) and pentose phosphate-TCA) that each require different regulation schemes. It is shown quantitatively that hexokinase, glucose 6-phosphate dehydrogenase and glyceraldehyde phosphate dehydrogenase, all branch points of pathways, play the largest roles in regulating central metabolism.

59 BASIC BIOLOGICAL SCIENCES↗

G4Boost: a machine learning-based tool for quadruplex identification and stability prediction

Background: G-quadruplexes (G4s), formed within guanine-rich nucleic acids, are secondary structures involved in important biological processes. Although every G4 motif has the potential to form a stable G4 structure, not every G4 motif would, and accurate energy-based methods are needed to assess their structural stability. Here, we present a decision tree-based prediction tool, G4Boost, to identify G4 motifs and predict their secondary structure folding probability and thermodynamic stability based on their sequences, nucleotide compositions, and estimated structural topologies. Results: G4Boost predicted the quadruplex folding state with an accuracy greater then 93% and an F1-score of 0.96, and the folding energy with an RMSE of 4.28 and R 2 of 0.95 only by the means of sequence intrinsic feature. G4Boost was successfully applied and validated to predict the stability of experimentally-determined G4 structures, including for plants and humans. Conclusion: G4Boost outperformed the three machine-learning based prediction tools, DeepG4, Quadron, and G4RNA Screener, in terms of both accuracy and F1-score, and can be highly useful for G4 prediction to understand gene regulation across species including plants and humans.

59 BASIC BIOLOGICAL SCIENCES↗

Influence of fixed charge concentration and water uptake on ion sorption in AMPS/PEGDA membranes

Water content and charge density strongly influence ion sorption in charged membranes. However, isolating the individual effect of each parameter on ion sorption can be difficult due to experimental challenges associated with independently controlling these two variables during membrane synthesis. This frustrates development and validation of fundamental models and structure/property relationships. In this study, three series of uncharged and negatively charged hydrogel membranes were prepared using poly(ethylene glycol) diacrylate (PEGDA) as a cross-linker and 2-acrylamido-2-methylpropanesulfonic acid (AMPS) as an ionic monomer. Here, water content and charge density were controlled by varying AMPS content and PEGDA chain length. Ion sorption in these materials was measured using aqueous NaCl solutions at concentrations ranging from 0.01 to 1.0 M. At constant charge density, salt sorption increased as water content increased. At fixed water content, salt sorption decreased as charge density increased. Salt sorption in membranes with the highest water content and charge density was predicted using the Donnan/Manning model, which accounts for solution and membrane phase thermodynamic non-idealities. However, this approach could not predict sorption in weakly charged and uncharged membranes, presumably due to additional membrane phase thermodynamic non-idealities associated with ion solvation and uncharged polymer segments.

36 MATERIALS SCIENCE↗

Creep Behavior and Phase Equilibria in Model Precipitate Strengthened Alumina-Forming Austenitic Alloys

Abstract Creep-rupture behavior and microstructural response in alumina-forming austenitic (AFA) alloys with two different precipitation strengthening mechanisms, “Laves-phase + M 23 C 6 carbide” and “coherent L1 2 γ′-Ni 3 (Al,Ti),” were explored as “model” cases of multi-phase, multi-scale heat-resistant AFA alloys for 650–750°C use. These alloys will be used to guide and verify computational alloy design and life-prediction modeling under an on-going eXtremeMAT project through the Office of Fossil Energy and Carbon Management, US Department of Energy. Computational thermodynamics were used to design and predict the amounts of strengthening and deteriorating secondary phases at 750°C. Creep-rupture lives of the alloys tested at 750°C and 100 MPa were in a range of 4000–9000 h, and the microstructure at the gage/grip after creep-rupture testing was compared with isothermally aged alloys for 1500 h, as well as the calculated phases. Detailed microstructure characterization includes phase identification, volume fraction measurement, and compositional analysis, which were correlated with the creep-rupture properties. High-temperature oxidation resistance was also screened and compared with commercial, chromia-forming heat-resistant steels. These model alloys also provide the basis for further design and optimization of next generation AFA alloys with improved creep resistance.

36 MATERIALS SCIENCE↗