Search Results (1,354)

Over the past decade, the number and diversity of identified protein post-translational modifications (PTMs) have grown significantly. However, most PTMs occur at relatively low abundance, making selective enrichment of modified peptides essential. To address this, we developed a thermodynamic model describing the free beads enrichment in suspension enrichment process and derived a theoretical relationship between material dosage and analyte recovery. The model predicts a non-linear trend, with enrichment efficiency increasing up to an optimal dosage and declining thereafter—a pattern confirmed by experimental data. We validated the model using centrifugation-based enrichment for glycosylated peptides and magnetic-based enrichment for phosphorylated peptides. In both cases, the results aligned with theoretical predictions. Additionally, the optimal dosage varied among peptides with the same modification type, highlighting the importance of tailoring enrichment strategies. This study provides a solid theoretical and experimental basis for optimizing PTMs enrichment and advancing more sensitive, accurate, and efficient mass spectrometry-based proteomic workflows. Full article

Levitation techniques reduce the available heterogeneous nucleation sites and provide stable access to deeply undercooled melts. However, some samples have repeatably demonstrated that, in the presence of strong stirring, solidification may be induced at moderate, sub-critical undercoolings. Dynamic nucleation is a mechanism by which solidification may be induced through flow effects within a sub-critically undercooled melt. In this mechanism, collapsing cavities within the melt produce very high-pressure shocks, which shift the local melting temperature. In these regions of locally shifted melt temperatures, thermodynamic conditions enable nuclei to grow and trigger solidification of the full sample. By deepening the local undercooling, dynamic nucleation enables solidification to occur in conditions where classical nucleation does not. Dynamic nucleation has been observed in several zirconium and zirconium-based samples in the Electromagnetic Levitator onboard the International Space Station (ISS-EML). The experiments presented here address conditions in which a zirconium sample alloyed with 2.5 atomic percent niobium spontaneously solidifies during electromagnetic levitation experiments with strong melt stirring. In these experimental conditions, classical nucleation predicts the sample to remain liquid. This solidification behavior is consistent with the solidification behavior observed in prior experiments on pure zirconium. Full article

Sanicro 25 (X7NiCrWCuCoNb25-23-3-3-2) steel is specifically designed for use in superheater components within the latest generation of conventional power plants. These power plants operate under conditions often referred to as super-ultra-supercritical, with steam parameters that can reach up to 30 MPa and temperatures of 653 °C for fresh steam and 672 °C for reheated steam. While last-generation supercritical power plants still rely on fossil fuels, they represent a significant step forward in more sustainable energy production. The most sophisticated facilities of this kind can achieve thermodynamic efficiencies exceeding 47%. This study aimed to conduct a detailed analysis of the initial precipitation processes occurring in Sanicro 25 steel within the temperature range of 700–900 °C. The temperature of 700 °C corresponds to the operational conditions of this material, particularly in secondary steam superheaters in thermal power plants that operate under ultra-supercritical parameters. Understanding precipitation processes is crucial for optimizing mechanical performance, particularly in terms of long-term strength and creep resistance. To accurately assess the microstructural changes that occur during the early stages of service, a digital twin approach was employed, which included CALPHAD simulations and experimental heat treatments. Experimental annealing tests were conducted in air within the temperature range of 700–900 °C. Precipitation behavior was simulated using the Thermo-Calc 2025a with Dictra software package. The results from Prisma simulations correlated well with the experimental data related to the kinetics of phase transformations; however, it was noted that the predicted sizes of the precipitates were generally smaller than those observed in experiments. Additionally, computational limitations were encountered during some simulations due to the complexity arising from the numerous alloying elements present in Sanicro 25 steel. The microstructural evolution was investigated using various methods, including light microscopy (LM), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). Full article

In this paper, the directed message-passing neural network architecture is used to predict several quantities of interest in gas chromatography: retention times, Clarke-Glew 3-point thermodynamic parameters for simulation, and retention indices. The retention index model was trained with 48,803 training samples and reached 1.9–2.6% accuracy, whereas the thermodynamic parameters and retention time were trained by using 230 training data samples yielding 17% accuracy. Furthermore, the accuracy as a function of the number of training samples is investigated, showing the necessity of large, accurate datasets for training deep learning-based models. Lastly, several uses of such a model for the identification of compounds and the optimization of GC parameters are discussed. Full article

The high spatial resolution of radar data enables the detailed resolution of typhoon vortices and their embedded structures; the assimilation of radar data in the initialization of numerical weather prediction exerts an important influence on the forecasting of typhoon track, intensity, and structures up to at least 12 h. For the case of typhoon Morakot (2009), Taiwan radar data was assimilated to adjust the dynamic and thermodynamic structures of the vortex in the model initialization by the three-dimensional variation data assimilation system in the Advanced Region Prediction System (ARPS). The radial wind was directly assimilated to tune the original unbalanced velocity fields through a 3-dimensional variation method, and complex cloud analysis was conducted by using the reflectivity data. The influence of radar data assimilation on typhoon prediction was examined at the stages of Morakot landing on Taiwan Island and subsequently going inland. The results showed that the assimilation made some improvement in the prediction of vortex intensity, track, and structures in the initialization and subsequent forecast. For example, besides deepening the central sea level pressure and enhancing the maximum surface wind speed, the radar data assimilation corrected the typhoon center movement to the best track and adjusted the size and inner-core structure of the vortex to be close to the observations. It was also shown that the specific humidity adjustment in the cloud analysis procedure during the assimilation time window played an important role, producing more hydrometeors and tuning the unbalanced moisture and temperature fields. The neighborhood-based ETS revealed that the assimilation with the specific humidity adjustment was propitious in improving forecast skill, specifically for smaller-scale reflectivity at the stage of Morakot landing, and for larger-scale reflectivity at the stage of Morakot going inland. The calculation of the intensity-scale skill score of the hourly precipitation forecast showed the assimilation with the specific humidity adjustment performed skillful forecasting for the spatial forecast-error scales of 30–160 km. Full article

Vacuum degassing (VD) is a critical refining step in electric arc furnace (EAF) steelmaking for producing clean steel with reduced nitrogen and hydrogen content. This study develops an Effective Equilibrium Reaction Zone (EERZ) model focused on denitrogenation (de-N) by simulating interfacial reactions at the bubble–steel interface (Z1). The model incorporates key process parameters such as argon flow rate, vacuum pressure, and initial nitrogen and sulfur concentrations. A robust empirical correlation was established between de-N efficiency and the mass of Z1, reducing prediction time from a day to under a minute. Additionally, the model was further improved by incorporating a dynamic surface exposure zone (Z_eye) to account for transient ladle eye effects on nitrogen removal under deep vacuum (<10 torr), validated using synchronized plant trials and Python-based video analysis. The integrated approach—combining thermodynamic-kinetic modeling, plant validation, and image-based diagnostics—provides a robust framework for optimizing VD control and enhancing nitrogen removal control in EAF-based steelmaking. Full article

Under global warming, persistent extreme heat events (PHEs) in China have increased significantly in both frequency and intensity, posing severe threats to agriculture and socioeconomic development. Combining observational analysis (1961–2019) and numerical simulations, this study investigates the distinct impacts of Northwest Pacific (NWP) and North Atlantic (NA) sea surface temperature (SST) anomalies on PHEs over China. Key findings include the following: (1) PHEs exhibit heterogeneous spatial distribution, with the Yangtze-Huai River Valley as the hotspot showing the highest frequency and intensity. A regime shift occurred post-2000, marked by a threefold increase in extreme indices (+3σ to +4σ). (2) Observational analyses reveal significant but independent correlations between PHEs and SST anomalies in the tropical NWP and mid-high latitude NA. (3) Numerical experiments demonstrate that NWP warming triggers a meridional dipole response (warming in southern China vs. cooling in the north) via the Pacific–Japan teleconnection pattern, characterized by an eastward-retreated and southward-shifted sub-tropical high (WPSH) coupled with an intensified South Asian High (SAH). In contrast, NA warming induces uniform warming across eastern China through a Eurasian Rossby wave train that modulates the WPSH northward. (4) Thermodynamically, NWP forcing dominates via asymmetric vertical motion and advection processes, while NA forcing primarily enhances large-scale subsidence and shortwave radiation. This study elucidates region-specific oceanic drivers of extreme heat, advancing mechanistic understanding for improved heatwave predictability. Full article

Background/Objective: In the pursuit of identifying novel therapeutic agents against breast cancer, a major priority is finding agents that effectively and safely inhibit the signaling pathways sustaining cancer cells. To better focus research efforts in validating such candidates, this in silico study assessed the pharmacokinetic profiles, thermodynamics, and binding affinity of chlorogenic acid and cinnamaldehyde with the upstream mediators of the Akt pathway implicated in breast cancer cells. Methods: Various software and online tools were used to conduct molecular docking of the small molecules with the proteins PI3K, Akt, and PDK1, and to examine their absorption, distribution, metabolism, elimination, and toxicity (ADMET) profile. Results: The results show strong binding energy (all within the range of those of FDA-approved drugs) and thermostability between the compounds and the proteins. The phytochemicals were predicted to have moderate oral bioavailability and tissue distribution, and were identified as substrates of drug metabolizing enzymes, but not deactivated. Conclusion: Although these predictive data warrant confirmation in a biological system, they suggest that the compounds have good pharmacokinetics and are strong inhibitors of the Akt pathway, with great potential to shut down breast cancer cell invasion and migration. These data also inform more efficient experimental designs for our planned in vivo studies. Full article

Stacking fault tetrahedra (SFTs) are typically considered improbable in high stacking fault energy metals like aluminum. Using molecular statics and dynamics simulations, we reveal the formation, growth, and transformation of SFTs in aluminum via vacancy aggregation. Three types—perfect, truncated, and defective SFTs—are characterized by their structure, formation energy, and binding energy across a range of vacancy cluster sizes. Formation energies of perfect and truncated SFTs follow a scaling relation; beyond a critical size, truncated SFTs become thermodynamically favored, indicating a size-dependent transformation pathway. Binding energy and structure evolution exhibit quasi-periodic behavior, where vacancies initially adsorb at the vertices or the midpoints of the edges of a perfect SFT, then aggregate along one facet, triggering fault nucleation and a binding energy jump as the system reconstructs into a new perfect SFT. Molecular dynamics simulations further confirm the SFT nucleation and growth via vacancy aggregation, consistent with thermodynamic predictions. SFTs exhibit notable thermal mobility, enabling coalescence and evolution into vacancy-type dislocation loops. BCC-like $V_5$ clusters are identified as potential nucleation precursors. These findings explain the nanoscale, low-temperature nature of SFTs in aluminum and offer new insights into defect evolution and control in FCC metals. Full article

Methods such as AlphaFold have revolutionized protein structure prediction, making quantitative prediction of the thermodynamic stability of individual proteins and their complexes one of the next frontiers in computational protein modeling. Here, we develop methods for using protein language models (PLMs) with protein mutational datasets related to protein tertiary and quaternary stability. First, we demonstrate that fine-tuning of a ProtT5 PLM enables accurate prediction of the largest protein mutant stability dataset available. Next, we show that mutational impacts on protein function can be captured by fine-tuning PLMs, using green fluorescent protein (GFP) brightness as a readout of folding and stability. In our final case study, we observe that PLMs can also be extended to protein complexes by identifying mutations that are stabilizing or destabilizing. Finally, we confirmed that state-of-the-art simulation methods (free energy perturbation) can refine the accuracy of predictions made by PLMs. This study highlights the versatility of PLMs and demonstrates their application towards the prediction of protein and complex stability. Full article

Isobaric vapor-liquid equilibrium (VLE) data for binary mixtures of biomass–derived ethyl levulinate and ethanol were measured using an apparatus comprising a modified Rose-Williams still and a condensation system. Measurements were taken at temperatures ranging from 329.58 K to 470.00 K and pressures of 40.0, 60.0 and 80.0 kPa. The thermodynamic consistency of the VLE data was evaluated using the Redlich-Kister area test, the Fredenslund test and the Van Ness point-to-point test. The data was correlated using three activity coefficient models: Wilson, NRTL and UNIQUAC. The Gibbs energy of mixing of the VLE data was analyzed to verify the suitability of the binary interaction parameters of these models. The activity coefficients and excess Gibbs free energy, calculated from the VLE experimental data and model correlation results, were analyzed to evaluate the models’ fit and the non–ideality of the binary system. The accuracy of the regression results was also assessed based on the root mean square deviation (RMSD) and average absolute deviation (AAD) for both temperature and the vapor phase mole fraction of ethyl levulinate. The results indicate that the NRTL model provided the best fit to the experimental data. Notably, the experimental data showed strong correlation with the predictions of all three models, suggesting their reliability for practical application. Full article

The discharge of synthetic dyes in industrial wastewaters poses a serious environmental threat as they are difficult to degrade naturally and are harmful to aquatic organisms. This study aimed to evaluate the feasibility of using clean untreated rice husk (CRH) as a sustainable and low-cost adsorbent for the removal of methylene blue (MB) from synthetic wastewater. This approach effectively avoids the energy-intensive grinding process by directly using whole unprocessed rice husk, highlighting its potential as a sustainable and cost-effective alternative to activated carbon. A series of batch adsorption experiments were conducted to evaluate the effects of key operating parameters such as initial dye concentration, contact time, pH, ionic strength, and temperature on the adsorption performance. Adsorption kinetics, isotherm models, and thermodynamic analysis were applied to elucidate the adsorption mechanism and behavior. The results showed that the maximum adsorption capacity of CRH for MB was 5.72 mg/g. The adsorption capacity was stable and efficient between pH 4 and 10, and reached the highest value at pH 12. The presence of sodium ions (Na⁺) and calcium ions (Ca²⁺) inhibited the adsorption efficiency, with calcium ions having a more significant effect. Kinetic analysis confirmed that the adsorption process mainly followed a pseudo-second-order model, suggesting the involvement of a chemisorption mechanism; notably, in the presence of ions, the Elovich model provided better predictions of the data. Thermodynamic evaluation showed that the adsorption was endothermic (ΔH° > 0) and spontaneous (ΔG° < 0), accompanied by an increase in the disorder of the solid–liquid interface (ΔS° > 0). The calculated activation energy (Ea) was 17.42 kJ/mol, further supporting the involvement of chemisorption. The equilibrium adsorption data were well matched to the Langmuir model at high concentrations (monolayer adsorption), while they were accurately described by the Freundlich model at lower concentrations (surface heterogeneity). The dimensionless separation factor (RL) confirmed that the adsorption process was favorable at all initial MB concentrations. The results of this study provide insights into the application of agricultural waste in environmental remediation and highlight the potential of untreated whole rice husk as a sustainable and economically viable alternative to activated carbon, which can help promote resource recovery and pollution control. Full article

Atmospheric climate science lacks the capacity to integrate thermodynamics with the gravitational potential of air in a classical quantum theory. To what extent can we identify Carnot’s ideal heat engine cycle in reversible isothermal and isentropic phases between dual temperatures partitioning heat flow with coupled work processes in the atmosphere? Using statistical action mechanics to describe Carnot’s cycle, the maximum rate of work possible can be integrated for the working gases as equal to variations in the absolute Gibbs energy, estimated as sustaining field quanta consistent with Carnot’s definition of heat as caloric. His treatise of 1824 even gave equations expressing work potential as a function of differences in temperature and the logarithm of the change in density and volume. Second, Carnot’s mechanical principle of cooling caused by gas dilation or warming by compression can be applied to tropospheric heat–work cycles in anticyclones and cyclones. Third, the virial theorem of Lagrange and Clausius based on least action predicts a more accurate temperature gradient with altitude near 6.5–6.9 °C per km, requiring that the Gibbs rotational quantum energies of gas molecules exchange reversibly with gravitational potential. This predicts a diminished role for the radiative transfer of energy from the atmosphere to the surface, in contrast to the Trenberth global radiative budget of ≈330 watts per square metre as downwelling radiation. The spectral absorptivity of greenhouse gas for surface radiation into the troposphere enables thermal recycling, sustaining air masses in Lagrangian action. This obviates the current paradigm of cooling with altitude by adiabatic expansion. The virial-action theorem must also control non-reversible heat–work Carnot cycles, with turbulent friction raising the surface temperature. Dissipative surface warming raises the surface pressure by heating, sustaining the weight of the atmosphere to varying altitudes according to latitude and seasonal angles of insolation. New predictions for experimental testing are now emerging from this virial-action hypothesis for climate, linking vortical energy potential with convective and turbulent exchanges of work and heat, proposed as the efficient cause setting the thermal temperature of surface materials. Full article

A novel and cost-effective methodology is introduced for the precise prediction of the melting time of metals and alloys in a 700 W domestic microwave oven, using a hybrid SiC–graphite susceptor to ensure efficient heating without direct interaction with microwaves. The study includes experimental trials with multiple alloys (Sn–Bi, Zn, Zamak, and Al–Si, among others) and variable masses, whose results made it possible to construct a dimensionless model, trained with XGBoost on easily measurable thermophysical properties (specific heat, density, thermal conductivity, mass, and melting temperature). The model achieves high accuracy, with a relative error below 5%, and metrics of MAE = 4.8 s, RMSE = 6.1 s, and R² = 0.9996. The generalization of the model to different microwave powers (600–1100 W) is also validated through analytical adjustment, without the need for additional experiments. The proposal is implemented as a Python application with a graphical interface, suitable for any academic or teaching laboratory, and its performance is compared with classical models. This approach effectively contributes to the democratization of thermal testing of metals in educational and research settings with limited resources, providing thermodynamic rigor and advanced artificial intelligence tools. Full article

Leptin is an adipocyte-derived hormone that orchestrates different physiological processes, including energy balance, thermogenesis, immune regulation, reproduction, and tissue remodeling. These effects are mediated through interaction with the CRH2 domain of the leptin receptor (Ob-R). While the structural aspects of the interaction between leptin and Ob-R have been first studied in humans and mice, comparative analyses of stability across mammalian species under physiologically relevant microenvironmental conditions remain limited. We performed a bioinformatics-driven structural, stability, and thermodynamic characterization of the leptin–CRH2 complex. This included structural homology modeling using a full-length template, interface mapping, and binding energy estimation. Additionally, we analyzed the effect of pH, ionic strength, and temperature on complex formation to mimic physiological and pathological tissue conditions to enhance clarity in the structural features and stability of the complex. Our results show that the interaction is primarily enthalpy-driven and is sensitive to temperature, ionic strength, and pH changes for all heterodimers analyzed here. The predicted binding free energy (ΔG) ranged from −10.50 to −16.81 kcal/mol across species. The integrated bioinformatic analyses suggest that subtle sequence variations influence the stability and environmental responsiveness of the complex. This study provides a molecular framework for understanding how leptin–Ob-R binding adapts across species and tissue contexts. Full article