WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7150
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Article A Physics-Informed Neural Network (PINN) Approach to Over-Equilibrium Dynamics in Conservatively Perturbed Linear Equilibrium Systems(MDPI, 2025) Dutta, Abhishek; Mukherjee, Bitan; Hosen, Sk Aftab; Turan, Meltem; Constales, Denis; Yablonsky, GregoryConservatively perturbed equilibrium (CPE) experiments yield transient concentration extrema that surpass steady-state equilibrium values. A physics-informed neural network (PINN) framework is introduced to simulate these over-equilibrium dynamics in linear chemical reaction networks without reliance on extensive time-series data. The PINN incorporates the reaction kinetics, stoichiometric invariants, and equilibrium constraints directly into its loss function, ensuring that the learned solution strictly satisfies physical conservation laws. Applied to three- and four-species reversible mechanisms (both acyclic and cyclic), the PINN surrogate matches conventional ODE integration results, reproducing the characteristic early concentration extrema (maxima or minima) in unperturbed species and the subsequent relaxation to equilibrium. It captures the timing and magnitude of these extrema with high accuracy while inherently preserving total mass. Through the physics-informed approach, the model achieves accurate results with minimal data and a compact network architecture, highlighting its parameter efficiency.Article Uncertainty Assessment of the Impacts of Climate Change on Streamflow in the Iznik Lake Watershed, Türkiye(MDPI, 2026) Tezel, Anil Caliskan; Akpinar, Adem; Bor, Asli; Elci, SebnemStudy region: This study focused on the Iznik Lake Watershed in northwestern T & uuml;rkiye. Study focus: Climate change is increasingly affecting water resources worldwide, raising concerns about future hydrological sustainability. This study investigates the impacts of climate change on river streamflow in the Iznik Lake Watershed, a critical freshwater resource in northwestern T & uuml;rkiye. To capture possible future conditions, downscaled climate projections were integrated with the SWAT+ hydrological model. Recognizing the inherent uncertainties in climate models and model parameterization, the analysis examined the relative influence of climate realizations, emission scenarios, and hydrological parameters on streamflow outputs. By quantifying both the magnitude of climate-induced changes and the contribution of different sources of uncertainty, the study provides insights that can guide decision-makers in future management planning and be useful for forthcoming modeling efforts. New hydrological insights for the region: Projections indicate wetter winters and springs but drier summers, with an overall warming trend in the study area. Based on simulations driven by four representative grid points, the results at the Karadere station, which represents the main inflow of the watershed, indicate modest changes in mean annual streamflow, ranging from -7% to +56% in the near future and from +19% to +54% in the far future. Maximum flows (Qmax) exhibit notable increases, ranging from +0.9% to +47% in the near future and from +21% to +63% in the far future, indicating a tendency toward higher peak discharges under future climate conditions. Low-flow conditions, especially in summer, exhibit the greatest relative variability due to near-zero baseline discharges. Relative change analysis revealed considerable differences in Karadere and Findicak sub-catchments, reflecting heterogeneous hydrological responses even within the same basin. Uncertainty analysis, conducted using both an ANOVA-based approach and Bayesian Model Averaging (BMA), highlighted the dominant influence of climate projections and potential evapotranspiration calculation methods, while land use change contributed negligibly to overall uncertainty.Article Advancing Hydrological Prediction With Hybrid Quantum Neural Networks: A Comparative Study for Mile Mughan Dam(MDPI, 2025) Abdi, Erfan; Sattari, Mohammad Taghi; Samadianfard, Saeed; Ahmad, SajjadPredicting dam inflow is critical for human life safety, water resource management, and hydroelectric power generation. While machine learning (ML) models address complex, nonlinear hydrological problems, quantum machine learning (QML) offers greater potential to overcome classical computational limits. This study compares a hybrid quantum neural network (HQNN) with the following two classical models: bidirectional CNN-LSTM and support vector regression (SVR). These models were evaluated to predict monthly inflow to the Mile Mughan Dam, a transboundary hydroelectric and irrigation dam located on the Aras River between Azerbaijan and Iran, using a 14-year dataset (2010-2023) under two scenarios. In total, 70% of data was used for training and 30% for testing. The first scenario encompassed meteorological variables plus three months of inflow lags, and the second included inflow lags only. Model performance was assessed using Coefficient of Determination (R2), Root Mean Squared Error (RMSE), Nash-Sutcliffe efficiency (NSE), Mean Absolute Percentage Error (MAPE), and graphical plots. HQNN showed superior performance across all metrics. In Scenario 1, HQNN achieved R2 = 0.915, RMSE = 37.318 MCM, NSE = 0.908, MAPE = 8.343%; CNN-BiLSTM had R2 = 0.867, RMSE = 46.506 MCM, NSE = 0.858, MAPE = 10.795%; SVR had R2 = 0.846, RMSE = 52.372 MCM, NSE = 0.821, MAPE = 12.772%. In Scenario 2, HQNN maintained strong performance (R2 = 0.855, RMSE = 48.56 MCM, NSE = 0.845, MAPE = 9.979%) and outperformed CNN-BiLSTM (R2 = 0.810, RMSE = 56.126 MCM, NSE = 0.793, MAPE = 11.456%) and SVR (R2 = 0.801, RMSE = 60.336 MCM, NSE = 0.761, MAPE = 12.901%). In Scenario 1 and Scenario 2, HQNN increased the prediction accuracy by 19.76% and 13.47%, respectively, compared to the CNN-BiLSTM model. These results confirm HQNN's reliability in both multivariate and univariate modeling.Article Investigation of Few-Layer Graphene-Ubiquitin Interactions with Optical Spectroscopy Techniques(MDPI, 2025) Gencay, Burcu; Guler, GunnurUnderstanding the molecular mechanisms of protein-nanoparticle interactions is crucial for enabling the development of new applications in biomedicine and nanotechnology. Ubiquitin, an important and structurally small functional protein, plays a central role in numerous cellular processes. Therefore, in the current study, we focused on the few-layer graphene (FLG)-Ubiquitin complexes formed by exfoliating FLG structures using only water. Optical spectroscopic techniques (Raman, FT-IR, UV-Vis and circular dichroism) were employed to investigate these complexes on the molecular level. Overall, both CD and FT-IR data reveal that the formation of the FLG-Ubiquitin complexes occurred without inducing disordered structures in the protein. Based on the existence of a blue shift (hypsochromic shift) in the UV-Vis data, the presence of a single tyrosine and two phenylalanine residues in ubiquitin enables the detection of FLG-induced micro-environmental changes, particularly influencing the protein's beta-sheet and alpha-helix structures. The CD spectral results and CDPro quantitative estimations are in line with ATR FT-IR results, confirming the absence of disordered structure formation while altering the protein's chirality. UV-Vis and CD spectroscopy results revealed concentration-dependent trends consistent with FLG-protein interactions that preserve the overall protein structure. This study has potential applications in both academic research and practical usage, particularly in biomedicine and nanotechnology specifically for FLG.Article Interventions in Historic Urban Sites After Earthquake Disasters(MDPI, 2025) Demir, Hatice Aysegul; Turan, Mine HamamciogluEarthquakes, fires, and climate change-related hazards increasingly threaten cultural heritage. Documenting and identifying the significance of heritage sites before disasters is essential for archival purposes and for guiding post-disaster interventions such as consolidation, reconstruction, or redesign. Although various post-disaster strategies exist in the literature, they often lack consideration of pre-disaster values and authentic qualities, limiting their effectiveness in value-based regeneration. This study proposes a framework for managing post-disaster interventions grounded in pre-disaster documentation of heritage values, authenticity, and integrity. The methodology includes seven phases: case selection; site survey and documentation; thematic analysis and mapping; quantification of qualitative data; synthesis of pre-disaster analysis results to define values, problems, and potentials; post-disaster assessment using aerial and terrestrial imagery; and development of targeted intervention strategies. This study focuses on two areas in Antakya, T & uuml;rkiye: Kurtulu & scedil; Street and Kuyulu Neighborhood, affected by the 2023 earthquake (M 7.7). These areas represent different historical layers: a Hellenistic grid plan with French-style buildings, and an organic Ottoman settlement morphology, respectively. Conservation data collected in 2019 inform the analysis. Mapping techniques evaluate attributes such as spatial characteristics, typologies, and structural systems. The study concludes that traces of pre-disaster spatial patterns and building features should inform post-disaster designs, ensuring sustainable, earthquake-resistant, and value-based interventions.Article A First Process-Oriented Characterization of Eriolobus Trilobatus (Labill. Ex Poiret) Bark From Turkey: Chemical, Morphological and Energy Properties(MDPI, 2025) Sen, Umut; Yucedag, Cengiz; Balci, Busra; Arici, Sefik; Kocar, Gunnur; Sat, Beyza; Pereira, HelenaFor the first time, Eriolobus trilobatus bark from Turkey has been characterized in terms of its chemical, extractive, fuel, and ash characteristics using SEM-EDS, wet chemical analysis, phenolic analysis, FT-IR, TGA, XRF, XRD, BET surface area measurement, proximate analysis, and ash fusion temperature (AFT) determination. The results showed that the bark contains 13% ash, dominated by calcium oxalate, and 15% extractives, largely composed of polar phenolic compounds with moderate radical-scavenging potential. Thermal decomposition of bark proceeds in four distinct stages, associated with the sequential degradation of extractives/hemicelluloses, cellulose, lignin/suberin, and inorganic fractions. The higher calorific value of 14.9 MJ/kg indicates moderate fuel quality compared with conventional woody biomass. Ash is mesoporous with a CaO-rich structure highly suitable for catalytic applications in biodiesel production and biomass gasification. Ash fusion analysis revealed a high flow temperature (1452 degrees C), indicating a very low slagging risk during thermochemical conversion. Overall, E. trilobatus bark is a promising material for value-added biorefinery pathways, enabling processes for the production of biochars, CaO-based catalysts, phenolic extracts, and sustainable energy. The valorization of E. trilobatus bark not only enhances the economic potential of forestry residues but also provides environmental co-benefits through carbon soil amendment and landscape applications.Article Characterisation of Electro-Brush Plated Nickel Coatings on P-Type (Zr,ti)co Half-Heusler Thermoelectric Materials for Stable Contact Layers(MDPI, 2025) Gurtaran, Mikdat; Zhang, Zhenxue; Li, Xiaoying; Dong, HanshanIn this study, a highly conductive nickel (Ni) layer was deposited onto a P-type (Zr,Ti)Co(Sn,Sb) half-Heusler (HH) thermoelectric (TE) material using a low-cost electro-brush plating technique. Before depositing Ni on the TE material, the plating process was optimised on a stainless steel (SS) substrate. An optimal medium-rate deposition voltage of 6V was identified on the SS substrate, with the desired thickness, superior mechanical performance, reduced sheet resistance and surface roughness, and enhanced electrical conductivity. The optimised deposition condition was then applied to the P-type (Zr,Ti)Co(Sn,Sb) material, resulting in a Ni layer that significantly enhanced its electrical and thermal stability. After thermal exposure at 500 degrees C for 10 h, the Ni coating effectively protected the TE surface against oxidation and sublimation, suggesting that the interfacial contact properties of P-type (Zr,Ti)Co(Sn,Sb) TE material can be effectively enhanced by depositing a highly conductive, oxidation-resistant Ni layer using the cost-effective, straightforward electro-brush plating technique.Article Comparative Stability of Synthetic and Natural Polymeric Micelles in Physiological Environments: Implications for Drug Delivery(MDPI, 2025) Polat, Hurriyet; Eren, Merve Cevik; Polat, Mehmet; Koss, Kyle M.; Polat, Onur K.Polymeric micelles are widely studied as nanocarriers for hydrophobic drugs, yet their structural stability under physiological conditions remains a major limitation. This review provides a comparative evaluation of synthetic and natural polymeric micelles with a focus on their stability under dilution and in protein-rich environments. The discussion integrates thermodynamic and kinetic factors governing micelle integrity and examines how molecular composition, hydrophobic segment length, and core-shell modifications influence disintegration behavior. While synthetic micelles commonly collapse below their critical micelle concentration during intravenous administration, natural polymeric micelles, such as those derived from chitosan, alginate, or heparin, exhibit improved resistance to dilution but remain vulnerable to protein-induced destabilization. Strategies such as core or shell cross-linking, surface functionalization, and natural polymer coatings are reviewed as promising approaches to enhance circulation stability and controlled drug release. The work provides a framework for designing micellar systems with balanced biocompatibility, biodegradability, and robustness suitable for clinical drug-delivery applications.Article Chemical Composition and Reactivity of Quercus Pubescens Bark and Bark Fractions for Thermochemical Biorefinery Applications(MDPI, 2025) Sen, Umut; Balci, Busra; Arici, Sefik; Sat, Beyza; Miranda, Isabel; Pereira, HelenaAdvancing circular bioeconomy in thermochemical biorefineries requires species-specific data that link biomass composition and thermochemical performance. Here, we provide the first integrated thermochemical dataset for Quercus pubescens bark combining FT-IR, XRD, XRF, TGA, and measured ash fusion temperatures (AFT). The results reveal that bark is enriched in phenolic extractives (21.2%) and inorganics (15%), with calcium oxalate monohydrate (COM) dominating the inorganic fraction, as confirmed by FT-IR and XRD. Thermal decomposition occurs between 150 degrees C and 690 degrees C. Pyrolysis follows diffusion-controlled kinetics, with apparent activation energies for bark and its fractions ranging between 70 and 103 kJ mol-1. Extraction increases the activation energy of bark. The ash exhibits a high AFT (softening: 1421 degrees C, flow: 1467 degrees C), placing this feedstock within the low-slagging, moderate-fouling range compared to other lignocellulosics. The observed COM-to-CaCO3/CaO transformation upon heating contributes to the elevated AFT. Reactivity analyses of bark fractions support thermochemical biorefinery routing of fractions: extracted bark (EB) and desuberinised bark (DB) are highly reactive and well-suited to combustion/gasification, whereas raw bark (B) and Klason lignin (KL) exhibit higher thermal stability and yield more persistent char, favoring slow pyrolysis for biochar production. Such routing strategies optimize energy recovery and also enable co-products with environmental co-benefits.Article Locoregional Treatment in De Novo Bone-Only Metastatic Breast Cancer: Prospective, Multi-Institutional Real-World Data, BOMETIN, Protocol MF14-1a(MDPI, 2025) Soran, Atilla; Demirors, Berkay; Aytac, Ozgur; Ozbas, Serdar; Dogan, Lutfi; Lucci, AnthonyIntroduction: The impact of locoregional treatment (LRT) on survival in de novo bone-only metastatic breast cancer (dnBOMBC) is controversial. This study aims to assess the effect of LRT on survival, utilizing international, prospectively acquired data in this cohort of patients. Materials and Methods: Patients with dnBOMBC were divided into two groups: those receiving systemic therapy only (ST) and those undergoing LRT. Further, patients who received LRT were divided into two subgroups: those who received ST after LRT (LRT+ST group) and those who received ST prior to LRT (ST+LRT group). Factors associated with disease progression, including solitary or multiple bone metastases, were analyzed. Results: There was a total of 744 patients with dnBOMBC treated at each of the participating institutions between 2014 and 2022, with 372 (50%) participants in each arm. Median follow-up was 48 months (32-66, 25-75%). Patients in the LRT group were significantly younger than the ST group [50 (42, 60) vs. 55 (44, 66), p = 0.0001]. There were no significant differences in grade, HER2 status, triple-negative status, receipt of hormonal therapy, or intervention to metastatic sites. During follow-up, 58% (n = 217) of patients in the ST group and 32% (n = 120) of patients in the LRT group died (p < 0.001). Local progression was observed in 20% of the patients in the ST group, whereas 9% progressed in the LRT group (p = 0.0001). Systemic progression occurred more in the ST group; 66% (n = 244) compared to 41% (n = 152) of patients in the LRT group (p < 0.001). The hazard of death was 64% lower in the LRT group than in the ST group (HR: 0.36, 95% CI: 0.29-0.45, p < 0.0001). The burden of metastatic disease differed significantly between the two groups, with a higher rate of solitary bone metastases in the LRT group compared to the ST group (50% vs. 24%, p < 0.001). However, the LRT group had better overall survival (OS) for both solitary (HR: 0.38, 95% Cl: 0.26-0.55) and multiple (HR: 0.38, 95% Cl: 0.29-0.51) bone metastasis patients. Within the LRT group, survival rates were similar whether the breast surgery was performed before or after ST. Multivariate Cox analysis showed that LRT and ER/PR positivity significantly decrease the hazard of death (p < 0.05). Conclusions: Analysis of this large multi-institutional patient cohort provides further evidence that LRT is associated with longer OS and lower locoregional recurrence rates in patients with dnBOMBC. In breast cancer patients with bone-only metastases at presentation, the decision for LRT should be made through a multidisciplinary approach with consideration of surgical therapy at the primary tumor.