Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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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 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 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 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.Article Enhancing Electron Transfer in Cytochrome P450 Systems: Insights From CYP119-Putidaredoxin Interface Engineering(MDPI, 2025) Kakimova, Akbota; Surmeli, Nur BasakCytochrome P450 enzymes (CYPs) are versatile biocatalysts capable of performing selective oxidation reactions valuable for industrial and pharmaceutical applications. However, their catalytic efficiency is often constrained by dependence on costly electron donors, the requirement for redox partners, and uncoupling reactions that divert reducing power toward reactive oxygen species. Improving electron transfer efficiency through optimized redox partner interactions is therefore critical for developing effective CYP-based biocatalysts. In this study, we investigated the interaction between CYP119, a thermophilic CYP from Sulfolobus acidocaldarius, and putidaredoxin (Pdx), the redox partner of P450cam. Using rational design and computational modeling with PyRosetta 3, 14 CYP119 variants were modeled and analyzed by docking simulations on the Rosie Docking Server. Structural analysis identified three key mutations (N34E, D77R, and N34E/D77R) for site-directed mutagenesis. These mutations (N34E, D77R, and N34E/D77R) enhanced Pdx binding affinity by 20-, 3-, and 12-fold, respectively, without affecting substrate binding. Catalytic assays using lauric acid and indirect assays to monitor electron transfer revealed that, despite improved complex formation, the N34E variant showed reduced electron transfer efficiency compared to D77R. These findings highlight the delicate balance between redox partner binding affinity and catalytic turnover, emphasizing that fine-tuning electron transfer interfaces are essential for engineering efficient CYP biocatalysts.Article UV-Shielding Biopolymer Coatings Loaded With Bioactive Compounds for Food Packaging Applications(MDPI, 2025) Gennaro, Matteo; Buyuktas, Duygu; Carullo, Daniele; Pinto, Andrea; Dallavalle, Sabrina; Farris, StefanoFour natural bioactive compounds with UV-absorbing properties-curcumin, quercetin, caffeic acid, and hymecromone-were incorporated into pectin-based coatings deposited on oriented polypropylene (OPP) to develop packaging films with UV-shielding capabilities. The effects of both bioactive compounds (used individually or in combination) and coating thickness (delta = 0.12-1.2 mu m) on the optical properties (UV-Vis transmittance and haze) of the coated OPP samples were investigated. Coating deposition enhanced the UV-barrier properties in relation to the type of bioactive compound, following the order of caffeic acid > hymecromone > curcumin > quercetin. Regardless of the type of bioactive compound used, no significant changes were observed in clarity, haze, and tensile parameters of OPP, whereas the pectin coatings dramatically improved the oxygen barrier performance of the plastic substrate. Additionally, a greater coating thickness resulted in a lower UV-light transmittance of coated PP films. Although the combination of hymecromone and caffeic acid did not exhibit a synergistic effect, it demonstrated an additive benefit, effectively broadening the wavelength range of UV protection in the final packaging materials. While this study highlights that a performance gap remains compared to commercially available UV-shielding materials, it underscores the potential of replacing synthetic UV-absorbing additives with natural compounds through coating technologies rather than masterbatch incorporation.Article Latent Psychological Pathways in Thermal Comfort Perception: the Mediating Role of Cognitive Uncertainty on Depression and Vigour(MDPI, 2025) Ozbey, Mehmet Furkan; Turhan, Cihan; Alkan, Nese; Akkurt, Gulden GokcenThermal comfort is the condition of mind that expresses satisfaction with the thermal environment, and it is assessed through subjective evaluation, according to the American Society of Heating, Refrigerating, and Air-Conditioning Engineers. While research has traditionally emphasised physical factors, growing evidence highlights the role of the state of mind in shaping thermal perception. In a prior Monte Carlo sensitivity analysis, six mood subscales-Anger, Confusion, Vigour, Tension, Depression, and Fatigue-were examined for how they affect the absolute difference between actual and predicted thermal sensation. Depression and vigour were found to be the most influential, while confusion appeared least impactful. However, to accurately assess the role of confusion, it is necessary to consider its potential interactions with other mood subscales. To this end, a mediation analysis was conducted using Hayes' PROCESS tool. The mediation analyses revealed that confusion partially mediated depression's effect in males and vigour's effect in females. These results suggest that, despite a weak direct impact, confusion critically influences thermal perception by altering the effects of key mood states. Accounting for the indirect effects of mood states may lead to more accurate predictions of human sensory experiences and improve the design of occupant-centred environments.Article Subinjectivity Relative To Cotorsion Pairs(MDPI, 2025) Alagoz, Yusuf; Alizade, Rafail; Buyukasik, Engin; Rozas, Juan Ramon Garcia; Oyonarte, LuisIn this paper, we define and study the X-subinjectivity domain of a module M where X=(A,B) is a complete cotorsion pair, which consists of those modules N such that, for every extension K of N with K/N in A, any homomorphism f:N -> M can be extended to a homomorphism g:K -> M. This approach allows us to characterize some classical rings in terms of these domains and generalize some known results. In particular, we classify the rings with X-indigent modules-that is, the modules whose X-subinjectivity domains are as small as possible-for the cotorsion pair X=(FC,FI), where FI is the class of FP-injective modules. Additionally, we determine the rings for which all (simple) right modules are either X-indigent or FP-injective. We further investigate X-indigent Abelian groups in the category of torsion Abelian groups for the well-known example of the flat cotorsion pair X=(FL,EC), where FL is the class of flat modules.