Search Results (479)

Chemical artificial intelligence increasingly relies on molecular property prediction models trained from proprietary compound libraries, bioassay records, and reaction-screening data. However, these data often contain commercially sensitive structures, confidential activity labels, and privacy-relevant experimental metadata, making direct centralization impractical. This paper proposes PrivMol, a privacy-preserving computational chemistry framework for federated molecular representation learning. PrivMol introduces two novel algorithms: Secure Substructure-Aware Federated Optimization and Differentially Private Molecular Gradient Calibration. The first algorithm decomposes molecular graphs into privacy-sensitive and task-relevant substructure regions, enabling local clients to train graph neural networks while transmitting only securely aggregated model updates. The second algorithm adaptively calibrates clipping and perturbation according to atom- and substructure-level contribution scores, reducing unnecessary utility loss on chemically informative fragments while retaining formal differential privacy guarantees. To improve robustness under heterogeneous chemical spaces, PrivMol incorporates local contrastive molecular alignment without exposing raw molecules, labels, scaffolds, substructure masks, or embeddings. Experimental evaluation on widely used public molecular benchmarks, including ESOL, FreeSolv, Lipophilicity, BBBP, BACE, HIV, and Tox21, demonstrates that PrivMol provides a favorable trade-off among prediction accuracy, communication efficiency, empirical leakage resistance, and privacy protection. The study offers a practical route toward secure collaborative chemical intelligence for computer-aided drug discovery, toxicology prediction, and materials informatics. Full article

Ectopic olfactory receptors (ORs) are G protein-coupled chemosensors expressed outside the olfactory epithelium, where they may couple local chemical inputs to cell-specific signaling. The oral cavity is continuously exposed to food-derived compounds, microbial metabolites, volatile organic compounds, and inflammation-associated metabolites, yet the molecular roles of oral ORs remain incompletely defined. This review critically synthesizes current evidence for OR expression and signaling in oral tissues and associated cell populations, with emphasis on ligand–receptor–signaling relationships and disease relevance. Functional OR signaling has been demonstrated in mammalian taste cells, while emerging transcriptomic studies in oral mucosa and transcriptomic/localization studies in the periodontal ligament indicate OR-related programs during tissue-specific or repair-associated states. Candidate metabolic axes, including short-chain fatty acids and lactate linked to OR51E1/OR51E2/Olfr78-related pathways in non-oral models, provide testable mechanistic hypotheses for microbiome–host communication in periodontitis and oral cancer; however, direct causal validation in oral disease models remains limited. We propose an evidence-tiered framework integrating spatial expression mapping, metabolomics-guided deorphanization, receptor perturbation, and longitudinal oral-fluid profiling. Oral ORs should currently be regarded as candidate molecular modulators and components of multimodal biomarker strategies rather than validated standalone diagnostic or therapeutic targets. Full article

Radix Paeoniae Alba, the dried root of Paeonia lactiflora Pall., contains characteristic monoterpene glycosides, but efficient recovery of these polar constituents remains challenging. This study developed an ionic liquid-assisted sequential ultrasound–microwave extraction method and evaluated paeoniflorin, oxypaeoniflorin and albiflorin by HPLC as multi-marker responses. Among the ionic liquids tested, 1-propyl-3-methylimidazolium dihydrogen phosphate showed the best extraction response. Box–Behnken response surface optimization gave practical extraction conditions of a solid-to-liquid ratio of 1:26 g/mL, ionic liquid concentration of 0.12 mol/L and ultrasound time of 22 min. Under these conditions, paeoniflorin and total marker glycosides reached 29.12 and 34.98 mg/g dry material, respectively, representing increases of 32.4% and 34.5% compared with conventional reflux extraction. UPLC-QTOF-MS profiling provided complementary chemical profile information for the optimized extract and tentatively annotated Paeonia-related monoterpene glycoside derivatives, galloylated glucose derivatives and polyphenolic constituents. Electrostatic potential, SAPT and non-covalent interaction analyses, supported by ¹H NMR chemical shift perturbation, suggested possible hydrogen bonding, electrostatic and dispersion interactions between paeoniflorin and the selected ionic liquid. These results support the optimized process as an efficient extraction approach and provide molecular interaction insights into ionic liquid-assisted recovery of monoterpene glycosides. Full article

Two-dimensional (2D) group-IV materials are promising for spintronics due to their silicon compatibility and tunable properties. In this work, we investigate the structural, electronic, magnetic, and optical properties of semi-hydrogenated 2D SiGe random alloys—where hydrogen atoms saturate only one side of the atomic plane—using density functional theory and many-body perturbation theory ($G{W}_0$). Substitutional disorder is modeled via representative high-symmetry configurations introduced by Baldereschi and co-workers to enable quasiparticle and optical simulations in large supercells. We demonstrate that these semi-hydrogenated alloys possess an intrinsic magnetic semiconducting ground state, arising from the electronic structure of the system, with an integer magnetic moment of $1{\mathsf{\mu }}_{\mathrm{B}}$ per primitive cell. The spin-resolved electronic structure features nearly flat frontier bands and a finite energy gap, which is significantly renormalized by quasiparticle corrections while maintaining robust spin polarization. These properties remain remarkably stable across different realizations of chemical disorder and over a wide range of alloy compositions considered in this work. Optical spectra calculated within the random phase approximation reveal a composition-dependent red-shift of the low-energy onset in the imaginary part of the dielectric function, consistent with the evolution of the quasiparticle electronic structure and the persistence of flat spin-polarized frontier bands. Our findings establish semi-hydrogenated 2D SiGe random alloys as a resilient model platform to explore interaction-driven magnetism in disordered two-dimensional systems, while simultaneously offering realistic prospects for spintronic and magneto-optoelectronic applications in the presence of chemical disorder. Full article

Hydrocarbon biodegradation in cold environments is constrained not only by microbial catabolic capacity but also by interfacial access to poorly soluble substrates and by the way remediation materials interact with microbial envelope-related structures. This study presents an uncertainty-aware low-temperature computational screening workflow for prioritizing functionalized oxide surface-patch models that may favor hydrocarbon association while avoiding excessive perturbation of simplified microbial-interface proxies. Twelve finite oxide–ligand candidates derived from TiO₂, ZnO, and CeO₂ patches functionalized with bare, catechol, glycerol, or citric acid states were evaluated against three hydrocarbon probes, hexane, toluene, and naphthalene, and two microbial-interface proxies. The workflow combined GFN2-xTB geometry optimization and relative interaction-energy screening, clean GFN2-xTB/ALPB rescoring with rescue tracking, short xTB-MD perturbation analysis, ORCA refinement of selected candidates, sensitivity analysis of ranking parameters, and integrated evidence classification. The analysis supports interfacial selectivity, rather than maximum adsorption strength, as the central design principle. TiO₂–catechol and TiO₂–glycerol remain experimentally testable primary candidates because their original screening profile combines chemically interpretable hydrocarbon association with comparatively mild microbial-proxy interaction descriptors. ZnO–catechol and ZnO–glycerol emerged as sensitivity-competitive secondary candidates under several scoring assumptions. Completed short xTB-MD trajectories further showed that TiO₂–glycerol produced moderate perturbation against the peptide proxy, whereas TiO₂–glycerol against NAG and ZnO–catechol against the peptide proxy showed very high proxy displacement. Overall, the workflow provides a transparent prioritization framework for experimental validation. Full article

An aeolian event and a fluvial episode affected Gale crater, Mars, prior to 3.6 billion years ago. Both were short-lived and catastrophic. The same two events also modified the Southern Highlands of the red planet during the same time interval. We show that events in Gale crater were a part of those that modified vast areas of the southern hemisphere of Mars. As such, the patterns documented in Gale crater are consistent with reshaping of large portions of Mars by short-lived catastrophic events by wind and water, although data from other regions are needed to establish this on a planetary scale. The study is based on data collected by the Curiosity rover during the past 14 years. The aeolian event excavated Gale crater and formed two distinct morphological provinces with two contrasting rock types. One was the cone-shaped ancestral Aeolis Mons, informally known as Mt. Sharp, that consists of sandstone, siltstone, and mudstone. The other was the nearly flat hollowed margin, the ancestral crater floor, that was initially covered by loose pebbles, cobbles, and boulders which were reworked and lithified to a conglomeratic rock unit later. Commonly reported Martian aeolian erosion rates cannot account for the abrasion and transport of 39,000 km³ of sediments out of Gale crater. This conclusion is supported by little modification of Gale crater during the past 3.6 billion years by ordinary winds. Our evaluation indicates that the excavation of Gale crater took place by a powerful aeolian perturbation that resembled a sand-blasting operation. It was short-lived, had extremely high erosion rates, and occurred during a cold and dry climate. The fluvial episode followed the aeolian event. The study of its sedimentary record indicates that it began with intense precipitation-driven great floods that eroded the ancestral Mt. Sharp, carved large canyons on its slope, and reworked gravels of the ancestral crater floor into giant bedforms. Flood waters also formed a deep lake that experienced one rise and one fall of lake-level and had a dynamic storm-driven sedimentation. The fluvial episode was also short-lived and indicates catastrophic actions of water during a warm and wet climate. As such, this study suggests that the extensive reshaping of the red planet during the Late Noachian period, including formation of valley networks, occurrence of hundreds of crater lakes, and excavation of numerous craters, were also due to short-lived, intense, climate-related perturbations by powerful wind and water rather than by ordinary, slow rate, long-duration processes. Another implication of the study is for the mineralogical evolution of Martian sedimentary rocks. It indicates that the Late Noachian period may have been mostly cold and dry, similar to the modern Mars. Its low water/rock ratio and cold temperatures halted chemical weathering that resulted in preservation of highly unstable minerals such as olivine and pyroxene. The fluvial perturbation with its high water/rock ratio was not long and/or warm enough to alter or significantly affect the mineralogy by weathering at the source region, or during the transport, or at the depositional site. Full article

Background: Bacterial adaptation to environmental and chemical stress involves coordinated, system-level responses collectively described as perturbome. Understanding conserved elements within core perturbomes may reveal strategic vulnerabilities for antimicrobial development. Methods: In this study, we implemented an integrative framework combining functional and comparative genomics, drug–target interactions and molecular docking to prioritize conserved stress-response targets in Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus. Results: A total of 147 genes from previously defined core perturbomes were analyzed through interactome reconstruction and functional enrichment. Interactome and functional analyses revealed significant connectivity and functional clustering, primarily associated with molecule biosynthesis, translation, transcriptional regulation, and energy metabolism. Orthology-based comparative genomics identified six conserved orthogroups shared across at least two species, representing key stress-adaptive nodes including fatty acid synthesis initiation, metabolic stress buffering, transcription termination (Rho), ATP synthesis, peptidoglycan remodeling, and UDP-glucose-mediated envelope biosynthesis. Drug–target interaction analyses suggested that these conserved proteins are modulated by enzymatic inhibitors, metabolite analogs, or active-site competitors. Structural and docking analyses focused on a selected protein, FabF (β-ketoacyl-ACP synthase II) and confirmed catalytically coherent binding of cerulenin within the active site, with high concordance between experimentally resolved and AlphaFold-predicted structures, supporting the reliability of structure-based prioritization. Conclusions: Overall, the results demonstrate that bacterial stress responses converge on evolutionarily conserved metabolic and regulatory elements essential for homeostasis and tolerance to perturbations, being the first work integrating core perturbome data from different microorganisms. The proposed perturbome-informed framework provides a rational strategy to identify robust, broad-spectrum antimicrobial targets and highlights opportunities for drug repurposing and future experimental validation. Full article

Neural ordinary differential equations (NODEs) have emerged as an effective methodology in artificial neural networks (ANNs) and deep learning for capturing unknown or unmodeled dynamics in compartmental and dynamical mathematical models arising from real-life applications, particularly under limited-data conditions, through learned data-driven corrections. Nevertheless, accurate one-step prediction errors do not necessarily guarantee reliable long-horizon rollouts. In this work, we study residual Neural ODE models of the form $\widehat{f}=f+h_{\theta }$ and derive a priori rollout-error estimates showing that long-time prediction behavior is generated by the incremental stability structure of the learned dynamics. Contracting regimes produce uniformly controlled rollout errors, whereas weakly contractive or expansive regimes can amplify persistent approximation errors over long time horizons. The analysis is illustrated on a flow-reactor chemical reaction network (CRN), where the washout parameter controls rollout reliability on the data-supported region. Numerical experiments further demonstrate that models with comparable empirical one-step prediction losses may exhibit substantially different multi-step behaviors. Rollout-error analysis and projected-gradient-descent (PGD) sensitivity directions additionally reveal that locally expansive regions align with worst-case perturbation amplification. Full article

Volcanic super-eruptions can perturb atmospheric composition and climate-relevant radiative properties in ways that are not captured by simple scaling from Pinatubo-like events. This study presents a reduced-order regime theory for the coupled evolution of stratospheric sulfur, sulfate aerosol burden, reactive halogens, ozone loss, stratospheric thermal adjustment, and aerosol residence time. The analysis is intended as an interpretive tool for organizing sulfur-rich volcanic scenarios, comparing literature-based benchmark classes, and designing chemistry–climate model experiments, rather than as an event-specific calibration or a substitute for three-dimensional models. Four control parameters structure the response: sulfur loading relative to microphysical saturation, effective halogen strength, ash-uptake efficiency, and dynamical lifetime sensitivity, with hemispheric asymmetry treated diagnostically. An external consistency check against published Pinatubo-like, idealized 10–40 teragrams of sulfur (Tg S), Toba-like, and Los Chocoyos-like responses is used to evaluate whether the reduced theory reproduces the expected rank ordering of aerosol saturation, forcing-efficiency decline, ozone-loss amplification, ash-driven sulfur suppression, and residence-time sensitivity. This comparison does not assign pointwise error margins against three-dimensional model output; it evaluates regime membership, sign of response, rank ordering, and broad magnitude behavior. The main conclusion is that volcanic super-eruption impacts are governed by interacting regime transitions rather than by sulfur mass alone. Microphysical saturation can limit forcing efficiency, halogens can shift the system toward chemically amplified ozone depletion, ash uptake can reduce the effective sulfur burden during the early phase, and dynamical state can control persistence and hemispheric expression. By separating these mechanisms, the study provides a compact basis for interpreting large volcanic perturbations to atmospheric chemistry and for designing targeted model experiments on extreme eruption scenarios. Full article

Mitochondrial reactive oxygen species (mtROS) are central regulators of cellular function, yet their biological roles are often reduced to an oxidative-stress/antioxidant dichotomy. This review reframes mtROS through the concept of mitohormesis, in which outcomes are neither inherently harmful nor beneficial but are determined by a defined set of contextual variables. We present a mechanistic framework in which mtROS effects depend on chemical species identity, sub-mitochondrial site of production, temporal dynamics, redox-buffering capacity, and metabolic state; together, these variables determine whether mtROS promote adaptive eustress or pathological distress. We then show that, across polyphenols, isothiocyanates, terpenoids, alkaloids, and quinones, the biologically relevant effects of natural redox-modulating compounds are mediated less by direct radical scavenging than by pro-hormetic mechanisms, including mild electron transport chain perturbation, nuclear factor erythroid 2-related factor 2/Kelch-like ECH-associated protein 1 (NRF2/KEAP1) activation, modulation of mitochondrial membrane potential, mitochondrial quality control, and NAD⁺/NADPH regulation. Applying this framework to disease reveals strong tissue and state dependence: neurodegeneration favors buffering expansion and mitophagy; metabolic disease may benefit from exercise-mimetic and NRF2-activating strategies; cardiovascular disease illustrates mitohormesis through ischemic preconditioning and CoQ10 supplementation; and cancer requires distinction between prevention and therapy because redox buffering can either protect normal tissue or support tumor survival. Finally, we argue that the failure of non-specific antioxidant supplementation is mechanistically predictable and propose context-aware, biomarker-guided, temporally optimized, and compartment-targeted redox interventions as a more rational translational path. Full article

Arsenic represents a ubiquitous element in the environment, characterized by high mobility, complex chemical speciation and a strong sensitivity to redox conditions and biological activity, with microbial processes play a central role in its biogeochemical cycling. The present review provides a comprehensive and integrative synthesis of arsenic biogeochemical cycling across terrestrial, freshwater and marine environments, in which chemical speciation is explicitly treated as the central unifying concept controlling arsenic mobility, transformation and bioavailability, linking geological, chemical and biological processes across environmental compartments. Natural processes regulating arsenic distribution are examined from mineralogical sources and soil–water interactions to biologically mediated transformations in aquatic and marine biotic compartments, largely driven by microbial activity, highlighting the contrast between inorganic arsenic dominance in abiotic reservoirs and the prevalence of organoarsenicals in tissues of living organisms. The review further explores arsenic behaviour under natural environmental alterations and in extreme or unconventional ecosystems, where redox constraints, sulphide chemistry or intense fluid–sediment exchanges lead to deviations from the baseline speciation patterns. Against this framework, anthropogenic perturbations are discussed through several documented case studies, illustrating how industrial releases, the long-term effects of mining activities, agricultural practices and the use of synthetic arsenical compounds may change arsenic pathways primarily by altering geochemical and biological controls rather than through a generalized increase in total arsenic content. Overall, the topics covered provide an integrated framework for interpreting arsenic dynamics across environmental systems, emphasizing the complex biogeochemical processes governing arsenic cycling. Full article

Oxalic acid is extensively used in industrial chemical processes, purification systems, hydrometallurgical operations, and advanced oxidation environments where rapid and environmentally sustainable analytical methodologies are increasingly required for process monitoring and quality control. In this study, a micro-Raman spectroscopy methodology was developed for the direct quantification of oxalic acid in aqueous systems at moderate-to-high concentrations (0.079–0.793 M). The analytical strategy was based on the integrated Raman response of the carbonyl stretching region (1700–1750 cm⁻¹), selected due to its strong concentration-dependent behavior, spectral definition, and reduced interference from the aqueous matrix. The proposed methodology demonstrated excellent analytical performance, including high linearity (R² > 0.998), satisfactory precision, and reliable concentration-dependent reproducibility throughout the evaluated concentration range. To evaluate operational robustness, matrix-matched standards incorporating temperature variation (25–40 °C), turbidity (0–57 mg/L), dissolved Ca²⁺ (0–58 mg/L), and dissolved Fe³⁺ (0–7 mg/L) were prepared to simulate chemically perturbed industrial environments. Principal Component Analysis (PCA) demonstrated that the carbonyl vibrational region retained organized concentration-dependent spectral behavior despite operational perturbations. Partial Least Squares (PLS) regression models developed under these matrix-informed conditions preserved strong predictive capability (R² ≈ 0.997), while preliminary prediction of process-related samples yielded excellent agreement between predicted and reference concentrations (R² = 0.990). Although operational perturbations produced substantial attenuation of Raman intensity, particularly at lower concentration levels, the carbonyl Raman band remained spectrally detectable and analytically interpretable throughout all evaluated conditions. Electronic-structure analysis using Natural Bond Orbital (NBO) and Atoms-in-Molecules (AIM) methodologies demonstrated that the strong analytical behavior of the ν(C=O) vibrational mode is associated with enhanced electron-density localization, covalent stabilization, and favorable polarizability characteristics of the carbonyl bond. The combined experimental, chemometric, and computational results demonstrate the feasibility of matrix-informed micro-Raman spectroscopy as a rapid, reagent-free, and operationally robust methodology for oxalic acid monitoring in chemically perturbed aqueous industrial systems. Full article

Microplastics (MPs) are increasingly detected environmental contaminants in both marine and freshwater ecosystems, with reported concentrations ranging from a few to thousands of particles per cubic meter depending on location and methodology. Although growing evidence suggests potential risks to aquatic organisms, the extent of their ecological and biological impacts is still under active investigation. Their size, persistence and capacity to transport chemical additives and co-contaminants allow them to enter biological systems by ingestion and respiration. When ingested, MPs cause oxidative stress, inflammation, and metabolic disorders, resulting in the destruction of vital tissues in major body organs including liver, gills, intestines, and brain. They also change gene expression, cause endocrine and immune pathway perturbation, induce apoptosis, and cause gut microbiome dysbiosis, all of which worsen the health and survival of the organism. MPs also serve as vectors of heavy metals, antibiotics, pesticides, and pathogens and enhance toxicity due to the Trojan horse effect and enable bioaccumulation in food webs. Due to their widespread presence in water, soil, air, and food, MP pollution has direct effects on human, animal, and ecosystem health. This review synthesizes current knowledge on the sources of MPs, the mode of exposure, and the mechanism of toxicity and new ecological implications. It also presents mitigation measures, and stresses a One Health paradigm as the key to taking concerted action on the international level to minimize MP pollution and protect both the environment and human health. Full article

Tyrosinase-related protein 1 (Tyrp1) is a melanosomal glycoprotein required for eumelanin biosynthesis through the oxidation of 5,6-dihydroxyindole-2-carboxylic acid (DHICA). Pathogenic variants in Tyrp1 cause oculocutaneous albinism type 3 (OCA3), but the molecular basis by which individual substitutions impair Tyrp1 stability and activity remains incompletely understood. Here, we examined wild-type Tyrp1 and three missense variants associated with OCA3: R356Q and R326H as OCA3-related variants, and D308N as a benign control; these were under conditions relevant to melanosome maturation. To assess stability, we developed a urea-induced unfolding assay in which His-tagged Tyrp1 variants were immobilized to Ni-NTA magnetic beads before chemical denaturation. R356Q was the most destabilized variant, with a ΔΔG of 0.695 kcal/mol at pH 5.0 (acidic conditions) and 1.998 kcal/mol at pH 7.4 (near-neutral conditions) relative to wild-type. R326H showed intermediate destabilization, whereas D308N behaved similarly to wild-type. DHICA oxidation assays in the presence of MBTH showed about 20% reduced catalytic activity for R356Q, particularly under acidic conditions. Molecular dynamics simulations and ligand docking were consistent with these findings and indicated that R356Q increases conformational flexibility and perturbs structural integrity. In contrast, glycosylation reduced conformational fluctuations and enhanced stability across Tyrp1 and mutant variants examined. Together, these results show that pH, glycosylation, and disease-associated substitutions collectively modulate Tyrp1 folding energetics and catalytic competence and identify R356Q as a strongly destabilizing OCA3 variant. By defining how disease-associated Tyrp1 substitutions affect protein stability and function, this study may provide a framework for interpreting genotype–phenotype relationships and improving molecular diagnosis of OCA3. Full article

Circulating fluidized bed boilers (CFBBs) are widely applied in energy, metallurgy, the chemical industry and other fields, mainly due to their high combustion efficiency and low pollution emissions. However, the CFBB combustion system, as a typical third-order plus time delay (TOPTD) system, has inherent characteristics: large inertia, significant time delays and strong coupling. Coupled with the difficulty in establishing an accurate mathematical model, traditional control methods struggle to achieve the desired control performance. Active disturbance rejection control (ADRC) has prominent advantages, such as low dependence on the controlled plant’s accurate model and strong disturbance rejection ability, but it has obvious limitations in dealing with systems with large inertia and large time delays. To address this problem, this paper proposes an input-compensated active disturbance rejection control (ICADRC) method. An input-compensated part composed of a second-order inertial link and a time delay link is introduced into the ESO input channel, which is specially optimized for the characteristics of TOPTD systems. A set of quantitative parameter tuning rules unique to ICADRC is established via the equivalent approximation method, and a dedicated MATLAB auto-tuning toolbox for ICADRC is developed for TOPTD systems. Simulation experiments are conducted on the CFBB combustion system, and the results show that the proposed ICADRC exhibits superior setpoint tracking performance, disturbance rejection performance and robustness compared with ADRC, DADRC, and SIMC-PI. Under nominal operating conditions, the ${\mathrm{IAE}}_{\mathrm{sum}}$ of ICADRC is reduced by 36.2% relative to DADRC and by 54.3% relative to SIMC-PI. Specifically, under fixed parameter perturbations, the variation amplitude of ICADRC’s performance index is only 2.1%, significantly lower than the 5.1% for DADRC, 6.1% for ADRC, and 7.3% for SIMC-PI. Full article