Kinetic Analysis Research Articles

Unlocking the unfolded structure of ubiquitin: Combining time-resolved x-ray solution scattering and molecular dynamics to generate unfolded ensembles.

The unfolding dynamics of ubiquitin were studied using a combination of x-ray solution scattering (XSS) and molecular dynamics (MD) simulations. The kinetic analysis of the XSS ubiquitin signals showed that the protein unfolds through a two-state process, independent of the presence of destabilizing salts. In order to characterize the ensemble of unfolded states in atomic detail, the experimental XSS results were used as a constraint in the MD simulations through the incorporation of x-ray scattering derived potential to drive the folded ubiquitin structure toward sampling unfolded states consistent with the XSS signals. We detail how biased MD simulations provide insight into unfolded states that are otherwise difficult to resolve and underscore how experimental XSS data can be combined with MD to efficiently sample structures away from the native state. Our results indicate that ubiquitin samples unfolded in states with a high degree of loss in secondary structure yet without a collapse to a molten globule or fully solvated extended chain. Finally, we propose how using biased-MD can significantly decrease the computational time and resources required to sample experimentally relevant nonequilibrium states.

Kinetic analysis of reversible solid-gas reactions in films: application to the decomposition of CaCO$$_3$$ and BaCO$$_3$$ carbonates

Kinetic analysis of reversible solid-gas reactions in films: application to the decomposition of CaCO$$_3$$ and BaCO$$_3$$ carbonates

Heterologous expression, characterization, and application of recombinant thermostable α-amylase from Geobacillus sp. DS3 for porous starch production

Novel Geobacillus sp. DS3, isolated from the Sikidang Crater in Dieng, exhibits promising characteristics for industrial applications, particularly in thermostable α-amylase production. Recombinant technology was used to express thermostable α-amylase in E. coli BL21(DE3) to overcome high-temperature production challenges. The study aimed to express, purify, characterize, and explore potential applications of this novel enzyme. The enzyme was successfully expressed in E. coli BL21(DE3) at 18 °C for 20 h with 0.5 mM IPTG induction. Purification with Ni-NTA column yielded 69.23 % from the initial crude enzyme, with a 3.6-fold increase in specific activity. The enzyme has a molecular weight of ±70 kDa (±58 kDa enzyme+11 kDa SUMO protein). It exhibited activity over a wide temperature range (30–90 °C) and pH range (6–8), with optimal activity at 70 °C and pH 6 with great stability at 60 °C. Kinetic analysis revealed Km and Vmax values of 324.03 mg/ml and 36.5 U/mg, respectively, with dextrin as the preferred substrate without cofactor addition. As a metalloenzyme, it showed the best activity in the presence of Ca2+. The enzyme was used for porous starch production and successfully immobilized with chitosan, exhibiting improved thermal stability. After the fourth reuse, the immobilized enzyme maintained 62 % activity compared to the initial immobilization.

Microstructural and kinetics analysis of FeB–Fe2B layer grown by pulsed-DC powder-pack boriding on AISI 316 L steel

Microstructural and kinetics analysis of FeB–Fe2B layer grown by pulsed-DC powder-pack boriding on AISI 316 L steel

Structural characteristics of cell wall pectic polysaccharides from wampee and their decreased binding with pectinase by wampee polyphenol

To investigate the structural characteristics of cell wall pectic polysaccharides from wampee, water soluble pectin (WSP), chelator-soluble pectin (CSP) and sodium carbonate-soluble pectin (SSP) were purified. And the inhibitory effects of wampee polyphenol (WPP) on pectinase when these cell wall pectic polysaccharides were used as substrates were also explored. Purified WSP (namely PWSP) had the lowest molecular weight (8.47 × 105 Da) and the highest GalA content (33.43%). While purified CSP (called PCSP) and SSP contained more abundant rhamnogalacturonan I side chains. All of them were low-methoxy pectin (DE < 50%). Enzyme activity and kinetics analysis showed that the inhibition of pectinase by wampee polyphenol was reversible and mixed type. When SSP was used as the substrate, WPP had the strongest inhibition (IC50 = 1.96 ± 0.06 mg/mL) on pectinase. Fluorescence quenching results indicated that WPP inhibited enzyme activity by interacting with substrates and enzymes. Therefore, WPP has the application potential in controlling softening of fruits and vegetables.

Quantitative Online Monitoring of an Immobilized Enzymatic Network by Ion Mobility-Mass Spectrometry.

The forward design of in vitro enzymatic reaction networks (ERNs) requires a detailed analysis of network kinetics and potentially hidden interactions between the substrates and enzymes. Although flow chemistry allows for a systematic exploration of how the networks adapt to continuously changing conditions, the analysis of the reaction products is often a bottleneck. Here, we report on the interface between a continuous stirred-tank reactor, in which an immobilized enzymatic network made of 12 enzymes is compartmentalized, and an ion mobility-mass spectrometer. Feeding uniformly 13C-labeled inputs to the enzymatic network generates all isotopically labeled reaction intermediates and products, which are individually detected by ion mobility-mass spectrometry (IMS-MS) based on their mass-to-charge ratios and inverse ion mobilities. The metabolic flux can be continuously and quantitatively monitored by diluting the ERN output with nonlabeled standards of known concentrations. The real-time quantitative data obtained by IMS-MS are then harnessed to train a model of network kinetics, which proves sufficiently predictive to control the ERN output after a single optimally designed experiment. The high resolution of the time-course data provided by this approach is an important stepping stone to design and control sizable and intricate ERNs.

Pressureless sintering kinetics analysis of Ti3SiC2 and Ti2AlC powdered MAX phases

This paper reports the pressureless sintering behavior and the activation energy of the powdered MAX phases Ti3SiC2 and Ti2AlC. A non-isothermal technique was used to determine the sintering kinetic parameter. The Ti3SiC2 and Ti2AlC MAX phases showed the maximum sintering rate at 1723 K, 0.14 and 0.10 µm/s, respectively. The sintering rate of the sample at different temperatures followed a cubic equation which was determined. The sintering activation energy (Ea) for the Ti3SiC2 and Ti2AlC samples was 362.1 kJ/mol and 640.3 kJ/mol, respectively.

Single-cell total-RNA profiling unveils regulatory hubs of transcription factors

Recent development of RNA velocity uses master equations to establish the kinetics of the life cycle of RNAs from unspliced RNA to spliced RNA (i.e., mature RNA) to degradation. To feed this kinetic analysis, simultaneous measurement of unspliced RNA and spliced RNA in single cells is greatly desired. However, the majority of single-cell RNA-seq chemistry primarily captures mature RNA species to measure gene expressions. Here, we develop a one-step total-RNA chemistry-based single-cell RNA-seq method: snapTotal-seq. We benchmark this method with multiple single-cell RNA-seq assays in their performance in kinetic analysis of cell cycle by RNA velocity. Next, with LASSO regression between transcription factors, we identify the critical regulatory hubs mediating the cell cycle dynamics. We also apply snapTotal-seq to profile the oncogene-induced senescence and identify the key regulatory hubs governing the entry of senescence. Furthermore, from the comparative analysis of unspliced RNA and spliced RNA, we identify a significant portion of genes whose expression changes occur in spliced RNA but not to the same degree in unspliced RNA, indicating these gene expression changes are mainly controlled by post-transcriptional regulation. Overall, we demonstrate that snapTotal-seq can provide enriched information about gene regulation, especially during the transition between cell states.

Exploring Negative Ion Behaviors and Their Influence on the Properties of DC Magnetron Sputtered ITO Films under Varied Power and Pressure Conditions

Abstract In this study, ITO films were deposited on silicon and quartz substrates by magnetron sputtering technology in pure argon. Using EQP plasma diagnostic technology, we study the effects of discharge power and discharge pressure on the ion flux and energy distribution function of incident on the substrate surface, with special attention to the production of high-energy negative oxygen ions, and elucidate the mechanism behind its production. At the same time, the structure and properties of ITO films were systematically characterized to understand the potential effects of high energy oxygen ions on the growth of ITO films. Combined with the kinetic property analysis of sputtering damage mechanism of transparent conductive oxide (TCO) thin films, it provides valuable physical understanding for the optimization of TCO thin film deposition process.

Treatability of BPA Containing Wastewater by Catalytic and Photocatalytic Ozone Processes Using n.TiO2

In this study, the treatment of synthetic wastewater containing 10 mg/L Bisphenol A (BPA) has been investigated by the catalytic and photocatalytic ozonation process. n.TiO2 nanocatalysts have been used in catalytic (COP) and photocatalytic (PCOP) ozonation processes. Optimum parameters have been determined as pH 6.32, 1200 mg/L ozone dose, 50 mg/L n.TiO2 catalyst dose and 12.5 min reaction time for COP. Optimum parameters have been found as pH 6.32, 1200 mg/L ozone dose, 50 mg/L n.TiO2 catalyst dose, 18 Watt UV light intensity, and 10 min reaction time for PCOP. The removal efficiencies of BPA have been obtained as 95.51% and 98.09% for COP and PCOP, respectively. Kinetic analyses showed that BPA removal has been carried out Pseudo second order kinetics with R2 values of 99.1 for both processes.

Manganese-rhodium nanoparticles: Adsorption on titanium oxide surfaces and catalyst for syngas reactions.

Manganese-rhodium (Mn-Rh) nanoparticles have emerged as a promising candidate for catalytic applications in the production of syngas, a critical precursor for a wide range of industrial processes. This study employs a comprehensive, theoretical, and computational approach to investigate the structural and electronic properties of Mn-Rh nanoparticles, with a specific focus on their interaction with titanium oxide (TiO2) surfaces and their potential as catalysts for syngas reactions. The density functional theory calculations are employed to explore the adsorption behavior of Mn-Rh nanoparticles on TiO2 surfaces. By analyzing the adsorption energies, geometries, and electronic structure at the nanoscale interface, we provide valuable insights into the stability and reactivity of Mn-Rh nanoparticles when immobilized on TiO2 supports. Furthermore, the catalytic performance of Mn-Rh nanoparticles in syngas production is thoroughly examined. Through detailed reaction mechanism studies and kinetic analysis, we elucidate the role of Mn and Rh in promoting syngas generation via carbon dioxide reforming and partial oxidation reactions. The findings demonstrate the potential of Mn-Rh nanoparticles as efficient catalysts for these crucial syngas reactions. This research work not only enhances our understanding of the fundamental properties of Mn-Rh nanoparticles but also highlights their application as catalysts for sustainable and industrially significant syngas production.

Hot Electrons in a Steady State: Interband vs Intraband Excitation of Plasmonic Gold.

Understanding the dynamics of "hot", highly energetic electrons resulting from nonradiative plasmon decay is crucial for optimizing applications in photocatalysis and energy conversion. This study presents an analysis of electron kinetics within plasmonic metals, focusing on the steady-state behavior during continuous-wave (CW) illumination. Using an inelastic spectroscopy technique, we quantify the temperature and lifetimes of distinct carrier populations during excitation. A significant finding is the monotonic increase in hot electron lifetime with decreases in electronic temperature. We also observe a 1.22× increase in hot electron temperature during intraband excitation compared to interband excitation and a corresponding 2.34× increase in carrier lifetime. The shorter lifetimes during interband excitation are hypothesized to result from direct recombination of nonthermal holes and hot electrons, highlighting steady-state kinetics. Our results help bridge the knowledge gap between ultrafast and steady-state spectroscopies, offering critical insights for optimizing plasmonic applications.

A novel relative-equilibrium graphical plot for rapid reversible tracer studies in dynamic PET imaging.

This study aims to address the issue of long scan durations required by traditional graphical analysis methods, such as the Logan plot and its variant, the reversible equilibrium (RE) Logan plot, for dynamic PET imaging of tracer kinetics. &#xD;Approach: We propose a relative RE Logan model that builds on the principles of the Logan plot and its variant to significantly reduce scan time without compromising the accuracy of tracer kinetics analysis. The model is supported by theoretical evidence and experimental validations, including two computer simulations and one clinical data analysis. &#xD;Main results: The proposed model demonstrates a significant linear relationship between the variable x and the slope DV_T of the RE Logan plot, and the variable x' and the slope DV_T' of the relative RE Logan plot. The Pearson correlation coefficients (r) of the linear fitting of the x' to the x equal 0.9849 in the simulated data and 0.9912 in the clinical data. Similarly, the r value for the linear fitting of DV_T' to DV_T equal 0.9989 and 0.9988 in the simulated data, and 0.9954 in the clinical data. &#xD;Significance: These results demonstrate the model's capability to maintain strong linear relationships and produce parametric images comparable to those of the traditional RE Logan plot, but with the considerable advantage of shorter scan durations. This innovation holds significant potential for enhancing the efficiency and feasibility of PET imaging in clinical settings.

In Vitro Ciclopirox Glucuronidation in Liver Microsomes from Humans and Various Experimental Animals.

Ciclopirox is a widely used antifungal drug, redisposition of which has drawn increasing attentions due to multiple promising activities. The drug undergoes extensive glucuronidation, which acts as a major obstacle in the ongoing novel application and still remains poorly understood. The current study aims to phenotype ciclopirox glucuronidation pathway and as well to decipher the related species differences. Ciclopirox glucuronidation was investigated in liver microsomes from humans (HLM) and various experimental animals. Assays with recombinant uridine diphosphate glucuronosyltransferases (UGTs), enzyme kinetic analyses and selective inhibitors were used to determine the role of individual UGTs in ciclopirox glucuronidation. HLM is highly active in ciclopirox glucuronidation withMichaelis-Menten constant (Km),maximum velocity (Vmax), and intrinsic clearance (CLint)values of 139 μM, 7.89 nmol/min/mg, and 56 μL/min/mg, respectively. UGT1A9 displays by far the highest activity, whereas several other isoforms (UGT1A6, UGT1A7, and UGT1A8) catalyze formation of traced glucuronides. Further kinetic analysis demonstrates that UGT1A9 has a closed Km value (167 μM) to HLM. UGT1A9 selective inhibitor (magnolol) can potently inhibit ciclopirox glucuronidation in HLM with the IC50 value of 0.12 μM. The reaction displays remarkable differences across liver microsomes from mice, rats, cynomolgus monkey, minipig, and beagle dog, with the CLint values in the range of 26-369 μL/min/mg. In addition, ciclopirox glucuronidation activities of experimental animals' liver microsomes were less sensitive to magnolol than that of HLM. Ciclopirox glucuronidation displays remarkable species differences with UGT1A9 as a dominant contributor in humans. It is suggested that the pharmacological or toxicological effects ofciclopirox may be UGT1A9 and species dependent.

Equilibrium adsorption, kinetic, thermodynamic, and breakthrough curves modelling of acetaminophen on Elaeagnus Angustifolia L. seeds-based granular activated carbon

ABSTRACT The widespread presence of pharmaceutical compounds as emerging environmental contaminants in aquatic environments has become a significant concern in recent years. In this study, synthesised granular activated carbon (GAC) derived from Elaeagnus Angustifolia L. seeds was utilised as an adsorbent to remove an emerging contaminant, acetaminophen (commercially known as paracetamol). The operating conditions for the chemical synthesis of the GAC, utilising ZnCl2 as an activating agent, included an impregnation ratio of 1:1, carbonisation at 500°C for 1 hour, and a heating rate of 5 °C/min. The efficacy of this adsorbent was assessed through both batch and fixed-bed column adsorption experiments under various operational parameters, including adsorbent mass (1–6 g/L), contact time, pH (2–10), temperature (20–60°C), inlet acetaminophen concentration (20–150 mg/L), and flow rate (0.5–1.5 mL/min). The results indicate that acetaminophen was better adsorbed in its neutral form rather than in its dissociated state. The findings also revealed that both the Langmuir (two-parameter) and Sips (three-parameter) models provided the best fit for the static adsorption equilibrium data. Furthermore, kinetic analysis indicated that the experimental data were best modelled by the Elovich model and governed by both external diffusion and intraparticle diffusion mechanisms. Therefore, the Yan-Viraraghavan model provided a good fit for the experimental breakthrough curves under various operating conditions. However, the adsorbed amounts of acetaminophen obtained from the column experiment indicated that the high-adsorbed amount of 204.11 mg/g was achieved with an inlet acetaminophen concentration of 150 mg/L, a bed depth of 6 cm, and a flow rate of 0.5 mL/min. These results highlight the potential of the synthesised GAC as a promising adsorbent for pharmaceutical wastewater treatment using fixed-bed column systems.

Ocr-mediated suppression of BrxX unveils a phage counter-defense mechanism.

The burgeoning crisis of antibiotic resistance has directed attention to bacteriophages as natural antibacterial agents capable of circumventing bacterial defenses. Central to this are the bacterial defense mechanisms, such as the BREX system, which utilizes the methyltransferase BrxX to protect against phage infection. This study presents the first in vitro characterization of BrxX from Escherichiacoli, revealing its substrate-specific recognition and catalytic activity. We demonstrate that BrxX exhibits nonspecific DNA binding but selectively methylates adenine within specific motifs. Kinetic analysis indicates a potential regulation of BrxX by the concentration of its co-substrate, S-adenosylmethionine, and suggests a role for other BREX components in modulating BrxX activity. Furthermore, we elucidate the molecular mechanism by which the T7 phage protein Ocr (Overcoming classical restriction) inhibits BrxX. Despite low sequence homology between BrxX from different bacterial species, Ocr effectively suppresses BrxX's enzymatic activity through high-affinity binding. Cryo-electron microscopy and biophysical analyses reveal that Ocr, a DNA mimic, forms a stable complex with BrxX, highlighting a conserved interaction interface across diverse BrxX variants. Our findings provide insights into the strategic counteraction by phages against bacterial defense systems and offer a foundational understanding of the complex interplay between phages and their bacterial hosts, with implications for the development of phage therapy to combat antibiotic resistance.

Equilibrium adsorption, kinetic, thermodynamic, and breakthrough curves modelling of acetaminophen on Elaeagnus Angustifolia L. seeds-based granular activated carbon

ABSTRACT The widespread presence of pharmaceutical compounds as emerging environmental contaminants in aquatic environments has become a significant concern in recent years. In this study, synthesised granular activated carbon (GAC) derived from Elaeagnus Angustifolia L. seeds was utilised as an adsorbent to remove an emerging contaminant, acetaminophen (commercially known as paracetamol). The operating conditions for the chemical synthesis of the GAC, utilising ZnCl2 as an activating agent, included an impregnation ratio of 1:1, carbonisation at 500°C for 1 hour, and a heating rate of 5 °C/min. The efficacy of this adsorbent was assessed through both batch and fixed-bed column adsorption experiments under various operational parameters, including adsorbent mass (1–6 g/L), contact time, pH (2–10), temperature (20–60°C), inlet acetaminophen concentration (20–150 mg/L), and flow rate (0.5–1.5 mL/min). The results indicate that acetaminophen was better adsorbed in its neutral form rather than in its dissociated state. The findings also revealed that both the Langmuir (two-parameter) and Sips (three-parameter) models provided the best fit for the static adsorption equilibrium data. Furthermore, kinetic analysis indicated that the experimental data were best modelled by the Elovich model and governed by both external diffusion and intraparticle diffusion mechanisms. Therefore, the Yan-Viraraghavan model provided a good fit for the experimental breakthrough curves under various operating conditions. However, the adsorbed amounts of acetaminophen obtained from the column experiment indicated that the high-adsorbed amount of 204.11 mg/g was achieved with an inlet acetaminophen concentration of 150 mg/L, a bed depth of 6 cm, and a flow rate of 0.5 mL/min. These results highlight the potential of the synthesised GAC as a promising adsorbent for pharmaceutical wastewater treatment using fixed-bed column systems.

Artificial neural networks (ANN)-genetic algorithm (GA) optimization on thermosonicated achocha juice: kinetic and thermodynamic perspectives of retained phytocompounds

The extraction of phytocompounds from Achocha (Cyclanthera pedata) vegetable juice using traditional methods often results in suboptimal yields and efficiency. This study aimed to enhance the extraction process through the application of thermosonication (TS). To achieve this, an artificial neural network (ANN) and a genetic algorithm (GA) were utilized to simulate and optimize the process parameters. The study investigated the influence of ultrasonic amplitude (30%–50%), temperature (30 °C–50 °C), and sonication duration (15–60 min) on total polyphenolic content (TPC), total flavonoid content (TFC), antioxidant activity (AOA), and ascorbic acid content (AA). Remarkably, the ANN-GA optimization resulted in optimal TS conditions: an ultrasonic amplitude of 40%, a temperature of 40 °C, and a sonication duration of 30 min. Subsequent analysis of extraction kinetics and thermodynamics across various temperatures (30 °C–50 °C) and extraction times (0–30 min) demonstrated R 2 (0.98821) and χ2 (1.74773) for TPC with activation energy (Ea) 26.0456, R 2 (0.99906) and χ2 (0.07215) for TFC with Ea 26.2336, R 2 (0.99867) and χ2 (0.03003) for AOA with Ea 26.0987, R 2 (0.99731) and χ2 (0.13719) for AA with Ea 26.0984, validating the pseudo second-order kinetic model. These findings indicate that increased temperature enhances the saturation concentration and rate constant of phytochemical extraction.

Kinetic and equilibrium analysis of penguin guano trace elements release to Antarctic seawater and snow meltwater

The present work extends the scope of prior studies through analysis, modelling and simulation of the As, Cd, Co, Cu, Fe Mn, Mo, Ni and Zn release from Gentoo (Pygoscelis papua) and Chinstrap (Pygoscelis antarcticus) penguin guano to the Southern Ocean seawater and to Antarctic snow meltwater. Laboratory experimental results have been modelled considering kinetic processes between water and guano using two element pools in the guano compartment; its application allows us to interpret behaviours and predict release concentrations of dissolved trace elements from guano which are potentially useful for incorporation as elements source into biogeochemical models applied in the Southern Ocean. Variations in quantities and release patterns depending on the type of guano and aqueous medium in contact have been identified. The release percentages from the guano to the aqueous medium, once the steady state has been reached, vary depending on the water medium and guano type in the ranges of 100–2.9 % for Mo; 91.5–68.6 % for Ni; 81.8–22.8 % As; 52.0–43.9 % Cu; 26.9–7.4 % Mn; 24.9–5.4 for Co; 4.4–3.2 % for Zn and 0.94–0.51 % for Fe. Considering a penguin population of 774,000 Gentoo and 8,000,000 Chinstrap, the estimated annual mass released to the both seawater and freshwater would be ≈18,500 kg for Cu, ≈1710 kg for Zn, ≈1944 kg for Fe, ≈1640 kg for Mn, ≈499 kg for As, ≈289 kg for Ni, ≈155 kg for Mo, ≈36.7 kg for Cd and ≈8.1 kg for Co. These contributions can be locally significant both in promoting phytoplankton growth and in their role as inhibitors of primary productivity.

Nitrogen configuration modulation of porous graphitic carbon nanosheets for superior capacitive energy storage

Carbon nanosheets with layer-stacked porous structures and surface functionalized groups are beneficial for efficient ion storage in supercapacitor electrode materials, but achieving high cost-effectiveness and controllable surface groups remains a significant challenge. Herein, the biomass-derived chitosan and sodium alginate are selected as raw materials for self-assembly reaction with phytic acid as a cross-linking agent. The protonated chitosan and sodium alginate form a cross-linked network structure through hydrogen bonding and electrostatic adsorption, which is subsequently carbonized and activated to synthesize porous graphitic carbon nanosheets (PNPCN-X). PNPCN-X realizes an efficient distribution of porous and graphitic structures. It's noteworthy that phytic acid facilitates the fixation of N atoms, and various N configurations can be adjusted by altering the content of phytic acid. Optimized PNPCN-1.5 exhibits a high content of structurally stable pyridinic-N and graphitic-N configurations, which are confirmed to serve as active sites substantially augmenting the ion adsorption capacity through Density Functional Theory (DFT) calculations. Benefiting from its exceptional physicochemical properties, PNPCN-1.5 achieves 322 F g−1 as electrode materials in the three-electrode system, while the symmetrical supercapacitor assembled with EMIMBF4 electrolyte attains 56.29 W h kg−1. Furthermore, various kinetic analyses extensively elucidate its capacitance distribution characteristics and ion diffusion rates.