Journal articles: 'Kinetic data structure'

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Tabak, H. H., C. Gao, S. Desai, and R. Govind. "Development of Predictive Structure-Biodegradation Relationship Models with the Use of Respirometrically Generated Biokinetic Data." Water Science and Technology 26, no. 3-4 (August 1, 1992): 763–72. http://dx.doi.org/10.2166/wst.1992.0457.

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Biodegradation is an important mechanism determining the fate of chemicals in the aquatic environment. In this paper, experimental data, determined from electrolytic respirometry, for 27 compounds were analyzed using first order and Monod kinetics. Additional data from the literature were also used in our analysis. A method based on group contribution to predict first-order and Monod kinetic rate constants was developed and validated. The group contribution approach gave reasonable results for a variety of compounds. More kinetic data are required to extend the group contribution approach.

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König, Matthias. "cy3sabiork: A Cytoscape app for visualizing kinetic data from SABIO-RK." F1000Research 5 (July 18, 2016): 1736. http://dx.doi.org/10.12688/f1000research.9211.1.

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Kinetic data of biochemical reactions are essential for the creation of kinetic models of biochemical networks. One of the main resources of such information is SABIO-RK, a curated database for kinetic data of biochemical reactions and their related information. Despite the importance for computational modelling there has been no simple solution to visualize the kinetic data from SABIO-RK. In this work, I present cy3sabiork, an app for querying and visualization of kinetic data from SABIO-RK in Cytoscape. The kinetic information is accessible via a combination of graph structure and annotations of nodes, with provided information consisting of: (I) reaction details, enzyme and organism; (II) kinetic law, formula, parameters; (III) experimental conditions; (IV) publication; (V) additional annotations. cy3sabiork creates an intuitive visualization of kinetic entries in form of a species-reaction-kinetics graph, which reflects the reaction-centered approach of SABIO-RK. Kinetic entries can be imported in SBML format from either the SABIO-RK web interface or via web service queries. The app allows for easy comparison of kinetic data, visual inspection of the elements involved in the kinetic record and simple access to the annotation information of the kinetic record. I applied cy3sabiork in the computational modelling of galactose metabolism in the human liver.

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Onodera, Andrea N., Wilson P. Gavião Neto, Maria Isabel Roveri, Wagner R. Oliveira, and Isabel CN Sacco. "Immediate effects of EVA midsole resilience and upper shoe structure on running biomechanics: a machine learning approach." PeerJ 5 (February 28, 2017): e3026. http://dx.doi.org/10.7717/peerj.3026.

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BackgroundResilience of midsole material and the upper structure of the shoe are conceptual characteristics that can interfere in running biomechanics patterns. Artificial intelligence techniques can capture features from the entire waveform, adding new perspective for biomechanical analysis. This study tested the influence of shoe midsole resilience and upper structure on running kinematics and kinetics of non-professional runners by using feature selection, information gain, and artificial neural network analysis.MethodsTwenty-seven experienced male runners (63 ± 44 km/week run) ran in four-shoe design that combined two resilience-cushioning materials (low and high) and two uppers (minimalist and structured). Kinematic data was acquired by six infrared cameras at 300 Hz, and ground reaction forces were acquired by two force plates at 1,200 Hz. We conducted a Machine Learning analysis to identify features from the complete kinematic and kinetic time series and from 42 discrete variables that had better discriminate the four shoes studied. For that analysis, we built an input data matrix of dimensions 1,080 (10 trials × 4 shoes × 27 subjects) × 1,254 (3 joints × 3 planes of movement × 101 data points + 3 vectors forces × 101 data points + 42 discrete calculated kinetic and kinematic features).ResultsThe applied feature selection by information gain and artificial neural networks successfully differentiated the two resilience materials using 200(16%) biomechanical variables with an accuracy of 84.8% by detecting alterations of running biomechanics, and the two upper structures with an accuracy of 93.9%.DiscussionThe discrimination of midsole resilience resulted in lower accuracy levels than did the discrimination of the shoe uppers. In both cases, the ground reaction forces were among the 25 most relevant features. The resilience of the cushioning material caused significant effects on initial heel impact, while the effects of different uppers were distributed along the stance phase of running. Biomechanical changes due to shoe midsole resilience seemed to be subject-dependent, while those due to upper structure seemed to be subject-independent.

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Roodt, Andreas. "Relevance of X-ray structure data to kinetic studies." Acta Crystallographica Section A Foundations of Crystallography 66, a1 (August 29, 2010): s6. http://dx.doi.org/10.1107/s0108767310099861.

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Kockara, S., M. Mete, V. Yip, B. Lee, and K. Aydin. "A soft kinetic data structure for lesion border detection." Bioinformatics 26, no. 12 (June 6, 2010): i21—i28. http://dx.doi.org/10.1093/bioinformatics/btq178.

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Aftandiliants, Ye G. "Modelling of structure forming in structural steels." Naukovij žurnal «Tehnìka ta energetika» 11, no. 4 (September 10, 2020): 13–22. http://dx.doi.org/10.31548/machenergy2020.04.013.

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The study showed that the influence of alloying elements on the secondary structure formation of the steels containing from 0.19 to 0.37 wt. % carbon; 0.82-1.82 silicon; 0.63-3.03 manganese; 1.01-3.09 chromium; 0.005-0.031 nitrogen; up to 0.25 wt.% vanadium and austenite grain size is determined by their change in the content of vanadium nitride phase in austenite, its alloying and overheating above tac3, and the dispersion of ferrite-pearlite, martensitic and bainitic structures is determined by austenite grain size and thermal kinetic parameters of phase transformations. Analytical dependencies are defined that describe the experimental data with a probability of 95% and an error of 10% to 18%. An analysis results of studying the structure formation of structural steel during tempering after quenching show that the dispersion and uniformity of the distribution of carbide and nitride phases in ferrite is controlled at complete austenite homogenization by diffusion mobility and the solubility limit of carbon and nitrogen in ferrite, and secondary phase quantity in case of the secondary phase presence in austenite more than 0.04 wt. %. Equations was obtained which, with a probability of 95% and an error of 0.7 to 2.6%, describe the real process.

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Khurana, Puneet, Lisa McWilliams, Jonathan Wingfield, Derek Barratt, and Bharath Srinivasan. "A Novel High-Throughput FLIPR Tetra–Based Method for Capturing Highly Confluent Kinetic Data for Structure–Kinetic Relationship Guided Early Drug Discovery." SLAS DISCOVERY: Advancing the Science of Drug Discovery 26, no. 5 (March 30, 2021): 684–97. http://dx.doi.org/10.1177/24725552211000676.

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Target engagement by small molecules is necessary for producing a physiological outcome. In the past, a lot of emphasis was placed on understanding the thermodynamics of such interactions to guide structure–activity relationships. It is becoming clearer, however, that understanding the kinetics of the interaction between a small-molecule inhibitor and the biological target [structure–kinetic relationship (SKR)] is critical for selection of the optimum candidate drug molecule for clinical trial. However, the acquisition of kinetic data in a high-throughput manner using traditional methods can be labor intensive, limiting the number of molecules that can be tested. As a result, in-depth kinetic studies are often carried out on only a small number of compounds, and usually at a later stage in the drug discovery process. Fundamentally, kinetic data should be used to drive key decisions much earlier in the drug discovery process, but the throughput limitations of traditional methods preclude this. A major limitation that hampers acquisition of high-throughput kinetic data is the technical challenge in collecting substantially confluent data points for accurate parameter estimation from time course analysis. Here, we describe the use of the fluorescent imaging plate reader (FLIPR), a charge-coupled device (CCD) camera technology, as a potential high-throughput tool for generating biochemical kinetic data with smaller time intervals. Subsequent to the design and optimization of the assay, we demonstrate the collection of highly confluent time-course data for various kinase protein targets with reasonable throughput to enable SKR-guided medicinal chemistry. We select kinase target 1 as a special case study with covalent inhibition, and demonstrate methods for rapid and detailed analysis of the resultant kinetic data for parameter estimation. In conclusion, this approach has the potential to enable rapid kinetic studies to be carried out on hundreds of compounds per week and drive project decisions with kinetic data at an early stage in drug discovery.

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Abolfazl Mostafavi, Mir, and Christopher Gold. "A global kinetic spatial data structure for a marine simulation." International Journal of Geographical Information Science 18, no. 3 (April 2004): 211–27. http://dx.doi.org/10.1080/13658810310001620942.

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Zheng, Xu-Li, Dong-Hui Quan, Hai-Long Zhang, Xiao-Hu Li, Qiang Chang, and Olli Sipilä. "A new data structure for accelerating kinetic Monte Carlo method." Research in Astronomy and Astrophysics 19, no. 12 (December 2019): 176. http://dx.doi.org/10.1088/1674-4527/19/12/176.

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LITTLE, David I., Peter C. POAT, and Ian G. GILES. "Residual Analysis in Determining the Error Structure in Enzyme Kinetic Data." European Journal of Biochemistry 124, no. 3 (March 3, 2005): 499–505. http://dx.doi.org/10.1111/j.1432-1033.1982.tb06621.x.

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Bardarov, Ventzislav, Pavlina Simeonova, Ludmila Neikova, Krum Bardarov, Vasil Simeonov, Stefan Tsakovski, and Kamen Kanev. "Statistical interpretation of medical data of patients with alcohol abuse." Open Medicine 7, no. 4 (August 1, 2012): 465–74. http://dx.doi.org/10.2478/s11536-012-0020-1.

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AbstractAn attempt is made to assess a set of biochemical, kinetic and anthropometric data for patients suffering from alcohol abuse (alcoholics) and healthy patients (non-alcoholics). The main goal is to identify the data set structure, finding groups of similarity among the clinical parameters or among the patients. Multivariate statistical methods (cluster analysis and principal components analysis) were used to assess the data collection. Several significant patterns of related parameters were found to be representative of the role of the liver function, kinetic and anthropometric indicators (conditionally named “liver function factor”, “ethanol metabolism factor”, “body weight factor”, and “acetaldehyde metabolic factor”). An effort is made to connect the role of kinetic parameters for acetaldehyde metabolism with biochemical, ethanol kinetic and anthropometric data in parallel.

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Umarani, R., and G. Radhakrishnan. "Structure–reactivity correlations of substituted 2-phenylthiazolidines." Canadian Journal of Chemistry 70, no. 7 (July 1, 1992): 2009–14. http://dx.doi.org/10.1139/v92-252.

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Systematic investigations of the kinetics of the reactions of ethyl bromoacetate (EBA) and of picryl bromide (PB) with 2-phenylthiazolidines (PT) in 100% ethanol were undertaken at 30, 35, 40, and 45 °C. The most incisive information concerning the Hammett equation comes from the extensive studies on the substituted 2-phenylthiazolidines, establishing linear Hammett plots with negative ρ values. The kinetic data, plotted in a Brønsted fashion against pKa of the corresponding thiazolidinium ions, yield linear relationships. The activation parameters were computed. The linear relationships between ΔH≠ and ΔS≠ signify a consistent mechanism throughout the series.

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Cendrowski, Krzysztof, Karolina Opała, and Ewa Mijowska. "Carbonized Lanthanum-Based Metal-Organic Framework with Parallel Arranged Channels for Azo-Dye Adsorption." Nanomaterials 10, no. 6 (May 30, 2020): 1053. http://dx.doi.org/10.3390/nano10061053.

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In this contribution, the synthesis of the metal−organic framework (MOF) based on lanthanum that exhibits trigonal prism shape is presented. The length of a single side of this structure ranges from 2 to 10 μm. The carbonized lanthanum-based organic framework (CMOF–La) maintained the original shape. However, the lanthanum oxide was reshaped in the form of rods during the carbonization. It resulted in the creation of parallel arranged channels. The unique structure of the carbonized structure motivated us to reveal its adsorption performance. Therefore, the adsorption kinetics of acid red 18 onto a carbonized metal−organic framework were conducted. Various physicochemical parameters such as initial dye concentration and pH of dye solution were investigated in an adsorption process. The adsorption was found to decrease with an increase in initial dye concentration. In addition, the increase in adsorption capacity was noticed when the solution was changed to basic. Optimal conditions were obtained at a low pH. Kinetic adsorption data were analyzed using the pseudo-first-order kinetic model, the pseudo-second-order kinetic model and the intraparticle diffusion model. The adsorption kinetics were well fitted using a pseudo-second-order kinetic model. It was found that the adsorption of anionic dye onto CMOF–La occurs by hydrophobic interactions between carbonized metal-organic framework and acid red 18.

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Zheng, Jingxue, Junchen Huang, Lin Tao, Zhi Li, and Qi Wang. "A Multifaceted Kinetic Model for the Thermal Decomposition of Calcium Carbonate." Crystals 10, no. 9 (September 22, 2020): 849. http://dx.doi.org/10.3390/cryst10090849.

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The existing kinetic models often consider the influence of a single factor alone on the chemical reaction and this is insufficient to completely describe the decomposition reaction of solids. Therefore, the existing kinetic models were improved using the pore structure model. The proposed model was verified using the thermal decomposition experiment on calcium carbonate. The equation has been modified as fα=n1−α1−1n−ln1−α−1m1−ψln1−α12. This led to the conclusion that the pore structure, generated during the thermal decomposition of calcite, has an important influence on the decomposition kinetics. The existing experimental data show that the improved model, with random pores as the main body, reasonably describes the thermal decomposition process of calcite.

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Hamdaoui, Mohamed, Nesma Sawssen Achour, and Sassi Ben Nasrallah. "The Influence of Woven Fabric Structure on Kinetics of Water Sorption." Journal of Engineered Fibers and Fabrics 9, no. 1 (March 2014): 155892501400900. http://dx.doi.org/10.1177/155892501400900112.

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In this paper, the results of an experimental study designed to determine the kinetics of water sorption on cotton fabrics are presented. The dynamic water sorption of cotton fabrics was gravimetrically investigated at 20°C by using an experimental device, which assured the vertical suspension of the cloth surface and permitted the measurement of the mass of liquid rising in the fabric. A good fit of the experimental data with the parallel exponential kinetics model was found. The results show that the weave structure and the number of yarns per centimeter had a significant influence on the model parameters and the kinetic rate of sorption.

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Bizi, Mohamed, and Fatima-Ezzahra EL Bachra. "Transport of Carbamazepine, Ciprofloxacin and Sulfamethoxazole in Activated Carbon: Solubility and Relationships between Structure and Diffusional Parameters." Molecules 26, no. 23 (December 2, 2021): 7318. http://dx.doi.org/10.3390/molecules26237318.

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The transport of carbamazepine, ciprofloxacin and sulfamethoxazole in the different pores of activated carbon in an aqueous solution is a dynamic process that is entirely dependent on the intrinsic parameters of these molecules and of the adsorbent. The macroscopic processes that take place are analyzed by interfacial diffusion and reaction models. Modeling of the experimental kinetic curves obtained following batch treatment of each solute at 2 µg/L in tap water showed (i) that the transport and sorption rates were controlled by external diffusion and intraparticle diffusion and (ii) that the effective diffusion coefficient for each solute, with the surface and pore diffusion coefficients, were linked by a linear relationship. A statistical analysis of the experimental data established correlations between the diffusional parameters and some geometrical parameters of these three molecules. Given the major discontinuities observed in the adsorption kinetics, the modeling of the experimental data required the use of traditional kinetic models, as well as a new kinetic model composed of the pseudo first or second order model and a sigmoidal expression. The predictions of this model were excellent. The solubility of each molecule below 60 °C was formulated by an empirical expression.

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Jia, Zhigang, Cong Han, Rui Chang, and Daqing Zhang. "Synthesis of carbon dots-assisted MgAl-LDH hollow microspheres with hierarchical structure for the effective removal of Congo red from wastewater." E3S Web of Conferences 269 (2021): 02003. http://dx.doi.org/10.1051/e3sconf/202126902003.

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Hierarchical hollow Mg-Al layered double hydroxide microspheres (HHMs) are successfully prepared by hydrothermal treatment in the presence of carbon dots (CDs). Morphology and structure of the as-prepared samples are characterized using XRD, SEM, FT-IR, and TEM techniques. The growth process of HHMs has been investigated in detail, and Ostwald ripening mechanism is suggested for the hierarchical growth of HHMs. Adsorption isotherms and adsorption kinetics of HHMs for congo red (CR) are investigated. Langmuir and Temkin model are more fitted to the experimental data of CR isotherm adsorption. Adsorption kinetic data obeys the pseudo-second-order kinetic model. Moreover, thermodynamic parameters (ΔGo, ΔHo and ΔSo) show that the CR adsorption onto HHMs is an endothermic and spontaneous process. The as-prepared HHMs could be a potential adsorbent for wastewater treatment containing anion dyes.

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Panday, Dinesh, Teena Kachawa, and Seema Kothari. "Kinetics and Correlation Analysis of Reactivity in the Oxidation of Some α-Hydroxy Acids by Benzimidazolium Dichromate." Progress in Reaction Kinetics and Mechanism 43, no. 3-4 (October 2018): 300–314. http://dx.doi.org/10.3184/146867818x15319903829236.

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Kinetic and mechanistic studies of the oxidation of mandelic acid and nine monosubstituted mandelic acids by benzimidazolium dichromate (BIDC) in dimethyl sulfoxide are discussed with an emphasis on correlation of structure and reactivity. The reactions were of first order with respect to BIDC. However, Michaelis-Menten type kinetics were observed with respect to hydroxy acids. The reactions are catalysed by protons. The deuterium isotope effect for the oxidation of mandelic acid ( kH/ kD = 5.91 at 298 K) indicated an α-C-H bond cleavage in the rate-determining step. An analysis of the solvent effect showed that the role of cationsolvation is major. The reaction showed an excellent correlation with the Hammett σ values, the reaction constant being negative. Based on the kinetic data, analysis of the solvent effect and results of structure-reactivity correlation along with some non-kinetic parameters, a mechanism involving rate-determining oxidative decomposition of the complex through hydride-ion transfer via a cyclic transition state to give the corresponding oxoacid is suggested.

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Smith, Colin A., Adam Mazur, Ashok K. Rout, Stefan Becker, Donghan Lee, Bert L. de Groot, and Christian Griesinger. "Enhancing NMR derived ensembles with kinetics on multiple timescales." Journal of Biomolecular NMR 74, no. 1 (December 14, 2019): 27–43. http://dx.doi.org/10.1007/s10858-019-00288-8.

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AbstractNuclear magnetic resonance (NMR) has the unique advantage of elucidating the structure and dynamics of biomolecules in solution at physiological temperatures, where they are in constant movement on timescales from picoseconds to milliseconds. Such motions have been shown to be critical for enzyme catalysis, allosteric regulation, and molecular recognition. With NMR being particularly sensitive to these timescales, detailed information about the kinetics can be acquired. However, nearly all methods of NMR-based biomolecular structure determination neglect kinetics, which introduces a large approximation to the underlying physics, limiting both structural resolution and the ability to accurately determine molecular flexibility. Here we present the Kinetic Ensemble approach that uses a hierarchy of interconversion rates between a set of ensemble members to rigorously calculate Nuclear Overhauser Effect (NOE) intensities. It can be used to simultaneously refine both temporal and structural coordinates. By generalizing ideas from the extended model free approach, the method can analyze the amplitudes and kinetics of motions anywhere along the backbone or side chains. Furthermore, analysis of a large set of crystal structures suggests that NOE data contains a surprising amount of high-resolution information that is better modeled using our approach. The Kinetic Ensemble approach provides the means to unify numerous types of experiments under a single quantitative framework and more fully characterize and exploit kinetically distinct protein states. While we apply the approach here to the protein ubiquitin and cross validate it with previously derived datasets, the approach can be applied to any protein for which NOE data is available.

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Chen, Qing, Anders Engström, Lars Höglund, Henrik Strandlund, and Bo Sundman. "Thermo-Calc Program Interface and Their Applications - Direct Insertion of Thermodynamic and Kinetic Data into Modelling of Materials Processing, Structure and Property." Materials Science Forum 475-479 (January 2005): 3145–48. http://dx.doi.org/10.4028/www.scientific.net/msf.475-479.3145.

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Thermodynamic and kinetic data are generally essential for quantitative modeling of materials processing, structure, and property. Thermo-Calc program interfaces, including TQ, TCAPI, and TC MATLAB Toolbox, provides a hierarchy of APIs for application programmers to access thermodynamic and kinetic data via the kernel of Thermo-Calc and DICTRA, the most widely used software and database system for multi-component phase equilibrium and phase transformation calculations. With these program interfaces, variation of thermodynamic and kinetic properties can be directly obtained in real time as the local temperature, pressure, or composition changes. The structure and usage of the Thermo-Calc program interfaces will be introduced in this article. Successful application examples will be illustrated.

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Choi, Jin Seung, Dong Won Kang, Jeong Woo Seo, Ju Young Kim, Seung Tae Yang, Dae Hyeok Kim, and Gye Rae Tack. "Changes in Gait Characteristics due to Outsole Structure of Shoe." Applied Mechanics and Materials 775 (July 2015): 28–33. http://dx.doi.org/10.4028/www.scientific.net/amm.775.28.

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The purpose of this study was to evaluate changes in kinematic and kinetic gait characteristics due to outsole structure of the shoe. In this experiment, cushioning shoe having cushion for heel (BOSS Corps., Korea) which is designed as a lever, MBT having an unstable rounded shoe (Masai Barefoot Technology, MBT, Swiss) and normal running shoe (Adidas, Germany) were compared. The experiment was performed walking on the straight walkway (10m x 3m) five times with preferred walking speed. 3D motion capture system was used to acquire kinematic and kinetic data using six infrared cameras and two force plates. For comparison among shoes, walking velocity, hip, knee and ankle joint angles (range of motion, trajectory), ground reaction force (loading rate, the decay rate, maximal vertical ground reaction force), and center of mass - center of pressure inclination angle (COM-COP angle) were used. The results showed that there were different effects of types of shoe on lower extremities. Joint angle trajectory of ankle, joint range of motion (ROM) of the hip, and peak force were significantly different among shoe types. MBT provided a decreased impact force. Cushioning shoe provided increased progressive force, decreased loading rate, and decreased COM-COP angle. For further study, it is necessary to analyze additional subjects (i.e., elderly) and long-term effects.

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Hoffman, Adam S., Sara Azzam, Kai Zhang, Yahong Xu, Yijin Liu, Simon R. Bare, and Dante A. Simonetti. "Direct observation of the kinetics of gas–solid reactions using in situ kinetic and spectroscopic techniques." Reaction Chemistry & Engineering 3, no. 5 (2018): 668–75. http://dx.doi.org/10.1039/c8re00020d.

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Dong, Xiao Ping, Jie Fu, Jun Hao Jin, and Chen Chen. "Adsorption of Basic Dye in Aqueous Solution by Mesoporous Carbon Materials." Advanced Materials Research 441 (January 2012): 559–63. http://dx.doi.org/10.4028/www.scientific.net/amr.441.559.

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Mesoporous carbon CMK-3 with high surface area and opened pore structure was used to adsorb the basic dye, Malachite green (MG). The equilibrium adsorption data was well described by the Langmuir model, and a very high Langmuir adsorption capacity was obtained by this adsorbent. The adsorption kinetics was found to be best represented by a pseudo-second-order kinetic model.

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Roodt, Andreas, Hendrik G. Visser, and Alice Brink. "Structure/reactivity relationships and mechanism from X-ray data and spectroscopic kinetic analysis." Crystallography Reviews 17, no. 4 (July 25, 2011): 241–80. http://dx.doi.org/10.1080/0889311x.2011.593032.

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Glöckner, Steffen, Khang Ngo, Björn Wagner, Andreas Heine, and Gerhard Klebe. "The Influence of Varying Fluorination Patterns on the Thermodynamics and Kinetics of Benzenesulfonamide Binding to Human Carbonic Anhydrase II." Biomolecules 10, no. 4 (March 27, 2020): 509. http://dx.doi.org/10.3390/biom10040509.

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The fluorination of lead-like compounds is a common tool in medicinal chemistry to alter molecular properties in various ways and with different goals. We herein present a detailed study of the binding of fluorinated benzenesulfonamides to human Carbonic Anhydrase II by complementing macromolecular X-ray crystallographic observations with thermodynamic and kinetic data collected with the novel method of kinITC. Our findings comprise so far unknown alternative binding modes in the crystalline state for some of the investigated compounds as well as complex thermodynamic and kinetic structure-activity relationships. They suggest that fluorination of the benzenesulfonamide core is especially advantageous in one position with respect to the kinetic signatures of binding and that a higher degree of fluorination does not necessarily provide for a higher affinity or more favorable kinetic binding profiles. Lastly, we propose a relationship between the kinetics of binding and ligand acidity based on a small set of compounds with similar substitution patterns.

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Bailleul, Alida M., and Casey M. Holliday. "Joint histology in Alligator mississippiensis challenges the identification of synovial joints in fossil archosaurs and inferences of cranial kinesis." Proceedings of the Royal Society B: Biological Sciences 284, no. 1851 (March 22, 2017): 20170038. http://dx.doi.org/10.1098/rspb.2017.0038.

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Archosaurs, like all vertebrates, have different types of joints that allow or restrict cranial kinesis, such as synovial joints and fibrous joints. In general, synovial joints are more kinetic than fibrous joints, because the former possess a fluid-filled cavity and articular cartilage that facilitate movement. Even though there is a considerable lack of data on the microstructure and the structure–function relationships in the joints of extant archosaurs, many functional inferences of cranial kinesis in fossil archosaurs have hinged on the assumption that elongated condylar joints are (i) synovial and/or (ii) kinetic. Cranial joint microstructure was investigated in an ontogenetic series of American alligators, Alligator mississippiensis . All the presumably synovial, condylar joints found within the head of the American alligator (the jaw joint, otic joint and laterosphenoid–postorbital (LS–PO) joint) were studied by means of paraffin histology and undecalcified histology paired with micro-computed tomography data to better visualize three-dimensional morphology. Results show that among the three condylar joints of A. mississippiensis , the jaw joint was synovial as expected, but the otherwise immobile otic and LS–PO joints lacked a synovial cavity. Therefore, condylar morphology does not always imply the presence of a synovial articulation nor mobility. These findings reveal an undocumented diversity in the joint structure of alligators and show that crocodylians and birds build novel, kinetic cranial joints differently. This complicates accurate identification of synovial joints and functional inferences of cranial kinesis in fossil archosaurs and tetrapods in general.

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Suchorski, Yuri, and Günther Rupprechter. "Catalysis by Imaging: From Meso- to Nano-scale." Topics in Catalysis 63, no. 15-18 (July 2, 2020): 1532–44. http://dx.doi.org/10.1007/s11244-020-01302-2.

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AbstractIn-situ imaging of catalytic reactions has provided insights into reaction front propagation, pattern formation and other spatio-temporal effects for decades. Most recently, analysis of the local image intensity opened a way towards evaluation of local reaction kinetics. Herein, our recent studies of catalytic CO oxidation on Pt(hkl) and Rh(hkl) via the kinetics by imaging approach, both on the meso- and nano-scale, are reviewed. Polycrystalline Pt and Rh foils and nanotips were used as µm- and nm-sized surface structure libraries as model systems for reactions in the 10–5–10–6 mbar pressure range. Isobaric light-off and isothermal kinetic transitions were visualized in-situ at µm-resolution by photoemission electron microscopy (PEEM), and at nm-resolution by field emission microscopy (FEM) and field ion microscopy (FIM). The local reaction kinetics of individual Pt(hkl) and Rh(hkl) domains and nanofacets of Pt and Rh nanotips were deduced from the local image intensity analysis. This revealed the structure-sensitivity of CO oxidation, both in the light-off and in the kinetic bistability: for different low-index Pt surfaces, differences of up to 60 K in the critical light-off temperatures and remarkable differences in the bistability ranges of differently oriented stepped Rh surfaces were observed. To prove the spatial coherence of light-off on nanotips, proper orthogonal decomposition (POD) as a spatial correlation analysis was applied to the FIM video-data. The influence of particular configurations of steps and kinks on kinetic transitions were analysed by using the average nearest neighbour number as a common descriptor. Perspectives of nanosized surface structure libraries for future model studies are discussed.

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Demyshev, Sergey, Olga Dymova, and Nadezhda Miklashevskaya. "Seasonal Variability of the Dynamics and Energy Transport in the Black Sea by Simulation Data." Water 14, no. 3 (January 24, 2022): 338. http://dx.doi.org/10.3390/w14030338.

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This paper presents an assessment of the seasonal variability of the velocity fields, mean and eddy kinetics, and available potential energies, and the energy conversion rates for the eddy and basin-scale circulation regimes. The data were obtained through the numerical modeling of the Black Sea circulation for 2011 and 2016. It revealed significant differences in the current structure in the southern and central sea parts for 2011 and 2016. In 2011, the Rim Current was an almost continuous cyclonic basin-scale gyre, while in 2016 a system of mesoscale anticyclones was observed in the southern part. The variability of the mean kinetic energy depends more on the circulation regime than on the season of the year, while the distribution of the mean available potential energy is predominantly seasonal. The eddy kinetic energy depends on both the circulation regime and the season. In winter, the energy transport from the mean current via a barotropic instability mechanism sustains the mesoscale eddy generation. In summer, the mesoscale variability in the basin-scale regime is provided by commensurate contributions of barotropic and baroclinic instability, and, in the eddy regime, mainly by the energy transport from the available potential energy through the baroclinic instability.

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Liu, Yan, Kaige Liu, Lin Zhang, and Zhaowen Zhang. "Removal of Rhodamine B from aqueous solution using magnetic NiFe nanoparticles." Water Science and Technology 72, no. 7 (June 30, 2015): 1243–49. http://dx.doi.org/10.2166/wst.2015.319.

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Surface-modified magnetic nano alloy particles Ni2.33Fe were prepared using a hydrothermal method and they were utilized for removing Rhodamine B (RhB) from aqueous solution. The magnetic nanoparticles were characterized by X-ray diffraction, scanning electron microscopy, thermogravimetric analysis and Fourier transform infrared spectroscopy, which confirmed that the surface of the magnetic product with a face-centered cubic-type structure was successfully modified by sodium citrate. Kinetics studies were conducted. The pseudo-second-order kinetic model was used for fitting the kinetic data successfully. The Freundlich and Langmuir adsorption models were employed for the mathematical description of adsorption equilibrium. It was found that the adsorption isotherm can be very satisfactorily fitted by the Freundlich model.

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Bystřický, Zdeněk, and Josef Jancar. "Morphogenesis of Photo-Polymerized Dimethacrylate Networks, Kinetics of Curing and Viscoelastic Parameters." Materials Science Forum 851 (April 2016): 207–14. http://dx.doi.org/10.4028/www.scientific.net/msf.851.207.

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The paper refers to the process of dimethacrylate networks morphogenesis. These stiff and highly cross-linked networks have been extensively used as a polymeric matrix of dental composites for decades. In the study, common co-monomer mixtures used in dental resin formulations were employed. This includes rigid aromatic base monomers, bisphenol A glycerolate dimethacrylate (Bis-GMA) and its ethoxylated alternative (Bis-EMA). Flexible aliphatic monomer, triethylene glycol dimethacrylate (TEGDMA), was used as the viscosity reducer. Kinetics of the polymerization process was studied regarding the structural differences and varying molar ratio of the co-monomers. Kinetic data provided the base for understanding the supra-molecular structure evolution. Consequently, an attempt to quantify the relationship between the resulting network morphology and complex viscoelastic moduli was made. Curing kinetics was studied using differential photo-calorimetry (DPC). Complex modulus was measured using dynamic-mechanical analysis (DMA). Thermal degradation kinetic data (TGA) were used in order to confirm the estimated morphology of cured networks. Reactivity of the monomer is derived from its molecular structure. The potential for non-covalent physical interactions along with monomer backbone rigidity significantly decrease polymerization rate and resulting double bond conversion. The diffusion-controlled kinetics dominates over the chemically controlled kinetics throughout most of the polymerization process. Dilution by the low viscous and flexible monomer shifts the diffusion-controlled kinetics to the later stages of the polymerization. However, the flexibility of the monomer backbone promotes the origination of structural heterogeneities, characterized by micro-gel domains formation. This is associated particularly with the anomalous pendant double bond reactivity and ineffective cross-linking.

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KIRKPATRICK, DAVID, JACK SNOEYINK, and BETTINA SPECKMANN. "KINETIC COLLISION DETECTION FOR SIMPLE POLYGONS." International Journal of Computational Geometry & Applications 12, no. 01n02 (February 2002): 3–27. http://dx.doi.org/10.1142/s0218195902000724.

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We design a simple and elegant kinetic data structure for detecting collisions between polygonal (but not necessarily convex) objects in motion in the plane. Our structure is compact, maintaining an active set of certificates whose number is proportional to a minimum-size set of separating polygons for the objects. It is also responsive; on the failure of a certificate invariants can be restored in time logarithmic in the total number of object vertices. It is difficult to characterize the efficiency of our structure for lack of a canonical definition of external events. Nevertheless we give an easy upper bound on the worst case number of certificate failures.

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Pfister, Niklas, Stefan Bauer, and Jonas Peters. "Learning stable and predictive structures in kinetic systems." Proceedings of the National Academy of Sciences 116, no. 51 (November 27, 2019): 25405–11. http://dx.doi.org/10.1073/pnas.1905688116.

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Learning kinetic systems from data is one of the core challenges in many fields. Identifying stable models is essential for the generalization capabilities of data-driven inference. We introduce a computationally efficient framework, called CausalKinetiX, that identifies structure from discrete time, noisy observations, generated from heterogeneous experiments. The algorithm assumes the existence of an underlying, invariant kinetic model, a key criterion for reproducible research. Results on both simulated and real-world examples suggest that learning the structure of kinetic systems benefits from a causal perspective. The identified variables and models allow for a concise description of the dynamics across multiple experimental settings and can be used for prediction in unseen experiments. We observe significant improvements compared to well-established approaches focusing solely on predictive performance, especially for out-of-sample generalization.

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Mysik, S. V. "Kinetic and Activation Characteristics of Structure Rearrangement Processes in Ethoxylated Isononylphenol Derivates." Radio Engineering, no. 1 (March 5, 2020): 17–30. http://dx.doi.org/10.36027/rdeng.0120.0000160.

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The paper presents the calculation results of the kinetic and activation characteristics of fast and ultrafast structure rearrangement processes in liquid hydroxyethylated derivates of isononylphenol (ОНФn). Parameters were calculated using the relaxation theory of acoustic spectroscopy of liquids based on the analysis of the acoustic spectra of speed and sound absorption of the hydroxyethylated derivates of isononylphenol. The paper shows that two simple regions of acoustic dispersion can describe the acoustic spectra in the frequency range from 12 MHz to 2 GHz and the temperature range from 253 K to 323 K. The dispersion region data in the hydroxyethylated derivates of isononylphenol correspond to the interconnected reactions of OH ... O bonding and breaking in chain associates and spatially branched network structures. It is noted that the change in the spatial structure of liquid hydroxyethylated derivates of isononylphenol can be considered as a set of the large number of independent (for non-collective processes) and interconnected (for collective processes) local rearrangements of the liquid structure as a result of the thermal motion of molecules. The proposed molecular mechanism of acoustic relaxation and the kinetic model of fast and ultrafast structure rearrangement processes of the hydroxyethylated derivates of isononylphenol made it possible to explain the main experimental results and to calculate the kinetic and activation characteristics of the structure rearrangement processes of the hydroxyethylated derivates of isononylphenol. This model and the kinetic and activation parameters of the hydroxyethylated derivates of isononylphenol can find application in development of various technologies for using nonionic surfactants.

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Ranke, Johannes, and Stefan Meinecke. "Error Models for the Kinetic Evaluation of Chemical Degradation Data." Environments 6, no. 12 (December 10, 2019): 124. http://dx.doi.org/10.3390/environments6120124.

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In the kinetic evaluation of chemical degradation data, degradation models are fitted to the data by varying degradation model parameters to obtain the best possible fit. Today, constant variance of the deviations of the observed data from the model is frequently assumed (error model “constant variance”). Allowing for a different variance for each observed variable (“variance by variable”) has been shown to be a useful refinement. On the other hand, experience gained in analytical chemistry shows that the absolute magnitude of the analytical error often increases with the magnitude of the observed value, which can be explained by an error component which is proportional to the true value. Therefore, kinetic evaluations of chemical degradation data using a two-component error model with a constant component (absolute error) and a component increasing with the observed values (relative error) are newly proposed here as a third possibility. In order to check which of the three error models is most adequate, they have been used in the evaluation of datasets obtained from pesticide evaluation dossiers published by the European Food Safety Authority (EFSA). For quantitative comparisons of the fits, the Akaike information criterion (AIC) was used, as the commonly used error level defined by the FOrum for the Coordination of pesticide fate models and their USe(FOCUS) is based on the assumption of constant variance. A set of fitting routines was developed within the mkin software package that allow for robust fitting of all three error models. Comparisons using parent only degradation datasets, as well as datasets with the formation and decline of transformation products showed that in many cases, the two-component error model proposed here provides the most adequate description of the error structure. While it was confirmed that the variance by variable error model often provides an improved representation of the error structure in kinetic fits with metabolites, it could be shown that in many cases, the two-component error model leads to a further improvement. In addition, it can be applied to parent only fits, potentially improving the accuracy of the fit towards the end of the decline curve, where concentration levels are lower.

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Islam, MN, N. Ahmed, MY Hossain, AKML Rahman, and A. Sultana. "Effect of pH on the adsorption kinetics of Cr(VI) on sodium chlorite treated coconut coir." Bangladesh Journal of Scientific and Industrial Research 51, no. 2 (June 12, 2016): 95–100. http://dx.doi.org/10.3329/bjsir.v51i2.28090.

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Coconut coir is a low cost bioadsorbent containing large amount of lignin. In this research work sodium chlorite treated coconut coir (SCT CC) was used to remove Cr(VI) from industrial wastewater by implementing adsorption technique through the investigation of the adsorption kinetics at different pH values. The maximum Cr(VI) adsorption capacity of SCT-CC at pH 2.00, 3.00, 5.00 and 7.00 was 24.75, 23.92, 16.07 and 6.31 mg Cr(VI) g-1 SCT-CC respectively with the dose of 7.5 g/L. The equilibrium established within three hours resulting the maximum removal (95%) of chromium. The adsorption kinetics of Cr(VI) on SCT-CC was found to be regulated by pH of the system. Rate of adsorption was the highest at pH 2.00 and the kinetic data well-fitted with Ho's pseudo second order kinetics. Fourier transform infrared (FT-IR) spectrometry analysis indicated that the carbonyl (C=O) groups and hydroxy (O-H) groups from the lignin structure in coconut coir may be involved in the mechanism of Cr(VI) adsorption and it showed good agreement with the kinetic data to elucidate the adsorption mechanismBangladesh J. Sci. Ind. Res. 51(2), 95-100, 2016

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Shuman, Cynthia F., Lotta Vrang, and U. Helena Danielson. "Improved Structure−Activity Relationship Analysis of HIV-1 Protease Inhibitors Using Interaction Kinetic Data." Journal of Medicinal Chemistry 47, no. 24 (November 2004): 5953–61. http://dx.doi.org/10.1021/jm0499110.

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Булыга, Д. В., and С. К. Евстропьев. "Кинетика адсорбции и фотокаталитического разложения диазокрасителя нанокомпозитом ZnO-MgO." Оптика и спектроскопия 130, no. 9 (2022): 1455. http://dx.doi.org/10.21883/os.2022.09.53309.3617-22.

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The synthesis of ZnO-MgO nanocomposite via modified Pechini method was performed. The crystalline structure and the morphology of nanocrystals were studied by X-ray diffraction analysis and scanning electron microscopy. The study on the kinetics of diazo dye adsorption and its photocatalytic decomposition on the surface of nanocomposite was performed. It was shown that the rate of adsorption process in aqueous solution is described by a kinetic equation of the first order. The application of the nanocomposite allows to significantly increase the efficiency of UV water treatment and its purification from the dye. However, a brief deviation of experimental data on the rate of photocatalytic degradation from the values of the widely used kinetic equation of the first order is observed.

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Gerasimov, Iliya, Denis Knyazkov, Andrey Shmakov, Oleg Korobeinichev, Nils Hansen, and Charles Westbrook. "Investigation of Methyl Pentanoate Flame Structure by Molecular-Beam Mass Spectrometry and Modeling." Siberian Journal of Physics 9, no. 3 (October 1, 2014): 49–62. http://dx.doi.org/10.54362/1818-7919-2014-9-3-49-62.

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The structure of four stoichiometric and fuel-rich premixed flames of methyl pentanoate stabilized at low (20 torr) and atmospheric pressures has been studied by molecular-beam mass spectrometry. The data obtained have been compared with results of numerical simulations, performed with implication of two detailed chemical kinetic mechanisms, one of which has been developed by the authors of this work. While both mechanisms have predicted concentration profiles for most of the species quite well, some discrepancies between experimental and modeling data have been observed for carbon monoxide and some intermediate products. Considerable differences in several profiles simulated with different mechanisms have been noted. Analysis of reaction paths in investigated flames has shown most of these differences to be caused by different reactions and kinetics used for isomerization of primary radicals of methyl pentanoate oxidation in these mechanisms

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Tomoaia, Gheorghe, Andrada Tomoaia-Cotisel, Maria Tomoaia-Cotisel, and Aurora Mocanu. "Kinetic study of adsorption of some biocompounds at the oil/water interface." Open Chemistry 3, no. 2 (June 1, 2005): 347–60. http://dx.doi.org/10.2478/bf02476001.

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AbstractThe adsorption kinetics of some local anesthetics, like dibucaine and tetracaine, and of stearic acid from bulk solutions at the oil/water interface was studied by using the pendent drop and ring methods. The anesthetics were dissolved in aqueous solutions (pH 2), and the fatty acid was dissolved in benzene, each biocompound at several different concentrations in bulk solutions. Kinetic equations for Langmuir mechanism of adsorption at oil/water interface were tested. The kinetic analysis shows that Langmuir kinetic approach describes the dynamic interfacial pressures within the limits of the experimental errors over a wide range of time and for different surfactant concentrations in bulk solutions. It is also concluded that this approach allows the calculation of the ratio of the adsorption and desorption rate constants of these biocompounds at the oil/water interface. Obtained results are in substantial agreement with earlier reported data for the surfactant adsorption as, well as with their molecular structure.

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Pulikkal, Ajmal Koya, and Lalduhawma Chhakchhuak. "Quantitative Assessment of Structure Reactivity Correlation on Rapid Kinetics of Halogenated Aromatic Compounds: A Hydrodynamic Voltammetry Study." ECS Meeting Abstracts MA2022-02, no. 60 (October 9, 2022): 2470. http://dx.doi.org/10.1149/ma2022-02602470mtgabs.

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Halogenations are mostly rapid and cannot be studied by the conventional method, hence, hydrodynamic voltammetry which is based on voltammetric principles can be adopted to study these fast reactions, provided either a reactant or a product in the reaction is electro reducible. These reactions are mostly electrophillic substitution reactions and second order when molecular halogens are used as a reagent. Rapid kinetic studies on some important halogenated aromatic compounds at rotating platinum electrode (RPE) using hydrodynamic voltammetry are summarized and reviewed for a period of the last few years. The advancement made to the technique as well as its application for mechanistic purposes, electrode kinetic measurements, pharmaceutical, and analytical applications have been addressed. As an investigative tool, kinetics has been used to obtain thermodynamic data that allows a quantitative comparison of the reactivity of the two substrates such as activation energy, velocity constants, frequency factors, and entropy change. This aids in configuring the mechanistic route, from among those theoretically possible by checking the compatibility with experimentally observed facts.

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Barysheva, Olga, Renat Sadykov, Yuri Khabibullin, and Elizaveta Zheltukhina. "Forecasting of an output of eco toxicants at thermal decomposition of chemical fuel." E3S Web of Conferences 140 (2019): 08002. http://dx.doi.org/10.1051/e3sconf/201914008002.

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Combustion of high-energy chemical fuels containing chlorine in the element structure can lead to formation in the particles of smoke of super eco toxicants—the polychlorinated dioxins and furans. The numerical experiment conducted was based on solution of the equations of chemical kinetics. The computational and theoretical researches directed to the solution of a problem of determination of parameters of combustion products of chemical fuels taking into account formation of harbingers of the polychlorinated dioxins were executed. The main data on the accepted method of determination of disequilibrium structures of products of burning the chlorine-containing chemical fuels were represented. Based on the analysis of references about mechanisms and speeds of chemical reactions of transformations of chlorine-containing connections, the kinetic model of formation of predecessors of dioxins is constructed. The carried-out calculations showed (assuming chemical balance) that process of formation of dioxins is significantly disequilibrious. The results of kinetic researches on emission of harbingers of dioxins showed the nature of the influence of different components of combustion products of chemical fuels on time for the different levels of temperatures.

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Hema, T., and K. S. Easwarakumar. "An Efficient Kinetic Range Query for One Dimensional Axis Parallel Segments." International Journal of Intelligent Information Technologies 14, no. 1 (January 2018): 48–62. http://dx.doi.org/10.4018/ijiit.2018010104.

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We present a kinetic data structure named Kinetic Interval Graph (KI-Graph) for performing efficient range search on moving one dimensional axis-parallel segments. This finds applications in Artificial Intelligence such as robotic motion. The structure requires O(n) storage. The time taken per update when a critical event occurs is O (1) thereby improving responsiveness when compared to the kinetic segment trees, while the overall updates across all segments at a time instance is at most n/2. Also, range query is performed efficiently in θ (k) time, where k segments are reported.

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Al-Gorair, Arej S., Asmaa Sayed, and Ghada A. Mahmoud. "Engineered Superabsorbent Nanocomposite Reinforced with Cellulose Nanocrystals for Remediation of Basic Dyes: Isotherm, Kinetic, and Thermodynamic Studies." Polymers 14, no. 3 (January 30, 2022): 567. http://dx.doi.org/10.3390/polym14030567.

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In this study, cellulose nanocrystals (CNCs) were produced from pea peels by acid hydrolysis to be used with pectin and acrylic acid (AAc) to form Pectin-PAAc/CNC nanocomposite by γ-irradiation. The structure, morphology, and properties of the nanocomposite were investigated using Fourier transform infrared spectroscopy (FTIR) and atomic force microscopy (AFM) techniques. The nanocomposite hydrogel was used for the removal of methylene blue dye (MB) from wastewater. The results revealed that the presence of CNCs in the polymeric matrix enhances the swelling and adsorption properties of Pectin-PAAc/CNC. The optimum adsorbate concentration is 70 mg/L. The kinetic experimental data were fit by pseudo-first-order (PFO), pseudo-second-order (PSO), and Avrami (Avr) kinetic models. It was found that the kinetic models fit the adsorption of MB well where the correlation coefficients of all kinetic models are higher than 0.97. The Avr kinetic model has the lowest ∆qe (normalized standard deviation) value, making it the most suitable one for describing the adsorption kinetics. The adsorption isotherm of MB by Pectin-PAAc follows the Brouers–Sotolongo model while that by Pectin-PAAc/CNC follows the Langmuir isotherm model. The negative values of ∆G confirmed the spontaneous nature of adsorption, and the positive value of ∆H indicated the endothermic nature of the adsorption.

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Choudhury, Subham, Michael Moret, Pierre Salvy, Daniel Weilandt, Vassily Hatzimanikatis, and Ljubisa Miskovic. "Reconstructing Kinetic Models for Dynamical Studies of Metabolism using Generative Adversarial Networks." Nature Machine Intelligence 4, no. 8 (August 30, 2022): 710–19. http://dx.doi.org/10.1038/s42256-022-00519-y.

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AbstractKinetic models of metabolism relate metabolic fluxes, metabolite concentrations and enzyme levels through mechanistic relations, rendering them essential for understanding, predicting and optimizing the behaviour of living organisms. However, due to the lack of kinetic data, traditional kinetic modelling often yields only a few or no kinetic models with desirable dynamical properties, making the analysis unreliable and computationally inefficient. We present REKINDLE (Reconstruction of Kinetic Models using Deep Learning), a deep-learning-based framework for efficiently generating kinetic models with dynamic properties matching the ones observed in cells. We showcase REKINDLE’s capabilities to navigate through the physiological states of metabolism using small numbers of data with significantly lower computational requirements. The results show that data-driven neural networks assimilate implicit kinetic knowledge and structure of metabolic networks and generate kinetic models with tailored properties and statistical diversity. We anticipate that our framework will advance our understanding of metabolism and accelerate future research in biotechnology and health.

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Putro, Jindrayani Nyoo, Felycia Edi Soetaredjo, Wenny Irawaty, Sandy Budi Hartono, Shella Permatasari Santoso, Jenni Lie, Maria Yuliana, et al. "Cellulose Nanocrystals (CNCs) and Its Modified Form from Durian Rind as Dexamethasone Carrier." Polymers 14, no. 23 (November 29, 2022): 5197. http://dx.doi.org/10.3390/polym14235197.

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In this study, CNCs were extracted from durian rind. Modification to CNCs with saponin was conducted at 50 °C for one h. CNCs and CNCs-saponin were employed as dexamethasone carriers. Modification to CNCs using saponin did not change the relative crystallinity of CNCs. CNCs’ molecular structure and surface chemistry did not alter significantly after modification. Both nanoparticles have surface charges independently of pH. Dexamethasone-released kinetics were studied at two different pH (7.4 and 5.8). Higuchi, Ritger–Peppas, first-order kinetic and sigmoidal equations were used to represent the released kinetic data. The sigmoidal equation was found to be superior to other models. The CNCs and CNCs-saponin showed burst release at 30 min. The study indicated that cell viability decreased by 30% after modification with saponin.

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Astola, Laura, Hans Stigter, Maria Victoria Gomez Roldan, Fred van Eeuwijk, Robert D. Hall, Marian Groenenboom, and Jaap J. Molenaar. "Parameter estimation in tree graph metabolic networks." PeerJ 4 (September 20, 2016): e2417. http://dx.doi.org/10.7717/peerj.2417.

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We study the glycosylation processes that convert initially toxic substrates to nutritionally valuable metabolites in the flavonoid biosynthesis pathway of tomato (Solanum lycopersicum) seedlings. To estimate the reaction rates we use ordinary differential equations (ODEs) to model the enzyme kinetics. A popular choice is to use a system of linear ODEs with constant kinetic rates or to use Michaelis–Menten kinetics. In reality, the catalytic rates, which are affected among other factors by kinetic constants and enzyme concentrations, are changing in time and with the approaches just mentioned, this phenomenon cannot be described. Another problem is that, in general these kinetic coefficients are not always identifiable. A third problem is that, it is not precisely known which enzymes are catalyzing the observed glycosylation processes. With several hundred potential gene candidates, experimental validation using purified target proteins is expensive and time consuming. We aim at reducing this task via mathematical modeling to allow for the pre-selection of most potential gene candidates. In this article we discuss a fast and relatively simple approach to estimate time varying kinetic rates, with three favorable properties: firstly, it allows for identifiable estimation of time dependent parameters in networks with a tree-like structure. Secondly, it is relatively fast compared to usually applied methods that estimate the model derivatives together with the network parameters. Thirdly, by combining the metabolite concentration data with a corresponding microarray data, it can help in detecting the genes related to the enzymatic processes. By comparing the estimated time dynamics of the catalytic rates with time series gene expression data we may assess potential candidate genes behind enzymatic reactions. As an example, we show how to apply this method to select prominent glycosyltransferase genes in tomato seedlings.

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Mantel, C. R., A. R. Schulz, K. Miyazawa, and H. E. Broxmeyer. "Kinetic selectivity of cholinephosphotransferase in mouse liver: the Km for CDP-choline depends on diacylglycerol structure." Biochemical Journal 289, no. 3 (February 1, 1993): 815–20. http://dx.doi.org/10.1042/bj2890815.

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The effects of different 1,2-diacyl-sn-glycerols on the kinetic properties of CDP-choline:1,2-diacylglycerol cholinephosphotransferase (EC 2.7.8.2) from mouse liver microsomes have been studied. Initial-velocity experiments were carried out with various concentrations of several species of diacylglycerol at different fixed concentrations of CDP-choline. Kinetic analysis of these data showed a family of intersecting lines consistent with a sequential kinetic mechanism of catalysis. The Km and Vmax. values derived from rate data revealed a pronounced effect of diacylglycerol species utilization on the Km value for CDP-choline. There was a biphasic relationship between diacylglycerol chain length and the Km for CDP-choline. Substitution of an unsaturated fatty acid in the sn-2 position of distearin also dramatically increased the CDP-choline Km value as well as the Vmax. 1,2-Dipalmitoyl-sn-glycerol was the preferred substrate over other disaturated species, but 1,2-dihexanoyl-sn-glycerol could not be utilized. These results demonstrate the kinetic mechanism of in vitro catalysis and suggest a regulatory role for CDP-choline concentration in the diacylglycerol species selectivity of cholinephosphotransferase resulting in the de novo biosynthesis of different molecular species of phosphatidylcholine.

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Hoffmann, Moritz, Martin Scherer, Tim Hempel, Andreas Mardt, Brian de Silva, Brooke E. Husic, Stefan Klus, et al. "Deeptime: a Python library for machine learning dynamical models from time series data." Machine Learning: Science and Technology 3, no. 1 (December 10, 2021): 015009. http://dx.doi.org/10.1088/2632-2153/ac3de0.

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Abstract Generation and analysis of time-series data is relevant to many quantitative fields ranging from economics to fluid mechanics. In the physical sciences, structures such as metastable and coherent sets, slow relaxation processes, collective variables, dominant transition pathways or manifolds and channels of probability flow can be of great importance for understanding and characterizing the kinetic, thermodynamic and mechanistic properties of the system. Deeptime is a general purpose Python library offering various tools to estimate dynamical models based on time-series data including conventional linear learning methods, such as Markov state models (MSMs), Hidden Markov Models and Koopman models, as well as kernel and deep learning approaches such as VAMPnets and deep MSMs. The library is largely compatible with scikit-learn, having a range of Estimator classes for these different models, but in contrast to scikit-learn also provides deep Model classes, e.g. in the case of an MSM, which provide a multitude of analysis methods to compute interesting thermodynamic, kinetic and dynamical quantities, such as free energies, relaxation times and transition paths. The library is designed for ease of use but also easily maintainable and extensible code. In this paper we introduce the main features and structure of the deeptime software. Deeptime can be found under https://deeptime-ml.github.io/.

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Barbosa, Thianne Silva Batista, Thiago Rodrigo Barbosa Barros, Tellys Lins Almeida Barbosa, Diogo Pierre Alves Rodrigues, and Meiry Gláucia Freire Rodrigues. "Oil removal from oil/water emulsion by Zeolitic Imidazolate Framework-8 (ZIF-8): A study of pH, and adsorption kinetic." Research, Society and Development 10, no. 14 (November 9, 2021): e444101422162. http://dx.doi.org/10.33448/rsd-v10i14.22162.

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Most traditional methods are only used to remove free oil from wastewater, and they are not efficient for separating oil-water emulsions. The adsorption separation process can be widely applied for the treatment of emulsions, mainly due to the cost and benefit of the process and the wide variety of materials that can be used as adsorbents, for example activated carbon, clays, zeolites, etc. Among the various types of porous materials called "Metal Organic Frameworks" (MOFs) are the zeolitic imidazolate (ZIFs) structures. The zeolitic structure of the ZIFs allows to exhibit high surface areas and thus to be promising adsorbents. To evaluate the adsorption capacity of ZIF-8 in the removal of emulsified oil, ZIF-8 was synthesized using Zn metal and as organic binder 2-methylimidazole (Hmim), dissolved in methanol at room temperature. ZIF-8 was characterized by X-ray diffraction (XRD) technique to determine the crystalline structure. To evaluate the capacity of the emulsified oil, a pH-influence test and chemical kinetics were determined. The best pH of the emulsion for removal was pH 6. The chemical kinetics performed at pH 6 presented the best fit with the pseudo-second model with correlation coefficient 0.93. According to the kinetic data, a removal percentage of 92.43% was found with only 30 min of removal.

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Izmodenov, Vladislav V. "Global structure of the heliosphere: 3D kinetic-MHD model and the interpretation of spacecraft data." Uspekhi Fizicheskih Nauk 188, no. 08 (April 2017): 881–93. http://dx.doi.org/10.3367/ufnr.2017.04.038293.

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Journal articles on the topic 'Kinetic data structure'

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