Simple Kinetics Research Articles

Accounting for Space—Quantification of Cell-To-Cell Transmission Kinetics Using Virus Dynamics Models.

Mathematical models based on ordinary differential equations (ODE) that describe the population dynamics of viruses and infected cells have been an essential tool to characterize and quantify viral infection dynamics. Although an important aspect of viral infection is the dynamics of viral spread, which includes transmission by cell-free virions and direct cell-to-cell transmission, models used so far ignored cell-to-cell transmission completely, or accounted for this process by simple mass-action kinetics between infected and uninfected cells. In this study, we show that the simple mass-action approach falls short when describing viral spread in a spatially-defined environment. Using simulated data, we present a model extension that allows correct quantification of cell-to-cell transmission dynamics within a monolayer of cells. By considering the decreasing proportion of cells that can contribute to cell-to-cell spread with progressing infection, our extension accounts for the transmission dynamics on a single cell level while still remaining applicable to standard population-based experimental measurements. While the ability to infer the proportion of cells infected by either of the transmission modes depends on the viral diffusion rate, the improved estimates obtained using our novel approach emphasize the need to correctly account for spatial aspects when analyzing viral spread.

Kinetics Study of Heterogeneous Bromine Release from the Reaction between Gaseous Ozone and Aqueous Bromide Solution.

The heterogeneous release of molecular bromine, Br2, from the reaction between gaseous ozone and aqueous bromide ion in seawater ice and sea salt aerosols is considered to be an initial source of reactive bromine species in the troposphere. Recent studies have demonstrated that the uptake of ozone by aqueous bromide solution is promoted by reactions at the gas-liquid interface. The present work investigated the heterogeneous reaction between gaseous ozone and aqueous bromide solution at atmospheric pressure and room temperature using a wetted wall flow reactor combined with a chemical ionization mass spectrometer. The emission rate of Br2 was measured as a function of gaseous ozone concentration, aqueous bromide concentration, and pH. In addition, we conducted a simple kinetics model simulation that included only bulk aqueous-phase reactions and compared the theoretical values with the experimentally determined values. The Br2 emission rates measured experimentally differ from the simulated rates at relatively high bromide concentration, as well as in the pH region of 6-9. These differences might be explained by different Br- concentration and/or deprotonation efficiency near the interface region and those in the bulk solution.

Probabilistic parameter estimation in a 2-step chemical kinetics model for n-dodecane jet autoignition

This paper demonstrates the development of a simple chemical kinetics model designed for autoignition of n-dodecane in air using Bayesian inference with a model-error representation. The model error, i.e. intrinsic discrepancy from a high-fidelity benchmark model, is represented by allowing additional variability in selected parameters. Subsequently, we quantify predictive uncertainties in the results of autoignition simulations of homogeneous reactors at realistic diesel engine conditions. We demonstrate that these predictive error bars capture model error as well. The uncertainty propagation is performed using non-intrusive spectral projection that can also be used in principle with larger scale computations, such as large eddy simulation. While the present calibration is performed to match a skeletal mechanism, it can be done with equal success using experimental data only (e.g. shock-tube measurements). Since our method captures the error associated with structural model simplifications, we believe that the optimised model could then lead to better qualified predictions of autoignition delay time in high-fidelity large eddy simulations than the existing detailed mechanisms. This methodology provides a way to reduce the cost of reaction kinetics in simulations systematically, while quantifying the accuracy of predictions of important target quantities.

Biosorption of fluoride from aqueous medium by Indian sandalwood (Santalum Album) leaf powder

Sandalwood leaf powder prepared from mature, dried Indian sandalwood (Santalum album) leaves was investigated to assess its ability to remove fluoride from aqueous solutions using adsorption process. Effects of solution pH, contact time, adsorbent amount and solution temperature on fluoride sorption had been investigated. The biosorbent was effective at the pH range of 5.0–7.0 and its fluoride removal capacity was found to be above 75.0%. The kinetics of the interactions was measured with pseudo first order Lagergren equation (mean k1: 2.22 × 10−2 min−1), simple second order kinetics (mean k2: 4.43 × 10−1 g/mg/min), and intra-particle diffusion (mean ki: 8.31 × 10−2 mg/g/min0.5) mechanism. The adsorption data gave good fits with Langmuir, Freundlich and Temkin isotherms and yielded Langmuir monolayer capacity of 4.66 mg/g. The negative values of the thermodynamic parameters, ΔH, ΔS and ΔG showed the adsorption process to be exothermic in nature and thermodynamically favourable at lower temperature. These results indicated that Sandalwood leaf powder might be an effective adsorbent for treatment of water contaminated with fluoride.

Identification of metabolites of MDR-1339, an inhibitor of β-amyloid protein aggregation, and kinetic characterization of the major metabolites in rats

We previously reported that MDR-1339, an inhibitor of β-amyloid protein aggregation, was likely to be eliminated by biotransformation in rats. The objective of this study was to determine the chemical identity of metabolites derived from this aggregate inhibitor and to characterize the kinetics of formation of these metabolites in rats. Using high performance liquid chromatography coupled with mass spectrometry with a hybrid triple quadrupole-linear ion trap, 7 metabolites and 1 potential metabolic intermediate were identified in RLM incubations containing MDR-1339. In addition to these, 3 glucuronide metabolites were detected in urine samples from rats receiving a 10 mg/kg oral dose of MDR-1339. When the kinetics of the formation of two major metabolites, M1 and M2, were analyzed assuming simple Michaelis-Menten kinetics, the Vmax and Km values were found to be 0.459 ± 0.0196 nmol/min/mg protein and 28.3 ± 3.07 μM for M1, and 0.101 ± 0.00537 nmol/min/mg protein and 14.7 ± 2.37 μM for M2, respectively. When chemically synthesized M1 and M2 were individually administered to rats intravenously at the dose of 5 mg/kg respectively, the volume of distribution and elimination clearance were determined to be 4590 ± 709 mL/kg and 68.4 ± 5.60 mL/min/kg for M1 and 15300 ± 8110 mL/kg and 98.0 ± 19.5 mL/min/kg for M2, respectively. When MDR-1339 was intravenously administered to rats at a dose of 5 mg/kg, the parent drug and M1 were readily detected for periods of up to 6 h after the administration, but M2 was observed only from 2 to 4 h. A standard moment analysis indicates that the formation clearance of M1 is 6.01 mL/min/kg, suggesting that 19.7% of the MDR-1339 dose was eliminated in rats. These observations indicate that the hepatic biotransformation of MDR-1339 results in the formation of at least 10 metabolites and that M1 is the major metabolite derived from this aggregation inhibitor in rats.

Kinetics of autoignition: a simple intuitive interpretation and its relation to the Livengood-Wu integral.

It is well known that the gas-phase autoignition phenomenon often involves branched chain reactions as well as the acceleration of reactions by thermal feedback. Despite the huge combustion kinetic mechanisms of large hydrocarbons found in practical fuels, chain reactions in the early stages of alkane autoignition exhibit simple kinetics since the pseudo-first-order assumption and the linear approximation are valid. In this study, this simple picture of autoignition will be presented starting from the H2-O2 system and then extending to practical fuel-air mixtures. The present interpretation gives the theoretical rationale for the Livengood-Wu integral which is known as an empirical method to predict the timing of knock in spark-ignition engines.

Kinetic modeling of ascorbic acid degradation of pineapple juice subjected to combined pressure-thermal treatment

A study was conducted to investigate and model kinetic degradation of ascorbic acid in freshly prepared pineapple juice subjected to various pressure (0.1, 300,450 and 600 MPa)-thermal (30, 75, 85 and 95 °C) treatment combinations. Experiments were conducted using a semi-custom made high pressure kinetic tester as well as an aluminum thermal kinetic tester. Thermal degradation of ascorbic acid was described with simple first order kinetics. The thermal rate constants (k75 -95 ◦C, 0.1 MPa) and activation energy (Ea) for ascorbic acid degradation reaction varied in the range of 0.004–0.006 per min and 14.22–29.78 kJ/mol, respectively. Within the experimental conditions of the study (300–600 MPa at 30 °C for holding times up to 15 min) high pressure processing did not alter ascorbic acid content (535.5–564.5 mg/kg). Combined pressure-thermal treatment (300–600 MPa at 75–95 °C) degraded ascorbic acid with increasing thermal intensity and was modeled using first order fractional conversion kinetics model. The lower asymptote value ([A]∞[A]0), rate constants (k75 -95 ◦C, 600 MPa) and Ea were in the range of 77–85%, 0.108 to 0.138 per min and 17.4–43.8 kJ/mol, respectively. Similarly, pressure sensitivity (ΔV≠) was ∼0 and −2.99 cm3/mol at 30 and 95 °C, respectively. Knowledge gained from the study can be useful for food processors to optimize high pressure treatment conditions for pineapple juice products.

Outlook on the Application of Metal-Liganded Bioactives for Stimuli-Responsive Release.

Direct metal-liganded bioactive coordination complexes are known to be sensitive to stimuli such as pH, light, ion activation, or redox cues. This results in the controlled release of the bioactive(s). Compared to other drug delivery strategies based on metal complexation, this type of coordination negates a multi-step drug loading methodology and offers customized physiochemical properties through judicious choice of modulating ancillary ligands. Bioactive release depends on simple dissociative kinetics. Nonetheless, there are challenges encountered when translating the pure coordination chemistry into the biological and physiological landscape. The stability of the metal–bioactive complex in the biological milieu may be compromised, disrupting the stimuli-responsive release mechanism, with premature release of the bioactive. Research has therefore progressed to the incorporation of metal-liganded bioactives with established drug delivery strategies to overcome these limitations. This review will highlight and critically assess current research interventions in order to predict the direction that pharmaceutical scientists could pursue to arrive at tailored and effective metal-liganded bioactive carriers for stimuli-responsive drug release.

The thermal theory based equation for correlation between temperature and flammability limits of hydrocarbons

Theoretical equation to evaluate the effect of temperature on the flammability limits of pure hydrocarbons was proposed in present study and compared with other methods available in the literatures. Theoretical equation was based on the thermal theory. Verification of the linear equation has been implemented on the cases of hydrogen, methane, propane, propylene, butylene, pentane and isobutane. The equation in this paper shows an average absolute relative error of 0.43% and 0.93% for lower and upper flammability limits, respectively. The equation possesses better prediction accuracy than other available methods at UFL. The reason for better accuracy is that the simple chemical kinetics about oxygen consumption was used to calculate reaction heat at upper flammability limit. Finally, the temperature range of application of theoretical equation was discussed in detail.

Feedback Kinetics in Mechanochemistry: The Importance of Cohesive States.

Although mechanochemical synthesis is becoming more widely applied and even commercialised, greater basic understanding is needed if the field is to progress on less of a trial-and-error basis. We report that a mechanochemical reaction in a ball mill exhibits unusual sigmoidal feedback kinetics that differ dramatically from the simple first-order kinetics for the same reaction in solution. An induction period is followed by a rapid increase in reaction rate before the rate decreases again as the reaction goes to completion. The origin of these unusual kinetics is found to be a feedback cycle involving both chemical and mechanical factors. During the reaction the physical form of the reaction mixture changes from a powder to a cohesive rubber-like state, and this results in the observed reaction rate increase. The study reveals that non-obvious and dynamic rheological changes in the reaction mixture must be appreciated to understand how mechanochemical reactions progress.

Surface-Mediated DNA Hybridization: Effects of DNA Conformation, Surface Chemistry, and Electrostatics.

Single-molecule Förster Resonance Energy Transfer (FRET) was used to study the dynamic association of mobile donor-labeled ssDNA oligonucleotides ("target") with covalently immobilized complementary acceptor-labeled ssDNA oligonucleotides ("probe"). While probe-target association events were resolved for all experiments, such FRET events were far more likely to occur in systems with complementarity and on hydrophobic, as compared to hydrophilic, surfaces. The distribution of donor-acceptor association-time intervals did not exhibit simple first-order kinetics, and when decomposed into a superposition of first-order processes, only a small fraction of events corresponded to a long-lived state that was presumed to represent true DNA hybridization, while the majority of association events were transient, representing nonspecific associations or partial hybridization. The structure of the DNA target and probe affected both the stability of the hybridized state, as well as the likelihood that an association between the two led to hybridization. In particular, the likelihood of hybridization decreased for longer target strands and for targets with stem-loop secondary structure. The presence of oligonucleotide secondary structure reduced the stability of hybridization, while greater complementarity increased stability of the hybridized state. Interestingly, increased ionic strength (i.e., greater electrostatic screening) increased the probability of hybridization but did not influence the lifetime of the hybridized state. Combined, these observations provide a nuanced view of surface-mediated DNA hybridization, where various factors independently influence the probability and stability of hybridization.

Fractal Charge Carrier Kinetics in TiO2

Charge carrier recombination kinetics of TiO2 powder samples were analyzed in the time domain ranging from 50 ns to 1 ms. The transient reflectance signals of the charge carriers observed by laser flash photolysis spectroscopy do not fit to simple second order kinetics as expected for the recombination of trapped electrons and holes. The deviation from second order reaction dynamics could rather be explained by the segregation of charge carriers and the fractal dimension of the semiconductor agglomerates. According to the fractal reaction kinetics, the time dependent rate coefficient kf (kf = k2,ft–h) has been employed instead of the second order rate constant k2, where the fractal parameter h describes the dimension of the system. This model could successfully be used to describe charge carrier signals in all observed time domains. Moreover, the model was compared with the concept developed by Shuttle et al., which proposes that the charge carrier signals decay following a power-law. The benefits of the ...

Nonexponential Kinetics of Loop Formation in Proteins and Peptides: A Signature of Rugged Free Energy Landscapes?

The kinetics of loop formation, i.e., the occurrence of contact between two atoms of a polypeptide, remains the focus of continuing interest. One of the reasons is that contact formation is the elementary event underlying processes such as folding and binding. More importantly, it is experimentally measurable and can be predicted theoretically for ideal polymers. Deviations from single exponential kinetics have sometimes been interpreted as a signature of rugged, protein-like, free energy landscapes. Here we present simulations, with different atomistic models, of short peptides with varied structural propensity, and of a structured protein. Results show exponential contact formation kinetics (or relaxation) at long times, and a power law relaxation at very short times. At intermediate times, a deviation from either power law or simple exponential kinetics is observed that appears to be characteristic of polypeptides with either specific or nonspecific attractive interactions but disappears if attractive interactions are absent. Our results agree with recent experimental measurements on peptides and proteins and offer a comprehensive interpretation for them.

Oxidation of the drug tiopronin by Cerium(IV) in perchloric acid media: Kinetic and mechanistic analyses

Although several analytical methods based on the Ce(IV) oxidations were developed for determinations of the drug tiopronin (MPG) and some biothiols, the kinetic and mechanistic aspects of oxidations of the thiol-containing molecules by Ce(IV) were poorly deciphered if not all. The oxidation of MPG by Ce(IV) has thus been characterized kinetically in perchloric acid media in this work. The oxidation reaction follows overall second-order kinetics: -d[Ce(IV)]tot/dt=k′[MPG]tot[Ce(IV)]tot, where k′ stands for the observed second-order rate constant and [Ce(IV)]tot and [MPG]tot pertain to the total concentrations of Ce(IV) and MPG, respectively. The relation between k′ and [H+] has been established in the region of 0.030M≤[H+]≤2.00M. Several additional reaction features are revealed by the rapid scan spectra, product identification and stoichiometric study. All these features are rationalized by a proposed reaction mechanism which involves Ce4+, Ce(OH)3+, and Ce(OH)22+ attacking on the sulfur atom of MPG in parallel and forming the rate-determining steps. These steps are followed by up to seven fast reactions. Rate constants of the rate-determining steps have been derived showing a reactivity trend: Ce4+>Ce(OH)3+>Ce(OH)22+. This trend, being observed for the first time in this work, suggests an outer-sphere electron transfer taking place in the rate-determining steps, which is strongly bolstered by the dependence of the Ce(IV)/Ce(III) redox potential on [H+] measured previously. Our kinetic and mechanistic analyses indicate that a rather complex reaction mechanism is operating behind the simple second-order kinetics.

Direct Observation of Insulin Association Dynamics with Time-Resolved X-ray Scattering.

Biological functions frequently require protein-protein interactions that involve secondary and tertiary structural perturbation. Here we study protein-protein dissociation and reassociation dynamics in insulin, a model system for protein oligomerization. Insulin dimer dissociation into monomers was induced by a nanosecond temperature-jump (T-jump) of ∼8 °C in aqueous solution, and the resulting protein and solvent dynamics were tracked by time-resolved X-ray solution scattering (TRXSS) on time scales of 10 ns to 100 ms. The protein scattering signals revealed the formation of five distinguishable transient species during the association process that deviate from simple two-state kinetics. Our results show that the combination of T-jump pump coupled to TRXSS probe allows for direct tracking of structural dynamics in nonphotoactive proteins.

Non-intrusive Assessment of Photosystem II and Photosystem I in Whole Coral Tissues

Reef building corals (phylum Cnidaria) harbour endosymbiotic dinoflagellate algae (genus Symbiodinium) that generate photosynthetic products to fuel their host’s metabolism. Non-invasive techniques such as chlorophyll (Chl) fluorescence analyses of Photosystem II (PSII) have been widely used to estimate the photosynthetic performance of Symbiodinium in hospite. However, since the spatial origin of PSII chlorophyll fluorescence in coral tissues is uncertain, such signals give limited information on depth-integrated photosynthetic performance of the whole tissue. In contrast, detection of absorbance changes in the near infrared (NIR) region integrates signals from deeper tissue layers due to weak absorption and multiple scattering of NIR light. While extensively utilised in higher plants, NIR bio-optical techniques are seldom applied to corals. We have developed a non-intrusive measurement method to examine photochemistry of intact corals, based on redox kinetics of the primary electron donor in Photosystem I (P700) and chlorophyll fluorescence kinetics (Fast-Repetition Rate fluorometry, FRRf). Since the redox state of P700 depends on the operation of both PSI and PSII, important information can be obtained on the PSII-PSI intersystem electron transfer kinetics. Under moderate, sub-lethal heat stress treatments (33 ˚C for ~20 min), the coral Pavona decussata exhibited down-regulation of PSII electron transfer kinetics, indicated by slower rates of electron transport from QA to plastoquinone (PQ) pool, and smaller relative size of oxidised PQ with concomitant decrease of a specifically-defined P700 kinetics area, which represents the active pool of PSII. The maximum quantum efficiency of PSII (Fv/Fm) and functional absorption cross-section of PSII (σPSII) remained unchanged. Based on the coordinated response of P700 parameters and PSII-PSI electron transport properties, we propose that simple P700 kinetics parameters as employed here serve as indicators of the integrity of PSII-PSI electron transfer dynamics in corals.

Characteristics of oxygenated PAHs in PM10 at Seoul, Korea

Seven particulate oxygenated-polycyclic aromatic hydrocarbons (oxy-PAHs) were analyzed in atmospheric particulate matter with an aerodynamic diameter of less than or equal to a nominal 10 μm (PM10) for the period between September 2006 and August 2007 in Seoul, South Korea. The major contributors of oxy-PAHs production were identified based on statistical analyses such as correlation coefficient relationship, principal component analysis (PCA), and simple reaction kinetics calculation. The results show that (1) the average concentrations of seven oxy-PAHs were 7.63 ± 4.32 ng/m3, with distinctive seasonal variations, being higher in winter (8.70 ± 3.90 ng/m3) and lower in summer (1.47 ± 0.73 ng/m3), similar to PAHs; (2) there were mixed contributions of primary emissions (e.g., vehicular emissions, biomass burning, long-range transport) and atmospheric reactions to oxy-PAH production; and (3) primary emissions might affect more than atmospheric reactions to the oxy-PAHs levels.

Oxidation in vitro of chromium(III) dietary supplements mer-[Cr(pic)3] and trans(S,S)-[Cr(Cys)2]\u2212 by hydrogen peroxide

Biological tests performed using 3T3 fibroblasts indicated low cytotoxicities for the complexes mer-[Cr(pic)3] and trans(S,S)-[Cr(Cys)2]−, where pic = picolinate anion and Cys = cysteine. Oxidation of these complexes by hydrogen peroxide was studied in NaOH and NaHCO3 media. Electronic (UV–Vis) and EPR spectroscopies were used to monitor the reaction course. Hydrogen peroxide oxidizes chromium(III) to both [CrV(O2)4]3− and CrVIO42− anions in alkaline media and practically completely to CrO42− anion in bicarbonate solution. The reactions follow consecutive biphasic or simple first-order kinetics. The first-order decay of [CrV(O2)4]3− anion at pH ≈ 8 was followed by EPR spectroscopy. Based on the obtained kinetic and spectroscopic data, mechanisms for the redox transformations of these chromium(III) complexes are proposed.

Point Kinetics Framework for Characterizing Prompt Neutron and Photon Signatures From Tagged Neutron Interrogation

The goal of this paper is to build a simple point kinetics model to predict the neutron and photon multiplicities induced by an associated particle imaging deuterium-tritium neutron generator interrogating uranium metal. A point kinetics framework is used to model the relationship between multiplication and radiation released from a 14.1-MeV neutron-induced fission chain in subcritical uranium. The goal of developing this point kinetics model is to tie the number of neutrons and photons released from a configuration to the multiplication of that configuration. The discussion is limited to building a model that describes the photon and neutron multiplicities released from a uranium inspection object, not considering the detection process. The addition of polyethylene shielding is also investigated. The point kinetics predictions are compared with the results from an MCNP-PoliMi simulation throughout as a way of measuring how closely the simple point kinetics model describes the complex propagation and transport of fission chain radiation in fissile material. The results show that the point kinetics does an excellent job of predicting the multiplicities released from the inspection objects, but at the cost of multiple additional inputs, some of which rely on the knowledge of geometric information from imaging.

Deciphering the Biochemical Pathway and Pharmacokinetic Study of Amyloid βeta-42 with Superparamagnetic Iron Oxide Nanoparticles (SPIONs) Using Systems Biology Approach.

Alzheimer's disease (AD) pathogenesis leads to the appearance of senile plaques due to the production and deposition of the β-amyloid peptide (Aβ). Superparamagnetic iron oxide nanoparticles (SPIONs) have potential role in the detection and imaging of Aβ plaques in AD. SPIONs have shown appropriate potential in the diagnosis and treatment of AD. In the present study, the pharmacokinetics of SPIONs and its effect in the biochemical pathway of AD were analyzed using collected information. During analysis, the interaction of SPIONs with amyloid beta-42 (Aβ42), a biomarker for AD progression, has been shown. Nodes represent the entities and edges represent the relation (interactions) of one node to another node. Aβ42 and their interaction with other entities making up biochemical network are involved in AD mechanism in presence of SPION. The kinetic simulation was done to investigate pharmacokinetics of SPIONs for AD, where concentration was assigned of nanoparticles and other entities were applied as a kinetic irreversible simple Michaelis-Menten or mass action kinetics. Simulation was done in presence and absence of SPIONs to investigate pharmacokinetic effect in AD and explore the mechanism of Aβ42 in presence of SPIONs. This study may lead to better understanding, which is required to target the metabolism of Aß42 peptide, a pivotal player in this pathology.