Realistic Kinetic Model Research Articles

Carrier recombination of organic-inorganic 3D halide perovskite single crystals

Organic-inorganic 3D halide perovskite materials recently have become one of the major players of hybrid semiconductors for photovoltaic and optoelectronic applications. The diffusion length of charge carriers is one of the critical parameters for justifying photovoltaic applications of materials. In this work, we propose a realistic kinetic model in order to fully understand carrier relaxation rate of photoexcited organic perovskites with a negligible exciton formation in photoluminescence lifetime measurements. We find that the extraction of carrier relaxation rate has to be made from multiple fluence-dependent photoluminescence lifetime measurements with global fittings, instead of a traditional single-fluence lifetime measurement. To demonstrate the validity of the model, two kinds of p-doped CH3NH3PbI3 single crystals were grown up by intentionally increasing defects. Global fittings of the kinetic model to the two kinds of single crystals yield doping density, trap density, and recombination constants. Our methodology provides a self-contained approach to determine diffusion lengths of organic 3D halide perovskite materials.

Battery-aware scheduling in low orbit: the GomX–3 case

Abstract When working with space systems the keyword is resources. For a satellite in orbit all resources are scarce and the most critical resource of all is power. It is therefore crucial to have detailed knowledge on how much power is available for an energy harvesting satellite in orbit at every time—especially when in eclipse, where it draws its power from onboard batteries. The challenge is to maximise operational performance of a satellite, while providing hard guarantees that critically low battery levels are avoided, taking into account these power restrictions. Classic approaches to workload scheduling and analysis are not suitable, because of heterogeneity, interdependencies and system dynamics involved. This paper addresses this problem by a two-step procedure to perform task scheduling for low-earth-orbit satellites exploiting formal methods. It combines time-bounded cost-optimal reachability analyses of priced timed automata networks with a realistic kinetic battery model capable of capturing capacity limits as well as stochastic fluctuations. We also discuss how the time-bounded analysis can be embedded into a workflow that exploits in-orbit current and voltage measurements so as to perpetuate the task scheduling. The core procedure has been exercised in-orbit for the automatic and resource-optimal day-ahead scheduling of G om X–3, a power-hungry 3-unit nanosatellite. We explain how this approach has overcome existing problems, has led to improved designs, and has provided new insights.

Mastering operational limitations of LEO satellites – The GomX-3 approach

When working with space systems the keyword is resources. For a satellite in orbit all resources are sparse and the most critical resource of all is power. It is therefore crucial to have detailed knowledge on how much power is available for an energy harvesting satellite in orbit at every time – especially when in eclipse, where it draws its power from onboard batteries. This paper addresses this problem by a two-step procedure to perform task scheduling for low-earth-orbit (LEO) satellites exploiting formal methods. It combines cost-optimal reachability analyses of priced timed automata networks with a realistic kinetic battery model capable of capturing capacity limits as well as stochastic fluctuations. The procedure is in use for the automatic and resource-optimal day-ahead scheduling of GomX-3, a power-hungry nanosatellite currently orbiting the earth. We explain how this approach has overcome existing problems, has led to improved designs, and has provided new insights.

LibRCGA: a C library for real-coded genetic algorithms for rapid parameter estimation of kinetic models

Kinetic modeling is a powerful tool to understand how a biochemical system behaves as a whole. To develop a realistic and predictive model, kinetic parameters need to be estimated so that a model fits experimental data. However, parameter estimation remains a major bottleneck in kinetic modeling. To accelerate parameter estimation, we developed a C library for real-coded genetic algorithms (libRCGA). In libRCGA, two real-coded genetic algorithms (RCGAs), viz. the Unimodal Normal Distribution Crossover with Minimal Generation Gap (UNDX/MGG) and the Real-coded Ensemble Crossover star with Just Generation Gap (REX star/JGG), are implemented in C language and paralleled by Message Passing Interface (MPI). We designed libRCGA to take advantage of high-performance computing environments and thus to significantly accelerate parameter estimation. Constrained optimization formulation is useful to construct a realistic kinetic model that satisfies several biological constraints. libRCGA employs stochastic ranking to efficiently solve constrained optimization problems. In the present paper, we demonstrate the performance of libRCGA through benchmark problems and in realistic parameter estimation problems. libRCGA is freely available for academic usage at http://kurata21.bio.kyutech.ac.jp/maeda/index.html.

Extending Reaction Mechanism Generator to Silicon Hydride Chemistry

Understanding the gas-phase chemistry of silicon hydrides is the first step to building a realistic kinetic model for chemical vapor deposition (CVD). Functionality for thermodynamic and kinetic data estimation of silicon hydrides was added to the open-source software Reaction Mechanism Generator (RMG). Using the updated RMG, a detailed kinetic model was built for SiH4 thermal decomposition. The generated model was used to perform reactor simulations at various process conditions for comparison to prior SiH4 decomposition experiments in a flow tube. Results show that the RMG-generated model can reasonably replicate experimental results for SiH4 concentration profiles at different temperatures and residence times. While the effect of changing initial SiH4 concentration is not captured, a first pass sensitivity analysis reveals that reasonable errors in reaction rates could contribute to the discrepancy.

Quantitative analysis of vesicle recycling at the calyx of Held synapse

Vesicle recycling is pivotal for maintaining reliable synaptic signaling, but its basic properties remain poorly understood. Here, we developed an approach to quantitatively analyze the kinetics of vesicle recycling with exquisite signal and temporal resolution at the calyx of Held synapse. The combination of this electrophysiological approach with electron microscopy revealed that ∼80% of vesicles (∼270,000 out of ∼330,000) in the nerve terminal are involved in recycling. Under sustained stimulation, recycled vesicles start to be reused in tens of seconds when ∼47% of the preserved vesicles in the recycling pool (RP) are depleted. The heterogeneity of vesicle recycling as well as two kinetic components of RP depletion revealed the existence of a replenishable pool of vesicles before the priming stage and led to a realistic kinetic model that assesses the size of the subpools of the RP. Thus, our study quantified the kinetics of vesicle recycling and kinetically dissected the whole vesicle pool in the calyceal terminal into the readily releasable pool (∼0.6%), the readily priming pool (∼46%), the premature pool (∼33%), and the resting pool (∼20%).

Synaptic GABA release prevents GABA transporter type-1 reversal during excessive network activity.

GABA transporters control extracellular GABA, which regulates the key aspects of neuronal and network behaviour. A prevailing view is that modest neuronal depolarization results in GABA transporter type-1 (GAT-1) reversal causing non-vesicular GABA release into the extracellular space during intense network activity. This has important implications for GABA uptake-targeting therapies. Here we combined a realistic kinetic model of GAT-1 with experimental measurements of tonic GABAA receptor currents in ex vivo hippocampal slices to examine GAT-1 operation under varying network conditions. Our simulations predict that synaptic GABA release during network activity robustly prevents GAT-1 reversal. We test this in the 0 Mg2+ model of epileptiform discharges using slices from healthy and chronically epileptic rats and find that epileptiform activity is associated with increased synaptic GABA release and is not accompanied by GAT-1 reversal. We conclude that sustained efflux of GABA through GAT-1 is unlikely to occur during physiological or pathological network activity.

Sorption selectivity and original kinetic analysis of an heterogeneous fatty acrylate esterification on a poly(styrene-divinylbenzene) sulfonated resin

The heterogeneous catalysis for esterification generally uses a poly(styrene-divinylbenzene) sulfonated resin. It presents a selective affinity with the chemical species involved in the reaction, and a coupled phenomenon of swelling. The components partitioning rests on still not precisely known interactions between the chemical species and the intern structure of catalyst. Although the chemical reaction is supposed to be located in the resin structure, most of the proposed kinetic models do not involve the sorbed components. Due to reaction processes, the sorption and kinetic phenomena cannot be independently studied. First part of the methodology is the analysis of selective sorption in absence of reaction at room temperature. The swelling phenomenon study at reaction temperature then allows the simultaneous determination of kinetic and sorption coupled parameters. It permits to design a more realistic kinetic model of the heterogeneous esterification reaction, to estimate the parameters and to validate them on experimental data obtained with esterification reactions in a batch reactor.

An introduction to tile-based self-assembly and a survey of recent results

We first give an introduction to the field of tile-based self-assembly, focusing primarily on theoretical models and their algorithmic nature. We start with a description of Winfree’s abstract Tile Assembly Model (aTAM) and survey a series of results in that model, discussing topics such as the shapes which can be built and the computations which can be performed, among many others. Next, we introduce the more experimentally realistic kinetic Tile Assembly Model (kTAM) and provide an overview of kTAM results, focusing especially on the kTAM’s ability to model errors and several results targeted at preventing and correcting errors. We then describe the 2-Handed Assembly Model (2HAM), which allows entire assemblies to combine with each other in pairs (as opposed to the restriction of single-tile addition in the aTAM and kTAM) and doesn’t require a specified seed. We give overviews of a series of 2HAM results, which tend to make use of geometric techniques not applicable in the aTAM. Finally, we discuss and define a wide array of more recently developed models and discuss their various tradeoffs in comparison to the previous models and to each other.

Interpretation and applicability of empirical tissue enhancement metrics in dynamic contrast-enhanced MRI based on a multiple pathway model

Computer simulations based on a physiologically realistic tracer kinetic model with multiple pathways was used to provide insights on the applicability and interpretation of tissue enhancement metrics such as the maximum slope, peak enhancement and area under curve, commonly used in dynamic contrast-enhanced (DCE) MRI. Results show that physiological conditions of the tissue that could affect the accuracy of the maximal slope method include a high blood flow, increased variability of flow within the vasculature or a low vascular volume. Interestingly, changes in permeability and interstitial volume might not affect the accuracy of the maximal slope method. Time-to-peak and peak value of the tissue enhancement curve are not strictly properties of the tissue alone, and they cannot be linearly related to intrinsic tissue parameters such as blood flow, blood volume, capillary permeability, interstitial volume and mean transit time. Similar to the normalized initial area under tissue concentration curve, an alternative estimate of the total tracer distribution volume can be simply given by the ratio of tracer concentration in the tissue and artery sampled at the final DCE scan.

Chemical morphogenesis: recent experimental advances in reaction-diffusion system design and control.

In his seminal 1952 paper, Alan Turing predicted that diffusion could spontaneously drive an initially uniform solution of reacting chemicals to develop stable spatially periodic concentration patterns. It took nearly 40 years before the first two unquestionable experimental demonstrations of such reaction-diffusion patterns could be made in isothermal single phase reaction systems. The number of these examples stagnated for nearly 20 years. We recently proposed a design method that made their number increase to six in less than 3 years. In this report, we formally justify our original semi-empirical method and support the approach with numerical simulations based on a simple but realistic kinetic model. To retain a number of basic properties of real spatial reactors but keep calculations to a minimal complexity, we introduce a new way to collapse the confined spatial direction of these reactors. Contrary to similar reduced descriptions, we take into account the effect of the geometric size in the confinement direction and the influence of the differences in the diffusion coefficient on exchange rates of species with their feed environment. We experimentally support the method by the observation of stationary patterns in red-ox reactions not based on oxihalogen chemistry. Emphasis is also brought on how one of these new systems can process different initial conditions and memorize them in the form of localized patterns of different geometries.

Motor Properties of Molecular Spiders

Molecular spiders are synthetic molecular motors featuring multiple legs such that each leg can interact with a substrate through binding and cleavage. Experimental studies of molecular spiders suggest that the motion of the spider on both a substrate matrix [R. Pei et al., J. Amer. Chem. Soc.128, 12693 (2006)] and a two dimensional substrate track [K. Lund et al, Nature 465, 206 (2010)] is biased towards uncleaved substrates. We first investigated the origin of the spider's biased motion by using Monte Carlo simulations of bipedal spiders on a 1D track based on a realistic chemical kinetic model [L.

Biased motion and molecular motor properties of bipedal spiders

Molecular spiders are synthetic molecular motors featuring multiple legs that each can interact with a substrate through binding and cleavage. Experimental studies suggest the motion of the spider in a matrix is biased toward uncleaved substrates and that spider properties such as processivity can be altered by changing the binding strength of the legs to substrate [R. Pei, S. K. Taylor, D. Stefanovic, S. Rudchenko, T. E. Mitchell, and M. N. Stojanovic, J. Am. Chem. Soc. 128, 12693 (2006)]. We investigate the origin of biased motion and molecular motor properties of bipedal spiders using Monte Carlo simulations. Our simulations combine a realistic chemical kinetic model, hand-over-hand or inchworm modes of stepping, and the use of a one-dimensional track. We find that stronger binding to substrate, cleavage and spider detachment from the track are contributing mechanisms to population bias. We investigate the contributions of stepping mechanism to speed, randomness parameter, processivity, coupling, and efficiency, and comment on how these molecular motor properties can be altered by changing experimentally tunable kinetic parameters.

Biased Motion and Molecular Motor Properties of Molecular Spiders

Molecular spiders are synthetic molecular motors featuring multiple legs that each can interact with a substrate through binding and cleavage. Experimental studies suggest the motion of the spider in a matrix is biased towards uncleaved substrates, and that spider properties such as processivity can be altered by changing the binding strength of the legs to substrate [R. Pei et al., J. Amer. Chem. Soc.128, 12693 (2006)]. We investigate the origin of biased motion and molecular motor properties of bipedal spiders using Monte Carlo simulations. Our simulations combine a realistic chemical kinetic model, hand-over-hand (HOH) or inchworm (IW) modes of stepping, and the use of a 1D track. We find that substrate cleavage and spider detachment from the track are both contributing mechanisms to population bias but are not necessary for biased motion on an asymmetric track. We investigate the contributions of stepping mechanism to speed, randomness parameter, processivity, coupling and efficiency, and comment on how these molecular motor properties can be altered by changing experimentally tunable kinetic parameters. We then consider the more general case where steps can occur by any mechanism, subject to steric constraints. We compare these results with the above for bipedal spiders and then simulate quadrupedal spiders to investigate the effect of leg number on motor performance.

Kinetic Model of the H2O2−SCN−−OH−−Cu2+ Oscillator and Its Application to the Interpretation of the Potentiometric Responses of Various Inert Electrodes Monitoring the Reaction Course

The high complexity of the kinetic mechanism of the H(2)O(2)-SCN(-)-OH(-)-Cu(2+) oscillator, involving numerous intermediates, causes the oscillations monitored potentiometrically with gold or glassy carbon electrodes to exhibit opposite phases compared with the oscillations recorded with palladium or platinum electrodes. Following our previous work on the outline explanation of these phenomena, involving the concept of the mixed potential, in this paper, we present their more detailed and advanced study. For that purpose, we built up a simplified but realistic kinetic model of the studied oscillator, involving nine intermediates. Of those nine species, Cu(OH)(3)(-), Cu(OH)(2)(-), and HO(2)(*) were found to be crucial for the explanation of the potentiometric responses of various electrodes, under an additional assumption that the interfacial exchange current density of the HO(2)(*)/HO(2)(-) couple increases in the series GC < Au < Pt. Calculated oscillatory variations of the mixed potential for various model electrodes, compared with experimental results, allowed us to conclude that the potentiometric oscillations are caused largely by the oscillations of the [Cu(OH)(3)(-)]/[Cu(OH)(2)(-)] concentration ratio, irrespective of the electrode material used as a potentiometric sensor. For the Au electrode, the increase of the potential within every oscillatory peak largely reflects the increase in the [Cu(OH)(3)(-)]/[Cu(OH)(2)(-)] ratio. The simultaneous shift of the relatively high Pt electrode potential toward more negative equilibrium potential of the Cu(OH)(3)(-)/Cu(OH)(2)(-) couple is caused by the increase of the exchange current density of the latter couple. Thus, even the opposite phases of the potentiometric oscillations are explainable in terms of the oscillatory behavior of the same redox couple. Understanding of such phenomena is crucial for the proper interpretation of potentiometric data in complex chemical systems.

Adsorption of Phenylacetylene on Si(100)-2 × 1: Kinetics and Structure of the Adlayer

Direct adsorption of phenylacetylene on clean silicon surface Si(100)-2 x 1 is studied in ultrahigh vacuum (UHV). The combination of scanning tunnel microscopy (STM) and surface differential reflectance spectroscopy (SDRS) with Monte Carlo calculations are put together to draw a realistic kinetic model of the evolution of the surface coverage as a function of the molecular exposure. STM images of weakly covered surfaces provide evidence of two very distinct adsorption geometries for phenylacetylene, with slightly different initial sticking probabilities. One configuration is detected with STM as a bright spot that occupies two dangling bonds of a single dimer, whereas the other configuration occupies three dangling bonds of adjacent dimers. These data are used to implement a Monte Carlo model which further serves to design an accurate kinetic model. The resulting evolution toward saturation is compared to the optical data from surface differential reflectance spectroscopy (SDRS). SDRS is an in situ technique that monitors the exact proportion of affected adsorption sites and therefore gives access to the surface coverage which is evaluated at 0.65. We investigate the effect of surface temperature on this adsorption mechanism and show that it has no major effect either on kinetics or on structure, unless it passes the threshold of dissociation measured at ca. 200 degrees C. This offers a comprehensive image of the whole adsorption process of phenylacetylene from initial up to complete saturation.

Insulin disposition in the lung following oral inhalation in humans : a meta-analysis of its pharmacokinetics.

Oral inhalation of insulin potentially offers non-invasive treatment and better glycaemic control in diabetes by virtue of its apparently faster absorption into the systemic circulation compared with subcutaneous injection. Nevertheless, the lung kinetics of inhaled insulin in humans have yet to be fully clarified because of the complexity of insulin-glucose (patho)physiology and the difficulty in approximating the inhaled dose. As a result, there remains considerable debate on the mechanisms of absorption and metabolism of insulin in the lung. To develop and apply a physiologically realistic insulin-glucose kinetic model to a meta-analysis of insulin-glucose profiles from well-controlled clinical studies of inhaled insulin published in the literature, and thereby, to derive the kinetic descriptors of insulin in the lung following inhalation through curve fitting. The model assumed first-order absorption (k(a,L)) and parallel non-absorptive loss (k(mm,L)), the latter primarily occurring via metabolism and mucociliary clearance in the lung, alongside two systemic compartments. Where necessary, glucose-dependent endogenous pancreatic insulin secretion was also taken into account by using blood glucose data as the second independent variable. Despite the model's simplicity and the use of mean data, 16 insulin-glucose profiles from ten clinical studies were successfully fitted to the model, yielding values for the rate constants k(a,L) and k(mm,L). Whole serum insulin profiles were rate-determined by k(a,L) and k(mm,L) combined, representing 'flip-flop' pharmacokinetics. The best estimate for k(a,L) was found to be 0.020-0.032 h(-1), effectively unchanged across doses (0.3-1.8 IU/kg), formulations (powder vs liquid) and subjects (healthy vs diabetic), suggesting passive diffusive absorption of insulin from the lung. In contrast, the values for k(mm,L) were much larger (0.5-1.6 h(-1)) and decreased with increasing inhaled dose. Therefore, it is likely that dose-dependent saturable lung metabolism controls the value of k(mm,L), alongside mucociliary clearance. As a result, the absolute bioavailability ranged from 1.5% to 4.8%. The modelling analysis also enabled derivation of increased values for both k(a,L) and k(mm,L) as a possible cause of faster absorption for deep inspiratory manoeuvres and increased absorption in smokers, and faster and increased absorption for insulin lispro. Although some of these results need to be substantiated experimentally, it appears that this modelling analysis has enabled unification of the literature information associated with the kinetics and mechanisms of insulin disposition in the lung following inhalation in humans.

Kinetics of nanocrystallization in FeCoNbB(Cu) alloys

HITPERM alloys (FeCoMBCu; M=Nb, Zr, Hf...) have been recently developed and proposed as competitive soft magnetic materials for high-temperature applications. To our knowledge, this work contains the first results on nanocrystallization isothermal kinetics for these alloys. Analysis of nanocrystallization of the studied FeCoNbB(Cu) alloys in the frame of the Johnson–Mehl–Avrami theory shows a slowing-down of the kinetics and anomalously low values of the Avrami exponent, in a similar way to that reported for FeSiBNbCu (FINEMET)-type alloys. Compositional effects of Co substitution and Cu addition are considered. A more realistic kinetic model developed by Hermann et al. accounts for the experimental data.

Theoretical and experimental studies of spatial bistability in the chlorine-dioxide–iodide reaction

The phenomenon of spatial bistability has recently been proposed to understand a number of paradoxical results obtained in experiments on nonequilibrium chemical patterns performed in open reactors made of a thin film of gel fed from one side. On the basis of a realistic kinetic model, we predict that the chlorine-dioxide–iodide reaction, taken as a prototypic example of a large class of reactions, should exhibit spatial bistability. The theoretical and numerical results are supported by experiments performed in specially designed reactors. This spatial bistability introduces an additional geometric dimension in the system which is generally overlooked. We elaborate on the role that this additional complexity can play in the observation of patterns associated to fronts in such reactors.

Pulsating wave propagation in reactive flows: flow-distributed oscillations

Stationary waves in a reactive flow with equal transport coefficients were recently generated by passing the oscillating Belousov-Zhabotinsky reaction medium through a tubular packed bed reactor while keeping the concentrations constant at the inflow boundary [M. Kaern and M. Menzinger, Phys. Rev. E 60, 3471 (1999)]. Here we study the effects of oscillatory boundary conditions, and observe traveling wave fronts that propagate in either a pulsating or a steady manner. The present experiment is isothermal and conditions are such that all species have identical transport properties. This excludes rapid thermal or activator diffusion and the wave pulsation appears to be induced by an essentially kinematic mechanism. Our experimental findings are supported by numerical simulations of the full reaction-diffusion-advection system using a realistic kinetic model. Finally, the kinematic essence of the mechanism inducing wave pulsation is captured in an iterative one-variable map.