Stochastic chemical kinetics and the quasi-steady-state assumption : application to the stochastic simulation algorithm and chemical master equation

Recently the application of the quasi-steady-state approximation (QSSA) to the stochastic simulation algorithm (SSA) was suggested for the purpose of speeding up stochastic simulations of chemical systems that involve both relatively fast and slow chemical reactions [Rao and Arkin, J. Chem. Phys. 118, 4999 (2003)] and further work has led to the nested and slow-scale SSA. Improved numerical efficiency is obtained by respecting the vastly different time scales characterizing the system and then by advancing only the slow reactions exactly, based on a suitable approximation to the fast reactions. We considerably extend these works by applying the QSSA to numerical methods for the direct solution of the chemical master equation (CME) and, in particular, to the finite state projection algorithm [Munsky and Khammash, J. Chem. Phys. 124, 044104 (2006)], in conjunction with Krylov methods. In addition, we point out some important connections to the literature on the (deterministic) total QSSA (tQSSA) and place the stochastic analogue of the QSSA within the more general framework of aggregation of Markov processes. We demonstrate the new methods on four examples: Michaelis–Menten enzyme kinetics, double phosphorylation, the Goldbeter–Koshland switch, and the mitogen activated protein kinase cascade. Overall, we report dramatic improvements by applying the tQSSA to the CME solver.

A quasi stationary approach to drying kinetics of cylindrical food particulates in a heat pump asisted fluid bed dryer

Experiments were undertaken to study drying kinetics of moist cylindrical shaped food particulates during fluidised bed drying. Cylindrical particles were prepared from Green beans with three different length:diameter ratios, 3:1, 2:1 and 1:1. A batch fluidised bed dryer connected to a heat pump system was used for the experimentation. A Heat pump and fluid bed combination was used to increase overall energy efficiency and achieve higher drying rates. Drying kinetics, were evaluated with non-dimensional moisture at three different drying temperatures of 30, 40 and 50o C. Numerous mathematical models can be used to calculate drying kinetics ranging from analytical models with simplified assumptions to empirical models built by regression using experimental data. Empirical models are commonly used for various food materials due to their simpler approach. However problems in accuracy, limits the applications of empirical models. Some limitations of empirical models could be reduced by using semi-empirical models based on heat and mass transfer of the drying operation. One such method is the quasi-stationary approach. In this study, a modified quasi-stationary approach was used to model drying kinetics of the cylindrical food particles at three drying temperatures.

Prediction of fluidization behaviour and a quasi-stationary approach to drying kinetics of irregular particulate food materials

Changes in fluidization behaviour behaviour was characterised for parallelepiped particles with three aspect ratios, 1:1, 2:1 and 3:1 and spherical particles. All drying experiments were conducted at 500C and 15 % RH using a heat pump dehumidifier system. Fluidization experiments were undertaken for the bed heights of 100, 80, 60 and 40 mm and at 10 moisture content levels. Due to irregularities in shape minimum fluidisation velocity of parallelepiped particulates (potato) could not fitted to any empirical model. Also a generalized equation was used to predict minimum fluidization velocity. The modified quasi-stationary method (MQSM) has been proposed to describe drying kinetics of parallelepiped particulates at 30o C, 40o C and 50o C that dry mostly in the falling rate period in a batch type fluid bed dryer.

Effects of inoculating dose on the kinetics of Chlamydia muridarum genital infection in female mice

Chlamydia trachomatis infections have been implicated in problems such as pelvic inflammatory disease and infertility in females. Although there are some studies examining the kinetics of ascending infection, there is limited information on the kinetics of pathology development and cellular infiltrate into the reproductive tissues in relation to the effects of inoculating dose, and a better understanding of these is needed. The murine model of female genital tract Chlamydia muridarum infection is frequently used as a model of human C. trachomatis reproductive tract infection. To investigate the kinetics of ascending genital infection and associated pathology development, female BALB/c mice were intravaginally infected with C. muridarum at doses ranging from 5102 to 2.6106 inclusion forming units. We found that the inoculating dose affects the course of infection and the ascension of bacteria, with the highest dose ascending rapidly to the oviducts. By comparison, the lowest dose resulted in the greatest bacterial load in the lower reproductive tract. Interestingly, we found that the dose did not significantly affect inflammatory cell infiltrate in the various regions. Overall, this data show the effects of infectious dose on the kinetics of ascending chlamydial infection and associated inflammatory infiltration in BALB/c mice.

Effect of inaccuracies in anthropometric data and linked-segment inverse dynamic modeling on kinetics of gait in persons with partial foot amputation

The accuracy of data derived from linked-segment models depends on how well the system has been represented. Previous investigations describing the gait of persons with partial foot amputation did not account for the unique anthropometry of the residuum or the inclusion of a prosthesis and footwear in the model and, as such, are likely to have underestimated the magnitude of the peak joint moments and powers. This investigation determined the effect of inaccuracies in the anthropometric input data on the kinetics of gait. Toward this end, a geometric model was developed and validated to estimate body segment parameters of various intact and partial feet. These data were then incorporated into customized linked-segment models, and the kinetic data were compared with that obtained from conventional models. Results indicate that accurate modeling increased the magnitude of the peak hip and knee joint moments and powers during terminal swing. Conventional inverse dynamic models are sufficiently accurate for research questions relating to stance phase. More accurate models that account for the anthropometry of the residuum, prosthesis, and footwear better reflect the work of the hip extensors and knee flexors to decelerate the limb during terminal swing phase.

Ticagrelor, a platelet aggregation inhibitor for the potential prevention and treatment of arterial thrombosis and acute coronary syndromes

Ticagrelor is an orally active ADP P2Y12 receptor antagonist in development by AstraZeneca plc for the reduction of recurrent ischemic events in patients with acute coronary syndromes (ACS). Prior to the development of ticagrelor, thienopyridine compounds, such as clopidogrel, were the focus of research into therapies for ACS. Although the thienopyridines are effective platelet aggregation inhibitors, they are prodrugs and, consequently, exert a slow onset of action. In addition, the variability in inter-individual metabolism of thienopyridine prodrugs has been associated with reduced efficacy in some patients. Ticagrelor is not a prodrug and exhibits a more rapid onset of action than the thienopyridine prodrugs. In clinical trials conducted to date, ticagrelor was a potent inhibitor of ADP-induced platelet aggregation and demonstrated effects that were comparable to clopidogrel. In a phase II, short-term trial, the bleeding profile of participants treated with ticagrelor was similar to that obtained with clopidogrel; however, an increased incidence of dyspnea was observed - an effect that has not been reported with the thienopyridines. Considering the occurrence of dyspnea, and the apparent non-superiority of ticagrelor to clopidogrel, it is difficult to justify a clear benefit to the continued development of ticagrelor. Outcomes from an ongoing phase III trial comparing ticagrelor with clopidogrel in 18,000 patients with ACS are likely to impact on the future development of ticagrelor.

Effects of pediatric obesity on joint kinematics and kinetics during 2 walking cadences

Objective: To determine whether differences existed in lower-extremity joint biomechanics during self-selected walking cadence (SW) and fast walking cadence (FW) in overweight- and normal-weight children.---------- Design: Survey.---------- Setting: Institutional gait study center.---------- Participants: Participants (N=20; mean age ± SD, 10.4±1.6y) from referred and volunteer samples were classified based on body mass index percentiles and stratified by age and sex. Exclusion criteria were a history of diabetes, neuromuscular disorder, or recent lower-extremity injury.---------- Main Outcome Measures: Sagittal, frontal, and transverse plane angular displacements (degrees) and peak moments (newton meters) at the hip, knee, and ankle joints.---------- Results: The level of significance was set at P less than .008. Compared with normal-weight children, overweight children had greater absolute peak joint moments at the hip (flexor, extensor, abductor, external rotator), the knee (flexor, extensor, abductor, adductor, internal rotator), and the ankle (plantarflexor, inverter, external/internal rotators). After including body weight as a covariate, overweight children had greater peak ankle dorsiflexor moments than normal-weight children. No kinematic differences existed between groups. Greater peak hip extensor moments and less peak ankle inverter moments occurred during FW than SW. There was greater angular displacement during hip flexion as well as less angular displacement at the hip (extension, abduction), knee (flexion, extension), and ankle (plantarflexion, inversion) during FW than SW.---------- Conclusions: Overweight children experienced increased joint moments, which can have long-term orthopedic implications and suggest a need for more nonweight-bearing activities within exercise prescription. The percent of increase in joint moments from SW to FW was not different for overweight and normal-weight children. These findings can be used in developing an exercise prescription that must involve weight-bearing activity.

Metadata aggregation : a critical component of research infrastructure for the future

The development of research data management infrastructure and services and making research data more discoverable and accessible to the research community is a key priority at the national, state and individual university level. This paper will discuss and reflect upon a collaborative project between Griffith University and the Queensland University of Technology to commission a Metadata Hub or Metadata Aggregation service based upon open source software components. It will describe the role that metadata aggregation services play in modern research infrastructure and argue that this role is a critical one.

A quasi-stationary approach to drying kinetics of different shaped food particulates in a heat pump assisted by fluid bed dryer

Experiments were undertaken to study drying kinetics of different shaped moist food particulates during heat pump assisted fluidised bed drying. Three particular geometrical shapes of parallelepiped, cylindrical and spheres were selected from potatoes (aspect ratio = 1:1, 2:1, 3:1), cut beans (length: diameter = 1:1, 2:1, 3:1) and peas respectively. A batch fluidised bed dryer connected to a heat pump system was used for the experimentation. A Heat pump and fluid bed combination was used to increase overall energy efficiency and achieve higher drying rates. Drying kinetics, were evaluated with non-dimensional moisture at three different drying temperatures of 30, 40 and 50o C. Due to complex hydrodynamics of the fluidised beds, drying kinetics are dryer or material specific. Numerous mathematical models can be used to calculate drying kinetics ranging from analytical models with simplified assumptions to empirical models built by regression using experimental data. Empirical models are commonly used for various food materials due to their simpler approach. However problems in accuracy, limits the applications of empirical models. Some limitations of empirical models could be reduced by using semi-empirical models based on heat and mass transfer of the drying operation. One such method is the quasi-stationary approach. In this study, a modified quasi-stationary approach was used to model drying kinetics of the cylindrical food particles at three drying temperatures.

Lateral shearing interferometry for analysis of tear film surface kinetics

Purpose: To date, there have been no measuring techniques available that could clearly identify all phases of tear film surface kinetics in one interblink interval. ----- ----- Methods: Using a series of cases, we show that lateral shearing interferometry equipped with a set of robust parameter estimation techniques is able to characterize up to five different phases of tear film surface kinetics that include: (i) initial fast tear film build-up phase, (ii) further slower tear film build-up phase, (iii) tear film stability, (iv) tear film thinning, and (v), after a detected break-up, subsequent tear film deterioration. ----- ----- Results: Several representative examples are given for estimating tear film surface kinetics in measurements in which the subjects were asked to blink and keep their eyes open as long as they could. ----- ----- Conclusions: Lateral shearing interferometry is a noninvasive technique that provides means for temporal characterization of tear film surface kinetics and the opportunity for the analysis of the two-step tear film build-up process.

Electron diffusion and back reaction in dye-sensitized solar cells : the effect of nonlinear recombination kinetics

The electron collection efficiency in dye-sensitized solar cells (DSCs) is usually related to the electron diffusion length, L = (Dτ)^1/2, where D is the diffusion coefficient of mobile electrons and τ is their lifetime, which is determined by electron transfer to the redox electrolyte. Analysis of incident photon-to-current efficiency (IPCE) spectra for front and rear illumination consistently gives smaller values of L than those derived from small amplitude methods. We show that the IPCE analysis is incorrect if recombination is not first-order in free electron concentration, and we demonstrate that the intensity dependence of the apparent L derived by first-order analysis of IPCE measurements and the voltage dependence of L derived from perturbation experiments can be fitted using the same reaction order, γ ≈ 0.8. The new analysis presented in this letter resolves the controversy over why L values derived from small amplitude methods are larger than those obtained from IPCE data.