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-steady performance prediction model for dynamic characteristics of a volute pump

A performance prediction model generally applicable for volute-type centrifugal pumps has been extended to predict the dynamic characteristics of a pump during its normal starting and stopping periods. Experiments have been conducted on a volute pump with different valve openings to study the dynamic behaviour of the pump during normal start-up and stopping, when a small length of discharge pipeline is connected to the discharge flange of the pump. Such experiments have also been conducted when the test pump was part of a hydraulic system, an experimental rig, where it is pumping against three similar pumps, known as supply pumps, connected in series, with the supply pumps kept idle or running. Instantaneous rotational speed, flowrate, and delivery and suction pressures of the pump were recorded and it was observed in all the tested cases that the change of pump behaviour during the transient period was quasi-steady, which validates the quasi-steady approach presented in this paper. The nature of variation of parameters during the transients has been discussed. The model-predicted dynamic head-capacity curves agree well with the experimental data for almost all the tested cases.

Bubble Behavior and Heat Transfer in Quasi-Steady Pool Boiling in Microgravity

Pool boiling of degassed FC-72 on a plane plate heater has been studied experimentally in microgravity. A quasi-steady heating method is adopted, in which the heating voltage is controlled to increase exponentially with time. Compared with terrestrial experiments, bubble behaviors are very different, and have direct effect on heat transfer. Small, primary bubbles attached on the surface seem to be able to suppress the activation of the cavities in the neighborhoods, resulting in a slow increase of the wall temperature with the heat flux. For the high subcooling, the coalesced bubble has a smooth surface and a small size. It is difficult to cover the whole heater surface, resulting in a special region of gradual transitional boiling in which nucleate boiling and local dry area can co-exist. No turning point corresponding to the transition from nucleate boiling to film boiling can be observed. On the contrary, the surface oscillation of the coalesced bubble at low subcooling may cause more activated nucleate sites, and then the surface temperature may keep constant or even fall down with the increasing heat flux. Furthermore, an abrupt transition to film boiling can also be observed. It is shown that heat transfer coefficient and CHF increase with the subcooling or pressure in microgravity, as observed in normal gravity.

Effects of initial soil fabric and mode of shearing on quasi-steady state line for monotonic undrained behavior

The effects of initial soil fabric and mode of shearing on quasi-steady state line in void ratiostress space are studied by employing the Distinct Element Method numerical analysis. The results show that the initial soil fabric and the mode of shearing have a profound effect on the location of the quasi-steady state line. The evolution of the soil fabric during the course of undrained shearing shows that the specimens with different initial soil fabrics reach quasi-steady state at various soil fabric conditions. At quasi-steady state, the soil fabric has a significant adjustment to change its behavior from contractive to dilative. As the stress state approaches the steady state, the soil fabrics of different initial conditions become similar. The numerical analysis results are compared qualitatively with the published experimental data and the effects of specimen reconstitution methods and mode of shearing found in the experimental studies canbe systematically explained by the numerical analysis. © 2009 Taylor & Francis Group.

Quasi steady state and dynamic hygrothermal performance of fibrous Hemp and Stone Wool insulations: Two innovative laboratory based investigations

Moisture and heat management properties of Hemp and Stone Wool insulations were studied by mounting them between a hot and a cold climate chamber. Both insulations were exposed to identical hygrothermal boundary conditions. Quasi steady state and dynamic tests were carried out at a range of relative humidity exposures. The likelihood of interstitial condensation was assessed and equivalent thermal conductivity values of the insulations were determined. The adsorption-desorption isotherms of the insulations were also determined in a dynamic vapour sorption (DVS) instrument. It was observed that the likelihood of condensation was higher in Stone Wool insulation than in Hemp insulation. Hemp insulation performed better in managing moisture due to its high hygric inertia and water absorption capacity. It was observed that the equivalent thermal conductivity of Stone Wool insulation was dependent on enthalpy flow and phase change of moisture. The equivalent thermal conductivity of Hemp insulation was close to its declared thermal conductivity in dynamic conditions when high relative humidity exposures were transient. In quasi steady state boundary conditions, when the insulation was allowed to reach the equilibrium moisture content at ranges of relative humidity, there was a moisture dependent increase of thermal conductivity in Hemp insulation.

Distribution, stability, bifurcations and catastrophe of steady rotation of a symmetrical heavy gyroscope with viscous-liquid-filled cavity

The number, the angles of orientation and the stability in Rumyantsev Movchan's sense of oblique steady rotations of a symmetric heavy gyroscope with a cavity completely filled with a uniform viscous liquid, possessing a fixed point 0 on its symmetric axis. are given for various values of the parameters. By taking the square of the upright component of the angular momentum M2 as a control parameter, three types of bifurcation diagrams of the steady rotations, two types of jumps and two kinds of local catastrophes, one being the symmetric reduced cusp type and the other being of the symmetric reduced butterfly type, are obtained. By taking account of the M2-damping owing to the moment of unavoidable faint friction, two different modes for the gyroscope, initially in a stable quasi-steady upright rotation with a nutation angle theta(s) equal to zero, to topple over are found.

Scaling of natural convection of an inclined flat plate : ramp cooling condition

A scaling analysis is performed for the transient boundary layer established adjacent to an inclined flat plate following a ramp cooling boundary condition. The imposed wall temperature decreases linearly up to a specific value over a specific time. It is revealed that if the ramp time is sufficiently large then the boundary layer reaches quasi-steady mode before the growth of the temperature is finished. However, if the ramp time is shorter then the steady state of the boundary layer may be reached after the growth of the temperature is completed. In this case, the ultimate steady state is the same as if the start up had been instantaneous. Note that the cold boundary layer adjacent to the plate is potentially unstable to Rayleigh-Bénard instability if the Rayleigh number exceeds a certain critical value for this cooling case. The onset of instability may set in at different stages of the boundary layer development. A proper identification of the time when the instability may set in is discussed. A numerical verification of the time for the onset of instability is presented in this study. Different flow regimes based on the stability of the boundary layer have also been discussed with numerical results.

Natural convection boundary-layer adjacent to an inclined flat plate subject to sudden and ramp heating

The natural convection thermal boundary layer adjacent to an inclined flat plate subject to sudden heating and a temperature boundary condition which follows a ramp function up until a specified time and then remains constant is investigated. The development of the flow from start-up to a steady-state has been described based on scaling analyses and verified by numerical simulations. Different flow regimes based on the Rayleigh number are discussed with numerical results for both boundary conditions. For ramp heating, the boundary layer flow depends on the comparison of the time at which the ramp heating is completed and the time at which the boundary layer completes its growth. If the ramp time is long compared with the steady state time, the layer reaches a quasi steady mode in which the growth of the layer is governed solely by the thermal balance between convection and conduction. On the other hand, if the ramp is completed before the layer becomes steady; the subsequent growth is governed by the balance between buoyancy and inertia, as for the case of instantaneous heating.

Natural convection in attics subject to instantaneous and ramp cooling boundary conditions

A fundamental study of the fluid dynamics inside an attic shaped triangular enclosure with cold upper walls and adiabatic horizontal bottom wall is reported in this study. The transient behaviour of the attic fluid which is relevant to our daily life is examined based on a scaling analysis. The transient phenomenon begins with the instantaneous cooling and the cooling with linear decreases of temperature up to some specific time (ramp time) and then maintain constant of the upper sloped walls. It is shown that both inclined walls develop a thermal boundary layer whose thicknesses increase towards steady-state or quasi-steady values. A proper identification of the timescales, the velocity and the thickness relevant to the flow that develops inside the cavity makes it possible to predict theoretically the basic flow features that will survive once the thermal flow in the enclosure reaches a steady state. A time scale for the cooling-down of the whole cavity together with the heat transfer scales through the inclined walls has also been obtained through scaling analysis. All scales are verified by the numerical simulations.

Scaling of free convection heat transfer in a triangular cavity for Pr>1

Unsteady natural convection inside a triangular cavity subject to a non-instantaneous heating on the inclined walls in the form of an imposed temperature which increases linearly up to a prescribed steady value over a prescribed time is reported. The development of the flow from start-up to a steady-state has been described based on scaling analyses and direct numerical simulations. The ramp temperature has been chosen in such a way that the boundary layer is reached a quasi-steady mode before the growth of the temperature is completed. In this mode the thermal boundary layer at first grows in thickness, then contracts with increasing time. However, if the imposed wall temperature growth period is sufficiently short, the boundary layer develops differently. It is seen that the shape of many houses are isosceles triangular cross-section. The heat transfer process through the roof of the attic-shaped space should be well understood. Because, in the building energy, one of the most important objectives for design and construction of houses is to provide thermal comfort for occupants. Moreover, in the present energy-conscious society it is also a requirement for houses to be energy efficient, i.e. the energy consumption for heating or air-conditioning houses must be minimized.

On the natural convection boundary layer adjacent to an inclined flat plate subject to ramp heating

An investigation of the natural convection boundary layer adjacent to an inclined semi-infinite plate subject to a temperature boundary condition which follows a ramp function up until some specified time and then remains constant is reported. The development of the flow from start-up to a steadystate has been described based on scaling analyses and verified by numerical simulations. Attention in this study has been given to fluids having a Prandtl number Pr less than unity. The boundary layer flow depends on the comparison of the time at which the ramp heating is completed and the time at which the boundary layer completes its growth. If the ramp time is long compared with the steady state time, the layer reaches a quasi steady mode in which the growth of the layer is governed solely by the thermal balance between convection and conduction. On the other hand, if the ramp is completed before the layer becomes steady; the subsequent growth is governed by the balance between buoyancy and inertia, as for the case of instantaneous heating.

A mathematical model for genetic regulation of the lactose operon

In this paper we construct a mathematical model for the genetic regulatory network of the lactose operon. This mathematical model contains transcription and translation of the lactose permease (LacY) and a reporter gene GFP. The probability of transcription of LacY is determined by 14 binding states out of all 50 possible binding states of the lactose operon based on the quasi-steady-state assumption for the binding reactions, while we calculate the probability of transcription for the reporter gene GFP based on 5 binding states out of 19 possible binding states because the binding site O2 is missing for this reporter gene. We have tested different mechanisms for the transport of thio-methylgalactoside (TMG) and the effect of different Hill coefficients on the simulated LacY expression levels. Using this mathematical model we have realized one of the experimental results with different LacY concentrations, which are induced by different concentrations of TMG.

An improved boundary layer scaling with ramp heating on a sloping plate

A scaling analysis for the natural convection boundary layer adjacent to an inclined semi-infinite plate subject to a non-instantaneous heating in the form of an imposed wall temperature which increases linearly up to a prescribed steady value over a prescribed time is reported. The development of the boundary layer flow from start-up to a steady-state has been described based on scaling analyses and verified by numerical simulations. The analysis reveals that, if the period of temperature growth on the wall is sufficiently long, the boundary layer reaches a quasi-steady mode before the growth of the temperature is completed. In this mode the thermal boundary layer at first grows in thickness and then contracts with increasing time. However, if the imposed wall temperature growth period is sufficiently short, the boundary layer develops differently, but after the wall temperature growth is completed, the boundary layer develops as though the startup had been instantaneous. The steady state values of the boundary layer for both cases are ultimately the same.