Search Results (8)

Our paper reviews some key concepts in chemical reaction network theory and mathematical epidemiology, and examines their intersection, with three goals. The first is to make the case that mathematical epidemiology (ME), and also related sciences like population dynamics, virology, ecology, etc., could benefit by adopting the universal language of essentially non-negative kinetic systems as developed by chemical reaction network (CRN) researchers. In this direction, our investigation of the relations between CRN and ME lead us to propose for the first time a definition of ME models, stated in Open Problem 1. Our second goal is to inform researchers outside ME of the convenient next generation matrix (NGM) approach for studying the stability of boundary points, which do not seem sufficiently well known. Last but not least, we want to help students and researchers who know nothing about either ME or CRN to learn them quickly, by offering them a Mathematica package “bootcamp”, including illustrating notebooks (and certain sections below will contain associated suggested notebooks; however, readers with experience may safely skip the bootcamp). We hope that the files indicated in the titles of various sections will be helpful, though of course improvement is always possible, and we ask the help of the readers for that. Full article

The existing natural gas transportation pipelines can withstand a hydrogen content of 0 to 50%, but further research is still needed on the pathways of NO and CO production under moderate or intense low oxygen dilution (MILD) combustion within this range of hydrogen blending. In this paper, we present a computational fluid dynamics (CFD) simulation of hydrogen-doped jet flame combustion in a jet in a hot coflow (JHC) burner. We conducted an in-depth study of the mechanisms by which NO and CO are produced at different locations within hydrogen-doped flames. Additionally, we established a chemical reaction network (CRN) model specifically for the JHC burner and calculated the detailed influence of hydrogen content on the mechanisms of NO and CO formation. The findings indicate that an increase in hydrogen content leads to an expansion of the main NO production region and a contraction of the main NO consumption region within the jet flame. This phenomenon is accompanied by a decline in the sub-reaction rates associated with both the prompt route and NO-reburning pathway via CH_i=0–3 radicals, alongside an increase in N₂O and thermal NO production rates. Consequently, this results in an overall enhancement of NO production and a reduction in NO consumption. In the context of MILD combustion, CO production primarily arises from the reduction of CO₂ through the reaction CH₂(S) + CO₂ ⇔ CO + CH₂O, the introduction of hydrogen into the system exerts an inhibitory effect on this reduction reaction while simultaneously enhancing the CO oxidation reaction, OH + CO ⇔ H + CO₂, this dual influence ultimately results in a reduction of CO production. Full article

The field of nitric oxide (NOx) production combined with turbulent flow is a complex issue of combustion, especially for the different time scales of reactions and flow in numerical simulations. Around this, a series of approach methods, including the empirical formula approach, the computational fluid dynamics (CFD) approach coupling with an infinite rate chemical reaction, the chemical reaction networks (CRNs), and the CFD approach coupling with CRNs, were classified, and we discussed its advantages and applicability. The empirical-formula approach can provide an average range of NOx concentration, and this method can be involved only in special scenarios. However, its simplicity and feasibility still promote practical use, and it is still widely applied in engineering. Moreover, with the help of artificial intelligence, this method was improved in regard to its accuracy. The CFD approach could describe the flow field comprehensively. In compliance with considering NOx formation as finite-rate chemical reactions, the NOx concentration distribution via simulation cannot match well with experimental results due to the restriction caused by the simplification of the combustion reaction. Considering NOx formation as a finite-rate chemical reaction, the CRNs approach was involved in CFD simulation, and the CRNs approach could forecast the NOx concentration distribution in the flow field. This article mainly focuses on the simulation method of nitric oxide (NOx) production in different combustion conditions. This review could help readers understand the details of the NOx formation mechanism and NOx formation prediction approach. Full article

The emerging field at the intersection of synthetic biology, network modelling, and control theory has grown in popularity in recent years. In this study, the aim is to design synthetic biomolecular controllers by exploiting the covalent modification cycle (CMC) enhanced with direct and indirect positive autoregulation (DPAR and IPAR). Two novel biomolecular controllers proposed, the Brink controller (BC) with DPAR (namely BC-DPAR) and the BC with IPAR (namely BC-IPAR), allow to (a) use fewer chemical reactions than purely designs based on dual chemical reaction networks (DCRNs), and (b) improve the stability of ultrasensitive response when designing biomolecular controllers. Following the conversion route from chemical reactions to DNA strand displacements, the integration of the two novel controllers and an enzymatic proteolysis model proposed aims to analyse the regulatory properties by exploring the tracking response of proteolysis products. Full article

DNA molecules can be adopted to design biomolecular control circuits that can effectively control biochemical reaction processes. However, the leak reaction in actual biochemical reactions causes a significant uncertainty for reactions. In this paper, the first-order time-delay system is selected as the controlled object. A two-degree-of-freedom internal model PID controller (2DOF IMC-PID) is constructed for the first time within the framework of chemical reaction networks (CRNs). Under this control strategy, the set-point tracking and disturbance suppression are tuned with individual controllers, respectively. The controller parameters are determined by two filtering parameters that affect the controller’s performance, so the parameter tuning is simpler and more targeted. Then, the 2DOF IMC-PID controller is implemented in DSD reaction networks, with less overshoot in the 2DOF IMC-PID control system than the traditional PID control system and the 2DOF PID control system. Finally, a 2DOF IMC-PID division gate control system is established to effectively inhibit the impacts of leak reactions on the computation results. Although the leak reaction occurs at the division gate, the ideal output can be produced by the 2DOF IMC-PID division gate control system. Full article

The computational ability of the chemical reaction networks (CRNs) using DNA as the substrate has been verified previously. To solve more complex computational problems and perform the computational steps as expected, the practical design of the basic modules of calculation and the steps in the reactions have become the basic requirements for biomolecular computing. This paper presents a method for solving nonlinear equations in the CRNs with DNA as the substrate. We used the basic calculation module of the CRNs with a gateless structure to design discrete and analog algorithms and realized the nonlinear equations that could not be solved in the previous work, such as exponential, logarithmic, and simple triangle equations. The solution of the equation uses the transformation method, Taylor expansion, and Newton iteration method, and the simulation verified this through examples. We used and improved the basic calculation module of the CRN++ programming language, optimized the error in the basic module, and analyzed the error’s variation over time. Full article

The Temkin reactor can be applied for industrial relevant catalyst testing with unmodified catalyst particles. It was assumed in the literature that this reactor behaves as a cascade of continuously stirred tank reactors (CSTR). However, this assumption was based only on outlet gas composition or inert residence time distribution measurements. The present work theoretically investigates the catalytic CO${}_2$ methanation as a test case on different catalyst geometries, a sphere, and a ring, inside a single Temkin reaction chamber under isothermal conditions. Axial gas-phase species profiles from detailed computational fluid dynamics (CFD) are compared with a CSTR and 1D plug-flow reactor (PFR) model using a sophisticated microkinetic model. In addition, a 1D chemical reactor network (CRN) model was developed, and model parameters were adjusted based on the CFD simulations. Whereas the ideal reactor models overpredict the axial product concentrations, the CRN model results agree well with the CFD simulations, especially under low to medium flow rates. This study shows that complex flow patterns greatly influence species fields inside the Temkin reactor. Although residence time measurements suggest CSTR-like behavior, the reactive flow cannot be described by either a CSTR or PFR model but with the developed CRN model. Full article

Future energy and transport scenarios will still rely on gas turbines for energy conversion and propulsion. Gas turbines will play a major role in energy transition and therefore gas turbine performance should be improved, and their pollutant emissions decreased. Consequently, designers must have accurate performance and emission prediction tools. Usually, pollutant emission prediction is limited to the combustion chamber as the composition at its outlet is considered to be “chemically frozen”. However, this assumption is not necessarily valid, especially with the increasing turbine inlet temperatures and operating pressures that benefit engine performance. In this work, Computational Fluid Dynamics (CFD) and Chemical Reactor Network (CRN) simulations were performed to analyse the progress of NO_x and CO species through the high-pressure turbine stator. Simulations considering turbulence-chemistry interaction were performed and compared with the finite-rate chemistry approach. The results show that progression of some relevant reactions continues to take place within the turbine stator. For an estimated cruise condition, both NO and CO concentrations are predicted to increase along the stator, while for the take-off condition, NO increases and CO decreases within the stator vanes. Reaction rates and concentrations are correlated with the flow structure for the cruise condition, especially in the near-wall flow field and the blade wakes. However, at the higher operating pressure and temperature encountered during take-off, reactions seem to be dependent on the residence time rather than on the flow structures. The inclusion of turbulence-chemistry interaction significantly changes the results, while heat transfer on the blade walls is shown to have minor effects. Full article