化学动力学过程模拟软件的开发

采用Borland C Builder 6.0可视化编程环境和基于面向对象的C 语言开发动力学模拟软件。该软件中对微分方程组的求解采用四阶龙格-库塔法。该软件适用于模拟各种化学动力学过程,用户可以根据不同情况设置复杂反应的任意步骤及其基元反应、相应反应速率常数及各物种的初始浓度和反应时间等。软件根据用户设定的参数自动计算出参与反应过程中各物种的浓度变化,同时提供Excel输出功能和绘图功能,可以直观地看到反应的动力学曲线。该软件不需要其他应用软件支持,可以在Windows 98/Me/2000/XP/2003下直接运行。程序涉及到的算法,需要较复杂的数据结构,程序采用C 语言提供的标准模板库,简化了程序设计并提高了运行效率。该软件模拟了一个包含平行-连串反应的化学动力学过程,运行速度较快,并得到精确的计算结果。     

数学软件Mathematica在化学反应工程中的应用

化学反应工程中会遇到大量复杂的数学模型求解和数学模型参数估值问题,以往依靠手工或编写计算机程序计算.本文采用数学软件Mathematica求解了若干化学反应工程中的数学问题,例如用FindRoot命令求取非理想反应器的轴向扩散模型中彼克列(Pe)准数,NonLinearFit命令进行反应动力学模型中的参数估值,符号计算和数值计算求反应器模拟中的定积分和微分方程的解.求解过程表明Mathematica强大的计算功能可以避免编程工作,且具有可视和图形化的特点,是求解化学反应工程中的数学问题的先进工具.     

The statistical dynamics of activity-led reactions

For any chemical reaction we construct a non-linear stochastic process in continuous or discrete time in which the concentrations obey a kinetic law, where the rates are proportional to the products of the activities. The main microscopic assumption can be interpreted as expressing the hypothesis of a collective effect related to saturation. The theory is unable to shed light on the problem of absolute rates. In the final section we suggest how the hypotheses of the model might be tested experimentally.     

ELSIM—a problem-solving environment for electrochemical kinetic simulations. Version 3.0-solution of governing equations associated with interfacial species,independent of spatial coordinates or in one-dimensional space geometry

A third version of the program ELSIM (for IBM compatible PCs) for the simulation of electrochemical transient methods has been elaborated upon. The program has been equipped with numerical algorithms that allow solution of kinetic problems characterized by the presence of interfacial species. Problems of this kind play an important role in electrochemical kinetic studies, among others in connection with electrocatalysis, modified electrodes or oscillatory systems. The user-written governing equations may take the form of differential—algebraic equations (for the concentrations of interfacial species) independent of spatial coordinates, or partial differential equations (for the concentrations of bulk species) in one-dimensional space geometry, coupled with differential—algebraic equations. Problem formulation has also been facilitated by the inclusion of a reaction compiler, which automatically generates the text of the above governing equations for user-written reaction mechanisms. Other new features include an option for the least-squares fitting of simulated transients to experimental curves, a hypertext help facility, and enhanced performance owing to the revised formula translation based on the three-address internal code generation, and on automatic differentiation.     

Computational study of band-crossing reactions

A numerical study of band-crossing reactions is conducted using a quasi-one-dimensional (1-D) computational model that accounts for species bulk advection, electromigration velocities, diffusion, and chemical reaction. The model is used to simulate chemical reactions between two initially distinct sample zones, referred to as "bands," that cross each other due to differences in electromigration velocities. The reaction is described in terms of a single step, reversible mechanism involving two reactants and one product. A parametric study is first conducted of the behavior of the species profiles, and results are interpreted in terms of the Damko/spl uml/hler number and of the ratios of the electromigration velocities of the reactant and product. Computed results are then used to explore the possibility of extracting forward and backward reaction rates based on time resolved observation of integral moments of species concentrations. In particular, it is shown that in the case of fast reactions, robust estimates can be obtained for high forward rates, but that small reverse rates may not be accurately observed.     

A general simulator for reaction-based biogeochemical processes

As more complex biogeochemical situations are being investigated (e.g., evolving reactivity, passivation of reactive surfaces, dissolution of sorbates), there is a growing need for biogeochemical simulators to flexibly and facilely address new reaction forms and rate laws. This paper presents an approach that accommodates this need to efficiently simulate general biogeochemical processes, while insulating the user from additional code development.The approach allows for the automatic extraction of fundamental reaction stoichiometry and thermodynamics from a standard chemistry database, and the symbolic entry of arbitrarily complex user-specified reaction forms, rate laws, and equilibria. The user-specified equilibria and kinetic rates (i.e., they are not defined in the format of the standardized database) are interpreted by the Maple V (Waterloo Maple) symbolic mathematical software package. FORTRAN 90 code is then generated by Maple for (1) the analytical Jacobian matrix (if preferred over the numerical Jacobian matrix) used in the Newton–Raphson solution procedure, and (2) the residual functions for governing equations, user-specified equilibrium expressions and rate laws. Matrix diagonalization eliminates the need to conceptualize the system of reactions as a tableau, which comprises a list of components, species, the stoichiometric matrix, and the formation equilibrium constant vector that forms the species from components (Morel and Hering, 1993), while identifying a minimum rank set of basis species with enhanced numerical convergence properties. The newly generated code, which is designed to operate in the BIOGEOCHEM biogeochemical simulator, is then compiled and linked into the BIOGEOCHEM executable. With these features, users can avoid recoding the simulator to accept new equilibrium expressions or kinetic rate laws, while still taking full advantage of the stoichiometry and thermodynamics provided by an existing chemical database. Thus, the approach introduces efficiencies in the specification of biogeochemical reaction networks and eliminates opportunities for mistakes in preparing input files and coding errors. Test problems are used to demonstrate the features of the procedure.     

Microcomputer simulation of steady-state enzyme kinetics for educational purposes

A BASIC program to assist the instruction of steady-state enzyme kinetics has been developed for the IBM PC microcomputer. Its purpose is to simulate laboratory experiments in order to minimize the time required to obtain kinetic data from which students deduce kinetic mechanisms and determine kinetic constants of enzyme-catalyzed reactions. The program randomly selects a kinetic scheme from various sequential, ping pong, and iso reaction sequences as well as values for the kinetic constants. The scheme and kinetic constants are unknown to the student at this time; the only thing he or she knows is the stoichiometry of the catalyzed reaction which can have two or three substrates and products. The student is prompted to enter values for concentrations of substrates and products; several different concentrations for each substrate and product can be entered in a single experiment. The program then calculates, displays and prints (if desired) the corresponding initial steady-state velocities. The student can perform as many experiments as desired until enough information is obtained to determine the kinetic mechanism and to calculate values for the kinetic constants.     

利用现代分析仪器结合化学计量学软件开设化学动力学实验

开设了“紫外光谱法在线测量连串反应动力学过程”的综合性实验。使用DAD紫外光谱仪在线测量邻苯二甲酸二乙酯在碱性条件下水解的连串反应,该反应体系中各组分的光谱重叠严重。利用化学计量学中的目标试验-数值遗传算法(TT—NGA)优化搜索动力学参数,采用Delphi7．0编写了处理实验数据的辅助教学软件TTNGA．exe,在Windows系统下该软件可方便使用。用该软件处理测得的动力学-光谱矩阵可以快速方便地获得各组分的纯光谱,动力学曲线和反应级数及速率常数。该实验的开设,培养了学生使用现代分析仪器并利用计算机技术和数学知识解决化学问题的能力,取得了良好的教学效果。     

Indistinguishability and identifiability of kinetic models for the MurC reaction in peptidoglycan biosynthesis

An important question in Systems Biology is the design of experiments that enable discrimination between two (or more) competing chemical pathway models or biological mechanisms. In this paper analysis is performed between two different models describing the kinetic mechanism of a three-substrate three-product reaction, namely the MurC reaction in the cytoplasmic phase of peptidoglycan biosynthesis. One model involves ordered substrate binding and ordered release of the three products; the competing model also assumes ordered substrate binding, but with fast release of the three products. The two versions are shown to be distinguishable; however, if standard quasi-steady-state assumptions are made distinguishability cannot be determined. Once model structure uniqueness is ensured the experimenter must determine if it is possible to successfully recover rate constant values given the experiment observations, a process known as structural identifiability. Structural identifiability analysis is carried out for both models to determine which of the unknown reaction parameters can be determined uniquely, or otherwise, from the ideal system outputs. This structural analysis forms an integrated step towards the modelling of the full pathway of the cytoplasmic phase of peptidoglycan biosynthesis.     

适定性分析在醇酮氧化动力学中的应用

在化工系统DCS先进控制领域和基于机理模型的化工类商品化软件中,大型装置的过程数学模型通常处于核心地位,同时这些场合也对模型的稳定性和动态特性有较高要求。而适定性分析有利于从物理意义和数学的角度分析模型的合理性,并指导正确的数值求解方法,从而产生高质量数学模型。本文结合醇酮氧化过程模拟的实践应用了Lipschitz条件、解的存在唯一性定理、解的延拓、解对初值的连续性和可微性定理和相关常微方程稳定性理论等数学工具,发现了文献中动力学方程组存在的问题,并对其进行了改进与提高;在实际应用中也取得了更好的效果;同时,对于其它类似的数学建模与求解问题也具有理论和实践的参考意义。     

Model complexity reduction of chemical reaction networks using mixed-integer quadratic programming

The model complexity reduction problem of large chemical reaction networks under isobaric and isothermal conditions is considered. With a given detailed kinetic mechanism and measured data of the key species over a finite time horizon, the complexity reduction is formulated in the form of a mixed-integer quadratic optimization problem where the objective function is derived from the parametric sensitivity matrix. The proposed method sequentially eliminates reactions from the mechanism and simultaneously tunes the remaining parameters until the pre-specified tolerance limit in the species concentration space is reached. The computational efficiency and numerical stability of the optimization are improved by a pre-reduction step followed by suitable scaling and initial conditioning of the Hessian involved. The proposed complexity reduction method is illustrated using three well-known case studies taken from reaction kinetics literature.     

基于动态特性补偿的绝热加速量热仪温度随动控制优化

针对绝热加速量热仪测试反应剧烈的样品时温度传感器存在动态测量误差,导致在进行反应热力学和动力学计算中出现偏差的现象,提出一种绝热反应过程中实时在系统动态特性补偿的方法。首先采用基于集中参数的方法对绝热反应过程进行模拟仿真,分析了影响进行反应热力学和动力学参数求取准确性的主要因素,其次利用粒子群算法的全局寻优能力,得到动态补偿器参数,并将其运用到绝热加速量热仪温度随动控制算法中。最后,通过标准样品对该补偿方法进行实验测试,验证了方法的有效性,研究结果对于提高化学反应热危险性评估准确性具有重要意义。     

PumpKin: A tool to find principal pathways in plasma chemical models

PumpKin is a software package to find all principal pathways, i.e. the dominant reaction sequences, in chemical reaction systems. Although many tools are available to integrate numerically arbitrarily complex chemical reaction systems, few tools exist in order to analyze the results and interpret them in relatively simple terms. In particular, due to the large disparity in the lifetimes of the interacting components, it is often useful to group reactions into pathways that recycle the fastest species. This allows a researcher to focus on the slow chemical dynamics, eliminating the shortest timescales. Based on the algorithm described by Lehmann (2004), PumpKin automates the process of finding such pathways, allowing the user to analyze complex kinetics and to understand the consumption and production of a certain species of interest. We designed PumpKin with an emphasis on plasma chemical systems but it can also be applied to atmospheric modeling and to industrial applications such as plasma medicine and plasma-assisted combustion.     

DIFS—a modelling and simulation tool for DGT induced trace metal remobilisation in sediments and soils

The technique of Diffusive Gradients in Thin-films (DGT) can measure in situ fluxes of trace metals in sediments. Interpretation of these measurements requires a numerical model of trace metal reaction and transport in sediments. The DIFS (DGT Induced Fluxes in Sediments) model has permitted quantitative interpretation of DGT measurements in terms of fundamental kinetic and equilibrium resupply parameters. DIFS is here further refined and developed into a software tool which both simulates temporal and spatial changes in concentrations of trace metals in solid and solution phases in sediments during in situ DGT deployments, and estimates resupply parameters from experimental data. The basis of the DIFS model is a pair of linked parabolic PDEs describing dissolved and sorbed trace metal concentrations in the sediment and DGT device. These are solved by the Method of Lines using standard ODE solvers. The solutions are processed to obtain the DGT response. The use of the software, in particular the format of the text file containing input parameters, is described. Illustrative examples of the type of behaviour predicted for DGT by DIFS are provided.     

The new mexico state university ring-star system: A distributed unix environment

A distributed version of the UNIX operations system is currently under development through a joint effort of New Mexico State University and the Hebrew University of Jerusalem. A microprocessor version of the UNIX kernel has been developed which will run on any PDP-11 or LSI-11 based processing element and allows processes to run in a UNIX ‘look-alike’ environment. Each process is fully transportable among all processors in the system. Although the preliminary version of the system was built in a star configuration, the system is currently being upgraded by the addition of a communication ring with 8-bit microprocessors as ring interface units. The current paper describes the software structure, the hardware structure and the communication protocol of the system.     

Fractional differential equations in electrochemistry

Electrochemistry was one of the first sciences to benefit from the fractional calculus. Electrodes may be thought of as “transducers” of chemical fluxes into electricity. In a typical electrochemical cell, chemical species, such as ions or dissolved molecules, move towards the electrodes by diffusion. Likewise, other species are liberated into solution by the electrode reaction and diffuse away from the electrode into the bulk solution. It is demonstrated in this paper that the electric current is linearly related to the temporal semiderivative of the concentrations, at the electrode, of the species involved in the electrochemical reaction. More usefully, the semiintegral of the current provides immediate access information about concentrations.     

Modeling the thermal stability of enzyme-based in vitro diagnostics biosensors

Performance of in vitro diagnostics biosensors may change over lifetime, particularly if environmental storage conditions such as temperature are not controlled. Biosensors are composed of diverse multiple components such as salts, polymers and biological components which may be differentially impacted by chemical and physical transformations induced by changes in temperature and exposure to humidity, oxygen and light. Mathematical models for predicting the influence of temperature on biosensor performance over time typically assume the changes follow first-order dynamics, with the temperature dependence of the rate of change described by an Arrhenius kinetic expression. However, the compositional diversity found in many biosensors may cause the assumption of first-order dynamics for sensor stability to be invalid. In this paper, a second-order dynamic model is developed to predict the change in biosensor performance over time for a single-use biosensor used in a point-of-care diagnostics system. The model consists of a reversible reaction followed by an irreversible reaction, with rate coefficients having Arrhenius temperature dependencies. The second-order dynamic model provides improved predictions, based on a comparison for two experimental datasets used for estimation, and on a validation dataset. The resulting model has applications for shelf-life prediction, designing accelerated testing experiments, biosensor improvement and the development of biosensor storage guidelines. Finally, it is shown that the concept of “mean kinetic temperature”, used widely in the pharmaceutical industry and based on first-order dynamics, can be applied successfully to a biosensor system exhibiting higher-order dynamic behaviour using a second-order model. This suggests that mean kinetic temperature concepts may be extended to in vitro diagnostics sensor applications.