Computational analysis of the roles of biochemical reactions in anomalous diffusion dynamics

Most biochemical processes in cells are usually modeled by reaction–diffusion(RD) equations. In these RD models,the diffusive process is assumed to be Gaussian. However, a growing number of studies have noted that intracellular diffusion is anomalous at some or all times, which may result from a crowded environment and chemical kinetics. This work aims to computationally study the effects of chemical reactions on the diffusive dynamics of RD systems by using both stochastic and deterministic algorithms. Numerical method to estimate the mean-square displacement(MSD) from a deterministic algorithm is also investigated. Our computational results show that anomalous diffusion can be solely due to chemical reactions. The chemical reactions alone can cause anomalous sub-diffusion in the RD system at some or all times.The time-dependent anomalous diffusion exponent is found to depend on many parameters, including chemical reaction rates, reaction orders, and chemical concentrations.     

An electrochemomechanical theory of defects in ionic solids. I. Theory

Charged defects diffuse through an ionic solid under electrochemical driving forces. Such a diffusion process can be affected by mechanical stresses in the solid. A deviation of defect concentration from its stoichiometric value during diffusion can cause volumetric strains in the solid. Such strains will result in mechanical stresses if the ionic solid is under mechanical constraint, or if the defect distribution is non-uniform. We develop a framework to account for the coupling between mechanical stresses and diffusion of charged defects in ionic solids. The framework consists of a system of nonlinear differential/algebraic equations governing the defect concentrations, electrostatic potential and the mechanical stresses. It is believed that this framework is the first fully coupled theory for the interaction between mechanical stresses and electrochemical forces in ionic solids.     

Thick film sensor based on NASICON for gas mixture detection

In recent years a new principle of solid state electrochemical gas sensors based on the kinetics of the controlled chemical reaction of gases with the electroactive species of a solid electrolyte is under development. In this kind of sensors a periodic voltage is applied to the solid state electrochemical cell and the current response is measured. The current-voltage relationship is dependent on the gas involved in the galvanic cell reactions and therefore all gases, which react on the surface of the sensor, can be simultaneously detected using only one sensor. In this paper, a thick film electrochemical sensor based on the kinetics of the controlled chemical reaction is presented. Paper presented at the 5th Euroconference on Solid State Ionics, Benalmádena, Spain, Sept. 13–20, 1998.     

Thermodynamic equilibrium for nitrogen species discharge: Comparison with global model

The equilibrium process of plasma nitrogen species by chemical kinetic reactions along various pressures is successfully investigated. The equilibrium process is required in industrial application to obtain the stable condition when heating up the material for having homogenous reaction. Nitrogen species densities is modeled by a continuity equation and extended Arrhenius form. These equations are used to integrate the change of density over the time. The integration is to acquire density and the reaction rate of each reaction where temperature and time dependence are imposed. A comparison is made with global model within pressure range of 1-100 mTorr and the temperature of electron is set to be higher than other nitrogen species. The results show that the chemical kinetic model only agrees for high pressure because of no power imposed; while the global model considers the external power along the pressure range then the electron and nitrogen species give highly quantity densities by factor of 3-5.     

Analysis of ignition of a porous energetic material

A theory of ignition is presented to analyse the effect of porosity on the time to ignition of a semi-infinite porous energetic solid subjected to a constant energy flux. An asymptotic perturbation analysis, based on the smallness of the gas-to-solid density ratio and the largeness of the activation energy, is utilized to describe the inert and transition stages leading to thermal runaway. As in the classical study of a nonporous solid, the transition stage consists of three spatial regions in the limit of large activation energy: a thin reactive–diffusive layer adjacent to the exposed surface of the material where chemical effects are first felt, a somewhat thicker transient–diffusive zone and, finally, an inert region where the temperature field is still governed solely by conductive heat transfer. Solutions in each region are constructed at each order with respect to the density-ratio parameter and matched to one another using asymptotic matching principles. It is found that the effects of porosity provide a leading-order reduction in the time to ignition relative to that for the nonporous problem, arising from the reduced amount of solid material that must be heated and the difference in thermal conductivities of the solid and gaseous phases. A positive correction to the leading-order ignition-delay time, however, is provided by the convective flow of gas out of the solid, which stems from the effects of thermal expansion and removes energy from the system. The latter phenomenon is absent from the corresponding calculation for the nonporous problem and produces a number of modifications at the next order in the analysis arising from the relative transport effects associated with the gas flow.     

Chemical reaction and diffusion: A comparison of molecular dynamics simulations with continuum solutions

Molecular dynamics simulations using the Lennard-Jones energy potential are compared with continuum solutions of reaction and diffusion in a dilute gas. The reaction model is a passive one in which high-energy bath atoms create a species, at dilute concentrations, which may have a very fast consumption reaction. This construction is designed based on typical fast reaction pathways involved in the fuel breakup in a hydrocarbon flame. Using reaction rates and diffusivities obtained from the molecular simulations allows the continuum solution to describe the reactive atom density spatial distribution with good accuracy. Based on this agreement, it is possible to estimate which reaction rates will produce negligible diffusive spreading, and hence, which species might be assumed to be in chemical equilibrium in continuum reacting flow calculations.     

Combustion in the future: The importance of chemistry

Combustion involves chemical reactions that are often highly exothermic. Combustion systems utilize the energy of chemical compounds released during this reactive process for transportation, to generate electric power, or to provide heat for various applications. Chemistry and combustion are interlinked in several ways. The outcome of a combustion process in terms of its energy and material balance, regarding the delivery of useful work as well as the generation of harmful emissions, depends sensitively on the molecular nature of the respective fuel. The design of efficient, low-emission combustion processes in compliance with air quality and climate goals suggests a closer inspection of the molecular properties and reactions of conventional, bio-derived, and synthetic fuels. Information about flammability, reaction intensity, and potentially hazardous combustion by-products is important also for safety considerations. Moreover, some of the compounds that serve as fuels can assume important roles in chemical energy storage and conversion. Combustion processes can furthermore be used to synthesize materials with attractive properties.A systematic understanding of the combustion behavior thus demands chemical knowledge. Desirable information includes properties of the thermodynamic states before and after the combustion reactions and relevant details about the dynamic processes that occur during the reactive transformations from the fuel and oxidizer to the products under the given boundary conditions. Combustion systems can be described, tailored, and improved by taking chemical knowledge into account. Combining theory, experiment, model development, simulation, and a systematic analysis of uncertainties enables qualitative or even quantitative predictions for many combustion situations of practical relevance.This article can highlight only a few of the numerous investigations on chemical processes for combustion and combustion-related science and applications, with a main focus on gas-phase reaction systems. It attempts to provide a snapshot of recent progress and a guide to exciting opportunities that drive such research beyond fossil combustion.     

Design and development of a controlled pressure/temperature set‐up for in situ studies of solid–gas processes and reactions in a synchrotron X‐ray powder diffraction station

A novel set‐up has been designed and used for synchrotron radiation X‐ray high‐resolution powder diffraction (SR‐HRPD) in transmission geometry (spinning capillary) for in situ solid–gas reactions and processes in an isobaric and isothermal environment. The pressure and temperature of the sample are controlled from 10^?3 to 1000 mbar and from 80 to 1000 K, respectively. To test the capacities of this novel experimental set‐up, structure deformation in the porous material zeolitic imidazole framework (ZIF‐8) by gas adsorption at cryogenic temperature has been studied under isothermal and isobaric conditions. Direct structure deformations by the adsorption of Ar and N₂ gases have been observed in situ, demonstrating that this set‐up is perfectly suitable for direct structural analysis under in operando conditions. The presented results prove the feasibility of this novel experimental station for the characterization in real time of solid–gas reactions and other solid–gas processes by SR‐HRPD.     

Nonequilibrium Zeldovich-von Neumann-Doring theory and reactive flow modeling of detonation

This paper discusses the Nonequilibrium Zeldovich-von Neumann-Doring (NEZND) theory of self-sustaining detonation waves and the Ignition and Growth reactive flow model of shock initiation and detonation wave propagation in solid explosives. The NEZND theory identified the nonequilibrium excitation processes that precede and follow the exothermic decomposition of a large high explosive molecule into several small reaction product molecules. The thermal energy deposited by the leading shock wave must be distributed to the vibrational modes of the explosive molecule before chemical reactions can occur. The induction time for the onset of the initial endothermic reactions can be calculated using high pressure-high temperature transition state theory. Since the chemical energy is released well behind the leading shock front of a detonation wave, a physical mechanism is required for this chemical energy to reinforce the leading shock front and maintain its overall constant velocity. This mechanism is the amplification of pressure wavelets in the reaction zone by the process of de-excitation of the initially highly vibrationally excited reaction product molecules. This process leads to the development of the three-dimensional structure of detonation waves observed for all explosives. For practical predictions of shock initiation and detonation in hydrodynamic codes, phenomenological reactive flow models have been developed. The Ignition and Growth reactive flow model of shock initiation and detonation in solid explosives has been very successful in describing the overall flow measured by embedded gauges and laser interferometry. This reactive flow model uses pressure and compression dependent reaction rates, because time-resolved experimental temperature data is not yet available. Since all chemical reaction rates are ultimately controlled by temperature, the next generation of reactive flow models will use temperature dependent reaction rates. Progress on a statistical hot spot ignition and growth reactive flow model with multistep Arrhenius chemical reaction pathways is discussed. The text was submitted by the authors in English.     

多孔颗粒内气体传递反应双阶段描述

本文采用双阶段模型描述多孔颗粒与气体的传递反应。反应分为两个阶段:气体反应物在扩散进入颗粒内部同时与颗粒发生反应的第一阶段;形成产物层后,扩散和反应用双区域模型来描述的第二阶段。分析发现,蒂勒数是描述过程特性的重要参数,同时反映反应和扩散速度的影响,且与总阻力存在一定关系。利用TGA进行了脱硫反应实验,分析了反应温度、颗粒大小等对反应的影响,实验结果很好地证实了理论分析结论。     

六硝基六氮杂异伍兹烷/2, 4, 6-三硝基甲苯共晶冲击起爆过程的分子动力学模拟

多尺度冲击技术可以准确的再现含能材料冲击起爆过程中冲击波阵面及反应区内的热力学和化学反应路径. 文本利用反应力场分子动力学(ReaxFF-MD)对六硝基六氮杂异伍兹烷/2, 4, 6-三硝基甲苯(CL20/TNT)1:1共晶沿<110>方向以6–10 km·s^-1的冲击速度进行冲击压缩模拟. 产物识别分析显示当冲击速度≥7 km·s^-1时, 冲击激发化学反应发生, 并且利用Rankine-Hugoniot守恒关系求得冲击起爆压力为24.56 GPa. 再者, 比较了冲击速度与粒子速度, 冲击速度与冲击诱发形变的关系, 当冲击速度为7–8 km·s^-1时, 冲击起爆发生, 系统经历弹- 塑性相变, 初级化学反应及次级化学反应, 并且相变与化学反应同时进行, 对于较高的冲击波速度(≥9 km·s^-1), 共晶系统内为过驱响应, 热力学参数均出现陡峭的梯度变化, 冲击波压缩材料直接阶跃至塑性变形阶段, 并且此阶段出现大量的碳原子.     

固体颗粒的结构演化与机械力化学效应

干法、室温振动研磨制备铝超微颗粒, 分别将研磨2 h, 4 h和8 h的铝粉, 在常温下超声水解得到白色Al(OH)₃胶体, 水解产品经干燥、研磨、焙烧后制备出多孔、片状γ -Al₂O₃纳米颗粒, 粒度分布在30---50 nm之间. 借助于X射线衍射(XRD)分析方法和透射电子显微镜(TEM), 研究固体颗粒在细化过程中的能量转换, 分析颗粒的微结构演化与机械力化学反应的关系, 确定理想的研磨时间. 研究结果表明: 固体颗粒在机械力的作用下产生大量的应变和位错缺陷, 使材料处于亚稳、高能活性状态, 易于诱发机械力化学反应, 在一定条件下晶体的表面能、应变能和层错能相互转化; 研磨2 h的铝颗粒内部, 晶格畸变和位错概率最大, 材料显示出极高的化学反应活性, 在超声波激发下, 储存在材料内部的能量被充分释放, 在较短的时间内, 水解生成Al(OH)₃纳米颗粒.     

Novel catalysts: Indium implanted SiO2 thin films

Interactions of Indium (In) and silicon (Si) atoms are known to catalyze certain organic chemical reactions with high efficiency. In an attempt of creating a material that manifests the interactions, In implanted SiO₂ thin films were prepared by ion beam injection and their catalytic abilities for organic chemical reactions were examined. It has been found that, with an injection energy of approximately 0.5 keV, a thin In film is formed on a SiO₂ substrate surface and the In implanted SiO₂ thin film can catalyze an organic chemical reaction. It has been also shown that there is an optimal ion dose for the highest catalytic ability in the film preparation process. Thin-film-type catalyzing materials such as the one proposed here may open a new way to enhance surface chemical reaction rates.     

气固反应的终止判断与酸性气体干式净化能限分析

借助成核—晶体生长模型，对气固反应过程中固体产物层的形成进行能耗分析，提出最小稳定晶核尺寸与成长后的晶粒相等的终止判据，与原来普遍使用的阅值孔隙率终止判据相补充，全面考虑气固反应的终止原因．在数值模拟中利用这些终止判据，预测垃圾焚烧炉排烟中HCI气体与钙吸收剂之间的干式反应程度，分析烟气干式净化的使用条件．     

二甲醚/空气对向流扩散燃烧反应历程的数值研究

本文采用详细化学反应动力学模型对二甲醚对向流扩散燃烧火焰进行了数值模拟,通过分析二甲醚燃烧过程中基元反应速度、关键中间产物和自由基,得到了二甲醚在对向流扩散燃烧中氧化的主要反应途径.结果表明,反应主要发生在高温区域(大于 800 K),CH2O、H2 和 CH4是重要的中间产物;OH、H 和 CH3是重要的自由基,在生成 CO、CO2和 H2O 的过程中起到关键性作用.     

The Use of Solid‐Phase Supports for Derivatization in Chromatography and Spectroscopy

Abstract

Derivatization, or chemical modification of analytes, is often required for species that are only weakly detectable by common spectroscopic methods. Derivatization is most commonly performed in homogeneous solution or using phase‐transfer catalyzed reactions. However, the use of solid phase supports for performing the same reactions has a number of advantages. The sample can be “cleaned up” on the same phase, eliminating interfering matrix components or excess reagent. The process naturally concentrates the analyte, providing higher sensitivity, but also, under favorable circumstances, provides for more efficient reactions relative to solutions of the same original concentration. This review explores the uses to which such supports have been put, primarily in fluorescence derivatization for chromatographic applications. Some of the considerations in applying these techniques are described, and they are shown to be an extremely useful format for derivatization.     

Automation of chemical kinetics: Status and challenges

Driven by synergic advancements in high performance computing and theory, the capability to estimate rate constants from first principles has evolved considerably recently. When this knowledge is coupled with a procedure to determine a list of all reactions relevant to describe the evolution of a reacting system, it becomes possible to envision a methodology to predict theoretically the reaction kinetics. However, if a thorough examination of all possible reaction channels is desired, the number of reactions for which a rate constant estimate is needed can become quite large. This determines the need for rate constant estimation automation. In the present work, the status of this rapidly evolving field is reviewed, with emphasis on recent advancements and present challenges. Thermochemistry is the field where automation is most advanced. Entropies, heat capacities, and enthalpies can be determined efficiently with accuracy comparable to experiments for most chemical species containing a limited number of atoms, while machine learning can be used to improve the computational predictions for large chemical species using reduced computational resources. Several approaches have been proposed to automatically investigate the reactivity over complex potential energy surfaces, while rate constants for elementary steps can be determined accurately for several reaction classes, such as abstraction, addition, beta-scission, and isomerization. Kinetic mechanisms can be automatically generated using methodologies that differ for level of complexity and required physical insight. Among the challenges that are still to be met are the estimation of rate constants for intrinsically multireference reaction classes, such as barrierless processes, the containment of the number of reactions to screen in mechanism development, and the integration of the existing automated software. It is suggested that the synergy between experiment and theory should evolve towards a stage where experiments are focused on the estimation of parameters where theoretical tools are least predictive, and vice versa.