F.E. in environmental engineering: Coupled thermo-hydro-mechanical processes in porous media including pollutant transport

Summary This paper presents a general model for the analysis of coupled thermo-hydro-mechanical problems in porous media with possible pollutant transport. The governing equations are described and discrete solution techniques using the finite element method in space and finite differences in time are shown. Emphasis is put on a direct solution procedure, where the coupled system of equations is solved without use of matrix partitioning. Both the Newton-Raphson method and fixed point method are employed. Application examples involving pollutant transport, heat and mass transfer in partially saturated geomaterials, dynamic strain localization and durability of concrete show the range of applicability of this model in the field of evironmental engineering.     

生物基因测序高性能计算日志的任务分析及建模

生物基因测序是生物信息学分析中最常用的高性能计算任务.旨在通过分析生物基因测序日志找出生物基因测序日志中的任务特性,构建一种通用的适合分析生物基因测序的任务模型,并应用于面向基因测序的高性能计算系统的任务调度及性能优化.基于任务日志,主要分析了生物基因测序日志中任务到达时间的规律特性、任务运行时间和任务的并行尺寸等特性,通过这些任务特性利用指数分布、伽马分布、正态分布以及线性拟合构建了相应的局部任务模型,然后提出一种局部模型融合的方法,将各个局部模型合并为统一的任务模型.通过两种通用的模型评测方法对任务模型进行的评测结果显示,最终的任务模型与原有任务日志的4种任务属性趋于相同的分布,验证了所构建的任务模型具有很好的通用性.     

Data base analysis for treatment of industrial wastewaters by biotechnology and incineration

A computer model, which combines a data base and a software application package, was developed to help decision makers choose between biological treatment and incineration for handling high strength wastewaters. Results of the analysis predict the fate of individual compounds and the economic feasibility for treatment by combined biodegradation/adsorption as compared to incineration. The data base used for analysis contains details on the biodegradability, biological inhibitory levels, and adsorption coefficients. Results will help the user decide the feasibility of biological treatment systems such as the widely used activated sludge/powdered activated carbon system or expanded-bed granular activated carbon reactors. A wide variety of industrial wastewaters were analyzed and the model predicted general trends for biological treatment. Results were generally in agreement with reported results.     

Computer-aided characterization for effective mechanical properties of porous tissue scaffolds

Performance of various functions of the tissue structure depends on porous scaffold microstructures with specific porosity characteristics that influence the behavior of the incorporated or ingrown cells. Understanding the mechanical properties of porous tissue scaffold is important for its biological and biomechanical tissue engineering application. This paper presents a computer aided characterization approach to evaluate the effective mechanical properties of porous tissue scaffold. An outline of a computer-aided tissue engineering approach for design and fabrication of porous tissue scaffold, procedure of computer-aided characterization and its interface with design model, development of a computational algorithm for finite element implementation and numerical solution of asymptotic homogenization theory is presented. Application of the algorithm to characterize the effective mechanical properties of porous poly-ε-caprolactone scaffold manufactured by precision extruding freeform deposition will also be presented, along with a parametric study of the process and design parameter to the structural properties of tissue scaffold.     

Square wave voltammetric detection of 2,4,6-trinitrotoluene and 2,4-dinitrotoluene on a gold electrode modified with self-assembled monolayers

Cantilever transducers, which are recognized as a promising platform for the next generation of chemical and biological sensors, are currently under extensive research. Here we report composite porous silicon-crystalline silicon microcantilevers made of SOI wafers, where the porous silicon surface provides an excellent interface for immobilization of the biosensing layer. We start with crystalline silicon cantilevers fabricated from SOI wafers and we establish a surface layer of porous silicon on the cantilevers by vapor phase stain etching. The processed porous silicon does not introduce significant static bending of the cantilevers indicating that it does not introduce significant residual stress. It does provide an excellent biocompatible material for immobilization of a wide variety of chemical and biological materials, resulting in enhanced sensitivity as demonstrated on the covalently immobilized antibody binding its complementary antigen.     

Numerical calculations of the effect of moisture content and moisture flow on ionic multi-species diffusion in the pore solution of porous materials

A method to analyse and calculate concentration profiles of different types of ions in the pore solution of porous materials such as concrete subjected to external wetting and drying is described. The equations in use have a solid theoretical meaning and are derived from a porous media technique, which is a special branch of the more general mixture theory. The effect of chemical action is ignored, making the presented model suitable to be implemented into codes dealing solely with chemical equilibrium.     

Non-Darcy flow in disordered porous media: A lattice Boltzmann study

It is well known that the Darcy law is insufficient for describing high-rate flows in porous media. However, it is still an open problem to establish a universal form for the nonlinear correction to Darcy law. In this work, we will investigate numerically the non-Darcy effect on incompressible flows through disordered porous media. Numerical simulations at pore-scale level are carried out with the Reynolds number varying from 0.02 to 30, which covers the Darcy and non-Darcy flow regimes. Three regimes are identified for flow through porous media, i.e., a linear Darcy regime at vanishing Reynolds number, a cubic transitional or weak inertial regime at low but finite Reynolds number, and a quadratic Forchheimer or strong inertial regime at larger Reynolds numbers. Finally, a general correlation is proposed to include the non-Darcy effect, as an extension to the common empirical expressions.     

Bio-PEPA: A framework for the modelling and analysis of biological systems

In this work we present Bio-PEPA, a process algebra for the modelling and the analysis of biochemical networks. It is a modification of PEPA, originally defined for the performance analysis of computer systems, in order to handle some features of biological models, such as stoichiometry and the use of general kinetic laws. Bio-PEPA may be seen as an intermediate, formal, compositional representation of biological systems, on which different kinds of analyses can be carried out. Bio-PEPA is enriched with some notions of equivalence. Specifically, the isomorphism and strong bisimulation for PEPA have been considered and extended to our language. Finally, we show the translation of a biological model into the new language and we report some analysis results.     

ADM机械化求解DLFFC多孔阳极理论数模

提出低温液相直接进料燃料电池的多孔阳极普遍化理论数学模型,为定量分析多孔阳极的电极极化提供理论依据。该理论效模为一非线性二阶常微分方程边值问题,用以描述多孔电极中过电位和浓度的分布。文中采用ADM机械化的方法得出逼近解析解,并与基于有限差分程序BAND(J)的数值解作了比较。计算结果显示使用前4-6项ADM逼近,解析解即可达到满意的精度。可以看出,作者提出的ADM机械化方法．避免了复杂的推导过程,是求解该类数模的一个简便、快速的有效工具。     

Onset of double-diffusive convection of a sparsely packed micropolar fluid in a porous medium layer saturated with a nanofluid

The onset of convection of a sparsely packed micropolar fluid in a porous medium layer saturated by a nanofluid is examined by using a linear and nonlinear stability analyses. The Darcy–Brinkman–Forchheimer model is employed for the porous medium layer. The model used for the nanofluid incorporates the effects of Brownian motion and thermophoresis. The critical Rayleigh number, wave number for stationary and oscillatory modes and frequency of oscillations are obtained analytically using linear theory, and the nonlinear analysis is made with minimal representation of the truncated Fourier series analysis involving only two terms. The effect of various parameters on the stationary and oscillatory convections is shown pictorially. The dependence of stationary or oscillatory convection on the porous parameter and parameters involved in micropolar fluids is also discussed. We also study the effect of time on transient Nusselt number and Sherwood number which are found to be oscillatory when time is small. However, when time becomes very large, both the transient Nusselt value and Sherwood value approach to their steady-state values.     

Combined Lattice Boltzmann and phase-field simulations for incompressible fluid flow in porous media

A Lattice-Boltzmann method for incompressible fluid flow is coupled with the dynamic equations of a phase-field model for multiple order parameters. The combined model approach is applied to computationally evaluate the permeability in porous media. At the boundaries between the solid and fluid phases of the porous microstructure, we employ a smooth formulation of a bounce-back condition related to the diffuse profile of the interfaces. We present simulations of fluid flow in both, static porous media with stationary non-moving interfaces and microstructures performing a dynamic evolution of the phase and grain boundaries. For the latter case, we demonstrate applications to dissolving grain structures with partial melt inclusions and computationally analyse the temporal evolution of the microporosity under wetting conditions at the melt-grain boundaries. In any development state of the material, the Darcy number and the hydraulic conductivity of the porous medium are evaluated for various types of fluid.     

Numerical study on two-phase flow through fractured porous media

Based on the flux equivalent principle of a single fracture,the discrete fracture concept was developed,in which the macroscopic fractures are explicitly described as(n-1)dimensional geometry element.On the fundamental of this simplification,the discrete-fractured model was developed which is suitable for all types of fractured porous media.The principle of discrete-fractured model was introduced in detail,and the general mathematical model was expressed subsequently.The fully coupling discrete-fractured ma...     

Single particle model for char oxidation

A general model describes the pore structure, mass transport and heterogeneous chemistry which occurs during the oxidation of porous coal char. The pore structure is depicted as a collection of pore trees, with a continuous size distribution and branching sequence. Oxygen diffuses into the pore tree and consumes carbon from the walls of the pores. The basic heterogeneous rate constants have been inferred from existing laboratory data on non-porous carbon and the char oxidation model is validated with data on porous carbon char.     

基于TDMA算法的污染扩散方程无量纲化方法研究

为了实现对污染扩散的量化分析和评估,提出一种基于TDMA算法的污染扩散方程无量纲化分析方法。采用双曲函数建立污染扩散方程,构建污染扩散的动力学模型,采用湍流度的动力学修正方法进行污染扩散的流场分析,构建污染扩散的多相非饱和多重孔隙分布模型,结合TDMA算法进行污染扩散的多孔介质中两相界面湍流场分析,分析污染源的基质孔隙和裂隙的流体压力,结合孔隙介质的弹性柔度张量评估方法,实现污染扩散方程无量纲化分析和定量评估。仿真结果表明,采用该方法进行污染扩散的量化评估的准确性较高,对污染扩散的动态拟合性能较强,提高了污染扩散的准确分析和预测能力。     

Numerical modeling of heat exchange and unsaturated–saturated flow in porous media

We discuss the numerical modeling of heat and mass transport in unsaturated–saturated porous media. The heat is transported by infiltrated water underlying capillary and gravitation driven forces. Heat energy is governed by molecular diffusion, convection, dispersion and exchange between the infiltrated water and porous media matrix. An unsaturated–saturated flow is considered with boundary conditions reflecting the external driven forces. The presented mathematical model is motivated by analysis of hygrothermal isolation properties of facades. The main contribution is focused on the determination of model parameters including soil parameters, dispersion coefficients, thermal transmission coefficient, thermal conductivity of porous media matrix and external transmission coefficients. The used mathematical model does not include the vapor transport and its phase exchange with water due to vaporization and condensation. It will be the next step of our research. Thus, practical applications of our model are limited. The developed numerical method is a good candidate for solving corresponding inverse problems. Numerical experiments support our method.     

On algorithmic analysis of transcriptional regulation by LTL model checking

Studies of cells in silico can greatly reduce the need for expensive and prolonged laboratory experimentation. The use of model checking for the analysis of biological networks has attracted much attention recently. The practical limitations are still the size of the model, and the time needed to generate the state space. This paper is focused on the model checking approach for analysis of piecewise-linear deterministic models of genetic regulatory networks. Firstly, the qualitative simulation algorithm of de Jong et al. that builds the heart of Genetic Network Analyzer (GNA) is revisited and its time complexity is studied in detail. Secondly, a novel algorithm that reduces the state space generation time is introduced. The new algorithm is developed as an abstraction of the original GNA algorithm. Finally, a fragment of linear time temporal logic for which the provided abstraction is conservative is identified. Efficiency of the new algorithm when implemented in the parallel model checking environment is demonstrated on a set of experiments performed on randomly modified biological models. In general, the achieved results bring a new insight into the field of qualitative simulation emerging in the context of systems biology.     

Generalized Buckley-Leverett problem

Analysis of the effect produced by thermal and gas treatment on oilfield reservoirs of the Bazhenov formation involves the dynamics of a porous saturated medium with a multiphase multicomponent fluid, taking into account the chemical and physicochemical transformations under thermal and gas injection. This work is a qualitative investigation into such processes based on a simplified partial model allowing analytical study. The process of hot water injection into hydrocarbon-saturated reservoirs is considered. The physical statement of the problem is the generalization of the BuckleyLeverett problem additionally taking into account mass and heat sources. The purpose is to study the mechanism of heat and mass transfer in a porous medium with allowance for chemical and physicochemical transformations. By way of example, an analytical solution of the problem is considered using a specific algebraic expression for the Buckley-Leverett function. Our research makes it possible to identify some qualitative features of the general model and to draw significant practical conclusions. The results can be applied to the investigation into a wide scope of processes of liquid-liquid displacement in a porous medium with two-phase and multicomponent fluid in the presence of heat and mass sources.     

Density-driven flow and solute transport problems. A 2-D numerical model based on the network simulation method

The network simulation method, based on the formal equivalence between physical systems and electrical networks, solves numerical problems of relatively mathematical complexity in a versatile, efficient and computationally fast way. In this paper, the method is applied for the first time to the design of a general purpose model for simulating two-dimensional transient density-driven flow and solute transport through porous media, a mathematical model made up by coupled, nonlinear differential equations. Using the Boussinesq approximation and the stream function formulation, the model is used to solve two typical problems related with groundwater flows. Isochlor concentration and stream function curves are presented and successfully compared with those of other authors. Simulation is carried out using the digital computer program Pspice with relatively low computing times.     

Using cellular automata for porous media simulation

A cellular automata (CA) approach is proposed for simulating a fluid flow through porous materials with tortuous channels at pore level. The approach aims to combine CA methods both for constructing computer representation of porous material morphology and for simulating fluid flow through it. Morphology representation is obtained using CA whose evolution exhibits self-organization and results in a stable configuration. The latter is then used for Lattice Gas CA application to simulate fluid flow through a porous material specimen and compute its permeability properties. Special boundary conditions are introduced allowing for different smoothness of solid pore walls surface. The model has been tested on a small 2D fragment in a PC and then implemented to investigate a porous carbon electrode of a hydrogen fuel cell on 128 processors of a multiprocessor cluster.     

Computer modelling in environmental geomechanics

This paper presents a general framework for the computational analysis of environmental geomechanics problems. It is based on heat and multiphase flow in deforming porous media where pollutant transport mechanisms can be added. The governing equations are derived and then discretised by means of the finite element method in space and finite differences in time. Appropriate solution methods are addressed. Examples given involve heat and mass transfer together with pollutant transport in deforming geomaterials and surface subsidence problems.