Reconstruction of arbitrary biochemical reaction networks: A compressive sensing approach

Reconstruction of biochemical reaction networks (BRN) and genetic regulatory networks (GRN) in particular is a central topic in systems biology which raises crucial theoretical challenges in system identification. Nonlinear Ordinary Differential Equations (ODEs) that involve polynomial and rational functions are typically used to model biochemical reaction networks. Such nonlinear models make the problem of determining the connectivity of biochemical networks from time-series experimental data quite difficult. In this paper, we present a network reconstruction algorithm that can deal with ODE model descriptions containing polynomial and rational functions. Rather than identifying the parameters of linear or nonlinear ODEs characterised by pre-defined equation structures, our methodology allows us to determine the nonlinear ODEs structure together with their associated parameters. To solve the network reconstruction problem, we cast it as a compressive sensing (CS) problem and use sparse Bayesian learning (SBL) algorithms as a computationally efficient and robust way to obtain its solution. © 2012 IEEE.

Seafloor interaction with steel catenary risers

This paper describes the key features of a seafloor-riser interaction model. The soil is represented in terms of non-linear load-deflection (P- y) relationships, which are also able to account for soil stiffness degradation due to cyclic loading. The analytical framework considers the riser-seafloor interaction problem in terms of a pipe resting on a bed of springs, and requires the iterative solution of a fourth-order ordinary differential equation. A series of simulations is used to illustrate the capabilities of the model. Thanks to the non-linear soil springs with stiffness degradation it is possible to simulate the trench formation process and estimate moments in a riser. Copyright © 2008 by The International Society of Offshore and Polar Engineers (ISOPE).

Optimization algorithms and ODE's in MDO

There is a need for a stronger theoretical understanding of Multidisciplinary Design Optimization (MDO) within the field. Having developed a differential geometry framework in response to this need, we consider how standard optimization algorithms can be modeled using systems of ordinary differential equations (ODEs) while also reviewing optimization algorithms which have been derived from ODE solution methods. We then use some of the framework's tools to show how our resultant systems of ODEs can be analyzed and their behaviour quantitatively evaluated. In doing so, we demonstrate the power and scope of our differential geometry framework, we provide new tools for analyzing MDO systems and their behaviour, and we suggest hitherto neglected optimization methods which may prove particularly useful within the MDO context. Copyright © 2013 by ASME.

STUDIES ON THE PURIFICATION AND RECLAMATION OF WASTE-WATER FROM A MEDIUM-SIZED CITY BY AN INTEGRATED BIOLOGICAL POND SYSTEM

The feasibility of an inexpensive wastewater treatment system is evaluated in this study. An integrated biological pond system was operated for more than 3 years to purify the wastewater from a medium-sized city, Central China. The experiment was conducted in 3 phases with different treatment combinations for testing their purification efficiencies. The pond system was divided into 3 functional regions: influent purification, effluent upgrading and multi-utilization. These regions were further divided into several zones and subzones. Various kinds of aquatic organisms, including macrophytes, algae, microorganisms and zooplankton, were effectively cooperating in the wastewater treatment in this system. The system attained high reductions of BOD5, COD, TSS, TN, TP and other pollutants. The purification efficiencies of this system were higher than those of most traditional oxidation ponds or ordinary macrophyte ponds. The mutagenic effect and numbers of bacteria and viruses declined significantly during the process of purification. After the wastewater flowed through the upgrading zone, the concentrations of pollutants and algae evidently decreased. Plant harvesting did not yield dramatic effects on reductions of the main pollutants, though it did significantly affect the biomass productivity of the macrophytes. The effluent from this system could be utilized in irrigation and aquaculture. Some aquatic products were harvested from this system and some biomass was utilized for food, fertilizer, fodder and some other uses. The wastewater was reclaimed for various purposes.

FREQUENCY RESPONSE OF FIBER RING RESONATOR AND ITS APPLICATION IN DFB LASER WAVELENGTH VARIATION MEASUREMENT

Frequency response of a fiber ring resonator (FRR) composed of an ordinary optical coupler and a segment of optical fiber is theoretically and experimentally investigated. The frequency response equation based oil small-signal modulation is derived and studied in detail. It is shown that the shape of the frequency response curve is very sensitive to the wavelength; as a result, the FRR can be applied to measure the wavelength of a lightwave source with high resolution. With this method, we demonstrate the measurement of tiny changes of wavelength of a DFB laser. (C) 2009 Wiley Periodicals. Inc. Microwave Opt Technol Lett 51 2444-2448, 2009 Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.24608

Electronic structure and optical property of semiconductor nanocrystallites

Semiconductor nanostructures show many special physical properties associated with quantum confinement effects, and have many applications in the opto-electronic and microelectronic fields. However, it is difficult to calculate their electronic states by the ordinary plane wave or linear combination of atomic orbital methods. In this paper, we review some of our works in this field, including semiconductor clusters, self-assembled quantum dots, and diluted magnetic semiconductor quantum dots. In semiconductor clusters we introduce energy bands and effective-mass Hamiltonian of wurtzite structure semiconductors, electronic structures and optical properties of spherical clusters, ellipsoidal clusters, and nanowires. In self-assembled quantum dots we introduce electronic structures and transport properties of quantum rings and quantum dots, and resonant tunneling of 3-dimensional quantum dots. In diluted magnetic semiconductor quantum dots we introduce magnetic-optical properties, and magnetic field tuning of the effective g factor in a diluted magnetic semiconductor quantum dot. (C) 2004 Elsevier B.V. All rights reserved.

Investigation of a chemically treated InP(100) surface during hydrophilic wafer bonding process

Surface micro-roughness, surface chemical properties, and surface wettability are three important aspects of wafer surfaces during a wafer cleaning process, which determine the bonding quality of ordinary direct wafer bonding. In this study, InP wafers are divided into four groups and treated by different chemical processes. Subsequently, the characteristics of the treated InP surfaces are carefully studied by X-ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM), and contact angle measurements. The optimal wafer treatment method for wafer bonding is determined by comparing the results of the processes as a whole. This optimization is later evaluated by a scanning electronic microscope (SEM), and the ridge waveguide 1.55 mu m Si-based InP/InGaAsP multi-quantum-well laser chips are also fabricated. (c) 2005 Elsevier B.V. All rights reserved.

Determination of the absorption for incident light propagating parallel through the guest-host polymer film waveguide

Guest host polymer thin films of polymethyl methacrylate (PMMA) incorporated with (4'-nitrobenzene)-3-azo-9-ethylcarbazole (NAEC) were fabricated by spin coating and then poled by the method of corona-onset poling at elevated temperature. The absorption mechanism of the polymeric film, which is very important for the optical transmission losses and directly relates to the orientation of chromophore NAEC in polymer PMMA, was investigated in detail. From the UV-visible absorption spectra for NAEC/PMMA film before and after being poled, we determined the change of absorption coefficient kappa with the wavelength and approximately calculated the maximum absorption A(parallel tomax) as 3.46 for incident light propagating parallel through the film, i.e. the ordinary polarized light, which cannot be directly measured in the spectro photometer. (C) 2002 Elsevier Science Ltd. All rights reserved.

A partially incoherent rate theory of long-range charge transfer in deoxyribose nucleic acid

A quantum chemistry based Green's function formulation of long-range charge transfer in deoxyribose nucleic acid (DNA) double helix is proposed. The theory takes into account the effects of DNA's electronic structure and its incoherent interaction with aqueous surroundings. In the implementation, the electronic tight-binding parameters for unsolvated DNA molecules are determined at the HF/6-31G* level, while those for individual nucleobase-water couplings are at a semiempirical level by fitting with experimental redox potentials. Numerical results include that: (i) the oxidative charge initially at the donor guanine site does hop sequentially over all guanine sites; however, the revealed rates can be of a much weaker distance dependence than that described by the ordinary Ohm's law; (ii) the aqueous surroundings-induced partial incoherences in thymine/adenine bridge bases lead them to deviate substantially from the superexchange regime; (iii) the time scale of the partially incoherent hole transport through the thymine/adenine pi stack in DNA is about 5 ps. (C) 2002 American Institute of Physics.

A VSLMS Style Tap-length Learning Algorithm for Structure Adaptation

Compared with the ordinary adaptive filter, the variable-length adaptive filter is more efficient (including smaller., lower power consumption and higher computational complexity output SNR) because of its tap-length learning algorithm, which is able to dynamically adapt its tap-length to the optimal tap-length that best balances the complexity and the performance of the adaptive filter. Among existing tap-length algorithms, the LMS-style Variable Tap-Length Algorithm (also called Fractional Tap-Length Algorithm or FT Algorithm) proposed by Y.Gong has the best performance because it has the fastest convergence rates and best stability. However, in some cases its performance deteriorates dramatically. To solve this problem, we first analyze the FT algorithm and point out some of its defects. Second, we propose a new FT algorithm called 'VSLMS' (Variable Step-size LMS) Style Tap-Length Learning Algorithm, which not only uses the concept of FT but also introduces a new concept of adaptive convergence slope. With this improvement the new FT algorithm has even faster convergence rates and better stability. Finally, we offer computer simulations to verify this improvement.

Hybrid numerical methods for exponential models of growth

A series of novel numerical methods for the exponential models of growth are proposed. Based on these methods, hybrid predictor-corrector methods are constructed. The hybrid numerical methods can increase the accuracy and the computing speed obviously, as well as enlarge the stability domain greatly. (c) 2005 Published by Elsevier Inc.

黄土高原降水计算插值与插值计算结果的对比分析

　收集黄土高原及周边地区74 个气象站1952 —2001 年降水数据, 用ArcGIS913 普通克里金(ordinary kriging) 插 值法采用计算插值(calculate then interpolate , CI) 和插值计算(interpolate then calculate , IC) 的方法生成黄土高原地区 1952 —2001 年50 a 平均年降水量和年降水量线性趋势系数空间分布表面, 并对其进行统计分析和地形分析。结果 表明: 1) 从插值结果统计值看, CI、IC 法生成的黄土高原地区50 a 平均年降水量和线性趋势系数空间分布表面平 均值分别为421165、421156 mm和- 01541 0、- 01423 1 mm/ a , 相似系数分别为99178 %和95199 % , 二者一致性良好; 2) 从插值结果表面光滑度看, IC 法稍优于CI 法,借用地形分析对生成表面进行坡度、坡向运算, 可作为评价表面 光滑度、空间数量变化特征和空间方向变化特征的直观方法; 3) 黄土高原地区50 a 平均年降水量具有东南多西北 少、南多北少、东多西少的分布规律, 其中服从东南西北、南北和东西方向递减的地带性分布规律区域占黄土高原 地区面积的89134 % , 非地带性分布规律区域占10166 %; 4) CI 和IC 法计算的黄土高原地区1952 —2001 年降水线 性趋势系数平均- 01541 0 和- 01423 1 mm/ a ,黄土高原地区年降水量有明显减少趋势。

土壤稳定入渗速率空间插值不确定性研究

以黄土丘陵沟壑第三副区的藉河流域为研究区,根据65个实测点数据,采用普通克里格法、反距离权重法、样条函数法等插值方法,分析了测点数量变化、栅格像元尺寸变化及插值方法的差异对土壤稳定入渗速率空间插值结果的影响,剖析了空间插值中的不确定性。结果表明:(1)参与插值站点越多,所得插值结果不确定性越小;(2)像元尺寸在25~800 m间变化对土壤稳定入渗速率的插值结果影响微弱;(3)不同插值方法对插值结果的精度影响较大,说明插值方法的差异对插值结果的不确定性有较大影响。

陕西省水蚀土壤因子指标插值方法比较研究

基于地统计学原理和半变异理论,采用地理信息系统技术定量研究了陕西省水蚀土壤因子指标的空间变异特征。分析比较了反距离权重法、样条函数法与普通克吕格法对陕西省土壤因子指标空间插值的精度。结果表明,研究区土壤抗冲系数具有中等强度的空间相关性,块金系数为32.29%,而稳渗速率、崩解速率、抗剪强度均表现为强烈的空间相关性,块金系数分别为13.19%,11.61%和12.98%。综合考虑平均相对误差、均方差及插值效果,认为普通克吕格法最好,更能反映土壤参数的空间特征并符合区域水土流失模型对数据的要求。对于普通克吕格法,稳渗速率的Lag步长为30 000 m,半方差理论模型为指数模型;抗冲系数、崩解速率、抗剪强度的Lag步长为55 000,半方差理论模型均为高斯模型。在空间分布上,各指标随土壤类型由北到南呈现明显的地带性规律。

Optical properties of delta-doped GaAs and GaAs/Al0.1Ga0.9As superlattices

Radiative transition in delta-doped GaAs superlattices with and without Al0.1Ga0.9As barriers is investigated by using photoluminescence at low temperatures. The experimental results show that the transition mechanism of delta-doped superlattices is very different from that of ordinary superlattices. Emission intensity of the transition from the electron first excited state to hole states is obviously stronger than that from the electron ground state to hole states due to larger overlap integral between wavefunctions of electrons in the first excited state and hole states. Based on the effective mass theory we have calculated the self-consistent potentials, optical transition matrix elements and photoluminescence spectra for two different samples. By using this model we can explain the main optical characteristics measured. Moreover, after taking into account the bandgap renormalization energy, good agreement between experiment and theory is obtained.