水稻模拟模型在高温敏感性研究中的应用

以调试校正较高精度的ORYZA2000模型参数及高温敏感性模拟验证为目的, 为模型适应性和本地化提供依据, 利用江苏省9个试验点5个水稻(Oryza sativa)品种的田间观测数据及当地逐日气象数据, 采用ORYZA2000最新版本(V2.13)水稻生长模型, 首先挑选出5个试验点3个品种的观测数据进行模型参数适应性调试校正, 确定了水稻发育生长阶段的各项参数, 然后用该参数对独立样本的4个试验点2个水稻品种地上部分各器官生物量、叶面积指数动态变化过程及最终产量进行了动态模拟。通过t检验和质量评价指标对模拟结果进行了显著性检验。利用通过检验的模型及其参数在假设环境温度不同时间段的持续升高条件下, 开展了高温对水稻生物量及产量影响的模拟研究, 模拟结果的影响幅度与实际高温处理结果的影响幅度进行了比较。结果表明: 1)经过调试校正获得较高精度的水稻发育阶段各参数, 较准确地模拟了水稻生物量和叶面积指数的动态累积过程, 模拟值与观测值基本一致, 说明校正后参数的合理性和有效性; 2)调整参数后高温敏感性模拟结果表明, 孕穗期到开花期温度连续3天、5天、7天升高到35 ℃时, 总生物量、穗生物量和总产量与对照(CK)相比分别下降了12%-25%; 不同时间段连续升高到38 ℃时下降18%-31%; 不同时间段升高到41 ℃时, 各生物量与对照相比分别下降了20%-38%。模型模拟值与控制试验室的观测数据的下降幅度基本一致, 表明经过参数校正的ORYZA2000可以应用于水稻对气温升高响应的预测。     

Application of a rice simulation model in high temperature sensitivity study

以调试校正较高精度的ORYZA2000模型参数及高温敏感性模拟验证为目的, 为模型适应性和本地化提供依据, 利用江苏省9个试验点5个水稻(Oryza sativa)品种的田间观测数据及当地逐日气象数据, 采用ORYZA2000最新版本(V2.13)水稻生长模型, 首先挑选出5个试验点3个品种的观测数据进行模型参数适应性调试校正, 确定了水稻发育生长阶段的各项参数, 然后用该参数对独立样本的4个试验点2个水稻品种地上部分各器官生物量、叶面积指数动态变化过程及最终产量进行了动态模拟。通过t检验和质量评价指标对模拟结果进行了显著性检验。利用通过检验的模型及其参数在假设环境温度不同时间段的持续升高条件下, 开展了高温对水稻生物量及产量影响的模拟研究, 模拟结果的影响幅度与实际高温处理结果的影响幅度进行了比较。结果表明: 1)经过调试校正获得较高精度的水稻发育阶段各参数, 较准确地模拟了水稻生物量和叶面积指数的动态累积过程, 模拟值与观测值基本一致, 说明校正后参数的合理性和有效性; 2)调整参数后高温敏感性模拟结果表明, 孕穗期到开花期温度连续3天、5天、7天升高到35 ℃时, 总生物量、穗生物量和总产量与对照(CK)相比分别下降了12%-25%; 不同时间段连续升高到38 ℃时下降18%-31%; 不同时间段升高到41 ℃时, 各生物量与对照相比分别下降了20%-38%。模型模拟值与控制试验室的观测数据的下降幅度基本一致, 表明经过参数校正的ORYZA2000可以应用于水稻对气温升高响应的预测。     

灌溉水稻生长发育和潜力产量的模拟模型

本文提出的HDRICE模型是灌溉水稻生长的生理生态模型,它由相互衍接的水稻形态发育、干物质积累和叶面积发育三模块组成。形态发育模块用以模拟逐日温度和日长对水稻发育的影响,其参数可反映水稻品种的基本营养性、感温性和感光性;干物质积累模块用以模拟冠层CO_2同化、作物的维持呼吸和生长呼吸及干物质分配等过程;叶面积发育模块用以模拟叶面积指数的动态。本文还讨论了模型的输入参数和模型检验。模型可应用于模拟水稻的生长发育,预测水稻品种潜在产量及为取得潜在产量所必需的群体数量指标。     

水稻一稻纵卷叶螟-天敌系统的优化管理

本研究是在水稻群体生长模型和纵卷叶螟种群生命系统模拟模型的基础上进行的。通过耦台水稻与纵卷叶螟相互关系模型,模拟了水稻-纵卷叶螟-天敌系统动态,估算了在不同条件下纵卷叶螟的产量损失率,结合经济核算确定不同条件组合下的经济阈值(多维动态经济阈值)。我们从稻田生态系统的整体出发,给出了稻纵卷叶螟管理系统流程图,图中将决策区分为趋势决策和实时决策,寓测报和防治于一体,以优化管理为目的。     

作物生长模拟模型参数校正与有效化的理论和实践

以ＧＯＳＳＹＭ 模型为例系统阐述了作物生长模拟模型有关参数校正和模型有效化的一般原理和方法,同时用新疆棉区的试验具体校正了品种参数、土壤参数和修改了部分模块,并对校正结果进行了验证．结果表明,两个试点土壤２０ ～４０ 、６０ ～８０ｃｍ 两个土层生长季水分动态观测值与土壤参数校正后模型的模拟值吻合较好;系５ 品种试验生育期６ 项生物指标动态模拟结果与实测值拟合的相关系数都在０ ．９ 以上,并且不同栽培条件的３ 个处理的模拟产量的相对误差平均为７ ．５ ％ ,模拟结果较理想．     

基于主成分分析水稻植株CH4排放估算模型

估算稻田甲烷（CH4）排放量是开展稻田甲烷排放研究的重要内容之一．通过观测南方红黄壤稻田不同水稻品种甲烷排放通量,测定了16个早稻、20个晚稻品种的植株节间组织的数量特征．选取株高、茎秆长度、茎秆维管束面积／茎壁横切面积、茎壁横切面积／节间横切面积、叶鞘横切面积／节间横切面积、气腔面积／茎壁横切面积、维管束总面积／茎壁横切面积等相关因子进行了主成分分析,建立基于水稻植株的CHa排放估算模型,早、晚稻估算模型相关系数分别为0．827、0．853．同时构造了综合评价函数,得出了水稻品种CH4排放综合分值,与实测结果相比较,吻合度较高．利用估算模型进行模拟,比较模拟值与实测值,相对误差较小,证明模型具有有效性和可行性,为估算水稻CH4排放提供参考依据,为评价水稻品种CH4排放高低提供经验参考．     

稻麦适宜氮素营养指标动态的模型设计

以水稻和小麦为研究对象,通过解析和提炼稻麦适宜氮素营养指标与品种类型、栽培技术、生态环境之间的定量关系,以基于生理发育时间（PDT）的相对生长度日和相对氮素营养指标为参数,建立了稻麦适宜氮素营养指标动态模型,并利用南京3年的大田试验资料对所建模型的可靠性和适应性进行了验证.结果表明：模型生成的水稻植株氮积累量和氮含量与实际观测值之间的平均根均方差（RMSE）分别为0.1245和0.1316;模拟的小麦植株氮积累量和氮含量与实际观测值之间的平均RMSE分别为0.1166和0.1301,表明模型对稻麦氮素营养指标动态具有较好的指导性,可为不同生态环境、品种类型和生产条件下的稻麦氮素营养诊断与管理调控提供定量化和精确化的指导.     

作物模型区域应用两种参数校准方法的比较

区域模拟的目的是利用有限的空间数据模拟出产量等作物性状的时空变异规律.然而站点作物模型应用到区域范围时涉及到数据归一化、参数简化、模型的校准和验证等问题.利用CERES-Rice模型对作物模型在我国的区域应用进行了尝试并对部分参数进行了校准.首先利用田间观测数据在各实验点上对模型进行了详细的站点校准,以验证模型在我国的模拟能力;其次,以我国水稻种植区(精确到亚区)为单位,运用平均值和标准差(RMSE)两种方法进行了区域校准和验证,即找出能反映出品种空间差异的代表性品种参数集;然后分别运用两种方法的校准结果,模拟水稻产量和成熟期,并将模拟结果与实测值进行了比较.结果表明:区域校准能反映出水稻生育期和产量的时空变化规律,其中RMSE法较平均值法效果好.目前作物模型区域应用过程中还存在大量的误差来源,有待进一步研究.     

水稻模型ORYZA2000在湖南双季稻区的验证与适应性评价

校准与验证水稻生长模型ORYZA2000,为模型本地化、区域化研究应用提供依据。本文采用湖南双季稻区作物田间观测数据,结合栽培管理措施、土壤以及同期逐日气象数据等资料对ORYZA2000进行参数校正,调试确定了早稻、晚稻有代表性品种的作物参数;利用独立的数据资料,对双季稻生育期、叶面积指数、生物量、产量等指标的模拟结果进行了详细地验证与适应性评价。结果表明：模型对双季稻品种的生育期模拟较好,开花期和成熟期的相对模拟误差为1—2d;早稻和晚稻叶面积指数的归一化均方根误差（NRMSE）均为24%,地上部总生物量、绿叶生物量、茎生物量和穗生物量的NRMSE值分别为18%、22%、22%、24%和19%、24%、28%、28%,产量的NRMSE值分别为11%和16%。校验的作物参数反映了湖南早稻和晚稻品种的生物学特性,参数值合理、有效。通过校准作物参数,ORYZA2000可较为准确地模拟双季稻生长发育及其生物量的动态累积过程,适应性较强,能够应用于双季稻生产。     

气候变化与水稻生长发育及产量形成关系的模拟研究

应用水稻生长日历模拟模型(RICAM1.3)模拟亚洲地区不同地点和不同气候条件下水稻的生育期和产量形成.其中3s-Beta模型被用于预测水稻开花期和描述水稻光温反应的3个连续阶段:基本营养生长期、光敏感期和光敏感后期.从时间与地理梯度的变化对水稻产量进行模拟,以中国、日本和菲律宾作为从北到南的地理梯度,以20世纪80年代气候变化作为时间梯度,应用RICAM1.3进行模拟.结果表明,模型具有广泛的适应性,能较好地模拟不同气候条件和不同水稻品种生育期的变化与产量的形成.     

From Molecular to Process Simulation: Novel Approaches to the Prediction of Phase Equilibria and PVT Behavior Based on Molecular/Quantum Mechanics and Molecular Dynamics Simulations

Abstract

Actually, in modern process simulators, more than 75% of the code implemented is dedicated to physical properties estimation, calculation and predictions. Data banks storing pure component parameters and binary interaction parameters for phase equilibrium calculations are extensively used and continuously implemented in actual process simulators. This gives an idea of the important role physical properties availability plays in process simulation.

In this paper we propose a new way for coupling molecular and process simulation. The basic machinery is to resort to molecular/quantum mechanics and molecular dynamics simulation techniques for generating the parameters of some equations of state that will subsequently be used for the prediction of phase equilibria and PVT behavior of small and polymeric molecules as well. This information, in turn, will be used as input in the process simulator, thus creating a final and well-defined bridge between molecular and process simulations in chemical engineering.     

树干径流单因子模拟实验分析

树干径流是发生在森林生态系统中的重要水文现象之一。已往,有关这方面的观测研究工作并不少见,但主要侧重于野外实际观测。由于影响因素错综复杂,单因子对干流影响的分析得不出比较满意的结果。     

Biochemical simulations: stochastic, approximate stochastic and hybrid approaches

Computer simulations have become an invaluable tool to studythe sometimes counterintuitive temporal dynamics of (bio-)chemicalsystems. In particular, stochastic simulation methods have attractedincreasing interest recently. In contrast to the well-knowndeterministic approach based on ordinary differential equations,they can capture effects that occur due to the underlying discretenessof the systems and random fluctuations in molecular numbers.Numerous stochastic, approximate stochastic and hybrid simulationmethods have been proposed in the literature. In this article,they are systematically reviewed in order to guide the researcherand help her find the appropriate method for a specific problem.      

Computerized scheme for the reaction of hemoglobin with ligands

A scheme for the reaction of hemoglobin with ligands is described, which postulates the functional heterogeneity of the chains, considers all possible combinations of the distribution of the ligand on the four chains of hemoglobin, and does not require simplifying assumptions about the hemoglobin reactivity. Ten tetrameric species are considered, together with 16 reactions between these species, each with an on and an off rate constant. The dissociation of hemoglobin tetramers into dimers is also considered, with four on and four off rate constants for the reactions between dimers, and ten equilibrium constants for the reactions between tetramers and dimers. Moreover, some side reactions, such as the trapping of ligands by a hemoglobin competitor, are included. A FORTRAN program, suitable for microcomputers, is described for handling this scheme, with some examples showing its advantages.     

Molecular Dynamics Simulation of Protein Folding with Supersecondary Structure Constraints

We integrate molecular dynamics simulation methods with a newly developed supersecondary structure prediction method and compute the structure of a protein molecule, crambin. The computed structure is similar to the crystal structure with an rms error of 3.94 Å.     

常规模拟定位和CT模拟定位的比较

目的:对比食管癌放射治疗中CT模拟定位和常规模拟定位的优劣。方法:对60例食管中、下段癌患者,同时行CT扫描和常规模拟定位;用三维计划系统制定治疗方案,比较分析这两种定位方法所描述靶区肿瘤的最大直径和等剂量分布情况。结果:两种定位方法肿瘤最大直径对比差别前后、右后、和左后分别为:2.0±0.5、4.3±1.2、1.4±0.35、4.0±1.1、1.5±0.4、3.6±1.2;等剂量曲线分布为60例和31例,差异有统计学意义。结论:CT模拟定位较常规模拟定位能更充分显示肿瘤外侵范围并反映其非对称性生长。     

Monte Carlo Study of Structural and Thermodynamic Properties of Liquid Chloroform Using a Five Site Model

A five site potential model combining Lennard–Jones plus Coulomb potential functions has been developed for chloroform molecule. The partial charges needed for Coulombic interactions were derived using the chelpg procedure implemented in the gaussian 92 program. These calculations were performed at the MP2 level with MC-311G* basis set for Cl and 6-311G** for C and H atoms. The parameters for the Lennard–Jones potentials were optimized to reproduce experimental values for the density and enthalpy of vaporization of the pure liquid at 298 K and 1 atm. The statistical mechanics calculations were performed with the Monte Carlo method in the isothermic and isobaric (NpT) ensemble. Besides the values obtained for density, ρ, and molar enthalpy of vaporization at constant pressure, Δ H_V, for liquid chloroform, results for molar volume, V_m, molar heat capacity, C_p, isobaric thermal expansivity, α_p, and isothermal compressibility, κ_T, for this pure liquid are also in very good agreement with experimental observations. Size effects on the values of thermodynamic properties were investigated. The potential model was also tested by computing the free energy for solvating one chloroform molecule into its own liquid at 298 K using a statistical perturbation approach. The result obtained compares well with the experimental value. Site–site pair correlation functions were calculated and are in good accordance with theoretical results available in the literature. Dipole–dipole correlation functions for the present five site model were also calculated at different carbon–carbon distances. These correlations were compared to those obtained using the four site model reported in the literature. An investigation of the solvent dependence of the relative free energy for cis/trans conversion of a hypothetical solute in TIP4P water and chloroform was accomplished. The results show strong interaction of water and chloroform molecules with the gauche conformer. The value obtained for the free energy barrier for cis/trans rotation in TIP4P water is higher than that for chloroform. This result is in agreement with the continuous theory for solvation as the conformer with higher dipole moment is more favoured by the solvent with higher dieletric constant. The results also show an increase in entropy as the solute goes from the cis to the trans geometry and this result is more appreciable in the aqueous solution. This revised version was published online in June 2006 with corrections to the Cover Date.     

An approach to generate noncontact ACL-injury prone situations on a computer using kinematic data of non-injury situations and Monte Carlo simulation

ACL-injuries are one of the most common knee injuries in noncontact sports. Kinematic data of injury prone situations provide important information to study the underlying ACL-injury mechanisms. However, these data are rare. In this work an approach is presented to generate injury prone situations for noncontact ACL-injuries on a computer. The injury prone situations are generated by a musculoskeletal simulation model using kinematic data of a non-injury situation and the method of Monte Carlo simulation. The approach is successfully applied to generate injury prone landings in downhill ski racing. The characteristics of the obtained injury prone landings are consistent with video recordings of injury cases.     

Molecular dynamics simulations of peptides and proteins with a continuum electrostatic model based on screened Coulomb potentials

A continuum electrostatics approach for molecular dynamics (MD) simulations of macromolecules is presented and analyzed for its performance on a peptide and a globular protein. The approach incorporates the screened Coulomb potential (SCP) continuum model of electrostatics, which was reported earlier. The model was validated in a broad set of tests some of which were based on Monte Carlo simulations that included single amino acids, peptides, and proteins. The implementation for large-scale MD simulations presented in this article is based on a pairwise potential that makes the electrostatic model suitable for fast analytical calculation of forces. To assess the suitability of the approach, a preliminary validation is conducted, which consists of (i) a 3-ns MD simulation of the immunoglobulin-binding domain of streptococcal protein G, a 56-residue globular protein and (ii) a 3-ns simulation of Dynorphin, a biological peptide of 17 amino acids. In both cases, the results are compared with those obtained from MD simulations using explicit water (EW) molecules in an all-atom representation. The initial structure of Dynorphin was assumed to be an alpha-helix between residues 1 and 9 as suggested from NMR measurements in micelles. The results obtained in the MD simulations show that the helical structure collapses early in the simulation, a behavior observed in the EW simulation and consistent with spectroscopic data that suggest that the peptide may adopt mainly an extended conformation in water. The dynamics of protein G calculated with the SCP implicit solvent model (SCP-ISM) reveals a stable structure that conserves all the elements of secondary structure throughout the entire simulation time. The average structures calculated from the trajectories with the implicit and explicit solvent models had a cRMSD of 1.1 A, whereas each average structure had a cRMSD of about 0.8A with respect to the X-ray structure. The main conformational differences of the average structures with respect to the crystal structure occur in the loop involving residues 8-14. Despite the overall similarity of the simulated dynamics with EW and SCP models, fluctuations of side-chains are larger when the implicit solvent is used, especially in solvent exposed side-chains. The MD simulation of Dynorphin was extended to 40 ns to study its behavior in an aqueous environment. This long simulation showed that the peptide has a tendency to form an alpha-helical structure in water, but the stabilization free energy is too weak, resulting in frequent interconversions between random and helical conformations during the simulation time. The results reported here suggest that the SCP implicit solvent model is adequate to describe electrostatic effects in MD simulation of both peptides and proteins using the same set of parameters. It is suggested that the present approach could form the basis for the development of a reliable and general continuum approach for use in molecular biology, and directions are outlined for attaining this long-term goal.