基于元胞自动机的城市生态安全格局模拟——以东莞市为例

以城市化快速发展的东莞市为研究对象,选取景观生态安全程度为评价标准,获取生态安全的元胞1 km×1 km范围内的城市化元胞数,将其嵌入元胞自动机(CA)转换规则中作为约束条件,控制城市发展,建立生态安全的城市CA,模拟生态安全的城市发展形态.结果表明: 东莞市综合景观生态安全指数从1988年的0.497降低到2005年的0.395,景观尺度上的生态安全下降.利用生态安全的CA模拟的2005年东莞市生态安全指数由实际的0.395增加到0.479,模拟的城市景观生态压力减小、生态安全状态和综合景观生态安全程度提高.CA可以作为探索生态安全城市研究的有效工具.     

基于元胞自动机的森林水源涵养量模型新方法——概念与理论框架

模型方法是定量评价森林水源涵养的重要途径。根据元胞自动机的基本理论,结合森林水源涵养效应的多尺度特征,提出了一个新的基于元胞自动机的森林水源涵养量计算模型。该模型将森林"水文响应单元"网格化作为元胞空间的基本单元,邻域定义为摩尔(Moore)型,元胞"水库"水量状态变化范围定义在一个连续的实数空间上。将元胞单元对不同降雨事件的响应分为不产生径流和产生径流两种情况,通过对蒸散发、邻域元胞间水量传输、深层渗漏等制定转换规则,模拟森林在不同尺度上的水源涵养动态特征。这种新模型方法将为森林水源涵养由小尺度(水文响应单元)向流域、景观尺度上推提供有效的定量研究途径,从而进一步推动森林水源涵养功能研究的深入。     

基于智能体模型的土地利用动态模拟研究进展

土地利用动态变化是全球变化和可持续发展研究的基础,对区域水循环、大气循环、环境质量、气候变化及陆地生态系统生产力等具有重要影响,也是造成生物多样性衰减的最主要原因.目前,建立于复杂性科学基础上的的智能体模型(ABM)成为土地利用动态模拟的重要方法.智能体模型能模拟个体或群体的行为及决策模式,从而能将政府、城市规划、房地产开发商、住户等社会群体及个人对土地利用产生的影响进行模拟,同时能对不同社会经济政策对土地动态影响进行模拟.智能体模型在元胞自动机基础上,加入了人为因素的智能体概念,从而能更好地模拟土地动态.在分析总结了智能体模型的相关概念和组织结构,并分析了其在土地利用动态、城市动态模拟及生态过程模拟等方面的应用与元胞自动机的关系,比较了常用的智能体模型的主要软件,最后概括了智能体模型优点、发展趋势及存在的主要问题.     

基于元胞自动机的城市空间动态模拟

城市空间动态的模拟与预测可以为城市可持续发展规划与管理提供重要的参考依据。SLEUTH元胞自动机模型在城市空间模拟中较强的适用性和可移植性,该模型通过对历史数据的蒙特卡洛迭代自动寻找城市增长误差最小的参数组合,解决了传统元胞自动机模型中转换规则不易确定的问题。以武汉市为研究案例,运用SLEUTH模型进行了城市空间动态模拟与情景预测。2007年至2011年的城市空间模拟结果显示,模拟结果与实际历史数据可以获得良好的空间匹配度,Lee-Sallee形状指数均在0.6以上,显示SLEUTH元胞自动机模型经过本地化校正后具有较强的适用性和满意的模拟精度。进而,设置了现状趋势、基本保护、严格保护等3种情景对武汉2025年城市空间动态进行了预测,结果显示,各情景模式下城市居住用地均明显增长,农业用地、林地、水域等均有所减少;现状趋势情景和基本保护情景下农田、林地、水域减少的幅度较大,会加剧区域的生境破碎、耕地功能下降、水资源匮乏、湖滨湿地萎缩等生态问题,说明这两种情景不能有效满足城市生态系统健康和可持续发展的需要。严格保护情景下,城市居住用地扩张的程度得到了明显的控制,水域和林地得到了有效的保护,对于重要的自然生态系统组分保护及其服务能力维持可以起到显著作用。     

软计算在生态模型中的应用

由于生态系统的高度复杂性和非线性以及空间数据采集技术的快速发展,近年来越来越多的软计算方法开始应用到生态模拟中来。软计算是个非常广泛的领域,在模式上主要包括元胞自动机、基于个体和盒式模式等;在方法上代表性的有人工神经网络、模糊数学、遗传算法、混沌理论等。重点介绍元胞自动机和规律方法在生态模型中的应用,具体实例包括种群动态模拟、水华预警和生境栖息地模拟。     

不同样本方案下遗传元胞自动机的土地利用模拟及景观评价

利用元胞自动机(cellular automata,CA)模拟土地利用情景,有助于理解其变化机理,并为土地资源持续利用提供空间决策支持.本文基于生物进化过程的遗传算法(genetic algo-rithm,GA)将CA参数编码成为染色体,在模拟结果与真实结果差异值的引导下,通过选择、杂交和变异算子使最优的染色体得以遗传和保留,从而建立智能优化的元胞自动机模型.以浙江省嘉兴市1992-2008年土地利用变化为例,分别利用6%(66个·km-2)和3%(33个·km-2)两种样本方案构建遗传CA模型进行土地利用变化模拟,并通过混淆矩阵、Kappa系数和景观指数对模拟结果进行评估.结果表明:遗传CA模拟结果能在数量、位置和景观格局上以超过80%的水平接近真实分类,且大样本量构建的遗传CA的模拟精度更高;2008年的模拟精度和景观综合指数低于2001年,表明遗传CA的模拟精度和景观综合指数随模拟时间而衰减.     

“生态位”元胞自动机在土地可持续规划模型中的应用

快速城市化带来了一系列的环境生态问题。有必要把生态学的概念引进城市规划中,以减少城市发展带来的弊端。提出了基于“生态位”的元胞自动机（CA）的新模型,并将其应用在土地利用规划中。探讨了如何通过“生态位”元胞自动机和GIS的结合进行城市土地可持续利用的规划。该模型可方便地探索不同土地利用政策下城市土地利用发展情景,能够为城市规划提供有用的决策支持。旨在探索通过模拟的手段对城市土地利用进行合理的规划。将该模型应用于快速发展的广州市,并取得了较有意义的结果。     

基于生态安全格局理论的国土空间生态修复分区模拟——以粤港澳大湾区为例

国土空间生态修复分区有助于推动生态修复工作的整体性和系统性。利用国土空间生态安全格局理论进行生态修复分区是一种较为经典的模式，但现有分区技术方案对高强度人类活动导致的土地利用景观变化考虑不足，不能很好的适应城市群尺度国土空间生态安全格局的塑造需求。设计了一种基于情景模拟的国土空间生态修复分区方案，该框架首先通过耦合空间马尔科夫链与元胞自动机模型模拟城镇化发展末期的土地利用景观格局；然后利用"生态源地-生态廊道-生态网络"理论构建国土空间生态安全格局基本骨架；最后根据最小累积阻力模型划分出生态修复关键区、调节区和双修区等类型。粤港澳大湾区案例研究表明：（1）土地利用景观变化对生态修复分区方案影响较大，不同景观格局导致的分区规模差异可达国土空间的10%左右；（2）国土空间生态修复分区需要充分考虑高强度人类活动对景观格局变化的潜在影响，进而使得生态修复分区政策更有利于国土空间生态安全格局塑造目标的实现。研究构建的国土空间生态修复分区技术方案可进一步深化生态安全格局理论在国土空间规划应用上的认知。     

基于种间竞争模型的毒杂草入侵空间分布模拟研究

以天然草场中毒杂草与可食牧草为研究对象,在种间竞争的生态数学模型的基础上引入入侵扩散因素建立毒杂草入侵扩散模型。采用元胞自动机理论将竞争模型扩展到空间网络进行模拟研究,分析毒杂草属的空间分布类型,为毒杂草的控制提供数据支持。研究表明:(1)在入侵扩散作用下,毒杂草与可食牧草的共存平衡点由一个增加为两个,增加了共存的可能性;(2)入侵扩散作用影响了毒杂草种群的空间分布特征,减少了种群空间分布的聚集程度。     

基于CA-Markov模型和多目标优化的大连市土地利用格局

运用马尔科夫转移矩阵、多准则评估以及元胞自动机耦合的CA-Markov模型,基于1990、2000、2010年土地利用图、地形因子和地理要素等,模拟大连市未来土地利用景观格局变化趋势.基于大连市土地利用结构、经济社会、自然环境等特点,结合大连市城市总体规划和土地利用规划,建立经济、社会、环境3个目标导向的模糊多目标优化模型,优化配置了大连市未来土地利用格局.结果表明:1990-2010年,大连的快速发展呈现出建设用地持续扩张而耕地、林地面积缩小的特点,以现有城市化速度发展,到2020年大连市景观格局土地覆盖将发生很大变化,景观破碎化程度将加剧.优化调整土地利用数量结构,能满足未来大连可持续发展的要求.     

农牧交错带西段景观结构和空间异质性分析

农牧交错地区是生态环境问题突出的地区。运用景观学理论,选取典型区域通过具体的景观特征指数分析了西北农牧交错景观的景观结构和景观空间异质性。结果表明地形地貌和人类作用是西北农牧交错区景观异质性的主导因素,地貌越破碎人类作用越强,景观也越破碎,斑块不规则性越高,景观多样性越高。进一步的景观样带分析显示,研究区景观结构呈一定的空间梯度变化,由南向北景观破碎度减小,斑块形状的不规则性降低。     

Zipping and Unzipping of Adenylate Kinase: Atomistic Insights into the Ensemble of Open ↔ Closed Transitions

Adenylate kinase (AdK), a phosphotransferase enzyme, plays an important role in cellular energy homeostasis. It undergoes a large conformational change between an open and a closed state, even in the absence of substrate. We investigate the apo-AdK transition at the atomic level both with free-energy calculations and with our new dynamic importance sampling (DIMS) molecular dynamics method. DIMS is shown to sample biologically relevant conformations as verified by comparing an ensemble of hundreds of DIMS transitions to AdK crystal structure intermediates. The simulations reveal in atomic detail how hinge regions partially and intermittently unfold during the transition. Conserved salt bridges are seen to have important structural and dynamic roles; in particular, four ionic bonds that open in a sequential, zipper-like fashion and, thus, dominate the free-energy landscape of the transition are identified. Transitions between the closed and open conformations only have to overcome moderate free-energy barriers. Unexpectedly, the closed state and the open state encompass broad free-energy basins that contain conformations differing in domain hinge motions by up to 40°. The significance of these extended states is discussed in relation to recent experimental Förster resonance energy transfer measurements. Taken together, these results demonstrate how a small number of cooperative key interactions can shape the overall dynamics of an enzyme and suggest an “all-or-nothing” mechanism for the opening and closing of AdK. Our efficient DIMS molecular dynamics computer simulation approach can provide a detailed picture of a functionally important macromolecular transition and thus help to interpret and suggest experiments to probe the conformational landscape of dynamic proteins such as AdK.     

A Multi-Paradigm Modeling Framework to Simulate Dynamic Reciprocity in a Bioreactor

Despite numerous technology advances, bioreactors are still mostly utilized as functional black-boxes where trial and error eventually leads to the desirable cellular outcome. Investigators have applied various computational approaches to understand the impact the internal dynamics of such devices has on overall cell growth, but such models cannot provide a comprehensive perspective regarding the system dynamics, due to limitations inherent to the underlying approaches. In this study, a novel multi-paradigm modeling platform capable of simulating the dynamic bidirectional relationship between cells and their microenvironment is presented. Designing the modeling platform entailed combining and coupling fully an agent-based modeling platform with a transport phenomena computational modeling framework. To demonstrate capability, the platform was used to study the impact of bioreactor parameters on the overall cell population behavior and vice versa. In order to achieve this, virtual bioreactors were constructed and seeded. The virtual cells, guided by a set of rules involving the simulated mass transport inside the bioreactor, as well as cell-related probabilistic parameters, were capable of displaying an array of behaviors such as proliferation, migration, chemotaxis and apoptosis. In this way the platform was shown to capture not only the impact of bioreactor transport processes on cellular behavior but also the influence that cellular activity wields on that very same local mass transport, thereby influencing overall cell growth. The platform was validated by simulating cellular chemotaxis in a virtual direct visualization chamber and comparing the simulation with its experimental analogue. The results presented in this paper are in agreement with published models of similar flavor. The modeling platform can be used as a concept selection tool to optimize bioreactor design specifications.     

Using motion planning to study RNA folding kinetics.

We propose a novel, motion planning based approach to approximately map the energy landscape of an RNA molecule. A key feature of our method is that it provides a sparse map that captures the main features of the energy landscape which can be analyzed to compute folding kinetics. Our method is based on probabilistic roadmap motion planners that we have previously successfully applied to protein folding. In this paper, we provide evidence that this approach is also well suited to RNA. We compute population kinetics and transition rates on our roadmaps using the master equation for a few moderately sized RNA and show that our results compare favorably with results of other existing methods.     

一种新的景观扩张指数的定义与实现

景观格局动态信息的定量表达始终是景观生态学研究的一个重要科学问题,景观格局指数是其中的一种重要方法,但其多是静态指数,难以有效定量表达景观格局的动态信息.因此,针对景观扩张过程以斑块扩张面积为基础提出了一种新的景观扩张指数,来表达景观格局的动态信息.并以妫水河流域1998-2009年的景观农田化过程为例,验证该指数的适用性,结果表明:该指数不仅能够定量表达斑块的空间扩张规模,而且可以准确识别斑块的空间扩张模式.根据扩张斑块与原斑块的空间位置关系,将景观的空间扩张模式划分为邻接扩张式和外部扩张式两种.提出的景观扩张指数在技术方法上计算简便,易于实现,完善了景观格局动态的量化表征科学方法.     

Evaluation of dynamic behavior forecasting parameters in the process of transition rule induction of unidimensional cellular automata

The simulation of the dynamics of a cellular systems based on cellular automata (CA) can be computationally expensive. This is particularly true when such simulation is part of a procedure of rule induction to find suitable transition rules for the CA. Several efforts have been described in the literature to make this problem more treatable. This work presents a study about the efficiency of dynamic behavior forecasting parameters (DBFPs) used for the induction of transition rules of CA for a specific problem: the classification by the majority rule. A total of 8 DBFPs were analyzed for the 31 best-performing rules found in the literature. Some of these DBFPs were highly correlated each other, meaning they yield the same information. Also, most rules presented values of the DBFPs very close each other. An evolutionary algorithm, based on gene expression programming, was developed for finding transition rules according a given preestablished behavior. The simulation of the dynamic behavior of the CA is not used to evaluate candidate transition rules. Instead, the average values for the DBFPs were used as reference. Experiments were done using the DBFPs separately and together. In both cases, the best induced transition rules were not acceptable solutions for the desired behavior of the CA. We conclude that, although the DBFPs represent interesting aspects of the dynamic behavior of CAs, the transition rule induction process still requires the simulation of the dynamics and cannot rely only on the DBFPs.     

Modeling of adhesion, protrusion, and contraction coordination for cell migration simulations

Cell migration is a highly complex, dynamical biological phenomenon that involves precise spatio-temporal coordination of distinctive sub-processes including adhesion, protrusion, and contraction of the cell. Observations of individual tumor cell migration reveal that cells generally exhibit either mesenchymal-type or amoeboid-type migration modes in native like environments. However, it has also been observed that some migrating cells are capable of morphologically adapting to their environment by modifying their type of migration. Recent studies suggest in fact that changes in biophysical and biomechanical properties of tumor cells can reversibly control their transition from one type of migration to the other. These changes may be caused by internal cell biomechanical mechanisms as well as mechanical and topological properties of the extracellular matrix. In order to understand the complex transition between the two modes and the role played by internal cellular mechanics during migration, we have developed a novel axisymmetric hyperviscoelastic cell model to simulate the dynamical behavior of a migrating cell. Numerical results from our study quantitatively demonstrate that the biomechanical properties of the cell may play an important role in the amoeboid-mesenchymal transition during migration. Our study will therefore not only help in creating a new platform for simulating cellular processes but will also provide insights into the role of sub-cellular mechanics in regulating various modes of migration during tumor invasion and metastasis.     

基于景观格局-服务的景观生态风险评价——以广州市为例

城市化对景观的结构和功能造成极大干扰,城市景观变化引起的生态风险受到城市生态建设的关注,但景观生态风险评价技术体系尚待深化,以促进风险防范决策。研究选取植被碳固定、土壤保持、水源涵养与提供和栖息地提供等景观服务改进景观脆弱度的评价方法,以广州市为案例研究区,评价了1990—2015年广州市城市景观生态风险及其时空变化特征。研究结果表明:(1)基于景观格局与服务的景观生态风险评价能够有效地评估城市景观生态风险的空间分布,但评价需要关注结果验证和辅助情景分析,方可为景观生态风险的预警和预测提供科学依据。(2)1990—2015年广州市的景观干扰度先增加后降低,2000年是景观干扰度变化的转折点;25年间,景观脆弱度不断增加,中脆弱度和高脆弱度比例之和维持在60%以上;2000年是景观生态风险的转折点,1990—2000年景观生态风险趋于增大,2000—2015年景观生态风险趋向降低;景观干扰度、脆弱度和生态风险在空间上呈现南部高于北部,西部高于东部的分布特征。(3)近25年,广州市景观生态风险与景观变化具有较好的空间一致性。维持低风险的比例为40.74%,基本都分布在北部山区,而维持高风险的比例为6.67%,由低风险向高风险的转变比例为32.28%,由高风险转变为低风险的比例为20.31%。