Potential Landscape and Flux Framework of Nonequilibrium Networks: Robustness, Dissipation, and Coherence of Biochemical Oscillations

We established a theoretical framework for studying nonequilibrium networks with two distinct natures essential for characterizing the global probabilistic dynamics: the underlying potential landscape and the corresponding curl flux. We applied the idea to a biochemical oscillation network and found that the underlying potential landscape for the oscillation limit cycle has a distinct closed ring valley (Mexican hat-like) shape when the fluctuations are small. This global landscape structure leads to attractions of the system to the ring valley.

Robustness and Coherence of a Three-Protein Circadian Oscillator: Landscape and Flux Perspectives

Three-protein circadian oscillations in cyanobacteria sustain for weeks. To understand how cellular oscillations function robustly in stochastic fluctuating environments, we used a stochastic model to uncover two natures of circadian oscillation: the potential landscape related to steady-state probability distribution of protein concentrations; and the corresponding flux related to speed of concentration changes which drive the oscillations. The barrier height of escaping from the oscillation attractor on the landscape provides a quantitative measure of the robustness and coherence for oscillations against intrinsic and external fluctuations. The difference between the locations of the zero total driving force and the extremal of the potential provides a possible experimental probe and quantification of the force from curl flux. These results, correlated with experiments, can help in the design of robust oscillatory networks.

Potential energy landscape and robustness of a gene regulatory network: Toggle switch

Finding a multidimensional potential landscape is the key for addressing important global issues, such as the robustness of cellular networks. We have uncovered the underlying potential energy landscape of a simple gene regulatory network: a toggle switch. This was realized by explicitly constructing the steady state probability of the gene switch in the protein concentration space in the presence of the intrinsic statistical fluctuations due to the small number of proteins in the cell. We explored the global phase space for the system. We found that the protein synthesis rate and the unbinding rate of proteins to the gene were small relative to the protein degradation rate; the gene switch is monostable with only one stable basin of attraction. When both the protein synthesis rate and the unbinding rate of proteins to the gene are large compared with the protein degradation rate, two global basins of attraction emerge for a toggle switch. These basins correspond to the biologically stable functional states. The potential energy barrier between the two basins determines the time scale of conversion from one to the other. We found as the protein synthesis rate and protein unbinding rate to the gene relative to the protein degradation rate became larger, the potential energy barrier became larger. This also corresponded to systems with less noise or the fluctuations on the protein numbers.

Bibarba bibarba: A new genus and species of Cobitinae (Pisces : Cypriniformes : Cobitidae) from Guangxi Province (China)

A new genus of Cobitinae, Bibarba gen. n., and a new species, B. bibarba sp. n., were discovered and are described for the Chengjiang River, a tributary of the Hongshuihe River in Guangxi Province of southern China. This river region is characterized by a Karst landscape, and the river that is inhabited by the new genus is a slowly moving stream with arenaceous and cobblestone beds. The new genus resembles Cobitis Linnaeus, 1758 (subfamily Cobitinae) in the shape and pigmentation pattern of their body, the absence of scales on their head, and the presence of a suborbital spine, but differs from it by a single Lamina circularis on the third pectoral fin ray instead of on the base of the second pectoral fin ray; two pairs of barbels (one rostral pair and one maxillo-mandibular pair) instead of three pairs of barbels (one rostral pair, one maxillary pair, and one maxillo-mandibular pair); a relatively thick and short suborbital spine with a strong medio-lateral process instead of a suborbital spine without or with a weakly formed medio-lateral process as in Cobitis; and the lack of a black stripe extending from the occiput through the eye to the insertion of the rostral barbel. The first two characters have not been reported in any other genus of the subfamily Cobitinae. A morphometric character analysis based on PCA reveals differences between B. bibarba and C. sinensis in body size, barbel length, interorbital width, pectoral fin length in males, and the position of the dorsal and ventral fins. Type specimens of the new species are kept in the Freshwater Fishes Museum of the Institute of Hydrobiology at the Chinese Academy of Sciences in Wuhan, Hubei Province. (c) 2007 Elsevier GmbH. All rights reserved.

Kinetics and Statistical Distributions of Single-Molecule Conformational Dynamics

We developed a coarse-grained yet microscopic detailed model to study the statistical fluctuations of single-molecule protein conformational dynamics of adenylate kinase. We explored the underlying conformational energy landscape and found that the system has two basins of attractions, open and closed conformations connected by two separate pathways. The kinetics is found to be nonexponential, consistent with single-molecule conformational dynamics experiments. Furthermore, we found that the statistical distribution of the kinetic times for the conformational transition has a long power law tail, reflecting the exponential density of state of the underlying landscape. We also studied the joint distribution of the two pathways and found memory effects.

Optimal specificity and function for flexible biomolecular recognition

Biomolecular associations often accompanied by large conformational changes, sometimes folding and unfolding. By exploring an exactly solvable model, we constructed the free energy landscape and established a general framework for studying the biomolecular flexible binding process. We derived an optimal criterion for the specificity and function for flexible biomolecular binding where the binding and conformational folding are coupled.

Optimal specificity and function for flexible biomolecular recognition

Biomolecular associations often accompanied by large conformational changes, sometimes folding and unfolding. By exploring an exactly solvable model, we constructed the free energy landscape and established a general framework for studying the biomolecular flexible binding process. We derived an optimal criterion for the specificity and function for flexible biomolecular binding where the binding and conformational folding are coupled.

Land-cover changes in an urban lake watershed in a mega-city, Central China

Urbanization can exert a profound influence on land covers and landscape characteristics. In this study, we characterize the impact of urbanization on land cover and lacustrine landscape and their consequences in a large urban lake watershed, Donghu Lake watershed (the largest urban lake in China), Central China, by using Landsat TM satellite images of three periods of 1987, 1993 and 1999 and ground-based information. We grouped the land covers into six categories: water body, vegetable land, forested land, shrub-grass land, open area and urban land, and calculated patch-related landscape indices to analyze the effects of urbanization on landscape features. We overlaid the land cover maps of the three periods to track the land cover change processes. The results indicated that urban land continuously expanded from 9.1% of the total watershed area in 1987, to 19.4% in 1993, and to 29.6% in 1999. The vegetable land increased from 7.0% in 1987, 11.9% in 1993, to 13.9% in 1999 to sustain the demands of vegetable for increased urban population. Concurrently, continuous reduction of other land cover types occurred between 1987 and 1999: water body decreased from 30.4% to 23.8%, and forested land from 33.6% to 24.3%. We found that the expansion of urban land has at least in part caused a decrease in relatively wild habitats, such as urban forest and lake water area. These alterations had resulted in significant negative environmental consequences, including decline of lakes, deterioration of water and air quality, and loss of biodiversity.

若尔盖自然保护区高原林蛙(Rana kukunoris)扩散模型与景观连接分析

揭示水体中繁殖的两栖动物在异质性景观中的空间扩散特点，探讨景观面积丧失和破碎化对于两栖动物的影响，为两栖动物的保护提供理论依据。本文以四川西北部若尔盖湿地自然保护区的高原林蛙(Rana kukunoris)为研究对象，通过运用地理信息系统及建立景观模型等方法，在分析若尔盖湿地自然保护区范围内现有景观格局的基础上，建立了高原林蛙的景观扩散模型，并模拟了“沼泽→草甸”的湿地逆演化过程下高原林蛙的空间分布与景观连接的变化特点。主要结果是： 1．若尔盖湿地自然保护区呈典型的沼泽—草甸式斑块—基质景观格局。草甸面积占整个景观面积的79.42%，景观蔓延度指数（CONTAG）为79.00远离最小值0而更趋向于最大值100，面积和景观蔓延度指数表明草甸是整个景观中面积占绝对优势且景观连接好的类型，构成了景观的基质，对景观的动态格局演变起主导作用。沼泽面积仅占整个景观面积的18.08%，但却是整个景观中斑块数目最多的单元，占所有斑块数的82.9%。因此沼泽斑块与草甸基质之间的动态结构对高原林蛙的扩散起着决定性的作用。 2．空间扩散模型表明，其它类型的景观不但扩展了高原林蛙的活动范围，而且也为高原林蛙在不同沼泽斑块间的连接提供了通道。高原林蛙的空间扩散区域使得彼此间成斑块化隔离状分布的沼泽形成了潜在景观功能连接，促进了不同斑块间物种的交流。小型沼泽作为垫脚石（stepping-stone），使得整个景观中的相隔距离较远的大型斑块联结为一个功能整体，促进了高原林蛙在整个景观中的相互动态联系。 3．模拟“沼泽→草甸”的湿地逆演化过程表明，大量小型沼泽湿地的消失将会 对在沼泽中繁殖并扩散到其它景观类型中去的高原林蛙造成潜在影响。逆演化过程不仅使沼泽斑块的分布范围，沼泽源斑块的面积和空间扩散面积减少，而且对景观连接也有很大影响。小型沼泽的消失，将使得景观斑块的功能连接变小，使得依靠小型沼泽作为跳板的动物在沼泽斑块之间的移动将变得更加困难。 本文是对生境丧失与破碎化影响下两栖动物的行为反应的一种尝试。影响模型的因素很多，包括动物对各种类型景观的偏好程度，地理数据的精度，及模型的可靠程度都是制约模型准确度的因素。 The spatial diffusion of water—breeding amphibian through heterogeneous landscape and the effects of landscape losing and fragmentation to amphibian were the core theory of the landscape ecology of amphibian. Geographical information system (GIS) and landscape model were used to model the diffused area of Rana kukunoris in Zoige Wetland Natural Reserve. Model was also used to analysis the spatial distribution variation of R. kukunoris and the change of landscape connectivity when simulated the retrogressive succession of landscape. The main results are below: 1. There was peatland—meadow pattern which was typical patch—matrix landscape pattern in Zoige Natural Reserve. The meadow area occupied 79.42% of the entire landscape area, contagion index (CONTAG) was 79.00 which was far away the minimum value (0) but tend to the maximum value (100). Both of these showed that meadow was the largest part and the most continue units. It was shown that meadow was matrix of the landscape, which evolved the leading role to the landscape dynamic pattern. Though their area only occupies 18.08% of entire landscape area, peatlands were according to 82.9% of the total patches. Dynamic of the pattern between peatlands and meadows decided the spatial diffusion of R. kukunoris. 2．The model indicated that the other types of landscape not only expanded diffusion of R. kukunoris, but also have provided the potential channels for frog's connections among different peatlands. The spatial diffusion zone of R. kukunoris forced isolated patch peatlands to be potential landscape functional connectivity. The small peatlands, as stepping-stone, made the large peatlands connect as a functional one and promoted the integrated and dynamic connectivity of R. kukunoris in the whole landscape. 3. The simulation of “peatlands→meadows”retrogressive succession process indicated that the decrease of small peatlands will have potential effect to R. kukunoris because they must bred in peatlands and diffuse to other type of the landscape. Retrogressive succession process not only made the decrease of distribution of peatlands, patches number of peatlands and diffused area of R. kukunoris, but also reduced the connectivity among source patches. As stepping-stone, the disappearance of small peatlands will made the migration of R. kukunoris among patches more difficult. The model was an experiment of the amphibian behavior reaction to habitat losing and fragmentation. There were many factors that could influence the accuracy of model, such as the preference of animals to each type of landscape, the geographical data precision, reliable degree of model.

黄土丘陵区退耕地植被景观时空变异特征

对黄土丘陵区退耕地植被特征的时空变异性进行了研究。结果表明,不同植被类型区植被特征之间差异不是很显著,仅延安与安塞在物种丰富度之间和安塞与吴旗在物种多样性之间存在较显著的差异(0.01

欧洲景观条约与景观生态学研究

In view of the growing social demand, the Council of Europe's Congress of Local and Regional Authorities (CLRAE) drew up the European Landscape Convention to promote landscape protection, management and planning, and to organize European co-operation on landscape issues in Europe. This paper summarizes the properties, origins, structure and content of the convention, and discusses the definitions on landscape and landscape policy to which the convention refers. Moreover, this paper sums up and concludes the perspective of landscape ecology in Europe.

Probing the kinetics of single molecule protein folding

We propose an approach to integrate the theory, simulations, and experiments in protein-folding kinetics. This is realized by measuring the mean and high-order moments of the first-passage time and its associated distribution. The full kinetics is revealed in the current theoretical framework through these measurements. In the experiments, information about the statistical properties of first-passage times can be obtained from the kinetic folding trajectories of single molecule experiments ( for example, fluorescence). Theoretical/simulation and experimental approaches can be directly related. We study in particular the temperature-varying kinetics to probe the underlying structure of the folding energy landscape. At high temperatures, exponential kinetics is observed; there are multiple parallel kinetic paths leading to the native state. At intermediate temperatures, nonexponential kinetics appears, revealing the nature of the distribution of local traps on the landscape and, as a result, discrete kinetic paths emerge. At very low temperatures, exponential kinetics is again observed; the dynamics on the underlying landscape is dominated by a single barrier.

长时记忆中图形不同特征的加工与提取

Information can be represented both conceptually and imaginarily in long-term memory. However, it seems that only conceptual representation appears, neglecting imaginary information, in most of the long-term memory (LTM) models. In the matter of fact, picture can be stored in LTM directly and conceptually. There is no evidence for what specific type of information, conceptual or imaginary, for the color, shape, or texture to be represented. However, it is evident that the shape and color can be represented separately in LMT. Further research is needed on whether features are represented separately or not, such as color and texture, texture and shape etc. Rehearsal plays important role in picture memory besides the types of storage and representation. Memory of picture is indeed enhanced by rehearsal. There are two types of rehearsal. One is for creating image, another is articulatory loop. Which one will be taken during picture memory process depends on the characteristics of stimuli, subjects' encoding preferences and/or task requirements. Nevertheless, the relation between two types of rehearsal is not very clear yet up to now. Different features could be activated at different time course or possibilities since they can be represented separately. Six experiments were conducted dealing with the characteristics of representation, rehearsal and retrieval of picture in LTM. From these experiments, further understanding of picture information processing was expected. It would add more evidence to the LTM models, and make practical sense to the computer visual identification. The first two experiments were based on the paradigm from Hanna et al.(1996) to investigate separable representation of texture and shape, texture and color. The results indicated that texture could be represented separately with color and shape respectively. It suggested that different features might be processed in different way during remembering. Another interest finding is that recognition performance for shape, color and texture are quite different. What for shape is highest, for color is lowest, and for texture is between of them. Three features of picture can be represented separately. How about the roles of rehearsal when they enter the LTM from short-term memory(STM)? The second three experiments assigned three different types of rehearsal, i. e. visual, verbal, and subject-run(might be both of visual and verbal). The findings are that performances of picture memory were affected significantly by different types of rehearsal. Both visual and verbal rehearsal played important role during remembering process. It seems that verbal rehearsal, which might enhance the relative strength of memory trace, was much more effective than visual one. In addition, subjects tended to choose those difficult-to-name, features to rehearse, to improve the memory performance. Only two features were changed in each of the first two experiments. They might interact (facilitate or disturb) each other when they were retrieved. So it was difficult to identify the retrieval difference between them. In the last experiment, easy-to-name pictures were studied, and only one feature could be recognized. The results indicated that the retrieval performances of three features(shape, color, and texture) were quite different. They were different on the relative strength of memory trace, with the shape was strongest, color was lightest, and texture was in between. No difference was found on the absolute strength of them.