In and out forests on combinatorial landscapes

Fitness landscape theory is a mathematical framework for numerical analysis of search algorithms on combinatorial optimization problems. We study a representation of fitness landscape as a weighted directed graph. We consider out forest and in forest structures in this graph and establish important relationships among the forest structures of a directed graph, the spectral properties of the Laplacian matrices, and the numbers of local optima of the landscape. These relationships provide a new approach for computing the numbers of local optima for various problem instances and neighborhood structures.     

Scoring confidence index: statistical evaluation of ligand binding mode predictions

Protein-ligand docking programs can generate a large number of possible binding orientations for each ligand candidate. The challenge is to identify the orientations closest to the native binding mode using a scoring method. Many different scoring functions have been developed for protein-ligand scoring, but their performance on binding mode prediction is often target-dependent. In this study, a statistical approach was employed to provide a confidence measure of scoring performance in finding close to the correct docked ligand orientations. It exploits the fact that the scores provided by an adequately performing scoring function generally improve as the ligand binding modes get closer to the correct native orientation. For such cases, the correlation coefficient of scores versus distances is expected to be highest when the most native-like orientation is used as a reference. This correlation coefficient, called the correlation-based score (CBScore), was used as an indicator of how far the docked pose was from the native orientation. The correlation between the original scores and CBScores as well as the range of CBScores were found to be good measures of scoring performance. They were combined into a single quantity, called the scoring confidence index. High values of the scoring confidence index were indicative of pronounced and relatively smooth binding energy landscapes with easily discernable global minima, resulting in reliable binding mode predictions. Low values of this index reflected rugged energy landscapes making the prediction of the correct binding mode very difficult and often unreliable. The diagnostic ability of the scoring confidence index was tested on a non-redundant set of 50 protein-ligand complexes scored with three commonly employed scoring functions: AffiScore, DrugScore and X-Score. Binding mode predictions were found to be three times more reliable for complexes with scoring confidence indices in the upper half than for cases with values in the lower half of the resulting range of 0–1.6. This new confidence measure of scoring performance is expected to be a valuable tool for virtual screening applications. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

On arithmetic and asymptotic properties of up-down numbers

Let σ=(σ₁,…,σ_N), where σ_i=±1, and let C(σ) denote the number of permutations π of 1,2,…,N+1, whose up-down signature sign(π(i+1)-π(i))=σ_i, for i=1,…,N. We prove that the set of all up-down numbers C(σ) can be expressed by a single universal polynomial Φ, whose coefficients are products of numbers from the Taylor series of the hyperbolic tangent function. We prove that Φ is a modified exponential, and deduce some remarkable congruence properties for the set of all numbers C(σ), for fixed N. We prove a concise upper bound for C(σ), which describes the asymptotic behaviour of the up-down function C(σ) in the limit C(σ)?(N+1)!.     

Spectroscopy of proteins at low temperature. Part I: Experiments with molecular ensembles

We discuss aspects of the physics of proteins at low temperature as they are reflected in highly resolved optical spectra of molecular probes. Typical probe molecules are heme-like dyes, aromatic amino acids, but also extended molecular aggregates in light harvesting complexes. We put emphasis on the interactions of the probe with its protein environment, on the range of these interactions, on their specific behavior in external fields, as well as on the characteristic parameters of the protein which can be determined with optical techniques at low temperatures but are not easily accessible otherwise. However, the focus of the review is on spectral diffusion physics of proteins, i.e. on their motion in conformational phase space, and on how this motion is reflected in the optical spectra. These structure changing-processes reflect the non-ergodic nature of low temperature proteins. They are most clearly detected at low temperature where the resolution of the experiment is close to the ultimate limit as given by the natural linewidth and where the dynamics become slow enough to be conveniently measured. In part I we discuss aspects of ensemble experiments, in part II we focus on experiments with single protein complexes. We offer lines of reasoning which may serve as guidelines for an understanding of the phenomena.     

The Fractal Nature of Riem/Diff I

This paper is devoted to large scale aspects of the geometry of the space of isometry classes of Riemannian metrics, with a 2-sided curvature bound, on a fixed compact smooth manifold of dimension at least five. Using a mix of tools from logic/computer science, and differential geometry and topology, we study the diameter functional and its critical points, as well as their distribution (density) within the space and the structure of their neighborhoods.     

城市河道系统的景观敏感性与景观规划

运用景观生态学的原理,通过对城市河道系统的景观敏感性与视觉美学敏感性的分析,指出景观系统的敏感性是指不同时间和空间尺度上系统对干扰的反应.揭示了城市化的快速发展使土地利用方式发生大规模改变的同时,城市河道及其沿岸景观系统在结构、形态上也发生巨大变化,导致河流水文、生态系统的破坏与功能的退化,城市水文洪涝灾害频发、水质污染严重和美学质量下降等问题,提出用景观规划探讨城市河道系统的保护、修复与补偿系统及可持续发展途径.     

基于3S的塔里木河中游景观格局变化特征分析

景观格局变化研究,是目前景观生态学的研究热点.本文把生态环境脆弱与人类活动的影响比较强烈的塔里木河中游选为研究靶区,利用遥感的手段获取试验区1973、1992和2000年景观格局的基础数据,在3S技术和景观生态学方法支持下,对塔里木河中游近30年土地利用和景观结构的时空变化特征进行了研究,对该地区的开发利用和生态环境保护提供科学依据.     

干旱区绿洲景观空间分异特征及其生态建设方略研究

基于景观生态学的相关原理,结合现代3s技术,通过对尉犁绿洲空间分异特征分析,探讨了该地区景观生态建设方略,旨在为该区域的景观生态设计、土地资源利用的合理化提供科学依据,这对实现其可持续发展和生态环境改善都有着重要的意义.     

Bioenergy Systems Planning Using Location–Allocation and Landscape Ecology Design Principles

Rural energy planning is a nexus of sustainable development issues, particularly the sustainable utilization of biomass resources, on which rural parts of the developing world remain critically dependent. A landscape based rural bioenergy planning framework is presented, which is based on location–allocation and landscape ecology principles and considers both domestic and commercial energy demands and energy flows, as well as the landscape impact of the required bioenergy production zones. p-median modelling principles underly the location–allocation formulation. Optimized bioenergy landscape designs are presented, which illustrate both accessibility and landscape ecology objectives.