The Statistics of the Number of Minima in a Random Energy Landscape

We consider random energy landscapes constructed from d-dimensional lattices or trees. The distribution of the number of local minima in such landscapes follows a large deviation principle and we derive the associated law exactly for dimension 1. Also of interest is the probability of the maximum possible number of minima; this probability scales exponentially with the number of sites. We calculate analytically the corresponding exponent for the Cayley tree and the two-leg ladder; for 2 to 5 dimensional hypercubic lattices, we compute the exponent numerically and compare to the Cayley tree case.Comment: 18 pages, 8 figures, added background on landscapes and reference

The structural role of the core literature in history

The intellectual landscapes of the humanities are mostly uncharted territory. Little is known on the ways published research of humanist scholars defines areas of intellectual activity. An open question relates to the structural role of core literature: highly cited sources, naturally playing a disproportionate role in the definition of intellectual landscapes. We introduce four indicators in order to map the structural role played by core sources into connecting different areas of the intellectual landscape of citing publications (i.e. communities in the bibliographic coupling network). All indicators factor out the influence of degree distributions by internalizing a null configuration model. By considering several datasets focused on history, we show that two distinct structural actions are performed by the core literature: a global one, by connecting otherwise separated communities in the landscape, or a local one, by rising connectivity within communities. In our study, the global action is mainly performed by small sets of scholarly monographs, reference works and primary sources, while the rest of the core, and especially most journal articles, acts mostly locally

Quantum adiabatic optimization and combinatorial landscapes

In this paper we analyze the performance of the Quantum Adiabatic Evolution algorithm on a variant of Satisfiability problem for an ensemble of random graphs parametrized by the ratio of clauses to variables, $\gamma=M/N$. We introduce a set of macroscopic parameters (landscapes) and put forward an ansatz of universality for random bit flips. We then formulate the problem of finding the smallest eigenvalue and the excitation gap as a statistical mechanics problem. We use the so-called annealing approximation with a refinement that a finite set of macroscopic variables (versus only energy) is used, and are able to show the existence of a dynamic threshold $\gamma=\gamma_d$ starting with some value of K -- the number of variables in each clause. Beyond dynamic threshold, the algorithm should take exponentially long time to find a solution. We compare the results for extended and simplified sets of landscapes and provide numerical evidence in support of our universality ansatz. We have been able to map the ensemble of random graphs onto another ensemble with fluctuations significantly reduced. This enabled us to obtain tight upper bounds on satisfiability transition and to recompute the dynamical transition using the extended set of landscapes.Comment: 41 pages, 10 figures; added a paragraph on paper's organization to the introduction, fixed reference

Using all-sky differential photometry to investigate how nocturnal clouds darken the night sky in rural areas

Artificial light at night has affected most of the natural nocturnal landscapes worldwide and the subsequent light pollution has diverse effects on flora, fauna and human well-being. To evaluate the environmental impacts of light pollution, it is crucial to understand both the natural and artificial components of light at night under all weather conditions. The night sky brightness for clear skies is relatively well understood and a reference point for a lower limit is defined. However, no such reference point exists for cloudy skies. While some studies have examined the brightening of the night sky by clouds in urban areas, the published data on the (natural) darkening by clouds is very sparse. Knowledge of reference points for the illumination of natural nocturnal environments however, is essential for experimental design and ecological modeling to assess the impacts of light pollution. Here we use differential all-sky photometry with a commercial digital camera to investigate how clouds darken sky brightness at two rural sites. The spatially resolved data enables us to identify and study the nearly unpolluted parts of the sky and to set an upper limit on ground illumination for overcast nights at sites without light pollution.Comment: 17 pages, 6 figure

Modelling and simulating change in reforesting mountain landscapes using a social-ecological framework

Natural reforestation of European mountain landscapes raises major environmental and societal issues. With local stakeholders in the Pyrenees National Park area (France), we studied agricultural landscape colonisation by ash (Fraxinus excelsior) to enlighten its impacts on biodiversity and other landscape functions of importance for the valley socio-economics. The study comprised an integrated assessment of land-use and land-cover change (LUCC) since the 1950s, and a scenario analysis of alternative future policy. We combined knowledge and methods from landscape ecology, land change and agricultural sciences, and a set of coordinated field studies to capture interactions and feedback in the local landscape/land-use system. Our results elicited the hierarchically-nested relationships between social and ecological processes. Agricultural change played a preeminent role in the spatial and temporal patterns of LUCC. Landscape colonisation by ash at the parcel level of organisation was merely controlled by grassland management, and in fact depended on the farmer's land management at the whole-farm level. LUCC patterns at the landscape level depended to a great extent on interactions between farm household behaviours and the spatial arrangement of landholdings within the landscape mosaic. Our results stressed the need to represent the local SES function at a fine scale to adequately capture scenarios of change in landscape functions. These findings orientated our modelling choices in the building an agent-based model for LUCC simulation (SMASH - Spatialized Multi-Agent System of landscape colonization by ASH). We discuss our method and results with reference to topical issues in interdisciplinary research into the sustainability of multifunctional landscapes

Highly Variable Genomic Landscape of Endogenous Retroviruses in the C57BL/6J Inbred Strain, Depending on Individual Mouse, Gender, Organ Type, and Organ Location.

Transposable repetitive elements, named the "TREome," represent ~40% of the mouse genome. We postulate that the germ line genome undergoes temporal and spatial diversification into somatic genomes in conjunction with the TREome activity. C57BL/6J inbred mice were subjected to genomic landscape analyses using a TREome probe from murine leukemia virus-type endogenous retroviruses (MLV-ERVs). None shared the same MLV-ERV landscape within each comparison group: (1) sperm and 18 tissues from one mouse, (2) six brain compartments from two females, (3) spleen and thymus samples from four age groups, (4) three spatial tissue sets from two females, and (5) kidney and liver samples from three females and three males. Interestingly, males had more genomic MLV-ERV copies than females; moreover, only in the males, the kidneys had higher MLV-ERV copies than the livers. Perhaps, the mouse-, gender-, and tissue/cell-dependent MLV-ERV landscapes are linked to the individual-specific and dynamic phenotypes of the C57BL/6J inbred population

Adaptation in tunably rugged fitness landscapes: The Rough Mount Fuji Model

Much of the current theory of adaptation is based on Gillespie's mutational landscape model (MLM), which assumes that the fitness values of genotypes linked by single mutational steps are independent random variables. On the other hand, a growing body of empirical evidence shows that real fitness landscapes, while possessing a considerable amount of ruggedness, are smoother than predicted by the MLM. In the present article we propose and analyse a simple fitness landscape model with tunable ruggedness based on the Rough Mount Fuji (RMF) model originally introduced by Aita et al. [Biopolymers 54:64-79 (2000)] in the context of protein evolution. We provide a comprehensive collection of results pertaining to the topographical structure of RMF landscapes, including explicit formulae for the expected number of local fitness maxima, the location of the global peak, and the fitness correlation function. The statistics of single and multiple adaptive steps on the RMF landscape are explored mainly through simulations, and the results are compared to the known behavior in the MLM model. Finally, we show that the RMF model can explain the large number of second-step mutations observed on a highly-fit first step backgound in a recent evolution experiment with a microvirid bacteriophage [Miller et al., Genetics 187:185-202 (2011)].Comment: 43 pages, 12 figures; revised version with new results on the number of fitness maxim

Three objectives of historical ecology: the case of litter collecting in Central European forests

Most ecosystems and landscapes worldwide are dominated or influenced by human impacts. Consequently, studies of pattern and processes of and within anthropogenic ecosystems and cultural landscapes have to consider human impacts and their historical development adequately. Three major objectives of historical ecology, i.e., the study of human impacts on ecosystems and landscapes over time, can be distinguished: (a) preserving cultural heritage in ecosystems and landscapes, (b) understanding historical trajectories of pattern and processes in ecosystems and landscapes, and (c) informing ecosystem and landscape management. In this paper, the application of these three major objectives of historical ecology is illustrated with a case study on litter collecting—a largely forgotten traditional forest use in Central Europe. Historical analyses do not allow—and should not be misused—to directly deduct management goals, as goals need to be set based on present needs and demands. Still, information on reference condition is relevant in the process of defining goals. Once specific goals are set, historical ecology may advise on how to best achieve and maintain desirable pattern and processes in ecosystems or landscap