The maximum empower principle: An invisible hand controlling the self-organizing development of forest plantations in south China

Derived from the maximum power principle (MPP), the maximum empower principle (MePP) is considered as the foundation of emergy theory and evaluation methods. However, it has often encountered some doubts since proposed, because of lacking sufficient empirical evidence. To test the validity of the MePP in the self-organization of forest ecosystems, this paper applied a process-based ecosystem model (Biome-BGC) to simulate the dynamics of biomass, litter and soil organic matter (SOM) of three forest plantations in south China during 1985–2007, and attempted to replicate their self-organizing processes. The simulated results and input flows were transformed to emergy as a common basis and, from the viewpoint of emergy synthesis, the dynamics of the production efficiency and empower of the three forest ecosystems were revealed along with their self-organizing developments over time. The results showed that three forest plantations had similar dynamic change patterns of emergy efficiency and empower, but the production efficiencies of them were not always consistent with their empower performances. The production efficiency firstly increased rapidly to maximums, and then decreased to optimal moderate values. However, the empower came to the maximums after the efficiency peaked and then fluctuated up and down, dependent on weather. These results implied that, a forest ecosystem in its self-organizing process tends toward maximum empower at optimal efficiency. Behind the maximum empower of the forest ecosystem is the desynchrony development of different components, e.g., biomass, litter and SOM; leaf, stem and root; biomass and biodiversity. As a whole, the MePP functions like an invisible hand controlling the general self-organizing development of forest ecosystems and pointing out the direction of their development.     

The strategy of ecosystem development: specific dissipation as an indicator of ecosystem maturity

The ratio of entropy generation rate to entropy embodied in structures relatively to the surroundings can be considered as an indicator of the ability of a self-organizing dissipative system to maintain itself far from equilibrium by pumping out entropy. The higher the ratio (which may be called the specific entropy production or the specific dissipation of a system), the lower the capacity of a system to convert the incoming low-entropy energy into internal organization. It appears that the ratio attains special significance for interpreting the evolution of biological systems, as the maximum expression of self-organizing systems, from the sub-cellular to the ecosystem scale. This paper proposes specific dissipation, written as the ratio of biological entropy production to exergy stored in the living biomass, as a thermodynamic orientor as well as an indicator of the development state of ecological systems. After having presented a method for estimating the specific dissipation in lakes, the adequacy of the proposed indicator is discussed and also tested by comparing its response to those of some classical ecological attributes (successional sequences of species, biodiversity, individual body size, structural organization and generation time of organisms) throughout the seasonal progression of the plankton community in Lake Trasimeno (Umbria, Italy). The results support the hypothesis that the minimization of specific dissipation is a primary criterion of evolution of ecological systems and also sustain the use of specific dissipation as an indicator of ecological maturity.     

Dissipation-error tradeoff in proofreading.

Chemical proofreading systems, of the kind believed responsible for the extremely high fidelity of DNA replication, achieve minimum error probability (equal to the product of the error probabilities of the writing and proofreading stages) only in the limit of infinite energy dissipation. However, a considerable degree of proofreading can be obtained in less strongly driven systems, dissipation only 0.1-1 kT/step.     

EAD: elasticity aware deduplication manager for datacenters with multi-tier storage systems

The popularity of Big Data applications places pressures on storage systems to efficiently scale to meet the demand. At the same time, new developments like solid-state drives have changed to traditional storage hierarchy. Cloud storage systems are transitioning towards a hybrid architecture consisting of large amounts of memory, solid-state disks (SSDs), and traditional magnetic hard disks (HD). This paper presents elasticity aware deduplication (EAD), a data deduplication framework designed for multi-tier cloud storage architectures consisting of SSD and HD. EAD dynamically adjusts the deduplication parameters at runtime in order to improve performance. Experimental results indicate that EAD is able to detect more than 98% of all duplicate data, but it only consumes less than 5% of expected memory space. Additionally, EAD saves approximately 74% of overall IO access cost compared to the traditional design.     

A comparison of phylogenetic network methods using computer simulation

Background

We present a series of simulation studies that explore the relative performance of several phylogenetic network approaches (statistical parsimony, split decomposition, union of maximum parsimony trees, neighbor-net, simulated history recombination upper bound, median-joining, reduced median joining and minimum spanning network) compared to standard tree approaches, (neighbor-joining and maximum parsimony) in the presence and absence of recombination.

Principal Findings

In the absence of recombination, all methods recovered the correct topology and branch lengths nearly all of the time when the substitution rate was low, except for minimum spanning networks, which did considerably worse. At a higher substitution rate, maximum parsimony and union of maximum parsimony trees were the most accurate. With recombination, the ability to infer the correct topology was halved for all methods and no method could accurately estimate branch lengths.

Conclusions

Our results highlight the need for more accurate phylogenetic network methods and the importance of detecting and accounting for recombination in phylogenetic studies. Furthermore, we provide useful information for choosing a network algorithm and a framework in which to evaluate improvements to existing methods and novel algorithms developed in the future.     

Quantifying robustness and dissipation cost of yeast cell cycle network: the funneled energy landscape perspectives

We study the origin of robustness of yeast cell cycle cellular network through uncovering its underlying energy landscape. This is realized from the information of the steady-state probabilities by solving a discrete set of kinetic master equations for the network. We discovered that the potential landscape of yeast cell cycle network is funneled toward the global minimum, G1 state. The ratio of the energy gap between G1 and average versus roughness of the landscape termed as robustness ratio (RR) becomes a quantitative measure of the robustness and stability for the network. The funneled landscape is quite robust against random perturbations from the inherent wiring or connections of the network. There exists a global phase transition between the more sensitive response or less self-degradation phase leading to underlying funneled global landscape with large RR, and insensitive response or more self-degradation phase leading to shallower underlying landscape of the network with small RR. Furthermore, we show that the more robust landscape also leads to less dissipation cost of the network. Least dissipation and robust landscape might be a realization of Darwinian principle of natural selection at cellular network level. It may provide an optimal criterion for network wiring connections and design.     

70% efficiency of bistate molecular machines explained by information theory,high dimensional geometry and evolutionary convergence

The relationship between information and energy is key to understanding biological systems. We can display the information in DNA sequences specifically bound by proteins by using sequence logos, and we can measure the corresponding binding energy. These can be compared by noting that one of the forms of the second law of thermodynamics defines the minimum energy dissipation required to gain one bit of information. Under the isothermal conditions that molecular machines function this is joules per bit ( is Boltzmann''s constant and T is the absolute temperature). Then an efficiency of binding can be computed by dividing the information in a logo by the free energy of binding after it has been converted to bits. The isothermal efficiencies of not only genetic control systems, but also visual pigments are near 70%. From information and coding theory, the theoretical efficiency limit for bistate molecular machines is ln 2 = 0.6931. Evolutionary convergence to maximum efficiency is limited by the constraint that molecular states must be distinct from each other. The result indicates that natural molecular machines operate close to their information processing maximum (the channel capacity), and implies that nanotechnology can attain this goal.     

Vascular metabolic dissipation in Murray's law

The metabolic dissipation in Murray's minimum energy hypothesis includes only the blood metabolism. The metabolic dissipation of the vascular tree, however, should also include the metabolism of passive and active components of the vessel wall. In this study, we extend the metabolic dissipation to include blood metabolism, as well as passive and active components of the vessel wall. The analysis is extended to the entire vascular arterial tree rather than a single vessel as in Murray's formulation. The calculations are based on experimentally measured morphological data of coronary artery network and the longitudinal distribution of blood pressure along the tree. Whereas the model includes multiple dissipation sources, the total metabolic consumption of a complex vascular tree is found to remain approximately proportional to the cumulative arterial volume of the unit. This implies that the previously described scaling relations for the various morphological features (volume, length, diameter, and flow) remain unchanged under the generalized condition of metabolic requirements of blood and blood vessel wall.     

Reverse Engineering of Oxygen Transport in the Lung: Adaptation to Changing Demands and Resources through Space-Filling Networks

The space-filling fractal network in the human lung creates a remarkable distribution system for gas exchange. Landmark studies have illuminated how the fractal network guarantees minimum energy dissipation, slows air down with minimum hardware, maximizes the gas- exchange surface area, and creates respiratory flexibility between rest and exercise. In this paper, we investigate how the fractal architecture affects oxygen transport and exchange under varying physiological conditions, with respect to performance metrics not previously studied.We present a renormalization treatment of the diffusion-reaction equation which describes how oxygen concentrations drop in the airways as oxygen crosses the alveolar membrane system. The treatment predicts oxygen currents across the lung at different levels of exercise which agree with measured values within a few percent. The results exhibit wide-ranging adaptation to changing process parameters, including maximum oxygen uptake rate at minimum alveolar membrane permeability, the ability to rapidly switch from a low oxygen uptake rate at rest to high rates at exercise, and the ability to maintain a constant oxygen uptake rate in the event of a change in permeability or surface area. We show that alternative, less than space-filling architectures perform sub-optimally and that optimal performance of the space-filling architecture results from a competition between underexploration and overexploration of the surface by oxygen molecules.     

Free energy dissipation of the pyruvate kinase reaction has a minimum at cell metabolite concentrations

The ratio of substrates and products (mass action ratio) for the reaction catalyzed by the enzyme pyruvate kinase is measured under the constraint of constant reaction rate for pyruvate kinase (EC 2.7.1.40) from brewers yeast and Eschcrichiacoli. For both organisms, a maximum of the ratio is found at concentrations comparable to those obtained from cell metabolite measurements. This observation suggests an optimum principle for free energy transduction in the glycolytic reaction pathway. as a maximum of the mass action ratio corresponds to a minimum dissipation of free energy.     

Towards an intelligent exploitation of heterogeneous and distributed resources in cooperative environments of eHealth

The objective of this research work is to empower healthcare information systems to deliver high quality information anytime and anywhere and to present distributed and heterogeneous resources access solutions which perfectly meet user requirements in different contexts. To reach this objective, we propose in this paper a new framework, called ONtology Oriented Framework for Pervasive Applications and Services (ONOF-PAS), and mainly based on: 1) interrelated ontological models representing the main entities in pervasive computing, such as Organization, Actor, Task, Service, Process, Object, Resources, etc.; 2) rule-based reasoning to infer the available and capable resources required by each task. The main functionality of the ONOF-PAS framework is to capture and to process the acquired knowledge about the user's context, the tasks they perform, the availability and capabilities of the required resources, and the organizations that own or manage these resources. Our framework allows healthcare information systems to infer the needed resources by linking each user-task with the required, available and capable resources taking into account the clinical conditions of the patients. The ONOF-PAS framework has been successfully applied in the telemedicine domain in order to provide practical and efficient resources access solutions that better meet the contexts and the expectations of the eHealth actors.     

Storage of a temporal pattern sequence in a network

Learning of single patterns and a temporal pattern sequence in a network when the coupling coefficients between the network elements change their values according to a definite coupling function is described. In contrast to technical systems (e.g. film, tape) where temporal sequences are often encoded in the storage location, the network stores information only by changing the values of the coupling coefficients. A network of 100 elements was simulated on an UNIVAC 1100/80 computer. Eight single patterns and a sequence of these patterns were offered at the input of the network. After the learning process the network reproduces every stored pattern as an output signal when only parts of it are fed in. The activity, that is the sum of all output signals, is regulated by an external control signal. By setting that control signal to a suitable value the network is able to reproduce the stored pattern sequence starting from any arbitrary pattern. Lowering the external control signal during that process causes the network to hold the last presented pattern until the external control signal is changed again. It is speculated that the coupling function implemented in the simulation may be anaogous to a characteristic describing the chemical process of cooperative binding.Supported by DFG (Ha 381/9 and Ha 381/11)     

Correlation Networks from Flows. The Case of Forced and Time-Dependent Advection-Diffusion Dynamics

Complex network theory provides an elegant and powerful framework to statistically investigate different types of systems such as society, brain or the structure of local and long-range dynamical interrelationships in the climate system. Network links in climate networks typically imply information, mass or energy exchange. However, the specific connection between oceanic or atmospheric flows and the climate network’s structure is still unclear. We propose a theoretical approach for verifying relations between the correlation matrix and the climate network measures, generalizing previous studies and overcoming the restriction to stationary flows. Our methods are developed for correlations of a scalar quantity (temperature, for example) which satisfies an advection-diffusion dynamics in the presence of forcing and dissipation. Our approach reveals that correlation networks are not sensitive to steady sources and sinks and the profound impact of the signal decay rate on the network topology. We illustrate our results with calculations of degree and clustering for a meandering flow resembling a geophysical ocean jet.     

In search of a thermodynamic description of biomass yields for the chemotrophic growth of microorganisms

Correlations for the prediction of biomass yields are valuable, and many proposals based on a number of parameters (Y(ATP), Y(Ave), eta(o), Y(c), Gibbs energy efficiencies, and enthalpy efficiencies) have been published. This article critically examines the properties of the proposed parameters with respect to the general applicability to chemotrophic growth systems, a clear relation to the Second Law of Thermodynamics, the absence of intrinsic problems, and a requirement of only black box information. It appears that none of the proposed parameters satisfies all these requirements. Particularly, the various energetic efficiency parameters suffer from major intrinsic problems. However, this article will show that the Gibbs energy dissipation per amount of produced biomass (kJ/C-mod) is a parameter which satisfies the requirements without having intrinsic problems. A simple correlation is found which provides the Gibbs energy dissipation/C-mol biomass as a function of the nature of the C-source (expressed as the carbon chain length and the degree of reduction). This dissipation appears to be nearly independent of the nature of the electron acceptor (e.g., O(2), No(3) (-), fermentation). Hence, a single correlation can describe a very wide range of microbial growth systems. In this respect, Gibbs energy dissipation is much more useful than heat production/C-mol biomass, which is strongly dependent on the electron acceptor used. Evidence is presented that even a net heat-uptake can occur in certain growth systems.The correlation of Gibbs energy dissipation thus obtained shows that dissipation/C-mol biomass increases for C-sources with smaller chain length (C(6) --> C(1)), and increases for both higher and lower degrees of reduction than 4. It appears that the dissipation/C-mol biomass can be regarded as a simple thermodynamic measure of the amount of biochemical "work" required to convert the carbon source into biomass by the proper irreversible carbon-carbon coupling and oxidation/reduction reactions. This is supported by the good correlation between the theoretical ATP requirement for biomass formation on different C-sources and the dissipation values (kJ/C-mol biomass) found. The established correlation for the Gibbs energy dissipation allows the prediction of the chemotrophic biomass yield on substrate with an error of 13% in the yield range 0.01 to 0.80 C-mol biomass/(C)-mol substrate for aerobic/anaerobic/denitrifying growth systems.     

Spatial graphs as templates for habitat networks in boreal landscapes

Network topology serves as a useful model for biological systems at various scales. Contrary to many biological systems, spatial reference is crucial for habitat networks. Boreal forest landscapes provide a wide gradient of spatial patterns and, thus, unique network structures. Assuming forest-dwelling organisms in general aim to minimize travel distances during foraging, dispersal, etc., linear links across the landscape matrix constitute expected movement routes among forested areas in boreal landscapes. We quantified the number and length of links in a set of 57 boreal forest landscapes for four hierarchically nested graphs in order to compare the incremental changes in characteristics of resulting graph measures. The forest cover graphs consisted of the same set of forest patches, and hierarchical link types extracted from real landscapes: nearest neighbour graph (NN), minimum spanning tree (MST), Gabriel graph (GG) and minimum planar graph (MPG). Most of the links in graphs were NN and GG links. Commonly links were 100–200?m in length, but link lengths particularly in the GG and MPG shorten when the proportion of forest in landscapes increased. Most nodes had 3–5 links each, but the number of links per node depended on node size and the proportion of forest cover. GG and MPG graphs retain the topology of the underlying node layout. Changes in node pattern alter the NN and MST graphs more than GG and MPG. Variation in regional network topologies is likely to affect connectivity patterns in a landscape and, thus, many ecological processes that occur at a local scale. An appropriate network analysis enables the discovery and comparison of distinctive network patterns. Understanding network topologies provide practical tools for land use planning and biodiversity management of broader areas that target functional habitat networks.     

青冈种群的能量损耗

１引言青冈（Ｃｙｃｌｏｂａｌａｎｏｐｓｉｓｇｌａｕｃａ）种群的能量损耗,是能量代谢中除能量积累外的另一部分。能量损耗过程是通过植物三大生理代谢活动中的呼吸和蒸腾两个作用而实现的。本文是继“青冈种群的能量积累”一文［１］的续篇,以便对青冈种群的能量代谢...     

DNA存储中的编码技术

脱氧核糖核酸(Deoxyribonucleic Acid, DNA)是一种天然的信息存储介质,具有存储密度高、存储时间长、损耗率低等特点。在传统存储方式不能满足信息增长的需求时,DNA数据存储技术逐渐成为研究热点。DNA编码是用尽可能少的碱基序列无错的存储数据信息,包括压缩(尽可能少的占用空间)、纠错(无错存储)和转换(数字信息转为碱基序列)3部分。DNA编码是DNA存储中的关键技术,它的结果直接影响存储性能的优劣和数据读写的完整。本文首先介绍DNA存储的发展历史,然后介绍DNA存储的框架,其中重点介绍DNA编码技术,最后对DNA存储中的编解码技术的未来发展方向进行讨论。     

Numerical study of the force network ensemble

The force network ensemble of Snoeijer et al. (Force network ensemble: a new approach to static granular matter, Phys. Rev. Lett. 92 (2004), 054302) is a convenient model to study networks of contact forces that are typically present in granular matter. Recently, we have shown that it is possible to extremely accurately determine the probability distribution of contact forces in the framework of this ensemble (van Eerd et al., Tail of the contact force distribution in static granular materials, Phys. Rev. E 75 (2007), 060302(R); Tighe et al., Entropy maximisation in the force network ensemble for granular solids, Phys. Rev. Lett. 100 (2008), 238001). In this work, we review several important details of these computations. In particular, we study in detail the angle-resolved contact force distribution, finite-size effects, the maximum allowed shear stress and the effect of walls. In addition, we investigate how well the force network ensemble resembles systems with ‘real’ interactions.     

Long-term variation of outdoor radon equilibrium equivalent concentration

Long-term variation of outdoor radon equilibrium equivalent concentration was investigated from 1982 to 1992 at a semi-natural location 10 km north of Munich, southern Germany. For this period the continuous measurement yielded a long-term average of 8.6 Bq·m^–3 (arithmetic mean) and 6.9 Bq·m^–3 (geometric mean), from which an average annual effective dose of 0.14 mSv due to outdoor radon can be derived. A long-term trend of the radon concentration was not detectable over the whole period of observation. However, by time series analysis, a long-term cyclic pattern was identified with two maxima (1984–1986, 1989–1991) and two minima (1982–1983, 1987–1988). The seasonal pattern is characterized by an autumn maximum and an early summer minimum. On average, the seasonal maximum in October was found to be higher by a factor of 2 than the June minimum. The diurnal variation of the radon concentration shows a maximum in the early morning and a minimum in the afternoon. On average, this maximum is a factor of 2 higher than the minimum. In the long term a seasonal pattern was observed for diurnal variation, with an average diurnal maximum to minimum ratio of 1.5 in winter compared with 3.5 in the summer months. The radon concentration is correlated with a meteorological parameter (stagnation index) which takes into account horizontal and vertical exchange processes and the wash-out of aerosols in the lower atmosphere.Dedicated to Prof. F. Waschsmann on the occasion of this 90th birthday