Exploring the Synergy Between Industrial Ecology and System of Systems to Understand Complexity

Two objectives are pursued in this article. First, from a methodological perspective, we explore the relationships among the constructs of complex adaptive systems, systems of systems, and industrial ecology. Through examination of central traits of each, we find that industrial ecology and system of systems present complementary frameworks for posing systemic problems in the context of sociotechnical applications. Furthermore, we contend that complexity science (the basis for the study of complex adaptive systems) provides a natural and necessary foundation and set of tools to analyze mechanisms such as evolution, emergence, and regulation in these applications. The second objective of the article is to illustrate the use of two tools from complexity sciences to address a network transition problem in air transportation framed from the system-of-systems viewpoint and shaped by an industrial ecology perspective. A stochastic simulation consisting of network theory analysis combined with agent-based modeling to study the evolution of an air transport network is presented. Patterns in agent behavior that lead to preferred outcomes across two scenarios are observed, and the implications of these results for decision makers are described. Furthermore, we highlight the necessity for future efforts to combine the merits of both system of systems and industrial ecology in tackling the issues of complexity in such large-scale, sociotechnical problems.     

Simultaneous modeling of phase and calorimetric behavior in an amphiphilic peptide/phospholipid model membrane

Differential scanning calorimetry (DSC) experiments have been performed on the amphiphilic peptide/1,2-bis(perdeuteriopalmitoyl)-sn-glycero-3-phosphocholine system for which partial phase diagrams have been measured by deuterium nuclear magnetic resonance. The solute concentration dependence of the transition enthalpy in such systems is often interpreted in terms of an annulus of lipid withdrawn, by the solvent, from participation in the transition while the bulk lipid melts with its fully enthalpy. This idea is equivalent to postulating ideal mixing between the lipid and the peptide/lipid complex, and there is little justification for such an assumption. Adaptation of regular solution theory to this system demonstrates that the peptide concentration dependence of the transition enthalpies can be incorporated into a thermodynamic model which reproduces the observed phase behavior fairly well without postulating that a complexing annulus of lipid around the peptide be withdrawn from participating in the chain-melting transition. The model parameters determined by simultaneous fitting of the phase behavior and transition enthalpies are used to simulate the DSC scan shapes. The asymmetry of the calorimetric scans for chi 2 less than or equal to 0.02 is reproduced by the model, but a broad component observed for higher concentration is not. In light of the results presented here, previous analyses of the calorimetric behavior of two-component systems in terms of symmetric transitions which do not account for the possible extent of a region of two-phase equilibrium must be questioned.     

The protein-solvent glass transition

The protein dynamical transition and its connection with the liquid-glass transition (GT) of hydration water and aqueous solvents are reviewed. The protein solvation shell exhibits a regular glass transition, characterized by steps in the specific heat and the thermal expansion coefficient at the calorimetric glass temperature T_G ≈ 170 K. It implies that the time scale of the structural α-relaxation has reached the experimental time window of 1–100 s. The protein dynamical transition, identified from elastic neutron scattering experiments by enhanced amplitudes of molecular motions exceeding the vibrational level [1], probes the α-process on a shorter time scale. The corresponding liquid-glass transition occurs at higher temperatures, typically 240 K. The GT is generally associated with diverging viscosities, the freezing of long-range translational diffusion in the supercooled liquid. Due to mutual hydrogen bonding, both, protein- and solvent relaxational degrees of freedom slow down in paralled near the GT. However, the freezing of protein motions, where surface-coupled rotational and librational degrees of freedom are arrested, is better characterized as a rubber-glass transition. In contrast, internal protein modes such as the rotation of side chains are not affected. Moreover, ligand binding experiments with myoglobin in various glass-forming solvents show, that only ligand entry and exit rates depend on the local viscosity near the protein surface, but protein-internal ligand migration is not coupled to the solvent. The GT leads to structural arrest on a macroscopic scale due to the microscopic cage effect on the scale of the intermolecular distance. Mode coupling theory provides a theoretical framework to understand the microcopic nature of the GT even in complex systems. The role of the α- and β-process in the dynamics of protein hydration water is evaluated. The protein-solvent GT is triggered by hydrogen bond fluctuations, which give rise to fast β-processes. High-frequency neutron scattering spectra indicate increasing hydrogen bond braking above T_G.     

Short-strong hydrogen bonds and a low barrier transition state for the proton transfer reaction in RNase A catalysis: a quantum chemical study

There is growing evidence that some enzymes catalyze reactions through the formation of short-strong hydrogen bonds as first suggested by Gerlt and Gassman. Support comes from several experimental and quantum chemical studies that include correlation energies on model systems. In the present study, the process of proton transfer between hydroxyl and imidazole groups, a model of the crucial step in the hydrolysis of RNA by the enzymes of the RNase A family, is investigated at the quantum mechanical level of density functional theory and perturbation theory at the MP2 level. The model focuses on the nature of the formation of a complex between the important residues of the protein and the hydroxyl group of the substrate. We have also investigated different configurations of the ground state that are important in the proton transfer reaction. The nature of bonding between the catalytic unit of the enzyme and the substrate in the model is investigated by Bader's atoms in molecule theory. The contributions of solvation and vibrational energies corresponding to the reactant, the transition state and the product configurations are also evaluated. Furthermore, the effect of protein environment is investigated by considering the catalytic unit surrounded by complete proteins--RNase A and Angiogenin. The results, in general, indicate the formation of a short-strong hydrogen bond and the formation of a low barrier transition state for the proton transfer model of the enzyme.     

A theoretical approach to "macroscopic fluctuations" effect

At present there is no generally accepted theory of the effect of macroscopic fluctuations. It the article, an attempt is made to relate this effect to some basic properties of quantum systems, in particular, to the formal absence of dynamic chaos in these systems. Based on this approach, it was shown why the level of the effect must be of the same order of magnitude as the level of noise and cannot exceed this level as the number of experiments increases. It was shown qualitatively what is the cause of the similarity of histograms observed in different experiments.     

Ten steps to investigate a cellular system with mathematical modeling

Cellular and intracellular processes are inherently complex due to the large number of components and interactions, which are often nonlinear and occur at different spatiotemporal scales. Because of this complexity, mathematical modeling is increasingly used to simulate such systems and perform experiments in silico, many orders of magnitude faster than real experiments and often at a higher spatiotemporal resolution. In this article, we will focus on the generic modeling process and illustrate it with an example model of membrane lipid turnover.     

Studying sensorimotor integration in insects

Sensorimotor integration is a field rich in theory backed by a large body of psychophysical evidence. Relating the underlying neural circuitry to these theories has, however, been more challenging. With a wide array of complex behaviors coordinated by their small brains, insects provide powerful model systems to study key features of sensorimotor integration at a mechanistic level. Insect neural circuits perform both hard-wired and learned sensorimotor transformations. They modulate their neural processing based on both internal variables, such as the animal's behavioral state, and external ones, such as the time of day. Here we present some studies using insect model systems that have produced insights, at the level of individual neurons, about sensorimotor integration and the various ways in which it can be modified by context.     

Beyond the Food Web Connections to a Deeper Industrial Ecology

Industrial ecology is a school of thought based, in part, upon a simple analogy between industrial systems and ecological systems in terms of their material and energy flows. This article argues for a more sophisticated connection between these diverse systems based on the fact that they are all complex self-organizing systems, operating far from thermodynamic equilibrium. As such, industrial and ecological systems have in common certain constraints and dynamic properties that move beyond the central metaphor of industrial ecology and could align these systems under a more comprehensive analytical framework. If incorporated at a fundamental level, the complex systems framework could add depth and sophistication to the field of industrial ecology.     

Direct measurement of single-molecule visco-elasticity in atomic force microscope force-extension experiments

Measuring the visco-elastic properties of biological macromolecules constitutes an important step towards the understanding of dynamic biological processes, such as cell adhesion, muscle function, or plant cell wall stability. Force spectroscopy techniques based on the atomic force microscope (AFM) are increasingly used to study the complex visco-elastic response of (bio-)molecules on a single-molecule level. These experiments either require that the AFM cantilever is actively oscillated or that the molecule is clamped at constant force to monitor thermal cantilever motion. Here we demonstrate that the visco-elasticity of single bio-molecules can readily be extracted from the Brownian cantilever motion during conventional force-extension measurements. It is shown that the characteristics of the cantilever determine the signal-to-noise (S/N) ratio and time resolution. Using a small cantilever, the visco-elastic properties of single dextran molecules were resolved with a time resolution of 8.3 ms. The presented approach can be directly applied to probe the dynamic response of complex bio-molecular systems or proteins in force-extension experiments. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Linking biodiversity and ecosystems: towards a unifying ecological theory

Community ecology and ecosystem ecology provide two perspectives on complex ecological systems that have largely complementary strengths and weaknesses. Merging the two perspectives is necessary both to ensure continued scientific progress and to provide society with the scientific means to face growing environmental challenges. Recent research on biodiversity and ecosystem functioning has contributed to this goal in several ways. By addressing a new question of high relevance for both science and society, by challenging existing paradigms, by tightly linking theory and experiments, by building scientific consensus beyond differences in opinion, by integrating fragmented disciplines and research fields, by connecting itself to other disciplines and management issues, it has helped transform ecology not only in content, but also in form. Creating a genuine evolutionary ecosystem ecology that links the evolution of species traits at the individual level, the dynamics of species interactions, and the overall functioning of ecosystems would give new impetus to this much-needed process of unification across ecological disciplines. Recent community evolution models are a promising step in that direction.     

Morphological analysis of information processing in basal ganglia of mammals

The article reviews published and own data on special features of organization of afferent cortical and infracortical correctional systems of the total striopallidaric nuclear complex in various species of mammals. The article focuses on analysis of organization of these flows in a dog being a classical object of behavioural experiments and a rare object of neuromorphological studies. It was discovered that the general trend towards segregated and converged flows of functionally different information at the level of striopallidum is retained in all tested mammals, being an evidence of the fundamental nature of the discussed principles of organization of the projection systems of basal ganglia. The reviewed morphological data confirm reliability of the presented concept of basal ganglia functioning.     

ER-mediated phagocytosis: a new membrane for new functions

Genomics and other high-throughput approaches, such as proteomics, are changing the way we study complex biological systems. In the past few years, these approaches have contributed markedly to improving our understanding of phagocytosis. Indeed, the ability to study biological systems by monitoring hundreds of proteins provides a level of resolution that is not attainable by the usual 'one protein at a time' approach. In this article, I discuss how proteomic approaches have revealed surprising findings that enable us to revisit established concepts, such as the origin of the phagosome membrane, and to propose new models of cell organization and the link between innate and adaptive immunity.     

生物实验信息管理模块建模技术研究

实验信息管理模块是生物实验室信息管理系统的核心,其设计的好坏直接关系到整个系统建设的成败。针对生物实验室实验流程灵活,数据流网络复杂等特点,研究设计了一套实验信息管理模块的模型,并将研究的模型用于基因测序实验室信息管理系统的开发并取得了成功。实践证明,该模型为实验室信息系统(LIMS)中实验管理模块的开发提供了理论支撑,并且提高了LIMS的开发效率。     

Menstruation, perimenopause, and chaos theory

This article argues that menstruation, including the transition to menopause, results from a specific kind of complex system, namely, one that is nonlinear, dynamical, and chaotic. A complexity-based perspective changes how we think about and research menstruation-related health problems and positive health. Chaotic systems are deterministic but not predictable, characterized by sensitivity to initial conditions and strange attractors. Chaos theory provides a coherent framework that qualitatively accounts for puzzling results from perimenopause research. It directs attention to variability within and between women, adaptation, lifespan development, and the need for complex explanations of disease. Whether the menstrual cycle is chaotic can be empirically tested, and a summary of our research on 20- to 40-year-old women is provided.     

Analyzing the mutual feedbacks between lake pollution and human behaviour in a mathematical social-ecological model

Does the adoption of environment-oriented actions by individuals necessarily improve the state of an ecosystem in the most effective way? We address this question with the example of eutrophication in shallow lakes. When exposed to fertilizers, such lakes can undergo a critical transition called eutrophication, resulting in a loss of biodiversity and ecosystem services. We couple a generic model of eutrophication with a best-response model of human behaviour, where agents can choose to pollute the lake at a high level (defection) or at a low level (cooperation). It is known that feedbacks between the interacting lake pollution and human behaviour can give rise to complex dynamics with multiple stable states and oscillations. Here, we analyze the impact of all model parameters on the shape of the nullclines. S-shaped nullclines are a condition for complex dynamics to occur. Moreover, we find that agents decreasing their pollution discharge into the lake is not necessarily the most effective way to reduce the pollution level in the lake. This is due to coexisting counterintuitive stable equilibria where the lake is in a clear state despite a high level of pollution discharge. We analyze the complex dynamics of the system and describe in detail Hopf, saddle-node, homoclinic and Bogdanov-Takens bifurcations. The complex dynamics with potential multistability and counterintuitive equilibria suggests that generic management recommendations holding for every level of pollution and of cooperation are impossible. Apart from the direct perturbation of an ecological variable, we identify three ways a management strategy can influence the social-ecological system: it can change the location, the resilience and the existence of stable equilibria.     

A methodology for designing and evaluating alternative cropping systems: Application on dairy and arable farms

To improve the sustainability of agricultural systems of the Lombardia region (northern Italy), a mixed indicator-model-expert approach was used. Starting from the results of a previous assessment of current management (ACT) in dairy and arable farms, alternative management scenarios at field level were designed in order to reduce nitrogen (N) losses whilst maintaining or improving the environmental and economic sustainability at the farming system level. By working with a group of experts supported by a mechanisation model and a cropping system model, two alternative N management scenarios were defined following a step-by-step decision procedure. The first scenario (FERT) is an improvement of the current fertiliser management scheme, applied at the same crops as in ACT and aimed at maintaining the same yields. The second scenario (ROT) is based on changes in crop rotations by introducing new crops to reduce N losses and to maintain economic profitability. The sustainability of the two scenarios was assessed and compared with agro-ecological and economic indicators. The results of FERT, indicate that the application of adequate N management plans tuned to the production target and the promotion of best management practices may help to reduce N surplus and consequently to save fossil energy and to decrease the costs of production. In the ROT scenario, the introduction of alfalfa cultivation reduces N surplus on maize, whereas intensive double cropping systems (two crops harvested in 12 months) increase N surplus and require higher energy consumptions and production costs compared to cultivating a summer crop only. However, in rotational systems more favourable weed population dynamics are expected compared to ACT. Both alternative scenarios were not implemented in practice, but they are realistic and are consistent with results of experiments where management options similar to those introduced in FERT and ROT were tested.This work indicates that the rational integration between scientific tools (indicators and models) and expert knowledge is adequate to deal with complex farming and cropping systems, which require a multidisciplinary approach.     

Global dynamics of biological systems from time-resolved omics experiments

The emergent properties of biological systems, organized around complex networks of irregularly connected elements, limit the applications of the direct scientific method to their study. The current lack of knowledge opens new perspectives to the inverse scientific paradigm where observations are accumulated and analysed by advanced data-mining techniques to enable a better understanding and the formulation of testable hypotheses about the structure and functioning of these systems. The current technology allows for the wide application of omics analytical methods in the determination of time-resolved molecular profiles of biological samples. Here it is proposed that the theory of dynamical systems could be the natural framework for the proper analysis and interpretation of such experiments. A new method is described, based on the techniques of non-linear time series analysis, which is providing a global view on the dynamics of biological systems probed with time-resolved omics experiments.     

Nonlinear blending: a useful general concept for the assessment of combination drug synergy

Human diseases may involve cellular signaling networks that contain redundant pathways, so that blocking a single pathway in the system cannot achieve the desired effect. As such, the use of drugs in combination are particularly effective interventions in networked systems. However, common synergy measures are often inadequate to quantify the effect of two different drugs in complex cellular systems. This article proposes a general approach to quantifying the synergy of two drugs in combination. This approach is called strong nonlinear blending. Drugs with different relative potencies, different effect maxima, or situations of potentiation or coalism pose no problem for strong nonlinear blending as a way to assess the increased response benefit to be gained by combining two drugs. This is important as testing drug combinations in complex biological systems are likely to produce a wide variety of possible response surfaces. It is also shown that for monotone increasing (or decreasing) dose response surfaces that strong nonlinear blending is equivalent to improved potency along a ray of constant dose ratio. This is important because fixed dose ratios form the basis for many preclinical and clinical combination drug experiments. Two examples are given involving HIV and cancer chemotherapy combination drug experiments.     

Frontal gel chromatography of interacting systems: theoretical and experimental evaluation of the shapes of elution profiles for systems of the type A + B in equilibrium C

A theoretical and experimental study has been made of the advancing elution profile in frontal gel chromatography of interacting systems for which the elution volume of the complex is smaller than that of the larger reactant. First, Gilbert-Jenkins theory is used to delineate the form of the elution profile from the magnitudes of the elution volumes and concentrations of reacting species. This procedure resulted in the detection of a misinterpretation of certain patterns obtained in a gel chromatographic study of the interaction between myoglobin and ovalbumin. Second, a numerical computational procedure, which incorporates both axial dispersion and concentration-dependence of species elution volumes, is used to establish the influence of these two factors on boundary shapes for such systems. Third, frontal gel chromatography on Sephadex G-75 is used to compare experimental behavior with theoretical profiles predicted for the electrostatic interaction between cytochrome c and soybean trypsin inhibitor (pH 6.8, I 0.01). Results of these experiments serve as a guide for future conduct of experiments aimed at characterization of biologically important, reversible complex formation between proteins and/or other macromolecules.     

Detection of Interactive Effects in Carcinogenesis

The multistage theory for cancer is used to derive models for independent effects and for interactive effects of two carcinogenic agents. The derivation assumes that a tumor is of single cell origin and that a normal cell is transformed to a cancer cell by undergoing a finite number of irreversible, heritable, mutation-like transitions. The interactions enter the proposed models at the level of single cell transition rates rather than, as is conventional, at the level of animal response proportions. Suggestions are given for the design and analysis of fixed time, binary response, two factor, cancer bioassay experiments.