Symmetry in Complex Systems

Complex systems with symmetry arise in many fields, at various length scales, including financial markets, social, transportation, telecommunication and power grid networks, world and country economies, ecosystems, molecular dynamics, immunology, living organisms, computational systems, and celestial and continuum mechanics. The emergence of new order and structure in complex systems means symmetry breaking and transition from unstable to stable states. Modeling complexity attracted many researchers from different areas, dealing both with theoretical concepts and practical applications. This Special Issue seeks to fill the gap between the theory of symmetry-based dynamics and its application to model and analyze complex systems. This Special Issue focuses on the synergies between the theory of symmetry-based dynamics and its application to model and analyze complex systems. It includes 7 manuscripts addressing novel issues and specific topics that illustrate symmetry in complex systems. In the follow-up the selected manuscripts are presented in alphabetic order.info:eu-repo/semantics/publishedVersio

Ab Initio Modeling of Ecosystems with Artificial Life

Artificial Life provides the opportunity to study the emergence and evolution of simple ecosystems in real time. We give an overview of the advantages and limitations of such an approach, as well as its relation to individual-based modeling techniques. The Digital Life system Avida is introduced and prospects for experiments with ab initio evolution (evolution "from scratch"), maintenance, as well as stability of ecosystems are discussed.Comment: 13 pages, 2 figure

Linked lives: the utility of an agent-based approach to modelling partnership and household formation in the context of social care

The UK’s population is aging, which presents a challenge as older people are the primary users of health and social care services. We present an agent-based model of the basic demographic processes that impinge on the supply of, and demand for, social care: namely mortality, fertility, health-status transitions, internal migration, and the formation and dissolution of partnerships and households. Agent-based modeling is used to capture the idea of “linked lives” and thus to represent hypotheses that are impossible to express in alternative formalisms. Simulation runs suggest that the per-taxpayer cost of state-funded social care could double over the next forty years. A key benefit of the approach is that we can treat the average cost of state-funded care as an outcome variable, and examine the projected effect of different sets of assumptions about the relevant social processes

Overcoming Metabolic Burden in Synthetic Biology: a CRISPR interference approach

Synthetic Biology is gaining an increasingly important role in the scientific community and dedicated research centers are rising all over the world. This discipline introduced the engineering principles of abstraction, modularity and standardization in the biology world; the application of these principles is allowing the design of complex biological systems to program living cells, realizing all sorts of desired function in many fields. These systems consist of DNA sequences, rationally combined to program the genetic instructions for cell behavior customization. Each part should behave as a biological brick for the design of complex genetic programs through functional building blocks; each module undergoes an extensive characterization to provide documentation on its functioning, enabling the rational design of complex circuits. Mathematical modeling accompanies all the design procedure as a tool to describe the behavior of each single genetic module, in a bottom-up fashion that should allow the prediction of more complex systems obtained by the interconnection of pre-characterized parts. However, many unpredictability sources hamper the ideally rational design of those synthetic genetic devices, mainly due to the tangled context-dependency behavior of those parts once placed into an intrinsically complex biological living system. Among others, the finite amount of translational resources in prokaryotic cells leads to an effect called metabolic burden, as a result of which hidden interactions between protein synthesis rates arise, leading to unexpected counterintuitive behaviors. To face this issue, two actions have been proposed in this study: firstly, a recently proposed mathematical modeling solution that included a description of the metabolic load exerted by the expression of recombinant genes have been applied on a case study, highlighting its worth of use and working boundaries; second, a CRISPR interference-based architecture have been developed to be used as an alternative to high resource usage transcriptional protein regulators, studying the underlying mechanism in several circuital configurations and optimizing each forming part in order to achieve the desired specifications. In Chapter 1, an introduction on synthetic biology is presented; in the second part, a brief overview on CRISPR technology and the overall aim of the study are reported. In Chapter 2, a case study evaluating the use of mathematical modeling to properly include metabolic burden in rational design of a set of transcriptional regulator cascades is reported. Firstly, the circuits and expected behavior are introduced, along with the discussion about experimental data, dissenting from what initially predicted. Secondly, the comparison between the use of a classical Hill equation-based model and an improved version that explicitly consider the translational load exerted by the expression of recombinant genes is reported. In Chapter 3, the design and deep characterization of a BioBrick$^{TM}$-compatible CRISPR interference-based repression set of modules is shown; expression optimization of the molecular players is reported and its usability as a low-burden alternative is demonstrated with experimental data and mathematical modeling. Working boundaries, peculiar aspects and rooms for improvements are then highlighted. In Chapter 4, preliminary studies aimed to improve the CRISPR interference system are reported and some of its context-dependencies are highlighted. Effects on repression efficiency due to alteration in the sequence of the RNA molecules addressing the CRISPR machinery to the desired target are discussed; evaluation of problems and opportunities related to the expression of more of this RNA guides are then highlighted. Lastly, an example of behavior of the system in presence of a competitor transcriptional regulator is reported. In Chapter 5 the overall conclusions of this thesis work are drawn

What is Autonomy?

A system is autonomous if it uses its own information to modify itself and its environment to enhance its survival, responding to both environmental and internal stimuli to modify its basic functions to increase its viability. Autonomy is the foundation of functionality, intentionality and meaning. Autonomous systems accommodate the unexpected through self-organizing processes, together with some constraints that maintain autonomy. Early versions of autonomy, such as autopoiesis and closure to efficient cause, made autonomous systems dynamically closed to information. This contrasts with recent work on open systems and information dynamics. On our account, autonomy is a matter of degree depending on the relative organization of the system and system environment interactions. A choice between third person openness and first person closure is not required

From Social Simulation to Integrative System Design

As the recent financial crisis showed, today there is a strong need to gain "ecological perspective" of all relevant interactions in socio-economic-techno-environmental systems. For this, we suggested to set-up a network of Centers for integrative systems design, which shall be able to run all potentially relevant scenarios, identify causality chains, explore feedback and cascading effects for a number of model variants, and determine the reliability of their implications (given the validity of the underlying models). They will be able to detect possible negative side effect of policy decisions, before they occur. The Centers belonging to this network of Integrative Systems Design Centers would be focused on a particular field, but they would be part of an attempt to eventually cover all relevant areas of society and economy and integrate them within a "Living Earth Simulator". The results of all research activities of such Centers would be turned into informative input for political Decision Arenas. For example, Crisis Observatories (for financial instabilities, shortages of resources, environmental change, conflict, spreading of diseases, etc.) would be connected with such Decision Arenas for the purpose of visualization, in order to make complex interdependencies understandable to scientists, decision-makers, and the general public.Comment: 34 pages, Visioneer White Paper, see http://www.visioneer.ethz.c