III. Ecosmos: A Revolutionary Fertile, Habitable, Solar-Bioplanet, Incubator Lifescape

2. Computational Systems Physics: Self-Organization, Active Matter

Furusawa, Chikara and Kunihiko Kaneko. Evolutionary Origin of Power-Laws in a Biochemical Reaction Network. Physical Review E. 73/011912, 2006. An example of how constant, “inevitable” properties and propensities can be extracted from all kinds of naturally occurring organic metabolic dynamics.

Therefore, one possible strategy for extracting the nature of intracellular dynamics is to search for universal laws with regard to the networks of intracellular reactions common to a class of cell models – albeit simple – and then to unravel the dynamics of evolution leading to such features. (011912-1)

Ghosh, Subhadip, et al. Enzymes as Active Matter. Annual Review of Condensed Matter. Vol. 12, 2020. Enzyme: a substance produced by a living organism which acts as a catalyst to bring about a specific biochemical reaction. Penn State biochemists contribute a further notice of this natural spontaneity in effect for metabolic processes. Are we persons “condensed Matter” or is the physical ecosmos coming to life. See also Stem Cell Populations as Self-Renewing Many-Particle Systems by David Jorg, et al in this same volume for another instance.

Nature has designed multifaceted cellular structures to support life. Cells contain a vast array of enzymes that collectively perform tasks by harnessing energy from chemical reactions. In the past decade, detailed investigations on enzymes that are freely dispersed in solution have revealed a concentration-dependent enhanced diffusion and chemotactic behavior during catalysis. The purpose of this article is to review the different classes of enzyme motility and discuss the possible mechanisms as gleaned from experimental observations and theoretical modeling. (Ghosh Abstract excerpt)

This article reviews the physical principles of stem cell populations as active many-particle systems that are able to self-renew, control their density, and recover from depletion. We illustrate the statistical hallmarks of homeostatic mechanisms from stem cell transient large-scale oscillation dynamics during recovery to the scaling behavior of clonal dynamics and front-like boundary propagation during regeneration. (Jorg Abstract)

Giardina, Irene. Collective Behavior in Animal Groups: Theoretical Models and Empirical Studies. HFSP Journal. 2/4, 2008. Noted more in Organic Societies, a Centre for Statistical Mechanics and Complexity, University of Rome, (Google for info) physicist achieves a novel advance for nonlinear science for not only is an exemplary complex, agent-based self-organization described for avian bird flocks, but this activity, widespread across animal communities from microbes and insects to primates and economies, is seen to imply and spring from a general, independent, informative source.

Goh, Segun, et al. Emergence of Criticality in the Transportation Passenger Flow: Scaling and Renormalization in the Seoul Bus System. PLoS One. 9/3, 2014. Seoul National University, Sungshin Women’s University, Seoul, and CNRS, Institut Jean Lamour, France physicists and geographers deftly discern in urban commuter traffic the presence of intrinsic self-organizing complex network phenomena. At the outset, the project is said to be a good example of statistical mechanics applied to social systems. We likewise cite this work as a microcosm of the worldwide discovery of a mathematical generative agency. Over the past two decades, intensely since 2010, an exemplary manifestation of these same nonlinear forms and dynamics has been found everywhere from cosmos to cities. A strong implication is then an independent, program-like source from which such a scale-invariant universality arises.

Social systems have recently attracted much attention, with attempts to understand social behavior with the aid of statistical mechanics applied to complex systems. Collective properties of such systems emerge from couplings between components, for example, individual persons, transportation nodes such as airports or subway stations, and administrative districts. Among various collective properties, criticality is known as a characteristic property of a complex system, which helps the systems to respond flexibly to external perturbations. This work considers the criticality of the urban transportation system entailed in the massive smart card data on the Seoul transportation network. Analyzing the passenger flow on the Seoul bus system during one week, we find explicit power-law correlations in the system, that is, power-law behavior of the strength correlation function of bus stops and verify scale invariance of the strength fluctuations.

Such criticality is probed by means of the scaling and renormalization analysis of the modified gravity model applied to the system. Here a group of nearby (bare) bus stops are transformed into a (renormalized) “block stop” and the scaling relations of the network density turn out to be closely related to the fractal dimensions of the system, revealing the underlying structure. Specifically, the resulting renormalized values of the gravity exponent and of the Hill coefficient give a good description of the Seoul bus system: The former measures the characteristic dimensionality of the network whereas the latter reflects the coupling between distinct transportation modes. It is thus demonstrated that such ideas of physics as scaling and renormalization can be applied successfully to social phenomena exemplified by the passenger flow. (Abstract)

Gompper, Gompper, Gerhard, et al. The 2019 Motile Active Matter Roadmap. Journal of Physics: Condensed Matter. 32/29, 2020. This is a broadly European state of the art collection for this fluid field, which is hardly a decade old. As the quotes note, some 40 researches post papers such as Active Brownian Particles: From Collective Phenomena to Fundamental Physics by Thomas Speck, Self-organized Collective Patterns by Fernando Peruani, and Patterns of Collective Motion in Huge Flocks of Starlings by Charlotte Hemelrijk. Its popularity and expansive subject increasingly attest to an animate, lively natural materiality.

Activity and autonomous motion are fundamental in living and engineering systems. The new field of active matter now focuses on the physical aspects of propulsion mechanisms, and on motility-induced collective behavior of a larger number of member agents. The scale ranges from microswimmers to cells, fish, birds, and people. A major challenge for understanding and designing active matter is their nonequilibrium nature due to persistent energy consumption. The vast complexity of phenomena and mechanisms involved in the self-organization and dynamics of motile active systems comprises a major challenge. Hence, going forward this important research area requires a concerted, synergetic, interdisciplinary approach. (Abstract excerpt)

Active matter is a novel class of nonequilibrium systems composed of a large number of autonomous agents. The scale of agents ranges from nanomotors, microswimmers, and cells, to crowds of fish, birds, and humans. Unraveling, predicting, and controlling the behavior of active matter is a truly interdisciplinary endeavor at the interface of biology, chemistry, ecology, engineering, mathematics, and physics. Recent progress in experimental and simulation methods, and theoretical advances, now allow for new insights into this behavior, which should ultimately lead to the design of novel synthetic active agents and materials. This Roadmap provides an overview of the state of the art, and discusses future research directions on natural and artificial active agents, and their collective behavior. (Gerhard Gompper, Roland Winkler, 3)

Green, Sara and Robert Batterman. Making Sense of Top-Down Causation: Universality and Functional Equivanence in Physics and Biology. Voosholz, J and M. Gabriel, eds.. Top_Down Causation and Emergence. Cambridge: MIT Press, 2021. In an 80th birthday Festschrift for George Ellis, University of Copenhagen and University of Pittsburgh philosophers make a latest strong case for this natural constructive method, (aka a universe which makes itself.) While doing so, they further affirm a persistent, analogic recurrence in kind across physical and biological phenomena.

Hagan, Michael and Aparna Baskaran. Emergent Self-Organization in Active Materials. Current Opinion in Cell Biology. 38/74, 2016. For the record, we ought to note that just a decade ago, as earlier entries show, a evidential recognition of such cellular spontaneity was rare and in abeyance. Here Brandeis University physicists provide a 2017 example of its common acceptance as metabolic physiology and anatomy becomes an exemplar of nonlinear complexity.

Biological systems exhibit large-scale self-organized dynamics and structures which enable organisms to perform the functions of life. The field of active matter strives to develop and understand microscopically driven nonequilibrium materials, with emergent properties comparable to those of living systems. This review will describe two recently developed classes of active matter systems, in which simple building blocks — self-propelled colloidal particles or extensile rod-like particles — self-organize to form macroscopic structures with features not possible in equilibrium systems. We summarize the recent experimental and theoretical progress on each of these systems, and we present simple descriptions of the physics underlying their emergent behaviors. (Abstract)

Hallatschek, Oskar, et al. Proliferating Active Matter. Nature Reviews Physics. May, 2023. Some 15 years after this field gained recognition (S. Ramaswamy), UC Berkeley, Leipzig University, University of Basel, MIT, University of Edinburgh, and Princeton University researchers including Ned Wingreen provide an extensive, 200 reference survey of a wealth of evidence across all manner of physical and biological phases such as particulate, colloidal, cellular flows and even avian flocks to acquire their own self-organized patterns and processes. Once more in mid 2023 a robust, organic integrity becomes well established.

Active matter locally dissipates energy to produce systematic motion. This Perspective highlights proliferation as a special type of activity that breaks particle number conservation and thereby gives rise to a unique set of collective phenomena characteristic of life. (editor)

The patterns of collective motion created by autonomous particles have fuelled active-matter research for two decades. But so far these studies have focused on candidate entities. In reality, living systems involve the growth and evolution of microbial biofilms, expansion of a tumour, the development from a fertilized egg into an embryo. Here we argue that unique features emerge because proliferation represents a distinct activity that consumes and dissipates energy, injects biomass, and leads to myriad dynamic scenarios. Complex, collective phenomena in these soft-matter phases moves us to propose expansive generation as another direction of active-matter physics, worthy of new dynamical universality classes. (Abstract edits)

Examples of Active Matter Proliferation: Growing cells, shapes and populations have often been studied in mathematical biology at a meanfield level so to observe phenomena in microbiology, development, ecology, epidemiology, group dynamics and evolution. Several generic model systems of active matter collectives have thus emerged. One prototypical example combining soft matter and growth is provided by microbial biofilms on solid, semisolid or liquid substrates into resilient communities. These surface bacteria are abundant in nature composed either of clonal cells or diverse species. Complex physical properties contribute to their expansive presence, evolutionary success and their
important role in human disease. (5)

Havlin, Shlomo, et al. Focus on Complex Networked Systems. www.iop.org/EJ/journal/1367-2630. Accessed December 2007. An introduction to a special section of 20 papers on this subject in the online resource The New Journal of Physics, published by the European Institute of Physics, in association with the American Institute of Physics, in their joint Virtual Journal in Science and Technology program. A salient feature is said to be their recursive, multifractal self-similarity.

Complex networks are becoming manifest in many fields of contemporary science, including mathematics, physics, computer science, biology, engineering, social sciences and economics. As part of a broad movement towards research in complex systems, scientists have recently found a striking degree of self-organization that emerges in networks representing seemingly diverse complex systems. (179) The last decade has witnessed a burst of research activity in the study of large systems made of many non-identical entities, whose interaction or interconnection patterns show complex network-like structures. (179)

Haw, Mark and Otti Croze. Physics Comes to Life. Physics World. February, 2012. A University of Strathclyde chemist and University of Glasgow mathematician contend that recent laboratory studies of aquatic schools of bacteria and algae, as typical many-body systems, require a 21st version of physical theories to explain. May it then be surmised that as statistical physics and complexity science converge, each approach can be deeply and beneficially revised. As a consequence, an ever stronger case bodes for an intrinsically organic cosmos.

Statistical mechanics, one of the 19th century’s most successful scientific theories, describes systems comprising billions of inanimate atoms and molecules. But does this fundamental theory work the same way when applied to swarms of non-equilibrium, self-propelling, environment-exploring swimmers? It turns out that a new “living” statistical mechanics is required to describe many aspects of microswimmer behaviors. (39-40)

Helbing, Dirk, et al, eds. Nonlinear Physics Everywhere From Molecules to Cities. European Physical Journal B. 63/3, 2008. A collection from the European Conference on Complex Systems 2007 in this periodical dedicated to “Condensed Matter and Complex Systems.” A typical paper is Why are Large Cities Faster?: Universal Scaling and Self-Similarity in Urban Organization and Dynamics by Luis Bettencourt, Jose Lobo, and Geoffrey West. An import might be to note two optional modes of study – either to discern the same complex network patterns and processes at each manifest, emergent scale, or trace an inference that this phenomena implies and springs from a common, mathematically creative source.

Herbert-Dufresne, Laurent, et al. Structural Preferential Attachment: Stochastic Process for the Growth of Scale-free, Self-similar Systems. Physical Review E. 85/026108, 2012. Département de Physique, de Génie Physique, et d'Optique, Université Laval, Québec, physicists contribute to this distillation of ubiquitous commonalities across nature and society. As such work proceeds, the presence and instantiation of a cosmic genetic code from galactic clusters to hemispheric civilizations seems ever more evident. For further team work, see A Preferential Attachment Approach to Community Structure at arXiv:1603.035566 which notes the apparent universality of this method.

Many complex systems have been shown to share universal properties of organization, such as scale independence, modularity, and self-similarity. We borrow tools from statistical physics in order to study structural preferential attachment (SPA), a recently proposed growth principle for the emergence of the aforementioned properties. We study the corresponding stochastic process in terms of its time evolution, its asymptotic behavior, and the scaling properties of its statistical steady state. Moreover, approximations are introduced to facilitate the modeling of real systems, mainly complex networks, using SPA. Finally, we investigate a particular behavior observed in the stochastic process, the peloton dynamics, and show how it predicts some features of real growing systems using prose samples as an example. (Abstract)

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