III. An Organic, Conducive, Habitable MultiUniVerse
2. Systems Chemistry
A section added in 2007 to gather novel advances in the nascent field of “supramolecular chemistry,” aka “constitutional dynamic and adaptive chemistry.” These terms, along with systems chemistry, are from the Nobel laureate Jean-Marie Lehn and colleagues to represent new appreciations of how the universal self-organizing principles are similarly being found to foster an emergent, nested complexity across chemical and biological precursor materialities.
How Does Life and the Universe Organize Itself?. www.huntsman.com. A site for Huntsman Advanced Materials – when accessed, type Lehn into its search box. An extensive news report on a February 21, 2008 talk in Basel by Nobel chemist Jean Marie Lehn on the revolutionary frontiers and implications of supramolecular chemistry, a field he founded. This advance which perceives material nature to possess a deep propensity for self-assembling dynamics not only promises many novel technologies but implies a profoundly different kind of animate cosmos with its own innate vitality. By intentionally facilitating these qualities of prior, innate self-organization and later selection, human intention can continue this emergent creation.
Constitutional dynamic chemistry introduces a paradigm shift with respect to constitutionally static chemistry. Whereas self-organization by design strives to achieve full control over the output molecular or supramolecular entity by explicit programming, self-organization by selection operates on dynamic constitutional diversity in response to either internal or external factors to achieve adaptation in a darwinistic fashion. By extending its characteristic features, supramolecular chemistry is thus leading towards the emergence of adaptive and evolutive chemistry.
Supramolecular Chemistry. www.nature.com/collections/wypqwypccc. A collation from the daily Nature Communications site of contributions to this 21st century scientific frontier. Its contents come in four categories: Physical Principles, Discrete Assemblies, Materials Design and Systems Chemistry For a sample, see Self-Selection of Dissipative Assemblies Driven by Primitive Chemical Reaction Networks by Tens-Solsona, Marta et al, Rich Complex Behavior of Self-Assembled Nanoparticles Far from Equilibrium by Serim Ilday, et al, and Chemical and Entropic Control on the Molecular Self-Assembly Process by Dan Packwood, et al. Some other collections are Complexity Research and Developmental Biology.
Supramolecular chemistry specializes in non-covalent interactions. These weak and reversible forces—such as hydrogen bonds, hydrophobic forces, van der Waals forces, and metal–ligand coordination—are key to understanding biological processes and self-assembling systems, and to constructing complex materials and molecular machinery. In the several decades since its conception, supramolecular chemistry has become a truly interdisciplinary research area, providing insights into and spurring developments across biology, chemistry, nanotechnology, materials science, and physics. In this collection, we highlight a selection of recent experimental and theoretical studies published in Nature Communications, which we hope reflect the true breadth of supramolecular chemistry as a discipline. The collection features advances in building discrete assemblies and extended material systems, all through the clever design of non-covalently organizing components.
Systems Chemistry. www.grc.org/systems-chemistry-conference/2018. A Gordon Research Conference over July 29 – August 3, 2018 at the Jordan Hotel at Sunday River Ski Resort in Newry, Maine, a fine summer venue. Notably, it is the first international meeting of this nascent field as it evokes a dynamic materiality akin to other realms of an ecosmos genesis. Some sessions are Bottom-up Construction of Complex Chemical Systems, Chemical Networks, Alternative Genetic Systems, Autocatalysis and Self-Replication, Chemical Reactivity Far from Equilibrium and so on. And the whole cast of advocates seem in attendance with David Lynn, Goren Ashkenasy, Sibren Otto and Rein Ulijn as Chairs onto main presenters Sara Imari Walker, Kepa Ruiz-Mirazo, Christine Keating, Henderson Cleaves, Niles Lehman, Jennifer Heemstra, Lee Cronin and more.
A difference between man-made processes and products and those in the living world is that the former are typically passive and static while the latter are active and dynamic. Life is the product of complex systems of molecular reactions; connections and interactions giving rise to a highly dynamic and functional whole. While research into complex systems is by now well established, chemistry embraced a "systems" view only recently. The design and study of dynamic, self-organized, multi-component chemical networks has been integrated under the umbrella of a fledgling Systems Chemistry. This meeting will offer an international venue for discussing breakthrough results in systems chemistry, for sharing new emerging methodology, and refinement of ideas across these new research directions. With the recent advances in instrumentation and analytical tools, complex chemical systems are opening new approaches for the construction and design of dynamic mesoscale materials. This diversity applies equally to scientists studying (i) supramolecular chemistry, (ii) origins of life, and (iii) far-from-equilibrium systems. (Summary edits)
Systems Chemistry. www.esf.org/conferences/08267. An October 2008 meeting held at Maratea, Italy by the European Science Foundation as part of its Action CM0703: Systems Chemistry initiative. This website will direct to the extensive program, which includes, e.g., George Cody: Geomimetic Biochemistry; Steven Benner: Systems Chemistry that Creates “Life;” Donna Blackmond: Chemical and Physical Models for the Evolution of Biological Homochirality; Peter Schuster: The Advent of Information and combinatorial Complexity; and Eors Szathmary: The Origin of the Genetic Code. Immediately followed by Chembiogenesis 2008 (Google) in the same venue, these efforts achieves a further rooting of living dynamics into conducive molecular realms. But the deeper ground of the physical cosmos remains absent and barren, a “systems physics” turn has yet to be taken.
Systems chemistry is the joint effort of prebiotic and supramolecular chemistry assisted by computer science from theoretical chemistry, biology, and complex systems research to tackle dynamic supersystem integration including at least one autocatalytic subsystem. It is the bottom-up pendant of systems biology towards synthetic biology. The integration approach will necessarily link to the question of asymmetric autocatalysis and chiral symmetry breaking, while the key challenge is to find the roots of Darwinian evolvability in chemical systems.
Andersen, Jakob, et al. An Intermediate Level of Abstraction for Computational Systems Chemistry. arXiv:1701.09097.. Andersen and Daniel Merkle, Earth-Life Science Institute, Tokyo, with Christoph Flamm and Peter Stadler, University of Vienna, introduce a Network View of Chemistry to expand this systems view. Life’s origin and a “universe of chemical compounds” are then be better appreciated.
Computational techniques are required for narrowing down the vast space of possibilities to plausible prebiotic scenarios, since precise information on the molecular composition, the dominant reaction chemistry, and the conditions for that era are scarce. The exploration of large chemical reaction networks is a central aspect in this endeavour. While quantum chemical methods can accurately predict the structures and reactivities of small molecules, they are not efficient enough to cope with large-scale reaction systems. The formalization of chemical reactions as graph grammars provides a generative system, well grounded in category theory, at the right level of abstraction for the analysis of large and complex reaction networks. An extension of the basic formalism into the realm of integer hyperflows allows for the identification of complex reaction patterns, such as auto-catalysis, in large reaction networks using optimization techniques. (Abstract)
Annila, Arto and Erkki Kolehmainen. On the Divide between Animate and Inanimate. Journal of Systems Chemistry. Online February, 2015. As the biological and physical sciences become (re)unified, University of Helsinki and University of Jyvaskyla, Finland, scientists contend, informed by new realizations of nature’s integral self-similarity, that this artificial, untenable separation and divide of inorganic and organic can at last be removed.
Vitalism was abandoned already for a long time ago, yet the impression that animate beings differ in some fundamental way from inanimate objects continues to thrive. Here, we argue that scale free patterns, found throughout nature, present convincing evidence that this demarcation is only imaginary. Therefore, all systems ought to be regarded alike, i.e., all are consuming free energy in least time. This way evolutionary processes can be understood as a series of changes from one state to another, so that flows of energy themselves naturally select those ways and means, such as species and societies or gadgets and galaxies to consume free energy in the least time in quest of attaining thermodynamic balance in respective surroundings. This holistic worldview, albeit an accurate account of nature, was shelved soon after its advent at the turn of the 18th century, because the general tenet did not meet that time expectations of a deterministic law, but now it is time to reconsider the old universal imperative against observations rather than expectations. (Abstract)
Ashkenasy, Goren, et al. Systems Chemistry. Chemical Society Reviews. 46/2543, 2017. GA, Ben-Gurion University of the Negev, Thomas Hermans, University of Strasbourg, Sijbren Otto, University of Goningen, and Annette Taylor, University of Sheffield introduce and survey an update collection on this integrative advance. For a flavor, some topics are dissipative non-equilibrium self-assembly, autocatalysis, and open-ended evolution. Among the papers are Exploring the Emergence of Complexity using Synthetic Replicators, Assessing Cooperativity in Supramolecular Systems (search Krbek) and Supramolecular Chemistry by the Nobel chemist and conceptual founder Jean-Marie Lehn.
This young field aims to develop complex molecular systems showing emergent properties; i.e. properties that go beyond the sum of the characteristics of the individual consituents of the system. This review gives an impression of the state of the art of the field by showing a diverse number of recent highlights, including out-of-equilibrium self-assembly, chemically fuelled molecular motion, compartmentalised chemical networks and designed oscillators. Subsequently a number of current challenges related to the design of complex chemical systems are discussed, including those of creating concurrent formation–destruction systems, continuously maintaining chemical systems away from equilibrium, incorporating feedback loops and pushing replication chemistry away from equilibrium. (Abstract)
Banzhaf, Wolfgang and Lidia Yamamoto. Artificial Chemistries. Cambridge: MIT Press, 2015. Memorial University of Newfoundland and University of Strasbourg interdisciplinary scientists achieve a 600 page resource for the multifaceted complex natural systems project which lately spans physical, evolutionary, biological and societal domains. The work opens by saying it has little to do with chemicals, but is all about the interactive dynamics between material entities from cosmos to culture. The title term has currency in the broad computational turn along with other evolutionary, genetic, neural net, and algorithmic versions. Its special contribution is an advanced, inclusive, insightful synthesis of the nascent field as it tries to express an intrinsic, universally recurrent program code that seems to be running everything. As the quotes convey, the endeavor is distinguished by an initial explication, albeit in abstract terms, of spontaneous complex adaptive networks, unto a better, intentional future as their creative utility may now pass to our comprehension. A 50 page bibliography with 959 entries is a copious guide in itself. See Banzhaf’s publication page for some two decades of writings on many facets such as genetic programming, molecular computing, and bioinformatics.
The field of Artificial Life (ALife) is now firmly established in the scientific world, but it has yet to achieve one of its original goals: an understanding of the emergence of life on Earth. The new field of Artificial Chemistries draws from chemistry, biology, computer science, mathematics, and other disciplines to work toward that goal. For if, as it has been argued, life emerged from primitive, prebiotic forms of self-organization, then studying models of chemical reaction systems could bring ALife closer to understanding the origins of life. In Artificial Chemistries (ACs), the emphasis is on creating new interactions rather than new materials. The results can be found both in the virtual world, in certain multiagent systems, and in the physical world, in new (artificial) reaction systems. (Publisher)
Barge, Laura, et al. From Chemical Gardens to Chemobrionics. Chemical Reviews. 115/8652, 2015. A 21 member international collaboration including Alan Mackay, Anne De Wit, Florence Haudin, Leroy Cronin and Julyan Cartwright write a scientific treatise of 50 pages and 275 references which covers historical studies of these spontaneous plant-like material forms from the 17th century to this 21st century resolve. As the quotes describe, the sciences of complex, self-organizing systems can now provide the theoretical explanations for their occasion. As the paper goes on, a major benefit is a better sense of an inherent prebiotic origin of life by virtue of these dynamic phenomena. For a popular review see The Fertile Physics of Chemical Gardens by Oliver Steinbock (search) et al in Physics Today for March 2016. In the mid 2010s, an emergent humankind seems at last able verify and discover an organic genesis cosmos.
Chemical gardens are perhaps the best example in chemistry of a self-organizing nonequilibrium process that creates complex structures. Many different chemical systems and materials can form these self-assembling structures, which span at least 8 orders of magnitude in size, from nanometers to meters. Key to this marvel is the self-propagation under fluid advection of reaction zones forming semipermeable precipitation membranes that maintain steep concentration gradients, with osmosis and buoyancy as the driving forces for fluid flow. Chemical gardens have been studied from the alchemists onward, but now in the 21st century we are beginning to understand how they can lead us to a new domain of self-organized structures of semipermeable membranes and amorphous as well as polycrystalline solids produced at the interface of chemistry, fluid dynamics, and materials science. We propose to call this emerging field chemobrionics. (8653)
Behler, Jorg. Neural Network Potential-Energy Surfaces in Chemistry. Physical Chemistry Chemical Physics. 13/17930, 2011. A Ruhr University Bochum theoretical chemist finds these cerebral dynamic topologies to be readily adaptable to chemical phenomena. See also Neural Network Molecular Dynamics Simulations of Solid-Liquid Interfaces by Suresh Natarajan and Behler in the same journal (Online September, 2016), and Constructing High-Dimensional Neural Network Potentials: A Tutorial Review by Behler in International Journal of Quantum Chemistry (115/16, 2015).
The accuracy of the results obtained in molecular dynamics or Monte Carlo simulations crucially depends on a reliable description of the atomic interactions. A large variety of efficient potentials has been proposed in the literature, but often the optimum functional form is difficult to find and strongly depends on the particular system. In recent years, artificial neural networks have become a promising new method to construct potentials for a wide range of systems. They offer a number of advantages: they are very general and applicable to systems as different as small molecules, semiconductors and metals; they are numerically very accurate and fast to evaluate; and they can be constructed using any electronic structure method. Significant progress has been made in recent years and a number of successful applications demonstrate the capabilities of neural network potentials. (Abstract)
Boeyens, Jan. The Grand Periodic Function. Scerri, Eric and Guillermo Restrepo, eds. Mendeleev to Oganesson: A Multidisciplinary Perspective on the Periodic Table. Oxford: Oxford University Press, 2017. In a latest volume on nature’s auspicious array of chemical elements, a chapter by the University of Pretoria chemist (search) which notes its structural essence. If of a mind, an independent geometry, a “cosmic self-similarity” with Fibonacci sequences, becomes evident. In regard, a science lecture hall at nearby UM Amherst has large wall PT on display. By any stretch this fecund materiality from which we arise and wonder is not an accident, but we cannot realize due to cultural constraints. And we should note that the title names – Dmitri Mendeleev (1834-1907) and Yuri Oganessian (1933- ) discoverer of the 118 atomic number - are a Russian chemist and physicist whose national country, as also America, yet seems bent on nuclear confrontation.
The ubiquitous symmetry, known as self-similarity, neatly accounts for the growing number of apparently unrelated regularities of Nature that derive form a single number pattern, based on the golden ratio. The unavoidable conclusion is that this pattern is generated by the typology of space-time. (137) It is no accident that the grand periodic function and all periodic phenomena are based on number theory, the golden ratio, logarithmic spirals, and self-similarity. The richest variety of periodic trends has been identified in chemistry and that is where a new number=based calculus is expected to develop. (138)
Breik, Keenan, et al. Programming Substrate-Independent Kinetic Barriers with Thermodynamic Binding Networks. arXiv:1810.12889. UT Austin and UC Davis researchers including David Doty press on with a frontier synthesis of chemical catalysis and energetic systems.
Engineering molecular systems that exhibit complex behavior requires the design of kinetic barriers. While programming such energy barriers seems to require knowledge of the specific substrate, we develop a novel substrate-independent approach. We extend the recently-developed model known as thermodynamic binding networks to programmable kinetic barriers that arise solely from the driving forces of bond formation and configurational entropy of separate complexes. Our model is robust such that several variations lead to equivalent energy barriers. Our results yield robust amplifiers using DNA strand displacement, a popular technology for engineering synthetic reaction pathways. (Abstract excerpt)