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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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VII. Pedia Sapiens: A Genesis Future on Earth and in the Heavens

1. Mind Over Matter: A Quantum, Atomic, Chemical Materiality

Thew, Rob, et al. Focus on Quantum Science and Technology Initiatives Around the World. Quantum Science and Technology. November, 2019. Editors from Switzerland, Canada, and Japan post a special collection for this radical worldwide ability to presently treat quantum phenomena as a common dynamic complex, network system which conveys content. Many unique applications with novel features then become possible such as faster computers and internet web.

Quantum physics has been a fascinating field of research for over a century, but is often seen as complex and difficult to understand. Information science was another primary development, but mostly as the reserve of complex and abstract mathematics. These technologies are sometimes seen as the first quantum revolution. Into the 21st century, a shift towards the development of products and applications by industrial companies has occurred, along with governments that realize the significance of these advances. This collection of Perspectives will provide insight into what is now a global pursuit. The first five papers cover established initiatives in Europe, Canada, Japan, Australia, and the USA. Further inputs from the UK and China will appear. So as 2020 approaches, we feel it is time to announce a second quantum revolution. (Summary excerpt.)

Tritschler, Ulrich and Helmut Colfen. Self-Assembled Hierarchically Structured Organic-Inorganic Composite Systems. Bioinspiration & Biomimetics. 11/3, 2017. In this journal University of Konstanz, Germany physical chemists seek to intentionally carry forth nature’s hard won, practical solutions to design and build novel, beneficial forms and features. See also in this journal Towards a Theoretical Clarification of Biomeimetics Using Conceptual Tools from Engineering Design by M. Drack, et al (13/1, 2018).

Designing bio-inspired, multifunctional organic–inorganic composite materials is one of the most popular current research objectives. This article reviews recent progress in synthesizing organic–inorganic composite materials via various self-assembly techniques and in this context highlights a recently developed bio-inspired synthesis concept for the fabrication of hierarchically structured, organic–inorganic composite materials. This one-step self-organization concept based on simultaneous liquid crystal formation of anisotropic inorganic nanoparticles and a functional liquid crystalline polymer turned out to be simple, fast, scalable and versatile, leading to various (multi-)functional composite materials, which exhibit hierarchical structuring over several length scales. (Abstract excerpt)

Van Anders, Greg, et al. Digital Alchemy for Materials Design: Colloids and Beyond. ACS Nano. 9/10, 2015. A team of University of Michigan materials scientists in coauthor Sharon Glotzer’ Lab describe breakthrough efforts to understand nature’s generative geometries, so as to take evolution forth to new creative, salutary phases. See an earlier entry here under Pablo Damasceno, and a March 2017 posting Digital Alchemist Seeks Rules of Emergence in Quanta Magazine with the subtitle Computational physicist Sharon Glotzer is uncovering the rules by which complex collective phenomena emerge from simple building blocks.

Starting with the early alchemists, a holy grail of science has been to make desired materials by modifying the attributes of basic building blocks. Building blocks that show promise for assembling new complex materials can be synthesized at the nanoscale with attributes that would astonish the ancient alchemists in their versatility. Here we show how to exploit the malleability of the valence of colloidal nanoparticle “elements” to directly and quantitatively link building-block attributes to bulk structure through a statistical thermodynamic framework we term “digital alchemy”. We use this framework to optimize building blocks for a given target structure and to determine which building-block attributes are most important to control for self-assembly, through a set of novel thermodynamic response functions, moduli, and susceptibilities. Moreover, our results give concrete solutions to the more general conceptual challenge of optimizing emergent behaviors in nature and can be applied to other types of matter. As examples, we apply digital alchemy to systems of truncated tetrahedra, rhombic dodecahedra, and isotropically interacting spheres that self-assemble diamond, fcc, and icosahedral quasicrystal structures, respectively. (Abstract)

Wadkawan, Vinod. Smart Structures. Oxford: Oxford University Press, 2007. As readers know, there is today a burst of books on “nanotechnology” as regnant mind may gain the ability to act upon the molecular and atomic depths of material device and function. This present volume by a Raja Ramanna Fellow at the Bhabha Research Centre, Mumbai, India is notable as a dedicated attempt to first articulate nature’s own method of dynamic self-organization and to then apply it everywhere as a direct, intentional continuation.

Wan, Kwok-Ho, et al. Quantum Generalization of Feedforward Neural Networks. Npj Quantum Information. 3/36, 2017. We cite this entry by Imperial College London mathematicians to report novel integrations between quantum phenomena and classical complex systems. Of especial note is an amenable employ of cerebral dynamics to nature’s fundamental realm. Why do neural nets so readily apply everywhere, what might this imply about universe and human? See also Topological Networks for Quantum Communication Between Distant Qubits in this journal (Lang, 3/47).

We propose a quantum generalisation of a classical neural network. The classical neurons are firstly rendered reversible by adding ancillary bits. Then they are generalised to being quantum reversible, i.e., unitary (the classical networks we generalise are called feedforward, and have step-function activation functions). The quantum network can be trained efficiently using gradient descent on a cost function to perform quantum generalisations of classical tasks. We demonstrate numerically that it can: (i) compress quantum states onto a minimal number of qubits, creating a quantum autoencoder, and (ii) discover quantum communication protocols such as teleportation. Our general recipe is theoretical and implementation-independent. The quantum neuron module can naturally be implemented photonically. (Abstract)

Quantum vs. classical: Can these neural networks show some form of quantum
supremacy? The comparison of classical and quantum neural networks is well-defined within our set-up, as the classical networks correspond to a particular parameter regime for the quantum networks. A key type of quantum supremacy is that the quantum network can take and process quantum inputs: it can for example process (+) and (-) differently. Thus, there are numerous quantum tasks it can do that the classical network cannot, including the two examples above. (36)

We often want computers to tell us something about the input data, e.g. if a given image corresponds to a cat or a dog. It seems the human brain learns this by looking at examples whilst getting feedback from a teacher, rather than being given an algorithm. Such an approach to programming is now revolutionising the ability of machines to learn. The approach uses simplified models of the brain: neural nets. Quantum information processing devices are now emerging as the next generation of information processors. One may hope that the neural net approach will be similarly powerful there. We therefore designed quantum neural nets, processing quantum superpositions. The nets work well in two example tasks: compressing data stored in superpositions, and rediscovering a protocol known as quantum teleportation. (Editor comment)

Warth, Benedict, et al. Metabolizing Data in the Cloud. Trends in Biotechnology. Online February, 2017. We cite this note from the Center for Metabolomics and Departments of Chemistry, Molecular and Computational Biology, Immunology and Microbial Science and Chemical Physiology, Scripps Research Institute, La Jolla, CA as an example of this enveloping global sensorium as it proceeds with a deep, interactive informomics learning project.

Cloud-based bioinformatic platforms address the fundamental demands of creating a flexible scientific environment, facilitating data processing and general accessibility independent of a countries’ affluence. These platforms have a multitude of advantages as demonstrated by omics technologies, helping to support both government and scientific mandates of a more open environment. (Abstract)

Wei, Bryan, et al. Complex Shapes Self-Assembled from Single-Stranded DNA Tiles. Nature. 485/623, 2012. Harvard University systems biophysicists find that deoxyribonucleic molecules can be molded by origami-like foldings into a myriad of topological arrays. By avail of its tendency to self-assemble into modular forms, a novel realm of vital nanoscale geometries is thus seen to open. The Letter is accompanied in the same issue by a review “The Importance of Being Modular” by Paul Rothemund and Ebbe Sloth Anderson.

Programmed self-assembly of strands of nucleic acid has proved highly effective for creating a wide range of structures with desired shapes. A particularly successful implementation is DNA origami, in which a long scaffold strand is folded by hundreds of short auxiliary strands into a complex shape. Modular strategies are in principle simpler and more versatile and have been used to assemble DNA or RNA tiles into periodic and algorithmic two-dimensional lattices, extended ribbons and tubes, three-dimensional crystals, polyhedra and simple finite two-dimensional shapes. (623)

Thus, the SST (single-stranded tile) method and DNA origami, and approaches that use multistranded DNA and RNA tiles, logic gates and kinetid hairpins, suggest the presence of a vast design space that remains to be explored for the creation of nucleic acid nanostructures, and more generally for information-directed molecular self-assembly. (626)

Willner, Alan. Communication with a Twist. IEEE Spectrum. August, 2016. A report on how a previously under-appreciated property of certain light beams, namely spiraling, corkscrew waves with an orbital angular momentum, can attain much higher levels of data transmission. A fiber optic cable which can carry this vortex pattern is now in the works. Our interest is still another instance of human ingenuity learning all about a natural genesis, in this case electromagnetic radiation, so as to be able to enhance a new radically intentional creation.

Windsor, Colin. Can the Development of Fusion Energy be Accelerated? Philosophical Transactions A. 377/20170446, 2019. A Tokamak Energy, UK engineer introduces the proceedings from a March 2018 Royal Society meeting on this issue of how to foster the research and construction of safer atomic fusion sources beyond calamity-prone fission reactors. Some papers are The European Roadmap towards Fusion Electricity, Towards a Compact Spherical Tokamak Pilot Plant, and Engineering Challenges for Accelerated Fusion.

This introduction reviews the unique opportunity of fusion power to deliver safe, carbon-free, abundant, base-load power. The differences from fission power are considered: especially why a Chernobyl, Three Mile Island or Fukushima accident could not happen with a fusion reactor. The Lawson triple product is introduced, along with tokamaks, or magnetic bottles, whose ability to approach close to fusion burn conditions has so far put them above their competitors. The question posed is whether the two developments of spherical tokamaks and high-temperature superconductors could lead to more economical fusion power plants and faster development than the current route. (Abstract)

Winpenny, Richard. Quantum Information Processing Using Molecular Nanomagnets as Qubits. Angewandte Chemie International. 47/7992, 2008. In another example, a University of Manchester chemist involves in and contributes to the genetic generation of life’s informational florescence.

Wolf, Edward. Graphene: A New Paradigm in Condensed Matter and Device Physics. New York: Oxford University Press, 2014. A NYU Polytechnic Institute physicist describes still another fantastic form latent in nature’s fertile materiality by which participatory human beings can find, avail and begin a new intentional creation.

The book is an introduction to the science and possible applications of Graphene, the first one-atom-thick crystalline form of matter. Discovered in 2004 by now Nobelists Geim and Novoselov, the single layer of graphite, a hexagonal network of carbon atoms, has astonishing electrical and mechanical properties. It supports the highest electrical current density of any material, far exceeding metals copper and silver. Its absolute minimum thickness, 0.34 nanometers, provides an inherent advantage in possible forms of digital electronics past the era of Moore's Law. (Publisher)

Yazdi, S. M. Hossein, et al. DNA-Based Storage. IEEE Transactions on Molecular, Biological and Multi-Scale Communications. 1/3, 2016. It seems, as evinced by new journals as this (search IEEE T-MBMC), that our sense of what constitutes a genome is steadily expanding. In typical entry, a team of University of Illinois theorists, who originally hail from Iran, Singapore, Spain, China, and Yugoslavia, study “chemical oligonucleotide” synthesis as if they were parsing literature with a mind to “edit” and improve. See also in issue 1/2, 2015, Coordinated Spatial Pattern Formation in Biomolecular Communications Networks by Yutaka Hori, et al for more potentials.

We provide an overview of current approaches to DNA-based storage system design and of accompanying synthesis, sequencing and editing methods. We also introduce and analyze a suite of new constrained coding schemes for both archival and random access DNA storage channels. The analytic contribution of our work is the construction and design of sequences over discrete alphabets that avoid pre-specified address patterns, have balanced base content, and exhibit other relevant substring constraints. These schemes adapt the stored signals to the DNA medium and thereby reduce the inherent error-rate of the system. (Yazdi Abstract)

This paper proposes a control theoretic framework to model and analyze the self-organized pattern formation of molecular concentrations in biomolecular communication networks, emerging applications in synthetic biology. In biomolecular communication networks, bionanomachines, or biological cells, communicate with each other using a cell-to-cell communication mechanism mediated by a diffusible signaling molecule, thereby the dynamics of molecular concentrations are approximately modeled as a reaction-diffusion system with a single diffuser. We first introduce a feedback model representation of the reaction- diffusion system and provide a systematic local stability/instability analysis tool using the root locus of the feedback system. The instability analysis then allows us to analytically derive the conditions for the self-organized spatial pattern formation, or Turing pattern formation, of the bionanomachines. (Hori Abstract)

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