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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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VIII. Pedia Sapiens: A New Genesis Future

1. Mind Over Matter: Quantum, Atomic, Chemical Connectomics

Su, Wu, et al. DNA-Templated Photonic Arrays and Assemblies: Design Principles and Future Opportunities. Chemistry A European Journal. 17/29, 2011. An example today the literature as human collaborative abilities take over material nature to begin an intentional re-creation good for cosmos and children. University of Leicester (Su and Vanessa Bonnard) and University of Strathclyde (Glenn Burley) researchers here join nucleotide and photon so as to enter a new Age of Life and Light. Whatever fantastic ordained reality that we do not yet understand is being revealed and offered to us?

Molecular photonics is a rapidly developing and multi-disciplinary field of research involving the construction of molecular assemblies comprising photoactive building blocks that are responsive to a light stimulus. A salient challenge in this field is the controlled assembly of these building blocks with nanoscale precision. DNA exhibits considerable promise as an architecture for the templated assembly of photoactive materials. In this Concept Article we describe the progress that has been made in the area of DNA photonics, in which DNA acts as a platform for the construction of optoelectronic assemblies, thin films and devices. (7983)

Tait, Steven. Surface Chemistry: Self-Assembling Sierpinski Triangles. Nature Chemistry. 7/5, 2015. A report on a technical paper Assembling Molecular Sierpinski Triangle Fractals in the same issue by Chinese and German scientists who found nature’s materiality to inherently form into these iconic geometries. To reflect a bit, from what kind of independent natural reality do these propensities arise, which are now passing to our sapient avail so as to begin, as the quotes alludes, a new cosmocene creation.

Defect-free Sierpiński triangles can be self-assembled on a silver surface through a combination of molecular design and thermal annealing. Three-fold halogen-bonding arrays and precise surface epitaxy preclude structural errors, thus enabling the high-level complexity of these supramolecular fractal patterns. (370) For the field of supramolecular chemistry – particularly for those researchers interested in surface functionalization and the realization of mathematical fractal designs – it is exciting to see the elements of rational instructed building block design, kinetic control, and error correction combined in harmony to produce such beautiful structures. As we look to the next challenges in the design of complex molecular systems and their use in novel materials, it is valuable to consider the importance of these particular elements and the principles for tuning molecular systems to achieve them. The final piece of the puzzle is to put them together to achieve spontaneous self-assembly in synthetic systems that approaches the elegance and complexity of self-assembled structures that we see all around us in the natural world. (371)

Tao, Kai, et al. Self-Assembling Peptide Semiconductors. Science. 358/885, 2017. We cite because Tel Aviv University biotechnologists describe how a facilitated passage from peptide biochemicals via oligomerized quantum dots can form semiconductor superstructures. Human intellect can lately delve into nature’s materiality so as to intentionally begin a new genesis, fittingly from the cradles of civilization.

For semiconductors, one often thinks of inorganic materials, such as doped silicon, or aromatic organic polymers and small molecules. Tao et al. review progress in making semiconductors based on self-assembling short peptides. The structures that form show extensive π and hydrogen bonding leading to a range of semiconductor properties, which can be tuned through doping or functionalization of the peptide sequences. These materials may shed light on biological semiconductors or provide an alternative for constructing biocompatible and therapeutic materials.

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)

Von Lilienfeld, Anatole, et al. Exploring Chemical Compound Space with Quantum-based Machine Learning. Nature Reviews Chemistry. 4/6, 2020. We cite this entry by University of Basel, Berlin and Luxembourg material scientists as an example, largely unawares so far, of humankinder abilities to take over and begin a new physical, elemental and in/organic chemical co-pro-creation.

Rational design of compounds with specific properties requires understanding and fast evaluation of molecular properties throughout the huge set of all potentially stable molecules. Recent melds of quantum-mechanical calculations with machine learning show promise for exploring wide swathes of chemical compound space. We propose that significant progress in the understanding of chemical reactivity can be made through a systematic combination of physical theories, comprehensive data sets of microscopic and macroscopic properties, and modern machine-learning methods. (Abstract excerpt)

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.

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