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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

Jin, Ren-Hua, et al. Biomimetic Synthesis of Shaped and Chiral Silica Entities Templated by Organic Objective Materials. Chemistry: A European Journal. 20/7198, 2014. This contribution by Kanagawa University, Japan, chemists, among thousands of its kind across the literature, applies biological topologies toward the creation of a new natural materiality. In regard, this frontier work could be seen as an intended passage to conscious human continuance for a new genesis future.

Organic molecules with accompanying self-organization have been a great subject in chemistry, material science and nanotechnology in the past two decades. One of the most important roles of organized organic molecules is the capability of templating complexly structured inorganic materials. The focus of this Minireview is on nanostructured silica with divergent morphologies and/or integrated chirality directed by organic templates of self-assembled polyamine/polypeptides/block copolymers, chiral organogels, self-organized chiral amphiphiles and chiral crystalline complexes, etc., by biomimetic silicification and conventional sol–gel reaction. Among them, biosilica (diatoms and sponges)-inspired biomimetic silicifications are particularly highlighted. (Abstract)

Johnson, George. A Shortcut Through Time: The Path to a Quantum Computer. New York: Knopf, 2003. A science writer narrates the players and their imaginations that portend an immense computational ability on an atomic scale.

Jones, Matthew and Chad Mirkin. Self-Assembly gets a New Direction. Nature. 491/42, 2012. For another example, this reviews of a materials science advance “Colloids with Valence and Specific Directional Bonding” by Yufeng Wang in the same issue, which is seen to “greatly expand the range of structures that can be assembled from small components.” Might it again be broached who are we fledgling creatures to gain mindful knowledge over matter so to begin a second genesis? Could one say to a child starting school “God needs your help,” with theologian Philip Hefner (search) that you are an intended “co-creators?”

The ability to design and assemble three-dimensional structures from colloidal particles is limited by the absence of specific directional bonds. As a result, complex or low-coordination structures, common in atomic and molecular systems, are rare in the colloidal domain. Here we demonstrate a general method for creating the colloidal analogues of atoms with valence: colloidal particles with chemically distinct surface patches that imitate hybridized atomic orbitals, including sp, sp2, sp3, sp3d, sp3d2 and sp3d3. Functionalized with DNA with single-stranded sticky ends, patches on different particles can form highly directional bonds through programmable, specific and reversible DNA hybridization. These features allow the particles to self-assemble into ‘colloidal molecules’ with triangular, tetrahedral and other bonding symmetries, and should also give access to a rich variety of new microstructured colloidal materials. (Wang, et al, Abstract)

Jorgensen, Mathias, et al. Atomistic Structure Learning. Journal of Chemical Physics. 151/054111, 2019. Interdisciplinary NanoScience Center, Aarhus University, Denmark researchers describe the conceptual formation of novel materials via a 2019 synthesis of deep neural nets, algorithmic computation, and an iterative elemental and (bio)molecular stereochemistry. A typical section is Atomistic Reinforcement Learning. Might we then witness and surmise the advent of collaborative humankinder take up and over of cosmic condensed matter formularies, quite as a self-creative genesis intends and requires?

One endeavor of modern physical chemistry is to use bottom-up approaches to design materials and drugs with desired properties. Here, we introduce an atomistic structure learning algorithm (ASLA) that utilizes a convolutional neural network to build 2D structures and planar compounds atom by atom. The algorithm takes no prior data or knowledge on atomic interactions but inquires a first-principles quantum mechanical program for thermodynamical stability. Using reinforcement learning, the algorithm accumulates knowledge of chemical compound space for a given number and type of atoms and stores this in the neural network, ultimately learning the blueprint for the optimal structural arrangement of the atoms. (Abstract)

Kaku, Michio. Physics of the Future: How Science Will Shape Human Destiny and Our Daily Lives by the Year 2100. New York: Doubleday, 2011. In his latest popular vista from the second decade of this century, the CCNY quantum physicist muses how we might become “the gods of our mythologies” with epic powers on the freeway to a new creation. While heavy on machine technologies, we note also for this summary quote.

All the technological revolutions described here are leading to a single point: the creation of a planetary civilization. This transition is perhaps the greatest in human history. In fact, the people living today are the most important ever to walk the surface of the planet, since they will determine whether we attain this goal or descent into chaos. (327)

Kalinin, Sergei, et al. Fire Up the Atom Forge. Nature. 539/485, 2016. Oak Ridge National Laboratory, Institute for Functional Imaging, Center for Nanophase Materials researchers describe novel abilities to manipulate individual atoms. As if “quantum Legos,” by reaching this datum an intentional phase of a new atomic and chemical nature may commence. See also a cited reference Dynamic Scan Control in STEM (Scanning transmission electron microscopy) in Advanced Structural and Chemical Imaging by Xiahan Sang, et al (Vol. 2/Art. 6, 2016), a new Springer journal. For another view see Atom-by-Atom Assembly by Manuel Endres, et al in Science (354/1024, 2016).

Materials could be made from scratch by enhancing a microscope that uses an electron beam to image the structure of crystals. Making the electron beam programmable — to vary how many electrons are fired, to where and for how long — would allow atoms to be moved, added or knocked out. The structure of the material needs to be monitored in real time so that progress can be followed and mistakes corrected. (Summary 487) Let us make a start: the ability to build new forms of matter from the atom up will mark a new chapter of nanoscience. (487)

Keane, Christopher. Chaos in Collective Health: Fractal Dynamics of Social Learning. Journal of Theoretical Biology. Online August, 2016. As the Abstract explains, a University of Pittsburgh professor of behavioral and community health sciences demonstrates how even such intense human activity can be modeled by common mathematical complexities which exhibit a reliable invariance across scales and situations. Again upon reflection, our collective cognizance can avail these independent forms and dynamics so as to achieve a palliative surcease of the human condition.

Physiology often exhibits non-linear, fractal patterns of adaptation. I show that such patterns of adaptation also characterize collective health behavior in a model of collective health. Protection in which individuals use highest payoff biased social learning to decide whether or not to protect against a spreading disease, but benefits of health are shared locally. This model results in collectives of protectors with an exponential distribution of sizes, smaller ones being much more likely. This distribution of protecting collectives, in turn, results in incidence patterns often seen in infectious disease which, although they seem to fluctuate randomly, actually have an underlying order, a fractal time trend pattern. The time trace of infection incidence shows a self-similarity coefficient consistent with a fractal distribution and anti-persistence, reflecting the negative feedback created by health protective behavior responding to disease, when the benefit of health is high enough to stimulate health protection.

When the benefit of health is too low to support any health protection, the self-similarity coefficient shows high persistence, reflecting positive feedback resulting the unmitigated spread of disease. Thus the self-similarity coefficient closely corresponds to the level of protection, demonstrating that what might otherwise be regarded as “noise” in incidence actually reflects the fact that protecting collectives form when the spreading disease is present locally but drop protection when disease subsides locally, mitigating disease intermittently. These results hold not only in a deterministic version of the model in a regular lattice network, but also in small-world networks with stochasticity in infection and efficacy of protection. The resulting non-linear and chaotic patterns of behavior and disease cannot be explained by traditional epidemiological methods but a simple agent-based model is sufficient to produce these results. (Abstract)

Keimer, Bernard and Joel Moore. The Physics of Quantum Materials. Nature Physics. 13/11, 2017. We cite this late 2017s entry by MPI Solid State Research and UC Berkeley physicists, among an increasing number, to report how novel abilities to engage this off-putting, arcane realm have now become amenable and commonplace. A “quantum collective phenomena” is found, along with other features more classical in kind, as human inquiry and innovation seems poised to take over material creation going forward.

The physical description of all materials is rooted in quantum mechanics, which describes how atoms bond and electrons interact at a fundamental level. In recent years there has been growing interest in material systems where quantum effects remain manifest over a wider range of energy and length scales such as superconductors, graphene, topological insulators, Weyl semimetals, quantum spin liquids, and spin ices. Many derive their properties from reduced dimensionality, in particular from confinement of electrons to two-dimensional sheets. Moreover, they tend to be materials in which electrons cannot be considered as independent particles but interact strongly and give rise to collective excitations known as quasiparticles. In all cases, however, quantum-mechanical effects fundamentally alter properties of the material. (Abstract excerpts)

Keinan, E. and I. Schechter, eds. Chemistry for the 21st Century. Weinheim, GDR: Wiley-VCH, 2001. A survey of the dawning ability to recreate material nature through computational studies and discrete atomic interactions. A typical article is “Quantum Alchemy.” In an introduction Jean Marie Lehn views this supramolecular phase as a “...general science of informed matter. The essence of chemistry is not only to discover but to invent, and above all, to create. The book of chemistry is not only to be read but to be written!”

Khajetoorians, Alexander, et al. Designer Quantum States of Matter Created Atom-by-Atom. arXiv:1904.11680. In an article to appear in Nature Reviews Physics, Radboud University, Delft University of Technology and Utrecht University scientists including Ingmar Swart review this future frontier as our globally collaborative human agency begins a second, intentional material creation. An Integrated Nanolab will then avail tunneling, spin lattices, topography, atomic resolution, quasiparticles, magnetism, spectroscopy qualities and much more.

With the advances in high resolution scanning tunneling microscopy as well as atomic-scale manipulation, it has become possible to create and characterize quantum states of matter bottom-up, atom-by-atom. We review recent advances in creating artificial electronic and spin lattices that lead to exotic quantum phases of matter from topological Dirac dispersion to complex magnetic order. We also project future perspectives in non-equilibrium dynamics, prototype technologies, engineered quantum phase transitions and topology, as well as the evolution of complexity from simplicity in this newly developing field. (Abstract)

Klishin, Andrei, et al. Statistical Physics of Design. New Journal of Physics. 20/103038, 2018. University of Michigan researchers including Greg van Anders post a novel entry which draws on basic nonequilibrium condensed matter principles with the aim to intentionally create novel, materials and structures. An update paper by this group is Robust Design in Systems Physics at arXiv:1805.02691 (second quote).

A key challenge in complex design problems that permeate science and engineering is the need to balance design objectives for specific design elements or subsystems with global system objectives. Here, using examples from arrangement problems, we show that the systems-level application of statistical physics principles, which we term "systems physics", provides a detailed characterization of subsystem design in terms of the concepts of stress and strain. Our approach generalizes straightforwardly to design problems in a wide range of other disciplines that require concrete understanding of how the pressure to meet overall design objectives drives the outcomes for component subsystems. (Abstract)

Ensuring robust outcomes and designs is a crucial challenge in the engineering of modern integrated systems that are comprised of many heterogeneous subsystems. Here, we show that the response of design elements to whole-system specification changes can be characterized, as materials are, using strong/weak and brittle/ductile dichotomies. We find these dichotomies emerge from a mesoscale treatment of early stage design problems that we cast in terms of stress--strain relationships. (1805.02691)

Koonin, Eugene and Michael Halperin. Sequence-Evolution-Function: Computational Approaches in Comparative Genomics. Norwell, MA: Kluwer Academic, 2003. A technical source. Chapter 8 is “Genomes and the Protein Universe.”

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