Recent Additions: New and Updated Entries in the Past 60 Days
Displaying entries 16 through 30 of 85 found.
Animate Cosmos > Organic
Liao, Qinqli, et al.
Density Functional Theory Calculations on the Interstellar Formation of Biomolecules.
Into October, a research report from the Laboratory form Guangxi University, China provides a good current illustrated proof of an apparent celestial precursor fertility which seeds itself with a complexifying sequence of the vital biochemicals on the way to life’s organic evolution. By now, as the quotes say, an inherent presence of such an array of metabolic compounds have been found to suffuse the astronomic reaches. Once more, circa 2023/2024, a grand, consummate discovery event by our planetary prodigy seems to indeed be forming in our midst/
The density functional theory (DFT) is the most versatile electronic structure method used in quantum chemical calculations, an d is increasingly applied in astrochemical research. This mini-review provides an overview of the applications of DFT calculations in understanding the chemistry that occurs in star-forming regions. We survey the formation of biologically-relevant compounds such as nucleobases in the interstellar medium, as well as biologically-relevant molecules such as sugars, and polycyclic aromatic hydrocarbons. We conclude by noting several research areas such as the formation pathways of chiral amino acids, complex sugars, and the role of environmental factors in the formation of interstellar biomolecules. (Excerpt)
Animate Cosmos > Organic
In our perspective, future research avenues should encompass the exploration of complex purine base formation, the elucidation of chiral amino acid synthesis pathways, comprehension of intricate sugar and biomolecule production, examination of the influence of metal ions and hydrogen bonding in ISM chemical reactions, refinement of computational models, and assessment of the impact of temperature and environmental variables on interstellar biomolecule formation. (9)
Density-functional theory (DFT) is a computational quantum mechanical modelling method used in physics, chemistry and materials science to investigate the electronic structure (or nuclear structure) (principally the ground state) of many-body systems, in particular atoms, molecules, and the condensed phases. (Wikipedia)
Oberg, Karin, et al.
Protoplanetary Disk Chemistry.
Harvard Smithsonian, University of Milan and Carnegie Institute for Science exochemists (see Oberg 2020) discuss the latest retrospective perceptions of how our orbital occasion, as it may gain a global sentience, came into material formation. See Bayesian Inference on the Isotopic Building Blocks of Mars and Earth. arXiv:2309.15290 for concurrent work. But we place this typical entry in our Ecosmos chapter lead section for its 2023 content quite attests to a phenomenal organic procreativity.
Planets form in disks of gas and dust around young stars. The disk molecular reservoirs and chemical evolution affect all aspects from the coagulation into pebbles to the material compositions of the mature planet. Here we review the protoplanetary disk chemistry of the volatile elements HOCNSP, and the links between disk and planet chemical compositions. Three takeaways are: (1) The disk chemical composition, including the organic reservoirs, is set by inheritance and in situ chemistry. (2) Disk gas and solid O/C/N/H ratios often deviate from stellar values. (3) Chemical, physical, and dynamical processes are often linked. (Excerpt)
Animate Cosmos > Organic
Sanchez, Ignacio, et al..
Solvent Constraints for Biopolymer Folding and Evolution in Extraterrestrial Environments..
We choose and place this entry by University of Buenos Aries astrochemists in our main organic ecosmos section because it well conveys an innately fertile essence on it’s own developmental course. Into this October, however might such a phenomenal biologic milieu and personal planet bearing result ever be able to dawn on us in.
We propose that spontaneous folding and molecular evolution of biopolymers are two universal aspects that must concur for life to happen. These aspects a related to the chemical composition of biopolymers and depend on the solvent in which they occur. We show that molecular information and energy landscape theories allow us to explore the limits that solvents impose on biopolymers. We consider water, alcohols, hydrocarbons, halogenated, aromatic media which may take part in alternative biochemistries. Many of these solvents have been found in molecular clouds or may be expected to occur in extrasolar planets. (Excerpt)
Animate Cosmos > Organic > quantum CS
Datta, Chandan, et al.
Catalysis of entanglement and other quantum resources.
Reports on Progress in Physics.
Quantum Optical Technologies, University of Warsaw physicists CD, Tulja Varun Kondra1, Marek Miller1 and Alexander Streltsov review past notices of this deeply evident propensity and then describe its latest theoretical basis along with thermodynamic aspects and applications. This observation is significant because it fills in a constant presence of such self-activating properties across every phenomenal domain. And as other diverse papers are now moved to state, a true natural universality is truly being discovered.
In chemistry, a catalyst is a substance which enables a chemical reaction or increases its rate, while remaining unchanged in the process. Instead of chemical reactions, quantum catalysis can enhance our ability to convert quantum states into each other under physical constraints. This article reviews new developments in quantum catalysis along with a historical overview of this research direction. We focus on catalytic entanglement and coherence, quantum thermodynamics and resource theories. We then review applications and recent efforts on a universal catalysis which does not depend on the states to be transformed. (Abstract)
Animate Cosmos > Organic > quantum CS
Today, chemical catalysis is broadly used in the chemical industry and is essential for many industrial processes. In addition, the importance of catalytic reactions in biochemistry cannot be overstated: to the point that the ability of living organisms to “catalyse chemical reactions efficiently and selectively” via metabolic pathways could be called one of the “fundamental conditions for life. Quantum catalysis is conceptually similar to chemical catalysis but differs from it in several important details. A simple analogy between quantum and chemical catalysis can be established by replacing “chemical reaction” with “quantum state transition”. With this, a quantum catalyst is a quantum system which enables otherwise impossible transitions between quantum states. (1)
Engelhardt, G., et al.
Photon-resolved Floquet theory in open quantum systems.
We record this typical entry out of a hundred each day on the arXiv.com site as one 2020s instance of this open territory being explored, settled and advantaged. Here Shenzhen Institute for Quantum Science and Engineering, Zhejiang University of Science and Technology, NTT Research, Sunnyvale, CA, MIT and Instituto de Ciencia de Materiales de Madrid, surely a global collaboration via instant communication and advance, describe a mathematical finesse amenable to their activities
Photon-resolved Floquet theory keeps track of the photon exchange of a quantum system with a coherent driving field. In this paper, we introduce a unifying methods for an analytical evaluation of low-order cumulants of photonic probability distributions. We find that the photon-flux fluctuations diverge can be related to an entanglement effect between the driven matter system and the driving field. As the framework is non-perturbative, it enhances spectroscopy and metrological views. (Excerpt)
Animate Cosmos > Organic > quantum CS
Pseiner, Johannes, et al..
Quantum interference between distant creation processes..
We record this entry by University of Vienna and MPI Science of Light physicists including Mario Krenn as an example in these 2020s of how research endeavors are able to freely range about and apply this foundational quantascape.
The search for macroscopic quantum phenomena is a fundamental pursuit in quantum mechanics. In this work, we introduce a novel approach to generate macroscopic quantum systems by demonstrating that the creation process of a quantum system can span a macroscopic distance. This new approach not only provides an exciting opportunity for foundational experiments in quantum physics.
Animate Cosmos > Organic > Biology Physics
Armengol-Collado, Joseh-Maria, et al.
Epithelia are multiscale active liquid crystals.
University of Leiden biophysicists including Luca Giomi post another current contribution that combines new understandings of complex living systems while proceeding on to ground their features in a conducive physical ground. See also Hexanematic crossover in epithelial monolayers depends on cell adhesion and cell density by Julia Eckert, et al in Nature Communications. (14/5762, 2023) and Biophysicists Uncover Powerful Symmetries in Living Tissue by Elise Cutts in Quanta (October 26, 2023) for an extensive news review.
Animate Cosmos > Organic > Biology Physics
Biological processes such as embryogenesis, wound healing and cancer rely on the ability of epithelial cells to coordinate their mechanical activity over length scales that are orders of magnitude larger than the cellular size. Although this process is regulated by signalling pathways, it has recently become evident that this coordination can be understood using physics tools, of which liquid crystal order is a prominent example. In this Letter, we combine in vitro experiments, numerical simulations and analysis to show that both nematic and hexatic order are present in epithelial layers. Our work provides a method to decipher epithelial structure and lead to a predictive mesoscopic theory of tissues. (Abstract)
If there’s one central idea in tissue biophysics, coauthor (Luca) Giomi said, it’s that structure gives rise to forces, and forces give rise to functions. In other words, controlling multiscale symmetry could be part of how tissues add up to more than the sum of their cells. There’s “a triangle of form, force and function.”. Cells use their shape to regulate forces, and these in turn serve mechanical functionality.” (Quanta)
Nematic: relating to or denoting a state of a liquid crystal in which the molecules are oriented in parallel but not arranged in well-defined planes. The hexatic phase is a state of matter that is between the solid and the isotropic liquid phases in two dimensional systems of particles.
Simpson, Kevin, et al.
Spatial biology of Ising-like synthetic genetic networks.
This contribution by Pontificia Universidad Católica de Chile, Santiago geneticists could exemplify the 2023 cross-discipline integrations as it at once cites theoretic reasons for complex genome systems which can now be seen to be deeply grounded in active physical principles. By so doing the whole dynamic operation is realized to embody a Ising model (see below) as it forms self-organizing fractal patterns.
Understandings of how spatial patterns of gene expression emerge from the interaction of individual gene networks remains a challenge in biology. We propose an experimental system with a theoretical framework that captures the emergence of short- and long-range correlation from interacting gene networks. Our method combines synthetic biology, statistical mechanics, and computational simulations to study the spatial behavior of synthetic gene networks. By this approach, we describe the spatial behavior of bi-stable and chemically coupled synthetic gene networks that self-organize into long-range correlations with power-law scalings. The resultant patterns are then found to resemble ferromagnetic and anti-ferromagnetic configurations of the Ising model near critical points. (Excerpt)
Animate Cosmos > cosmos
Here, we apply a theoretical framework based on the Ising model to study how spatial correlations emerge from chemically coupled, bistable SGNs in Escherichia coli colonies. Ww construct synthetic toggle switches whose states are based on quorum sensing signaling. These SGNs self-organize in long-range spatial correlations and fractal patterns reminiscent of ferromagnetic systems of the Ising model. (2)
Our findings shed light on the spatial biology of coupled and bistable gene networks in growing cell populations. This emergent spatial behavior could provide insights into the study and engineering of self-organizing gene patterns in eukaryotic tissues and bacterial consortia. (12)
The Ising model, after the physicist Ernst Ising, is a mathematical model of ferromagnetism in statistical mechanics. It consists of discrete variables that represent magnetic dipole moments of atomic "spins" that can be in one of two states.
Awwad, Yassir and Tomislav Prokopec.
Large-Scale Geometry of the Universe..
We cite this entry by Utrecht university physicists among a growing cadre as evidence of how by 2022 an integral Earthumanity survey has become able to theoretically and empirically consider the vast celestial expanse of an entire galactic (e)cosmos. See also, for example, A Three-dimensional Map of the Milky Way by Iwanek Patryk, et al at 2212.00035.
Animate Cosmos > cosmos > Geological
Tiberiu, Gabriel and Alexandru Nicolin-Żaczek..
Motifs in earthquake networks: Romania, Italy, United States of America.
University of Bucharest seismology theorists describe a sophisticated mathematical analysis which arrays from physical substrates through layers of complexities and connectivities onto geologic environmental issues. As a result, further abilities to understand so as to better predict are achieved. This especial contribution goes on to prompt a number of points. Researchers now have a full, open, worldwide accessibility to scientific publications along with high technical acumen due to global education opportunities. As now has become common in such papers, the first paragraph, (noted below), lists an array of similar findings across diverse domains.
We present a detailed description of seismic activity in Romania, Italy, and Japan, as well as the California zone, based on the statistical analysis of their underlying earthquake networks. Our results on network connectivity motifs do allow for a complex description and reinforce the current understanding of seismicity as a critical phenomenon. The distributions on node connectivity, three-, and four-node motifs are consistent with power-law, i.e., scale-free over large earthquake intervals. The main message is these seismic zones have power-law components, over orders of magnitude, independent of discretization. (Abstract)
Animate Cosmos > Information
The apparent ubiquity of power laws has now been proven in almost every field of the science of complex critical systems such as linguistics, musicology, and biology to meteorology, environmental studies, economics, and computer science. (1) One of the most striking properties of complex systems is the possibility to self-organize into a critical state (1)
Morphological Computing as Logic Underlying Cognition in Human, Animal, and Intelligent Machines.
The veteran Chalmers University of Technology, Sweden information/computation polyscholar provides a timely synopsis of her integrative thought and collegial conferences over the past decade. In so doing she has achieved an integral survey of these 21st century endeavors as they seek to identify, express and quantify nature’s apparent program-like source and its language-like articulation. In regard, typical sections are Info-Computational Nature, Evolution as a Driver of Cognition in Living Organisms; Computing Cells: Self-generating Systems; Cognition in Nature and Artifacts as Computation of Information and Connecting Morphological Computing and Cognition in Nature to Logic. See also her current paper Computational Natural Philosophy: A Thread from Presocratics through Turing to ChatGPT at arXiv:2309.13094. Altogether Gordana Dodig-Crnkovic contributes a unique, woman wise, visionary perception going forward.
This work reviews the interconnections between logic, epistemology, and natural sciences that connect mathematics, physics, chemistry, biology, and cognition. Altogether they imply a scale-invariant, self-organizing dynamics across organizational tiers of nature. Our exemplary human language was evolved by living organisms from its basal cognition of unicellular organisms. The Extended Evolutionary Synthesis is essential for understanding the human-level relationship between logic and information processing/computational epistemology. We conclude that more research is needed to elucidate the details of the mechanisms linking natural phenomena with the logic of agency in nature. (Excerpt)
Animate Cosmos > Information > Quant Info
The basic tenets of my conception include: • All existing nature (universe) is a network of networks of computational processes on informational structures. • Nature is described as structure (information) with dynamics (computation) • Self-organizing nature – active matter drives spontaneous processes of complexification in a universe far from thermic equilibrium. • Cognition is seen as a result of computation of information (morphogenesis) • The “mind” as a result of cognition is extended in nature – embodied, embedded, and enactive. • Info-computational formulation of The Extended Evolutionary Synthesis EES explains the generation of novel biological forms and behaviors and the emergence of increasingly complex cognitive agents (minds). The theory of evolution followed from Darwinism to Neo-Darwinism, to the Modern Synthesis, and currently to its EES info-computational form as a process of learning under variable environmental constraints. (15-16)
Ariswalla, Xerxes, et al..
Pregeometry, Formal Language and Constructivist Foundations of Physics.
XA, Pompeu Fabra University, Barcelona, Hatem Elshatlawy, Aachen University, Germany and Dean Rickles, University of Sydney, consider how a latter meld of Gottfried Leibniz, Alan Turing, John Wheeler and Stephen Wolfram and a nod to Galileo, could give credence to, inform and parse the actual presence of nature’s implicate textual and/or program-like essence. Since its content goes into musings about formal languages, coherentism, and more, longer quotes are added. See also Ruliology: Linking Computation, Observers and Physical Law by this team at 2308.16068. Our take is that this current year seems to be defined by many novel language and program-based versions, which seem to be lately joining with each other. As an attempt to integrate Wheeler and Wolfram, this paper seeks to explore and exercise such foundational realms. See also, for example, BEND: Benchmarking DNA Language Models on biologically meaningful tasks by Frederikke Isa Marin, et al at 2311.12570.
How does one formalize the structures necessary for the foundations of physics? This work is an endeavor toward a metaphysics of pregeometric structures since recent notions of quantum geometry may add a new dimension. We discuss relevant philosophies due to Leibniz, Wheeler, as well as modern topos theory and more. We note evidence of a formal language as a conceptual basis. Our approach is to be seen as a constructivist view, whereof syntactic types realize proofs and programs. This perspective addresses the crucial issue of how spatiality may be realized in ways that link computation to physics, such as the Wolfram model. (Excerpt)
Animate Cosmos > Thermodynamics
The term “pregeometry” was first coined by John A. Wheeler as an approach to the foundations of physics that ought to encompass any underlying explanation of spacetime or quantum gravity. One may argue that this term merely functions as a placeholder for whatever more elementary structure is eventually found to serve its intended function. As an historic anecdote, it was also the inadequacy of most seemingly plausible structures that led Wheeler to his ideas encapsulated in the phrase “It from Bit”. As we will discuss here, higher homotopical constructions in formal languages, expressed using higher categories, turn out to operationalize such a framework of pregeometry. This exercise may be seen as a modern day incarnation of Wheeler’s original intuition. (2)
Apart from Wheeler, language-theoretic approaches to the foundations of physics have also been proposed in several earlier studie]. More recently, the Wolfram Model, Constructor Theory, Categorical Quantum Mechanics, and other versions, can all be seen as instances of syntactic formalisms within a broader language-theoretic framework. The key point is that the context of formal language subsumes these theories and models, and provides the appropriate foundation for various notions of pregeometry and geometry proposed in theories of quantum gravity. (3)
Buchholz, Detlev and Klaus Fredenhagen..
Arrow of Time and Quantum Physics.
Foundations of Physics.
After noting a century of pro and con conjecture, University of Gottingen and University of Hamburg physicists develop and reach a 2020s worldwide consensus that a temporal flow does indeed go forward, detached from and unhindered by the second thermal law.
We discuss the consequences of the hypothesis that the (non-reversible) arrow of time is intrinsic in any and all systems. Within the context of local quantum physics it is shown how such a semi-group action of time can be extended to the group of spacetime translations in Minkowski space. It is explained how the description of operations in classical terms combined with constraints imposed by the arrow of time leads to a quantum theoretical framework. These results suggest that the arrow of time is fundamental in nature and not merely a consequence of statistical effects on which the Second Law is based. (Excerpt)
Animate Cosmos > Thermodynamics
The Arrow of Time is Alive and Well but Forbidden Under the Received View of Physics.
In this eprint The University of Maryland physicist and author of The Transactional Interpretation of Quantum Mechanics (2022) defends the actual reality of a directional cosmic duration, along with noting its many prior twists and turns.
This essay offers a meta-level analysis in the sociology and history of physics in the context of the "Arrow of Time" or so-called "Two Times" problem. In effect, it argues that the two topics are intertwined, and it is only by coming to grips with the sociological aspects, involving adherence to certain metaphysical, epistemological and methodological beliefs and practices, that real progress can be made in the physics. (Abstract)
Animate Cosmos > Thermodynamics
The Second Law: Resolving the Mystery of the Second Law of Thermodynamics.
Online: Wolfram Media,
Since the 1980s, the polymath philosopher and software designer has developed a cellular automata computational method which has gained a wide and deep applicability. For his whole scale achievements, please visit his home site at stephenwolfram.com. See also his latest edition How Did We Get Here? The Tangled History of the Second Law of Thermodynamics at arXiv:2311.10722.
Ever since it was first formulated a century and a half ago, the Second Law of thermodynamics has an air of mystery about it. In this book, Stephen Wolfram builds on recent breakthroughs in the foundations of physics to propose that it emerges as a general feature of computational processes by virtue of their interplay with our similar activities as observers. In the book, Wolfram tells the story of his own quest as well as trace the whole history of the Second Law. We next sample its Table of Contents.
The Basic Arc of the Story · Heat Engines and the Beginnings of Thermodynamics · The Second Law Is Formulated · The Concept of Entropy · "Deriving" the Second Law from Molecular Dynamics · The Concept of Ergodicity · Maxwell's Demon · Coarse Graining and the "Modern Formulation" · The Second Law and Quantum Mechanics · Continuous Versus Discrete · So Where Does This Leave the Second Law?
A cellular automaton is a collection of cells arranged in a grid of specified shape, such that each cell changes state as a function of time, according to a defined set of rules driven by the states of neighboring cells.