The theory of everything

Agency

Agency is action aimed at goals selected by an agent. A deterministic world view leaves scant room for agency. To reconcile the arguments, we represent action as nested control systems, ranging from clearly deterministic to clearly volitional. Negative feedback minimizes deviations from setpoints (goals). Goals are determined by higher modules in a hierarchy of systems, ranging from gamma-efferent spindles through reflexes to operant responses; these last, and the larger system that contains them, called the Self, comprise volitional agents. When operants become habitual they descend to closed teleonomic systems-automaticity. Change in emotional states, and unpredicted changes in the context-raise them back to full volitional systems. At the highest level is the Self-the brain's model of the agent. When aroused out of open teleonomic functioning, it must reconsider means and ends. It does so by simulating action plans, using the same neural systems it uses to effect them. The simulated stimuli and responses are conscious, approximating their perceptions as experienced in real time; this verisimilitude gives them their hedonic value. Positive feedback plays a key role in these complex adaptive systems, as it focuses and holds attention on the most salient percepts and goals, permitting the self-organization of action plans. The Self is not a separate entity, but a colloquy of command modules wearing the avatar of the agent. This system is put into correspondence with Grossberg's Adaptive Resonance Theory. Free will and determinism emerge not as binary opposites, but the modulating inputs to a spectrum of systems.

Materials Nanoarchitectonics for Advanced Devices

Advances in nanotechnology have made it possible to observe and evaluate structures down to the atomic and molecular level. The next step in the development of functional materials is to apply the knowledge of nanotechnology to materials sciences. This is the role of nanoarchitectonics, which is a concept of post-nanotechnology. Nanoarchitectonics is defined as a methodology to create functional materials using nanounits such as atoms, molecules, and nanomaterials as building blocks. Nanoarchitectonics is very general and is not limited to materials or applications, and thus nanoarchitecture is applied in many fields. In particular, in the evolution from nanotechnology to nanoarchitecture, it is useful to consider the contribution of nanoarchitecture in device applications. There may be a solution to the widely recognized problem of integrating top-down and bottom-up approaches in the design of functional systems. With this in mind, this review discusses examples of nanoarchitectonics in developments of advanced devices. Some recent examples are introduced through broadly dividing them into organic molecular nanoarchitectonics and inorganic materials nanoarchitectonics. Examples of organic molecular nanoarchitecture include a variety of control structural elements, such as π-conjugated structures, chemical structures of complex ligands, steric hindrance effects, molecular stacking, isomerization and color changes due to external stimuli, selective control of redox reactions, and doping control of organic semiconductors by electron transfer reactions. Supramolecular chemical processes such as association and intercalation of organic molecules are also important in controlling device properties. The nanoarchitectonics of inorganic materials often allows for control of size, dimension, and shape, and their associated physical properties can also be controlled. In addition, there are specific groups of materials that are suitable for practical use, such as nanoparticles and graphene. Therefore, nanoarchitecture of inorganic materials also has a more practical aspect. Based on these aspects, this review finally considers the future of materials nanoarchitectonics for further advanced devices.

Lateral nanoarchitectonics from nano to life: ongoing challenges in interfacial chemical science

Lateral nanoarchitectonics is a method of precisely designing functional materials from atoms, molecules, and nanomaterials (so-called nanounits) in two-dimensional (2D) space using knowledge of nanotechnology. Similar strategies can be seen in biological systems; in particular, biological membranes ingeniously arrange and organise functional units within a single layer of units to create powerful systems for photosynthesis or signal transduction and others. When our major lateral nanoarchitectural approaches such as layer-by-layer (LbL) assembly and Langmuir-Blodgett (LB) films are compared with biological membranes, one finds that lateral nanoarchitectonics has potential to become a powerful tool for designing advanced functional nanoscale systems; however, it is still rather not well-developed with a great deal of unexplored possibilities. Based on such a discussion, this review article examines the current status of lateral nanoarchitectonics from the perspective of in-plane functional structure organisation at different scales. These include the extension of functions at the molecular level by on-surface synthesis, monolayers at the air-water interface, 2D molecular patterning, supramolecular polymers, macroscopic manipulation and functionality of molecular machines, among others. In many systems, we have found that while the targets are very attractive, the research is still in its infancy, and many challenges remain. Therefore, it is important to look at the big picture from different perspectives in such a comprehensive review. This review article will provide such an opportunity and help us set a direction for lateral nanotechnology toward more advanced functional organization.

Concluding remarks

The Faraday Discussion on Correlated electronic structure took place from the 17th to the 19th of July 2024 in London, UK. The Discussion encompassed various facets of electron correlation, ranging from its formal definition and quantification to emerging frontiers in electronic structure theory, with applications in the solid state, integration with machine learning, and quantum computing.

Seeing with an extra sense

Science foremost derives from our curiosity about the world. Can we make sense of the phenomena we see around us? Given that understanding, can we predict previously unimagined phenomena? How do things work? Can we use what we discover to invent new technologies? One class of questions that has mesmerized observers, dating at least to early cave paintings of hunters and their prey, surrounds the nature of the phenomenon we refer to as life. Over the centuries, scientists have found a broad array of surprisingly different techniques for observing, measuring, characterizing and explaining the living world. Microscopes provide a dazzling view of a previously unseen reality that tells us how living organisms are made up and how their components are organized and move. The tools of molecular science tell us the sequence and structure of the macromolecules that fill cells. The data explosion that has attended the development of a new generation of high-throughput tools for querying the living world demands that we have some way of accounting for those data that both provide intuition and make dangerous predictions with no after-the-fact parametric wiggle room. In this special issue of Current Biology, leading researchers explore how physical approaches have contributed to various fields of biology. Here, to introduce this special issue, I consider some of the ways in which viewing the living through a physical lens allows us to see things that might otherwise remain hidden.

Interface-Interactive Nanoarchitectonics: Solid and/or Liquid

The methodology of nanoarchitectonics is to construct functional materials using nanounits such as atoms, molecules, and nanoobjects, just like architecting buildings. Nanoarchitectonics pursues the ultimate concept of materials science through the integration of related fields. In this review paper, under the title of interface-interactive nanoarchitectonics, several examples of structure fabrication and function development at interfaces will be discussed, highlighting the importance of architecting materials with nanoscale considerations. Two sections provide some examples at the solid and liquid surfaces. In solid interfacial environments, molecular structures can be precisely observed and analyzed with theoretical calculations. Solid surfaces are a prime site for nanoarchitectonics at the molecular level. Nanoarchitectonics of solid surfaces has the potential to pave the way for cutting-edge functionality and science based on advanced observation and analysis. Liquid surfaces are more kinetic and dynamic than solid interfaces, and their high fluidity offers many possibilities for structure fabrications by nanoarchitectonics. The latter feature has advantages in terms of freedom of interaction and diversity of components, therefore, liquid surfaces may be more suitable environments for the development of functionalities. The final section then discusses what is needed for the future of material creation in nanoarchitectonics.

Phantom energy in the nonlinear response of a quantum many-body scar state

Quantum many-body scars are notable as nonthermal, low-entanglement states that exist at high energies. In this study, we used attractively interacting dysprosium gases to create scar states that are stable enough to be driven into a strongly nonlinear regime while retaining their character. We measured how the kinetic and total energies evolve after quenching the confining potential. Although the bare interactions are attractive, the atoms behave as if they repel each other: Their kinetic energy paradoxically decreases as the gas is compressed. The missing "phantom" energy is quantified by benchmarking our experimental results against generalized hydrodynamics calculations. We present evidence that the missing kinetic energy is carried by undetected, very high momentum atoms.

Liquid-Liquid Interfacial Nanoarchitectonics

Science in the small world has become a crucial key that has the potential to revolutionize materials technology. This trend is embodied in the postnanotechnology concept of nanoarchitectonics. The goal of nanoarchitectonics is to create bio-like functional structures, in which self-organized and hierarchical structures are working efficiently. Liquid-liquid interface like environments such as cell membrane surface are indispensable for the expression of biological functions through the accumulation and organization of functional materials. From this viewpoint, it is necessary to reconsider the liquid-liquid interface as a medium where nanoarchitectonics can play an active role. In this review, liquid-liquid interfacial nanoarchitectonics is classified by component materials such as organic, inorganic, carbon, and bio, and recent research examples are discussed. Examples discussed in this paper include molecular aggregates, supramolecular polymers, conductive polymers film, crystal-like capsules, block copolymer assemblies, covalent organic framework (COF) films, complex crystals, inorganic nanosheets, colloidosomes, fullerene assemblies, all-carbon π-conjugated graphite nanosheets, carbon nanoskins and fullerphene thin films at liquid-liquid interfaces. Furthermore, at the liquid-liquid interface using perfluorocarbons and aqueous phases, cell differentiation controls are discussed with the self-assembled structure of biomaterials. The significance of liquid-liquid interfacial nanoarchitectonics in the future development of materials will then be discussed.

Bio-gel nanoarchitectonics in tissue engineering

Given the creation of materials based on nanoscale science, nanotechnology must be combined with other disciplines. This role is played by the new concept of nanoarchitectonics, the process of constructing functional materials from nanocomponents. Nanoarchitectonics may be highly compatible with applications in biological systems. Conversely, it would be meaningful to consider nanoarchitectonics research oriented toward biological applications with a focus on materials systems. Perhaps, hydrogels are promising as a model medium to realize nanoarchitectonics in biofunctional materials science. In this review, we will provide an overview of some of the defined targets, especially for tissue engineering. Specifically, we will discuss (i) hydrogel bio-inks for 3D bioprinting, (ii) dynamic hydrogels as an artificial extracellular matrix (ECM), and (iii) topographical hydrogels for tissue organization. Based on these backgrounds and conceptual evolution, the construction strategies and functions of bio-gel nanoarchitectonics in medical applications and tissue engineering will be discussed.

Liquid-Liquid and Liquid-Solid Interfacial Nanoarchitectonics

Nanoscale science is becoming increasingly important and prominent, and further development will necessitate integration with other material chemistries. In other words, it involves the construction of a methodology to build up materials based on nanoscale knowledge. This is also the beginning of the concept of post-nanotechnology. This role belongs to nanoarchitectonics, which has been rapidly developing in recent years. However, the scope of application of nanoarchitectonics is wide, and it is somewhat difficult to compile everything. Therefore, this review article will introduce the concepts of liquid and interface, which are the keywords for the organization of functional material systems in biological systems. The target interfaces are liquid-liquid interface, liquid-solid interface, and so on. Recent examples are summarized under the categories of molecular assembly, metal-organic framework and covalent organic framework, and living cell. In addition, the latest research on the liquid interfacial nanoarchitectonics of organic semiconductor film is also discussed. The final conclusive section summarizes these features and discusses the necessary components for the development of liquid interfacial nanoarchitectonics.

Molecular machines working at interfaces: physics, chemistry, evolution and nanoarchitectonics

As a post-nanotechnology concept, nanoarchitectonics combines nanotechnology with advanced materials science. Molecular machines made by assembling molecular units and their organizational bodies are also products of nanoarchitectonics. They can be regarded as the smallest functional materials. Originally, studies on molecular machines analyzed the average properties of objects dispersed in solution by spectroscopic methods. Researchers' playgrounds partially shifted to solid interfaces, because high-resolution observation of molecular machines is usually done on solid interfaces under high vacuum and cryogenic conditions. Additionally, to ensure the practical applicability of molecular machines, operation under ambient conditions is necessary. The latter conditions are met in dynamic interfacial environments such as the surface of water at room temperature. According to these backgrounds, this review summarizes the trends of molecular machines that continue to evolve under the concept of nanoarchitectonics in interfacial environments. Some recent examples of molecular machines in solution are briefly introduced first, which is followed by an overview of studies of molecular machines and similar supramolecular structures in various interfacial environments. The interfacial environments are classified into (i) solid interfaces, (ii) liquid interfaces, and (iii) various material and biological interfaces. Molecular machines are expanding their activities from the static environment of a solid interface to the more dynamic environment of a liquid interface. Molecular machines change their field of activity while maintaining their basic functions and induce the accumulation of individual molecular machines into macroscopic physical properties molecular machines through macroscopic mechanical motions can be employed to control molecular machines. Moreover, research on molecular machines is not limited to solid and liquid interfaces; interfaces with living organisms are also crucial.

Layer-by-layer designer nanoarchitectonics for physical and chemical communications in functional materials

Nanoarchitectonics, as a post-nanotechnology concept, constructs functional materials and structures using nanounits of atoms, molecules, and nanomaterials as materials. With the concept of nanoarchitectonics, asymmetric structures, and hierarchical organization, rather than mere assembly and organization of structures, can be produced, where rational physical and chemical communications will lead to the development of more advanced functional materials. Layer-by-layer assembly can be a powerful tool for this purpose, as exemplified in this feature paper. This feature article explores the possibility of constructing advanced functional systems based on recent examples of layer-by-layer assembly. We will illustrate both the development of more basic methods and more advanced nanoarchitectonics systems aiming towards practical applications. Specifically, the following sections will provide examples of (i) advancement in basics and methods, (ii) physico-chemical aspects and applications, (iii) bio-chemical aspects and applications, and (iv) bio-medical applications. It can be concluded that materials nanoarchitectonics based on layer-by-layer assembly is a useful method for assembling asymmetric structures and hierarchical organization, and is a powerful technique for developing functions through physical and chemical communication.

Confined Space Nanoarchitectonics for Dynamic Functions and Molecular Machines

Nanotechnology has advanced the techniques for elucidating phenomena at the atomic, molecular, and nano-level. As a post nanotechnology concept, nanoarchitectonics has emerged to create functional materials from unit structures. Consider the material function when nanoarchitectonics enables the design of materials whose internal structure is controlled at the nanometer level. Material function is determined by two elements. These are the functional unit that forms the core of the function and the environment (matrix) that surrounds it. This review paper discusses the nanoarchitectonics of confined space, which is a field for controlling functional materials and molecular machines. The first few sections introduce some of the various dynamic functions in confined spaces, considering molecular space, materials space, and biospace. In the latter two sections, examples of research on the behavior of molecular machines, such as molecular motors, in confined spaces are discussed. In particular, surface space and internal nanospace are taken up as typical examples of confined space. What these examples show is that not only the central functional unit, but also the surrounding spatial configuration is necessary for higher functional expression. Nanoarchitectonics will play important roles in the architecture of such a total system.

2D Materials Nanoarchitectonics for 3D Structures/Functions

It has become clear that superior material functions are derived from precisely controlled nanostructures. This has been greatly accelerated by the development of nanotechnology. The next step is to assemble materials with knowledge of their nano-level structures. This task is assigned to the post-nanotechnology concept of nanoarchitectonics. However, nanoarchitectonics, which creates intricate three-dimensional functional structures, is not always easy. Two-dimensional nanoarchitectonics based on reactions and arrangements at the surface may be an easier target to tackle. A better methodology would be to define a two-dimensional structure and then develop it into a three-dimensional structure and function. According to these backgrounds, this review paper is organized as follows. The introduction is followed by a summary of the three issues; (i) 2D to 3D dynamic structure control: liquid crystal commanded by the surface, (ii) 2D to 3D rational construction: a metal-organic framework (MOF) and a covalent organic framework (COF); (iii) 2D to 3D functional amplification: cells regulated by the surface. In addition, this review summarizes the important aspects of the ultimate three-dimensional nanoarchitectonics as a perspective. The goal of this paper is to establish an integrated concept of functional material creation by reconsidering various reported cases from the viewpoint of nanoarchitectonics, where nanoarchitectonics can be regarded as a method for everything in materials science.

Materials Nanoarchitectonics at Dynamic Interfaces: Structure Formation and Functional Manipulation

The next step in nanotechnology is to establish a methodology to assemble new functional materials based on the knowledge of nanotechnology. This task is undertaken by nanoarchitectonics. In nanoarchitectonics, we architect functional material systems from nanounits such as atoms, molecules, and nanomaterials. In terms of the hierarchy of the structure and the harmonization of the function, the material created by nanoarchitectonics has similar characteristics to the organization of the functional structure in biosystems. Looking at actual biofunctional systems, dynamic properties and interfacial environments are key. In other words, nanoarchitectonics at dynamic interfaces is important for the production of bio-like highly functional materials systems. In this review paper, nanoarchitectonics at dynamic interfaces will be discussed, looking at recent typical examples. In particular, the basic topics of "molecular manipulation, arrangement, and assembly" and "material production" will be discussed in the first two sections. Then, in the following section, "fullerene assembly: from zero-dimensional unit to advanced materials", we will discuss how various functional structures can be created from the very basic nanounit, the fullerene. The above examples demonstrate the versatile possibilities of architectonics at dynamic interfaces. In the last section, these tendencies will be summarized, and future directions will be discussed.

The shift from quantitative to qualitative thinking-problems and prospects as viewed from Husserl's and Hegel's philosophy

This article contrasts the views of the philosophers Husserl and Hegel on quantification in science and compares their proposals for conducting rigorous qualitative research. Both deem quantification integral to science, but furthermore proposed methodologies to investigate qualitative necessities achieved by a shift in conscious activity and awareness. However, their methodologies differ significantly. While Husserl rejects idealization and instead proposes intuitive means to ideate qualitative essential relations, Hegel suggests idealizing less one-sidedly, namely, qualitatively over and above quantitatively. The article first examines how quantification is achieved and how it contrasts with measuring. This contrast reveals that measuring implies knowledge of qualities. These qualities, however, thus far remain oddly external to the mathematical relations linking the various established equations. The article then follows Husserl's reconstruction of the development of science to illustrate the dismissal of many experiential qualities and how philosophy further amplified skepticism about science on qualities. Husserl's notion of the life-world and the method of eidetic variation are then introduced as means to counterbalance mathematical proceedings in science. However, this method reveals both eidetic qualitative structures and psychical structures without being able to distinguish between them. It is thus susceptible to idiosyncratic, traditional, and cultural biases. Subsequently, Hegel's description of the shift in conscious experience that sets qualitative from quantitative thinking apart is introduced. This shift may overcome the biases, but it faces skepticism that calls for further investigation of the experience of different kinds of thinking.

Efficient, Formal, Material, and Final Causes in Biology and Technology

This paper considers how a classification of causal effects as comprising efficient, formal, material, and final causation can provide a useful understanding of how emergence takes place in biology and technology, with formal, material, and final causation all including cases of downward causation; they each occur in both synchronic and diachronic forms. Taken together, they underlie why all emergent levels in the hierarchy of emergence have causal powers (which is Noble's principle of biological relativity) and so why causal closure only occurs when the upwards and downwards interactions between all emergent levels are taken into account, contra to claims that some underlying physics level is by itself causality complete. A key feature is that stochasticity at the molecular level plays an important role in enabling agency to emerge, underlying the possibility of final causation occurring in these contexts.

Molecular nanoarchitectonics: unification of nanotechnology and molecular/materials science

The development of nanotechnology has provided an opportunity to integrate a wide range of phenomena and disciplines from the atomic scale, the molecular scale, and the nanoscale into materials. Nanoarchitectonics as a post-nanotechnology concept is a methodology for developing functional material systems using units such as atoms, molecules, and nanomaterials. Especially, molecular nanoarchitectonics has been strongly promoted recently by incorporating nanotechnological methods into organic synthesis. Examples of research that have attracted attention include the direct observation of organic synthesis processes at the molecular level with high resolution, and the control of organic syntheses with probe microscope tips. These can also be considered as starting points for nanoarchitectonics. In this review, these examples of molecular nanoarchitectonics are introduced, and future prospects of nanoarchitectonics are discussed. The fusion of basic science and the application of practical functional materials will complete materials chemistry for everything.

Biomass Nanoarchitectonics for Supercapacitor Applications

Nanoarchitectonics integrates nanotechnology with numerous scientific disciplines to create innovative and novel functional materials from nano-units (atoms, molecules, and nanomaterials). The objective of nanoarchitectonics concept is to develop functional materials and systems with rationally architected functional units. This paper explores the progress and potential of this field using biomass nanoarchitectonics for supercapacitor applications as examples of energetic materials and devices. Strategic design of nanoporous carbons that exhibit ultra-high surface area and hierarchically pore architectures comprising micro- and mesopore structure and controlled pore size distributions are of great significance in energy-related applications, including in high-performance supercapacitors, lithium-ion batteries, and fuel cells. Agricultural wastes or natural biomass are lignocellulosic materials and are excellent carbon sources for the preparation of hierarchically porous carbons with an ultra-high surface area that are attractive materials in high-performance supercapacitor applications due to high electrical and ion conduction, extreme porosity, and exceptional chemical and thermal stability. In this review, we will focus on the latest advancements in the fabrication of hierarchical porous carbon materials from different biomass by chemical activation method. Particularly, the importance of biomass-derived ultra-high surface area porous carbons, hierarchical architectures with interconnected pores in high-energy storage, and high-performance supercapacitors applications will be discussed. Finally, the current challenges and outlook for the further improvement of carbon materials derived from biomass or agricultural wastes in the advancements of supercapacitor devices will be discussed.

Information geometry for multiparameter models: new perspectives on the origin of simplicity

Complex models in physics, biology, economics, and engineering are oftensloppy, meaning that the model parameters are not well determined by the model predictions for collective behavior. Many parameter combinations can vary over decades without significant changes in the predictions. This review uses information geometry to explore sloppiness and its deep relation to emergent theories. We introduce themodel manifoldof predictions, whose coordinates are the model parameters. Itshyperribbonstructure explains why only a few parameter combinations matter for the behavior. We review recent rigorous results that connect the hierarchy of hyperribbon widths to approximation theory, and to the smoothness of model predictions under changes of the control variables. We discuss recent geodesic methods to find simpler models on nearby boundaries of the model manifold-emergent theories with fewer parameters that explain the behavior equally well. We discuss a Bayesian prior which optimizes the mutual information between model parameters and experimental data, naturally favoring points on the emergent boundary theories and thus simpler models. We introduce a 'projected maximum likelihood' prior that efficiently approximates this optimal prior, and contrast both to the poor behavior of the traditional Jeffreys prior. We discuss the way the renormalization group coarse-graining in statistical mechanics introduces a flow of the model manifold, and connect stiff and sloppy directions along the model manifold with relevant and irrelevant eigendirections of the renormalization group. Finally, we discuss recently developed 'intensive' embedding methods, allowing one to visualize the predictions of arbitrary probabilistic models as low-dimensional projections of an isometric embedding, and illustrate our method by generating the model manifold of the Ising model.

Molecular Machines and Microrobots: Nanoarchitectonics Developments and On-Water Performances

This review will focus on micromachines and microrobots, which are objects at the micro-level with similar machine functions, as well as nano-level objects such as molecular machines and nanomachines. The paper will initially review recent examples of molecular machines and microrobots that are not limited to interfaces, noting the diversity of their functions. Next, examples of molecular machines and micromachines/micro-robots functioning at the air-water interface will be discussed. The behaviors of molecular machines are influenced significantly by the specific characteristics of the air-water interface. By placing molecular machines at the air-water interface, the scientific horizon and depth of molecular machine research will increase dramatically. On the other hand, for microrobotics, more practical and advanced systems have been reported, such as the development of microrobots and microswimmers for environmental remediations and biomedical applications. The research currently being conducted on the surface of water may provide significant basic knowledge for future practical uses of molecular machines and microrobots.

Full Configuration Interaction Excited-State Energies in Large Active Spaces from Subspace Iteration with Repeated Random Sparsification

We present a stable and systematically improvable quantum Monte Carlo (QMC) approach to calculating excited-state energies, which we implement using our fast randomized iteration method for the full configuration interaction problem (FCI-FRI). Unlike previous excited-state quantum Monte Carlo methods, our approach, which is based on an asymmetric variant of subspace iteration, avoids the use of dot products of random vectors and instead relies upon trial vectors to maintain orthogonality and estimate eigenvalues. By leveraging recent advances, we apply our method to calculate ground- and excited-state energies of challenging molecular systems in large active spaces, including the carbon dimer with 8 electrons in 108 orbitals (8e,108o), an oxo-Mn(salen) transition metal complex (28e,28o), ozone (18e,87o), and butadiene (22e,82o). In the majority of these test cases, our approach yields total excited-state energies that agree with those from state-of-the-art methods─including heat-bath CI, the density matrix renormalization group approach, and FCIQMC─to within sub-milliHartree accuracy. In all cases, estimated excitation energies agree to within about 0.1 eV.

Fidelity Mechanics: Analogues of the Four Thermodynamic Laws and Landauer's Principle

Fidelity mechanics is formalized as a framework for investigating critical phenomena in quantum many-body systems. Fidelity temperature is introduced for quantifying quantum fluctuations, which, together with fidelity entropy and fidelity internal energy, constitute three basic state functions in fidelity mechanics, thus enabling us to formulate analogues of the four thermodynamic laws and Landauer's principle at zero temperature. Fidelity flows, which are irreversible, are defined and may be interpreted as an alternative form of renormalization group flows. Thus, fidelity mechanics offers a means to characterize both stable and unstable fixed points: divergent fidelity temperature for unstable fixed points and zero-fidelity temperature and (locally) maximal fidelity entropy for stable fixed points. In addition, fidelity entropy behaves differently at an unstable fixed point for topological phase transitions and at a stable fixed point for topological quantum states of matter. A detailed analysis of fidelity mechanical-state functions is presented for six fundamental models-the quantum spin-1/2 XY model, the transverse-field quantum Ising model in a longitudinal field, the quantum spin-1/2 XYZ model, the quantum spin-1/2 XXZ model in a magnetic field, the quantum spin-1 XYZ model, and the spin-1/2 Kitaev model on a honeycomb lattice for illustrative purposes. We also present an argument to justify why the thermodynamic, psychological/computational, and cosmological arrows of time should align with each other, with the psychological/computational arrow of time being singled out as a master arrow of time.

Molecule-to-Material-to-Bio Nanoarchitectonics with Biomedical Fullerene Nanoparticles

Nanoarchitectonics integrates nanotechnology with various other fields, with the goal of creating functional material systems from nanoscale units such as atoms, molecules, and nanomaterials. The concept bears strong similarities to the processes and functions seen in biological systems. Therefore, it is natural for materials designed through nanoarchitectonics to truly shine in bio-related applications. In this review, we present an overview of recent work exemplifying how nanoarchitectonics relates to biology and how it is being applied in biomedical research. First, we present nanoscale interactions being studied in basic biology and how they parallel nanoarchitectonics concepts. Then, we overview the state-of-the-art in biomedical applications pursuant to the nanoarchitectonics framework. On this basis, we take a deep dive into a particular building-block material frequently seen in nanoarchitectonics approaches: fullerene. We take a closer look at recent research on fullerene nanoparticles, paying special attention to biomedical applications in biosensing, gene delivery, and radical scavenging. With these subjects, we aim to illustrate the power of nanomaterials and biomimetic nanoarchitectonics when applied to bio-related applications, and we offer some considerations for future perspectives.

Materials nanoarchitectonics in a two-dimensional world within a nanoscale distance from the liquid phase

Promoted understanding of nanotechnology has enabled the construction of functional materials with nanoscale-regulated structures. Accordingly, materials science requires one-step further innovation by coupling nanotechnology with the other materials sciences. As a post-nanotechnology concept, nanoarchitectonics has recently been proposed. It is a methodology to architect functional material systems using atomic, molecular, and nanomaterial unit-components. One of the attractive methodologies would be to develop nanoarchitectonics in a defined dimensional environment with certain dynamism, such as liquid interfaces. However, nanoarchitectonics at liquid interfaces has not been fully explored because of difficulties in direct observations and evaluations with high-resolutions. This unsatisfied situation in the nanoscale understanding of liquid interfaces may keep liquid interfaces as unexplored and attractive frontiers in nanotechnology and nanoarchitectonics. Research efforts related to materials nanoarchitectonics on liquid interfaces have been continuously made. As exemplified in this review paper, a wide range of materials can be organized and functionalized on liquid interfaces, including organic molecules, inorganic nanomaterials, hybrids, organic semiconductor thin films, proteins, and stem cells. Two-dimensional nanocarbon sheets have been fabricated by molecular reactions at dynamically moving interfaces, and metal-organic frameworks and covalent organic frameworks have been fabricated by specific interactions and reactions at liquid interfaces. Therefore, functions such as sensors, devices, energy-related applications, and cell control are being explored. In fact, the potential for the nanoarchitectonics of functional materials in two-dimensional nanospaces at liquid surfaces is sufficiently high. On the basis of these backgrounds, this short review article describes recent approaches to materials nanoarchitectonics in a liquid-based two-dimensional world, i.e., interfacial regions within a nanoscale distance from the liquid phase.

A free energy principle for generic quantum systems

The Free Energy Principle (FEP) states that under suitable conditions of weak coupling, random dynamical systems with sufficient degrees of freedom will behave so as to minimize an upper bound, formalized as a variational free energy, on surprisal (a.k.a., self-information). This upper bound can be read as a Bayesian prediction error. Equivalently, its negative is a lower bound on Bayesian model evidence (a.k.a., marginal likelihood). In short, certain random dynamical systems evince a kind of self-evidencing. Here, we reformulate the FEP in the formal setting of spacetime-background free, scale-free quantum information theory. We show how generic quantum systems can be regarded as observers, which with the standard freedom of choice assumption become agents capable of assigning semantics to observational outcomes. We show how such agents minimize Bayesian prediction error in environments characterized by uncertainty, insufficient learning, and quantum contextuality. We show that in its quantum-theoretic formulation, the FEP is asymptotically equivalent to the Principle of Unitarity. Based on these results, we suggest that biological systems employ quantum coherence as a computational resource and - implicitly - as a communication resource. We summarize a number of problems for future research, particularly involving the resources required for classical communication and for detecting and responding to quantum context switches.

Toward a theory of evolution as multilevel learning

We apply the theory of learning to physically renormalizable systems in an attempt to outline a theory of biological evolution, including the origin of life, as multilevel learning. We formulate seven fundamental principles of evolution that appear to be necessary and sufficient to render a universe observable and show that they entail the major features of biological evolution, including replication and natural selection. It is shown that these cornerstone phenomena of biology emerge from the fundamental features of learning dynamics such as the existence of a loss function, which is minimized during learning. We then sketch the theory of evolution using the mathematical framework of neural networks, which provides for detailed analysis of evolutionary phenomena. To demonstrate the potential of the proposed theoretical framework, we derive a generalized version of the Central Dogma of molecular biology by analyzing the flow of information during learning (back propagation) and predicting (forward propagation) the environment by evolving organisms. The more complex evolutionary phenomena, such as major transitions in evolution (in particular, the origin of life), have to be analyzed in the thermodynamic limit, which is described in detail in the paper by Vanchurin et al. [V. Vanchurin, Y. I. Wolf, E. V. Koonin, M. I. Katsnelson, Proc. Natl. Acad. Sci. U.S.A. 119, 10.1073/pnas.2120042119 (2022)].

Toward a theory of evolution as multilevel learning

We apply the theory of learning to physically renormalizable systems in an attempt to outline a theory of biological evolution, including the origin of life, as multilevel learning. We formulate seven fundamental principles of evolution that appear to be necessary and sufficient to render a universe observable and show that they entail the major features of biological evolution, including replication and natural selection. It is shown that these cornerstone phenomena of biology emerge from the fundamental features of learning dynamics such as the existence of a loss function, which is minimized during learning. We then sketch the theory of evolution using the mathematical framework of neural networks, which provides for detailed analysis of evolutionary phenomena. To demonstrate the potential of the proposed theoretical framework, we derive a generalized version of the Central Dogma of molecular biology by analyzing the flow of information during learning (back propagation) and predicting (forward propagation) the environment by evolving organisms. The more complex evolutionary phenomena, such as major transitions in evolution (in particular, the origin of life), have to be analyzed in the thermodynamic limit, which is described in detail in the paper by Vanchurin et al. [V. Vanchurin, Y. I. Wolf, E. V. Koonin, M. I. Katsnelson, Proc. Natl. Acad. Sci. U.S.A. 119, 10.1073/pnas.2120042119 (2022)].

Porous carbon nanoarchitectonics for the environment: detection and adsorption

As a post-nanotechnology concept, nanoarchitectonics has emerged from the 20th century to the 21st century. This review summarizes the recent progress in the field of metal-free porous carbon nanoarchitectonics.

Regulation of stem cell fate and function by using bioactive materials with nanoarchitectonics for regenerative medicine

Nanoarchitectonics has emerged as a post-nanotechnology concept. As one of the applications of nanoarchitectonics, this review paper discusses the control of stem cell fate and function as an important issue. For hybrid nanoarchitectonics involving living cells, it is crucial to understand how biomaterials and their nanoarchitected structures regulate behaviours and fates of stem cells. In this review, biomaterials for the regulation of stem cell fate are firstly discussed. Besides multipotent differentiation, immunomodulation is an important biological function of mesenchymal stem cells (MSCs). MSCs can modulate immune cells to treat multiple immune- and inflammation-mediated diseases. The following sections summarize the recent advances of the regulation of the immunomodulatory functions of MSCs by biophysical signals. In the third part, we discussed how biomaterials direct the self-organization of pluripotent stem cells for organoid. Bioactive materials are constructed which mimic the biophysical cues of in vivo microenvironment such as elasticity, viscoelasticity, biodegradation, fluidity, topography, cell geometry, and etc. Stem cells interpret these biophysical cues by different cytoskeletal forces. The different cytoskeletal forces lead to substantial transcription and protein expression, which affect stem cell fate and function. Regulations of stem cells could not be utilized only for tissue repair and regenerative medicine but also potentially for production of advanced materials systems. Materials nanoarchitectonics with integration of stem cells and related biological substances would have high impacts in science and technology of advanced materials.

Idealizations and analogies: Explaining critical phenomena

The "universality" of critical phenomena is much discussed in philosophy of scientific explanation, idealizations and philosophy of physics. Lange and Reutlinger recently opposed Batterman concerning the role of some deliberate distortions in unifying a large class of phenomena, regardless of microscopic constitution. They argue for an essential explanatory role for "commonalities" rather than that of idealizations. Building on Batterman's insight, this article aims to show that assessing the differences between the universality of critical phenomena and two paradigmatic cases of "commonality strategy"-the ideal gas model and the harmonic oscillator model-is necessary to avoid the objections raised by Lange and Reutlinger. Taking these universal explanations as benchmarks for critical phenomena reveals the importance of the different roles played by analogies underlying the use of the models. A special combination of physical and formal analogies allows one to explain the epistemic autonomy of the universality of critical phenomena through an explicative loop.

Ecological Values Theory: Beyond Conformity, Goal-Seeking, and Rule-Following in Action and Interaction

Values have long been considered important for psychology but are frequently characterized as beliefs, goals, rules, or norms. Ecological values theory locates them, not in people or in objects, but in ecosystem relationships and the demands those relationships place on fields of action within the system. To test the worth of this approach, we consider skilled coordination tasks in social psychology (e.g., negotiating disagreements, synchrony and asynchrony in interactions, and selectivity in social learning) and perception-action (e.g., driving vehicles and carrying a child). Evidence suggests that a diverse array of values (e.g., truth, social solidarity, justice, flexibility, safety, and comfort) work in a cooperative tension to guide actions. Values emerge as critical constraints on action that differ from goals, rules, and natural laws, and yet provide the larger context in which they can function effectively. Prospects and challenges for understanding values and their role in action, including theoretical and methodological issues, are considered.

The Superconducting Critical Temperature

Two principles govern the critical temperature for superconducting transitions: (1) intrinsic strength of the pair coupling and (2) the effect of the many-body environments on the efficiency of that coupling. Most discussions take into account only the former, but we argue that the properties of unconventional superconductors are governed more often by the latter, through dynamical symmetry relating to normal and superconducting states. Differentiating these effects is essential to charting a path to the highest-temperature superconductors.

Structure, scale and emergence

In this paper I consider the structures that chemists and physicists attribute at the molecular scale to substances and materials of various kinds, and how they relate to structures and processes at other scales. I argue that the structure of a substance is the set of properties and relations which are preserved across all the conditions in which it can be said to exist. In short, structure is abstraction. On the basis of this view, and using concrete examples, I argue that structures, and therefore the chemical substances and other materials to which they are essential, are emergent. Firstly, structures themselves are scale-dependent because they can only exist within certain physical conditions, and a single substance may have different structures at different scales (of length, time and energy). Secondly, the distinctness of both substances and structures is a scale-dependent relationship: above a certain point, two distinct possibilities may become one. Thirdly, the necessary conditions for composition, for both substances and molecular species, are scale-dependent. To know whether a group of nuclei and electrons form a molecule it is not enough to consider energy alone: one also has to know about their environment and the lifetime over which the group robustly hangs together.

Causal Geometry

Information geometry has offered a way to formally study the efficacy of scientific models by quantifying the impact of model parameters on the predicted effects. However, there has been little formal investigation of causation in this framework, despite causal models being a fundamental part of science and explanation. Here, we introduce causal geometry, which formalizes not only how outcomes are impacted by parameters, but also how the parameters of a model can be intervened upon. Therefore, we introduce a geometric version of "effective information"-a known measure of the informativeness of a causal relationship. We show that it is given by the matching between the space of effects and the space of interventions, in the form of their geometric congruence. Therefore, given a fixed intervention capability, an effective causal model is one that is well matched to those interventions. This is a consequence of "causal emergence," wherein macroscopic causal relationships may carry more information than "fundamental" microscopic ones. We thus argue that a coarse-grained model may, paradoxically, be more informative than the microscopic one, especially when it better matches the scale of accessible interventions-as we illustrate on toy examples.

Levels of biological plausibility

Notions of mechanism, emergence, reduction and explanation are all tied to levels of analysis. I cover the relationship between lower and higher levels, suggest a level of mechanism approach for neuroscience in which the components of a mechanism can themselves be further decomposed and argue that scientists' goals are best realized by focusing on pragmatic concerns rather than on metaphysical claims about what is ‘real'. Inexplicably, neuroscientists are enchanted by both reduction and emergence. A fascination with reduction is misplaced given that theory is neither sufficiently developed nor formal to allow it, whereas metaphysical claims of emergence bring physicalism into question. Moreover, neuroscience's existence as a discipline is owed to higher-level concepts that prove useful in practice. Claims of biological plausibility are shown to be incoherent from a level of mechanism view and more generally are vacuous. Instead, the relevant findings to address should be specified so that model selection procedures can adjudicate between competing accounts. Model selection can help reduce theoretical confusions and direct empirical investigations. Although measures themselves, such as behaviour, blood-oxygen-level-dependent (BOLD) and single-unit recordings, are not levels of analysis, like levels, no measure is fundamental and understanding how measures relate can hasten scientific progress.

This article is part of the theme issue ‘Key relationships between non-invasive functional neuroimaging and the underlying neuronal activity'.

The Causal Closure of Physics in Real World Contexts

The causal closure of physics is usually discussed in a context free way. Here I discuss it in the context of engineering systems and biology, where strong emergence takes place due to a combination of upwards emergence and downwards causation (Ellis, Emergence in Solid State Physics and Biology, 2020, arXiv:2004.13591). Firstly, I show that causal closure is strictly limited in terms of spatial interactions because these are cases that are of necessity strongly interacting with the environment. Effective Spatial Closure holds ceteris parabus, and can be violated by Black Swan Events. Secondly, I show that causal closure in the hierarchy of emergence is a strictly interlevel affair, and in the cases of engineering and biology encompasses all levels from the social level to the particle physics level. However Effective Causal Closure can usefully be defined for a restricted set of levels, and one can experimentally determine Effective Theories that hold at each level. This does not however imply those effective theories are causally complete by themselves. In particular, the particle physics level is not causally complete by itself in the contexts of solid state physics (because of interlevel wave-particle duality), digital computers (where algorithms determine outcomes), or biology (because of time dependent constraints). Furthermore Inextricably Intertwined Levels occur in all these contexts.

Coordination Dynamics: A Foundation for Understanding Social Behavior

Humans' interactions with each other or with socially competent machines exhibit lawful coordination patterns at multiple levels of description. According to Coordination Dynamics, such laws specify the flow of coordination states produced by functional synergies of elements (e.g., cells, body parts, brain areas, people…) that are temporarily organized as single, coherent units. These coordinative structures or synergies may be mathematically characterized as informationally coupled self-organizing dynamical systems (Coordination Dynamics). In this paper, we start from a simple foundation, an elemental model system for social interactions, whose behavior has been captured in the Haken-Kelso-Bunz (HKB) model. We follow a tried and tested scientific method that tightly interweaves experimental neurobehavioral studies and mathematical models. We use this method to further develop a body of empirical research that advances the theory toward more generalized forms. In concordance with this interdisciplinary spirit, the present paper is written both as an overview of relevant advances and as an introduction to its mathematical underpinnings. We demonstrate HKB's evolution in the context of social coordination along several directions, with its applicability growing to increasingly complex scenarios. In particular, we show that accommodating for symmetry breaking in intrinsic dynamics and coupling, multiscale generalization and adaptation are principal evolutions. We conclude that a general framework for social coordination dynamics is on the horizon, in which models support experiments with hypothesis generation and mechanistic insights.

Rethinking Causation for Data-intensive Biology: Constraints, Cancellations, and Quantized Organisms: Causality in complex organisms is sculpted by constraints rather than instigators, with outcomes perhaps better described by quantized patterns than rectilinear pathways

Complex organisms thwart the simple rectilinear causality paradigm of "necessary and sufficient," with its experimental strategy of "knock down and overexpress." This Essay organizes the eccentricities of biology into four categories that call for new mathematical approaches; recaps for the biologist the philosopher's recent refinements to the causation concept and the mathematician's computational tools that handle some but not all of the biological eccentricities; and describes overlooked insights that make causal properties of physical hierarchies such as emergence and downward causation straightforward. Reviewing and extrapolating from similar situations in physics, it is suggested that new mathematical tools for causation analysis incorporating feedback, signal cancellation, nonlinear dependencies, physical hierarchies, and fixed constraints rather than instigative changes will reveal unconventional biological behaviors. These include "eigenisms," organisms that are limited to quantized states; trajectories that steer a system such as an evolving species toward optimal states; and medical control via distributed "sheets" rather than single control points.

The information theory of individuality

Despite the near universal assumption of individuality in biology, there is little agreement about what individuals are and few rigorous quantitative methods for their identification. Here, we propose that individuals are aggregates that preserve a measure of temporal integrity, i.e., "propagate" information from their past into their futures. We formalize this idea using information theory and graphical models. This mathematical formulation yields three principled and distinct forms of individuality-an organismal, a colonial, and a driven form-each of which varies in the degree of environmental dependence and inherited information. This approach can be thought of as a Gestalt approach to evolution where selection makes figure-ground (agent-environment) distinctions using suitable information-theoretic lenses. A benefit of the approach is that it expands the scope of allowable individuals to include adaptive aggregations in systems that are multi-scale, highly distributed, and do not necessarily have physical boundaries such as cell walls or clonal somatic tissue. Such individuals might be visible to selection but hard to detect by observers without suitable measurement principles. The information theory of individuality allows for the identification of individuals at all levels of organization from molecular to cultural and provides a basis for testing assumptions about the natural scales of a system and argues for the importance of uncertainty reduction through coarse-graining in adaptive systems.