Conformational changes of proteins and other biomolecules play a fundamental role in their functional mechanism. Single pair Förster resonance energy transfer offers the possibility to detect these conformational changes and dynamics, and to characterize their underlying kinetics. Using spFRET on microscopes with different modes of detection, dynamic timescales ranging from nanoseconds to seconds can be quantified. Confocal microscopy can be used as a means to analyze dynamics in the range of nanoseconds to milliseconds, while total internal (...) reflection fluorescence microscopy offers information about conformational changes on timescales of milliseconds to seconds. While the existence of dynamics can be directly inferred from the FRET efficiency time trace or the correlation of FRET efficiency and fluorescence lifetime, additional computational approaches are required to extract the kinetic rates of these dynamics, a short overview of which is given in this review. The functional mechanism of proteins is often driven by underlying conformational changes. These intramolecular changes and dynamics can be investigated using single pair Förster resonance energy transfer. The kinetic timescales of the dynamics in the range of nanoseconds to seconds is then quantified using different experimental and analytical implementations. (shrink)

Protein structure is dynamic: the intrinsic flexibility of polypeptides facilitates a range of conformational fluctuations, and individual protein chains can assemble into complexes. Proteins are also dynamic in evolution: significant variations in secondary, tertiary and quaternary structure can be observed among divergent members of a protein family. Recent work has highlighted intriguing similarities between these structural and evolutionary dynamics occurring at various levels. Here we review evidence showing how evolutionary changes in protein sequence and structure are often closely (...) related to local protein flexibility and disorder, large‐scale motions and quaternary structure assembly. We suggest that these correspondences can be largely explained by neutral evolution, while deviations between structural and evolutionary dynamics can provide valuable functional insights. Finally, we address future prospects for the field and practical applications that arise from a deeper understanding of the intimate relationship between protein structure, dynamics, function and evolution. (shrink)

© The Author, 2017. Published by Oxford University Press. All rights reserved. In this article, we introduce a lightweight dynamic epistemic logical framework for automated planning under initial uncertainty. We generalize the standard conformant planning problem in AI in two crucial aspects: first, the planning goal can be any formula expressed in an epistemic propositional dynamic logic ; second, procedural constraints of the desired plan specified by regular expressions can be imposed. We then reduce the problem of generalized conformant planning (...) to the model checking problem of our logic. Although our conformant planning problem is much more general than the standard one with Boolean goals and no procedural constraints, the complexity is still PSPACE-complete which is equally hard as standard conformant planning over explicit transition systems. (shrink)

In this paper, an integrated, cognitive view of different mechanisms, reasons and pathways to norm compliance is presented. After a short introduction, theories of norm compliance are reviewed, and found to group in four main typologies: the rational choice model of norm compliance; theories based on conditional preferences to conformity, theories of thoughtless conformity, and theories of norm internalization. In the third section of the paper, the normative architecture EMIL-A is presented. Previous work discussed the epistemic module of this normative (...) architecture, allowing for the generation of normative beliefs being formed. The fourth and fifth sections present the pragmatic modules of EMIL-A, i.e. norm adoption—leading to normative goals—and norm compliance—leading to their execution. Not only are several alternative reasons for norm adoption shown, but also several pathways to norm compliance are identified. Finally, a summary and ideas for future works conclude the paper. (shrink)

A general framework by which dynamic interactions within a protein will promote the necessary series of structural changes, or “conformational cycle,” required for function is proposed. It is suggested that the free‐energy landscape of a protein is biased toward this conformational cycle. Fluctuations into higher energy, although thermally accessible, conformations drive the conformational cycle forward. The amino acid interaction network is defined as those intraprotein interactions that contribute most to the free‐energy landscape. Some network connections are consistent (...) in every structural state, while others periodically change their interaction strength according to the conformational cycle. It is reviewed here that structural transitions change these periodic network connections, which then predisposes the protein toward the next set of network changes, and hence the next structural change. These concepts are illustrated by recent work on tryptophan synthase. Disruption of these dynamic connections may lead to aberrant protein function and disease states. (shrink)

A Higgsless model for strong, electroweak and gravitational interactions is proposed. This model is based on the local symmetry group SU(3)×SU(2)L×U(1)×C,where C is the local conformal symmetry group. The natural minimal conformally invariant form of total Lagrangian is postulated. It contains all standard model fields and gravitational interaction. Using the unitary gauge and the conformal scale fixing conditions, we can eliminate all four real components of the Higgs doublet in this model. However, the masses of vector mesons, leptons, and quarks (...) are automatically generated and are given by the same formulas as in the conventional standard model. In this manner one gets the mass generation without the mechanism of spontaneous symmetry breaking and without the remaining real dynamical Higgs field. The gravitational sector is analyzed, and it is shown that the model admits in the classical limit the Einsteinian form of gravitational interactions. (shrink)

We review the relativistic classical and quantum mechanics of Stueckelberg, and introduce the compensation fields necessary for the gauge covariance of the Stueckelbert–Schrödinger equation. To achieve this, one must introduce a fifth, Lorentz scalar, compensation field, in addition to the four vector fields with compensate the action of the space-time derivatives. A generalized Lorentz force can be derived from the classical Hamilton equations associated with this evolution function. We show that the fifth (scalar) field can be eliminated through the introduction (...) of a conformal metric on the spacetime manifold. The geodesic equation associated with this metric coincides with the Lorentz force, and is therefore dynamically equivalent. Since the generalized Maxwell equations for the five dimensional fields provide an equation relating the fifth field with the spacetime density of events, one can derive the spacetime event density associated with the Friedmann–Robertson–Walker solution of the Einstein equations. The resulting density, in the conformal coordinate space, is isotropic and homogeneous, decreasing as the square of the Robertson–Walker scale factor. Using the Einstein equations, one see that both for the static and matter dominated models, the conformal time slice in which the events which generate the world lines are contained becomes progressively thinner as the inverse square of the scale factor, establishing a simple correspondence between the configurations predicted by the underlying Friedmann–Robertson–Walker dynamical model and the configurations in the conformal coordinates. (shrink)

We review some recent developments in the conformal gravity theory that has been advanced as a candidate alternative to standard Einstein gravity. As a quantum theory the conformal theory is both renormalizable and unitary, with unitarity being obtained because the theory is a PT symmetric rather than a Hermitian theory. We show that in the theory there can be no a priori classical curvature, with all curvature having to result from quantization. In the conformal theory gravity requires no independent quantization (...) of its own, with it being quantized solely by virtue of its being coupled to a quantized matter source. Moreover, because it is this very coupling that fixes the strength of the gravitational field commutators, the gravity sector zero-point energy density and pressure fluctuations are then able to identically cancel the zero-point fluctuations associated with the matter sector. In addition, we show that when the conformal symmetry is spontaneously broken, the zero-point structure automatically readjusts so as to identically cancel the cosmological constant term that dynamical mass generation induces. We show that the macroscopic classical theory that results from the quantum conformal theory incorporates global physics effects that provide for a detailed accounting of a comprehensive set of 138 galactic rotation curves with no adjustable parameters other than the galactic mass to light ratios, and with the need for no dark matter whatsoever. With these global effects eliminating the need for dark matter, we see that invoking dark matter in galaxies could potentially be nothing more than an attempt to describe global physics effects in purely local galactic terms. Finally, we review some recent work by ’t Hooft in which a connection between conformal gravity and Einstein gravity has been found. (shrink)

Compactified Minkowski spacetime is suggested by conformal covariance of Maxwell equations, while E. Cartan's definition of simple spinors leads to the idea of compactified momentum space. Assuming both diffeomorphic to (S 3 × S 1 )/Z 2 , one may obtain in the conformally flat stereographic projection field theories both infrared and ultraviolet regularized. On the compact manifold themselves instead, Fourier integrals of wave-field oscillations would have to be replaced by Fourier series summed over indices of spherical eigenfunctions: n, l, (...) m, m′. Tentatively identifying those wave structures with spacetime itself (in the frame of Big-Bang) and/or with matter and radiation distribution, some large-scale (hydrogenic) and small-scale (lattice) space structures are conjectured. (shrink)

By briefly reviewing three well-known scientific revolutions in fundamental physics (the discovery of inertia, of special relativity and of general relativity), I claim that problems that were supposed to be crying for a dynamical explanation in the old paradigm ended up receiving a structural explanation in the new one. This claim is meant to give more substance to Kuhn’s view that revolutions are accompanied by a shift in what needs to be explained, while suggesting at the same time the existence (...) of a pattern that is common to all of the discussed case-studies. It remains to be seen whether also quantum mechanics, in particular entanglement, conforms to this pattern. (shrink)

The mathematical and physical aspects of the conformal symmetry of space-time and of physical laws are analyzed. In particular, the group classification of conformally flat space-times, the conformal compactifications of space-time, and the problem of imbedding of the flat space-time in global four-dimensional curved spaces with non-trivial topological and geometrical structure are discussed in detail. The wave equations on the compactified space-times are analyzed also, and the set of their elementary solutions constructed. Finally, the implications of global compactified space-times for (...) cosmology are discussed. It is argued that the recent discovery of periodic structure of matter distribution on large distances strongly suggests that the global cosmological space-time should be close. Next we analyze the inflation scalar field in the inflationary model of universe evolution considered on the spatially compact Robertson-Walker space-time. It is shown that the energy distribution in this model is periodic and the periods and density decrease with increasing distance, in striking agreement with experimental data. Our model of the universe also provides a definite predictions for the energy distribution, polar and azimuthal, considered as a function of angles θ and φ. These predictions should be tested with the new astronomical data. (shrink)

The SARS‐CoV‐2 virus is responsible for the COVID‐19 pandemic the world experience since 2019. The protein responsible for the first steps of cell invasion, the spike protein, has probably received the most attention in light of its central role during infection. Computational approaches are among the tools employed by the scientific community in the enormous effort to study this new affliction. One of these methods, namely molecular dynamics (MD), has been used to characterize the function of the spike protein (...) at the atomic level and unveil its structural features from a dynamic perspective. In this review, we focus on these main findings, including spike protein flexibility, rare S protein conformational changes, cryptic epitopes, the role of glycans, drug repurposing, and the effect of spike protein variants. (shrink)

Here I discuss findings that suggest a universal mechanism for proteins (and RNA) to recognize and interact with various binding partners by selectively binding to different conformations that pre‐exist in the free protein's conformational ensemble. The tandem RNA recognition motif domains of splicing factor U2AF65 fluctuate in solution between a predominately closed conformation in which the RNA binding site of one of the domains is blocked, and a lowly populated open conformation in which both RNA binding pockets are accessible. (...) RNA binding to U2AF65 may thus occur through the weakly populated open conformation, and the binding interaction stabilizes the open conformation. The conformational diversity observed in U2AF65 might also facilitate binding to diverse RNA sequences as found in the polypyrimidine tracts that help define 3′ splice sites. Similar binding pathways in other systems have important consequences in biological regulation, molecular evolution, and information storage. (shrink)

Chaos distributes with a covert method to condense the dynamic of complexity and satisfies the security requirements of a cryptographic system. This study gives an ability online/offline ID-based short signature scheme using conformable fractional chaotic maps. Furthermore, we establish its security under IBSS existential unforgeability of identity-based short signature under chosen message attack in the random oracle model. Some of the stimulating preparations of obtainable processes are that they give a multiperiod application of the offline storage, which licenses the agent (...) to recycle the offline pre-registered data in time series, rather than one-period usage in all past IBSS processes. (shrink)

In this paper, we study the evolution of knowledge in multi-agent conformant planning over transition systems. We propose a dynamic epistemic logical framework with modalities of distributed knowledge to handle the epistemic reasoning in such scenarios, and we reduce a problem of multi-agent conformant planning to a model checking problem. We prove that multi-agent conformant planning is Pspace-complete on the size of the dynamic epistemic model.

In this paper, I outline two strands of evidence for the conclusion that the dynamical approach to cognitive science both seeks and provides covering law explanations. Two of the most successful dynamical models—Kelso’s model of rhythmic finger movement and Thelen et al.’s model of infant perseverative reaching—can be seen to provide explanations which conform to the famous explanatory scheme first put forward by Hempel and Oppenheim. In addition, many prominent advocates of the dynamical approach also express the provision of this (...) kind of explanation as a goal of dynamical cognitive science. I conclude by briefly outlining two consequences. First, dynamical cognitive science’s explanatory style may strengthen its links to the so-called “situated” approach to cognition, but, secondly, it may also undermine the widespread intuition that dynamics is related to emergentism in the philosophy of mind. (shrink)

In this paper, we propose a dynamic epistemic framework to capture the knowledge evolution in multi-agent systems where agents are not able to observe. We formalize multi-agent conformant planning with group knowledge, and reduce planning problems to model checking problems. We prove that multi-agent conformant planning with group knowledge is Pspace -complete on the size of dynamic epistemic models. We also consider the alternative Kripke semantics, and show that for each Kripke model with perfect recall and no miracles, there is (...) an equivalent dynamic epistemic model and vice versa. (shrink)

Barbour’s interpretation of Mach’s principle led him to postulate that gravity should be formulated as a dynamical theory of spatial conformal geometry, or in his terminology, “shapes.” Recently, it was shown that the dynamics of General Relativity can indeed be formulated as the dynamics of shapes. This new Shape Dynamics theory, unlike earlier proposals by Barbour and his collaborators, implements local spatial conformal invariance as a gauge symmetry that replaces refoliation invariance in General Relativity. It is the (...) purpose of this paper to answer frequent questions about (new) Shape Dynamics, such as its relation to Poincaré invariance, General Relativity, Constant Mean (extrinsic) Curvature gauge, earlier Shape Dynamics, and finally the conformal approach to the initial value problem of General Relativity. Some of these relations can be clarified by considering a simple model: free electrodynamics and its dual shift symmetric formulation. This model also serves as an example where symmetry trading is used for usual gauge theories. (shrink)

Dynamics of complex systems is often hierarchically organized on different time scales. To understand the physics of such hierarchy, here Brownian motion of a particle moving through a fluctuating medium with slowly varying temperature is studied as an analytically tractable example, and a kinetic theory is formulated for describing the states of the particle. What is peculiar here is that the (inverse) temperature is treated as a dynamical variable. Dynamical hierarchy is introduced in conformity with the adiabatic scheme. Then, (...) a new analytical method is developed to show how the Fokker–Planck equation admits as a stationary solution the Maxwellian distribution modulated by the temperature fluctuations, the distribution of which turns out to be determined by the drift term. A careful comment is also made on so-called superstatistics. (shrink)

Microtubules form a highly dynamic filament network in all eukaryotic cells. Individual microtubules grow by tubulin dimer subunit addition and frequently switch between phases of growth and shortening. These unique dynamics are powered by GTP hydrolysis and drive microtubule network remodeling, which is central to eukaryotic cell biology and morphogenesis. Yet, our knowledge of the molecular events at growing microtubule ends remains incomplete. Here, recent ultrastructural, biochemical and cell biological data are integrated to develop a realistic model of growing (...) microtubule ends comprised of structurally distinct but biochemically overlapping zones. Proteins that recognize microtubule lattice conformations associated with specific tubulin guanosine nucleotide states may independently control major structural transitions at growing microtubule ends. A model is proposed in which tubulin dimer addition and subsequent closure of the MT wall are optimized in cells to achieve rapid physiological microtubule growth. (shrink)

Comparative scholarship on judicial review has paid a lot of attention to the causal impact of politics on judicial decision-making. However, the slower-moving, macro-social process through which judicial review influences societal conceptions of the law/politics relation is less well understood. Drawing on the political science literature on institutional change, The Politico-Legal Dynamics of Judicial Review tests a typological theory of the evolution of judicial review regimes - complexes of legitimating ideas about the law/politics relation. The theory posits that such (...) regimes tend to conform to one of four main types - democratic or authoritarian legalism, or democratic or authoritarian instrumentalism. Through case studies of Australia, India, and Zimbabwe and a comparative chapter analyzing ten additional societies, the book then explores how actually-existing judicial review regimes transition between these types. This process of ideational development, Roux concludes, is distinct both from the everyday business of constitutional politics and changes to the formal constitution. (shrink)

In a 2008 paper, Walmsley argued that the explanations employed in the dynamical approach to cognitive science, as exemplified by the Haken, Kelso and Bunz model of rhythmic finger movement, and the model of infant preservative reaching developed by Esther Thelen and her colleagues, conform to Carl Hempel and Paul Oppenheim’s deductive-nomological model of explanation (also known as the covering law model). Although we think Walmsley’s approach is methodologically sound in that it starts with an analysis of scientific practice rather (...) than a general philosophical framework, we nevertheless feel that there are two problems with his paper. First, he focuses only on the deductivenomological model and so neglects the important fact that explanations are causal. Second, the explanations offered by the dynamical approach do not take the deductive-nomological format, because they do not deduce the explananda from exceptionless laws. Because of these two points, Walmsley makes the dynamical explanations in cognitive science appear problematic, while in fact they are not. (shrink)

In this work we study dimensional theoretical properties of some a±ne dynamical systems. By dimensional theoretical properties we mean Hausdor® dimension and box- counting dimension of invariant sets and ergodic measures on theses sets. Especially we are interested in two problems. First we ask whether the Hausdor® and box- counting dimension of invariant sets coincide. Second we ask whether there exists an ergodic measure of full Hausdor® dimension on these invariant sets. If this is not the case we ask the (...) question, whether at least the variational principle for Haus- dor® dimension holds, which means that there is a sequence of ergodic measures such that their Hausdor® dimension approximates the Hausdor® dimension of the invariant set. It seems to be well accepted by experts that these questions are of great importance in developing a dimension theory of dynamical systems (see the book of Pesin about dimension theory of dynamical systems [PE2]). Dimensional theoretical properties of conformal dynamical systems are fairly well understood today. For example there are general theorems about conformal repellers and hyperbolic sets for conformal di®eomorphisms (see chapter 7 of [PE2]). On the other hand the existence of two di®erent rates of expansion or contraction forces problems that are not captured by a general theory this days. At this stage of de- velopment of the dimension theory of dynamical systems it seems natural to study non conformal examples. This is the ¯rst step to understand the mechanisms that determine dimensional theoretical properties of non conformal dynamical systems. A±ne dynamical systems represent simple examples of non conformal systems. They are easy to de¯ne, but studying their dimensional theoretical properties does never- theless provide challenging mathematical problems and exemplify interesting phe- nomena. We consider here a special class of self-a±ne repellers in dimension two, depending on four parameters (see 2.1.). Furthermore we study a class of attractors of piecewise a±ne maps in dimension three depending on four parameters as well. The last object of our work are projections of these maps that are known as gener- alized Baker's transformations (see 2.2.). The contents of our work is the following: In chapter two we give an overview about some main results in the area of di- mension theory of a±ne dynamical systems and de¯ne the systems we study in this work. We will explain, what is known about the dimensional theoretical properties of these systems and describe what our new results are. In chapter three we then apply symbolic dynamics to our systems. We will introduce explicit shift codings 4 and ¯nd representations of all ergodic measures for our systems using these codings. From chapter four to chapter eight we study dimensional theoretical properties, which our systems generally or generically have. In chapter four we will prove a formula for the box-counting dimension of the repellers and the attractors (see the- orem 4.1.). Then in chapter ¯ve we apply general dimensional theoretical results for ergodic measures found by Ledrappier and Young [LY] and Barreira, Schmeling and Pesin [BPS] to our systems. These results relate the dimension of ergodic measures to metric entropy and Lyapunov exponents. Using this approach we will be able to reduce questions about the dimension of ergodic measures in our context to ques- tions about certain overlapping and especially overlapping self-similar measures on the line. These overlapping self-similar measures are studied in chapter six. Our main theorem extends a result of Peres and Solomyak [PS2] concerning the absolute continuity resp. singularity of symmetric self-similar measures to asymmetric ones (see theorem 6.1.3.). In chapter seven we bring our results together. We prove that we generically (in the sense of Lebesgue measure on a part of the parameter space) have the iden- tity of box-counting and Hausdor® dimension for the repellers and the attractors. (see theorem 7.1.1. and corollary 7.1.2.). This result suggest that one can expect that the identity of box-counting dimension and Hausdor® dimension holds at least generically in some natural classes of non conformal dynamical systems. Furthermore we will see in chapter seven that there generically exists an ergodic measure of full Hausdor® dimension for the repellers. On the other hand the vari- ational principle for Hausdor® dimension is not generic for the attractors. It holds only if we assume a certain symmetry (see theorem 7.1.1.). For generalized Baker's transformations we will ¯nd a part of the parameter space where there generically is an ergodic measure of full dimension and a part where the variational principle for Hausdor® dimension does not hold (see theorem 7.1.3.). Roughly speaking the reason why the variational principle does not hold here is, that if there exists both a stable and an unstable direction one can not generically maximize the dimension in the stable and in the unstable direction at the same time. In an other setting this phenomenon was observed before by Manning and McCluskey [MM]. In chapter eight we extend some results of the last section to invariant sets that correspond to special Markov chains instead of full shifts (see theorem 8.1.1.). In the last two chapters of our work we are interested in number theoretical excep- tions to our generic results. The starting point of our considerations in section nine are results of ErdÄos [ER1] and Alexander and Yorke [AY] that establish singularity and a decrease of dimension for in¯nite convolved Bernoulli measures under special conditions. Using a generalized notion of the Garsia entropy ([GA1/2]) we are able 5 to understand the consequences of number theoretical peculiarities in broader class of overlapping measures (see theorem 9.1.1.). In chapter ten we then analyze number theoretical peculiarities in the context of our dynamical systems. We restrict our attention to a symmetric situation where we generically have the existence of a Bernoulli measure of full dimension and the identity of Hausdor® and box-counting dimension for all of our systems. In the ¯rst section of chapter ten we ¯nd parameter values such that the variational principle for Hausdor® dimension does not hold for the attractors and for the Fat Baker's transformations (see theorem 10.1.1.). These are the ¯rst known examples of dynamical systems for which the variational principle for Hausdor® dimension does not hold because of number theoretical peculiarities of parameter values. For the repellers we have been able to show that under certain number theoretical conditions there is at least no Bernoulli measure of full Hausdor® dimension; the question if the variational principle for Hausdor® dimension holds remains open in this situation. In the second section of chapter ten we will show that the identity for Hausdor® and box-counting dimension can drops because there are number theoretical pecu- liarities. In the context of Weierstrass-like functions this phenomenon was observed by Przytycki and Urbanski [PU]. Our theorem extends this result to a larger class of sets, invariant under dynamical systems (see theorem 10.2.1). At the end of this work the reader will ¯nd two appendices, a list of notations and the list of references. In appendix A we introduce the notions of dimension we use in this work and collect some general facts in dimension theory. In appendix B we state the facts about Pisot-Vijayarghavan number, we need in our analysis of number theoretical peculiarities. The list of notations contains general notations and a table with a summary of notations we use to describe the dynamical systems that we study. Acknowledgments I wish to thank my supervisor JÄorg Schmeling for a lot of valuable discussion and all his help. Also thanks to Luis Barreira for his great hospitality in Lisboa and many interesting comments. This work was done while I was supported by "Promotionstipendium gem. NaFÄoG der Freien UniversitÄat Berlin". (shrink)

Alternative non‐B‐DNA conformations formed under physiological conditions by sequences called flipons include left‐handed Z‐DNA, three‐stranded triplexes, and four‐stranded i‐motifs and quadruplexes. These conformations accumulate and release energy to enable the local assembly of cellular machines in a context specific manner. In these transactions, nucleosomes store power, serving like rechargeable batteries, while flipons smooth energy flows from source to sink by acting as capacitors or resistors. Here, I review the known biological roles for flipons. I present recent and unequivocal findings showing (...) how innate immune responses are regulated by Z‐flipons that identify endogenous RNAs as self. Evidence is also presented supporting important roles for other flipon classes. In these examples, the dynamic exchange of energy between flipons and nucleosomes enables rapid switching of genetic programs without altering flipon sequence. The increased phenotypic diversity enabled by flipons drives their natural selection, with adaptations evolving faster than is possible by codon mutation alone. (shrink)

The etiology of Tauopathies, a diverse class of neurodegenerative diseases associated with the Microtubule Associated Protein (MAP) Tau, is usually described by a common mechanism in which Tau dysfunction results in the loss of axonal microtubule stability. Here, we reexamine and build upon the canonical disease model to encompass other Tau functions. In addition to regulating microtubule dynamics, Tau acts as a modulator of motor proteins, a signaling hub, and a scaffolding protein. This diverse array of functions is related (...) to the dynamic nature of Tau isoform expression, post‐translational modification (PTM), and conformational flexibility. Thus, there is no single mechanism that can describe Tau dysfunction. The effects of specific pathogenic mutations or aberrant PTMs need to be examined on all of the various functions of Tau in order to understand the unique etiology of each disease state. (shrink)

Counterfactual reasoning research typically demonstrates contrast effects—nearly winning evokes frustration, whereas nearly losing evokes exhilaration. The present work, however, describes conditions under which assimilative responses (i.e., when judgements are pulled towards a comparison standard) also occur. Participants solved analogies and learned that they had either nearly attained a target score or nearly failed to attain it. Participants in the no trajectory condition received this feedback in the absence of any prior feedback, whereas those in the trajectory condition received feedback after (...) having received prior feedback conforming to either an ascending or descending pattern. Participants then provided perceptions of their verbal intelligence. Assimilation effects were observed in the trajectory conditions but attenuated in the no trajectory conditions. Discussion focuses on the role of feedback dynamics in determining responses to close-call counterfactuals. (shrink)

The objective of this article is to see whether desire for recognition might contain an emancipatory aspect. Could this desire be a political ally? The argumentative strategy is to fully acknowledge the oppressive mechanisms at work before trying to find a way to other outcomes, including emancipation, with which desire for recognition has been associated in the tradition from Hegel. Through a re-interpretation of the master-and-slave dialectic, supplemented by sociological research on status expectations, I suggest a way out of the (...) vicious circle, where desire produced by power finds satisfaction through a preexisting other, resulting in an endless dynamic of compulsive conformity and regressive assertion of status. The hold of this dynamic must not be underestimated, yet, as I argue, both desire and what satisfies desire are liable to change, through struggle. The transformation of the generalized other, which provides recognition, is seen to be a crucial feature of all collective struggle. The very source of recognition is transformed, behind the backs of the actors, in turn affecting their desire. This can but must not lead to the emancipatory outcomes which are traditionally tied to recognition in the Hegelian tradition. (shrink)

Human brains exhibit complex dynamic behaviour measured by external recordings of electric (EEG) and magnetic fields (MEG). These data reveal synaptic field oscillations in neocortex at millisecond temporal and centimetre spatial scales. We suggest that the neural networks underlying behaviour and cognition may be viewed as embedded in these synaptic action fields, analogous to social networks embedded in a culture. These synaptic fields may facilitate the binding of disparate networks to produce a behaviour and consciousness that appears unified to external (...) observers. EEG, MEG, anatomy, physiology, and complex physical systems are considered here to suggest fundamental physical and biological properties of human brains that may be required for human consciousness to occur. We do not claim that these tissue properties are necessarily causal; however, they appear to be strongly correlated with human consciousness. Emphasis is placed on the hierarchical structure of brains, non-local connections between distant cortical regions, and resonant interactions between networks. While several of these ideas are supported by both experimental data and mathematical theory, the mathematics is replaced by metaphor for this paper. One conjecture is that the schizophrenias and other diseases occur when neural networks fail to conform to global synaptic fields. Perhaps consciousness is a resonance phenomenon and only properly tuned brains can orchestrate the beautiful music of sentience. (shrink)

Understanding what is distinctive about the role of models in science requires characterizing broad patterns in how these models evolve in the face of experimental results. That is, we must examine not just model statics—how the model relates to theory, or represents the world, at some point in time—but also model dynamics—how the model both generates new experimental results and is modified in response to them. Visual representations of structure play a central role in the theoretical reasoning of organic (...) chemists. Not surprisingly, these representations have changed in important ways–in response to experimental and theoretical developments– throughout the history of organic chemistry. In many cases it is appropriate to understand the visual representations used by organic chemists as models. The evolution of the structural representations of organic chemists therefore provides a clear example of the dynamics of scientific modeling. In this paper I use a conception of scientific modeling drawn from the work of Mary Hesse to examine how the concept of a molecular conformation was incorporated into the visual representations of structure used by organic chemists. (shrink)

In this review paper, we discuss how gravity and spin can be obtained as the realization of the local Conformal-Affine group of symmetry transformations. In particular, we show how gravitation is a gauge theory which can be obtained starting from some local invariance as the Poincaré local symmetry. We review previous results where the inhomogeneous connection coefficients, transforming under the Lorentz group, give rise to gravitational gauge potentials which can be used to define covariant derivatives accommodating minimal couplings of matter, (...) gauge fields (and then spin connections). After we show, in a self-contained approach, how the tetrads and the Lorentz group can be used to induce the spacetime metric and then the Invariance Induced Gravity can be directly obtained both in holonomic and anholonomic pictures. Besides, we show how tensor valued connection forms act as auxiliary dynamical fields associated with the dilation, special conformal and deformation (shear) degrees of freedom, inherent to the bundle manifold. As a result, this allows to determine the bundle curvature of the theory and then to construct boundary topological invariants which give rise to a prototype (source free) gravitational Lagrangian. Finally, the Bianchi identities, the covariant field equations and the gauge currents are obtained determining completely the dynamics. (shrink)

What van Gelder calls the dynamical hypothesis is only a special case of what we here dub the general dynamical hypothesis. His terminology makes it easy to overlook important alternative dynamical approaches in cognitive science. Connectionist models typically conform to the general dynamical hypothesis, but not to van Gelder's.

Here we review concepts related to an ensemble description of G-protein-coupled receptors. The ensemble is characterized by both inactive and active states, whose equilibrium populations and exchange rates depend sensitively on ligand, environment, and allosteric factors. This review focuses on the adenosine A2 receptor, a prototypical class A GPCR. 19F Nuclear Magnetic Resonance studies show that apo A2AR is characterized by a broad ensemble of conformers, spanning inactive to active states, and resembling states defined earlier for rhodopsin. In keeping with (...) ideas associated with a conformational selection mechanism, addition of agonist serves to allosterically restrict the overall degrees of freedom at the G protein binding interface and bias both states and functional dynamics to facilitate G protein binding and subsequent activation. While the ligand does not necessarily “induce” activation, it does bias sampling of states, increase the cooperativity of the activation process and thus, the lifetimes of functional activation intermediates, while restricting conformational dynamics to that needed for activation. GPCRs represent a ubiquitous class of transmembrane receptors, responsible for cell signaling and cell homeostasis. Their activation gives rise to conformational changes that allow the receptor to engage downstream partners. Activation can be thought of in terms of a free energy landscape associated with distinct conformers, responsible for the process. Here, the action of ligands is seen to alter this landscape by enabling transitions between key intermediates. (shrink)

Advocates of dynamical systems theory (DST) sometimes employ revolutionary rhetoric. In an attempt to clarify how DST models differ from others in cognitive science, I focus on two issues raised by DST: the role for representations in mental models and the conception of explanation invoked. Two features of representations are their role in standing-in for features external to the system and their format. DST advocates sometimes claim to have repudiated the need for stand-ins in DST models, but I argue that (...) they are mistaken. Nonetheless, DST does offer new ideas as to the format of representations employed in cognitive systems. With respect to explanation, I argue that some DST models are better seen as conforming to the covering-law conception of explanation than to the mechanistic conception of explanation implicit in most cognitive science research. But even here, I argue, DST models are a valuable complement to more mechanistic cognitive explanations. (shrink)

We study vertex operators in 4D conformal field theory derived from quantized gravity, whose dynamics is governed by the Wess-Zumino action by Riegert and the Weyl action. Conformal symmetry is equal to diffeomorphism symmetry in the ultraviolet limit, which mixes positive-metric and negative-metric modes of the gravitational field and thus these modes cannot be treated separately in physical operators. In this paper, we construct gravitational vertex operators such as the Ricci scalar, defined as space-time volume integrals of them are (...) invariant under conformal transformations. Short distance singularities of these operator products are computed and it is shown that their coefficients have physically correct signs. Furthermore, we show that conformal algebra holds even in the system perturbed by the cosmological constant vertex operator as in the case of the Liouville theory shown by Curtright and Thorn. (shrink)

Exactly how do the sign/symbol/token systems of endo- and exo-biosemiosis differ from those of cognitive semiosis? Do the biological messages that integrate metabolism have conceptual meaning? Semantic information has two subsets: Descriptive and Prescriptive. Prescriptive information instructs or directly produces nontrivial function. In cognitive semiosis, prescriptive information requires anticipation and “choice with intent” at bona fide decision nodes. Prescriptive information either tells us what choices to make, or it is a recordation of wise choices already made. Symbol systems allow recordation (...) of deliberate choices and the transmission of linear digital prescriptive information. Formal symbol selection can be instantiated into physicality using physical symbol vehicles (tokens). Material symbol systems (MSS) formally assign representational meaning to physical objects. Even verbal semiosis instantiates meaning into physical sound waves using an MSS. Formal function can also be incorporated into physicality through the use of dynamically-inert (dynamically-incoherent or -decoupled) configurable switch-settings in conceptual circuits. This paper examines the degree to which biosemiosis conforms to the essential formal criteria of prescriptive semiosis and cybernetic management. (shrink)

In conformity with the dynamical perspective advocated by van Gelder, a more psychological approach can highlight the intrinsic temporality of human cognition, revealing the inadequacies of representationalism as a framework for the modeling of mind.

The dynamic mother-daughter relationship can be loving and supportive at best as well as contentious and tragic. It is a relationship predicated on maternal instinct which can provide direction and support for deep insight into notions of womanhood, personal and political philosophies. However, in providing this guidance, ironically this same maternal guidance can act to stifle the growth of an adolescent daughter as she transitions into womanhood. Jamaica Kincaid’s ‘Annie John’ can be seen as an exemplar of this transition. Annie (...) has to contend with not only her mother’s maternal pressure on her to conform, but she must also adhere to cultural expectations of a creolized culture predicated on both Africana and British understandings of femininity, social expectations, womanhood, and etiquette. This challenges Annie’s own emerging philosophy and desire for independence and self-definition. As discussed in this paper, success can be achieved outside and beyond the mother-daughter dynamic once a daughter has had the opportunity to consider, realize, defy the hypocrisy of being encouraged to be independent whilst being forced to follow one’s mother’s notion of womanhood. In a valiant attempt to avoid the tragedy of replicating her mother’s own flaws, Annie John’s personal growth was no easy feat and created at times a contentious dynamic. However, this journey not only facilitated her success and independence so that she could travel beyond the shores of Antigua, it demonstrated an independence of thought that African Caribbean creolized women must experience in order to realize their own success. (shrink)

A massless Weyl-invariant dynamics of a scalar, a Dirac spinor, and electromagnetic fields is formulated in a Weyl space, W4, allowing for conformal rescalings of the metric and of all fields with nontrivial Weyl weight together with the associated transformations of the Weyl vector fields κμ, representing the D(1) gauge fields, with D(1) denoting the dilatation group. To study the appearance of nonzero masses in the theory the Weyl symmetry is broken explicitly and the corresponding reduction of the Weyl (...) space W4 to a pseudo-Riemannian space V4 is investigated assuming the breaking to be determined by an expression involving the curvature scalar R of the W4 and the mass of the scalar, selfinteracting field. Thereby also the spinor field acquires a mass proportional to the modulus Φ of the scalar field in a Higgs-type mechanism formulated here in a Weyl-geometric setting with Φ providing a potential for the Weyl vector fields κμ. After the Weyl-symmetry breaking, one obtains generally covariant and U(1) gauge covariant field equations coupled to the metric of the underlying V4. This metric is determined by Einstein's equations, with a gravitational coupling constant depending on Φ, coupled to the energy momentum tensors of the now massive fields involved together with the (massless) radiation fields. (shrink)

Almost 40 years since the discovery of microtubule dynamic instability, the molecular mechanisms underlying microtubule dynamics remain an area of intense research interest. The “standard model” of microtubule dynamics implicates a “cap” of GTP‐bound tubulin dimers at the growing microtubule end as the main determinant of microtubule stability. Loss of the GTP‐cap leads to microtubule “catastrophe,” a switch‐like transition from microtubule growth to shrinkage. However, recent studies, using biochemical in vitro reconstitution, cryo‐EM, and computational modeling approaches, challenge the (...) simple GTP‐cap model. Instead, a new perspective on the mechanisms of microtubule dynamics is emerging. In this view, highly dynamic transitions between different structural conformations of the growing microtubule end – which may or may not be directly linked to the nucleotide content at the microtubule end – ultimately drive microtubule catastrophe. (shrink)

If one formulates Helmholtz's ideas about perception in terms of modern-day theories one arrives at a model of perceptual inference and learning that can explain a remarkable range of neurobiological facts. Using constructs from statistical physics it can be shown that the problems of inferring what cause our sensory inputs and learning causal regularities in the sensorium can be resolved using exactly the same principles. Furthermore, inference and learning can proceed in a biologically plausible fashion. The ensuing scheme rests on (...) Empirical Bayes and hierarchical models of how sensory information is generated. The use of hierarchical models enables the brain to construct prior expectations in a dynamic and context-sensitive fashion. This scheme provides a principled way to understand many aspects of the brain's organisation and responses. In this paper, we suggest that these perceptual processes are just one emergent property of systems that conform to a free-energy principle. The free-energy considered here represents a bound on the surprise inherent in any exchange with the environment, under expectations encoded by its state or configuration. A system can minimise free-energy by changing its configuration to change the way it samples the environment, or to change its expectations. These changes correspond to action and perception, respectively, and lead to an adaptive exchange with the environment that is characteristic of biological systems. This treatment implies that the system's state and structure encode an implicit and probabilistic model of the environment. We will look at models entailed by the brain and how minimisation of free-energy can explain its dynamics and structure. (shrink)

If one formulates Helmholtz’s ideas about perception in terms of modern-day theories one arrives at a model of perceptual inference and learning that can explain a remarkable range of neurobiological facts. Using constructs from statistical physics it can be shown that the problems of inferring what cause our sensory inputs and learning causal regularities in the sensorium can be resolved using exactly the same principles. Furthermore, inference and learning can proceed in a biologically plausible fashion. The ensuing scheme rests on (...) Empirical Bayes and hierarchical models of how sensory information is generated. The use of hierarchical models enables the brain to construct prior expectations in a dynamic and context-sensitive fashion. This scheme provides a principled way to understand many aspects of the brain’s organisation and responses. In this paper, we suggest that these perceptual processes are just one emergent property of systems that conform to a free-energy principle. The free-energy considered here represents a bound on the surprise inherent in any exchange with the environment, under expectations encoded by its state or configuration. A system can minimise free-energy by changing its configuration to change the way it samples the environment, or to change its expectations. These changes correspond to action and perception, respectively, and lead to an adaptive exchange with the environment that is characteristic of biological systems. This treatment implies that the system’s state and structure encode an implicit and probabilistic model of the environment. We will look at models entailed by the brain and how minimisation of free-energy can explain its dynamics and structure. (shrink)

The relation of the conformal group to various earlier proposed relativistic quantum mechanical dynamical groups (and other related groups) is studied in the framework of projective geometry, by explicitly constructing the contractions of the six-dimensional coordinate transformations. Five-dimensional realizations are then derived. An attempt is made to improve our physical insight through geometry.

Harmony is a concept essential to Confucianism and to the way of life of past and present people in East Asia. Integrating methods of textual exegesis, historical investigation, comparative analysis, and philosophical argumentation, this book presents a comprehensive treatment of the Confucian philosophy of harmony. The book traces the roots of the concept to antiquity, examines its subsequent development, and explicates its theoretical and practical significance for the contemporary world. It argues that, contrary to a common view in the West, (...) Confucian harmony is not mere agreement but has to be achieved and maintained with creative tension. Under the influence of a Weberian reading of Confucianism as "adjustment" to a world with an underlying fixed cosmic order, Confucian harmony has been systematically misinterpreted in the West as presupposing an invariable grand scheme of things that pre-exists in the world to which humanity has to conform. The book shows that Confucian harmony is a dynamic, generative process, which seeks to balance and reconcile differences and conflicts through creativity. Illuminating one of the most important concepts in Chinese philosophy and intellectual history, this book is of interest to students of Chinese studies, history and philosophy in general and eastern philosophy in particular. (shrink)

Findings in dynamic unit formation suggest that completion processes reflect the optics of our world. Dynamic unit formation may depend on patterns of motion signals that are consistent with the causes of optical changes. In addition, dynamic completion conforms to a local curvature minimization constraint. Such relational aspects of vision are important to consider in linking perceptual experience and neural activity.

The Z‐conformation, recently elucidated in crystals of synthetic alternating dG‐dC polymers, is a dramatically different structure for DNA. Despite suggestive locations of alternating purine‐pyrimidine tracts in chromosomes and intriguing functional hypotheses, unequivocal demonstrations of the Z‐conformation in vivo are not proving easy. Perhaps the Z‐conformation should be considered largely as a dynamic structure transiently forming in torsionally stressed chromatin.

The concept of cooperative communities that enforce norm conformity through reward, as well as shaming, ridicule, and ostracism, has been central to anthropology since the work of Durkheim. Prevailing approaches from evolutionary theory explain the willingness to exert sanctions to enforce norms as self-interested behavior, while recent experimental studies suggest that altruistic rewarding and punishing—“strong reciprocity”—play an important role in promoting cooperation. This paper will use data from 308 conversations among the Ju/’hoansi (!Kung) Bushmen (a) to examine the dynamics (...) of norm enforcement, (b) to evaluate the costs of punishment in a forager society and understand how they are reduced, and (c) to determine whether hypotheses that center on individual self-interest provide sufficient explanations for bearing the costs of norm enforcement, or whether there is evidence for strong reciprocity. (shrink)

Taxa and homologues can in our view be construed both as kinds and as individuals. However, the conceptualization of taxa as natural kinds in the sense of homeostatic property cluster kinds has been criticized by some systematists, as it seems that even such kinds cannot evolve due to their being homeostatic. We reply by arguing that the treatment of transformational and taxic homologies, respectively, as dynamic and static aspects of the same homeostatic property cluster kind represents a good perspective for (...) supporting the conceptualization of taxa as kinds. The focus on a phenomenon of homology based on causal processes (e.g., connectivity, activity-function, genetics, inheritance, and modularity) and implying relationship with modification yields a notion of natural kinds conforming to the phylogenetic-evolutionary framework. Nevertheless, homeostatic property cluster kinds in taxonomic and evolutionary practice must be rooted in the primacy of epistemological classification (homology as observational properties) over metaphysical generalization (series of transformation and common ancestry as unobservational processes). The perspective of individuating characters exclusively by historical-transformational independence instead of their developmental, structural, and functional independence fails to yield a sufficient practical interplay between theory and observation. Purely ontological and ostensional perspectives in evolution and phylogeny (e.g., an ideographic character concept and PhyloCode’s ‘individualism’ of clades) may be pragmatically contested in the case of urgent issues in biodiversity research, conservation, and systematics. (shrink)

The brain is composed of electrically excitable neuronal networks regulated by the activity of voltage-gated ion channels. Further portraying the molecular composition of the brain, however, will not reveal anything remotely reminiscent of a feeling, a sensation or a conscious experience. In classical physics, addressing the mind–brain problem is a formidable task because no physical mechanism is able to explain how the brain generates the unobservable, inner psychological world of conscious experiences and how in turn those conscious experiences steer the (...) underlying brain processes toward desired behavior. Yet, this setback does not establish that consciousness is non-physical. Modern quantum physics affirms the interplay between two types of physical entities in Hilbert space: unobservable quantum states, which are vectors describing what exists in the physical world, and quantum observables, which are operators describing what can be observed in quantum measurements. Quantum no-go theorems further provide a framework for studying quantum brain dynamics, which has to be governed by a physically admissible Hamiltonian. Comprising consciousness of unobservable quantum information integrated in quantum brain states explains the origin of the inner privacy of conscious experiences and revisits the dynamic timescale of conscious processes to picosecond conformational transitions of neural biomolecules. The observable brain is then an objective construction created from classical bits of information, which are bound by Holevo’s theorem, and obtained through the measurement of quantum brain observables. Thus, quantum information theory clarifies the distinction between the unobservable mind and the observable brain, and supports a solid physical foundation for consciousness research. (shrink)