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  • Top-down effects in the brain
    Phys. Life Rev. (IF 13.783) Pub Date : 2018-07-09
    George Ellis

    The purpose of this investigation is to demonstrate that one is unable to understand the operation of the brain without taking top-down effects into account. This is demonstrated by looking in turn at evolutionary and developmental aspects, then at functional aspects related to sensory systems, learning processes, and motor processes that lead to action on the world. It is also clear in terms of the effects of a society on brains located in that society. The possibility of top down affects exists both because of multiple realisability of higher level processes at lower levels, and because lower level elements are adapted to perform their higher level functions. These top-down processes validate a non-reductionist approach to how the brain works.

  • The body talks: Sensorimotor communication and its brain and kinematic signatures
    Phys. Life Rev. (IF 13.783) Pub Date : 2018-06-30
    Giovanni Pezzulo, Francesco Donnarumma, Haris Dindo, Alessandro D'Ausilio, Ivana Konvalinka, Cristiano Castelfranchi

    Human communication is a traditional topic of research in many disciplines such as psychology, linguistics and philosophy, all of which mainly focused on language, gestures and deictics. However, these do not constitute the sole channels of communication, especially during online social interaction, where instead an additional critical role may be played by sensorimotor communication (SMC). SMC refers here to (often subtle) communicative signals embedded within pragmatic actions – for example, a soccer player carving his body movements in ways that inform a partner about his intention, or to feint an adversary; or the many ways we offer a glass of wine, rudely or politely. SMC is a natural form of communication that does not require any prior convention or any specific code. It amounts to the continuous and flexible exchange of bodily signals, with or without awareness, to enhance coordination success; and it is versatile, as sensorimotor signals can be embedded within every action. SMC is at the center of recent interest in neuroscience, cognitive psychology, human-robot interaction and experimental semiotics; yet, we still lack a coherent and comprehensive synthesis to account for its multifaceted nature. Some fundamental questions remain open, such as which interactive scenarios promote or not promote SMC, what aspects of social interaction can be properly called communicative and which ones entail a mere transfer of information, and how many forms of SMC exist and what we know (or still don't know) about them from an empirical viewpoint. The present work brings together all these separate strands of research within a unified overarching, multidisciplinary framework for SMC, which combines evidence from kinematic studies of human-human interaction and computational modeling of social exchanges.

  • Does being multi-headed make you better at solving problems? A survey of Physarum-based models and computations
    Phys. Life Rev. (IF 13.783) Pub Date : 2018-05-22
    Chao Gao, Chen Liu, Daniel Schenz, Xuelong Li, Zili Zhang, Marko Jusup, Zhen Wang, Madeleine Beekman, Toshiyuki Nakagaki

    Physarum polycephalum, a single-celled, multinucleate slime mould, is a seemingly simple organism, yet it exhibits quasi-intelligent behaviour during extension, foraging, and as it adapts to dynamic environments. For these reasons, Physarum is an attractive target for modelling with the underlying goal to uncover the physiological mechanisms behind the exhibited quasi-intelligence and/or to devise novel algorithms for solving complex computational problems. The recent increase in modelling studies on Physarum has prompted us to review the latest developments in this field in the context of modelling and computing alike. Specifically, we cover models based on (i) morphology, (ii) taxis, and (iii) positive feedback dynamics found in top-down and bottom-up modelling techniques. We also survey the application of each of these core features of Physarum to solving difficult computational problems with real-world applications. Finally, we highlight some open problems in the field and present directions for future research.

  • Creativity, information, and consciousness: The information dynamics of thinking
    Phys. Life Rev. (IF 13.783) Pub Date : 2018-05-07
    Geraint A. Wiggins

    This paper presents a theory of the basic operation of mind, Information Dynamics of Thinking, which is intended for computational implementation and thence empirical testing. It is based on the information theory of Shannon, and treats the mind/brain as an information processing organ that aims to be information-efficient, in that it predicts its world, so as to use information efficiently, and regularly re-represents it, so as to store information efficiently. The theory is presented in context of a background review of various research areas that impinge upon its development. Consequences of the theory and testable hypotheses arising from it are discussed.

  • Muscleless motor synergies and actions without movements: From motor neuroscience to cognitive robotics
    Phys. Life Rev. (IF 13.783) Pub Date : 2018-04-27
    Vishwanathan Mohan, Ajaz Bhat, Pietro Morasso

    Emerging trends in neurosciences are providing converging evidence that cortical networks in predominantly motor areas are activated in several contexts related to ‘action’ that do not cause any overt movement. Indeed for any complex body, human or embodied robot inhabiting unstructured environments, the dual processes of shaping motor output during action execution and providing the self with information related to feasibility, consequence and understanding of potential actions (of oneself/others) must seamlessly alternate during goal-oriented behaviors, social interactions. While prominent approaches like Optimal Control, Active Inference converge on the role of forward models, they diverge on the underlying computational basis. In this context, revisiting older ideas from motor control like the Equilibrium Point Hypothesis and synergy formation, this article offers an alternative perspective emphasizing the functional role of a ‘plastic, configurable’ internal representation of the body (body-schema) as a critical link enabling the seamless continuum between motor control and imagery. With the central proposition that both “real and imagined” actions are consequences of an internal simulation process achieved though passive goal-oriented animation of the body schema, the computational/neural basis of muscleless motor synergies (and ensuing simulated actions without movements) is explored. The rationale behind this perspective is articulated in the context of several interdisciplinary studies in motor neurosciences (for example, intracranial depth recordings from the parietal cortex, FMRI studies highlighting a shared cortical basis for action ‘execution, imagination and understanding’), animal cognition (in particular, tool-use and neuro-rehabilitation experiments, revealing how coordinated tools are incorporated as an extension to the body schema) and pertinent challenges towards building cognitive robots that can seamlessly “act, interact, anticipate and understand” in unstructured natural living spaces.

  • Rethinking foundations of language from a multidisciplinary perspective
    Phys. Life Rev. (IF 13.783) Pub Date : 2018-04-21
    Tao Gong, Lan Shuai, Yicheng Wu

    The issue of language foundations has been of great controversy ever since it was first raised in Lenneberg's (1967) monograph Biological Foundations of Language. Based on a survey of recent findings relevant to the study of language acquisition and evolution, we propose that: (i) the biological predispositions for language are largely domain-general, not necessarily language-specific or human-unique; (ii) the socio-cultural environment of language serves as another important foundation of language, which helps shape language components, induce and drive language shift; and (iii) language must have coevolved with the cognitive mechanisms associated with it through intertwined biological and cultural evolution. In addition to theoretical issues, this paper also evaluates the primary approaches recently joining the endeavor of studying language foundations and evolution, including human experiments and computer simulations. Most of the evidence surveyed in this paper comes from a variety of disciplines, and methodology therein complements each other to form a global picture of language foundations. These reflect the complexity of the issue of language foundations and the necessity of taking a multidisciplinary perspective to address it.

  • Physics of mind: Experimental confirmations of theoretical predictions
    Phys. Life Rev. (IF 13.783) Pub Date : 2018-04-02
    Félix Schoeller, Leonid Perlovsky, Dmitry Arseniev

    What is common among Newtonian mechanics, statistical physics, thermodynamics, quantum physics, the theory of relativity, astrophysics and the theory of superstrings? All these areas of physics have in common a methodology, which is discussed in the first few lines of the review. Is a physics of the mind possible? Is it possible to describe how a mind adapts in real time to changes in the physical world through a theory based on a few basic laws? From perception and elementary cognition to emotions and abstract ideas allowing high-level cognition and executive functioning, at nearly all levels of study, the mind shows variability and uncertainties. Is it possible to turn psychology and neuroscience into so-called “hard” sciences? This review discusses several established first principles for the description of mind and their mathematical formulations. A mathematical model of mind is derived from these principles. This model includes mechanisms of instincts, emotions, behavior, cognition, concepts, language, intuitions, and imagination. We clarify fundamental notions such as the opposition between the conscious and the unconscious, the knowledge instinct and aesthetic emotions, as well as humans' universal abilities for symbols and meaning. In particular, the review discusses in length evolutionary and cognitive functions of aesthetic emotions and musical emotions. Several theoretical predictions are derived from the model, some of which have been experimentally confirmed. These empirical results are summarized and we introduce new theoretical developments. Several unsolved theoretical problems are proposed, as well as new experimental challenges for future research.

  • Shock wave-induced permeabilization of mammalian cells
    Phys. Life Rev. (IF 13.783) Pub Date : 2018-03-21
    Luz M. López-Marín, Ana Leonor Rivera, Francisco Fernández, Achim M. Loske

    Controlled permeabilization of mammalian cell membranes is fundamental to develop gene and cell therapies based on macromolecular cargo delivery, a process that emerged against an increasing number of health afflictions, including genetic disorders, cancer and infections. Viral vectors have been successfully used for macromolecular delivery; however, they may have unpredictable side effects and have been limited to life-threatening cases. Thus, several chemical and physical methods have been explored to introduce drugs, vaccines, and nucleic acids into cells. One of the most appealing physical methods to deliver genes into cells is shock wave-induced poration. High-speed microjets of fluid, emitted due to the collapse of microbubbles after shock wave passage, represent the most significant mechanism that contributes to cell membrane poration by this technique. Herein, progress in shock wave-induced permeabilization of mammalian cells is presented. After covering the main concepts related to molecular strategies whose applications depend on safer drug delivery methods, the physics behind shock wave phenomena is described. Insights into the use of shock waves for cell membrane permeation are discussed, along with an overview of the two major biomedical applications thereof—i.e., genetic modification and anti-cancer shock wave-assisted chemotherapy. The aim of this review is to summarize 30 years of data showing underwater shock waves as a safe, noninvasive method for macromolecular delivery into mammalian cells, encouraging the development of further research, which is still required before the introduction of this promising tool into clinical practice.

  • Modeling thrombosis in silico: Frontiers, challenges, unresolved problems and milestones
    Phys. Life Rev. (IF 13.783) Pub Date : 2018-03-05
    A.V. Belyaev, J.L. Dunster, J.M. Gibbins, M.A. Panteleev, V. Volpert

    Hemostasis is a complex physiological mechanism that functions to maintain vascular integrity under any conditions. Its primary components are blood platelets and a coagulation network that interact to form the hemostatic plug, a combination of cell aggregate and gelatinous fibrin clot that stops bleeding upon vascular injury. Disorders of hemostasis result in bleeding or thrombosis, and are the major immediate cause of mortality and morbidity in the world. Regulation of hemostasis and thrombosis is immensely complex, as it depends on blood cell adhesion and mechanics, hydrodynamics and mass transport of various species, huge signal transduction networks in platelets, as well as spatiotemporal regulation of the blood coagulation network. Mathematical and computational modeling has been increasingly used to gain insight into this complexity over the last 30 years, but the limitations of the existing models remain profound. Here we review state-of-the-art-methods for computational modeling of thrombosis with the specific focus on the analysis of unresolved challenges. They include: a) fundamental issues related to physics of platelet aggregates and fibrin gels; b) computational challenges and limitations for solution of the models that combine cell adhesion, hydrodynamics and chemistry; c) biological mysteries and unknown parameters of processes; d) biophysical complexities of the spatiotemporal networks' regulation. Both relatively classical approaches and innovative computational techniques for their solution are considered; the subjects discussed with relation to thrombosis modeling include coarse-graining, continuum versus particle-based modeling, multiscale models, hybrid models, parameter estimation and others. Fundamental understanding gained from theoretical models are highlighted and a description of future prospects in the field and the nearest possible aims are given.

  • Seeing mental states: An experimental strategy for measuring the observability of other minds
    Phys. Life Rev. (IF 13.783) Pub Date : 2017-10-06
    Cristina Becchio, Atesh Koul, Caterina Ansuini, Cesare Bertone, Andrea Cavallo

    Is it possible to perceive others' mental states? Are mental states visible in others' behavior? In contrast to the traditional view that mental states are hidden and not directly accessible to perception, in recent years a phenomenologically-motivated account of social cognition has emerged: direct social perception. However, despite numerous published articles that both defend and critique direct perception, researchers have made little progress in articulating the conditions under which direct perception of others' mental states is possible. This paper proposes an empirically anchored approach to the observability of others' mentality – not just in the weak sense of discussing relevant empirical evidence for and against the phenomenon of interest, but also, and more specifically, in the stronger sense of identifying an experimental strategy for measuring the observability of mental states and articulating the conditions under which mental states are observable. We conclude this article by reframing the problem of direct perception in terms of establishing a definable and measurable relationship between movement features and perceived mental states.

  • Answering Schrödinger's question: A free-energy formulation
    Phys. Life Rev. (IF 13.783) Pub Date : 2017-09-20
    Maxwell James Désormeau Ramstead, Paul Benjamin Badcock, Karl John Friston

    The free-energy principle (FEP) is a formal model of neuronal processes that is widely recognised in neuroscience as a unifying theory of the brain and biobehaviour. More recently, however, it has been extended beyond the brain to explain the dynamics of living systems, and their unique capacity to avoid decay. The aim of this review is to synthesise these advances with a meta-theoretical ontology of biological systems called variational neuroethology, which integrates the FEP with Tinbergen's four research questions to explain biological systems across spatial and temporal scales. We exemplify this framework by applying it to Homo sapiens, before translating variational neuroethology into a systematic research heuristic that supplies the biological, cognitive, and social sciences with a computationally tractable guide to discovery.

  • Network science of biological systems at different scales: A review
    Phys. Life Rev. (IF 13.783) Pub Date : 2017-11-03
    Marko Gosak, Rene Markovič, Jurij Dolenšek, Marjan Slak Rupnik, Marko Marhl, Andraž Stožer, Matjaž Perc

    Network science is today established as a backbone for description of structure and function of various physical, chemical, biological, technological, and social systems. Here we review recent advances in the study of complex biological systems that were inspired and enabled by methods of network science. First, we present research highlights ranging from determination of the molecular interaction network within a cell to studies of architectural and functional properties of brain networks and biological transportation networks. Second, we focus on synergies between network science and data analysis, which enable us to determine functional connectivity patterns in multicellular systems. Until now, this intermediate scale of biological organization received the least attention from the network perspective. As an example, we review the methodology for the extraction of functional beta cell networks in pancreatic islets of Langerhans by means of advanced imaging techniques. Third, we concentrate on the emerging field of multilayer networks and review the first endeavors and novel perspectives offered by this framework in exploring biological complexity. We conclude by outlining challenges and directions for future research that encompass utilization of the multilayer network formalism in exploring intercellular communication patterns in tissues, and we advocate for network science being one of the key pillars for assessing physiological function of complex biological systems—from organelles to organs—in health and disease.

  • At the root of the paradox
    Phys. Life Rev. (IF 13.783) Pub Date : 2017-12-28
    Eugen Wassiliwizky

    Eerola et al.'s multi-layered model for the pleasure taken in music-elicited sadness is an important step in integrating explanatory accounts from different disciplines. Here, I would like to point out two theoretical inconsistencies that lie at the very root of the paradox and can have a major impact on future studies: first, the conflation of the transformation hypothesis and the co-activation hypothesis of sadness and pleasure, and second, the conflation of sadness that is elicited by musical instruments and that which is elicited by lyrics.

  • Cellular mechanosensing of the biophysical microenvironment: A review of mathematical models of biophysical regulation of cell responses
    Phys. Life Rev. (IF 13.783) Pub Date : 2017-06-21
    Bo Cheng, Min Lin, Guoyou Huang, Yuhui Li, Baohua Ji, Guy M. Genin, Vikram S. Deshpande, Tian Jian Lu, Feng Xu

    Cells in vivo reside within complex microenvironments composed of both biochemical and biophysical cues. The dynamic feedback between cells and their microenvironments hinges upon biophysical cues that regulate critical cellular behaviors. Understanding this regulation from sensing to reaction to feedback is therefore critical, and a large effort is afoot to identify and mathematically model the fundamental mechanobiological mechanisms underlying this regulation. This review provides a critical perspective on recent progress in mathematical models for the responses of cells to the biophysical cues in their microenvironments, including dynamic strain, osmotic shock, fluid shear stress, mechanical force, matrix rigidity, porosity, and matrix shape. The review highlights key successes and failings of existing models, and discusses future opportunities and challenges in the field.

  • How much free energy is absorbed upon breaking DNA base pairs?: Comment on “DNA melting and energetics of the double helix” by Maxim Frank-Kamenetskii et al.
    Phys. Life Rev. (IF 13.783) Pub Date : 2018-03-07
    John SantaLucia Jr.

    Highlights • Sequence dependence of DNA melting. • Comparison of nearest-neighbor parameters from different laboratories. • Entropic origin of salt dependence of DNA melting.

  • A critical analysis towards research perspectives
    Phys. Life Rev. (IF 13.783) Pub Date : 2017-10-09
    M. Dolfin, L. Leonida, N. Outada

    We take advantage of the challenging comments to the modeling approach we proposed in [35] to look ahead at a number of applications of the methods to the alternative questions these comments raise. In turn, our effort results in a number of interesting and valuable research perspectives. The presentation goes along three main lines. In the first line, we summarize briefly the aims and results in [35]. In the second section we give a technical the issues raised and, finally, the focus moves to the above mentioned research perspectives.

  • Energetics: An emerging frontier in cellular mechanosensing
    Phys. Life Rev. (IF 13.783) Pub Date : 2017-09-29
    Bo Cheng, Min Lin, Guoyou Huang, Yuhui Li, Baohua Ji, Guy M. Genin, Vikram S. Deshpande, Tian Jian Lu, Feng Xu

    How do cells can sense the substrate stiffness? Our recent review highlighted a range of theoretical models and simulations that have been proposed to answer this important question. In response to this review, three leading groups in the field noted some important omissions not only from our review itself but also from the field. These groups noted, correctly, that much of our understanding of cellular mechanosensing arises from models that take advantage of equilibrium thermodynamics, and that this is inappropriate because living cells are never in thermodynamic equilibrium. In this response, we highlight some promising research aimed at resolving this conundrum.

  • An integrative review of the enjoyment of sadness associated with music
    Phys. Life Rev. (IF 13.783) Pub Date : 2017-11-23
    Tuomas Eerola, Jonna K. Vuoskoski, Henna-Riikka Peltola, Vesa Putkinen, Katharina Schäfer

    The recent surge of interest towards the paradoxical pleasure produced by sad music has generated a handful of theories and an array of empirical explorations on the topic. However, none of these have attempted to weigh the existing evidence in a systematic fashion. The present work puts forward an integrative framework laid out over three levels of explanation – biological, psycho-social, and cultural – to compare and integrate the existing findings in a meaningful way. First, we review the evidence pertinent to experiences of pleasure associated with sad music from the fields of neuroscience, psychophysiology, and endocrinology. Then, the psychological and interpersonal mechanisms underlying the recognition and induction of sadness in the context of music are combined with putative explanations ranging from social surrogacy and nostalgia to feelings of being moved. Finally, we address the cultural aspects of the paradox – the extent to which it is embedded in the Western notion of music as an aesthetic, contemplative object – by synthesising findings from history, ethnography, and empirical studies. Furthermore, we complement these explanations by considering the particularly significant meanings that sadness portrayed in art can evoke in some perceivers. Our central claim is that one cannot attribute the enjoyment of sadness fully to any one of these levels, but to a chain of functionalities afforded by each level. Each explanatory level has several putative explanations and its own shift towards positive valence, but none of them deliver the full transformation from a highly negative experience to a fully enjoyable experience alone. The current evidence within this framework ranges from weak to non-existent at the biological level, moderate at the psychological level, and suggestive at the cultural level. We propose a series of focussed topics for future investigation that would allow to deconstruct the drivers and constraints of the processes leading to pleasurable music-related sadness.

  • DNA melting and energetics of the double helix
    Phys. Life Rev. (IF 13.783) Pub Date : 2017-11-14
    Alexander Vologodskii, Maxim D. Frank-Kamenetskii

    Studying melting and energetics of the DNA double helix has been one of the major topics of molecular biophysics over the past six decades. The main objective of this article is to overview the current state of the field and to emphasize that there are still serious gaps in our understanding of the issue. We start with a concise description of the commonly accepted theoretical model of the DNA melting. We then concentrate on studies devoted to the comparison with experiment of theoretically predicted melting profiles of DNAs with known sequences. For long DNA molecules, such comparison is significant from the basic-science viewpoint while an accurate theoretical description of melting of short duplexes is necessary for various very important applications in biotechnology. Several sets of DNA melting parameters, proposed within the framework of the nearest neighbor model, are compared and analyzed. The analysis leads to a conclusion that in case of long DNA molecules the consensus set of nearest neighbor parameters describes well the experimental melting profiles. Unexpectedly, for short DNA duplexes the same set of parameters hardly yields any improvement as compared to the simplest model, which completely ignores the effect of heterogeneous stacking. Possible causes of this striking observation are discussed. We then overview the issue of separation of base-pairing and base-stacking contributions into the double helix stability. The recent experimental attempts to solve the problem are extensively analyzed. It is concluded that the double helix is essentially stabilized by stacking interaction between adjacent base pairs. Base pairing between complementary pairs does not appreciably contribute into the duplex stability. In the final section of the article, kinetic aspects of the DNA melting phenomenon are discussed. The main emphasis is made on the hysteresis effects often observed in melting of long DNA molecules. It is argued that the phenomenon can be well described via an accurate theoretical treatment of the random-walk model of melting kinetics of an isolated helical segment in DNA.

  • Modeling human behavior in economics and social science
    Phys. Life Rev. (IF 13.783) Pub Date : 2017-06-29
    M. Dolfin, L. Leonida, N. Outada

    The complex interactions between human behaviors and social economic sciences is critically analyzed in this paper in view of possible applications of mathematical modeling as an attainable interdisciplinary approach to understand and simulate the aforementioned dynamics. The quest is developed along three steps: Firstly an overall analysis of social and economic sciences indicates the main requirements that a contribution of mathematical modeling should bring to these sciences; subsequently the focus moves to an overview of mathematical tools and to the selection of those which appear, according to the authors bias, appropriate to the modeling; finally, a survey of applications is presented looking ahead to research perspectives.

  • Ligand diffusion in proteins via enhanced sampling in molecular dynamics
    Phys. Life Rev. (IF 13.783) Pub Date : 2017-04-01
    J. Rydzewski, W. Nowak

    Computational simulations in biophysics describe the dynamics and functions of biological macromolecules at the atomic level. Among motions particularly important for life are the transport processes in heterogeneous media. The process of ligand diffusion inside proteins is an example of a complex rare event that can be modeled using molecular dynamics simulations. The study of physical interactions between a ligand and its biological target is of paramount importance for the design of novel drugs and enzymes. Unfortunately, the process of ligand diffusion is difficult to study experimentally. The need for identifying the ligand egress pathways and understanding how ligands migrate through protein tunnels has spurred the development of several methodological approaches to this problem. The complex topology of protein channels and the transient nature of the ligand passage pose difficulties in the modeling of the ligand entry/escape pathways by canonical molecular dynamics simulations. In this review, we report a methodology involving a reconstruction of the ligand diffusion reaction coordinates and the free-energy profiles along these reaction coordinates using enhanced sampling of conformational space. We illustrate the above methods on several ligand–protein systems, including cytochromes and G-protein-coupled receptors. The methods are general and may be adopted to other transport processes in living matter.

  • Topodynamics of metastable brains
    Phys. Life Rev. (IF 13.783) Pub Date : 2017-03-23
    Arturo Tozzi, James F. Peters, Andrew A. Fingelkurts, Alexander A. Fingelkurts, Pedro C. Marijuán

    The brain displays both the anatomical features of a vast amount of interconnected topological mappings as well as the functional features of a nonlinear, metastable system at the edge of chaos, equipped with a phase space where mental random walks tend towards lower energetic basins. Nevertheless, with the exception of some advanced neuro-anatomic descriptions and present-day connectomic research, very few studies have been addressing the topological path of a brain embedded or embodied in its external and internal environment. Herein, by using new formal tools derived from algebraic topology, we provide an account of the metastable brain, based on the neuro-scientific model of Operational Architectonics of brain–mind functioning. We introduce a “topodynamic” description that shows how the relationships among the countless intertwined spatio-temporal levels of brain functioning can be assessed in terms of projections and mappings that take place on abstract structures, equipped with different dimensions, curvatures and energetic constraints. Such a topodynamical approach, apart from providing a biologically plausible model of brain function that can be operationalized, is also able to tackle the issue of a long-standing dichotomy: it throws indeed a bridge between the subjective, immediate datum of the naïve complex of sensations and mentations and the objective, quantitative, data extracted from experimental neuro-scientific procedures. Importantly, it opens the door to a series of new predictions and future directions of advancement for neuroscientific research.

  • There and back again: Two views on the protein folding puzzle
    Phys. Life Rev. (IF 13.783) Pub Date : 2017-01-27
    Alexei V. Finkelstein, Azat J. Badretdin, Oxana V. Galzitskaya, Dmitry N. Ivankov, Natalya S. Bogatyreva, Sergiy O. Garbuzynskiy

    The ability of protein chains to spontaneously form their spatial structures is a long-standing puzzle in molecular biology. Experimentally measured folding times of single-domain globular proteins range from microseconds to hours: the difference (10–11 orders of magnitude) is the same as that between the life span of a mosquito and the age of the universe. This review describes physical theories of rates of overcoming the free-energy barrier separating the natively folded (N) and unfolded (U) states of protein chains in both directions: “U-to-N” and “N-to-U”. In the theory of protein folding rates a special role is played by the point of thermodynamic (and kinetic) equilibrium between the native and unfolded state of the chain; here, the theory obtains the simplest form. Paradoxically, a theoretical estimate of the folding time is easier to get from consideration of protein unfolding (the “N-to-U” transition) rather than folding, because it is easier to outline a good unfolding pathway of any structure than a good folding pathway that leads to the stable fold, which is yet unknown to the folding protein chain. And since the rates of direct and reverse reactions are equal at the equilibrium point (as follows from the physical “detailed balance” principle), the estimated folding time can be derived from the estimated unfolding time. Theoretical analysis of the “N-to-U” transition outlines the range of protein folding rates in a good agreement with experiment. Theoretical analysis of folding (the “U-to-N” transition), performed at the level of formation and assembly of protein secondary structures, outlines the upper limit of protein folding times (i.e., of the time of search for the most stable fold). Both theories come to essentially the same results; this is not a surprise, because they describe overcoming one and the same free-energy barrier, although the way to the top of this barrier from the side of the unfolded state is very different from the way from the side of the native state; and both theories agree with experiment. In addition, they predict the maximal size of protein domains that fold under solely thermodynamic (rather than kinetic) control and explain the observed maximal size of the “foldable” protein domains.

  • Move me, astonish me… delight my eyes and brain: The Vienna Integrated Model of top-down and bottom-up processes in Art Perception (VIMAP) and corresponding affective, evaluative, and neurophysiological correlates
    Phys. Life Rev. (IF 13.783) Pub Date : 2017-02-27
    Matthew Pelowski, Patrick S. Markey, Michael Forster, Gernot Gerger, Helmut Leder

    This paper has a rather audacious purpose: to present a comprehensive theory explaining, and further providing hypotheses for the empirical study of, the multiple ways by which people respond to art. Despite common agreement that interaction with art can be based on a compelling, and occasionally profound, psychological experience, the nature of these interactions is still under debate. We propose a model, The Vienna Integrated Model of Art Perception (VIMAP), with the goal of resolving the multifarious processes that can occur when we perceive and interact with visual art. Specifically, we focus on the need to integrate bottom-up, artwork-derived processes, which have formed the bulk of previous theoretical and empirical assessments, with top-down mechanisms which can describe how individuals adapt or change within their processing experience, and thus how individuals may come to particularly moving, disturbing, transformative, as well as mundane, results. This is achieved by combining several recent lines of theoretical research into a new integrated approach built around three processing checks, which we argue can be used to systematically delineate the possible outcomes in art experience. We also connect our model's processing stages to specific hypotheses for emotional, evaluative, and physiological factors, and address main topics in psychological aesthetics including provocative reactions—chills, awe, thrills, sublime—and difference between “aesthetic” and “everyday” emotional response. Finally, we take the needed step of connecting stages to functional regions in the brain, as well as broader core networks that may coincide with the proposed cognitive checks, and which taken together can serve as a basis for future empirical and theoretical art research.

  • Dependency distance: A new perspective on syntactic patterns in natural languages
    Phys. Life Rev. (IF 13.783) Pub Date : 2017-03-27
    Haitao Liu, Chunshan Xu, Junying Liang

    Dependency distance, measured by the linear distance between two syntactically related words in a sentence, is generally held as an important index of memory burden and an indicator of syntactic difficulty. Since this constraint of memory is common for all human beings, there may well be a universal preference for dependency distance minimization (DDM) for the sake of reducing memory burden. This human-driven language universal is supported by big data analyses of various corpora that consistently report shorter overall dependency distance in natural languages than in artificial random languages and long-tailed distributions featuring a majority of short dependencies and a minority of long ones. Human languages, as complex systems, seem to have evolved to come up with diverse syntactic patterns under the universal pressure for dependency distance minimization. However, there always exist a small number of long-distance dependencies in natural languages, which may reflect some other biological or functional constraints. Language system may adapt itself to these sporadic long-distance dependencies. It is these universal constraints that have shaped such a rich diversity of syntactic patterns in human languages.

  • Generalizing dependency distance: Comment on “Dependency distance: A new perspective on syntactic patterns in natural languages” by Haitao Liu et al.
    Phys. Life Rev. (IF 13.783) Pub Date : 2017-06-23
    Richard Futrell, Roger Levy, Edward Gibson

    With the support of the comprehensive review in Liu et al. [14], we consider dependency distance minimization to be firmly established as a quantitative property of syntactic trees. In this comment, we consider future empirical and theoretical directions for this concept, including a recent information-theoretic reinterpretation of dependency locality effects as proposed by Futrell and Levy [4].

Some contents have been Reproduced with permission of the American Chemical Society.
Some contents have been Reproduced by permission of The Royal Society of Chemistry.
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