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Dynamic systems theory

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https://www.readbyqxmd.com/read/29043353/machine-learnt-bond-order-potential-to-model-metal-organic-co-c-heterostructures
#1
Badri Narayanan, Henry Chan, Alper Kinaci, Fatih G Sen, Stephen K Gray, Maria K Y Chan, Subramanian K R S Sankaranarayanan
A fundamental understanding of the inter-relationships between structure, morphology, atomic scale dynamics, chemistry, and physical properties of mixed metallic-covalent systems is essential to design novel functional materials for applications in flexible nano-electronics, energy storage and catalysis. To achieve such knowledge, it is imperative to develop robust and computationally efficient atomistic models that describe atomic interactions accurately within a single framework. Here, we present a unified Tersoff-Brenner type bond order potential (BOP) for a Co-C system, trained against lattice parameters, cohesive energies, equation of state, and elastic constants of different crystalline phases of cobalt as well as orthorhombic Co2C derived from density functional theory (DFT) calculations...
October 18, 2017: Nanoscale
https://www.readbyqxmd.com/read/29042301/towards-a-first-implementation-of-the-wlimes-approach-in-living-system-studies-advancing-the-diagnostics-and-therapy-in-personalized-medicine
#2
Plamen L Simeonov, Andrée C Ehresmann
The goal of this paper is to advance an extensible theory of living systems using an approach to biomathematics and biocomputation that suitably addresses self-organized, self-referential and anticipatory systems with multi-temporal multi-agents. Our first step is to provide foundations for modelling of emergent and evolving dynamic multi-level organic complexes and their sustentative processes in artificial and natural life systems. Main applications are in life sciences, medicine, ecology and astrobiology, as well as robotics, industrial automation, man-machine interface and creative design...
October 14, 2017: Bio Systems
https://www.readbyqxmd.com/read/29040327/epizootic-to-enzootic-transition-of-a-fungal-disease-in-tropical-andean-frogs-are-surviving-species-still-susceptible
#3
Alessandro Catenazzi, Andrea Swei, Jacob Finkle, Emily Foreyt, Lauren Wyman, Vance T Vredenburg
The fungal pathogen Batrachochytrium dendrobatidis (Bd), which causes the disease chytridiomycosis, has been linked to catastrophic amphibian declines throughout the world. Amphibians differ in their vulnerability to chytridiomycosis; some species experience epizootics followed by collapse while others exhibit stable host/pathogen dynamics where most amphibian hosts survive in the presence of Bd (e.g., in the enzootic state). Little is known about the factors that drive the transition between the two disease states within a community, or whether populations of species that survived the initial epizootic are stable, yet this information is essential for conservation and theory...
2017: PloS One
https://www.readbyqxmd.com/read/29038487/the-microbiome-beyond-the-horizon-of-ecological-and-evolutionary-theory
#4
REVIEW
Britt Koskella, Lindsay J Hall, C Jessica E Metcalf
The ecological and evolutionary study of community formation, diversity, and stability is rooted in general theory and reinforced by decades of system-specific empirical work. Deploying these ideas to study the assembly, complexity, and dynamics of microbial communities living in and on eukaryotes has proved seductive, but challenging. The success of this research endeavour depends on our capacity to observe and characterize the distributions, abundances, and functional traits of microbiota, representing an array of technical and analytical challenges...
October 16, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/29037042/structural-monitoring-of-the-onset-of-excited-state-aromaticity-in-a-liquid-crystal-phase
#5
Masaki Hada, Shohei Saito, Sei'ichi Tanaka, Ryuma Sato, Masahiko Yoshimura, Kazuhiro Mouri, Kyohei Matsuo, Shigehiro Yamaguchi, Mitsuo Hara, Yasuhiko Hayashi, Fynn Roehricht, Rainer Herges, Yasuteru Shigeta, Ken Onda, R J Dwayne Miller
Aromaticity of photoexcited molecules is an important concept in organic chemistry. Its theory, Baird's rule for triplet aromaticity since 1972, gives the rationale of photoinduced conformational changes and photochemical reactivities of cyclic π-conjugated systems. However, it is still challenging to monitor the dynamic structural change induced by the ex-cited-state aromaticity, particularly in condensed materials. Here we report direct structural observation of a molecular motion and a subsequent packing deformation accompanied by the excited-state aromaticity...
October 16, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29035765/a-force-based-mechanistic-model-for-describing-activated-sludge-settling-process
#6
Guihua Xu, Fengjun Yin, Yuanjian Xu, Han-Qing Yu
Sludge settling as the last step in the biological wastewater treatment process substantially affects the system performance, and thus the design and control optimization of the sludge settling process has been frequently investigated with mathematical modeling tools. So far, these models are developed on the basis of the solid flux theory with numerous parameters and complicated boundary conditions, and their prediction results are often unsatisfactory. In this work, a new force-based mechanical model with five parameters was developed, in which five forces were adopted and Newton's law, rather than the flux theory, was used to describe the sludge settling process...
October 10, 2017: Water Research
https://www.readbyqxmd.com/read/29035237/robust-adaptive-fuzzy-control-of-a-class-of-uncertain-nonlinear-systems-with-unstable-dynamics-and-mismatched-disturbances
#7
Ding Zhai, Liwei An, Jiuxiang Dong, Qingling Zhang
This paper studies the robust stabilization problem for a class of uncertain nonlinear systems with unstable zero dynamics. The considered zero dynamic is not assumed to be input-to-state practically stable and contains nonlinear uncertainties and mismatched external disturbances. A new robust adaptive fuzzy control method is developed by combining H∞ theory with backstepping technique. First, an ideal C¹ virtual control function is designed, which can guarantee the zero dynamic asymptotically stable with a suboptimal H∞ performance...
October 16, 2017: IEEE Transactions on Cybernetics
https://www.readbyqxmd.com/read/29034937/hybrid-particle-continuum-simulations-coupling-brownian-dynamics-and-local-dynamic-density-functional-theory
#8
Shuanhu Qi, Friederike Schmid
We present a multiscale hybrid particle-field scheme for the simulation of relaxation and diffusion behavior of soft condensed matter systems. It combines particle-based Brownian dynamics and field-based local dynamics in an adaptive sense such that particles can switch their level of resolution on the fly. The switching of resolution is controlled by a tuning function which can be chosen at will according to the geometry of the system. As an application, the hybrid scheme is used to study the kinetics of interfacial broadening of a polymer blend, and is validated by comparing the results to the predictions from pure Brownian dynamics and pure local dynamics calculations...
October 16, 2017: Soft Matter
https://www.readbyqxmd.com/read/29034353/the-default-mode-network-in-autism
#9
Aarthi Padmanabhan, Charles J Lynch, Marie Schaer, Vinod Menon
Autism spectrum disorder (ASD) is characterized by deficits in social communication and interaction. Since its discovery as a major functional brain system, the default mode network (DMN) has been implicated in a number of psychiatric disorders, including ASD. Here we review converging multimodal evidence for DMN dysfunction in the context of specific components of social cognitive dysfunction in ASD: 'self-referential processing' - the ability to process social information relative to oneself and 'theory of mind' or 'mentalizing' - the ability to infer the mental states such as beliefs, intentions, and emotions of others...
September 2017: Biological Psychiatry: Cognitive Neuroscience and Neuroimaging
https://www.readbyqxmd.com/read/29033780/evolutionary-musicology-meets-embodied-cognition-biocultural-coevolution-and-the-enactive-origins-of-human-musicality
#10
REVIEW
Dylan van der Schyff, Andrea Schiavio
Despite evolutionary musicology's interdisciplinary nature, and the diverse methods it employs, the field has nevertheless tended to divide into two main positions. Some argue that music should be understood as a naturally selected adaptation, while others claim that music is a product of culture with little or no relevance for the survival of the species. We review these arguments, suggesting that while interesting and well-reasoned positions have been offered on both sides of the debate, the nature-or-culture (or adaptation vs...
2017: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/29031703/comparative-approximations-of-criticality-in-a-neural-and-quantum-regime
#11
REVIEW
Jesse Sterling Bettinger
Under a variety of conditions, non-linear systems with many degrees of freedom tend to evolve towards complexity and criticality. Over the last few decades, a steady proliferation of models re: nonlinear and far-from-equilibrium thermodynamics of metastable, many-valued systems arose, serving as attributes of a 'critical' attractor landscape. Building off recent data citing trademark aspects of criticality in the brain-including: power-laws, scale-free (1/f) behavior (scale invariance, or scale independence, critical slowing, and avalanches-it has been conjectured that operating at criticality entails functional advantages such as: optimized neural computation and information processing; memory; large dynamical ranges; long-range communication; and "enhanced ability to react to highly diverse stimuli...
October 11, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/29031276/isotopic-effects-in-vibrational-relaxation-dynamics-of-h-on-a-si-100-surface
#12
F Bouakline, U Lorenz, G Melani, G K Paramonov, P Saalfrank
In a recent paper [U. Lorenz and P. Saalfrank, Chem. Phys. 482, 69 (2017)], we proposed a robust scheme to set up a system-bath model Hamiltonian, describing the coupling of adsorbate vibrations (system) to surface phonons (bath), from first principles. The method is based on an embedded cluster approach, using orthogonal coordinates for system and bath modes, and an anharmonic phononic expansion of the system-bath interaction up to second order. In this contribution, we use this model Hamiltonian to calculate vibrational relaxation rates of H-Si and D-Si bending modes, coupled to a fully H(D)-covered Si(100)-(2×1) surface, at zero temperature...
October 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29029962/answering-schr%C3%A3-dinger-s-question-a-free-energy-formulation
#13
REVIEW
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...
September 20, 2017: Physics of Life Reviews
https://www.readbyqxmd.com/read/29029075/improving-health-systems-performance-in-low-and-middle-income-countries-a-system-dynamics-model-of-the-pay-for-performance-initiative-in-afghanistan
#14
O Alonge, S Lin, T Igusa, D H Peters
System dynamics methods were used to explore effective implementation pathways for improving health systems performance through pay-for-performance (P4P) schemes. A causal loop diagram was developed to delineate primary causal relationships for service delivery within primary health facilities. A quantitative stock-and-flow model was developed next. The stock-and-flow model was then used to simulate the impact of various P4P implementation scenarios on quality and volume of services. Data from the Afghanistan national facility survey in 2012 was used to calibrate the model...
September 23, 2017: Health Policy and Planning
https://www.readbyqxmd.com/read/29028542/spectral-diffusion-and-dynamic-nuclear-polarization-beyond-the-high-temperature-approximation
#15
W Th Wenckebach
Dynamic Nuclear Polarization (DNP) has proven itself most powerful for the orientation of nuclear spins in polarized targets and for hyperpolarization in magnetic resonance imaging (MRI). Unfortunately, the theoretical description of some of the processes involved in DNP invokes the high temperature approximation, in which Boltzmann factors are expanded up to first order, while the high electron and nuclear spin polarization required for many applications do not justify such an approximation. A previous article extended the description of one of the mechanisms of DNP-thermal mixing-beyond the high temperature approximation (Wenckebach, 2017)...
October 4, 2017: Journal of Magnetic Resonance
https://www.readbyqxmd.com/read/29023087/simulations-of-graphene-nanoflake-as-a-nanovector-to-improve-znpc-phototherapy-toxicity-from-vacuum-to-cell-membrane
#16
Eric Duverger, Fabien Picaud, Louise Stauffer, Philippe Sonnet
We propose a new approach to improve photodynamic therapy by transporting Zn-Phthalocyanine (ZnPc) in biological systems via a graphene nanoflake, to increase its targeting. Indeed, by means of time dependent density functional theory simulations, we show that the ZnPc molecule in interaction with a graphene nanoflake preserves its optical properties not only in the vacuum but also in the water. Moreover, molecular dynamic simulations demonstrate that the graphene nanoflake-ZnPc association, as a carrier, permits to stabilize the ZnPc/graphene nanoflake system on the cellular membrane, which was not possible when using ZnPc alone...
October 12, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29022403/developmental-approach-for-behavior-learning-using-primitive-motion-skills
#17
Farhan Dawood, Chu Kiong Loo
Imitation learning through self-exploration is essential in developing sensorimotor skills. Most developmental theories emphasize that social interactions, especially understanding of observed actions, could be first achieved through imitation, yet the discussion on the origin of primitive imitative abilities is often neglected, referring instead to the possibility of its innateness. This paper presents a developmental model of imitation learning based on the hypothesis that humanoid robot acquires imitative abilities as induced by sensorimotor associative learning through self-exploration...
August 6, 2017: International Journal of Neural Systems
https://www.readbyqxmd.com/read/29021555/bypassing-the-kohn-sham-equations-with-machine-learning
#18
Felix Brockherde, Leslie Vogt, Li Li, Mark E Tuckerman, Kieron Burke, Klaus-Robert Müller
Last year, at least 30,000 scientific papers used the Kohn-Sham scheme of density functional theory to solve electronic structure problems in a wide variety of scientific fields. Machine learning holds the promise of learning the energy functional via examples, bypassing the need to solve the Kohn-Sham equations. This should yield substantial savings in computer time, allowing larger systems and/or longer time-scales to be tackled, but attempts to machine-learn this functional have been limited by the need to find its derivative...
October 11, 2017: Nature Communications
https://www.readbyqxmd.com/read/29020767/confinement-of-iodine-molecules-into-triple-helical-chains-within-robust-metal-organic-frameworks
#19
Xinran Zhang, Ivan da Silva, Harry G W Godfrey, Samantha K Callear, Sergey A Sapchenko, Yongqiang Cheng, Inigo J Vitorica-Yrezabal, Mark D Frogley, Gianfelice Cinque, Chiu C Tang, Carlotta Giacobbe, Catherine Dejoie, Svemir Rudic, Anibal J Ramirez-Cuesta, Melissa A Denecke, Sihai Yang, Martin Schröder
During the nuclear waste disposal process, radioactive iodine in fission product can be released. The widespread implementation of sustainable nuclear energy thus requires the development of efficient iodine stores that have simultaneously high capacity, stability and more importantly, storage density (and hence minimised system volume). Here, we report high I2 adsorption in a series of robust porous metal-organic materials, MFM-300(M) (M = Al, Sc, Fe, In). MFM-300(Sc) exhibits fully reversible I2 uptake of 1...
October 11, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29019282/negotiating-gender-norms-to-support-men-in-psychological-distress
#20
Aisling Keohane, Noel Richardson
Underpinning a general pattern of higher suicide rates in men is the assumption that men do not ask for help or utilize the health-care system during times of psychological distress. There has been a failure to grapple with the dynamic of when, how and from whom men might ask for help during times of psychological distress, and what key barriers or enabling factors are likely to influence potential help-givers' capacity or willingness to offer help to men in psychological distress. The aim of this study was to investigate how masculine norms impact men's help-seeking as well as care givers' behaviors and willingness to support men in need of psychological help or perceived to be at risk of suicide...
October 1, 2017: American Journal of Men's Health
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