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Dynamic systems theory

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https://www.readbyqxmd.com/read/28548893/dynamic-decision-making-learning-processes-and-new-research-directions
#1
Cleotilde Gonzalez, Pegah Fakhari, Jerome Busemeyer
OBJECTIVE: The aim of this manuscript is to provide a review of contemporary research and applications on dynamic decision making (DDM). BACKGROUND: Since early DDM studies, there has been little systematic progress in understanding decision making in complex, dynamic systems. Our review contributes to better understanding of decision making processes in dynamic tasks. METHOD: We discuss new research directions in DDM to highlight the value of simplification in the study of complex decision processes, divided into experimental and theoretical/computational approaches, and focus on problems involving control tasks and search-and-choice tasks...
May 1, 2017: Human Factors
https://www.readbyqxmd.com/read/28548847/simulating-the-electronic-circular-dichroism-spectra-of-photo-reversible-peptide-conformations
#2
Hugo Gattuso, Cristina García-Iriepa, Diego Sampedro, Antonio Monari, Marco Marazzi
Electronic circular dichroism (CD) spectroscopy of peptides is one of the most important experimental char-acterization tools to get insights regarding their structure. Nevertheless, even though highly useful, the reliable simulations of CD spectra result in a complex task. Here, we propose a combination of quantum mechanics/molecular mechanics (QM/MM) methods with a semi-empirical Hamiltonian based on the Frankel excitons theory to efficiently describe the behavior of a 27-amino acid α-helical peptide in water...
May 26, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28548537/dispersive-time-delay-dynamical-systems
#3
Alexander Pimenov, Svetlana Slepneva, Guillaume Huyet, Andrei G Vladimirov
We present a theoretical approach to investigate the effect of dispersion in dynamical systems commonly described by time-delay models. The introduction of a polarization equation provides a means to introduce dispersion as a distributed delay term. The expansion of this term in power series, as usually performed to study the propagation of waves in spatially extended systems, can lead to the appearance of spurious instabilities. This approach is illustrated using a long cavity laser, where in the normal dispersion regime both the experiment and theory show a stable operation, while a modulation instability, commonly referred as the Benjamin-Feir instability, is observed in the anomalous dispersion regime...
May 12, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28542901/mechanisms-and-implications-of-a-type-iv-functional-response-for-short-term-intake-rate-of-dry-matter-in-large-mammalian-herbivores
#4
J C Mezzalira, O J F Bonnet, P C de F Carvalho, L Fonseca, C Bremm, C C Mezzalira, E A Laca
1.The functional response (i.e. the relationship between consumers' intake rate and resource density) is central in plant-herbivore interactions. Its shape and the biological processes leading to it have significant implications for both foraging theory and ecology of grazing systems. 2.A type IV functional response (i.e. dome-shaped relationship) of short-term intake rate of dry matter (intake while grazing) has rarely been reported for large herbivores and the conditions that can lead to it are poorly understood...
May 19, 2017: Journal of Animal Ecology
https://www.readbyqxmd.com/read/28542896/diverse-responses-of-species-to-landscape-fragmentation-in-a-simple-food-chain
#5
Jinbao Liao, Daniel Bearup, Bernd Blasius
1.Habitat destruction, characterized by habitat loss and fragmentation, is a key driver of species extinction in spatial extended communities. Recently, there has been some progress in the theory of spatial food webs, however to date practically little is known about how habitat configurational fragmentation influences multi-trophic food web dynamics. 2.To explore how habitat fragmentation affects species persistence in food webs, we introduce a modelling framework that describes the site occupancy of species in a tri-trophic system...
May 24, 2017: Journal of Animal Ecology
https://www.readbyqxmd.com/read/28542167/corticosterone-oscillations-during-mania-induction-in-the-lateral-hypothalamic-kindled-rat-experimental-observations-and-mathematical-modeling
#6
Osama A Abulseoud, Man Choi Ho, Doo-Sup Choi, Ana Stanojević, Željko Čupić, Ljiljana Kolar-Anić, Vladana Vukojević
Changes in the hypothalamic-pituitary-adrenal (HPA) axis activity constitute a key component of bipolar mania, but the extent and nature of these alterations are not fully understood. We use here the lateral hypothalamic-kindled (LHK) rat model to deliberately induce an acute manic-like episode and measure serum corticosterone concentrations to assess changes in HPA axis activity. A mathematical model is developed to succinctly describe the entwined biochemical transformations that underlay the HPA axis and emulate by numerical simulations the considerable increase in serum corticosterone concentration induced by LHK...
2017: PloS One
https://www.readbyqxmd.com/read/28537945/making-sense-of-effective-partnerships-among-senior-leaders-in-the-national-health-service
#7
Mahima Mitra, Timothy Hoff, Paul Brankin, Sue Dopson
BACKGROUND: Changing health care systems depend on strong organizational leadership that realizes the collaborative potential of both physician and nonphysician leaders. PURPOSE: The aim of this study was to seek insight into the everyday health care leader experience by examining 24 physician and nonphysician leaders working in the U.K. National Health Service. We explored (a) how they make sense of and act with respect to specific collaborative tensions in their interactions and (b) which aspects of their everyday leadership contexts heighten the probability for producing and resolving such tensions...
May 22, 2017: Health Care Management Review
https://www.readbyqxmd.com/read/28537607/colloid-oil-water-interface-interactions-in-the-presence-of-multiple-salts-charge-regulation-and-dynamics
#8
J C Everts, S Samin, N A Elbers, J E S van der Hoeven, A van Blaaderen, R van Roij
We theoretically and experimentally investigate colloid-oil-water-interface interactions of charged, sterically stabilized, poly(methyl-methacrylate) colloidal particles dispersed in a low-polar oil (dielectric constant ε = 5-10) that is in contact with an adjacent water phase. In this model system, the colloidal particles cannot penetrate the oil-water interface due to repulsive van der Waals forces with the interface whereas the multiple salts that are dissolved in the oil are free to partition into the water phase...
May 24, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28536441/fractional-transport-of-photons-in-deterministic-aperiodic-structures
#9
Luca Dal Negro, Sandeep Inampudi
The propagation of optical pulses through primary types of deterministic aperiodic structures is numerically studied in time domain using the rigorous transfer matrix method in combination with analytical fractional transport models. We demonstrate tunable anomalous photon transport, including the elusive logarithmic Sinai sub-diffusion in photonic systems for the first time. Our results are in excellent agreement with the scaling theory of transport in aperiodic media with fractal spectra, and additionally demonstrate logarithmic sub-diffusion in the presence of multifractality...
May 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28535343/tuning-adsorption-duration-to-control-the-diffusion-of-a-nanoparticle-in-adsorbing-polymers
#10
Xuezheng Cao, Holger Merlitz, Chen-Xu Wu
Controlling the nanoparticle (NP) diffusion in polymers is a prerequisite to obtain polymer nanocomposites (PNCs) with desired dynamical and rheological properties, and to achieve targeted delivery of nanomedicine in biological systems. Here we determinate the suppression mechanism of direct NP-polymer attraction to hamper the NP mobility in adsorbing polymers, and then quantify the dependence of the effective viscosity \eta_{eff} felt by the NP on the adsorption duration \tau_{ads} of polymers on the NP, using scaling theory analysis and molecular dynamics (MD) simulations...
May 23, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28535148/stochastic-gene-expression-conditioned-on-large-deviations
#11
Jordan M Horowitz, Rahul V Kulkarni
The intrinsic stochasticity of gene expression can give rise to large fluctuations and rare events that drive phenotypic variation in a population of genetically identical cells. Characterizing the fluctuations that give rise to such rare events motivates the analysis of large deviations in stochastic models of gene expression. Recent developments in non-equilibrium statistical mechanics have led to a framework for analyzing Markovian processes conditioned on rare events and for representing such processes by conditioning-free driven Markovian processes...
May 23, 2017: Physical Biology
https://www.readbyqxmd.com/read/28534622/solute-partitioning-in-micelles-combining-molecular-dynamics-simulations-cosmomic-and-experiments
#12
Denitsa Yordanova, Eric Ritter, Thomas Gerlach, Jan-Hendrik Jensen, Irina Smirnova, Sven Jakobtorweihen
The partition equilibria of solutes between micelles and an aqueous phase is a key factor in many applications. Depending on the task, many micelle-solute combinations are possible. Therefore, theoretical methods to predict the partition behavior in micellar systems are needed. Here, two predictive methods are evaluated and compared. First, it is shown how molecular dynamics simulations (MD) with the umbrella sampling method can be used to calculate free energy profiles in micellar systems. The second applied method is an extension of the COSMO-RS theory to anisotropic systems termed COSMOmic...
May 23, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28531219/pyldm-an-open-source-package-for-lifetime-density-analysis-of-time-resolved-spectroscopic-data
#13
Gabriel F Dorlhiac, Clyde Fare, Jasper J van Thor
Ultrafast spectroscopy offers temporal resolution for probing processes in the femto- and picosecond regimes. This has allowed for investigation of energy and charge transfer in numerous photoactive compounds and complexes. However, analysis of the resultant data can be complicated, particularly in more complex biological systems, such as photosystems. Historically, the dual approach of global analysis and target modelling has been used to elucidate kinetic descriptions of the system, and the identity of transient species respectively...
May 22, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28530269/a-critical-comparison-of-coarse-grained-structure-based-approaches-and-atomic-models-of-protein-folding
#14
Jie Hu, Tao Chen, Moye Wang, Hue Sun Chan, Zhuqing Zhang
Structure-based coarse-grained Gō-like models have been used extensively in deciphering protein folding mechanisms because of their simplicity and tractability. Meanwhile, explicit-solvent molecular dynamics (MD) simulations with physics-based all-atom force fields have been applied successfully to simulate folding/unfolding transitions for several small, fast-folding proteins. To explore the degree to which coarse-grained Gō-like models and their extensions to incorporate nonnative interactions are capable of producing folding processes similar to those in all-atom MD simulations, here we systematically compare the computed unfolded states, transition states, and transition paths obtained using coarse-grained models and all-atom explicit-solvent MD simulations...
May 22, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28530167/biofilm-community-succession-a-neutral-perspective
#15
Stephen Woodcock, William T Sloan
Although biofilms represent one of the dominant forms of life in aqueous environments, our understanding of the assembly and development of their microbial communities remains relatively poor. In recent years, several studies have addressed this and have extended the concepts of succession theory in classical ecology into microbial systems. From these datasets, niche-based conceptual models have been developed explaining observed biodiversity patterns and their dynamics. These models have not, however, been formulated mathematically and so remain untested...
May 22, 2017: Microbiology
https://www.readbyqxmd.com/read/28529962/picosecond-sulfur-k-edge-x-ray-absorption-spectroscopy-with-applications-to-excited-state-proton-transfer
#16
Benjamin E Van Kuiken, Matthew R Ross, Matthew L Strader, Amy A Cordones, Hana Cho, Jae Hyuk Lee, Robert W Schoenlein, Munira Khalil
Picosecond X-ray absorption (XA) spectroscopy at the S K-edge (∼2.4 keV) is demonstrated and used to monitor excited state dynamics in a small organosulfur molecule (2-Thiopyridone, 2TP) following optical excitation. Multiple studies have reported that the thione (2TP) is converted into the thiol (2-Mercaptopyridine, 2MP) following photoexcitation. However, the timescale and photochemical pathway of this reaction remain uncertain. In this work, time-resolved XA spectroscopy at the S K-edge is used to monitor the formation and decay of two transient species following 400 nm excitation of 2TP dissolved in acetonitrile...
July 2017: Structural Dynamics (Melville, N.Y.)
https://www.readbyqxmd.com/read/28528256/evaluation-of-artificial-time-series-microarray-data-for-dynamic-gene-regulatory-network-inference
#17
P Xenitidis, I Seimenis, S Kakolyris, A Adamopoulos
High-throughput technology like microarrays is widely used in the inference of gene regulatory networks (GRNs). We focused on time series data since we are interested in the dynamics of GRNs and the identification of dynamic networks. We evaluated the amount of information that exists in artificial time series microarray data and the ability of an inference process to produce accurate models based on them. We used dynamic artificial gene regulatory networks in order to create artificial microarray data. Key features that characterize microarray data such as the time separation of directly triggered genes, the percentage of directly triggered genes and the triggering function type were altered in order to reveal the limits that are imposed by the nature of microarray data on the inference process...
May 17, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28528255/molecular-structure-second-and-third-order-nonlinear-optical-properties-and-dft-studies-of-a-novel-non-centrosymmetric-chalcone-derivative-2e-3-4-fluorophenyl-1-4-1e-4-fluorophenyl-methylene-amino-phenyl-prop-2-en-1-one
#18
Shivaraj R Maidur, Parutagouda Shankaragouda Patil, Anusha Ekbote, Tze Shyang Chia, Ching Kheng Quah
In the present work, the title chalcone, (2E)-3-(4-fluorophenyl)-1-(4-{[(1E)-(4-fluorophenyl) methylene]amino}phenyl)prop-2-en-1-one (abbreviated as FAMFC), was synthesized and structurally characterized by single-crystal X-ray diffraction. The compound is crystallized in the monoclinic system with non-centrosymmetric space group P21 and hence it satisfies the essential condition for materials to exhibit second-order nonlinear optical properties. The molecular structure was further confirmed by using FT-IR and (1)H NMR spectroscopic techniques...
May 9, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28528137/fuzzy-dynamic-output-feedback-h%C3%A2-control-for-continuous-time-t-s-fuzzy-systems-under-imperfect-premise-matching
#19
Tao Zhao, Songyi Dian
This paper addresses a fuzzy dynamic output feedback H∞ control design problem for continuous-time nonlinear systems via T-S fuzzy model. The stability of the fuzzy closed-loop system which is formed by a T-S fuzzy model and a fuProd. Type: FTPzzy dynamic output feedback H∞ controller connected in a closed loop is investigated with Lyapunov stability theory. The proposed fuzzy controller does not share the same membership functions and number of rules with T-S fuzzy systems, which can enhance design flexibility...
May 17, 2017: ISA Transactions
https://www.readbyqxmd.com/read/28527457/role-of-quantum-coherence-in-shaping-the-line-shape-of-an-exciton-interacting-with-a-spatially-and-temporally-correlated-bath
#20
Rajesh Dutta, Kaushik Bagchi, Biman Bagchi
Kubo's fluctuation theory of line shape forms the backbone of our understanding of optical and vibrational line shapes, through such concepts as static heterogeneity and motional narrowing. However, the theory does not properly address the effects of quantum coherences on optical line shape, especially in extended systems where a large number of eigenstates are present. In this work, we study the line shape of an exciton in a one-dimensional lattice consisting of regularly placed and equally separated optical two level systems...
May 21, 2017: Journal of Chemical Physics
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