GDSCalc: A Web-Based Application for Evaluating Discrete Graph Dynamical Systems
Elmeligy Abdelhamid, Sherif H.; Kuhlman, Chris J.; Marathe, Madhav V.; Mortveit, Henning S.; Ravi, S. S.
2015-01-01
Discrete dynamical systems are used to model various realistic systems in network science, from social unrest in human populations to regulation in biological networks. A common approach is to model the agents of a system as vertices of a graph, and the pairwise interactions between agents as edges. Agents are in one of a finite set of states at each discrete time step and are assigned functions that describe how their states change based on neighborhood relations. Full characterization of state transitions of one system can give insights into fundamental behaviors of other dynamical systems. In this paper, we describe a discrete graph dynamical systems (GDSs) application called GDSCalc for computing and characterizing system dynamics. It is an open access system that is used through a web interface. We provide an overview of GDS theory. This theory is the basis of the web application; i.e., an understanding of GDS provides an understanding of the software features, while abstracting away implementation details. We present a set of illustrative examples to demonstrate its use in education and research. Finally, we compare GDSCalc with other discrete dynamical system software tools. Our perspective is that no single software tool will perform all computations that may be required by all users; tools typically have particular features that are more suitable for some tasks. We situate GDSCalc within this space of software tools. PMID:26263006
NASA Astrophysics Data System (ADS)
Wuensche, Andrew
DDLab is interactive graphics software for creating, visualizing, and analyzing many aspects of Cellular Automata, Random Boolean Networks, and Discrete Dynamical Networks in general and studying their behavior, both from the time-series perspective — space-time patterns, and from the state-space perspective — attractor basins. DDLab is relevant to research, applications, and education in the fields of complexity, self-organization, emergent phenomena, chaos, collision-based computing, neural networks, content addressable memory, genetic regulatory networks, dynamical encryption, generative art and music, and the study of the abstract mathematical/physical/dynamical phenomena in their own right.
Systoles in discrete dynamical systems
NASA Astrophysics Data System (ADS)
Fernandes, Sara; Grácio, Clara; Ramos, Carlos Correia
2013-01-01
The fruitful relationship between Geometry and Graph Theory has been explored by several authors benefiting also the Theory of discrete dynamical systems seen as Markov chains in graphs. In this work we will further explore the relation between these areas, giving a geometrical interpretation of notions from dynamical systems. In particular, we relate the topological entropy with the systole, here defined in the context of discrete dynamical systems. We show that for continuous interval maps the systole is trivial; however, for the class of interval maps with one discontinuity point the systole acquires relevance from the point of view of the dynamical behavior. Moreover, we define the geodesic length spectrum associated to a Markov interval map and we compute the referred spectrum in several examples.
Discreteness effects in population dynamics
NASA Astrophysics Data System (ADS)
Guevara Hidalgo, Esteban; Lecomte, Vivien
2016-05-01
We analyse numerically the effects of small population size in the initial transient regime of a simple example population dynamics. These effects play an important role for the numerical determination of large deviation functions of additive observables for stochastic processes. A method commonly used in order to determine such functions is the so-called cloning algorithm which in its non-constant population version essentially reduces to the determination of the growth rate of a population, averaged over many realizations of the dynamics. However, the averaging of populations is highly dependent not only on the number of realizations of the population dynamics, and on the initial population size but also on the cut-off time (or population) considered to stop their numerical evolution. This may result in an over-influence of discreteness effects at initial times, caused by small population size. We overcome these effects by introducing a (realization-dependent) time delay in the evolution of populations, additional to the discarding of the initial transient regime of the population growth where these discreteness effects are strong. We show that the improvement in the estimation of the large deviation function comes precisely from these two main contributions.
Web-Based Implementation of Discrete Mathematics
ERIC Educational Resources Information Center
Love, Tanzy; Keinert, Fritz; Shelley, Mack
2006-01-01
The Department of Mathematics at Iowa State University teaches a freshman-level Discrete Mathematics course with total enrollment of about 1,800 students per year. The traditional format includes large lectures, with about 150 students each, taught by faculty and temporary instructors in two class sessions per week and recitation sections, with…
Constraint Web Service Composition Based on Discrete Particle Swarm Optimization
NASA Astrophysics Data System (ADS)
Fang, Xianwen; Fan, Xiaoqin; Yin, Zhixiang
Web service composition provides an open, standards-based approach for connecting web services together to create higher-level business processes. The Standards are designed to reduce the complexity required to compose web services, hence reducing time and costs, and increase overall efficiency in businesses. This paper present independent global constrains web service composition optimization methods based on Discrete Particle Swarm Optimization (DPSO) and associate Petri net (APN). Combining with the properties of APN, an efficient DPSO algorithm is presented which is used to search a legal firing sequence in the APN model. Using legal firing sequences of the Petri net makes the service composition locating space based on DPSO shrink greatly. Finally, for comparing our methods with the approximating methods, the simulation experiment is given out. Theoretical analysis and experimental results indicate that this method owns both lower computation cost and higher success ratio of service composition.
Terminal Dynamics Approach to Discrete Event Systems
NASA Technical Reports Server (NTRS)
Zak, Michail; Meyers, Ronald
1995-01-01
This paper presents and discusses a mathematical formalism for simulation of discrete event dynamic (DED)-a special type of 'man-made' systems to serve specific purposes of information processing. The main objective of this work is to demonstrate that the mathematical formalism for DED can be based upon a terminal model of Newtonian dynamics which allows one to relax Lipschitz conditions at some discrete points.!.
Dynamic discretization method for solving Kepler's equation
NASA Astrophysics Data System (ADS)
Feinstein, Scott A.; McLaughlin, Craig A.
2006-09-01
Kepler’s equation needs to be solved many times for a variety of problems in Celestial Mechanics. Therefore, computing the solution to Kepler’s equation in an efficient manner is of great importance to that community. There are some historical and many modern methods that address this problem. Of the methods known to the authors, Fukushima’s discretization technique performs the best. By taking more of a system approach and combining the use of discretization with the standard computer science technique known as dynamic programming, we were able to achieve even better performance than Fukushima. We begin by defining Kepler’s equation for the elliptical case and describe existing solution methods. We then present our dynamic discretization method and show the results of a comparative analysis. This analysis will demonstrate that, for the conditions of our tests, dynamic discretization performs the best.
Attractors for discrete periodic dynamical systems
John E. Franke; James F. Selgrade
2003-01-01
A mathematical framework is introduced to study attractors of discrete, nonautonomous dynamical systems which depend periodically on time. A structure theorem for such attractors is established which says that the attractor of a time-periodic dynamical system is the unin of attractors of appropriate autonomous maps. If the nonautonomous system is a perturbation of an...
Novel web service selection model based on discrete group search.
Zhai, Jie; Shao, Zhiqing; Guo, Yi; Zhang, Haiteng
2014-01-01
In our earlier work, we present a novel formal method for the semiautomatic verification of specifications and for describing web service composition components by using abstract concepts. After verification, the instantiations of components were selected to satisfy the complex service performance constraints. However, selecting an optimal instantiation, which comprises different candidate services for each generic service, from a large number of instantiations is difficult. Therefore, we present a new evolutionary approach on the basis of the discrete group search service (D-GSS) model. With regard to obtaining the optimal multiconstraint instantiation of the complex component, the D-GSS model has competitive performance compared with other service selection models in terms of accuracy, efficiency, and ability to solve high-dimensional service composition component problems. We propose the cost function and the discrete group search optimizer (D-GSO) algorithm and study the convergence of the D-GSS model through verification and test cases.
Dynamic Web Pages: Performance Impact on Web Servers.
ERIC Educational Resources Information Center
Kothari, Bhupesh; Claypool, Mark
2001-01-01
Discussion of Web servers and requests for dynamic pages focuses on experimentally measuring and analyzing the performance of the three dynamic Web page generation technologies: CGI, FastCGI, and Servlets. Develops a multivariate linear regression model and predicts Web server performance under some typical dynamic requests. (Author/LRW)
Discrete model for DNA-promoter dynamics
NASA Astrophysics Data System (ADS)
Salerno, Mario
1991-10-01
We introduce a discrete model for DNA that takes into account the information about specific base sequences along the double helix. We use this model to study nonlinear wave dynamics of the T7A1 DNA promoter. As results we show the existence in the promoter of a dynamically active region in which static solitons acquire finite velocities, which contrasts with regions where solitons simply remain static. Furthermore, when they pass through this region moving solitons are accelerated, decelerated, or reflected, depending on their initial velocities. The possibility that these dynamical effects play a role in the mechanism of genetic activation is suggested.
Dynamical Properties of Discrete Reaction Networks
Paulevé, Loïc; Craciun, Gheorghe; Koeppl, Heinz
2013-01-01
Reaction networks are commonly used to model the dynamics of populations subject to transformations that follow an imposed stoichiometry. This paper focuses on the efficient characterisation of dynamical properties of Discrete Reaction Networks (DRNs). DRNs can be seen as modeling the underlying discrete nondeterministic transitions of stochastic models of reaction networks. In that sense, a proof of non-reachability in a given DRN has immediate implications for any concrete stochastic model based on that DRN, independent of the choice of kinetic laws and constants. Moreover, if we assume that stochastic kinetic rates are given by the mass-action law (or any other kinetic law that gives non-vanishing probability to each reaction if the required number of interacting substrates is present), then reachability properties are equivalent in the two settings. The analysis of two types of global dynamical properties of DRNs is addressed: irreducibility, i.e., the ability to reach any discrete state from any other state; and recurrence, i.e., the ability to return to any initial state. Our results consider both the verification of such properties when species are present in a large copy number, and in the general case. The necessary and sufficient conditions obtained involve algebraic conditions on the network reactions which in most cases can be verified using linear programming. Finally, the relationship of DRN irreducibility and recurrence with dynamical properties of stochastic and continuous models of reaction networks is discussed. PMID:23722628
Energy Levels of 'Hydrogen Atom' in Discrete Time Dynamics
Khrennikov, Andrei; Volovich, Yaroslav
2006-01-04
We analyze dynamical consequences of a conjecture that there exists a fundamental (indivisible) quant of time. In particular we study the problem of discrete energy levels of hydrogen atom. We are able to reconstruct potential which in discrete time formalism leads to energy levels of unperturbed hydrogen atom. We also consider linear energy levels of quantum harmonic oscillator and show how they are produced in the discrete time formalism. More generally, we show that in discrete time formalism finite motion in central potential leads to discrete energy spectrum, the property which is common for quantum mechanical theory. Thus deterministic (but discrete time{exclamation_point}) dynamics is compatible with discrete energy levels.
Discrete Molecular Dynamics Simulation of Biomolecules
NASA Astrophysics Data System (ADS)
Ding, Feng
2011-10-01
Discrete molecular dynamics (DMD) simulation of hard spheres was the first implementation of molecular dynamics (MD) in history. DMD simulations are computationally more efficient than continuous MD simulations due to simplified interaction potentials. However, also due to these simplified potentials, DMD has often been associated with coarse-grained modeling, and hence continuous MD has become the dominant approach used to study the internal dynamics of biomolecules. With the recent advances in DMD methodology, including the development of high-resolution models for biomolecules and approaches to increase DMD efficiency, DMD simulations are emerging as an important tool in the field of molecular modeling, including the study of protein folding, protein misfolding and aggregation, and protein engineering. Recently, DMD methodology has been applied to modeling RNA folding and protein-ligand recognition. With these improvements to DMD methodology and the continuous increase in available computational power, we expect a growing role of DMD simulations in our understanding of biology.
Time Discretization Approach to Dynamic Localization Conditions
NASA Astrophysics Data System (ADS)
Papp, E.
An alternative wavefunction to the description of the dynamic localization of a charged particle moving on a one-dimensional lattice under the influence of a periodic time dependent electric field is written down. For this purpose the method of characteristics such as applied by Dunlap and Kenkre [Phys. Rev. B 34, 3625 (1986)] has been modified by using a different integration variable. Handling this wavefunction one is faced with the selection of admissible time values. This results in a conditionally exactly solvable problem, now by accounting specifically for the implementation of a time discretization working in conjunction with a related dynamic localization condition. In addition, one resorts to the strong field limit, which amounts to replace, to leading order, the large order zeros of the Bessel function J0(z), used before in connection with the cosinusoidal modulation, by integral multiples of π. Here z stands for the ratio between the field amplitude and the frequency. The modulation function of the electric field vanishes on the nodal points of the time grid, which stands for an effective field-free behavior. This opens the way to propose quickly tractable dynamic localization conditions for arbitrary periodic modulations. We have also found that the present time discretization approach produces the minimization of the mean square displacement characterizing the usual exact wavefunction. Other realizations and comparisons have also been presented.
Evolving dynamic web pages using web mining
NASA Astrophysics Data System (ADS)
Menon, Kartik; Dagli, Cihan H.
2003-08-01
The heterogeneity and the lack of structure that permeates much of the ever expanding information sources on the WWW makes it difficult for the user to properly and efficiently access different web pages. Different users have different needs from the same web page. It is necessary to train the system to understand the needs and demands of the users. In other words there is a need for efficient and proper web mining. In this paper issues and possible ways of training the system and providing high level of organization for semi structured data available on the web is discussed. Web pages can be evolved based on history of query searches, browsing, links traversed and observation of the user behavior like book marking and time spent on viewing. Fuzzy clustering techniques help in grouping natural users and groups, neural networks, association rules and web traversals patterns help in efficient sequential anaysis based on previous searches and queries by the user. In this paper we analyze web server logs using above mentioned techniques to know more about user interactions. Analyzing these web server logs help to closely understand the user behavior and his/her web access pattern.
Dynamical Localization for Discrete Anderson Dirac Operators
NASA Astrophysics Data System (ADS)
Prado, Roberto A.; de Oliveira, César R.; Carvalho, Silas L.
2017-04-01
We establish dynamical localization for random Dirac operators on the d-dimensional lattice, with d\\in { 1, 2, 3} , in the three usual regimes: large disorder, band edge and 1D. These operators are discrete versions of the continuous Dirac operators and consist in the sum of a discrete free Dirac operator with a random potential. The potential is a diagonal matrix formed by different scalar potentials, which are sequences of independent and identically distributed random variables according to an absolutely continuous probability measure with bounded density and of compact support. We prove the exponential decay of fractional moments of the Green function for such models in each of the above regimes, i.e., (j) throughout the spectrum at larger disorder, (jj) for energies near the band edges at arbitrary disorder and (jjj) in dimension one, for all energies in the spectrum and arbitrary disorder. Dynamical localization in theses regimes follows from the fractional moments method. The result in the one-dimensional regime contrast with one that was previously obtained for 1D Dirac model with Bernoulli potential.
Fast Fourier transform discrete dislocation dynamics
NASA Astrophysics Data System (ADS)
Graham, J. T.; Rollett, A. D.; LeSar, R.
2016-12-01
Discrete dislocation dynamics simulations have been generally limited to modeling systems described by isotropic elasticity. Effects of anisotropy on dislocation interactions, which can be quite large, have generally been ignored because of the computational expense involved when including anisotropic elasticity. We present a different formalism of dislocation dynamics in which the dislocations are represented by the deformation tensor, which is a direct measure of the slip in the lattice caused by the dislocations and can be considered as an eigenstrain. The stresses arising from the dislocations are calculated with a fast Fourier transform (FFT) method, from which the forces are determined and the equations of motion are solved. Use of the FFTs means that the stress field is only available at the grid points, which requires some adjustments/regularizations to be made to the representation of the dislocations and the calculation of the force on individual segments, as is discussed hereinafter. A notable advantage of this approach is that there is no computational penalty for including anisotropic elasticity. We review the method and apply it in a simple dislocation dynamics calculation.
Non-Lipschitz Dynamics Approach to Discrete Event Systems
NASA Technical Reports Server (NTRS)
Zak, M.; Meyers, R.
1995-01-01
This paper presents and discusses a mathematical formalism for simulation of discrete event dynamics (DED) - a special type of 'man- made' system designed to aid specific areas of information processing. A main objective is to demonstrate that the mathematical formalism for DED can be based upon the terminal model of Newtonian dynamics which allows one to relax Lipschitz conditions at some discrete points.
A Dynamic and Individualized Web System.
ERIC Educational Resources Information Center
Connolly, Christopher G.
Many universities have striven to provide their students, parents, faculty, staff, and alumni with robust, useful, and informative Web sites. Villanova University (Villanova, Pennsylvania) has spent the last 12 months overhauling its static Web site to a dynamic and individualized Web system. At the outset, the term "portal" was adopted by the…
A Few Continuous and Discrete Dynamical Systems
NASA Astrophysics Data System (ADS)
Zhang, Yufeng; Rui, Wenjuan
2016-08-01
Starting from a 2-unimodular group, we construct its new Lie algebras for which the positive-order Lax pairs and the negative-order Lax pairs are introduced, respectively. With the help of the resulting structure equation of the group we generate some partial differential equations including the well-known MKdV equation, the sine-Gordon equation, the hyperbolic sine-Gordon equation and other new nonlinear evolution equations. With the aid of the Tu scheme combined with the given Lax pairs, we obtain the isospectral and nonisospectral hierarchies of evolution equations, from which we generate two sets of symmetries of a generalized nonlinear Schrödinger (gNLS) equation. Finally, we discretize the Lax pairs to obtain a set of coupled semi-discrete equations. As their reduction, we produce the semi-discrete MKdV equation and semi-discrete NLS equation.
Reprint of: Dynamics of discrete screw dislocations on glide directions
NASA Astrophysics Data System (ADS)
Alicandro, R.; De Luca, L.; Garroni, A.; Ponsiglione, M.
2016-12-01
We consider a simple discrete model for screw dislocations in crystals. Using a variational discrete scheme we study the motion of a configuration of dislocations toward low energy configurations. We deduce an effective fully overdamped dynamics that follows the maximal dissipation criterion introduced in Cermelli and Gurtin (1999) and predicts motion along the glide directions of the crystal.
Dynamics of discrete screw dislocations on glide directions
NASA Astrophysics Data System (ADS)
Alicandro, R.; De Luca, L.; Garroni, A.; Ponsiglione, M.
2016-07-01
We consider a simple discrete model for screw dislocations in crystals. Using a variational discrete scheme we study the motion of a configuration of dislocations toward low energy configurations. We deduce an effective fully overdamped dynamics that follows the maximal dissipation criterion introduced in Cermelli and Gurtin (1999) and predicts motion along the glide directions of the crystal.
The dynamics of assembling food webs.
Fahimipour, Ashkaan K; Hein, Andrew M
2014-05-01
Community assembly is central to ecology, yet ecologists have amassed little quantitative information about how food webs assemble. Theory holds that colonisation rate is a primary driver of community assembly. We present new data from a mesocosm experiment to test the hypothesis that colonisation rate also determines the assembly dynamics of food webs. By manipulating colonisation rate and measuring webs through time, we show how colonisation rate governs structural changes during assembly. Webs experiencing different colonisation rates had stable topologies despite significant species turnover, suggesting that some features of network architecture emerge early and change little through assembly. But webs experiencing low colonisation rates showed less variation in the magnitudes of trophic fluxes, and were less likely to develop coupled fast and slow resource channels--a common feature of published webs. Our results reveal that food web structure develops according to repeatable trajectories that are strongly influenced by colonisation rate. © 2014 John Wiley & Sons Ltd/CNRS.
Generations of solvable discrete-time dynamical systems
NASA Astrophysics Data System (ADS)
Bihun, Oksana; Calogero, Francesco
2017-05-01
A technique is introduced which allows to generate—starting from any solvable discrete-time dynamical system involving N time-dependent variables—new, generally nonlinear, generations of discrete-time dynamical systems, also involving N time-dependent variables and being as well solvable by algebraic operations (essentially by finding the N zeros of explicitly known polynomials of degree N). The dynamical systems constructed using this technique may also feature large numbers of arbitrary constants, and they need not be autonomous. The solvable character of these models allows to identify special cases with remarkable time evolutions: for instance, isochronous or asymptotically isochronous discrete-time dynamical systems. The technique is illustrated by a few examples.
Hamiltonian dynamics and constrained variational calculus: continuous and discrete settings
NASA Astrophysics Data System (ADS)
de León, Manuel; Jiménez, Fernando; Martín de Diego, David
2012-05-01
The aim of this paper is to study the relationship between Hamiltonian dynamics and constrained variational calculus. We describe both using the notion of Lagrangian submanifolds of convenient symplectic manifolds and using the so-called Tulczyjew triples. The results are also extended to the case of discrete dynamics and nonholonomic mechanics. Interesting applications to the geometrical integration of Hamiltonian systems are obtained.
Dispersal dynamics in food webs.
Melián, Carlos J; Křivan, Vlastimil; Altermatt, Florian; Starý, Petr; Pellissier, Loïc; De Laender, Frederik
2015-02-01
Studies of food webs suggest that limited nonrandom dispersal can play an important role in structuring food webs. It is not clear, however, whether density-dependent dispersal fits empirical patterns of food webs better than density-independent dispersal. Here, we study a spatially distributed food web, using a series of population-dispersal models that contrast density-independent and density-dependent dispersal in landscapes where sampled sites are either homogeneously or heterogeneously distributed. These models are fitted to empirical data, allowing us to infer mechanisms that are consistent with the data. Our results show that models with density-dependent dispersal fit the α, β, and γ tritrophic richness observed in empirical data best. Our results also show that density-dependent dispersal leads to a critical distance threshold beyond which site similarity (i.e., β tritrophic richness) starts to decrease much faster. Such a threshold can also be detected in the empirical data. In contrast, models with density-independent dispersal do not predict such a threshold. Moreover, preferential dispersal from more centrally located sites to peripheral sites does not provide a better fit to empirical data when compared with symmetric dispersal between sites. Our results suggest that nonrandom dispersal in heterogeneous landscapes is an important driver that shapes local and regional richness (i.e., α and γ tritrophic richness, respectively) as well as the distance-decay relationship (i.e., β tritrophic richness) in food webs.
Bahi, Jacques M; Contassot-Vivier, Sylvain
2009-08-01
This paper brings a correction to the formulation of the basins of fixed-point states of fully asynchronous discrete-time discrete-state dynamic networks presented in our paper that appeared in the IEEE Transactions on Neural Networks, vol. 17, no. 2, pp. 397-408, March 2006. In our subsequent works on totally asynchronous systems, we have discovered that the formulation given in that previous paper lacks an additional condition. We present in this paper why the previous formulation is incomplete and give the correct formulation.
Identifying the topology of networks with discrete-time dynamics
NASA Astrophysics Data System (ADS)
Guo, Shu-Juan; Fu, Xin-Chu
2010-07-01
We suggest a method for identifying the topology of networks with discrete-time dynamics based on the dynamical evolution supported by the networks. The Frobenius matrix norm and Lasalle's invariance principle are used in this work. The network concerned can be directed or undirected, weighted or unweighted, and the local dynamics of each node can be nonidentical. The connections among the nodes can be all unknown or partially known. Finally, several examples are illustrated to verify the theoretical results.
Dynamics of a discrete auroral arc
NASA Technical Reports Server (NTRS)
Bruening, K.; Goertz, C. K.
1986-01-01
Porcupine Flight 4 data were used to determine the field-aligned currents associated with a southward moving discrete auroral arc in the postmidnight sector. Three different methods were used for determining the field-aligned current which should give identical results if the arcs are quasi-stationary and no parallel electric field exists between the payload and the dynamo region of the ionosphere. As long as the rocket is above the arc, the three methods agree. The integral of precipitating electron flux, the local magnetic field perturbations, and the divergence of the horizontal Pedersen current all indicate an upward current of 5 + or - 3 microamperes/sq m. Immediately north of the arc a strong downward current of about 10-20 microamperes/sq m is detected. The magnitude, however, is not well known because the rocket's velocity relative to the arc cannot be clearly established. Further north of the southward moving arc, the two methods that can be applied (magnetic field perturbations and divergence of the horizontal Pedersen current) yield contradictory results not only about the magnitude of the current but also about the direction of the current. It is suggested that this discrepancy is due to time-dependent electric field.
Dynamics of a discrete auroral arc
NASA Astrophysics Data System (ADS)
Bruening, K.; Goertz, C. K.
1986-06-01
Porcupine Flight 4 data were used to determine the field-aligned currents associated with a southward moving discrete auroral arc in the postmidnight sector. Three different methods were used for determining the field-aligned current which should give identical results if the arcs are quasi-stationary and no parallel electric field exists between the payload and the dynamo region of the ionosphere. As long as the rocket is above the arc, the three methods agree. The integral of precipitating electron flux, the local magnetic field perturbations, and the divergence of the horizontal Pedersen current all indicate an upward current of 5 + or - 3 microamperes/sq m. Immediately north of the arc a strong downward current of about 10-20 microamperes/sq m is detected. The magnitude, however, is not well known because the rocket's velocity relative to the arc cannot be clearly established. Further north of the southward moving arc, the two methods that can be applied (magnetic field perturbations and divergence of the horizontal Pedersen current) yield contradictory results not only about the magnitude of the current but also about the direction of the current. It is suggested that this discrepancy is due to time-dependent electric field.
On the Importance of the Dynamics of Discretizations
NASA Technical Reports Server (NTRS)
Sweby, Peter K.; Yee, H. C.; Rai, ManMohan (Technical Monitor)
1995-01-01
It has been realized recently that the discrete maps resulting from numerical discretizations of differential equations can possess asymptotic dynamical behavior quite different from that of the original systems. This is the case not only for systems of Ordinary Differential Equations (ODEs) but in a more complicated manner for Partial Differential Equations (PDEs) used to model complex physics. The impact of the modified dynamics may be mild and even not observed for some numerical methods. For other classes of discretizations the impact may be pronounced, but not always obvious depending on the nonlinear model equations, the time steps, the grid spacings and the initial conditions. Non-convergence or convergence to periodic solutions might be easily recognizable but convergence to incorrect but plausible solutions may not be so obvious - even for discretized parameters within the linearized stability constraint. Based on our past four years of research, we will illustrate some of the pathology of the dynamics of discretizations, its possible impact and the usage of these schemes for model nonlinear ODEs, convection-diffusion equations and grid adaptations.
On the Importance of the Dynamics of Discretizations
NASA Technical Reports Server (NTRS)
Sweby, Peter K.; Yee, H. C.; Rai, ManMohan (Technical Monitor)
1995-01-01
It has been realized recently that the discrete maps resulting from numerical discretizations of differential equations can possess asymptotic dynamical behavior quite different from that of the original systems. This is the case not only for systems of Ordinary Differential Equations (ODEs) but in a more complicated manner for Partial Differential Equations (PDEs) used to model complex physics. The impact of the modified dynamics may be mild and even not observed for some numerical methods. For other classes of discretizations the impact may be pronounced, but not always obvious depending on the nonlinear model equations, the time steps, the grid spacings and the initial conditions. Non-convergence or convergence to periodic solutions might be easily recognizable but convergence to incorrect but plausible solutions may not be so obvious - even for discretized parameters within the linearized stability constraint. Based on our past four years of research, we will illustrate some of the pathology of the dynamics of discretizations, its possible impact and the usage of these schemes for model nonlinear ODEs, convection-diffusion equations and grid adaptations.
Human dynamics revealed through Web analytics.
Gonçalves, Bruno; Ramasco, José J
2008-08-01
The increasing ubiquity of Internet access and the frequency with which people interact with it raise the possibility of using the Web to better observe, understand, and monitor several aspects of human social behavior. Web sites with large numbers of frequently returning users are ideal for this task. If these sites belong to companies or universities, their usage patterns can furnish information about the working habits of entire populations. In this work, we analyze the properly anonymized logs detailing the access history to Emory University's Web site. Emory is a medium-sized university located in Atlanta, Georgia. We find interesting structure in the activity patterns of the domain and study in a systematic way the main forces behind the dynamics of the traffic. In particular, we find that linear preferential linking, priority-based queuing, and the decay of interest for the contents of the pages are the essential ingredients to understand the way users navigate the Web.
Human dynamics revealed through Web analytics
NASA Astrophysics Data System (ADS)
Gonçalves, Bruno; Ramasco, José J.
2008-08-01
The increasing ubiquity of Internet access and the frequency with which people interact with it raise the possibility of using the Web to better observe, understand, and monitor several aspects of human social behavior. Web sites with large numbers of frequently returning users are ideal for this task. If these sites belong to companies or universities, their usage patterns can furnish information about the working habits of entire populations. In this work, we analyze the properly anonymized logs detailing the access history to Emory University’s Web site. Emory is a medium-sized university located in Atlanta, Georgia. We find interesting structure in the activity patterns of the domain and study in a systematic way the main forces behind the dynamics of the traffic. In particular, we find that linear preferential linking, priority-based queuing, and the decay of interest for the contents of the pages are the essential ingredients to understand the way users navigate the Web.
Nutrient dynamics and food-web stability
DeAngelis, D.L.; Mulholland, P.J.; Palumbo, A.V.; Steinman, A.D.; Huston, M.A.; Elwood, J.W. )
1989-01-01
The importance of nutrient limitation and recycling in ecosystems is widely recognized. Nutrients, defined in the broad sense as all material elements vital to biological functions, are in such small supply that they limit production in many ecosystems. Such limitation can affect ecosystem properties, including the structure and dynamics of the food webs that link species through their feeding relationships. What are the effects of limiting nutrients on the stability of ecosystem food webs Most of the literature on food web stability centers around the dynamics of population numbers and/or biomasses. Nevertheless, a growing body of theoretical and empirical research considers the role that both nutrient limitation and recycling can play in stability. In this paper, it is the authors objective to summarize the current understanding of several important types of stability. The theoretical and empirical evidence relating these types of stability and nutrient cycling is described. A central generalization is produced in each case.
A scheme for designing extreme multistable discrete dynamical systems
NASA Astrophysics Data System (ADS)
Chakraborty, Priyanka
2017-09-01
In this paper, we propose a scheme for designing discrete extreme multistable systems coupling two identical dynamical systems. Existence of infinitely many attractors in the system is obtained via partial synchronization between two systems for a given set of parameters. We give a conjecture that extreme multistable systems can be designed by coupling two m-dimensional dynamical systems in such a way that i (1 ≤ i≤ m-1) number of state variables of the two systems synchronize completely and (m-i) number of state variables keep constant difference. We demonstrate the applicability of our scheme in two-dimensional (2D) as well as three-dimensional (3D) discrete dynamical systems. In particular, we discuss our scheme taking coupled 2D Hénon maps, coupled 2D Duffing maps and coupled 3D Hénon maps. We have analytically shown the existence of fixed points and period-2 orbits in the coupled system with the variation of initial conditions. These analytically derived conditions matched very well with the numerical simulation results. Variation of the largest Lyapunov exponent with the initial conditions is shown to confirm the existence of extreme multistability in the model. Our scheme may be useful for designing physically, chemically and biologically useful multistable discrete dynamical systems.
Lattice fluid dynamics from perfect discretizations of continuum flows
Katz, E.; Wiese, U.
1998-11-01
We use renormalization group methods to derive equations of motion for large scale variables in fluid dynamics. The large scale variables are averages of the underlying continuum variables over cubic volumes and naturally exist on a lattice. The resulting lattice dynamics represents a perfect discretization of continuum physics, i.e., grid artifacts are completely eliminated. Perfect equations of motion are derived for static, slow flows of incompressible, viscous fluids. For Hagen-Poiseuille flow in a channel with a square cross section the equations reduce to a perfect discretization of the Poisson equation for the velocity field with Dirichlet boundary conditions. The perfect large scale Poisson equation is used in a numerical simulation and is shown to represent the continuum flow exactly. For nonsquare cross sections one can use a numerical iterative procedure to derive flow equations that are approximately perfect. {copyright} {ital 1998} {ital The American Physical Society}
A biased filter for linear discrete dynamic systems.
NASA Technical Reports Server (NTRS)
Chang, J. W.; Hoerl, A. E.; Leathrum, J. F.
1972-01-01
A recursive estimator, the ridge filter, was developed for the linear discrete dynamic estimation problem. Theorems were established to show that the ridge filter can be, on the average, closer to the expected value of the system state than the Kalman filter. On the other hand, Kalman filter, on the average, is closer to the instantaneous system state than the ridge filter. The ridge filter has been formulated in such a way that the computational features of the Kalman filter are preserved.
Pinning synchronization of discrete dynamical networks with delay coupling
NASA Astrophysics Data System (ADS)
Cheng, Ranran; Peng, Mingshu; Zuo, Jun
2016-05-01
The purpose of this paper is to investigate the pinning synchronization analysis for nonlinear coupled delayed discrete dynamical networks with the identical or nonidentical topological structure. Based on the Lyapunov stability theory, pinning control method and linear matrix inequalities, several adaptive synchronization criteria via two kinds of pinning control method are obtained. Two examples based on Rulkov chaotic system are included to illustrate the effectiveness and verification of theoretical analysis.
Recursive multibody dynamics and discrete-time optimal control
NASA Technical Reports Server (NTRS)
Deleuterio, G. M. T.; Damaren, C. J.
1989-01-01
A recursive algorithm is developed for the solution of the simulation dynamics problem for a chain of rigid bodies. Arbitrary joint constraints are permitted, that is, joints may allow translational and/or rotational degrees of freedom. The recursive procedure is shown to be identical to that encountered in a discrete-time optimal control problem. For each relevant quantity in the multibody dynamics problem, there exists an analog in the context of optimal control. The performance index that is minimized in the control problem is identified as Gibbs' function for the chain of bodies.
Dynamic modelling and analysis of space webs
NASA Astrophysics Data System (ADS)
Yu, Yang; Baoyin, HeXi; Li, JunFeng
2011-04-01
Future space missions demand operations on large flexible structures, for example, space webs, the lightweight cable nets deployable in space, which can serve as platforms for very large structures or be used to capture orbital objects. The interest in research on space webs is likely to increase in the future with the development of promising applications such as Furoshiki sat-ellite of JAXA, Robotic Geostationary Orbit Restorer (ROGER) of ESA and Grapple, Retrieve And Secure Payload (GRASP) of NASA. Unlike high-tensioned nets in civil engineering, space webs may be low-tensioned or tensionless, and extremely flexible, owing to the microgravity in the orbit and the lack of support components, which may cause computational difficulties. Mathematical models are necessary in the analysis of space webs, especially in the conceptual design and evaluation for prototypes. A full three-dimensional finite element (FE) model was developed in this work. Trivial truss elements were adopted to reduce the computational complexity. Considering cable is a compression-free material and its tensile stiffness is also variable, we introduced the cable material constitutive relationship to work out an accurate and feasible model for prototype analysis and design. In the static analysis, the stress distribution and global deformation of the webs were discussed to get access to the knowledge of strength of webs with different types of meshes. In the dynamic analysis, special attention was paid to the impact problem. The max stress and global deformation were investigated. The simulation results indicate the interesting phenomenon which may be worth further research.
Applications of Discrete Molecular Dynamics in biology and medicine.
Proctor, Elizabeth A; Dokholyan, Nikolay V
2016-04-01
Discrete Molecular Dynamics (DMD) is a physics-based simulation method using discrete energetic potentials rather than traditional continuous potentials, allowing microsecond time scale simulations of biomolecular systems to be performed on personal computers rather than supercomputers or specialized hardware. With the ongoing explosion in processing power even in personal computers, applications of DMD have similarly multiplied. In the past two years, researchers have used DMD to model structures of disease-implicated protein folding intermediates, study assembly of protein complexes, predict protein-protein binding conformations, engineer rescue mutations in disease-causative protein mutants, design a protein conformational switch to control cell signaling, and describe the behavior of polymeric dispersants for environmental cleanup of oil spills, among other innovative applications.
Discrete dynamic modeling of T cell survival signaling networks
NASA Astrophysics Data System (ADS)
Zhang, Ranran
2009-03-01
Biochemistry-based frameworks are often not applicable for the modeling of heterogeneous regulatory systems that are sparsely documented in terms of quantitative information. As an alternative, qualitative models assuming a small set of discrete states are gaining acceptance. This talk will present a discrete dynamic model of the signaling network responsible for the survival and long-term competence of cytotoxic T cells in the blood cancer T-LGL leukemia. We integrated the signaling pathways involved in normal T cell activation and the known deregulations of survival signaling in leukemic T-LGL, and formulated the regulation of each network element as a Boolean (logic) rule. Our model suggests that the persistence of two signals is sufficient to reproduce all known deregulations in leukemic T-LGL. It also indicates the nodes whose inactivity is necessary and sufficient for the reversal of the T-LGL state. We have experimentally validated several model predictions, including: (i) Inhibiting PDGF signaling induces apoptosis in leukemic T-LGL. (ii) Sphingosine kinase 1 and NFκB are essential for the long-term survival of T cells in T-LGL leukemia. (iii) T box expressed in T cells (T-bet) is constitutively activated in the T-LGL state. The model has identified potential therapeutic targets for T-LGL leukemia and can be used for generating long-term competent CTL necessary for tumor and cancer vaccine development. The success of this model, and of other discrete dynamic models, suggests that the organization of signaling networks has an determining role in their dynamics. Reference: R. Zhang, M. V. Shah, J. Yang, S. B. Nyland, X. Liu, J. K. Yun, R. Albert, T. P. Loughran, Jr., Network Model of Survival Signaling in LGL Leukemia, PNAS 105, 16308-16313 (2008).
Parallel Stochastic discrete event simulation of calcium dynamics in neuron.
Ishlam Patoary, Mohammad Nazrul; Tropper, Carl; McDougal, Robert A; Zhongwei, Lin; Lytton, William W
2017-09-26
The intra-cellular calcium signaling pathways of a neuron depends on both biochemical reactions and diffusions. Some quasi-isolated compartments (e.g. spines) are so small and calcium concentrations are so low that one extra molecule diffusing in by chance can make a nontrivial difference in its concentration (percentage-wise). These rare events can affect dynamics discretely in such way that they cannot be evaluated by a deterministic simulation. Stochastic models of such a system provide a more detailed understanding of these systems than existing deterministic models because they capture their behavior at a molecular level. Our research focuses on the development of a high performance parallel discrete event simulation environment, Neuron Time Warp (NTW), which is intended for use in the parallel simulation of stochastic reaction-diffusion systems such as intra-calcium signaling. NTW is integrated with NEURON, a simulator which is widely used within the neuroscience community. We simulate two models, a calcium buffer and a calcium wave model. The calcium buffer model is employed in order to verify the correctness and performance of NTW by comparing it to a serial deterministic simulation in NEURON. We also derived a discrete event calcium wave model from a deterministic model using the stochastic IP3R structure.
Convergence time towards periodic orbits in discrete dynamical systems.
San Martín, Jesús; Porter, Mason A
2014-01-01
We investigate the convergence towards periodic orbits in discrete dynamical systems. We examine the probability that a randomly chosen point converges to a particular neighborhood of a periodic orbit in a fixed number of iterations, and we use linearized equations to examine the evolution near that neighborhood. The underlying idea is that points of stable periodic orbit are associated with intervals. We state and prove a theorem that details what regions of phase space are mapped into these intervals (once they are known) and how many iterations are required to get there. We also construct algorithms that allow our theoretical results to be implemented successfully in practice.
Essential uncontrollability of discrete linear, time-invariant, dynamical systems
NASA Technical Reports Server (NTRS)
Cliff, E. M.
1975-01-01
The concept of a 'best approximating m-dimensional subspace' for a given set of vectors in n-dimensional whole space is introduced. Such a subspace is easily described in terms of the eigenvectors of an associated Gram matrix. This technique is used to approximate an achievable set for a discrete linear time-invariant dynamical system. This approximation characterizes the part of the state space that may be reached using modest levels of control. If the achievable set can be closely approximated by a proper subspace of the whole space then the system is 'essentially uncontrollable'. The notion finds application in studies of failure-tolerant systems, and in decoupling.
On control of continuous dynamical polysystems in discrete times
Khryashchev, S. M.
2015-03-10
This paper considers control systems with a finite number of control parameters, i.e. dynamical polysystems. It is assumed that control switchings can occur only at certain discrete times. Statistical methods in number theory are used to investigate the controllability of these systems. Existence of control switching times is established through analysis of Diophantine equations. The values of control switching times are found through suitable numerical methods. Certain assertions on the controllability of the polysystems of the class under consideration are proved. Some examples are considered.
Experiments of reconstructing discrete atmospheric dynamic models from data (I)
NASA Astrophysics Data System (ADS)
Lin, Zhenshan; Zhu, Yanyu; Deng, Ziwang
1995-03-01
In this paper, we give some experimental results of our study in reconstructing discrete atmospheric dynamic models from data. After a great deal of numerical experiments, we found that the logistic map, x n + 1 = 1- μx {2/n}, could be used in monthly mean temperature prediction when it was approaching the chaotic region, and its predictive results were in reverse states to the practical data. This means that the nonlinear developing behavior of the monthly mean temperature system is bifurcating back into the critical chaotic states from the chaotic ones.
Novel coupling scheme to control dynamics of coupled discrete systems
NASA Astrophysics Data System (ADS)
Shekatkar, Snehal M.; Ambika, G.
2015-08-01
We present a new coupling scheme to control spatio-temporal patterns and chimeras on 1-d and 2-d lattices and random networks of discrete dynamical systems. The scheme involves coupling with an external lattice or network of damped systems. When the system network and external network are set in a feedback loop, the system network can be controlled to a homogeneous steady state or synchronized periodic state with suppression of the chaotic dynamics of the individual units. The control scheme has the advantage that its design does not require any prior information about the system dynamics or its parameters and works effectively for a range of parameters of the control network. We analyze the stability of the controlled steady state or amplitude death state of lattices using the theory of circulant matrices and Routh-Hurwitz criterion for discrete systems and this helps to isolate regions of effective control in the relevant parameter planes. The conditions thus obtained are found to agree well with those obtained from direct numerical simulations in the specific context of lattices with logistic map and Henon map as on-site system dynamics. We show how chimera states developed in an experimentally realizable 2-d lattice can be controlled using this scheme. We propose this mechanism can provide a phenomenological model for the control of spatio-temporal patterns in coupled neurons due to non-synaptic coupling with the extra cellular medium. We extend the control scheme to regulate dynamics on random networks and adapt the master stability function method to analyze the stability of the controlled state for various topologies and coupling strengths.
Detectability of Discrete Event Systems with Dynamic Event Observation
Shu, Shaolong; Lin, Feng
2009-01-01
Our previous work considers detectability of discrete event systems which is to determine the current state and subsequent states of a system based on event observation. We assume that event observation is static, that is, if an event is observable, then all its occurrences are observable. However, in practical systems such as sensor networks, event observation often needs to be dynamic, that is, the occurrences of same events may or may not be observable, depending on the state of the system. In this paper, we generalize static event observation into dynamic event observation and consider the detectability problem under dynamic event observation. We define four types of detectabilities. To check detectabilities, we construct the observer with exponential complexity. To reduce computational complexity, we can also construct a detector with polynomial complexity to check strong detectabilities. Dynamic event observation can be implemented in two possible ways: a passive observation and an active observation. For the active observation, we discuss how to find minimal event observation policies that preserve four types of detectabilities respectively. PMID:20161618
Novel discretization schemes for the numerical simulation of membrane dynamics
NASA Astrophysics Data System (ADS)
Kolsti, Kyle F.
Motivated by the demands of simulating flapping wings of Micro Air Vehicles, novel numerical methods were developed and evaluated for the dynamic simulation of membranes. For linear membranes, a mixed-form time-continuous Galerkin method was employed using trilinear space-time elements. Rather than time-marching, the entire space-time domain was discretized and solved simultaneously. Second-order rates of convergence in both space and time were observed in numerical studies. Slight high-frequency noise was filtered during post-processing. For geometrically nonlinear membranes, the model incorporated two new schemes that were independently developed and evaluated. Time marching was performed using quintic Hermite polynomials uniquely determined by end-point jerk constraints. The single-step, implicit scheme was significantly more accurate than the most common Newmark schemes. For a simple harmonic oscillator, the scheme was found to be symplectic, frequency-preserving, and conditionally stable. Time step size was limited by accuracy requirements rather than stability. The spatial discretization scheme employed a staggered grid, grouping of nonlinear terms, and polygon shape functions in a strong-form point collocation formulation. The observed rate of convergence was two for both displacement and strain. Validation against existing experimental data showed the method to be accurate until hyperelastic effects dominate.
Analytic Perturbation Analysis of Discrete Event Dynamic Systems
Uryasev, S.
1994-09-01
This paper considers a new Analytic Perturbation Analysis (APA) approach for Discrete Event Dynamic Systems (DEDS) with discontinuous sample-path functions with respect to control parameters. The performance functions for DEDS usually are formulated as mathematical expectations, which can be calculated only numerically. APA is based on new analytic formulas for the gradients of expectations of indicator functions; therefore, it is called an analytic perturbation analysis. The gradient of performance function may not coincide with the expectation of a gradient of sample-path function (i.e., the interchange formula for the gradient and expectation sign may not be valid). Estimates of gradients can be obtained with one simulation run of the models.
Dynamic intermittency in discrete erodible-bed avalanches
NASA Astrophysics Data System (ADS)
Arran, Matthew; Vriend, Nathalie
2016-11-01
The coexistence of fluid-like and solid-like behaviour in granular matter allows avalanches of grains to flow on the surface of a static but erodible bed. For sufficiently slow inflow, these avalanches are discrete, with previous experimentalists reporting that avalanche fronts pass a given point quasi-periodically. We report instead observations of dynamic intermittency between two regimes, one in which avalanches occur quasi-periodically and another in which the intervals between them are irregular. Finding the first regime consistent with existing models, we introduce a model for the second regime within the framework of Self-Organised Criticality, and describe the transition between the regimes with reference to the state of the erodible bed.
Dynamics of Sequence -Discrete Bacterial Populations Inferred Using Metagenomes
Stevens, Sarah; Bendall, Matthew; Kang, Dongwan; Froula, Jeff; Egan, Rob; Chan, Leong-Keat; Tringe, Susannah; McMahon, Katherine; Malmstrom, Rex
2014-03-14
From a multi-year metagenomic time series of two dissimilar Wisconsin lakes we have assembled dozens of genomes using a novel approach that bins contigs into distinct genome based on sequence composition, e.g. kmer frequencies, and contig coverage patterns at various times points. Next, we investigated how these genomes, which represent sequence-discrete bacterial populations, evolved over time and used the time series to discover the population dynamics. For example, we explored changes in single nucleotide polymorphism (SNP) frequencies as well as patterns of gene gain and loss in multiple populations. Interestingly, SNP diversity was purged at nearly every genome position in some populations during the course of this study, suggesting these populations may have experienced genome-wide selective sweeps. This represents the first direct, time-resolved observations of periodic selection in natural populations, a key process predicted by the ecotype model of bacterial diversification.
Dynamics of movement patterning in learning a discrete multiarticular action.
Chow, Jia Yi; Davids, Keith; Button, Chris; Rein, Robert
2008-07-01
From a nonlinear dynamics perspective, presence of movement variability before a change in preferred movement patterns is hypothesized to afford the necessary adaptability and flexibility for seeking novel functional behaviors. In this study, four novice participants practiced a discrete multiarticular movement for 12 sessions over 4 weeks. Cluster analysis procedures revealed how changes between preferred movement patterns were affected with and without the presence of variability in movement clusters before a defined change. Performance improved in all participants as a function of practice. Participants typically showed evidence of change between preferred movement clusters and higher variability in the use of movement clusters within a session. However, increasing variability in movement clusters was not always accompanied by transition from one preferred movement cluster to another. In summary, it was observed that intentional and informational constraints play an important role in influencing the specific pathway of change for individual learners as they search for new preferred movement patterns.
Displaying R spatial statistics on Google dynamic maps with web applications created by Rwui
2012-01-01
Background The R project includes a large variety of packages designed for spatial statistics. Google dynamic maps provide web based access to global maps and satellite imagery. We describe a method for displaying directly the spatial output from an R script on to a Google dynamic map. Methods This is achieved by creating a Java based web application which runs the R script and then displays the results on the dynamic map. In order to make this method easy to implement by those unfamiliar with programming Java based web applications, we have added the method to the options available in the R Web User Interface (Rwui) application. Rwui is an established web application for creating web applications for running R scripts. A feature of Rwui is that all the code for the web application being created is generated automatically so that someone with no knowledge of web programming can make a fully functional web application for running an R script in a matter of minutes. Results Rwui can now be used to create web applications that will display the results from an R script on a Google dynamic map. Results may be displayed as discrete markers and/or as continuous overlays. In addition, users of the web application may select regions of interest on the dynamic map with mouse clicks and the coordinates of the region of interest will automatically be made available for use by the R script. Conclusions This method of displaying R output on dynamic maps is designed to be of use in a number of areas. Firstly it allows statisticians, working in R and developing methods in spatial statistics, to easily visualise the results of applying their methods to real world data. Secondly, it allows researchers who are using R to study health geographics data, to display their results directly onto dynamic maps. Thirdly, by creating a web application for running an R script, a statistician can enable users entirely unfamiliar with R to run R coded statistical analyses of health geographics
Displaying R spatial statistics on Google dynamic maps with web applications created by Rwui.
Newton, Richard; Deonarine, Andrew; Wernisch, Lorenz
2012-09-24
The R project includes a large variety of packages designed for spatial statistics. Google dynamic maps provide web based access to global maps and satellite imagery. We describe a method for displaying directly the spatial output from an R script on to a Google dynamic map. This is achieved by creating a Java based web application which runs the R script and then displays the results on the dynamic map. In order to make this method easy to implement by those unfamiliar with programming Java based web applications, we have added the method to the options available in the R Web User Interface (Rwui) application. Rwui is an established web application for creating web applications for running R scripts. A feature of Rwui is that all the code for the web application being created is generated automatically so that someone with no knowledge of web programming can make a fully functional web application for running an R script in a matter of minutes. Rwui can now be used to create web applications that will display the results from an R script on a Google dynamic map. Results may be displayed as discrete markers and/or as continuous overlays. In addition, users of the web application may select regions of interest on the dynamic map with mouse clicks and the coordinates of the region of interest will automatically be made available for use by the R script. This method of displaying R output on dynamic maps is designed to be of use in a number of areas. Firstly it allows statisticians, working in R and developing methods in spatial statistics, to easily visualise the results of applying their methods to real world data. Secondly, it allows researchers who are using R to study health geographics data, to display their results directly onto dynamic maps. Thirdly, by creating a web application for running an R script, a statistician can enable users entirely unfamiliar with R to run R coded statistical analyses of health geographics data. Fourthly, we envisage an
Zhang, Hong; Abhyankar, Shrirang; Constantinescu, Emil; ...
2017-01-24
Sensitivity analysis is an important tool for describing power system dynamic behavior in response to parameter variations. It is a central component in preventive and corrective control applications. The existing approaches for sensitivity calculations, namely, finite-difference and forward sensitivity analysis, require a computational effort that increases linearly with the number of sensitivity parameters. In this paper, we investigate, implement, and test a discrete adjoint sensitivity approach whose computational effort is effectively independent of the number of sensitivity parameters. The proposed approach is highly efficient for calculating sensitivities of larger systems and is consistent, within machine precision, with the function whosemore » sensitivity we are seeking. This is an essential feature for use in optimization applications. Moreover, our approach includes a consistent treatment of systems with switching, such as dc exciters, by deriving and implementing the adjoint jump conditions that arise from state-dependent and time-dependent switchings. The accuracy and the computational efficiency of the proposed approach are demonstrated in comparison with the forward sensitivity analysis approach. In conclusion, this paper focuses primarily on the power system dynamics, but the approach is general and can be applied to hybrid dynamical systems in a broader range of fields.« less
Constant pressure and temperature discrete-time Langevin molecular dynamics
Grønbech-Jensen, Niels; Farago, Oded
2014-11-21
We present a new and improved method for simultaneous control of temperature and pressure in molecular dynamics simulations with periodic boundary conditions. The thermostat-barostat equations are built on our previously developed stochastic thermostat, which has been shown to provide correct statistical configurational sampling for any time step that yields stable trajectories. Here, we extend the method and develop a set of discrete-time equations of motion for both particle dynamics and system volume in order to seek pressure control that is insensitive to the choice of the numerical time step. The resulting method is simple, practical, and efficient. The method is demonstrated through direct numerical simulations of two characteristic model systems—a one-dimensional particle chain for which exact statistical results can be obtained and used as benchmarks, and a three-dimensional system of Lennard-Jones interacting particles simulated in both solid and liquid phases. The results, which are compared against the method of Kolb and Dünweg [J. Chem. Phys. 111, 4453 (1999)], show that the new method behaves according to the objective, namely that acquired statistical averages and fluctuations of configurational measures are accurate and robust against the chosen time step applied to the simulation.
Discrete Dynamic Bayesian Network Analysis of fMRI Data
Burge, John; Lane, Terran; Link, Hamilton; Qiu, Shibin; Clark, Vincent P.
2010-01-01
We examine the efficacy of using discrete Dynamic Bayesian Networks (dDBNs), a data-driven modeling technique employed in machine learning, to identify functional correlations among neuroanatomical regions of interest. Unlike many neuroimaging analysis techniques, this method is not limited by linear and/or Gaussian noise assumptions. It achieves this by modeling the time series of neuroanatomical regions as discrete, as opposed to continuous, random variables with multinomial distributions. We demonstrated this method using an fMRI dataset collected from healthy and demented elderly subjects and identify correlates based on a diagnosis of dementia. The results are validated in three ways. First, the elicited correlates are shown to be robust over leave-one-out cross-validation and, via a Fourier bootstrapping method, that they were not likely due to random chance. Second, the dDBNs identified correlates that would be expected given the experimental paradigm. Third, the dDBN's ability to predict dementia is competitive with two commonly employed machine-learning classifiers: the support vector machine and the Gaussian naïve Bayesian network. We also verify that the dDBN selects correlates based on non-linear criteria. Finally, we provide a brief analysis of the correlates elicited from Buckner et al.'s data that suggests that demented elderly subjects have reduced involvement of entorhinal and occipital cortex and greater involvement of the parietal lobe and amygdala in brain activity compared with healthy elderly (as measured via functional correlations among BOLD measurements). Limitations and extensions to the dDBN method are discussed. PMID:17990301
An implicit finite element method for discrete dynamic fracture
Gerken, Jobie M.
1999-12-01
A method for modeling the discrete fracture of two-dimensional linear elastic structures with a distribution of small cracks subject to dynamic conditions has been developed. The foundation for this numerical model is a plane element formulated from the Hu-Washizu energy principle. The distribution of small cracks is incorporated into the numerical model by including a small crack at each element interface. The additional strain field in an element adjacent to this crack is treated as an externally applied strain field in the Hu-Washizu energy principle. The resulting stiffness matrix is that of a standard plane element. The resulting load vector is that of a standard plane element with an additional term that includes the externally applied strain field. Except for the crack strain field equations, all terms of the stiffness matrix and load vector are integrated symbolically in Maple V so that fully integrated plane stress and plane strain elements are constructed. The crack strain field equations are integrated numerically. The modeling of dynamic behavior of simple structures was demonstrated within acceptable engineering accuracy. In the model of axial and transverse vibration of a beam and the breathing mode of vibration of a thin ring, the dynamic characteristics were shown to be within expected limits. The models dominated by tensile forces (the axially loaded beam and the pressurized ring) were within 0.5% of the theoretical values while the shear dominated model (the transversely loaded beam) is within 5% of the calculated theoretical value. The constant strain field of the tensile problems can be modeled exactly by the numerical model. The numerical results should therefore, be exact. The discrepancies can be accounted for by errors in the calculation of frequency from the numerical results. The linear strain field of the transverse model must be modeled by a series of constant strain elements. This is an approximation to the true strain field, so some
Folding a protein by discretizing its backbone torsional dynamics
NASA Astrophysics Data System (ADS)
Fernández, Ariel
1999-05-01
The aim of this work is to provide a coarse codification of local conformational constraints associated with each folding motif of a peptide chain in order to obtain a rough solution to the protein folding problem. This is accomplished by implementing a discretized version of the soft-mode dynamics on a personal computer (PC). Our algorithm mimics a parallel process as it evaluates concurrent folding possibilities by pattern recognition. It may be implemented in a PC as a sequence of perturbation-translation-renormalization (p-t-r) cycles performed on a matrix of local topological constraints (LTM). This requires suitable representational tools and a periodic quenching of the dynamics required for renormalization. We introduce a description of the peptide chain based on a local discrete variable the values of which label the basins of attraction of the Ramachandran map for each residue. Thus, the local variable indicates the basin in which the torsional coordinates of each residue lie at a given time. In addition, a coding of local topological constraints associated with each secondary and tertiary structural motif is introduced. Our treatment enables us to adopt a computation time step of 81 ps, a value far larger than hydrodynamic drag time scales. Folding pathways are resolved as transitions between patterns of locally encoded structural signals that change within the 10 μs-100 ms time scale range. These coarse folding pathways are generated by the periodic search for structural patterns in the time-evolving LTM. Each pattern is recorded as a contact matrix, an operation subject to a renormalization feedback loop. The validity of our approach is tested vis-a-vis experimentally-probed folding pathways eventually generating tertiary interactions in proteins which recover their active structure under in vitro renaturation conditions. As an illustration, we focus on determining significant folding intermediates and late kinetic bottlenecks that occur within the
Modelling machine ensembles with discrete event dynamical system theory
NASA Technical Reports Server (NTRS)
Hunter, Dan
1990-01-01
Discrete Event Dynamical System (DEDS) theory can be utilized as a control strategy for future complex machine ensembles that will be required for in-space construction. The control strategy involves orchestrating a set of interactive submachines to perform a set of tasks for a given set of constraints such as minimum time, minimum energy, or maximum machine utilization. Machine ensembles can be hierarchically modeled as a global model that combines the operations of the individual submachines. These submachines are represented in the global model as local models. Local models, from the perspective of DEDS theory , are described by the following: a set of system and transition states, an event alphabet that portrays actions that takes a submachine from one state to another, an initial system state, a partial function that maps the current state and event alphabet to the next state, and the time required for the event to occur. Each submachine in the machine ensemble is presented by a unique local model. The global model combines the local models such that the local models can operate in parallel under the additional logistic and physical constraints due to submachine interactions. The global model is constructed from the states, events, event functions, and timing requirements of the local models. Supervisory control can be implemented in the global model by various methods such as task scheduling (open-loop control) or implementing a feedback DEDS controller (closed-loop control).
Green’s function molecular dynamics meets discrete dislocation plasticity
NASA Astrophysics Data System (ADS)
Venugopalan, Syam P.; Müser, Martin H.; Nicola, Lucia
2017-09-01
Metals deform plastically at the asperity level when brought in contact with a counter body even when the nominal contact pressure is small. Modeling the plasticity of solids with rough surfaces is challenging due to the multi-scale nature of surface roughness and the length-scale dependence of plasticity. While discrete-dislocation plasticity (DDP) simulations capture size-dependent plasticity by keeping track of the motion of individual dislocations, only simple two-dimensional surface geometries have so far been studied with DDP. The main computational bottleneck in contact problems modeled by DDP is the calculation of the dislocation image fields. We address this issue by combining two-dimensional DDP with Green’s function molecular dynamics. The resulting method allows for an efficient boundary-value-method based treatment of elasticity in the presence of dislocations. We demonstrate that our method captures plasticity quantitatively from single to many dislocations and that it scales more favorably with system size than conventional methods. We also derive the relevant Green’s functions for elastic slabs of finite width allowing arbitrary boundary conditions on top and bottom surface to be simulated.
Modelling machine ensembles with discrete event dynamical system theory
NASA Technical Reports Server (NTRS)
Hunter, Dan
1990-01-01
Discrete Event Dynamical System (DEDS) theory can be utilized as a control strategy for future complex machine ensembles that will be required for in-space construction. The control strategy involves orchestrating a set of interactive submachines to perform a set of tasks for a given set of constraints such as minimum time, minimum energy, or maximum machine utilization. Machine ensembles can be hierarchically modeled as a global model that combines the operations of the individual submachines. These submachines are represented in the global model as local models. Local models, from the perspective of DEDS theory , are described by the following: a set of system and transition states, an event alphabet that portrays actions that takes a submachine from one state to another, an initial system state, a partial function that maps the current state and event alphabet to the next state, and the time required for the event to occur. Each submachine in the machine ensemble is presented by a unique local model. The global model combines the local models such that the local models can operate in parallel under the additional logistic and physical constraints due to submachine interactions. The global model is constructed from the states, events, event functions, and timing requirements of the local models. Supervisory control can be implemented in the global model by various methods such as task scheduling (open-loop control) or implementing a feedback DEDS controller (closed-loop control).
Dynamic hybrid algorithms for MAP inference in discrete MRFs.
Alahari, Karteek; Kohli, Pushmeet; Torr, Philip H S
2010-10-01
In this paper, we present novel techniques that improve the computational and memory efficiency of algorithms for solving multilabel energy functions arising from discrete mrfs or crfs. These methods are motivated by the observations that the performance of minimization algorithms depends on: 1) the initialization used for the primal and dual variables and 2) the number of primal variables involved in the energy function. Our first method (dynamic alpha-expansion) works by "recycling" results from previous problem instances. The second method simplifies the energy function by "reducing" the number of unknown variables present in the problem. Further, we show that it can also be used to generate a good initialization for the dynamic alpha-expansion algorithm by "reusing" dual variables. We test the performance of our methods on energy functions encountered in the problems of stereo matching and color and object-based segmentation. Experimental results show that our methods achieve a substantial improvement in the performance of alpha-expansion, as well as other popular algorithms such as sequential tree-reweighted message passing and max-product belief propagation. We also demonstrate the applicability of our schemes for certain higher order energy functions, such as the one described in [1], for interactive texture-based image and video segmentation. In most cases, we achieve a 10-15 times speed-up in the computation time. Our modified alpha-expansion algorithm provides similar performance to Fast-PD, but is conceptually much simpler. Both alpha-expansion and Fast-PD can be made orders of magnitude faster when used in conjunction with the "reduce" scheme proposed in this paper.
Signatures of discrete breathers in coherent state quantum dynamics.
Igumenshchev, Kirill; Ovchinnikov, Misha; Maniadis, Panagiotis; Prezhdo, Oleg
2013-02-07
In classical mechanics, discrete breathers (DBs) - a spatial time-periodic localization of energy - are predicted in a large variety of nonlinear systems. Motivated by a conceptual bridging of the DB phenomena in classical and quantum mechanical representations, we study their signatures in the dynamics of a quantum equivalent of a classical mechanical point in phase space - a coherent state. In contrast to the classical point that exhibits either delocalized or localized motion, the coherent state shows signatures of both localized and delocalized behavior. The transition from normal to local modes have different characteristics in quantum and classical perspectives. Here, we get an insight into the connection between classical and quantum perspectives by analyzing the decomposition of the coherent state into system's eigenstates, and analyzing the spacial distribution of the wave-function density within these eigenstates. We find that the delocalized and localized eigenvalue components of the coherent state are separated by a mixed region, where both kinds of behavior can be observed. Further analysis leads to the following observations. Considered as a function of coupling, energy eigenstates go through avoided crossings between tunneling and non-tunneling modes. The dominance of tunneling modes in the high nonlinearity region is compromised by the appearance of new types of modes - high order tunneling modes - that are similar to the tunneling modes but have attributes of non-tunneling modes. Certain types of excitations preferentially excite higher order tunneling modes, allowing one to study their properties. Since auto-correlation functions decrease quickly in highly nonlinear systems, short-time dynamics are sufficient for modeling quantum DBs. This work provides a foundation for implementing modern semi-classical methods to model quantum DBs, bridging classical and quantum mechanical signatures of DBs, and understanding spectroscopic experiments that
Development and evaluation of a dynamic web-based application.
Hsieh, Yichuan; Brennan, Patricia Flatley
2007-10-11
Traditional consumer health informatics (CHI) applications that were developed for lay public on the Web were commonly written in a Hypertext Markup Language (HTML). As genetics knowledge rapidly advances and requires updating information in a timely fashion, a different content structure is therefore needed to facilitate information delivery. This poster will present the process of developing a dynamic database-driven Web CHI application.
Emerging Technologies: Making the Web Dynamic--DOM and DAV
ERIC Educational Resources Information Center
Godwin-Jones, Robert
2004-01-01
Five years ago, in the January, 1998, issue of "Language Learning & Technology," this author wrote a column on Dynamic Web Page Creation, discussing options for Web interactivity and bemoaning incompatibilities among browsers. In the current column the author explores what has changed since 1998, new options that have arrived, and…
Web-based dynamic Delphi: a new survey instrument
NASA Astrophysics Data System (ADS)
Yao, JingTao; Liu, Wei-Ning
2006-04-01
We present a mathematical model for a dynamic Delphi survey method which takes advantages of Web technology. A comparative study on the performance of the conventional Delphi method and the dynamic Delphi instrument is conducted. It is suggested that a dynamic Delphi survey may form a consensus quickly. However, the result may not be robust due to the judgement leaking issues.
FPGA Implementation of Discrete-Time Neuronal Network for Dynamic Image Segmentation
NASA Astrophysics Data System (ADS)
Fujimoto, Ken'ichi; Musashi, Mio; Yoshinaga, Tetsuya
We have developed a discrete-time dynamical system for dynamic image segmentation. It consists of a global inhibitor and modified chaotic neurons that can generate oscillatory responses. Dynamic image segmentation is performed using its oscillatory responses. This letter presents an implementation of our system in a field programmable gate array (FPGA) device and a successful result of dynamic image segmentation.
The GBT Dynamic Scheduling System: Powered by the Web
NASA Astrophysics Data System (ADS)
Marganian, P.; Clark, M.; McCarty, M.; Sessoms, E.; Shelton, A.
2009-09-01
The web technologies utilized for the Robert C. Byrd Green Bank Telescope's (GBT) new Dynamic Scheduling System are discussed, focusing on languages, frameworks, and tools. We use a popular Python web framework, TurboGears, to take advantage of the extensive web services the system provides. TurboGears is a model-view-controller framework, which aggregates SQLAlchemy, Genshi, and CherryPy respectively. On top of this framework, Javascript (Prototype, script.aculo.us, and JQuery) and cascading style sheets (Blueprint) are used for desktop-quality web pages.
Integrated Information in Discrete Dynamical Systems: Motivation and Theoretical Framework
Balduzzi, David; Tononi, Giulio
2008-01-01
This paper introduces a time- and state-dependent measure of integrated information, φ, which captures the repertoire of causal states available to a system as a whole. Specifically, φ quantifies how much information is generated (uncertainty is reduced) when a system enters a particular state through causal interactions among its elements, above and beyond the information generated independently by its parts. Such mathematical characterization is motivated by the observation that integrated information captures two key phenomenological properties of consciousness: (i) there is a large repertoire of conscious experiences so that, when one particular experience occurs, it generates a large amount of information by ruling out all the others; and (ii) this information is integrated, in that each experience appears as a whole that cannot be decomposed into independent parts. This paper extends previous work on stationary systems and applies integrated information to discrete networks as a function of their dynamics and causal architecture. An analysis of basic examples indicates the following: (i) φ varies depending on the state entered by a network, being higher if active and inactive elements are balanced and lower if the network is inactive or hyperactive. (ii) φ varies for systems with identical or similar surface dynamics depending on the underlying causal architecture, being low for systems that merely copy or replay activity states. (iii) φ varies as a function of network architecture. High φ values can be obtained by architectures that conjoin functional specialization with functional integration. Strictly modular and homogeneous systems cannot generate high φ because the former lack integration, whereas the latter lack information. Feedforward and lattice architectures are capable of generating high φ but are inefficient. (iv) In Hopfield networks, φ is low for attractor states and neutral states, but increases if the networks are optimized to
Integrated information in discrete dynamical systems: motivation and theoretical framework.
Balduzzi, David; Tononi, Giulio
2008-06-13
This paper introduces a time- and state-dependent measure of integrated information, phi, which captures the repertoire of causal states available to a system as a whole. Specifically, phi quantifies how much information is generated (uncertainty is reduced) when a system enters a particular state through causal interactions among its elements, above and beyond the information generated independently by its parts. Such mathematical characterization is motivated by the observation that integrated information captures two key phenomenological properties of consciousness: (i) there is a large repertoire of conscious experiences so that, when one particular experience occurs, it generates a large amount of information by ruling out all the others; and (ii) this information is integrated, in that each experience appears as a whole that cannot be decomposed into independent parts. This paper extends previous work on stationary systems and applies integrated information to discrete networks as a function of their dynamics and causal architecture. An analysis of basic examples indicates the following: (i) phi varies depending on the state entered by a network, being higher if active and inactive elements are balanced and lower if the network is inactive or hyperactive. (ii) phi varies for systems with identical or similar surface dynamics depending on the underlying causal architecture, being low for systems that merely copy or replay activity states. (iii) phi varies as a function of network architecture. High phi values can be obtained by architectures that conjoin functional specialization with functional integration. Strictly modular and homogeneous systems cannot generate high phi because the former lack integration, whereas the latter lack information. Feedforward and lattice architectures are capable of generating high phi but are inefficient. (iv) In Hopfield networks, phi is low for attractor states and neutral states, but increases if the networks are optimized
Dynamic Scheduling for Web Monitoring Crawler
2009-02-27
publication changes in web pages caused by particular events, such as accidents, financial crisis, and sports games . 2. A group of web pages P = {P1, P2, P3...Period We monitored sports news web pages during Beijing Olympic Games . As each game held in the Olympic can be regarded as an event, it is possible to...expect articles about the games would be published according to progresses of the games . For example, if some Olympians won or lost in the game , the
DIVE in the cosmic web: voids with Delaunay triangulation from discrete matter tracer distributions
NASA Astrophysics Data System (ADS)
Zhao, Cheng; Tao, Charling; Liang, Yu; Kitaura, Francisco-Shu; Chuang, Chia-Hsun
2016-07-01
We present a novel parameter-free cosmological void finder (DIVE, Delaunay TrIangulation Void findEr) based on Delaunay Triangulation (DT), which efficiently computes the empty spheres constrained by a discrete set of tracers. We define the spheres as DT voids, and describe their properties, including a universal density profile together with an intrinsic scatter. We apply this technique on 100 halo catalogues with volumes of 2.5 h-1Gpc side each, with a bias and number density similar to the Baryon Oscillation Spectroscopic Survey CMASS luminous red galaxies, performed with the PATCHY code. Our results show that there are two main species of DT voids, which can be characterized by the radius: they have different responses to halo redshift space distortions, to number density of tracers, and reside in different dark matter environments. Based on dynamical arguments using the tidal field tensor, we demonstrate that large DT voids are hosted in expanding regions, whereas the haloes used to construct them reside in collapsing ones. Our approach is therefore able to efficiently determine the troughs of the density field from galaxy surveys, and can be used to study their clustering. We further study the power spectra of DT voids, and find that the bias of the two populations are different, demonstrating that the small DT voids are essentially tracers of groups of haloes.
Discrete Dynamical Systems Meet the Classic Monkey-and-the-Bananas Problem.
ERIC Educational Resources Information Center
Gannon, Gerald E.; Martelli, Mario U.
2001-01-01
Presents a solution of the three-sailors-and-the-bananas problem and attempts a generalization. Introduces an interesting way of looking at the mathematics with an idea drawn from discrete dynamical systems. (KHR)
Discrete Dynamical Systems Meet the Classic Monkey-and-the-Bananas Problem.
ERIC Educational Resources Information Center
Gannon, Gerald E.; Martelli, Mario U.
2001-01-01
Presents a solution of the three-sailors-and-the-bananas problem and attempts a generalization. Introduces an interesting way of looking at the mathematics with an idea drawn from discrete dynamical systems. (KHR)
USDA-ARS?s Scientific Manuscript database
Composed of linear difference equations, a discrete dynamic system model was designed to reconstruct transcriptional regulations in gene regulatory networks in response to 5-hydroxymethylfurfural, a bioethanol conversion inhibitor for ethanologenic yeast Saccharomyces cerevisiae. The modeling aims ...
Dong, Lu; Zhong, Xiangnan; Sun, Changyin; He, Haibo
2016-04-08
This paper presents the design of a novel adaptive event-triggered control method based on the heuristic dynamic programming (HDP) technique for nonlinear discrete-time systems with unknown system dynamics. In the proposed method, the control law is only updated when the event-triggered condition is violated. Compared with the periodic updates in the traditional adaptive dynamic programming (ADP) control, the proposed method can reduce the computation and transmission cost. An actor-critic framework is used to learn the optimal event-triggered control law and the value function. Furthermore, a model network is designed to estimate the system state vector. The main contribution of this paper is to design a new trigger threshold for discrete-time systems. A detailed Lyapunov stability analysis shows that our proposed event-triggered controller can asymptotically stabilize the discrete-time systems. Finally, we test our method on two different discrete-time systems, and the simulation results are included.
Dynamical behavior of fractional-order Hastings-Powell food chain model and its discretization
NASA Astrophysics Data System (ADS)
Matouk, A. E.; Elsadany, A. A.; Ahmed, E.; Agiza, H. N.
2015-10-01
In this work, the dynamical behavior of fractional-order Hastings-Powell food chain model is investigated and a new discretization method of the fractional-order system is introduced. A sufficient condition for existence and uniqueness of the solution of the proposed system is obtained. Local stability of the equilibrium points of the fractional-order system is studied. Furthermore, the necessary and sufficient conditions of stability of the discretized system are also studied. It is shown that the system's fractional parameter has effect on the stability of the discretized system which shows rich variety of dynamical behaviors such as Hopf bifurcation, an attractor crisis and chaotic attractors. Numerical simulations show the tea-cup chaotic attractor of the fractional-order system and the richer dynamical behavior of the corresponding discretized system.
Internet: Growth dynamics of the World-Wide Web
NASA Astrophysics Data System (ADS)
Huberman, Bernardo A.; Adamic, Lada A.
1999-09-01
The exponential growth of the World-Wide Web has transformed it into an ecology of knowledge in which highly diverse information is linked in an extremely complex and arbitrary manner. But even so, as we show here, there is order hidden in the web. We find that web pages are distributed among sites according to a universal power law: many sites have only a few pages, whereas very few sites have hundreds of thousands of pages. This universal distribution can be explained by using a simple stochastic dynamical growth model.
On the Dynamics of Some Discretizations of Convection-Diffusion Equations
NASA Technical Reports Server (NTRS)
Sweby, Peter K.; Yee, H. C.; Rai, Man Mohan (Technical Monitor)
1995-01-01
Numerical discretizations of differential equations which model physical processes can possess dynamics quite different from that of the equations themselves. Recently the emphasis has been on the the dynamics of numerical discretizations for Ordinary Differential Equations (ODEs). For Partial Differential Equations (PDEs) using a method of lines approach the situation is more complex. First, the spatial discretisation may introduce dynamics not present in the original equations; second, the solution of the resulting system of ODEs is open to the modified dynamics of the ODE solver used. These two effects may interact in a complex manner. In this talk we present some results of our recent work on the dynamics of discretizations of convection-diffusion equations, including those produced using Total Variation Diminishing (TVD) schemes and adaptive grid techniques. A more general overview of the area may be found on our accompanying poster presentation.
Timing in cognition and EEG brain dynamics: discreteness versus continuity.
Fingelkurts, Andrew A; Fingelkurts, Alexander A
2006-09-01
This article provides an overview of recent developments in solving the timing problem (discreteness vs. continuity) in cognitive neuroscience. Both theoretical and empirical studies have been considered, with an emphasis on the framework of operational architectonics (OA) of brain functioning (Fingelkurts and Fingelkurts in Brain Mind 2:291-29, 2001; Neurosci Biobehav Rev 28:827-836, 2005). This framework explores the temporal structure of information flow and interarea interactions within the network of functional neuronal populations by examining topographic sharp transition processes in the scalp EEG, on the millisecond scale. We conclude, based on the OA framework, that brain functioning is best conceptualized in terms of continuity-discreteness unity which is also the characteristic property of cognition. At the end we emphasize where one might productively proceed for the future research.
Simulating Food Web Dynamics along a Gradient: Quantifying Human Influence
Jordán, Ferenc; Gjata, Nerta; Mei, Shu; Yule, Catherine M.
2012-01-01
Realistically parameterized and dynamically simulated food-webs are useful tool to explore the importance of the functional diversity of ecosystems, and in particular relations between the dynamics of species and the whole community. We present a stochastic dynamical food web simulation for the Kelian River (Borneo). The food web was constructed for six different locations, arrayed along a gradient of increasing human perturbation (mostly resulting from gold mining activities) along the river. Along the river, the relative importance of grazers, filterers and shredders decreases with increasing disturbance downstream, while predators become more dominant in governing eco-dynamics. Human activity led to increased turbidity and sedimentation which adversely impacts primary productivity. Since the main difference between the study sites was not the composition of the food webs (structure is quite similar) but the strengths of interactions and the abundance of the trophic groups, a dynamical simulation approach seemed to be useful to better explain human influence. In the pristine river (study site 1), when comparing a structural version of our model with the dynamical model we found that structurally central groups such as omnivores and carnivores were not the most important ones dynamically. Instead, primary consumers such as invertebrate grazers and shredders generated a greater dynamical response. Based on the dynamically most important groups, bottom-up control is replaced by the predominant top-down control regime as distance downstream and human disturbance increased. An important finding, potentially explaining the poor structure to dynamics relationship, is that indirect effects are at least as important as direct ones during the simulations. We suggest that our approach and this simulation framework could serve systems-based conservation efforts. Quantitative indicators on the relative importance of trophic groups and the mechanistic modeling of eco-dynamics
Simulating food web dynamics along a gradient: quantifying human influence.
Jordán, Ferenc; Gjata, Nerta; Mei, Shu; Yule, Catherine M
2012-01-01
Realistically parameterized and dynamically simulated food-webs are useful tool to explore the importance of the functional diversity of ecosystems, and in particular relations between the dynamics of species and the whole community. We present a stochastic dynamical food web simulation for the Kelian River (Borneo). The food web was constructed for six different locations, arrayed along a gradient of increasing human perturbation (mostly resulting from gold mining activities) along the river. Along the river, the relative importance of grazers, filterers and shredders decreases with increasing disturbance downstream, while predators become more dominant in governing eco-dynamics. Human activity led to increased turbidity and sedimentation which adversely impacts primary productivity. Since the main difference between the study sites was not the composition of the food webs (structure is quite similar) but the strengths of interactions and the abundance of the trophic groups, a dynamical simulation approach seemed to be useful to better explain human influence. In the pristine river (study site 1), when comparing a structural version of our model with the dynamical model we found that structurally central groups such as omnivores and carnivores were not the most important ones dynamically. Instead, primary consumers such as invertebrate grazers and shredders generated a greater dynamical response. Based on the dynamically most important groups, bottom-up control is replaced by the predominant top-down control regime as distance downstream and human disturbance increased. An important finding, potentially explaining the poor structure to dynamics relationship, is that indirect effects are at least as important as direct ones during the simulations. We suggest that our approach and this simulation framework could serve systems-based conservation efforts. Quantitative indicators on the relative importance of trophic groups and the mechanistic modeling of eco-dynamics
Hamiltonian dynamics for complex food webs.
Kozlov, Vladimir; Vakulenko, Sergey; Wennergren, Uno
2016-03-01
We investigate stability and dynamics of large ecological networks by introducing classical methods of dynamical system theory from physics, including Hamiltonian and averaging methods. Our analysis exploits the topological structure of the network, namely the existence of strongly connected nodes (hubs) in the networks. We reveal new relations between topology, interaction structure, and network dynamics. We describe mechanisms of catastrophic phenomena leading to sharp changes of dynamics and hence completely altering the ecosystem. We also show how these phenomena depend on the structure of interaction between species. We can conclude that a Hamiltonian structure of biological interactions leads to stability and large biodiversity.
Hamiltonian dynamics for complex food webs
NASA Astrophysics Data System (ADS)
Kozlov, Vladimir; Vakulenko, Sergey; Wennergren, Uno
2016-03-01
We investigate stability and dynamics of large ecological networks by introducing classical methods of dynamical system theory from physics, including Hamiltonian and averaging methods. Our analysis exploits the topological structure of the network, namely the existence of strongly connected nodes (hubs) in the networks. We reveal new relations between topology, interaction structure, and network dynamics. We describe mechanisms of catastrophic phenomena leading to sharp changes of dynamics and hence completely altering the ecosystem. We also show how these phenomena depend on the structure of interaction between species. We can conclude that a Hamiltonian structure of biological interactions leads to stability and large biodiversity.
NASA Astrophysics Data System (ADS)
Wang, Tong; Ding, Yongsheng; Zhang, Lei; Hao, Kuangrong
2016-08-01
This paper considered the synchronisation of continuous complex dynamical networks with discrete-time communications and delayed nodes. The nodes in the dynamical networks act in the continuous manner, while the communications between nodes are discrete-time; that is, they communicate with others only at discrete time instants. The communication intervals in communication period can be uncertain and variable. By using a piecewise Lyapunov-Krasovskii function to govern the characteristics of the discrete communication instants, we investigate the adaptive feedback synchronisation and a criterion is derived to guarantee the existence of the desired controllers. The globally exponential synchronisation can be achieved by the controllers under the updating laws. Finally, two numerical examples including globally coupled network and nearest-neighbour coupled networks are presented to demonstrate the validity and effectiveness of the proposed control scheme.
Variational discretizations for the dynamics of fluid-conveying flexible tubes
NASA Astrophysics Data System (ADS)
Gay-Balmaz, François; Putkaradze, Vakhtang
2016-11-01
We derive a variational approach for discretizing fluid-structure interactions, with a particular focus on the dynamics of fluid-conveying elastic tubes. Our method is based on a discretization of the fluid's back-to-labels map and a Lie group discretization of the tube's variables, coupled with an appropriately formulated discrete version of the fluid conservation law. This approach allows the development of geometric numerical schemes for the dynamics of fluid-conveying collapsible tubes, which preserve several intrinsic geometric properties of the continuous system, such as symmetries and symplecticity. In addition, our approach can also be used to derive simplified, but geometrically consistent, low-component models for further analytical and numerical analysis of the system. xml:lang="fr"
Geometry and dynamics in the Fresnel transforms of discrete systems.
Wolf, Kurt Bernardo; Krötzsch, Guillermo
2007-09-01
Free propagation in continuous optical and mechanical systems is generated by the momentum-squared operator and results in a shear of the phase space plane along the position coordinate. We examine three discrete versions of the Fresnel transform in periodic systems through their Wigner function on a toroidal phase space. But since it is topologically impossible to continuously and globally shear a torus, we examine a fourth version of the Fresnel transform on a spherical phase space, in a model based on the Lie algebra of angular momentum, where the corresponding Fresnel transform wrings the sphere.
Direct determination of discrete harmonic bath parameters from molecular dynamics simulations.
Walters, Peter L; Allen, Thomas C; Makri, Nancy
2017-01-15
We present a direct procedure for determining the parameters of a discrete harmonic bath modeling the influence of a complex condensed phase environment on the system of interest. The procedure employs an efficient discretization of the spectral density into modes that correspond to equal fractions of the reorganization energy. The new procedure uses directly the classical correlation function (available from molecular dynamics calculations) as input, avoiding numerical computation of the spectral density by means of a discrete Fourier transform. Convergence is obtained using a shorter time length of the correlation function, leading to significant computational savings. © 2016 Wiley Periodicals, Inc.
NASA Astrophysics Data System (ADS)
Zañudo, Jorge G. T.; Albert, Réka
2013-06-01
Discrete dynamic models are a powerful tool for the understanding and modeling of large biological networks. Although a lot of progress has been made in developing analysis tools for these models, there is still a need to find approaches that can directly relate the network structure to its dynamics. Of special interest is identifying the stable patterns of activity, i.e., the attractors of the system. This is a problem for large networks, because the state space of the system increases exponentially with network size. In this work, we present a novel network reduction approach that is based on finding network motifs that stabilize in a fixed state. Notably, we use a topological criterion to identify these motifs. Specifically, we find certain types of strongly connected components in a suitably expanded representation of the network. To test our method, we apply it to a dynamic network model for a type of cytotoxic T cell cancer and to an ensemble of random Boolean networks of size up to 200. Our results show that our method goes beyond reducing the network and in most cases can actually predict the dynamical repertoire of the nodes (fixed states or oscillations) in the attractors of the system.
Food-web dynamics in a large river discontinuum
Cross, Wyatt F.; Baxter, Colden V.; Rosi-Marshall, Emma J.; Hall, Robert O.; Kennedy, Theodore A.; Donner, Kevin C.; Kelly, Holly A. Wellard; Seegert, Sarah E.Z.; Behn, Kathrine E.; Yard, Michael D.
2013-01-01
Nearly all ecosystems have been altered by human activities, and most communities are now composed of interacting species that have not co-evolved. These changes may modify species interactions, energy and material flows, and food-web stability. Although structural changes to ecosystems have been widely reported, few studies have linked such changes to dynamic food-web attributes and patterns of energy flow. Moreover, there have been few tests of food-web stability theory in highly disturbed and intensely managed freshwater ecosystems. Such synthetic approaches are needed for predicting the future trajectory of ecosystems, including how they may respond to natural or anthropogenic perturbations. We constructed flow food webs at six locations along a 386-km segment of the Colorado River in Grand Canyon (Arizona, USA) for three years. We characterized food-web structure and production, trophic basis of production, energy efficiencies, and interaction-strength distributions across a spatial gradient of perturbation (i.e., distance from Glen Canyon Dam), as well as before and after an experimental flood. We found strong longitudinal patterns in food-web characteristics that strongly correlated with the spatial position of large tributaries. Above tributaries, food webs were dominated by nonnative New Zealand mudsnails (62% of production) and nonnative rainbow trout (100% of fish production). The simple structure of these food webs led to few dominant energy pathways (diatoms to few invertebrate taxa to rainbow trout), large energy inefficiencies (i.e., Below large tributaries, invertebrate production declined ∼18-fold, while fish production remained similar to upstream sites and comprised predominately native taxa (80–100% of production). Sites below large tributaries had increasingly reticulate and detritus-based food webs with a higher prevalence of omnivory, as well as interaction strength distributions more typical of theoretically stable food webs (i
Lehtinen, Arttu; Granberg, Fredric; Laurson, Lasse; Nordlund, Kai; Alava, Mikko J
2016-01-01
The stress-driven motion of dislocations in crystalline solids, and thus the ensuing plastic deformation process, is greatly influenced by the presence or absence of various pointlike defects such as precipitates or solute atoms. These defects act as obstacles for dislocation motion and hence affect the mechanical properties of the material. Here we combine molecular dynamics studies with three-dimensional discrete dislocation dynamics simulations in order to model the interaction between different kinds of precipitates and a 1/2〈111〉{110} edge dislocation in BCC iron. We have implemented immobile spherical precipitates into the ParaDis discrete dislocation dynamics code, with the dislocations interacting with the precipitates via a Gaussian potential, generating a normal force acting on the dislocation segments. The parameters used in the discrete dislocation dynamics simulations for the precipitate potential, the dislocation mobility, shear modulus, and dislocation core energy are obtained from molecular dynamics simulations. We compare the critical stresses needed to unpin the dislocation from the precipitate in molecular dynamics and discrete dislocation dynamics simulations in order to fit the two methods together and discuss the variety of the relevant pinning and depinning mechanisms.
Navier-Stokes Dynamics by a Discrete Boltzmann Model
NASA Technical Reports Server (NTRS)
Rubinstein, Robet
2010-01-01
This work investigates the possibility of particle-based algorithms for the Navier-Stokes equations and higher order continuum approximations of the Boltzmann equation; such algorithms would generalize the well-known Pullin scheme for the Euler equations. One such method is proposed in the context of a discrete velocity model of the Boltzmann equation. Preliminary results on shock structure are consistent with the expectation that the shock should be much broader than the near discontinuity predicted by the Pullin scheme, yet narrower than the prediction of the Boltzmann equation. We discuss the extension of this essentially deterministic method to a stochastic particle method that, like DSMC, samples the distribution function rather than resolving it completely.
Extinction dynamics of a discrete population in an oasis
NASA Astrophysics Data System (ADS)
Berti, Stefano; Cencini, Massimo; Vergni, Davide; Vulpiani, Angelo
2015-07-01
Understanding the conditions ensuring the persistence of a population is an issue of primary importance in population biology. The first theoretical approach to the problem dates back to the 1950s with the Kierstead, Slobodkin, and Skellam (KiSS) model, namely a continuous reaction-diffusion equation for a population growing on a patch of finite size L surrounded by a deadly environment with infinite mortality, i.e., an oasis in a desert. The main outcome of the model is that only patches above a critical size allow for population persistence. Here we introduce an individual-based analog of the KiSS model to investigate the effects of discreteness and demographic stochasticity. In particular, we study the average time to extinction both above and below the critical patch size of the continuous model and investigate the quasistationary distribution of the number of individuals for patch sizes above the critical threshold.
Discrete-time pilot model. [human dynamics and digital simulation
NASA Technical Reports Server (NTRS)
Cavalli, D.
1978-01-01
Pilot behavior is considered as a discrete-time process where the decision making has a sequential nature. This model differs from both the quasilinear model which follows from classical control theory and from the optimal control model which considers the human operator as a Kalman estimator-predictor. An additional factor considered is that the pilot's objective may not be adequately formulated as a quadratic cost functional to be minimized, but rather as a more fuzzy measure of the closeness with which the aircraft follows a reference trajectory. All model parameters, in the digital program simulating the pilot's behavior, were successfully compared in terms of standard-deviation and performance with those of professional pilots in IFR configuration. The first practical application of the model was in the study of its performance degradation when the aircraft model static margin decreases.
NASA Astrophysics Data System (ADS)
Huang, Yandong; Rüdiger, Sten; Shuai, Jianwei
2013-12-01
The random opening and closing of ion channels establishes channel noise, which can be approximated and included into stochastic differential equations (Langevin approach). The Langevin approach is often incorporated to model stochastic ion channel dynamics for systems with a large number of channels. Here, we introduce a discretization procedure of a channel-based Langevin approach to simulate the stochastic channel dynamics with small and intermediate numbers of channels. We show that our Langevin approach with discrete channel open fractions can give a good approximation of the original Markov dynamics even for only 10 K channels. We suggest that the better approximation by the discretized Langevin approach originates from the improved representation of events that trigger action potentials.
Collisionless Dynamics and the Cosmic Web
NASA Astrophysics Data System (ADS)
Hahn, Oliver
2016-10-01
I review the nature of three-dimensional collapse in the Zeldovich approximation, how it relates to the underlying nature of the three-dimensional Lagrangian manifold and naturally gives rise to a hierarchical structure formation scenario that progresses through collapse from voids to pancakes, filaments and then halos. I then discuss how variations of the Zeldovich approximation (based on the gravitational or the velocity potential) have been used to define classifications of the cosmic large-scale structure into dynamically distinct parts. Finally, I turn to recent efforts to devise new approaches relying on tessellations of the Lagrangian manifold to follow the fine-grained dynamics of the dark matter fluid into the highly non-linear regime and both extract the maximum amount of information from existing simulations as well as devise new simulation techniques for cold collisionless dynamics.
Discrete and continuous dynamics modeling of a mass moving on a flexible structure
NASA Technical Reports Server (NTRS)
Herman, Deborah Ann
1992-01-01
A general discrete methodology for modeling the dynamics of a mass that moves on the surface of a flexible structure is developed. This problem was motivated by the Space Station/Mobile Transporter system. A model reduction approach is developed to make the methodology applicable to large structural systems. To validate the discrete methodology, continuous formulations are also developed. Three different systems are examined: (1) simply-supported beam, (2) free-free beam, and (3) free-free beam with two points of contact between the mass and the flexible beam. In addition to validating the methodology, parametric studies were performed to examine how the system's physical properties affect its dynamics.
Nonlinear Maps for Design of Discrete Time Models of Neuronal Network Dynamics
2016-02-29
Performance/Technic~ 02-01-2016- 02-29-2016 4. TITLE AND SUBTITLE Sa. CONTRACT NUMBER Nonlinear Maps for Design of Discrete-Time Models of Neuronal...Network Dynamics Sb. GRANT NUMBER N00014-16-1-2252 Sc. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Sd. PROJECT NUMBER Nikolai Rulkov Se. TASK NUMBER Sf...N00014-16-1-2252 Report #1 Performance/Technical Monthly Report Nonlinear Maps for Design of Discrete-Time Models of Neuronal Network Dynamics
Studying Human Dynamics Through Web Analytics
NASA Astrophysics Data System (ADS)
Ramasco, Jose; Goncalves, Bruno
2008-03-01
When Tim Berners Lee, a physicist at the European Center for Nuclear Research (CERN) first conceived the World Wide Web (WWW) in 1990 as a way to facilitate the sharing of scientific information and results among the centers different researchers and groups, even the most ingenious of science fiction writers could not have imagined the role it would come to play in the following decades. The increasing ubiquitousness of Internet access and the frequency with which people interact with it raise the possibility of using it to better observe, understand, and even monitor several aspects of human social behavior. Websites with large numbers of frequently returning users, such as search engines, company or university websites, are ideal for this task. The properly anonymized logs detailing the access history to Emory University's website is studied. We find that a small number of users is responsible for a finite fraction of the total activity. A saturation phenomenon is observed where, certain connections age, becoming less attractive to new activity over time. Finally, by measuring the average activity as a function of the day of the week, we find that productivity seems to be higher on Tuesdays and Wednesdays, with Sundays being the least active day.
Dynamics of Discrete Breathers in a Pt3Al Crystal
NASA Astrophysics Data System (ADS)
Starostenkov, M. D.; Potekaev, A. I.; Dmitriev, S. V.; Zakharov, P. V.; Eremin, A. M.; Kulagina, V. V.
2016-01-01
The discrete breathers in a Pt3Al crystal, which exhibit soft (DB1) and hard (DB2) nonlinearity, are shown to possess a number of principal differences. Unlike an immobile and stable DB1, a DB2 breather is mainly localized on four Al atoms and is stretched along one of the close-packed rows of crystals. On the other hand, DB2 can displace hundreds of nanometers along one of the directions of close packing. Having localized a considerable amount of energy, both DB1 and DB2 breathers slowly emit it during their lifetime. A collision of DB1 and DB2 results in part of their energy being released into the Al sublattice, the larger part lost by DB2 that is destroyed faster than DB1. The DB2 breather can effectively transport the energy throughout the crystal, and a collision of DBs results in its considerable localization in the crystal. A capability of transferring the energy can thus give rise to structural transformations far from the focus of excitation of such localized objects.
NASA Astrophysics Data System (ADS)
Zhang, Z.; Toyer, S.; Brizhinev, D.; Ledger, M.; Taylor, K.; Purss, M. B. J.
2016-12-01
We are witnessing a rapid proliferation of geoscientific and geospatial data from an increasing variety of sensors and sensor networks. This data presents great opportunities to resolve cross-disciplinary problems. However, working with it often requires an understanding of file formats and protocols seldom used outside of scientific computing, potentially limiting the data's value to other disciplines. In this paper, we present a new approach to serving satellite coverage data on the web, which improves ease-of-access using the principles of linked data. Linked data adapts the concepts and protocols of the human-readable web to machine-readable data; the number of developers familiar with web technologies makes linked data a natural choice for bringing coverages to a wider audience. Our approach to using linked data also makes it possible to efficiently service high-level SPARQL queries: for example, "Retrieve all Landsat ETM+ observations of San Francisco between July and August 2016" can easily be encoded in a single query. We validate the new approach, which we call QBCov, with a reference implementation of the entire stack, including a simple web-based client for interacting with Landsat observations. In addition to demonstrating the utility of linked data for publishing coverages, we investigate the heretofore unexplored relationship between Discrete Global Grid Systems (DGGS) and linked data. Our conclusions are informed by the aforementioned reference implementation of QBCov, which is backed by a hierarchical file format designed around the rHEALPix DGGS. Not only does the choice of a DGGS-based representation provide an efficient mechanism for accessing large coverages at multiple scales, but the ability of DGGS to produce persistent, unique identifiers for spatial regions is especially valuable in a linked data context. This suggests that DGGS has an important role to play in creating sustainable and scalable linked data infrastructures. QBCov is being
Dynamics of The Tranquil Cosmic Web
NASA Astrophysics Data System (ADS)
Nusser, Adi
2016-10-01
The phase space distribution of matter out to ~ 100 \\rm Mpc is probed by two types of observational data: galaxy redshift surveys and peculiar motions of galaxies. Important information on the process of structure formation and deviations from standard gravity have been extracted from the accumulating data. The remarkably simple Zel'dovich approximation is the basis for much of our insight into the dynamics of structure formation and the development of data analyses methods. Progress in the methodology and some recent results is reviewed.
Static and dynamic explanations for patterns in food webs.
Lawton, J H; Warren, P H
1988-09-01
Ten interesting patterns can be discerned in compendia of published food webs, and are not all easily dismissed as artefacts of poor data. A variety of theoretical explanations have been put forward to explain one, or more, of these patterns; for example, five reasons have been advanced for why food chains are short. Two bodies of theory each satisfactorily account for a majority (but not all) of the patterns, but draw on very different assumptions. One group of theoretical explanations is based on dynamic interactions between species, modelled by Lotka-Volterra equations. The other takes a static view of food web assembly, and assumes a trophic cascade, or hierarchy of feeding links, in which species body sizes appear to play a crucial role. On present evidence, it is not possible to distinguish between the relative contributions of either of these possibilities in the creation of structure in real food webs. Copyright © 1988. Published by Elsevier Ltd.
Liao, Bolin; Zhang, Yunong; Jin, Long
2016-02-01
In this paper, a new Taylor-type numerical differentiation formula is first presented to discretize the continuous-time Zhang neural network (ZNN), and obtain higher computational accuracy. Based on the Taylor-type formula, two Taylor-type discrete-time ZNN models (termed Taylor-type discrete-time ZNNK and Taylor-type discrete-time ZNNU models) are then proposed and discussed to perform online dynamic equality-constrained quadratic programming. For comparison, Euler-type discrete-time ZNN models (called Euler-type discrete-time ZNNK and Euler-type discrete-time ZNNU models) and Newton iteration, with interesting links being found, are also presented. It is proved herein that the steady-state residual errors of the proposed Taylor-type discrete-time ZNN models, Euler-type discrete-time ZNN models, and Newton iteration have the patterns of O(h(3)), O(h(2)), and O(h), respectively, with h denoting the sampling gap. Numerical experiments, including the application examples, are carried out, of which the results further substantiate the theoretical findings and the efficacy of Taylor-type discrete-time ZNN models. Finally, the comparisons with Taylor-type discrete-time derivative model and other Lagrange-type discrete-time ZNN models for dynamic equality-constrained quadratic programming substantiate the superiority of the proposed Taylor-type discrete-time ZNN models once again.
Emerging hierarchies in dynamically adapting webs
NASA Astrophysics Data System (ADS)
Katifori, Eleni; Graewer, Johannes; Magnasco, Marcelo; Modes, Carl
Transport networks play a key role across four realms of eukaryotic life: slime molds, fungi, plants, and animals. In addition to the developmental algorithms that build them, many also employ adaptive strategies to respond to stimuli, damage, and other environmental changes. We model these adapting network architectures using a generic dynamical system on weighted graphs and find in simulation that these networks ultimately develop a hierarchical organization of the final weighted architecture accompanied by the formation of a system-spanning backbone. We quantify the hierarchical organization of the networks by developing an algorithm that decomposes the architecture to multiple scales and analyzes how the organization in each scale relates to that of the scale above and below it. The methodologies developed in this work are applicable to a wide range of systems including the slime mold physarum polycephalum, human microvasculature, and force chains in granular media.
ERIC Educational Resources Information Center
Winkel, Brian
2012-01-01
We give an example of cross coursing in which a subject or approach in one course in undergraduate mathematics is used in a completely different course. This situation crosses falling body modelling in an upper level differential equations course into a modest discrete dynamical systems unit of a first-year mathematics course. (Contains 1 figure.)
ERIC Educational Resources Information Center
Winkel, Brian
2012-01-01
We give an example of cross coursing in which a subject or approach in one course in undergraduate mathematics is used in a completely different course. This situation crosses falling body modelling in an upper level differential equations course into a modest discrete dynamical systems unit of a first-year mathematics course. (Contains 1 figure.)
Bifurcations and dynamics of a discrete predator-prey system.
Asheghi, Rasoul
2014-01-01
In this paper, we study the dynamics behaviour of a stratum of plant-herbivore which is modelled through the following F(x, y)=(f(x, y), g(x, y)) two-dimensional map with four parameters defined by [Formula: see text] where x ≥ 0, y ≥ 0, and the real parameters a, b, r, k are all positive. We will focus on the case a ≠ b. We study the stability of fixed points and do the analysis of the period-doubling and the Neimark-Sacker bifurcations in a standard way.
Quantum circuit dynamics via path integrals: Is there a classical action for discrete-time paths?
NASA Astrophysics Data System (ADS)
Penney, Mark D.; Enshan Koh, Dax; Spekkens, Robert W.
2017-07-01
It is straightforward to compute the transition amplitudes of a quantum circuit using the sum-over-paths methodology when the gates in the circuit are balanced, where a balanced gate is one for which all non-zero transition amplitudes are of equal magnitude. Here we consider the question of whether, for such circuits, the relative phases of different discrete-time paths through the configuration space can be defined in terms of a classical action, as they are for continuous-time paths. We show how to do so for certain kinds of quantum circuits, namely, Clifford circuits where the elementary systems are continuous-variable systems or discrete systems of odd-prime dimension. These types of circuit are distinguished by having phase-space representations that serve to define their classical counterparts. For discrete systems, the phase-space coordinates are also discrete variables. We show that for each gate in the generating set, one can associate a symplectomorphism on the phase-space and to each of these one can associate a generating function, defined on two copies of the configuration space. For discrete systems, the latter association is achieved using tools from algebraic geometry. Finally, we show that if the action functional for a discrete-time path through a sequence of gates is defined using the sum of the corresponding generating functions, then it yields the correct relative phases for the path-sum expression. These results are likely to be relevant for quantizing physical theories where time is fundamentally discrete, characterizing the classical limit of discrete-time quantum dynamics, and proving complexity results for quantum circuits.
Dynamics in a three species food-web system
NASA Astrophysics Data System (ADS)
Gupta, K.; Gakkhar, S.
2016-04-01
In this paper, the dynamics of a three species food-web system is discussed. The food-web comprises of one predator and two logistically growing competing species. The predator species is taking food from one of the competitors with Holling type II functional response. Another competitor is the amensal species for the predator of first species. The system is shown to be positive and bounded. The stability of various axial points, boundary points and interior point has been investigated. The persistence of the system has been studied. Numerical simulation has been performed to show the occurrence of Hopf bifurcation and stable limit cycle about the interior point. The presence of second competitor and its interaction with predator gives more complex dynamics than the simple prey-predator system. The existence of transcritical bifurcation has been established about two axial points. The existence of periodic attractor having period-2 solution has been shown, when amensal coefficient is chosen as bifurcation parameter.
Discrete-time dynamic systems synchronization: Information transmission and model matching
NASA Astrophysics Data System (ADS)
Tôrres, Leonardo A. B.
2007-04-01
Some recently published results have highlighted the role of synchronization phenomena in recovering perturbation signals injected in nonlinear continuous-time oscillators. In the present contribution, those results are extended to the realm of discrete-time systems. It is also shown that the synchronization of nonlinear discrete-time systems provide very interesting ramifications to the problem of measuring the discrepancy between mathematical models and the corresponding original dynamical system from which the data were measured. Moreover, the noise impact on the proposed approach is discussed.
Dynamics of Quantal Heating in Electron Systems with Discrete Spectra
NASA Astrophysics Data System (ADS)
Mayer, William; Dietrich, Scott; Vitkalov, Sergey; Bykov, Alexey
2015-03-01
The temporal evolution of quantal Joule heating of 2D electrons in GaAs quantum well placed in quantizing magnetic fields is studied using a difference frequency method. The method is based on measurements of the electron conductivity oscillating at the beat frequency f =f1 -f2 between two microwaves applied to 2D system at frequencies f1 and f2. The method provides direct access to the dynamical characteristics of the heating and yields the inelastic scattering time τin of 2D electrons. The obtained τin is strongly temperature dependent, varying from 0.13 ns at 5.5K to 1 ns at 2.4K in magnetic field B=0.333T. When temperature T exceeds the Landau level separation the relaxation rate 1 /τin is proportional to T2, indicating the electron-electron interaction as the dominant mechanism limiting the quantal heating. At lower temperatures the rate tends to be proportional to T3, indicating considerable contribution from electron-phonon scattering. This work was supported by the National Science Foundation (DMR 1104503), the Russian Foundation for Basic Research (project no.14-02-01158) and the Ministry of Education and Science of the Russian Federation.
Discrete Adjoint-Based Design Optimization of Unsteady Turbulent Flows on Dynamic Unstructured Grids
NASA Technical Reports Server (NTRS)
Nielsen, Eric J.; Diskin, Boris; Yamaleev, Nail K.
2009-01-01
An adjoint-based methodology for design optimization of unsteady turbulent flows on dynamic unstructured grids is described. The implementation relies on an existing unsteady three-dimensional unstructured grid solver capable of dynamic mesh simulations and discrete adjoint capabilities previously developed for steady flows. The discrete equations for the primal and adjoint systems are presented for the backward-difference family of time-integration schemes on both static and dynamic grids. The consistency of sensitivity derivatives is established via comparisons with complex-variable computations. The current work is believed to be the first verified implementation of an adjoint-based optimization methodology for the true time-dependent formulation of the Navier-Stokes equations in a practical computational code. Large-scale shape optimizations are demonstrated for turbulent flows over a tiltrotor geometry and a simulated aeroelastic motion of a fighter jet.
Wei, Qinglai; Liu, Derong; Lin, Qiao
2016-08-03
In this paper, a novel local value iteration adaptive dynamic programming (ADP) algorithm is developed to solve infinite horizon optimal control problems for discrete-time nonlinear systems. The focuses of this paper are to study admissibility properties and the termination criteria of discrete-time local value iteration ADP algorithms. In the discrete-time local value iteration ADP algorithm, the iterative value functions and the iterative control laws are both updated in a given subset of the state space in each iteration, instead of the whole state space. For the first time, admissibility properties of iterative control laws are analyzed for the local value iteration ADP algorithm. New termination criteria are established, which terminate the iterative local ADP algorithm with an admissible approximate optimal control law. Finally, simulation results are given to illustrate the performance of the developed algorithm.
Makarenko, A. V.
2016-10-15
A new class of bifurcations is defined in discrete dynamical systems, and methods for their diagnostics and the analysis of their properties are presented. The TQ-bifurcations considered are implemented in discrete mappings and are related to the qualitative rearrangement of the shape of trajectories in an extended space of states. Within the demonstration of the main capabilities of the toolkit, an analysis is carried out of a logistic mapping in a domain to the right of the period-doubling limit point. Five critical values of the parameter are found for which the geometric structure of the trajectories of the mapping experiences a qualitative rearrangement. In addition, an analysis is carried out of the so-called “trace map,” which arises in the problems of quantum-mechanical description of various properties of discrete crystalline and quasicrystalline lattices.
A discrete geometric approach for simulating the dynamics of thin viscous threads
Audoly, B.; Clauvelin, N.; Brun, P.-T.; Bergou, M.; Grinspun, E.; Wardetzky, M.
2013-11-15
We present a numerical model for the dynamics of thin viscous threads based on a discrete, Lagrangian formulation of the smooth equations. The model makes use of a condensed set of coordinates, called the centerline/spin representation: the kinematic constraints linking the centerline's tangent to the orientation of the material frame is used to eliminate two out of three degrees of freedom associated with rotations. Based on a description of twist inspired from discrete differential geometry and from variational principles, we build a full-fledged discrete viscous thread model, which includes in particular a discrete representation of the internal viscous stress. Consistency of the discrete model with the classical, smooth equations for thin threads is established formally. Our numerical method is validated against reference solutions for steady coiling. The method makes it possible to simulate the unsteady behavior of thin viscous threads in a robust and efficient way, including the combined effects of inertia, stretching, bending, twisting, large rotations and surface tension.
Remarks on discrete and continuous large-scale models of DNA dynamics.
Klapper, I; Qian, H
1998-01-01
We present a comparison of the continuous versus discrete models of large-scale DNA conformation, focusing on issues of relevance to molecular dynamics. Starting from conventional expressions for elastic potential energy, we derive elastic dynamic equations in terms of Cartesian coordinates of the helical axis curve, together with a twist function representing the helical or excess twist. It is noted that the conventional potential energies for the two models are not consistent. In addition, we derive expressions for random Brownian forcing for the nonlinear elastic dynamics and discuss the nature of such forces in a continuous system. PMID:9591677
NASA Astrophysics Data System (ADS)
Guo, Shu-Juan; Fu, Xin-Chu
2010-07-01
In this paper, by applying Lasalle's invariance principle and some results about the trace of a matrix, we propose a method for estimating the topological structure of a discrete dynamical network based on the dynamical evolution of the network. The network concerned can be directed or undirected, weighted or unweighted, and the local dynamics of each node can be nonidentical. The connections among the nodes can be all unknown or partially known. Finally, two examples, including a Hénon map and a central network, are illustrated to verify the theoretical results.
NASA Astrophysics Data System (ADS)
Xun, Zhi-Peng; Zhang, Zhe; Chen, Yi-Li; Wu, Ling; Tang, Gang
2017-04-01
In order to investigate the influences of large height differences and overhangs on the dynamic scaling behavior of discrete models, meanwhile reducing the finite-size effects, the Etching model is modified to reduce large height differences, and the overhangs in Ballistic Deposition surfaces are removed under certain principles. Numerical simulations are carried out for the modified models, and the results show that the modified surfaces lead to good dynamic scaling behavior even on small system length scales. The values of the dynamic scaling exponents are in excellent agreement with theoretical predictions of the Kardar-Parisi-Zhang equation in (1 + 1) dimensions.
Prototyping Dynamic Earth Science Data Visualization on the Web
NASA Astrophysics Data System (ADS)
Roberts, J. T.; Zhou, A. Y.; Rodriguez, J.; Hall, J. R.; Thompson, C. K.
2016-12-01
Current solutions for rapid map-based visualization of Earth Science data products on the web typically provide static image representations of the data that have been transformed or abstracted away from the actual source data values. The color pixels within these images are generally confined to 256 bins, which represent a limited precision of values. The accuracy of these values may be sufficient for introductory analysis, but inadequate for scientific analysis.New technologies are emerging that enable visualizations based on the underlying source data values of the imagery within a web browser. By having interactive access to source data values, high quality analysis within a web application can be achieved by leveraging server-side data access instead of downloading entire data files and processing them locally. This enables on-the-fly tasks ranging from hovering over a point to see its raw value, dynamically applying a color palette, modifying the color scale (e.g., from linear to logarithmic) to highlight variations in the data, or performing statistical analysis of data values within a selected region. This presentation highlights findings from an ongoing effort by NASA's Global Imagery Browse Services to investigate various technologies and file formats that make these types of dynamic data visualizations possible.
NASA Astrophysics Data System (ADS)
Rastogi, Vikas
2016-09-01
The main focus of the paper is touted as effects of discrete damping on the dynamic analysis of rotating shaft. The whole analysis is being carried out through extended Lagrangian formulation for a discrete - continuous system. The variation formulation for this system is possible, considering the continuous system as one-dimensional. The generalized formulation for one dimensional continuous rotary shaft with discrete external damper has been obtained through principle of variation. Using this extended formulation, the invariance of umbra-Lagrangian density through extended Noether's theorem is achieved. Rayleigh beam model is used to model the shaft. Amplitude equation of rotor is obtained theoretically and validated through simulation results. The simulation results reveal the important phenomena of limiting dynamics of the rotor shaft, which is due to an imbalance of material damping and stiffness of the rotor shaft. The regenerative energy in the rotor shaft, induced due to elasticity/stiffness of the rotor shaft, is dissipated partially through the in-span discrete damper and also through the dissipative coupling between drive and the rotor shaft. In such cases, the shaft speed will not increase with increase in excitation frequency of the rotor but the slip between the drive and the shaft increases due to loading of drive.
h2-norm optimal model reduction for large scale discrete dynamical MIMO systems
NASA Astrophysics Data System (ADS)
Bunse-Gerstner, A.; Kubalinska, D.; Vossen, G.; Wilczek, D.
2010-01-01
Modeling strategies often result in dynamical systems of very high dimension. It is then desirable to find systems of the same form but of lower complexity, whose input-output behavior approximates the behavior of the original system. Here we consider linear time-invariant discrete-time dynamical systems. The cornerstone of this paper is a relation between optimal model reduction in the h2-norm and (tangential) rational Hermite interpolation. First order necessary conditions for h2-optimal model reduction are presented for discrete Multiple-Input-Multiple-Output (MIMO) systems. These conditions suggest a specific choice of interpolation data and a novel algorithm aiming for anh2-optimal model reduction for MIMO systems. It is also shown that the conditions are equivalent to two known gramian-based first order necessary conditions. Numerical experiments demonstrate the approximation quality of the method.
Discrete Time McKean–Vlasov Control Problem: A Dynamic Programming Approach
Pham, Huyên Wei, Xiaoli
2016-12-15
We consider the stochastic optimal control problem of nonlinear mean-field systems in discrete time. We reformulate the problem into a deterministic control problem with marginal distribution as controlled state variable, and prove that dynamic programming principle holds in its general form. We apply our method for solving explicitly the mean-variance portfolio selection and the multivariate linear-quadratic McKean–Vlasov control problem.
Discrete scale invariant quantum dynamics and universal quantum beats in Bose gases
NASA Astrophysics Data System (ADS)
Maki, J.; Jiang, S. J.; Zhou, F.
2017-06-01
We study the signature of classical scale invariance in the far-from-equilibrium quantum dynamics of two-dimensional Bose gases. We show that the density profile displays a scale invariant logarithmic singularity near the center. In addition, the density oscillates due to quantum beats with universal structures. Namely, the frequencies of the beats can be connected with one another by a universal discrete scale transformation induced by the classical scale invariance. The experimental applicability of these results is then discussed.
A discrete dynamics model for synchronization of pulse-coupled oscillators.
Schultz, A; Wechsler, H
1998-01-01
Biological information processing systems employ a variety of feature types. It has been postulated that oscillator synchronization is the mechanism for binding these features together to realize coherent perception. A discrete dynamic model of a coupled system of oscillators is presented. The network of oscillators converges to a state where subpopulations of cells become phase synchronized. It has potential applications to describing biological perception as well as for the construction of multifeature pattern recognition systems. It is shown that this model can be used to detect the presence of short line segments in the boundary contour of an object. The Hough transform, which is the standard method for detecting curve segments of a specified shape in an image was found not to be effective for this application. Implementation of the discrete dynamics model of oscillator synchronization is much easier than the differential equation models that have appeared in the literature. A systematic numerical investigation of the convergence properties of the model has been performed and it is shown that the discrete dynamics model can scale up to large number of oscillators.
Distributing flight dynamics products via the World Wide Web
NASA Technical Reports Server (NTRS)
Woodard, Mark; Matusow, David
1996-01-01
The NASA Flight Dynamics Products Center (FDPC), which make available selected operations products via the World Wide Web, is reported on. The FDPC can be accessed from any host machine connected to the Internet. It is a multi-mission service which provides Internet users with unrestricted access to the following standard products: antenna contact predictions; ground tracks; orbit ephemerides; mean and osculating orbital elements; earth sensor sun and moon interference predictions; space flight tracking data network summaries; and Shuttle transport system predictions. Several scientific data bases are available through the service.
Dynamics of pairwise motions in the Cosmic Web
NASA Astrophysics Data System (ADS)
Hellwing, Wojciech A.
2016-10-01
We present results of analysis of the dark matter (DM) pairwise velocity statistics in different Cosmic Web environments. We use the DM velocity and density field from the Millennium 2 simulation together with the NEXUS+ algorithm to segment the simulation volume into voxels uniquely identifying one of the four possible environments: nodes, filaments, walls or cosmic voids. We show that the PDFs of the mean infall velocities v 12 as well as its spatial dependence together with the perpendicular and parallel velocity dispersions bear a significant signal of the large-scale structure environment in which DM particle pairs are embedded. The pairwise flows are notably colder and have smaller mean magnitude in wall and voids, when compared to much denser environments of filaments and nodes. We discuss on our results, indicating that they are consistent with a simple theoretical predictions for pairwise motions as induced by gravitational instability mechanism. Our results indicate that the Cosmic Web elements are coherent dynamical entities rather than just temporal geometrical associations. In addition it should be possible to observationally test various Cosmic Web finding algorithms by segmenting available peculiar velocity data and studying resulting pairwise velocity statistics.
Successional dynamics in the seasonally forced diamond food web.
Klausmeier, Christopher A; Litchman, Elena
2012-07-01
Plankton seasonal succession is a classic example of nonequilibrium community dynamics. Despite the fact that it has been well studied empirically, it lacks a general quantitative theory. Here we investigate a food web model that includes a resource, two phytoplankton, and a shared grazer-the diamond food web-in a seasonal environment. The model produces a number of successional trajectories that have been widely discussed in the context of the verbal Plankton Ecology Group model of succession, such as a spring bloom of a good competitor followed by a grazer-induced clear-water phase, setting the stage for the late-season dominance of a grazer-resistant species. It also predicts a novel, counterintuitive trajectory where the grazer-resistant species has both early- and late-season blooms. The model often generates regular annual cycles but sometimes produces multiyear cycles or chaos, even with identical forcing each year. Parameterizing the model, we show how the successional trajectory depends on nutrient supply and the length of the growing season, two key parameters that vary among water bodies. This model extends nonequilibrium theory to food webs and is a first step toward a quantitative theory of plankton seasonal succession.
Eisenhauer, Philipp; Heckman, James J.; Mosso, Stefano
2015-01-01
We compare the performance of maximum likelihood (ML) and simulated method of moments (SMM) estimation for dynamic discrete choice models. We construct and estimate a simplified dynamic structural model of education that captures some basic features of educational choices in the United States in the 1980s and early 1990s. We use estimates from our model to simulate a synthetic dataset and assess the ability of ML and SMM to recover the model parameters on this sample. We investigate the performance of alternative tuning parameters for SMM. PMID:26494926
Discrete-time dynamic user-optimal departure time/route choice model
Chen, H.K.; Hsueh, C.F.
1998-05-01
This paper concerns a discrete-time, link-based, dynamic user-optimal departure time/route choice model using the variational inequality approach. The model complies with a dynamic user-optimal equilibrium condition in which for each origin-destination pair, the actual route travel times experienced by travelers, regardless the departure time, is equal and minimal. A nested diagonalization procedure is proposed to solve the model. Numerical examples are then provided for demonstration and detailed elaboration for multiple solutions and Braess`s paradox.
Discrete Molecular Dynamics Approach to the Study of Disordered and Aggregating Proteins.
Emperador, Agustí; Orozco, Modesto
2017-03-14
We present a refinement of the Coarse Grained PACSAB force field for Discrete Molecular Dynamics (DMD) simulations of proteins in aqueous conditions. As the original version, the refined method provides good representation of the structure and dynamics of folded proteins but provides much better representations of a variety of unfolded proteins, including some very large, impossible to analyze by atomistic simulation methods. The PACSAB/DMD method also reproduces accurately aggregation properties, providing good pictures of the structural ensembles of proteins showing a folded core and an intrinsically disordered region. The combination of accuracy and speed makes the method presented here a good alternative for the exploration of unstructured protein systems.
Stochastic aspects of one-dimensional discrete dynamical systems: Benford's law
NASA Astrophysics Data System (ADS)
Snyder, Mark A.; Curry, James H.; Dougherty, Anne M.
2001-08-01
Benford's law owes its discovery to the ``Grubby Pages Hypothesis,'' a 19th century observation made by Simon Newcomb that the beginning pages of logarithm books were grubbier than the last few pages, implying that scientists referenced the values toward the front of the books more frequently. If a data set satisfies Benford's law, then it's significant digits will have a logarithmic distribution, which favors smaller significant digits. In this article we demonstrate two ways of creating discrete one-dimensional dynamical systems that satisfy Benford's law. We also develop a numerical simulation methodology that we use to study dynamical systems when analytical results are not readily available.
NASA Technical Reports Server (NTRS)
Dupnick, E.
1973-01-01
Description of the development and operation of a vehicle-scheduling algorithm which has applications to the NASA problem of assigning payloads to space delivery vehicles. The algorithm is based on a discrete, integer-valued, nonserial, dynamic-programming solution to the classical problem of developing resource utilization plans with limited resources. The algorithm places special emphasis on incorporating interpayload (precedence) relationships; maintaining optimal alternate schedule definitions (a unique feature of dynamic programming) in the event of contingencies (namely, resource inventory changes) without problem resolution; and, by using a special information storage technique, reducing the computational complexity of solving realistic problems.
A discrete approach to stochastic parametrization and dimension reduction in nonlinear dynamics
NASA Astrophysics Data System (ADS)
Lu, F.; Chorin, A. J.
2015-12-01
Prediction for a high-dimensional nonlinear dynamic system often encounters difficulties: the system may be too complicated to solve in full, and initial data may be missing because only a small subset of variables is observed. However, only a small subset of the variables may be of interest and need to be predicted. We present a solution by developing a discrete stochastic reduced system for the variables of interest, in which one formulates discrete solvable approximate equations for these variables and uses data and statistical methods to account for the impact of the other variables. The stochastic reduced system can capture the long-time statistical properties of the full system as well as the short-time dynamics, and hence make reliable predictions. A key ingredient in the construction of the stochastic reduced system is a discrete-time stochastic parametrization based on the NARMAX (nonlinear autoregression moving average with exogenous input) model. As an example, this construction is applied to the Lorenz 96 system.
NASA Astrophysics Data System (ADS)
Liu, Jie; Sun, Xingsheng; Li, Kun; Jiang, Chao; Han, Xu
2015-11-01
Aiming at structures containing random parameters with multi-peak probability density functions (PDFs) or great variable coefficients, an analytical method of probability density function discretization and approximation (PDFDA) is proposed for dynamic load identification. Dynamic loads are expressed as the functions of time and random parameters in time domain and the forward model is established through the discretized convolution integral of loads and the corresponding unit-pulse response functions. The PDF of each random parameter is discretized into several subintervals and in each subinterval the original PDF curve is approximated via uniform distribution PDF with equal probability value. Then the joint distribution model is built and hence the equivalent deterministic equations are solved to identify unknown loads. Inverse analysis is operated separately at each variable in the joint distribution model through regularization because of noise-contaminated measured responses. In order to assess the accuracy of identified results, PDF curves and statistical properties of loads are achieved based on the specially assumed distributions of identified loads. Numerical simulations demonstrate the efficiency and superiority of the presented method.
NASA Astrophysics Data System (ADS)
Lai, Pik-Yin
2017-02-01
Reconstructing network connection topology and interaction strengths solely from measurement of the dynamics of the nodes is a challenging inverse problem of broad applicability in various areas of science and engineering. For a discrete-time step network under noises whose noise-free dynamics is stationary, we derive general analytic results relating the weighted connection matrix of the network to the correlation functions obtained from time-series measurements of the nodes for networks with one-dimensional intrinsic node dynamics. Information about the intrinsic node dynamics and the noise strengths acting on the nodes can also be obtained. Based on these results, we develop a scheme that can reconstruct the above information of the network using only the time-series measurements of node dynamics as input. Reconstruction formulas for higher-dimensional node dynamics are also derived and illustrated with a two-dimensional node dynamics network system. Furthermore, we extend our results and obtain a reconstruction scheme even for the cases when the noise-free dynamics is periodic. We demonstrate that our method can give accurate reconstruction results for weighted directed networks with linear or nonlinear node dynamics of various connection topologies, and with linear or nonlinear couplings.
NASA Astrophysics Data System (ADS)
Tancock, M. J.; Lane, S. N.; Hardy, R. J.
2012-12-01
There has been a significant amount of research conducted in order to understand the flow fields at natural river confluences. Much of this has been made possible due to advances in the use of Computational Fluid Dynamics (CFD). However, much of this research has been conducted on river confluences with negligible water surface slopes and any understanding of the sediment dynamics is largely implied from the flow fields. Therefore, a key challenge is to understand the flow and sediment dynamics of steep river confluences with dynamic boundaries. Two numerical modelling developments are presented which together are capable of increasing our understanding of the sediment dynamics of steep river confluences. The first is the application of a Height-of-Liquid (HOL) model within a CFD framework to explicitly solve the water surface elevation. This is a time-dependent, multiphase treatment of the fluid dynamics which solves for the change in volume of water and air in each vertical column of the mesh. The second is the development of a reduced complexity discrete particle transport model which uses the change in momentum on a spherical particle to predict the transport paths through the flow field determined from CFD simulations. The performance of the two models is tested using field data from a series of highly dynamic, steep gravel-bed confluences on a braidplain of the Borgne d'Arolla, Switzerland. The HOL model is validated against the water surface elevation and flow velocity data and is demonstrated to provide a reliable representation of the flow field in fast-flowing, supercritical flows. In order to validate the discrete particle model, individual particles were tracked using electronic tacheometry. The model is demonstrated to accurately represent the particle tracks obtained in the field and provides a new methodology to understand the dynamic morphology of braid plains.
NASA Astrophysics Data System (ADS)
Chang, Wei-Der; Yan, Jun-Juh
2006-10-01
In this paper, we propose a novel genetic algorithm (GA) with a multi-crossover fashion to estimate the associated coefficients for a class of nonlinear discrete-time multivariable dynamical systems. Unlike the traditional crossover method of using two chromosomes, the proposed method uses three chromosomes to achieve a crossover. According to the adjusting direction by crossing three chromosomes, more excellent offspring can be produced. To solve the identification problem of multivariable nonlinear discrete-time systems, each of estimated system coefficients represents a gene, and a collection of genes is referred to as a chromosome in the view of GA. The chromosomes in the population are then evolved using the proposed multi-crossover method. An illustrative example of multivariable nonlinear systems is given to demonstrate the effectiveness, as compared with the traditional crossover method, of the proposed method.
2014-01-01
Berth allocation is the forefront operation performed when ships arrive at a port and is a critical task in container port optimization. Minimizing the time ships spend at berths constitutes an important objective of berth allocation problems. This study focuses on the discrete dynamic berth allocation problem (discrete DBAP), which aims to minimize total service time, and proposes an iterated greedy (IG) algorithm to solve it. The proposed IG algorithm is tested on three benchmark problem sets. Experimental results show that the proposed IG algorithm can obtain optimal solutions for all test instances of the first and second problem sets and outperforms the best-known solutions for 35 out of 90 test instances of the third problem set. PMID:25295295
Lin, Shih-Wei; Ying, Kuo-Ching; Wan, Shu-Yen
2014-01-01
Berth allocation is the forefront operation performed when ships arrive at a port and is a critical task in container port optimization. Minimizing the time ships spend at berths constitutes an important objective of berth allocation problems. This study focuses on the discrete dynamic berth allocation problem (discrete DBAP), which aims to minimize total service time, and proposes an iterated greedy (IG) algorithm to solve it. The proposed IG algorithm is tested on three benchmark problem sets. Experimental results show that the proposed IG algorithm can obtain optimal solutions for all test instances of the first and second problem sets and outperforms the best-known solutions for 35 out of 90 test instances of the third problem set.
Discrete Adjoint-Based Design for Unsteady Turbulent Flows On Dynamic Overset Unstructured Grids
NASA Technical Reports Server (NTRS)
Nielsen, Eric J.; Diskin, Boris
2012-01-01
A discrete adjoint-based design methodology for unsteady turbulent flows on three-dimensional dynamic overset unstructured grids is formulated, implemented, and verified. The methodology supports both compressible and incompressible flows and is amenable to massively parallel computing environments. The approach provides a general framework for performing highly efficient and discretely consistent sensitivity analysis for problems involving arbitrary combinations of overset unstructured grids which may be static, undergoing rigid or deforming motions, or any combination thereof. General parent-child motions are also accommodated, and the accuracy of the implementation is established using an independent verification based on a complex-variable approach. The methodology is used to demonstrate aerodynamic optimizations of a wind turbine geometry, a biologically-inspired flapping wing, and a complex helicopter configuration subject to trimming constraints. The objective function for each problem is successfully reduced and all specified constraints are satisfied.
Beyler, Andrew P; Marshall, Lisa F; Cui, Jian; Brokmann, Xavier; Bawendi, Moungi G
2013-10-25
We measure the anomalous spectral diffusion of single colloidal quantum dots over eight temporal decades simultaneously by combining single-molecule spectroscopy and photon-correlation Fourier spectroscopy. Our technique distinguishes between discrete and continuous dynamics and directly reveals that the quasicontinuous spectral diffusion observed using conventional spectroscopy is composed of rapid, discrete spectral jumps. Despite their multiple time scales, these dynamics can be captured by a single mechanism whose parameters vary widely between dots and over time in individual dots.
NASA Astrophysics Data System (ADS)
Liu, Chao; Zhang, Qingling; Zhang, Xue; Duan, Xiaodong
2009-09-01
A differential-algebraic model system which considers a prey-predator system with stage structure for prey and harvest effort on predator is proposed. By using the differential-algebraic system theory and bifurcation theory, dynamic behavior of the proposed model system with and without discrete time delay is investigated. Local stability analysis of the model system without discrete time delay reveals that there is a phenomenon of singularity induced bifurcation due to variation of the economic interest of harvesting, and a state feedback controller is designed to stabilize the proposed model system at the interior equilibrium; Furthermore, local stability of the model system with discrete time delay is studied. It reveals that the discrete time delay has a destabilizing effect in the population dynamics, and a phenomenon of Hopf bifurcation occurs as the discrete time delay increases through a certain threshold. Finally, numerical simulations are carried out to show the consistency with theoretical analysis obtained in this paper.
Geraci, Joseph; Dharsee, Moyez; Nuin, Paulo; Haslehurst, Alexandria; Koti, Madhuri; Feilotter, Harriet E; Evans, Ken
2014-03-01
We introduce a novel method for visualizing high dimensional data via a discrete dynamical system. This method provides a 2D representation of the relationship between subjects according to a set of variables without geometric projections, transformed axes or principal components. The algorithm exploits a memory-type mechanism inherent in a certain class of discrete dynamical systems collectively referred to as the chaos game that are closely related to iterative function systems. The goal of the algorithm was to create a human readable representation of high dimensional patient data that was capable of detecting unrevealed subclusters of patients from within anticipated classifications. This provides a mechanism to further pursue a more personalized exploration of pathology when used with medical data. For clustering and classification protocols, the dynamical system portion of the algorithm is designed to come after some feature selection filter and before some model evaluation (e.g. clustering accuracy) protocol. In the version given here, a univariate features selection step is performed (in practice more complex feature selection methods are used), a discrete dynamical system is driven by this reduced set of variables (which results in a set of 2D cluster models), these models are evaluated for their accuracy (according to a user-defined binary classification) and finally a visual representation of the top classification models are returned. Thus, in addition to the visualization component, this methodology can be used for both supervised and unsupervised machine learning as the top performing models are returned in the protocol we describe here. Butterfly, the algorithm we introduce and provide working code for, uses a discrete dynamical system to classify high dimensional data and provide a 2D representation of the relationship between subjects. We report results on three datasets (two in the article; one in the appendix) including a public lung cancer
Global dynamics in a stage-structured discrete-time population model with harvesting.
Liz, Eduardo; Pilarczyk, Paweł
2012-03-21
The purpose of this paper is to analyze the effect of constant effort harvesting upon global dynamics of a discrete-time population model with juvenile and adult stages. We consider different scenarios, including adult-only mortality, juvenile-only mortality, and equal mortality of juveniles and adults. In addition to analytical study of equilibria of the system, we analyze global dynamics by means of an automated set-oriented rigorous numerical method. We obtain a comprehensive overview of the dynamics as the harvest rate and survival probability change. In particular, we determine the range of parameters for which the population abundance gets larger in spite of an increase in the harvest rate (so-called hydra effect), and for which subsequent increases in harvesting effort can magnify fluctuations in population abundance (destabilize it) and then stabilize it again (so-called bubble effect). Copyright © 2011 Elsevier Ltd. All rights reserved.
NASA Astrophysics Data System (ADS)
Spellings, Matthew; Marson, Ryan L.; Anderson, Joshua A.; Glotzer, Sharon C.
2017-04-01
Faceted shapes, such as polyhedra, are commonly found in systems of nanoscale, colloidal, and granular particles. Many interesting physical phenomena, like crystal nucleation and growth, vacancy motion, and glassy dynamics are challenging to model in these systems because they require detailed dynamical information at the individual particle level. Within the granular materials community the Discrete Element Method has been used extensively to model systems of anisotropic particles under gravity, with friction. We provide an implementation of this method intended for simulation of hard, faceted nanoparticles, with a conservative Weeks-Chandler-Andersen (WCA) interparticle potential, coupled to a thermodynamic ensemble. This method is a natural extension of classical molecular dynamics and enables rigorous thermodynamic calculations for faceted particles.
United-Atom Discrete Molecular Dynamics of Proteins Using Physics-Based Potentials.
Emperador, Agustí; Meyer, Tim; Orozco, Modesto
2008-12-09
We present a method for the efficient simulation of the equilibrium dynamics of proteins based on the well established discrete molecular dynamics algorithm, which avoids integration of Newton equations of motion at short time steps, allowing then the derivation of very large trajectories for proteins with a reduced computational cost. In the presented implementation we used an all heavy-atoms description of proteins, with simple potentials describing the conformational region around the experimental structure based on local physical interactions (covalent structure, hydrogen bonds, hydrophobic contacts, solvation, steric hindrance, and bulk dispersion interactions). The method shows a good ability to describe the flexibility of 33 diverse proteins in water as determined by atomistic molecular dynamics simulation and can be useful for massive simulation of proteins in crowded environments or for refinement of protein structure in large complexes.
Discrete-time dynamic network model for the spread of susceptible-infective-recovered diseases
NASA Astrophysics Data System (ADS)
Chauhan, Sanjeev Kumar
2017-07-01
We propose a discrete-time dynamic network model describing the spread of susceptible-infective-recovered diseases in a population. We consider the case in which the nodes in the network change their links due to social mixing dynamics as well as in response to the disease. The model shows the behavior that, as we increase social mixing, disease spread is inhibited in certain cases, while in other cases it is enhanced. We also extend this dynamic network model to take into account the case of hidden infection. Here we find that, as expected, the disease spreads more readily if there is a time period after contracting the disease during which an individual is infective but is not known to have the disease.
Dynamic quantised feedback stabilisation of discrete-time linear system with white noise input
NASA Astrophysics Data System (ADS)
Ji, Mingming; He, Xing; Zhang, Weidong
2015-09-01
In this paper, we mainly focus on the problem of quantised feedback stabilisation of a stochastic discrete-time linear system with white noise input. The dynamic quantiser is used here. The stability of the system under state quantisation and input quantisation is analysed in detail, respectively. Both the convergence of the state's mean and the boundedness of the state's covariance matrix norm should be considered when analysing its stability. It is shown that for the two situations of the state quantisation and the input quantisation, if the system without noise input can be stabilised by a linear feedback law, it must be stabilised by the dynamic quantised feedback control policy. The sufficient conditions that the dynamic quantiser should satisfy are given. Using the results obtained in this paper, one can test whether the stochastic system is stabilisable or not. Numerical examples are given to show the effectiveness of the results.
Modeling and 2-D discrete simulation of dislocation dynamics for plastic deformation of metal
NASA Astrophysics Data System (ADS)
Liu, Juan; Cui, Zhenshan; Ou, Hengan; Ruan, Liqun
2013-05-01
Two methods are employed in this paper to investigate the dislocation evolution during plastic deformation of metal. One method is dislocation dynamic simulation of two-dimensional discrete dislocation dynamics (2D-DDD), and the other is dislocation dynamics modeling by means of nonlinear analysis. As screw dislocation is prone to disappear by cross-slip, only edge dislocation is taken into account in simulation. First, an approach of 2D-DDD is used to graphically simulate and exhibit the collective motion of a large number of discrete dislocations. In the beginning, initial grains are generated in the simulation cells according to the mechanism of grain growth and the initial dislocation is randomly distributed in grains and relaxed under the internal stress. During the simulation process, the externally imposed stress, the long range stress contribution of all dislocations and the short range stress caused by the grain boundaries are calculated. Under the action of these forces, dislocations begin to glide, climb, multiply, annihilate and react with each other. Besides, thermal activation process is included. Through the simulation, the distribution of dislocation and the stress-strain curves can be obtained. On the other hand, based on the classic dislocation theory, the variation of the dislocation density with time is described by nonlinear differential equations. Finite difference method (FDM) is used to solve the built differential equations. The dislocation evolution at a constant strain rate is taken as an example to verify the rationality of the model.
NASA Astrophysics Data System (ADS)
El-Sayed, A. M. A.; Elsonbaty, A.; Elsadany, A. A.; Matouk, A. E.
2016-12-01
This paper presents an analytical framework to investigate the dynamical behavior of a new fractional-order hyperchaotic circuit system. A sufficient condition for existence, uniqueness and continuous dependence on initial conditions of the solution of the proposed system is derived. The local stability of all the system’s equilibrium points are discussed using fractional Routh-Hurwitz test. Then the analytical conditions for the existence of a pitchfork bifurcation in this system with fractional-order parameter less than 1/3 are provided. Conditions for the existence of Hopf bifurcation in this system are also investigated. The dynamics of discretized form of our fractional-order hyperchaotic system are explored. Chaos control is also achieved in discretized system using delay feedback control technique. The numerical simulation are presented to confirm our theoretical analysis via phase portraits, bifurcation diagrams and Lyapunov exponents. A text encryption algorithm is presented based on the proposed fractional-order system. The results show that the new system exhibits a rich variety of dynamical behaviors such as limit cycles, chaos and transient phenomena where fractional-order derivative represents a key parameter in determining system qualitative behavior.
Restricted feedback control in discrete-time dynamical systems with memory
NASA Astrophysics Data System (ADS)
Workman, Kathryn G.; Zhao, Shuang; Cain, John W.
2014-04-01
When an equilibrium state of a physical or biological system suffers a loss of stability (e.g., via a bifurcation), it may be both possible and desirable to stabilize the equilibrium via closed-loop feedback control. Significant effort has been devoted towards using such control to prevent oscillatory or chaotic behavior in dynamical systems, both continuous-time and discrete-time. Regarding control in discrete-time systems, most prior attempts to stabilize unstable equilibria require that the system be perturbed once during each time step. However, there are examples of systems for which this is neither feasible nor possible. In this paper, we analyze a restricted feedback control method for discrete-time systems (restricted in the sense that the controller's perturbations may be applied only in every other time step). We apply our theoretical analysis to a specific example from cardiac electrophysiology in which this sort of restricted feedback control is especially relevant. The example is a useful test case for the theory, and one for which an experimental setup is rather straightforward.
Parallel Discrete Molecular Dynamics Simulation With Speculation and In-Order Commitment*†
Khan, Md. Ashfaquzzaman; Herbordt, Martin C.
2011-01-01
Discrete molecular dynamics simulation (DMD) uses simplified and discretized models enabling simulations to advance by event rather than by timestep. DMD is an instance of discrete event simulation and so is difficult to scale: even in this multi-core era, all reported DMD codes are serial. In this paper we discuss the inherent difficulties of scaling DMD and present our method of parallelizing DMD through event-based decomposition. Our method is microarchitecture inspired: speculative processing of events exposes parallelism, while in-order commitment ensures correctness. We analyze the potential of this parallelization method for shared-memory multiprocessors. Achieving scalability required extensive experimentation with scheduling and synchronization methods to mitigate serialization. The speed-up achieved for a variety of system sizes and complexities is nearly 6× on an 8-core and over 9× on a 12-core processor. We present and verify analytical models that account for the achieved performance as a function of available concurrency and architectural limitations. PMID:21822327
Parallel Discrete Molecular Dynamics Simulation With Speculation and In-Order Commitment.
Khan, Md Ashfaquzzaman; Herbordt, Martin C
2011-07-20
Discrete molecular dynamics simulation (DMD) uses simplified and discretized models enabling simulations to advance by event rather than by timestep. DMD is an instance of discrete event simulation and so is difficult to scale: even in this multi-core era, all reported DMD codes are serial. In this paper we discuss the inherent difficulties of scaling DMD and present our method of parallelizing DMD through event-based decomposition. Our method is microarchitecture inspired: speculative processing of events exposes parallelism, while in-order commitment ensures correctness. We analyze the potential of this parallelization method for shared-memory multiprocessors. Achieving scalability required extensive experimentation with scheduling and synchronization methods to mitigate serialization. The speed-up achieved for a variety of system sizes and complexities is nearly 6× on an 8-core and over 9× on a 12-core processor. We present and verify analytical models that account for the achieved performance as a function of available concurrency and architectural limitations.
Parallel discrete molecular dynamics simulation with speculation and in-order commitment
NASA Astrophysics Data System (ADS)
Khan, Md. Ashfaquzzaman; Herbordt, Martin C.
2011-07-01
Discrete molecular dynamics simulation (DMD) uses simplified and discretized models enabling simulations to advance by event rather than by timestep. DMD is an instance of discrete event simulation and so is difficult to scale: even in this multi-core era, all reported DMD codes are serial. In this paper we discuss the inherent difficulties of scaling DMD and present our method of parallelizing DMD through event-based decomposition. Our method is microarchitecture inspired: speculative processing of events exposes parallelism, while in-order commitment ensures correctness. We analyze the potential of this parallelization method for shared-memory multiprocessors. Achieving scalability required extensive experimentation with scheduling and synchronization methods to mitigate serialization. The speed-up achieved for a variety of system sizes and complexities is nearly 6× on an 8-core and over 9× on a 12-core processor. We present and verify analytical models that account for the achieved performance as a function of available concurrency and architectural limitations.
Mesoscale dynamic coupling of finite- and discrete-element methods for fluid-particle interactions.
Srivastava, S; Yazdchi, K; Luding, S
2014-08-06
A new method for two-way fluid-particle coupling on an unstructured mesoscopically coarse mesh is presented. In this approach, we combine a (higher order) finite-element method (FEM) on the moving mesh for the fluid with a soft sphere discrete-element method for the particles. The novel feature of the proposed scheme is that the FEM mesh is a dynamic Delaunay triangulation based on the positions of the moving particles. Thus, the mesh can be multi-purpose: it provides (i) a framework for the discretization of the Navier-Stokes equations, (ii) a simple tool for detecting contacts between moving particles, (iii) a basis for coarse-graining or upscaling, and (iv) coupling with other physical fields (temperature, electromagnetic, etc.). This approach is suitable for a wide range of dilute and dense particulate flows, because the mesh resolution adapts with particle density in a given region. Two-way momentum exchange is implemented using semi-empirical drag laws akin to other popular approaches; for example, the discrete particle method, where a finite-volume solver on a coarser, fixed grid is used. We validate the methodology with several basic test cases, including single- and double-particle settling with analytical and empirical expectations, and flow through ordered and random porous media, when compared against finely resolved FEM simulations of flow through fixed arrays of particles.
Recent Progress in Discrete Dislocation Dynamics and Its Applications to Micro Plasticity
NASA Astrophysics Data System (ADS)
Po, Giacomo; Mohamed, Mamdouh S.; Crosby, Tamer; Erel, Can; El-Azab, Anter; Ghoniem, Nasr
2014-10-01
We present a self-contained review of the discrete dislocation dynamics (DDD) method for the numerical investigation of plasticity in crystals, focusing on recent development and implementation progress. The review covers the theoretical foundations of DDD within the framework of incompatible elasticity, its numerical implementation via the nodal method, the extension of the method to finite domains and several implementation details. Applications of the method to current topics in micro-plasticity are presented, including the size effects in nano-indentation, the evolution of the dislocation microstructure in persistent slip bands, and the phenomenon of dislocation avalanches in micro-pillar compression.
Non-Markovian autoresonant dynamics of tunneling from discrete to continuum modes
Barak, Assaf; Segev, Mordechai
2011-09-15
We study the autoresonant dynamics of a discrete level coupled to a continuum, and show that passing adiabatically through a linear resonance, above a well-defined threshold, yields a transition to nonlinear phase locking and linear non-Markovian decay to the continuum. This process results in broadening of the population of the continuum modes beyond its natural linewidth. This concept can be employed to alter spontaneous emission, where driving an atom into phase locking with continuum modes will yield the emission of short pulses.
Chaos analysis and delayed-feedback control in a discrete dynamic coupled map traffic model
NASA Astrophysics Data System (ADS)
Fang, Yaling; Shi, Zhongke
2015-03-01
The presence of chaos in traffic flow is studied using a modified discrete dynamic coupled map model which is derived from both the flow-density-speed fundamental diagram and Del Castillo's speed-density model. The modified model employs occupancy as its new variable and introduces a coupling strength with the consideration of effect of the front adjacent vehicle. And we analyze its stability of the control system and provide a procedure to design the decentralized delayed-feedback controllers for the traffic control system. These theoretical results are illustrated by numerical simulations.
H∞ control of combustion in diesel engines using a discrete dynamics model
NASA Astrophysics Data System (ADS)
Hirata, Mitsuo; Ishizuki, Sota; Suzuki, Masayasu
2016-09-01
This paper proposes a control method for combustion in diesel engines using a discrete dynamics model. The proposed two-degree-of-freedom control scheme achieves not only good feedback properties such as disturbance suppression and robust stability but also a good transient response. The method includes a feedforward controller constructed from the inverse model of the plant, and a feedback controller designed by an Hcontrol method, which reduces the effect of the turbocharger lag. The effectiveness of the proposed method is evaluated via numerical simulations.
A Dynamic Discrete Dislocation Plasticity study of elastodynamic shielding of stationary cracks
NASA Astrophysics Data System (ADS)
Gurrutxaga-Lerma, B.; Balint, D. S.; Dini, D.; Sutton, A. P.
2017-01-01
Employing Dynamic Discrete Dislocation Plasticity (D3P), an elastodynamic analysis of the shielding of a stationary crack tip by dislocations is studied. Dislocations are generated via Frank-Read sources, and make a negligible contribution to the shielding of the crack tip, whereas dislocations generated at the crack tip via homogeneous nucleation dominate the shielding. Their effect is found to be highly localised around the crack, leading to a magnification of the shielding when compared to time-independent, elastostatic predictions. The resulting attenuation of KI(t) is computed, and is found to be directly proportional to the applied load and to √{ t }.
Dynamics of a Discretely Reinforced Cylindrical Shell Under a Local Impulsive Load
NASA Astrophysics Data System (ADS)
Lugovoi, P. Z.; Sirenko, V. N.; Skosarenko, Yu. V.; Batutina, T. Ya.
2017-03-01
A procedure and software for studying the dynamics of a reinforced cylindrical shell on an elastic foundation are developed. The shell is under local loads distributed over small areas and varying linearly during a short time. The stringers are described by a structurally orthotropic model and the ring ribs by a discrete model. The candidate solution is expanded into series of natural modes. The influence of a local load on the deformation parameters of the shell is studied using a test example. Conclusions on the effect of the pulse shape, the time of action of the external forces, and the reinforcement on the strain state of the shell are drawn
Dynamical behavior of a discrete time Hogg-Huberman model with three resources
NASA Astrophysics Data System (ADS)
Inoue, M.; Tanaka, T.; Takagi, N.; Shibata, J.
2002-09-01
The dynamical behavior of a discrete time Hogg-Huberman model with three resources 1-3 is investigated. The payoff function of resource 3 is assumed to be the same function as that of resource 2. It is found that when the control parameter takes certain values there are various states which are called the monopoly state of resource 1, and synchronized and asynchronized chaotic states with respect to the fractions of agents using resources 2 and 3. The effect of a reward mechanism based on the actual performance of agents is also calculated in this system.
Nonlinear Maps for Design of Discrete-Time Models of Neuronal Network Dynamics
2016-03-31
2016 Performance/Technic~ 03-01-2016- 03-31-2016 4. TITLE AND SUBTITLE Sa. CONTRACT NUMBER Nonlinear Maps for Design of Discrete-Time Models of...Neuronal Network Dynamics Sb. GRANT NUMBER N00014-16-1-2252 Sc. PROGRAM ELEMENT NUMBER 6. AUTHOR{S) Sd. PROJECT NUMBER Nikolai Rulkov Se. TASK NUMBER...they apperar in the report, e.g . 1F665702D1257. Sc. PROGRAM ELEMENT NUMBER. Enter all program element numbers as they appear in the report, e.g
Dissipative soliton dynamics in a discrete magnetic nano-dot chain
Lee, Kyeong-Dong; You, Chun-Yeol; Song, Hyon-Seok; Shin, Sung-Chul; Park, Byong-Guk
2014-02-03
Soliton dynamics is studied in a discrete magnetic nano-dot chain by means of micromagnetic simulations together with an analytic model equation. A soliton under a dissipative system is driven by an applied field. The field-driven dissipative soliton enhances its mobility nonlinearly, as the characteristic frequency and the intrinsic Gilbert damping decrease. During the propagation, the soliton emits spin waves which act as an extrinsic damping channel. The characteristic frequency, the maximum velocity, and the localization length of the soliton are found to be proportional to the threshold field, the threshold velocity, and the initial mobility, respectively.
Non-Deterministic Modelling of Food-Web Dynamics
Planque, Benjamin; Lindstrøm, Ulf; Subbey, Sam
2014-01-01
A novel approach to model food-web dynamics, based on a combination of chance (randomness) and necessity (system constraints), was presented by Mullon et al. in 2009. Based on simulations for the Benguela ecosystem, they concluded that observed patterns of ecosystem variability may simply result from basic structural constraints within which the ecosystem functions. To date, and despite the importance of these conclusions, this work has received little attention. The objective of the present paper is to replicate this original model and evaluate the conclusions that were derived from its simulations. For this purpose, we revisit the equations and input parameters that form the structure of the original model and implement a comparable simulation model. We restate the model principles and provide a detailed account of the model structure, equations, and parameters. Our model can reproduce several ecosystem dynamic patterns: pseudo-cycles, variation and volatility, diet, stock-recruitment relationships, and correlations between species biomass series. The original conclusions are supported to a large extent by the current replication of the model. Model parameterisation and computational aspects remain difficult and these need to be investigated further. Hopefully, the present contribution will make this approach available to a larger research community and will promote the use of non-deterministic-network-dynamics models as ‘null models of food-webs’ as originally advocated. PMID:25299245
Dynamic Space for Rent: Using Commercial Web Hosting to Develop a Web 2.0 Intranet
ERIC Educational Resources Information Center
Hodgins, Dave
2010-01-01
The explosion of Web 2.0 into libraries has left many smaller academic libraries (and other libraries with limited computing resources or support) to work in the cloud using free Web applications. The use of commercial Web hosting is an innovative approach to the problem of inadequate local resources. While the idea of insourcing IT will seem…
Dynamic Space for Rent: Using Commercial Web Hosting to Develop a Web 2.0 Intranet
ERIC Educational Resources Information Center
Hodgins, Dave
2010-01-01
The explosion of Web 2.0 into libraries has left many smaller academic libraries (and other libraries with limited computing resources or support) to work in the cloud using free Web applications. The use of commercial Web hosting is an innovative approach to the problem of inadequate local resources. While the idea of insourcing IT will seem…
NASA Astrophysics Data System (ADS)
Krajewski, Florian R.; Müser, Martin H.
2005-03-01
The commensurate Frenkel Kontorova (FK) model is studied using path-integral molecular dynamics (PIMD). We focus on the highly discrete case, in which the embedding potential has a much greater maximum curvature than the harmonic potential connecting two particles in the FK chain. When efficient sampling methods are used, the dynamical interpretation of adiabatic PIMD appears to represent quite accurately the true time correlation functions of this highly correlated many-body system. We have found that the discrete, quantum FK model shows different behavior than its continuum version. The spectral density does not show the characteristic ω-2Θ(ω-ωc) cusp of the continuum solution in the pinned phase (m>mc). We also identify a dynamical quantum hysteresis in addition to the regular classical hysteresis when an external force is applied to the FK chain. In the unpinned phase (m⩽mc), we find a linear response damping coefficient which is finite and only weakly dependent on temperature T at small values of T.
Dynamics and energy spectra of aperiodic discrete-time quantum walks
NASA Astrophysics Data System (ADS)
Lo Gullo, N.; Ambarish, C. V.; Busch, Th.; Dell'Anna, L.; Chandrashekar, C. M.
2017-07-01
We investigate the role of different aperiodic sequences in the dynamics of single quantum particles in discrete space and time. For this we consider three aperiodic sequences, namely, the Fibonacci, Thue-Morse, and Rudin-Shapiro sequences, as examples of tilings the diffraction spectra of which have pure point, singular continuous, and absolutely continuous support, respectively. Our interest is to understand how the order, intrinsically introduced by the deterministic rule used to generate the aperiodic sequences, is reflected in the dynamical properties of the quantum system. For this system we consider a single particle undergoing a discrete-time quantum walk (DTQW), where the aperiodic sequences are used to distribute the coin operations at different lattice positions (inhomogeneous DTQW) or by applying the same coin operation at all lattice sites at a given time but choosing different coin operation at each time step according to the chosen aperiodic sequence (time dependent DTQW). We study the energy spectra and the spreading of an initially localized wave packet for different cases, finding that in the case of Fibonacci and Thue-Morse tilings the system is superdiffusive, whereas in the Rudin-Shapiro case it is strongly subdiffusive. Trying to understand this behavior in terms of the energy spectra, we look at the survival amplitude as a function of time. By means of the echo we present strong evidence that, although the three orderings are very different as evidenced by their diffraction spectra, the energy spectra are all singular continuous except for the inhomogeneous DTQW with the Rudin-Shapiro sequence where it is discrete. This is in agreement with the observed strong localization both in real space and in the Hilbert space. Our paper is particularly interesting because quantum walks can be engineered in laboratories by means of ultracold gases or in optical waveguides, and therefore would be a perfect playground to study singular continuous energy
Optimal discrete-time dynamic output-feedback design - A w-domain approach
NASA Technical Reports Server (NTRS)
Ha, Cheolkeun; Ly, Uy-Loi
1991-01-01
An alternative method for optimal digital control design is described in this paper. The method is based on the usage of the w-transform and has many attractive design features. One of these is its immediate connection with frequency loop-shaping techniques that are now popular and effective for multivariable control synthesis in continuous-time domain. Furthermore, any design algorithms originally developed for continuous-time systems can now be immediately extended to the discrete-time domain. The main results presented in this paper are the exact problem formulation and solution of an optimal discrete-time dynamic output-feedback design in the w-domain involving a quadratic performance index to random disturbances. In addition, necessary conditions for optimality are obtained for the numerical solution of the optimal output-feedback compensator design. A numerical example is presented illustrating its application to the design of a low-order dynamic compensator in a stability augmentation system of a commercial transport.
Complex dynamics of a delayed discrete neural network of two nonidentical neurons
Chen, Yuanlong; Huang, Tingwen; Huang, Yu
2014-03-15
In this paper, we discover that a delayed discrete Hopfield neural network of two nonidentical neurons with self-connections and no self-connections can demonstrate chaotic behaviors. To this end, we first transform the model, by a novel way, into an equivalent system which has some interesting properties. Then, we identify the chaotic invariant set for this system and show that the dynamics of this system within this set is topologically conjugate to the dynamics of the full shift map with two symbols. This confirms chaos in the sense of Devaney. Our main results generalize the relevant results of Huang and Zou [J. Nonlinear Sci. 15, 291–303 (2005)], Kaslik and Balint [J. Nonlinear Sci. 18, 415–432 (2008)] and Chen et al. [Sci. China Math. 56(9), 1869–1878 (2013)]. We also give some numeric simulations to verify our theoretical results.
NASA Technical Reports Server (NTRS)
Bainum, P. M.; Sellappan, R.
1978-01-01
Attitude control techniques for the pointing and stabilization of very large, inherently flexible spacecraft systems were investigated. The attitude dynamics and control of a long, homogeneous flexible beam whose center of mass is assumed to follow a circular orbit was analyzed. First order effects of gravity gradient were included. A mathematical model which describes the system rotations and deflections within the orbital plane was developed by treating the beam as a number of discretized mass particles connected by massless, elastic structural elements. The uncontrolled dynamics of the system are simulated and, in addition, the effects of the control devices were considered. The concept of distributed modal control, which provides a means for controlling a system mode independently of all other modes, was examined. The effect of varying the number of modes in the model as well as the number and location of the control devices were also considered.
Zhong, Xiangnan; He, Haibo; Zhang, Huaguang; Wang, Zhanshan
2014-12-01
In this paper, we develop and analyze an optimal control method for a class of discrete-time nonlinear Markov jump systems (MJSs) with unknown system dynamics. Specifically, an identifier is established for the unknown systems to approximate system states, and an optimal control approach for nonlinear MJSs is developed to solve the Hamilton-Jacobi-Bellman equation based on the adaptive dynamic programming technique. We also develop detailed stability analysis of the control approach, including the convergence of the performance index function for nonlinear MJSs and the existence of the corresponding admissible control. Neural network techniques are used to approximate the proposed performance index function and the control law. To demonstrate the effectiveness of our approach, three simulation studies, one linear case, one nonlinear case, and one single link robot arm case, are used to validate the performance of the proposed optimal control method.
Construction of discrete-continual models in structure analysis for extreme dynamic loadings
NASA Astrophysics Data System (ADS)
Bolotin, V. V.; Trifonov, O. V.
2009-12-01
We propose a new method for constructing design models of high-rise buildings and structures, which is based on the treatment of the set of bearing structures as discrete-continual inelastic damageable system admitting large spatial displacements and rotations. We derive a relation for the virtual work functional with respect to increments of integral stress characteristics, which can be viewed as a starting point for solving applied problems of simulation of structural dynamics under the action of extreme forces. To take into account the processes of damage and failure of buildings and structures, we propose a generalized scheme for constructing a nonlinear physical model of deformation on the level of integral stress characteristics in the bearing structures of a storey. As an example of application of this model, we consider the problem of dynamic behavior of a multistorey building under a spatial seismic load.
Complex dynamics of a delayed discrete neural network of two nonidentical neurons
Chen, Yuanlong; Huang, Tingwen; Huang, Yu
2014-03-15
In this paper, we discover that a delayed discrete Hopfield neural network of two nonidentical neurons with self-connections and no self-connections can demonstrate chaotic behaviors. To this end, we first transform the model, by a novel way, into an equivalent system which has some interesting properties. Then, we identify the chaotic invariant set for this system and show that the dynamics of this system within this set is topologically conjugate to the dynamics of the full shift map with two symbols. This confirms chaos in the sense of Devaney. Our main results generalize the relevant results of Huang and Zou [J. Nonlinear Sci. 15, 291–303 (2005)], Kaslik and Balint [J. Nonlinear Sci. 18, 415–432 (2008)] and Chen et al. [Sci. China Math. 56(9), 1869–1878 (2013)]. We also give some numeric simulations to verify our theoretical results.
Social Dynamics in Web Page through Inter-Agent Interaction
NASA Astrophysics Data System (ADS)
Takeuchi, Yugo; Katagiri, Yasuhiro
Social persuasion abounds in human-human interactions. Attitudes and behaviors of people are invariably influenced by the attitudes and behaviors of other people as well as our social roles/relationships toward them. In the pedagogic scene, the relationship between teacher and learner produces one of the most typical interactions, in which the teacher makes the learner spontaneously study what he/she teaches. This study is an attempt to elucidate the nature and effectiveness of social persuasion in human-computer interaction environments. We focus on the social dynamics of multi-party interactions that involve both human-agent and inter-agent interactions. An experiment is conducted in a virtual web-instruction setting employing two types of agents: conductor agents who accompany and guide each learner throughout his/her learning sessions, and domain-expert agents who provide explanations and instructions for each stage of the instructional materials. In this experiment, subjects are assigned two experimental conditions: the authorized condition, in which an agent respectfully interacts with another agent, and the non-authorized condition, in which an agent carelessly interacts with another agent. The results indicate performance improvements in the authorized condition of inter-agent interactions. An analysis is given from the perspective of the transfer of authority from inter-agent to human-agent interactions based on social conformity. We argue for pedagogic advantages of social dynamics created by multiple animated character agents.
Dynamic selection mechanism for quality of service aware web services
NASA Astrophysics Data System (ADS)
D'Mello, Demian Antony; Ananthanarayana, V. S.
2010-02-01
A web service is an interface of the software component that can be accessed by standard Internet protocols. The web service technology enables an application to application communication and interoperability. The increasing number of web service providers throughout the globe have produced numerous web services providing the same or similar functionality. This necessitates the use of tools and techniques to search the suitable services available over the Web. UDDI (universal description, discovery and integration) is the first initiative to find the suitable web services based on the requester's functional demands. However, the requester's requirements may also include non-functional aspects like quality of service (QoS). In this paper, the authors define a QoS model for QoS aware and business driven web service publishing and selection. The authors propose a QoS requirement format for the requesters, to specify their complex demands on QoS for the web service selection. The authors define a tree structure called quality constraint tree (QCT) to represent the requester's variety of requirements on QoS properties having varied preferences. The paper proposes a QoS broker based architecture for web service selection, which facilitates the requesters to specify their QoS requirements to select qualitatively optimal web service. A web service selection algorithm is presented, which ranks the functionally similar web services based on the degree of satisfaction of the requester's QoS requirements and preferences. The paper defines web service provider qualities to distinguish qualitatively competitive web services. The paper also presents the modelling and selection mechanism for the requester's alternative constraints defined on the QoS. The authors implement the QoS broker based system to prove the correctness of the proposed web service selection mechanism.
Discrete Dynamics Model for the Speract-Activated Ca2+ Signaling Network Relevant to Sperm Motility
Espinal, Jesús; Aldana, Maximino; Guerrero, Adán; Wood, Christopher
2011-01-01
Understanding how spermatozoa approach the egg is a central biological issue. Recently a considerable amount of experimental evidence has accumulated on the relation between oscillations in intracellular calcium ion concentration ([Ca]) in the sea urchin sperm flagellum, triggered by peptides secreted from the egg, and sperm motility. Determination of the structure and dynamics of the signaling pathway leading to these oscillations is a fundamental problem. However, a biochemically based formulation for the comprehension of the molecular mechanisms operating in the axoneme as a response to external stimulus is still lacking. Based on experiments on the S. purpuratus sea urchin spermatozoa, we propose a signaling network model where nodes are discrete variables corresponding to the pathway elements and the signal transmission takes place at discrete time intervals according to logical rules. The validity of this model is corroborated by reproducing previous empirically determined signaling features. Prompted by the model predictions we performed experiments which identified novel characteristics of the signaling pathway. We uncovered the role of a high voltage-activated channel as a regulator of the delay in the onset of fluctuations after activation of the signaling cascade. This delay time has recently been shown to be an important regulatory factor for sea urchin sperm reorientation. Another finding is the participation of a voltage-dependent calcium-activated channel in the determination of the period of the fluctuations. Furthermore, by analyzing the spread of network perturbations we find that it operates in a dynamically critical regime. Our work demonstrates that a coarse-grained approach to the dynamics of the signaling pathway is capable of revealing regulatory sperm navigation elements and provides insight, in terms of criticality, on the concurrence of the high robustness and adaptability that the reproduction processes are predicted to have developed
The discrete-continuum connection in dislocation dynamics: I. Time coarse graining of cross slip
NASA Astrophysics Data System (ADS)
Xia, Shengxu; Belak, James; El-Azab, Anter
2016-10-01
A recent continuum dislocation dynamics formalism (Xia and El-Azab 2015 Model. Simul. Mater. Sci. Eng. 23 055009) has been enriched by incorporating an improved cross slip model. 3D discrete dislocation dynamics simulations were used to collect cross slip rate data in the form of time series that were analysed to estimate the correlation time for cross slip, which was subsequently used as a time scale for local window averaging of the collected cross slip rate data. This time averaging filters out the cross slip rate fluctuations over time intervals less than the correlation time, thus resulting in relatively smoother time series for the cross slip rates. The coarse grained series were further cast in the form of smooth trends with superposed fluctuations and implemented in continuum dislocation dynamics simulations using a Monte Carlo scheme. This approach resulted in a significant improvement of the predicted stress-strain response and a more realistic dislocation cell structure evolution. The similitude law for the average cell size evolution with inverse of stress, however, remains unaffected by the cross slip rates used in continuum dislocation dynamics.
Sparsified-dynamics modeling of discrete point vortices with graph theory
NASA Astrophysics Data System (ADS)
Taira, Kunihiko; Nair, Aditya
2014-11-01
We utilize graph theory to derive a sparsified interaction-based model that captures unsteady point vortex dynamics. The present model builds upon the Biot-Savart law and keeps the number of vortices (graph nodes) intact and reduces the number of inter-vortex interactions (graph edges). We achieve this reduction in vortex interactions by spectral sparsification of graphs. This approach drastically reduces the computational cost to predict the dynamical behavior, sharing characteristics of reduced-order models. Sparse vortex dynamics are illustrated through an example of point vortex clusters interacting amongst themselves. We track the centroids of the individual vortex clusters to evaluate the error in bulk motion of the point vortices in the sparsified setup. To further improve the accuracy in predicting the nonlinear behavior of the vortices, resparsification strategies are employed for the sparsified interaction-based models. The model retains the nonlinearity of the interaction and also conserves the invariants of discrete vortex dynamics; namely the Hamiltonian, linear impulse, and angular impulse as well as circulation. Work supported by US Army Research Office (W911NF-14-1-0386) and US Air Force Office of Scientific Research (YIP: FA9550-13-1-0183).
Event-driven Monte Carlo: Exact dynamics at all time scales for discrete-variable models
NASA Astrophysics Data System (ADS)
Mendoza-Coto, Alejandro; Díaz-Méndez, Rogelio; Pupillo, Guido
2016-06-01
We present an algorithm for the simulation of the exact real-time dynamics of classical many-body systems with discrete energy levels. In the same spirit of kinetic Monte Carlo methods, a stochastic solution of the master equation is found, with no need to define any other phase-space construction. However, unlike existing methods, the present algorithm does not assume any particular statistical distribution to perform moves or to advance the time, and thus is a unique tool for the numerical exploration of fast and ultra-fast dynamical regimes. By decomposing the problem in a set of two-level subsystems, we find a natural variable step size, that is well defined from the normalization condition of the transition probabilities between the levels. We successfully test the algorithm with known exact solutions for non-equilibrium dynamics and equilibrium thermodynamical properties of Ising-spin models in one and two dimensions, and compare to standard implementations of kinetic Monte Carlo methods. The present algorithm is directly applicable to the study of the real-time dynamics of a large class of classical Markovian chains, and particularly to short-time situations where the exact evolution is relevant.
A dynamic model of mobile concrete pump boom based on discrete time transfer matrix method
NASA Astrophysics Data System (ADS)
Ren, Wu; Wu, Yunxin; Zhang, Zhaowei
2013-12-01
Mobile concrete pump boom is typical multibody large-scale motion manipulator. Due to posture constantly change in working process, kinematic rule and dynamic characteristic are difficult to solve. A dynamics model of a mobile concrete pump boom is established based on discrete time transfer matrix method (DTTMM). The boom system is divided into sub-structure A and substructure B. Sub-structure A is composed by the 1st boom and hydraulic actuator as well as the support. And substructure B is consists of the other three booms and corresponding hydraulic actuators. In the model, the booms and links are regarded as rigid elements and the hydraulic cylinders are equivalent to spring-damper. The booms are driven by the controllable hydraulic actuators. The overall dynamic equation and transfer matrix of the model can be assembled by sub-structures A and B. To get a precise result, step size and integration parameters are studied then. Next the tip displacement is calculated and compared with the result of ADAMS software. The displacement and rotation angle curves of the proposed method fit well with the ADAMS model. Besides it is convenient in modeling and saves time. So it is suitable for mobile concrete pump boom real-time monitoring and dynamic analysis. All of these provide reference to boom optimize and engineering application of such mechanisms.
Kroenlein, Kenneth; Muzny, Chris D; Diky, Vladimir; Kazakov, Andrei F; Chirico, Robert D; Magee, Joseph W; Abdulagatov, Ilmutdin; Frenkel, Michael
2011-06-27
ThermoData Engine (TDE) is the first full-scale software implementation of the dynamic data evaluation concept, as reported recently in this journal. In the present paper, we describe the development of a World Wide Web-based interface to TDE evaluations of pure compound properties, including critical properties, phase boundary equilibria (vapor pressures, sublimation pressures, and crystal-liquid boundary pressures), densities, energetic properties, and transport properties. This includes development of a system for caching evaluation results to maintain high availability and an advanced window-in-window interface that leverages modern Web-browser technologies. Challenges associated with bringing the principal advantages of the TDE technology to the Web are described, as are compromises to maintain general access and speed of interaction while remaining true to the tenets of dynamic data evaluation. Future extensions of the interface and associated Web-services are outlined.
NASA Astrophysics Data System (ADS)
Gurrutxaga-Lerma, Benat; Sutton, Adrian; Eakins, Daniel; Balint, Daniel; Dini, Daniele
2013-06-01
This talk intends to offer some insight as to how Discrete Dislocation Plasticity (DDP) can be adapted to simulate plastic relaxation processes under weak shock loading and high strain rates. In those circumstances, dislocations are believed to be the main cause of plastic relaxation in crystalline solids. Direct simulation of dislocations as the dynamic agents of plastic relaxation in those cases remains a challenge. DDP, where dislocations are modelled as discrete discontinuities in elastic continuum media, is often unable to adequately simulate plastic relaxation because it treats dislocation motion quasi-statically, thus neglecting the time-dependent nature of the elastic fields and assuming that they instantaneously acquire the shape and magnitude predicted by elastostatics. Under shock loading, this assumption leads to several artefacts that can only be overcome with a fully time-dependent formulation of the elastic fields. In this talk one of such formulations for the creation, annihilation and arbitrary motion of straight edge dislocations will be presented. These solutions are applied in a two-dimensional model of time-dependent plastic relaxation under shock loading, and some relevant results will be presented. EPSRC CDT in Theory and Simulation of Materials
Discrete states and carrier-phonon scattering in quantum dot population dynamics
Man, Minh Tan; Lee, Hong Seok
2015-01-01
The influence of the growth conditions of multilayer CdTe/ZnTe quantum dots (QDs) on Si substrate upon their carrier dynamics is studied using intensity integration and broadening photoluminescence. The unusual temperature dependence of the line broadening is explained using a model for interband transitions that involves a lowest discrete electronic state (1Se) with different discrete hole states (1S3/2 and 2S3/2) and a 1P transition. These transitions are expected to play a critical role in both the thermally activated energy and the line broadening of the QDs. We also demonstrate that a thermally activated transition between two different states occurs with band low-temperature quenching, with values separated by 5.8–16 meV. The main nonradiative process is thermal escape assisted by carrier scattering via emission of longitudinal phonons through the hole states at high temperature, with an average energy of 19.3–20.2 meV. PMID:25652600
Policy iteration adaptive dynamic programming algorithm for discrete-time nonlinear systems.
Liu, Derong; Wei, Qinglai
2014-03-01
This paper is concerned with a new discrete-time policy iteration adaptive dynamic programming (ADP) method for solving the infinite horizon optimal control problem of nonlinear systems. The idea is to use an iterative ADP technique to obtain the iterative control law, which optimizes the iterative performance index function. The main contribution of this paper is to analyze the convergence and stability properties of policy iteration method for discrete-time nonlinear systems for the first time. It shows that the iterative performance index function is nonincreasingly convergent to the optimal solution of the Hamilton-Jacobi-Bellman equation. It is also proven that any of the iterative control laws can stabilize the nonlinear systems. Neural networks are used to approximate the performance index function and compute the optimal control law, respectively, for facilitating the implementation of the iterative ADP algorithm, where the convergence of the weight matrices is analyzed. Finally, the numerical results and analysis are presented to illustrate the performance of the developed method.
Long-term memory contribution as applied to the motion of discrete dynamical systems
NASA Astrophysics Data System (ADS)
Stanislavsky, A. A.
2006-12-01
We consider the evolution of logistic maps under long-term memory. The memory effects are characterized by one parameter, α. If it equals to zero, any memory is absent. This leads to the ordinary discrete dynamical systems. For α =1 the memory becomes full, and each subsequent state of the corresponding discrete system accumulates all past states with the same weight just as the ordinary integral of first order does in the continuous space. The case with 0<α<1 has the long-term memory effects. The characteristic features are also observed for the fractional integral depending on time, and the parameter α is equivalent to the order index of the fractional integral. We study the evolution of the bifurcation diagram among α =0 and α =0.15. The main result of this work is that the long-term memory effects make difficulties for developing the chaos motion in such logistic maps. The parameter α resembles a governing parameter for the bifurcation diagram. For α >0.15 the memory effects win over chaos.
NASA Astrophysics Data System (ADS)
Derakhshani, S. M.; Schott, D. L.; Lodewijks, G.
2013-06-01
Dust emissions can have significant effects on the human health, environment and industry equipment. Understanding the dust generation process helps to select a suitable dust preventing approach and also is useful to evaluate the environmental impact of dust emission. To describe these processes, numerical methods such as Computational Fluid Dynamics (CFD) are widely used, however nowadays particle based methods like Discrete Element Method (DEM) allow researchers to model interaction between particles and fluid flow. In this study, air flow over a stockpile, dust emission, erosion and surface deformation of granular material in the form of stockpile are studied by using DEM and CFD as a coupled method. Two and three dimensional simulations are respectively developed for CFD and DEM methods to minimize CPU time. The standard κ-ɛ turbulence model is used in a fully developed turbulent flow. The continuous gas phase and the discrete particle phase link to each other through gas-particle void fractions and momentum transfer. In addition to stockpile deformation, dust dispersion is studied and finally the accuracy of stockpile deformation results obtained by CFD-DEM modelling will be validated by the agreement with the existing experimental data.
Animal diversity and ecosystem functioning in dynamic food webs
NASA Astrophysics Data System (ADS)
Schneider, Florian D.; Brose, Ulrich; Rall, Björn C.; Guill, Christian
2016-10-01
Species diversity is changing globally and locally, but the complexity of ecological communities hampers a general understanding of the consequences of animal species loss on ecosystem functioning. High animal diversity increases complementarity of herbivores but also increases feeding rates within the consumer guild. Depending on the balance of these counteracting mechanisms, species-rich animal communities may put plants under top-down control or may release them from grazing pressure. Using a dynamic food-web model with body-mass constraints, we simulate ecosystem functions of 20,000 communities of varying animal diversity. We show that diverse animal communities accumulate more biomass and are more exploitative on plants, despite their higher rates of intra-guild predation. However, they do not reduce plant biomass because the communities are composed of larger, and thus energetically more efficient, plant and animal species. This plasticity of community body-size structure reconciles the debate on the consequences of animal species loss for primary productivity.
Animal diversity and ecosystem functioning in dynamic food webs
Schneider, Florian D.; Brose, Ulrich; Rall, Björn C.; Guill, Christian
2016-01-01
Species diversity is changing globally and locally, but the complexity of ecological communities hampers a general understanding of the consequences of animal species loss on ecosystem functioning. High animal diversity increases complementarity of herbivores but also increases feeding rates within the consumer guild. Depending on the balance of these counteracting mechanisms, species-rich animal communities may put plants under top-down control or may release them from grazing pressure. Using a dynamic food-web model with body-mass constraints, we simulate ecosystem functions of 20,000 communities of varying animal diversity. We show that diverse animal communities accumulate more biomass and are more exploitative on plants, despite their higher rates of intra-guild predation. However, they do not reduce plant biomass because the communities are composed of larger, and thus energetically more efficient, plant and animal species. This plasticity of community body-size structure reconciles the debate on the consequences of animal species loss for primary productivity. PMID:27703157
Animal diversity and ecosystem functioning in dynamic food webs.
Schneider, Florian D; Brose, Ulrich; Rall, Björn C; Guill, Christian
2016-10-05
Species diversity is changing globally and locally, but the complexity of ecological communities hampers a general understanding of the consequences of animal species loss on ecosystem functioning. High animal diversity increases complementarity of herbivores but also increases feeding rates within the consumer guild. Depending on the balance of these counteracting mechanisms, species-rich animal communities may put plants under top-down control or may release them from grazing pressure. Using a dynamic food-web model with body-mass constraints, we simulate ecosystem functions of 20,000 communities of varying animal diversity. We show that diverse animal communities accumulate more biomass and are more exploitative on plants, despite their higher rates of intra-guild predation. However, they do not reduce plant biomass because the communities are composed of larger, and thus energetically more efficient, plant and animal species. This plasticity of community body-size structure reconciles the debate on the consequences of animal species loss for primary productivity.
Perturbed dynamics of discrete-time switched nonlinear systems with delays and uncertainties.
Liu, Xingwen; Cheng, Jun
2016-05-01
This paper addresses the dynamics of a class of discrete-time switched nonlinear systems with time-varying delays and uncertainties and subject to perturbations. It is assumed that the nominal switched nonlinear system is robustly uniformly exponentially stable. It is revealed that there exists a maximal Lipschitz constant, if perturbation satisfies a Lipschitz condition with any Lipschitz constant less than the maximum, then the perturbed system can preserve the stability property of the nominal system. In situations where the perturbations are known, it is proved that there exists an upper bound of coefficient such that the perturbed system remains exponentially stable provided that the perturbation is scaled by any coefficient bounded by the upper bound. A numerical example is provided to illustrate the proposed theoretical results.
NASA Astrophysics Data System (ADS)
Khraishi, Tariq A.; Zbib, Hussein M.; de La Rubia, Tomas Diaz; Victoria, Max
2002-04-01
When irradiated, metals undergo significant internal damage accumulation and degradation of mechanical properties. Damage takes the form of a high number density of nanosize defect clusters (stacking-fault tetrahedrons (SFTs) or interstitial loops). The alteration of mechanical properties is manifested in a hardening behavior and localized plastic deformation in defect-free channels. This work uses discrete dislocation dynamics (DD) to capture these effects. It sets the framework for the elastic interaction between gliding dislocations and defect clusters and details a scheme for loop unfaulting and absorption into dislocations. Here, it is shown that SFTs represents weaker pinning points for dislocation motion than parent dislocation loops. It is also shown that appreciable yield drop can be attributed to high density of defects decorating the dislocations. Strong obstacles cause dislocations in Cu to continually double cross slip causing the formation of defect-free channels. Finally, the correlation between yield stress increase and defect number density is in excellent agreement with the experiment.
Flow Dynamics of green sand in the DISAMATIC moulding process using Discrete element method (DEM)
NASA Astrophysics Data System (ADS)
Hovad, E.; Larsen, P.; Walther, J. H.; Thorborg, J.; Hattel, J. H.
2015-06-01
The DISAMATIC casting process production of sand moulds is simulated with DEM (discrete element method). The main purpose is to simulate the dynamics of the flow of green sand, during the production of the sand mould with DEM. The sand shot is simulated, which is the first stage of the DISAMATIC casting process. Depending on the actual casting geometry the mould can be geometrically quite complex involving e.g. shadowing effects and this is directly reflected in the sand flow during the moulding process. In the present work a mould chamber with “ribs” at the walls is chosen as a baseline geometry to emulate some of these important conditions found in the real moulding process. The sand flow is simulated with the DEM and compared with corresponding video footages from the interior of the chamber during the moulding process. The effect of the rolling resistance and the static friction coefficient is analysed and discussed in relation to the experimental findings.
Dynamical Localization for Discrete and Continuous Random Schrödinger Operators
NASA Astrophysics Data System (ADS)
Germinet, F.; De Bièvre, S.
We show for a large class of random Schrödinger operators Ho on and on that dynamical localization holds, i.e. that, with probability one, for a suitable energy interval I and for q a positive real,
Discrete dynamic system oriented on the formation of prebiotic dipeptides from Rode's experiment.
Polanco, Carlos; Samaniego, José Lino; Buhse, Thomas; Castañón González, Jorge Alberto
2014-01-01
This work attempts to rationalize the possible prebiotic profile of the first dipeptides of about 4 billion years ago based on a computational discrete dynamic system that uses the final yields of the dipeptides obtained in Rode's experiments of salt-induced peptide formation (Rode et al., 1999, Peptides 20: 773-786). The system built a prebiotic scenario that allowed us to observe that (i) the primordial peptide generation was strongly affected by the abundances of the amino acid monomers, (ii) small variations in the concentration of the monomers have almost no effect on the final distribution pattern of the dipeptides and (iii) the most plausible chemical reaction of prebiotic peptide bond formation can be linked to Rode's hypothesis of a salt-induced scenario. The results of our computational simulations were related to former simulations of the Miller, and Fox & Harada experiments on amino acid monomer and oligomer generation, respectively, offering additional information to our approach.
Pierce, Clay; Colvin, Michael E.; Stewart, Timothy W.
2012-01-01
Continuous harvest over an annual period is a common assumption of continuous biomass dynamics models (CBDMs); however, fish are frequently harvested in a discrete manner. We developed semidiscrete biomass dynamics models (SDBDMs) that allow discrete harvest events and evaluated differences between CBDMs and SDBDMs using an equilibrium yield analysis with varying levels of fishing mortality (F). Equilibrium fishery yields for CBDMs and SDBDMS were similar at low fishing mortalities and diverged as F approached and exceeded maximum sustained yield (FMSY). Discrete harvest resulted in lower equilibrium yields at high levels of Frelative to continuous harvest. The effect of applying harvest continuously when it was in fact discrete was evaluated by fitting CBDMs and SDBDMs to time series data generated from a hypothetical fish stock undergoing discrete harvest and evaluating parameter estimates bias. Violating the assumption of continuous harvest resulted in biased parameter estimates for CBDM while SDBDM parameter estimates were unbiased. Biased parameter estimates resulted in biased biological reference points derived from CBDMs. Semidiscrete BDMs outperformed continuous BDMs and should be used when harvest is discrete, when the time and magnitude of harvest are known, and when F is greater than FMSY.
Discrete Molecular Dynamics Can Predict Helical Prestructured Motifs in Disordered Proteins
Han, Kyou-Hoon; Dokholyan, Nikolay V.; Tompa, Péter; Kalmár, Lajos; Hegedűs, Tamás
2014-01-01
Intrinsically disordered proteins (IDPs) lack a stable tertiary structure, but their short binding regions termed Pre-Structured Motifs (PreSMo) can form transient secondary structure elements in solution. Although disordered proteins are crucial in many biological processes and designing strategies to modulate their function is highly important, both experimental and computational tools to describe their conformational ensembles and the initial steps of folding are sparse. Here we report that discrete molecular dynamics (DMD) simulations combined with replica exchange (RX) method efficiently samples the conformational space and detects regions populating α-helical conformational states in disordered protein regions. While the available computational methods predict secondary structural propensities in IDPs based on the observation of protein-protein interactions, our ab initio method rests on physical principles of protein folding and dynamics. We show that RX-DMD predicts α-PreSMos with high confidence confirmed by comparison to experimental NMR data. Moreover, the method also can dissect α-PreSMos in close vicinity to each other and indicate helix stability. Importantly, simulations with disordered regions forming helices in X-ray structures of complexes indicate that a preformed helix is frequently the binding element itself, while in other cases it may have a role in initiating the binding process. Our results indicate that RX-DMD provides a breakthrough in the structural and dynamical characterization of disordered proteins by generating the structural ensembles of IDPs even when experimental data are not available. PMID:24763499
A new method for the control of discrete nonlinear dynamic systems using neural networks.
Adetona, O; Garcia, E; Keel, L H
2000-01-01
A new controller design method for nonaffine nonlinear dynamic systems is presented in this paper. An identified neural network model of the nonlinear plant is used in the proposed method. The method is based on a new control law that is developed for any discrete deterministic time-invariant nonlinear dynamic system in a subregion Phi(x) of an asymptotically stable equilibrium point of the plant. The performance of the control law is not necessarily dependent on the distance between the current state of the plant and the equilibrium state if the nonlinear dynamic system satisfies some mild requirements in Phi(x). The control law is simple to implement and is based on a novel linearization of the input-output model of the plant at each instant in time. It can be used to control both minimum phase and nonminimum phase nonaffine nonlinear plants. Extensive empirical studies have confirmed that the control law can be used to control a relatively general class of highly nonlinear multiinput-multioutput (MIMO) plants.
Discrete event performance prediction of speculatively parallel temperature-accelerated dynamics
Zamora, Richard James; Voter, Arthur F.; Perez, Danny; ...
2016-12-01
Due to its unrivaled ability to predict the dynamical evolution of interacting atoms, molecular dynamics (MD) is a widely used computational method in theoretical chemistry, physics, biology, and engineering. Despite its success, MD is only capable of modeling time scales within several orders of magnitude of thermal vibrations, leaving out many important phenomena that occur at slower rates. The Temperature Accelerated Dynamics (TAD) method overcomes this limitation by thermally accelerating the state-to-state evolution captured by MD. Due to the algorithmically complex nature of the serial TAD procedure, implementations have yet to improve performance by parallelizing the concurrent exploration of multiplemore » states. Here we utilize a discrete event-based application simulator to introduce and explore a new Speculatively Parallel TAD (SpecTAD) method. We investigate the SpecTAD algorithm, without a full-scale implementation, by constructing an application simulator proxy (SpecTADSim). Finally, following this method, we discover that a nontrivial relationship exists between the optimal SpecTAD parameter set and the number of CPU cores available at run-time. Furthermore, we find that a majority of the available SpecTAD boost can be achieved within an existing TAD application using relatively simple algorithm modifications.« less
Discrete event performance prediction of speculatively parallel temperature-accelerated dynamics
Zamora, Richard James; Voter, Arthur F.; Perez, Danny; Santhi, Nandakishore; Mniszewski, Susan M.; Thulasidasan, Sunil; Eidenbenz, Stephan J.
2016-12-01
Due to its unrivaled ability to predict the dynamical evolution of interacting atoms, molecular dynamics (MD) is a widely used computational method in theoretical chemistry, physics, biology, and engineering. Despite its success, MD is only capable of modeling time scales within several orders of magnitude of thermal vibrations, leaving out many important phenomena that occur at slower rates. The Temperature Accelerated Dynamics (TAD) method overcomes this limitation by thermally accelerating the state-to-state evolution captured by MD. Due to the algorithmically complex nature of the serial TAD procedure, implementations have yet to improve performance by parallelizing the concurrent exploration of multiple states. Here we utilize a discrete event-based application simulator to introduce and explore a new Speculatively Parallel TAD (SpecTAD) method. We investigate the SpecTAD algorithm, without a full-scale implementation, by constructing an application simulator proxy (SpecTADSim). Finally, following this method, we discover that a nontrivial relationship exists between the optimal SpecTAD parameter set and the number of CPU cores available at run-time. Furthermore, we find that a majority of the available SpecTAD boost can be achieved within an existing TAD application using relatively simple algorithm modifications.
Dynamics of Investor Attention on the Social Web
ERIC Educational Resources Information Center
Li, Xian
2013-01-01
The World Wide Web has been revolutionizing how investors produce and consume information while participating in financial markets. Both the amount of information and the speed it flows around have achieved unprecedented magnitudes. The preeminent change is the growth of investor communities on the social web, which give rise to multidimensional…
Dynamics of Investor Attention on the Social Web
ERIC Educational Resources Information Center
Li, Xian
2013-01-01
The World Wide Web has been revolutionizing how investors produce and consume information while participating in financial markets. Both the amount of information and the speed it flows around have achieved unprecedented magnitudes. The preeminent change is the growth of investor communities on the social web, which give rise to multidimensional…
NASA Technical Reports Server (NTRS)
Yee, H. C.; Sweby, P. K.
1995-01-01
The global asymptotic nonlinear behavior of 1 1 explicit and implicit time discretizations for four 2 x 2 systems of first-order autonomous nonlinear ordinary differential equations (ODES) is analyzed. The objectives are to gain a basic understanding of the difference in the dynamics of numerics between the scalars and systems of nonlinear autonomous ODEs and to set a baseline global asymptotic solution behavior of these schemes for practical computations in computational fluid dynamics. We show how 'numerical' basins of attraction can complement the bifurcation diagrams in gaining more detailed global asymptotic behavior of time discretizations for nonlinear differential equations (DEs). We show how in the presence of spurious asymptotes the basins of the true stable steady states can be segmented by the basins of the spurious stable and unstable asymptotes. One major consequence of this phenomenon which is not commonly known is that this spurious behavior can result in a dramatic distortion and, in most cases, a dramatic shrinkage and segmentation of the basin of attraction of the true solution for finite time steps. Such distortion, shrinkage and segmentation of the numerical basins of attraction will occur regardless of the stability of the spurious asymptotes, and will occur for unconditionally stable implicit linear multistep methods. In other words, for the same (common) steady-state solution the associated basin of attraction of the DE might be very different from the discretized counterparts and the numerical basin of attraction can be very different from numerical method to numerical method. The results can be used as an explanation for possible causes of error, and slow convergence and nonconvergence of steady-state numerical solutions when using the time-dependent approach for nonlinear hyperbolic or parabolic PDES.
Caroff, Jildaz; Mihalea, Cristian; Da Ros, Valerio; Yagi, Takanobu; Iacobucci, Marta; Ikka, Léon; Moret, Jacques; Spelle, Laurent
2017-07-01
Recent reports have revealed a worsening of aneurysm occlusion between WEB treatment baseline and angiographic follow-up due to "compression" of the device. We utilized computational fluid dynamics (CFD) in order to determine whether the underlying mechanism of this worsening is flow related. We included data from all consecutive patients treated in our institution with a WEB for unruptured aneurysms located either at the middle cerebral artery or basilar tip. The CFD study was performed using pre-operative 3D rotational angiography. From digital subtraction follow-up angiographies patients were dichotomized into two groups: one with WEB "compression" and one without. We performed statistical analyses to determine a potential correlation between WEB compression and CFD inflow ratio. Between July 2012 and June 2015, a total of 22 unruptured middle cerebral artery or basilar tip aneurysms were treated with a WEB device in our department. Three patients were excluded from the analysis and the mean follow-up period was 17months. Eleven WEBs presented "compression" during follow-up. Interestingly, device "compression" was statistically correlated to the CFD inflow ratio (P=0.018), although not to aneurysm volume, aspect ratio or neck size. The mechanisms underlying the worsening of aneurysm occlusion in WEB-treated patients due to device compression are most likely complex as well as multifactorial. However, it is apparent from our pilot study that a high arterial inflow is, at least, partially involved. Further theoretical and animal research studies are needed to increase our understanding of this phenomenon. Copyright © 2017 Elsevier Masson SAS. All rights reserved.
A Dynamic Recommender System for Improved Web Usage Mining and CRM Using Swarm Intelligence
Alphy, Anna; Prabakaran, S.
2015-01-01
In modern days, to enrich e-business, the websites are personalized for each user by understanding their interests and behavior. The main challenges of online usage data are information overload and their dynamic nature. In this paper, to address these issues, a WebBluegillRecom-annealing dynamic recommender system that uses web usage mining techniques in tandem with software agents developed for providing dynamic recommendations to users that can be used for customizing a website is proposed. The proposed WebBluegillRecom-annealing dynamic recommender uses swarm intelligence from the foraging behavior of a bluegill fish. It overcomes the information overload by handling dynamic behaviors of users. Our dynamic recommender system was compared against traditional collaborative filtering systems. The results show that the proposed system has higher precision, coverage, F1 measure, and scalability than the traditional collaborative filtering systems. Moreover, the recommendations given by our system overcome the overspecialization problem by including variety in recommendations. PMID:26229978
A Dynamic Recommender System for Improved Web Usage Mining and CRM Using Swarm Intelligence.
Alphy, Anna; Prabakaran, S
2015-01-01
In modern days, to enrich e-business, the websites are personalized for each user by understanding their interests and behavior. The main challenges of online usage data are information overload and their dynamic nature. In this paper, to address these issues, a WebBluegillRecom-annealing dynamic recommender system that uses web usage mining techniques in tandem with software agents developed for providing dynamic recommendations to users that can be used for customizing a website is proposed. The proposed WebBluegillRecom-annealing dynamic recommender uses swarm intelligence from the foraging behavior of a bluegill fish. It overcomes the information overload by handling dynamic behaviors of users. Our dynamic recommender system was compared against traditional collaborative filtering systems. The results show that the proposed system has higher precision, coverage, F1 measure, and scalability than the traditional collaborative filtering systems. Moreover, the recommendations given by our system overcome the overspecialization problem by including variety in recommendations.
Generalized coherent states for discrete and continuous dynamics and their applications
NASA Astrophysics Data System (ADS)
Sadiq, Muhammad
We investigate new forms of generalized coherent states for several systems with no direct reference to their group structures. A general procedure of constructing a set of coherent states, as proposed by Perelomov, is to use an irreducible representation of a Lie group acting on an extremal state (e.g., vacuum state). However, Klauder put forth a set of conditions to define coherent states in a way free from any underlying group structure. First we critically examine Klauder's coherent states, as modified by Gazeau and Klauder, which are defined over energy eigenstates of a physical system, and construct a new modified class of coherent states satisfying Klauder's criteria. Our set of coherent states is a natural generalization of the harmonic oscillator coherent states and encompasses both the discrete and continuous spectra in a unified manner. We apply our formulation to a particle in a one-dimensional box, a particle in the Poschl-Teller potential, and the compactified Coulomb problem in order to demonstrate explicitly the limiting procedure for going from the coherent states for discrete dynamics to those for continuous dynamics. We also discuss the path integral with our coherent states. Secondly, we construct two different classes of coherent states for a cubic SU(2) or Higgs algebra. The first class is constructed by following a Perelomov-like procedure so as to retain the usual SU(2) limit; and the second one is the cubic SU(2) version of our generalized coherent states similar to those of Gazeau and Klauder. The final topic we discuss in this thesis is related to quantum computation with coherent states. We show that simulation of a dynamical quantum system can be performed on a coherent quantum computer as a Quantum Fourier Transform operator to the extremal state belonging to the irreducible representation of the group. The states obtained in this manner are termed as Perelomov type coherent states. Our construction here is based on applying the
NASA Astrophysics Data System (ADS)
Savin, Sergey; Büchner, Jörg; Zelenyi, Lev; Kronberg, Elena; Kozak, Lyudmila; Blecki, Jan; Lezhen, Liudmila; Nemecek, Zdenek; Safrankova, Jana; Skalsky, Alexander; Budaev, Vyacheslav; Amata, Ermanno
We explore interactions of Supersonic Plasma Streams (SPS) with the Earth magnetosphere in the context of the planetary and astrophysical magnetospheres and of that of laboratory plasmas. The interactions can be inherently non-local and non-equilibrium, and even explosive due to both solar wind (SW) induced and self-generated coherent structures in the multiscale system with the scales ranging from the micro to global scales. We concentrate on the main fundamental processes arising from the SPS cascading and interactions with surface and cavity resonances in the Earth’s magnetosphere, using multi-spacecraft data (SPECTR-R, DOUBLE STAR, CLUSTER, GEOTAIL, ACE, WIND etc.). We will address the following key problems to advance our understanding of anomalous transport and boundary dynamics: - generalizations of the SPS generation mechanisms, e.g., by bow shock (BS) surface or magnetosheath (MSH) cavity resonances, triggering by interplanetary shocks, solar wind (SW) dynamic pressure jumps, foreshock nonlinear structures, etc. - the clarification of BS rippling mechanisms requires base on the relevant databases from the CLUSTER/ DOUBLE STAR/ GEOTAIL/SPECTR-R/ ACE/ WIND spacecraft, which will be used for a statistical analysis targeting the SPS statistical features as extreme events. - substantial part of the SW kinetic energy can be pumped into the BS membrane and MSH cavity modes and initiate further cascades towards higher frequencies. Accordingly we present the multipoint studies of the SPS and of related nonlinear discrete cascades (carried generally by the SPS), along with the transformation of discrete cascades of the dynamic pressure into turbulent cascades. - investigation of spectral and bi-spectral cross-correlations in SW, foreshock, MSH and in vicinity of BS and magnetopause (MP) would demonstrate that both inflow and outflow into/ from magnetosphere can be modulated by the SPS and by the related outer magnetospheric resonances as well. We demonstrate in
Angeles, J G C; Ouyang, Z; Aguirre, A M; Lammers, P J; Song, M
2009-09-01
Fungal-plant root associations involve nutrient exchanges, between the partners and the soil, particularly phosphate, that benefit both organisms. Discrete dynamical system (DDS) models are reconstructed to capture gene regulation in the arbuscular mycorrhizae Glomus versiforme-Medicago trunculata root symbiosis. Previously published time-course gene expression data derived from various days post-inoculation were clustered to identify genes co-regulated in mycorrhizal roots. Uncolonised roots grown with high phosphate provide a key nutritional control condition. First-order linear DDS models were created using a data-driven method to fit to the observed gene expression data. The result of the modelling constitutes active gene interactions in the regulatory network of the plant root at 8, 15, 22, 31 and 36 days post-inoculation. These genes are involved in basic metabolism, development, oxidative stress and defense pathways, and show consistent dynamic behaviours in the model. The functions of previously unannotated genes were further elucidated from the developed system maps.
Dorn, Martin; Hekmat, Dariusch
2016-03-01
Preparative packed-bed chromatography using polymer-based, compressible, porous resins is a powerful method for purification of macromolecular bioproducts. During operation, a complex, hysteretic, thus, history-dependent packed bed behavior is often observed but theoretical understanding of the causes is limited. Therefore, a rigorous modeling approach of the chromatography column on the particle scale has been made which takes into account interparticle micromechanics and fluid-particle interactions for the first time. A three-dimensional deterministic model was created by applying Computational Fluid Dynamics (CFD) coupled with the Discrete Element Method (DEM). The column packing behavior during either flow or mechanical compression was investigated in-silico and in laboratory experiments. A pronounced axial compression-relaxation profile was identified that differed for both compression strategies. Void spaces were clearly visible in the packed bed after compression. It was assumed that the observed bed inhomogeneity was because of a force-chain network at the particle scale. The simulation satisfactorily reproduced the measured behavior regarding packing compression as well as pressure-flow dependency. Furthermore, the particle Young's modulus and particle-wall friction as well as interparticle friction were identified as crucial parameters affecting packing dynamics. It was concluded that compaction of the chromatographic bed is rather because of particle rearrangement than particle deformation. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 32:363-371, 2016. © 2015 American Institute of Chemical Engineers.
Dynamics of exciton-polaritons in discrete lattices under incoherent localized pumping
NASA Astrophysics Data System (ADS)
Yulin, A. V.; Chestnov, I. Yu.; Ma, X.; Schumacher, S.; Peschel, U.; Egorov, O. A.
2016-08-01
The paper deals with the spontaneous coherence building up between exciton-polaritons trapped in an array of deep potential wells in the presence of an incoherent pump. A theoretical approach based on a standard tight-binding mean-field approximation is used to reduce the continuous periodic problem to a discrete model. The typical dynamics of the nonlinear exciton-polariton system for the cases of spatially uniform and for localized pumps are discussed. Special attention is paid to the "staggered" coherent steady states with π jumps in the phases between neighboring sites and to "uniform" states with a smooth phase distribution. It is shown that, apart from the states with a single frequency, mixed states with spectra with several harmonics can form in the system. The selection mechanism that controls the type of steady state growing from a weak noise is studied. It is found that in the case of localized pumps the decaying tails of the solutions play a crucial role in the dynamics of the polaritons. The applicability of the obtained theoretical results for a qualitative explanation of the complex phenomena observed in recent experiments is discussed.
Zholtkevych, G N; Bespalov, G Yu; Nosov, K V; Abhishek, Mahalakshmi
2013-12-01
Mathematical modeling is a convenient way for characterization of complex ecosystems. This approach was applied to study the dynamics of zooplankton in Lake Sevan (Armenia) at different stages of anthropogenic eutrophication with the use of a novel method called discrete modeling of dynamical systems with feedback (DMDS). Simulation demonstrated that the application of this method helps in characterization of inter- and intra-component relationships in a natural ecosystem. This method describes all possible pairwise inter-component relationships like "plus-plus," "minus-minus," "plus-minus," "plus-zero," "minus-zero," and "zero-zero" that occur in most ecosystems. Based on the results, a working hypothesis was formulated. It was found that the sensitivity to weak external influence in zooplanktons was the greatest during the mid period of eutrophication in Lake Sevan, whereas in the final stages of eutrophication, an outbreak in the biomass production of cyanobacteria was evident. To support this approach, a weak external disturbance in the form of magnetic storm was used to see its effect on species Daphnia longispina sevanica. A statistically significant correlation between the frequency of magnetic storms and the number of this species was revealed and an increase in the number of toxic cyanobacteria species as a consequence of eutrophication. This paper, for the first time, suggests a DMDS method, to diagnose impact of anthropogenic eutrophication on environment.
Discrete-time nonlinear HJB solution using approximate dynamic programming: convergence proof.
Al-Tamimi, Asma; Lewis, Frank L; Abu-Khalaf, Murad
2008-08-01
Convergence of the value-iteration-based heuristic dynamic programming (HDP) algorithm is proven in the case of general nonlinear systems. That is, it is shown that HDP converges to the optimal control and the optimal value function that solves the Hamilton-Jacobi-Bellman equation appearing in infinite-horizon discrete-time (DT) nonlinear optimal control. It is assumed that, at each iteration, the value and action update equations can be exactly solved. The following two standard neural networks (NN) are used: a critic NN is used to approximate the value function, whereas an action network is used to approximate the optimal control policy. It is stressed that this approach allows the implementation of HDP without knowing the internal dynamics of the system. The exact solution assumption holds for some classes of nonlinear systems and, specifically, in the specific case of the DT linear quadratic regulator (LQR), where the action is linear and the value quadratic in the states and NNs have zero approximation error. It is stressed that, for the LQR, HDP may be implemented without knowing the system A matrix by using two NNs. This fact is not generally appreciated in the folklore of HDP for the DT LQR, where only one critic NN is generally used.
NASA Astrophysics Data System (ADS)
Delfau, Jean-Baptiste; Ollivier, Hélène; López, Cristóbal; Blasius, Bernd; Hernández-García, Emilio
2016-10-01
Brownian particles interacting via repulsive soft-core potentials can spontaneously aggregate, despite repelling each other, and form periodic crystals of particle clusters. We study this phenomenon in low-dimensional situations (one and two dimensions) at two levels of description: by performing numerical simulations of the discrete particle dynamics and by linear and nonlinear analysis of the corresponding Dean-Kawasaki equation for the macroscopic particle density. Restricting to low dimensions and neglecting fluctuation effects, we gain analytical insight into the mechanisms of the instability leading to clustering which turn out to be the interplay among diffusion, the intracluster forces, and the forces between neighboring clusters. We show that the deterministic part of the Dean-Kawasaki equation provides a good description of the particle dynamics, including width and shape of the clusters and over a wide range of parameters, and analyze with weakly nonlinear techniques the nature of the pattern-forming bifurcation in one and two dimensions. Finally, we briefly discuss the case of attractive forces.
TOPSAN: a dynamic web database for structural genomics.
Ellrott, Kyle; Zmasek, Christian M; Weekes, Dana; Sri Krishna, S; Bakolitsa, Constantina; Godzik, Adam; Wooley, John
2011-01-01
The Open Protein Structure Annotation Network (TOPSAN) is a web-based collaboration platform for exploring and annotating structures determined by structural genomics efforts. Characterization of those structures presents a challenge since the majority of the proteins themselves have not yet been characterized. Responding to this challenge, the TOPSAN platform facilitates collaborative annotation and investigation via a user-friendly web-based interface pre-populated with automatically generated information. Semantic web technologies expand and enrich TOPSAN's content through links to larger sets of related databases, and thus, enable data integration from disparate sources and data mining via conventional query languages. TOPSAN can be found at http://www.topsan.org.
Discrete two-sex models of population dynamics: On modelling the mating function
NASA Astrophysics Data System (ADS)
Bessa-Gomes, Carmen; Legendre, Stéphane; Clobert, Jean
2010-09-01
Although sexual reproduction has long been a central subject of theoretical ecology, until recently its consequences for population dynamics were largely overlooked. This is now changing, and many studies have addressed this issue, showing that when the mating system is taken into account, the population dynamics depends on the relative abundance of males and females, and is non-linear. Moreover, sexual reproduction increases the extinction risk, namely due to the Allee effect. Nevertheless, different studies have identified diverse potential consequences, depending on the choice of mating function. In this study, we investigate the consequences of three alternative mating functions that are frequently used in discrete population models: the minimum; the harmonic mean; and the modified harmonic mean. We consider their consequences at three levels: on the probability that females will breed; on the presence and intensity of the Allee effect; and on the extinction risk. When we consider the harmonic mean, the number of times the individuals of the least abundant sex mate exceeds their mating potential, which implies that with variable sex-ratios the potential reproductive rate is no longer under the modeller's control. Consequently, the female breeding probability exceeds 1 whenever the sex-ratio is male-biased, which constitutes an obvious problem. The use of the harmonic mean is thus only justified if we think that this parameter should be re-defined in order to represent the females' breeding rate and the fact that females may reproduce more than once per breeding season. This phenomenon buffers the Allee effect, and reduces the extinction risk. However, when we consider birth-pulse populations, such a phenomenon is implausible because the number of times females can reproduce per birth season is limited. In general, the minimum or modified harmonic mean mating functions seem to be more suitable for assessing the impact of mating systems on population dynamics.
TADSim: Discrete Event-based Performance Prediction for Temperature Accelerated Dynamics
Mniszewski, Susan M.; Junghans, Christoph; Voter, Arthur F.; Perez, Danny; Eidenbenz, Stephan J.
2015-04-16
Next-generation high-performance computing will require more scalable and flexible performance prediction tools to evaluate software--hardware co-design choices relevant to scientific applications and hardware architectures. Here, we present a new class of tools called application simulators—parameterized fast-running proxies of large-scale scientific applications using parallel discrete event simulation. Parameterized choices for the algorithmic method and hardware options provide a rich space for design exploration and allow us to quickly find well-performing software--hardware combinations. We demonstrate our approach with a TADSim simulator that models the temperature-accelerated dynamics (TAD) method, an algorithmically complex and parameter-rich member of the accelerated molecular dynamics (AMD) family of molecular dynamics methods. The essence of the TAD application is captured without the computational expense and resource usage of the full code. We accomplish this by identifying the time-intensive elements, quantifying algorithm steps in terms of those elements, abstracting them out, and replacing them by the passage of time. We use TADSim to quickly characterize the runtime performance and algorithmic behavior for the otherwise long-running simulation code. We extend TADSim to model algorithm extensions, such as speculative spawning of the compute-bound stages, and predict performance improvements without having to implement such a method. Validation against the actual TAD code shows close agreement for the evolution of an example physical system, a silver surface. Finally, focused parameter scans have allowed us to study algorithm parameter choices over far more scenarios than would be possible with the actual simulation. This has led to interesting performance-related insights and suggested extensions.
TADSim: Discrete Event-based Performance Prediction for Temperature Accelerated Dynamics
Mniszewski, Susan M.; Junghans, Christoph; Voter, Arthur F.; ...
2015-04-16
Next-generation high-performance computing will require more scalable and flexible performance prediction tools to evaluate software--hardware co-design choices relevant to scientific applications and hardware architectures. Here, we present a new class of tools called application simulators—parameterized fast-running proxies of large-scale scientific applications using parallel discrete event simulation. Parameterized choices for the algorithmic method and hardware options provide a rich space for design exploration and allow us to quickly find well-performing software--hardware combinations. We demonstrate our approach with a TADSim simulator that models the temperature-accelerated dynamics (TAD) method, an algorithmically complex and parameter-rich member of the accelerated molecular dynamics (AMD) family ofmore » molecular dynamics methods. The essence of the TAD application is captured without the computational expense and resource usage of the full code. We accomplish this by identifying the time-intensive elements, quantifying algorithm steps in terms of those elements, abstracting them out, and replacing them by the passage of time. We use TADSim to quickly characterize the runtime performance and algorithmic behavior for the otherwise long-running simulation code. We extend TADSim to model algorithm extensions, such as speculative spawning of the compute-bound stages, and predict performance improvements without having to implement such a method. Validation against the actual TAD code shows close agreement for the evolution of an example physical system, a silver surface. Finally, focused parameter scans have allowed us to study algorithm parameter choices over far more scenarios than would be possible with the actual simulation. This has led to interesting performance-related insights and suggested extensions.« less
NASA Astrophysics Data System (ADS)
Gao, Yuan; Zhuang, Zhuo; You, XiaoChuan
2011-04-01
We develop a new hierarchical dislocation-grain boundary (GB) interaction model to predict the mechanical behavior of polycrystalline metals at micro and submicro scales by coupling 3D Discrete Dislocation Dynamics (DDD) simulation with the Molecular Dynamics (MD) simulation. At the microscales, the DDD simulations are responsible for capturing the evolution of dislocation structures; at the nanoscales, the MD simulations are responsible for obtaining the GB energy and ISF energy which are then transferred hierarchically to the DDD level. In the present model, four kinds of dislocation-GB interactions, i.e. transmission, absorption, re-emission and reflection, are all considered. By this methodology, the compression of a Cu micro-sized bi-crystal pillar is studied. We investigate the characteristic mechanical behavior of the bi-crystal compared with that of the single-crystal. Moreover, the comparison between the present penetrable model of GB and the conventional impenetrable model also shows the accuracy and efficiency of the present model.
NASA Technical Reports Server (NTRS)
Saether, Erik; Hochhalter, Jacob D.; Glaessgen, Edward H.; Mishin, Yuri
2014-01-01
A multiscale modeling methodology is developed for structurally-graded material microstructures. Molecular dynamic (MD) simulations are performed at the nanoscale to determine fundamental failure mechanisms and quantify material constitutive parameters. These parameters are used to calibrate material processes at the mesoscale using discrete dislocation dynamics (DD). Different grain boundary interactions with dislocations are analyzed using DD to predict grain-size dependent stress-strain behavior. These relationships are mapped into crystal plasticity (CP) parameters to develop a computationally efficient finite element-based DD/CP model for continuum-level simulations and complete the multiscale analysis by predicting the behavior of macroscopic physical specimens. The present analysis is focused on simulating the behavior of a graded microstructure in which grain sizes are on the order of nanometers in the exterior region and transition to larger, multi-micron size in the interior domain. This microstructural configuration has been shown to offer improved mechanical properties over homogeneous coarse-grained materials by increasing yield stress while maintaining ductility. Various mesoscopic polycrystal models of structurally-graded microstructures are generated, analyzed and used as a benchmark for comparison between multiscale DD/CP model and DD predictions. A final series of simulations utilize the DD/CP analysis method exclusively to study macroscopic models that cannot be analyzed by MD or DD methods alone due to the model size.
Principles of Discrete Time Mechanics
NASA Astrophysics Data System (ADS)
Jaroszkiewicz, George
2014-04-01
1. Introduction; 2. The physics of discreteness; 3. The road to calculus; 4. Temporal discretization; 5. Discrete time dynamics architecture; 6. Some models; 7. Classical cellular automata; 8. The action sum; 9. Worked examples; 10. Lee's approach to discrete time mechanics; 11. Elliptic billiards; 12. The construction of system functions; 13. The classical discrete time oscillator; 14. Type 2 temporal discretization; 15. Intermission; 16. Discrete time quantum mechanics; 17. The quantized discrete time oscillator; 18. Path integrals; 19. Quantum encoding; 20. Discrete time classical field equations; 21. The discrete time Schrodinger equation; 22. The discrete time Klein-Gordon equation; 23. The discrete time Dirac equation; 24. Discrete time Maxwell's equations; 25. The discrete time Skyrme model; 26. Discrete time quantum field theory; 27. Interacting discrete time scalar fields; 28. Space, time and gravitation; 29. Causality and observation; 30. Concluding remarks; Appendix A. Coherent states; Appendix B. The time-dependent oscillator; Appendix C. Quaternions; Appendix D. Quantum registers; References; Index.
GENERAL: Symplectic-energy-first integrators of discrete mechanico-electrical dynamical systems
NASA Astrophysics Data System (ADS)
Fu, Jing-Li; Chen, Ben-Yong; Tang, Yi-Fa; Fu, Hao
2008-11-01
A discrete total variation calculus with variable time steps is presented for mechanico-electrical systems where there exist non-potential and dissipative forces. By using this discrete variation calculus, the symplectic-energy-first integrators for mechanico-electrical systems are derived. To do this, the time step adaptation is employed. The discrete variational principle and the Euler-Lagrange equation are derived for the systems. By using this discrete algorithm it is shown that mechanico-electrical systems are not symplectic and their energies are not conserved unless they are Lagrange mechanico-electrical systems. A practical example is presented to illustrate these results.
Sensor Web Dynamic Measurement Techniques and Adaptive Observing Strategies
NASA Technical Reports Server (NTRS)
Talabac, Stephen J.
2004-01-01
Sensor Web observing systems may have the potential to significantly improve our ability to monitor, understand, and predict the evolution of rapidly evolving, transient, or variable environmental features and events. This improvement will come about by integrating novel data collection techniques, new or improved instruments, emerging communications technologies and protocols, sensor mark-up languages, and interoperable planning and scheduling systems. In contrast to today's observing systems, "event-driven" sensor webs will synthesize real- or near-real time measurements and information from other platforms and then react by reconfiguring the platforms and instruments to invoke new measurement modes and adaptive observation strategies. Similarly, "model-driven" sensor webs will utilize environmental prediction models to initiate targeted sensor measurements or to use a new observing strategy. The sensor web concept contrasts with today's data collection techniques and observing system operations concepts where independent measurements are made by remote sensing and in situ platforms that do not share, and therefore cannot act upon, potentially useful complementary sensor measurement data and platform state information. This presentation describes NASA's view of event-driven and model-driven Sensor Webs and highlights several research and development activities at the Goddard Space Flight Center.
Bellmore, J. Ryan; Benjamin, Joseph R.; Newsom, Michael; Bountry, Jennifer A.; Dombroski, Daniel
2017-01-01
Restoration is frequently aimed at the recovery of target species, but also influences the larger food web in which these species participate. Effects of restoration on this broader network of organisms can influence target species both directly and indirectly via changes in energy flow through food webs. To help incorporate these complexities into river restoration planning we constructed a model that links river food web dynamics to in-stream physical habitat and riparian vegetation conditions. We present an application of the model to the Methow River, Washington (USA), a location of on-going restoration aimed at recovering salmon. Three restoration strategies were simulated: riparian vegetation restoration, nutrient augmentation via salmon carcass addition, and side-channel reconnection. We also added populations of nonnative aquatic snails and fish to the modeled food web to explore how changes in food web structure mediate responses to restoration. Simulations suggest that side-channel reconnection may be a better strategy than carcass addition and vegetation planting for improving conditions for salmon in this river segment. However, modeled responses were strongly sensitive to changes in the structure of the food web. The addition of nonnative snails and fish modified pathways of energy through the food web, which negated restoration improvements. This finding illustrates that forecasting responses to restoration may require accounting for the structure of food webs, and that changes in this structure—as might be expected with the spread of invasive species—could compromise restoration outcomes. Unlike habitat-based approaches to restoration assessment that focus on the direct effects of physical habitat conditions on single species of interest, our approach dynamically links the success of target organisms to the success of competitors, predators, and prey. By elucidating the direct and indirect pathways by which restoration affects target species
Bellmore, J Ryan; Benjamin, Joseph R; Newsom, Michael; Bountry, Jennifer A; Dombroski, Daniel
2017-04-01
Restoration is frequently aimed at the recovery of target species, but also influences the larger food web in which these species participate. Effects of restoration on this broader network of organisms can influence target species both directly and indirectly via changes in energy flow through food webs. To help incorporate these complexities into river restoration planning, we constructed a model that links river food web dynamics to in-stream physical habitat and riparian vegetation conditions. We present an application of the model to the Methow River, Washington, USA, a location of on-going restoration aimed at recovering salmon. Three restoration strategies were simulated: riparian vegetation restoration, nutrient augmentation via salmon carcass addition, and side channel reconnection. We also added populations of nonnative aquatic snails and fish to the modeled food web to explore how changes in food web structure mediate responses to restoration. Simulations suggest that side channel reconnection may be a better strategy than carcass addition and vegetation planting for improving conditions for salmon in this river segment. However, modeled responses were strongly sensitive to changes in the structure of the food web. The addition of nonnative snails and fish modified pathways of energy through the food web, which negated restoration improvements. This finding illustrates that forecasting responses to restoration may require accounting for the structure of food webs, and that changes in this structure, as might be expected with the spread of invasive species, could compromise restoration outcomes. Unlike habitat-based approaches to restoration assessment that focus on the direct effects of physical habitat conditions on single species of interest, our approach dynamically links the success of target organisms to the success of competitors, predators, and prey. By elucidating the direct and indirect pathways by which restoration affects target species
Using Web Services and XML Harvesting to Achieve a Dynamic Web Site. Computers in Small Libraries
ERIC Educational Resources Information Center
Roberts, Gary
2005-01-01
Exploiting and contextualizing free information is a natural part of library culture. In this column, Gary Roberts, the information systems and reference librarian at Herrick Library, Alfred University in Alfred, NY, describes how to use XML content on a Web site to link to hundreds of free and useful resources. He gives a general overview of the…
NASA Astrophysics Data System (ADS)
Bertin, N.; Upadhyay, M. V.; Pradalier, C.; Capolungo, L.
2015-09-01
In this paper, we propose a novel full-field approach based on the fast Fourier transform (FFT) technique to compute mechanical fields in periodic discrete dislocation dynamics (DDD) simulations for anisotropic materials: the DDD-FFT approach. By coupling the FFT-based approach to the discrete continuous model, the present approach benefits from the high computational efficiency of the FFT algorithm, while allowing for a discrete representation of dislocation lines. It is demonstrated that the computational time associated with the new DDD-FFT approach is significantly lower than that of current DDD approaches when large number of dislocation segments are involved for isotropic and anisotropic elasticity, respectively. Furthermore, for fine Fourier grids, the treatment of anisotropic elasticity comes at a similar computational cost to that of isotropic simulation. Thus, the proposed approach paves the way towards achieving scale transition from DDD to mesoscale plasticity, especially due to the method’s ability to incorporate inhomogeneous elasticity.
Ab initio folding of proteins using all-atom discrete molecular dynamics
Ding, Feng; Tsao, Douglas; Nie, Huifen; Dokholyan, Nikolay V.
2008-01-01
Summary Discrete molecular dynamics (DMD) is a rapid sampling method used in protein folding and aggregation studies. Until now, DMD was used to perform simulations of simplified protein models in conjunction with structure-based force fields. Here, we develop an all-atom protein model and a transferable force field featuring packing, solvation, and environment-dependent hydrogen bond interactions. Using the replica exchange method, we perform folding simulations of six small proteins (20–60 residues) with distinct native structures. In all cases, native or near-native states are reached in simulations. For three small proteins, multiple folding transitions are observed and the computationally-characterized thermodynamics are in quantitative agreement with experiments. The predictive power of all-atom DMD highlights the importance of environment-dependent hydrogen bond interactions in modeling protein folding. The developed approach can be used for accurate and rapid sampling of conformational spaces of proteins and protein-protein complexes, and applied to protein engineering and design of protein-protein interactions. PMID:18611374
Munsky, Brian; Fox, Zachary; Neuert, Gregor
2015-09-01
The production and degradation of RNA transcripts is inherently subject to biological noise that arises from small gene copy numbers in individual cells. As a result, cellular RNA levels can exhibit large fluctuations over time and from one cell to the next. This article presents a range of precise single-molecule experimental techniques, based upon RNA fluorescence in situ hybridization, which can be used to measure the fluctuations of RNA at the single-cell level. A class of models for gene activation and deactivation is postulated in order to capture complex stochastic effects of chromatin modifications or transcription factor interactions. A computational tool, known as the finite state projection approach, is introduced to accurately and efficiently analyze these models in order to predict how probability distributions of RNA change over time in response to changing environmental conditions. These single-molecule experiments, discrete stochastic models, and computational analyses are systematically integrated to identify models of gene regulation dynamics. To illustrate the power and generality of our integrated experimental and computational approach, we explore cases that include different models for three different RNA types (sRNA, mRNA and nascent RNA), three different experimental techniques and three different biological species (bacteria, yeast and human cells). Copyright © 2015. Published by Elsevier Inc.
Shirvanyants, David; Ding, Feng; Tsao, Douglas; Ramachandran, Srinivas; Dokholyan, Nikolay V
2012-07-26
Until now it has been impractical to observe protein folding in silico for proteins larger than 50 residues. Limitations of both force field accuracy and computational efficiency make the folding problem very challenging. Here we employ discrete molecular dynamics (DMD) simulations with an all-atom force field to fold fast-folding proteins. We extend the DMD force field by introducing long-range electrostatic interactions to model salt-bridges and a sequence-dependent semiempirical potential accounting for natural tendencies of certain amino acid sequences to form specific secondary structures. We enhance the computational performance by parallelizing the DMD algorithm. Using a small number of commodity computers, we achieve sampling quality and folding accuracy comparable to the explicit-solvent simulations performed on high-end hardware. We demonstrate that DMD can be used to observe equilibrium folding of villin headpiece and WW domain, study two-state folding kinetics, and sample near-native states in ab initio folding of proteins of ∼100 residues.
Dynamical and statistical behavior of discrete combustion waves: a theoretical and numerical study.
Bharath, Naine Tarun; Rashkovskiy, Sergey A; Tewari, Surya P; Gundawar, Manoj Kumar
2013-04-01
We present a detailed theoretical and numerical study of combustion waves in a discrete one-dimensional disordered system. The distances between neighboring reaction cells were modeled with a gamma distribution. The results show that the random structure of the microheterogeneous system plays a crucial role in the dynamical and statistical behavior of the system. This is a consequence of the nonlinear interaction of the random structure of the system with the thermal wave. An analysis of the experimental data on the combustion of a gasless system (Ti + xSi) and a wide range of thermite systems was performed in view of the developed model. We have shown that the burning rate of the powder system sensitively depends on its internal structure. The present model allows for reproducing theoretically the experimental data for a wide range of pyrotechnic mixtures. We show that Arrhenius' macrokinetics at combustion of disperse systems can take place even in the absence of Arrhenius' microkinetics; it can have a purely thermal nature and be related to their heterogeneity and to the existence of threshold temperature. It is also observed that the combustion of disperse systems always occurs in the microheterogeneous mode according to the relay-race mechanism.
Value Iteration Adaptive Dynamic Programming for Optimal Control of Discrete-Time Nonlinear Systems.
Wei, Qinglai; Liu, Derong; Lin, Hanquan
2016-03-01
In this paper, a value iteration adaptive dynamic programming (ADP) algorithm is developed to solve infinite horizon undiscounted optimal control problems for discrete-time nonlinear systems. The present value iteration ADP algorithm permits an arbitrary positive semi-definite function to initialize the algorithm. A novel convergence analysis is developed to guarantee that the iterative value function converges to the optimal performance index function. Initialized by different initial functions, it is proven that the iterative value function will be monotonically nonincreasing, monotonically nondecreasing, or nonmonotonic and will converge to the optimum. In this paper, for the first time, the admissibility properties of the iterative control laws are developed for value iteration algorithms. It is emphasized that new termination criteria are established to guarantee the effectiveness of the iterative control laws. Neural networks are used to approximate the iterative value function and compute the iterative control law, respectively, for facilitating the implementation of the iterative ADP algorithm. Finally, two simulation examples are given to illustrate the performance of the present method.
Finite-approximation-error-based discrete-time iterative adaptive dynamic programming.
Wei, Qinglai; Wang, Fei-Yue; Liu, Derong; Yang, Xiong
2014-12-01
In this paper, a new iterative adaptive dynamic programming (ADP) algorithm is developed to solve optimal control problems for infinite horizon discrete-time nonlinear systems with finite approximation errors. First, a new generalized value iteration algorithm of ADP is developed to make the iterative performance index function converge to the solution of the Hamilton-Jacobi-Bellman equation. The generalized value iteration algorithm permits an arbitrary positive semi-definite function to initialize it, which overcomes the disadvantage of traditional value iteration algorithms. When the iterative control law and iterative performance index function in each iteration cannot accurately be obtained, for the first time a new "design method of the convergence criteria" for the finite-approximation-error-based generalized value iteration algorithm is established. A suitable approximation error can be designed adaptively to make the iterative performance index function converge to a finite neighborhood of the optimal performance index function. Neural networks are used to implement the iterative ADP algorithm. Finally, two simulation examples are given to illustrate the performance of the developed method.
Adaptive Dynamic Programming for Discrete-Time Zero-Sum Games.
Wei, Qinglai; Liu, Derong; Lin, Qiao; Song, Ruizhuo
2017-01-27
In this paper, a novel adaptive dynamic programming (ADP) algorithm, called "iterative zero-sum ADP algorithm," is developed to solve infinite-horizon discrete-time two-player zero-sum games of nonlinear systems. The present iterative zero-sum ADP algorithm permits arbitrary positive semidefinite functions to initialize the upper and lower iterations. A novel convergence analysis is developed to guarantee the upper and lower iterative value functions to converge to the upper and lower optimums, respectively. When the saddle-point equilibrium exists, it is emphasized that both the upper and lower iterative value functions are proved to converge to the optimal solution of the zero-sum game, where the existence criteria of the saddle-point equilibrium are not required. If the saddle-point equilibrium does not exist, the upper and lower optimal performance index functions are obtained, respectively, where the upper and lower performance index functions are proved to be not equivalent. Finally, simulation results and comparisons are shown to illustrate the performance of the present method.
Dynamical and statistical behavior of discrete combustion waves: A theoretical and numerical study
NASA Astrophysics Data System (ADS)
Bharath, Naine Tarun; Rashkovskiy, Sergey A.; Tewari, Surya P.; Gundawar, Manoj Kumar
2013-04-01
We present a detailed theoretical and numerical study of combustion waves in a discrete one-dimensional disordered system. The distances between neighboring reaction cells were modeled with a gamma distribution. The results show that the random structure of the microheterogeneous system plays a crucial role in the dynamical and statistical behavior of the system. This is a consequence of the nonlinear interaction of the random structure of the system with the thermal wave. An analysis of the experimental data on the combustion of a gasless system (Ti + xSi) and a wide range of thermite systems was performed in view of the developed model. We have shown that the burning rate of the powder system sensitively depends on its internal structure. The present model allows for reproducing theoretically the experimental data for a wide range of pyrotechnic mixtures. We show that Arrhenius’ macrokinetics at combustion of disperse systems can take place even in the absence of Arrhenius’ microkinetics; it can have a purely thermal nature and be related to their heterogeneity and to the existence of threshold temperature. It is also observed that the combustion of disperse systems always occurs in the microheterogeneous mode according to the relay-race mechanism.
Food web dynamics in a seasonally varying wetland
DeAngelis, D.L.; Trexler, J.C.; Donalson, D.D.
2008-01-01
A spatially explicit model is developed to simulate the small fish community and its underlying food web, in the freshwater marshes of the Everglades. The community is simplified to a few small fish species feeding on periphyton and invertebrates. Other compartments are detritus, crayfish, and a piscivorous fish species. This unit food web model is applied to each of the 10,000 spatial cells on a 100 x 100 pixel landscape. Seasonal variation in water level is assumed and rules are assigned for fish movement in response to rising and falling water levels, which can cause many spatial cells to alternate between flooded and dry conditions. It is shown that temporal variations of water level on a spatially heterogeneous landscape can maintain at least three competing fish species. In addition, these environmental factors can strongly affect the temporal variation of the food web caused by top-down control from the piscivorous fish.
Bengoetxea, Ana; Leurs, Françoise; Hoellinger, Thomas; Cebolla, Ana M; Dan, Bernard; McIntyre, Joseph; Cheron, Guy
2014-01-01
In this study we employed a dynamic recurrent neural network (DRNN) in a novel fashion to reveal characteristics of control modules underlying the generation of muscle activations when drawing figures with the outstretched arm. We asked healthy human subjects to perform four different figure-eight movements in each of two workspaces (frontal plane and sagittal plane). We then trained a DRNN to predict the movement of the wrist from information in the EMG signals from seven different muscles. We trained different instances of the same network on a single movement direction, on all four movement directions in a single movement plane, or on all eight possible movement patterns and looked at the ability of the DRNN to generalize and predict movements for trials that were not included in the training set. Within a single movement plane, a DRNN trained on one movement direction was not able to predict movements of the hand for trials in the other three directions, but a DRNN trained simultaneously on all four movement directions could generalize across movement directions within the same plane. Similarly, the DRNN was able to reproduce the kinematics of the hand for both movement planes, but only if it was trained on examples performed in each one. As we will discuss, these results indicate that there are important dynamical constraints on the mapping of EMG to hand movement that depend on both the time sequence of the movement and on the anatomical constraints of the musculoskeletal system. In a second step, we injected EMG signals constructed from different synergies derived by the PCA in order to identify the mechanical significance of each of these components. From these results, one can surmise that discrete-rhythmic movements may be constructed from three different fundamental modules, one regulating the co-activation of all muscles over the time span of the movement and two others elliciting patterns of reciprocal activation operating in orthogonal directions.
A discrete stage-structured model of California newt population dynamics during a period of drought
Jones, Marjorie T.; Milligan, William R.; Kats, Lee B.; Vandergon, Thomas L.; Honeycutt, Rodney L.; Fisher, Robert N.; Davis, Courtney L.; Lucas, Timothy A.
2017-01-01
We introduce a mathematical model for studying the population dynamics under drought of the California newt (Taricha torosa), a species of special concern in the state of California. Since 2012, California has experienced a record-setting drought, and multiple studies predict drought conditions currently underway will persist and even increase in severity. Recent declines and local extinctions of California newt populations in Santa Monica Mountain streams motivate our study of the impact of drought on newt population sizes. Although newts are terrestrial salamanders, they migrate to streams each spring to breed and lay eggs. Since egg and larval stages occur in water, a precipitation deficit due to drought conditions reduces the space for newt egg-laying and the necessary habitat for larval development. To mathematically forecast newt population dynamics, we develop a nonlinear system of discrete equations that includes demographic parameters such as survival rates for newt life stages and egg production, which depend on habitat availability and rainfall. We estimate these demographic parameters using 15 years of stream survey data collected from Cold Creek in Los Angeles County, California, and our model captures the observed decline of the parameterized Cold Creek newt population. Based upon data analysis, we predict how the number of available newt egg-laying sites varies with annual precipitation. Our model allows us to make predictions about how the length and severity of drought can affect the likelihood of persistence and the time to critical endangerment of a local newt population. We predict that sustained severe drought will critically endanger the newt population but that the newt population can rebound if a drought is sufficiently short.
Bengoetxea, Ana; Leurs, Françoise; Hoellinger, Thomas; Cebolla, Ana M.; Dan, Bernard; McIntyre, Joseph; Cheron, Guy
2014-01-01
In this study we employed a dynamic recurrent neural network (DRNN) in a novel fashion to reveal characteristics of control modules underlying the generation of muscle activations when drawing figures with the outstretched arm. We asked healthy human subjects to perform four different figure-eight movements in each of two workspaces (frontal plane and sagittal plane). We then trained a DRNN to predict the movement of the wrist from information in the EMG signals from seven different muscles. We trained different instances of the same network on a single movement direction, on all four movement directions in a single movement plane, or on all eight possible movement patterns and looked at the ability of the DRNN to generalize and predict movements for trials that were not included in the training set. Within a single movement plane, a DRNN trained on one movement direction was not able to predict movements of the hand for trials in the other three directions, but a DRNN trained simultaneously on all four movement directions could generalize across movement directions within the same plane. Similarly, the DRNN was able to reproduce the kinematics of the hand for both movement planes, but only if it was trained on examples performed in each one. As we will discuss, these results indicate that there are important dynamical constraints on the mapping of EMG to hand movement that depend on both the time sequence of the movement and on the anatomical constraints of the musculoskeletal system. In a second step, we injected EMG signals constructed from different synergies derived by the PCA in order to identify the mechanical significance of each of these components. From these results, one can surmise that discrete-rhythmic movements may be constructed from three different fundamental modules, one regulating the co-activation of all muscles over the time span of the movement and two others elliciting patterns of reciprocal activation operating in orthogonal directions
A discrete stage-structured model of California newt population dynamics during a period of drought.
Jones, Marjorie T; Milligan, William R; Kats, Lee B; Vandergon, Thomas L; Honeycutt, Rodney L; Fisher, Robert N; Davis, Courtney L; Lucas, Timothy A
2017-02-07
We introduce a mathematical model for studying the population dynamics under drought of the California newt (Taricha torosa), a species of special concern in the state of California. Since 2012, California has experienced a record-setting drought, and multiple studies predict drought conditions currently underway will persist and even increase in severity. Recent declines and local extinctions of California newt populations in Santa Monica Mountain streams motivate our study of the impact of drought on newt population sizes. Although newts are terrestrial salamanders, they migrate to streams each spring to breed and lay eggs. Since egg and larval stages occur in water, a precipitation deficit due to drought conditions reduces the space for newt egg-laying and the necessary habitat for larval development. To mathematically forecast newt population dynamics, we develop a nonlinear system of discrete equations that includes demographic parameters such as survival rates for newt life stages and egg production, which depend on habitat availability and rainfall. We estimate these demographic parameters using 15 years of stream survey data collected from Cold Creek in Los Angeles County, California, and our model captures the observed decline of the parameterized Cold Creek newt population. Based upon data analysis, we predict how the number of available newt egg-laying sites varies with annual precipitation. Our model allows us to make predictions about how the length and severity of drought can affect the likelihood of persistence and the time to critical endangerment of a local newt population. We predict that sustained severe drought will critically endanger the newt population but that the newt population can rebound if a drought is sufficiently short.
Using a Simulation To Teach Food Web Dynamics.
ERIC Educational Resources Information Center
Rueter, John G.; Perrin, Nancy A.
1999-01-01
Reports on research that tested the effect of using a computer simulation to teach the concept of a food web to nonbiology majors in a large introductory course. Concludes that the use of the simulation resulted in significantly better performance on an open-ended essay question for those students who used the software, particularly for average…
Using a Simulation To Teach Food Web Dynamics.
ERIC Educational Resources Information Center
Rueter, John G.; Perrin, Nancy A.
1999-01-01
Reports on research that tested the effect of using a computer simulation to teach the concept of a food web to nonbiology majors in a large introductory course. Concludes that the use of the simulation resulted in significantly better performance on an open-ended essay question for those students who used the software, particularly for average…
The Spider's Web: Creativity and Survival in Dynamic Balance.
ERIC Educational Resources Information Center
Cohen, Bill
2001-01-01
The spider's web is presented as a model for Indigenous education and community transformation, grounded in Okanagan philosophy. Children are at the center and benefit from the influence of extended family and community. The model's relevance for language revitalization, cultural maintenance, and educational planning and assessment is discussed.…
The Spider's Web: Creativity and Survival in Dynamic Balance.
ERIC Educational Resources Information Center
Cohen, Bill
2001-01-01
The spider's web is presented as a model for Indigenous education and community transformation, grounded in Okanagan philosophy. Children are at the center and benefit from the influence of extended family and community. The model's relevance for language revitalization, cultural maintenance, and educational planning and assessment is discussed.…
NASA Astrophysics Data System (ADS)
Schmidt, Burkhard; Lorenz, Ulf
2017-04-01
WavePacket is an open-source program package for the numerical simulation of quantum-mechanical dynamics. It can be used to solve time-independent or time-dependent linear Schrödinger and Liouville-von Neumann-equations in one or more dimensions. Also coupled equations can be treated, which allows to simulate molecular quantum dynamics beyond the Born-Oppenheimer approximation. Optionally accounting for the interaction with external electric fields within the semiclassical dipole approximation, WavePacket can be used to simulate experiments involving tailored light pulses in photo-induced physics or chemistry. The graphical capabilities allow visualization of quantum dynamics 'on the fly', including Wigner phase space representations. Being easy to use and highly versatile, WavePacket is well suited for the teaching of quantum mechanics as well as for research projects in atomic, molecular and optical physics or in physical or theoretical chemistry. The present Part I deals with the description of closed quantum systems in terms of Schrödinger equations. The emphasis is on discrete variable representations for spatial discretization as well as various techniques for temporal discretization. The upcoming Part II will focus on open quantum systems and dimension reduction; it also describes the codes for optimal control of quantum dynamics. The present work introduces the MATLAB version of WavePacket 5.2.1 which is hosted at the Sourceforge platform, where extensive Wiki-documentation as well as worked-out demonstration examples can be found.
Model Driven Development of Web Services and Dynamic Web Services Composition
2005-01-01
Web Services (WS) has emerged as a new component-based software develop- ment paradigm in a network -centric environment based on the Service Oriented...tion of legacy distributed software system toward WS applications ; 2) the innovation of new infrastructure, and languages in support of WS application ...approach is presented toward reengineering legacy software systems to WS applications , rather than rewriting the whole legacy software system from
There must be a better way! Managing a corporate web site dynamically from a database
j.z. cohen
1998-10-21
This document is a set of slides available from http://www1.y12.org/lmes_sti/html/ycsdinf-98-8/index.htm that describes limitations of static web pages for conveying information, a plan for overcoming these limitations by generating web pages dynamically from a database, expected advantages and disadvantages of this method, design for a system using the method, and future plans.
Martinez-Pedrero, Fernando; Tierno, Pietro; Johansen, Tom H.; Straube, Arthur V.
2016-01-01
The emergence of wave fronts in dissipative driven systems is a fascinating phenomenon which can be found in a broad range of physical and biological disciplines. Here we report the direct experimental observation of discrete fronts propagating along chains of paramagnetic colloidal particles, the latter propelled above a traveling wave potential generated by a structured magnetic substrate. We develop a rigorously reduced theoretical framework and describe the dynamics of the system in terms of a generalized one-dimensional dissipative Frenkel-Kontorova model. The front dynamics is explored in a wide range of field parameters close to and far from depinning, where the discrete and continuum limits apply. We show how symmetry breaking and finite size of chains are used to control the direction of front propagation, a universal feature relevant to different systems and important for real applications. PMID:26837286
JBrowse: a dynamic web platform for genome visualization and analysis.
Buels, Robert; Yao, Eric; Diesh, Colin M; Hayes, Richard D; Munoz-Torres, Monica; Helt, Gregg; Goodstein, David M; Elsik, Christine G; Lewis, Suzanna E; Stein, Lincoln; Holmes, Ian H
2016-04-12
JBrowse is a fast and full-featured genome browser built with JavaScript and HTML5. It is easily embedded into websites or apps but can also be served as a standalone web page. Overall improvements to speed and scalability are accompanied by specific enhancements that support complex interactive queries on large track sets. Analysis functions can readily be added using the plugin framework; most visual aspects of tracks can also be customized, along with clicks, mouseovers, menus, and popup boxes. JBrowse can also be used to browse local annotation files offline and to generate high-resolution figures for publication. JBrowse is a mature web application suitable for genome visualization and analysis.
NASA Astrophysics Data System (ADS)
Zhu, Ling; van de Ven, Glenn; Watkins, Laura L.; Posti, Lorenzo
2016-11-01
We present a new discrete chemo-dynamical axisymmetric modelling technique, which we apply to the dwarf spheroidal galaxy Sculptor. The major improvement over previous Jeans models is that realistic chemical distributions are included directly in the dynamical modelling of the discrete data. This avoids loss of information due to spatial binning and eliminates the need for hard cuts to remove contaminants and to separate stars based on their chemical properties. Using a combined likelihood in position, metallicity and kinematics, we find that our models naturally separate Sculptor stars into a metal-rich and a metal-poor population. Allowing for non-spherical symmetry, our approach provides a central slope of the dark matter density of γ = 0.5 ± 0.3. The metal-rich population is nearly isotropic (with β _r^{red} = 0.0± 0.1), while the metal-poor population is tangentially anisotropic (with β _r^{blue} = -0.2± 0.1) around the half-light radius of 0.26 kpc. A weak internal rotation of the metal-rich population is revealed with vmax/σ0 = 0.15 ± 0.15. We run tests using mock data to show that a discrete data set with ˜6000 stars is required to distinguish between a core (γ = 0) and cusp (γ = 1), and to constrain the possible internal rotation to better than 1σ confidence with our model. We conclude that our discrete chemo-dynamical modelling technique provides a flexible and powerful tool to robustly constrain the internal dynamics of multiple populations, and the total mass distribution in a stellar system.
Naji, Ali; Atzberger, Paul J; Brown, Frank L H
2009-04-03
We introduce a simulation strategy to consistently couple continuum biomembrane dynamics to the motion of discrete biological macromolecules residing within or on the membrane. The methodology is used to study the diffusion of integral membrane proteins that impart a curvature on the bilayer surrounding them. Such proteins exhibit a substantial reduction in diffusion coefficient relative to "flat" proteins; this effect is explained by elementary hydrodynamic considerations.
Discrete Molecular Dynamics Study of Oligomer Formation by N-Terminally Truncated Amyloid β-Protein
Meral, Derya; Urbanc, Brigita
2013-01-01
In Alzheimer’s disease (AD), amyloid β-protein (Aβ) self–assembles into toxic oligomers. Of the two predominant Aβ alloforms, Aβ1–40 and Aβ1–42, the latter is particularly strongly linked to AD. N-terminally truncated and pyroglutamated Aβ peptides were recently shown to seed Aβ aggregation and contribute significantly to Aβ–mediated toxicity, yet their folding and assembly were not explored computationally. Discrete molecular dynamics (DMD) approach previously captured in vitro–derived distinct Aβ1–40 and Aβ1–42 oligomer size distributions and predicted that the more toxic Aβ1–42 oligomers had more flexible and solvent exposed N-termini than Aβ1–40 oligomers. Here, we examined oligomer formation of Aβ3–40, Aβ3–42, Aβ11–40, and Aβ11–42 by the DMD approach. The four N-terminally truncated peptides showed increased oligomerization propensity relative to the full–length peptides, consistent with in vitro findings. Conformations formed by Aβ3–40/42 had significantly more flexible and solvent–exposed N-termini than Aβ1–40/42 conformations. In contrast, in Aβ11–40/42 conformations the N-termini formed more contacts and were less accessible to the solvent. The compactness of the Aβ11–40/42 conformations was in part facilitated by Val12. Two single amino acid substitutions that reduced and abolished hydrophobicity at position 12, respectively, resulted in a proportionally increased structural variability. Our results suggest that Aβ11–40 and Aβ11–42 oligomers might be less toxic than Aβ1–40 and Aβ1–42 oligomers and offer a plausible explanation for the experimentally–observed increased toxicity of Aβ3–40 and Aβ3–42 and their pyroglutamated forms. PMID:23500806
An Agent-Based Discrete Collagen Fiber Network Model of Dynamic Traction Force-Induced Remodeling.
Reinhardt, James W; Gooch, Keith
2017-09-21
We developed an agent-based model that incorporates repetitively applied traction force within a discrete fiber network to understand how microstructural properties of the network influence mechanical properties and traction force-induced remodeling. An important difference between our model and similar finite-element models is that by implementing more biologically-realistic dynamic traction, we can explore a greater range of matrix remodeling. Here, we validated our model by reproducing qualitative trends observed in three sets of experimental data reported by others: tensile and shear testing of cell-free collagen gels, collagen remodeling around a single isolated cell, and collagen remodeling between pairs of cells. In response to tensile and shear strain, simulated acellular networks exhibited biphasic stress-strain curves indicative of strain-stiffening. Our data support the notion that strain-stiffening might occur as individual fibrils successively align along the axis of strain and become engaged in tension. In simulations with a single, contractile cell, peak collagen displacement occurred closest to the cell and decreased with increasing distance. In simulations with two cells, compaction of collagen between cells appeared inversely related to the initial distance between cells. Further analysis revealed strain energy was relatively uniform around the outer surface of cells separated by 250 microns, but became increasingly non-uniform as the distance between cells decreased. This pattern was partly attributable to the pattern of collagen compaction. These findings are of interest because fibril alignment, density, and strain energy may each contribute to contact guidance during tissue morphogenesis.
Degree correlations in a dynamically generated model food web
NASA Astrophysics Data System (ADS)
Rikvold, Per Arne
2010-02-01
We explore aspects of the community structures generated by a simple predator-prey model of biological coevolution, using large-scale kinetic Monte Carlo simulations. The model accounts for interspecies and intraspecies competition for resources, as well as adaptive foraging behavior. It produces a metastable low-diversity phase and a stable high-diversity phase. The structures and joint indegree-outdegree distributions of the food webs generated in the latter phase are discussed.
ERIC Educational Resources Information Center
Dehinbo, Johnson
2011-01-01
The widespread use of the Internet and the World Wide Web led to the availability of many platforms for developing dynamic Web application and the problem of choosing the most appropriate platform that will be easy to use for undergraduate students of web applications development in tertiary institutions. Students beginning to learn web…
A discrete momentum-conserving explicit algorithm for rigid body dynamics analysis
NASA Technical Reports Server (NTRS)
Park, K. C.; Chiou, J. C.
1993-01-01
A discrete momentum-conserving explicit time integration is presented. The accurate feature and simplicity of the present algorithm are realized by a mid-point implicit formula for integrating the Euler parameters and a second-order discrete momentum-conserving form of the central difference algorithm, respectively. The accuracy and robustness of the algorithm is demonstrated by example problems which exhibit large overall rigid motions under holonomic constraints.
A discrete momentum-conserving explicit algorithm for multibody dynamics analysis
NASA Technical Reports Server (NTRS)
Park, K. C.; Chiou, J. C.
1992-01-01
A discrete momentum-conserving, explicit time integration is presented. The accurate feature and simplicity of the present algorithm are realized by a mid-point implicit formula for integrating the Euler parameters and a second-order discrete momentum-conserving form of the central difference algorithm, respectively. The accuracy and robustness of the algorithm is demonstrated by example problems which exhibit large overall rigid motions under holonomic constraints.
Sivak, David A; Chodera, John D; Crooks, Gavin E
2014-06-19
When simulating molecular systems using deterministic equations of motion (e.g., Newtonian dynamics), such equations are generally numerically integrated according to a well-developed set of algorithms that share commonly agreed-upon desirable properties. However, for stochastic equations of motion (e.g., Langevin dynamics), there is still broad disagreement over which integration algorithms are most appropriate. While multiple desiderata have been proposed throughout the literature, consensus on which criteria are important is absent, and no published integration scheme satisfies all desiderata simultaneously. Additional nontrivial complications stem from simulating systems driven out of equilibrium using existing stochastic integration schemes in conjunction with recently developed nonequilibrium fluctuation theorems. Here, we examine a family of discrete time integration schemes for Langevin dynamics, assessing how each member satisfies a variety of desiderata that have been enumerated in prior efforts to construct suitable Langevin integrators. We show that the incorporation of a novel time step rescaling in the deterministic updates of position and velocity can correct a number of dynamical defects in these integrators. Finally, we identify a particular splitting (related to the velocity Verlet discretization) that has essentially universally appropriate properties for the simulation of Langevin dynamics for molecular systems in equilibrium, nonequilibrium, and path sampling contexts.
2015-01-01
When simulating molecular systems using deterministic equations of motion (e.g., Newtonian dynamics), such equations are generally numerically integrated according to a well-developed set of algorithms that share commonly agreed-upon desirable properties. However, for stochastic equations of motion (e.g., Langevin dynamics), there is still broad disagreement over which integration algorithms are most appropriate. While multiple desiderata have been proposed throughout the literature, consensus on which criteria are important is absent, and no published integration scheme satisfies all desiderata simultaneously. Additional nontrivial complications stem from simulating systems driven out of equilibrium using existing stochastic integration schemes in conjunction with recently developed nonequilibrium fluctuation theorems. Here, we examine a family of discrete time integration schemes for Langevin dynamics, assessing how each member satisfies a variety of desiderata that have been enumerated in prior efforts to construct suitable Langevin integrators. We show that the incorporation of a novel time step rescaling in the deterministic updates of position and velocity can correct a number of dynamical defects in these integrators. Finally, we identify a particular splitting (related to the velocity Verlet discretization) that has essentially universally appropriate properties for the simulation of Langevin dynamics for molecular systems in equilibrium, nonequilibrium, and path sampling contexts. PMID:24555448
Dynamics of the Lake Michigan food web, 1970-2000
Madenjian, Charles P.; Fahnenstiel, Gary L.; Johengen, Thomas H.; Nalepa, Thomas F.; Vanderploeg, Henry A.; Fleischer, Guy W.; Schneeberger, Philip J.; Benjamin, Darren M.; Smith, Emily B.; Bence, James R.; Rutherford, Edward S.; Lavis, Dennis S.; Robertson, Dale M.; Jude, David J.; Ebener, Mark P.
2002-01-01
Herein, we document changes in the Lake Michigan food web between 1970 and 2000 and identify the factors responsible for these changes. Control of sea lamprey (Petromyzon marinus) and alewife (Alosa pseudoharengus) populations in Lake Michigan, beginning in the 1950s and 1960s, had profound effects on the food web. Recoveries of lake whitefish (Coregonus clupeaformis) and burbot (Lota lota) populations, as well as the buildup of salmonine populations, were attributable, at least in part, to sea lamprey control. Based on our analyses, predation by salmonines was primarily responsible for the reduction in alewife abundance during the 1970s and early 1980s. In turn, the decrease in alewife abundance likely contributed to recoveries of deepwater sculpin (Myoxocephalus thompsoni), yellow perch (Perca flavescens), and burbot populations during the 1970s and 1980s. Decrease in the abundance of all three dominant benthic macroinvertebrate groups, including Diporeia, oligochaetes, and sphaeriids, during the 1980s in nearshore waters (50 m deep) of Lake Michigan, was attributable to a decrease in primary production linked to a decline in phosphorus loadings. Continued decrease in Diporeia abundance during the 1990s was associated with the zebra mussel (Dreissena polymorpha) invasion, but specific mechanisms for zebra mussels affecting Diporeia abundance remain unidentified.
Howard, Ian S; Ingram, James N; Wolpert, Daniel M
2011-04-01
Rhythmic and discrete arm movements occur ubiquitously in everyday life, and there is a debate as to whether these two classes of movements arise from the same or different underlying neural mechanisms. Here we examine interference in a motor-learning paradigm to test whether rhythmic and discrete movements employ at least partially separate neural representations. Subjects were required to make circular movements of their right hand while they were exposed to a velocity-dependent force field that perturbed the circularity of the movement path. The direction of the force-field perturbation reversed at the end of each block of 20 revolutions. When subjects made only rhythmic or only discrete circular movements, interference was observed when switching between the two opposing force fields. However, when subjects alternated between blocks of rhythmic and discrete movements, such that each was uniquely associated with one of the perturbation directions, interference was significantly reduced. Only in this case did subjects learn to corepresent the two opposing perturbations, suggesting that different neural resources were employed for the two movement types. Our results provide further evidence that rhythmic and discrete movements employ at least partially separate control mechanisms in the motor system.
Limitations of discrete-time approaches to continuous-time contagion dynamics
NASA Astrophysics Data System (ADS)
Fennell, Peter G.; Melnik, Sergey; Gleeson, James P.
2016-11-01
Continuous-time Markov process models of contagions are widely studied, not least because of their utility in predicting the evolution of real-world contagions and in formulating control measures. It is often the case, however, that discrete-time approaches are employed to analyze such models or to simulate them numerically. In such cases, time is discretized into uniform steps and transition rates between states are replaced by transition probabilities. In this paper, we illustrate potential limitations to this approach. We show how discretizing time leads to a restriction on the values of the model parameters that can accurately be studied. We examine numerical simulation schemes employed in the literature, showing how synchronous-type updating schemes can bias discrete-time formalisms when compared against continuous-time formalisms. Event-based simulations, such as the Gillespie algorithm, are proposed as optimal simulation schemes both in terms of replicating the continuous-time process and computational speed. Finally, we show how discretizing time can affect the value of the epidemic threshold for large values of the infection rate and the recovery rate, even if the ratio between the former and the latter is small.
Ingram, James N.; Wolpert, Daniel M.
2011-01-01
Rhythmic and discrete arm movements occur ubiquitously in everyday life, and there is a debate as to whether these two classes of movements arise from the same or different underlying neural mechanisms. Here we examine interference in a motor-learning paradigm to test whether rhythmic and discrete movements employ at least partially separate neural representations. Subjects were required to make circular movements of their right hand while they were exposed to a velocity-dependent force field that perturbed the circularity of the movement path. The direction of the force-field perturbation reversed at the end of each block of 20 revolutions. When subjects made only rhythmic or only discrete circular movements, interference was observed when switching between the two opposing force fields. However, when subjects alternated between blocks of rhythmic and discrete movements, such that each was uniquely associated with one of the perturbation directions, interference was significantly reduced. Only in this case did subjects learn to corepresent the two opposing perturbations, suggesting that different neural resources were employed for the two movement types. Our results provide further evidence that rhythmic and discrete movements employ at least partially separate control mechanisms in the motor system. PMID:21273324
Folding of pig gastric mucin non-glycosylated domains: a discrete molecular dynamics study.
Barz, Bogdan; Turner, Bradley S; Bansil, Rama; Urbanc, Brigita
2012-09-01
Mucin glycoproteins consist of tandem-repeating glycosylated regions flanked by non-repetitive protein domains with little glycosylation. These non-repetitive domains are involved in polymerization of mucin and play an important role in the pH-dependent gelation of gastric mucin, which is essential for protecting the stomach from autodigestion. We examine folding of the non-repetitive sequence of PGM-2X (242 amino acids) and the von Willebrand factor vWF-C1 domain (67 amino acids) at neutral and low pH using discrete molecular dynamics (DMD) in an implicit solvent combined with a four-bead peptide model. Using the same implicit solvent parameters, folding of both domains is simulated at neutral and low pH. In contrast to vWF-C1, PGM-2X folding is strongly affected by pH as indicated by changes in the contact order, radius of gyration, free-energy landscape, and the secondary structure. Whereas the free-energy landscape of vWF-C1 shows a single minimum at both neutral and low pH, the free-energy landscape of PGM-2X is characterized by multiple minima that are more numerous and shallower at low pH. Detailed structural analysis shows that PGM-2X partially unfolds at low pH. This partial unfolding is facilitated by the C-terminal region GLU236-PRO242, which loses contact with the rest of the domain due to effective "mean-field" repulsion among highly positively charged N- and C-terminal regions. Consequently, at low pH, hydrophobic amino acids are more exposed to the solvent. In vWF-C1, low pH induces some structural changes, including an increased exposure of CYS at position 67, but these changes are small compared to those found in PGM-2X. For PGM-2X, the DMD-derived average β-strand propensity increases from 0.26 ± 0.01 at neutral pH to 0.38 ± 0.01 at low pH. For vWF-C1, the DMD-derived average β-strand propensity is 0.32 ± 0.02 at neutral pH and 0.35 ± 0.02 at low pH. The DMD-derived structural information provides insight into pH-induced changes in the
NASA Technical Reports Server (NTRS)
Housner, J. M.; Mcgowan, P. E.
1986-01-01
A computerized procedure is presented for calculating instantaneous velocity changes due to discrete imposition of constraints, impact or discrete inertial changes. Such discrete changes are impulsive in nature, involve wave propagation and therefore usually require detailed modeling for accurate prediction. It is demonstrated that when modeling is coarse, physically unrealistic results can be produced. The present procedure, which concentrates on finite element analysis, reduces the need for detailed modeling by assuming that only those velocities in the neighborhood of grid points involved in the constraint or those rigidly connected to grid points involved in the constraint need be considered in calculating velocity changes. The procedure utilizes Newton's second law and as such conserves momentum where valid. Sample problems are provided.
NASA Technical Reports Server (NTRS)
Housner, J. M.; Mcgowan, P. E.
1986-01-01
A computerized procedure is presented for calculating instantaneous velocity changes due to discrete imposition of constraints, impact or discrete inertial changes. Such discrete changes are impulsive in nature, involve wave propagation and therefore usually require detailed modeling for accurate prediction. It is demonstrated that when modeling is coarse, physically unrealistic results can be produced. The present procedure, which concentrates on finite element analysis, reduces the need for detailed modeling by assuming that only those velocities in the neighborhood of grid points involved in the constraint or those rigidly connected to grid points involved in the constraint need be considered in calculating velocity changes. The procedure utilizes Newton's second law and as such conserves momentum where valid. Sample problems are provided.
Systematic generation of nonlinear discretized dynamic equilibrium equations of spinning cantilevers
NASA Technical Reports Server (NTRS)
El-Essawi, M.; Utku, S.; Salama, M.
1982-01-01
General nonlinear discretized governing equations of motion of spinning elastic solids and structures are adjusted for the case of a spinning cantilever with initial geometric imperfections. Consideration is given to second degree nonlinearities in the strain-displacement and velocity-displacement relationships. Parameters of the discretization are developed to include the type and number of the coordinate functions used in the admissible trial solution in order to unify the discretization approaches associated with stationarity principles. The coordinate functions comprise both sets of continuous and piecewise continuous functions employed in the Rayleigh-Ritz and the finite element methods, respectively. Coefficient matrices are provided which contain the energy density expressions and which are adaptable to computer programming.
From a discrete to a continuum model of cell dynamics in one dimension
NASA Astrophysics Data System (ADS)
Murray, Philip J.; Edwards, Carina M.; Tindall, Marcus J.; Maini, Philip K.
2009-09-01
Multiscale modeling is emerging as one of the key challenges in mathematical biology. However, the recent rapid increase in the number of modeling methodologies being used to describe cell populations has raised a number of interesting questions. For example, at the cellular scale, how can the appropriate discrete cell-level model be identified in a given context? Additionally, how can the many phenomenological assumptions used in the derivation of models at the continuum scale be related to individual cell behavior? In order to begin to address such questions, we consider a discrete one-dimensional cell-based model in which cells are assumed to interact via linear springs. From the discrete equations of motion, the continuous Rouse [P. E. Rouse, J. Chem. Phys. 21, 1272 (1953)] model is obtained. This formalism readily allows the definition of a cell number density for which a nonlinear “fast” diffusion equation is derived. Excellent agreement is demonstrated between the continuum and discrete models. Subsequently, via the incorporation of cell division, we demonstrate that the derived nonlinear diffusion model is robust to the inclusion of more realistic biological detail. In the limit of stiff springs, where cells can be considered to be incompressible, we show that cell velocity can be directly related to cell production. This assumption is frequently made in the literature but our derivation places limits on its validity. Finally, the model is compared with a model of a similar form recently derived for a different discrete cell-based model and it is shown how the different diffusion coefficients can be understood in terms of the underlying assumptions about cell behavior in the respective discrete models.
Rapid contemporary evolution and clonal food web dynamics.
Jones, Laura E; Becks, Lutz; Ellner, Stephen P; Hairston, Nelson G; Yoshida, Takehito; Fussmann, Gregor F
2009-06-12
Character evolution that affects ecological community interactions often occurs contemporaneously with temporal changes in population size, potentially altering the very nature of those dynamics. Such eco-evolutionary processes may be most readily explored in systems with short generations and simple genetics. Asexual and cyclically parthenogenetic organisms such as microalgae, cladocerans and rotifers, which frequently dominate freshwater plankton communities, meet these requirements. Multiple clonal lines can coexist within each species over extended periods, until either fixation occurs or a sexual phase reshuffles the genetic material. When clones differ in traits affecting interspecific interactions, within-species clonal dynamics can have major effects on the population dynamics. We first consider a simple predator-prey system with two prey genotypes, parametrized with data from a well-studied experimental system, and explore how the extent of differences in defence against predation within the prey population determine dynamic stability versus instability of the system. We then explore how increased potential for evolution affects the community dynamics in a more general community model with multiple predator and multiple prey genotypes. These examples illustrate how microevolutionary 'details' that enhance or limit the potential for heritable phenotypic change can have significant effects on contemporaneous community-level dynamics and the persistence and coexistence of species.
Liu, Yanchen; Shi, Hanchang; Shi, Huiming; Wang, Zhiqiang
2010-10-01
The aim of study was proposed a new control model feasible on-line implemented by Programmable Logic Controller (PLC) to enhance nitrogen removal against the fluctuation of influent in Carrousel oxidation ditch. The discrete-time control model was established by confirmation model of operational conditions based on a expert access, which was obtained by a simulation using Activated Sludge Model 2-D (ASM2-D) and Computation Fluid Dynamics (CFD), and discrete-time control model to switch between different operational stages. A full-scale example is provided to demonstrate the feasibility of the proposed operation and the procedure of the control design. The effluent quality was substantially improved, to the extent that it met the new wastewater discharge standards of NH(3)-N<5mg/L and TN<15 mg/L enacted in China throughout a one-day period with fluctuation of influent.
ERIC Educational Resources Information Center
Ünal, Erhan; Çakir, Hasan
2017-01-01
The purpose of this study was to design a problem based collaborative learning environment supported by dynamic web technologies and to examine students' views about this learning environment. The study was designed as a qualitative research. Some 36 students who took an Object Oriented Programming I-II course at the department of computer…
Prototype of a Mobile Social Network for Education Using Dynamic Web Service
ERIC Educational Resources Information Center
Hoentsch, Sandra Costa Pinto; Carvalho, Felipe Oliveira; Santos, Luiz Marcus Monteiro de Almeida; Ribeiro, Admilson de Ribamar Lima
2012-01-01
This article presents the proposal of a social network site SocialNetLab that belongs to the Department of Computing-Federal University of Sergipe and which aims to locate and notify users of a nearby friend independently of the location technology available in the equipment through dynamic Web Service; to serve as a laboratory for research in…
Sociometry: An Approach for Assessing Group Dynamics in Web-Based Courses
ERIC Educational Resources Information Center
Daugherty, Martha; Turner, Jeff
2003-01-01
Student interactivity in web-based educational environments has shown to increase academic learning and motivation (Jiang, 1998; Petraglia, 1998). However, instructors often find it difficult to assess the quality of online group dynamics without visual observations of student behaviors. The purpose of this study was to investigate the use of…
"Dynamic Syllabi for Dummies": Posting Class Assignments on the World Wide Web.
ERIC Educational Resources Information Center
Kornblith, Gary J.
1998-01-01
Argues that instructors need to recognize and adapt to students who are increasingly computer savvy. Relates the process of developing dynamic World Wide Web syllabi for undergraduate history courses. Provides an outline of suggestions and warnings for creating interesting and educational syllabi. Suggests that the best syllabi incorporate Web…
NASA Astrophysics Data System (ADS)
Hancock, W.; Weatherley, D.; Wruck, B.; Chitombo, G. P.
2012-04-01
The flow dynamics of granular materials is of broad interest in both the geosciences (e.g. landslides, fault zone evolution, and brecchia pipe formation) and many engineering disciplines (e.g chemical engineering, food sciences, pharmaceuticals and materials science). At the interface between natural and human-induced granular media flow, current underground mass-mining methods are trending towards the induced failure and subsequent gravitational flow of large volumes of broken rock, a method known as cave mining. Cave mining relies upon the undercutting of a large ore body, inducement of fragmentation of the rock and subsequent extraction of ore from below, via hopper-like outlets. Design of such mines currently relies upon a simplified kinematic theory of granular flow in hoppers, known as the ellipsoid theory of mass movement. This theory assumes that the zone of moving material grows as an ellipsoid above the outlet of the silo. The boundary of the movement zone is a shear band and internal to the movement zone, the granular material is assumed to have a uniformly high bulk porosity compared with surrounding stagnant regions. There is however, increasing anecdotal evidence and field measurements suggesting this theory fails to capture the full complexity of granular material flow within cave mines. Given the practical challenges obstructing direct measurement of movement both in laboratory experiments and in-situ, the Discrete Element Method (DEM [1]) is a popular alternative to investigate granular media flow. Small-scale DEM studies (c.f. [3] and references therein) have confirmed that movement within DEM silo flow models matches that predicted by ellipsoid theory, at least for mono-disperse granular material freely outflowing at a constant rate. A major draw-back of these small-scale DEM studies is that the initial bulk porosity of the simulated granular material is significantly higher than that of broken, prismatic rock. In this investigation, more
ERIC Educational Resources Information Center
Flaherty, Brian P.
2008-01-01
Developmental research often involves studying change across 2 or more processes or constructs simultaneously. A natural question in this work is whether change in these 2 processes is related or independent. Associative latent transition analysis (ALTA) was designed to test hypotheses about the degree to which change in 2 discrete latent…
NASA Astrophysics Data System (ADS)
Feldstein, Y. I.; Vorobjev, V. G.; Zverev, V. L.; Förster, M.
2014-05-01
Research results about planetary-scale auroral distributions are presented in a historical retrospective, beginning with the first "maps of isochasms" - lines of equal visibility of auroras in the firmament (Fig. 2) - up to "isoaurora maps" - lines of equal occurrence frequency of auroras in the zenith (Fig. 4). The exploration of auroras in Russia from Lomonosov in the 18th century (Fig. 1) until the start of the International Geophysical Year (IGY) in 1957 is shortly summed up. A generalised pattern of discrete auroral forms along the auroral oval during geomagnetically very quiet intervals is presented in Fig. 5. The changes of discrete auroral forms versus local time exhibit a fixed pattern with respect to the sun. The auroral forms comprise rays near noon, homogeneous arcs during the evening, and rayed arcs and bands during the night and in the morning. This fixed auroral pattern is unsettled during disturbances, which occur sometimes even during very quiet intervals. The azimuths of extended auroral forms vary with local time. Such variations in the orientation of extended forms above stations in the auroral zone have been used by various investigators to determine the position of the auroral oval (Fig. 9). Auroral luminosity of the daytime and nighttime sectors differ owing to different luminosity forms, directions of motion of the discrete forms, the height of the luminescent layers, and the spectral composition (predominant red emissions during daytime and green emissions during the night). Schemes that summarise principal peculiarities of daytime luminosity, its structure in MLT (magnetic local time) and MLat (magnetic latitude) coordinates, and the spectral composition of the luminosity are presented in Figs. 15 and 19. We discuss in detail the daytime sector dynamics of individual discrete forms for both quiet conditions and auroral substorms. The most important auroral changes during substorms occur in the nighttime sector. We present the evolution of
Regime shifts in marine communities: a complex systems perspective on food web dynamics.
Yletyinen, Johanna; Bodin, Örjan; Weigel, Benjamin; Nordström, Marie C; Bonsdorff, Erik; Blenckner, Thorsten
2016-02-24
Species composition and habitats are changing at unprecedented rates in the world's oceans, potentially causing entire food webs to shift to structurally and functionally different regimes. Despite the severity of these regime shifts, elucidating the precise nature of their underlying processes has remained difficult. We address this challenge with a new analytic approach to detect and assess the relative strength of different driving processes in food webs. Our study draws on complexity theory, and integrates the network-centric exponential random graph modelling (ERGM) framework developed within the social sciences with community ecology. In contrast to previous research, this approach makes clear assumptions of direction of causality and accommodates a dynamic perspective on the emergence of food webs. We apply our approach to analysing food webs of the Baltic Sea before and after a previously reported regime shift. Our results show that the dominant food web processes have remained largely the same, although we detect changes in their magnitudes. The results indicate that the reported regime shift may not be a system-wide shift, but instead involve a limited number of species. Our study emphasizes the importance of community-wide analysis on marine regime shifts and introduces a novel approach to examine food webs.
Regime shifts in marine communities: a complex systems perspective on food web dynamics
Yletyinen, Johanna; Bodin, Örjan; Weigel, Benjamin; Nordström, Marie C.; Bonsdorff, Erik; Blenckner, Thorsten
2016-01-01
Species composition and habitats are changing at unprecedented rates in the world's oceans, potentially causing entire food webs to shift to structurally and functionally different regimes. Despite the severity of these regime shifts, elucidating the precise nature of their underlying processes has remained difficult. We address this challenge with a new analytic approach to detect and assess the relative strength of different driving processes in food webs. Our study draws on complexity theory, and integrates the network-centric exponential random graph modelling (ERGM) framework developed within the social sciences with community ecology. In contrast to previous research, this approach makes clear assumptions of direction of causality and accommodates a dynamic perspective on the emergence of food webs. We apply our approach to analysing food webs of the Baltic Sea before and after a previously reported regime shift. Our results show that the dominant food web processes have remained largely the same, although we detect changes in their magnitudes. The results indicate that the reported regime shift may not be a system-wide shift, but instead involve a limited number of species. Our study emphasizes the importance of community-wide analysis on marine regime shifts and introduces a novel approach to examine food webs. PMID:26888032
Post-launch analysis of the deployment dynamics of a space web sounding rocket experiment
NASA Astrophysics Data System (ADS)
Mao, Huina; Sinn, Thomas; Vasile, Massimiliano; Tibert, Gunnar
2016-10-01
Lightweight deployable space webs have been proposed as platforms or frames for a construction of structures in space where centrifugal forces enable deployment and stabilization. The Suaineadh project was aimed to deploy a 2 × 2m2 space web by centrifugal forces in milli-gravity conditions and act as a test bed for the space web technology. Data from former sounding rocket experiments, ground tests and simulations were used to design the structure, the folding pattern and control parameters. A developed control law and a reaction wheel were used to control the deployment. After ejection from the rocket, the web was deployed but entanglements occurred since the web did not start to deploy at the specified angular velocity. The deployment dynamics was reconstructed from the information recorded in inertial measurement units and cameras. The nonlinear torque of the motor used to drive the reaction wheel was calculated from the results. Simulations show that if the Suaineadh started to deploy at the specified angular velocity, the web would most likely have been deployed and stabilized in space by the motor, reaction wheel and controller used in the experiment.
Applying Dynamic Fuzzy Petri Net to Web Learning System
ERIC Educational Resources Information Center
Chen, Juei-Nan; Huang, Yueh-Min; Chu, William
2005-01-01
This investigation presents a DFPN (Dynamic Fuzzy Petri Net) model to increase the flexibility of the tutoring agent's behaviour and thus provide a learning content structure for a lecture course. The tutoring agent is a software assistant for a single user, who may be an expert in an e-Learning course. Based on each learner's behaviour, the…
Joyfully Map Social Dynamics When Designing Web-Based Courses
ERIC Educational Resources Information Center
Ahamer, Gilbert
2013-01-01
This paper provides a concept and a notation for optimizing the design of social processes in gaming and learning for individuals, groups of individuals and society as a whole. Traditional approaches to the mapping and designing of the emerging social dynamics in a joyful, social education setting have fallen short of producing desirable results…
Joyfully Map Social Dynamics When Designing Web-Based Courses
ERIC Educational Resources Information Center
Ahamer, Gilbert
2013-01-01
This paper provides a concept and a notation for optimizing the design of social processes in gaming and learning for individuals, groups of individuals and society as a whole. Traditional approaches to the mapping and designing of the emerging social dynamics in a joyful, social education setting have fallen short of producing desirable results…
NASA Astrophysics Data System (ADS)
Rey, Sergio J.; Kang, Wei; Wolf, Levi
2016-10-01
Discrete Markov chain models (DMCs) have been widely applied to the study of regional income distribution dynamics and convergence. This popularity reflects the rich body of DMC theory on the one hand and the ability of this framework to provide insights on the internal and external properties of regional income distribution dynamics on the other. In this paper we examine the properties of tests for spatial effects in DMC models of regional distribution dynamics. We do so through a series of Monte Carlo simulations designed to examine the size, power and robustness of tests for spatial heterogeneity and spatial dependence in transitional dynamics. This requires that we specify a data generating process for not only the null, but also alternatives when spatial heterogeneity or spatial dependence is present in the transitional dynamics. We are not aware of any work which has examined these types of data generating processes in the spatial distribution dynamics literature. Results indicate that tests for spatial heterogeneity and spatial dependence display good power for the presence of spatial effects. However, tests for spatial heterogeneity are not robust to the presence of strong spatial dependence, while tests for spatial dependence are sensitive to the spatial configuration of heterogeneity. When the spatial configuration can be considered random, dependence tests are robust to the dynamic spatial heterogeneity, but not so to the process mean heterogeneity when the difference in process means is large relative to the variance of the time series.
Zhang, Huaguang; Song, Ruizhuo; Wei, Qinglai; Zhang, Tieyan
2011-12-01
In this paper, a novel heuristic dynamic programming (HDP) iteration algorithm is proposed to solve the optimal tracking control problem for a class of nonlinear discrete-time systems with time delays. The novel algorithm contains state updating, control policy iteration, and performance index iteration. To get the optimal states, the states are also updated. Furthermore, the "backward iteration" is applied to state updating. Two neural networks are used to approximate the performance index function and compute the optimal control policy for facilitating the implementation of HDP iteration algorithm. At last, we present two examples to demonstrate the effectiveness of the proposed HDP iteration algorithm.
NASA Astrophysics Data System (ADS)
Chang, K.-J.; Chen, R.-F.; Chan, Y.-C.; Kuo, C.-Y.; Weng, C.-H.
2012-04-01
transported debris was about 30 - 90 m thick, covered on the preexisting debris deposit hill and around the river channel. The debris formed a dammed lake, with a maximum volume of 45 Mm3. Based on DTMs data sets, field observations, the discrete element method - PFC3D is adapts to analyze the triggering mechanism and sling dynamic process. The presence and the coupling effect from the strong ground excitation and high pore water pressure is the essential factor to triggering the landslide event. The results shows that the best fit between the deposit topography of the post-event DTM and numerical simulations, the fictional coefficient of the sliding surface is as low as 0.087. The maximum sliding speed is as high as 87.2 m/s, the result coincide with the seismic record from the nearby strong motion seismic record.
Demopoulos, Amanda; McClain-Counts, Jennifer; Ross, Steve W.; Brooke, Sandra; Mienis, Furu
2017-01-01
Examination of food webs and trophic niches provide insights into organisms' functional ecology, yet few studies have examined trophodynamics within submarine canyons, where the interaction of canyon morphology and oceanography influences habitat provision and food deposition. Using stable isotope analysis and Bayesian ellipses, we documented deep-sea food-web structure and trophic niches in Baltimore Canyon and the adjacent open slopes in the US Mid-Atlantic Region. Results revealed isotopically diverse feeding groups, comprising approximately 5 trophic levels. Regression analysis indicated that consumer isotope data are structured by habitat (canyon vs. slope), feeding group, and depth. Benthic feeders were enriched in 13C and 15N relative to suspension feeders, consistent with consuming older, more refractory organic matter. In contrast, canyon suspension feeders had the largest and more distinct isotopic niche, indicating they consume an isotopically discrete food source, possibly fresher organic material. The wider isotopic niche observed for canyon consumers indicated the presence of feeding specialists and generalists. High dispersion in δ13C values for canyon consumers suggests that the isotopic composition of particulate organic matter changes, which is linked to depositional dynamics, resulting in discrete zones of organic matter accumulation or resuspension. Heterogeneity in habitat and food availability likely enhances trophic diversity in canyons. Given their abundance in the world's oceans, our results from Baltimore Canyon suggest that submarine canyons may represent important havens for trophic diversity.
Biological vs. Physical Mixing Effects on Benthic Food Web Dynamics
Braeckman, Ulrike; Provoost, Pieter; Moens, Tom; Soetaert, Karline; Middelburg, Jack J.; Vincx, Magda; Vanaverbeke, Jan
2011-01-01
Biological particle mixing (bioturbation) and solute transfer (bio-irrigation) contribute extensively to ecosystem functioning in sediments where physical mixing is low. Macrobenthos transports oxygen and organic matter deeper into the sediment, thereby likely providing favourable niches to lower trophic levels (i.e., smaller benthic animals such as meiofauna and bacteria) and thus stimulating mineralisation. Whether this biological transport facilitates fresh organic matter assimilation by the metazoan lower part of the food web through niche establishment (i.e., ecosystem engineering) or rather deprives them from food sources, is so far unclear. We investigated the effects of the ecosystem engineers Lanice conchilega (bio-irrigator) and Abra alba (bioturbator) compared to abiotic physical mixing events on survival and food uptake of nematodes after a simulated phytoplankton bloom. The 13C labelled diatom Skeletonema costatum was added to 4 treatments: (1) microcosms containing the bioturbator, (2) microcosms containing the bio-irrigator, (3) control microcosms and (4) microcosms with abiotic manual surface mixing. Nematode survival and subsurface peaks in nematode density profiles were most pronounced in the bio-irrigator treatment. However, nematode specific uptake (Δδ13C) of the added diatoms was highest in the physical mixing treatment, where macrobenthos was absent and the diatom 13C was homogenised. Overall, nematodes fed preferentially on bulk sedimentary organic material rather than the added diatoms. The total C budget (µg C m−2), which included TO13C remaining in the sediment, respiration, nematode and macrobenthic uptake, highlighted the limited assimilation by the metazoan benthos and the major role of bacterial respiration. In summary, bioturbation and especially bio-irrigation facilitated the lower trophic levels mainly over the long-term through niche establishment. Since the freshly added diatoms represented only a limited food source for
Biological vs. physical mixing effects on benthic food web dynamics.
Braeckman, Ulrike; Provoost, Pieter; Moens, Tom; Soetaert, Karline; Middelburg, Jack J; Vincx, Magda; Vanaverbeke, Jan
2011-03-24
Biological particle mixing (bioturbation) and solute transfer (bio-irrigation) contribute extensively to ecosystem functioning in sediments where physical mixing is low. Macrobenthos transports oxygen and organic matter deeper into the sediment, thereby likely providing favourable niches to lower trophic levels (i.e., smaller benthic animals such as meiofauna and bacteria) and thus stimulating mineralisation. Whether this biological transport facilitates fresh organic matter assimilation by the metazoan lower part of the food web through niche establishment (i.e., ecosystem engineering) or rather deprives them from food sources, is so far unclear. We investigated the effects of the ecosystem engineers Lanice conchilega (bio-irrigator) and Abra alba (bioturbator) compared to abiotic physical mixing events on survival and food uptake of nematodes after a simulated phytoplankton bloom. The (13)C labelled diatom Skeletonema costatum was added to 4 treatments: (1) microcosms containing the bioturbator, (2) microcosms containing the bio-irrigator, (3) control microcosms and (4) microcosms with abiotic manual surface mixing. Nematode survival and subsurface peaks in nematode density profiles were most pronounced in the bio-irrigator treatment. However, nematode specific uptake (Δδ(13)C) of the added diatoms was highest in the physical mixing treatment, where macrobenthos was absent and the diatom (13)C was homogenised. Overall, nematodes fed preferentially on bulk sedimentary organic material rather than the added diatoms. The total C budget (µg C m(-2)), which included TO(13)C remaining in the sediment, respiration, nematode and macrobenthic uptake, highlighted the limited assimilation by the metazoan benthos and the major role of bacterial respiration. In summary, bioturbation and especially bio-irrigation facilitated the lower trophic levels mainly over the long-term through niche establishment. Since the freshly added diatoms represented only a limited food source
Networked Physics Curriculum:. From Static Web to Dynamic Java
NASA Astrophysics Data System (ADS)
Bothun, G. D.; Kevan, S. D.; Micklavzina, S.; Mason, D.
We describe our efforts at the University of Oregon to use Web-based Instructional Technology (IT) supplemented with interactive Java virtual experiments to change the standard pedagogy associated with large, introductory undergraduate classes in physics and astronomy. We begin by examining some of the problems associated with the standard pedagogy in these classes and how these problems motivated our development of networked courseware. Although we identify and describe five empirical positive outcomes associated with IT, we conclude that the use of HTML-based course material and assignments does not substantially alter the standard pedagogy as this medium alone is not conducive to interactive exercises. To build interactivity into our courseware, we have undertaken a vigorous effort of creating Java-based experiments which are grounded in physical reality and duplicate the kinds of experiments that are done in the physical lab. In so doing, we build experimentation into a curriculum for large lecture-based classes in which the standard pedagogy and resource constraints normally preclude lab sections. The main goal is to create a networked environment where the student can easily retrieve the notes and the demonstrations that were done in class as well as to engage in experiments that are designed to illustrate basic principles. In so doing, we hope to move to a more learner-centered environment which is driven by student inquiry. Five specific Java experiments are described here and each is accompanied by a snapshot of the experimental apparatus and controls. An appendix contains the relevant URLs of the experiments, courseware, and animation described herein.
NASA Technical Reports Server (NTRS)
Jameson, Antony
1994-01-01
The effect of artificial diffusion on discrete shock structures is examined for a family of schemes which includes scalar diffusion, convective upwind and split pressure (CUSP) schemes, and upwind schemes with characteristics splitting. The analysis leads to conditions on the diffusive flux such that stationary discrete shocks can contain a single interior point. The simplest formulation which meets these conditions is a CUSP scheme in which the coefficients of the pressure differences is fully determined by the coefficient of convective diffusion. It is also shown how both the characteristic and CUSP schemes can be modified to preserve constant stagnation enthalpy in steady flow, leading to four variants, the E and H-characteristic schemes, and the E and H-CUSP schemes. Numerical results are presented which confirm the properties of these schemes.
Autonomous learning by simple dynamical systems with a discrete-time formulation
NASA Astrophysics Data System (ADS)
Bilen, Agustín M.; Kaluza, Pablo
2017-05-01
We present a discrete-time formulation for the autonomous learning conjecture. The main feature of this formulation is the possibility to apply the autonomous learning scheme to systems in which the errors with respect to target functions are not well-defined for all times. This restriction for the evaluation of functionality is a typical feature in systems that need a finite time interval to process a unit piece of information. We illustrate its application on an artificial neural network with feed-forward architecture for classification and a phase oscillator system with synchronization properties. The main characteristics of the discrete-time formulation are shown by constructing these systems with predefined functions.
Discrete simulation of the dynamics of spread of extreme opinions in a society
NASA Astrophysics Data System (ADS)
Stauffer, Dietrich; Sahimi, Muhammad
2006-05-01
We propose a discrete model for how opinions about a given “extreme” subject, about which various groups of a population have different degrees of enthusiasm for or susceptibility to, such as fanaticism, extreme social and political positions, and terrorism, may spread. The model, in a certain limit, is the discrete analogue of a deterministic continuum model suggested by others. We carry out extensive computer simulation of the model by utilizing it on lattices with infinite- or short-range interactions, and on symmetric and hierarchical (or directed) Barabási-Albert scale-free networks. Several interesting features of the model are demonstrated, and comparison is made with the deterministic continuum model.
Kengne, E; Lakhssassi, A
2015-03-01
We consider a lossless one-dimensional nonlinear discrete bi-inductance electrical transmission line made of N identical unit cells. When lattice effects are considered, we use the reductive perturbation method in the semidiscrete limit to show that the dynamics of modulated waves can be modeled by the classical nonlinear Schrödinger (CNLS) equation, which describes the modulational instability and the propagation of bright and dark solitons on a continuous-wave background. Our theoretical analysis based on the CNLS equation predicts either two or four frequency regions with different behavior concerning the modulational instability of a plane wave. With the help of the analytical solutions of the CNLS equation, we investigate analytically the effects of the linear capacitance CS on the dynamics of matter-wave solitons in the network. Our results reveal that the linear parameter CS can be used to manipulate the motion of bright, dark, and kink soliton in the network.
On the discrete-time dynamics of a class of self-stabilizing MCA extraction algorithms.
Kong, Xiangyu; Hu, Changhua; Han, Chongzhao
2010-01-01
The minor component analysis (MCA) deals with the recovery of the eigenvector associated to the smallest eigenvalue of the autocorrelation matrix of the input dada, and it is a very important tool for signal processing and data analysis. This brief analyzes the convergence and stability of a class of self-stabilizing MCA algorithms via a deterministic discrete-time (DDT) method. Some sufficient conditions are obtained to guarantee the convergence of these learning algorithms. Simulations are carried out to further illustrate the theoretical results achieved. It can be concluded that these self-stabilizing algorithms can efficiently extract the minor component (MC), and they outperform some existing MCA methods.
Avalanche dynamics of magnetic flux in a two-dimensional discrete superconductor
Ginzburg, S. L.; Nakin, A. V.; Savitskaya, N. E.
2006-11-15
The critical state of a two-dimensional discrete superconductor in an external magnetic field is studied. This state is found to be self-organized in the generalized sense, i.e., is a set of metastable states that transform to each other by means of avalanches. An avalanche is characterized by the penetration of a magnetic flux to the system. The sizes of the occurring avalanches, i.e., changes in the magnetic flux, exhibit the power-law distribution. It is also shown that the size of the avalanche occurring in the critical state and the external magnetic field causing its change are statistically independent quantities.
Business Models of E-Government: Research on Dynamic E-Government Based on Web Services
NASA Astrophysics Data System (ADS)
Li, Yan; Yang, Jiumin
Government transcends all sectors in a society. It provides not only the legal, political and economic infrastructure to support other sectors, but also exerts significant influence on the social factors that contribute to their development. With its maturity of technologies and management, e-government will eventually enter into the time of 'one-stop' services. Among others, the technology of Web services is the major contributor to this achievement. Web services provides a new way of standard-based software technology, letting programmers combine existing computer system in new ways over the Internet within one business or across many, and would thereby bring about profound and far-reaching impacts on e-government. This paper introduced the business modes of e-government, architecture of dynamic e-government and its key technologies. Finally future prospect of dynamic e-government was also briefly discussed.
Shaitan, K V; Orshanskiy, I A
2015-01-01
In this study we suggested a dynamics simulation for the formation of protofiber of spider web nanofiber. It was shown that a bundle of parallel polyalanine β-strands of sufficient length is arranged through self-assembly into a stable right-handed super helix. By numerical analysis we investigated the rheological properties and provided in nonlinear regime a generalization of the model of Singer for description of the rheological behaviour of super helix.
Mixotrophy and intraguild predation - dynamic consequences of shifts between food web motifs
NASA Astrophysics Data System (ADS)
Karnatak, Rajat; Wollrab, Sabine
2017-06-01
Mixotrophy is ubiquitous in microbial communities of aquatic systems with many flagellates being able to use autotroph as well as heterotroph pathways for energy acquisition. The usage of one over the other pathway is associated with resource availability and the coupling of alternative pathways has strong implications for system stability. We investigated the impact of dominance of different energy pathways related to relative resource availability on system dynamics in the setting of a tritrophic food web motif. This motif consists of a mixotroph feeding on a purely autotroph species while competing for a shared resource. In addition, the autotroph can use an additional exclusive food source. By changing the relative abundance of shared vs. exclusive food source, we shift the food web motif from an intraguild predation motif to a food chain motif. We analyzed the dependence of system dynamics on absolute and relative resource availability. In general, the system exhibits a transition from stable to oscillatory dynamics with increasing nutrient availability. However, this transition occurs at a much lower nutrient level for the food chain in comparison to the intraguild predation motif. A similar transition is also observed with variations in the relative abundance of food sources for a range of nutrient levels. We expect this shift in food web motifs to occur frequently in microbial communities and therefore the results from our study are highly relevant for natural systems.
Kooistra, Lammert; Bergsma, Aldo; Chuma, Beatus; de Bruin, Sytze
2009-01-01
This paper describes the development of a sensor web based approach which combines earth observation and in situ sensor data to derive typical information offered by a dynamic web mapping service (WMS). A prototype has been developed which provides daily maps of vegetation productivity for the Netherlands with a spatial resolution of 250 m. Daily available MODIS surface reflectance products and meteorological parameters obtained through a Sensor Observation Service (SOS) were used as input for a vegetation productivity model. This paper presents the vegetation productivity model, the sensor data sources and the implementation of the automated processing facility. Finally, an evaluation is made of the opportunities and limitations of sensor web based approaches for the development of web services which combine both satellite and in situ sensor sources. PMID:22574019
Kooistra, Lammert; Bergsma, Aldo; Chuma, Beatus; de Bruin, Sytze
2009-01-01
This paper describes the development of a sensor web based approach which combines earth observation and in situ sensor data to derive typical information offered by a dynamic web mapping service (WMS). A prototype has been developed which provides daily maps of vegetation productivity for the Netherlands with a spatial resolution of 250 m. Daily available MODIS surface reflectance products and meteorological parameters obtained through a Sensor Observation Service (SOS) were used as input for a vegetation productivity model. This paper presents the vegetation productivity model, the sensor data sources and the implementation of the automated processing facility. Finally, an evaluation is made of the opportunities and limitations of sensor web based approaches for the development of web services which combine both satellite and in situ sensor sources.
Feng, Rui; Xenos, Michalis; Girdhar, Gaurav; Kang, Wei; Davenport, James W; Deng, Yuefan; Bluestein, Danny
2012-01-01
Flow and stresses induced by blood flow acting on the blood cellular constituents can be represented to a certain extent by a continuum mechanics approach down to the order of the μm level. However, the molecular effects of, e.g., adhesion/aggregation bonds of blood clotting can be on the order of nm. The coupling of the disparate length and timescales between such molecular levels and macroscopic transport represents a major computational challenge. To address this challenge, a multiscale numerical approach based on discrete particle dynamics (DPD) methodology derived from molecular dynamics (MD) principles is proposed. The feasibility of the approach was firstly tested for its ability to simulate viscous flow conditions. Simulations were conducted in low Reynolds numbers flows (Re = 25-33) through constricted tubes representing blood vessels with various degrees of stenosis. Multiple discrete particles interacting with each other were simulated, with 1.24-1.36 million particles representing the flow domain and 0.4 million particles representing the vessel wall. The computation was carried out on the massive parallel supercomputer NY BlueGene/L employing NAMD-a parallel MD package for high performance computing (HPC). Typical recirculation zones were formed distal to the stenoses. The velocity profiles and recirculation zones were in excellent agreement with computational fluid dynamics (CFD) 3D Navier-Stokes viscous fluid flow simulations and with classic numerical and experimental results by YC Fung in constricted tubes. This feasibility analysis demonstrates the potential of a methodology that widely departs from a continuum approach to simulate multiscale phenomena such as flow induced blood clotting.
Bayesian analysis of the dynamic cosmic web in the SDSS galaxy survey
NASA Astrophysics Data System (ADS)
Leclercq, Florent; Jasche, Jens; Wandelt, Benjamin
2015-06-01
Recent application of the Bayesian algorithm \\textsc{borg} to the Sloan Digital Sky Survey (SDSS) main sample galaxies resulted in the physical inference of the formation history of the observed large-scale structure from its origin to the present epoch. In this work, we use these inferences as inputs for a detailed probabilistic cosmic web-type analysis. To do so, we generate a large set of data-constrained realizations of the large-scale structure using a fast, fully non-linear gravitational model. We then perform a dynamic classification of the cosmic web into four distinct components (voids, sheets, filaments, and clusters) on the basis of the tidal field. Our inference framework automatically and self-consistently propagates typical observational uncertainties to web-type classification. As a result, this study produces accurate cosmographic classification of large-scale structure elements in the SDSS volume. By also providing the history of these structure maps, the approach allows an analysis of the origin and growth of the early traces of the cosmic web present in the initial density field and of the evolution of global quantities such as the volume and mass filling fractions of different structures. For the problem of web-type classification, the results described in this work constitute the first connection between theory and observations at non-linear scales including a physical model of structure formation and the demonstrated capability of uncertainty quantification. A connection between cosmology and information theory using real data also naturally emerges from our probabilistic approach. Our results constitute quantitative chrono-cosmography of the complex web-like patterns underlying the observed galaxy distribution.
Bayesian analysis of the dynamic cosmic web in the SDSS galaxy survey
Leclercq, Florent; Wandelt, Benjamin
2015-06-01
Recent application of the Bayesian algorithm \\textsc(borg) to the Sloan Digital Sky Survey (SDSS) main sample galaxies resulted in the physical inference of the formation history of the observed large-scale structure from its origin to the present epoch. In this work, we use these inferences as inputs for a detailed probabilistic cosmic web-type analysis. To do so, we generate a large set of data-constrained realizations of the large-scale structure using a fast, fully non-linear gravitational model. We then perform a dynamic classification of the cosmic web into four distinct components (voids, sheets, filaments, and clusters) on the basis of the tidal field. Our inference framework automatically and self-consistently propagates typical observational uncertainties to web-type classification. As a result, this study produces accurate cosmographic classification of large-scale structure elements in the SDSS volume. By also providing the history of these structure maps, the approach allows an analysis of the origin and growth of the early traces of the cosmic web present in the initial density field and of the evolution of global quantities such as the volume and mass filling fractions of different structures. For the problem of web-type classification, the results described in this work constitute the first connection between theory and observations at non-linear scales including a physical model of structure formation and the demonstrated capability of uncertainty quantification. A connection between cosmology and information theory using real data also naturally emerges from our probabilistic approach. Our results constitute quantitative chrono-cosmography of the complex web-like patterns underlying the observed galaxy distribution.
NASA Astrophysics Data System (ADS)
Tran, Quoc Anh; Chevalier, Bastien; Benz, Miguel; Breul, Pierre; Gourvès, Roland
2017-06-01
The recent technological developments made on the light dynamic penetration test Panda 3 ® provide a dynamic load-penetration curve σp - sp for each impact. This curve is influenced by the mechanical and physical properties of the investigated granular media. In order to analyze and exploit the load-penetration curve, a numerical model of penetration test using 3D Discrete Element Method is proposed for reproducing tests in dynamic conditions in granular media. All parameters of impact used in this model have at first been calibrated by respecting mechanical and geometrical properties of the hammer and the rod. There is a good agreement between experimental results and the ones obtained from simulations in 2D or 3D. After creating a sample, we will simulate the Panda 3 ®. It is possible to measure directly the dynamic load-penetration curve occurring at the tip for each impact. Using the force and acceleration measured in the top part of the rod, it is possible to separate the incident and reflected waves and then calculate the tip's load-penetration curve. The load-penetration curve obtained is qualitatively similar with that obtained by experimental tests. In addition, the frequency analysis of the measured signals present also a good compliance with that measured in reality when the tip resistance is qualitatively similar.
The global dynamics of a discrete juvenile-adult model with continuous and seasonal reproduction.
Ackleh, Azmy S; Chiquet, Ross A
2009-03-01
A general discrete juvenile-adult population model with time-dependent birth rate and nonlinear survivorship rates is studied. When breeding is continuous, it is shown that the model has a unique globally asymptotically stable positive equilibrium provided the net reproductive number is larger than one. If it is smaller than one, then the extinction equilibrium is globally asymptotically stable. When breeding is seasonal, it is shown that there exists a unique globally asymptotically stable periodic solution provided the net reproductive number is larger than one. When this value is less than one, the population goes to extinction. Conditions on the birth rate where the population with seasonal breeding survives while the population with continuous breeding becomes extinct are provided.
Attractors of relaxation discrete-time systems with chaotic dynamics on a fast time scale
Maslennikov, Oleg V.; Nekorkin, Vladimir I.
2016-07-15
In this work, a new type of relaxation systems is considered. Their prominent feature is that they comprise two distinct epochs, one is slow regular motion and another is fast chaotic motion. Unlike traditionally studied slow-fast systems that have smooth manifolds of slow motions in the phase space and fast trajectories between them, in this new type one observes, apart the same geometric objects, areas of transient chaos. Alternating periods of slow regular motions and fast chaotic ones as well as transitions between them result in a specific chaotic attractor with chaos on a fast time scale. We formulate basic properties of such attractors in the framework of discrete-time systems and consider several examples. Finally, we provide an important application of such systems, the neuronal electrical activity in the form of chaotic spike-burst oscillations.
VEDA: a web-based virtual environment for dynamic atomic force microscopy.
Melcher, John; Hu, Shuiqing; Raman, Arvind
2008-06-01
We describe here the theory and applications of virtual environment dynamic atomic force microscopy (VEDA), a suite of state-of-the-art simulation tools deployed on nanoHUB (www.nanohub.org) for the accurate simulation of tip motion in dynamic atomic force microscopy (dAFM) over organic and inorganic samples. VEDA takes advantage of nanoHUB's cyberinfrastructure to run high-fidelity dAFM tip dynamics computations on local clusters and the teragrid. Consequently, these tools are freely accessible and the dAFM simulations are run using standard web-based browsers without requiring additional software. A wide range of issues in dAFM ranging from optimal probe choice, probe stability, and tip-sample interaction forces, power dissipation, to material property extraction and scanning dynamics over hetereogeneous samples can be addressed.
Invited Article: VEDA: A web-based virtual environment for dynamic atomic force microscopy
NASA Astrophysics Data System (ADS)
Melcher, John; Hu, Shuiqing; Raman, Arvind
2008-06-01
We describe here the theory and applications of virtual environment dynamic atomic force microscopy (VEDA), a suite of state-of-the-art simulation tools deployed on nanoHUB (www.nanohub.org) for the accurate simulation of tip motion in dynamic atomic force microscopy (dAFM) over organic and inorganic samples. VEDA takes advantage of nanoHUB's cyberinfrastructure to run high-fidelity dAFM tip dynamics computations on local clusters and the teragrid. Consequently, these tools are freely accessible and the dAFM simulations are run using standard web-based browsers without requiring additional software. A wide range of issues in dAFM ranging from optimal probe choice, probe stability, and tip-sample interaction forces, power dissipation, to material property extraction and scanning dynamics over hetereogeneous samples can be addressed.
Cavity master equation for the continuous time dynamics of discrete-spin models
NASA Astrophysics Data System (ADS)
Aurell, E.; Del Ferraro, G.; Domínguez, E.; Mulet, R.
2017-05-01
We present an alternate method to close the master equation representing the continuous time dynamics of interacting Ising spins. The method makes use of the theory of random point processes to derive a master equation for local conditional probabilities. We analytically test our solution studying two known cases, the dynamics of the mean-field ferromagnet and the dynamics of the one-dimensional Ising system. We present numerical results comparing our predictions with Monte Carlo simulations in three different models on random graphs with finite connectivity: the Ising ferromagnet, the random field Ising model, and the Viana-Bray spin-glass model.
A new dimension: Evolutionary food web dynamics in two dimensional trait space.
Ritterskamp, Daniel; Bearup, Daniel; Blasius, Bernd
2016-09-21
Species within a habitat are not uniformly distributed. However this aspect of community structure, which is fundamental to many conservation activities, is neglected in the majority of models of food web assembly. To address this issue, we introduce a model which incorporates a second dimension, which can be interpreted as space, into the trait space used in evolutionary food web models. Our results show that the additional trait axis allows the emergence of communities with a much greater range of network structures, similar to the diversity observed in real ecological communities. Moreover, the network properties of the food webs obtained are in good agreement with those of empirical food webs. Community emergence follows a consistent pattern with spread along the second trait axis occurring before the assembly of higher trophic levels. Communities can reach either a static final structure, or constantly evolve. We observe that the relative importance of competition and predation is a key determinant of the network structure and the evolutionary dynamics. The latter are driven by the interaction-competition and predation-between small groups of species. The model remains sufficiently simple that we are able to identify the factors, and mechanisms, which determine the final community state.
Magnitude judgments of loudness change for discrete, dynamic, and hybrid stimuli.
Pastore, Richard E; Flint, Jesse
2011-04-01
Recent investigations of loudness change within stimuli have identified differences as a function of direction of change and power range (e.g., Canévet, Acustica, 62, 2136-2142, 1986; Neuhoff, Nature, 395, 123-124, 1998), with claims of differences between dynamic and static stimuli. Experiment 1 provides the needed direct empirical evaluation of loudness change across static, dynamic, and hybrid stimuli. Consistent with recent findings for dynamic stimuli, quantitative and qualitative differences in pattern of loudness change were found as a function of power change direction. With identical patterns of loudness change, only quantitative differences were found across stimulus type. In Experiment 2, Points of Subjective loudness Equality (PSE) provided additional information about loudness judgments for the static and dynamic stimuli. Because the quantitative differences across stimulus type exceed the magnitude that could be expected based upon temporal integration by the auditory system, other factors need to be, and are, considered.
Wang, Fei-Yue; Jin, Ning; Liu, Derong; Wei, Qinglai
2011-01-01
In this paper, we study the finite-horizon optimal control problem for discrete-time nonlinear systems using the adaptive dynamic programming (ADP) approach. The idea is to use an iterative ADP algorithm to obtain the optimal control law which makes the performance index function close to the greatest lower bound of all performance indices within an ε-error bound. The optimal number of control steps can also be obtained by the proposed ADP algorithms. A convergence analysis of the proposed ADP algorithms in terms of performance index function and control policy is made. In order to facilitate the implementation of the iterative ADP algorithms, neural networks are used for approximating the performance index function, computing the optimal control policy, and modeling the nonlinear system. Finally, two simulation examples are employed to illustrate the applicability of the proposed method.
Zhang, Huaguang; Jiang, He; Luo, Chaomin; Xiao, Geyang
2016-10-03
In this paper, we investigate the nonzero-sum games for a class of discrete-time (DT) nonlinear systems by using a novel policy iteration (PI) adaptive dynamic programming (ADP) method. The main idea of our proposed PI scheme is to utilize the iterative ADP algorithm to obtain the iterative control policies, which not only ensure the system to achieve stability but also minimize the performance index function for each player. This paper integrates game theory, optimal control theory, and reinforcement learning technique to formulate and handle the DT nonzero-sum games for multiplayer. First, we design three actor-critic algorithms, an offline one and two online ones, for the PI scheme. Subsequently, neural networks are employed to implement these algorithms and the corresponding stability analysis is also provided via the Lyapunov theory. Finally, a numerical simulation example is presented to demonstrate the effectiveness of our proposed approach.
Dynamical Behavior of a Malaria Model with Discrete Delay and Optimal Insecticide Control
NASA Astrophysics Data System (ADS)
Kar, Tuhin Kumar; Jana, Soovoojeet
In this paper we have proposed and analyzed a simple three-dimensional mathematical model related to malaria disease. We consider three state variables associated with susceptible human population, infected human population and infected mosquitoes, respectively. A discrete delay parameter has been incorporated to take account of the time of incubation period with infected mosquitoes. We consider the effect of insecticide control, which is applied to the mosquitoes. Basic reproduction number is figured out for the proposed model and it is shown that when this threshold is less than unity then the system moves to the disease-free state whereas for higher values other than unity, the system would tend to an endemic state. On the other hand if we consider the system with delay, then there may exist some cases where the endemic equilibrium would be unstable although the numerical value of basic reproduction number may be greater than one. We formulate and solve the optimal control problem by considering insecticide as the control variable. Optimal control problem assures to obtain better result than the noncontrol situation. Numerical illustrations are provided in support of the theoretical results.
Martínez-Rosell, Gerard; Giorgino, Toni; De Fabritiis, Gianni
2017-07-24
Protein preparation is a critical step in molecular simulations that consists of refining a Protein Data Bank (PDB) structure by assigning titration states and optimizing the hydrogen-bonding network. In this application note, we describe ProteinPrepare, a web application designed to interactively support the preparation of protein structures. Users can upload a PDB file, choose the solvent pH value, and inspect the resulting protonated residues and hydrogen-bonding network within a 3D web interface. Protonation states are suggested automatically but can be manually changed using the visual aid of the hydrogen-bonding network. Tables and diagrams provide estimated pKa values and charge states, with visual indication for cases where review is required. We expect the graphical interface to be a useful instrument to assess the validity of the preparation, but nevertheless, a script to execute the preparation offline with the High-Throughput Molecular Dynamics (HTMD) environment is also provided for noninteractive operations.
Effects of picture amount on preference, balance, and dynamic feel of Web pages.
Chiang, Shu-Ying; Chen, Chien-Hsiung
2012-04-01
This study investigates the effects of picture amount on subjective evaluation. The experiment herein adopted two variables to define picture amount: column ratio and picture size. Six column ratios were employed: 7:93,15:85, 24:76, 33:67, 41:59, and 50:50. Five picture sizes were examined: 140 x 81, 220 x 127, 300 x 173, 380 x 219, and 460 x 266 pixels. The experiment implemented a within-subject design; 104 participants were asked to evaluate 30 web page layouts. Repeated measurements revealed that the column ratio and picture size have significant effects on preference, balance, and dynamic feel. The results indicated the most appropriate picture amount for display: column ratios of 15:85 and 24:76, and picture sizes of 220 x 127, 300 x 173, and 380 x 219. The research findings can serve as the basis for the application of design guidelines for future web page interface design.
Data compression of discrete sequence: A tree based approach using dynamic programming
NASA Technical Reports Server (NTRS)
Shivaram, Gurusrasad; Seetharaman, Guna; Rao, T. R. N.
1994-01-01
A dynamic programming based approach for data compression of a ID sequence is presented. The compression of an input sequence of size N to that of a smaller size k is achieved by dividing the input sequence into k subsequences and replacing the subsequences by their respective average values. The partitioning of the input sequence is carried with the intention of reducing the mean squared error in the reconstructed sequence. The complexity involved in finding the partitions which would result in such an optimal compressed sequence is reduced by using the dynamic programming approach, which is presented.
Markov state modeling and dynamical coarse-graining via discrete relaxation path sampling
NASA Astrophysics Data System (ADS)
Fačkovec, B.; Vanden-Eijnden, E.; Wales, D. J.
2015-07-01
A method is derived to coarse-grain the dynamics of complex molecular systems to a Markov jump process (MJP) describing how the system jumps between cells that fully partition its state space. The main inputs are relaxation times for each pair of cells, which are shown to be robust with respect to positioning of the cell boundaries. These relaxation times can be calculated via molecular dynamics simulations performed in each cell separately and are used in an efficient estimator for the rate matrix of the MJP. The method is illustrated through applications to Sinai billiards and a cluster of Lennard-Jones discs.
Nedorezov, L V; Sadykov, A M; Sadykova, D L
2010-01-01
Considered is a mathematical model for dynamics of an isolated population with non-overlapping generations. The individuals' birth process (emergence of new-generation individuals) is assumed to have a discrete nature (there exist some fixed time moments at which the new generations emerge), while the death process is assumed to be continuous. In addition, the birth rate is assumed to be a function of the number of individuals survived till the moment of reproduction, the function being non-monotone: there exists an optimal value of the population size at which the birth rate reaches its maximum (Alley principle). Analysis of the discrete-continuous models has revealed that each of the new models has a rich set of dynamical regimes. New models are compared with a number of well-known discrete ones (like Skellam, Moran-Ricker, Hassell, Maynard Smith-Slatkin models, and others) when approximating an empirical time series on fluctuations of a green oak moth population (Korzukhin, Semevsky, 1992). Neither of the models can provide for a satisfactory description of the green oak moth dynamics. It is also shown that usage of the discrete-continuous models for approximation of real datasets enables one to find several important population parameters, which can hardly (or cannot) be found by means of traditional discrete models.
NASA Astrophysics Data System (ADS)
Hachuła, Piotr; Nockowska-Rosiak, Magdalena; Schmeidel, Ewa
2017-07-01
An analysis of dynamics of demand-inventory model formulated with a system of three first order difference equations with three parameters. The origin, rules, assumptions and example of application are presented. The numerical analysis is performed using bifurcation diagrams and phase portraits. Graphical observation of evolution of trajectories suggests chaotic behaviour occurrence.
Investigations of dynamic behavior of composite bridges with open web girders
NASA Astrophysics Data System (ADS)
Kartopol'tsev, Andrei; Kartopol'tsev, Vladimir; Kolmakov, Boris
2017-01-01
The paper presents investigation of the dynamic behavior of composite bridges with open web girders. The bridge span is made of reinforced concrete layers with a metal pan underneath. The dynamic tests of the bridge structure are carried out using the multichannel vibrodiagnostic test kit for measuring the eigenfrequency. The software application LIRA is used to develop the finite element model (FEM) of the bridge after its mathematical simulation. The FE model is subjected to loads identical to the experimental ones, and the dynamic behavior of the bridge is simulated to measure the multimode eigenfrequences. A careful comparison between the calculations and experimental results shows good agreement for the investigated parameters of the bridge structure.
Stratification of discharge in noble gases from the viewpoint of the discrete dynamics
Golubovskii, Yu. Pelyukhova, E.; Sigeneger, F.; Nekuchaev, V.
2015-03-15
Based on the analysis of electron phase trajectories in sinusoidal electric fields, a new point of view on discharge stratification is proposed. It is shown that the positive column can be considered as a spatial resonator in which electric fields with a fundamental period length L{sub S} or higher mode length q/p L{sub S} establish, where p and q are integers and p > q. The fundamental mode length L{sub S} is equivalent to the distance on which electrons gain energy equal to the lowest excitation threshold. This distance determines a length of the S-striation. Unlike kinetic theory, in the presented model resonance properties of the discharge column are not connected with elastic collision energy losses. A point map is used to obtain the resonance trajectories of electrons in the phase plane. Stable points for the positions of inelastic collisions in the resonance trajectories have been found at the positions of field maxima in the case of integer ratios p/q . For non-integer ratios p/q , multiple resonance trajectories arise according to a more complex stability criterion. From this point of view, S-, P-, and R-striations in noble gas discharges can be explained. Due to energy losses in elastic collisions, initial electron energy distribution functions converge to the resonance trajectories (the so-called “bunch effect”). The findings of the discrete model agree with results of kinetic theory and experiment. The new approach avoids difficulties of the kinetic theory in the case of exceptionally large relaxation lengths which can even exceed the positive column length.
Polyakov, Pavel D; Duval, Jérôme F L
2014-02-07
We report a comprehensive theory to evaluate the kinetics of complex formation between metal ions and charged spherical nanoparticles. The latter consist of an ion-impermeable core surrounded by a soft shell layer characterized by a discrete axisymmetric 2D distribution of charged sites that bind metal ions. The theory explicitly integrates the conductive diffusion of metal ions from bulk solution toward the respective locations of the reactive sites within the particle shell volume. The kinetic constant k for outer-sphere nanoparticle-metal association is obtained from the sum of the contributions stemming from all reactive sites, each evaluated from the corresponding incoming flux of metal ions derived from steady-state Poisson-Nernst-Planck equations. Illustrations are provided to capture the basic intertwined impacts of particle size, overall particle charge, spatial heterogeneity in site distribution, type of particle (hard, core-shell or porous) and concentration of the background electrolyte on k. As a limit, k converges with predictions from previously reported analytical expressions derived for porous particles with low and high charge density, cases that correspond to coulombic and mean-field (smeared-out) electrostatic treatments, respectively. The conditions underlying the applicability of these latter approaches are rigorously identified in terms of (i) the extent of overlap between electric double layers around charged neighbouring sites, and (ii) the magnitude of the intraparticulate metal concentration gradient. For the first time, the proposed theory integrates the differentiated impact of the local potential around the charged binding sites amidst the overall particle field, together with that of the so-far discarded intraparticulate flux of metal ions.
Jang, Sumin; Choubey, Sandeep; Furchtgott, Leon; Zou, Ling-Nan; Doyle, Adele; Menon, Vilas; Loew, Ethan B; Krostag, Anne-Rachel; Martinez, Refugio A; Madisen, Linda; Levi, Boaz P; Ramanathan, Sharad
2017-03-15
The complexity of gene regulatory networks that lead multipotent cells to acquire different cell fates makes a quantitative understanding of differentiation challenging. Using a statistical framework to analyze single-cell transcriptomics data, we infer the gene expression dynamics of early mouse embryonic stem (mES) cell differentiation, uncovering discrete transitions across nine cell states. We validate the predicted transitions across discrete states using flow cytometry. Moreover, using live-cell microscopy, we show that individual cells undergo abrupt transitions from a naïve to primed pluripotent state. Using the inferred discrete cell states to build a probabilistic model for the underlying gene regulatory network, we further predict and experimentally verify that these states have unique response to perturbations, thus defining them functionally. Our study provides a framework to infer the dynamics of differentiation from single cell transcriptomics data and to build predictive models of the gene regulatory networks that drive the sequence of cell fate decisions during development.
Model of discrete dynamics of asset price relations based on the minimal arbitrage principle
NASA Astrophysics Data System (ADS)
Kostanjčar, Zvonko; Hengster-Movrić, Kristian; Jeren, Branko
2011-06-01
In this paper we present a deterministic and a probabilistic model of the dynamics of the price relations for a number of assets on the market. The formalism is based on the asset space introduced in a theory by Illinski. We derive, from an action functional for the system of price relations in that space, the corresponding difference equations, which constitute the deterministic description. Furthermore, we obtain the probability density function of the probabilistic model of market dynamics from the same action functional. The deterministic solution corresponds to a geometric sequence for the interest, whereas the derived probability density describes the probability of the next value of the price relations in dependence on their prior value. The formalism is completely developed for systems (markets) with two and three assets, but exactly the same approach is applicable to the systems consisting of an arbitrary number of assets.
Minimax terminal approach problem in two-level hierarchical nonlinear discrete-time dynamical system
Shorikov, A. F.
2015-11-30
We consider a discrete–time dynamical system consisting of three controllable objects. The motions of all objects are given by the corresponding vector nonlinear or linear discrete–time recurrent vector relations, and control system for its has two levels: basic (first or I level) that is dominating and subordinate level (second or II level) and both have different criterions of functioning and united a priori by determined informational and control connections defined in advance. For the dynamical system in question, we propose a mathematical formalization in the form of solving a multistep problem of two-level hierarchical minimax program control over the terminal approach process with incomplete information and give a general scheme for its solving.
Dynamic behavior of discrete-time multiagent systems with general communication structures
NASA Astrophysics Data System (ADS)
Xiao, Feng; Wang, Long
2006-10-01
In this paper, we discuss the dynamic behavior of networks of dynamic agents with general communication topologies. We first analyze the basic case: systems with communication topologies that have spanning trees, i.e., the systems that solve consensus problems. We establish an algebraic condition to characterize each agent's contributions to the final state. And we also study the influence of time-delays on each agent's contributions. Then, we investigate the general case: systems with weakly connected topologies. By using matrix theory, we prove that the states of internal agents will converge to a convex combination of boundary agents in the absence or presence of communication time-delays, and we also show that the coefficients of the convex combination are independent of time-delays even if the delays are time-varying. These results have broad applications in other areas, e.g., study of swarm behavior, formation control of vehicles, etc.
Discrete Dislocation Dynamics Simulations of Twin Size-Effects in Magnesium
2015-01-01
dynamics simulations to study the mechanical behavior of micro-twinned Mg. Strong strain hardening was captured by current simulations, which is...significant grain refinement and strong hardening . In addition, Knezevic et al. [3] showed that compression twins in the tension-twinned grains attribute to...the hardening behavior. Moreover, Barnett et al. [4] observed the formation of low angle boundaries arising from the dislocation-TB interaction, which
Dynamically Coupled Food-web and Hydrodynamic Modeling with ADH-CASM
NASA Astrophysics Data System (ADS)
Piercy, C.; Swannack, T. M.
2012-12-01
Oysters and freshwater mussels are "ecological engineers," modifying the local water quality by filtering zooplankton and other suspended particulate matter from the water column and flow hydraulics by impinging on the near-bed flow environment. The success of sessile, benthic invertebrates such as oysters depends on environmental factors including but not limited to temperature, salinity, and flow regime. Typically food-web and other types of ecological models use flow and water quality data as direct input without regard to the feedback between the ecosystem and the physical environment. The USACE-ERDC has developed a coupled hydrodynamic-ecological modeling approach that dynamically couples a 2-D hydrodynamic and constituent transport model, Adaptive Hydraulics (ADH), with a bioenergetics food-web model, the Comprehensive Aquatics Systems Model (CASM), which captures the dynamic feedback between aquatic ecological systems and the environment. We present modeling results from restored oyster reefs in the Great Wicomico River on the western shore of the Chesapeake Bay, which quantify ecosystem services such as the influence of the benthic ecosystem on water quality. Preliminary results indicate that while the influence of oyster reefs on bulk flow dynamics is limited due to the localized influence of oyster reefs, large reefs and the associated benthic ecosystem can create measurable changes in the concentrations of nitrogen, phosphorus, and carbon in the areas around reefs. We also present a sensitivity analysis to quantify the relative sensitivity of the coupled ADH-CASM model to both hydrodynamic and ecological parameter choice.
Web-based experiments for the study of collective social dynamics in cultural markets
Salganik, Matthew J.; Watts, Duncan J.
2013-01-01
Social scientists are often interested in understanding how the dynamics of social systems are driven by the behavior of individuals that make up those systems. However, this process is hindered by the difficulty of experimentally studying how individual behavioral tendencies lead to collective social dynamics in large groups of people interacting over time. In this paper we investigate the role of social influence, a process well studied at the individual level, on the puzzling nature of success for cultural products such as books, movies, and music. Using a “multiple-worlds” experimental design we are able to isolate the causal effect of an individual level mechanism on collective social outcomes. We employ this design in a web-based experiment in which 2,930 participants listened to, rated, and download 48 songs by up-and-coming bands. Surprisingly, despite relatively large differences in the demographics, behavior, and preferences of participants, the experimental results at both the individual and collective level were similar to those found in Salganik, Dodds, and Watts (2006). Further, by comparing results from two distinct pools of participants we are able to gain new insights into the role of individual behavior on collective outcomes. We conclude with a discussion of the strengths and weaknesses of web-based experiments to address questions of collective social dynamics. PMID:25164996
Web-based experiments for the study of collective social dynamics in cultural markets.
Salganik, Matthew J; Watts, Duncan J
2009-07-01
Social scientists are often interested in understanding how the dynamics of social systems are driven by the behavior of individuals that make up those systems. However, this process is hindered by the difficulty of experimentally studying how individual behavioral tendencies lead to collective social dynamics in large groups of people interacting over time. In this study, we investigate the role of social influence, a process well studied at the individual level, on the puzzling nature of success for cultural products such as books, movies, and music. Using a "multiple-worlds" experimental design, we are able to isolate the causal effect of an individual-level mechanism on collective social outcomes. We employ this design in a Web-based experiment in which 2,930 participants listened to, rated, and downloaded 48 songs by up-and-coming bands. Surprisingly, despite relatively large differences in the demographics, behavior, and preferences of participants, the experimental results at both the individual and collective levels were similar to those found in Salganik, Dodds, and Watts (2006). Further, by comparing results from two distinct pools of participants, we are able to gain new insights into the role of individual behavior on collective outcomes. We conclude with a discussion of the strengths and weaknesses of Web-based experiments to address questions of collective social dynamics.
Development of a laboratory niche Web site.
Dimenstein, Izak B; Dimenstein, Simon I
2013-10-01
This technical note presents the development of a methodological laboratory niche Web site. The "Grossing Technology in Surgical Pathology" (www.grossing-technology.com) Web site is used as an example. Although common steps in creation of most Web sites are followed, there are particular requirements for structuring the template's menu on methodological laboratory Web sites. The "nested doll principle," in which one object is placed inside another, most adequately describes the methodological approach to laboratory Web site design. Fragmentation in presenting the Web site's material highlights the discrete parts of the laboratory procedure. An optimally minimal triad of components can be recommended for the creation of a laboratory niche Web site: a main set of media, a blog, and an ancillary component (host, contact, and links). The inclusion of a blog makes the Web site a dynamic forum for professional communication. By forming links and portals, cloud computing opens opportunities for connecting a niche Web site with other Web sites and professional organizations. As an additional source of information exchange, methodological laboratory niche Web sites are destined to parallel both traditional and new forms, such as books, journals, seminars, webinars, and internal educational materials.
Jones, Reese E.; Zimmerman, Jonathan A.; Po, Giacomo; ...
2016-02-01
Accurate simulation of the plastic deformation of ductile metals is important to the design of structures and components to performance and failure criteria. Many techniques exist that address the length scales relevant to deformation processes, including dislocation dynamics (DD), which models the interaction and evolution of discrete dislocation line segments, and crystal plasticity (CP), which incorporates the crystalline nature and restricted motion of dislocations into a higher scale continuous field framework. While these two methods are conceptually related, there have been only nominal efforts focused at the global material response that use DD-generated information to enhance the fidelity of CPmore » models. To ascertain to what degree the predictions of CP are consistent with those of DD, we compare their global and microstructural response in a number of deformation modes. After using nominally homogeneous compression and shear deformation dislocation dynamics simulations to calibrate crystal plasticity ow rule parameters, we compare not only the system-level stress-strain response of prismatic wires in torsion but also the resulting geometrically necessary dislocation density fields. To establish a connection between explicit description of dislocations and the continuum assumed with crystal plasticity simulations we ascertain the minimum length-scale at which meaningful dislocation density fields appear. Furthermore, our results show that, for the case of torsion, that the two material models can produce comparable spatial dislocation density distributions.« less
Jones, Reese E.; Zimmerman, Jonathan A.; Po, Giacomo; Mandadapu, Kranthi
2016-02-01
Accurate simulation of the plastic deformation of ductile metals is important to the design of structures and components to performance and failure criteria. Many techniques exist that address the length scales relevant to deformation processes, including dislocation dynamics (DD), which models the interaction and evolution of discrete dislocation line segments, and crystal plasticity (CP), which incorporates the crystalline nature and restricted motion of dislocations into a higher scale continuous field framework. While these two methods are conceptually related, there have been only nominal efforts focused at the global material response that use DD-generated information to enhance the fidelity of CP models. To ascertain to what degree the predictions of CP are consistent with those of DD, we compare their global and microstructural response in a number of deformation modes. After using nominally homogeneous compression and shear deformation dislocation dynamics simulations to calibrate crystal plasticity ow rule parameters, we compare not only the system-level stress-strain response of prismatic wires in torsion but also the resulting geometrically necessary dislocation density fields. To establish a connection between explicit description of dislocations and the continuum assumed with crystal plasticity simulations we ascertain the minimum length-scale at which meaningful dislocation density fields appear. Furthermore, our results show that, for the case of torsion, that the two material models can produce comparable spatial dislocation density distributions.
DLSanalysis.org: a web interface for analysis of dynamic light scattering data.
Hansen, Steen
2017-06-21
A web interface ( www.DLSanalysis.org ) for indirect Laplace transformation of dynamic light scattering data is presented. When experimental data are uploaded to the server they are processed in a few seconds, and the result is displayed on the screen in the form of a size distribution together with the experimental data and the fit to the data. No other user input than the experimental data is necessary, but various options for the analysis may be selected. No local installation of software or registration is necessary. The result of the analysis can be downloaded.
ERIC Educational Resources Information Center
Wang, Tzu-Hua
2010-01-01
This research combines the idea of cake format dynamic assessment defined by Sternberg and Grigorenko (2001) and the "graduated prompt approach" proposed by (Campione and Brown, 1985) and (Campione and Brown, 1987) to develop a multiple-choice Web-based dynamic assessment system. This research adopts a quasi-experimental design to…
Dynamics of two discrete vortices with different circulations composed of pure electron plasmas
Soga, Yukihiro; Mihara, Yasuhiro; Park, Youngsoo
2015-06-29
Two-dimensional dynamics of two vortex strings with different circulations were experimentally observed. The strings were composed of pure electron plasmas and were confined in a Malmberg–Penning trap. When one of the two vortices trapped in a conventional potential well had weak circulation, the orbits of the two vortices contradicted the point vortex theory. This disagreement stems from an unavoidable external electric field that exerts a different additional E × B drift velocity on each vortex. We resolved the discrepancy between observation and theory by applying a stepwise potential to the end electrodes, which produced a less non-ideal electric field.
Transient dynamics and food-web complexity in the Lotka-Volterra cascade model.
Chen, X.; Cohen, J. E.
2001-01-01
How does the long-term behaviour near equilibrium of model food webs correlate with their short-term transient dynamics? Here, simulations of the Lotka -Volterra cascade model of food webs provide the first evidence to answer this question. Transient behaviour is measured by resilience, reactivity, the maximum amplification of a perturbation and the time at which the maximum amplification occurs. Model food webs with a higher probability of local asymptotic stability may be less resilient and may have a larger transient growth of perturbations. Given a fixed connectance, the sizes and durations of transient responses to perturbations increase with the number of species. Given a fixed number of species, as connectance increases, the sizes and durations of transient responses to perturbations may increase or decrease depending on the type of link that is varied. Reactivity is more sensitive to changes in the number of donor-controlled links than to changes in the number of recipient-controlled links, while resilience is more sensitive to changes in the number of recipient-controlled links than to changes in the number of donor-controlled links. Transient behaviour is likely to be one of the important factors affecting the persistence of ecological communities. PMID:11345334
PCB Food Web Dynamics Quantify Nutrient and Energy Flow in Aquatic Ecosystems.
McLeod, Anne M; Paterson, Gordon; Drouillard, Ken G; Haffner, G Douglas
2015-11-03
Measuring in situ nutrient and energy flows in spatially and temporally complex aquatic ecosystems represents a major ecological challenge. Food web structure, energy and nutrient budgets are difficult to measure, and it is becoming more important to quantify both energy and nutrient flow to determine how food web processes and structure are being modified by multiple stressors. We propose that polychlorinated biphenyl (PCB) congeners represent an ideal tracer to quantify in situ energy and nutrient flow between trophic levels. Here, we demonstrate how an understanding of PCB congener bioaccumulation dynamics provides multiple direct measurements of energy and nutrient flow in aquatic food webs. To demonstrate this novel approach, we quantified nitrogen (N), phosphorus (P) and caloric turnover rates for Lake Huron lake trout, and reveal how these processes are regulated by both growth rate and fish life history. Although minimal nutrient recycling was observed in young growing fish, slow growing, older lake trout (>5 yr) recycled an average of 482 Tonnes·yr(-1) of N, 45 Tonnes·yr(-1) of P and assimilated 22 TJ yr(-1) of energy. Compared to total P loading rates of 590 Tonnes·yr(-1), the recycling of primarily bioavailable nutrients by fish plays an important role regulating the nutrient states of oligotrophic lakes.
Alteration of island food-web dynamics following major disturbance by hurricanes.
Spiller, David A; Schoener, Thomas W
2007-01-01
Major abiotic disturbance can be an important factor influencing food-web dynamics, particularly in areas impacted by the recent increase in hurricane activity. We present a unique set of data on key food-web processes occurring on 10 small islands for three relatively calm years and then four subsequent years during which two hurricanes passed directly over the study site. Herbivory, as measured by leaf damage, was 3.2 times higher in the year after the first hurricane (2000) than in the previous year and was 1.7 times higher in the year after the second hurricane (2002) than in 2001. The effect of a top predator (the lizard, Anolis sagrei) on herbivory strengthened continuously after the first hurricane and overall was 2.4 times stronger during the disturbance period than before. Overall abundance of lizards was 30% lower during the disturbance period than before, and abundances of web spiders and hymenopteran parasitoids were 66% and 59% lower, respectively. We suggest that increased herbivory observed on all islands was caused, at least in part, by the overall reduction in predation by both lizards and arthropods, whereas magnification of the lizard effect on herbivory was caused by reduced compensatory predation by arthropods.
McDonough, J M
2009-06-01
Outline of the derivation and mathematical and physical interpretations are presented for a discrete dynamical system known as the "poor man's Navier-Stokes equation." Numerical studies demonstrate that velocity fields produced by this dynamical system are similar to those seen in laboratory experiments and in detailed simulations, and they lead to scaling for the turbulence kinetic energy spectrum in accord with Kolmogorov K41 theory.
Poblete, Simón; Wysocki, Adam; Gompper, Gerhard; Winkler, Roland G
2014-09-01
We investigate the hydrodynamic properties of a spherical colloid model, which is composed of a shell of point particles by hybrid mesoscale simulations, which combine molecular dynamics simulations for the sphere with the multiparticle collision dynamics approach for the fluid. Results are presented for the center-of-mass and angular velocity correlation functions. The simulation results are compared with theoretical results for a rigid colloid obtained as a solution of the Stokes equation with no-slip boundary conditions. Similarly, analytical results of a point-particle model are presented, which account for the finite size of the simulated system. The simulation results agree well with both approaches on appropriative time scales; specifically, the long-time correlations are quantitatively reproduced. Moreover, a procedure is proposed to obtain the infinite-system-size diffusion coefficient based on a combination of simulation results and analytical predictions. In addition, we present the velocity field in the vicinity of the colloid and demonstrate its close agreement with the theoretical prediction. Our studies show that a point-particle model of a sphere is very well suited to describe the hydrodynamic properties of spherical colloids, with a significantly reduced numerical effort.
Dynamics of a discrete chain of bi-stable elements: A biomimetic shock absorbing mechanism
NASA Astrophysics Data System (ADS)
Cohen, T.; Givli, S.
2014-03-01
A biomimetic shock absorbing mechanism, inspired by the bi-stable elongation behavior of the giant protein titin, is examined. A bi-stable element, composed of three mass particles with monotonous interaction forces, is suggested to facilitate an internal degree of freedom of finite mass which contributes significantly to dissipation upon unlocking of an internal link. An essential feature of the suggested element is that it undergoes reversible rapture and therefore retrieves its initial configuration once unloaded. The quasistatic and dynamic behaviors are investigated showing similarity to the common tri-linear bi-stable response, with two steady phases separated by a spinodal region. The dynamic behavior of a chain of elements is also examined, for several loading scenarios, showing that the suggested mechanism serves as an efficient shock absorber in a sub-critical dampening environment, as compared with a simple mass on spring system. Propagation of shock waves and refraction waves in an element chain is observed and the effect of natural imperfections is considered.
NASA Astrophysics Data System (ADS)
Dorostkar, Omid; Guyer, Robert A.; Johnson, Paul A.; Marone, Chris; Carmeliet, Jan
2017-05-01
The presence of fault gouge has considerable influence on slip properties of tectonic faults and the physics of earthquake rupture. The presence of fluids within faults also plays a significant role in faulting and earthquake processes. In this paper, we present 3-D discrete element simulations of dry and fluid-saturated granular fault gouge and analyze the effect of fluids on stick-slip behavior. Fluid flow is modeled using computational fluid dynamics based on the Navier-Stokes equations for an incompressible fluid and modified to take into account the presence of particles. Analysis of a long time train of slip events shows that the (1) drop in shear stress, (2) compaction of granular layer, and (3) the kinetic energy release during slip all increase in magnitude in the presence of an incompressible fluid, compared to dry conditions. We also observe that on average, the recurrence interval between slip events is longer for fluid-saturated granular fault gouge compared to the dry case. This observation is consistent with the occurrence of larger events in the presence of fluid. It is found that the increase in kinetic energy during slip events for saturated conditions can be attributed to the increased fluid flow during slip. Our observations emphasize the important role that fluid flow and fluid-particle interactions play in tectonic fault zones and show in particular how discrete element method (DEM) models can help understand the hydromechanical processes that dictate fault slip.
NASA Astrophysics Data System (ADS)
Yang, Hui; Li, Zhenhuan; Huang, Minsheng
2014-12-01
Unlike common single crystals, the nickel-based single crystal superalloy shows surprisingly anomalous flow strength (i.e. with the increase of temperature, the yield strength first increases to a peak value and then decreases) and tension-compression (TC) asymmetry. A comprehensive three-dimensional discrete dislocation dynamics (3D-DDD) procedure was developed to model these abnormal mechanical properties. For this purpose, a series of complicated dynamic evolution details of Kear-Wilsdorf (KW) locks, which are closely related to the flow strength anomaly and TC asymmetry, were incorporated into this 3D-DDD framework. Moreover, the activation of the cubic slip system, which is the origin of the decrease in yield strength with increasing temperature at relatively high temperatures, was especially taken into account by introducing a competition criterion between the unlocking of the KW locks and the activation of the cubic slip system. To test our framework, a series of 3D-DDD simulations were performed on a representative volume cell model with a cuboidal Ni3Al precipitate phase embedded in a nickel matrix. Results show that the present 3D-DDD procedure can successfully capture the dynamic evolution of KW locks, the flow strength anomaly and TC asymmetry. Then, the underlying dislocation mechanisms leading to these abnormal mechanical responses were investigated and discussed in detail. Finally, a cyclic deformation of the nickel-based single crystal superalloy was modeled by using the present DDD model, with a special focus on the influence of KW locks on the Bauschinger effect and cyclic softening.
Turing pattern dynamics and adaptive discretization for a super-diffusive Lotka-Volterra model.
Bendahmane, Mostafa; Ruiz-Baier, Ricardo; Tian, Canrong
2016-05-01
In this paper we analyze the effects of introducing the fractional-in-space operator into a Lotka-Volterra competitive model describing population super-diffusion. First, we study how cross super-diffusion influences the formation of spatial patterns: a linear stability analysis is carried out, showing that cross super-diffusion triggers Turing instabilities, whereas classical (self) super-diffusion does not. In addition we perform a weakly nonlinear analysis yielding a system of amplitude equations, whose study shows the stability of Turing steady states. A second goal of this contribution is to propose a fully adaptive multiresolution finite volume method that employs shifted Grünwald gradient approximations, and which is tailored for a larger class of systems involving fractional diffusion operators. The scheme is aimed at efficient dynamic mesh adaptation and substantial savings in computational burden. A numerical simulation of the model was performed near the instability boundaries, confirming the behavior predicted by our analysis.
Heckman, James J; Raut, Lakshmi K
2016-03-01
This paper formulates a structural dynamic programming model of preschool investment choices of altruistic parents and then empirically estimates the structural parameters of the model using the NLSY79 data. The paper finds that preschool investment significantly boosts cognitive and non-cognitive skills, which enhance earnings and school outcomes. It also finds that a standard Mincer earnings function, by omitting measures of non-cognitive skills on the right-hand side, overestimates the rate of return to schooling. From the estimated equilibrium Markov process, the paper studies the nature of within generation earnings distribution, intergenerational earnings mobility, and schooling mobility. The paper finds that a tax-financed free preschool program for the children of poor socioeconomic status generates positive net gains to the society in terms of average earnings, higher intergenerational earnings mobility, and schooling mobility.
Heckman, James J.; Raut, Lakshmi K.
2015-01-01
This paper formulates a structural dynamic programming model of preschool investment choices of altruistic parents and then empirically estimates the structural parameters of the model using the NLSY79 data. The paper finds that preschool investment significantly boosts cognitive and non-cognitive skills, which enhance earnings and school outcomes. It also finds that a standard Mincer earnings function, by omitting measures of non-cognitive skills on the right-hand side, overestimates the rate of return to schooling. From the estimated equilibrium Markov process, the paper studies the nature of within generation earnings distribution, intergenerational earnings mobility, and schooling mobility. The paper finds that a tax-financed free preschool program for the children of poor socioeconomic status generates positive net gains to the society in terms of average earnings, higher intergenerational earnings mobility, and schooling mobility. PMID:26709326
Parameter estimation for dynamical systems with discrete events and logical operations.
Fröhlich, Fabian; Theis, Fabian J; Rädler, Joachim O; Hasenauer, Jan
2017-04-01
Ordinary differential equation (ODE) models are frequently used to describe the dynamic behaviour of biochemical processes. Such ODE models are often extended by events to describe the effect of fast latent processes on the process dynamics. To exploit the predictive power of ODE models, their parameters have to be inferred from experimental data. For models without events, gradient based optimization schemes perform well for parameter estimation, when sensitivity equations are used for gradient computation. Yet, sensitivity equations for models with parameter- and state-dependent events and event-triggered observations are not supported by existing toolboxes. In this manuscript, we describe the sensitivity equations for differential equation models with events and demonstrate how to estimate parameters from event-resolved data using event-triggered observations in parameter estimation. We consider a model for GFP expression after transfection and a model for spiking neurons and demonstrate that we can improve computational efficiency and robustness of parameter estimation by using sensitivity equations for systems with events. Moreover, we demonstrate that, by using event-outputs, it is possible to consider event-resolved data, such as time-to-event data, for parameter estimation with ODE models. By providing a user-friendly, modular implementation in the toolbox AMICI, the developed methods are made publicly available and can be integrated in other systems biology toolboxes. We implement the methods in the open-source toolbox Advanced MATLAB Interface for CVODES and IDAS (AMICI, https://github.com/ICB-DCM/AMICI ). jan.hasenauer@helmholtz-muenchen.de. Supplementary data are available at Bioinformatics online.
Development of an internal dynamic web site to promote quality assurance in a clinical laboratory.
Pernet, Pascal; Mario, Nathalie; Vaubourdolle, Michel
2004-01-01
In clinical laboratories, one challenging quality assurance objective is to maintain standardized practices. Meeting this objective entails ensuring information flow, which is necessary to smooth running of the laboratory. To facilitate information flow, we developed an internal quality Web site on our local network. The dynamic generated pages of the site were constructed with EasyPHP v.1.6, a complete freeware package providing PHP dynamic language and databases. The site comprises various sections: general news, specific laboratory units news, documents (quality manual, guidelines, emergency processes), schedules, National Quality Control results, forum, etc. Five to 10 pages are updated each week. This work was facilitated by the use of PHP-written pages and data tables, which enable us to record in real time the operation of our assurance quality project and to improve traceability. This approach could be extended to other aspects of quality management and could help meet the future IS015189 standard requirements.
The effects of mixotrophy on the stability and dynamics of a simple planktonic food web model.
Jost, Christian; Lawrence, Cathryn A; Campolongo, Francesca; van de Bund, Wouter; Hill, Sheryl; DeAngelis, Don L
2004-08-01
Recognition of the microbial loop as an important part of aquatic ecosystems disrupted the notion of simple linear food chains. However, current research suggests that even the microbial loop paradigm is a gross simplification of microbial interactions due to the presence of mixotrophs-organisms that both photosynthesize and graze. We present a simple food web model with four trophic species, three of them arranged in a food chain (nutrients-autotrophs-herbivores) and the fourth as a mixotroph with links to both the nutrients and the autotrophs. This model is used to study the general implications of inclusion of the mixotrophic link in microbial food webs and the specific predictions for a parameterization that describes open ocean mixed layer plankton dynamics. The analysis indicates that the system parameters reside in a region of the parameter space where the dynamics converge to a stable equilibrium rather than displaying periodic or chaotic solutions. However, convergence requires weeks to months, suggesting that the system would never reach equilibrium in the ocean due to alteration of the physical forcing regime. Most importantly, the mixotrophic grazing link seems to stabilize the system in this region of the parameter space, particularly when nutrient recycling feedback loops are included.
The effects of mixotrophy on the stability and dynamics of a simple planktonic food web
Jost, Christian; Lawrence, Cathryn A.; Campolongo, Francesca; Wouter, van de Bund; Hill, Sheryl; DeAngelis, Donald L.
2004-01-01
Recognition of the microbial loop as an important part of aquatic ecosystems disrupted the notion of simple linear food chains. However, current research suggests that even the microbial loop paradigm is a gross simplification of microbial interactions due to the presence of mixotrophs—organisms that both photosynthesize and graze. We present a simple food web model with four trophic species, three of them arranged in a food chain (nutrients–autotrophs–herbivores) and the fourth as a mixotroph with links to both the nutrients and the autotrophs. This model is used to study the general implications of inclusion of the mixotrophic link in microbial food webs and the specific predictions for a parameterization that describes open ocean mixed layer plankton dynamics. The analysis indicates that the system parameters reside in a region of the parameter space where the dynamics converge to a stable equilibrium rather than displaying periodic or chaotic solutions. However, convergence requires weeks to months, suggesting that the system would never reach equilibrium in the ocean due to alteration of the physical forcing regime. Most importantly, the mixotrophic grazing link seems to stabilize the system in this region of the parameter space, particularly when nutrient recycling feedback loops are included.
Identification of continuous-time models for nonlinear dynamic systems from discrete data
NASA Astrophysics Data System (ADS)
Guo, Yuzhu; Guo, Ling Zhong; Billings, Stephen A.; Wei, Hua-Liang
2016-09-01
A new iOFR-MF (iterative orthogonal forward regression--modulating function) algorithm is proposed to identify continuous-time models from noisy data by combining the MF method and the iOFR algorithm. In the new method, a set of candidate terms, which describe different dynamic relationships among the system states or between the input and output, are first constructed. These terms are then modulated using the MF method to generate the data matrix. The iOFR algorithm is next applied to build the relationships between these modulated terms, which include detecting the model structure and estimating the associated parameters. The relationships between the original variables are finally recovered from the model of the modulated terms. Both nonlinear state-space models and a class of higher order nonlinear input-output models are considered. The new direct method is compared with the traditional finite difference method and results show that the new method performs much better than the finite difference method. The new method works well even when the measurements are severely corrupted by noise. The selection of appropriate MFs is also discussed.
NASA Astrophysics Data System (ADS)
Xie, Zheng; Ye, Zheng; Ma, Yu-Jie
2009-12-01
Numerical simulation of antennae is a topic in computational electromagnetism, which is concerned with the numerical study of Maxwell equations. By discrete exterior calculus and the lattice gauge theory with coefficient R, we obtain the Bianchi identity on prism lattice. By defining an inner product of discrete differential forms, we derive the source equation and continuity equation. Those equations compose the discrete Maxwell equations in vacuum case on discrete manifold, which are implemented on Java development platform to simulate the Gaussian pulse radiation on antennaes.
ADAM: analysis of discrete models of biological systems using computer algebra.
Hinkelmann, Franziska; Brandon, Madison; Guang, Bonny; McNeill, Rustin; Blekherman, Grigoriy; Veliz-Cuba, Alan; Laubenbacher, Reinhard
2011-07-20
Many biological systems are modeled qualitatively with discrete models, such as probabilistic Boolean networks, logical models, Petri nets, and agent-based models, to gain a better understanding of them. The computational complexity to analyze the complete dynamics of these models grows exponentially in the number of variables, which impedes working with complex models. There exist software tools to analyze discrete models, but they either lack the algorithmic functionality to analyze complex models deterministically or they are inaccessible to many users as they require understanding the underlying algorithm and implementation, do not have a graphical user interface, or are hard to install. Efficient analysis methods that are accessible to modelers and easy to use are needed. We propose a method for efficiently identifying attractors and introduce the web-based tool Analysis of Dynamic Algebraic Models (ADAM), which provides this and other analysis methods for discrete models. ADAM converts several discrete model types automatically into polynomial dynamical systems and analyzes their dynamics using tools from computer algebra. Specifically, we propose a method to identify attractors of a discrete model that is equivalent to solving a system of polynomial equations, a long-studied problem in computer algebra. Based on extensive experimentation with both discrete models arising in systems biology and randomly generated networks, we found that the algebraic algorithms presented in this manuscript are fast for systems with the structure maintained by most biological systems, namely sparseness and robustness. For a large set of published complex discrete models, ADAM identified the attractors in less than one second. Discrete modeling techniques are a useful tool for analyzing complex biological systems and there is a need in the biological community for accessible efficient analysis tools. ADAM provides analysis methods based on mathematical algorithms as a web
NASA Astrophysics Data System (ADS)
Smolarkiewicz, Piotr K.; Kühnlein, Christian; Wedi, Nils P.
2014-04-01
A numerical framework is developed for consistent integrations of the soundproof and fully compressible nonhydrostatic equations of motion for all-scale atmospheric flows; i.e., low Mach number, high Reynolds number, rotating stratified flows under gravity. The reduced anelastic and pseudo-incompressible soundproof equations and the fully compressible Euler equations are combined into a common form of conservation laws for mass, momentum and entropy that facilitates the design of a sole principal algorithm for its integration, with minimal alterations for accommodating each special case. The development extends a proven numerical framework for integrating the soundproof equations. It relies on non-oscillatory forward-in-time transport methods, applied consistently to all dependent variables of the system at hand, and with buoyant and rotational modes of motion treated implicitly in the integration. When the fully compressible equations are solved, the framework admits congruent schemes with explicit or implicit representation of acoustic modes, so the former can provide a reference for the latter. The consistency of the framework minimises the numerical differences between the soundproof and compressible integrators, thus admitting conclusive comparisons between compressible and soundproof solutions, unobscured by algorithmic disparities. For the large-time-step implicit schemes, technical differences between the soundproof and compressible integrators reduce to the selection of either a prescribed or a numerically prognosed density, and extension of the generalised Poisson solver to a bespoke Helmholtz solver. The numerical advancements and merits of the approach are illustrated with canonical simulations of planetary baroclinic instability, an archetype of global weather, and the breaking of a deep stratospheric gravity waves, an example of nonhydrostatic mesoscale dynamics.
NASA Astrophysics Data System (ADS)
Gao, Siwen; Fivel, Marc; Ma, Anxin; Hartmaier, Alexander
2015-03-01
In the characteristic γ / γ ‧ microstructure of single crystal superalloys, misfit stresses occur due to a significant lattice mismatch of those two phases. The magnitude of this lattice mismatch depends on the chemical composition of both phases as well as on temperature. Furthermore, the lattice mismatch of γ and γ ‧ phases can be either positive or negative in sign. The internal stresses caused by such lattice mismatch play a decisive role for the micromechanical processes that lead to the observed macroscopic athermal deformation behavior of these high-temperature alloys. Three-dimensional discrete dislocation dynamics (DDD) simulations are applied to investigate dislocation glide in γ matrix channels and shearing of γ ‧ precipitates by superdislocations under externally applied uniaxial stresses, by fully taking into account internal misfit stresses. Misfit stress fields are calculated by the fast Fourier transformation (FFT) method and hybridized with DDD simulations. For external loading along the crystallographic [001] direction of the single crystal, it was found that the different internal stress states for negative and positive lattice mismatch result in non-uniform dislocation movement and different dislocation patterns in horizontal and vertical γ matrix channels. Furthermore, positive lattice mismatch produces a lower deformation rate than negative lattice mismatch under the same tensile loading, but for an increasing magnitude of lattice mismatch, the deformation resistance always diminishes. Hence, the best deformation performance is expected to result from alloys with either small positive, or even better, vanishing lattice mismatch between γ and γ ‧ phase.
Longstaff, M G; Mahant, P R; Stacy, M A; Van Gemmert, A W A; Leis, B C; Stelmach, G E
2003-03-01
To systematically investigate the ability of Parkinson's disease patients to discretely and dynamically scale the size of continuous movements and to assess the impact of movement size on outcome variability. Ten patients with Parkinson's disease (mean age 72 years) were compared with 12 healthy elderly controls (mean age 70 years). The subjects wrote with a stylus on a graphics tablet. In experiment 1 they drew circles, matching the size of five target circles ranging in magnitude from a radius of 0.5 cm up to 2.5 cm. In experiment 2 they drew spirals with a radius of at least 2 cm. In both experiments the drawings were initially performed as accurately as possible then as fast and accurately as possible. In both experiments the patients and controls drew at a similar speed. The within trial variability of the pen trajectory was greater for patients than controls, and increased disproportionately with the size of the movement. When the emphasis was on size rather than variability (circles), the patients' drawing movements were the same size as controls. When the emphasis was on accuracy of pen trajectory (that is, minimum variability) rather than size (spirals), the patients' drawing movements were smaller than controls. The movements made by Parkinson's disease patients are hypometric partly as an adaptive strategy used to reduce movement variability. This strategy is used primarily when the requirement to make accurate movements outweighs the need to make large movements.
Longstaff, M; Mahant, P; Stacy, M; Van Gemmert, A W A; Leis, B; Stelmach, G
2003-01-01
Objectives: To systematically investigate the ability of Parkinson's disease patients to discretely and dynamically scale the size of continuous movements and to assess the impact of movement size on outcome variability. Methods: Ten patients with Parkinson's disease (mean age 72 years) were compared with 12 healthy elderly controls (mean age 70 years). The subjects wrote with a stylus on a graphics tablet. In experiment 1 they drew circles, matching the size of five target circles ranging in magnitude from a radius of 0.5 cm up to 2.5 cm. In experiment 2 they drew spirals with a radius of at least 2 cm. In both experiments the drawings were initially performed as accurately as possible then as fast and accurately as possible. Results: In both experiments the patients and controls drew at a similar speed. The within trial variability of the pen trajectory was greater for patients than controls, and increased disproportionately with the size of the movement. When the emphasis was on size rather than variability (circles), the patients' drawing movements were the same size as controls. When the emphasis was on accuracy of pen trajectory (that is, minimum variability) rather than size (spirals), the patients' drawing movements were smaller than controls. Conclusions: The movements made by Parkinson's disease patients are hypometric partly as an adaptive strategy used to reduce movement variability. This strategy is used primarily when the requirement to make accurate movements outweighs the need to make large movements. PMID:12588912
Fan, Haidong; Aubry, Sylvie; Arsenlis, Athanasios; El-Awady, Jaafar A.
2015-04-13
The mechanical response of micro-twinned polycrystalline magnesium was studied through three-dimensional discrete dislocation dynamics (DDD). A systematic interaction model between dislocations and (1012) tension twin boundaries (TBs) was proposed and introduced into the DDD framework. In addition, a nominal grain boundary (GB) model agreeing with experimental results was also introduced to mimic the GB’s barrier effect. The current simulation results show that TBs act as a strong obstacle to gliding dislocations, which contributes significantly to the hardening behavior of magnesium. On the other hand, the deformation accommodated by twinning plays a softening role. Therefore, the concave shape of the Mg stress-strain curve results from the competition between dislocation-TB induced hardening and twinning deformation induced softening. At low strain levels, twinning deformation induced softening dominates and a decreasing hardening rate is observed in Stage-I. In Stage-II, both the hardening and softening effects decline, but twinning deformation induced softening declines faster, which leads to an increasing hardening rate.
Inertia-Controlled Twinning in Ni-Mn-Ga Actuators: A Discrete Twin-Boundary Dynamics Study
NASA Astrophysics Data System (ADS)
Faran, Eilon; Riccardi, Leonardo; Shilo, Doron
2017-07-01
A discrete twin-boundary modeling approach is applied for simulating the dynamic magnetomechanical response of a Ni-Mn-Ga actuator over a wide frequency range. The model is based on experimentally measured kinetic relation of individual twin boundaries and takes into account inertial forces due to acceleration of the actuator's mass. The calculated results show good agreement with experimental measurements performed on a specially designed Ni-Mn-Ga linear spring-mass actuator. In addition, the simulation reveals several new effects that have not been considered before and can be applied to the design of improved actuators. It is identified that the demagnetization effect plays a role of an "effective spring" and results in a resonance-type response. The effects of the actuator's mass and the twin-boundary density on the resonance response and the actuator performance are explored numerically. In particular, it is shown that mass-inertia poses an inherent upper limit over the actuator's bandwidth, which is approximately constant and equals to about 200 Hz.
Fan, Haidong; Aubry, Sylvie; Arsenlis, Athanasios; ...
2015-04-13
The mechanical response of micro-twinned polycrystalline magnesium was studied through three-dimensional discrete dislocation dynamics (DDD). A systematic interaction model between dislocations and (1012) tension twin boundaries (TBs) was proposed and introduced into the DDD framework. In addition, a nominal grain boundary (GB) model agreeing with experimental results was also introduced to mimic the GB’s barrier effect. The current simulation results show that TBs act as a strong obstacle to gliding dislocations, which contributes significantly to the hardening behavior of magnesium. On the other hand, the deformation accommodated by twinning plays a softening role. Therefore, the concave shape of the Mgmore » stress-strain curve results from the competition between dislocation-TB induced hardening and twinning deformation induced softening. At low strain levels, twinning deformation induced softening dominates and a decreasing hardening rate is observed in Stage-I. In Stage-II, both the hardening and softening effects decline, but twinning deformation induced softening declines faster, which leads to an increasing hardening rate.« less
Synchronous Discrete Harmonic Oscillator
Antippa, Adel F.; Dubois, Daniel M.
2008-10-17
We introduce the synchronous discrete harmonic oscillator, and present an analytical, numerical and graphical study of its characteristics. The oscillator is synchronous when the time T for one revolution covering an angle of 2{pi} in phase space, is an integral multiple N of the discrete time step {delta}t. It is fully synchronous when N is even. It is pseudo-synchronous when T/{delta}t is rational. In the energy conserving hyperincursive representation, the phase space trajectories are perfectly stable at all time scales, and in both synchronous and pseudo-synchronous modes they cycle through a finite number of phase space points. Consequently, both the synchronous and the pseudo-synchronous hyperincursive modes of time-discretization provide a physically realistic and mathematically coherent, procedure for dynamic, background independent, discretization of spacetime. The procedure is applicable to any stable periodic dynamical system, and provokes an intrinsic correlation between space and time, whereby space-discretization is a direct consequence of background-independent time-discretization. Hence, synchronous discretization moves the formalism of classical mechanics towards that of special relativity. The frequency of the hyperincursive discrete harmonic oscillator is ''blue shifted'' relative to its continuum counterpart. The frequency shift has the precise value needed to make the speed of the system point in phase space independent of the discretizing time interval {delta}t. That is the speed of the system point is the same on the polygonal (in the discrete case) and the circular (in the continuum case) phase space trajectories.
NASA Astrophysics Data System (ADS)
Sengupta, Sayantan; Guha, Abhijit
2017-09-01
This paper presents a systematic computational study of the flow in a shrouded rotor cavity (with depth of the order of 100 μm) with multiple discrete inflows revealing the physics of how an initially non-axisymmetric flow evolves, both in the Lagrangian and Eulerian frameworks, towards axisymmetry. The approach to axisymmetry happens faster for the tangential velocity as compared to the radial component. The non-uniform inlet condition for the radial and tangential velocities, consisting of high velocity at the inlet openings and zero velocity on the shroud wall in between two consecutive inlets, gives rise to an oscillatory variation in the velocity of a fluid particle, with progressively decreasing amplitude, if one tracks its motion along a surface streamline. The rate of decay of the amplitude increases, i.e., equivalently the approach to the axisymmetric condition happens at a greater radial location, as the number of inlets, Ninlet, is increased. When the rotational speed of the discs, Ω, is increased, the distribution of radial velocity (Ur) is significantly altered, which may result even in a change of the fundamental shape of its z-profile, changing from parabolic to flat to W-shaped. The fluid has to negotiate with two different non-uniformities within a short radial distance (Δrc): one in the θ-direction because of the presence of discrete inlets and the other in the z-direction due to the no-slip condition on the disc surface. An increase in Δrc from zero to a finite value assists in the attainment of the axisymmetric condition for both tangential and radial velocities, i.e., the axisymmetry is obtained at a larger radial location. The subtle and complex fluid dynamics of the approach to axisymmetry is comprehensively analysed by following the progressive development of the z-profiles of Ur along a surface streamline located on the middle-plane of the inter-disc-spacing for an eight-inlet flow-configuration. Two sets of velocity profiles are
Microbial food web dynamics along a soil chronosequence of a glacier forefield
NASA Astrophysics Data System (ADS)
Esperschütz, J.; Pérez-de-Mora, A.; Schreiner, K.; Welzl, G.; Buegger, F.; Zeyer, J.; Hagedorn, F.; Munch, J. C.; Schloter, M.
2011-11-01
Microbial food webs are critical for efficient nutrient turnover providing the basis for functional and stable ecosystems. However, the successional development of such microbial food webs and their role in "young" ecosystems is unclear. Due to a continuous glacier retreat since the middle of the 19th century, glacier forefields have expanded offering an excellent opportunity to study food web dynamics in soils at different developmental stages. In the present study, litter degradation and the corresponding C fluxes into microbial communities were investigated along the forefield of the Damma glacier (Switzerland). 13C-enriched litter of the pioneering plant Leucanthemopsis alpina (L.) Heywood was incorporated into the soil at sites that have been free from ice for approximately 10, 60, 100 and more than 700 years. The structure and function of microbial communities were identified by 13C analysis of phospholipid fatty acids (PLFA) and phospholipid ether lipids (PLEL). Results showed increasing microbial diversity and biomass, and enhanced proliferation of bacterial groups as ecosystem development progressed. Initially, litter decomposition proceeded faster at the more developed sites, but at the end of the experiment loss of litter mass was similar at all sites, once the more easily-degradable litter fraction was processed. As a result incorporation of 13C into microbial biomass was more evident during the first weeks of litter decomposition. 13C enrichments of both PLEL and PLFA biomarkers following litter incorporation were observed at all sites, suggesting similar microbial foodwebs at all stages of soil development. Nonetheless, the contribution of bacteria, especially actinomycetes to litter turnover became more pronounced as soil age increased in detriment of archaea, fungi and protozoa, more prominent in recently deglaciated terrain.
The Impact of 850,000 Years of Climate Changes on the Structure and Dynamics of Mammal Food Webs
Nenzén, Hedvig K.; Montoya, Daniel; Varela, Sara
2014-01-01
Most evidence of climate change impacts on food webs comes from modern studies and little is known about how ancient food webs have responded to climate changes in the past. Here, we integrate fossil evidence from 71 fossil sites, body-size relationships and actualism to reconstruct food webs for six large mammal communities that inhabited the Iberian Peninsula at different times during the Quaternary. We quantify the long-term dynamics of these food webs and study how their structure changed across the Quaternary, a period for which fossil data and climate changes are well known. Extinction, immigration and turnover rates were correlated with climate changes in the last 850 kyr. Yet, we find differences in the dynamics and structural properties of Pleistocene versus Holocene mammal communities that are not associated with glacial-interglacial cycles. Although all Quaternary mammal food webs were highly nested and robust to secondary extinctions, general food web properties changed in the Holocene. These results highlight the ability of communities to re-organize with the arrival of phylogenetically similar species without major structural changes, and the impact of climate change and super-generalist species (humans) on Iberian Holocene mammal communities. PMID:25207754
The impact of 850,000 years of climate changes on the structure and dynamics of mammal food webs.
Nenzén, Hedvig K; Montoya, Daniel; Varela, Sara
2014-01-01
Most evidence of climate change impacts on food webs comes from modern studies and little is known about how ancient food webs have responded to climate changes in the past. Here, we integrate fossil evidence from 71 fossil sites, body-size relationships and actualism to reconstruct food webs for six large mammal communities that inhabited the Iberian Peninsula at different times during the Quaternary. We quantify the long-term dynamics of these food webs and study how their structure changed across the Quaternary, a period for which fossil data and climate changes are well known. Extinction, immigration and turnover rates were correlated with climate changes in the last 850 kyr. Yet, we find differences in the dynamics and structural properties of Pleistocene versus Holocene mammal communities that are not associated with glacial-interglacial cycles. Although all Quaternary mammal food webs were highly nested and robust to secondary extinctions, general food web properties changed in the Holocene. These results highlight the ability of communities to re-organize with the arrival of phylogenetically similar species without major structural changes, and the impact of climate change and super-generalist species (humans) on Iberian Holocene mammal communities.
Bioaccumulation Dynamics of Arsenate at the Base of Aquatic Food Webs.
Lopez, Adeline R; Hesterberg, Dean R; Funk, David H; Buchwalter, David B
2016-06-21
Periphyton is an important food source at the base of freshwater ecosystems that tends to bioconcentrate trace elements making them trophically available. The potential for arsenic-a trace element of particular concern due to its widespread occurrence, toxicity, and carcinogenicity-to bioconcentrate in periphyton and thus be available to benthic grazers is less well characterized. To better understand arsenate bioaccumulation dynamics in lotic food webs, we used a radiotracer approach to characterize accumulation in periphyton and subsequent trophic transfer to benthic grazers. Periphyton bioconcentrated As between 3,200-9,700-fold (dry weight) over 8 days without reaching steady state, suggesting that periphyton is a major sink for arsenate. However, As-enriched periphyton as a food source for the mayfly Neocloeon triangulifer resulted in negligible As accumulation in a full lifecycle exposure. Additional studies estimate dietary assimilation efficiency in several primary consumers ranging from 22% in the mayfly N. triangulifer to 75% in the mayfly Isonychia sp. X-ray fluorescence mapping revealed that As was predominantly associated with iron oxides in periphyton. We speculate that As adsorption to Fe in periphyton may play a role in reducing dietary bioavailability. Together, these results suggest that trophic movement of As in lotic food webs is relatively low, though species differences in bioaccumulation patterns are important.
Ims, Rolf A; Henden, John-André; Thingnes, Anders V; Killengreen, Siw T
2013-01-01
Production cycles in birds are proposed as prime cases of indirect interactions in food webs. They are thought to be driven by predators switching from rodents to bird nests in the crash phase of rodent population cycles. Although rodent cycles are geographically widespread and found in different rodent taxa, bird production cycles appear to be most profound in the high Arctic where lemmings dominate. We hypothesized that this may be due to arctic lemmings inducing stronger predator responses than boreal voles. We tested this hypothesis by estimating predation rates in dummy bird nests during a rodent cycle in low-Arctic tundra. Here, the rodent community consists of a spatially variable mix of one lemming (Lemmus lemmus) and two vole species (Myodes rufocanus and Microtus oeconomus) with similar abundances. In consistence with our hypothesis, lemming peak abundances predicted well crash-phase nest predation rates, whereas the vole abundances had no predictive ability. Corvids were found to be the most important nest predators. Lemmings appear to be accessible to the whole predator community which makes them particularly powerful drivers of food web dynamics.
The Focal Adhesion Analysis Server: a web tool for analyzing focal adhesion dynamics.
Berginski, Matthew E; Gomez, Shawn M
2013-01-01
The Focal Adhesion Analysis Server (FAAS) is a web-based implementation of a set of computer vision algorithms designed to quantify the behavior of focal adhesions in cells imaged in 2D cultures. The input consists of one or more images of a labeled focal adhesion protein. The outputs of the system include a range of static and dynamic measurements for the adhesions present in each image as well as how these properties change over time. The user is able to adjust several parameters important for proper focal adhesion identification. This system provides a straightforward tool for the global, unbiased assessment of focal adhesion behavior common in optical microscopy studies. The webserver is available at: http://faas.bme.unc.edu/.
Nfon, Erick; Armitage, James M; Cousins, Ian T
2011-11-15
A dynamic combined fate and food web model was developed to estimate the food web transfer of chemicals in small aquatic ecosystems (i.e. ponds). A novel feature of the modeling approach is that aquatic macrophytes (submerged aquatic vegetation) were included in the fate model and were also a food item in the food web model. The paper aims to investigate whether macrophytes are effective at mitigating chemical exposure and to compare the modeling approach developed here with previous modeling approaches recommended in the European Union (EU) guideline for risk assessment of pesticides. The model was used to estimate bioaccumulation of three hypothetical chemicals of varying hydrophobicity in a pond food web comprising 11 species. Three different macrophyte biomass densities were simulated in the model experiments to determine the influence of macrophytes on fate and bioaccumulation. Macrophytes were shown to have a significant effect on the fate and food web transfer of highly hydrophobic compounds with log KOW>=5. Modeled peak concentrations in biota were highest for the scenarios with the lowest macrophyte biomass density. The distribution and food web transfer of the hypothetical compound with the lowest hydrophobicity (log KOW=3) was not affected by the inclusion of aquatic macrophytes in the pond environment. For the three different hypothetical chemicals and at all macrophyte biomass densities, the maximum predicted concentrations in the top predator in the food web model were at least one order of magnitude lower than the values estimated using methods suggested in EU guidelines. The EU guideline thus provides a highly conservative estimate of risk. In our opinion, and subject to further model evaluation, a realistic assessment of dynamic food web transfer and risk can be obtained using the model presented here.
Sime-Ngando, Télesphore
2012-01-01
Parasitism is one of the earlier and common ecological interactions in the nature, occurring in almost all environments. Microbial parasites typically are characterized by their small size, short generation time, and high rates of reproduction, with simple life cycle occurring generally within a single host. They are diverse and ubiquitous in aquatic ecosystems, comprising viruses, prokaryotes, and eukaryotes. Recently, environmental 18S rDNA surveys of microbial eukaryotes have unveiled major infecting agents in pelagic systems, consisting primarily of the fungal order of Chytridiales (chytrids). Chytrids are considered the earlier branch of the Eumycetes and produce motile, flagellated zoospores, characterized by a small size (2–6 μm), and a single, posterior flagellum. The existence of these dispersal propagules includes chytrids within the so-called group of zoosporic fungi, which are particularly adapted to the plankton lifestyle where they infect a wide variety of hosts, including fishes, eggs, zooplankton, algae, and other aquatic fungi but primarily freshwater phytoplankton. Related ecological implications are huge because chytrids can killed their hosts, release substrates for microbial processes, and provide nutrient-rich particles as zoospores and short fragments of filamentous inedible hosts for the grazer food chain. Furthermore, based on the observation that phytoplankton chytridiomycosis preferentially impacts the larger size species, blooms of such species (e.g., filamentous cyanobacteria) may not totally represent trophic bottlenecks. Besides, chytrid epidemics represent an important driving factor in phytoplankton seasonal successions. In this review, I summarize the knowledge on the diversity, community structure, quantitative importance, and functional roles of fungal chytrids, primarily those who are parasites of phytoplankton, and infer the ecological implications and potentials for the food web dynamics and properties. I reach the
ERIC Educational Resources Information Center
Sinclair, Margaret P.
2005-01-01
A case study, originally set up to identify and describe some benefits and limitations of using dynamic web-based geometry sketches, provided an opportunity to examine peer interactions in a lab. Since classes were held in a computer lab, teachers and pairs faced the challenges of working and communicating in a lab environment. Research has shown…
ERIC Educational Resources Information Center
O'Connor, Eileen
2013-01-01
With the advent of web 2.0 and virtual technologies and new understandings about learning within a global, networked environment, online course design has moved beyond the constraints of text readings, papers, and discussion boards. This next generation of online courses needs to dynamically and actively integrate the wide-ranging distribution of…
YouGenMap: a web platform for dynamic multi-comparative mapping and visualization of genetic maps
Keith Batesole; Kokulapalan Wimalanathan; Lin Liu; Fan Zhang; Craig S. Echt; Chun Liang
2014-01-01
Comparative genetic maps are used in examination of genome organization, detection of conserved gene order, and exploration of marker order variations. YouGenMap is an open-source web tool that offers dynamic comparative mapping capability of users' own genetic mapping between 2 or more map sets. Users' genetic map data and optional gene annotations are...
NASA Technical Reports Server (NTRS)
Steeman, Gerald; Connell, Christopher
2000-01-01
Many librarians may feel that dynamic Web pages are out of their reach, financially and technically. Yet we are reminded in library and Web design literature that static home pages are a thing of the past. This paper describes how librarians at the Institute for Defense Analyses (IDA) library developed a database-driven, dynamic intranet site using commercial off-the-shelf applications. Administrative issues include surveying a library users group for interest and needs evaluation; outlining metadata elements; and, committing resources from managing time to populate the database and training in Microsoft FrontPage and Web-to-database design. Technical issues covered include Microsoft Access database fundamentals, lessons learned in the Web-to-database process (including setting up Database Source Names (DSNs), redesigning queries to accommodate the Web interface, and understanding Access 97 query language vs. Standard Query Language (SQL)). This paper also offers tips on editing Active Server Pages (ASP) scripting to create desired results. A how-to annotated resource list closes out the paper.
NASA Astrophysics Data System (ADS)
Zhang, Lijun; Zhao, Jiemei; Qi, Xue; Jia, Heming
2013-06-01
The problem of tracking control for a class of uncertain non-affine discrete-time nonlinear systems with internal dynamics is addressed. The fixed point theorem is first employed to ensure the control problem in question is solvable and well-defined. Based on it, an adaptive output feedback control scheme based on neural network (NN) is presented. The proposed control algorithm consists of two parts: a dynamic compensator is introduced to stabilise the linear portion of the tracking error system; a single-hidden-layer neural network (SHL NN) approximation mechanism is introduced to cancel the uncertainties resulting from the non-affine function, where the recursive weight update rules of NN estimation are derived from the discrete-time version of Lyapunov control theory. Ultimate boundedness of the error signals is shown through Lyapunov's direct method and the discrete-time version of input-to-state stability (ISS) theory. Finally, a model of automatical underwater vehicle (AUV) is considered to show the effectiveness of the proposed control scheme.
Jang, Sumin; Choubey, Sandeep; Furchtgott, Leon; Zou, Ling-Nan; Doyle, Adele; Menon, Vilas; Loew, Ethan B; Krostag, Anne-Rachel; Martinez, Refugio A; Madisen, Linda; Levi, Boaz P; Ramanathan, Sharad
2017-01-01
The complexity of gene regulatory networks that lead multipotent cells to acquire different cell fates makes a quantitative understanding of differentiation challenging. Using a statistical framework to analyze single-cell transcriptomics data, we infer the gene expression dynamics of early mouse embryonic stem (mES) cell differentiation, uncovering discrete transitions across nine cell states. We validate the predicted transitions across discrete states using flow cytometry. Moreover, using live-cell microscopy, we show that individual cells undergo abrupt transitions from a naïve to primed pluripotent state. Using the inferred discrete cell states to build a probabilistic model for the underlying gene regulatory network, we further predict and experimentally verify that these states have unique response to perturbations, thus defining them functionally. Our study provides a framework to infer the dynamics of differentiation from single cell transcriptomics data and to build predictive models of the gene regulatory networks that drive the sequence of cell fate decisions during development. DOI: http://dx.doi.org/10.7554/eLife.20487.001 PMID:28296635
NASA Astrophysics Data System (ADS)
Yoon, Jeoung Seok; Zang, Arno; Zimmermann, Günter; Stephansson, Ove
2016-04-01
Operation of fluid injection into and withdrawal from the subsurface for various purposes has been known to induce earthquakes. Such operations include hydraulic fracturing for shale gas extraction, hydraulic stimulation for Enhanced Geothermal System development and waste water disposal. Among these, several damaging earthquakes have been reported in the USA in particular in the areas of high-rate massive amount of wastewater injection [1] mostly with natural fault systems. Oil and gas production have been known to induce earthquake where pore fluid pressure decreases in some cases by several tens of Mega Pascal. One recent seismic event occurred in November 2013 near Azle, Texas where a series of earthquakes began along a mapped ancient fault system [2]. It was studied that a combination of brine production and waste water injection near the fault generated subsurface pressures sufficient to induced earthquakes on near-critically stressed faults. This numerical study aims at investigating the occurrence mechanisms of such earthquakes induced by fluid injection [3] and withdrawal by using hydro-geomechanical coupled dynamic simulator (Itasca's Particle Flow Code 2D). Generic models are setup to investigate the sensitivity of several parameters which include fault orientation, frictional properties, distance from the injection well to the fault, amount of fluid withdrawal around the injection well, to the response of the fault systems and the activation magnitude. Fault slip movement over time in relation to the diffusion of pore pressure is analyzed in detail. Moreover, correlations between the spatial distribution of pore pressure change and the locations of induced seismic events and fault slip rate are investigated. References [1] Keranen KM, Weingarten M, Albers GA, Bekins BA, Ge S, 2014. Sharp increase in central Oklahoma seismicity since 2008 induced by massive wastewater injection, Science 345, 448, DOI: 10.1126/science.1255802. [2] Hornbach MJ, DeShon HR
NASA Astrophysics Data System (ADS)
Yu, Fajun
2017-02-01
Starting from a discrete spectral problem, we derive a hierarchy of nonlinear discrete equations which include the Ablowitz-Ladik (AL) equation. We analytically study the discrete rogue-wave (DRW) solutions of AL equation with three free parameters. The trajectories of peaks and depressions of profiles for the first- and second-order DRWs are produced by means of analytical and numerical methods. In particular, we study the solutions with dispersion in parity-time ( P T ) symmetric potential for Ablowitz-Musslimani equation. And we consider the non-autonomous DRW solutions, parameters controlling and their interactions with variable coefficients, and predict the long-living rogue wave solutions. Our results might provide useful information for potential applications of synthetic P T symmetric systems in nonlinear optics and condensed matter physics.
Mercury Dynamics in Aquatic Food Webs of the Finger Lakes, New York
NASA Astrophysics Data System (ADS)
Cleckner, L.; Razavi, N. R.; Halfman, J. D.; Cushman, S. F.; Foust, J.; Gilman, B.
2016-12-01
Mercury (Hg) contamination of fish is a global concern due to the deleterious health effects in humans and wildlife associated with ingesting fish with elevated concentrations. A key to understanding elevated fish Hg concentrations is to examine methyl Hg dynamics at the base of food webs, including algae and zooplankton. Predicting determinants of methyl Hg concentrations in lower trophic level biota remains an active area of research. This study was conducted to assess Hg concentrations in biota of the Finger Lakes (New York, USA), a region where fisheries are an important economic driver, but where no comprehensive assessment of food web Hg dynamics has been completed to date. Sources of Hg in the region include atmospheric pollution from an active coal-fired power plant. The objectives of this study were to: 1) determine if fish Hg concentrations were of concern, 2) assess differences in Hg accumulation among lakes and determine predictors of fish Hg concentrations, and 3) evaluate the predictive power of monthly zooplankton methyl Hg concentrations on fish Hg concentrations. From May - October 2015, suspended particulate matter, zooplankton, and benthos were sampled monthly in five of the Finger Lakes (Honeoye, Canandaigua, Seneca, Cayuga, and Owasco Lakes). Fish were sampled once over the same study period and species were targeted from all trophic levels. Results for top predatory fish including Lake Trout (Salvelinus namaycush), Largemouth Bass (Micropterus salmoides), and Walleye (Sander vitreus) showed significant differences among lakes, and elevated concentrations are above US Environmental Protection Agency's screening value (300 ng/g wet weight). No clear pattern in Hg levels among lakes was evident in lower trophic level fishes such as Yellow Perch (Perca flavescens) and Golden Shiner (Notemigonus crysoleucas), but concentrations were low. Benthivorous Brown Bullhead (Ameiurus nebulosus) exhibited significant differences in Hg among lakes with
NASA Astrophysics Data System (ADS)
Aquilanti, Vincenzo; Marinelli, Dimitri; Marzuoli, Annalisa
2013-05-01
The action of the quantum mechanical volume operator, introduced in connection with a symmetric representation of the three-body problem and recently recognized to play a fundamental role in discretized quantum gravity models, can be given as a second-order difference equation which, by a complex phase change, we turn into a discrete Schrödinger-like equation. The introduction of discrete potential-like functions reveals the surprising crucial role here of hidden symmetries, first discovered by Regge for the quantum mechanical 6j symbols; insight is provided into the underlying geometric features. The spectrum and wavefunctions of the volume operator are discussed from the viewpoint of the Hamiltonian evolution of an elementary ‘quantum of space’, and a transparent asymptotic picture of the semiclassical and classical regimes emerges. The definition of coordinates adapted to the Regge symmetry is exploited for the construction of a novel set of discrete orthogonal polynomials, characterizing the oscillatory components of torsion-like modes.
Visinets: a web-based pathway modeling and dynamic visualization tool.
Spychala, Jozef; Spychala, Pawel; Gomez, Shawn; Weinreb, Gabriel E
2015-01-01
In this report we describe a novel graphically oriented method for pathway modeling and a software package that allows for both modeling and visualization of biological networks in a user-friendly format. The Visinets mathematical approach is based on causal mapping (CMAP) that has been fully integrated with graphical interface. Such integration allows for fully graphical and interactive process of modeling, from building the network to simulation of the finished model. To test the performance of Visinets software we have applied it to: a) create executable EGFR-MAPK pathway model using an intuitive graphical way of modeling based on biological data, and b) translate existing ordinary differential equation (ODE) based insulin signaling model into CMAP formalism and compare the results. Our testing fully confirmed the potential of the CMAP method for broad application for pathway modeling and visualization and, additionally, showed significant advantage in computational efficiency. Furthermore, we showed that Visinets web-based graphical platform, along with standardized method of pathway analysis, may offer a novel and attractive alternative for dynamic simulation in real time for broader use in biomedical research. Since Visinets uses graphical elements with mathematical formulas hidden from the users, we believe that this tool may be particularly suited for those who are new to pathway modeling and without the in-depth modeling skills often required when using other software packages.
Yokohama, Noriya; Tsuchimoto, Tadashi; Oishi, Masamichi; Itou, Katsuya
2007-01-20
It has been noted that the downtime of medical informatics systems is often long. Many systems encounter downtimes of hours or even days, which can have a critical effect on daily operations. Such systems remain especially weak in the areas of database and medical imaging data. The scheme design shows the three-layer architecture of the system: application, database, and storage layers. The application layer uses the DICOM protocol (Digital Imaging and Communication in Medicine) and HTTP (Hyper Text Transport Protocol) with AJAX (Asynchronous JavaScript+XML). The database is designed to decentralize in parallel using cluster technology. Consequently, restoration of the database can be done not only with ease but also with improved retrieval speed. In the storage layer, a network RAID (Redundant Array of Independent Disks) system, it is possible to construct exabyte-scale parallel file systems that exploit storage spread. Development and evaluation of the test-bed has been successful in medical information data backup and recovery in a network environment. This paper presents a schematic design of the new medical informatics system that can be accommodated from a recovery and the dynamic Web application for medical imaging distribution using AJAX.
Visinets: A Web-Based Pathway Modeling and Dynamic Visualization Tool
Spychala, Pawel; Gomez, Shawn
2015-01-01
In this report we describe a novel graphically oriented method for pathway modeling and a software package that allows for both modeling and visualization of biological networks in a user-friendly format. The Visinets mathematical approach is based on causal mapping (CMAP) that has been fully integrated with graphical interface. Such integration allows for fully graphical and interactive process of modeling, from building the network to simulation of the finished model. To test the performance of Visinets software we have applied it to: a) create executable EGFR-MAPK pathway model using an intuitive graphical way of modeling based on biological data, and b) translate existing ordinary differential equation (ODE) based insulin signaling model into CMAP formalism and compare the results. Our testing fully confirmed the potential of the CMAP method for broad application for pathway modeling and visualization and, additionally, showed significant advantage in computational efficiency. Furthermore, we showed that Visinets web-based graphical platform, along with standardized method of pathway analysis, may offer a novel and attractive alternative for dynamic simulation in real time for broader use in biomedical research. Since Visinets uses graphical elements with mathematical formulas hidden from the users, we believe that this tool may be particularly suited for those who are new to pathway modeling and without the in-depth modeling skills often required when using other software packages. PMID:26020230
Owen-Smith, Norman; Mills, M G L
2008-04-01
Shifting prey selection has been identified as a mechanism potentially regulating predator-prey interactions, but it may also lead to different outcomes, especially in more complex systems with multiple prey species available. We assessed changing prey selection by lions, the major predator for 12 large herbivore species in South Africa's Kruger National Park. The database was provided by records of found carcasses ascribed to kills by lions assembled over 70 years, coupled with counts of changing prey abundance extending over 30 years. Wildebeest and zebra constituted the most favored prey species during the early portion of the study period, while selection for buffalo rose in the south of the park after a severe drought increased their vulnerability. Rainfall had a negative influence on the proportional representation of buffalo in lion kills, but wildebeest and zebra appeared less susceptible to being killed under conditions of low rainfall. Selection by lions for alternative prey species, including giraffe, kudu, waterbuck, and warthog, was influenced by the changing relative abundance and vulnerability of the three principal prey species. Simultaneous declines in the abundance of rarer antelope species were associated with a sharp increase in selection for these species at a time when all three principal prey species were less available. Hence shifting prey selection by lions affected the dynamics of herbivore populations in different ways: promoting contrasting responses by principal prey species to rainfall variation, while apparently being the main cause of sharp declines by alternative prey species under certain conditions. Accordingly, adaptive responses by predators, to both the changing relative abundance of the principal prey species, and other conditions affecting the relative vulnerability of various species, should be taken into account to understand the interactive dynamics of multispecies predator-prey webs.
NASA Astrophysics Data System (ADS)
Mendonça, J. Ricardo G.; Gevorgyan, Yeva
2017-05-01
We investigate one-dimensional elementary probabilistic cellular automata (PCA) whose dynamics in first-order mean-field approximation yields discrete logisticlike growth models for a single-species unstructured population with nonoverlapping generations. Beginning with a general six-parameter model, we find constraints on the transition probabilities of the PCA that guarantee that the ensuing approximations make sense in terms of population dynamics and classify the valid combinations thereof. Several possible models display a negative cubic term that can be interpreted as a weak Allee factor. We also investigate the conditions under which a one-parameter PCA derived from the more general six-parameter model can generate valid population growth dynamics. Numerical simulations illustrate the behavior of some of the PCA found.
Mendonça, J Ricardo G; Gevorgyan, Yeva
2017-05-01
We investigate one-dimensional elementary probabilistic cellular automata (PCA) whose dynamics in first-order mean-field approximation yields discrete logisticlike growth models for a single-species unstructured population with nonoverlapping generations. Beginning with a general six-parameter model, we find constraints on the transition probabilities of the PCA that guarantee that the ensuing approximations make sense in terms of population dynamics and classify the valid combinations thereof. Several possible models display a negative cubic term that can be interpreted as a weak Allee factor. We also investigate the conditions under which a one-parameter PCA derived from the more general six-parameter model can generate valid population growth dynamics. Numerical simulations illustrate the behavior of some of the PCA found.
NASA Technical Reports Server (NTRS)
Mizell, Carolyn Barrett; Malone, Linda
2007-01-01
The development process for a large software development project is very complex and dependent on many variables that are dynamic and interrelated. Factors such as size, productivity and defect injection rates will have substantial impact on the project in terms of cost and schedule. These factors can be affected by the intricacies of the process itself as well as human behavior because the process is very labor intensive. The complex nature of the development process can be investigated with software development process models that utilize discrete event simulation to analyze the effects of process changes. The organizational environment and its effects on the workforce can be analyzed with system dynamics that utilizes continuous simulation. Each has unique strengths and the benefits of both types can be exploited by combining a system dynamics model and a discrete event process model. This paper will demonstrate how the two types of models can be combined to investigate the impacts of human resource interactions on productivity and ultimately on cost and schedule.
NASA Technical Reports Server (NTRS)
Tsang, W. L.; Glover, J. D.; Bach, R. E.
1981-01-01
Two off-line schemes are proposed for the identification of unknown noise covariance matrices Q and R of a discrete-time dynamic system. The first scheme is based on a maximum a posteriori cost function utilizing smoothed state estimates, while the second is based on a maximum likelihood cost function utilizing filtered state estimates. Sensitivity of the cost functions to Q and R is analyzed for the following cases: (1) single-input single-output systems; (2) multiinput single-output systems; and (3) single-input multioutput systems with a diagonal R. Identifiability criteria are presented for the cases considered and demonstrated by examples.
NASA Astrophysics Data System (ADS)
Takayanagi, Toshiyuki; Shiga, Motoyuki
2002-08-01
The structures and vibrational frequencies of Cl 2-helium clusters have been studied using the path integral molecular dynamics method combined with the discrete-variable-representation approach. It is found that the Cl 2-helium clusters form clear shell structures comprised of rings around the Cl 2 bond. The vibrational frequencies calculated show a monotonically increasing red shift with an increase in cluster size. It can be concluded that the first solvation shell and its density around T-shaped configurations play the most important role in the observed frequency shifts.
NASA Astrophysics Data System (ADS)
Burke, Mark E.
2010-11-01
Dubois coined the term incursion, for an inclusive or implicit recursion, to describe a discrete-time anticipatory system which computes its future states by reference to its future states as well as its current and past states. In this paper, we look at a model which has been proposed in the context of a social system which has functionally differentiated subsystems. The model is derived from a discrete-time compartmental SIS epidemic model. We analyse a low order instance of the model both in its form as a recursion with no anticipatory capacity, and also as an incursion with associated anticipatory capacity. The properties of the incursion are compared and contrasted with those of the underlying recursion.
J. Ryan Bellmore; Joseph R. Benjamin; Michael Newsom; Jennifer A. Bountry; Daniel Dombroski
2017-01-01
Restoration is frequently aimed at the recovery of target species, but also influences the larger food web in which these species participate. Effects of restoration on this broader network of organisms can influence target species both directly and indirectly via changes in energy flow through food webs. To help incorporate these complexities into river restoration...
GEO Label Web Services for Dynamic and Effective Communication of Geospatial Metadata Quality
NASA Astrophysics Data System (ADS)
Lush, Victoria; Nüst, Daniel; Bastin, Lucy; Masó, Joan; Lumsden, Jo
2014-05-01
We present demonstrations of the GEO label Web services and their integration into a prototype extension of the GEOSS portal (http://scgeoviqua.sapienzaconsulting.com/web/guest/geo_home), the GMU portal (http://gis.csiss.gmu.edu/GADMFS/) and a GeoNetwork catalog application (http://uncertdata.aston.ac.uk:8080/geonetwork/srv/eng/main.home). The GEO label is designed to communicate, and facilitate interrogation of, geospatial quality information with a view to supporting efficient and effective dataset selection on the basis of quality, trustworthiness and fitness for use. The GEO label which we propose was developed and evaluated according to a user-centred design (UCD) approach in order to maximise the likelihood of user acceptance once deployed. The resulting label is dynamically generated from producer metadata in ISO or FDGC format, and incorporates user feedback on dataset usage, ratings and discovered issues, in order to supply a highly informative summary of metadata completeness and quality. The label was easily incorporated into a community portal as part of the GEO Architecture Implementation Programme (AIP-6) and has been successfully integrated into a prototype extension of the GEOSS portal, as well as the popular metadata catalog and editor, GeoNetwork. The design of the GEO label was based on 4 user studies conducted to: (1) elicit initial user requirements; (2) investigate initial user views on the concept of a GEO label and its potential role; (3) evaluate prototype label visualizations; and (4) evaluate and validate physical GEO label prototypes. The results of these studies indicated that users and producers support the concept of a label with drill-down interrogation facility, combining eight geospatial data informational aspects, namely: producer profile, producer comments, lineage information, standards compliance, quality information, user feedback, expert reviews, and citations information. These are delivered as eight facets of a wheel
Sooria, P M; Jyothibabu, R; Anjusha, A; Vineetha, G; Vinita, J; Lallu, K R; Paul, M; Jagadeesan, L
2015-07-01
The paper presents the ecology and dynamics of plankton food web in the Cochin backwaters (CBW), the largest monsoonal estuary along the west coast of India. The data source is a time series measurement carried out in the CBW during the Spring Intermonsoon (March-May) and the Southwest Monsoon (June-September). The plankton food web consisting of autotrophic/heterotrophic picoplankton, autotrophic/heterotrophic nanoplankton, microzooplankton, and mesozooplankton was quantified in relation to the seasonal hydrographical settings in the CBW. The study showed that significant changes in the abundance and dynamics of plankton food web components were governed mostly by the spatial and seasonal changes in hydrography rather than short-term changes induced by tide. During the Spring Intermonsoon, all plankton consumers in the CBW was higher than the Southwest Monsoon, and the trophic interaction was more effective in upstream where there was a close coupling between all prey components and their consumers. During the Southwest Monsoon, on the other hand, the trophic interaction was more effective downstream where the abundance of all plankton consumers was significantly higher than the upstream. Based on statistical analyses NMDS/SIMPROF and RDA, we demarcated the spatial difference/mismatch in the prey and consumer distribution in the CBW and showed that a more efficient plankton food web exists in the mesohaline regions during both seasons. This suggests that a noticeable spatial shift occurs seasonally in the active plankton food web zone in the CBW; it is upstream during the Spring Intermonsoon and downstream during the Southwest Monsoon.
Discrete Newtonian cosmology: perturbations
NASA Astrophysics Data System (ADS)
Ellis, George F. R.; Gibbons, Gary W.
2015-03-01
In a previous paper (Gibbons and Ellis 2014 Discrete Newtonian cosmology Class. Quantum Grav. 31 025003), we showed how a finite system of discrete particles interacting with each other via Newtonian gravitational attraction would lead to precisely the same dynamical equations for homothetic motion as in the case of the pressure-free Friedmann-Lemaître-Robertson-Walker cosmological models of general relativity theory, provided the distribution of particles obeys the central configuration equation. In this paper we show that one can obtain perturbed such Newtonian solutions that give the same linearized structure growth equations as in the general relativity case. We also obtain the Dmitriev-Zel’dovich equations for subsystems in this discrete gravitational model, and show how it leads to the conclusion that voids have an apparent negative mass.
NASA Astrophysics Data System (ADS)
Klette, Reinhard; Jiang, Ruyi; Morales, Sandino; Vaudrey, Tobi
Applying computer technology, such as computer vision in driver assistance, implies that processes and data are modeled as being discretized rather than being continuous. The area of stereo vision provides various examples how concepts known in discrete mathematics (e.g., pixel adjacency graphs, belief propagation, dynamic programming, max-flow/min-cut, or digital straight lines) are applied when aiming for efficient and accurate pixel correspondence solutions. The paper reviews such developments for a reader in discrete mathematics who is interested in applied research (in particular, in vision-based driver assistance). As a second subject, the paper also discusses lane detection and tracking, which is a particular task in driver assistance; recently the Euclidean distance transform proved to be a very appropriate tool for obtaining a fairly robust solution.
Methylation plotter: a web tool for dynamic visualization of DNA methylation data.
Mallona, Izaskun; Díez-Villanueva, Anna; Peinado, Miguel A
2014-01-01
Methylation plotter is a Web tool that allows the visualization of methylation data in a user-friendly manner and with publication-ready quality. The user is asked to introduce a file containing the methylation status of a genomic region. This file can contain up to 100 samples and 100 CpGs. Optionally, the user can assign a group for each sample (i.e. whether a sample is a tumoral or normal tissue). After the data upload, the tool produces different graphical representations of the results following the most commonly used styles to display this type of data. They include an interactive plot that summarizes the status of every CpG site and for every sample in lollipop or grid styles. Methylation values ranging from 0 (unmethylated) to 1 (fully methylated) are represented using a gray color gradient. A practical feature of the tool allows the user to choose from different types of arrangement of the samples in the display: for instance, sorting by overall methylation level, by group, by unsupervised clustering or just following the order in which data were entered. In addition to the detailed plot, Methylation plotter produces a methylation profile plot that summarizes the status of the scrutinized region, a boxplot that sums up the differences between groups (if any) and a dendrogram that classifies the data by unsupervised clustering. Coupled with this analysis, descriptive statistics and testing for differences at both CpG and group levels are provided. The implementation is based in R/shiny, providing a highly dynamic user interface that generates quality graphics without the need of writing R code. Methylation plotter is freely available at http://gattaca.imppc.org:3838/methylation_plotter/.
Methylation plotter: a web tool for dynamic visualization of DNA methylation data
2014-01-01
Methylation plotter is a Web tool that allows the visualization of methylation data in a user-friendly manner and with publication-ready quality. The user is asked to introduce a file containing the methylation status of a genomic region. This file can contain up to 100 samples and 100 CpGs. Optionally, the user can assign a group for each sample (i.e. whether a sample is a tumoral or normal tissue). After the data upload, the tool produces different graphical representations of the results following the most commonly used styles to display this type of data. They include an interactive plot that summarizes the status of every CpG site and for every sample in lollipop or grid styles. Methylation values ranging from 0 (unmethylated) to 1 (fully methylated) are represented using a gray color gradient. A practical feature of the tool allows the user to choose from different types of arrangement of the samples in the display: for instance, sorting by overall methylation level, by group, by unsupervised clustering or just following the order in which data were entered. In addition to the detailed plot, Methylation plotter produces a methylation profile plot that summarizes the status of the scrutinized region, a boxplot that sums up the differences between groups (if any) and a dendrogram that classifies the data by unsupervised clustering. Coupled with this analysis, descriptive statistics and testing for differences at both CpG and group levels are provided. The implementation is based in R/shiny, providing a highly dynamic user interface that generates quality graphics without the need of writing R code. Methylation plotter is freely available at http://gattaca.imppc.org:3838/methylation_plotter/. PMID:25260021
NASA Technical Reports Server (NTRS)
Yee, H. C.; Sweby, P. K.
1995-01-01
The global asymptotic nonlinear behavior of 11 explicit and implicit time discretizations for four 2 x 2 systems of first-order autonomous nonlinear ordinary differential equations (ODEs) is analyzed. The objectives are to gain a basic understanding of the difference in the dynamics of numerics between the scalars and systems of nonlinear autonomous ODEs and to set a baseline global asymptotic solution behavior of these schemes for practical computations in computational fluid dynamics. We show how 'numerical' basins of attraction can complement the bifurcation diagrams in gaining more detailed global asymptotic behavior of time discretizations for nonlinear differential equations (DEs). We show how in the presence of spurious asymptotes the basins of the true stable steady states can be segmented by the basins of the spurious stable and unstable asymptotes. One major consequence of this phenomenon which is not commonly known is that this spurious behavior can result in a dramatic distortion and, in most cases, a dramatic shrinkage and segmentation of the basin of attraction of the true solution for finite time steps. Such distortion, shrinkage and segmentation of the numerical basins of attraction will occur regardless of the stability of the spurious asymptotes, and will occur for unconditionally stable implicit linear multistep methods. In other words, for the same (common) steady-state solution the associated basin of attraction of the DE might be very different from the discretized counterparts and the numerical basin of attraction can be very different from numerical method to numerical method. The results can be used as an explanation for possible causes of error, and slow convergence and nonconvergence of steady-state numerical solutions when using the time-dependent approach for nonlinear hyperbolic or parabolic PDEs.
Groothuis-Oudshoorn, Catharina GM; Vollenbroek-Hutten, Miriam MR; IJzerman, Maarten J
2017-01-01
Background Patient-centered design that addresses patients’ preferences and needs is considered an important aim for improving health care systems. At present, within the field of pain rehabilitation, patients’ preferences regarding telerehabilitation remain scarcely explored and little is known about the optimal combination between human and electronic contact from the patients’ perspective. In addition, limited evidence is available about the best way to explore patients’ preferences. Therefore, the assessment of patients’ preferences regarding telemedicine is an important step toward the design of effective patient-centered care. Objective To identify which telerehabilitation treatment options patients with chronic pain are most likely to accept as alternatives to conventional rehabilitation and assess which treatment attributes are most important to them. Methods A discrete choice experiment with 15 choice tasks, combining 6 telerehabilitation treatment characteristics, was designed. Each choice task consisted of 2 hypothetical treatment scenarios and 1 opt-out scenario. Relative attribute importance was estimated using a bivariate probit regression analysis. One hundred and thirty surveys were received, of which 104 were usable questionnaires; thus, resulting in a total of 1547 observations. Results Physician communication mode, the use of feedback and monitoring technology (FMT), and exercise location were key drivers of patients’ treatment preferences (P<.001). Patients were willing to accept less frequent physician consultation offered mainly through video communication, provided that they were offered FMT and some face-to-face consultation and could exercise outside their home environment at flexible exercise hours. Home-based telerehabilitation scenarios with minimal physician supervision were the least preferred. A reduction in health care premiums would make these telerehabilitation scenarios as attractive as conventional clinic
Sørensen, V; Ingvaldsen, R P; Whiting, H T
2001-07-01
The purpose of this experiment was to explore the application of co-ordination dynamics to the analysis of discrete rather than cyclical movements. Subjects, standing in a fixed position, were required to return table-tennis balls delivered to different spatial locations in the direction of a fixed target. This was achieved in condition 1 by systematically scaling, from left to right and vice versa, the 'spatial location' of the ball-identified as a control parameter. In condition 2, the control condition, the spatial location was varied randomly over the same range. The changes between regimes of the stroke co-ordination pattern, defined at two different levels, (1) organisational--forehand or backhand drive. and (2) kinematic-the distance of the bat at ball-bat contact relative to the leading edge of the table, were identified as collective variables, the values of which changed spontaneously at the transition points exposed by the control parameter. The switch between regimes was shown to be dependent upon the direction of scaling, i.e. a hysteresis effect was identified in both conditions. These findings confirm that the conceptual and methodological frameworks of co-ordination dynamics can be applied, appropriately, to the analysis of discrete movements. Moreover, it would seem that control parameter values (spatial location of the ball) do not necessarily have to be scaled in a systematic way in order to produce the required effects.
NASA Astrophysics Data System (ADS)
Peng, Shouyong; Urbanc, Brigita; Ding, Feng; Cruz, Luis; Buldyrev, Sergey; Dokholyan, Nikolay; Stanley, H. E.
2003-03-01
New evidence shows that oligomeric forms of Amyloid-Beta are potent neurotoxins that play a major role in neurodegeneration of Alzheimer's disease. Detailed knowledge of the structure and assembly dynamics of Amyloid-Beta is important for the development of new therapeutic strategies. Here we apply a two-atom model with Go interactions to model aggregation of Amyloid-Beta (1-40) peptides using the discrete molecular dynamics simulation. At temperatures above the transition temperature from an alpha-helical to random coil, we obtain two types of parallel beta-sheet structures, (a) a helical beta-sheet structure at a lower temperature and (b) a parallel beta-sheet structure at a higher temperature, both with inter-sheet distance of 10 A and with free edges which possibly enable further fibrillar elongation.
Khan, Basir Ahamed; Sardar, Subhankar; Sarkar, Pranab; Adhikari, Satrajit
2014-12-11
The major portion of the algorithm of the time-dependent discrete variable representation (TDDVR) method is recently parallelized using the shared-memory parallelization scheme with the aim of performing dynamics on relatively large molecular systems. Because of the astronomical importance of naphthalene and anthracene, we have investigated their radical cations as models for theoretical simulation of complex photoelectron spectra and nonradiative decay process using the newly implemented parallel TDDVR code. The strong vibronic coupling among the six lowest doublet electronic states makes these polynuclear hydrocarbons dynamically important. The aim of the present investigation is to show the efficiency of our current TDDVR algorithm to perform dynamics on large dimensional quantum systems in vibronically coupled electronic manifold. Both the sequential and the parallelized TDDVR algorithms are almost linear scalable for an increase in number of processors. Because a significant speed-up is achieved by cycling in the correct way over arrays, all of the simulations are performed within a reasonable wall clock time. Our theoretical spectra well reproduce the features of the corresponding experimental analog. The dynamical outcomes, for example, population, photoelectron spectra, and diffused interstellar bands, etc., of our quantum-classical approach show good agreement with the findings of the well-established quantum dynamical method, that is, multi configuration time-dependent Hartree (MCTDH) approach.
Microscopic derivation of discrete hydrodynamics.
Español, Pep; Anero, Jesús G; Zúñiga, Ignacio
2009-12-28
By using the standard theory of coarse graining based on Zwanzig's projection operator, we derive the dynamic equations for discrete hydrodynamic variables. These hydrodynamic variables are defined in terms of the Delaunay triangulation. The resulting microscopically derived equations can be understood, a posteriori, as a discretization on an arbitrary irregular grid of the Navier-Stokes equations. The microscopic derivation provides a set of discrete equations that exactly conserves mass, momentum, and energy and the dissipative part of the dynamics produces strict entropy increase. In addition, the microscopic derivation provides a practical implementation of thermal fluctuations in a way that the fluctuation-dissipation theorem is satisfied exactly. This paper points toward a close connection between coarse-graining procedures from microscopic dynamics and discretization schemes for partial differential equations.
NASA Astrophysics Data System (ADS)
Roganov, E. A.; Roganova, N. A.; Aleksandrov, A. I.; Ukolova, A. V.
2017-01-01
We implement a web portal which dynamically creates documents in more than 30 different formats including html, pdf and docx from a single original material source. It is obtained by using a number of free software such as Markdown (markup language), Pandoc (document converter), MathJax (library to display mathematical notation in web browsers), framework Ruby on Rails. The portal enables the creation of documents with a high quality visualization of mathematical formulas, is compatible with a mobile device and allows one to search documents by text or formula fragments. Moreover, it gives professors the ability to develop the latest technology educational materials, without qualified technicians' assistance, thus improving the quality of the whole educational process.
NASA Astrophysics Data System (ADS)
Dahlke, H. E.; Easton, Z. M.; Fuka, D. R.; Rao, N. S.; Steenhuis, T. S.
2008-12-01
To optimize NPS pollution reduction efficiency of Best Management Practices (BMPs) in NY State, various models have been developed that can effectively delineate runoff and contaminant source areas in the landscape. In the Finger Lakes region with shallow, permeable soils, underlain by a restricting layer, saturation excess runoff is the dominant mechanism of nutrient transport. In watersheds characterized by these conditions, runoff originates from areas in the landscape that expand and contract seasonally and are therefore often termed as variable source areas (VSAs). Hence, consideration should be given to the spatial distribution of VSA in the watershed during the planning process of BMPs. However, in practice the applied hydrological models often require extensive expertise and effort to be used on a routine basis for BMP planning. In order to simplify the BMP planning process, we developed an interactive web-based tool for Salmon Creek watershed, NY that locates VSA and calculates their probability of saturation. The interactive web tool incorporates hydrologic, geographic and land management information in an ESRI ArcIMS framework and presents the resulting VSA maps online. For the web tool we developed a Python-based application that calculates the surface runoff potential of the 230 km2 Salmon Creek watershed on the basis of a water balance model and free precipitation and temperature data from the National Climatic Data Center. Areas of high surface runoff potential are distributed via a soil topographic index to capture VSA dynamics. Further, the application is used to calculate a one to two day prediction of the spatial extent of VSA using free web- provided weather forecasts. The web tool is designed to interactively assist planners and especially farmers in the BMP planning process on a simplified expertise level. It can be used on a daily basis to locate fields with low runoff risk that could, potentially receive more liberal nutrient applications
NASA Astrophysics Data System (ADS)
Malard, J. J.; Rojas, M.; Adamowski, J. F.; Anandaraja, N.; Tuy, H.; Melgar-Quiñonez, H.
2016-12-01
While several well-validated crop growth models are currently widely used, very few crop pest models of the same caliber have been developed or applied, and pest models that take trophic interactions into account are even rarer. This may be due to several factors, including 1) the difficulty of representing complex agroecological food webs in a quantifiable model, and 2) the general belief that pesticides effectively remove insect pests from immediate concern. However, pests currently claim a substantial amount of harvests every year (and account for additional control costs), and the impact of insects and of their trophic interactions on agricultural crops cannot be ignored, especially in the context of changing climates and increasing pressures on crops across the globe. Unfortunately, most integrated pest management frameworks rely on very simple models (if at all), and most examples of successful agroecological management remain more anecdotal than scientifically replicable. In light of this, there is a need for validated and robust agroecological food web models that allow users to predict the response of these webs to changes in management, crops or climate, both in order to predict future pest problems under a changing climate as well as to develop effective integrated management plans. Here we present Tiko'n, a Python-based software whose API allows users to rapidly build and validate trophic web agroecological models that predict pest dynamics in the field. The programme uses a Bayesian inference approach to calibrate the models according to field data, allowing for the reuse of literature data from various sources and reducing the need for extensive field data collection. We apply the model to the cononut black-headed caterpillar (Opisina arenosella) and associated parasitoid data from Sri Lanka, showing how the modeling framework can be used to rapidly develop, calibrate and validate models that elucidate how the internal structures of food webs
Decoupled diversity dynamics in green and brown webs during primary succession in a saltmarsh.
Schrama, Maarten; van der Plas, Fons; Berg, Matty P; Olff, Han
2017-01-01
Terrestrial ecosystems are characterized by a strong functional connection between the green (plant-herbivore-based) and brown (detritus-detritivore-based) parts of the food web, which both develop over successional time. However, the interlinked changes in green and brown food web diversity patterns in relation to key ecosystem processes are rarely studied. Here, we demonstrate changes in species richness, diversity and evenness over a wide range of invertebrate green and brown trophic groups during 100 years of primary succession in a saltmarsh ecosystem, using a well-calibrated chronosequence. We contrast two hypotheses on the relationship between green and brown food web diversity across succession: (i) 'coupled diversity hypothesis', which predicts that all trophic groups covary similarly with the main drivers of successional ecosystem assembly vs. (ii) the 'decoupled diversity hypothesis', where green and brown trophic groups diversity respond to different drivers during succession. We found that, while species richness for plants and invertebrate herbivores (green web groups) both peaked at intermediate productivity and successional age, the diversity of macrodetritivores, microarthropod microbivores and secondary consumers (brown web groups) continuously increased towards the latest successional stages. These results suggest that green web trophic groups are mainly driven by vegetation parameters, such as the amount of bare soil, vegetation biomass production and vegetation height, while brown web trophic groups are mostly driven by the production and standing stock of dead organic material and soil development. Our results show that plant diversity cannot simply be used as a proxy for the diversity of all other species groups that drive ecosystem functioning, as brown and green diversity components in our ecosystem responded differently to successional gradients.
Using Innovative Outliers to Detect Discrete Shifts in Dynamics in Group-Based State-Space Models
ERIC Educational Resources Information Center
Chow, Sy-Miin; Hamaker, Ellen L.; Allaire, Jason C.
2009-01-01
Outliers are typically regarded as data anomalies that should be discarded. However, dynamic or "innovative" outliers can be appropriately utilized to capture unusual but substantively meaningful shifts in a system's dynamics. We extend De Jong and Penzer's 1998 approach for representing outliers in single-subject state-space models to a…
NASA Astrophysics Data System (ADS)
Shorikov, A. F.
2016-12-01
This article discusses the discrete-time dynamical system consisting from two controlled objects and described by a linear recurrent vector equations in the presence of uncertain perturbations. This dynamical system has two levels of a control: dominant level (the first level or the level I) and subordinate level (the second level or the level II) and both have different linear terminal criterions of functioning and united a priori by determined information and control connections. It is assumed that the sets constraining all a priori undefined parameters are known and they are a finite sets or convex, closed and bounded polyhedrons in the corresponding finite-dimensional vector spaces. For the dynamical system in question, we propose a mathematical formalization in the form of solving two-level hierarchical minimax program control problem with incomplete information. In this article for solving of the investigated problem is proposed the algorithm that has a form of a recurrent procedure of solving a linear programming and a finite optimization problems. The results obtained in this article can be used for computer simulation of an actual dynamical processes and for designing controlling and navigation systems.
Observability of discretized partial differential equations
NASA Technical Reports Server (NTRS)
Cohn, Stephen E.; Dee, Dick P.
1988-01-01
It is shown that complete observability of the discrete model used to assimilate data from a linear partial differential equation (PDE) system is necessary and sufficient for asymptotic stability of the data assimilation process. The observability theory for discrete systems is reviewed and applied to obtain simple observability tests for discretized constant-coefficient PDEs. Examples are used to show how numerical dispersion can result in discrete dynamics with multiple eigenvalues, thereby detracting from observability.
Zhao, Renjie; Evans, James W.; Oliveira, Tiago J.
2016-04-08
Here, a discrete version of deposition-diffusion equations appropriate for description of step flow on a vicinal surface is analyzed for a two-dimensional grid of adsorption sites representing the stepped surface and explicitly incorporating kinks along the step edges. Model energetics and kinetics appropriately account for binding of adatoms at steps and kinks, distinct terrace and edge diffusion rates, and possible additional barriers for attachment to steps. Analysis of adatom attachment fluxes as well as limiting values of adatom densities at step edges for nonuniform deposition scenarios allows determination of both permeability and kinetic coefficients. Behavior of these quantities is assessed as a function of key system parameters including kink density, step attachment barriers, and the step edge diffusion rate.
Zhao, Renjie; Evans, James W.; Oliveira, Tiago J.
2016-04-08
Here, a discrete version of deposition-diffusion equations appropriate for description of step flow on a vicinal surface is analyzed for a two-dimensional grid of adsorption sites representing the stepped surface and explicitly incorporating kinks along the step edges. Model energetics and kinetics appropriately account for binding of adatoms at steps and kinks, distinct terrace and edge diffusion rates, and possible additional barriers for attachment to steps. Analysis of adatom attachment fluxes as well as limiting values of adatom densities at step edges for nonuniform deposition scenarios allows determination of both permeability and kinetic coefficients. Behavior of these quantities is assessedmore » as a function of key system parameters including kink density, step attachment barriers, and the step edge diffusion rate.« less
NASA Astrophysics Data System (ADS)
Zhao, Jian-Fu
2012-07-01
Boiling in microgravity is an increasing significant subject of investigation. Motivation for the study comes not only from many potential space applications due to its high efficiency to transfer high heat flux with liquid-vapor phase change, but also from powerful platform of microgravity to reveal the mechanism of heat transfer underneath the phenomenon of boiling. In the present paper, the growth of a discrete bubble during nucleate pool boiling and heat transfer in short-term microgravity is studied experimentally utilizing the drop tower Beijing. A P-doped N-type square silicon chip with the dimensions of 10x10x0.5 mm ^{3} was used as the heater. Two 0.25-mm diameters copper wires for power supply was soldered to the side surfaces of the chip at the opposite ends. The normal resistant of the chip is 75 Ω. The chip was heated by using Joule effect. A D.C. power supply of constant current was used to input energy to the heater element. A 0.12-mm diameter, T-type thermocouple adhered on the centre of the backside of the chip was used for the measurement of wall temperature, while two other T-type thermocouples were used for the bulk liquid temperature. FC-72 was used as working fluid. The concentration of air was determined by using Henry law as 0.0046 moles gas/mole liquid. The pressure and the bulk liquid temperature in the boiling chamber were nominally 102.0 kPa and 12.0 °C, respectively. The shapes of the bubbles were recorded using a high speed camera at a speed of 250 fps with a shutter speed of 1/2000 s. Based on the image manipulation, the effective diameter of the discrete bubble is obtained. The experiments were conducted utilizing the drop tower Beijing, which can provide a short-term microgravity condition. The residual gravity of 10 ^{-2 ... -3} g _{0} can be maintained throughout the short duration of 3.6 s. To avoid the influence of natural convection in normal gravity environment, the heating switched on at the release of the drop capsule
Di Maio, V; Lánský, P; Rodriguez, R
2004-03-01
Different variants of stochastic leaky integrate-and-fire model for the membrane depolarisation of neurons are investigated. The model is driven by a constant input and equidistant pulses of fixed amplitude. These two types of signal are considered under the influence of three types of noise: white noise, jitter on interpulse distance, and noise in the amplitude of pulses. The results of computational experiments demonstrate the enhancement of the signal by noise in subthreshold regime and deterioration of the signal if it is sufficiently strong to carry the information in absence of noise. Our study holds mainly to central neurons that process discrete pulses although an application in sensory system is also available.
NASA Astrophysics Data System (ADS)
Alber, Mark; Chen, Nan; Glimm, Tilmann; Lushnikov, Pavel M.
2006-01-01
The Cellular Potts Model (CPM) has been used for simulating various biological phenomena such as differential adhesion, fruiting body formation of the slime mold Dictyostelium discoideum, angiogenesis, cancer invasion, chondrogenesis in embryonic vertebrate limbs, and many others. In this paper, we derive continuous limit of discrete one dimensional CPM with the chemotactic interactions between cells in the form of a Fokker-Planck equation for the evolution of the cell probability density function. This equation is then reduced to the classical macroscopic Keller-Segel model. In particular, all coefficients of the Keller-Segel model are obtained from parameters of the CPM. Theoretical results are verified numerically by comparing Monte Carlo simulations for the CPM with numerics for the Keller-Segel model.
Weinberg, Seth H.; Smith, Gregory D.
2012-01-01
Cardiac myocyte calcium signaling is often modeled using deterministic ordinary differential equations (ODEs) and mass-action kinetics. However, spatially restricted “domains” associated with calcium influx are small enough (e.g., 10−17 liters) that local signaling may involve 1–100 calcium ions. Is it appropriate to model the dynamics of subspace calcium using deterministic ODEs or, alternatively, do we require stochastic descriptions that account for the fundamentally discrete nature of these local calcium signals? To address this question, we constructed a minimal Markov model of a calcium-regulated calcium channel and associated subspace. We compared the expected value of fluctuating subspace calcium concentration (a result that accounts for the small subspace volume) with the corresponding deterministic model (an approximation that assumes large system size). When subspace calcium did not regulate calcium influx, the deterministic and stochastic descriptions agreed. However, when calcium binding altered channel activity in the model, the continuous deterministic description often deviated significantly from the discrete stochastic model, unless the subspace volume is unrealistically large and/or the kinetics of the calcium binding are sufficiently fast. This principle was also demonstrated using a physiologically realistic model of calmodulin regulation of L-type calcium channels introduced by Yue and coworkers. PMID:23509597
Bang, Jae Beum; Yoon, Yoo Sang; Lee, Young Hwan; Lee, Sam Beom
2014-12-01
The importance of team dynamics with regard to clinical performance is being emphasized to improve patient safety and the quality of health care. The aim of this study was to examine the correlation and differences in team dynamics and team clinical performance in a web-based simulation (WS) and high-fidelity simulation (HS) in the medical students. The simulations were held for 15 teams of fourth year medical students (n=52). They were given two clinical cases, dyspnea (case 1) and chest pain (case 2) by WS and then HS. The scores on the team dynamics and the team's clinical performance were analyzed by paired t-test and multiple regression using SPSS version 21.0 (IBM Corp.). The teamwork scores on case 2 (22.67 ± 6.58) were higher than for case 1 in the HS (20.47 ± 7.22). Team clinical performance scores were the same the WS and HS. Team clinical performances were significantly associated with team dynamics in both cases by HS. Teamwork scores of team dynamics were each explanation on case 1 (74.9%), case 2 (63.4%) in the HS. The team dynamics and clinical performance can improve if undergraduate medical students have more opportunities. They should be trained in these endeavors to become future doctors for which scenario-based simulations could be valuable.
Weaver, Daniel M.; Coghlan, Stephen M.; Zydlewski, Joseph; Hogg, Robert S.; Canton, Michael
2015-01-01
Anadromous fishes serve as vectors of marine-derived nutrients into freshwaters that are incorporated into aquatic and terrestrial food webs. Pacific salmonines Oncorhynchus spp. exemplify the importance of migratory fish as links between marine and freshwater systems; however, little attention has been given to sea lamprey (Petromyzon marinus Linnaeus, 1758) in Atlantic coastal systems. A first step to understanding the role of sea lamprey in freshwater food webs is to characterize the composition and rate of nutrient inputs. We conducted laboratory and field studies characterizing the elemental composition and the decay rates and subsequent water enriching effects of sea lamprey carcasses. Proximate tissue analysis demonstrated lamprey carcass nitrogen:phosphorus ratios of 20.2:1 (±1.18 SE). In the laboratory, carcass decay resulted in liberation of phosphorus within 1 week and nitrogen within 3 weeks. Nutrient liberation was accelerated at higher temperatures. In a natural stream, carcass decomposition resulted in an exponential decline in biomass, and after 24 days, the proportion of initial biomass remaining was 27% (±3.0% SE). We provide quantitative results as to the temporal dynamics of sea lamprey carcass decomposition and subsequent nutrient liberation. These nutrient subsidies may arrive at a critical time to maximize enrichment of stream food webs.
Wang, Jun-Sheng; Yang, Guang-Hong
2017-07-25
This paper studies the optimal output-feedback control problem for unknown linear discrete-time systems with stochastic measurement and process noise. A dithered Bellman equation with the innovation covariance matrix is constructed via the expectation operator given in the form of a finite summation. On this basis, an output-feedback-based approximate dynamic programming method is developed, where the terms depending on the innovation covariance matrix are available with the aid of the innovation covariance matrix identified beforehand. Therefore, by iterating the Bellman equation, the resulting value function can converge to the optimal one in the presence of the aforementioned noise, and the nearly optimal control laws are delivered. To show the effectiveness and the advantages of the proposed approach, a simulation example and a velocity control experiment on a dc machine are employed.
NASA Astrophysics Data System (ADS)
Beretta, Gian P.
2008-09-01
A rate equation for a discrete probability distribution is discussed as a route to describe smooth relaxation towards the maximum entropy distribution compatible at all times with one or more linear constraints. The resulting dynamics follows the path of steepest entropy ascent compatible with the constraints. The rate equation is consistent with the Onsager theorem of reciprocity and the fluctuation-dissipation theorem. The mathematical formalism was originally developed to obtain a quantum theoretical unification of mechanics and thermodinamics. It is presented here in a general, non-quantal formulation as a part of an effort to develop tools for the phenomenological treatment of non-equilibrium problems with applications in engineering, biology, sociology, and economics. The rate equation is also extended to include the case of assigned time-dependences of the constraints and the entropy, such as for modeling non-equilibrium energy and entropy exchanges.
Takada, Mayura B; Miyashita, Tadashi
2014-09-01
Landscapes in nature can be viewed as a continuum of small total habitable area with high fragmentation to widely spreading habitats. The dispersal-mediated rescue effect predominates in the former landscapes, while classical density-dependent processes generally prevail in widely spread habitats. A similar principle should be applied to populations of organisms utilizing microhabitats in limited supply. To test this hypothesis, we examined the population dynamics of a web spider, Neriene brongersmai, in 16 populations with varying degrees of microhabitat availability, and we explored whether: (i) high microhabitat availability improves survival rate during density-independent movement, while the resultant high density reduces survival rate in a density-dependent manner; and (ii) temporal population stability increases with microhabitat availability at the population level. Furthermore, we conducted two types of field experiments to verify whether high microhabitat availability actually reduces mortality associated with web-site movement. Field observations revealed that demographic change in N. brongersmai populations was affected by three factors at different stages, namely the microhabitat limitation from the early to late juvenile stages, the density dependence from the late juvenile to adult stages and the food limitation from the adult to the next early juvenile stages. In addition, there was a tendency for a positive association between population stability and microhabitat availability at the population level. A small-scale experiment, where the frequency of spider web relocation was equalized artificially, revealed that high microhabitat availability elevated the survival rate during a movement event between web-sites. The larger spatiotemporal scale experiment also revealed an improved spider survival rate following treatment with high microhabitat availability, even though spider density was kept at a relatively low level. The population dynamics of N
From Static to Dynamic: Choosing and Implementing a Web-Based CMS
ERIC Educational Resources Information Center
Kneale, Ruth
2008-01-01
Working as systems librarian for the Advanced Technology Solar Telescope (ATST), a project for the National Solar Observatory (NSO) based in Tucson, Arizona, a large part of the author's responsibilities involve running the web site. She began looking into content management systems (CMSs), specifically ones for website control. A CMS is generally…
From Static to Dynamic: Choosing and Implementing a Web-Based CMS
ERIC Educational Resources Information Center
Kneale, Ruth
2008-01-01
Working as systems librarian for the Advanced Technology Solar Telescope (ATST), a project for the National Solar Observatory (NSO) based in Tucson, Arizona, a large part of the author's responsibilities involve running the web site. She began looking into content management systems (CMSs), specifically ones for website control. A CMS is generally…
SEASONAL DYNAMICS OF PCB ACCUMULATION IN A GREAT LAKES FOOD WEB. (R825151)
Seston, sediment, settling organic matter, and food web members were
collected from Grand Traverse Bay, Lake Michigan, between April 1997 and
September 1998 to examine PCB and toxaphene biomagnification. Stable isotopes of
nitrogen and carbon were analyzed in sampl...
Fitting dynamical x-ray diffraction data over the World Wide Web.
Stepanov, S.; Forrest, R.; Biosciences Division; Univ. of Houston
2008-01-01
The first implementation of fitting X-ray Bragg diffraction profiles from strained multilayer crystals at a remote web-based X-ray software server is presented. The algorithms and the software solutions involved in the process are described. The suggested technology can be applied to a wide range of scientific research and has the potential to promote remote collaborations across scientific communities.
Tundra fire disturbance homogonizes belowground food web structure, function and dynamics
NASA Astrophysics Data System (ADS)
Moore, J. C.; Pressler, Y.; Koltz, A.; Asmus, A.; Simpson, R.
2016-12-01
Tundra fires on Alaska's North Slope are on the rise due to increased lightning strikes since 2000. On July 16, 2007 lightning ignited the Anaktuvuk River fire, burning a 40-by-10 mile swath of tundra about 24 miles north of Toolik Field Station. The fire burned 401 square miles, was visible from space, and released more than 2.3 million tons of carbon into the atmosphere. A large amount of the organic layer of the soil was burned, changing the over all composition of the site and exposing deeper soil horizons. Due to fundamental transitions in soil characteristics and vegetation we hypothesized that the belowground food web community would be affected both in terms of biomass and location within the soil profile. Microbial biomass was reduced with burn severity. In the lower organic horizon there was a significant reduction in fungal biomass but we did not observe this effect in the upper organic soil. We did not observe a significant effect of burn severity on individual group biomass within higher trophic levels. Canonical Discriminant Analysis using the biomass estimates of the functional groups in the food webs found that the webs are becoming increasingly homogenized in the severely burned site compared to the moderately burned and unburned sites. The unburned soils differed significantly from soil at both burn sites; the greatest effects on food web structure were at the lower organic depth, whereas. We modeled the effects of the fire on soil organic matter processing rates and energy flow through the three food webs. The model estimated a decrease in C and N mineralization with fire severity, due in large part to the loss of organic material. While the organic horizon at the unburned site had 12 times greater C and N mineralization than the mineral soils, we observed little to no difference in C and N mineralization between the organic and mineral soil horizons in the moderately and severely burned sites. Our results show that the fire significantly altered
NASA Astrophysics Data System (ADS)
Zhang, M.; Cooper, L. W.; Biasatti, D. M.; Kedra, M.; Grebmeier, J. M.
2016-02-01
Food web dynamics in the Chukchi Sea have been previously evaluated using bulk analysis of stable carbon and nitrogen isotopes of organisms. However, recent advances in compound-specific stable isotope analysis of amino acids indicate the potential to better identify the contributions of different dietary sources (e.g., pelagic vs. benthic, ice algae vs. phytoplankton) and to resolve complexities of food web structure that are difficult to address with bulk isotope analysis. Here we combine amino acid δ13C and δ15N data measured from primary producers and tissues of bivalves, polychaetes and other benthic invertebrates collected during two cruises in the summer of 2013 and 2015 in the Pacific Arctic. The results showed spatial variation of carbon isotope values in amino acids with difference up to 6 per mil for each individual species or taxa studied, indicating a shift in the food-web baseline geographically. Furthermore, the spatial variation in isotopic values was related to environmental factors, specifically sea ice extent, and total organic carbon, total organic nitrogen and the carbon/nitrogen ratio of the organic fractions of surface sediments. Results also indicated that trophic levels, as estimated by differences in the nitrogen isotope composition of glutamic acid and phenylalanine [Δ15Nglu-phe (δ15Nglu - δ15Nphe)], varied spatially by 0.5 to 1.5 trophic levels for certain species or taxa such as Macoma calcarea, Maldanidae and Ampelisca, indicating trophic level shifts that were associated with the food quality of organic matter in the organic fraction of the sediments. These results can be potentially used to predict future food web change in this high latitude marine system that is known for its ecological importance and on-going environmental changes, including warming and sea ice decline.
ADAM: Analysis of Discrete Models of Biological Systems Using Computer Algebra
2011-01-01
Background Many biological systems are modeled qualitatively with discrete models, such as probabilistic Boolean networks, logical models, Petri nets, and agent-based models, to gain a better understanding of them. The computational complexity to analyze the complete dynamics of these models grows exponentially in the number of variables, which impedes working with complex models. There exist software tools to analyze discrete models, but they either lack the algorithmic functionality to analyze complex models deterministically or they are inaccessible to many users as they require understanding the underlying algorithm and implementation, do not have a graphical user interface, or are hard to install. Efficient analysis methods that are accessible to modelers and easy to use are needed. Results We propose a method for efficiently identifying attractors and introduce the web-based tool Analysis of Dynamic Algebraic Models (ADAM), which provides this and other analysis methods for discrete models. ADAM converts several discrete model types automatically into polynomial dynamical systems and analyzes their dynamics using tools from computer algebra. Specifically, we propose a method to identify attractors of a discrete model that is equivalent to solving a system of polynomial equations, a long-studied problem in computer algebra. Based on extensive experimentation with both discrete models arising in systems biology and randomly generated networks, we found that the algebraic algorithms presented in this manuscript are fast for systems with the structure maintained by most biological systems, namely sparseness and robustness. For a large set of published complex discrete models, ADAM identified the attractors in less than one second. Conclusions Discrete modeling techniques are a useful tool for analyzing complex biological systems and there is a need in the biological community for accessible efficient analysis tools. ADAM provides analysis methods based on
NASA Astrophysics Data System (ADS)
Munsky, Brian
2015-03-01
MAPK signal-activated transcription plays central roles in myriad biological processes including stress adaptation responses and cell fate decisions. Recent single-cell and single-molecule experiments have advanced our ability to quantify the spatial, temporal, and stochastic fluctuations for such signals and their downstream effects on transcription regulation. This talk explores how integrating such experiments with discrete stochastic computational analyses can yield quantitative and predictive understanding of transcription regulation in both space and time. We use single-molecule mRNA fluorescence in situ hybridization (smFISH) experiments to reveal locations and numbers of multiple endogenous mRNA species in 100,000's of individual cells, at different times and under different genetic and environmental perturbations. We use finite state projection methods to precisely and efficiently compute the full joint probability distributions of these mRNA, which capture measured spatial, temporal and correlative fluctuations. By combining these experimental and computational tools with uncertainty quantification, we systematically compare models of varying complexity and select those which give optimally precise and accurate predictions in new situations. We use these tools to explore two MAPK-activated gene regulation pathways. In yeast adaptation to osmotic shock, we analyze Hog1 kinase activation of transcription for three different genes STL1 (osmotic stress), CTT1 (oxidative stress) and HSP12 (heat shock). In human osteosarcoma cells under serum induction, we analyze ERK activation of c-Fos transcription.
Weise, Louis D; Panfilov, Alexander V
2013-01-01
We introduce an electromechanical model for human cardiac tissue which couples a biophysical model of cardiac excitation (Tusscher, Noble, Noble, Panfilov, 2006) and tension development (adjusted Niederer, Hunter, Smith, 2006 model) with a discrete elastic mass-lattice model. The equations for the excitation processes are solved with a finite difference approach, and the equations of the mass-lattice model are solved using Verlet integration. This allows the coupled problem to be solved with high numerical resolution. Passive mechanical properties of the mass-lattice model are described by a generalized Hooke's law for finite deformations (Seth material). Active mechanical contraction is initiated by changes of the intracellular calcium concentration, which is a variable of the electrical model. Mechanical deformation feeds back on the electrophysiology via stretch-activated ion channels whose conductivity is controlled by the local stretch of the medium. We apply the model to study how stretch-activated currents affect the action potential shape, restitution properties, and dynamics of spiral waves, under constant stretch, and dynamic stretch caused by active mechanical contraction. We find that stretch conditions substantially affect these properties via stretch-activated currents. In constantly stretched medium, we observe a substantial decrease in conduction velocity, and an increase of action potential duration; whereas, with dynamic stretch, action potential duration is increased only slightly, and the conduction velocity restitution curve becomes biphasic. Moreover, in constantly stretched medium, we find an increase of the core size and period of a spiral wave, but no change in rotation dynamics; in contrast, in the dynamically stretching medium, we observe spiral drift. Our results may be important to understand how altered stretch conditions affect the heart's functioning.
NASA Astrophysics Data System (ADS)
Charles, Alexandre; Ballard, Patrick
2016-08-01
The dynamics of mechanical systems with a finite number of degrees of freedom (discrete mechanical systems) is governed by the Lagrange equation which is a second-order differential equation on a Riemannian manifold (the configuration manifold). The handling of perfect (frictionless) unilateral constraints in this framework (that of Lagrange's analytical dynamics) was undertaken by Schatzman and Moreau at the beginning of the 1980s. A mathematically sound and consistent evolution problem was obtained, paving the road for many subsequent theoretical investigations. In this general evolution problem, the only reaction force which is involved is a generalized reaction force, consistently with the virtual power philosophy of Lagrange. Surprisingly, such a general formulation was never derived in the case of frictional unilateral multibody dynamics. Instead, the paradigm of the Coulomb law applying to reaction forces in the real world is generally invoked. So far, this paradigm has only enabled to obtain a consistent evolution problem in only some very few specific examples and to suggest numerical algorithms to produce computational examples (numerical modeling). In particular, it is not clear what is the evolution problem underlying the computational examples. Moreover, some of the few specific cases in which this paradigm enables to write down a precise evolution problem are known to show paradoxes: the Painlevé paradox (indeterminacy) and the Kane paradox (increase in kinetic energy due to friction). In this paper, we follow Lagrange's philosophy and formulate the frictional unilateral multibody dynamics in terms of the generalized reaction force and not in terms of the real-world reaction force. A general evolution problem that governs the dynamics is obtained for the first time. We prove that all the solutions are dissipative; that is, this new formulation is free of Kane paradox. We also prove that some indeterminacy of the Painlevé paradox is fixed in this
Weise, Louis D.; Panfilov, Alexander V.
2013-01-01
We introduce an electromechanical model for human cardiac tissue which couples a biophysical model of cardiac excitation (Tusscher, Noble, Noble, Panfilov, 2006) and tension development (adjusted Niederer, Hunter, Smith, 2006 model) with a discrete elastic mass-lattice model. The equations for the excitation processes are solved with a finite difference approach, and the equations of the mass-lattice model are solved using Verlet integration. This allows the coupled problem to be solved with high numerical resolution. Passive mechanical properties of the mass-lattice model are described by a generalized Hooke's law for finite deformations (Seth material). Active mechanical contraction is initiated by changes of the intracellular calcium concentration, which is a variable of the electrical model. Mechanical deformation feeds back on the electrophysiology via stretch-activated ion channels whose conductivity is controlled by the local stretch of the medium. We apply the model to study how stretch-activated currents affect the action potential shape, restitution properties, and dynamics of spiral waves, under constant stretch, and dynamic stretch caused by active mechanical contraction. We find that stretch conditions substantially affect these properties via stretch-activated currents. In constantly stretched medium, we observe a substantial decrease in conduction velocity, and an increase of action potential duration; whereas, with dynamic stretch, action potential duration is increased only slightly, and the conduction velocity restitution curve becomes biphasic. Moreover, in constantly stretched medium, we find an increase of the core size and period of a spiral wave, but no change in rotation dynamics; in contrast, in the dynamically stretching medium, we observe spiral drift. Our results may be important to understand how altered stretch conditions affect the heart's functioning. PMID:23527160
Tadonléké, R D; Jugnia, L B; Sime-Ngando, T; Devaux, J; Romagoux, J C
2002-01-01
Phytoplankton dynamics, bacterial standing stocks and living microbial biomass (derived from ATP measurements, 0.7-200 mm size class) were examined in 1996 in the newly flooded (1995) Sep Reservoir ('Massif Central,' France), for evidence of the importance of the microbial food web relative to the traditional food chain. Phosphate concentrations were low, N:P ratios were high, and phosphate losses converted into carbon accounted for <50% of phytoplankton biomass and production, indicating that P was limiting phytoplankton development during the study. The observed low availability of P contrasts with the high release of "directly" assimilable P often reported in newly flooded reservoirs, suggesting that factors determining nutrient dynamics in such ecosystems are complex. The phosphate availability, but also the water column stability, seemed to be among the major factors determining phytoplankton dynamics, as (i) large-size phytoplankton species were prominent during the period of increasing water column stability, whereas small-size species dominated phytoplankton assemblages during the period of decreasing stability, and (ii) a Dinobryon divergens bloom occurred during a period when inorganic P was undetectable, coinciding with the lowest values of bacterial standing stocks. Indication of grazing limitation of bacterial populations by the mixotrophic chrysophyte D. divergens (in late spring) and by other potential grazers (mainly rotifers in summer) seemed to be confirmed by the Model II or functional slopes of the bacterial vs phytoplankton regressions, which were always <0.63. Phytoplankton biomass was not correlated with phosphorus sources and its contribution was remarkably low relative to the living microbial biomass which, in contrast, was positively correlated with total phosphorus in summer. We conclude that planktonic microheterotrophs are strongly implicated in the phosphorus dynamics in the Sep Reservoir, and thus support the idea that an important
NASA Astrophysics Data System (ADS)
Dalguer Gudiel, L. A.; Irikura, K.
2001-12-01
We performed a 3D model to simulate the dynamic rupture of a pre-existing fault and near-source ground motion of actual earthquakes solving the elastodynamic equation of motion using the 3D Discrete Element Method (DEM). The DEM is widely employed in engineering to designate lumped mass models in a truss arrangement, as opposed to FEM (Finite Element) models that may also consist of lumped masses, but normally require to mount a full stiffness matrix for response determination. The term has also been used for models of solids consisting of assemblies of discrete elements, such as spheres in elastic contact, employed in the analysis of perforation or penetration of concrete or rock. It should be noted that the designation Lattice Models, common in Physics, may be more adequate, although it omits reference to a fundamental property of the approach, which is the lumped-mass representation. In the present DEM formulation, the method models any orthotropic elastic solid. It is constructed by a three dimensional periodic truss-like structures using cubic elements that consists of lumping masses in nodal points, which are interconnected by unidimensional elements. The method was previously used in 2D to simulate in a simplified way the 1999 Chi-chi (Taiwan) earthquake (Dalguer et. al., 2000). Now the method was extended to resolve 3D problems. We apply the model to simulate the dynamic rupture process and near source ground motion of the 1999 Chi-chi (Taiwan) and the 2000 Tottori (Japan) earthquakes. The attractive feature in the problem under consideration is the possibility of introducing internal cracks or fractures with little computational effort and without increasing the number of degrees of freedom. For the 3D dynamic spontaneous rupture simulation of these eartquakes we need to know: the geometry of the fault, the initial stress distribution along the fault, the stress drop distribution, the strength of the fault to break and the critical slip (because slip
Update on Small Modular Reactors Dynamic System Modeling Tool: Web Application
Hale, Richard Edward; Cetiner, Sacit M.; Fugate, David L.; Batteh, John J; Tiller, Michael M.
2015-01-01
Previous reports focused on the development of component and system models as well as end-to-end system models using Modelica and Dymola for two advanced reactor architectures: (1) Advanced Liquid Metal Reactor and (2) fluoride high-temperature reactor (FHR). The focus of this report is the release of the first beta version of the web-based application for model use and collaboration, as well as an update on the FHR model. The web-based application allows novice users to configure end-to-end system models from preconfigured choices to investigate the instrumentation and controls implications of these designs and allows for the collaborative development of individual component models that can be benchmarked against test systems for potential inclusion in the model library. A description of this application is provided along with examples of its use and a listing and discussion of all the models that currently exist in the library.
NASA Technical Reports Server (NTRS)
Gottlieb, D.; Turkel, E.
1980-01-01
New methods are introduced for the time integration of the Fourier and Chebyshev methods of solution for dynamic differential equations. These methods are unconditionally stable, even though no matrix inversions are required. Time steps are chosen by accuracy requirements alone. For the Fourier method both leapfrog and Runge-Kutta methods are considered. For the Chebyshev method only Runge-Kutta schemes are tested. Numerical calculations are presented to verify the analytic results. Applications to the shallow water equations are presented.
Prinz, Jan-Hendrik; Chondera, John D; Pande, Vijay S; Swope, William C; Smith, Jeremy C; Noe, F
2011-01-01
Parallel tempering (PT) molecular dynamics simulations have been extensively investigated as a means of efficient sampling of the configurations of biomolecular systems. Recent work has demonstrated how the short physical trajectories generated in PT simulations of biomolecules can be used to construct the Markov models describing biomolecular dynamics at each simulated temperature. While this approach describes the temperature-dependent kinetics, it does not make optimal use of all available PT data, instead estimating the rates at a given temperature using only data from that temperature. This can be problematic, as some relevant transitions or states may not be sufficiently sampled at the temperature of interest, but might be readily sampled at nearby temperatures. Further, the comparison of temperature-dependent properties can suffer from the false assumption that data collected from different temperatures are uncorrelated. We propose here a strategy in which, by a simple modification of the PT protocol, the harvested trajectories can be reweighted, permitting data from all temperatures to contribute to the estimated kinetic model. The method reduces the statistical uncertainty in the kinetic model relative to the single temperature approach and provides estimates of transition probabilities even for transitions not observed at the temperature of interest. Further, the method allows the kinetics to be estimated at temperatures other than those at which simulations were run. We illustrate this method by applying it to the generation of a Markov model of the conformational dynamics of the solvated terminally blocked alanine peptide.
Composition of Web Services Using Markov Decision Processes and Dynamic Programming
Uc-Cetina, Víctor; Moo-Mena, Francisco; Hernandez-Ucan, Rafael
2015-01-01
We propose a Markov decision process model for solving the Web service composition (WSC) problem. Iterative policy evaluation, value iteration, and policy iteration algorithms are used to experimentally validate our approach, with artificial and real data. The experimental results show the reliability of the model and the methods employed, with policy iteration being the best one in terms of the minimum number of iterations needed to estimate an optimal policy, with the highest Quality of Service attributes. Our experimental work shows how the solution of a WSC problem involving a set of 100,000 individual Web services and where a valid composition requiring the selection of 1,000 services from the available set can be computed in the worst case in less than 200 seconds, using an Intel Core i5 computer with 6 GB RAM. Moreover, a real WSC problem involving only 7 individual Web services requires less than 0.08 seconds, using the same computational power. Finally, a comparison with two popular reinforcement learning algorithms, sarsa and Q-learning, shows that these algorithms require one or two orders of magnitude and more time than policy iteration, iterative policy evaluation, and value iteration to handle WSC problems of the same complexity. PMID:25874247
Composition of web services using Markov decision processes and dynamic programming.
Uc-Cetina, Víctor; Moo-Mena, Francisco; Hernandez-Ucan, Rafael
2015-01-01
We propose a Markov decision process model for solving the Web service composition (WSC) problem. Iterative policy evaluation, value iteration, and policy iteration algorithms are used to experimentally validate our approach, with artificial and real data. The experimental results show the reliability of the model and the methods employed, with policy iteration being the best one in terms of the minimum number of iterations needed to estimate an optimal policy, with the highest Quality of Service attributes. Our experimental work shows how the solution of a WSC problem involving a set of 100,000 individual Web services and where a valid composition requiring the selection of 1,000 services from the available set can be computed in the worst case in less than 200 seconds, using an Intel Core i5 computer with 6 GB RAM. Moreover, a real WSC problem involving only 7 individual Web services requires less than 0.08 seconds, using the same computational power. Finally, a comparison with two popular reinforcement learning algorithms, sarsa and Q-learning, shows that these algorithms require one or two orders of magnitude and more time than policy iteration, iterative policy evaluation, and value iteration to handle WSC problems of the same complexity.
NASA Astrophysics Data System (ADS)
Zhu, Ling; Romanowsky, Aaron J.; van de Ven, Glenn; Long, R. J.; Watkins, Laura L.; Pota, Vincenzo; Napolitano, Nicola R.; Forbes, Duncan A.; Brodie, Jean; Foster, Caroline
2016-11-01
We construct a suite of discrete chemo-dynamical models of the giant elliptical galaxy NGC 5846. These models are a powerful tool to constrain both the mass distribution and internal dynamics of multiple tracer populations. We use Jeans models to simultaneously fit stellar kinematics within the effective radius Re, planetary nebula (PN) radial velocities out to 3 Re, and globular cluster (GC) radial velocities and colours out to 6 Re. The best-fitting model is a cored dark matter halo which contributes ˜10 per cent of the total mass within 1 Re, and 67 per cent ± 10 per cent within 6 Re, although a cusped dark matter halo is also acceptable. The red GCs exhibit mild rotation with vmax/σ0 ˜ 0.3 in the region R > Re, aligned with but counter-rotating to the stars in the inner parts, while the blue GCs and PNe kinematics are consistent with no rotation. The red GCs are tangentially anisotropic, the blue GCs are mildly radially anisotropic, and the PNe vary from radially to tangentially anisotropic from the inner to the outer region. This is confirmed by general made-to-measure models. The tangential anisotropy of the red GCs in the inner regions could stem from the preferential destruction of red GCs on more radial orbits, while their outer tangential anisotropy - similar to the PNe in this region - has no good explanation. The mild radial anisotropy of the blue GCs is consistent with an accretion scenario.
Minisuperspace models of discrete systems
NASA Astrophysics Data System (ADS)
Baytaş, Bekir; Bojowald, Martin
2017-04-01
A discrete quantum spin system is presented in which several modern methods of canonical quantum gravity can be tested with promising results. In particular, features of interacting dynamics are analyzed with an emphasis on homogeneous configurations and the dynamical building-up and stability of long-range correlations. Different types of homogeneous minisuperspace models are introduced for the system, including one based on condensate states, and shown to capture different aspects of the discrete system. They are evaluated with effective methods and by means of continuum limits, showing good agreement with operator calculations whenever the latter are available. As a possibly quite general result, it is concluded that an analysis of the building-up of long-range correlations in discrete systems requires nonperturbative solutions of the dynamical equations. Some questions related to stability can be analyzed perturbatively but suggest that matter couplings may be relevant for this question in the context of quantum cosmology.
NASA Astrophysics Data System (ADS)
di, L.; Yu, G.; Chen, N.
2007-12-01
The self-adaptation concept is the central piece of the control theory widely and successfully used in engineering and military systems. Such a system contains a predictor and a measurer. The predictor takes initial condition and makes an initial prediction and the measurer then measures the state of a real world phenomenon. A feedback mechanism is built in that automatically feeds the measurement back to the predictor. The predictor takes the measurement against the prediction to calculate the prediction error and adjust its internal state based on the error. Thus, the predictor learns from the error and makes a more accurate prediction in the next step. By adopting the self-adaptation concept, we proposed the Self-adaptive Earth Predictive System (SEPS) concept for enabling the dynamic coupling between the sensor web and the Earth system models. The concept treats Earth System Models (ESM) and Earth Observations (EO) as integral components of the SEPS coupled by the SEPS framework. EO measures the Earth system state while ESM predicts the evolution of the state. A feedback mechanism processes EO measurements and feeds them into ESM during model runs or as initial conditions. A feed-forward mechanism analyzes the ESM predictions against science goals for scheduling optimized/targeted observations. The SEPS framework automates the Feedback and Feed-forward mechanisms (the FF-loop). Based on open consensus-based standards, a general SEPS framework can be developed for supporting the dynamic, interoperable coupling between ESMs and EO. Such a framework can support the plug-in-and-play capability of both ESMs and diverse sensors and data systems as long as they support the standard interfaces. This presentation discusses the SEPS concept, the service-oriented architecture (SOA) of SEPS framework, standards of choices for the framework, and the implementation. The presentation also presents examples of SEPS to demonstrate dynamic, interoperable, and live coupling of
Ulanova, N G; Belova, I N; Logofet, D O
2008-01-01
Presented is a synthesis of field, theoretical and modelling studies on joint dynamics of two species--common birch (Betula pendula Roth) and wood small reed (Calamagrostis epigeios (L.) Roth)--overgrowing a spruce forest clear-cut. A nonlinear matrix model for population dynamics of two species, which both possess non-trivial population structures and compete for a resource in common was developed as an expansion of the linear models for single-species, age-stage-structured population dynamics. Constant values of the age-stage-specific survival and reproduction rates have been modified with some decreasing functions of the (competitive group) abundances in the competitor species or/and the species itself. Special aggregation of the age-stage structure for each of the competitor species has reduced the dimension of the nonlinear matrix operator down to the level that admits accurate calibration of the model parameters on the observation data, as well as the search for an equilibrium and its stability analysis. When calibrated, the nonlinear model exhibits convergence to the steady equilibrium--a state of the phytocoenosis that is interpreted as young, closed-canopy, birch forest with suppressed woodreed population. The model illustrates the observed course of forest renewal: the appearance of birch germs and the growth of birch population overpass the woodreed competitive resistance and result in formation of young birch forest, where the birch exerts a strong suppressive impact on both the woodreed growth and the own young growth. Remarked is a potential of the model as an object of more general mathematical study and a tool to predict the course of forest renewal.
Stability analysis of a discrete Hutchinson equation with discrete and distributed delay
NASA Astrophysics Data System (ADS)
Suryanto, A.; Yanti, I.; Kusumawinahyu, W. M.
2014-02-01
In this paper a Hutchinson equation with discrete and distributed delay is discretized by the Euler method. The dynamics of the obtained discrete system is then investigated. Specifically the stability of the positive fixed point is analyzed. It is found that for sufficiently small time-step of integration, the positive equilibrium undergoes a Neimark-Sacker bifurcation which is controlled by the discrete time delay. The results of analysis are then confirmed by some numerical simulations.
Microbial food web dynamics along a soil chronosequence of a glacier forefield
NASA Astrophysics Data System (ADS)
Esperschütz, J.; Pérez-de-Mora, A.; Schreiner, K.; Welzl, G.; Buegger, F.; Zeyer, J.; Hagedorn, F.; Munch, J. C.; Schloter, M.
2011-02-01
Microbial food webs are critical for efficient nutrient turnover providing the basis for functional and stable ecosystems. However, the successional development of such microbial food webs and their role in "young" ecosystems is unclear. Due to a continuous glacier retreat since the middle of the 19th century, glacier forefields have expanded offering an excellent opportunity to study food web development at differently developed soils. In the present study, litter degradation and the corresponding C fluxes into microbial communities were investigated along the forefield of the Damma glacier (Switzerland). 13C-enriched litter of the pioneering plant Leucanthemopsis alpina (L.) Heywood was incorporated into the soil at sites that have been free from ice for approximately 10, 60, 100 and more than 700 years. The structure and function of microbial communities were identified by 13C analysis of phospholipid fatty acids (PLFA) and phospholipid ether lipids (PLEL). Results showed increasing microbial diversity and biomass, and enhanced proliferation of bacterial groups as ecosystem development progressed. Initially, litter decomposition proceeded faster at the more developed sites, but at the end of the experiment loss of litter mass was similar at all sites, once the more easily-degradable litter fraction was processed. As a result incorporation of 13C into microbial biomass was more evident during the first weeks of litter decomposition. 13C enrichments of both PLEL and PUFA biomarkers following litter incorporation were observed at all sites, suggesting similar microbial foodwebs at all stages of soil development. Nonetheless, the contribution of bacteria and actinomycetes to litter turnover became more pronounced as soil age increased in detriment of archaea, fungi and protozoa, more prominent in recently deglaciated terrain.
The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation
Kawaji, Hideya; Severin, Jessica; Lizio, Marina; Waterhouse, Andrew; Katayama, Shintaro; Irvine, Katharine M; Hume, David A; Forrest, Alistair RR; Suzuki, Harukazu; Carninci, Piero; Hayashizaki, Yoshihide; Daub, Carsten O
2009-01-01
In FANTOM4, an international collaborative research project, we collected a wide range of genome-scale data, including 24 million mRNA 5'-reads (CAGE tags) and microarray expression profiles along a differentiation time course of the human THP-1 cell line and under 52 systematic siRNA perturbations. In addition, data regarding chromatin status derived from ChIP-chip to elucidate the transcriptional regulatory interactions are included. Here we present these data to the research community as an integrated web resource. PMID:19374775
The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation.
Kawaji, Hideya; Severin, Jessica; Lizio, Marina; Waterhouse, Andrew; Katayama, Shintaro; Irvine, Katharine M; Hume, David A; Forrest, Alistair R R; Suzuki, Harukazu; Carninci, Piero; Hayashizaki, Yoshihide; Daub, Carsten O
2009-01-01
In FANTOM4, an international collaborative research project, we collected a wide range of genome-scale data, including 24 million mRNA 5'-reads (CAGE tags) and microarray expression profiles along a differentiation time course of the human THP-1 cell line and under 52 systematic siRNA perturbations. In addition, data regarding chromatin status derived from ChIP-chip to elucidate the transcriptional regulatory interactions are included. Here we present these data to the research community as an integrated web resource.
Chaos in Periodic Discrete Systems
NASA Astrophysics Data System (ADS)
Shi, Yuming; Zhang, Lijuan; Yu, Panpan; Huang, Qiuling
This paper focuses on chaos in periodic discrete systems, whose state space may vary with time. Some close relationships between some chaotic dynamical behaviors of a periodic discrete system and its autonomous induced system are given. Based on these relationships, several criteria of chaos are established and some sufficient conditions for no chaos are given for periodic discrete systems. Further, it is shown that a finite-dimensional linear periodic discrete system is not chaotic in the sense of Li-Yorke or Wiggins. In particular, an interesting problem of whether nonchaotic rules may generate a chaotic system is studied, with some examples provided, one of which surprisingly shows that a composition of globally asymptotically stable maps can be chaotic. In addition, some properties of sign pattern matrices of non-negative square matrices are given for convenience of the study.
NASA Astrophysics Data System (ADS)
Agaoglou, M.; Charalampidis, E. G.; Ioannidou, T. A.; Kevrekidis, P. G.
2017-09-01
A discrete analogue of the extended Bogomolny-Prasad-Sommerfeld (BPS) Skyrme model that admits time-dependent solutions is presented. Using the spacing h of adjacent lattice nodes as a parameter, we identify the spatial profile of the solution and the continuation of the relevant branch of solutions over the lattice spacing for different values of the potential (free) parameter α . In particular, we explore the dynamics and stability of the obtained solutions, finding that, while they generally seem to be prone to instabilities, for suitable values of the lattice spacing and for sufficiently large values of α , they may be long-lived in direct numerical simulations.
NASA Astrophysics Data System (ADS)
Christaki, U.; Lefèvre, D.; Georges, C.; Colombet, J.; Catala, P.; Courties, C.; Sime-Ngando, T.; Blain, S.; Obernosterer, I.
2014-12-01
Microbial food web dynamics were determined during the onset of several spring phytoplankton blooms induced by natural iron fertilization off Kerguelen Island in the Southern Ocean (KEOPS2). The abundances of heterotrophic bacteria and heterotrophic nanoflagellates, bacterial heterotrophic production, bacterial respiration, and bacterial growth efficiency, were consistently higher in surface waters of the iron-fertilized sites than at the reference site in HNLC (high nutrient low chlorophyll) waters. The abundance of virus-like particles remained unchanged, but viral production increased by a factor of 6 in iron-fertilized waters. Bacterial heterotrophic production was significantly related to heterotrophic nanoflagellate abundance and viral production across all sites, with bacterial production explaining about 70 and 85%, respectively, of the variance of each in the mixed layer (ML). Estimated rates of grazing and viral lysis, however, indicated that heterotrophic nanoflagellates accounted for a substantially higher loss of bacterial production (50%) than viruses (11%). Combining these results with rates of primary production and export determined for the study area, a budget for the flow of carbon through the microbial food web and higher trophic levels during the early (KEOPS2) and the late phase (KEOPS1) of the Kerguelen bloom is provided.
NASA Astrophysics Data System (ADS)
Christaki, U.; Lefèvre, D.; Georges, C.; Colombet, J.; Catala, P.; Courties, C.; Sime-Ngando, T.; Blain, S.; Obernosterer, I.
2014-05-01
Microbial food web dynamics were determined during the onset of several spring phytoplankton blooms induced by natural iron fertilization off Kerguelen Island in the Southern Ocean (KEOPS2). The abundances of heterotrophic bacteria and heterotrophic nanoflagellates, bacterial heterotrophic production, bacterial respiration, and bacterial growth efficiency, were consistently higher in surface waters of the iron-fertilized sites than at the reference site in HNLC (high nutrient low chlorophyll) waters. The abundance of viral like particles remained unchanged, but viral production increased by a factor of 6 in iron-fertilized waters. Bacterial heterotrophic production was significantly related to heterotrophic nanoflagellate abundance and viral production across all sites, with bacterial production explaining about 70 and 85%, respectively, of the variance of each in the mixed layer (ML). Estimated rates of grazing and viral lysis, however, indicated that heterotrophic nanoflagellates accounted for a substantially higher loss of bacterial production (50%) than viruses (11%). Combining these results with rates of primary production and export determined for the study area, a budget for the flow of carbon through the microbial food web and higher levels during the early (KEOPS2) and the late phase (KEOPS1) of the Kerguelen bloom is provided.
An indicator-based evaluation of Black Sea food web dynamics during 1960-2000
NASA Astrophysics Data System (ADS)
Akoglu, Ekin; Salihoglu, Baris; Libralato, Simone; Oguz, Temel; Solidoro, Cosimo
2014-06-01
Four Ecopath mass-balance models were implemented for evaluating the structure and function of the Black Sea ecosystem using several ecological indicators during four distinctive periods (1960s, 1980-1987, 1988-1994 and 1995-2000). The results exemplify how the Black Sea ecosystem structure started to change after the 1960s as a result of a series of trophic transformations, i.e., shifts in the energy flow pathways through the food web. These transformations were initiated by anthropogenic factors, such as eutrophication and overfishing, that led to the transfer of large quantities of energy to the trophic dead-end species, which had no natural predators in the ecosystem, i.e., jellyfish whose biomass increased from 0.03 g C m- 2 in 1960-1969 to 0.933 g C m- 2 in 1988-1994. Concurrently, an alternative short pathway for energy transfer was formed that converted significant amounts of system production back to detritus. This decreased the transfer efficiency of energy flow from the primary producers to the higher trophic levels from 9% in the 1960s to 3% between 1980 and 1987. We conclude that the anchovy stock collapse and successful establishment of the alien comb-jelly Mnemiopsis in 1989 were rooted in the trophic interactions in the food web, all of which were exacerbated because of the long-term establishment of a combination of anthropogenic stressors.
Using web-based training to enhance perceptual-cognitive skills in complex dynamic offside events.
Put, Koen; Wagemans, Johan; Spitz, Jochim; Williams, A Mark; Helsen, Werner F
2016-01-01
In association football, the difficulty in making offside decisions depends on both perceptual and cognitive processes. Therefore, the objectives of the present study were to enhance the decision-making skills of assistant referees by further developing their ability to (1) time slice the incoming information flow into series of isolated time frames during an ongoing offside situation and (2) use this information to mentally read off the spatial positions of the key-role players. Training (n = 10) and control groups (n = 10) were exposed to a pre- and post-test, consisting of an offside decision-making and frame recognition test. In the latter, assistant referees were asked to indicate which of five photos best represented the spatial position of the defender and attacker at the moment of the pass. Only the training group received 12 web-based offside training sessions. First, the training group improved in mentally freezing, holding and scanning the mental picture of the offside situation in short-term memory from pre- to post-test, as evidenced by an increased recognition accuracy. Second, the improvement in recognition accuracy resulted in enhanced performance on the offside decision-making task. The benefits of web-based training are highlighted.
NASA Astrophysics Data System (ADS)
Consoli, Antonio; Sanchez, Jorge R.; Horche, Paloma R.; Esquivias, Ignacio
2014-07-01
presented. The proposed tool is addressed to the students of optical communication courses, encouraging self consolidation of the subjects learned in lectures. The semiconductor laser model is based on the well known rate equations for the carrier density, photon density and optical phase. The direct modulation of the laser is considered with input parameters which can be selected by the user. Different options for the waveform, amplitude and frequency of the injected current are available, together with the bias point. Simulation results are plotted for carrier density and output power versus time. Instantaneous frequency variations of the laser output are numerically shifted to the audible frequency range and sent to the computer loudspeakers. This results in an intuitive description of the "chirp" phenomenon due to amplitude-phase coupling, typical of directly modulated semiconductor lasers. In this way, the student can actually listen to the time resolved spectral content of the laser output. By changing the laser parameters and/or the modulation parameters, consequent variation of the laser output can be appreciated in intuitive manner. The proposed educational tool has been previously implemented by the same authors with locally executable software. In the present manuscript, we extend our previous work to a web based platform, offering improved distribution and allowing its use to the wide audience of the web.
Using qualitative eye-tracking data to inform audio presentation of dynamic Web content
NASA Astrophysics Data System (ADS)
Brown, Andy; Jay, Caroline; Harper, Simon
2010-12-01
Presenting Web content through screen readers can be a challenging task, but this is the only means of access for many blind and visually impaired users. The difficulties are more acute when the information forms part of an interactive process, such as the increasingly common "Web 2.0 applications". If the process is to be completed correctly and efficiently it is vital that appropriate information is given to the user at an appropriate time. Designing a non-visual interface that achieves these aims is a non-trivial task, for which several approaches are possible. The one taken here is to use eye-tracking to understand how sighted users interact with the content, and to gain insight into how they benefit from the information, then apply this understanding to design a non-visual user interface. This paper describes how this technique was applied to develop audio interfaces for two common types of interaction-auto-suggest lists and pop-up calendars. Although the resulting interfaces were quite different, one largely mirroring the visual representation and the other not, evaluations showed that the approach was effective, with both audio implementations effective and popular with participants.
medplot: a web application for dynamic summary and analysis of longitudinal medical data based on R.
Ahlin, Črt; Stupica, Daša; Strle, Franc; Lusa, Lara
2015-01-01
In biomedical studies the patients are often evaluated numerous times and a large number of variables are recorded at each time-point. Data entry and manipulation of longitudinal data can be performed using spreadsheet programs, which usually include some data plotting and analysis capabilities and are straightforward to use, but are not designed for the analyses of complex longitudinal data. Specialized statistical software offers more flexibility and capabilities, but first time users with biomedical background often find its use difficult. We developed medplot, an interactive web application that simplifies the exploration and analysis of longitudinal data. The application can be used to summarize, visualize and analyze data by researchers that are not familiar with statistical programs and whose knowledge of statistics is limited. The summary tools produce publication-ready tables and graphs. The analysis tools include features that are seldom available in spreadsheet software, such as correction for multiple testing, repeated measurement analyses and flexible non-linear modeling of the association of the numerical variables with the outcome. medplot is freely available and open source, it has an intuitive graphical user interface (GUI), it is accessible via the Internet and can be used within a web browser, without the need for installing and maintaining programs locally on the user's computer. This paper describes the application and gives detailed examples describing how to use the application on real data from a clinical study including patients with early Lyme borreliosis.
Le Meur, Nolwenn; Lamirault, Guillaume; Bihouée, Audrey; Steenman, Marja; Bédrine-Ferran, Hélène; Teusan, Raluca; Ramstein, Gérard; Léger, Jean J.
2004-01-01
We propose a freely accessible web-based pipeline, which processes raw microarray scan data to obtain experimentally consolidated gene expression values. The tool MADSCAN, which stands for MicroArray Data Suites of Computed ANalysis, makes a practical choice among the numerous methods available for filtering, normalizing and scaling of raw microarray expression data in a dynamic and automatic way. Different statistical methods have been adapted to extract reliable information from replicate gene spots as well as from replicate microarrays for each biological situation under study. A carefully constructed experimental design thus allows to detect outlying expression values and to identify statistically significant expression values, together with a list of quality controls with proposed threshold values. The integrated processing procedure described here, based on multiple measurements per gene, is decisive for reliably monitoring subtle gene expression changes typical for most biological events. PMID:15475389
Coolbaugh, Crystal L; Raymond Jr, Stephen C
2015-01-01
Background Computer tailored, Web-based interventions have emerged as an effective approach to promote physical activity. Existing programs, however, do not adjust activities according to the participant’s compliance or physiologic adaptations, which may increase risk of injury and program attrition in sedentary adults. To address this limitation, objective activity monitor (AM) and heart rate data could be used to guide personalization of physical activity, but improved Web-based frameworks are needed to test such interventions. Objective The objective of this study is to (1) develop a personalized physical activity prescription (PPAP) app that combines dynamic Web-based guidance with multi-sensor AM data to promote physical activity and (2) to assess the feasibility of using this system in the field. Methods The PPAP app was constructed using an open-source software platform and a custom, multi-sensor AM capable of accurately measuring heart rate and physical activity. A novel algorithm was written to use a participant’s compliance and physiologic response to aerobic training (ie, changes in daily resting heart rate) recorded by the AM to create daily, personalized physical activity prescriptions. In addition, the PPAP app was designed to (1) manage the transfer of files from the AM to data processing software and a relational database, (2) provide interactive visualization features such as calendars and training tables to encourage physical activity, and (3) enable remote administrative monitoring of data quality and participant compliance. A 12-week feasibility study was performed to assess the utility and limitations of the PPAP app used by sedentary adults in the field. Changes in physical activity level and resting heart rate were monitored throughout the intervention. Results The PPAP app successfully created daily, personalized physical activity prescriptions and an interactive Web environment to guide and promote physical activity by the participants
Coolbaugh, Crystal L; Raymond, Stephen C; Hawkins, David A
2015-06-04
Computer tailored, Web-based interventions have emerged as an effective approach to promote physical activity. Existing programs, however, do not adjust activities according to the participant's compliance or physiologic adaptations, which may increase risk of injury and program attrition in sedentary adults. To address this limitation, objective activity monitor (AM) and heart rate data could be used to guide personalization of physical activity, but improved Web-based frameworks are needed to test such interventions. The objective of this study is to (1) develop a personalized physical activity prescription (PPAP) app that combines dynamic Web-based guidance with multi-sensor AM data to promote physical activity and (2) to assess the feasibility of using this system in the field. The PPAP app was constructed using an open-source software platform and a custom, multi-sensor AM capable of accurately measuring heart rate and physical activity. A novel algorithm was written to use a participant's compliance and physiologic response to aerobic training (ie, changes in daily resting heart rate) recorded by the AM to create daily, personalized physical activity prescriptions. In addition, the PPAP app was designed to (1) manage the transfer of files from the AM to data processing software and a relational database, (2) provide interactive visualization features such as calendars and training tables to encourage physical activity, and (3) enable remote administrative monitoring of data quality and participant compliance. A 12-week feasibility study was performed to assess the utility and limitations of the PPAP app used by sedentary adults in the field. Changes in physical activity level and resting heart rate were monitored throughout the intervention. The PPAP app successfully created daily, personalized physical activity prescriptions and an interactive Web environment to guide and promote physical activity by the participants. The varied compliance of the
Study on dynamic services composition of web services based on BPEL
NASA Astrophysics Data System (ADS)
Gao, Jinyue; Huang, Fei; Zhang, Gongxuan
2013-12-01
From the core concepts of SOA (Service-Oriented Architecture) ——"Service" starting the service composition is discussed in detail, from the service relationships network modeling, services dynamic composition approach based on Business Process Execution Language BPEL (Business Process Execution Language) is proposed in this paper, meanwhile two concepts of service agent and service quality are described, which achieve the service process dynamic execution.
NASA Astrophysics Data System (ADS)
Gao, Siwen; Rajendran, Mohan Kumar; Fivel, Marc; Ma, Anxin; Shchyglo, Oleg; Hartmaier, Alexander; Steinbach, Ingo
2015-10-01
Three-dimensional discrete dislocation dynamics (DDD) simulations in combination with the phase-field method are performed to investigate the influence of different realistic Ni-base single crystal superalloy microstructures with the same volume fraction of {γ\\prime} precipitates on plastic deformation at room temperature. The phase-field method is used to generate realistic microstructures as the boundary conditions for DDD simulations in which a constant high uniaxial tensile load is applied along different crystallographic directions. In addition, the lattice mismatch between the γ and {γ\\prime} phases is taken into account as a source of internal stresses. Due to the high antiphase boundary energy and the rare formation of superdislocations, precipitate cutting is not observed in the present simulations. Therefore, the plastic deformation is mainly caused by dislocation motion in γ matrix channels. From a comparison of the macroscopic mechanical response and the dislocation evolution for different microstructures in each loading direction, we found that, for a given {γ\\prime} phase volume fraction, the optimal microstructure should possess narrow and homogeneous γ matrix channels.
NASA Astrophysics Data System (ADS)
Ouyanga, Chaojun; Lia, Zhenhuan; Huanga, Minsheng; Hua, Lili; Houa, Chuantao
2009-11-01
2D discrete dislocation dynamic modeling of compressed micro-pillars attached on a huge base is executed to study the size-dependent microplastic behavior of micro-pillars and the corresponding size effect. In addition to the conventional dimensional parameters of the micro-pillar such as the micro-pillar size and the height-to-width ratio, the micro-pillar taper angle and the dislocation slip plane orientation angle in the micro-pillar are also considered to address the size effect and its rich underlying mechanism. Computational results show that there are at least two operating mechanisms responsible for the plastic behavior of micro-pillars. One is associated with the dislocation free slip-out from the micro-pillar sidewall; the other is related to the dislocation pile-up at the base and the top end of the pillar. The overall mechanism governing the size effect of the micro-pillar rests with multi-factors, including the micro-pillar size, the height-to-width ratio, the micro-pillar taper and the slip plane orientation angle; however, whether the "free slip band" exists or not is the most important denotation. The well-known Schmid law still validates in the slender micro-pillars due to existence of the free slip band, whereas it may fail in the podgier micro-pillars due to absence of the free slip band; as a result, a complicated even "reverse" size effect appears.
NASA Astrophysics Data System (ADS)
Lee, Hee-Seung; Tuckerman, Mark E.
2008-12-01
An efficient computational approach to perform Car-Parrinello ab initio molecular dynamics (CPAIMD) simulations under cluster (free) boundary conditions is presented. The general approach builds upon a recent real-space CPAIMD formalism using discrete variable representation (DVR) basis sets [Y. Liu et al., Phys. Rev. B 12, 125110 (2003); H.-S. Lee and M. E. Tuckerman, J. Phys. Chem. A 110, 5549 (2006)]. In order to satisfy cluster boundary conditions, a DVR based on sinc functions is utilized to expand the Kohn-Sham orbitals and electron density. Poisson's equation is solved in order to calculate the Hartree potential via an integral representation of the 1/r singularity. Excellent convergence properties are achieved with respect to the number of grid points (or DVR functions) and the size of the simulation cell. A straightforward implementation of the present approach leads to near linear scaling [O(N4/3)] of the computational cost with respect to the system size (N) for the solution of Poisson's equation. The accuracy and stability of CPAIMD simulations based on sinc DVR are tested for a model problem as well as for N2 and a water dimer.
Lee, Hee-Seung; Tuckerman, Mark E
2008-12-14
An efficient computational approach to perform Car-Parrinello ab initio molecular dynamics (CPAIMD) simulations under cluster (free) boundary conditions is presented. The general approach builds upon a recent real-space CPAIMD formalism using discrete variable representation (DVR) basis sets [Y. Liu et al., Phys. Rev. B 12, 125110 (2003); H.-S. Lee and M. E. Tuckerman, J. Phys. Chem. A 110, 5549 (2006)]. In order to satisfy cluster boundary conditions, a DVR based on sinc functions is utilized to expand the Kohn-Sham orbitals and electron density. Poisson's equation is solved in order to calculate the Hartree potential via an integral representation of the 1/r singularity. Excellent convergence properties are achieved with respect to the number of grid points (or DVR functions) and the size of the simulation cell. A straightforward implementation of the present approach leads to near linear scaling [O(N(4/3))] of the computational cost with respect to the system size (N) for the solution of Poisson's equation. The accuracy and stability of CPAIMD simulations based on sinc DVR are tested for a model problem as well as for N(2) and a water dimer.
Christobel, M.; Tamil Selvi, S.; Benedict, Shajulin
2015-01-01
One of the most significant and the topmost parameters in the real world computing environment is energy. Minimizing energy imposes benefits like reduction in power consumption, decrease in cooling rates of the computing processors, provision of a green environment, and so forth. In fact, computation time and energy are directly proportional to each other and the minimization of computation time may yield a cost effective energy consumption. Proficient scheduling of Bag-of-Tasks in the grid environment ravages in minimum computation time. In this paper, a novel discrete particle swarm optimization (DPSO) algorithm based on the particle's best position (pbDPSO) and global best position (gbDPSO) is adopted to find the global optimal solution for higher dimensions. This novel DPSO yields better schedule with minimum computation time compared to Earliest Deadline First (EDF) and First Come First Serve (FCFS) algorithms which comparably reduces energy. Other scheduling parameters, such as job completion ratio and lateness, are also calculated and compared with EDF and FCFS. An energy improvement of up to 28% was obtained when Makespan Conservative Energy Reduction (MCER) and Dynamic Voltage Scaling (DVS) were used in the proposed DPSO algorithm. PMID:26075296
Christobel, M; Tamil Selvi, S; Benedict, Shajulin
2015-01-01
One of the most significant and the topmost parameters in the real world computing environment is energy. Minimizing energy imposes benefits like reduction in power consumption, decrease in cooling rates of the computing processors, provision of a green environment, and so forth. In fact, computation time and energy are directly proportional to each other and the minimization of computation time may yield a cost effective energy consumption. Proficient scheduling of Bag-of-Tasks in the grid environment ravages in minimum computation time. In this paper, a novel discrete particle swarm optimization (DPSO) algorithm based on the particle's best position (pbDPSO) and global best position (gbDPSO) is adopted to find the global optimal solution for higher dimensions. This novel DPSO yields better schedule with minimum computation time compared to Earliest Deadline First (EDF) and First Come First Serve (FCFS) algorithms which comparably reduces energy. Other scheduling parameters, such as job completion ratio and lateness, are also calculated and compared with EDF and FCFS. An energy improvement of up to 28% was obtained when Makespan Conservative Energy Reduction (MCER) and Dynamic Voltage Scaling (DVS) were used in the proposed DPSO algorithm.
Caughey, W S; Shimada, H; Choc, M G; Tucker, M P
1981-01-01
Infrared spectra for the carbon monoxide complex with myoglobin isolated as the oxygenyl species from bovine heart muscle were carefully examined in the C--O stretch region as either the pH or the temperature was varied. Deconvolutions of these spectra into bands of Gaussian shape suggest the presence of four bands near 1938(I), 1944(II), 1954(III), and 1965(IV) cm-1 with halfband widths of about 18, 9, 9, and 10 cm-1, respectively. The relative intensities of the four bands varied with changes in pH or temperature. 13C NMR spectra and other evidence indicate that the four C--O stretch bands arise from four discrete rapidly interconverting conformers: CI, CII, CIII, and CIV. Under conditions of physiological pH and temperature, the relative stabilities are CI approximately CII much greater than CIII approximately CIV. The delta H and delta S values for conformer interconversions are estimated to range from -8 to 34 kJ/mol and -27 to 87 J.mol-1 K-1, respectively; therefore the structures of the conformers may be expected to vary significantly. These findings provide evidence for a highly flexible, dynamic structure at the ligand-binding site of bovine myoglobin, even when ligands are bound. PMID:6942409
Dynamic taxonomies applied to a web-based relational database for geo-hydrological risk mitigation
NASA Astrophysics Data System (ADS)
Sacco, G. M.; Nigrelli, G.; Bosio, A.; Chiarle, M.; Luino, F.
2012-02-01
In its 40 years of activity, the Research Institute for Geo-hydrological Protection of the Italian National Research Council has amassed a vast and varied collection of historical documentation on landslides, muddy-debris flows, and floods in northern Italy from 1600 to the present. Since 2008, the archive resources have been maintained through a relational database management system. The database is used for routine study and research purposes as well as for providing support during geo-hydrological emergencies, when data need to be quickly and accurately retrieved. Retrieval speed and accuracy are the main objectives of an implementation based on a dynamic taxonomies model. Dynamic taxonomies are a general knowledge management model for configuring complex, heterogeneous information bases that support exploratory searching. At each stage of the process, the user can explore or browse the database in a guided yet unconstrained way by selecting the alternatives suggested for further refining the search. Dynamic taxonomies have been successfully applied to such diverse and apparently unrelated domains as e-commerce and medical diagnosis. Here, we describe the application of dynamic taxonomies to our database and compare it to traditional relational database query methods. The dynamic taxonomy interface, essentially a point-and-click interface, is considerably faster and less error-prone than traditional form-based query interfaces that require the user to remember and type in the "right" search keywords. Finally, dynamic taxonomy users have confirmed that one of the principal benefits of this approach is the confidence of having considered all the relevant information. Dynamic taxonomies and relational databases work in synergy to provide fast and precise searching: one of the most important factors in timely response to emergencies.
NASA Astrophysics Data System (ADS)
Gao, Siwen; Fivel, Marc; Ma, Anxin; Hartmaier, Alexander
2017-05-01
A three-dimensional (3D) discrete dislocation dynamics (DDD) creep model is developed to investigate creep behavior under uniaxial tensile stress along the crystallographic [001] direction in Ni-base single crystal superalloys, which takes explicitly account of dislocation glide, climb and vacancy diffusion, but neglects phase transformation like rafting of γ‧ precipitates. The vacancy diffusion model takes internal stresses by dislocations and mismatch strains into account and it is coupled to the dislocation dynamics model in a numerically efficient way. This model is helpful for understanding the fundamental creep mechanisms in superalloys and clarifying the effects of dislocation glide and climb on creep deformation. In cases where the precipitate cutting rarely occurs, e.g. due to the high anti-phase boundary energy and the lack of superdislocations, the dislocation glide in the γ matrix and the dislocation climb along the γ/γ‧ interface dominate plastic deformation. The simulation results show that a high temperature or a high stress both promote dislocation motion and multiplication, so as to cause a large creep strain. Dislocation climb accelerated by high temperature only produces a small plastic strain, but relaxes the hardening caused by the filling γ channels and lets dislocations further glide and multiply. The strongest variation of vacancy concentration occurs in the horizontal channels, where more mixed dislocations exit and tend to climb. The increasing internal stresses due to the increasing dislocation density are easily overcome by dislocations under a high external stress that leads to a long-term dislocation glide accompanied by multiplication.
Dorostkar, Omid; Guyer, Robert A.; Johnson, Paul A.; ...
2017-05-01
The presence of fault gouge has considerable influence on slip properties of tectonic faults and the physics of earthquake rupture. The presence of fluids within faults also plays a significant role in faulting and earthquake processes. In this study, we present 3-D discrete element simulations of dry and fluid-saturated granular fault gouge and analyze the effect of fluids on stick-slip behavior. Fluid flow is modeled using computational fluid dynamics based on the Navier-Stokes equations for an incompressible fluid and modified to take into account the presence of particles. Analysis of a long time train of slip events shows that themore » (1) drop in shear stress, (2) compaction of granular layer, and (3) the kinetic energy release during slip all increase in magnitude in the presence of an incompressible fluid, compared to dry conditions. We also observe that on average, the recurrence interval between slip events is longer for fluid-saturated granular fault gouge compared to the dry case. This observation is consistent with the occurrence of larger events in the presence of fluid. It is found that the increase in kinetic energy during slip events for saturated conditions can be attributed to the increased fluid flow during slip. Finally, our observations emphasize the important role that fluid flow and fluid-particle interactions play in tectonic fault zones and show in particular how discrete element method (DEM) models can help understand the hydromechanical processes that dictate fault slip.« less
Trophic positioning of meiofauna revealed by stable isotopes and food web analyses.
Schmid-Araya, Jenny M; Schmid, Peter E; Tod, Steven P; Esteban, Genoveva F
2016-11-01
Despite important advances in the ecology of river food webs, the strength and nature of the connection between the meio- and macrofaunal components of the web are still debated. Some unresolved issues are the effects of the inclusion of meiofaunal links and their temporal variations on the overall river food web properties, and the significance of autochthonous and allochthonous material for these components. In the present study, we conducted analyses of gut content of macro- and meiofauna and stable isotope analyses of meiofauna to examine seasonal food webs of a chalk stream. The results of the gut content analyses, confirmed by the δ(13) C signatures, revealed a seasonal shift from a dependence on autochthonous (biofilm) to allochthonous food sources. Here, we demonstrate that aggregating basal or meiofaunal species into single categories affects key web properties such as web size, links, linkage density, and predator-prey ratios. More importantly, seasonal variation in attributes characterized the entire web and these changes persist regardless of taxonomic resolution. Furthermore, our analyses evidenced discrete variations in δ(15) N across the meiofauna community with a trophic structure that confirms gut content analyses, placing the meiofauna high in the food web. We, therefore, conclude that small-body-sized taxa can occur high in dynamic river food webs, questioning assumptions that trophic position increases with body size and that webs are static.
Food web dynamics in the Scotia Sea in summer: A stable isotope study
NASA Astrophysics Data System (ADS)
Stowasser, G.; Atkinson, A.; McGill, R. A. R.; Phillips, R. A.; Collins, M. A.; Pond, D. W.
2012-01-01
The pelagic food web of the Scotia Sea was studied by analysing natural abundances of nitrogen and carbon stable isotopes of primary producers and pelagic consumers, sampled from the seasonal ice edge in the south to the Antarctic Polar Front in the north. The analysis covered, within a single mid-summer period, particulate organic matter (POM) and 38 taxa, ranging from suspension feeding copepods and salps to omnivorous euphausiids, pelagic fish and higher, land-based predators including fur seals, penguins and flying birds. Spatial variation in δ 15N of POM correlated well with nutrient availability and primary productivity. Latitudinal differences in δ 13C of POM were closely linked to variations in temperature, nutrients and productivity depending on the frontal region sampled. This translated to equivalent (although smaller) regional δ 13C differences among higher trophic levels. The trophic positions of species based on isotope values broadly agreed with previously published dietary data with three important exceptions. First, the carnivorous amphipod Themisto gaudichaudii had anomalously low δ 15N values. Second, Euphausia superba had δ 15N values that were also surprisingly low, considering the abundant literature suggesting its omnivory. Third, the copepod Rhincalanus gigas, considered a suspension feeder, had unexpectedly high δ 15N values rather more in keeping with omnivorous feeding. The consumer δ 15N values ranged from 1.2‰ (min.) measured in Salpa thompsoni (designated here as trophic level (TL) 2 across all regions) to 15.2‰ (max.) measured in white-chinned petrels ( Procellaria aequinoctialis, calculated as TL5 relative to the TL2 of salps). Excluding seabirds, the resulting food chain length of 3.7 TL (above POM at TL1) was lower than in most other Southern Ocean and temperate marine pelagic ecosystems. The majority (60%) of vertebrate predators occupied only 1-1.5 trophic levels above the herbivorous suspension feeders such as krill
Toxaphene congeners in the Canadian Great Lakes basin: temporal and spatial food web dynamics.
Whittle, D M; Kiriluk, R M; Carswell, A A; Keir, M J; MacEachen, D C
2000-01-01
Samples of a top predator fish species, lake trout (Salvelinus namaycush) and predominant forage species including smelt (Osmerus mordax), alewife (Alosa pseudoharengus), slimy sculpin (Cottus cognatus), deepwater sculpin (Myoxocephalus quadricornis) and lake herring (Coregonus artedii) were, collected from throughout 4 of the 5 Great Lakes (Superior, Huron, Erie and Ontario) (Fig. 1). Lake trout were also collected from three isolated lake systems (Lakes Nipigon, Simcoe and Opeongo), all located within the basin. All the samples were analysed for body burdens of total toxaphene and 22 toxaphene congeners. In addition, from each of the Great Lakes sites samples of major invertebrate dietary items, which included Mysis relicta, Diporeia hoyi and plankton, were similarly analysed. Whole lake trout samples, archived at -80 degrees C, were reanalysed to determine historical trends of toxaphene congeners plus carbon and nitrogen stable isotope signatures. The Lake Superior food web consistently had the highest levels of total toxaphene of all the Great Lakes monitored. The primary source of toxaphene to Lake Superior has been identified as atmospheric transport and deposition from sites in the southern US, Mexico and Central America (Hoff, R.M., Strachan, W.M.J., Sweet, C.W., Chan, C.H., Shackelton, M., Bidleman, T.F., Brice, K.A., Burnison, D.A., Cussion, S., Gatz, D.F., Harlin, K., Schroeder, W.H., 1996. Atmospheric deposition of toxic chemicals to the Great Lakes: A review of data through 1994. Atmospheric Environ. 30, 3505-3527). Of the offsystem lakes surveyed. Lake Nipigon, situated due north of Lake Superior and with a Lake Basin area of about 6% of Lake Superior (Hendendorf, C.E., 1982. J. Great Lakes Res. 8(3), 379-412) had total toxaphene levels in lake trout equivalent to about 50% of those found in lake trout from Lake Superior. Temporal trend toxaphene congener analysis was conducted on archived whole fish samples collected over the period 1980 through to
Food-web dynamics and trophic-level interactions in a multispecies community of freshwater unionids
Nichols, S.J.; Garling, D.
2000-01-01
We compared feeding habits and trophic-level relationships of unionid species in a detritus-dominated river and an alga-dominated lake using biochemical analyses, gut contents, and stable-isotope ratios. The δ13C ratios for algae and other food-web components show that all unionids from both the river and the lake used bacterial carbons, not algal carbons, as their main dietary source, in spite of positive selection and concentration of diatoms and green algae from the water column in the gut and mantle cavity. Algae did provide key nutrients such as vitamins A and D and phytosterols that were bioaccumulated in the tissues of all species. The δ15N ratios for the multispecies unionid community in the Huron River indicated some differences in nitrogen enrichment between species, the greatest enrichment being found in Pyganadon grandis. These δ15N ratios indicate that unionids may not always feed as primary consumers or omnivores. Stable-isotope data were critical for delineating diets and trophic-level interactions of this group of filter-feeders. Further refinements in identifying bacterial and picoplankton components of the fine particulate organic matter are needed to complete our understanding of resource partitioning between multispecies unionid populations.
Coupling News Sentiment with Web Browsing Data Improves Prediction of Intra-Day Price Dynamics
Ranco, Gabriele; Bordino, Ilaria; Bormetti, Giacomo; Caldarelli, Guido; Lillo, Fabrizio; Treccani, Michele
2016-01-01
The new digital revolution of big data is deeply changing our capability of understanding society and forecasting the outcome of many social and economic systems. Unfortunately, information can be very heterogeneous in the importance, relevance, and surprise it conveys, affecting severely the predictive power of semantic and statistical methods. Here we show that the aggregation of web users’ behavior can be elicited to overcome this problem in a hard to predict complex system, namely the financial market. Specifically, our in-sample analysis shows that the combined use of sentiment analysis of news and browsing activity of users of Yahoo! Finance greatly helps forecasting intra-day and daily price changes of a set of 100 highly capitalized US stocks traded in the period 2012–2013. Sentiment analysis or browsing activity when taken alone have very small or no predictive power. Conversely, when considering a news signal where in a given time interval we compute the average sentiment of the clicked news, weighted by the number of clicks, we show that for nearly 50% of the companies such signal Granger-causes hourly price returns. Our result indicates a “wisdom-of-the-crowd” effect that allows to exploit users’ activity to identify and weigh properly the relevant and surprising news, enhancing considerably the forecasting power of the news sentiment. PMID:26808833
Coupling News Sentiment with Web Browsing Data Improves Prediction of Intra-Day Price Dynamics.
Ranco, Gabriele; Bordino, Ilaria; Bormetti, Giacomo; Caldarelli, Guido; Lillo, Fabrizio; Treccani, Michele
2016-01-01
The new digital revolution of big data is deeply changing our capability of understanding society and forecasting the outcome of many social and economic systems. Unfortunately, information can be very heterogeneous in the importance, relevance, and surprise it conveys, affecting severely the predictive power of semantic and statistical methods. Here we show that the aggregation of web users' behavior can be elicited to overcome this problem in a hard to predict complex system, namely the financial market. Specifically, our in-sample analysis shows that the combined use of sentiment analysis of news and browsing activity of users of Yahoo! Finance greatly helps forecasting intra-day and daily price changes of a set of 100 highly capitalized US stocks traded in the period 2012-2013. Sentiment analysis or browsing activity when taken alone have very small or no predictive power. Conversely, when considering a news signal where in a given time interval we compute the average sentiment of the clicked news, weighted by the number of clicks, we show that for nearly 50% of the companies such signal Granger-causes hourly price returns. Our result indicates a "wisdom-of-the-crowd" effect that allows to exploit users' activity to identify and weigh properly the relevant and surprising news, enhancing considerably the forecasting power of the news sentiment.
Meshkat, Nicolette; Kuo, Christine Er-zhen; DiStefano, Joseph
2014-01-01
Parameter identifiability problems can plague biomodelers when they reach the quantification stage of development, even for relatively simple models. Structural identifiability (SI) is the primary question, usually understood as knowing which of P unknown biomodel parameters p1,…, pi,…, pP are-and which are not-quantifiable in principle from particular input-output (I-O) biodata. It is not widely appreciated that the same database also can provide quantitative information about the structurally unidentifiable (not quantifiable) subset, in the form of explicit algebraic relationships among unidentifiable pi. Importantly, this is a first step toward finding what else is needed to quantify particular unidentifiable parameters of interest from new I-O experiments. We further develop, implement and exemplify novel algorithms that address and solve the SI problem for a practical class of ordinary differential equation (ODE) systems biology models, as a user-friendly and universally-accessible web application (app)-COMBOS. Users provide the structural ODE and output measurement models in one of two standard forms to a remote server via their web browser. COMBOS provides a list of uniquely and non-uniquely SI model parameters, and-importantly-the combinations of parameters not individually SI. If non-uniquely SI, it also provides the maximum number of different solutions, with important practical implications. The behind-the-scenes symbolic differential algebra algorithms are based on computing Gröbner bases of model attributes established after some algebraic transformations, using the computer-algebra system Maxima. COMBOS was developed for facile instructional and research use as well as modeling. We use it in the classroom to illustrate SI analysis; and have simplified complex models of tumor suppressor p53 and hormone regulation, based on explicit computation of parameter combinations. It's illustrated and validated here for models of moderate complexity, with
Ben Said, Mohamed; Le Mignot, Loic; Richard, Jean Baptiste; Le Bihan, Christine; Toubiana, Laurent; Jais, Jean-Philippe; Landais, Paul
2006-01-01
A Multi-Source Information System (MSIS), has been designed for the Renal Epidemiology and Information Network (REIN) dedicated to End-Stage Renal Disease (ESRD). MSIS aims at providing reliable follow-up data for ESRD patients. It is based on an n-tier architecture, made out of a universal client, a dynamic Web server connected to a production database and to a data warehouse. MSIS is operational since 2002 and progressively deployed in 9 regions in France. It includes 16,677 patients. We show that the analysis of MSIS web log files allows evaluating the use of the system and the workload in a public-health perspective.
Lewis, Paul A.; Cunningham, Joan E.
2016-01-01
Background In the context of breast cancer, axillary web syndrome (AWS), also called lymphatic cording, typically presents in the weeks after axillary surgery. This painful condition, likely lymphofibrotic in origin, restricts upper extremity range of motion (ROM). There is no established treatment, although physical therapy and other approaches have been used to variable effect. This report describes treatment of a female client with AWS, who had recently undergone a unilateral simple mastectomy with sentinel node biopsy plus axillary dissection. Methods The client presented with pain upon movement (self-reported as 5 on the 0–10 Oxford Pain Scale), visible cording and restricted use of the ipsilateral upper extremity. Clinical assessment included determining the extent of AWS cording (taut, from axilla to wrist) and measuring glenohumeral joint ROM (140° flexion by goniometer). A therapeutic massage with movement protocol, termed dynamic angular petrissage, was administered over two sessions: Swedish massage combined with dynamically taking the limb through all possible angles of movement (passive ROM), controlling stretch and tension while simultaneously and segmentally applying petrissage and non-petrissage techniques to the underlying soft tissue. Careful attention was taken to not break the cord. Home care consisted of prescribed exercises performed by the patient. Results After Session One, pain was reduced (to 0/10), ROM improved (to 170° flexion), and cording was visibly reduced. After Session Two the cord was residually apparent only on hyperextension, with no ROM restrictions in glenohumeral joint flexion. Follow-up at three months revealed absence of visual or palpable evidence of cording, unrestricted glenohumeral joint ROM, and absence of movement-associated pain. Conclusion The signs and symptoms of AWS were quickly and effectively eliminated, without causing any pain or discomfort to the client. We propose that dynamic angular petrissage may be
NASA Astrophysics Data System (ADS)
Byrnes, Joseph S.; Toomey, Douglas R.; Hooft, Emilie E. E.; Nábělek, John; Braunmiller, Jochen
2017-08-01
We use the delay times of teleseismic S phases recorded by ocean bottom seismometers during the plate-scale Cascadia Initiative community experiment to constrain the heterogeneity of seismic velocity structure beneath young oceanic lithosphere. Our study area covers the entire Juan de Fuca (JdF) and Gorda plates, from their creation at the JdF and Gorda Ridges to their subduction beneath the North American continent, and the entire length of the Blanco transform fault. The range of the observed Vs anomalies requires variations in the melt fraction of the asthenosphere. The data require that low Vs anomalies extend to depths of at least 200 km, which is within the carbonatite melting regime. In the upper 200 km of the mantle, Vs increases rapidly to the east of the JdF Ridge, while there is no clear relationship with the age of the lithosphere in the Gorda region. The distribution of melt is asymmetric about both the JdF and Gorda Ridges. Dynamic upwelling - due to the buoyancy of the mantle - and accompanying downwelling can explain the rapid decrease in melt fraction to the east of the JdF Ridge, the asymmetry about the JdF Ridge, and the sinuous pattern of upwelling near the Blanco transform fault. Finally, mantle flow beneath the diffuse Gorda and Explorer plate boundaries is distinct from that beneath the discrete plate boundary of the JdF Ridge. In particular, shear between the Pacific and JdF plates appears to dominate mantle deformation over seafloor spreading beneath the Gorda Ridge.
Yifat, Jonathan; Gannot, Israel
2015-03-01
Early detection of malignant tumors plays a crucial role in the survivability chances of the patient. Therefore, new and innovative tumor detection methods are constantly searched for. Tumor-specific magnetic-core nano-particles can be used with an alternating magnetic field to detect and treat tumors by hyperthermia. For the analysis of the method effectiveness, the bio-heat transfer between the nanoparticles and the tissue must be carefully studied. Heat diffusion in biological tissue is usually analyzed using the Pennes Bio-Heat Equation, where blood perfusion plays an important role. Malignant tumors are known to initiate an angiogenesis process, where endothelial cell migration from neighboring vasculature eventually leads to the formation of a thick blood capillary network around them. This process allows the tumor to receive its extensive nutrition demands and evolve into a more progressive and potentially fatal tumor. In order to assess the effect of angiogenesis on the bio-heat transfer problem, we have developed a discrete stochastic 3D model & simulation of tumor-induced angiogenesis. The model elaborates other angiogenesis models by providing high resolution 3D stochastic simulation, capturing of fine angiogenesis morphological features, effects of dynamic sprout thickness functions, and stochastic parent vessel generator. We show that the angiogenesis realizations produced are well suited for numerical bio-heat transfer analysis. Statistical study on the angiogenesis characteristics was derived using Monte Carlo simulations. According to the statistical analysis, we provide analytical expression for the blood perfusion coefficient in the Pennes equation, as a function of several parameters. This updated form of the Pennes equation could be used for numerical and analytical analyses of the proposed detection and treatment method.
Renormdynamics, discrete dynamics and quanputers
NASA Astrophysics Data System (ADS)
Makhaldiani, Nugzar
2017-03-01
In the Standard Model of Particle Physics (SM), the values of the coupling constants and masses of particles evolve according to the Renormdynamic motion equations. In SM, minimal supersymmetric extension of the SM, standard pion-nucleon field theory and other models is shown how to define the values of coupling constants and masses. Why supersymmetry is So universal?
The discrete-time compensated Kalman filter
NASA Technical Reports Server (NTRS)
Lee, W. H.; Athans, M.
1978-01-01
A suboptimal dynamic compensator to be used in conjunction with the ordinary discrete time Kalman filter was derived. The resultant compensated Kalman Filter has the property that steady state bias estimation errors, resulting from modelling errors, were eliminated.
Comparing the Discrete and Continuous Logistic Models
ERIC Educational Resources Information Center
Gordon, Sheldon P.
2008-01-01
The solutions of the discrete logistic growth model based on a difference equation and the continuous logistic growth model based on a differential equation are compared and contrasted. The investigation is conducted using a dynamic interactive spreadsheet. (Contains 5 figures.)
Comparing the Discrete and Continuous Logistic Models
ERIC Educational Resources Information Center
Gordon, Sheldon P.
2008-01-01
The solutions of the discrete logistic growth model based on a difference equation and the continuous logistic growth model based on a differential equation are compared and contrasted. The investigation is conducted using a dynamic interactive spreadsheet. (Contains 5 figures.)
A web-based relational database for monitoring and analyzing mosquito population dynamics.
Sucaet, Yves; Van Hemert, John; Tucker, Brad; Bartholomay, Lyric
2008-07-01
Mosquito population dynamics have been monitored on an annual basis in the state of Iowa since 1969. The primary goal of this project was to integrate light trap data from these efforts into a centralized back-end database and interactive website that is available through the internet at http://iowa-mosquito.ent.iastate.edu. For comparative purposes, all data were categorized according to the week of the year and normalized according to the number of traps running. Users can readily view current, weekly mosquito abundance compared with data from previous years. Additional interactive capabilities facilitate analyses of the data based on mosquito species, distribution, or a time frame of interest. All data can be viewed in graphical and tabular format and can be downloaded to a comma separated value (CSV) file for import into a spreadsheet or more specialized statistical software package. Having this long-term dataset in a centralized database/website is useful for informing mosquito and mosquito-borne disease control and for exploring the ecology of the species represented therein. In addition to mosquito population dynamics, this database is available as a standardized platform that could be modified and applied to a multitude of projects that involve repeated collection of observational data. The development and implementation of this tool provides capacity for the user to mine data from standard spreadsheets into a relational database and then view and query the data in an interactive website.
NASA Astrophysics Data System (ADS)
Reitz, Meredith; Stark, Colin; Hung, Chi-Yao; Smith, Breannan; Grinspin, Eitan; Capart, Herve; Li, Liming; Crone, Timothy; Hsu, Leslie; Ling, Hoe
2014-05-01
A complete theoretical understanding of geophysical granular flow is essential to the reliable assessment of landslide and debris flow hazard and for the design of mitigation strategies, but several key challenges remain. Perhaps the most basic is a general treatment of the processes of internal energy dissipation, which dictate the runout velocity and the shape and scale of the affected area. Currently, dissipation is best described by macroscopic, empirical friction coefficients only indirectly related to the grain-scale physics. Another challenge is describing the forces exerted at the boundaries of the flow, which dictate the entrainment of further debris and the erosion of cohesive surfaces. While the granular effects on these boundary forces have been shown to be large compared to predictions from continuum approximations, the link between granular effects and erosion or entrainment rates has not been settled. Here we present preliminary results of a multi-disciplinary study aimed at improving our understanding of granular flow energy dissipation and boundary forces, through an effort to connect grain-scale physics to macroscopic behaviors. Insights into grain-scale force distributions and energy dissipation mechanisms are derived from discrete contact-dynamics simulations. Macroscopic erosion and flow behaviors are documented from a series of granular flow experiments, in which a rotating drum half-filled with grains is placed within a centrifuge payload, in order to drive effective gravity levels up to ~100g and approach the forces present in natural systems. A continuum equation is used to characterize the flowing layer depth and velocity resulting from the force balance between the down-slope pull of gravity and the friction at the walls. In this presentation we will focus on the effect of granular-specific physics such as force chain networks and grain-grain collisions, derived from the contact dynamics simulations. We will describe our efforts to
NASA Astrophysics Data System (ADS)
Liou, C.; Hulbert, S.
We present the architecture, design, and implementation details of the ADASS XII web site. The web site was implemented in Zope, a high-performance application server, web server, and content management system rolled into one. Zope includes a robust, scalable object database, web services architecture, and powerful programming capabilities. The web site was built to conform to HTML, CSS, and accessibility standards as adopted by the W3C. This dynamic web site also taps into a back-end Sybase database while requiring a minimal amount of coding. We offer this site as a prototype web site suitable for reuse in supporting future ADASS meetings.
Venner, Samuel; Chadès, Iadine; Bel-Venner, Marie-Claude; Pasquet, Alain; Charpillet, François; Leborgne, Raymond
2006-08-21
Dynamic state-dependent models have been widely developed since 1990s for solving questions in evolutionary ecology. Up to now, these models were mainly run over finite-time horizon. However, for many biological questions an infinite-time horizon perspective could be more appropriate, especially when the end of the modeled period is state- rather than time-dependent. Despite this approach is widely used in the field of economics and operational research, thus far no work has been providing biologists with a general method to solve infinite-time horizon problems. Here we present such a method, through the exhaustive description of an algorithm that we implement to determine the strategy an organism should follow to reach a particular state as fast as possible while limiting mortality risk. To illustrate that method we explored web-building behavior in an orb-weaving spider. How are adult females predicted to build their successive webs to gain energy, grow, and lay their first clutch as fast as possible, without suffering from either predation or starvation? From this example, we first show how an optimal strategy over infinite-time horizon can be processed and selected. Second, we analyse variations of the optimal web-building strategy along with the spider's body weight and predation risk during web building. Our model yields two main predictions: (1) spiders reduce their web size as they are gaining weight due to body-mass-dependent cost of web-building behavior, and (2) this reduction in web size starts at lower weight under higher predation risk.