Directory of Open Access Journals (Sweden)
Le Novère Nicolas
2010-03-01
Full Text Available Abstract Background Most cellular signal transduction mechanisms depend on a few molecular partners whose roles depend on their position and movement in relation to the input signal. This movement can follow various rules and take place in different compartments. Additionally, the molecules can form transient complexes. Complexation and signal transduction depend on the specific states partners and complexes adopt. Several spatial simulator have been developed to date, but none are able to model reaction-diffusion of realistic multi-state transient complexes. Results Meredys allows for the simulation of multi-component, multi-feature state molecular species in two and three dimensions. Several compartments can be defined with different diffusion and boundary properties. The software employs a Brownian dynamics engine to simulate reaction-diffusion systems at the reactive particle level, based on compartment properties, complex structure, and hydro-dynamic radii. Zeroth-, first-, and second order reactions are supported. The molecular complexes have realistic geometries. Reactive species can contain user-defined feature states which can modify reaction rates and outcome. Models are defined in a versatile NeuroML input file. The simulation volume can be split in subvolumes to speed up run-time. Conclusions Meredys provides a powerful and versatile way to run accurate simulations of molecular and sub-cellular systems, that complement existing multi-agent simulation systems. Meredys is a Free Software and the source code is available at http://meredys.sourceforge.net/.
Multi-scale simulation of reaction-diffusion systems
Vijaykumar, A.
2017-01-01
In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green’s Function
Reaction-diffusion controlled growth of complex structures
Noorduin, Willem; Mahadevan, L.; Aizenberg, Joanna
2013-03-01
Understanding how the emergence of complex forms and shapes in biominerals came about is both of fundamental and practical interest. Although biomineralization processes and organization strategies to give higher order architectures have been studied extensively, synthetic approaches to mimic these self-assembled structures are highly complex and have been difficult to emulate, let alone replicate. The emergence of solution patterns has been found in reaction-diffusion systems such as Turing patterns and the BZ reaction. Intrigued by this spontaneous formation of complexity we explored if similar processes can lead to patterns in the solid state. We here identify a reaction-diffusion system in which the shape of the solidified products is a direct readout of the environmental conditions. Based on insights in the underlying mechanism, we developed a toolbox of engineering strategies to deterministically sculpt patterns and shapes, and combine different morphologies to create a landscape of hierarchical multi scale-complex tectonic architectures with unprecedented levels of complexity. These findings may hold profound implications for understanding, mimicking and ultimately expanding upon nature's morphogenesis strategies, allowing the synthesis of advanced highly complex microscale materials and devices. WLN acknowledges the Netherlands Organization for Scientific Research for financial support
International Nuclear Information System (INIS)
Owolabi, Kolade M.
2016-01-01
The aim of this paper is to examine pattern formation in the sub— and super-diffusive scenarios and compare it with that of classical or standard diffusive processes in two-component fractional reaction-diffusion systems that modeled a predator-prey dynamics. The focus of the work concentrates on the use of two separate mathematical techniques, we formulate a Fourier spectral discretization method as an efficient alternative technique to solve fractional reaction-diffusion problems in higher-dimensional space, and later advance the resulting systems of ODEs in time with the adaptive exponential time-differencing solver. Obviously, the fractional Fourier approach is able to achieve spectral convergence up to machine precision regardless of the fractional order α, owing to the fact that our approach is able to give full diagonal representation of the fractional operator. The complexity of the dynamics in this system is theoretically discussed and graphically displayed with some examples and numerical simulations in one, two and three dimensions.
Stochastic modeling and simulation of reaction-diffusion system with Hill function dynamics.
Chen, Minghan; Li, Fei; Wang, Shuo; Cao, Young
2017-03-14
Stochastic simulation of reaction-diffusion systems presents great challenges for spatiotemporal biological modeling and simulation. One widely used framework for stochastic simulation of reaction-diffusion systems is reaction diffusion master equation (RDME). Previous studies have discovered that for the RDME, when discretization size approaches zero, reaction time for bimolecular reactions in high dimensional domains tends to infinity. In this paper, we demonstrate that in the 1D domain, highly nonlinear reaction dynamics given by Hill function may also have dramatic change when discretization size is smaller than a critical value. Moreover, we discuss methods to avoid this problem: smoothing over space, fixed length smoothing over space and a hybrid method. Our analysis reveals that the switch-like Hill dynamics reduces to a linear function of discretization size when the discretization size is small enough. The three proposed methods could correctly (under certain precision) simulate Hill function dynamics in the microscopic RDME system.
Flexible single molecule simulation of reaction-diffusion processes
International Nuclear Information System (INIS)
Hellander, Stefan; Loetstedt, Per
2011-01-01
An algorithm is developed for simulation of the motion and reactions of single molecules at a microscopic level. The molecules diffuse in a solvent and react with each other or a polymer and molecules can dissociate. Such simulations are of interest e.g. in molecular biology. The algorithm is similar to the Green's function reaction dynamics (GFRD) algorithm by van Zon and ten Wolde where longer time steps can be taken by computing the probability density functions (PDFs) and then sample from the distribution functions. Our computation of the PDFs is much less complicated than GFRD and more flexible. The solution of the partial differential equation for the PDF is split into two steps to simplify the calculations. The sampling is without splitting error in two of the coordinate directions for a pair of molecules and a molecule-polymer interaction and is approximate in the third direction. The PDF is obtained either from an analytical solution or a numerical discretization. The errors due to the operator splitting, the partitioning of the system, and the numerical approximations are analyzed. The method is applied to three different systems involving up to four reactions. Comparisons with other mesoscopic and macroscopic models show excellent agreement.
Event-triggered synchronization for reaction-diffusion complex networks via random sampling
Dong, Tao; Wang, Aijuan; Zhu, Huiyun; Liao, Xiaofeng
2018-04-01
In this paper, the synchronization problem of the reaction-diffusion complex networks (RDCNs) with Dirichlet boundary conditions is considered, where the data is sampled randomly. An event-triggered controller based on the sampled data is proposed, which can reduce the number of controller and the communication load. Under this strategy, the synchronization problem of the diffusion complex network is equivalently converted to the stability of a of reaction-diffusion complex dynamical systems with time delay. By using the matrix inequality technique and Lyapunov method, the synchronization conditions of the RDCNs are derived, which are dependent on the diffusion term. Moreover, it is found the proposed control strategy can get rid of the Zeno behavior naturally. Finally, a numerical example is given to verify the obtained results.
Simulations of pattern dynamics for reaction-diffusion systems via SIMULINK.
Wang, Kaier; Steyn-Ross, Moira L; Steyn-Ross, D Alistair; Wilson, Marcus T; Sleigh, Jamie W; Shiraishi, Yoichi
2014-04-11
Investigation of the nonlinear pattern dynamics of a reaction-diffusion system almost always requires numerical solution of the system's set of defining differential equations. Traditionally, this would be done by selecting an appropriate differential equation solver from a library of such solvers, then writing computer codes (in a programming language such as C or Matlab) to access the selected solver and display the integrated results as a function of space and time. This "code-based" approach is flexible and powerful, but requires a certain level of programming sophistication. A modern alternative is to use a graphical programming interface such as Simulink to construct a data-flow diagram by assembling and linking appropriate code blocks drawn from a library. The result is a visual representation of the inter-relationships between the state variables whose output can be made completely equivalent to the code-based solution. As a tutorial introduction, we first demonstrate application of the Simulink data-flow technique to the classical van der Pol nonlinear oscillator, and compare Matlab and Simulink coding approaches to solving the van der Pol ordinary differential equations. We then show how to introduce space (in one and two dimensions) by solving numerically the partial differential equations for two different reaction-diffusion systems: the well-known Brusselator chemical reactor, and a continuum model for a two-dimensional sheet of human cortex whose neurons are linked by both chemical and electrical (diffusive) synapses. We compare the relative performances of the Matlab and Simulink implementations. The pattern simulations by Simulink are in good agreement with theoretical predictions. Compared with traditional coding approaches, the Simulink block-diagram paradigm reduces the time and programming burden required to implement a solution for reaction-diffusion systems of equations. Construction of the block-diagram does not require high-level programming
An adaptive algorithm for simulation of stochastic reaction-diffusion processes
International Nuclear Information System (INIS)
Ferm, Lars; Hellander, Andreas; Loetstedt, Per
2010-01-01
We propose an adaptive hybrid method suitable for stochastic simulation of diffusion dominated reaction-diffusion processes. For such systems, simulation of the diffusion requires the predominant part of the computing time. In order to reduce the computational work, the diffusion in parts of the domain is treated macroscopically, in other parts with the tau-leap method and in the remaining parts with Gillespie's stochastic simulation algorithm (SSA) as implemented in the next subvolume method (NSM). The chemical reactions are handled by SSA everywhere in the computational domain. A trajectory of the process is advanced in time by an operator splitting technique and the timesteps are chosen adaptively. The spatial adaptation is based on estimates of the errors in the tau-leap method and the macroscopic diffusion. The accuracy and efficiency of the method are demonstrated in examples from molecular biology where the domain is discretized by unstructured meshes.
Accurate numerical simulation of reaction-diffusion processes for heavy oil recovery
Energy Technology Data Exchange (ETDEWEB)
Govind, P.A.; Srinivasan, S. [Society of Petroleum Engineers, Richardson, TX (United States)]|[Texas Univ., Austin, TX (United States)
2008-10-15
This study evaluated a reaction-diffusion simulation tool designed to analyze the displacement of carbon dioxide (CO{sub 2}) in a simultaneous injection of carbon dioxide and elemental sodium in a heavy oil reservoir. Sodium was used due to the exothermic reaction of sodium with in situ that occurs when heat is used to reduce oil viscosity. The process also results in the formation of sodium hydroxide that reduces interfacial tension at the bitumen interface. A commercial simulation tool was used to model the sodium transport mechanism to the reaction interface through diffusion as well as the reaction zone's subsequent displacement. The aim of the study was to verify if the in situ reaction was able to generate sufficient heat to reduce oil viscosity and improve the displacement of the heavy oil. The study also assessed the accuracy of the reaction front simulation tool, in which an alternate method was used to model the propagation front as a moving heat source. The sensitivity of the simulation results were then evaluated in relation to the diffusion coefficient in order to understand the scaling characteristics of the reaction-diffusion zone. A pore-scale simulation was then up-scaled to grid blocks. Results of the study showed that when sodium suspended in liquid CO{sub 2} is injected into reservoirs, it diffuses through the carrier phase and interacts with water. A random walk diffusion algorithm with reactive dissipation was implemented to more accurately characterize reaction and diffusion processes. It was concluded that the algorithm modelled physical dispersion while neglecting the effect of numerical dispersion. 10 refs., 3 tabs., 24 figs.
Energy Technology Data Exchange (ETDEWEB)
Hepburn, I.; De Schutter, E., E-mail: erik@oist.jp [Computational Neuroscience Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495 (Japan); Theoretical Neurobiology & Neuroengineering, University of Antwerp, Antwerp 2610 (Belgium); Chen, W. [Computational Neuroscience Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495 (Japan)
2016-08-07
Spatial stochastic molecular simulations in biology are limited by the intense computation required to track molecules in space either in a discrete time or discrete space framework, which has led to the development of parallel methods that can take advantage of the power of modern supercomputers in recent years. We systematically test suggested components of stochastic reaction-diffusion operator splitting in the literature and discuss their effects on accuracy. We introduce an operator splitting implementation for irregular meshes that enhances accuracy with minimal performance cost. We test a range of models in small-scale MPI simulations from simple diffusion models to realistic biological models and find that multi-dimensional geometry partitioning is an important consideration for optimum performance. We demonstrate performance gains of 1-3 orders of magnitude in the parallel implementation, with peak performance strongly dependent on model specification.
The two-regime method for optimizing stochastic reaction-diffusion simulations
Flegg, M. B.
2011-10-19
Spatial organization and noise play an important role in molecular systems biology. In recent years, a number of software packages have been developed for stochastic spatio-temporal simulation, ranging from detailed molecular-based approaches to less detailed compartment-based simulations. Compartment-based approaches yield quick and accurate mesoscopic results, but lack the level of detail that is characteristic of the computationally intensive molecular-based models. Often microscopic detail is only required in a small region (e.g. close to the cell membrane). Currently, the best way to achieve microscopic detail is to use a resource-intensive simulation over the whole domain. We develop the two-regime method (TRM) in which a molecular-based algorithm is used where desired and a compartment-based approach is used elsewhere. We present easy-to-implement coupling conditions which ensure that the TRM results have the same accuracy as a detailed molecular-based model in the whole simulation domain. Therefore, the TRM combines strengths of previously developed stochastic reaction-diffusion software to efficiently explore the behaviour of biological models. Illustrative examples and the mathematical justification of the TRM are also presented.
International Nuclear Information System (INIS)
Mittal, R.C.; Rohila, Rajni
2016-01-01
In this paper, we have applied modified cubic B-spline based differential quadrature method to get numerical solutions of one dimensional reaction-diffusion systems such as linear reaction-diffusion system, Brusselator system, Isothermal system and Gray-Scott system. The models represented by these systems have important applications in different areas of science and engineering. The most striking and interesting part of the work is the solution patterns obtained for Gray Scott model, reminiscent of which are often seen in nature. We have used cubic B-spline functions for space discretization to get a system of ordinary differential equations. This system of ODE’s is solved by highly stable SSP-RK43 method to get solution at the knots. The computed results are very accurate and shown to be better than those available in the literature. Method is easy and simple to apply and gives solutions with less computational efforts.
Alternans and Spiral Breakup in an Excitable Reaction-Diffusion System: A Simulation Study.
Gani, M Osman; Ogawa, Toshiyuki
2014-01-01
The determination of the mechanisms of spiral breakup in excitable media is still an open problem for researchers. In the context of cardiac electrophysiological activities, spiral breakup exhibits complex spatiotemporal pattern known as ventricular fibrillation. The latter is the major cause of sudden cardiac deaths all over the world. In this paper, we numerically study the instability of periodic planar traveling wave solution in two dimensions. The emergence of stable spiral pattern is observed in the considered model. This pattern occurs when the heart is malfunctioning (i.e., ventricular tachycardia). We show that the spiral wave breakup is a consequence of the transverse instability of the planar traveling wave solutions. The alternans, that is, the oscillation of pulse widths, is observed in our simulation results. Moreover, we calculate the widths of spiral pulses numerically and observe that the stable spiral pattern bifurcates to an oscillatory wave pattern in a one-parameter family of solutions. The spiral breakup occurs far below the bifurcation when the maximum and the minimum excited states become more distinct, and hence the alternans becomes more pronounced.
Hallock, Michael J; Stone, John E; Roberts, Elijah; Fry, Corey; Luthey-Schulten, Zaida
2014-05-01
Simulation of in vivo cellular processes with the reaction-diffusion master equation (RDME) is a computationally expensive task. Our previous software enabled simulation of inhomogeneous biochemical systems for small bacteria over long time scales using the MPD-RDME method on a single GPU. Simulations of larger eukaryotic systems exceed the on-board memory capacity of individual GPUs, and long time simulations of modest-sized cells such as yeast are impractical on a single GPU. We present a new multi-GPU parallel implementation of the MPD-RDME method based on a spatial decomposition approach that supports dynamic load balancing for workstations containing GPUs of varying performance and memory capacity. We take advantage of high-performance features of CUDA for peer-to-peer GPU memory transfers and evaluate the performance of our algorithms on state-of-the-art GPU devices. We present parallel e ciency and performance results for simulations using multiple GPUs as system size, particle counts, and number of reactions grow. We also demonstrate multi-GPU performance in simulations of the Min protein system in E. coli . Moreover, our multi-GPU decomposition and load balancing approach can be generalized to other lattice-based problems.
The two-regime method for optimizing stochastic reaction-diffusion simulations
Flegg, M. B.; Chapman, S. J.; Erban, R.
2011-01-01
Spatial organization and noise play an important role in molecular systems biology. In recent years, a number of software packages have been developed for stochastic spatio-temporal simulation, ranging from detailed molecular-based approaches
Zhu, Xiaolu; Yang, Hao
2017-12-01
The recently emerged four-dimensional (4D) biofabrication technique aims to create dynamic three-dimensional (3D) biological structures that can transform their shapes or functionalities with time when an external stimulus is imposed or when cell postprinting self-assembly occurs. The evolution of 3D pattern of branching geometry via self-assembly of cells is critical for 4D biofabrication of artificial organs or tissues with branched geometry. However, it is still unclear that how the formation and evolution of these branching pattern are biologically encoded. We study the 4D fabrication of lung branching structures utilizing a simulation model on the reaction-diffusion mechanism, which is established using partial differential equations of four variables, describing the reaction and diffusion process of morphogens with time during the development process of lung branching. The simulation results present the forming process of 3D branching pattern, and also interpret the behaviors of side branching and tip splitting as the stalk growing, through 3D visualization of numerical simulation.
Stochastic reaction-diffusion algorithms for macromolecular crowding
Sturrock, Marc
2016-06-01
Compartment-based (lattice-based) reaction-diffusion algorithms are often used for studying complex stochastic spatio-temporal processes inside cells. In this paper the influence of macromolecular crowding on stochastic reaction-diffusion simulations is investigated. Reaction-diffusion processes are considered on two different kinds of compartmental lattice, a cubic lattice and a hexagonal close packed lattice, and solved using two different algorithms, the stochastic simulation algorithm and the spatiocyte algorithm (Arjunan and Tomita 2010 Syst. Synth. Biol. 4, 35-53). Obstacles (modelling macromolecular crowding) are shown to have substantial effects on the mean squared displacement and average number of molecules in the domain but the nature of these effects is dependent on the choice of lattice, with the cubic lattice being more susceptible to the effects of the obstacles. Finally, improvements for both algorithms are presented.
Reaction Diffusion and Chemotaxis for Decentralized Gathering on FPGAs
Directory of Open Access Journals (Sweden)
Bernard Girau
2009-01-01
and rapid simulations of the complex dynamics of this reaction-diffusion model. Then we describe the FPGA implementation of the environment together with the agents, to study the major challenges that must be solved when designing a fast embedded implementation of the decentralized gathering model. We analyze the results according to the different goals of these hardware implementations.
Owolabi, Kolade M.
2018-03-01
In this work, we are concerned with the solution of non-integer space-fractional reaction-diffusion equations with the Riemann-Liouville space-fractional derivative in high dimensions. We approximate the Riemann-Liouville derivative with the Fourier transform method and advance the resulting system in time with any time-stepping solver. In the numerical experiments, we expect the travelling wave to arise from the given initial condition on the computational domain (-∞, ∞), which we terminate in the numerical experiments with a large but truncated value of L. It is necessary to choose L large enough to allow the waves to have enough space to distribute. Experimental results in high dimensions on the space-fractional reaction-diffusion models with applications to biological models (Fisher and Allen-Cahn equations) are considered. Simulation results reveal that fractional reaction-diffusion equations can give rise to a range of physical phenomena when compared to non-integer-order cases. As a result, most meaningful and practical situations are found to be modelled with the concept of fractional calculus.
Shi, Kuangyu; Bayer, Christine; Gaertner, Florian C; Astner, Sabrina T; Wilkens, Jan J; Nüsslin, Fridtjof; Vaupel, Peter; Ziegler, Sibylle I
2017-02-01
Positron-emission tomography (PET) with hypoxia specific tracers provides a noninvasive method to assess the tumor oxygenation status. Reaction-diffusion models have advantages in revealing the quantitative relation between in vivo imaging and the tumor microenvironment. However, there is no quantitative comparison of the simulation results with the real PET measurements yet. The lack of experimental support hampers further applications of computational simulation models. This study aims to compare the simulation results with a preclinical [ 18 F]FMISO PET study and to optimize the reaction-diffusion model accordingly. Nude mice with xenografted human squamous cell carcinomas (CAL33) were investigated with a 2 h dynamic [ 18 F]FMISO PET followed by immunofluorescence staining using the hypoxia marker pimonidazole and the endothelium marker CD 31. A large data pool of tumor time-activity curves (TAC) was simulated for each mouse by feeding the arterial input function (AIF) extracted from experiments into the model with different configurations of the tumor microenvironment. A measured TAC was considered to match a simulated TAC when the difference metric was below a certain, noise-dependent threshold. As an extension to the well-established Kelly model, a flow-limited oxygen-dependent (FLOD) model was developed to improve the matching between measurements and simulations. The matching rate between the simulated TACs of the Kelly model and the mouse PET data ranged from 0 to 28.1% (on average 9.8%). By modifying the Kelly model to an FLOD model, the matching rate between the simulation and the PET measurements could be improved to 41.2-84.8% (on average 64.4%). Using a simulation data pool and a matching strategy, we were able to compare the simulated temporal course of dynamic PET with in vivo measurements. By modifying the Kelly model to a FLOD model, the computational simulation was able to approach the dynamic [ 18 F]FMISO measurements in the investigated
Turing Patterns in a Reaction-Diffusion System
International Nuclear Information System (INIS)
Wu Yanning; Wang Pingjian; Hou Chunju; Liu Changsong; Zhu Zhengang
2006-01-01
We have further investigated Turing patterns in a reaction-diffusion system by theoretical analysis and numerical simulations. Simple Turing patterns and complex superlattice structures are observed. We find that the shape and type of Turing patterns depend on dynamical parameters and external periodic forcing, and is independent of effective diffusivity rate σ in the Lengyel-Epstein model. Our numerical results provide additional insight into understanding the mechanism of development of Turing patterns and predicting new pattern formations.
Reaction-Diffusion Automata Phenomenology, Localisations, Computation
Adamatzky, Andrew
2013-01-01
Reaction-diffusion and excitable media are amongst most intriguing substrates. Despite apparent simplicity of the physical processes involved the media exhibit a wide range of amazing patterns: from target and spiral waves to travelling localisations and stationary breathing patterns. These media are at the heart of most natural processes, including morphogenesis of living beings, geological formations, nervous and muscular activity, and socio-economic developments. This book explores a minimalist paradigm of studying reaction-diffusion and excitable media using locally-connected networks of finite-state machines: cellular automata and automata on proximity graphs. Cellular automata are marvellous objects per se because they show us how to generate and manage complexity using very simple rules of dynamical transitions. When combined with the reaction-diffusion paradigm the cellular automata become an essential user-friendly tool for modelling natural systems and designing future and emergent computing arch...
Field theory of propagating reaction-diffusion fronts
International Nuclear Information System (INIS)
Escudero, C.
2004-01-01
The problem of velocity selection of reaction-diffusion fronts has been widely investigated. While the mean-field limit results are well known theoretically, there is a lack of analytic progress in those cases in which fluctuations are to be taken into account. Here, we construct an analytic theory connecting the first principles of the reaction-diffusion process to an effective equation of motion via field-theoretic arguments, and we arrive at results already confirmed by numerical simulations
Reaction-diffusion pulses: a combustion model
International Nuclear Information System (INIS)
Campos, Daniel; Llebot, Josep Enric; Fort, Joaquim
2004-01-01
We focus on a reaction-diffusion approach proposed recently for experiments on combustion processes, where the heat released by combustion follows first-order reaction kinetics. This case allows us to perform an exhaustive analytical study. Specifically, we obtain the exact expressions for the speed of the thermal pulses, their maximum temperature and the condition of self-sustenance. Finally, we propose two generalizations of the model, namely, the case of several reactants burning together, and that of time-delayed heat conduction. We find an excellent agreement between our analytical results and simulations
Reaction-diffusion pulses: a combustion model
Energy Technology Data Exchange (ETDEWEB)
Campos, Daniel [Grup de FIsica EstadIstica, Dept. de FIsica, Universitat Autonoma de Barcelona, E-08193 Bellaterrra (Spain); Llebot, Josep Enric [Grup de FIsica EstadIstica, Dept. de FIsica, Universitat Autonoma de Barcelona, E-08193 Bellaterrra (Spain); Fort, Joaquim [Dept. de FIsica, Univ. de Girona, Campus de Montilivi, 17071 Girona, Catalonia (Spain)
2004-07-02
We focus on a reaction-diffusion approach proposed recently for experiments on combustion processes, where the heat released by combustion follows first-order reaction kinetics. This case allows us to perform an exhaustive analytical study. Specifically, we obtain the exact expressions for the speed of the thermal pulses, their maximum temperature and the condition of self-sustenance. Finally, we propose two generalizations of the model, namely, the case of several reactants burning together, and that of time-delayed heat conduction. We find an excellent agreement between our analytical results and simulations.
Pattern dynamics of the reaction-diffusion immune system.
Zheng, Qianqian; Shen, Jianwei; Wang, Zhijie
2018-01-01
In this paper, we will investigate the effect of diffusion, which is ubiquitous in nature, on the immune system using a reaction-diffusion model in order to understand the dynamical behavior of complex patterns and control the dynamics of different patterns. Through control theory and linear stability analysis of local equilibrium, we obtain the optimal condition under which the system loses stability and a Turing pattern occurs. By combining mathematical analysis and numerical simulation, we show the possible patterns and how these patterns evolve. In addition, we establish a bridge between the complex patterns and the biological mechanism using the results from a previous study in Nature Cell Biology. The results in this paper can help us better understand the biological significance of the immune system.
Diffusive instabilities in hyperbolic reaction-diffusion equations
Zemskov, Evgeny P.; Horsthemke, Werner
2016-03-01
We investigate two-variable reaction-diffusion systems of the hyperbolic type. A linear stability analysis is performed, and the conditions for diffusion-driven instabilities are derived. Two basic types of eigenvalues, real and complex, are described. Dispersion curves for both types of eigenvalues are plotted and their behavior is analyzed. The real case is related to the Turing instability, and the complex one corresponds to the wave instability. We emphasize the interesting feature that the wave instability in the hyperbolic equations occurs in two-variable systems, whereas in the parabolic case one needs three reaction-diffusion equations.
Parametric spatiotemporal oscillation in reaction-diffusion systems.
Ghosh, Shyamolina; Ray, Deb Shankar
2016-03-01
We consider a reaction-diffusion system in a homogeneous stable steady state. On perturbation by a time-dependent sinusoidal forcing of a suitable scaling parameter the system exhibits parametric spatiotemporal instability beyond a critical threshold frequency. We have formulated a general scheme to calculate the threshold condition for oscillation and the range of unstable spatial modes lying within a V-shaped region reminiscent of Arnold's tongue. Full numerical simulations show that depending on the specificity of nonlinearity of the models, the instability may result in time-periodic stationary patterns in the form of standing clusters or spatially localized breathing patterns with characteristic wavelengths. Our theoretical analysis of the parametric oscillation in reaction-diffusion system is corroborated by full numerical simulation of two well-known chemical dynamical models: chlorite-iodine-malonic acid and Briggs-Rauscher reactions.
Laser spot detection based on reaction diffusion
Czech Academy of Sciences Publication Activity Database
Vázquez-Otero, Alejandro; Khikhlukha, Danila; Solano-Altamirano, J. M.; Dormido, R.; Duro, N.
2016-01-01
Roč. 16, č. 3 (2016), s. 1-11, č. článku 315. ISSN 1424-8220 R&D Projects: GA MŠk EF15_008/0000162 Grant - others:ELI Beamlines(XE) CZ.02.1.01/0.0/0.0/15_008/0000162 Institutional support: RVO:68378271 Keywords : laser spot detection * laser beam detection * reaction diffusion models * Fitzhugh-Nagumo model * reaction diffusion computation * Turing patterns Subject RIV: BL - Plasma and Gas Discharge Physics OBOR OECD: Fluids and plasma physics (including surface physics) Impact factor: 2.677, year: 2016
Reaction-diffusion systems in intracellular molecular transport and control.
Soh, Siowling; Byrska, Marta; Kandere-Grzybowska, Kristiana; Grzybowski, Bartosz A
2010-06-07
Chemical reactions make cells work only if the participating chemicals are delivered to desired locations in a timely and precise fashion. Most research to date has focused on active-transport mechanisms, although passive diffusion is often equally rapid and energetically less costly. Capitalizing on these advantages, cells have developed sophisticated reaction-diffusion (RD) systems that control a wide range of cellular functions-from chemotaxis and cell division, through signaling cascades and oscillations, to cell motility. These apparently diverse systems share many common features and are "wired" according to "generic" motifs such as nonlinear kinetics, autocatalysis, and feedback loops. Understanding the operation of these complex (bio)chemical systems requires the analysis of pertinent transport-kinetic equations or, at least on a qualitative level, of the characteristic times of the constituent subprocesses. Therefore, in reviewing the manifestations of cellular RD, we also describe basic theory of reaction-diffusion phenomena.
Laser Spot Detection Based on Reaction Diffusion
Alejandro Vázquez-Otero; Danila Khikhlukha; J. M. Solano-Altamirano; Raquel Dormido; Natividad Duro
2016-01-01
Center-location of a laser spot is a problem of interest when the laser is used for processing and performing measurements. Measurement quality depends on correctly determining the location of the laser spot. Hence, improving and proposing algorithms for the correct location of the spots are fundamental issues in laser-based measurements. In this paper we introduce a Reaction Diffusion (RD) system as the main computational framework for robustly finding laser spot centers. The method presente...
Reaction diffusion equations with boundary degeneracy
Directory of Open Access Journals (Sweden)
Huashui Zhan
2016-03-01
Full Text Available In this article, we consider the reaction diffusion equation $$ \\frac{\\partial u}{\\partial t} = \\Delta A(u,\\quad (x,t\\in \\Omega \\times (0,T, $$ with the homogeneous boundary condition. Inspired by the Fichera-Oleinik theory, if the equation is not only strongly degenerate in the interior of $\\Omega$, but also degenerate on the boundary, we show that the solution of the equation is free from any limitation of the boundary condition.
Reaction-diffusion fronts with inhomogeneous initial conditions
Energy Technology Data Exchange (ETDEWEB)
Bena, I [Departement de Physique Theorique, Universite de Geneve, CH-1211 Geneva 4 (Switzerland); Droz, M [Departement de Physique Theorique, Universite de Geneve, CH-1211 Geneva 4 (Switzerland); Martens, K [Departement de Physique Theorique, Universite de Geneve, CH-1211 Geneva 4 (Switzerland); Racz, Z [Institute for Theoretical Physics, Eoetvoes University, 1117 Budapest (Hungary)
2007-02-14
Properties of reaction zones resulting from A+B {yields} C type reaction-diffusion processes are investigated by analytical and numerical methods. The reagents A and B are separated initially and, in addition, there is an initial macroscopic inhomogeneity in the distribution of the B species. For simple two-dimensional geometries, exact analytical results are presented for the time evolution of the geometric shape of the front. We also show using cellular automata simulations that the fluctuations can be neglected both in the shape and in the width of the front.
Simulation in Complex Modelling
DEFF Research Database (Denmark)
Nicholas, Paul; Ramsgaard Thomsen, Mette; Tamke, Martin
2017-01-01
This paper will discuss the role of simulation in extended architectural design modelling. As a framing paper, the aim is to present and discuss the role of integrated design simulation and feedback between design and simulation in a series of projects under the Complex Modelling framework. Complex...... performance, engage with high degrees of interdependency and allow the emergence of design agency and feedback between the multiple scales of architectural construction. This paper presents examples for integrated design simulation from a series of projects including Lace Wall, A Bridge Too Far and Inflated...... Restraint developed for the research exhibition Complex Modelling, Meldahls Smedie Gallery, Copenhagen in 2016. Where the direct project aims and outcomes have been reported elsewhere, the aim for this paper is to discuss overarching strategies for working with design integrated simulation....
Multiscale Reaction-Diffusion Algorithms: PDE-Assisted Brownian Dynamics
Franz, Benjamin
2013-06-19
Two algorithms that combine Brownian dynami cs (BD) simulations with mean-field partial differential equations (PDEs) are presented. This PDE-assisted Brownian dynamics (PBD) methodology provides exact particle tracking data in parts of the domain, whilst making use of a mean-field reaction-diffusion PDE description elsewhere. The first PBD algorithm couples BD simulations with PDEs by randomly creating new particles close to the interface, which partitions the domain, and by reincorporating particles into the continuum PDE-description when they cross the interface. The second PBD algorithm introduces an overlap region, where both descriptions exist in parallel. It is shown that the overlap region is required to accurately compute variances using PBD simulations. Advantages of both PBD approaches are discussed and illustrative numerical examples are presented. © 2013 Society for Industrial and Applied Mathematics.
Laser Spot Detection Based on Reaction Diffusion.
Vázquez-Otero, Alejandro; Khikhlukha, Danila; Solano-Altamirano, J M; Dormido, Raquel; Duro, Natividad
2016-03-01
Center-location of a laser spot is a problem of interest when the laser is used for processing and performing measurements. Measurement quality depends on correctly determining the location of the laser spot. Hence, improving and proposing algorithms for the correct location of the spots are fundamental issues in laser-based measurements. In this paper we introduce a Reaction Diffusion (RD) system as the main computational framework for robustly finding laser spot centers. The method presented is compared with a conventional approach for locating laser spots, and the experimental results indicate that RD-based computation generates reliable and precise solutions. These results confirm the flexibility of the new computational paradigm based on RD systems for addressing problems that can be reduced to a set of geometric operations.
Laser Spot Detection Based on Reaction Diffusion
Directory of Open Access Journals (Sweden)
Alejandro Vázquez-Otero
2016-03-01
Full Text Available Center-location of a laser spot is a problem of interest when the laser is used for processing and performing measurements. Measurement quality depends on correctly determining the location of the laser spot. Hence, improving and proposing algorithms for the correct location of the spots are fundamental issues in laser-based measurements. In this paper we introduce a Reaction Diffusion (RD system as the main computational framework for robustly finding laser spot centers. The method presented is compared with a conventional approach for locating laser spots, and the experimental results indicate that RD-based computation generates reliable and precise solutions. These results confirm the flexibility of the new computational paradigm based on RD systems for addressing problems that can be reduced to a set of geometric operations.
Simulations with complex measure
International Nuclear Information System (INIS)
Markham, J.K.; Kieu, T.D.
1997-01-01
A method is proposed to handle the sign problem in the simulation of systems having indefinite or complex-valued measures. In general, this new approach, which is based on renormalisation blocking, is shown to yield statistical errors smaller that the crude Monte Carlo method using absolute values of the original measures. The improved method is applied to the 2D Ising model with temperature generalised to take on complex values. It is also adapted to implement Monte Carlo Renormalisation Group calculations of the magnetic and thermal critical exponents. 10 refs., 4 tabs., 7 figs
Control of transversal instabilities in reaction-diffusion systems
Totz, Sonja; Löber, Jakob; Totz, Jan Frederik; Engel, Harald
2018-05-01
In two-dimensional reaction-diffusion systems, local curvature perturbations on traveling waves are typically damped out and vanish. However, if the inhibitor diffuses much faster than the activator, transversal instabilities can arise, leading from flat to folded, spatio-temporally modulated waves and to spreading spiral turbulence. Here, we propose a scheme to induce or inhibit these instabilities via a spatio-temporal feedback loop. In a piecewise-linear version of the FitzHugh–Nagumo model, transversal instabilities and spiral turbulence in the uncontrolled system are shown to be suppressed in the presence of control, thereby stabilizing plane wave propagation. Conversely, in numerical simulations with the modified Oregonator model for the photosensitive Belousov–Zhabotinsky reaction, which does not exhibit transversal instabilities on its own, we demonstrate the feasibility of inducing transversal instabilities and study the emerging wave patterns in a well-controlled manner.
Gan, Qintao; Lv, Tianshi; Fu, Zhenhua
2016-04-01
In this paper, the synchronization problem for a class of generalized neural networks with time-varying delays and reaction-diffusion terms is investigated concerning Neumann boundary conditions in terms of p-norm. The proposed generalized neural networks model includes reaction-diffusion local field neural networks and reaction-diffusion static neural networks as its special cases. By establishing a new inequality, some simple and useful conditions are obtained analytically to guarantee the global exponential synchronization of the addressed neural networks under the periodically intermittent control. According to the theoretical results, the influences of diffusion coefficients, diffusion space, and control rate on synchronization are analyzed. Finally, the feasibility and effectiveness of the proposed methods are shown by simulation examples, and by choosing different diffusion coefficients, diffusion spaces, and control rates, different controlled synchronization states can be obtained.
Exact analytical solutions for nonlinear reaction-diffusion equations
International Nuclear Information System (INIS)
Liu Chunping
2003-01-01
By using a direct method via the computer algebraic system of Mathematica, some exact analytical solutions to a class of nonlinear reaction-diffusion equations are presented in closed form. Subsequently, the hyperbolic function solutions and the triangular function solutions of the coupled nonlinear reaction-diffusion equations are obtained in a unified way
Speed ot travelling waves in reaction-diffusion equations
International Nuclear Information System (INIS)
Benguria, R.D.; Depassier, M.C.; Mendez, V.
2002-01-01
Reaction diffusion equations arise in several problems of population dynamics, flame propagation and others. In one dimensional cases the systems may evolve into travelling fronts. Here we concentrate on a reaction diffusion equation which arises as a simple model for chemotaxis and present results for the speed of the travelling fronts. (Author)
Nonlinear analysis of a reaction-diffusion system: Amplitude equations
Energy Technology Data Exchange (ETDEWEB)
Zemskov, E. P., E-mail: zemskov@ccas.ru [Russian Academy of Sciences, Dorodnicyn Computing Center (Russian Federation)
2012-10-15
A reaction-diffusion system with a nonlinear diffusion term is considered. Based on nonlinear analysis, the amplitude equations are obtained in the cases of the Hopf and Turing instabilities in the system. Turing pattern-forming regions in the parameter space are determined for supercritical and subcritical instabilities in a two-component reaction-diffusion system.
ReaDDy--a software for particle-based reaction-diffusion dynamics in crowded cellular environments.
Directory of Open Access Journals (Sweden)
Johannes Schöneberg
Full Text Available We introduce the software package ReaDDy for simulation of detailed spatiotemporal mechanisms of dynamical processes in the cell, based on reaction-diffusion dynamics with particle resolution. In contrast to other particle-based reaction kinetics programs, ReaDDy supports particle interaction potentials. This permits effects such as space exclusion, molecular crowding and aggregation to be modeled. The biomolecules simulated can be represented as a sphere, or as a more complex geometry such as a domain structure or polymer chain. ReaDDy bridges the gap between small-scale but highly detailed molecular dynamics or Brownian dynamics simulations and large-scale but little-detailed reaction kinetics simulations. ReaDDy has a modular design that enables the exchange of the computing core by efficient platform-specific implementations or dynamical models that are different from Brownian dynamics.
Mixed, Nonsplit, Extended Stability, Stiff Integration of Reaction Diffusion Equations
Alzahrani, Hasnaa H.
2016-01-01
A tailored integration scheme is developed to treat stiff reaction-diffusion prob- lems. The construction adapts a stiff solver, namely VODE, to treat reaction im- plicitly together with explicit treatment of diffusion. The second-order Runge
Study of ODE limit problems for reaction-diffusion equations
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Jacson Simsen
2018-01-01
Full Text Available In this work we study ODE limit problems for reaction-diffusion equations for large diffusion and we study the sensitivity of nonlinear ODEs with respect to initial conditions and exponent parameters. Moreover, we prove continuity of the flow and weak upper semicontinuity of a family of global attractors for reaction-diffusion equations with spatially variable exponents when the exponents go to 2 in \\(L^{\\infty}(\\Omega\\ and the diffusion coefficients go to infinity.
Spatiotemporal Patterns in a Ratio-Dependent Food Chain Model with Reaction-Diffusion
Directory of Open Access Journals (Sweden)
Lei Zhang
2014-01-01
Full Text Available Predator-prey models describe biological phenomena of pursuit-evasion interaction. And this interaction exists widely in the world for the necessary energy supplement of species. In this paper, we have investigated a ratio-dependent spatially extended food chain model. Based on the bifurcation analysis (Hopf and Turing, we give the spatial pattern formation via numerical simulation, that is, the evolution process of the system near the coexistence equilibrium point (u2*,v2*,w2*, and find that the model dynamics exhibits complex pattern replication. For fixed parameters, on increasing the control parameter c1, the sequence “holes → holes-stripe mixtures → stripes → spots-stripe mixtures → spots” pattern is observed. And in the case of pure Hopf instability, the model exhibits chaotic wave pattern replication. Furthermore, we consider the pattern formation in the case of which the top predator is extinct, that is, the evolution process of the system near the equilibrium point (u1*,v1*,0, and find that the model dynamics exhibits stripes-spots pattern replication. Our results show that reaction-diffusion model is an appropriate tool for investigating fundamental mechanism of complex spatiotemporal dynamics. It will be useful for studying the dynamic complexity of ecosystems.
Soft tissue deformation modelling through neural dynamics-based reaction-diffusion mechanics.
Zhang, Jinao; Zhong, Yongmin; Gu, Chengfan
2018-05-30
Soft tissue deformation modelling forms the basis of development of surgical simulation, surgical planning and robotic-assisted minimally invasive surgery. This paper presents a new methodology for modelling of soft tissue deformation based on reaction-diffusion mechanics via neural dynamics. The potential energy stored in soft tissues due to a mechanical load to deform tissues away from their rest state is treated as the equivalent transmembrane potential energy, and it is distributed in the tissue masses in the manner of reaction-diffusion propagation of nonlinear electrical waves. The reaction-diffusion propagation of mechanical potential energy and nonrigid mechanics of motion are combined to model soft tissue deformation and its dynamics, both of which are further formulated as the dynamics of cellular neural networks to achieve real-time computational performance. The proposed methodology is implemented with a haptic device for interactive soft tissue deformation with force feedback. Experimental results demonstrate that the proposed methodology exhibits nonlinear force-displacement relationship for nonlinear soft tissue deformation. Homogeneous, anisotropic and heterogeneous soft tissue material properties can be modelled through the inherent physical properties of mass points. Graphical abstract Soft tissue deformation modelling with haptic feedback via neural dynamics-based reaction-diffusion mechanics.
A fractional reaction-diffusion description of supply and demand
Benzaquen, Michael; Bouchaud, Jean-Philippe
2018-02-01
We suggest that the broad distribution of time scales in financial markets could be a crucial ingredient to reproduce realistic price dynamics in stylised Agent-Based Models. We propose a fractional reaction-diffusion model for the dynamics of latent liquidity in financial markets, where agents are very heterogeneous in terms of their characteristic frequencies. Several features of our model are amenable to an exact analytical treatment. We find in particular that the impact is a concave function of the transacted volume (aka the "square-root impact law"), as in the normal diffusion limit. However, the impact kernel decays as t-β with β = 1/2 in the diffusive case, which is inconsistent with market efficiency. In the sub-diffusive case the decay exponent β takes any value in [0, 1/2], and can be tuned to match the empirical value β ≈ 1/4. Numerical simulations confirm our theoretical results. Several extensions of the model are suggested. Contribution to the Topical Issue "Continuous Time Random Walk Still Trendy: Fifty-year History, Current State and Outlook", edited by Ryszard Kutner and Jaume Masoliver.
Rethinking pattern formation in reaction-diffusion systems
Halatek, J.; Frey, E.
2018-05-01
The present theoretical framework for the analysis of pattern formation in complex systems is mostly limited to the vicinity of fixed (global) equilibria. Here we present a new theoretical approach to characterize dynamical states arbitrarily far from (global) equilibrium. We show that reaction-diffusion systems that are driven by locally mass-conserving interactions can be understood in terms of local equilibria of diffusively coupled compartments. Diffusive coupling generically induces lateral redistribution of the globally conserved quantities, and the variable local amounts of these quantities determine the local equilibria in each compartment. We find that, even far from global equilibrium, the system is well characterized by its moving local equilibria. We apply this framework to in vitro Min protein pattern formation, a paradigmatic model for biological pattern formation. Within our framework we can predict and explain transitions between chemical turbulence and order arbitrarily far from global equilibrium. Our results reveal conceptually new principles of self-organized pattern formation that may well govern diverse dynamical systems.
An analytic algorithm for the space-time fractional reaction-diffusion equation
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M. G. Brikaa
2015-11-01
Full Text Available In this paper, we solve the space-time fractional reaction-diffusion equation by the fractional homotopy analysis method. Solutions of different examples of the reaction term will be computed and investigated. The approximation solutions of the studied models will be put in the form of convergent series to be easily computed and simulated. Comparison with the approximation solution of the classical case of the studied modeled with their approximation errors will also be studied.
Delay-induced Turing-like waves for one-species reaction-diffusion model on a network
Petit, Julien; Carletti, Timoteo; Asllani, Malbor; Fanelli, Duccio
2015-09-01
A one-species time-delay reaction-diffusion system defined on a complex network is studied. Traveling waves are predicted to occur following a symmetry-breaking instability of a homogeneous stationary stable solution, subject to an external nonhomogeneous perturbation. These are generalized Turing-like waves that materialize in a single-species populations dynamics model, as the unexpected byproduct of the imposed delay in the diffusion part. Sufficient conditions for the onset of the instability are mathematically provided by performing a linear stability analysis adapted to time-delayed differential equations. The method here developed exploits the properties of the Lambert W-function. The prediction of the theory are confirmed by direct numerical simulation carried out for a modified version of the classical Fisher model, defined on a Watts-Strogatz network and with the inclusion of the delay.
Towards reaction-diffusion computing devices based on minority-carrier transport in semiconductors
International Nuclear Information System (INIS)
Asai, Tetsuya; Adamatzky, Andrew; Amemiya, Yoshihito
2004-01-01
Reaction-diffusion (RD) chemical systems are known to realize sensible computation when both data and results of the computation are encoded in concentration profiles of chemical species; the computation is implemented via spreading and interaction of either diffusive or phase waves. Thin-layer chemical systems are thought of therefore as massively-parallel locally-connected computing devices, where micro-volume of the medium is analogous to an elementary processor. Practical applications of the RD chemical systems are reduced however due to very low speed of traveling waves which makes real-time computation senseless. To overcome the speed-limitations while preserving unique features of RD computers we propose a semiconductor RD computing device where minority carriers diffuse as chemical species and reaction elements are represented by p-n-p-n diodes. We offer blue-prints of the RD semiconductor devices, and study in computer simulation propagation phenomena of the density wave of minority carriers. We then demonstrate what computational problems can be solved in RD semiconductor devices and evaluate space-time complexity of computation in the devices
Stability analysis of non-autonomous reaction-diffusion systems: the effects of growing domains
Madzvamuse, Anotida; Gaffney, Eamonn A.; Maini, Philip K.
2009-01-01
By using asymptotic theory, we generalise the Turing diffusively-driven instability conditions for reaction-diffusion systems with slow, isotropic domain growth. There are two fundamental biological differences between the Turing conditions on fixed and growing domains, namely: (i) we need not enforce cross nor pure kinetic conditions and (ii) the restriction to activator-inhibitor kinetics to induce pattern formation on a growing biological system is no longer a requirement. Our theoretical findings are confirmed and reinforced by numerical simulations for the special cases of isotropic linear, exponential and logistic growth profiles. In particular we illustrate an example of a reaction-diffusion system which cannot exhibit a diffusively-driven instability on a fixed domain but is unstable in the presence of slow growth. © Springer-Verlag 2009.
Stability analysis of non-autonomous reaction-diffusion systems: the effects of growing domains
Madzvamuse, Anotida
2009-08-29
By using asymptotic theory, we generalise the Turing diffusively-driven instability conditions for reaction-diffusion systems with slow, isotropic domain growth. There are two fundamental biological differences between the Turing conditions on fixed and growing domains, namely: (i) we need not enforce cross nor pure kinetic conditions and (ii) the restriction to activator-inhibitor kinetics to induce pattern formation on a growing biological system is no longer a requirement. Our theoretical findings are confirmed and reinforced by numerical simulations for the special cases of isotropic linear, exponential and logistic growth profiles. In particular we illustrate an example of a reaction-diffusion system which cannot exhibit a diffusively-driven instability on a fixed domain but is unstable in the presence of slow growth. © Springer-Verlag 2009.
Dichotomous-noise-induced pattern formation in a reaction-diffusion system
Das, Debojyoti; Ray, Deb Shankar
2013-06-01
We consider a generic reaction-diffusion system in which one of the parameters is subjected to dichotomous noise by controlling the flow of one of the reacting species in a continuous-flow-stirred-tank reactor (CSTR) -membrane reactor. The linear stability analysis in an extended phase space is carried out by invoking Furutzu-Novikov procedure for exponentially correlated multiplicative noise to derive the instability condition in the plane of the noise parameters (correlation time and strength of the noise). We demonstrate that depending on the correlation time an optimal strength of noise governs the self-organization. Our theoretical analysis is corroborated by numerical simulations on pattern formation in a chlorine-dioxide-iodine-malonic acid reaction-diffusion system.
Pattern formation in reaction diffusion systems with finite geometry
International Nuclear Information System (INIS)
Borzi, C.; Wio, H.
1990-04-01
We analyze the one-component, one-dimensional, reaction-diffusion equation through a simple inverse method. We confine the system and fix the boundary conditions as to induce pattern formation. We analyze the stability of those patterns. Our goal is to get information about the reaction term out of the preknowledgment of the pattern. (author). 5 refs
Analytically solvable models of reaction-diffusion systems
Energy Technology Data Exchange (ETDEWEB)
Zemskov, E P; Kassner, K [Institut fuer Theoretische Physik, Otto-von-Guericke-Universitaet, Universitaetsplatz 2, 39106 Magdeburg (Germany)
2004-05-01
We consider a class of analytically solvable models of reaction-diffusion systems. An analytical treatment is possible because the nonlinear reaction term is approximated by a piecewise linear function. As particular examples we choose front and pulse solutions to illustrate the matching procedure in the one-dimensional case.
Turing instability in reaction-diffusion systems with nonlinear diffusion
Energy Technology Data Exchange (ETDEWEB)
Zemskov, E. P., E-mail: zemskov@ccas.ru [Russian Academy of Sciences, Dorodnicyn Computing Center (Russian Federation)
2013-10-15
The Turing instability is studied in two-component reaction-diffusion systems with nonlinear diffusion terms, and the regions in parametric space where Turing patterns can form are determined. The boundaries between super- and subcritical bifurcations are found. Calculations are performed for one-dimensional brusselator and oregonator models.
Delay-induced wave instabilities in single-species reaction-diffusion systems
Otto, Andereas; Wang, Jian; Radons, Günter
2017-11-01
The Turing (wave) instability is only possible in reaction-diffusion systems with more than one (two) components. Motivated by the fact that a time delay increases the dimension of a system, we investigate the presence of diffusion-driven instabilities in single-species reaction-diffusion systems with delay. The stability of arbitrary one-component systems with a single discrete delay, with distributed delay, or with a variable delay is systematically analyzed. We show that a wave instability can appear from an equilibrium of single-species reaction-diffusion systems with fluctuating or distributed delay, which is not possible in similar systems with constant discrete delay or without delay. More precisely, we show by basic analytic arguments and by numerical simulations that fast asymmetric delay fluctuations or asymmetrically distributed delays can lead to wave instabilities in these systems. Examples, for the resulting traveling waves are shown for a Fisher-KPP equation with distributed delay in the reaction term. In addition, we have studied diffusion-induced instabilities from homogeneous periodic orbits in the same systems with variable delay, where the homogeneous periodic orbits are attracting resonant periodic solutions of the system without diffusion, i.e., periodic orbits of the Hutchinson equation with time-varying delay. If diffusion is introduced, standing waves can emerge whose temporal period is equal to the period of the variable delay.
Simulating social complexity a handbook
Meyer, Ruth
2013-01-01
Social systems are among the most complex known. This poses particular problems for those who wish to understand them. The complexity often makes analytic approaches infeasible and natural language approaches inadequate for relating intricate cause and effect. However, individual- and agent-based computational approaches hold out the possibility of new and deeper understanding of such systems. Simulating Social Complexity examines all aspects of using agent- or individual-based simulation. This approach represents systems as individual elements having each their own set of differing states and internal processes. The interactions between elements in the simulation represent interactions in the target systems. What makes these elements "social" is that they are usefully interpretable as interacting elements of an observed society. In this, the focus is on human society, but can be extended to include social animals or artificial agents where such work enhances our understanding of human society. The phenom...
Distributed order reaction-diffusion systems associated with Caputo derivatives
Saxena, R. K.; Mathai, A. M.; Haubold, H. J.
2014-08-01
This paper deals with the investigation of the solution of an unified fractional reaction-diffusion equation of distributed order associated with the Caputo derivatives as the time-derivative and Riesz-Feller fractional derivative as the space-derivative. The solution is derived by the application of the joint Laplace and Fourier transforms in compact and closed form in terms of the H-function. The results derived are of general nature and include the results investigated earlier by other authors, notably by Mainardi et al. ["The fundamental solution of the space-time fractional diffusion equation," Fractional Calculus Appl. Anal. 4, 153-202 (2001); Mainardi et al. "Fox H-functions in fractional diffusion," J. Comput. Appl. Math. 178, 321-331 (2005)] for the fundamental solution of the space-time fractional equation, including Haubold et al. ["Solutions of reaction-diffusion equations in terms of the H-function," Bull. Astron. Soc. India 35, 681-689 (2007)] and Saxena et al. ["Fractional reaction-diffusion equations," Astrophys. Space Sci. 305, 289-296 (2006a)] for fractional reaction-diffusion equations. The advantage of using the Riesz-Feller derivative lies in the fact that the solution of the fractional reaction-diffusion equation, containing this derivative, includes the fundamental solution for space-time fractional diffusion, which itself is a generalization of fractional diffusion, space-time fraction diffusion, and time-fractional diffusion, see Schneider and Wyss ["Fractional diffusion and wave equations," J. Math. Phys. 30, 134-144 (1989)]. These specialized types of diffusion can be interpreted as spatial probability density functions evolving in time and are expressible in terms of the H-function in compact forms. The convergence conditions for the double series occurring in the solutions are investigated. It is interesting to observe that the double series comes out to be a special case of the Srivastava-Daoust hypergeometric function of two variables
Numerical solution of a reaction-diffusion equation
International Nuclear Information System (INIS)
Moyano, Edgardo A.; Scarpettini, Alberto F.
2000-01-01
The purpose of the present work to continue the observations and the numerical experiences on a reaction-diffusion model, that is a simplified form of the neutronic flux equation. The model is parabolic, nonlinear, with Dirichlet boundary conditions. The purpose is to approximate non trivial solutions, asymptotically stables for t → ∞, that is solutions that tend to the elliptic problem, in the Lyapunov sense. It belongs to the so-called reaction-diffusion equations of semi linear kind, that is, linear equations in the heat operator and they have a nonlinear reaction function, in this case f (u, a, b) = u (a - b u), being u concentration, a and b parameters. The study of the incidence of these parameters take an interest to the neutronic flux physics. So that we search non trivial, positive and bounded solutions. The used algorithm is based on the concept of monotone and ordered sequences, and on the existence theorem of Amann and Sattinger. (author)
Maximum Principles for Discrete and Semidiscrete Reaction-Diffusion Equation
Directory of Open Access Journals (Sweden)
Petr Stehlík
2015-01-01
Full Text Available We study reaction-diffusion equations with a general reaction function f on one-dimensional lattices with continuous or discrete time ux′ (or Δtux=k(ux-1-2ux+ux+1+f(ux, x∈Z. We prove weak and strong maximum and minimum principles for corresponding initial-boundary value problems. Whereas the maximum principles in the semidiscrete case (continuous time exhibit similar features to those of fully continuous reaction-diffusion model, in the discrete case the weak maximum principle holds for a smaller class of functions and the strong maximum principle is valid in a weaker sense. We describe in detail how the validity of maximum principles depends on the nonlinearity and the time step. We illustrate our results on the Nagumo equation with the bistable nonlinearity.
An Application of Equivalence Transformations to Reaction Diffusion Equations
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Mariano Torrisi
2015-10-01
Full Text Available In this paper, we consider a quite general class of advection reaction diffusion systems. By using an equivalence generator, derived in a previous paper, the authors apply a projection theorem to determine some special forms of the constitutive functions that allow the extension by one of the two-dimensional principal Lie algebra. As an example, a special case is discussed at the end of the paper.
Attractor of reaction-diffusion equations in Banach spaces
Directory of Open Access Journals (Sweden)
José Valero
2001-04-01
Full Text Available In this paper we prove first some abstract theorems on existence of global attractors for differential inclusions generated by w-dissipative operators. Then these results are applied to reaction-diffusion equations in which the Babach space Lp is used as phase space. Finally, new results concerning the fractal dimension of the global attractor in the space L2 are obtained.
Multiple Scale Reaction-Diffusion-Advection Problems with Moving Fronts
Nefedov, Nikolay
2016-06-01
In this work we discuss the further development of the general scheme of the asymptotic method of differential inequalities to investigate stability and motion of sharp internal layers (fronts) for nonlinear singularly perturbed parabolic equations, which are called in applications reaction-diffusion-advection equations. Our approach is illustrated for some new important cases of initial boundary value problems. We present results on stability and on the motion of the fronts.
Reaction diffusion voronoi diagrams: from sensors data to computing
Czech Academy of Sciences Publication Activity Database
Vázquez-Otero, Alejandro (ed.); Faigl, J.; Dormido, R.; Duro, N.
2015-01-01
Roč. 15, č. 6 (2015), s. 12736-12764 ISSN 1424-8220 R&D Projects: GA MŠk ED1.1.00/02.0061 Grant - others:ELI Beamlines(XE) CZ.1.05/1.1.00/02.0061 Institutional support: RVO:68378271 Keywords : reaction diffusion * FitzHugh–Nagumo * path planning * navigation * exploration Subject RIV: BD - Theory of Information Impact factor: 2.033, year: 2015
Square Turing patterns in reaction-diffusion systems with coupled layers
Energy Technology Data Exchange (ETDEWEB)
Li, Jing [State Key Laboratory for Mesoscopic Physics and School of Physics, Peking University, Beijing 100871 (China); Wang, Hongli, E-mail: hlwang@pku.edu.cn, E-mail: qi@pku.edu.cn [State Key Laboratory for Mesoscopic Physics and School of Physics, Peking University, Beijing 100871 (China); Center for Quantitative Biology, Peking University, Beijing 100871 (China); Ouyang, Qi, E-mail: hlwang@pku.edu.cn, E-mail: qi@pku.edu.cn [State Key Laboratory for Mesoscopic Physics and School of Physics, Peking University, Beijing 100871 (China); Center for Quantitative Biology, Peking University, Beijing 100871 (China); The Peking-Tsinghua Center for Life Sciences, Beijing 100871 (China)
2014-06-15
Square Turing patterns are usually unstable in reaction-diffusion systems and are rarely observed in corresponding experiments and simulations. We report here an example of spontaneous formation of square Turing patterns with the Lengyel-Epstein model of two coupled layers. The squares are found to be a result of the resonance between two supercritical Turing modes with an appropriate ratio. Besides, the spatiotemporal resonance of Turing modes resembles to the mode-locking phenomenon. Analysis of the general amplitude equations for square patterns reveals that the fixed point corresponding to square Turing patterns is stationary when the parameters adopt appropriate values.
Externally controlled anisotropy in pattern-forming reaction-diffusion systems.
Escala, Dario M; Guiu-Souto, Jacobo; Muñuzuri, Alberto P
2015-06-01
The effect of centrifugal forces is analyzed in a pattern-forming reaction-diffusion system. Numerical simulations conducted on the appropriate extension of the Oregonator model for the Belousov-Zhabotinsky reaction show a great variety of dynamical behaviors in such a system. In general, the system exhibits an anisotropy that results in new types of patterns or in a global displacement of the previous one. We consider the effect of both constant and periodically modulated centrifugal forces on the different types of patterns that the system may exhibit. A detailed analysis of the patterns and behaviors observed for the different parameter values considered is presented here.
Reaction diffusion and solid state chemical kinetics handbook
Dybkov, V I
2010-01-01
This monograph deals with a physico-chemical approach to the problem of the solid-state growth of chemical compound layers and reaction-diffusion in binary heterogeneous systems formed by two solids; as well as a solid with a liquid or a gas. It is explained why the number of compound layers growing at the interface between the original phases is usually much lower than the number of chemical compounds in the phase diagram of a given binary system. For example, of the eight intermetallic compounds which exist in the aluminium-zirconium binary system, only ZrAl3 was found to grow as a separate
Global dynamics of a reaction-diffusion system
Directory of Open Access Journals (Sweden)
Yuncheng You
2011-02-01
Full Text Available In this work the existence of a global attractor for the semiflow of weak solutions of a two-cell Brusselator system is proved. The method of grouping estimation is exploited to deal with the challenge in proving the absorbing property and the asymptotic compactness of this type of coupled reaction-diffusion systems with cubic autocatalytic nonlinearity and linear coupling. It is proved that the Hausdorff dimension and the fractal dimension of the global attractor are finite. Moreover, the existence of an exponential attractor for this solution semiflow is shown.
A Weak Comparison Principle for Reaction-Diffusion Systems
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José Valero
2012-01-01
Full Text Available We prove a weak comparison principle for a reaction-diffusion system without uniqueness of solutions. We apply the abstract results to the Lotka-Volterra system with diffusion, a generalized logistic equation, and to a model of fractional-order chemical autocatalysis with decay. Moreover, in the case of the Lotka-Volterra system a weak maximum principle is given, and a suitable estimate in the space of essentially bounded functions L∞ is proved for at least one solution of the problem.
On the solutions of fractional reaction-diffusion equations
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Jagdev Singh
2013-05-01
Full Text Available In this paper, we obtain the solution of a fractional reaction-diffusion equation associated with the generalized Riemann-Liouville fractional derivative as the time derivative and Riesz-Feller fractional derivative as the space-derivative. The results are derived by the application of the Laplace and Fourier transforms in compact and elegant form in terms of Mittag-Leffler function and H-function. The results obtained here are of general nature and include the results investigated earlier by many authors.
Explosive instabilities of reaction-diffusion equations including pinch effects
International Nuclear Information System (INIS)
Wilhelmsson, H.
1992-01-01
Particular solutions of reaction-diffusion equations for temperature are obtained for explosively unstable situations. As a result of the interplay between inertial, diffusion, pinch and source processes certain 'bell-shaped' distributions may grow explosively in time with preserved shape of the spatial distribution. The effect of the pinch, which requires a density inhomogeneity, is found to diminish the effect of diffusion, or inversely to support the inertial and source processes in creating the explosion. The results may be described in terms of elliptic integrals or. more simply, by means of expansions in the spatial coordinate. An application is the temperature evolution of a burning fusion plasma. (au) (18 refs.)
A reaction-diffusion model of ROS-induced ROS release in a mitochondrial network.
Directory of Open Access Journals (Sweden)
Lufang Zhou
2010-01-01
Full Text Available Loss of mitochondrial function is a fundamental determinant of cell injury and death. In heart cells under metabolic stress, we have previously described how the abrupt collapse or oscillation of the mitochondrial energy state is synchronized across the mitochondrial network by local interactions dependent upon reactive oxygen species (ROS. Here, we develop a mathematical model of ROS-induced ROS release (RIRR based on reaction-diffusion (RD-RIRR in one- and two-dimensional mitochondrial networks. The nodes of the RD-RIRR network are comprised of models of individual mitochondria that include a mechanism of ROS-dependent oscillation based on the interplay between ROS production, transport, and scavenging; and incorporating the tricarboxylic acid (TCA cycle, oxidative phosphorylation, and Ca(2+ handling. Local mitochondrial interaction is mediated by superoxide (O2.- diffusion and the O2.(--dependent activation of an inner membrane anion channel (IMAC. In a 2D network composed of 500 mitochondria, model simulations reveal DeltaPsi(m depolarization waves similar to those observed when isolated guinea pig cardiomyocytes are subjected to a localized laser-flash or antioxidant depletion. The sensitivity of the propagation rate of the depolarization wave to O(2.- diffusion, production, and scavenging in the reaction-diffusion model is similar to that observed experimentally. In addition, we present novel experimental evidence, obtained in permeabilized cardiomyocytes, confirming that DeltaPsi(m depolarization is mediated specifically by O2.-. The present work demonstrates that the observed emergent macroscopic properties of the mitochondrial network can be reproduced in a reaction-diffusion model of RIRR. Moreover, the findings have uncovered a novel aspect of the synchronization mechanism, which is that clusters of mitochondria that are oscillating can entrain mitochondria that would otherwise display stable dynamics. The work identifies the
Simulating geometrically complex blast scenarios
Directory of Open Access Journals (Sweden)
Ian G. Cullis
2016-04-01
Full Text Available The effects of blast waves generated by energetic and non-energetic sources are of continuing interest to the ballistics research community. Modern conflicts are increasingly characterised by asymmetric urban warfare, with improvised explosive devices (IEDs often playing a dominant role on the one hand and an armed forces requirement for minimal collateral effects from their weapons on the other. These problems are characterised by disparate length- and time-scales and may also be governed by complex physics. There is thus an increasing need to be able to rapidly assess and accurately predict the effects of energetic blast in topologically complex scenarios. To this end, this paper presents a new QinetiQ-developed advanced computational package called EAGLE-Blast, which is capable of accurately resolving the generation, propagation and interaction of blast waves around geometrically complex shapes such as vehicles and buildings. After a brief description of the numerical methodology, various blast scenario simulations are described and the results compared with experimental data to demonstrate the validation of the scheme and its ability to describe these complex scenarios accurately and efficiently. The paper concludes with a brief discussion on the use of the code in supporting the development of algorithms for fast running engineering models.
A discrete model to study reaction-diffusion-mechanics systems.
Weise, Louis D; Nash, Martyn P; Panfilov, Alexander V
2011-01-01
This article introduces a discrete reaction-diffusion-mechanics (dRDM) model to study the effects of deformation on reaction-diffusion (RD) processes. The dRDM framework employs a FitzHugh-Nagumo type RD model coupled to a mass-lattice model, that undergoes finite deformations. The dRDM model describes a material whose elastic properties are described by a generalized Hooke's law for finite deformations (Seth material). Numerically, the dRDM approach combines a finite difference approach for the RD equations with a Verlet integration scheme for the equations of the mass-lattice system. Using this framework results were reproduced on self-organized pacemaking activity that have been previously found with a continuous RD mechanics model. Mechanisms that determine the period of pacemakers and its dependency on the medium size are identified. Finally it is shown how the drift direction of pacemakers in RDM systems is related to the spatial distribution of deformation and curvature effects.
A discrete model to study reaction-diffusion-mechanics systems.
Directory of Open Access Journals (Sweden)
Louis D Weise
Full Text Available This article introduces a discrete reaction-diffusion-mechanics (dRDM model to study the effects of deformation on reaction-diffusion (RD processes. The dRDM framework employs a FitzHugh-Nagumo type RD model coupled to a mass-lattice model, that undergoes finite deformations. The dRDM model describes a material whose elastic properties are described by a generalized Hooke's law for finite deformations (Seth material. Numerically, the dRDM approach combines a finite difference approach for the RD equations with a Verlet integration scheme for the equations of the mass-lattice system. Using this framework results were reproduced on self-organized pacemaking activity that have been previously found with a continuous RD mechanics model. Mechanisms that determine the period of pacemakers and its dependency on the medium size are identified. Finally it is shown how the drift direction of pacemakers in RDM systems is related to the spatial distribution of deformation and curvature effects.
Traveling wavefront solutions to nonlinear reaction-diffusion-convection equations
International Nuclear Information System (INIS)
Indekeu, Joseph O; Smets, Ruben
2017-01-01
Physically motivated modified Fisher equations are studied in which nonlinear convection and nonlinear diffusion is allowed for besides the usual growth and spread of a population. It is pointed out that in a large variety of cases separable functions in the form of exponentially decaying sharp wavefronts solve the differential equation exactly provided a co-moving point source or sink is active at the wavefront. The velocity dispersion and front steepness may differ from those of some previously studied exact smooth traveling wave solutions. For an extension of the reaction-diffusion-convection equation, featuring a memory effect in the form of a maturity delay for growth and spread, also smooth exact wavefront solutions are obtained. The stability of the solutions is verified analytically and numerically. (paper)
Traveling wavefront solutions to nonlinear reaction-diffusion-convection equations
Indekeu, Joseph O.; Smets, Ruben
2017-08-01
Physically motivated modified Fisher equations are studied in which nonlinear convection and nonlinear diffusion is allowed for besides the usual growth and spread of a population. It is pointed out that in a large variety of cases separable functions in the form of exponentially decaying sharp wavefronts solve the differential equation exactly provided a co-moving point source or sink is active at the wavefront. The velocity dispersion and front steepness may differ from those of some previously studied exact smooth traveling wave solutions. For an extension of the reaction-diffusion-convection equation, featuring a memory effect in the form of a maturity delay for growth and spread, also smooth exact wavefront solutions are obtained. The stability of the solutions is verified analytically and numerically.
Guiding brine shrimp through mazes by solving reaction diffusion equations
Singal, Krishma; Fenton, Flavio
Excitable systems driven by reaction diffusion equations have been shown to not only find solutions to mazes but to also to find the shortest path between the beginning and the end of the maze. In this talk we describe how we can use the Fitzhugh-Nagumo model, a generic model for excitable media, to solve a maze by varying the basin of attraction of its two fixed points. We demonstrate how two dimensional mazes are solved numerically using a Java Applet and then accelerated to run in real time by using graphic processors (GPUs). An application of this work is shown by guiding phototactic brine shrimp through a maze solved by the algorithm. Once the path is obtained, an Arduino directs the shrimp through the maze using lights from LEDs placed at the floor of the Maze. This method running in real time could be eventually used for guiding robots and cars through traffic.
Pattern formation in three-dimensional reaction-diffusion systems
Callahan, T. K.; Knobloch, E.
1999-08-01
Existing group theoretic analysis of pattern formation in three dimensions [T.K. Callahan, E. Knobloch, Symmetry-breaking bifurcations on cubic lattices, Nonlinearity 10 (1997) 1179-1216] is used to make specific predictions about the formation of three-dimensional patterns in two models of the Turing instability, the Brusselator model and the Lengyel-Epstein model. Spatially periodic patterns having the periodicity of the simple cubic (SC), face-centered cubic (FCC) or body-centered cubic (BCC) lattices are considered. An efficient center manifold reduction is described and used to identify parameter regimes permitting stable lamellæ, SC, FCC, double-diamond, hexagonal prism, BCC and BCCI states. Both models possess a special wavenumber k* at which the normal form coefficients take on fixed model-independent ratios and both are described by identical bifurcation diagrams. This property is generic for two-species chemical reaction-diffusion models with a single activator and inhibitor.
Reaction-diffusion modeling of hydrogen in beryllium
Energy Technology Data Exchange (ETDEWEB)
Wensing, Mirko; Matveev, Dmitry; Linsmeier, Christian [Forschungszentrum Juelich GmbH, Institut fuer Energie- und Klimaforschung - Plasmaphysik (Germany)
2016-07-01
Beryllium will be used as first-wall material for the future fusion reactor ITER as well as in the breeding blanket of DEMO. In both cases it is important to understand the mechanisms of hydrogen retention in beryllium. In earlier experiments with beryllium low-energy binding states of hydrogen were observed by thermal desorption spectroscopy (TDS) which are not yet well understood. Two candidates for these states are considered: beryllium-hydride phases within the bulk and surface effects. The retention of deuterium in beryllium is studied by a reaction rate approach using a coupled reaction diffusion system (CRDS)-model relying on ab initio data from density functional theory calculations (DFT). In this contribution we try to assess the influence of surface recombination.
Mixed, Nonsplit, Extended Stability, Stiff Integration of Reaction Diffusion Equations
Alzahrani, Hasnaa H.
2016-07-26
A tailored integration scheme is developed to treat stiff reaction-diffusion prob- lems. The construction adapts a stiff solver, namely VODE, to treat reaction im- plicitly together with explicit treatment of diffusion. The second-order Runge-Kutta- Chebyshev (RKC) scheme is adjusted to integrate diffusion. Spatial operator is de- scretised by second-order finite differences on a uniform grid. The overall solution is advanced over S fractional stiff integrations, where S corresponds to the number of RKC stages. The behavior of the scheme is analyzed by applying it to three simple problems. The results show that it achieves second-order accuracy, thus, preserving the formal accuracy of the original RKC. The presented development sets the stage for future extensions, particularly, to multidimensional reacting flows with detailed chemistry.
Reaction diffusion in chromium-zircaloy-2 system
International Nuclear Information System (INIS)
Xiang Wenxin; Ying Shihao
2001-01-01
Reaction diffusion in the chromium-zircaloy-2 diffusion couples is investigated in the temperature range of 1023 - 1123 K. Scanning electron microscope (SEM) and energy dispersive spectrum (EDS) were used to measure the thickness of the reaction layer and to determine the Zr, Fe and Cr concentration penetrate profile in reaction layer, respectively. The growth kinetics of reaction layer has been studied and the results show that the growth of intermetallic compound is controlled by the process of volume diffusion as the layer growth approximately obeys the parabolic law. Interdiffusion coefficients were calculated using Boltzmann-Matano-Heumann model. Calculated interdiffusion coefficients were compared with those obtained on the condition that Cr dissolves in Zr and merely forms dilute solid solution. The comparison indicates that Cr diffuses in dilute solid solution is five orders of magnitude faster than in Zr(Fe, Cr) 2 intermetallic compound
Arjunan, Satya Nanda Vel; Tomita, Masaru
2010-03-01
Many important cellular processes are regulated by reaction-diffusion (RD) of molecules that takes place both in the cytoplasm and on the membrane. To model and analyze such multicompartmental processes, we developed a lattice-based Monte Carlo method, Spatiocyte that supports RD in volume and surface compartments at single molecule resolution. Stochasticity in RD and the excluded volume effect brought by intracellular molecular crowding, both of which can significantly affect RD and thus, cellular processes, are also supported. We verified the method by comparing simulation results of diffusion, irreversible and reversible reactions with the predicted analytical and best available numerical solutions. Moreover, to directly compare the localization patterns of molecules in fluorescence microscopy images with simulation, we devised a visualization method that mimics the microphotography process by showing the trajectory of simulated molecules averaged according to the camera exposure time. In the rod-shaped bacterium Escherichia coli, the division site is suppressed at the cell poles by periodic pole-to-pole oscillations of the Min proteins (MinC, MinD and MinE) arising from carefully orchestrated RD in both cytoplasm and membrane compartments. Using Spatiocyte we could model and reproduce the in vivo MinDE localization dynamics by accounting for the previously reported properties of MinE. Our results suggest that the MinE ring, which is essential in preventing polar septation, is largely composed of MinE that is transiently attached to the membrane independently after recruited by MinD. Overall, Spatiocyte allows simulation and visualization of complex spatial and reaction-diffusion mediated cellular processes in volumes and surfaces. As we showed, it can potentially provide mechanistic insights otherwise difficult to obtain experimentally. The online version of this article (doi:10.1007/s11693-009-9047-2) contains supplementary material, which is available to
Critical behavior in reaction-diffusion systems exhibiting absorbing phase transition
Ódor, G
2003-01-01
Phase transitions of reaction-diffusion systems with site occupation restriction and with particle creation that requires n>1 parents and where explicit diffusion of single particles (A) exists are reviewed. Arguments based on mean-field approximation and simulations are given which support novel kind of non-equilibrium criticality. These are in contradiction with the implications of a suggested phenomenological, multiplicative noise Langevin equation approach and with some of recent numerical analysis. Simulation results for the one and two dimensional binary spreading 2A -> 4A, 4A -> 2A model display a new type of mean-field criticality characterized by alpha=1/3 and beta=1/2 critical exponents suggested in cond-mat/0210615.
Drawert, Brian; Engblom, Stefan; Hellander, Andreas
2012-06-22
Experiments in silico using stochastic reaction-diffusion models have emerged as an important tool in molecular systems biology. Designing computational software for such applications poses several challenges. Firstly, realistic lattice-based modeling for biological applications requires a consistent way of handling complex geometries, including curved inner- and outer boundaries. Secondly, spatiotemporal stochastic simulations are computationally expensive due to the fast time scales of individual reaction- and diffusion events when compared to the biological phenomena of actual interest. We therefore argue that simulation software needs to be both computationally efficient, employing sophisticated algorithms, yet in the same time flexible in order to meet present and future needs of increasingly complex biological modeling. We have developed URDME, a flexible software framework for general stochastic reaction-transport modeling and simulation. URDME uses Unstructured triangular and tetrahedral meshes to resolve general geometries, and relies on the Reaction-Diffusion Master Equation formalism to model the processes under study. An interface to a mature geometry and mesh handling external software (Comsol Multiphysics) provides for a stable and interactive environment for model construction. The core simulation routines are logically separated from the model building interface and written in a low-level language for computational efficiency. The connection to the geometry handling software is realized via a Matlab interface which facilitates script computing, data management, and post-processing. For practitioners, the software therefore behaves much as an interactive Matlab toolbox. At the same time, it is possible to modify and extend URDME with newly developed simulation routines. Since the overall design effectively hides the complexity of managing the geometry and meshes, this means that newly developed methods may be tested in a realistic setting already at
Stability and Hopf Bifurcation of a Reaction-Diffusion Neutral Neuron System with Time Delay
Dong, Tao; Xia, Linmao
2017-12-01
In this paper, a type of reaction-diffusion neutral neuron system with time delay under homogeneous Neumann boundary conditions is considered. By constructing a basis of phase space based on the eigenvectors of the corresponding Laplace operator, the characteristic equation of this system is obtained. Then, by selecting time delay and self-feedback strength as the bifurcating parameters respectively, the dynamic behaviors including local stability and Hopf bifurcation near the zero equilibrium point are investigated when the time delay and self-feedback strength vary. Furthermore, the direction of the Hopf bifurcation and the stability of bifurcating periodic solutions are obtained by using the normal form and the center manifold theorem for the corresponding partial differential equation. Finally, two simulation examples are given to verify the theory.
Schwarz, Karsten; Rieger, Heiko
2013-03-01
We present an efficient Monte Carlo method to simulate reaction-diffusion processes with spatially varying particle annihilation or transformation rates as it occurs for instance in the context of motor-driven intracellular transport. Like Green's function reaction dynamics and first-passage time methods, our algorithm avoids small diffusive hops by propagating sufficiently distant particles in large hops to the boundaries of protective domains. Since for spatially varying annihilation or transformation rates the single particle diffusion propagator is not known analytically, we present an algorithm that generates efficiently either particle displacements or annihilations with the correct statistics, as we prove rigorously. The numerical efficiency of the algorithm is demonstrated with an illustrative example.
A Reaction-Diffusion-Based Coding Rate Control Mechanism for Camera Sensor Networks
Directory of Open Access Journals (Sweden)
Naoki Wakamiya
2010-08-01
Full Text Available A wireless camera sensor network is useful for surveillance and monitoring for its visibility and easy deployment. However, it suffers from the limited capacity of wireless communication and a network is easily overflown with a considerable amount of video traffic. In this paper, we propose an autonomous video coding rate control mechanism where each camera sensor node can autonomously determine its coding rate in accordance with the location and velocity of target objects. For this purpose, we adopted a biological model, i.e., reaction-diffusion model, inspired by the similarity of biological spatial patterns and the spatial distribution of video coding rate. Through simulation and practical experiments, we verify the effectiveness of our proposal.
A reaction-diffusion-based coding rate control mechanism for camera sensor networks.
Yamamoto, Hiroshi; Hyodo, Katsuya; Wakamiya, Naoki; Murata, Masayuki
2010-01-01
A wireless camera sensor network is useful for surveillance and monitoring for its visibility and easy deployment. However, it suffers from the limited capacity of wireless communication and a network is easily overflown with a considerable amount of video traffic. In this paper, we propose an autonomous video coding rate control mechanism where each camera sensor node can autonomously determine its coding rate in accordance with the location and velocity of target objects. For this purpose, we adopted a biological model, i.e., reaction-diffusion model, inspired by the similarity of biological spatial patterns and the spatial distribution of video coding rate. Through simulation and practical experiments, we verify the effectiveness of our proposal.
Automatic simplification of systems of reaction-diffusion equations by a posteriori analysis.
Maybank, Philip J; Whiteley, Jonathan P
2014-02-01
Many mathematical models in biology and physiology are represented by systems of nonlinear differential equations. In recent years these models have become increasingly complex in order to explain the enormous volume of data now available. A key role of modellers is to determine which components of the model have the greatest effect on a given observed behaviour. An approach for automatically fulfilling this role, based on a posteriori analysis, has recently been developed for nonlinear initial value ordinary differential equations [J.P. Whiteley, Model reduction using a posteriori analysis, Math. Biosci. 225 (2010) 44-52]. In this paper we extend this model reduction technique for application to both steady-state and time-dependent nonlinear reaction-diffusion systems. Exemplar problems drawn from biology are used to demonstrate the applicability of the technique. Copyright © 2014 Elsevier Inc. All rights reserved.
International Nuclear Information System (INIS)
Xu Rui; Chaplain, M.A.J.; Davidson, F.A.
2006-01-01
In this paper, we first investigate a stage-structured competitive model with time delays, harvesting, and nonlocal spatial effect. By using an iterative technique recently developed by Wu and Zou (Wu J, Zou X. Travelling wave fronts of reaction-diffusion systems with delay. J Dynam Differen Equat 2001;13:651-87), sufficient conditions are established for the existence of travelling front solution connecting the two boundary equilibria in the case when there is no positive equilibrium. The travelling wave front corresponds to an invasion by a stronger species which drives the weaker species to extinction. Secondly, we consider a stage-structured competitive model with time delays and nonlocal spatial effect when the domain is finite. We prove the global stability of each of the nonnegative equilibria and demonstrate that the more complex model studied here admits three possible long term behaviors: coexistence, bistability and dominance as is the case for the standard Lotka-Voltera competitive model
Reaction Diffusion Voronoi Diagrams: From Sensors Data to Computing
Directory of Open Access Journals (Sweden)
Alejandro Vázquez-Otero
2015-05-01
Full Text Available In this paper, a new method to solve computational problems using reaction diffusion (RD systems is presented. The novelty relies on the use of a model configuration that tailors its spatiotemporal dynamics to develop Voronoi diagrams (VD as a part of the system’s natural evolution. The proposed framework is deployed in a solution of related robotic problems, where the generalized VD are used to identify topological places in a grid map of the environment that is created from sensor measurements. The ability of the RD-based computation to integrate external information, like a grid map representing the environment in the model computational grid, permits a direct integration of sensor data into the model dynamics. The experimental results indicate that this method exhibits significantly less sensitivity to noisy data than the standard algorithms for determining VD in a grid. In addition, previous drawbacks of the computational algorithms based on RD models, like the generation of volatile solutions by means of excitable waves, are now overcome by final stable states.
Decay to Equilibrium for Energy-Reaction-Diffusion Systems
Haskovec, Jan
2018-02-06
We derive thermodynamically consistent models of reaction-diffusion equations coupled to a heat equation. While the total energy is conserved, the total entropy serves as a driving functional such that the full coupled system is a gradient flow. The novelty of the approach is the Onsager structure, which is the dual form of a gradient system, and the formulation in terms of the densities and the internal energy. In these variables it is possible to assume that the entropy density is strictly concave such that there is a unique maximizer (thermodynamical equilibrium) given linear constraints on the total energy and suitable density constraints. We consider two particular systems of this type, namely, a diffusion-reaction bipolar energy transport system, and a drift-diffusion-reaction energy transport system with confining potential. We prove corresponding entropy-entropy production inequalities with explicitly calculable constants and establish the convergence to thermodynamical equilibrium, first in entropy and later in L norm using Cziszár–Kullback–Pinsker type inequalities.
Decay to Equilibrium for Energy-Reaction-Diffusion Systems
Haskovec, Jan; Hittmeir, Sabine; Markowich, Peter A.; Mielke, Alexander
2018-01-01
We derive thermodynamically consistent models of reaction-diffusion equations coupled to a heat equation. While the total energy is conserved, the total entropy serves as a driving functional such that the full coupled system is a gradient flow. The novelty of the approach is the Onsager structure, which is the dual form of a gradient system, and the formulation in terms of the densities and the internal energy. In these variables it is possible to assume that the entropy density is strictly concave such that there is a unique maximizer (thermodynamical equilibrium) given linear constraints on the total energy and suitable density constraints. We consider two particular systems of this type, namely, a diffusion-reaction bipolar energy transport system, and a drift-diffusion-reaction energy transport system with confining potential. We prove corresponding entropy-entropy production inequalities with explicitly calculable constants and establish the convergence to thermodynamical equilibrium, first in entropy and later in L norm using Cziszár–Kullback–Pinsker type inequalities.
Stochastic flows, reaction-diffusion processes, and morphogenesis
International Nuclear Information System (INIS)
Kozak, J.J.; Hatlee, M.D.; Musho, M.K.; Politowicz, P.A.; Walsh, C.A.
1983-01-01
Recently, an exact procedure has been introduced [C. A. Walsh and J. J. Kozak, Phys. Rev. Lett.. 47: 1500 (1981)] for calculating the expected walk length for a walker undergoing random displacements on a finite or infinite (periodic) d-dimensional lattice with traps (reactive sites). The method (which is based on a classification of the symmetry of the sites surrounding the central deep trap and a coding of the fate of the random walker as it encounters a site of given symmetry) is applied here to several problems in lattice statistics for each of which exact results are presented. First, we assess the importance of lattice geometry in influencing the efficiency of reaction-diffusion processs in simple and multiple trap systems by reporting values of for square (cubic) versus hexagonal lattices in d = 2,3. We then show how the method may be applied to variable-step (distance-dependent) walks for a single walker on a given lattice and also demonstrate the calculation of the expected walk length for the case of multiple walkers. Finally, we make contact with recent discussions of ''mixing'' by showing that the degree of chaos associated with flows in certain lattice-systems can be calibrated by monitoring the lattice walks induced by the Poincare map of a certain parabolic function
Evolution of density profiles for reaction-diffusion processes
International Nuclear Information System (INIS)
Ondarza-Rovira, R.
1990-01-01
The purpose of this work is to study the reaction diffusion equations for the concentration of one species in one spatial dimension. Nonlinear diffusion equations paly an important role in several fields: Physics, Kinetic Chemistry, Poblational Biology, Neurophysics, etc. The study of the behavior of solutions, with nonlinear diffusion coefficient, and monomial creation and annihilation terms, is considered. It is found, that when the exponent of the annihilation term is smaller than the one of the creation term, unstable equilibrium solutions may exist, for which solutions above it explode in finite time, but solutions below it decay exponentially. By means of the reduction to quadratures technique, it is found that is possible to obtain travelling wave solution in those cases when the annihilation term is greater than the creation term. This method of solution always permits to know the propagation velocity of the front, even if the concentration cannot be written in closed form. The portraits of the solutions in phase space show the existence of solutions which velocities may be smaller or greater than the ones found analytically. Linear and nonlinear diffusion equations, differ significantly in that the former are of change of solutions are considered. This is reminiscent of the fact that linear diffusion yields infinite propagation speed, even though the speed of the front is finite. When the strength of the annihilation term increases, as compared with that of the creation term, arbitrary initial conditions (studied numerically) relax to stable platforms that move indefinitly with constant speed. (Author)
Hybrid approaches for multiple-species stochastic reaction-diffusion models
Spill, Fabian; Guerrero, Pilar; Alarcon, Tomas; Maini, Philip K.; Byrne, Helen
2015-10-01
Reaction-diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or animals, which move and/or react in a stochastic manner. If the number of entities is large, accounting for each individual is inefficient, and often partial differential equation (PDE) models are used in which the stochastic behaviour of individuals is replaced by a description of the averaged, or mean behaviour of the system. In some situations the number of individuals is large in certain regions and small in others. In such cases, a stochastic model may be inefficient in one region, and a PDE model inaccurate in another. To overcome this problem, we develop a scheme which couples a stochastic reaction-diffusion system in one part of the domain with its mean field analogue, i.e. a discretised PDE model, in the other part of the domain. The interface in between the two domains occupies exactly one lattice site and is chosen such that the mean field description is still accurate there. In this way errors due to the flux between the domains are small. Our scheme can account for multiple dynamic interfaces separating multiple stochastic and deterministic domains, and the coupling between the domains conserves the total number of particles. The method preserves stochastic features such as extinction not observable in the mean field description, and is significantly faster to simulate on a computer than the pure stochastic model.
Hybrid approaches for multiple-species stochastic reaction-diffusion models.
Spill, Fabian
2015-10-01
Reaction-diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or animals, which move and/or react in a stochastic manner. If the number of entities is large, accounting for each individual is inefficient, and often partial differential equation (PDE) models are used in which the stochastic behaviour of individuals is replaced by a description of the averaged, or mean behaviour of the system. In some situations the number of individuals is large in certain regions and small in others. In such cases, a stochastic model may be inefficient in one region, and a PDE model inaccurate in another. To overcome this problem, we develop a scheme which couples a stochastic reaction-diffusion system in one part of the domain with its mean field analogue, i.e. a discretised PDE model, in the other part of the domain. The interface in between the two domains occupies exactly one lattice site and is chosen such that the mean field description is still accurate there. In this way errors due to the flux between the domains are small. Our scheme can account for multiple dynamic interfaces separating multiple stochastic and deterministic domains, and the coupling between the domains conserves the total number of particles. The method preserves stochastic features such as extinction not observable in the mean field description, and is significantly faster to simulate on a computer than the pure stochastic model.
Hybrid approaches for multiple-species stochastic reaction-diffusion models.
Spill, Fabian; Guerrero, Pilar; Alarcon, Tomas; Maini, Philip K; Byrne, Helen
2015-01-01
Reaction-diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or animals, which move and/or react in a stochastic manner. If the number of entities is large, accounting for each individual is inefficient, and often partial differential equation (PDE) models are used in which the stochastic behaviour of individuals is replaced by a description of the averaged, or mean behaviour of the system. In some situations the number of individuals is large in certain regions and small in others. In such cases, a stochastic model may be inefficient in one region, and a PDE model inaccurate in another. To overcome this problem, we develop a scheme which couples a stochastic reaction-diffusion system in one part of the domain with its mean field analogue, i.e. a discretised PDE model, in the other part of the domain. The interface in between the two domains occupies exactly one lattice site and is chosen such that the mean field description is still accurate there. In this way errors due to the flux between the domains are small. Our scheme can account for multiple dynamic interfaces separating multiple stochastic and deterministic domains, and the coupling between the domains conserves the total number of particles. The method preserves stochastic features such as extinction not observable in the mean field description, and is significantly faster to simulate on a computer than the pure stochastic model.
Heterogeneity induces spatiotemporal oscillations in reaction-diffusion systems
Krause, Andrew L.; Klika, Václav; Woolley, Thomas E.; Gaffney, Eamonn A.
2018-05-01
We report on an instability arising in activator-inhibitor reaction-diffusion (RD) systems with a simple spatial heterogeneity. This instability gives rise to periodic creation, translation, and destruction of spike solutions that are commonly formed due to Turing instabilities. While this behavior is oscillatory in nature, it occurs purely within the Turing space such that no region of the domain would give rise to a Hopf bifurcation for the homogeneous equilibrium. We use the shadow limit of the Gierer-Meinhardt system to show that the speed of spike movement can be predicted from well-known asymptotic theory, but that this theory is unable to explain the emergence of these spatiotemporal oscillations. Instead, we numerically explore this system and show that the oscillatory behavior is caused by the destabilization of a steady spike pattern due to the creation of a new spike arising from endogeneous activator production. We demonstrate that on the edge of this instability, the period of the oscillations goes to infinity, although it does not fit the profile of any well-known bifurcation of a limit cycle. We show that nearby stationary states are either Turing unstable or undergo saddle-node bifurcations near the onset of the oscillatory instability, suggesting that the periodic motion does not emerge from a local equilibrium. We demonstrate the robustness of this spatiotemporal oscillation by exploring small localized heterogeneity and showing that this behavior also occurs in the Schnakenberg RD model. Our results suggest that this phenomenon is ubiquitous in spatially heterogeneous RD systems, but that current tools, such as stability of spike solutions and shadow-limit asymptotics, do not elucidate understanding. This opens several avenues for further mathematical analysis and highlights difficulties in explaining how robust patterning emerges from Turing's mechanism in the presence of even small spatial heterogeneity.
Simulating complex noise barrier reflections
Eerden, F.J.M. van der; Lutgendorf, D.; Roo, F. de
2011-01-01
Within the EU FP7 QUIESST project, QUIeting the Environment for a Sustainable Surface Transport, a test method is being developed for the reflectivity of noise barriers. The method needs to account for a complex shape of barriers and the use of various types of absorbing materials. The performance
Glider-based computing in reaction-diffusion hexagonal cellular automata
International Nuclear Information System (INIS)
Adamatzky, Andrew; Wuensche, Andrew; De Lacy Costello, Benjamin
2006-01-01
A three-state hexagonal cellular automaton, discovered in [Wuensche A. Glider dynamics in 3-value hexagonal cellular automata: the beehive rule. Int J Unconvention Comput, in press], presents a conceptual discrete model of a reaction-diffusion system with inhibitor and activator reagents. The automaton model of reaction-diffusion exhibits mobile localized patterns (gliders) in its space-time dynamics. We show how to implement the basic computational operations with these mobile localizations, and thus demonstrate collision-based logical universality of the hexagonal reaction-diffusion cellular automaton
Sheng, Yin; Zhang, Hao; Zeng, Zhigang
2017-10-01
This paper is concerned with synchronization for a class of reaction-diffusion neural networks with Dirichlet boundary conditions and infinite discrete time-varying delays. By utilizing theories of partial differential equations, Green's formula, inequality techniques, and the concept of comparison, algebraic criteria are presented to guarantee master-slave synchronization of the underlying reaction-diffusion neural networks via a designed controller. Additionally, sufficient conditions on exponential synchronization of reaction-diffusion neural networks with finite time-varying delays are established. The proposed criteria herein enhance and generalize some published ones. Three numerical examples are presented to substantiate the validity and merits of the obtained theoretical results.
Wang, Xiaohu; Lu, Kening; Wang, Bixiang
2018-01-01
In this paper, we study the Wong-Zakai approximations given by a stationary process via the Wiener shift and their associated long term behavior of the stochastic reaction-diffusion equation driven by a white noise. We first prove the existence and uniqueness of tempered pullback attractors for the Wong-Zakai approximations of stochastic reaction-diffusion equation. Then, we show that the attractors of Wong-Zakai approximations converges to the attractor of the stochastic reaction-diffusion equation for both additive and multiplicative noise.
Amplitude equations for a sub-diffusive reaction-diffusion system
International Nuclear Information System (INIS)
Nec, Y; Nepomnyashchy, A A
2008-01-01
A sub-diffusive reaction-diffusion system with a positive definite memory operator and a nonlinear reaction term is analysed. Amplitude equations (Ginzburg-Landau type) are derived for short wave (Turing) and long wave (Hopf) bifurcation points
Study on monostable and bistable reaction-diffusion equations by iteration of travelling wave maps
Yi, Taishan; Chen, Yuming
2017-12-01
In this paper, based on the iterative properties of travelling wave maps, we develop a new method to obtain spreading speeds and asymptotic propagation for monostable and bistable reaction-diffusion equations. Precisely, for Dirichlet problems of monostable reaction-diffusion equations on the half line, by making links between travelling wave maps and integral operators associated with the Dirichlet diffusion kernel (the latter is NOT invariant under translation), we obtain some iteration properties of the Dirichlet diffusion and some a priori estimates on nontrivial solutions of Dirichlet problems under travelling wave transformation. We then provide the asymptotic behavior of nontrivial solutions in the space-time region for Dirichlet problems. These enable us to develop a unified method to obtain results on heterogeneous steady states, travelling waves, spreading speeds, and asymptotic spreading behavior for Dirichlet problem of monostable reaction-diffusion equations on R+ as well as of monostable/bistable reaction-diffusion equations on R.
International Nuclear Information System (INIS)
Liang Jinling; Cao Jinde
2003-01-01
Employing general Halanay inequality, we analyze the global exponential stability of a class of reaction-diffusion recurrent neural networks with time-varying delays. Several new sufficient conditions are obtained to ensure existence, uniqueness and global exponential stability of the equilibrium point of delayed reaction-diffusion recurrent neural networks. The results extend and improve the earlier publications. In addition, an example is given to show the effectiveness of the obtained result
Cross-diffusional effect in a telegraph reaction diffusion Lotka-Volterra two competitive system
International Nuclear Information System (INIS)
Abdusalam, H.A; Fahmy, E.S.
2003-01-01
It is known now that, telegraph equation is more suitable than ordinary diffusion equation in modelling reaction diffusion in several branches of sciences. Telegraph reaction diffusion Lotka-Volterra two competitive system is considered. We observed that this system can give rise to diffusive instability only in the presence of cross-diffusion. Local and global stability analysis in the cross-diffusional effect are studied by considering suitable Lyapunov functional
Directory of Open Access Journals (Sweden)
Herman N C Berghuijs
Full Text Available The rate of photosynthesis depends on the CO2 partial pressure near Rubisco, Cc, which is commonly calculated by models using the overall mesophyll resistance. Such models do not explain the difference between the CO2 level in the intercellular air space and Cc mechanistically. This problem can be overcome by reaction-diffusion models for CO2 transport, production and fixation in leaves. However, most reaction-diffusion models are complex and unattractive for procedures that require a large number of runs, like parameter optimisation. This study provides a simpler reaction-diffusion model. It is parameterized by both leaf physiological and leaf anatomical data. The anatomical data consisted of the thickness of the cell wall, cytosol and stroma, and the area ratios of mesophyll exposed to the intercellular air space to leaf surfaces and exposed chloroplast to exposed mesophyll surfaces. The model was used directly to estimate photosynthetic parameters from a subset of the measured light and CO2 response curves; the remaining data were used for validation. The model predicted light and CO2 response curves reasonably well for 15 days old tomato (cv. Admiro leaves, if (photorespiratory CO2 release was assumed to take place in the inner cytosol or in the gaps between the chloroplasts. The model was also used to calculate the fraction of CO2 produced by (photorespiration that is re-assimilated in the stroma, and this fraction ranged from 56 to 76%. In future research, the model should be further validated to better understand how the re-assimilation of (photorespired CO2 is affected by environmental conditions and physiological parameters.
Bifurcation analysis of a delay reaction-diffusion malware propagation model with feedback control
Zhu, Linhe; Zhao, Hongyong; Wang, Xiaoming
2015-05-01
With the rapid development of network information technology, information networks security has become a very critical issue in our work and daily life. This paper attempts to develop a delay reaction-diffusion model with a state feedback controller to describe the process of malware propagation in mobile wireless sensor networks (MWSNs). By analyzing the stability and Hopf bifurcation, we show that the state feedback method can successfully be used to control unstable steady states or periodic oscillations. Moreover, formulas for determining the properties of the bifurcating periodic oscillations are derived by applying the normal form method and center manifold theorem. Finally, we conduct extensive simulations on large-scale MWSNs to evaluate the proposed model. Numerical evidences show that the linear term of the controller is enough to delay the onset of the Hopf bifurcation and the properties of the bifurcation can be regulated to achieve some desirable behaviors by choosing the appropriate higher terms of the controller. Furthermore, we obtain that the spatial-temporal dynamic characteristics of malware propagation are closely related to the rate constant for nodes leaving the infective class for recovered class and the mobile behavior of nodes.
Traveling and Pinned Fronts in Bistable Reaction-Diffusion Systems on Networks
Kouvaris, Nikos E.; Kori, Hiroshi; Mikhailov, Alexander S.
2012-01-01
Traveling fronts and stationary localized patterns in bistable reaction-diffusion systems have been broadly studied for classical continuous media and regular lattices. Analogs of such non-equilibrium patterns are also possible in networks. Here, we consider traveling and stationary patterns in bistable one-component systems on random Erdös-Rényi, scale-free and hierarchical tree networks. As revealed through numerical simulations, traveling fronts exist in network-organized systems. They represent waves of transition from one stable state into another, spreading over the entire network. The fronts can furthermore be pinned, thus forming stationary structures. While pinning of fronts has previously been considered for chains of diffusively coupled bistable elements, the network architecture brings about significant differences. An important role is played by the degree (the number of connections) of a node. For regular trees with a fixed branching factor, the pinning conditions are analytically determined. For large Erdös-Rényi and scale-free networks, the mean-field theory for stationary patterns is constructed. PMID:23028746
GPU Accelerated Surgical Simulators for Complex Morhpology
DEFF Research Database (Denmark)
Mosegaard, Jesper; Sørensen, Thomas Sangild
2005-01-01
a springmass system in order to simulate a complex organ such as the heart. Computations are accelerated by taking advantage of modern graphics processing units (GPUs). Two GPU implementations are presented. They vary in their generality of spring connections and in the speedup factor they achieve...
Cherniha, Roman
2017-01-01
This book presents several fundamental results in solving nonlinear reaction-diffusion equations and systems using symmetry-based methods. Reaction-diffusion systems are fundamental modeling tools for mathematical biology with applications to ecology, population dynamics, pattern formation, morphogenesis, enzymatic reactions and chemotaxis. The book discusses the properties of nonlinear reaction-diffusion systems, which are relevant for biological applications, from the symmetry point of view, providing rigorous definitions and constructive algorithms to search for conditional symmetry (a nontrivial generalization of the well-known Lie symmetry) of nonlinear reaction-diffusion systems. In order to present applications to population dynamics, it focuses mainly on two- and three-component diffusive Lotka-Volterra systems. While it is primarily a valuable guide for researchers working with reaction-diffusion systems and those developing the theoretical aspects of conditional symmetry conception,...
International Nuclear Information System (INIS)
Moore, Peter K.
2003-01-01
Solving systems of reaction-diffusion equations in three space dimensions can be prohibitively expensive both in terms of storage and CPU time. Herein, I present a new incomplete assembly procedure that is designed to reduce storage requirements. Incomplete assembly is analogous to incomplete factorization in that only a fixed number of nonzero entries are stored per row and a drop tolerance is used to discard small values. The algorithm is incorporated in a finite element method-of-lines code and tested on a set of reaction-diffusion systems. The effect of incomplete assembly on CPU time and storage and on the performance of the temporal integrator DASPK, algebraic solver GMRES and preconditioner ILUT is studied
Control of complex physically simulated robot groups
Brogan, David C.
2001-10-01
Actuated systems such as robots take many forms and sizes but each requires solving the difficult task of utilizing available control inputs to accomplish desired system performance. Coordinated groups of robots provide the opportunity to accomplish more complex tasks, to adapt to changing environmental conditions, and to survive individual failures. Similarly, groups of simulated robots, represented as graphical characters, can test the design of experimental scenarios and provide autonomous interactive counterparts for video games. The complexity of writing control algorithms for these groups currently hinders their use. A combination of biologically inspired heuristics, search strategies, and optimization techniques serve to reduce the complexity of controlling these real and simulated characters and to provide computationally feasible solutions.
A reaction-diffusion model to capture disparity selectivity in primary visual cortex.
Directory of Open Access Journals (Sweden)
Mohammed Sultan Mohiuddin Siddiqui
Full Text Available Decades of experimental studies are available on disparity selective cells in visual cortex of macaque and cat. Recently, local disparity map for iso-orientation sites for near-vertical edge preference is reported in area 18 of cat visual cortex. No experiment is yet reported on complete disparity map in V1. Disparity map for layer IV in V1 can provide insight into how disparity selective complex cell receptive field is organized from simple cell subunits. Though substantial amounts of experimental data on disparity selective cells is available, no model on receptive field development of such cells or disparity map development exists in literature. We model disparity selectivity in layer IV of cat V1 using a reaction-diffusion two-eye paradigm. In this model, the wiring between LGN and cortical layer IV is determined by resource an LGN cell has for supporting connections to cortical cells and competition for target space in layer IV. While competing for target space, the same type of LGN cells, irrespective of whether it belongs to left-eye-specific or right-eye-specific LGN layer, cooperate with each other while trying to push off the other type. Our model captures realistic 2D disparity selective simple cell receptive fields, their response properties and disparity map along with orientation and ocular dominance maps. There is lack of correlation between ocular dominance and disparity selectivity at the cell population level. At the map level, disparity selectivity topography is not random but weakly clustered for similar preferred disparities. This is similar to the experimental result reported for macaque. The details of weakly clustered disparity selectivity map in V1 indicate two types of complex cell receptive field organization.
Hopf bifurcation in a delayed reaction-diffusion-advection population model
Chen, Shanshan; Lou, Yuan; Wei, Junjie
2018-04-01
In this paper, we investigate a reaction-diffusion-advection model with time delay effect. The stability/instability of the spatially nonhomogeneous positive steady state and the associated Hopf bifurcation are investigated when the given parameter of the model is near the principle eigenvalue of an elliptic operator. Our results imply that time delay can make the spatially nonhomogeneous positive steady state unstable for a reaction-diffusion-advection model, and the model can exhibit oscillatory pattern through Hopf bifurcation. The effect of advection on Hopf bifurcation values is also considered, and our results suggest that Hopf bifurcation is more likely to occur when the advection rate increases.
International Nuclear Information System (INIS)
Li Zuoan; Li Kelin
2009-01-01
In this paper, we investigate a class of impulsive fuzzy cellular neural networks with distributed delays and reaction-diffusion terms. By employing the delay differential inequality with impulsive initial conditions and M-matrix theory, we find some sufficient conditions ensuring the existence, uniqueness and global exponential stability of equilibrium point for impulsive fuzzy cellular neural networks with distributed delays and reaction-diffusion terms. In particular, the estimate of the exponential converging index is also provided, which depends on the system parameters. An example is given to show the effectiveness of the results obtained here.
International Nuclear Information System (INIS)
Wang Jian; Lu Junguo
2008-01-01
In this paper, we study the global exponential stability of fuzzy cellular neural networks with delays and reaction-diffusion terms. By constructing a suitable Lyapunov functional and utilizing some inequality techniques, we obtain a sufficient condition for the uniqueness and global exponential stability of the equilibrium solution for a class of fuzzy cellular neural networks with delays and reaction-diffusion terms. The result imposes constraint conditions on the network parameters independently of the delay parameter. The result is also easy to check and plays an important role in the design and application of globally exponentially stable fuzzy neural circuits
WNT and DKK Determine Hair Follicle Spacing Through a Reaction-Diffusion Mechanism
Sick, Stefanie; Reinker, Stefan; Timmer, Jens; Schlake, Thomas
2006-12-01
Mathematical reaction-diffusion models have been suggested to describe formation of animal pigmentation patterns and distribution of epidermal appendages. However, the crucial signals and in vivo mechanisms are still elusive. Here we identify WNT and its inhibitor DKK as primary determinants of murine hair follicle spacing, using a combined experimental and computational modeling approach. Transgenic DKK overexpression reduces overall appendage density. Moderate suppression of endogenous WNT signaling forces follicles to form clusters during an otherwise normal morphogenetic program. These results confirm predictions of a WNT/DKK-specific mathematical model and provide in vivo corroboration of the reaction-diffusion mechanism for epidermal appendage formation.
Polyanin, A. D.; Sorokin, V. G.
2017-12-01
The paper deals with nonlinear reaction-diffusion equations with one or several delays. We formulate theorems that allow constructing exact solutions for some classes of these equations, which depend on several arbitrary functions. Examples of application of these theorems for obtaining new exact solutions in elementary functions are provided. We state basic principles of construction, selection, and use of test problems for nonlinear partial differential equations with delay. Some test problems which can be suitable for estimating accuracy of approximate analytical and numerical methods of solving reaction-diffusion equations with delay are presented. Some examples of numerical solutions of nonlinear test problems with delay are considered.
Dynamic Analysis of a Reaction-Diffusion Rumor Propagation Model
Zhao, Hongyong; Zhu, Linhe
2016-06-01
The rapid development of the Internet, especially the emergence of the social networks, leads rumor propagation into a new media era. Rumor propagation in social networks has brought new challenges to network security and social stability. This paper, based on partial differential equations (PDEs), proposes a new SIS rumor propagation model by considering the effect of the communication between the different rumor infected users on rumor propagation. The stabilities of a nonrumor equilibrium point and a rumor-spreading equilibrium point are discussed by linearization technique and the upper and lower solutions method, and the existence of a traveling wave solution is established by the cross-iteration scheme accompanied by the technique of upper and lower solutions and Schauder’s fixed point theorem. Furthermore, we add the time delay to rumor propagation and deduce the conditions of Hopf bifurcation and stability switches for the rumor-spreading equilibrium point by taking the time delay as the bifurcation parameter. Finally, numerical simulations are performed to illustrate the theoretical results.
A SIMULATION MODEL OF THE GAS COMPLEX
Directory of Open Access Journals (Sweden)
Sokolova G. E.
2016-06-01
Full Text Available The article considers the dynamics of gas production in Russia, the structure of sales in the different market segments, as well as comparative dynamics of selling prices on these segments. Problems of approach to the creation of the gas complex using a simulation model, allowing to estimate efficiency of the project and determine the stability region of the obtained solutions. In the presented model takes into account the unit repayment of the loan, allowing with the first year of simulation to determine the possibility of repayment of the loan. The model object is a group of gas fields, which is determined by the minimum flow rate above which the project is cost-effective. In determining the minimum source flow rate for the norm of discount is taken as a generalized weighted average percentage on debt and equity taking into account risk premiums. He also serves as the lower barrier to internal rate of return below which the project is rejected as ineffective. Analysis of the dynamics and methods of expert evaluation allow to determine the intervals of variation of the simulated parameters, such as the price of gas and the exit gas complex at projected capacity. Calculated using the Monte Carlo method, for each random realization of the model simulated values of parameters allow to obtain a set of optimal for each realization of values minimum yield of wells, and also allows to determine the stability region of the solution.
A reaction-diffusion model of CO2 influx into an oocyte
Somersalo, Erkki; Occhipinti, Rossana; Boron, Walter F.; Calvetti, Daniela
2012-01-01
We have developed and implemented a novel mathematical model for simulating transients in surface pH (pHS) and intracellular pH (pHi) caused by the influx of carbon dioxide (CO2) into a Xenopus oocyte. These transients are important tools for studying gas channels. We assume that the oocyte is a sphere surrounded by a thin layer of unstirred fluid, the extracellular unconvected fluid (EUF), which is in turn surrounded by the well-stirred bulk extracellular fluid (BECF) that represents an infinite reservoir for all solutes. Here, we assume that the oocyte plasma membrane is permeable only to CO2. In both the EUF and intracellular space, solute concentrations can change because of diffusion and reactions. The reactions are the slow equilibration of the CO2 hydration-dehydration reactions and competing equilibria among carbonic acid (H2CO3)/bicarbonate ( HCO3-) and a multitude of non-CO2/HCO3- buffers. Mathematically, the model is described by a coupled system of reaction-diffusion equations that—assuming spherical radial symmetry—we solved using the method of lines with appropriate stiff solvers. In agreement with experimental data (Musa-Aziz et al, PNAS 2009, 106:5406–5411), the model predicts that exposing the cell to extracellular 1.5% CO2/10 mM HCO3- (pH 7.50) causes pHi to fall and pHS to rise rapidly to a peak and then decay. Moreover, the model provides insights into the competition between diffusion and reaction processes when we change the width of the EUF, membrane permeability to CO2, native extra-and intracellular carbonic anhydrase-like activities, the non-CO2/HCO3- (intrinsic) intracellular buffering power, or mobility of intrinsic intracellular buffers. PMID:22728674
Existence of global solutions to reaction-diffusion systems via a Lyapunov functional
Directory of Open Access Journals (Sweden)
Said Kouachi
2001-10-01
Full Text Available The purpose of this paper is to construct polynomial functionals (according to solutions of the coupled reaction-diffusion equations which give $L^{p}$-bounds for solutions. When the reaction terms are sufficiently regular, using the well known regularizing effect, we deduce the existence of global solutions. These functionals are obtained independently of work done by Malham and Xin [11].
Evans functions and bifurcations of nonlinear waves of some nonlinear reaction diffusion equations
Zhang, Linghai
2017-10-01
The main purposes of this paper are to accomplish the existence, stability, instability and bifurcation of the nonlinear waves of the nonlinear system of reaction diffusion equations ut =uxx + α [ βH (u - θ) - u ] - w, wt = ε (u - γw) and to establish the existence, stability, instability and bifurcation of the nonlinear waves of the nonlinear scalar reaction diffusion equation ut =uxx + α [ βH (u - θ) - u ], under different conditions on the model constants. To establish the bifurcation for the system, we will study the existence and instability of a standing pulse solution if 0 1; the existence and instability of two standing wave fronts if 2 (1 + αγ) θ = αβγ and 0 traveling wave front as well as the existence and instability of a standing pulse solution if 0 traveling wave front as well as the existence and instability of an upside down standing pulse solution if 0 traveling wave back of the nonlinear scalar reaction diffusion equation ut =uxx + α [ βH (u - θ) - u ] -w0, where w0 = α (β - 2 θ) > 0 is a positive constant, if 0 motivation to study the existence, stability, instability and bifurcations of the nonlinear waves is to study the existence and stability/instability of infinitely many fast/slow multiple traveling pulse solutions of the nonlinear system of reaction diffusion equations. The existence and stability of infinitely many fast multiple traveling pulse solutions are of great interests in mathematical neuroscience.
Bifurcation Analysis of Gene Propagation Model Governed by Reaction-Diffusion Equations
Directory of Open Access Journals (Sweden)
Guichen Lu
2016-01-01
Full Text Available We present a theoretical analysis of the attractor bifurcation for gene propagation model governed by reaction-diffusion equations. We investigate the dynamical transition problems of the model under the homogeneous boundary conditions. By using the dynamical transition theory, we give a complete characterization of the bifurcated objects in terms of the biological parameters of the problem.
Czech Academy of Sciences Publication Activity Database
Eisner, J.; Väth, Martin
2016-01-01
Roč. 135, April (2016), s. 158-193 ISSN 0362-546X Institutional support: RVO:67985840 Keywords : reaction-diffusion system * turing instability * global bifurcation Subject RIV: BA - General Mathematics Impact factor: 1.192, year: 2016 http://www.sciencedirect.com/science/article/pii/S0362546X16000146
Large-time behavior of solutions to a reaction-diffusion system with distributed microstructure
Muntean, A.
2009-01-01
Abstract We study the large-time behavior of a class of reaction-diffusion systems with constant distributed microstructure arising when modeling diffusion and reaction in structured porous media. The main result of this Note is the following: As t ¿ 8 the macroscopic concentration vanishes, while
Boundedness for a system of reaction-diffusion equations with more general Arrhenius term. Pt. 1
International Nuclear Information System (INIS)
Okoya, S.S.
1992-11-01
In this paper, we consider an extended model of a coupled nonlinear reaction-diffusion equation with Neumann-Neumann boundary conditions. We obtain upper linear growth bound for one of the components. We also find the corresponding bound for the case of Dirichlet-Dirichlet boundary conditions. (author). 12 refs
Dynamical Behaviors of Stochastic Reaction-Diffusion Cohen-Grossberg Neural Networks with Delays
Directory of Open Access Journals (Sweden)
Li Wan
2012-01-01
Full Text Available This paper investigates dynamical behaviors of stochastic Cohen-Grossberg neural network with delays and reaction diffusion. By employing Lyapunov method, Poincaré inequality and matrix technique, some sufficient criteria on ultimate boundedness, weak attractor, and asymptotic stability are obtained. Finally, a numerical example is given to illustrate the correctness and effectiveness of our theoretical results.
Concentration fluctuations in non-isothermal reaction-diffusion systems. II. The nonlinear case
Bedeaux, D.; Ortiz de Zárate, J.M.; Pagonabarraga, I.; Sengers, J.V.; Kjelstrup, S.
2011-01-01
In this paper, we consider a simple reaction-diffusion system, namely, a binary fluid mixture with an association-dissociation reaction between two species. We study fluctuations at hydrodynamic spatiotemporal scales when this mixture is driven out of equilibrium by the presence of a temperature
The entropy dissipation method for spatially inhomogeneous reaction-diffusion-type systems
Di Francesco, M.; Fellner, K.; Markowich, P. A
2008-01-01
and reaction terms and admit fewer conservation laws than the size of the system. In particular, we successfully apply the entropy approach to general linear systems and to a nonlinear example of a reaction-diffusion-convection system arising in solid
Minimum-complexity helicopter simulation math model
Heffley, Robert K.; Mnich, Marc A.
1988-01-01
An example of a minimal complexity simulation helicopter math model is presented. Motivating factors are the computational delays, cost, and inflexibility of the very sophisticated math models now in common use. A helicopter model form is given which addresses each of these factors and provides better engineering understanding of the specific handling qualities features which are apparent to the simulator pilot. The technical approach begins with specification of features which are to be modeled, followed by a build up of individual vehicle components and definition of equations. Model matching and estimation procedures are given which enable the modeling of specific helicopters from basic data sources such as flight manuals. Checkout procedures are given which provide for total model validation. A number of possible model extensions and refinement are discussed. Math model computer programs are defined and listed.
Simulating Complex Window Systems using BSDF Data
Energy Technology Data Exchange (ETDEWEB)
Konstantoglou, Maria; Jonsson, Jacob; Lee, Eleanor
2009-06-22
Nowadays, virtual models are commonly used to evaluate the performance of conventional window systems. Complex fenestration systems can be difficult to simulate accurately not only because of their geometry but also because of their optical properties that scatter light in an unpredictable manner. Bi-directional Scattering Distribution Functions (BSDF) have recently been developed based on a mixture of measurements and modelling to characterize the optics of such systems. This paper describes the workflow needed to create then use these BSDF datasets in the Radiance lighting simulation software. Limited comparisons are made between visualizations produced using the standard ray-tracing method, the BSDF method, and that taken in a full-scale outdoor mockup.
Computer simulations of dendrimer-polyelectrolyte complexes.
Pandav, Gunja; Ganesan, Venkat
2014-08-28
We carry out a systematic analysis of static properties of the clusters formed by complexation between charged dendrimers and linear polyelectrolyte (LPE) chains in a dilute solution under good solvent conditions. We use single chain in mean-field simulations and analyze the structure of the clusters through radial distribution functions of the dendrimer, cluster size, and charge distributions. The effects of LPE length, charge ratio between LPE and dendrimer, the influence of salt concentration, and the dendrimer generation number are examined. Systems with short LPEs showed a reduced propensity for aggregation with dendrimers, leading to formation of smaller clusters. In contrast, larger dendrimers and longer LPEs lead to larger clusters with significant bridging. Increasing salt concentration was seen to reduce aggregation between dendrimers as a result of screening of electrostatic interactions. Generally, maximum complexation was observed in systems with an equal amount of net dendrimer and LPE charges, whereas either excess LPE or dendrimer concentrations resulted in reduced clustering between dendrimers.
Stamova, Ivanka; Stamov, Gani
2017-12-01
In this paper, we propose a fractional-order neural network system with time-varying delays and reaction-diffusion terms. We first develop a new Mittag-Leffler synchronization strategy for the controlled nodes via impulsive controllers. Using the fractional Lyapunov method sufficient conditions are given. We also study the global Mittag-Leffler synchronization of two identical fractional impulsive reaction-diffusion neural networks using linear controllers, which was an open problem even for integer-order models. Since the Mittag-Leffler stability notion is a generalization of the exponential stability concept for fractional-order systems, our results extend and improve the exponential impulsive control theory of neural network system with time-varying delays and reaction-diffusion terms to the fractional-order case. The fractional-order derivatives allow us to model the long-term memory in the neural networks, and thus the present research provides with a conceptually straightforward mathematical representation of rather complex processes. Illustrative examples are presented to show the validity of the obtained results. We show that by means of appropriate impulsive controllers we can realize the stability goal and to control the qualitative behavior of the states. An image encryption scheme is extended using fractional derivatives. Copyright © 2017 Elsevier Ltd. All rights reserved.
Entropy methods for reaction-diffusion equations: slowly growing a-priori bounds
Desvillettes, Laurent; Fellner, Klemens
2008-01-01
In the continuation of [Desvillettes, L., Fellner, K.: Exponential Decay toward Equilibrium via Entropy Methods for Reaction-Diffusion Equations. J. Math. Anal. Appl. 319 (2006), no. 1, 157-176], we study reversible reaction-diffusion equations via entropy methods (based on the free energy functional) for a 1D system of four species. We improve the existing theory by getting 1) almost exponential convergence in L1 to the steady state via a precise entropy-entropy dissipation estimate, 2) an explicit global L∞ bound via interpolation of a polynomially growing H1 bound with the almost exponential L1 convergence, and 3), finally, explicit exponential convergence to the steady state in all Sobolev norms.
An Efficient Implicit FEM Scheme for Fractional-in-Space Reaction-Diffusion Equations
Burrage, Kevin
2012-01-01
Fractional differential equations are becoming increasingly used as a modelling tool for processes associated with anomalous diffusion or spatial heterogeneity. However, the presence of a fractional differential operator causes memory (time fractional) or nonlocality (space fractional) issues that impose a number of computational constraints. In this paper we develop efficient, scalable techniques for solving fractional-in-space reaction diffusion equations using the finite element method on both structured and unstructured grids via robust techniques for computing the fractional power of a matrix times a vector. Our approach is show-cased by solving the fractional Fisher and fractional Allen-Cahn reaction-diffusion equations in two and three spatial dimensions, and analyzing the speed of the traveling wave and size of the interface in terms of the fractional power of the underlying Laplacian operator. © 2012 Society for Industrial and Applied Mathematics.
Liu, Bingchen; Dong, Mengzhen; Li, Fengjie
2018-04-01
This paper deals with a reaction-diffusion problem with coupled nonlinear inner sources and nonlocal boundary flux. Firstly, we propose the critical exponents on nonsimultaneous blow-up under some conditions on the initial data. Secondly, we combine the scaling technique and the Green's identity method to determine four kinds of simultaneous blow-up rates. Thirdly, the lower and the upper bounds of blow-up time are derived by using Sobolev-type differential inequalities.
Reaction-diffusion processes in zero transverse dimensions as toy models for high-energy QCD
International Nuclear Information System (INIS)
Armesto, Nestor; Bondarenko, Sergey; Quiroga-Arias, Paloma; Milhano, Jose Guilherme
2008-01-01
We examine numerically different zero-dimensional reaction-diffusion processes as candidate toy models for high-energy QCD evolution. Of the models examined-Reggeon Field Theory, Directed Percolation and Reversible Processes-only the latter shows the behaviour commonly expected, namely an increase of the scattering amplitude with increasing rapidity. Further, we find that increasing recombination terms, quantum loops and the heuristic inclusion of a running of the couplings, generically slow down the evolution.
Numerical Solutions of Singularly Perturbed Reaction Diffusion Equation with Sobolev Gradients
Directory of Open Access Journals (Sweden)
Nauman Raza
2013-01-01
Full Text Available Critical points related to the singular perturbed reaction diffusion models are calculated using weighted Sobolev gradient method in finite element setting. Performance of different Sobolev gradients has been discussed for varying diffusion coefficient values. A comparison is shown between the weighted and unweighted Sobolev gradients in two and three dimensions. The superiority of the method is also demonstrated by showing comparison with Newton's method.
International Nuclear Information System (INIS)
Cherniha, Roman
2010-01-01
New definitions of Q-conditional symmetry for systems of PDEs are presented, which generalize the standard notation of non-classical (conditional) symmetry. It is shown that different types of Q-conditional symmetry of a system generate a hierarchy of conditional symmetry operators. A class of two-component nonlinear reaction-diffusion systems is examined to demonstrate the applicability of the definitions proposed and it is shown when different definitions of Q-conditional symmetry lead to the same operators.
Traveling Wave Solutions of Reaction-Diffusion Equations Arising in Atherosclerosis Models
Directory of Open Access Journals (Sweden)
Narcisa Apreutesei
2014-05-01
Full Text Available In this short review article, two atherosclerosis models are presented, one as a scalar equation and the other one as a system of two equations. They are given in terms of reaction-diffusion equations in an infinite strip with nonlinear boundary conditions. The existence of traveling wave solutions is studied for these models. The monostable and bistable cases are introduced and analyzed.
Liu, Ping; Shi, Junping
2018-01-01
The bifurcation of non-trivial steady state solutions of a scalar reaction-diffusion equation with nonlinear boundary conditions is considered using several new abstract bifurcation theorems. The existence and stability of positive steady state solutions are proved using a unified approach. The general results are applied to a Laplace equation with nonlinear boundary condition and bistable nonlinearity, and an elliptic equation with superlinear nonlinearity and sublinear boundary conditions.
Passivity analysis for uncertain BAM neural networks with time delays and reaction-diffusions
Zhou, Jianping; Xu, Shengyuan; Shen, Hao; Zhang, Baoyong
2013-08-01
This article deals with the problem of passivity analysis for delayed reaction-diffusion bidirectional associative memory (BAM) neural networks with weight uncertainties. By using a new integral inequality, we first present a passivity condition for the nominal networks, and then extend the result to the case with linear fractional weight uncertainties. The proposed conditions are expressed in terms of linear matrix inequalities, and thus can be checked easily. Examples are provided to demonstrate the effectiveness of the proposed results.
International Nuclear Information System (INIS)
Lou, X.; Cui, B.
2008-01-01
In this paper we consider the problem of exponential stability for recurrent neural networks with multiple time varying delays and reaction-diffusion terms. The activation functions are supposed to be bounded and globally Lipschitz continuous. By means of Lyapunov functional, sufficient conditions are derived, which guarantee global exponential stability of the delayed neural network. Finally, a numerical example is given to show the correctness of our analysis. (author)
A minimally-resolved immersed boundary model for reaction-diffusion problems
Pal Singh Bhalla, A; Griffith, BE; Patankar, NA; Donev, A
2013-01-01
We develop an immersed boundary approach to modeling reaction-diffusion processes in dispersions of reactive spherical particles, from the diffusion-limited to the reaction-limited setting. We represent each reactive particle with a minimally-resolved "blob" using many fewer degrees of freedom per particle than standard discretization approaches. More complicated or more highly resolved particle shapes can be built out of a collection of reactive blobs. We demonstrate numerically that the blo...
Contribution to an effective design method for stationary reaction-diffusion patterns
Energy Technology Data Exchange (ETDEWEB)
Szalai, István; Horváth, Judit [Laboratory of Nonlinear Chemical Dynamics, Institute of Chemistry, Eötvös Loránd University, P.O. Box 32, H-1518 Budapest 112 (Hungary); De Kepper, Patrick [Centre de Recherche Paul Pascal, CNRS, University of Bordeaux, 115, Avenue Schweitzer, F-33600 Pessac (France)
2015-06-15
The British mathematician Alan Turing predicted, in his seminal 1952 publication, that stationary reaction-diffusion patterns could spontaneously develop in reacting chemical or biochemical solutions. The first two clear experimental demonstrations of such a phenomenon were not made before the early 1990s when the design of new chemical oscillatory reactions and appropriate open spatial chemical reactors had been invented. Yet, the number of pattern producing reactions had not grown until 2009 when we developed an operational design method, which takes into account the feeding conditions and other specificities of real open spatial reactors. Since then, on the basis of this method, five additional reactions were shown to produce stationary reaction-diffusion patterns. To gain a clearer view on where our methodical approach on the patterning capacity of a reaction stands, numerical studies in conditions that mimic true open spatial reactors were made. In these numerical experiments, we explored the patterning capacity of Rabai's model for pH driven Landolt type reactions as a function of experimentally attainable parameters that control the main time and length scales. Because of the straightforward reversible binding of protons to carboxylate carrying polymer chains, this class of reaction is at the base of the chemistry leading to most of the stationary reaction-diffusion patterns presently observed. We compare our model predictions with experimental observations and comment on agreements and differences.
Contribution to an effective design method for stationary reaction-diffusion patterns
International Nuclear Information System (INIS)
Szalai, István; Horváth, Judit; De Kepper, Patrick
2015-01-01
The British mathematician Alan Turing predicted, in his seminal 1952 publication, that stationary reaction-diffusion patterns could spontaneously develop in reacting chemical or biochemical solutions. The first two clear experimental demonstrations of such a phenomenon were not made before the early 1990s when the design of new chemical oscillatory reactions and appropriate open spatial chemical reactors had been invented. Yet, the number of pattern producing reactions had not grown until 2009 when we developed an operational design method, which takes into account the feeding conditions and other specificities of real open spatial reactors. Since then, on the basis of this method, five additional reactions were shown to produce stationary reaction-diffusion patterns. To gain a clearer view on where our methodical approach on the patterning capacity of a reaction stands, numerical studies in conditions that mimic true open spatial reactors were made. In these numerical experiments, we explored the patterning capacity of Rabai's model for pH driven Landolt type reactions as a function of experimentally attainable parameters that control the main time and length scales. Because of the straightforward reversible binding of protons to carboxylate carrying polymer chains, this class of reaction is at the base of the chemistry leading to most of the stationary reaction-diffusion patterns presently observed. We compare our model predictions with experimental observations and comment on agreements and differences
Huang, Rui; Jin, Chunhua; Mei, Ming; Yin, Jingxue
2018-01-01
This paper deals with the existence and stability of traveling wave solutions for a degenerate reaction-diffusion equation with time delay. The degeneracy of spatial diffusion together with the effect of time delay causes us the essential difficulty for the existence of the traveling waves and their stabilities. In order to treat this case, we first show the existence of smooth- and sharp-type traveling wave solutions in the case of c≥c^* for the degenerate reaction-diffusion equation without delay, where c^*>0 is the critical wave speed of smooth traveling waves. Then, as a small perturbation, we obtain the existence of the smooth non-critical traveling waves for the degenerate diffusion equation with small time delay τ >0 . Furthermore, we prove the global existence and uniqueness of C^{α ,β } -solution to the time-delayed degenerate reaction-diffusion equation via compactness analysis. Finally, by the weighted energy method, we prove that the smooth non-critical traveling wave is globally stable in the weighted L^1 -space. The exponential convergence rate is also derived.
Huang, Rui; Jin, Chunhua; Mei, Ming; Yin, Jingxue
2018-06-01
This paper deals with the existence and stability of traveling wave solutions for a degenerate reaction-diffusion equation with time delay. The degeneracy of spatial diffusion together with the effect of time delay causes us the essential difficulty for the existence of the traveling waves and their stabilities. In order to treat this case, we first show the existence of smooth- and sharp-type traveling wave solutions in the case of c≥c^* for the degenerate reaction-diffusion equation without delay, where c^*>0 is the critical wave speed of smooth traveling waves. Then, as a small perturbation, we obtain the existence of the smooth non-critical traveling waves for the degenerate diffusion equation with small time delay τ >0. Furthermore, we prove the global existence and uniqueness of C^{α ,β }-solution to the time-delayed degenerate reaction-diffusion equation via compactness analysis. Finally, by the weighted energy method, we prove that the smooth non-critical traveling wave is globally stable in the weighted L^1-space. The exponential convergence rate is also derived.
Simulation and Optimisation of CLIC's recombination complex
Costa, Raul; Barroso, Manuel
In this thesis we present the first Placet2 recombination simulations of the drive beam recombination complex (DBRC) design for the compact linear collider (CLIC). We start by presenting a review of the CLIC project and the DBRC’s role and design within it. We then discuss some of the core principles of beam dynamics and how tracking codes like Placet2 implement them. We follow that by presenting the design issues raised by our simulations and our proposed strategy to address them, key among which is a previously unknown parabolic dependency of the longitudinal position to the momentum (T 566 ), which threat- ens the efficiency of the power extraction structures. Through iterative opti- misation of the design, we eliminated this aberration both in the delay loop and in combiner ring 1. We also found the beam’s horizontal emittance to be significantly over the design budget (150 μm) and attempted to meet that budget, reaching 157 μm. In order to obtain this emittance value, an update to the combiner ring...
Theories and simulations of complex social systems
Mago, Vijay
2014-01-01
Research into social systems is challenging due to their complex nature. Traditional methods of analysis are often difficult to apply effectively as theories evolve over time. This can be due to a lack of appropriate data, or too much uncertainty. It can also be the result of problems which are not yet understood well enough in the general sense so that they can be classified, and an appropriate solution quickly identified. Simulation is one tool that deals well with these challenges, fits in well with the deductive process, and is useful for testing theory. This field is still relatively new, and much of the work is necessarily innovative, although it builds upon a rich and varied foundation. There are a number of existing modelling paradigms being applied to complex social systems research. Additionally, new methods and measures are being devised through the process of conducting research. We expect that readers will enjoy the collection of high quality research works from new and accomplished researchers. ...
Automatic Algorithm Selection for Complex Simulation Problems
Ewald, Roland
2012-01-01
To select the most suitable simulation algorithm for a given task is often difficult. This is due to intricate interactions between model features, implementation details, and runtime environment, which may strongly affect the overall performance. An automated selection of simulation algorithms supports users in setting up simulation experiments without demanding expert knowledge on simulation. Roland Ewald analyzes and discusses existing approaches to solve the algorithm selection problem in the context of simulation. He introduces a framework for automatic simulation algorithm selection and
Mielke, Alexander; Mittnenzweig, Markus
2018-04-01
We discuss how the recently developed energy dissipation methods for reaction diffusion systems can be generalized to the non-isothermal case. For this, we use concave entropies in terms of the densities of the species and the internal energy, where the importance is that the equilibrium densities may depend on the internal energy. Using the log-Sobolev estimate and variants for lower-order entropies as well as estimates for the entropy production of the nonlinear reactions, we give two methods to estimate the relative entropy by the total entropy production, namely a somewhat restrictive convexity method, which provides explicit decay rates, and a very general, but weaker compactness method.
Nonlinear waves in reaction-diffusion systems: The effect of transport memory
International Nuclear Information System (INIS)
Manne, K. K.; Hurd, A. J.; Kenkre, V. M.
2000-01-01
Motivated by the problem of determining stress distributions in granular materials, we study the effect of finite transport correlation times on the propagation of nonlinear wave fronts in reaction-diffusion systems. We obtain results such as the possibility of spatial oscillations in the wave-front shape for certain values of the system parameters and high enough wave-front speeds. We also generalize earlier known results concerning the minimum wave-front speed and shape-speed relationships stemming from the finiteness of the correlation times. Analytic investigations are made possible by a piecewise linear representation of the nonlinearity. (c) 2000 The American Physical Society
Spatiotemporal chaos of self-replicating spots in reaction-diffusion systems.
Wang, Hongli; Ouyang, Qi
2007-11-23
The statistical properties of self-replicating spots in the reaction-diffusion Gray-Scott model are analyzed. In the chaotic regime of the system, the spots that dominate the spatiotemporal chaos grow and divide in two or decay into the background randomly and continuously. The rates at which the spots are created and decay are observed to be linearly dependent on the number of spots in the system. We derive a probabilistic description of the spot dynamics based on the statistical independence of spots and thus propose a characterization of the spatiotemporal chaos dominated by replicating spots.
On one model problem for the reaction-diffusion-advection equation
Davydova, M. A.; Zakharova, S. A.; Levashova, N. T.
2017-09-01
The asymptotic behavior of the solution with boundary layers in the time-independent mathematical model of reaction-diffusion-advection arising when describing the distribution of greenhouse gases in the surface atmospheric layer is studied. On the basis of the asymptotic method of differential inequalities, the existence of a boundary-layer solution and its asymptotic Lyapunov stability as a steady-state solution of the corresponding parabolic problem is proven. One of the results of this work is the determination of the local domain of the attraction of a boundary-layer solution.
Nefedov, Nikolay
2017-02-01
This is an extended variant of the paper presented at MURPHYS-HSFS 2016 conference in Barcelona. We discuss further development of the asymptotic method of differential inequalities to investigate existence and stability of sharp internal layers (fronts) for nonlinear singularly perturbed periodic parabolic problems and initial boundary value problems with blow-up of fronts for reaction-diffusion-advection equations. In particular, we consider periodic solutions with internal layer in the case of balanced reaction. For the initial boundary value problems we prove the existence of fronts and give their asymptotic approximation including the new case of blowing-up fronts. This case we illustrate by the generalised Burgers equation.
Existence and exponential stability of traveling waves for delayed reaction-diffusion systems
Hsu, Cheng-Hsiung; Yang, Tzi-Sheng; Yu, Zhixian
2018-03-01
The purpose of this work is to investigate the existence and exponential stability of traveling wave solutions for general delayed multi-component reaction-diffusion systems. Following the monotone iteration scheme via an explicit construction of a pair of upper and lower solutions, we first obtain the existence of monostable traveling wave solutions connecting two different equilibria. Then, applying the techniques of weighted energy method and comparison principle, we show that all solutions of the Cauchy problem for the considered systems converge exponentially to traveling wave solutions provided that the initial perturbations around the traveling wave fronts belong to a suitable weighted Sobolev space.
International Nuclear Information System (INIS)
Wang Linshan; Zhang Zhe; Wang Yangfan
2008-01-01
Some criteria for the global stochastic exponential stability of the delayed reaction-diffusion recurrent neural networks with Markovian jumping parameters are presented. The jumping parameters considered here are generated from a continuous-time discrete-state homogeneous Markov process, which are governed by a Markov process with discrete and finite state space. By employing a new Lyapunov-Krasovskii functional, a linear matrix inequality (LMI) approach is developed to establish some easy-to-test criteria of global exponential stability in the mean square for the stochastic neural networks. The criteria are computationally efficient, since they are in the forms of some linear matrix inequalities
Nonlinear waves in reaction-diffusion systems: The effect of transport memory
Manne, K. K.; Hurd, A. J.; Kenkre, V. M.
2000-04-01
Motivated by the problem of determining stress distributions in granular materials, we study the effect of finite transport correlation times on the propagation of nonlinear wave fronts in reaction-diffusion systems. We obtain results such as the possibility of spatial oscillations in the wave-front shape for certain values of the system parameters and high enough wave-front speeds. We also generalize earlier known results concerning the minimum wave-front speed and shape-speed relationships stemming from the finiteness of the correlation times. Analytic investigations are made possible by a piecewise linear representation of the nonlinearity.
Directory of Open Access Journals (Sweden)
Luisa Malaguti
2011-01-01
Full Text Available The paper deals with a degenerate reaction-diffusion equation, including aggregative movements and convective terms. The model also incorporates a real parameter causing the change from a purely diffusive to a diffusive-aggregative and to a purely aggregative regime. Existence and qualitative properties of traveling wave solutions are investigated, and estimates of their threshold speeds are furnished. Further, the continuous dependence of the threshold wave speed and of the wave profiles on a real parameter is studied, both when the process maintains its diffusion-aggregation nature and when it switches from it to another regime.
Energy Technology Data Exchange (ETDEWEB)
Wang, Chi-Jen [Iowa State Univ., Ames, IA (United States)
2013-01-01
In this thesis, we analyze both the spatiotemporal behavior of: (A) non-linear “reaction” models utilizing (discrete) reaction-diffusion equations; and (B) spatial transport problems on surfaces and in nanopores utilizing the relevant (continuum) diffusion or Fokker-Planck equations. Thus, there are some common themes in these studies, as they all involve partial differential equations or their discrete analogues which incorporate a description of diffusion-type processes. However, there are also some qualitative differences, as shall be discussed below.
Adaptive exponential synchronization of delayed neural networks with reaction-diffusion terms
International Nuclear Information System (INIS)
Sheng Li; Yang Huizhong; Lou Xuyang
2009-01-01
This paper presents an exponential synchronization scheme for a class of neural networks with time-varying and distributed delays and reaction-diffusion terms. An adaptive synchronization controller is derived to achieve the exponential synchronization of the drive-response structure of neural networks by using the Lyapunov stability theory. At the same time, the update laws of parameters are proposed to guarantee the synchronization of delayed neural networks with all parameters unknown. It is shown that the approaches developed here extend and improve the ideas presented in recent literatures.
The entropy dissipation method for spatially inhomogeneous reaction-diffusion-type systems
Di Francesco, M.
2008-12-08
We study the long-time asymptotics of reaction-diffusion-type systems that feature a monotone decaying entropy (Lyapunov, free energy) functional. We consider both bounded domains and confining potentials on the whole space for arbitrary space dimensions. Our aim is to derive quantitative expressions for (or estimates of) the rates of convergence towards an (entropy minimizing) equilibrium state in terms of the constants of diffusion and reaction and with respect to conserved quantities. Our method, the so-called entropy approach, seeks to quantify convergence to equilibrium by using functional inequalities, which relate quantitatively the entropy and its dissipation in time. The entropy approach is well suited to nonlinear problems and known to be quite robust with respect to model variations. It has already been widely applied to scalar diffusion-convection equations, and the main goal of this paper is to study its generalization to systems of partial differential equations that contain diffusion and reaction terms and admit fewer conservation laws than the size of the system. In particular, we successfully apply the entropy approach to general linear systems and to a nonlinear example of a reaction-diffusion-convection system arising in solid-state physics as a paradigm for general nonlinear systems. © 2008 The Royal Society.
Directory of Open Access Journals (Sweden)
Dmitry V. Lukyanenko
2017-01-01
Full Text Available This work develops a theory of the asymptotic-numerical investigation of the moving fronts in reaction-diffusion-advection models. By considering the numerical solution of the singularly perturbed Burgers’s equation we discuss a method of dynamically adapted mesh construction that is able to significantly improve the numerical solution of this type of equations. For the construction we use a priori information that is based on the asymptotic analysis of the problem. In particular, we take into account the information about the speed of the transition layer, its width and structure. Our algorithms are able to reduce significantly complexity and enhance stability of the numerical calculations in comparison with classical approaches for solving this class of problems. The numerical experiment is presented to demonstrate the effectiveness of the proposed method.The article is published in the authors’ wording.
SUPERCOMPUTER SIMULATION OF CRITICAL PHENOMENA IN COMPLEX SOCIAL SYSTEMS
Directory of Open Access Journals (Sweden)
Petrus M.A. Sloot
2014-09-01
Full Text Available The paper describes a problem of computer simulation of critical phenomena in complex social systems on a petascale computing systems in frames of complex networks approach. The three-layer system of nested models of complex networks is proposed including aggregated analytical model to identify critical phenomena, detailed model of individualized network dynamics and model to adjust a topological structure of a complex network. The scalable parallel algorithm covering all layers of complex networks simulation is proposed. Performance of the algorithm is studied on different supercomputing systems. The issues of software and information infrastructure of complex networks simulation are discussed including organization of distributed calculations, crawling the data in social networks and results visualization. The applications of developed methods and technologies are considered including simulation of criminal networks disruption, fast rumors spreading in social networks, evolution of financial networks and epidemics spreading.
Lecca, Paola; Morpurgo, Daniele
2012-01-01
Reaction-diffusion based models have been widely used in the literature for modeling the growth of solid tumors. Many of the current models treat both diffusion/consumption of nutrients and cell proliferation. The majority of these models use classical transport/mass conservation equations for describing the distribution of molecular species in tumor spheroids, and the Fick's law for describing the flux of uncharged molecules (i.e oxygen, glucose). Commonly, the equations for the cell movement and proliferation are first order differential equations describing the rate of change of the velocity of the cells with respect to the spatial coordinates as a function of the nutrient's gradient. Several modifications of these equations have been developed in the last decade to explicitly indicate that the tumor includes cells, interstitial fluids and extracellular matrix: these variants provided a model of tumor as a multiphase material with these as the different phases. Most of the current reaction-diffusion tumor models are deterministic and do not model the diffusion as a local state-dependent process in a non-homogeneous medium at the micro- and meso-scale of the intra- and inter-cellular processes, respectively. Furthermore, a stochastic reaction-diffusion model in which diffusive transport of the molecular species of nutrients and chemotherapy drugs as well as the interactions of the tumor cells with these species is a novel approach. The application of this approach to he scase of non-small cell lung cancer treated with gemcitabine is also novel. We present a stochastic reaction-diffusion model of non-small cell lung cancer growth in the specification formalism of the tool Redi, we recently developed for simulating reaction-diffusion systems. We also describe how a spatial gradient of nutrients and oncological drugs affects the tumor progression. Our model is based on a generalization of the Fick's first diffusion law that allows to model diffusive transport in non
International Nuclear Information System (INIS)
Lu Junguo
2008-01-01
In this paper, the global exponential stability and periodicity for a class of reaction-diffusion delayed recurrent neural networks with Dirichlet boundary conditions are addressed by constructing suitable Lyapunov functionals and utilizing some inequality techniques. We first prove global exponential converge to 0 of the difference between any two solutions of the original reaction-diffusion delayed recurrent neural networks with Dirichlet boundary conditions, the existence and uniqueness of equilibrium is the direct results of this procedure. This approach is different from the usually used one where the existence, uniqueness of equilibrium and stability are proved in two separate steps. Furthermore, we prove periodicity of the reaction-diffusion delayed recurrent neural networks with Dirichlet boundary conditions. Sufficient conditions ensuring the global exponential stability and the existence of periodic oscillatory solutions for the reaction-diffusion delayed recurrent neural networks with Dirichlet boundary conditions are given. These conditions are easy to check and have important leading significance in the design and application of reaction-diffusion recurrent neural networks with delays. Finally, two numerical examples are given to show the effectiveness of the obtained results
Reaction time for trimolecular reactions in compartment-based reaction-diffusion models
Li, Fei; Chen, Minghan; Erban, Radek; Cao, Yang
2018-05-01
Trimolecular reaction models are investigated in the compartment-based (lattice-based) framework for stochastic reaction-diffusion modeling. The formulae for the first collision time and the mean reaction time are derived for the case where three molecules are present in the solution under periodic boundary conditions. For the case of reflecting boundary conditions, similar formulae are obtained using a computer-assisted approach. The accuracy of these formulae is further verified through comparison with numerical results. The presented derivation is based on the first passage time analysis of Montroll [J. Math. Phys. 10, 753 (1969)]. Montroll's results for two-dimensional lattice-based random walks are adapted and applied to compartment-based models of trimolecular reactions, which are studied in one-dimensional or pseudo one-dimensional domains.
Cluster geometry and survival probability in systems driven by reaction-diffusion dynamics
International Nuclear Information System (INIS)
Windus, Alastair; Jensen, Henrik J
2008-01-01
We consider a reaction-diffusion model incorporating the reactions A→φ, A→2A and 2A→3A. Depending on the relative rates for sexual and asexual reproduction of the quantity A, the model exhibits either a continuous or first-order absorbing phase transition to an extinct state. A tricritical point separates the two phase lines. While we comment on this critical behaviour, the main focus of the paper is on the geometry of the population clusters that form. We observe the different cluster structures that arise at criticality for the three different types of critical behaviour and show that there exists a linear relationship for the survival probability against initial cluster size at the tricritical point only.
Critical regimes driven by recurrent mobility patterns of reaction-diffusion processes in networks
Gómez-Gardeñes, J.; Soriano-Paños, D.; Arenas, A.
2018-04-01
Reaction-diffusion processes1 have been widely used to study dynamical processes in epidemics2-4 and ecology5 in networked metapopulations. In the context of epidemics6, reaction processes are understood as contagions within each subpopulation (patch), while diffusion represents the mobility of individuals between patches. Recently, the characteristics of human mobility7, such as its recurrent nature, have been proven crucial to understand the phase transition to endemic epidemic states8,9. Here, by developing a framework able to cope with the elementary epidemic processes, the spatial distribution of populations and the commuting mobility patterns, we discover three different critical regimes of the epidemic incidence as a function of these parameters. Interestingly, we reveal a regime of the reaction-diffussion process in which, counter-intuitively, mobility is detrimental to the spread of disease. We analytically determine the precise conditions for the emergence of any of the three possible critical regimes in real and synthetic networks.
Semi-analytical solutions of the Schnakenberg model of a reaction-diffusion cell with feedback
Al Noufaey, K. S.
2018-06-01
This paper considers the application of a semi-analytical method to the Schnakenberg model of a reaction-diffusion cell. The semi-analytical method is based on the Galerkin method which approximates the original governing partial differential equations as a system of ordinary differential equations. Steady-state curves, bifurcation diagrams and the region of parameter space in which Hopf bifurcations occur are presented for semi-analytical solutions and the numerical solution. The effect of feedback control, via altering various concentrations in the boundary reservoirs in response to concentrations in the cell centre, is examined. It is shown that increasing the magnitude of feedback leads to destabilization of the system, whereas decreasing this parameter to negative values of large magnitude stabilizes the system. The semi-analytical solutions agree well with numerical solutions of the governing equations.
Vorticity field, helicity integral and persistence of entanglement in reaction-diffusion systems
International Nuclear Information System (INIS)
Trueba, J L; Arrayas, M
2009-01-01
We show that a global description of the stability of entangled structures in reaction-diffusion systems can be made by means of a helicity integral. A vorticity vector field is defined for these systems, as in electromagnetism or fluid dynamics. We have found under which conditions the helicity is conserved or lost through the boundaries of the medium, so the entanglement of structures observed is preserved or disappears during time evolution. We illustrate the theory with an example of knotted entanglement in a FitzHugh-Nagumo model. For this model, we introduce new non-trivial initial conditions using the Hopf fibration and follow the time evolution of the entanglement. (fast track communication)
Vorticity field, helicity integral and persistence of entanglement in reaction-diffusion systems
Energy Technology Data Exchange (ETDEWEB)
Trueba, J L; Arrayas, M [Area de Electromagnetismo, Universidad Rey Juan Carlos, Camino del Molino s/n, 28943 Fuenlabrada, Madrid (Spain)
2009-07-17
We show that a global description of the stability of entangled structures in reaction-diffusion systems can be made by means of a helicity integral. A vorticity vector field is defined for these systems, as in electromagnetism or fluid dynamics. We have found under which conditions the helicity is conserved or lost through the boundaries of the medium, so the entanglement of structures observed is preserved or disappears during time evolution. We illustrate the theory with an example of knotted entanglement in a FitzHugh-Nagumo model. For this model, we introduce new non-trivial initial conditions using the Hopf fibration and follow the time evolution of the entanglement. (fast track communication)
Yuvan, Steven; Bier, Martin
2018-02-01
Two decades ago Bak et al. (1997) [3] proposed a reaction-diffusion model to describe market fluctuations. In the model buyers and sellers diffuse from opposite ends of a 1D interval that represents a price range. Trades occur when buyers and sellers meet. We show analytically and numerically that the model well reproduces the square-root relation between traded volumes and price changes that is observed in real-life markets. The result is remarkable as this relation has commonly been explained in terms of more elaborate trader strategies. We furthermore explain why the square-root relation is robust under model modifications and we show how real-life bond market data exhibit the square-root relation.
Grytskyy, Dmytro; Diesmann, Markus; Helias, Moritz
2016-06-01
Self-organized structures in networks with spike-timing dependent synaptic plasticity (STDP) are likely to play a central role for information processing in the brain. In the present study we derive a reaction-diffusion-like formalism for plastic feed-forward networks of nonlinear rate-based model neurons with a correlation sensitive learning rule inspired by and being qualitatively similar to STDP. After obtaining equations that describe the change of the spatial shape of the signal from layer to layer, we derive a criterion for the nonlinearity necessary to obtain stable dynamics for arbitrary input. We classify the possible scenarios of signal evolution and find that close to the transition to the unstable regime metastable solutions appear. The form of these dissipative solitons is determined analytically and the evolution and interaction of several such coexistent objects is investigated.
Cluster geometry and survival probability in systems driven by reaction-diffusion dynamics
Energy Technology Data Exchange (ETDEWEB)
Windus, Alastair; Jensen, Henrik J [The Institute for Mathematical Sciences, 53 Prince' s Gate, South Kensington, London SW7 2PG (United Kingdom)], E-mail: h.jensen@imperial.ac.uk
2008-11-15
We consider a reaction-diffusion model incorporating the reactions A{yields}{phi}, A{yields}2A and 2A{yields}3A. Depending on the relative rates for sexual and asexual reproduction of the quantity A, the model exhibits either a continuous or first-order absorbing phase transition to an extinct state. A tricritical point separates the two phase lines. While we comment on this critical behaviour, the main focus of the paper is on the geometry of the population clusters that form. We observe the different cluster structures that arise at criticality for the three different types of critical behaviour and show that there exists a linear relationship for the survival probability against initial cluster size at the tricritical point only.
Existence of weak solutions to a nonlinear reaction-diffusion system with singular sources
Directory of Open Access Journals (Sweden)
Ida de Bonis
2017-09-01
Full Text Available We discuss the existence of a class of weak solutions to a nonlinear parabolic system of reaction-diffusion type endowed with singular production terms by reaction. The singularity is due to a potential occurrence of quenching localized to the domain boundary. The kind of quenching we have in mind is due to a twofold contribution: (i the choice of boundary conditions, modeling in our case the contact with an infinite reservoir filled with ready-to-react chemicals and (ii the use of a particular nonlinear, non-Lipschitz structure of the reaction kinetics. Our working techniques use fine energy estimates for approximating non-singular problems and uniform control on the set where singularities are localizing.
Regularity of random attractors for fractional stochastic reaction-diffusion equations on Rn
Gu, Anhui; Li, Dingshi; Wang, Bixiang; Yang, Han
2018-06-01
We investigate the regularity of random attractors for the non-autonomous non-local fractional stochastic reaction-diffusion equations in Hs (Rn) with s ∈ (0 , 1). We prove the existence and uniqueness of the tempered random attractor that is compact in Hs (Rn) and attracts all tempered random subsets of L2 (Rn) with respect to the norm of Hs (Rn). The main difficulty is to show the pullback asymptotic compactness of solutions in Hs (Rn) due to the noncompactness of Sobolev embeddings on unbounded domains and the almost sure nondifferentiability of the sample paths of the Wiener process. We establish such compactness by the ideas of uniform tail-estimates and the spectral decomposition of solutions in bounded domains.
Global dynamics of a nonlocal delayed reaction-diffusion equation on a half plane
Hu, Wenjie; Duan, Yueliang
2018-04-01
We consider a delayed reaction-diffusion equation with spatial nonlocality on a half plane that describes population dynamics of a two-stage species living in a semi-infinite environment. A Neumann boundary condition is imposed accounting for an isolated domain. To describe the global dynamics, we first establish some a priori estimate for nontrivial solutions after investigating asymptotic properties of the nonlocal delayed effect and the diffusion operator, which enables us to show the permanence of the equation with respect to the compact open topology. We then employ standard dynamical system arguments to establish the global attractivity of the nontrivial equilibrium. The main results are illustrated by the diffusive Nicholson's blowfly equation and the diffusive Mackey-Glass equation.
Anomalous dimension in a two-species reaction-diffusion system
Vollmayr-Lee, Benjamin; Hanson, Jack; McIsaac, R. Scott; Hellerick, Joshua D.
2018-01-01
We study a two-species reaction-diffusion system with the reactions A+A\\to (0, A) and A+B\\to A , with general diffusion constants D A and D B . Previous studies showed that for dimensions d≤slant 2 the B particle density decays with a nontrivial, universal exponent that includes an anomalous dimension resulting from field renormalization. We demonstrate via renormalization group methods that the scaled B particle correlation function has a distinct anomalous dimension resulting in the asymptotic scaling \\tilde CBB(r, t) ˜ tφf(r/\\sqrt{t}) , where the exponent ϕ results from the renormalization of the square of the field associated with the B particles. We compute this exponent to first order in \
Asymptotic behavior of equilibrium states of reaction-diffusion systems with mass conservation
Chern, Jann-Long; Morita, Yoshihisa; Shieh, Tien-Tsan
2018-01-01
We deal with a stationary problem of a reaction-diffusion system with a conservation law under the Neumann boundary condition. It is shown that the stationary problem turns to be the Euler-Lagrange equation of an energy functional with a mass constraint. When the domain is the finite interval (0 , 1), we investigate the asymptotic profile of a strictly monotone minimizer of the energy as d, the ratio of the diffusion coefficient of the system, tends to zero. In view of a logarithmic function in the leading term of the potential, we get to a scaling parameter κ satisfying the relation ε : =√{ d } =√{ log κ } /κ2. The main result shows that a sequence of minimizers converges to a Dirac mass multiplied by the total mass and that by a scaling with κ the asymptotic profile exhibits a parabola in the nonvanishing region. We also prove the existence of an unstable monotone solution when the mass is small.
Mode-locking in advection-reaction-diffusion systems: An invariant manifold perspective
Locke, Rory A.; Mahoney, John R.; Mitchell, Kevin A.
2018-01-01
Fronts propagating in two-dimensional advection-reaction-diffusion systems exhibit a rich topological structure. When the underlying fluid flow is periodic in space and time, the reaction front can lock to the driving frequency. We explain this mode-locking phenomenon using the so-called burning invariant manifolds (BIMs). In fact, the mode-locked profile is delineated by a BIM attached to a relative periodic orbit (RPO) of the front element dynamics. Changes in the type (and loss) of mode-locking can be understood in terms of local and global bifurcations of the RPOs and their BIMs. We illustrate these concepts numerically using a chain of alternating vortices in a channel geometry.
Oscillatory pulses and wave trains in a bistable reaction-diffusion system with cross diffusion.
Zemskov, Evgeny P; Tsyganov, Mikhail A; Horsthemke, Werner
2017-01-01
We study waves with exponentially decaying oscillatory tails in a reaction-diffusion system with linear cross diffusion. To be specific, we consider a piecewise linear approximation of the FitzHugh-Nagumo model, also known as the Bonhoeffer-van der Pol model. We focus on two types of traveling waves, namely solitary pulses that correspond to a homoclinic solution, and sequences of pulses or wave trains, i.e., a periodic solution. The effect of cross diffusion on wave profiles and speed of propagation is analyzed. We find the intriguing result that both pulses and wave trains occur in the bistable cross-diffusive FitzHugh-Nagumo system, whereas only fronts exist in the standard bistable system without cross diffusion.
Dynamics of interface in three-dimensional anisotropic bistable reaction-diffusion system
International Nuclear Information System (INIS)
He Zhizhu; Liu, Jing
2010-01-01
This paper presents a theoretical investigation of dynamics of interface (wave front) in three-dimensional (3D) reaction-diffusion (RD) system for bistable media with anisotropy constructed by means of anisotropic surface tension. An equation of motion for the wave front is derived to carry out stability analysis of transverse perturbations, which discloses mechanism of pattern formation such as labyrinthine in 3D bistable media. Particularly, the effects of anisotropy on wave propagation are studied. It was found that, sufficiently strong anisotropy can induce dynamical instabilities and lead to breakup of the wave front. With the fast-inhibitor limit, the bistable system can further be described by a variational dynamics so that the boundary integral method is adopted to study the dynamics of wave fronts.
Monostable traveling waves for a time-periodic and delayed nonlocal reaction-diffusion equation
Li, Panxiao; Wu, Shi-Liang
2018-04-01
This paper is concerned with a time-periodic and delayed nonlocal reaction-diffusion population model with monostable nonlinearity. Under quasi-monotone or non-quasi-monotone assumptions, it is known that there exists a critical wave speed c_*>0 such that a periodic traveling wave exists if and only if the wave speed is above c_*. In this paper, we first prove the uniqueness of non-critical periodic traveling waves regardless of whether the model is quasi-monotone or not. Further, in the quasi-monotone case, we establish the exponential stability of non-critical periodic traveling fronts. Finally, we illustrate the main results by discussing two types of death and birth functions arising from population biology.
Scalable implicit methods for reaction-diffusion equations in two and three space dimensions
Energy Technology Data Exchange (ETDEWEB)
Veronese, S.V.; Othmer, H.G. [Univ. of Utah, Salt Lake City, UT (United States)
1996-12-31
This paper describes the implementation of a solver for systems of semi-linear parabolic partial differential equations in two and three space dimensions. The solver is based on a parallel implementation of a non-linear Alternating Direction Implicit (ADI) scheme which uses a Cartesian grid in space and an implicit time-stepping algorithm. Various reordering strategies for the linearized equations are used to reduce the stride and improve the overall effectiveness of the parallel implementation. We have successfully used this solver for large-scale reaction-diffusion problems in computational biology and medicine in which the desired solution is a traveling wave that may contain rapid transitions. A number of examples that illustrate the efficiency and accuracy of the method are given here; the theoretical analysis will be presented.
Large-scale computing techniques for complex system simulations
Dubitzky, Werner; Schott, Bernard
2012-01-01
Complex systems modeling and simulation approaches are being adopted in a growing number of sectors, including finance, economics, biology, astronomy, and many more. Technologies ranging from distributed computing to specialized hardware are explored and developed to address the computational requirements arising in complex systems simulations. The aim of this book is to present a representative overview of contemporary large-scale computing technologies in the context of complex systems simulations applications. The intention is to identify new research directions in this field and
Directory of Open Access Journals (Sweden)
Shahid Hasnain
2017-07-01
Full Text Available This research paper represents a numerical approximation to non-linear three dimension reaction diffusion equation with non-linear source term from population genetics. Since various initial and boundary value problems exist in three dimension reaction diffusion phenomena, which are studied numerically by different numerical methods, here we use finite difference schemes (Alternating Direction Implicit and Fourth Order Douglas Implicit to approximate the solution. Accuracy is studied in term of L2, L∞ and relative error norms by random selected grids along time levels for comparison with analytical results. The test example demonstrates the accuracy, efficiency and versatility of the proposed schemes. Numerical results showed that Fourth Order Douglas Implicit scheme is very efficient and reliable for solving 3-D non-linear reaction diffusion equation.
Hasnain, Shahid; Saqib, Muhammad; Mashat, Daoud Suleiman
2017-07-01
This research paper represents a numerical approximation to non-linear three dimension reaction diffusion equation with non-linear source term from population genetics. Since various initial and boundary value problems exist in three dimension reaction diffusion phenomena, which are studied numerically by different numerical methods, here we use finite difference schemes (Alternating Direction Implicit and Fourth Order Douglas Implicit) to approximate the solution. Accuracy is studied in term of L2, L∞ and relative error norms by random selected grids along time levels for comparison with analytical results. The test example demonstrates the accuracy, efficiency and versatility of the proposed schemes. Numerical results showed that Fourth Order Douglas Implicit scheme is very efficient and reliable for solving 3-D non-linear reaction diffusion equation.
Computer simulation of complexity in plasmas
International Nuclear Information System (INIS)
Hayashi, Takaya; Sato, Tetsuya
1998-01-01
By making a comprehensive comparative study of many self-organizing phenomena occurring in magnetohydrodynamics and kinetic plasmas, we came up with a hypothetical grand view of self-organization. This assertion is confirmed by a recent computer simulation for a broader science field, specifically, the structure formation of short polymer chains, where the nature of the interaction is completely different from that of plasmas. It is found that the formation of the global orientation order proceeds stepwise. (author)
Simulating Complex Systems by Cellular Automata
Kroc, Jiri; Hoekstra, Alfons G
2010-01-01
Deeply rooted in fundamental research in Mathematics and Computer Science, Cellular Automata (CA) are recognized as an intuitive modeling paradigm for Complex Systems. Already very basic CA, with extremely simple micro dynamics such as the Game of Life, show an almost endless display of complex emergent behavior. Conversely, CA can also be designed to produce a desired emergent behavior, using either theoretical methodologies or evolutionary techniques. Meanwhile, beyond the original realm of applications - Physics, Computer Science, and Mathematics – CA have also become work horses in very different disciplines such as epidemiology, immunology, sociology, and finance. In this context of fast and impressive progress, spurred further by the enormous attraction these topics have on students, this book emerges as a welcome overview of the field for its practitioners, as well as a good starting point for detailed study on the graduate and post-graduate level. The book contains three parts, two major parts on th...
International Nuclear Information System (INIS)
Wang Xiaohu; Xu Daoyi
2009-01-01
In this paper, the global exponential stability of impulsive fuzzy cellular neural networks with mixed delays and reaction-diffusion terms is considered. By establishing an integro-differential inequality with impulsive initial condition and using the properties of M-cone and eigenspace of the spectral radius of nonnegative matrices, several new sufficient conditions are obtained to ensure the global exponential stability of the equilibrium point for fuzzy cellular neural networks with delays and reaction-diffusion terms. These results extend and improve the earlier publications. Two examples are given to illustrate the efficiency of the obtained results.
Smart modeling and simulation for complex systems practice and theory
Ren, Fenghui; Zhang, Minjie; Ito, Takayuki; Tang, Xijin
2015-01-01
This book aims to provide a description of these new Artificial Intelligence technologies and approaches to the modeling and simulation of complex systems, as well as an overview of the latest scientific efforts in this field such as the platforms and/or the software tools for smart modeling and simulating complex systems. These tasks are difficult to accomplish using traditional computational approaches due to the complex relationships of components and distributed features of resources, as well as the dynamic work environments. In order to effectively model the complex systems, intelligent technologies such as multi-agent systems and smart grids are employed to model and simulate the complex systems in the areas of ecosystem, social and economic organization, web-based grid service, transportation systems, power systems and evacuation systems.
Simulation of dust voids in complex plasmas
Goedheer, W. J.; Land, V.
2008-12-01
In dusty radio-frequency (RF) discharges under micro-gravity conditions often a void is observed, a dust free region in the discharge center. This void is generated by the drag of the positive ions pulled out of the discharge by the electric field. We have developed a hydrodynamic model for dusty RF discharges in argon to study the behaviour of the void and the interaction between the dust and the plasma background. The model is based on a recently developed theory for the ion drag force and the charging of the dust. With this model, we studied the plasma inside the void and obtained an understanding of the way it is sustained by heat generated in the surrounding dust cloud. When this heating mechanism is suppressed by lowering the RF power, the plasma density inside the void decreases, even below the level where the void collapses, as was recently shown in experiments on board the International Space Station. In this paper we present results of simulations of this collapse. At reduced power levels the collapsed central cloud behaves as an electronegative plasma with corresponding low time-averaged electric fields. This enables the creation of relatively homogeneous Yukawa balls, containing more than 100 000 particles. On earth, thermophoresis can be used to balance gravity and obtain similar dust distributions.
Numerical simulations and mathematical models of flows in complex geometries
DEFF Research Database (Denmark)
Hernandez Garcia, Anier
The research work of the present thesis was mainly aimed at exploiting one of the strengths of the Lattice Boltzmann methods, namely, the ability to handle complicated geometries to accurately simulate flows in complex geometries. In this thesis, we perform a very detailed theoretical analysis...... and through the Chapman-Enskog multi-scale expansion technique the dependence of the kinetic viscosity on each scheme is investigated. Seeking for optimal numerical schemes to eciently simulate a wide range of complex flows a variant of the finite element, off-lattice Boltzmann method [5], which uses...... the characteristic based integration is also implemented. Using the latter scheme, numerical simulations are conducted in flows of different complexities: flow in a (real) porous network and turbulent flows in ducts with wall irregularities. From the simulations of flows in porous media driven by pressure gradients...
International Nuclear Information System (INIS)
Adamatzky, Andrew; Lacy Costello, Benjamin de
2003-01-01
A reaction-diffusion chemical computer in this context is a planar uniform chemical reactor, where data and results of a computation are represented by concentration profiles of reactants and the computation itself is implemented via the spreading and interaction of diffusive and phase waves. This class of chemical computers are efficient at solving problems with a 'natural' parallelism where data sets are decomposable onto a large number of geographically neighboring domains which are then processed in parallel. Typical problems of this type include image processing, geometrical transformations and optimisation. When chemical based devices are used to solve such problems questions regarding their reproducible, efficiency and the accuracy of their computations arise. In addition to these questions what are the limitations of reaction-diffusion chemical processors--what type of problems cannot currently and are unlikely ever to be solved? To answer the questions we study how a Voronoi diagram is constructed and how it is inverted in a planar chemical processor. We demonstrate that a Voronoi diagram is computed only partially in the chemical processor. We also prove that given a specific Voronoi diagram it is impossible to reconstruct the planar set (from which diagram was computed) in the reaction-diffusion chemical processor. In the Letter we open the first ever line of enquiry into the computational inability of reaction-diffusion chemical computers
Czech Academy of Sciences Publication Activity Database
Klika, Václav; Baker, R. E.; Headon, D.; Gaffney, E. A.
2012-01-01
Roč. 74, č. 4 (2012), s. 935-957 ISSN 0092-8240 Institutional research plan: CEZ:AV0Z20760514 Keywords : reaction-diffusion * receptor-mediated patterning * turing models Subject RIV: BO - Biophysics Impact factor: 2.023, year: 2012 http://www.springerlink.com/content/9713544x6871w4n6/?MUD=MP
Czech Academy of Sciences Publication Activity Database
Eisner, Jan; Kučera, Milan; Väth, Martin
2016-01-01
Roč. 61, č. 1 (2016), s. 1-25 ISSN 0862-7940 R&D Projects: GA ČR GA13-12580S Institutional support: RVO:67985904 ; RVO:67985840 Keywords : reaction-diffusion system * unlateral condition * variational inequality Subject RIV: EG - Zoology; BA - General Mathematics (MU-W) Impact factor: 0.618, year: 2016
Ranking important nodes in complex networks by simulated annealing
International Nuclear Information System (INIS)
Sun Yu; Yao Pei-Yang; Shen Jian; Zhong Yun; Wan Lu-Jun
2017-01-01
In this paper, based on simulated annealing a new method to rank important nodes in complex networks is presented. First, the concept of an importance sequence (IS) to describe the relative importance of nodes in complex networks is defined. Then, a measure used to evaluate the reasonability of an IS is designed. By comparing an IS and the measure of its reasonability to a state of complex networks and the energy of the state, respectively, the method finds the ground state of complex networks by simulated annealing. In other words, the method can construct a most reasonable IS. The results of experiments on real and artificial networks show that this ranking method not only is effective but also can be applied to different kinds of complex networks. (paper)
Image-Based Measurement of H2O2 Reaction-Diffusion in Wounded Zebrafish Larvae.
Jelcic, Mark; Enyedi, Balázs; Xavier, João B; Niethammer, Philipp
2017-05-09
Epithelial injury induces rapid recruitment of antimicrobial leukocytes to the wound site. In zebrafish larvae, activation of the epithelial NADPH oxidase Duox at the wound margin is required early during this response. Before injury, leukocytes are near the vascular region, that is, ∼100-300 μm away from the injury site. How Duox establishes long-range signaling to leukocytes is unclear. We conceived that extracellular hydrogen peroxide (H 2 O 2 ) generated by Duox diffuses through the tissue to directly regulate chemotactic signaling in these cells. But before it can oxidize cellular proteins, H 2 O 2 must get past the antioxidant barriers that protect the cellular proteome. To test whether, or on which length scales this occurs during physiological wound signaling, we developed a computational method based on reaction-diffusion principles that infers H 2 O 2 degradation rates from intravital H 2 O 2 -biosensor imaging data. Our results indicate that at high tissue H 2 O 2 levels the peroxiredoxin-thioredoxin antioxidant chain becomes overwhelmed, and H 2 O 2 degradation stalls or ceases. Although the wound H 2 O 2 gradient reaches deep into the tissue, it likely overcomes antioxidant barriers only within ∼30 μm of the wound margin. Thus, Duox-mediated long-range signaling may require other spatial relay mechanisms besides extracellular H 2 O 2 diffusion. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.
Quantitative modeling of the reaction/diffusion kinetics of two-chemistry photopolymers
Kowalski, Benjamin Andrew
Optically driven diffusion in photopolymers is an appealing material platform for a broad range of applications, in which the recorded refractive index patterns serve either as images (e.g. data storage, display holography) or as optical elements (e.g. custom GRIN components, integrated optical devices). A quantitative understanding of the reaction/diffusion kinetics is difficult to obtain directly, but is nevertheless necessary in order to fully exploit the wide array of design freedoms in these materials. A general strategy for characterizing these kinetics is proposed, in which key processes are decoupled and independently measured. This strategy enables prediction of a material's potential refractive index change, solely on the basis of its chemical components. The degree to which a material does not reach this potential reveals the fraction of monomer that has participated in unwanted reactions, reducing spatial resolution and dynamic range. This approach is demonstrated for a model material similar to commercial media, achieving quantitative predictions of index response over three orders of exposure dose (~1 to ~103 mJ cm-2) and three orders of feature size (0.35 to 500 microns). The resulting insights enable guided, rational design of new material formulations with demonstrated performance improvement.
Fourier spectral methods for fractional-in-space reaction-diffusion equations
Bueno-Orovio, Alfonso
2014-04-01
© 2014, Springer Science+Business Media Dordrecht. Fractional differential equations are becoming increasingly used as a powerful modelling approach for understanding the many aspects of nonlocality and spatial heterogeneity. However, the numerical approximation of these models is demanding and imposes a number of computational constraints. In this paper, we introduce Fourier spectral methods as an attractive and easy-to-code alternative for the integration of fractional-in-space reaction-diffusion equations described by the fractional Laplacian in bounded rectangular domains of ℝ. The main advantages of the proposed schemes is that they yield a fully diagonal representation of the fractional operator, with increased accuracy and efficiency when compared to low-order counterparts, and a completely straightforward extension to two and three spatial dimensions. Our approach is illustrated by solving several problems of practical interest, including the fractional Allen–Cahn, FitzHugh–Nagumo and Gray–Scott models, together with an analysis of the properties of these systems in terms of the fractional power of the underlying Laplacian operator.
A reaction-diffusion model for radiation-induced bystander effects.
Olobatuyi, Oluwole; de Vries, Gerda; Hillen, Thomas
2017-08-01
We develop and analyze a reaction-diffusion model to investigate the dynamics of the lifespan of a bystander signal emitted when cells are exposed to radiation. Experimental studies by Mothersill and Seymour 1997, using malignant epithelial cell lines, found that an emitted bystander signal can still cause bystander effects in cells even 60 h after its emission. Several other experiments have also shown that the signal can persist for months and even years. Also, bystander effects have been hypothesized as one of the factors responsible for the phenomenon of low-dose hyper-radiosensitivity and increased radioresistance (HRS/IRR). Here, we confirm this hypothesis with a mathematical model, which we fit to Joiner's data on HRS/IRR in a T98G glioma cell line. Furthermore, we use phase plane analysis to understand the full dynamics of the signal's lifespan. We find that both single and multiple radiation exposure can lead to bystander signals that either persist temporarily or permanently. We also found that, in an heterogeneous environment, the size of the domain exposed to radiation and the number of radiation exposures can determine whether a signal will persist temporarily or permanently. Finally, we use sensitivity analysis to identify those cell parameters that affect the signal's lifespan and the signal-induced cell death the most.
Dóka, Éva; Lente, Gábor
2017-04-13
This work presents a rigorous mathematical study of the effect of unavoidable inhomogeneities in laser flash photolysis experiments. There are two different kinds of inhomegenities: the first arises from diffusion, whereas the second one has geometric origins (the shapes of the excitation and detection light beams). Both of these are taken into account in our reported model, which gives rise to a set of reaction-diffusion type partial differential equations. These equations are solved by a specially developed finite volume method. As an example, the aqueous reaction between the sulfate ion radical and iodide ion is used, for which sufficiently detailed experimental data are available from an earlier publication. The results showed that diffusion itself is in general too slow to influence the kinetic curves on the usual time scales of laser flash photolysis experiments. However, the use of the absorbances measured (e.g., to calculate the molar absorption coefficients of transient species) requires very detailed mathematical consideration and full knowledge of the geometrical shapes of the excitation laser beam and the separate detection light beam. It is also noted that the usual pseudo-first-order approach to evaluating the kinetic traces can be used successfully even if the usual large excess condition is not rigorously met in the reaction cell locally.
Mean field effects for counterpropagating traveling wave solutions of reaction-diffusion systems
International Nuclear Information System (INIS)
Bernoff, A.J.; Kuske, R.; Matkowsky, B.J.; Volpert, V.
1995-01-01
In many problems, one observes traveling waves that propagate with constant velocity and shape in the χ direction, say, are independent of y, and z and describe transitions between two equilibrium states. As parameters of the system are varied, these traveling waves can become unstable and give rise to waves having additional structure, such as traveling waves in the y and z directions, which can themselves be subject to instabilities as parameters are further varied. To investigate this scenario the authors consider a system of reaction-diffusion equations with a traveling wave solution as a basic state. They determine solutions bifurcating from the basic state that describe counterpropagating traveling wave in directions orthogonal to the direction of propagation of the basic state and determine their stability. Specifically, they derive long wave modulation equations for the amplitudes of the counterpropagating traveling waves that are coupled to an equation for a mean field, generated by the translation of the basic state in the direction of its propagation. The modulation equations are then employed to determine stability boundaries to long wave perturbations for both unidirectional and counterpropagating traveling waves. The stability analysis is delicate because the results depend on the order in which transverse and longitudinal perturbation wavenumbers are taken to zero. For the unidirectional wave they demonstrate that it is sufficient to consider the cases of (1) purely transverse perturbations, (2) purely longitudinal perturbations, and (3) longitudinal perturbations with a small transverse component. These yield Eckhaus type, zigzag type, and skew type instabilities, respectively
A Reaction-Diffusion Model for Synapse Growth and Long-Term Memory
Liu, Kang; Lisman, John; Hagan, Michael
Memory storage involves strengthening of synaptic transmission known as long-term potentiation (LTP). The late phase of LTP is associated with structural processes that enlarge the synapse. Yet, synapses must be stable, despite continual subunit turnover, over the lifetime of an encoded memory. These considerations suggest that synapses are variable-size stable structure (VSSS), meaning they can switch between multiple metastable structures with different sizes. The mechanisms underlying VSSS are poorly understood. While experiments and theory have suggested that the interplay between diffusion and receptor-scaffold interactions can lead to a preferred stable size for synaptic domains, such a mechanism cannot explain how synapses adopt widely different sizes. Here we develop a minimal reaction-diffusion model of VSSS for synapse growth, incorporating the recent observation from super-resolution microscopy that neural activity can build compositional heterogeneities within synaptic domains. We find that introducing such heterogeneities can change the stable domain size in a controlled manner. We discuss a potential connection between this model and experimental data on synapse sizes, and how it provides a possible mechanism to structurally encode graded long-term memory. We acknowledge the support from NSF INSPIRE Award number IOS-1526941 (KL, MFH, JL) and the Brandeis Center for Bioinspired Soft Materials, an NSF MRSEC, DMR- 1420382 (MFH).
A nonlocal and periodic reaction-diffusion-advection model of a single phytoplankton species.
Peng, Rui; Zhao, Xiao-Qiang
2016-02-01
In this article, we are concerned with a nonlocal reaction-diffusion-advection model which describes the evolution of a single phytoplankton species in a eutrophic vertical water column where the species relies solely on light for its metabolism. The new feature of our modeling equation lies in that the incident light intensity and the death rate are assumed to be time periodic with a common period. We first establish a threshold type result on the global dynamics of this model in terms of the basic reproduction number R0. Then we derive various characterizations of R0 with respect to the vertical turbulent diffusion rate, the sinking or buoyant rate and the water column depth, respectively, which in turn give rather precise conditions to determine whether the phytoplankton persist or become extinct. Our theoretical results not only extend the existing ones for the time-independent case, but also reveal new interesting effects of the modeling parameters and the time-periodic heterogeneous environment on persistence and extinction of the phytoplankton species, and thereby suggest important implications for phytoplankton growth control.
Directory of Open Access Journals (Sweden)
Inci Cilingir Sungu
2015-01-01
Full Text Available A new application of the hybrid generalized differential transform and finite difference method is proposed by solving time fractional nonlinear reaction-diffusion equations. This method is a combination of the multi-time-stepping temporal generalized differential transform and the spatial finite difference methods. The procedure first converts the time-evolutionary equations into Poisson equations which are then solved using the central difference method. The temporal differential transform method as used in the paper takes care of stability and the finite difference method on the resulting equation results in a system of diagonally dominant linear algebraic equations. The Gauss-Seidel iterative procedure then used to solve the linear system thus has assured convergence. To have optimized convergence rate, numerical experiments were done by using a combination of factors involving multi-time-stepping, spatial step size, and degree of the polynomial fit in time. It is shown that the hybrid technique is reliable, accurate, and easy to apply.
New mechanism of spiral wave initiation in a reaction-diffusion-mechanics system.
Directory of Open Access Journals (Sweden)
Louis D Weise
Full Text Available Spiral wave initiation in the heart muscle is a mechanism for the onset of dangerous cardiac arrhythmias. A standard protocol for spiral wave initiation is the application of a stimulus in the refractory tail of a propagating excitation wave, a region that we call the "classical vulnerable zone." Previous studies of vulnerability to spiral wave initiation did not take the influence of deformation into account, which has been shown to have a substantial effect on the excitation process of cardiomyocytes via the mechano-electrical feedback phenomenon. In this work we study the effect of deformation on the vulnerability of excitable media in a discrete reaction-diffusion-mechanics (dRDM model. The dRDM model combines FitzHugh-Nagumo type equations for cardiac excitation with a discrete mechanical description of a finite-elastic isotropic material (Seth material to model cardiac excitation-contraction coupling and stretch activated depolarizing current. We show that deformation alters the "classical," and forms a new vulnerable zone at longer coupling intervals. This mechanically caused vulnerable zone results in a new mechanism of spiral wave initiation, where unidirectional conduction block and rotation directions of the consequently initiated spiral waves are opposite compared to the mechanism of spiral wave initiation due to the "classical vulnerable zone." We show that this new mechanism of spiral wave initiation can naturally occur in situations that involve wave fronts with curvature, and discuss its relation to supernormal excitability of cardiac tissue. The concept of mechanically induced vulnerability may lead to a better understanding about the onset of dangerous heart arrhythmias via mechano-electrical feedback.
New mechanism of spiral wave initiation in a reaction-diffusion-mechanics system.
Weise, Louis D; Panfilov, Alexander V
2011-01-01
Spiral wave initiation in the heart muscle is a mechanism for the onset of dangerous cardiac arrhythmias. A standard protocol for spiral wave initiation is the application of a stimulus in the refractory tail of a propagating excitation wave, a region that we call the "classical vulnerable zone." Previous studies of vulnerability to spiral wave initiation did not take the influence of deformation into account, which has been shown to have a substantial effect on the excitation process of cardiomyocytes via the mechano-electrical feedback phenomenon. In this work we study the effect of deformation on the vulnerability of excitable media in a discrete reaction-diffusion-mechanics (dRDM) model. The dRDM model combines FitzHugh-Nagumo type equations for cardiac excitation with a discrete mechanical description of a finite-elastic isotropic material (Seth material) to model cardiac excitation-contraction coupling and stretch activated depolarizing current. We show that deformation alters the "classical," and forms a new vulnerable zone at longer coupling intervals. This mechanically caused vulnerable zone results in a new mechanism of spiral wave initiation, where unidirectional conduction block and rotation directions of the consequently initiated spiral waves are opposite compared to the mechanism of spiral wave initiation due to the "classical vulnerable zone." We show that this new mechanism of spiral wave initiation can naturally occur in situations that involve wave fronts with curvature, and discuss its relation to supernormal excitability of cardiac tissue. The concept of mechanically induced vulnerability may lead to a better understanding about the onset of dangerous heart arrhythmias via mechano-electrical feedback.
Route complexity and simulated physical ageing negatively influence wayfinding
Zijlstra, Emma; Hagedoorn, Mariet; Krijnen, Wim P.; Schans, van der Cornelis; Mobach, Mark P.
The aim of this age-simulation field experiment was to assess the influence of route complexity and physical ageing on wayfinding. Seventy-five people (aged 18-28) performed a total of 108 wayfinding tasks (i.e., 42 participants performed two wayfinding tasks and 33 performed one wayfinding task),
Visualization and simulation of complex flows in biomedical engineering
Imai, Yohsuke; Ishikawa, Takuji; Oliveira, Mónica
2014-01-01
This book focuses on the most recent advances in the application of visualization and simulation methods to understand the flow behavior of complex fluids used in biomedical engineering and other related fields. It shows the physiological flow behavior in large arteries, microcirculation, respiratory systems and in biomedical microdevices.
Quantum simulations of small electron-hole complexes
International Nuclear Information System (INIS)
Lee, M.A.; Kalia, R.K.; Vashishta, P.D.
1984-09-01
The Green's Function Monte Carlo method is applied to the calculation of the binding energies of electron-hole complexes in semiconductors. The quantum simulation method allows the unambiguous determination of the ground state energy and the effects of band anisotropy on the binding energy. 22 refs., 1 fig
International Nuclear Information System (INIS)
Han, Renji; Dai, Binxiang
2017-01-01
Highlights: • We model general two-dimensional reaction-diffusion with nonlocal delay. • The existence of unique positive steady state is studied. • The bilinear form for the proposed system is given. • The existence, direction of Hopf bifurcation are given by symmetry method. - Abstract: A nonlocal delayed reaction-diffusive two-species model with Dirichlet boundary condition and general functional response is investigated in this paper. Based on the Lyapunov–Schmidt reduction, the existence, bifurcation direction and stability of Hopf bifurcating periodic orbits near the positive spatially nonhomogeneous steady-state solution are obtained, where the time delay is taken as the bifurcation parameter. Moreover, the general results are applied to a diffusive Lotka–Volterra type food-limited population model with nonlocal delay effect, and it is found that diffusion and nonlocal delay can also affect the other dynamic behavior of the system by numerical experiments.
International Nuclear Information System (INIS)
Wu Shiliang; Li Wantong
2009-01-01
This paper deals with the global asymptotic stability and uniqueness (up to translation) of bistable traveling fronts in a class of reaction-diffusion systems. The known results do not apply in solving these problems because the reaction terms do not satisfy the required monotone condition. To overcome the difficulty, a weak monotone condition is proposed for the reaction terms, which is called interval monotone condition. Under such a weak monotone condition, the existence and comparison theorem of solutions is first established for reaction-diffusion systems on R by appealing to the theory of abstract differential equations. The global asymptotic stability and uniqueness (up to translation) of bistable traveling fronts are then proved by the elementary super- and sub-solution comparison and squeezing methods for nonlinear evolution equations. Finally, these abstract results are applied to a two species competition-diffusion model and a system modeling man-environment-man epidemics.
Effects of intrinsic stochasticity on delayed reaction-diffusion patterning systems
Woolley, Thomas E.; Baker, Ruth E.; Gaffney, Eamonn A.; Maini, Philip K.; Seirin-Lee, Sungrim
2012-01-01
Cellular gene expression is a complex process involving many steps, including the transcription of DNA and translation of mRNA; hence the synthesis of proteins requires a considerable amount of time, from ten minutes to several hours. Since diffusion-driven instability has been observed to be sensitive to perturbations in kinetic delays, the application of Turing patterning mechanisms to the problem of producing spatially heterogeneous differential gene expression has been questioned. In deterministic systems a small delay in the reactions can cause a large increase in the time it takes a system to pattern. Recently, it has been observed that in undelayed systems intrinsic stochasticity can cause pattern initiation to occur earlier than in the analogous deterministic simulations. Here we are interested in adding both stochasticity and delays to Turing systems in order to assess whether stochasticity can reduce the patterning time scale in delayed Turing systems. As analytical insights to this problem are difficult to attain and often limited in their use, we focus on stochastically simulating delayed systems. We consider four different Turing systems and two different forms of delay. Our results are mixed and lead to the conclusion that, although the sensitivity to delays in the Turing mechanism is not completely removed by the addition of intrinsic noise, the effects of the delays are clearly ameliorated in certain specific cases. © 2012 American Physical Society.
Effects of intrinsic stochasticity on delayed reaction-diffusion patterning systems
Woolley, Thomas E.
2012-05-22
Cellular gene expression is a complex process involving many steps, including the transcription of DNA and translation of mRNA; hence the synthesis of proteins requires a considerable amount of time, from ten minutes to several hours. Since diffusion-driven instability has been observed to be sensitive to perturbations in kinetic delays, the application of Turing patterning mechanisms to the problem of producing spatially heterogeneous differential gene expression has been questioned. In deterministic systems a small delay in the reactions can cause a large increase in the time it takes a system to pattern. Recently, it has been observed that in undelayed systems intrinsic stochasticity can cause pattern initiation to occur earlier than in the analogous deterministic simulations. Here we are interested in adding both stochasticity and delays to Turing systems in order to assess whether stochasticity can reduce the patterning time scale in delayed Turing systems. As analytical insights to this problem are difficult to attain and often limited in their use, we focus on stochastically simulating delayed systems. We consider four different Turing systems and two different forms of delay. Our results are mixed and lead to the conclusion that, although the sensitivity to delays in the Turing mechanism is not completely removed by the addition of intrinsic noise, the effects of the delays are clearly ameliorated in certain specific cases. © 2012 American Physical Society.
The need for simulation in complex industrial systems
Directory of Open Access Journals (Sweden)
Aboura Khalid
2012-10-01
Full Text Available We discuss the concept of simulation and its application in the resolution of problems in complex industrial systems. Most problems of serious scale, be it an inventory problem, a production and distribution problem, a management of resources or process improvement, all real world problems require a mix of generic, data algorithmic and Ad-hoc solutions making the best of available information. We describe two projects in which analytical solutions were applied or contemplated. The first case study uses linear programming in the optimal allocation of advertising resources by a major internet service provider. The second study, in a series of projects, analyses options for the expansion of the production and distribution network of mining products, as part of a sensitive strategic business review. Using the examples, we make the case for the need of simulation in complex industrial problems where analytical solutions may be attempted but where the size and complexity of the problem forces a Monte Carlo approach.
Nefedov, N. N.; Nikulin, E. I.
2018-01-01
A singularly perturbed periodic in time problem for a parabolic reaction-diffusion equation in a two-dimensional domain is studied. The case of existence of an internal transition layer under the conditions of balanced and unbalanced rapid reaction is considered. An asymptotic expansion of a solution is constructed. To justify the asymptotic expansion thus constructed, the asymptotic method of differential inequalities is used. The Lyapunov asymptotic stability of a periodic solution is investigated.
Dinesh Kumar, S.; Nageshwar Rao, R.; Pramod Chakravarthy, P.
2017-11-01
In this paper, we consider a boundary value problem for a singularly perturbed delay differential equation of reaction-diffusion type. We construct an exponentially fitted numerical method using Numerov finite difference scheme, which resolves not only the boundary layers but also the interior layers arising from the delay term. An extensive amount of computational work has been carried out to demonstrate the applicability of the proposed method.
International Nuclear Information System (INIS)
Moyano, Edgardo A.; Scarpettini, Alberto F.
2003-01-01
A semi linear model of weakly coupled parabolic p.d.e. with reaction-diffusion is investigated. The system describes fission gas transfer from grain interior of UO 2 to grain boundaries. The problem is studied in a bounded domain. Using the upper-lower solutions method, two monotone sequences for the finite differences equations are constructed. Reasons are mentioned that allow to affirm that in the proposed functional sector the algorithm converges to the unique solution of the differential system. (author)
Chen, Wu-Hua; Luo, Shixian; Zheng, Wei Xing
2016-12-01
This paper presents a new impulsive synchronization criterion of two identical reaction-diffusion neural networks with discrete and unbounded distributed delays. The new criterion is established by applying an impulse-time-dependent Lyapunov functional combined with the use of a new type of integral inequality for treating the reaction-diffusion terms. The impulse-time-dependent feature of the proposed Lyapunov functional can capture more hybrid dynamical behaviors of the impulsive reaction-diffusion neural networks than the conventional impulse-time-independent Lyapunov functions/functionals, while the new integral inequality, which is derived from Wirtinger's inequality, overcomes the conservatism introduced by the integral inequality used in the previous results. Numerical examples demonstrate the effectiveness of the proposed method. Later, the developed impulsive synchronization method is applied to build a spatiotemporal chaotic cryptosystem that can transmit an encrypted image. The experimental results verify that the proposed image-encrypting cryptosystem has the advantages of large key space and high security against some traditional attacks.
Directory of Open Access Journals (Sweden)
Matthew J Simpson
Full Text Available Many processes during embryonic development involve transport and reaction of molecules, or transport and proliferation of cells, within growing tissues. Mathematical models of such processes usually take the form of a reaction-diffusion partial differential equation (PDE on a growing domain. Previous analyses of such models have mainly involved solving the PDEs numerically. Here, we present a framework for calculating the exact solution of a linear reaction-diffusion PDE on a growing domain. We derive an exact solution for a general class of one-dimensional linear reaction-diffusion process on 0
Simpson, Matthew J
2015-01-01
Many processes during embryonic development involve transport and reaction of molecules, or transport and proliferation of cells, within growing tissues. Mathematical models of such processes usually take the form of a reaction-diffusion partial differential equation (PDE) on a growing domain. Previous analyses of such models have mainly involved solving the PDEs numerically. Here, we present a framework for calculating the exact solution of a linear reaction-diffusion PDE on a growing domain. We derive an exact solution for a general class of one-dimensional linear reaction-diffusion process on 0exact solutions with numerical approximations confirms the veracity of the method. Furthermore, our examples illustrate a delicate interplay between: (i) the rate at which the domain elongates, (ii) the diffusivity associated with the spreading density profile, (iii) the reaction rate, and (iv) the initial condition. Altering the balance between these four features leads to different outcomes in terms of whether an initial profile, located near x = 0, eventually overcomes the domain growth and colonizes the entire length of the domain by reaching the boundary where x = L(t).
Measuring cognitive load: performance, mental effort and simulation task complexity.
Haji, Faizal A; Rojas, David; Childs, Ruth; de Ribaupierre, Sandrine; Dubrowski, Adam
2015-08-01
Interest in applying cognitive load theory in health care simulation is growing. This line of inquiry requires measures that are sensitive to changes in cognitive load arising from different instructional designs. Recently, mental effort ratings and secondary task performance have shown promise as measures of cognitive load in health care simulation. We investigate the sensitivity of these measures to predicted differences in intrinsic load arising from variations in task complexity and learner expertise during simulation-based surgical skills training. We randomly assigned 28 novice medical students to simulation training on a simple or complex surgical knot-tying task. Participants completed 13 practice trials, interspersed with computer-based video instruction. On trials 1, 5, 9 and 13, knot-tying performance was assessed using time and movement efficiency measures, and cognitive load was assessed using subjective rating of mental effort (SRME) and simple reaction time (SRT) on a vibrotactile stimulus-monitoring secondary task. Significant improvements in knot-tying performance (F(1.04,24.95) = 41.1, p cognitive load (F(2.3,58.5) = 57.7, p load among novices engaged in simulation-based learning. These measures can be used to track cognitive load during skills training. Mental effort ratings are also sensitive to small differences in intrinsic load arising from variations in the physical complexity of a simulation task. The complementary nature of these subjective and objective measures suggests their combined use is advantageous in simulation instructional design research. © 2015 John Wiley & Sons Ltd.
Optimal control of an invasive species using a reaction-diffusion model and linear programming
Bonneau, Mathieu; Johnson, Fred A.; Smith, Brian J.; Romagosa, Christina M.; Martin, Julien; Mazzotti, Frank J.
2017-01-01
Managing an invasive species is particularly challenging as little is generally known about the species’ biological characteristics in its new habitat. In practice, removal of individuals often starts before the species is studied to provide the information that will later improve control. Therefore, the locations and the amount of control have to be determined in the face of great uncertainty about the species characteristics and with a limited amount of resources. We propose framing spatial control as a linear programming optimization problem. This formulation, paired with a discrete reaction-diffusion model, permits calculation of an optimal control strategy that minimizes the remaining number of invaders for a fixed cost or that minimizes the control cost for containment or protecting specific areas from invasion. We propose computing the optimal strategy for a range of possible model parameters, representing current uncertainty on the possible invasion scenarios. Then, a best strategy can be identified depending on the risk attitude of the decision-maker. We use this framework to study the spatial control of the Argentine black and white tegus (Salvator merianae) in South Florida. There is uncertainty about tegu demography and we considered several combinations of model parameters, exhibiting various dynamics of invasion. For a fixed one-year budget, we show that the risk-averse strategy, which optimizes the worst-case scenario of tegus’ dynamics, and the risk-neutral strategy, which optimizes the expected scenario, both concentrated control close to the point of introduction. A risk-seeking strategy, which optimizes the best-case scenario, focuses more on models where eradication of the species in a cell is possible and consists of spreading control as much as possible. For the establishment of a containment area, assuming an exponential growth we show that with current control methods it might not be possible to implement such a strategy for some of the
Large-Eddy Simulations of Flows in Complex Terrain
Kosovic, B.; Lundquist, K. A.
2011-12-01
Large-eddy simulation as a methodology for numerical simulation of turbulent flows was first developed to study turbulent flows in atmospheric by Lilly (1967). The first LES were carried by Deardorff (1970) who used these simulations to study atmospheric boundary layers. Ever since, LES has been extensively used to study canonical atmospheric boundary layers, in most cases flat plate boundary layers under the assumption of horizontal homogeneity. Carefully designed LES of canonical convective and neutrally stratified and more recently stably stratified atmospheric boundary layers have contributed significantly to development of better understanding of these flows and their parameterizations in large scale models. These simulations were often carried out using codes specifically designed and developed for large-eddy simulations of horizontally homogeneous flows with periodic lateral boundary conditions. Recent developments in multi-scale numerical simulations of atmospheric flows enable numerical weather prediction (NWP) codes such as ARPS (Chow and Street, 2009), COAMPS (Golaz et al., 2009) and Weather Research and Forecasting model, to be used nearly seamlessly across a wide range of atmospheric scales from synoptic down to turbulent scales in atmospheric boundary layers. Before we can with confidence carry out multi-scale simulations of atmospheric flows, NWP codes must be validated for accurate performance in simulating flows over complex or inhomogeneous terrain. We therefore carry out validation of WRF-LES for simulations of flows over complex terrain using data from Askervein Hill (Taylor and Teunissen, 1985, 1987) and METCRAX (Whiteman et al., 2008) field experiments. WRF's nesting capability is employed with a one-way nested inner domain that includes complex terrain representation while the coarser outer nest is used to spin up fully developed atmospheric boundary layer turbulence and thus represent accurately inflow to the inner domain. LES of a
The future of simulation technologies for complex cardiovascular procedures.
Cates, Christopher U; Gallagher, Anthony G
2012-09-01
Changing work practices and the evolution of more complex interventions in cardiovascular medicine are forcing a paradigm shift in the way doctors are trained. Implantable cardioverter defibrillator (ICD), transcatheter aortic valve implantation (TAVI), carotid artery stenting (CAS), and acute stroke intervention procedures are forcing these changes at a faster pace than in other disciplines. As a consequence, cardiovascular medicine has had to develop a sophisticated understanding of precisely what is meant by 'training' and 'skill'. An evolving conclusion is that procedure training on a virtual reality (VR) simulator presents a viable current solution. These simulations should characterize the important performance characteristics of procedural skill that have metrics derived and defined from, and then benchmarked to experienced operators (i.e. level of proficiency). Simulation training is optimal with metric-based feedback, particularly formative trainee error assessments, proximate to their performance. In prospective, randomized studies, learners who trained to a benchmarked proficiency level on the simulator performed significantly better than learners who were traditionally trained. In addition, cardiovascular medicine now has available the most sophisticated virtual reality simulators in medicine and these have been used for the roll-out of interventions such as CAS in the USA and globally with cardiovascular society and industry partnered training programmes. The Food and Drug Administration has advocated the use of VR simulation as part of the approval of new devices and the American Board of Internal Medicine has adopted simulation as part of its maintenance of certification. Simulation is rapidly becoming a mainstay of cardiovascular education, training, certification, and the safe adoption of new technology. If cardiovascular medicine is to continue to lead in the adoption and integration of simulation, then, it must take a proactive position in the
Siegfried, Robert
2014-01-01
Robert Siegfried presents a framework for efficient agent-based modeling and simulation of complex systems. He compares different approaches for describing structure and dynamics of agent-based models in detail. Based on this evaluation the author introduces the "General Reference Model for Agent-based Modeling and Simulation" (GRAMS). Furthermore he presents parallel and distributed simulation approaches for execution of agent-based models -from small scale to very large scale. The author shows how agent-based models may be executed by different simulation engines that utilize underlying hard
Complex saddle points and the sign problem in complex Langevin simulation
International Nuclear Information System (INIS)
Hayata, Tomoya; Hidaka, Yoshimasa; Tanizaki, Yuya
2016-01-01
We show that complex Langevin simulation converges to a wrong result within the semiclassical analysis, by relating it to the Lefschetz-thimble path integral, when the path-integral weight has different phases among dominant complex saddle points. Equilibrium solution of the complex Langevin equation forms local distributions around complex saddle points. Its ensemble average approximately becomes a direct sum of the average in each local distribution, where relative phases among them are dropped. We propose that by taking these phases into account through reweighting, we can solve the wrong convergence problem. However, this prescription may lead to a recurrence of the sign problem in the complex Langevin method for quantum many-body systems.
Complexant Identification in Hanford Waste Simulant Sr/TRU Filtrate
International Nuclear Information System (INIS)
Bannochie, C.J.
2003-01-01
This project was designed to characterize the available multidentate ligand species and metal ion complexes of iron, strontium and manganese formed with the parent chelators, complexing agents and their fragment products. Complex identification was applied to AN-102 and AN-107 filtrate simulants for Hanford waste after an oxidation reaction with sodium permanganate to create a freshly precipitated manganese dioxide solid for adsorption of transuranic elements. Separation efficiency of different ligands was investigated based on the exchange capability of different ion exchange and ion exclusion analytical columns including Dionex IonPac AS-5A, AS-10, AS-11 and AS-6. The elution programs developed with different mobile phase concentrations were based on the change in the effective charge of the anionic species and therefore the retention on the stationary phase. In the present work, qualitative and quantitative assessments of multidentate ligands were investigated. Identification methods for the metal ion complexes responsible for solubilizing Fe, Mn and Sr were applied to aged and fresh simulant waste filtrates. Although concentration measurements of both fresh and 3-week aged filtrates showed that the degradation process occurs mainly due to the harsh chemical environment, it was found that the concentration of iron and manganese did not increase, within the error of the analytical measurements, after three weeks when compared with fresh filtrate
Choi, Eunsong
Computer simulations are an integral part of research in modern condensed matter physics; they serve as a direct bridge between theory and experiment by systemactically applying a microscopic model to a collection of particles that effectively imitate a macroscopic system. In this thesis, we study two very differnt condensed systems, namely complex fluids and frustrated magnets, primarily by simulating classical dynamics of each system. In the first part of the thesis, we focus on ionic liquids (ILs) and polymers--the two complementary classes of materials that can be combined to provide various unique properties. The properties of polymers/ILs systems, such as conductivity, viscosity, and miscibility, can be fine tuned by choosing an appropriate combination of cations, anions, and polymers. However, designing a system that meets a specific need requires a concrete understanding of physics and chemistry that dictates a complex interplay between polymers and ionic liquids. In this regard, molecular dynamics (MD) simulation is an efficient tool that provides a molecular level picture of such complex systems. We study the behavior of Poly (ethylene oxide) (PEO) and the imidazolium based ionic liquids, using MD simulations and statistical mechanics. We also discuss our efforts to develop reliable and efficient classical force-fields for PEO and the ionic liquids. The second part is devoted to studies on geometrically frustrated magnets. In particular, a microscopic model, which gives rise to an incommensurate spiral magnetic ordering observed in a pyrochlore antiferromagnet is investigated. The validation of the model is made via a comparison of the spin-wave spectra with the neutron scattering data. Since the standard Holstein-Primakoff method is difficult to employ in such a complex ground state structure with a large unit cell, we carry out classical spin dynamics simulations to compute spin-wave spectra directly from the Fourier transform of spin trajectories. We
Simulation of Weak Signals of Nanotechnology Innovation in Complex System
Directory of Open Access Journals (Sweden)
Sun Hi Yoo
2018-02-01
Full Text Available It is especially indispensable for new businesses or industries to predict the innovation of new technologies. This requires an understanding of how the complex process of innovation, which is accomplished through more efficient products, processes, services, technologies, or ideas, is adopted and diffused in the market, government, and society. Furthermore, detecting “weak signals” (signs of change in science and technology (S&T is also important to foretell events associated with innovations in technology. Thus, we explore the dynamic behavior of weak signals of a specific technological innovation using the agent-based simulating tool NetLogo. This study provides a deeper understanding of the early stages of complex technology innovation, and the models are capable of analyzing initial complex interaction structures between components of technologies and between agents engaged in collective invention.
International Nuclear Information System (INIS)
Ahmadi, A.; Meyer, M.; Rouzineau, D.; Prevost, M.; Alix, P.; Laloue, N.
2010-01-01
This paper gives the first step of the development of a rigorous multicomponent reactive separation model. Such a model is highly essential to further the optimization of acid gases removal plants (CO 2 capture, gas treating, etc.) in terms of size and energy consumption, since chemical solvents are conventionally used. Firstly, two main modelling approaches are presented: the equilibrium-based and the rate-based approaches. Secondly, an extended rate-based model with rigorous modelling methodology for diffusion-reaction phenomena is proposed. The film theory and the generalized Maxwell-Stefan equations are used in order to characterize multicomponent interactions. The complete chain of chemical reactions is taken into account. The reactions can be kinetically controlled or at chemical equilibrium, and they are considered for both liquid film and liquid bulk. Thirdly, the method of numerical resolution is described. Coupling the generalized Maxwell-Stefan equations with chemical equilibrium equations leads to a highly non-linear Differential-Algebraic Equations system known as DAE index 3. The set of equations is discretized with finite-differences as its integration by Gear method is complex. The resulting algebraic system is resolved by the Newton- Raphson method. Finally, the present model and the associated methods of numerical resolution are validated for the example of esterification of methanol. This archetype non-electrolytic system permits an interesting analysis of reaction impact on mass transfer, especially near the phase interface. The numerical resolution of the model by Newton-Raphson method gives good results in terms of calculation time and convergence. The simulations show that the impact of reactions at chemical equilibrium and that of kinetically controlled reactions with high kinetics on mass transfer is relatively similar. Moreover, the Fick's law is less adapted for multicomponent mixtures where some abnormalities such as counter
International Nuclear Information System (INIS)
Ferreri, J. C.; Carmen, A. del
1998-01-01
A numerical study of the dynamics of pattern evolution in reaction-diffusion systems is performed, although limited to one spatial dimension. The diffusion coefficients are nonlinear, based on powers of the scalar variables. The system keeps the dynamics of previous studies in the literature, but the presence of nonlinear diffusion generates a field of strong nonlinear interactions due to the presence of receding travelling waves. This field is limited by the plane of symmetry of the space domain and the last born outgoing travelling wave. These effects are discussed. (author). 10 refs., 7 figs
Directory of Open Access Journals (Sweden)
Qiankun Song
2007-06-01
Full Text Available Impulsive bidirectional associative memory neural network model with time-varying delays and reaction-diffusion terms is considered. Several sufficient conditions ensuring the existence, uniqueness, and global exponential stability of equilibrium point for the addressed neural network are derived by M-matrix theory, analytic methods, and inequality techniques. Moreover, the exponential convergence rate index is estimated, which depends on the system parameters. The obtained results in this paper are less restrictive than previously known criteria. Two examples are given to show the effectiveness of the obtained results.
Directory of Open Access Journals (Sweden)
Cao Jinde
2007-01-01
Full Text Available Impulsive bidirectional associative memory neural network model with time-varying delays and reaction-diffusion terms is considered. Several sufficient conditions ensuring the existence, uniqueness, and global exponential stability of equilibrium point for the addressed neural network are derived by M-matrix theory, analytic methods, and inequality techniques. Moreover, the exponential convergence rate index is estimated, which depends on the system parameters. The obtained results in this paper are less restrictive than previously known criteria. Two examples are given to show the effectiveness of the obtained results.
Paul, Shibashis; Ghosh, Shyamolina; Ray, Deb Shankar
2018-02-01
We consider a reaction-diffusion system with linear, stochastic activator-inhibitor kinetics where the time evolution of concentration of a species at any spatial location depends on the relative average concentration of its neighbors. This self-regulating nature of kinetics brings in spatial correlation between the activator and the inhibitor. An interplay of this correlation in kinetics and disparity of diffusivities of the two species leads to symmetry breaking non-equilibrium transition resulting in stationary pattern formation. The role of initial noise strength and the linear reaction terms has been analyzed for pattern selection.
Challenges to the development of complex virtual reality surgical simulations.
Seymour, N E; Røtnes, J S
2006-11-01
Virtual reality simulation in surgical training has become more widely used and intensely investigated in an effort to develop safer, more efficient, measurable training processes. The development of virtual reality simulation of surgical procedures has begun, but well-described technical obstacles must be overcome to permit varied training in a clinically realistic computer-generated environment. These challenges include development of realistic surgical interfaces and physical objects within the computer-generated environment, modeling of realistic interactions between objects, rendering of the surgical field, and development of signal processing for complex events associated with surgery. Of these, the realistic modeling of tissue objects that are fully responsive to surgical manipulations is the most challenging. Threats to early success include relatively limited resources for development and procurement, as well as smaller potential for return on investment than in other simulation industries that face similar problems. Despite these difficulties, steady progress continues to be made in these areas. If executed properly, virtual reality offers inherent advantages over other training systems in creating a realistic surgical environment and facilitating measurement of surgeon performance. Once developed, complex new virtual reality training devices must be validated for their usefulness in formative training and assessment of skill to be established.
Complex Langevin Simulations of QCD at Finite Density - Progress Report
Sinclair, D. K.; Kogut, J. B.
2018-03-01
We simulate lattice QCD at finite quark-number chemical potential to study nuclear matter, using the complex Langevin equation (CLE). The CLE is used because the fermion determinant is complex so that standard methods relying on importance sampling fail. Adaptive methods and gauge-cooling are used to prevent runaway solutions. Even then, the CLE is not guaranteed to give correct results. We are therefore performing extensive testing to determine under what, if any, conditions we can achieve reliable results. Our earlier simulations at β = 6/g2 = 5.6, m = 0.025 on a 124 lattice reproduced the expected phase structure but failed in the details. Our current simulations at β = 5.7 on a 164 lattice fail in similar ways while showing some improvement. We are therefore moving to even weaker couplings to see if the CLE might produce the correct results in the continuum (weak-coupling) limit, or, if it still fails, whether it might reproduce the results of the phase-quenched theory. We also discuss action (and other dynamics) modifications which might improve the performance of the CLE.
High performance ultrasonic field simulation on complex geometries
Chouh, H.; Rougeron, G.; Chatillon, S.; Iehl, J. C.; Farrugia, J. P.; Ostromoukhov, V.
2016-02-01
Ultrasonic field simulation is a key ingredient for the design of new testing methods as well as a crucial step for NDT inspection simulation. As presented in a previous paper [1], CEA-LIST has worked on the acceleration of these simulations focusing on simple geometries (planar interfaces, isotropic materials). In this context, significant accelerations were achieved on multicore processors and GPUs (Graphics Processing Units), bringing the execution time of realistic computations in the 0.1 s range. In this paper, we present recent works that aim at similar performances on a wider range of configurations. We adapted the physical model used by the CIVA platform to design and implement a new algorithm providing a fast ultrasonic field simulation that yields nearly interactive results for complex cases. The improvements over the CIVA pencil-tracing method include adaptive strategies for pencil subdivisions to achieve a good refinement of the sensor geometry while keeping a reasonable number of ray-tracing operations. Also, interpolation of the times of flight was used to avoid time consuming computations in the impulse response reconstruction stage. To achieve the best performance, our algorithm runs on multi-core superscalar CPUs and uses high performance specialized libraries such as Intel Embree for ray-tracing, Intel MKL for signal processing and Intel TBB for parallelization. We validated the simulation results by comparing them to the ones produced by CIVA on identical test configurations including mono-element and multiple-element transducers, homogeneous, meshed 3D CAD specimens, isotropic and anisotropic materials and wave paths that can involve several interactions with interfaces. We show performance results on complete simulations that achieve computation times in the 1s range.
Lattice dynamics and molecular dynamics simulation of complex materials
International Nuclear Information System (INIS)
Chaplot, S.L.
1997-01-01
In this article we briefly review the lattice dynamics and molecular dynamics simulation techniques, as used for complex ionic and molecular solids, and demonstrate a number of applications through examples of our work. These computational studies, along with experiments, have provided microscopic insight into the structure and dynamics, phase transitions and thermodynamical properties of a variety of materials including fullerene, high temperature superconducting oxides and geological minerals as a function of pressure and temperature. The computational techniques also allow the study of the structures and dynamics associated with disorder, defects, surfaces, interfaces etc. (author)
SimulaTE: simulating complex landscapes of transposable elements of populations.
Kofler, Robert
2018-04-15
Estimating the abundance of transposable elements (TEs) in populations (or tissues) promises to answer many open research questions. However, progress is hampered by the lack of concordance between different approaches for TE identification and thus potentially unreliable results. To address this problem, we developed SimulaTE a tool that generates TE landscapes for populations using a newly developed domain specific language (DSL). The simple syntax of our DSL allows for easily building even complex TE landscapes that have, for example, nested, truncated and highly diverged TE insertions. Reads may be simulated for the populations using different sequencing technologies (PacBio, Illumina paired-ends) and strategies (sequencing individuals and pooled populations). The comparison between the expected (i.e. simulated) and the observed results will guide researchers in finding the most suitable approach for a particular research question. SimulaTE is implemented in Python and available at https://sourceforge.net/projects/simulates/. Manual https://sourceforge.net/p/simulates/wiki/Home/#manual; Test data and tutorials https://sourceforge.net/p/simulates/wiki/Home/#walkthrough; Validation https://sourceforge.net/p/simulates/wiki/Home/#validation. robert.kofler@vetmeduni.ac.at.
Numerical simulation of radiation fog in complex terrain
Zhang, X.; Musson-Genon, L.; Carissimo, B.; Dupont, E.
2009-09-01
The interest for micro-scale modeling of the atmosphere is growing for environmental applications related, for example, to energy production, transport and urban development. The turbulence in the stable layers where pollutant dispersion is low and can lead to strong pollution events. This could be further complicated by the presence of clouds or fog and is specifically difficult in urban or industrial area due to the presence of buildings. In this context, radiation fog formation and dissipation over complex terrain were therefore investigated with a state-of-the-art model. This study is divided into two phases. The first phase is a pilot stage, which consist of employing a database from the ParisFog campaign which took place in the south of Paris during winter 2006-07 to assess the ability of the cloud model to reproduce the detailed structure of radiation fog. The second phase use the validated model for the study of influence of complex terrain on fog evolution. Special attention is given to the detailed and complete simulations and validation technique used is to compare the simulated results using the 3D cloud model of computational fluid dynamical software Code_Saturne with one of the best collected in situ data during the ParisFog campaign. Several dynamical, microphysical parameterizations and simulation conditions have been described. The resulting 3D cloud model runs at a horizontal resolution of 30 m and a vertical resolution comparable to the 1D model. First results look very promising and are able to reproduce the spatial distribution of fog. The analysis of the behavior of the different parameterized physical processes suggests that the subtle balance between the various processes is achieved.
Cohen, Daniel; Vlaev, Ivo; McMahon, Laurie; Harvey, Sarah; Mitchell, Andy; Borovoi, Leah; Darzi, Ara
2017-05-11
The Health and Social Care Act 2012 represents the most complex National Health Service reforms in history. High-quality clinical leadership is important for successful implementation of health service reform. However, little is known about the effectiveness of current leadership training. This study describes the use of a behavioral simulation to improve the knowledge and leadership of a cohort of medical doctors expected to take leadership roles in the National Health Service. A day-long behavioral simulation (The Crucible) was developed and run based on a fictitious but realistic health economy. Participants completed pre- and postsimulation questionnaires generating qualitative and quantitative data. Leadership skills, knowledge, and behavior change processes described by the "theory of planned behavior" were self-assessed pre- and postsimulation. Sixty-nine medical doctors attended. Participants deemed the simulation immersive and relevant. Significant improvements were shown in perceived knowledge, capability, attitudes, subjective norms, intentions, and leadership competency following the program. Nearly one third of participants reported that they had implemented knowledge and skills from the simulation into practice within 4 weeks. This study systematically demonstrates the effectiveness of behavioral simulation for clinical management training and understanding of health policy reform. Potential future uses and strategies for analysis are discussed. High-quality care requires understanding of health systems and strong leadership. Policymakers should consider the use of behavioral simulation to improve understanding of health service reform and development of leadership skills in clinicians, who readily adopt skills from simulation into everyday practice.
[Interest of complex tasks on laparoscopic virtual reality simulator].
Valentin, L; Rabischong, B; Compan, C; Botchorichvili, R; Pereira, B; Avan, P
2016-03-01
The purpose of this study was to assess the contribution of complex tasks on virtual reality simulator (VRS) for novice surgeons in laparoscopy learning. Fifty-five medical students were prospectively randomized in two groups (A: basic skills, n=28 and B: basic and complex skills, n=27) and then trained during two sessions on VRS. Evaluations took place before and after each training. These evaluations consisted of the achievement of an intracorporeal suture, recorded on video, with the left then with the right hand. Two independent experts evaluated those gestures blindly. A significant progression in terms of times and technical scores was observed in both groups between the first and the last evaluations (P between 0.001 and 0.04). Students in group B improved slower and longer than those in group A. However, left and right hands results confused did not highlight significant differences between the two groups. At the third session, the first hand to train is significantly faster in group B than in group A (P=0.04). This study found only a late and minimal impact of complex skills to reduce the execution time of intracorporeal suture. It also showed an slower and longer overall progression for those who use them compared to subjects using basic skills only. Copyright © 2015 Elsevier Masson SAS. All rights reserved.
MOLECULAR SIMULATION OF PHASE EQUILIBRIA FOR COMPLEX FLUIDS
Energy Technology Data Exchange (ETDEWEB)
Athanassios Z. Panagiotopoulos
2009-09-09
The general area of this project was the development and application of novel molecular simulation methods for prediction of thermodynamic and structural properties of complex polymeric, surfactant and ionic fluids. Over this project period, we have made considerable progress in developing novel algorithms to meet the computational challenges presented by the strong or long-range interactions in these systems and have generated data for well-defined mod-els that can be used to test theories and compare to experimental data. Overall, 42 archival papers and many invited and contributed presentations and lectures have been based on work supported by this project. 6 PhD, 1 M.S. and 2 postdoctoral students have been associated with this work, as listed in the body of the report.
Molecular Simulation Of Phase Equilibria For Complex Fluids
International Nuclear Information System (INIS)
Panagiotopoulos, Athanassios Z.
2009-01-01
The general area of this project was the development and application of novel molecular simulation methods for prediction of thermodynamic and structural properties of complex polymeric, surfactant and ionic fluids. Over this project period, we have made considerable progress in developing novel algorithms to meet the computational challenges presented by the strong or long-range interactions in these systems and have generated data for well-defined mod-els that can be used to test theories and compare to experimental data. Overall, 42 archival papers and many invited and contributed presentations and lectures have been based on work supported by this project. 6 PhD, 1 M.S. and 2 postdoctoral students have been associated with this work, as listed in the body of the report.
Simulation of complex pharmacokinetic models in Microsoft Excel.
Meineke, Ingolf; Brockmöller, Jürgen
2007-12-01
With the arrival of powerful personal computers in the office numerical methods are accessible to everybody. Simulation of complex processes therefore has become an indispensible tool in research and education. In this paper Microsoft EXCEL is used as a platform for a universal differential equation solver. The software is designed as an add-in aiming at a minimum of required user input to perform a given task. Four examples are included to demonstrate both, the simplicity of use and the versatility of possible applications. While the layout of the program is admittedly geared to the needs of pharmacokineticists, it can be used in any field where sets of differential equations are involved. The software package is available upon request.
Spiral patterns near Turing instability in a discrete reaction diffusion system
International Nuclear Information System (INIS)
Li, Meifeng; Han, Bo; Xu, Li; Zhang, Guang
2013-01-01
In this paper, linear stability analysis is applied to an exponential discrete Lotka–Volterra system, which describes the competition between two identical species. Conditions for the Turing instability are obtained and the emergence of spiral patterns is demonstrated by means of numerical simulations in the vicinity of the bifurcation point. Moreover, the impact of crucial system parameters on the stability and coherence of spiral patterns is illustrated on several examples
International Nuclear Information System (INIS)
Lu Junguo; Lu Linji
2009-01-01
In this paper, global exponential stability and periodicity of a class of reaction-diffusion recurrent neural networks with distributed delays and Dirichlet boundary conditions are studied by constructing suitable Lyapunov functionals and utilizing some inequality techniques. We first prove global exponential convergence to 0 of the difference between any two solutions of the original neural networks, the existence and uniqueness of equilibrium is the direct results of this procedure. This approach is different from the usually used one where the existence, uniqueness of equilibrium and stability are proved in two separate steps. Secondly, we prove periodicity. Sufficient conditions ensuring the existence, uniqueness, and global exponential stability of the equilibrium and periodic solution are given. These conditions are easy to verify and our results play an important role in the design and application of globally exponentially stable neural circuits and periodic oscillatory neural circuits.
D'Ambrosio, Raffaele; Moccaldi, Martina; Paternoster, Beatrice
2018-05-01
In this paper, an adapted numerical scheme for reaction-diffusion problems generating periodic wavefronts is introduced. Adapted numerical methods for such evolutionary problems are specially tuned to follow prescribed qualitative behaviors of the solutions, making the numerical scheme more accurate and efficient as compared with traditional schemes already known in the literature. Adaptation through the so-called exponential fitting technique leads to methods whose coefficients depend on unknown parameters related to the dynamics and aimed to be numerically computed. Here we propose a strategy for a cheap and accurate estimation of such parameters, which consists essentially in minimizing the leading term of the local truncation error whose expression is provided in a rigorous accuracy analysis. In particular, the presented estimation technique has been applied to a numerical scheme based on combining an adapted finite difference discretization in space with an implicit-explicit time discretization. Numerical experiments confirming the effectiveness of the approach are also provided.
Adam, A. M. A.; Bashier, E. B. M.; Hashim, M. H. A.; Patidar, K. C.
2017-07-01
In this work, we design and analyze a fitted numerical method to solve a reaction-diffusion model with time delay, namely, a delayed version of a population model which is an extension of the logistic growth (LG) equation for a food-limited population proposed by Smith [F.E. Smith, Population dynamics in Daphnia magna and a new model for population growth, Ecology 44 (1963) 651-663]. Seeing that the analytical solution (in closed form) is hard to obtain, we seek for a robust numerical method. The method consists of a Fourier-pseudospectral semi-discretization in space and a fitted operator implicit-explicit scheme in temporal direction. The proposed method is analyzed for convergence and we found that it is unconditionally stable. Illustrative numerical results will be presented at the conference.
Brandt-Pollmann, U; Lebiedz, D; Diehl, M; Sager, S; Schlöder, J
2005-09-01
Theoretical and experimental studies related to manipulation of pattern formation in self-organizing reaction-diffusion processes by appropriate control stimuli become increasingly important both in chemical engineering and cellular biochemistry. In a model study, we demonstrate here exemplarily the application of an efficient nonlinear model predictive control (NMPC) algorithm to real-time optimal feedback control of pattern formation in a bacterial chemotaxis system modeled by nonlinear partial differential equations. The corresponding drift-diffusion model type is representative for many (bio)chemical systems involving nonlinear reaction dynamics and nonlinear diffusion. We show how the computed optimal feedback control strategy exploits the system inherent physical property of wave propagation to achieve desired control aims. We discuss various applications of our approach to optimal control of spatiotemporal dynamics.
Global-Scale Hydrology: Simple Characterization of Complex Simulation
Koster, Randal D.
1999-01-01
Atmospheric general circulation models (AGCMS) are unique and valuable tools for the analysis of large-scale hydrology. AGCM simulations of climate provide tremendous amounts of hydrological data with a spatial and temporal coverage unmatched by observation systems. To the extent that the AGCM behaves realistically, these data can shed light on the nature of the real world's hydrological cycle. In the first part of the seminar, I will describe the hydrological cycle in a typical AGCM, with some emphasis on the validation of simulated precipitation against observations. The second part of the seminar will focus on a key goal in large-scale hydrology studies, namely the identification of simple, overarching controls on hydrological behavior hidden amidst the tremendous amounts of data produced by the highly complex AGCM parameterizations. In particular, I will show that a simple 50-year-old climatological relation (and a recent extension we made to it) successfully predicts, to first order, both the annual mean and the interannual variability of simulated evaporation and runoff fluxes. The seminar will conclude with an example of a practical application of global hydrology studies. The accurate prediction of weather statistics several months in advance would have tremendous societal benefits, and conventional wisdom today points at the use of coupled ocean-atmosphere-land models for such seasonal-to-interannual prediction. Understanding the hydrological cycle in AGCMs is critical to establishing the potential for such prediction. Our own studies show, among other things, that soil moisture retention can lead to significant precipitation predictability in many midlatitude and tropical regions.
Dynamics of embedded curves by doubly-nonlocal reaction-diffusion systems
von Brecht, James H.; Blair, Ryan
2017-11-01
We study a class of nonlocal, energy-driven dynamical models that govern the motion of closed, embedded curves from both an energetic and dynamical perspective. Our energetic results provide a variety of ways to understand physically motivated energetic models in terms of more classical, combinatorial measures of complexity for embedded curves. This line of investigation culminates in a family of complexity bounds that relate a rather broad class of models to a generalized, or weighted, variant of the crossing number. Our dynamic results include global well-posedness of the associated partial differential equations, regularity of equilibria for these flows as well as a more detailed investigation of dynamics near such equilibria. Finally, we explore a few global dynamical properties of these models numerically.
Effect of noise on defect chaos in a reaction-diffusion model.
Wang, Hongli; Ouyang, Qi
2005-06-01
The influence of noise on defect chaos due to breakup of spiral waves through Doppler and Eckhaus instabilities is investigated numerically with a modified Fitzhugh-Nagumo model. By numerical simulations we show that the noise can drastically enhance the creation and annihilation rates of topological defects. The noise-free probability distribution function for defects in this model is found not to fit with the previously reported squared-Poisson distribution. Under the influence of noise, the distributions are flattened, and can fit with the squared-Poisson or the modified-Poisson distribution. The defect lifetime and diffusive property of defects under the influence of noise are also checked in this model.
Quantum Mechanical Simulations of Complex Nanostructures for Photovoltaic Applications
Energy Technology Data Exchange (ETDEWEB)
Wu, Zhigang [Colorado School of Mines, Golden, CO (United States)
2017-05-31
A quantitative understanding of the electronic excitations in nanostructures, especially complex nanostructures, is crucial for making new-generation photovoltaic (PV) cells based on nanotechnology, which have high efficiency and low cost. Yet current quantum mechanical simulation methods are either computationally too expensive or not accurate and reliable enough, hindering the rational design of the nanoscale PV cells. The PI seeks to develop new methodologies to overcome the challenges in this very difficult and long-lasting problem, pushing the field forward so that electronic excitations can be accurately predicted for systems involving thousands of atoms. The primary objective of this project is to develop new approaches for electronic excitation calculations that are more accurate than traditional density functional theory (DFT) and are applicable to systems larger than what current beyond-DFT methods can treat. In this proposal, the PI will first address the excited-state problem within the DFT framework to obtain quasiparticle energies from both Kohn-Sham (KS) eigenvalues and orbitals; and the electron-hole binding energy will be computed based on screened Coulomb interaction of corresponding DFT orbitals. The accuracy of these approaches will be examined against many-body methods of GW/BSE and quantum Monte Carlo (QMC). The PI will also work on improving the accuracy and efficiency of the GW/BSE and QMC methods in electronic excitation computations by using better KS orbitals obtained from orbital-dependent DFT as inputs. Then an extended QMC database of ground- and excited-state properties will be developed, and this will be spot checked and supplemented with data from GW/BSE calculations. The investigation will subsequently focus on the development of an improved exchange-correlation (XC) density functional beyond the current generalized gradient approximation (GGA) level of parameterization, with parameters fitted to the QMC database. This will allow
Direct Numerical Simulation of Turbulent Flow Over Complex Bathymetry
Yue, L.; Hsu, T. J.
2017-12-01
Direct numerical simulation (DNS) is regarded as a powerful tool in the investigation of turbulent flow featured with a wide range of time and spatial scales. With the application of coordinate transformation in a pseudo-spectral scheme, a parallelized numerical modeling system was created aiming at simulating flow over complex bathymetry with high numerical accuracy and efficiency. The transformed governing equations were integrated in time using a third-order low-storage Runge-Kutta method. For spatial discretization, the discrete Fourier expansion was adopted in the streamwise and spanwise direction, enforcing the periodic boundary condition in both directions. The Chebyshev expansion on Chebyshev-Gauss-Lobatto points was used in the wall-normal direction, assuming there is no-slip on top and bottom walls. The diffusion terms were discretized with a Crank-Nicolson scheme, while the advection terms dealiased with the 2/3 rule were discretized with an Adams-Bashforth scheme. In the prediction step, the velocity was calculated in physical domain by solving the resulting linear equation directly. However, the extra terms introduced by coordinate transformation impose a strict limitation to time step and an iteration method was applied to overcome this restriction in the correction step for pressure by solving the Helmholtz equation. The numerical solver is written in object-oriented C++ programing language utilizing Armadillo linear algebra library for matrix computation. Several benchmarking cases in laminar and turbulent flow were carried out to verify/validate the numerical model and very good agreements are achieved. Ongoing work focuses on implementing sediment transport capability for multiple sediment classes and parameterizations for flocculation processes.
Design and Developmental Research on the VV&A of Complex Simulation System
Directory of Open Access Journals (Sweden)
Liu Li
2016-01-01
Full Text Available The Verification, Validation and Accreditation (VV&A of a complex simulation system is a complex systems engineering. Based on the brief introduction to the concept of VV&A, this paper puts forward its design principles, approaches and basic contents, expounds the typical developing process and predicts its up-to-date technology developing trend of complex simulation system.
Modelling and simulation of gas explosions in complex geometries
Energy Technology Data Exchange (ETDEWEB)
Saeter, Olav
1998-12-31
This thesis presents a three-dimensional Computational Fluid Dynamics (CFD) code (EXSIM94) for modelling and simulation of gas explosions in complex geometries. It gives the theory and validates the following sub-models : (1) the flow resistance and turbulence generation model for densely packed regions, (2) the flow resistance and turbulence generation model for single objects, and (3) the quasi-laminar combustion model. It is found that a simple model for flow resistance and turbulence generation in densely packed beds is able to reproduce the medium and large scale MERGE explosion experiments of the Commission of European Communities (CEC) within a band of factor 2. The model for a single representation is found to predict explosion pressure in better agreement with the experiments with a modified k-{epsilon} model. This modification also gives a slightly improved grid independence for realistic gas explosion approaches. One laminar model is found unsuitable for gas explosion modelling because of strong grid dependence. Another laminar model is found to be relatively grid independent and to work well in harmony with the turbulent combustion model. The code is validated against 40 realistic gas explosion experiments. It is relatively grid independent in predicting explosion pressure in different offshore geometries. It can predict the influence of ignition point location, vent arrangements, different geometries, scaling effects and gas reactivity. The validation study concludes with statistical and uncertainty analyses of the code performance. 98 refs., 96 figs, 12 tabs.
Ducrot, Arnaud; Giletti, Thomas
2014-09-01
In this work we study the asymptotic behaviour of the Kermack-McKendrick reaction-diffusion system in a periodic environment with non-diffusive susceptible population. This problem was proposed by Kallen et al. as a model for the spatial spread for epidemics, where it can be reasonable to assume that the susceptible population is motionless. For arbitrary dimensional space we prove that large classes of solutions of such a system have an asymptotic spreading speed in large time, and that the infected population has some pulse-like asymptotic shape. The analysis of the one-dimensional problem is more developed, as we are able to uncover a much more accurate description of the profile of solutions. Indeed, we will see that, for some initially compactly supported infected population, the profile of the solution converges to some pulsating travelling wave with minimal speed, that is to some entire solution moving at a constant positive speed and whose profile's shape is periodic in time.
Saliba, Daniel; Al-Ghoul, Mazen
2016-11-01
We report the synthesis of magnesium-aluminium layered double hydroxide (LDH) using a reaction-diffusion framework (RDF) that exploits the multiscale coupling of molecular diffusion with chemical reactions, nucleation and growth of crystals. In an RDF, the hydroxide anions are allowed to diffuse into an organic gel matrix containing the salt mixture needed for the precipitation of the LDH. The chemical structure and composition of the synthesized magnesium-aluminium LDHs are determined using powder X-ray diffraction (PXRD), thermo-gravimetric analysis, differential scanning calorimetry, solid-state nuclear magnetic resonance (SSNMR), Fourier transform infrared and energy dispersive X-ray spectroscopy. This novel technique also allows the investigation of the mechanism of intercalation of some fluorescent probes, such as the neutral three-dimensional rhodamine B (RhB) and the negatively charged two-dimensional 8-hydroxypyrene-1,3,6-trisulfonic acid (HPTS), using in situ steady-state fluorescence spectroscopy. The incorporation of these organic dyes inside the interlayer region of the LDH is confirmed via fluorescence microscopy, solid-state lifetime, SSNMR and PXRD. The activation energies of intercalation of the corresponding molecules (RhB and HPTS) are computed and exhibit dependence on the geometry of the involved probe (two or three dimensions), the charge of the fluorescent molecule (anionic, cationic or neutral) and the cationic ratio of the corresponding LDH. This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.
Simulation-based modeling of building complexes construction management
Shepelev, Aleksandr; Severova, Galina; Potashova, Irina
2018-03-01
The study reported here examines the experience in the development and implementation of business simulation games based on network planning and management of high-rise construction. Appropriate network models of different types and levels of detail have been developed; a simulation model including 51 blocks (11 stages combined in 4 units) is proposed.
International Nuclear Information System (INIS)
Ghorai, Santu; Poria, Swarup
2016-01-01
Spatiotemporal dynamics of a predator–prey system in presence of spatial diffusion is investigated in presence of additional food exists for predators. Conditions for stability of Hopf as well as Turing patterns in a spatial domain are determined by making use of the linear stability analysis. Impact of additional food is clear from these conditions. Numerical simulation results are presented in order to validate the analytical findings. Finally numerical simulations are carried out around the steady state under zero flux boundary conditions. With the help of numerical simulations, the different types of spatial patterns (including stationary spatial pattern, oscillatory pattern, and spatiotemporal chaos) are identified in this diffusive predator–prey system in presence of additional food, depending on the quantity, quality of the additional food and the spatial domain and other parameters of the model. The key observation is that spatiotemporal chaos can be controlled supplying suitable additional food to predator. These investigations may be useful to understand complex spatiotemporal dynamics of population dynamical models in presence of additional food.
Large-eddy simulation of atmospheric flow over complex terrain
DEFF Research Database (Denmark)
Bechmann, Andreas
2007-01-01
The present report describes the development and validation of a turbulence model designed for atmospheric flows based on the concept of Large-Eddy Simulation (LES). The background for the work is the high Reynolds number k - #epsilon# model, which has been implemented on a finite-volume code...... turbulence model is able to handle both engineering and atmospheric flows and can be run in both RANS or LES mode. For LES simulations a time-dependent wind field that accurately represents the turbulent structures of a wind environment must be prescribed at the computational inlet. A method is implemented...... where the turbulent wind field from a separate LES simulation can be used as inflow. To avoid numerical dissipation of turbulence special care is paid to the numerical method, e.g. the turbulence model is calibrated with the specific numerical scheme used. This is done by simulating decaying isotropic...
Environmental management policy analysis using complex system simulation
International Nuclear Information System (INIS)
Van Eeckhout, E.; Roberts, D.; Oakes, R.; Shieh, A.; Hardie, W.; Pope, P.
1999-01-01
The two primary modules of Envirosim (the model of Los Alamos TA-55 and the WIPP transport/storage model) have been combined into one application, with the simulated waste generated by TA-55 operations being fed to storage, packaging, and transport simulation entities. Three simulation scenarios were executed which demonstrate the usefulness of Envirosim as a policy analysis tool for use in planning shipments to WIPP. A graphical user interface (GUI) has been implemented using IDL (Interactive Data Language) which allows the analyst to easily view simulation results. While IDL is not necessarily the graphics interface that would be selected for a production version of Envirosim, it does provide some powerful data manipulation capabilities, and it runs on a variety of platforms
BRAND program complex for neutron-physical experiment simulation by the Monte-Carlo method
International Nuclear Information System (INIS)
Androsenko, A.A.; Androsenko, P.A.
1984-01-01
Possibilities of the BRAND program complex for neutron and γ-radiation transport simulation by the Monte-Carlo method are described in short. The complex includes the following modules: geometric module, source module, detector module, modules of simulation of a vector of particle motion direction after interaction and a free path. The complex is written in the FORTRAN langauage and realized by the BESM-6 computer
Complex Langevin simulation of real time quantum evolution
International Nuclear Information System (INIS)
Ilgenfritz, E.M.; Kripfganz, J.
1986-07-01
Complex Langevin methods are used to study the time evolution of quantum mechanical wave packets. We do not need any Feynman ε regularization for the numerical evaluation of the double time path integral. (author)
Simulation and Analysis of Complex Biological Processes: an Organisation Modelling Perspective
Bosse, T.; Jonker, C.M.; Treur, J.
2005-01-01
This paper explores how the dynamics of complex biological processes can be modelled and simulated as an organisation of multiple agents. This modelling perspective identifies organisational structure occurring in complex decentralised processes and handles complexity of the analysis of the dynamics
Simulation Gaming as a Social Development Instrument : Dealing with Complex Problems
Klievink, B.; Janssen, M.
Improving public service delivery is a very complex domain and the complexity is difficult to grasp by stakeholders having various degree of knowledge and involvement. An emergent and promising method for dealing with complex problems is simulation gaming, which can be used to capitalize the
Usability and Information access challenges in complex simulation models
CSIR Research Space (South Africa)
Naidoo, S
2008-07-01
Full Text Available -sensitive help and meaningful feedback when errors occur Legibility Ease with which visual content can be understood Task Completion Whether a user can complete a task within appropriate task time when performing. Minimal action Capability of the software... by the user interface may result in some operations not being visible to the user although available in the simulation tool. The challenge has been to develop simulation tools that can be used by the users with minimal effort required both to operate...
Simulation and Efficient Measurements of Intensities for Complex Imaging Sequences
DEFF Research Database (Denmark)
Jensen, Jørgen Arendt; Rasmussen, Morten Fischer; Stuart, Matthias Bo
2014-01-01
on the sequence to simulate both intensity and mechanical index (MI) according to FDA rules. A 3 MHz BK Medical 8820e convex array transducer is used with the SARUS scanner. An Onda HFL-0400 hydrophone and the Onda AIMS III system measures the pressure field for three imaging schemes: a fixed focus, single...
Complex adaptative systems and computational simulation in Archaeology
Directory of Open Access Journals (Sweden)
Salvador Pardo-Gordó
2017-07-01
Full Text Available Traditionally the concept of ‘complexity’ is used as a synonym for ‘complex society’, i.e., human groups with characteristics such as urbanism, inequalities, and hierarchy. The introduction of Nonlinear Systems and Complex Adaptive Systems to the discipline of archaeology has nuanced this concept. This theoretical turn has led to the rise of modelling as a method of analysis of historical processes. This work has a twofold objective: to present the theoretical current characterized by generative thinking in archaeology and to present a concrete application of agent-based modelling to an archaeological problem: the dispersal of the first ceramic production in the western Mediterranean.
Directory of Open Access Journals (Sweden)
Roman Cherniha
2018-04-01
Full Text Available This review is devoted to search for Lie and Q-conditional (nonclassical symmetries and exact solutions of a class of reaction-diffusion-convection equations with exponential nonlinearities. A complete Lie symmetry classification of the class is derived via two different algorithms in order to show that the result depends essentially on the type of equivalence transformations used for the classification. Moreover, a complete description of Q-conditional symmetries for PDEs from the class in question is also presented. It is shown that all the well-known results for reaction-diffusion equations with exponential nonlinearities follow as particular cases from the results derived for this class of reaction-diffusion-convection equations. The symmetries obtained for constructing exact solutions of the relevant equations are successfully applied. The exact solutions are compared with those found by means of different techniques. Finally, an application of the exact solutions for solving boundary-value problems arising in population dynamics is presented.
Modelling and simulating in-stent restenosis with complex automata
Hoekstra, A.G.; Lawford, P.; Hose, R.
2010-01-01
In-stent restenosis, the maladaptive response of a blood vessel to injury caused by the deployment of a stent, is a multiscale system involving a large number of biological and physical processes. We describe a Complex Automata Model for in-stent restenosis, coupling bulk flow, drug diffusion, and
Simulation of Wind Farms in Flat & Complex terrain using CFD
DEFF Research Database (Denmark)
Prospathopoulos, John; Cabezon, D.; Politis, E.S.
2010-01-01
, the combination of the induction factor method along with the turbulence correction provides satisfactory results. In the complex terrain case, there are some significant discrepancies with the measurements, which are discussed. In this case, the induction factor method does not provide satisfactory results....
Computed tomography of von Meyenburg complex simulating micro-abscesses
International Nuclear Information System (INIS)
Sada, P.N.; Ramakrishna, B.
1994-01-01
A case is presented of a bile duct hamartoma in a 44 year old man being evaluated for abdominal pain. The computed tomography (CT) findings suggested micro-abscesses in the liver and a CT guided tru-cut biopsy showed von Meyenburg complex. 9 refs., 3 figs
Large-eddy simulation of atmospheric flow over complex terrain
Energy Technology Data Exchange (ETDEWEB)
Bechmann, A.
2006-11-15
The present report describes the development and validation of a turbulence model designed for atmospheric flows based on the concept of Large-Eddy Simulation (LES). The background for the work is the high Reynolds number k - epsilon model, which has been implemented on a finite-volume code of the incompressible Reynolds-averaged Navier-Stokes equations (RANS). The k - epsilon model is traditionally used for RANS computations, but is here developed to also enable LES. LES is able to provide detailed descriptions of a wide range of engineering flows at low Reynolds numbers. For atmospheric flows, however, the high Reynolds numbers and the rough surface of the earth provide difficulties normally not compatible with LES. Since these issues are most severe near the surface they are addressed by handling the near surface region with RANS and only use LES above this region. Using this method, the developed turbulence model is able to handle both engineering and atmospheric flows and can be run in both RANS or LES mode. For LES simulations a time-dependent wind field that accurately represents the turbulent structures of a wind environment must be prescribed at the computational inlet. A method is implemented where the turbulent wind field from a separate LES simulation can be used as inflow. To avoid numerical dissipation of turbulence special care is paid to the numerical method, e.g. the turbulence model is calibrated with the specific numerical scheme used. This is done by simulating decaying isotropic and homogeneous turbulence. Three atmospheric test cases are investigated in order to validate the behavior of the presented turbulence model. Simulation of the neutral atmospheric boundary layer, illustrates the turbulence model ability to generate and maintain the turbulent structures responsible for boundary layer transport processes. Velocity and turbulence profiles are in good agreement with measurements. Simulation of the flow over the Askervein hill is also
Tcaciuc, A Patricia; Borrelli, Raffaella; Zaninetta, Luciano M; Gschwend, Philip M
2018-01-24
Passive sampling is becoming a widely used tool for assessing freely dissolved concentrations of hydrophobic organic contaminants in environmental media. For certain media and target analytes, the time to reach equilibrium exceeds the deployment time, and in such cases, the loss of performance reference compounds (PRCs), loaded in the sampler before deployment, is one of the common ways used to assess the fractional equilibration of target analytes. The key assumption behind the use of PRCs is that their release is solely diffusion driven. But in this work, we show that PRC transformations in the sediment can have a measurable impact on the PRC releases and even allow estimation of that compound's transformation rate in the environment of interest. We found that in both field and lab incubations, the loss of the 13 C 2,4'-DDT PRC from a polyethylene (PE) passive sampler deployed at the sediment-water interface was accelerated compared to the loss of other PRCs ( 13 C-labeled PCBs, 13 C-labeled DDE and DDD). The DDT PRC loss was also accompanied by accumulation in the PE of its degradation product, 13 C 2,4'-DDD. Using a 1D reaction-diffusion model, we deduced the in situ degradation rates of DDT from the measured PRC loss. The in situ degradation rates increased with depth into the sediment bed (0.14 d -1 at 0-10 cm and 1.4 d -1 at 30-40 cm) and although they could not be independently validated, these rates compared favorably with literature values. This work shows that passive sampling users should be cautious when choosing PRCs, as degradation processes can affect some PRC's releases from the passive sampler. More importantly, this work opens up the opportunity for novel applications of passive samplers, particularly with regard to investigating in situ degradation rates, pathways, and products for both legacy and emerging contaminants. However, further work is needed to confirm that the rates deduced from model fitting of PRC loss are a true reflection of DDT
A Bacterial-Based Algorithm to Simulate Complex Adaptative Systems
González Rodríguez, Diego; Hernández Carrión, José Rodolfo
2014-01-01
Paper presented at the 13th International Conference on Simulation of Adaptive Behavior which took place at Castellón, Spain in 2014, July 22-25. Bacteria have demonstrated an amazing capacity to overcome envi-ronmental changes by collective adaptation through genetic exchanges. Using a distributed communication system and sharing individual strategies, bacteria propagate mutations as innovations that allow them to survive in different envi-ronments. In this paper we present an agent-based...
Integrating Multibody Simulation and CFD: toward Complex Multidisciplinary Design Optimization
Pieri, Stefano; Poloni, Carlo; Mühlmeier, Martin
This paper describes the use of integrated multidisciplinary analysis and optimization of a race car model on a predefined circuit. The objective is the definition of the most efficient geometric configuration that can guarantee the lowest lap time. In order to carry out this study it has been necessary to interface the design optimization software modeFRONTIER with the following softwares: CATIA v5, a three dimensional CAD software, used for the definition of the parametric geometry; A.D.A.M.S./Motorsport, a multi-body dynamic simulation software; IcemCFD, a mesh generator, for the automatic generation of the CFD grid; CFX, a Navier-Stokes code, for the fluid-dynamic forces prediction. The process integration gives the possibility to compute, for each geometrical configuration, a set of aerodynamic coefficients that are then used in the multiboby simulation for the computation of the lap time. Finally an automatic optimization procedure is started and the lap-time minimized. The whole process is executed on a Linux cluster running CFD simulations in parallel.
Learning to manage complexity through simulation: students' challenges and possible strategies.
Gormley, Gerard J; Fenwick, Tara
2016-06-01
Many have called for medical students to learn how to manage complexity in healthcare. This study examines the nuances of students' challenges in coping with a complex simulation learning activity, using concepts from complexity theory, and suggests strategies to help them better understand and manage complexity.Wearing video glasses, participants took part in a simulation ward-based exercise that incorporated characteristics of complexity. Video footage was used to elicit interviews, which were transcribed. Using complexity theory as a theoretical lens, an iterative approach was taken to identify the challenges that participants faced and possible coping strategies using both interview transcripts and video footage.Students' challenges in coping with clinical complexity included being: a) unprepared for 'diving in', b) caught in an escalating system, c) captured by the patient, and d) unable to assert boundaries of acceptable practice.Many characteristics of complexity can be recreated in a ward-based simulation learning activity, affording learners an embodied and immersive experience of these complexity challenges. Possible strategies for managing complexity themes include: a) taking time to size up the system, b) attuning to what emerges, c) reducing complexity, d) boundary practices, and e) working with uncertainty. This study signals pedagogical opportunities for recognizing and dealing with complexity.
Numerical simulation of flow over bariers in complex terrain
Czech Academy of Sciences Publication Activity Database
Bodnár, Tomáš; Beneš, L.; Kozel, Karel
2008-01-01
Roč. 31, 5-6 (2008), s. 619-632 ISSN 1124-1896 R&D Projects: GA AV ČR 1ET400760405 Institutional research plan: CEZ:AV0Z20760514 Keywords : boundary layer * complex terrain * finite difference Subject RIV: DG - Athmosphere Sciences, Meteorology Impact factor: 0.277, year: 2008 http://prometeo.sif.it:8080/papers/?pid=ncc9331
Directory of Open Access Journals (Sweden)
Demongeot Jacques
2004-06-01
Full Text Available Abstract Background The transport of intra-cellular particles by microtubules is a major biological function. Under appropriate in vitro conditions, microtubule preparations behave as a 'complex' system and show 'emergent' phenomena. In particular, they form dissipative structures that self-organise over macroscopic distances by a combination of reaction and diffusion. Results Here, we show that self-organisation also gives rise to a collective transport of colloidal particles along a specific direction. Particles, such as polystyrene beads, chromosomes, nuclei, and vesicles are carried at speeds of several microns per minute. The process also results in the macroscopic self-organisation of these particles. After self-organisation is completed, they show the same pattern of organisation as the microtubules. Numerical simulations of a population of growing and shrinking microtubules, incorporating experimentally realistic reaction dynamics, predict self-organisation. They forecast that during self-organisation, macroscopic parallel arrays of oriented microtubules form which cross the reaction space in successive waves. Such travelling waves are capable of transporting colloidal particles. The fact that in the simulations, the aligned arrays move along the same direction and at the same speed as the particles move, suggest that this process forms the underlying mechanism for the observed transport properties. Conclusions This process constitutes a novel physical chemical mechanism by which chemical energy is converted into collective transport of colloidal particles along a given direction. Self-organisation of this type provides a new mechanism by which intra cellular particles such as chromosomes and vesicles can be displaced and simultaneously organised by microtubules. It is plausible that processes of this type occur in vivo.
Glade, Nicolas; Demongeot, Jacques; Tabony, James
2004-01-01
Background The transport of intra-cellular particles by microtubules is a major biological function. Under appropriate in vitro conditions, microtubule preparations behave as a 'complex' system and show 'emergent' phenomena. In particular, they form dissipative structures that self-organise over macroscopic distances by a combination of reaction and diffusion. Results Here, we show that self-organisation also gives rise to a collective transport of colloidal particles along a specific direction. Particles, such as polystyrene beads, chromosomes, nuclei, and vesicles are carried at speeds of several microns per minute. The process also results in the macroscopic self-organisation of these particles. After self-organisation is completed, they show the same pattern of organisation as the microtubules. Numerical simulations of a population of growing and shrinking microtubules, incorporating experimentally realistic reaction dynamics, predict self-organisation. They forecast that during self-organisation, macroscopic parallel arrays of oriented microtubules form which cross the reaction space in successive waves. Such travelling waves are capable of transporting colloidal particles. The fact that in the simulations, the aligned arrays move along the same direction and at the same speed as the particles move, suggest that this process forms the underlying mechanism for the observed transport properties. Conclusions This process constitutes a novel physical chemical mechanism by which chemical energy is converted into collective transport of colloidal particles along a given direction. Self-organisation of this type provides a new mechanism by which intra cellular particles such as chromosomes and vesicles can be displaced and simultaneously organised by microtubules. It is plausible that processes of this type occur in vivo. PMID:15176973
Ngada, Narcisse
2015-06-15
The complexity and cost of building and running high-power electrical systems make the use of simulations unavoidable. The simulations available today provide great understanding about how systems really operate. This paper helps the reader to gain an insight into simulation in the field of power converters for particle accelerators. Starting with the definition and basic principles of simulation, two simulation types, as well as their leading tools, are presented: analog and numerical simulations. Some practical applications of each simulation type are also considered. The final conclusion then summarizes the main important items to keep in mind before opting for a simulation tool or before performing a simulation.
Temperature field simulation of complex structures in fire environment
International Nuclear Information System (INIS)
Li Weifen; Hao Zhiming; Li Minghai
2010-01-01
In this paper, the typical model of the system of dangerous goods - steel - wood composite structure including components of explosives is used as the research object. Using MARC program, the temperature field of the structure in the fire environment is simulated. Radiation, conduction and convection heat transfer within the gap of the structure are taken into account, contact heat transfer is also considered. The phenomenon of thermal decomposition of wood in high temperature is deal with by equivalent method. The results show that the temperature of the explosives is not high in the fire environment. The timber inside the composite structure has played a very good insulation effect of explosives.
Simulations of photochemical smog formation in complex urban areas
Muilwijk, C.; Schrijvers, P. J. C.; Wuerz, S.; Kenjereš, S.
2016-12-01
In the present study we numerically investigated the dispersion of photochemical reactive pollutants in complex urban areas by applying an integrated Computational Fluid Dynamics (CFD) and Computational Reaction Dynamics (CRD) approach. To model chemical reactions involved in smog generation, the Generic Reaction Set (GRS) approach is used. The GRS model was selected since it does not require detailed modeling of a large set of reactive components. Smog formation is modeled first in the case of an intensive traffic emission, subjected to low to moderate wind conditions in an idealized two-dimensional street canyon with a building aspect ratio (height/width) of one. It is found that Reactive Organic Components (ROC) play an important role in the chemistry of smog formation. In contrast to the NOx/O3 photochemical steady state model that predicts a depletion of the (ground level) ozone, the GRS model predicts generation of ozone. Secondly, the effect of direct sunlight and shadow within the street canyon on the chemical reaction dynamics is investigated for three characteristic solar angles (morning, midday and afternoon). Large differences of up to one order of magnitude are found in the ozone production for different solar angles. As a proof of concept for real urban areas, the integrated CFD/CRD approach is applied for a real scale (1 × 1 km2) complex urban area (a district of the city of Rotterdam, The Netherlands) with high traffic emissions. The predicted pollutant concentration levels give realistic values that correspond to moderate to heavy smog. It is concluded that the integrated CFD/CRD method with the GRS model of chemical reactions is both accurate and numerically robust, and can be used for modeling of smog formation in complex urban areas.
An advanced modelling tool for simulating complex river systems.
Trancoso, Ana Rosa; Braunschweig, Frank; Chambel Leitão, Pedro; Obermann, Matthias; Neves, Ramiro
2009-04-01
The present paper describes MOHID River Network (MRN), a 1D hydrodynamic model for river networks as part of MOHID Water Modelling System, which is a modular system for the simulation of water bodies (hydrodynamics and water constituents). MRN is capable of simulating water quality in the aquatic and benthic phase and its development was especially focused on the reproduction of processes occurring in temporary river networks (flush events, pools formation, and transmission losses). Further, unlike many other models, it allows the quantification of settled materials at the channel bed also over periods when the river falls dry. These features are very important to secure mass conservation in highly varying flows of temporary rivers. The water quality models existing in MOHID are base on well-known ecological models, such as WASP and ERSEM, the latter allowing explicit parameterization of C, N, P, Si, and O cycles. MRN can be coupled to the basin model, MOHID Land, with computes runoff and porous media transport, allowing for the dynamic exchange of water and materials between the river and surroundings, or it can be used as a standalone model, receiving discharges at any specified nodes (ASCII files of time series with arbitrary time step). These features account for spatial gradients in precipitation which can be significant in Mediterranean-like basins. An interface has been already developed for SWAT basin model.
Stabilizing simulations of complex stochastic representations for quantum dynamical systems
Energy Technology Data Exchange (ETDEWEB)
Perret, C; Petersen, W P, E-mail: wpp@math.ethz.ch [Seminar for Applied Mathematics, ETH, Zurich (Switzerland)
2011-03-04
Path integral representations of quantum dynamics can often be formulated as stochastic differential equations (SDEs). In a series of papers, Corney and Drummond (2004 Phys. Rev. Lett. 93 260401), Deuar and Drummond (2001 Comput. Phys. Commun. 142 442-5), Drummond and Gardnier (1980 J. Phys. A: Math. Gen. 13 2353-68), Gardiner and Zoller (2004 Quantum Noise: A Handbook of Markovian and Non-Markovian Quantum Stochastic Methods with Applications to Quantum Optics (Springer Series in Synergetics) 3rd edn (Berlin: Springer)) and Gilchrist et al (1997 Phys. Rev. A 55 3014-32) and their collaborators have derived SDEs from coherent states representations for density matrices. Computationally, these SDEs are attractive because they seem simple to simulate. They can be quite unstable, however. In this paper, we consider some of the instabilities and propose a few remedies. Particularly, because the variances of the simulated paths typically grow exponentially, the processes become de-localized in relatively short times. Hence, the issues of boundary conditions and stable integration methods become important. We use the Bose-Einstein Hamiltonian as an example. Our results reveal that it is possible to significantly extend integration times and show the periodic structure of certain functionals.
Computer simulations of discharges from a lignite power plant complex
International Nuclear Information System (INIS)
Koukouliou, V.; Horyna, J.; Perez-Sanchez, D.
2008-01-01
This paper describes work carried out within the IAEA EMRAS program NORM working group to test the predictions of three computer models against measured radionuclide concentrations resulting from discharges from a lignite power plant complex. This complex consists of two power plants with a total of five discharge stacks, situated approximately 2-5 kilometres from a city of approximately 10,000 inhabitants. Monthly measurements of mean wind speed and direction, dust loading, and 238 U activities in fallout samples, as well as mean annual values of 232 Th activity in the nearest city sampling sites were available for the study. The models used in the study were Pc-CREAM (a detailed impact assessment model), and COMPLY and CROM (screening models). In applying the models to this scenario it was noted that the meteorological data provided was not ideal for testing, and that a number of assumptions had to be made, particularly for the simpler models. However, taking the gaps and uncertainties in the data into account, the model predictions from PC-CREAM were generally in good agreement with the measured data, and the results from different models were also generally consistent with each other. However, the COMPLY predictions were generally lower than those from PC-CREAM. This is of concern, as the aim of a screening model (COMPLY) is to provide conservative estimates of contaminant concentrations. Further investigation of this problem is required. The general implications of the results for further model development are discussed. (author)
Combining molecular dynamics with mesoscopic Green’s function reaction dynamics simulations
Energy Technology Data Exchange (ETDEWEB)
Vijaykumar, Adithya, E-mail: vijaykumar@amolf.nl [FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam (Netherlands); van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam (Netherlands); Bolhuis, Peter G. [van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam (Netherlands); Rein ten Wolde, Pieter, E-mail: p.t.wolde@amolf.nl [FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam (Netherlands)
2015-12-07
In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green’s Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. We propose a novel approach that combines GFRD for simulating the system at the mesoscopic scale where particles are far apart, with a microscopic technique such as Langevin dynamics or Molecular Dynamics (MD), for simulating the system at the microscopic scale where reactants are in close proximity. This scheme defines the regions where the particles are close together and simulated with high microscopic resolution and those where they are far apart and simulated with lower mesoscopic resolution, adaptively on the fly. The new multi-scale scheme, called MD-GFRD, is generic and can be used to efficiently simulate reaction-diffusion systems at the particle level.
Combining molecular dynamics with mesoscopic Green’s function reaction dynamics simulations
International Nuclear Information System (INIS)
Vijaykumar, Adithya; Bolhuis, Peter G.; Rein ten Wolde, Pieter
2015-01-01
In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green’s Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. We propose a novel approach that combines GFRD for simulating the system at the mesoscopic scale where particles are far apart, with a microscopic technique such as Langevin dynamics or Molecular Dynamics (MD), for simulating the system at the microscopic scale where reactants are in close proximity. This scheme defines the regions where the particles are close together and simulated with high microscopic resolution and those where they are far apart and simulated with lower mesoscopic resolution, adaptively on the fly. The new multi-scale scheme, called MD-GFRD, is generic and can be used to efficiently simulate reaction-diffusion systems at the particle level
A new approach for turbulent simulations in complex geometries
Israel, Daniel M.
Historically turbulence modeling has been sharply divided into Reynolds averaged Navier-Stokes (RANS), in which all the turbulent scales of motion are modeled, and large-eddy simulation (LES), in which only a portion of the turbulent spectrum is modeled. In recent years there have been numerous attempts to couple these two approaches either by patching RANS and LES calculations together (zonal methods) or by blending the two sets of equations. In order to create a proper bridging model, that is, a single set of equations which captures both RANS and LES like behavior, it is necessary to place both RANS and LES in a more general framework. The goal of the current work is threefold: to provide such a framework, to demonstrate how the Flow Simulation Methodology (FSM) fits into this framework, and to evaluate the strengths and weaknesses of the current version of the FSM. To do this, first a set of filtered Navier-Stokes (FNS) equations are introduced in terms of an arbitrary generalized filter. Additional exact equations are given for the second order moments and the generalized subfilter dissipation rate tensor. This is followed by a discussion of the role of implicit and explicit filters in turbulence modeling. The FSM is then described with particular attention to its role as a bridging model. In order to evaluate the method a specific implementation of the FSM approach is proposed. Simulations are presented using this model for the case of a separating flow over a "hump" with and without flow control. Careful attention is paid to error estimation, and, in particular, how using flow statistics and time series affects the error analysis. Both mean flow and Reynolds stress profiles are presented, as well as the phase averaged turbulent structures and wall pressure spectra. Using the phase averaged data it is possible to examine how the FSM partitions the energy between the coherent resolved scale motions, the random resolved scale fluctuations, and the subfilter
Wind-farm simulation over moderately complex terrain
Segalini, Antonio; Castellani, Francesco
2017-05-01
A comparison between three independent software to estimate the power production and the flow field in a wind farm is conducted, validating them against SCADA (Supervisory, Control And Data Acquisition) data. The three software were ORFEUS, WindSim and WAsP: ORFEUS and WAsP are linearised solvers, while WindSim is fully nonlinear. A wake model (namely a prescribed velocity deficit associated to the turbines) is used by WAsP, while ORFEUS and WindSim use the actuator-disc method to account for the turbines presence. The comparison indicates that ORFEUS and WAsP perform slightly better than WindSim in the assessment of the polar efficiency. The wakes simulated with ORFEUS appear more persistent than the ones of WindSim, which uses a two-equation closure model for the turbulence effects.
DEVELOPING INDUSTRIAL ROBOT SIMULATION MODEL TUR10-K USING “UNIVERSAL MECHANISM” SOFTWARE COMPLEX
Directory of Open Access Journals (Sweden)
Vadim Vladimirovich Chirkov
2018-02-01
Full Text Available Manipulation robots are complex spatial mechanical systems having five or six degrees of freedom, and sometimes more. For this reason, modeling manipulative robots movement, even in the kinematic formulation, is a complex mathematical task. If one moves from kinematic modeling of motion to dynamic modeling then there must be taken into account the inertial properties of the modeling object. In this case, analytical constructing of such a complex object mathematical model as a manipulation robot becomes practically impossible. Therefore, special computer-aided design systems, called CAE-systems, are used for modeling complex mechanical systems. The purpose of the paper is simulation model construction of a complex mechanical system, such as the industrial robot TUR10-K, to obtain its dynamic characteristics. Developing such models makes it possible to reduce the complexity of designing complex systems process and to obtain the necessary characteristics. Purpose. Developing the simulation model of the industrial robot TUR10-K and obtaining dynamic characteristics of the mechanism. Methodology: the article is used a computer simulation method. Results: There is obtained the simulation model of the robot and its dynamic characteristics. Practical implications: the results can be used in the mechanical systems design and various simulation models.
Simulation As a Method To Support Complex Organizational Transformations in Healthcare
Rothengatter, D.C.F.; Katsma, Christiaan; van Hillegersberg, Jos
2010-01-01
In this paper we study the application of simulation as a method to support information system and process design in complex organizational transitions. We apply a combined use of a collaborative workshop approach with the use of a detailed and accurate graphical simulation model in a hospital that
International Nuclear Information System (INIS)
Zimakov, V.N.; Chernykh, V.P.
1998-01-01
The problems on creating calculational-simulating (CSC) and their application by developing the program and program-technical means for computer-aided process control systems at NPP are considered. The abo- ve complex is based on the all-mode real time mathematical model, functioning at a special complex of computerized means
A Simulation for Managing Complexity in Sales and Operations Planning Decisions
DuHadway, Scott; Dreyfus, David
2017-01-01
Within the classroom it is often difficult to convey the complexities and intricacies that go into making sales and operations planning decisions. This article describes an in-class simulation that allows students to gain hands-on experience with the complexities in making forecasting, inventory, and supplier selection decisions as part of the…
Genetic Simulation Tools for Post-Genome Wide Association Studies of Complex Diseases
Amos, Christopher I.; Bafna, Vineet; Hauser, Elizabeth R.; Hernandez, Ryan D.; Li, Chun; Liberles, David A.; McAllister, Kimberly; Moore, Jason H.; Paltoo, Dina N.; Papanicolaou, George J.; Peng, Bo; Ritchie, Marylyn D.; Rosenfeld, Gabriel; Witte, John S.
2014-01-01
Genetic simulation programs are used to model data under specified assumptions to facilitate the understanding and study of complex genetic systems. Standardized data sets generated using genetic simulation are essential for the development and application of novel analytical tools in genetic epidemiology studies. With continuing advances in high-throughput genomic technologies and generation and analysis of larger, more complex data sets, there is a need for updating current approaches in genetic simulation modeling. To provide a forum to address current and emerging challenges in this area, the National Cancer Institute (NCI) sponsored a workshop, entitled “Genetic Simulation Tools for Post-Genome Wide Association Studies of Complex Diseases” at the National Institutes of Health (NIH) in Bethesda, Maryland on March 11-12, 2014. The goals of the workshop were to: (i) identify opportunities, challenges and resource needs for the development and application of genetic simulation models; (ii) improve the integration of tools for modeling and analysis of simulated data; and (iii) foster collaborations to facilitate development and applications of genetic simulation. During the course of the meeting the group identified challenges and opportunities for the science of simulation, software and methods development, and collaboration. This paper summarizes key discussions at the meeting, and highlights important challenges and opportunities to advance the field of genetic simulation. PMID:25371374
International Nuclear Information System (INIS)
Zhao Yi; Small, Michael; Coward, David; Howell, Eric; Zhao Chunnong; Ju Li; Blair, David
2006-01-01
We describe the application of complexity estimation and the surrogate data method to identify deterministic dynamics in simulated gravitational wave (GW) data contaminated with white and coloured noises. The surrogate method uses algorithmic complexity as a discriminating statistic to decide if noisy data contain a statistically significant level of deterministic dynamics (the GW signal). The results illustrate that the complexity method is sensitive to a small amplitude simulated GW background (SNR down to 0.08 for white noise and 0.05 for coloured noise) and is also more robust than commonly used linear methods (autocorrelation or Fourier analysis)
Bagli, Enrico; Guidi, Vincenzo
2013-08-01
A toolkit for the simulation of coherent interactions between high-energy charged particles and complex crystal structures, called DYNECHARM++ has been developed. The code has been written in C++ language taking advantage of this object-oriented programing method. The code is capable to evaluating the electrical characteristics of complex atomic structures and to simulate and track the particle trajectory within them. Calculation method of electrical characteristics based on their expansion in Fourier series has been adopted. Two different approaches to simulate the interaction have been adopted, relying on the full integration of particle trajectories under the continuum potential approximation and on the definition of cross-sections of coherent processes. Finally, the code has proved to reproduce experimental results and to simulate interaction of charged particles with complex structures.
Juckem, Paul F.; Clark, Brian R.; Feinstein, Daniel T.
2017-05-04
The U.S. Geological Survey, National Water-Quality Assessment seeks to map estimated intrinsic susceptibility of the glacial aquifer system of the conterminous United States. Improved understanding of the hydrogeologic characteristics that explain spatial patterns of intrinsic susceptibility, commonly inferred from estimates of groundwater age distributions, is sought so that methods used for the estimation process are properly equipped. An important step beyond identifying relevant hydrogeologic datasets, such as glacial geology maps, is to evaluate how incorporation of these resources into process-based models using differing levels of detail could affect resulting simulations of groundwater age distributions and, thus, estimates of intrinsic susceptibility.This report describes the construction and calibration of three groundwater-flow models of northeastern Wisconsin that were developed with differing levels of complexity to provide a framework for subsequent evaluations of the effects of process-based model complexity on estimations of groundwater age distributions for withdrawal wells and streams. Preliminary assessments, which focused on the effects of model complexity on simulated water levels and base flows in the glacial aquifer system, illustrate that simulation of vertical gradients using multiple model layers improves simulated heads more in low-permeability units than in high-permeability units. Moreover, simulation of heterogeneous hydraulic conductivity fields in coarse-grained and some fine-grained glacial materials produced a larger improvement in simulated water levels in the glacial aquifer system compared with simulation of uniform hydraulic conductivity within zones. The relation between base flows and model complexity was less clear; however, the relation generally seemed to follow a similar pattern as water levels. Although increased model complexity resulted in improved calibrations, future application of the models using simulated particle
A Framework for the Interactive Handling of High-Dimensional Simulation Data in Complex Geometries
Benzina, Amal; Buse, Gerrit; Butnaru, Daniel; Murarasu, Alin; Treib, Marc; Varduhn, Vasco; Mundani, Ralf-Peter
2013-01-01
Flow simulations around building infrastructure models involve large scale complex geometries, which when discretized in adequate detail entail high computational cost. Moreover, tasks such as simulation insight by steering or optimization require many such costly simulations. In this paper, we illustrate the whole pipeline of an integrated solution for interactive computational steering, developed for complex flow simulation scenarios that depend on a moderate number of both geometric and physical parameters. A mesh generator takes building information model input data and outputs a valid cartesian discretization. A sparse-grids-based surrogate model—a less costly substitute for the parameterized simulation—uses precomputed data to deliver approximated simulation results at interactive rates. Furthermore, a distributed multi-display visualization environment shows building infrastructure together with flow data. The focus is set on scalability and intuitive user interaction.
Flow MRI simulation in complex 3D geometries: Application to the cerebral venous network.
Fortin, Alexandre; Salmon, Stéphanie; Baruthio, Joseph; Delbany, Maya; Durand, Emmanuel
2018-02-05
Develop and evaluate a complete tool to include 3D fluid flows in MRI simulation, leveraging from existing software. Simulation of MR spin flow motion is of high interest in the study of flow artifacts and angiography. However, at present, only a few simulators include this option and most are restricted to static tissue imaging. An extension of JEMRIS, one of the most advanced high performance open-source simulation platforms to date, was developed. The implementation of a Lagrangian description of the flow allows simulating any MR experiment, including both static tissues and complex flow data from computational fluid dynamics. Simulations of simple flow models are compared with real experiments on a physical flow phantom. A realistic simulation of 3D flow MRI on the cerebral venous network is also carried out. Simulations and real experiments are in good agreement. The generality of the framework is illustrated in 2D and 3D with some common flow artifacts (misregistration and inflow enhancement) and with the three main angiographic techniques: phase contrast velocimetry (PC), time-of-flight, and contrast-enhanced imaging MRA. The framework provides a versatile and reusable tool for the simulation of any MRI experiment including physiological fluids and arbitrarily complex flow motion. © 2018 International Society for Magnetic Resonance in Medicine.
Thrive or overload? The effect of task complexity on novices' simulation-based learning.
Haji, Faizal A; Cheung, Jeffrey J H; Woods, Nicole; Regehr, Glenn; de Ribaupierre, Sandrine; Dubrowski, Adam
2016-09-01
Fidelity is widely viewed as an important element of simulation instructional design based on its purported relationship with transfer of learning. However, higher levels of fidelity may increase task complexity to a point at which novices' cognitive resources become overloaded. In this experiment, we investigate the effects of variations in task complexity on novices' cognitive load and learning during simulation-based procedural skills training. Thirty-eight medical students were randomly assigned to simulation training on a simple or complex lumbar puncture (LP) task. Participants completed four practice trials on this task (skill acquisition). After 10 days of rest, all participants completed one additional trial on their assigned task (retention) and one trial on a 'very complex' simulation designed to be similar to the complex task (transfer). We assessed LP performance and cognitive load on each trial using multiple measures. In both groups, LP performance improved significantly during skill acquisition (p ≤ 0.047, f = 0.29-0.96) and was maintained at retention. The simple task group demonstrated superior performance compared with the complex task group throughout these phases (p ≤ 0.002, d = 1.13-2.31). Cognitive load declined significantly in the simple task group (p Education.
Simulation of complex data structures for planning of studies with focus on biomarker comparison.
Schulz, Andreas; Zöller, Daniela; Nickels, Stefan; Beutel, Manfred E; Blettner, Maria; Wild, Philipp S; Binder, Harald
2017-06-13
There are a growing number of observational studies that do not only focus on single biomarkers for predicting an outcome event, but address questions in a multivariable setting. For example, when quantifying the added value of new biomarkers in addition to established risk factors, the aim might be to rank several new markers with respect to their prediction performance. This makes it important to consider the marker correlation structure for planning such a study. Because of the complexity, a simulation approach may be required to adequately assess sample size or other aspects, such as the choice of a performance measure. In a simulation study based on real data, we investigated how to generate covariates with realistic distributions and what generating model should be used for the outcome, aiming to determine the least amount of information and complexity needed to obtain realistic results. As a basis for the simulation a large epidemiological cohort study, the Gutenberg Health Study was used. The added value of markers was quantified and ranked in subsampling data sets of this population data, and simulation approaches were judged by the quality of the ranking. One of the evaluated approaches, the random forest, requires original data at the individual level. Therefore, also the effect of the size of a pilot study for random forest based simulation was investigated. We found that simple logistic regression models failed to adequately generate realistic data, even with extensions such as interaction terms or non-linear effects. The random forest approach was seen to be more appropriate for simulation of complex data structures. Pilot studies starting at about 250 observations were seen to provide a reasonable level of information for this approach. We advise to avoid oversimplified regression models for simulation, in particular when focusing on multivariable research questions. More generally, a simulation should be based on real data for adequately reflecting
Simulation of complex data structures for planning of studies with focus on biomarker comparison
Directory of Open Access Journals (Sweden)
Andreas Schulz
2017-06-01
Full Text Available Abstract Background There are a growing number of observational studies that do not only focus on single biomarkers for predicting an outcome event, but address questions in a multivariable setting. For example, when quantifying the added value of new biomarkers in addition to established risk factors, the aim might be to rank several new markers with respect to their prediction performance. This makes it important to consider the marker correlation structure for planning such a study. Because of the complexity, a simulation approach may be required to adequately assess sample size or other aspects, such as the choice of a performance measure. Methods In a simulation study based on real data, we investigated how to generate covariates with realistic distributions and what generating model should be used for the outcome, aiming to determine the least amount of information and complexity needed to obtain realistic results. As a basis for the simulation a large epidemiological cohort study, the Gutenberg Health Study was used. The added value of markers was quantified and ranked in subsampling data sets of this population data, and simulation approaches were judged by the quality of the ranking. One of the evaluated approaches, the random forest, requires original data at the individual level. Therefore, also the effect of the size of a pilot study for random forest based simulation was investigated. Results We found that simple logistic regression models failed to adequately generate realistic data, even with extensions such as interaction terms or non-linear effects. The random forest approach was seen to be more appropriate for simulation of complex data structures. Pilot studies starting at about 250 observations were seen to provide a reasonable level of information for this approach. Conclusions We advise to avoid oversimplified regression models for simulation, in particular when focusing on multivariable research questions. More generally
Tutorial at CNS 2013: Managing complex workflows in neural simulation and data analysis
Grün, Sonja; Davison, Andrew
2013-01-01
In our attempts to uncover the mechanisms that govern brain processing on the level of interacting neurons, neuroscientists have taken on the challenge of tackling the sheer complexity exhibited by neuronal networks. Neuronal simulations are nowadays performed with a high degree of detail, covering large, heterogeneous networks. Experimentally, electrophysiologists can simultaneously record from hundreds of neurons in complicated behavioral paradigms. The data streams of simulation and experi...
Large Eddy Simulations of Complex Flows in IC-Engine's Exhaust Manifold and Turbine
Fjällman, Johan
2014-01-01
The thesis deals with the flow in pipe bends and radial turbines geometries that are commonly found in an Internal Combustion Engine (ICE). The development phase of internal combustion engines relies more and more on simulations as an important complement to experiments. This is partly because of the reduction in development cost and the shortening of the development time. This is one of the reasons for the need of more accurate and predictive simulations. By using more complex computational ...
Modelling and simulation of floods in alpine catchments equipped with complex hydropower schemes
Bieri, Martin; Schleiss, Anton; Frankhauser, A.
2010-01-01
The simulation of run-off in an alpine catchment area equipped with complex hydropower schemes is presented by the help of an especially developed tool, called Routing System, which can combine hydrological modelling and operation of hydraulic elements. In the hydrological forecasting tool tridimensional rainfall, temperature and evapotranspiration distributions are taken into account for simulating the dominant hydrological processes, as glacier melt, snow pack constitution and melt, soil in...
International Nuclear Information System (INIS)
Vieira, Leonardo S.; Donatelli, Joao L.; Cruz, Manuel E.
2006-01-01
In this work we present the development and implementation of an integrated approach for mathematical exergoeconomic optimization of complex thermal systems. By exploiting the computational power of a professional process simulator, the proposed integrated approach permits the optimization routine to ignore the variables associated with the thermodynamic balance equations and thus deal only with the decision variables. To demonstrate the capabilities of the integrated approach, it is here applied to a complex cogeneration system, which includes all the major components of a typical thermal plant, and requires more than 800 variables for its simulation
Lei, Qun-Li; Hadinoto, Kunn; Ni, Ran
2017-04-18
The delivery and dissolution of poorly soluble drugs is challenging in the pharmaceutical industry. One way to significantly improve the delivery efficiency is to incorporate these hydrophobic small molecules into a colloidal polyelectrolyes(PE)-drug complex in their ionized states. Despite its huge application value, the general mechanism of PE collapse and complex formation in this system has not been well understood. In this work, by combining a mean-field theory with extensive molecular simulations, we unveil the phase behaviors of the system under dilute and salt-free conditions. We find that the complexation is a first-order-like phase transition triggered by the hydrophobic attraction between the drug molecules. Importantly, the valence ratio between the drug molecule and PE monomer plays a crucial role in determining the stability and morphology of the complex. Moreover, the sign of the zeta potential and the net charge of the complex are found to be inverted as the hydrophobicity of the drug molecules increases. Both theory and simulation indicate that the complexation point and complex morphology and the electrostatic properties of the complex have a weak dependence on chain length. Finally, the dynamics aspect of PE-drug complexation is also explored, and it is found that the complex can be trapped into a nonequilibrium glasslike state when the hydropobicity of the drug molecule is too strong. Our work gives a clear physical picture behind the PE-drug complexation phenomenon and provides guidelines to fabricate the colloidal PE-drug complex with the desired physical characteristics.
Kraus, E. I.; Shabalin, I. I.; Shabalin, T. I.
2018-04-01
The main points of development of numerical tools for simulation of deformation and failure of complex technical objects under nonstationary conditions of extreme loading are presented. The possibility of extending the dynamic method for construction of difference grids to the 3D case is shown. A 3D realization of discrete-continuum approach to the deformation and failure of complex technical objects is carried out. The efficiency of the existing software package for 3D modelling is shown.
Efficient Simulation Modeling of an Integrated High-Level-Waste Processing Complex
International Nuclear Information System (INIS)
Gregory, Michael V.; Paul, Pran K.
2000-01-01
An integrated computational tool named the Production Planning Model (ProdMod) has been developed to simulate the operation of the entire high-level-waste complex (HLW) at the Savannah River Site (SRS) over its full life cycle. ProdMod is used to guide SRS management in operating the waste complex in an economically efficient and environmentally sound manner. SRS HLW operations are modeled using coupled algebraic equations. The dynamic nature of plant processes is modeled in the form of a linear construct in which the time dependence is implicit. Batch processes are modeled in discrete event-space, while continuous processes are modeled in time-space. The ProdMod methodology maps between event-space and time-space such that the inherent mathematical discontinuities in batch process simulation are avoided without sacrificing any of the necessary detail in the batch recipe steps. Modeling the processes separately in event- and time-space using linear constructs, and then coupling the two spaces, has accelerated the speed of simulation compared to a typical dynamic simulation. The ProdMod simulator models have been validated against operating data and other computer codes. Case studies have demonstrated the usefulness of the ProdMod simulator in developing strategies that demonstrate significant cost savings in operating the SRS HLW complex and in verifying the feasibility of newly proposed processes
Simulation of drift dynamics of arbitrary carrier distributions in complex semiconductor detectors
De Castro Manzano, Pablo
2014-01-01
An extensible open-source C++ software for the simulation of elec- trons and holes drift in semiconductor detectors of complex geometries has been developed in order to understand transient currents and charge collection efficiencies of arbitrary charge distributions. The simulation is based on Ramo’s theorem formalism to obtain induced currents in the electrodes. Efficient open source C++ numerical libraries are used to ob- tain the electric and weighting field using finite-element methods and to simulate the carrier transport. A graphical user interface is also provided. The tool has already been proved useful to model laser induced transient currents
Improvement of computer complex and interface system for compact nuclear simulator
International Nuclear Information System (INIS)
Lee, D. Y.; Park, W. M.; Cha, K. H.; Jung, C. H.; Park, J. C.
1999-01-01
CNS(Compact Nuclear Simulator) was developed at the end of 1980s, and have been used as training simulator for staffs of KAERI during 10 years. The operator panel interface cards and the graphic interface cards were designed with special purpose only for CNS. As these interface cards were worn out for 10 years, it was very difficult to get spare parts and to repair them. And the interface cards were damaged by over current happened by shortage of lamp in the operator panel. To solve these problem, the project 'Improvement of Compact Nuclear Simulator' was started from 1997. This paper only introduces about the improvement of computer complex and interface system
Simulation of complex detection systems in neutrinoless double beta decay experiments
International Nuclear Information System (INIS)
Larrea, A.; Morales, A.; Morales, J.; Nunez-Lagos, R.; Puimedon, J.; Villar, J.A.
1988-01-01
The estimated efficiency of several detection systems dedicated to the search of the neutrinoless double beta decay of 76 Ge is reported. In order to perform this work, we have developed the GEOM macro library system which can handle highly complex geometries in simulation problems, allowing to include an accurate description of the experimental setup in a very simple way. Also an internal mechanism for checking the correct location of every boundary defining the geometrical regions is included. The present version of GEOM is implemented in the EGS4 code of Monte Carlo simulation of photons and electron/positron showers, but it can be easily extended to other simulation codes. (orig.)
Directory of Open Access Journals (Sweden)
Heidi Koldsø
2014-10-01
Full Text Available Cell membranes are complex multicomponent systems, which are highly heterogeneous in the lipid distribution and composition. To date, most molecular simulations have focussed on relatively simple lipid compositions, helping to inform our understanding of in vitro experimental studies. Here we describe on simulations of complex asymmetric plasma membrane model, which contains seven different lipids species including the glycolipid GM3 in the outer leaflet and the anionic lipid, phosphatidylinositol 4,5-bisphophate (PIP2, in the inner leaflet. Plasma membrane models consisting of 1500 lipids and resembling the in vivo composition were constructed and simulations were run for 5 µs. In these simulations the most striking feature was the formation of nano-clusters of GM3 within the outer leaflet. In simulations of protein interactions within a plasma membrane model, GM3, PIP2, and cholesterol all formed favorable interactions with the model α-helical protein. A larger scale simulation of a model plasma membrane containing 6000 lipid molecules revealed correlations between curvature of the bilayer surface and clustering of lipid molecules. In particular, the concave (when viewed from the extracellular side regions of the bilayer surface were locally enriched in GM3. In summary, these simulations explore the nanoscale dynamics of model bilayers which mimic the in vivo lipid composition of mammalian plasma membranes, revealing emergent nanoscale membrane organization which may be coupled both to fluctuations in local membrane geometry and to interactions with proteins.
Towards socio-material approaches in simulation-based education: lessons from complexity theory.
Fenwick, Tara; Dahlgren, Madeleine Abrandt
2015-04-01
Review studies of simulation-based education (SBE) consistently point out that theory-driven research is lacking. The literature to date is dominated by discourses of fidelity and authenticity - creating the 'real' - with a strong focus on the developing of clinical procedural skills. Little of this writing incorporates the theory and research proliferating in professional studies more broadly, which show how professional learning is embodied, relational and situated in social - material relations. A key concern for medical educators concerns how to better prepare students for the unpredictable and dynamic ambiguity of professional practice; this has stimulated the movement towards socio-material theories in education that address precisely this question. Among the various socio-material theories that are informing new developments in professional education, complexity theory has been of particular importance for medical educators interested in updating current practices. This paper outlines key elements of complexity theory, illustrated with examples from empirical study, to argue its particular relevance for improving SBE. Complexity theory can make visible important material dynamics, and their problematic consequences, that are not often noticed in simulated experiences in medical training. It also offers conceptual tools that can be put to practical use. This paper focuses on concepts of emergence, attunement, disturbance and experimentation. These suggest useful new approaches for designing simulated settings and scenarios, and for effective pedagogies before, during and following simulation sessions. Socio-material approaches such as complexity theory are spreading through research and practice in many aspects of professional education across disciplines. Here, we argue for the transformative potential of complexity theory in medical education using simulation as our focus. Complexity tools open questions about the socio-material contradictions inherent in
Collaborative Management of Complex Major Construction Projects: AnyLogic-Based Simulation Modelling
Directory of Open Access Journals (Sweden)
Na Zhao
2016-01-01
Full Text Available Complex supply chain system collaborative management of major construction projects effectively integrates the different participants in the construction project. This paper establishes a simulation model based on AnyLogic to reveal the collaborative elements in the complex supply chain management system and the modes of action as well as the transmission problems of the intent information. Thus it is promoting the participants to become an organism with coordinated development and coevolution. This study can help improve the efficiency and management of the complex system of major construction projects.
Using multi-criteria analysis of simulation models to understand complex biological systems
Maureen C. Kennedy; E. David. Ford
2011-01-01
Scientists frequently use computer-simulation models to help solve complex biological problems. Typically, such models are highly integrated, they produce multiple outputs, and standard methods of model analysis are ill suited for evaluating them. We show how multi-criteria optimization with Pareto optimality allows for model outputs to be compared to multiple system...
Appreciating the Complexity of Project Management Execution: Using Simulation in the Classroom
Hartman, Nathan S.; Watts, Charles A.; Treleven, Mark D.
2013-01-01
As the popularity and importance of project management increase, so does the need for well-prepared project managers. This article discusses our experiences using a project management simulation in undergraduate and MBA classes to help students better grasp the complexity of project management. This approach gives students hands-on experience with…
Jiménez, P.A.; González-Rouco, J.F.; García-Bustamante, E.; Navarro, J.; Montávez, J.P.; Vilà-Guerau de Arellano, J.; Dudhia, J.; Muñoz-Roldan, A.
2010-01-01
This study analyzes the daily-mean surface wind variability over an area characterized by complex topography through comparing observations and a 2-km-spatial-resolution simulation performed with the Weather Research and Forecasting (WRF) model for the period 1992–2005. The evaluation focuses on the
Directory of Open Access Journals (Sweden)
Michael Deegan
2014-05-01
Full Text Available While public-sector management problems are steeped in positivistic and socially constructed complexity, public management education in the management of complexity lags behind that of business schools, particularly in the application of simulation-based learning. This paper describes a Simulation-Based Learning Environment for public management education that includes a coupled case study and System Dynamics simulation surrounding flood protection, a domain where stewardship decisions regarding public infrastructure and investment have direct and indirect effects on businesses and the public. The Pointe Claire case and CoastalProtectSIM simulation provide a platform for policy experimentation under conditions of exogenous uncertainty (weather and climate change as well as endogenous effects generated by structure. We discuss the model in some detail, and present teaching materials developed to date to support the use of our work in public administration curricula. Our experience with this case demonstrates the potential of this approach to motivate sustainable learning about complexity in public management settings and enhance learners’ competency to deal with complex dynamic problems.
An electromechanical based deformable model for soft tissue simulation.
Zhong, Yongmin; Shirinzadeh, Bijan; Smith, Julian; Gu, Chengfan
2009-11-01
Soft tissue deformation is of great importance to surgery simulation. Although a significant amount of research efforts have been dedicated to simulating the behaviours of soft tissues, modelling of soft tissue deformation is still a challenging problem. This paper presents a new deformable model for simulation of soft tissue deformation from the electromechanical viewpoint of soft tissues. Soft tissue deformation is formulated as a reaction-diffusion process coupled with a mechanical load. The mechanical load applied to a soft tissue to cause a deformation is incorporated into the reaction-diffusion system, and consequently distributed among mass points of the soft tissue. Reaction-diffusion of mechanical load and non-rigid mechanics of motion are combined to govern the simulation dynamics of soft tissue deformation. An improved reaction-diffusion model is developed to describe the distribution of the mechanical load in soft tissues. A three-layer artificial cellular neural network is constructed to solve the reaction-diffusion model for real-time simulation of soft tissue deformation. A gradient based method is established to derive internal forces from the distribution of the mechanical load. Integration with a haptic device has also been achieved to simulate soft tissue deformation with haptic feedback. The proposed methodology does not only predict the typical behaviours of living tissues, but it also accepts both local and large-range deformations. It also accommodates isotropic, anisotropic and inhomogeneous deformations by simple modification of diffusion coefficients.
Chou, S. C.; Zolino, M. M.; Gomes, J. L.; Bustamante, J. F.; Lima-e-Silva, P. P.
2012-04-01
The Eta Model is used operationally by CPTEC to produce weather forecasts over South America since 1997. The model has gone through upgrades. In order to prepare the model for operational higher resolution forecasts, the model is configured and tested over a region of complex topography located near the coast of Southeast Brazil. The Eta Model was configured, with 2-km horizontal resolution and 50 layers. The Eta-2km is a second nesting, it is driven by Eta-15km, which in its turn is driven by Era-Interim reanalyses. The model domain includes the two Brazilians cities, Rio de Janeiro and Sao Paulo, urban areas, preserved tropical forest, pasture fields, and complex terrain and coastline. Mountains can rise up to about 700m. The region suffers frequent events of floods and landslides. The objective of this work is to evaluate high resolution simulations of wind and temperature in this complex area. Verification of model runs uses observations taken from the nuclear power plant. Accurate near-surface wind direction and magnitude are needed for the plant emergency plan and winds are highly sensitive to model spatial resolution and atmospheric stability. Verification of two cases during summer shows that model has clear diurnal cycle signal for wind in that region. The area is characterized by weak winds which makes the simulation more difficult. The simulated wind magnitude is about 1.5m/s, which is close to observations of about 2m/s; however, the observed change of wind direction of the sea breeze is fast whereas it is slow in the simulations. Nighttime katabatic flow is captured by the simulations. Comparison against Eta-5km runs show that the valley circulation is better described in the 2-km resolution run. Simulated temperatures follow closely the observed diurnal cycle. Experiments improving some surface conditions such as the surface temperature and land cover show simulation error reduction and improved diurnal cycle.
Hu, Eric Y; Bouteiller, Jean-Marie C; Song, Dong; Baudry, Michel; Berger, Theodore W
2015-01-01
Chemical synapses are comprised of a wide collection of intricate signaling pathways involving complex dynamics. These mechanisms are often reduced to simple spikes or exponential representations in order to enable computer simulations at higher spatial levels of complexity. However, these representations cannot capture important nonlinear dynamics found in synaptic transmission. Here, we propose an input-output (IO) synapse model capable of generating complex nonlinear dynamics while maintaining low computational complexity. This IO synapse model is an extension of a detailed mechanistic glutamatergic synapse model capable of capturing the input-output relationships of the mechanistic model using the Volterra functional power series. We demonstrate that the IO synapse model is able to successfully track the nonlinear dynamics of the synapse up to the third order with high accuracy. We also evaluate the accuracy of the IO synapse model at different input frequencies and compared its performance with that of kinetic models in compartmental neuron models. Our results demonstrate that the IO synapse model is capable of efficiently replicating complex nonlinear dynamics that were represented in the original mechanistic model and provide a method to replicate complex and diverse synaptic transmission within neuron network simulations.
MacDonald, G; Mackenzie, J A; Nolan, M; Insall, R H
2016-03-15
In this paper, we devise a moving mesh finite element method for the approximate solution of coupled bulk-surface reaction-diffusion equations on an evolving two dimensional domain. Fundamental to the success of the method is the robust generation of bulk and surface meshes. For this purpose, we use a novel moving mesh partial differential equation (MMPDE) approach. The developed method is applied to model problems with known analytical solutions; these experiments indicate second-order spatial and temporal accuracy. Coupled bulk-surface problems occur frequently in many areas; in particular, in the modelling of eukaryotic cell migration and chemotaxis. We apply the method to a model of the two-way interaction of a migrating cell in a chemotactic field, where the bulk region corresponds to the extracellular region and the surface to the cell membrane.
International Nuclear Information System (INIS)
Abdelmalek, Salem; Kouachi, Said
2007-01-01
To prove global existence for solutions of m-component reaction-diffusion systems presents fundamental difficulties in the case in which some components of the system satisfy Neumann boundary conditions while others satisfy nonhomogeneous Dirichlet boundary conditions and nonhomogeneous Robin boundary conditions. The purpose of this paper is to prove the existence of a global solution using a single inequality for the polynomial growth condition of the reaction terms. Our technique is based on the construction of polynomial functionals. This result generalizes those obtained recently by Kouachi et al (at press), Kouachi (2002 Electron. J. Diff. Eqns 2002 1), Kouachi (2001 Electron. J. Diff. Eqns 2001 1) and independently by Malham and Xin (1998 Commun. Math. Phys. 193 287)
Energy Technology Data Exchange (ETDEWEB)
Yun, Sung Mi; Kang, Christina S. [Department of Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 143-701 (Korea, Republic of); Kim, Jonghwa [Department of Industrial Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 143-701 (Korea, Republic of); Kim, Han S., E-mail: hankim@konkuk.ac.kr [Department of Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 143-701 (Korea, Republic of)
2015-04-28
Highlights: • Remediation of complex contaminated soil achieved by sequential soil flushing. • Removal of Zn, Pb, and heavy petroleum oils using 0.05 M citric acid and 2% SDS. • Unified desorption distribution coefficients modeled and experimentally determined. • Nonequilibrium models for the transport behavior of complex contaminants in soils. - Abstract: The removal of heavy metals (Zn and Pb) and heavy petroleum oils (HPOs) from a soil with complex contamination was examined by soil flushing. Desorption and transport behaviors of the complex contaminants were assessed by batch and continuous flow reactor experiments and through modeling simulations. Flushing a one-dimensional flow column packed with complex contaminated soil sequentially with citric acid then a surfactant resulted in the removal of 85.6% of Zn, 62% of Pb, and 31.6% of HPO. The desorption distribution coefficients, K{sub Ubatch} and K{sub Lbatch}, converged to constant values as C{sub e} increased. An equilibrium model (ADR) and nonequilibrium models (TSNE and TRNE) were used to predict the desorption and transport of complex contaminants. The nonequilibrium models demonstrated better fits with the experimental values obtained from the column test than the equilibrium model. The ranges of K{sub Ubatch} and K{sub Lbatch} were very close to those of K{sub Ufit} and K{sub Lfit} determined from model simulations. The parameters (R, β, ω, α, and f) determined from model simulations were useful for characterizing the transport of contaminants within the soil matrix. The results of this study provide useful information for the operational parameters of the flushing process for soils with complex contamination.
Seirin Lee, S.
2010-03-23
Turing\\'s pattern formation mechanism exhibits sensitivity to the details of the initial conditions suggesting that, in isolation, it cannot robustly generate pattern within noisy biological environments. Nonetheless, secondary aspects of developmental self-organisation, such as a growing domain, have been shown to ameliorate this aberrant model behaviour. Furthermore, while in-situ hybridisation reveals the presence of gene expression in developmental processes, the influence of such dynamics on Turing\\'s model has received limited attention. Here, we novelly focus on the Gierer-Meinhardt reaction diffusion system considering delays due the time taken for gene expression, while incorporating a number of different domain growth profiles to further explore the influence and interplay of domain growth and gene expression on Turing\\'s mechanism. We find extensive pathological model behaviour, exhibiting one or more of the following: temporal oscillations with no spatial structure, a failure of the Turing instability and an extreme sensitivity to the initial conditions, the growth profile and the duration of gene expression. This deviant behaviour is even more severe than observed in previous studies of Schnakenberg kinetics on exponentially growing domains in the presence of gene expression (Gaffney and Monk in Bull. Math. Biol. 68:99-130, 2006). Our results emphasise that gene expression dynamics induce unrealistic behaviour in Turing\\'s model for multiple choices of kinetics and thus such aberrant modelling predictions are likely to be generic. They also highlight that domain growth can no longer ameliorate the excessive sensitivity of Turing\\'s mechanism in the presence of gene expression time delays. The above, extensive, pathologies suggest that, in the presence of gene expression, Turing\\'s mechanism would generally require a novel and extensive secondary mechanism to control reaction diffusion patterning. © 2010 Society for Mathematical Biology.
Energy Technology Data Exchange (ETDEWEB)
Paik, Joongcheol [University of Minnesota; Sotiropoulos, Fotis [University of Minnesota; Sale, Michael J [ORNL
2005-06-01
A numerical method is developed for carrying out unsteady Reynolds-averaged Navier-Stokes (URANS) simulations and detached-eddy simulations (DESs) in complex 3D geometries. The method is applied to simulate incompressible swirling flow in a typical hydroturbine draft tube, which consists of a strongly curved 90 degree elbow and two piers. The governing equations are solved with a second-order-accurate, finite-volume, dual-time-stepping artificial compressibility approach for a Reynolds number of 1.1 million on a mesh with 1.8 million nodes. The geometrical complexities of the draft tube are handled using domain decomposition with overset (chimera) grids. Numerical simulations show that unsteady statistical turbulence models can capture very complex 3D flow phenomena dominated by geometry-induced, large-scale instabilities and unsteady coherent structures such as the onset of vortex breakdown and the formation of the unsteady rope vortex downstream of the turbine runner. Both URANS and DES appear to yield the general shape and magnitude of mean velocity profiles in reasonable agreement with measurements. Significant discrepancies among the DES and URANS predictions of the turbulence statistics are also observed in the straight downstream diffuser.
de Vries, R
2004-02-15
Electrostatic complexation of flexible polyanions with the whey proteins alpha-lactalbumin and beta-lactoglobulin is studied using Monte Carlo simulations. The proteins are considered at their respective isoelectric points. Discrete charges on the model polyelectrolytes and proteins interact through Debye-Huckel potentials. Protein excluded volume is taken into account through a coarse-grained model of the protein shape. Consistent with experimental results, it is found that alpha-lactalbumin complexes much more strongly than beta-lactoglobulin. For alpha-lactalbumin, strong complexation is due to localized binding to a single large positive "charge patch," whereas for beta-lactoglobulin, weak complexation is due to diffuse binding to multiple smaller charge patches. Copyright 2004 American Institute of Physics
Directory of Open Access Journals (Sweden)
Y. Zhao
2017-06-01
Full Text Available Local line rolling forming is a common forming approach for the complex curvature plate of ships. However, the processing mode based on artificial experience is still applied at present, because it is difficult to integrally determine relational data for the forming shape, processing path, and process parameters used to drive automation equipment. Numerical simulation is currently the major approach for generating such complex relational data. Therefore, a highly precise and effective numerical computation method becomes crucial in the development of the automated local line rolling forming system for producing complex curvature plates used in ships. In this study, a three-dimensional elastoplastic finite element method was first employed to perform numerical computations for local line rolling forming, and the corresponding deformation and strain distribution features were acquired. In addition, according to the characteristics of strain distributions, a simplified deformation simulation method, based on the deformation obtained by applying strain was presented. Compared to the results of the three-dimensional elastoplastic finite element method, this simplified deformation simulation method was verified to provide high computational accuracy, and this could result in a substantial reduction in calculation time. Thus, the application of the simplified deformation simulation method was further explored in the case of multiple rolling loading paths. Moreover, it was also utilized to calculate the local line rolling forming for the typical complex curvature plate of ships. Research findings indicated that the simplified deformation simulation method was an effective tool for rapidly obtaining relationships between the forming shape, processing path, and process parameters.
Del Carpio R., Maikol; Hashemi, M. Javad; Mosqueda, Gilberto
2017-10-01
This study examines the performance of integration methods for hybrid simulation of large and complex structural systems in the context of structural collapse due to seismic excitations. The target application is not necessarily for real-time testing, but rather for models that involve large-scale physical sub-structures and highly nonlinear numerical models. Four case studies are presented and discussed. In the first case study, the accuracy of integration schemes including two widely used methods, namely, modified version of the implicit Newmark with fixed-number of iteration (iterative) and the operator-splitting (non-iterative) is examined through pure numerical simulations. The second case study presents the results of 10 hybrid simulations repeated with the two aforementioned integration methods considering various time steps and fixed-number of iterations for the iterative integration method. The physical sub-structure in these tests consists of a single-degree-of-freedom (SDOF) cantilever column with replaceable steel coupons that provides repeatable highlynonlinear behavior including fracture-type strength and stiffness degradations. In case study three, the implicit Newmark with fixed-number of iterations is applied for hybrid simulations of a 1:2 scale steel moment frame that includes a relatively complex nonlinear numerical substructure. Lastly, a more complex numerical substructure is considered by constructing a nonlinear computational model of a moment frame coupled to a hybrid model of a 1:2 scale steel gravity frame. The last two case studies are conducted on the same porotype structure and the selection of time steps and fixed number of iterations are closely examined in pre-test simulations. The generated unbalance forces is used as an index to track the equilibrium error and predict the accuracy and stability of the simulations.
GPU-accelerated depth map generation for X-ray simulations of complex CAD geometries
Grandin, Robert J.; Young, Gavin; Holland, Stephen D.; Krishnamurthy, Adarsh
2018-04-01
Interactive x-ray simulations of complex computer-aided design (CAD) models can provide valuable insights for better interpretation of the defect signatures such as porosity from x-ray CT images. Generating the depth map along a particular direction for the given CAD geometry is the most compute-intensive step in x-ray simulations. We have developed a GPU-accelerated method for real-time generation of depth maps of complex CAD geometries. We preprocess complex components designed using commercial CAD systems using a custom CAD module and convert them into a fine user-defined surface tessellation. Our CAD module can be used by different simulators as well as handle complex geometries, including those that arise from complex castings and composite structures. We then make use of a parallel algorithm that runs on a graphics processing unit (GPU) to convert the finely-tessellated CAD model to a voxelized representation. The voxelized representation can enable heterogeneous modeling of the volume enclosed by the CAD model by assigning heterogeneous material properties in specific regions. The depth maps are generated from this voxelized representation with the help of a GPU-accelerated ray-casting algorithm. The GPU-accelerated ray-casting method enables interactive (> 60 frames-per-second) generation of the depth maps of complex CAD geometries. This enables arbitrarily rotation and slicing of the CAD model, leading to better interpretation of the x-ray images by the user. In addition, the depth maps can be used to aid directly in CT reconstruction algorithms.
Stinchcombe, Arne; Gagnon, Sylvain; Zhang, J Jane; Montembeault, Patricia; Bedard, Michel
2011-12-01
The purpose of the study was to explore age differences in attentional demand in response to driving situations of varying complexity within the context of a simulated assessment protocol. It was hypothesized that as road complexity increased, an indicator of attentional demand (i.e., latency to respond to a secondary task) would increase and, independent of the road complexity, older adults would exhibit greater attentional demand in comparison with younger and middle-aged drivers. Drivers from 3 age categories (i.e., young, middle-aged, and older) completed an assessment protocol in a STISIM driving simulator (Systems Technology, Inc., Hawthorne, CA) during which participants responded to a series of strategically placed secondary tasks (i.e., peripheral detection tasks, PDTs). Situations where secondary tasks occurred were grouped according to whether they were straight-road, crossing-path, or lane-change events. Two global indices of driving safety as well as several cognitive measures external to the driving simulator were also collected. The results supported the hypothesis in that complex driving situations elicited greater attentional demand among drivers of all ages. Older adults showed greater attentional demand in comparison to young and middle-aged adults even after controlling for baseline response time. Older drivers also scored poorer on a global measure of driving safety. The findings are highly consistent with the literature on road complexity and attention that show that increased driving complexity is associated with poorer performance on tasks designed to concurrently assess attention, an effect that is more pronounced for older drivers. The results point to intrinsic and extrinsic factors that contribute to motor vehicle collisions (MVCs) among older drivers. The relevance of these findings is discussed in relation to interventions and future research aimed at improving road safety.
International Nuclear Information System (INIS)
Tahvili, Sahar; Österberg, Jonas; Silvestrov, Sergei; Biteus, Jonas
2014-01-01
One of the most important factors in the operations of many cooperations today is to maximize profit and one important tool to that effect is the optimization of maintenance activities. Maintenance activities is at the largest level divided into two major areas, corrective maintenance (CM) and preventive maintenance (PM). When optimizing maintenance activities, by a maintenance plan or policy, we seek to find the best activities to perform at each point in time, be it PM or CM. We explore the use of stochastic simulation, genetic algorithms and other tools for solving complex maintenance planning optimization problems in terms of a suggested framework model based on discrete event simulation
Directory of Open Access Journals (Sweden)
Salvatore Butticè
2014-05-01
Full Text Available Xanthogranulomatous pyelonephritis is a rare and peculiar form of chronic pyelonephritis and is generally associated with renal lithiasis. Its incidence is higher in females. The peculiarity of this disease is that it requires a differential diagnosis, because it can often simulate dramatic pathologic conditions. In fact, in the literature are also described cases in association with squamous cell carcinoma of the kidney The radiologic clinical findings simulate renal masses, sometimes in association with caval thrombus. We describe a case of xanthogranulomatous pyelonephritis with radiologic aspects of a complex cyst of Bosniak class III in a man 40-year old.
Fast and Low-Complexity Simulations of the Inquiry Time in Bluetooth
DEFF Research Database (Denmark)
Figueiras, Joao; Schwefel, Hans-Peter
2006-01-01
The timing behavior of the Inquiry Procedure in Bluetooth is relevant for several important functionalities, in particular topology formation and localization. The detailed Inquiry procedure is rather complex and simulation models may become inefficient if they implement the full detailed...... specification. This paper presents an abstracted model to approximate the distribution of Bluetooth inquiry time for scenarios in which multiple Bluetooth nodes perform the inquiry procedure. The abstracted model leads to a simple algorithm which can be used in simulation models to generate samples from...
Mizell, Carolyn; Malone, Linda
2007-01-01
It is very difficult for project managers to develop accurate cost and schedule estimates for large, complex software development projects. None of the approaches or tools available today can estimate the true cost of software with any high degree of accuracy early in a project. This paper provides an approach that utilizes a software development process simulation model that considers and conveys the level of uncertainty that exists when developing an initial estimate. A NASA project will be analyzed using simulation and data from the Software Engineering Laboratory to show the benefits of such an approach.
Energy Technology Data Exchange (ETDEWEB)
Tahvili, Sahar [Mälardalen University (Sweden); Österberg, Jonas; Silvestrov, Sergei [Division of Applied Mathematics, Mälardalen University (Sweden); Biteus, Jonas [Scania CV (Sweden)
2014-12-10
One of the most important factors in the operations of many cooperations today is to maximize profit and one important tool to that effect is the optimization of maintenance activities. Maintenance activities is at the largest level divided into two major areas, corrective maintenance (CM) and preventive maintenance (PM). When optimizing maintenance activities, by a maintenance plan or policy, we seek to find the best activities to perform at each point in time, be it PM or CM. We explore the use of stochastic simulation, genetic algorithms and other tools for solving complex maintenance planning optimization problems in terms of a suggested framework model based on discrete event simulation.
Marsh, C.; Pomeroy, J. W.; Wheater, H. S.
2017-12-01
Accurate management of water resources is necessary for social, economic, and environmental sustainability worldwide. In locations with seasonal snowcovers, the accurate prediction of these water resources is further complicated due to frozen soils, solid-phase precipitation, blowing snow transport, and snowcover-vegetation-atmosphere interactions. Complex process interactions and feedbacks are a key feature of hydrological systems and may result in emergent phenomena, i.e., the arising of novel and unexpected properties within a complex system. One example is the feedback associated with blowing snow redistribution, which can lead to drifts that cause locally-increased soil moisture, thus increasing plant growth that in turn subsequently impacts snow redistribution, creating larger drifts. Attempting to simulate these emergent behaviours is a significant challenge, however, and there is concern that process conceptualizations within current models are too incomplete to represent the needed interactions. An improved understanding of the role of emergence in hydrological systems often requires high resolution distributed numerical hydrological models that incorporate the relevant process dynamics. The Canadian Hydrological Model (CHM) provides a novel tool for examining cold region hydrological systems. Key features include efficient terrain representation, allowing simulations at various spatial scales, reduced computational overhead, and a modular process representation allowing for an alternative-hypothesis framework. Using both physics-based and conceptual process representations sourced from long term process studies and the current cold regions literature allows for comparison of process representations and importantly, their ability to produce emergent behaviours. Examining the system in a holistic, process-based manner can hopefully derive important insights and aid in development of improved process representations.
Complex of electrostatic accelerators for simulation and diagnostics of radiation damage
International Nuclear Information System (INIS)
Antuf'ev, Yu.P.; Belyaev, V.Kh.; Vergunov, A.D.
1983-01-01
The installation for simulation and diagnostics of radiation damage of materials is described. The installation consists of two electrostatic accelerators of vertical type for 5 MV and horizontal type for 800 kV. The accelerating complex ensures accelerated ion beam production in the independent operation regime as well as in the two beams target simultaneous irradiation regime, energy range of accelerated single-charged ions is 80 keV ... 5 MeV, homogeneity is better than +-0.05%. Oilless vacuum pumping out system is realized at the accelerating complex
Deposition Velocities of Non-Newtonian Slurries in Pipelines: Complex Simulant Testing
Energy Technology Data Exchange (ETDEWEB)
Poloski, Adam P.; Bonebrake, Michael L.; Casella, Andrew M.; Johnson, Michael D.; Toth, James J.; Adkins, Harold E.; Chun, Jaehun; Denslow, Kayte M.; Luna, Maria; Tingey, Joel M.
2009-07-01
) was performed at each yield stress condition. Unlike the previous simulant, the sizes and densities of the particles that can deposit in the piping are a result of the simulant precipitation process; there is expected to be a complex mixture of particles of various sizes and densities that make it difficult to predict a stability map. The objective of the testing is to observe whether behavior consistent with the stability-map concept occurs in complex simulants with mixtures of different sizes and densities.
A novel approach to simulate gene-environment interactions in complex diseases
Directory of Open Access Journals (Sweden)
Nicodemi Mario
2010-01-01
Full Text Available Abstract Background Complex diseases are multifactorial traits caused by both genetic and environmental factors. They represent the major part of human diseases and include those with largest prevalence and mortality (cancer, heart disease, obesity, etc.. Despite a large amount of information that has been collected about both genetic and environmental risk factors, there are few examples of studies on their interactions in epidemiological literature. One reason can be the incomplete knowledge of the power of statistical methods designed to search for risk factors and their interactions in these data sets. An improvement in this direction would lead to a better understanding and description of gene-environment interactions. To this aim, a possible strategy is to challenge the different statistical methods against data sets where the underlying phenomenon is completely known and fully controllable, for example simulated ones. Results We present a mathematical approach that models gene-environment interactions. By this method it is possible to generate simulated populations having gene-environment interactions of any form, involving any number of genetic and environmental factors and also allowing non-linear interactions as epistasis. In particular, we implemented a simple version of this model in a Gene-Environment iNteraction Simulator (GENS, a tool designed to simulate case-control data sets where a one gene-one environment interaction influences the disease risk. The main aim has been to allow the input of population characteristics by using standard epidemiological measures and to implement constraints to make the simulator behaviour biologically meaningful. Conclusions By the multi-logistic model implemented in GENS it is possible to simulate case-control samples of complex disease where gene-environment interactions influence the disease risk. The user has full control of the main characteristics of the simulated population and a Monte
De Lucia, Marco; Kempka, Thomas; Jatnieks, Janis; Kühn, Michael
2017-04-01
.: "Flexible Simulation Framework to Couple Processes in Complex 3D Models for Subsurface Utilization Assessment.", Energy Procedia, 97, 2016 p. 494-501.
Rahman Prize Lecture: Lattice Boltzmann simulation of complex states of flowing matter
Succi, Sauro
Over the last three decades, the Lattice Boltzmann (LB) method has gained a prominent role in the numerical simulation of complex flows across an impressively broad range of scales, from fully-developed turbulence in real-life geometries, to multiphase flows in micro-fluidic devices, all the way down to biopolymer translocation in nanopores and lately, even quark-gluon plasmas. After a brief introduction to the main ideas behind the LB method and its historical developments, we shall present a few selected applications to complex flow problems at various scales of motion. Finally, we shall discuss prospects for extreme-scale LB simulations of outstanding problems in the physics of fluids and its interfaces with material sciences and biology, such as the modelling of fluid turbulence, the optimal design of nanoporous gold catalysts and protein folding/aggregation in crowded environments.
3-D FDTD simulation of shear waves for evaluation of complex modulus imaging.
Orescanin, Marko; Wang, Yue; Insana, Michael
2011-02-01
The Navier equation describing shear wave propagation in 3-D viscoelastic media is solved numerically with a finite differences time domain (FDTD) method. Solutions are formed in terms of transverse scatterer velocity waves and then verified via comparison to measured wave fields in heterogeneous hydrogel phantoms. The numerical algorithm is used as a tool to study the effects on complex shear modulus estimation from wave propagation in heterogeneous viscoelastic media. We used an algebraic Helmholtz inversion (AHI) technique to solve for the complex shear modulus from simulated and experimental velocity data acquired in 2-D and 3-D. Although 3-D velocity estimates are required in general, there are object geometries for which 2-D inversions provide accurate estimations of the material properties. Through simulations and experiments, we explored artifacts generated in elastic and dynamic-viscous shear modulus images related to the shear wavelength and average viscosity.
Examination of Level Crossings on ETCS Equipped Lines with Complex Simulation
Bela Vincze; Geza Tarnai
2004-01-01
Because of the lack of former experiences with the new ETCS system, several experiments and tests have to be carried out with various technologies before any installation. For such a new system, it is also very important to have well documented test results of the existing installations for further designing or demonstational purposes. This paper driefly describes a complex simulation tool, which has been developed in in order fulfill these demands, and a study concerning with a particular ET...
PANTHERE, simulation software of dose flow rates for complex nuclear installations
International Nuclear Information System (INIS)
Longeot, M.; Dupont, B.; Coatanea, C.; Schumm, S.; Zweers, M.; Malvagi, F.; Trama, J.C.
2010-01-01
The authors present the PANTHERE simulation software developed by EDF-SEPTEN to determine gamma dose flow rate in any point of complex industrial installations. They present the current industrial version (PANTHEREV1) and its different applications, and more particularly an investigation in the field of qualification of hardware under irradiation in case of severe accident. They present the currently under development version (PANTHEREV2) which will be exploited in 2011
Brand, Bethany L; Webermann, Aliya R; Frankel, A Steven
Few assessors receive training in assessing dissociation and complex dissociative disorders (DDs). Potential differential diagnoses include anxiety, mood, psychotic, substance use, and personality disorders, as well as exaggeration and malingering. Individuals with DDs typically elevate on many clinical and validity scales on psychological tests, yet research indicates that they can be distinguished from DD simulators. Becoming informed about the testing profiles of DD individuals and DD simulators can improve the accuracy of differential diagnoses in forensic settings. In this paper, we first review the testing profiles of individuals with complex DDs and contrast them with DD simulators on assessment measures used in forensic contexts, including the Minnesota Multiphasic Personality Inventory-2 (MMPI-2), Personality Assessment Inventory (PAI), and the Structured Inventory of Reported Symptoms (SIRS), as well as dissociation-specific measures such as the Dissociative Experiences Scale (DES) and Structured Clinical Interview for DSM-IV Dissociative Disorders (SCID-D-R). We then provide recommendations for assessing complex trauma and dissociation through the aforementioned assessments. Copyright © 2016 Elsevier Ltd. All rights reserved.
A dynamic simulation model of the Savannah River Site high level waste complex
International Nuclear Information System (INIS)
Gregory, M.V.; Aull, J.E.; Dimenna, R.A.
1994-01-01
A detailed, dynamic simulation entire high level radioactive waste complex at the Savannah River Site has been developed using SPEEDUP(tm) software. The model represents mass transfer, evaporation, precipitation, sludge washing, effluent treatment, and vitrification unit operation processes through the solution of 7800 coupled differential and algebraic equations. Twenty-seven discrete chemical constituents are tracked through the unit operations. The simultaneous simultaneous simulation of concurrent batch and continuous processes is achieved by several novel, customized SPEEDUP(tm) algorithms. Due to the model's computational burden, a high-end work station is required: simulation of a years operation of the complex requires approximately three CPU hours on an IBM RS/6000 Model 590 processor. The model will be used to develop optimal high level waste (HLW) processing strategies over a thirty year time horizon. It will be employed to better understand the dynamic inter-relationships between different HLW unit operations, and to suggest strategies that will maximize available working tank space during the early years of operation and minimize overall waste processing cost over the long-term history of the complex. Model validation runs are currently underway with comparisons against actual plant operating data providing an excellent match
Chemodynamics of EDTA in a simulated mixed waste: the Hanford Site's complex concentrate waste
International Nuclear Information System (INIS)
Toste, A.P.; Ohnuki, Toshihiko
1999-01-01
Enormous stockpiles of mixed wastes at the USDOE's Hanford Site, the original US plutonium production facility, await permanent disposal. One mixed waste derived from reprocessing spent fuel was found to contain numerous nuclear related organics including chelating agents like EDTA and complexing agents, which have been used as decontamination agents, etc. Their presence in actual mixed wastes indicates that the organic content of nuclear wastes is dynamic and complicate waste management efforts. The subjects of this report is the chemo-degradation of EDTA degradation in a simulant Hanford's complex concentrate waste. The simulant was prepared by adding EDTA to an inorganic matrix, which was formulated based on past analyses of the actual waste. Aliquots of the EDTA simulant were withdrawn at different time points, derivatized via methylation and analyzed by gas chromatography and Gc/MS to monitor the disappearance of EDTA and the appearance of its' degradation products. This report also compares the results of EDTA's chemo-degradation to the g-radiolysis of EDTA in the simulant, the subject of a recently published article. Finally based on the results of these two studies, an assesment of the potential impact of EDTA degradation on the management of mixed wastes is offered. (J.P.N.)
Hettinger, Lawrence J.; Kirlik, Alex; Goh, Yang Miang; Buckle, Peter
2015-01-01
Accurate comprehension and analysis of complex sociotechnical systems is a daunting task. Empirically examining, or simply envisioning the structure and behaviour of such systems challenges traditional analytic and experimental approaches as well as our everyday cognitive capabilities. Computer-based models and simulations afford potentially useful means of accomplishing sociotechnical system design and analysis objectives. From a design perspective, they can provide a basis for a common mental model among stakeholders, thereby facilitating accurate comprehension of factors impacting system performance and potential effects of system modifications. From a research perspective, models and simulations afford the means to study aspects of sociotechnical system design and operation, including the potential impact of modifications to structural and dynamic system properties, in ways not feasible with traditional experimental approaches. This paper describes issues involved in the design and use of such models and simulations and describes a proposed path forward to their development and implementation. Practitioner Summary: The size and complexity of real-world sociotechnical systems can present significant barriers to their design, comprehension and empirical analysis. This article describes the potential advantages of computer-based models and simulations for understanding factors that impact sociotechnical system design and operation, particularly with respect to process and occupational safety. PMID:25761227
A novel approach for modelling complex maintenance systems using discrete event simulation
International Nuclear Information System (INIS)
Alrabghi, Abdullah; Tiwari, Ashutosh
2016-01-01
Existing approaches for modelling maintenance rely on oversimplified assumptions which prevent them from reflecting the complexity found in industrial systems. In this paper, we propose a novel approach that enables the modelling of non-identical multi-unit systems without restrictive assumptions on the number of units or their maintenance characteristics. Modelling complex interactions between maintenance strategies and their effects on assets in the system is achieved by accessing event queues in Discrete Event Simulation (DES). The approach utilises the wide success DES has achieved in manufacturing by allowing integration with models that are closely related to maintenance such as production and spare parts systems. Additional advantages of using DES include rapid modelling and visual interactive simulation. The proposed approach is demonstrated in a simulation based optimisation study of a published case. The current research is one of the first to optimise maintenance strategies simultaneously with their parameters while considering production dynamics and spare parts management. The findings of this research provide insights for non-conflicting objectives in maintenance systems. In addition, the proposed approach can be used to facilitate the simulation and optimisation of industrial maintenance systems. - Highlights: • This research is one of the first to optimise maintenance strategies simultaneously. • New insights for non-conflicting objectives in maintenance systems. • The approach can be used to optimise industrial maintenance systems.
Directory of Open Access Journals (Sweden)
Joshua Rodewald
2016-10-01
Full Text Available Supply networks existing today in many industries can behave as complex adaptive systems making them more difficult to analyze and assess. Being able to fully understand both the complex static and dynamic structures of a complex adaptive supply network (CASN are key to being able to make more informed management decisions and prioritize resources and production throughout the network. Previous efforts to model and analyze CASN have been impeded by the complex, dynamic nature of the systems. However, drawing from other complex adaptive systems sciences, information theory provides a model-free methodology removing many of those barriers, especially concerning complex network structure and dynamics. With minimal information about the network nodes, transfer entropy can be used to reverse engineer the network structure while local transfer entropy can be used to analyze the network structure’s dynamics. Both simulated and real-world networks were analyzed using this methodology. Applying the methodology to CASNs allows the practitioner to capitalize on observations from the highly multidisciplinary field of information theory which provides insights into CASN’s self-organization, emergence, stability/instability, and distributed computation. This not only provides managers with a more thorough understanding of a system’s structure and dynamics for management purposes, but also opens up research opportunities into eventual strategies to monitor and manage emergence and adaption within the environment.
Modeling and Simulation of Project Management through the PMBOK® Standard Using Complex Networks
Directory of Open Access Journals (Sweden)
Luz Stella Cardona-Meza
2017-01-01
Full Text Available Discussion about project management, in both the academic literature and industry, is predominantly based on theories of control, many of which have been developed since the 1950s. However, issues arise when these ideas are applied unilaterally to all types of projects and in all contexts. In complex environments, management problems arise from assuming that results, predicted at the start of a project, can be sufficiently described and delivered as planned. Thus, once a project reaches a critical size, a calendar, and a certain level of ambiguity and interconnection, the analysis centered on control does not function adequately. Projects that involve complex situations can be described as adaptive complex systems, consistent in multiple interdependent dynamic components, multiple feedback processes, nonlinear relations, and management of hard data (process dynamics and soft data (executive team dynamics. In this study, through a complex network, the dynamic structure of a project and its trajectories are simulated using inference processes. Finally, some numerical simulations are described, leading to a decision making tool that identifies critical processes, thereby obtaining better performance outcomes of projects.
FACET: A simulation software framework for modeling complex societal processes and interactions
Energy Technology Data Exchange (ETDEWEB)
Christiansen, J. H.
2000-06-02
FACET, the Framework for Addressing Cooperative Extended Transactions, was developed at Argonne National Laboratory to address the need for a simulation software architecture in the style of an agent-based approach, but with sufficient robustness, expressiveness, and flexibility to be able to deal with the levels of complexity seen in real-world social situations. FACET is an object-oriented software framework for building models of complex, cooperative behaviors of agents. It can be used to implement simulation models of societal processes such as the complex interplay of participating individuals and organizations engaged in multiple concurrent transactions in pursuit of their various goals. These transactions can be patterned on, for example, clinical guidelines and procedures, business practices, government and corporate policies, etc. FACET can also address other complex behaviors such as biological life cycles or manufacturing processes. To date, for example, FACET has been applied to such areas as land management, health care delivery, avian social behavior, and interactions between natural and social processes in ancient Mesopotamia.
Large eddy simulation modeling of particle-laden flows in complex terrain
Salesky, S.; Giometto, M. G.; Chamecki, M.; Lehning, M.; Parlange, M. B.
2017-12-01
The transport, deposition, and erosion of heavy particles over complex terrain in the atmospheric boundary layer is an important process for hydrology, air quality forecasting, biology, and geomorphology. However, in situ observations can be challenging in complex terrain due to spatial heterogeneity. Furthermore, there is a need to develop numerical tools that can accurately represent the physics of these multiphase flows over complex surfaces. We present a new numerical approach to accurately model the transport and deposition of heavy particles in complex terrain using large eddy simulation (LES). Particle transport is represented through solution of the advection-diffusion equation including terms that represent gravitational settling and inertia. The particle conservation equation is discretized in a cut-cell finite volume framework in order to accurately enforce mass conservation. Simulation results will be validated with experimental data, and numerical considerations required to enforce boundary conditions at the surface will be discussed. Applications will be presented in the context of snow deposition and transport, as well as urban dispersion.
Preoperative surgical planning and simulation of complex cranial base tumors in virtual reality
Institute of Scientific and Technical Information of China (English)
YI Zhi-qiang; LI Liang; MO Da-peng; ZHANG Jia-yong; ZHANG Yang; BAO Sheng-de
2008-01-01
@@ The extremely complex anatomic relationships among bone,tumor,blood vessels and cranial nerves remains a big challenge for cranial base tumor surgery.Therefore.a good understanding of the patient specific anatomy and a preoperative planning are helpful and crocial for the neurosurgeons.Three dimensional (3-D) visualization of various imaging techniques have been widely explored to enhance the comprehension of volumetric data for surgical planning.1 We used the Destroscope Virtual Reality (VR) System (Singapore,Volume Interaction Pte Ltd,software:RadioDexterTM 1.0) to optimize preoperative plan in the complex cranial base tumors.This system uses patient-specific,coregistered,fused radiology data sets that may be viewed stereoscopically and can be manipulated in a virtual reality environment.This article describes our experience with the Destroscope VR system in preoperative surgical planning and simulation for 5 patients with complex cranial base tumors and evaluates the clinical usefulness of this system.
Jain, Vaibhav; Maiti, Prabal K.; Bharatam, Prasad V.
2016-09-01
Computational studies performed on dendrimer-drug complexes usually consider 1:1 stoichiometry, which is far from reality, since in experiments more number of drug molecules get encapsulated inside a dendrimer. In the present study, molecular dynamic (MD) simulations were implemented to characterize the more realistic molecular models of dendrimer-drug complexes (1:n stoichiometry) in order to understand the effect of high drug loading on the structural properties and also to unveil the atomistic level details. For this purpose, possible inclusion complexes of model drug Nateglinide (Ntg) (antidiabetic, belongs to Biopharmaceutics Classification System class II) with amine- and acetyl-terminated G4 poly(amidoamine) (G4 PAMAM(NH2) and G4 PAMAM(Ac)) dendrimers at neutral and low pH conditions are explored in this work. MD simulation analysis on dendrimer-drug complexes revealed that the drug encapsulation efficiency of G4 PAMAM(NH2) and G4 PAMAM(Ac) dendrimers at neutral pH was 6 and 5, respectively, while at low pH it was 12 and 13, respectively. Center-of-mass distance analysis showed that most of the drug molecules are located in the interior hydrophobic pockets of G4 PAMAM(NH2) at both the pH; while in the case of G4 PAMAM(Ac), most of them are distributed near to the surface at neutral pH and in the interior hydrophobic pockets at low pH. Structural properties such as radius of gyration, shape, radial density distribution, and solvent accessible surface area of dendrimer-drug complexes were also assessed and compared with that of the drug unloaded dendrimers. Further, binding energy calculations using molecular mechanics Poisson-Boltzmann surface area approach revealed that the location of drug molecules in the dendrimer is not the decisive factor for the higher and lower binding affinity of the complex, but the charged state of dendrimer and drug, intermolecular interactions, pH-induced conformational changes, and surface groups of dendrimer do play an
Gamble, Andree S
2017-03-01
Simulation in health education has been shown to increase confidence, psychomotor and professional skills, and thus positively impact on student preparedness for clinical placement. It is recognised as a valuable tool to expose and engage students in realistic patient care encounters without the potential to cause patient harm. Although inherent challenges exist in the development and implementation of simulation, variability in clinical placement time, availability and quality dictates the need to provide students with learning opportunities they may otherwise not experience. With this, and a myriad of other issues providing the impetus for improved clinical preparation, 28 final semester undergraduate nursing students in a paediatric nursing course were involved in an extended multi-scenario simulated clinical shift prior to clinical placement. The simulation focussed on a complex ward experience, giving students the opportunity to demonstrate a variety of psychomotor skills, decision making, leadership, team work and other professional attributes integral for successful transition into the clinical arena. Evaluation data were collected at 3 intermittent points; post-simulation, post clinical placement, and 3 months after commencing employment as a Registered Nurse. Quantitative and qualitative analysis suggested positive impacts on critical nursing concepts and psychomotor skills resulted for participants in both clinical placement and beyond into the first months of employment. Copyright © 2017 Elsevier Ltd. All rights reserved.
Energy Technology Data Exchange (ETDEWEB)
Potter, Kristin C [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Brunhart-Lupo, Nicholas J [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Bush, Brian W [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Gruchalla, Kenny M [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Bugbee, Bruce [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Krishnan, Venkat K [National Renewable Energy Laboratory (NREL), Golden, CO (United States)
2017-10-09
We have developed a framework for the exploration, design, and planning of energy systems that combines interactive visualization with machine-learning based approximations of simulations through a general purpose dataflow API. Our system provides a visual inter- face allowing users to explore an ensemble of energy simulations representing a subset of the complex input parameter space, and spawn new simulations to 'fill in' input regions corresponding to new enegery system scenarios. Unfortunately, many energy simula- tions are far too slow to provide interactive responses. To support interactive feedback, we are developing reduced-form models via machine learning techniques, which provide statistically sound esti- mates of the full simulations at a fraction of the computational cost and which are used as proxies for the full-form models. Fast com- putation and an agile dataflow enhance the engagement with energy simulations, and allow researchers to better allocate computational resources to capture informative relationships within the system and provide a low-cost method for validating and quality-checking large-scale modeling efforts.
Simulation of tracer dispersion from elevated and surface releases in complex terrain
Hernández, J. F.; Cremades, L.; Baldasano, J. M.
A new version of an advanced mesoscale dispersion modeling system for simulating passive air pollutant dispersion in the real atmospheric planetary boundary layer (PBL), is presented. The system comprises a diagnostic mass-consistent meteorological model and a Lagrangian particle dispersion model (LADISMO). The former version of LADISMO, developed according to Zannetti (Air pollution modelling, 1990), was based on the Monte Carlo technique and included calculation of higher-order moments of vertical random forcing for convective conditions. Its ability to simulate complex flow dispersion has been stated in a previous paper (Hernández et al. 1995, Atmospheric Environment, 29A, 1331-1341). The new version follows Thomson's scheme (1984, Q. Jl Roy. Met. Soc.110, 1107-1120). It is also based on Langevin equation and follows the ideas given by Brusasca et al. (1992, Atmospheric Environment26A, 707-723) and Anfossi et al. (1992, Nuovo Cemento 15c, 139-158). The model is used to simulate the dispersion and predict the ground level concentration (g.l.c.) of a tracer (SF 6) released from both an elevated source ( case a) and a ground level source ( case b) in a highly complex mountainous terrain during neutral and synoptically dominated conditions ( case a) and light and apparently stable conditions ( case b). The last case is considered as being a specially difficult task to simulate. In fact, few works have reported situations with valley drainage flows in complex terrains and real stable atmospheric conditions with weak winds. The model assumes that nearly calm situations associated to strong stability and air stagnation, make the lowest layers of PBL poorly diffusive (Brusasca et al., 1992, Atmospheric Environment26A, 707-723). Model results are verified against experimental data from Guardo-90 tracer experiments, an intensive field campaign conducted in the Carrion river valley (Northern Spain) to study atmospheric diffusion within a steep walled valley in mountainous
Simulation of 125I-induced DNA strand breaks in a CAP-DNA complex
International Nuclear Information System (INIS)
Li, W.; Friedland, W.; Jacob, P.
2000-01-01
DNA strand breakage induced by decay of 125 I incorporated into the pyrimidine of a small piece of DNA with a specific base pair sequence has been investigated theoretically and experimentally (Lobachevsky and Martin 2000a, 2000b; Nikjoo et al., 1996; Pomplun and Terrissol, 1994; Charlton and Humm, 1988). Recently an attempt was made to analyse the DNA kinks in a CAP-DNA complex with 125 I induced DNA strand breakage (Karamychev et al., 1999). This method could be used as a so called radioprobing for such DNa distortions like other chemical and biological assays, provided that it has been tested and confirmed in a corresponding theoretical simulation. In the measurement, the distribution of the first breaks on the DNA strands starting from their labeled end can be determined. Based on such first breakage distributions, the simulation calculation could then be used to derive information on the structure of a given DNA-protein complex. The biophysical model PARTRAC has been applied successfully in simulating DNA damage induced by irradiation (Friedland et al., 1998; 1999). In the present study PARTRAC is adapted to a DNA-protein complex in which a specific sequence of 30 base pairs of DNA is connected with the catabolite gene activator protein (CAP). This report presents the first step of the analysis in which the CAP-DNA model used in NIH is overlaid with electron track structures in liquid water and the strand breaks due to direct ionization and due to radical attack are simulated. The second step will be to take into account the neutralization of the heavily charged tellurium and the protective effect of the CAP protein against radical attack. (orig.)
Wang, Wei; Huang, Li; Liang, Xuedong
2018-01-06
This paper investigates the reliability of complex emergency logistics networks, as reliability is crucial to reducing environmental and public health losses in post-accident emergency rescues. Such networks' statistical characteristics are analyzed first. After the connected reliability and evaluation indices for complex emergency logistics networks are effectively defined, simulation analyses of network reliability are conducted under two different attack modes using a particular emergency logistics network as an example. The simulation analyses obtain the varying trends in emergency supply times and the ratio of effective nodes and validates the effects of network characteristics and different types of attacks on network reliability. The results demonstrate that this emergency logistics network is both a small-world and a scale-free network. When facing random attacks, the emergency logistics network steadily changes, whereas it is very fragile when facing selective attacks. Therefore, special attention should be paid to the protection of supply nodes and nodes with high connectivity. The simulation method provides a new tool for studying emergency logistics networks and a reference for similar studies.
International Nuclear Information System (INIS)
Toste, A.P.; Osborn, B.C.; Polach, K.J.; Lechner-Fish, T.J.
1995-01-01
Reanalysis of the organics in a mixed waste, an organic complexant waste, from the U.S. Department of Energy's Hanford Site, has yielded an 80.4% accounting of the waste's total organic content. In addition to several complexing and chelating agents (citrate, EDTA, HEDTA and NTA), 38 chelator/complexor fragments have been identified, compared to only 11 in the original analysis, all presumably formed via organic degradation. Moreover, a mis identification, methanetricarboxylic acid, has been re-identified as the chelator fragment N-(methylamine)imino-diacetic acid (MAIDA). A nonradioactive simulant of the actual waste, containing the parent organics (citrate, EDTA, HEDTA and NTA), was formulated and stored in the dark at ambient temperature for 90 days. Twenty chelator and complexor fragments were identified in the simulant, along with several carboxylic acids, confirming that myriad chelator and complexor fragments are formed via degradation of the parent organics. Moreover, their abundance in the simulant (60.9% of the organics identified) argues that the harsh chemistries of mixed wastes like Hanford's organic degradation, even in the absence of radiation. (author). 26 refs., 2 tabs
On the Simulation-Based Reliability of Complex Emergency Logistics Networks in Post-Accident Rescues
Wang, Wei; Huang, Li; Liang, Xuedong
2018-01-01
This paper investigates the reliability of complex emergency logistics networks, as reliability is crucial to reducing environmental and public health losses in post-accident emergency rescues. Such networks’ statistical characteristics are analyzed first. After the connected reliability and evaluation indices for complex emergency logistics networks are effectively defined, simulation analyses of network reliability are conducted under two different attack modes using a particular emergency logistics network as an example. The simulation analyses obtain the varying trends in emergency supply times and the ratio of effective nodes and validates the effects of network characteristics and different types of attacks on network reliability. The results demonstrate that this emergency logistics network is both a small-world and a scale-free network. When facing random attacks, the emergency logistics network steadily changes, whereas it is very fragile when facing selective attacks. Therefore, special attention should be paid to the protection of supply nodes and nodes with high connectivity. The simulation method provides a new tool for studying emergency logistics networks and a reference for similar studies. PMID:29316614
Understanding Crew Decision-Making in the Presence of Complexity: A Flight Simulation Experiment
Young, Steven D.; Daniels, Taumi S.; Evans, Emory; deHaag, Maarten Uijt; Duan, Pengfei
2013-01-01
Crew decision making and response have long been leading causal and contributing factors associated with aircraft accidents. Further, it is anticipated that future aircraft and operational environments will increase exposure to risks related to these factors if proactive steps are not taken to account for ever-increasing complexity. A flight simulation study was designed to collect data to help in understanding how complexity can, or may, be manifest. More specifically, an experimental apparatus was constructed that allowed for manipulation of information complexity and uncertainty, while also manipulating operational complexity and uncertainty. Through these manipulations, and the aid of experienced airline pilots, several issues have been discovered, related most prominently to the influence of information content, quality, and management. Flight crews were immersed in an environment that included new operational complexities suggested for the future air transportation system as well as new technological complexities (e.g. electronic flight bags, expanded data link services, synthetic and enhanced vision systems, and interval management automation). In addition, a set of off-nominal situations were emulated. These included, for example, adverse weather conditions, traffic deviations, equipment failures, poor data quality, communication errors, and unexpected clearances, or changes to flight plans. Each situation was based on one or more reference events from past accidents or incidents, or on a similar case that had been used in previous developmental tests or studies. Over the course of the study, 10 twopilot airline crews participated, completing over 230 flights. Each flight consisted of an approach beginning at 10,000 ft. Based on the recorded data and pilot and research observations, preliminary results are presented regarding decision-making issues in the presence of the operational and technological complexities encountered during the flights.
Wright-Maley, Cory
2014-01-01
A slavery simulation that took place as part of a field trip for students of a Hartford junior high academy led a father to file a human rights suit against the school district, and for one official to comment that simulations of complex and tragic human phenomena have "no place in an educational system." In light of these conclusions,…
Directory of Open Access Journals (Sweden)
Marco A. Velasco
2016-10-01
Full Text Available Scaffolds are essential in bone tissue engineering, as they provide support to cells and growth factors necessary to regenerate tissue. In addition, they meet the mechanical function of the bone while it regenerates. Currently, the multiple methods for designing and manufacturing scaffolds are based on regular structures from a unit cell that repeats in a given domain. However, these methods do not resemble the actual structure of the trabecular bone which may work against osseous tissue regeneration. To explore the design of porous structures with similar mechanical properties to native bone, a geometric generation scheme from a reaction-diffusion model and its manufacturing via a material jetting system is proposed. This article presents the methodology used, the geometric characteristics and the modulus of elasticity of the scaffolds designed and manufactured. The method proposed shows its potential to generate structures that allow to control the basic scaffold properties for bone tissue engineering such as the width of the channels and porosity. The mechanical properties of our scaffolds are similar to trabecular tissue present in vertebrae and tibia bones. Tests on the manufactured scaffolds show that it is necessary to consider the orientation of the object relative to the printing system because the channel geometry, mechanical properties and roughness are heavily influenced by the position of the surface analyzed with respect to the printing axis. A possible line for future work may be the establishment of a set of guidelines to consider the effects of manufacturing processes in designing stages.
World, We Have Problems: Simulation for Large Complex, Risky Projects, and Events
Elfrey, Priscilla
2010-01-01
Prior to a spacewalk during the NASA STS/129 mission in November 2009, Columbia Broadcasting System (CBS) correspondent William Harwood reported astronauts, "were awakened again", as they had been the day previously. Fearing something not properly connected was causing a leak, the crew, both on the ground and in space, stopped and checked everything. The alarm proved false. The crew did complete its work ahead of schedule, but the incident reminds us that correctly connecting hundreds and thousands of entities, subsystems and systems, finding leaks, loosening stuck valves, and adding replacements to very large complex systems over time does not occur magically. Everywhere major projects present similar pressures. Lives are at - risk. Responsibility is heavy. Large natural and human-created disasters introduce parallel difficulties as people work across boundaries their countries, disciplines, languages, and cultures with known immediate dangers as well as the unexpected. NASA has long accepted that when humans have to go where humans cannot go that simulation is the sole solution. The Agency uses simulation to achieve consensus, reduce ambiguity and uncertainty, understand problems, make decisions, support design, do planning and troubleshooting, as well as for operations, training, testing, and evaluation. Simulation is at the heart of all such complex systems, products, projects, programs, and events. Difficult, hazardous short and, especially, long-term activities have a persistent need for simulation from the first insight into a possibly workable idea or answer until the final report perhaps beyond our lifetime is put in the archive. With simulation we create a common mental model, try-out breakdowns of machinery or teamwork, and find opportunity for improvement. Lifecycle simulation proves to be increasingly important as risks and consequences intensify. Across the world, disasters are increasing. We anticipate more of them, as the results of global warming
Linear-algebraic bath transformation for simulating complex open quantum systems
International Nuclear Information System (INIS)
Huh, Joonsuk; Mostame, Sarah; Fujita, Takatoshi; Aspuru-Guzik, Alán; Yung, Man-Hong
2014-01-01
In studying open quantum systems, the environment is often approximated as a collection of non-interacting harmonic oscillators, a configuration also known as the star-bath model. It is also well known that the star-bath can be transformed into a nearest-neighbor interacting chain of oscillators. The chain-bath model has been widely used in renormalization group approaches. The transformation can be obtained by recursion relations or orthogonal polynomials. Based on a simple linear algebraic approach, we propose a bath partition strategy to reduce the system-bath coupling strength. As a result, the non-interacting star-bath is transformed into a set of weakly coupled multiple parallel chains. The transformed bath model allows complex problems to be practically implemented on quantum simulators, and it can also be employed in various numerical simulations of open quantum dynamics. (paper)
Analysis and computer simulation for transient flow in complex system of liquid piping
International Nuclear Information System (INIS)
Mitry, A.M.
1985-01-01
This paper is concerned with unsteady state analysis and development of a digital computer program, FLUTRAN, that performs a simulation of transient flow behavior in a complex system of liquid piping. The program calculates pressure and flow transients in the liquid filled piping system. The analytical model is based on the method of characteristics solution to the fluid hammer continuity and momentum equations. The equations are subject to wide variety of boundary conditions to take into account the effect of hydraulic devices. Water column separation is treated as a boundary condition with known head. Experimental tests are presented that exhibit transients induced by pump failure and valve closure in the McGuire Nuclear Station Low Level Intake Cooling Water System. Numerical simulation is conducted to compare theory with test data. Analytical and test data are shown to be in good agreement and provide validation of the model
Stress influences decisions to break a safety rule in a complex simulation task in females.
Starcke, Katrin; Brand, Matthias; Kluge, Annette
2016-07-01
The current study examines the effects of acutely induced laboratory stress on a complex decision-making task, the Waste Water Treatment Simulation. Participants are instructed to follow a certain decision rule according to safety guidelines. Violations of this rule are associated with potential high rewards (working faster and earning more money) but also with the risk of a catastrophe (an explosion). Stress was induced with the Trier Social Stress Test while control participants underwent a non-stress condition. In the simulation task, stressed females broke the safety rule more often than unstressed females: χ(2) (1, N=24)=10.36, pbreak the safety rule because stressed female participants focused on the potential high gains while they neglected the risk of potential negative consequences. Copyright © 2016 Elsevier B.V. All rights reserved.
Remote sensing reflectance simulation of coastal optical complex water in the East China Sea
He, Shuo; Lou, Xiulin; Zhang, Huaguo; Zheng, Gang
2018-02-01
In this work, remote sensing reflectance (Rrs) spectra of the Zhejiang coastal water in the East China Sea (ECS) were simulated by using the Hydrolight software with field data as input parameters. The seawater along the Zhejiang coast is typical Case II water with complex optical properties. A field observation was conducted in the Zhejiang coastal region in late May of 2016, and the concentration of ocean color constituents (pigment, SPM and CDOM), IOPs (absorption and backscattering coefficients) and Rrs were measured at 24 stations of 3 sections covering the turbid to clear inshore coastal waters. Referring to these ocean color field data, an ocean color model suitable for the Zhejiang coastal water was setup and applied in the Hydrolight. A set of 11 remote sensing reflectance spectra above water surface were modeled and calculated. Then, the simulated spectra were compared with the filed measurements. Finally, the spectral shape and characteristics of the remote sensing reflectance spectra were analyzed and discussed.
Comparison of Different Measurement Techniques and a CFD Simulation in Complex Terrain
International Nuclear Information System (INIS)
Schulz, Christoph; Lutz, Thorsten; Hofsäß, Martin; Anger, Jan; Wen Cheng, Po; Rautenberg, Alexander; Bange, Jens
2016-01-01
This paper deals with a comparison of data collected by measurements and a simulation for a complex terrain test site in southern Germany. Lidar, met mast, unmanned aerial vehicle (UAV) measurements of wind speed and direction and Computational Fluid Dynamics (CFD) data are compared to each other. The site is characterised regarding its flow features and the suitability for a wind turbine test field. A Delayed-Detached-Eddy- Simulation (DES) was employed using measurement data to generate generic turbulent inflow. A good agreement of the wind profiles between the different approaches was reached. The terrain slope leads to a speed-up, a change of turbulence intensity as well as to flow angle variations. (paper)
A dynamic globalization model for large eddy simulation of complex turbulent flow
Energy Technology Data Exchange (ETDEWEB)
Choi, Hae Cheon; Park, No Ma; Kim, Jin Seok [Seoul National Univ., Seoul (Korea, Republic of)
2005-07-01
A dynamic subgrid-scale model is proposed for large eddy simulation of turbulent flows in complex geometry. The eddy viscosity model by Vreman [Phys. Fluids, 16, 3670 (2004)] is considered as a base model. A priori tests with the original Vreman model show that it predicts the correct profile of subgrid-scale dissipation in turbulent channel flow but the optimal model coefficient is far from universal. Dynamic procedures of determining the model coefficient are proposed based on the 'global equilibrium' between the subgrid-scale dissipation and viscous dissipation. An important feature of the proposed procedures is that the model coefficient determined is globally constant in space but varies only in time. Large eddy simulations with the present dynamic model are conducted for forced isotropic turbulence, turbulent channel flow and flow over a sphere, showing excellent agreements with previous results.
Beneficiation of Stillwater Complex Rock for the Production of Lunar Simulants
Rickman, D. L.; Young, C.; Stoeser, D.; Edmunson, J.
2014-01-01
The availability of pure, high calcium plagioclase would be a significant asset in any attempt to manufacture high-quality lunar simulants. A suitable plagioclase product can be obtained from materials obtained from the Stillwater Complex of Montana. The access, geology, petrology, and mineralogy of the relevant rocks and the mill tailings are described here. This study demonstrates successful plagioclase recovery from mill tailings produced by the Stillwater Mine Company. Hydrogen peroxide was used to remove carboxymethyl cellulose from the tailing. The characteristics of the plagioclase products are shown and locked grains are identified as a limit to achievable purity. Based on the experimental results, flowsheets were developed showing how these resources could be processed and made into 'separates' of (1) high calcium plagioclase and (2) orthopyroxene/clinopyroxene with the thought that they would be combined later to make simulant.
Information-Theoretic Approaches for Evaluating Complex Adaptive Social Simulation Systems
Energy Technology Data Exchange (ETDEWEB)
Omitaomu, Olufemi A [ORNL; Ganguly, Auroop R [ORNL; Jiao, Yu [ORNL
2009-01-01
In this paper, we propose information-theoretic approaches for comparing and evaluating complex agent-based models. In information theoretic terms, entropy and mutual information are two measures of system complexity. We used entropy as a measure of the regularity of the number of agents in a social class; and mutual information as a measure of information shared by two social classes. Using our approaches, we compared two analogous agent-based (AB) models developed for regional-scale social-simulation system. The first AB model, called ABM-1, is a complex AB built with 10,000 agents on a desktop environment and used aggregate data; the second AB model, ABM-2, was built with 31 million agents on a highperformance computing framework located at Oak Ridge National Laboratory, and fine-resolution data from the LandScan Global Population Database. The initializations were slightly different, with ABM-1 using samples from a probability distribution and ABM-2 using polling data from Gallop for a deterministic initialization. The geographical and temporal domain was present-day Afghanistan, and the end result was the number of agents with one of three behavioral modes (proinsurgent, neutral, and pro-government) corresponding to the population mindshare. The theories embedded in each model were identical, and the test simulations focused on a test of three leadership theories - legitimacy, coercion, and representative, and two social mobilization theories - social influence and repression. The theories are tied together using the Cobb-Douglas utility function. Based on our results, the hypothesis that performance measures can be developed to compare and contrast AB models appears to be supported. Furthermore, we observed significant bias in the two models. Even so, further tests and investigations are required not only with a wider class of theories and AB models, but also with additional observed or simulated data and more comprehensive performance measures.
A large-eddy simulation based power estimation capability for wind farms over complex terrain
Senocak, I.; Sandusky, M.; Deleon, R.
2017-12-01
There has been an increasing interest in predicting wind fields over complex terrain at the micro-scale for resource assessment, turbine siting, and power forecasting. These capabilities are made possible by advancements in computational speed from a new generation of computing hardware, numerical methods and physics modelling. The micro-scale wind prediction model presented in this work is based on the large-eddy simulation paradigm with surface-stress parameterization. The complex terrain is represented using an immersed-boundary method that takes into account the parameterization of the surface stresses. Governing equations of incompressible fluid flow are solved using a projection method with second-order accurate schemes in space and time. We use actuator disk models with rotation to simulate the influence of turbines on the wind field. Data regarding power production from individual turbines are mostly restricted because of proprietary nature of the wind energy business. Most studies report percentage drop of power relative to power from the first row. There have been different approaches to predict power production. Some studies simply report available wind power in the upstream, some studies estimate power production using power curves available from turbine manufacturers, and some studies estimate power as torque multiplied by rotational speed. In the present work, we propose a black-box approach that considers a control volume around a turbine and estimate the power extracted from the turbine based on the conservation of energy principle. We applied our wind power prediction capability to wind farms over flat terrain such as the wind farm over Mower County, Minnesota and the Horns Rev offshore wind farm in Denmark. The results from these simulations are in good agreement with published data. We also estimate power production from a hypothetical wind farm in complex terrain region and identify potential zones suitable for wind power production.
Directory of Open Access Journals (Sweden)
Chiara Biscarini
2013-01-01
Full Text Available The numerical simulation of fast-moving fronts originating from dam or levee breaches is a challenging task for small scale engineering projects. In this work, the use of fully three-dimensional Navier-Stokes (NS equations and lattice Boltzmann method (LBM is proposed for testing the validity of, respectively, macroscopic and mesoscopic mathematical models. Macroscopic simulations are performed employing an open-source computational fluid dynamics (CFD code that solves the NS combined with the volume of fluid (VOF multiphase method to represent free-surface flows. The mesoscopic model is a front-tracking experimental variant of the LBM. In the proposed LBM the air-gas interface is represented as a surface with zero thickness that handles the passage of the density field from the light to the dense phase and vice versa. A single set of LBM equations represents the liquid phase, while the free surface is characterized by an additional variable, the liquid volume fraction. Case studies show advantages and disadvantages of the proposed LBM and NS with specific regard to the computational efficiency and accuracy in dealing with the simulation of flows through complex geometries. In particular, the validation of the model application is developed by simulating the flow propagating through a synthetic urban setting and comparing results with analytical and experimental laboratory measurements.
GATE Monte Carlo simulation in radiation therapy for complex and dynamic beams in IMRT
International Nuclear Information System (INIS)
Benhalouche, Saadia
2014-01-01
Radiotherapy is one of the three methods of cancer treatment along with surgery and chemotherapy. It has evolved with the development of treatment techniques such as IMRT and VMAT along with IGRT for patient positioning. The aim is to effectively treat tumors while limiting the dose to healthy organs. In our work, we use the GATE Monte Carlo simulation platform to model a LINAC for a 6 MV photon beam. The resulting model is then validated with a dosimetric study by calculating relevant parameters for the beam quality. The LINAC model is then used for simulating clinical IMRT treatment plans in the ORL domain. Simulation results are compared with experimental measurements. We also explored the possibility of modeling the LINAC portal imaging system. This technique referred to as MV-CBCT combine the LINAC source with a flat panel detector to acquire 3D images of the patient. This part was validated first by acquiring 2D projections on patient and anthropomorphic phantom, and by reconstructing 3D volumes. Here again, validation was performed by comparing simulated and actual images. As a second step, a dosimetric validation was done by evaluating the dose deposited by IMRT beams, by means of portal signal only. We show in the present work the ability of GATE to perform complex IMRT treatments and portal images as they are performed routinely for dosimetric quality control. (author) [fr
International Nuclear Information System (INIS)
Vieira, Leonardo S.; Donatelli, Joao L.; Cruz, Manuel E.
2009-01-01
In this paper, the application of an iterative exergoeconomic methodology for improvement of thermal systems to a complex combined-cycle cogeneration plant is presented. The methodology integrates exergoeconomics with a professional process simulator, and represents an alternative to conventional mathematical optimization techniques, because it reduces substantially the number of variables to be considered in the improvement process. By exploiting the computational power of a simulator, the integrated approach permits the optimization routine to ignore the variables associated with the thermodynamic equations, and thus to deal only with the economic equations and objective function. In addition, the methodology combines recent available exergoeconomic techniques with qualitative and quantitative criteria to identify only those decision variables, which matter for the improvement of the system. To demonstrate the strengths of the methodology, it is here applied to a 24-component cogeneration plant, which requires O(10 3 ) variables for its simulation. The results which are obtained, are compared to those reached using a conventional mathematical optimization procedure, also coupled to the process simulator. It is shown that, for engineering purposes, improvement of the system is often more cost effective and less time consuming than optimization of the system.
Numerical simulation of complex turbulent Flow over a backward-facing step
International Nuclear Information System (INIS)
Silveira Neto, A.
1991-06-01
A statistical and topological study of a complex turbulent flow over a backward-facing step is realized by means of Direct and Large-Eddy Simulations. Direct simulations are performed in an isothermal and in a stratified two-dimensional case. In the isothermal case coherent structures have been obtained by the numerical simulation in the mixing layer downstream of the step. In a second step a thermal stratification is imposed on this flow. The coherent structures are in this case produced in the immediate vicinity of the step and disappear dowstream for increasing stratification. Afterwards, large-eddy simulations are carried out in the three-dimensional case. The subgrid-scale model is a local adaptation to the physical space of the spectral eddy-viscosity concept. The statistics of turbulence are in good agreement with the experimental data, corresponding to a small step configuration. Furthermore, calculations at higher step configuration show that the eddy structure of the flow presents striking analogies with the plane shear layers, with large billows shed behind the step, and intense longitudinal vortices strained between these billows [fr
Activity and stability of a complex bacterial soil community under simulated Martian conditions
Hansen, Aviaja Anna; Merrison, Jonathan; Nørnberg, Per; Aagaard Lomstein, Bente; Finster, Kai
2005-04-01
A simulation experiment with a complex bacterial soil community in a Mars simulation chamber was performed to determine the effect of Martian conditions on community activity, stability and survival. At three different depths in the soil core short-term effects of Martian conditions with and without ultraviolet (UV) exposure corresponding to 8 Martian Sol were compared. Community metabolic activities and functional diversity, measured as glucose respiration and versatility in substrate utilization, respectively, decreased after UV exposure, whereas they remained unaffected by Martian conditions without UV exposure. In contrast, the numbers of culturable bacteria and the genetic diversity were unaffected by the simulated Martian conditions both with and without UV exposure. The genetic diversity of the soil community and of the colonies grown on agar plates were evaluated by denaturant gradient gel electrophoresis (DGGE) on DNA extracts. Desiccation of the soil prior to experimentation affected the functional diversity by decreasing the versatility in substrate utilization. The natural dominance of endospores and Gram-positive bacteria in the investigated Mars-analogue soil may explain the limited effect of the Mars incubations on the survival and community structure. Our results suggest that UV radiation and desiccation are major selecting factors on bacterial functional diversity in terrestrial bacterial communities incubated under simulated Martian conditions. Furthermore, these results suggest that forward contamination of Mars is a matter of great concern in future space missions.
Directory of Open Access Journals (Sweden)
Roger P. Pawlowski
2012-01-01
Full Text Available An approach for incorporating embedded simulation and analysis capabilities in complex simulation codes through template-based generic programming is presented. This approach relies on templating and operator overloading within the C++ language to transform a given calculation into one that can compute a variety of additional quantities that are necessary for many state-of-the-art simulation and analysis algorithms. An approach for incorporating these ideas into complex simulation codes through general graph-based assembly is also presented. These ideas have been implemented within a set of packages in the Trilinos framework and are demonstrated on a simple problem from chemical engineering.
Development of a numerical methodology for flowforming process simulation of complex geometry tubes
Varela, Sonia; Santos, Maite; Arroyo, Amaia; Pérez, Iñaki; Puigjaner, Joan Francesc; Puigjaner, Blanca
2017-10-01
Nowadays, the incremental flowforming process is widely explored because of the usage of complex tubular products is increasing due to the light-weighting trend and the use of expensive materials. The enhanced mechanical properties of finished parts combined with the process efficiency in terms of raw material and energy consumption are the key factors for its competitiveness and sustainability, which is consistent with EU industry policy. As a promising technology, additional steps for extending the existing flowforming limits in the production of tubular products are required. The objective of the present research is to further expand the current state of the art regarding limitations on tube thickness and diameter, exploring the feasibility to flowform complex geometries as tubes of elevated thickness of up to 60 mm. In this study, the analysis of the backward flowforming process of 7075 aluminum tubular preform is carried out to define the optimum process parameters, machine requirements and tooling geometry as demonstration case. Numerical simulation studies on flowforming of thin walled tubular components have been considered to increase the knowledge of the technology. The calculation of the rotational movement of the mesh preform, the high ratio thickness/length and the thermomechanical condition increase significantly the computation time of the numerical simulation model. This means that efficient and reliable tools able to predict the forming loads and the quality of flowformed thick tubes are not available. This paper aims to overcome this situation by developing a simulation methodology based on FEM simulation code including new strategies. Material characterization has also been performed through tensile test to able to design the process. Finally, to check the reliability of the model, flowforming tests at industrial environment have been developed.
Modeling and simulation for fewer-axis grinding of complex surface
Li, Zhengjian; Peng, Xiaoqiang; Song, Ci
2017-10-01
As the basis of fewer-axis grinding of complex surface, the grinding mathematical model is of great importance. A mathematical model of the grinding wheel was established, and then coordinate and normal vector of the wheel profile could be calculated. Through normal vector matching at the cutter contact point and the coordinate system transformation, the grinding mathematical model was established to work out the coordinate of the cutter location point. Based on the model, interference analysis was simulated to find out the right position and posture of workpiece for grinding. Then positioning errors of the workpiece including the translation positioning error and the rotation positioning error were analyzed respectively, and the main locating datum was obtained. According to the analysis results, the grinding tool path was planned and generated to grind the complex surface, and good form accuracy was obtained. The grinding mathematical model is simple, feasible and can be widely applied.
Simulating Engineering Flows through Complex Porous Media via the Lattice Boltzmann Method
Directory of Open Access Journals (Sweden)
Vesselin Krassimirov Krastev
2018-03-01
Full Text Available In this paper, recent achievements in the application of the lattice Boltzmann method (LBM to complex fluid flows are reported. More specifically, we focus on flows through reactive porous media, such as the flow through the substrate of a selective catalytic reactor (SCR for the reduction of gaseous pollutants in the automotive field; pulsed-flow analysis through heterogeneous catalyst architectures; and transport and electro-chemical phenomena in microbial fuel cells (MFC for novel waste-to-energy applications. To the authors’ knowledge, this is the first known application of LBM modeling to the study of MFCs, which represents by itself a highly innovative and challenging research area. The results discussed here essentially confirm the capabilities of the LBM approach as a flexible and accurate computational tool for the simulation of complex multi-physics phenomena of scientific and technological interest, across physical scales.
Thermal plume above a simulated sitting person with different complexity of body geometry
DEFF Research Database (Denmark)
Zukowska, Daria; Melikov, Arsen Krikor; Popiolek, Zbigniew J.
2007-01-01
Occupants are one of the main heat sources in rooms. They generate thermal plumes with characteristics, which depend on geometry, surface temperature and area of the human body in contact with the surrounding air as well as temperature, velocity and turbulence intensity distribution in the room....... The characteristics of the thermal plume generated by a sitting person were studied using four human body simulators with different complexity of geometry but equal surface area: a vertical cylinder, a rectangular box, a dummy, and a thermal manikin. The results show that the dummy and the thermal manikin generate...
Neutron-induced complex reaction analysis with 3D nuclear track simulation
International Nuclear Information System (INIS)
Sajo-Bohus, L.; Palfalvi, J.K.; Akatov, Yu.; Arevalo, O.; Greaves, E.D.; Nemeth, P.; Palacios, D.; Szabo, J.; Eoerdoegh, I.
2005-01-01
Complex (multiple) etched tracks are analysed through digitised images and 3D simulation by a purpose-built algorithm. From a binary track image an unfolding procedure is followed to generate a 3D track model, from which several track parameters are estimated. The method presented here allows the deposited energy, that originated from particle fragmentation or carbon spallation by means of induced tracks in commercially available PADC detectors, to be estimated. Results of evaluated nuclear tracks related to 12 C (n,3αn ' ) reaction are presented here. The detectors were exposed on the ISS in 2001
COMPLEX SIMULATION MODEL OF TRAIN BREAKING-UP PROCESS AT THE HUMPS
Directory of Open Access Journals (Sweden)
E. B. Demchenko
2015-11-01
Full Text Available Purpose. One of the priorities of station sorting complex functioning improvement is the breaking-up process energy consumptions reduction, namely: fuel consumption for train pushing and electric energy consumption for cut braking. In this regard, an effective solution of the problem of energy consumption reduction at breaking-up subsystem requires a comprehensive handling of train pushing and cut rolling down processes. At the same time, the analysis showed that the current task of pushing process improvement and cut rolling down effectiveness increase are solved separately. To solve this problem it is necessary to develop the complex simulation model of train breaking up process at humps. Methodology. Pushing process simulation was done based on adapted under the shunting conditions traction calculations. In addition, the features of shunting locomotives work at the humps were taken into account. In order to realize the current pushing mode the special algorithm of hump locomotive controlling, which along with the safety shunting operation requirements takes into account behavioral factors associated with engineer control actions was applied. This algorithm provides train smooth acceleration and further movement with speed, which is close to the set speed. Hump locomotive fuel consumptions were determined based on the amount of mechanical work performed by locomotive traction. Findings. The simulation model of train pushing process was developed and combined with existing cut rolling down model. Cut initial velocity is determined during simulation process. The obtained initial velocity is used for further cut rolling process modeling. In addition, the modeling resulted in sufficiently accurate determination of the fuel rates consumed for train breaking-up. Originality. The simulation model of train breaking-up process at the humps, which in contrast to the existing models allows reproducing complexly all the elements of this process in detail
The effects of model complexity and calibration period on groundwater recharge simulations
Moeck, Christian; Van Freyberg, Jana; Schirmer, Mario
2017-04-01
A significant number of groundwater recharge models exist that vary in terms of complexity (i.e., structure and parametrization). Typically, model selection and conceptualization is very subjective and can be a key source of uncertainty in the recharge simulations. Another source of uncertainty is the implicit assumption that model parameters, calibrated over historical periods, are also valid for the simulation period. To the best of our knowledge there is no systematic evaluation of the effect of the model complexity and calibration strategy on the performance of recharge models. To address this gap, we utilized a long-term recharge data set (20 years) from a large weighting lysimeter. We performed a differential split sample test with four groundwater recharge models that vary in terms of complexity. They were calibrated using six calibration periods with climatically contrasting conditions in a constrained Monte Carlo approach. Despite the climatically contrasting conditions, all models performed similarly well during the calibration. However, during validation a clear effect of the model structure on model performance was evident. The more complex, physically-based models predicted recharge best, even when calibration and prediction periods had very different climatic conditions. In contrast, more simplistic soil-water balance and lumped model performed poorly under such conditions. For these models we found a strong dependency on the chosen calibration period. In particular, our analysis showed that this can have relevant implications when using recharge models as decision-making tools in a broad range of applications (e.g. water availability, climate change impact studies, water resource management, etc.).
Directory of Open Access Journals (Sweden)
Robert S. Pierce
2017-10-01
Full Text Available Increasing demand for weight reduction and greater fuel efficiency continues to spur the use of composite materials in commercial aircraft structures. Subsequently, as composite aerostructures become larger and more complex, traditional autoclave manufacturing methods are becoming prohibitively expensive. This has prompted renewed interest in out-of-autoclave processing techniques in which resins are introduced into a reinforcing preform. However, the success of these resin infusion methods is highly dependent upon operator skill and experience, particularly in the development of new manufacturing strategies for complex parts. Process modeling, as a predictive computational tool, aims to address the issues of reliability and waste that result from traditional trial-and-error approaches. Basic modeling attempts, many of which are still used in industry, generally focus on simulating fluid flow through an isotropic porous reinforcement material. However, recent efforts are beginning to account for the multiscale and multidisciplinary complexity of woven materials, in simulations that can provide greater fidelity. In particular, new multi-physics process models are able to better predict the infusion behavior through textiles by considering the effect of fabric deformation on permeability and porosity properties within the reinforcing material. In addition to reviewing previous research related to process modeling and the current state of the art, this paper highlights the recent validation of a multi-physics process model against the experimental infusion of a complex double dome component. By accounting for deformation-dependent flow behavior, the multi-physics process model was able to predict realistic flow behavior, demonstrating considerable improvement over basic isotropic permeability models.
Energy Technology Data Exchange (ETDEWEB)
Buck, D. R. [Iowa State Univ., Ames, IA (United States)
2000-09-12
Theoretical simulations and ultrafast pump-probe laser spectroscopy experiments were used to study photosynthetic pigment-protein complexes and antennae found in green sulfur bacteria such as Prosthecochloris aestuarii, Chloroflexus aurantiacus, and Chlorobium tepidum. The work focused on understanding structure-function relationships in energy transfer processes in these complexes through experiments and trying to model that data as we tested our theoretical assumptions with calculations. Theoretical exciton calculations on tubular pigment aggregates yield electronic absorption spectra that are superimpositions of linear J-aggregate spectra. The electronic spectroscopy of BChl c/d/e antennae in light harvesting chlorosomes from Chloroflexus aurantiacus differs considerably from J-aggregate spectra. Strong symmetry breaking is needed if we hope to simulate the absorption spectra of the BChl c antenna. The theory for simulating absorption difference spectra in strongly coupled photosynthetic antenna is described, first for a relatively simple heterodimer, then for the general N-pigment system. The theory is applied to the Fenna-Matthews-Olson (FMO) BChl a protein trimers from Prosthecochloris aestuarii and then compared with experimental low-temperature absorption difference spectra of FMO trimers from Chlorobium tepidum. Circular dichroism spectra of the FMO trimer are unusually sensitive to diagonal energy disorder. Substantial differences occur between CD spectra in exciton simulations performed with and without realistic inhomogeneous distribution functions for the input pigment diagonal energies. Anisotropic absorption difference spectroscopy measurements are less consistent with 21-pigment trimer simulations than 7-pigment monomer simulations which assume that the laser-prepared states are localized within a subunit of the trimer. Experimental anisotropies from real samples likely arise from statistical averaging over states with diagonal energies shifted by
Johnson, Sylvester, IV
A CAE (Computer Aided Engineering) tool called SEEL (Simulation of Electron Energy Loss) is described in detail. SEEL simulates in any material the energy loss and trajectories of electrons in the complex, multilayered nanostructures typical of ULSI, at beam energies from 1 to 50 keV. Structures and materials are defined in the input file rather than in the source code of the program, for which flowcharts are included in addition to an explanation of the algorithms implemented. Satisfactory comparisons of simulated with experimental results are made of both secondary electron (SE) and backscattered electron (BSE) linescans across an array of MOS gate structures capped by rough oxide. Many other comparisons are made. The effects of varying line edge slopes on SE linescan peak shape are simulated and analyzed. A data library containing the simulated variation of the FWHM, peak height, and peak location with slope for different materials, line heights or trench depths, widths, beam energies, and nominal diameters could be used to find the edge location relative to the peak for improvement of the accuracy of linewidth measurement algorithms. An investigation indicates that the use of such a library would be complicated by the effect of surface roughness on the SE signal at the edge of a feature. SEEL can be used as the first module in a series of programs that simulate energy deposition in resist structures and correct the exposure of a circuit pattern. Pixel by pixel convolution for prediction of the proximity effect is time-consuming. Another method of proximity effect prediction based on the reciprocity of the RED is described. Such programs could be used to reduce the number of iterations in the lab required to optimize resist structures and exposure parameters. For both smooth and rough interfaces between a bottom layer of PMMA in a multilayer resist structure and a W film, the simulated exposure contrast declines from that with an oxide film beneath the structure
Mental simulation of drawing actions enhances delayed recall of a complex figure.
De Lucia, Natascia; Trojano, Luigi; Senese, Vincenzo Paolo; Conson, Massimiliano
2016-10-01
Motor simulation implies that the same motor representations involved in action execution are re-enacted during observation or imagery of actions. Neurofunctional data suggested that observation of letters or abstract paintings can elicit simulation of writing or drawing gestures. We performed four behavioural experiments on right-handed healthy participants to test whether observation of a static and complex geometrical figure implies re-enactment of drawing actions. In Experiment 1, participants had to observe the stimulus without explicit instruction (observation-only condition), while performing irrelevant finger tapping (motor dual task), or while articulating irrelevant verbal material (verbal dual task). Delayed drawing of the stimulus was less accurate in the motor dual-task (interfering with simulation of hand actions) than in verbal dual-task and observation-only conditions. In Experiment 2, delayed drawing in the observation only was as accurate as when participants encoded the stimulus by copying it; in both conditions, accuracy was higher than when participants were instructed to observe the stimulus to recall it later verbally (observe to recall), thus being discouraged from engaging motor simulation. In Experiment 3, delayed drawing was as accurate in the observation-only condition as when participants imagined copying the stimulus; accuracy in both conditions was higher than in the observe-to-recall condition. In Experiment 4, in the observe-only condition participants who observed the stimulus with their right arm hidden behind their back were significantly less accurate than participants who had their left arm hidden. These findings converge in suggesting that mere observation of a geometrical stimulus can activate motor simulation and re-enactment of drawing actions.
International Nuclear Information System (INIS)
Patil, Sunil; Tafti, Danesh
2012-01-01
Highlights: ► Large eddy simulation. ► Wall layer modeling. ► Synthetic inlet turbulence. ► Swirl flows. - Abstract: Large eddy simulations of complex high Reynolds number flows are carried out with the near wall region being modeled with a zonal two layer model. A novel formulation for solving the turbulent boundary layer equation for the effective tangential velocity in a generalized co-ordinate system is presented and applied in the near wall zonal treatment. This formulation reduces the computational time in the inner layer significantly compared to the conventional two layer formulations present in the literature and is most suitable for complex geometries involving body fitted structured and unstructured meshes. The cost effectiveness and accuracy of the proposed wall model, used with the synthetic eddy method (SEM) to generate inlet turbulence, is investigated in turbulent channel flow, flow over a backward facing step, and confined swirling flows at moderately high Reynolds numbers. Predictions are compared with available DNS, experimental LDV data, as well as wall resolved LES. In all cases, there is at least an order of magnitude reduction in computational cost with no significant loss in prediction accuracy.
Ballet, Pascal; Rivière, Jérémy; Pothet, Alain; Théron, Michaël; Pichavant, Karine; Abautret, Frank; Fronville, Alexandra; Rodin, Vincent
2017-01-01
International audience; Modelling and teaching complex biological systems is a difficult process. Multi-Agent Based Simulations (MABS) have proved to be an appropriate approach both in research and education when dealing with such systems including emergent, self-organizing phenomena. This chapter presents NetBioDyn, an original software aimed at biologists (students, teachers, researchers) to easily build and simulate complex biological mechanisms observed in multicellular and molecular syst...
Idealized tropical cyclone simulations of intermediate complexity: A test case for AGCMs
Directory of Open Access Journals (Sweden)
Kevin Reed
2012-04-01
Full Text Available The paper introduces a moist, deterministic test case of intermediate complexity for Atmospheric General Circulation Models (AGCMs. We suggest pairing an AGCM dynamical core with simple physical parameterizations to test the evolution of a single, idealized, initially weak vortex into a tropical cyclone. The initial conditions are based on an initial vortex seed that is in gradient-wind and hydrostatic balance. The suggested ``simple-physics'' package consists of parameterizations of bulk aerodynamic surface fluxes for moisture, sensible heat and momentum, boundary layer diffusion, and large-scale condensation. Such a configuration includes the important driving mechanisms for tropical cyclones, and leads to a rapid intensification of the initial vortex over a forecast period of ten days. The simple-physics test paradigm is not limited to tropical cyclones, and can be universally applied to other flow fields. The physical parameterizations are described in detail to foster model intercomparisons.The characteristics of the intermediate-complexity test case are demonstrated with the help of four hydrostatic dynamical cores that are part of the Community Atmosphere Model version 5 (CAM 5 developed at the National Center for Atmospheric Research (NCAR. In particular, these are the Finite-Volume, Spectral Element, and spectral transform Eulerian and semi-Lagrangian dynamical cores that are coupled to the simple-physics suite. The simulations show that despite the simplicity of the physics forcings the models develop the tropical cyclone at horizontal grid spacings of about 55 km and finer. The simple-physics simulations reveal essential differences in the storm's structure and strength due to the choice of the dynamical core. Similar differences are also seen in complex full-physics aqua-planet experiments with CAM 5 which serve as a motivator for this work. The results suggest that differences in complex full-physics simulations can be, at least
Simulation of complex fracture networks influenced by natural fractures in shale gas reservoir
Directory of Open Access Journals (Sweden)
Zhao Jinzhou
2014-10-01
Full Text Available When hydraulic fractures intersect with natural fractures, the geometry and complexity of a fracture network are determined by the initiation and propagation pattern which is affected by a number of factors. Based on the fracture mechanics, the criterion for initiation and propagation of a fracture was introduced to analyze the tendency of a propagating angle and factors affecting propagating pressure. On this basis, a mathematic model with a complex fracture network was established to investigate how the fracture network form changes with different parameters, including rock mechanics, in-situ stress distribution, fracture properties, and frac treatment parameters. The solving process of this model was accelerated by classifying the calculation nodes on the extending direction of the fracture by equal pressure gradients, and solving the geometrical parameters prior to the iteration fitting flow distribution. With the initiation and propagation criterion as the bases for the propagation of branch fractures, this method decreased the iteration times through eliminating the fitting of the fracture length in conventional 3D fracture simulation. The simulation results indicated that the formation with abundant natural fractures and smaller in-situ stress difference is sufficient conditions for fracture network development. If the pressure in the hydraulic fractures can be kept at a high level by temporary sealing or diversion, the branch fractures will propagate further with minor curvature radius, thus enlarging the reservoir stimulation area. The simulated shape of fracture network can be well matched with the field microseismic mapping in data point range and distribution density, validating the accuracy of this model.
Automated builder and database of protein/membrane complexes for molecular dynamics simulations.
Directory of Open Access Journals (Sweden)
Sunhwan Jo
2007-09-01
Full Text Available Molecular dynamics simulations of membrane proteins have provided deeper insights into their functions and interactions with surrounding environments at the atomic level. However, compared to solvation of globular proteins, building a realistic protein/membrane complex is still challenging and requires considerable experience with simulation software. Membrane Builder in the CHARMM-GUI website (http://www.charmm-gui.org helps users to build such a complex system using a web browser with a graphical user interface. Through a generalized and automated building process including system size determination as well as generation of lipid bilayer, pore water, bulk water, and ions, a realistic membrane system with virtually any kinds and shapes of membrane proteins can be generated in 5 minutes to 2 hours depending on the system size. Default values that were elaborated and tested extensively are given in each step to provide reasonable options and starting points for both non-expert and expert users. The efficacy of Membrane Builder is illustrated by its applications to 12 transmembrane and 3 interfacial membrane proteins, whose fully equilibrated systems with three different types of lipid molecules (DMPC, DPPC, and POPC and two types of system shapes (rectangular and hexagonal are freely available on the CHARMM-GUI website. One of the most significant advantages of using the web environment is that, if a problem is found, users can go back and re-generate the whole system again before quitting the browser. Therefore, Membrane Builder provides the intuitive and easy way to build and simulate the biologically important membrane system.
Directory of Open Access Journals (Sweden)
Chantal Basurto
2015-12-01
Full Text Available Complex Fenestration Systems (CFS are advanced daylighting systems that are placed on the upper part of a window to improve the indoor daylight distribution within rooms. Due to their double function of daylight redirection and solar protection, they are considered as a solution to mitigate the unfavorable effects due to the admission of direct sunlight in buildings located in prevailing sunny climates (risk of glare and overheating. Accordingly, an adequate assessment of their performance should include an annual evaluation of the main aspects relevant to the use of daylight in such regions: the indoor illuminance distribution, thermal comfort, and visual comfort of the occupant’s. Such evaluation is possible with the use of computer simulations combined with the bi-directional scattering distribution function (BSDF data of these systems. This study explores the use of available methods to assess the visible and thermal annual performance of five different CFS using advanced computer simulations. To achieve results, an on-site daylight monitoring was carried out in a building located in a predominantly sunny climate location, and the collected data was used to create and calibrate a virtual model used to carry-out the simulations. The results can be employed to select the CFS, which improves visual and thermal interior environment for the occupants.
CFD Numerical Simulation of the Complex Turbulent Flow Field in an Axial-Flow Water Pump
Directory of Open Access Journals (Sweden)
Wan-You Li
2014-09-01
Full Text Available Further optimal design of an axial-flow water pump calls for a thorough recognition of the characteristics of the complex turbulent flow field in the pump, which is however extremely difficult to be measured using the up-to-date experimental techniques. In this study, a numerical simulation procedure based on computational fluid dynamics (CFD was elaborated in order to obtain the fully three-dimensional unsteady turbulent flow field in an axial-flow water pump. The shear stress transport (SST k-ω model was employed in the CFD calculation to study the unsteady internal flow of the axial-flow pump. Upon the numerical simulation results, the characteristics of the velocity field and pressure field inside the impeller region were discussed in detail. The established model procedure in this study may provide guidance to the numerical simulations of turbomachines during the design phase or the investigation of flow and pressure field characteristics and performance. The presented information can be of reference value in further optimal design of the axial-flow pump.
In-flight simulation of high agility through active control: Taming complexity by design
Padfield, Gareth D.; Bradley, Roy
1993-01-01
The motivation for research into helicopter agility stems from the realization that marked improvements relative to current operational types are possible, yet there is a dearth of useful criteria for flying qualities at high performance levels. Several research laboratories are currently investing resources in developing second generation airborne rotorcraft simulators. The UK's focus has been the exploitation of agility through active control technology (ACT); this paper reviews the results of studies conducted to date. The conflict between safety and performance in flight research is highlighted and the various forms of safety net to protect against system failures are described. The role of the safety pilot, and the use of actuator and flight envelope limiting are discussed. It is argued that the deep complexity of a research ACT system can only be tamed through a requirement specification assembled using design principles and cast in an operational simulation form. Work along these lines conducted at DRA is described, including the use of the Jackson System Development method and associated Ada simulation.
Modelling of turbulence and combustion for simulation of gas explosions in complex geometries
Energy Technology Data Exchange (ETDEWEB)
Arntzen, Bjoern Johan
1998-12-31
This thesis analyses and presents new models for turbulent reactive flows for CFD (Computational Fluid Dynamics) simulation of gas explosions in complex geometries like offshore modules. The course of a gas explosion in a complex geometry is largely determined by the development of turbulence and the accompanying increased combustion rate. To be able to model the process it is necessary to use a CFD code as a starting point, provided with a suitable turbulence and combustion model. The modelling and calculations are done in a three-dimensional finite volume CFD code, where complex geometries are represented by a porosity concept, which gives porosity on the grid cell faces, depending on what is inside the cell. The turbulent flow field is modelled with a k-{epsilon} turbulence model. Subgrid models are used for production of turbulence from geometry not fully resolved on the grid. Results from laser doppler anemometry measurements around obstructions in steady and transient flows have been analysed and the turbulence models have been improved to handle transient, subgrid and reactive flows. The combustion is modelled with a burning velocity model and a flame model which incorporates the burning velocity into the code. Two different flame models have been developed: SIF (Simple Interface Flame model), which treats the flame as an interface between reactants and products, and the {beta}-model where the reaction zone is resolved with about three grid cells. The flame normally starts with a quasi laminar burning velocity, due to flame instabilities, modelled as a function of flame radius and laminar burning velocity. As the flow field becomes turbulent, the flame uses a turbulent burning velocity model based on experimental data and dependent on turbulence parameters and laminar burning velocity. The laminar burning velocity is modelled as a function of gas mixture, equivalence ratio, pressure and temperature in reactant. Simulations agree well with experiments. 139
Deen, N.G.; van Sint Annaland, M.; Kuipers, J.A.M.
2007-01-01
In this paper a simulation model is presented for the Direct Numerical Simulation (DNS) of complex multi-fluid flows in which simultaneously (moving) deformable (drops or bubbles) and non-deformable (moving) elements (particles) are present, possibly with the additional presence of free surfaces.
Deen, N.G.; van Sint Annaland, M.; Kuipers, J.A.M.
2009-01-01
In this paper a simulation model is presented for the Direct Numerical Simulation (DNS) of complex multi-fluid flows in which simultaneously (moving) deformable (drops or bubbles) and non-deformable (moving) elements (particles) are present, possibly with the additional presence of free surfaces.
A GENERAL PHYSIOLOGICAL AND TOXICOKINETIC (GPAT) MODEL FOR SIMULATION OF COMPLEX TOLUENE EXPOSURE SCENARIOS IN HUMANS. E M Kenyon1, T Colemen2, C R Eklund1 and V A Benignus3. 1U.S. EPA, ORD, NHEERL, ETD, PKB, RTP, NC, USA; 2Biological Simulators, Inc., Jackson MS, USA, 3U.S. EP...
Hickmott, Curtis W.
Cellular core tooling is a new technology which has the capability to manufacture complex integrated monolithic composite structures. This novel tooling method utilizes thermoplastic cellular cores as inner tooling. The semi-rigid nature of the cellular cores makes them convenient for lay-up, and under autoclave temperature and pressure they soften and expand providing uniform compaction on all surfaces including internal features such as ribs and spar tubes. This process has the capability of developing fully optimized aerospace structures by reducing or eliminating assembly using fasteners or bonded joints. The technology is studied in the context of evaluating its capabilities, advantages, and limitations in developing high quality structures. The complex nature of these parts has led to development of a model using the Finite Element Analysis (FEA) software Abaqus and the plug-in COMPRO Common Component Architecture (CCA) provided by Convergent Manufacturing Technologies. This model utilizes a "virtual autoclave" technique to simulate temperature profiles, resin flow paths, and ultimately deformation from residual stress. A model has been developed simulating the temperature profile during curing of composite parts made with the cellular core technology. While modeling of composites has been performed in the past, this project will look to take this existing knowledge and apply it to this new manufacturing method capable of building more complex parts and develop a model designed specifically for building large, complex components with a high degree of accuracy. The model development has been carried out in conjunction with experimental validation. A double box beam structure was chosen for analysis to determine the effects of the technology on internal ribs and joints. Double box beams were manufactured and sectioned into T-joints for characterization. Mechanical behavior of T-joints was performed using the T-joint pull-off test and compared to traditional
Understanding and revisiting the most complex perovskite system via atomistic simulations
Yang, Yali; Xu, Bin; Xu, Changsong; Ren, Wei; Bellaiche, Laurent
2018-05-01
A first-principles-based effective Hamiltonian is developed and used, along with direct ab initio techniques, to investigate finite-temperature properties of the system commonly coined the most complex perovskite, that is NaNbO3. Such simulations successfully reproduce the existence of seven different phases in its phase diagram. The decomposition of the total energy of this effective Hamiltonian into different terms, altogether with the values of the parameters associated with these terms, also allow us to shed some light into puzzling features of such a compound. Examples include revealing the microscopic reasons of why R 3 c is its ground state and why it solely adopts in-phase tiltings at high temperatures versus complex nanotwins for intermediate temperatures. The results of the computations also call for a revisiting of the so-called P ,R , and S states, in the sense that an unexpected and previously overlooked inhomogeneous electrical polarization is numerically found in the P state while complex tiltings associated with the simultaneous condensation of several k points are predicted for the controversial R and S phases.
Network reliability analysis of complex systems using a non-simulation-based method
International Nuclear Information System (INIS)
Kim, Youngsuk; Kang, Won-Hee
2013-01-01
Civil infrastructures such as transportation, water supply, sewers, telecommunications, and electrical and gas networks often establish highly complex networks, due to their multiple source and distribution nodes, complex topology, and functional interdependence between network components. To understand the reliability of such complex network system under catastrophic events such as earthquakes and to provide proper emergency management actions under such situation, efficient and accurate reliability analysis methods are necessary. In this paper, a non-simulation-based network reliability analysis method is developed based on the Recursive Decomposition Algorithm (RDA) for risk assessment of generic networks whose operation is defined by the connections of multiple initial and terminal node pairs. The proposed method has two separate decomposition processes for two logical functions, intersection and union, and combinations of these processes are used for the decomposition of any general system event with multiple node pairs. The proposed method is illustrated through numerical network examples with a variety of system definitions, and is applied to a benchmark gas transmission pipe network in Memphis TN to estimate the seismic performance and functional degradation of the network under a set of earthquake scenarios.
Soltani Nehzad, Amir; Lukkien, Johan J.; Mak, Rudolf H.; Verhoeven, Richard; van den Heuvel, Martijn M.H.P.; Skavhaug, A.; Guiochet, J.; Schoitsch, E.; Bitsch, F.
2016-01-01
Simulations are widely used in the engineering workflow of complex mechatronic embedded systems in various domains, such as healthcare, railway, automotive and aerospace, for analyzing, testing and validating purposes. This paper focuses on the development and test of the control software of complex
Energy Technology Data Exchange (ETDEWEB)
Montoya, M.L. [GKSS-Forschungszentrum Geesthacht GmbH (Germany). Inst. fuer Hydrophysik
1999-07-01
Climatic conditions during the lst interglacial (125,000 years before present) are investigated with two climate models of different complexity: The atmosphere-ocean general circulation model ECHAM-1/LSG and the climate system model of intermediate complexity CLIMBER-2. In particular the role of vegetation at the last interglacial maximum, and its importance for a consistent simulation of the Mid-Holocene climate, has been investigated (EU project ASPEN: Air-Sea Wave Processes in Climate Change Models). Comparison of the results of the two models reveals a broad agreement in most large-scale features. Nevertheless, discrepancies are also detected. Essentially, the models differ in their ocean circulation responses. Profiting of the fast turnaround time of CLIMBER-2, a number of sensitivity experiments have been performed to try to explain the possible reasons for these differences, and to analyze additional effects not included in the previous simulations. In particular, the role of vegetation at the last interglacial maximum has been investigated. Comparison of the simulated responses against CLIMAP reconstructed SSTs for Marine Isotope Stage 5e shows a satisfactory agreement within the data uncertainties. (orig.) [German] Die klimatischen Bedingungen waehrend der letzten interglazialen Periode (vor 125 000 Jahren) werden anhand zweier Klimamodelle unterschiedlicher Komplexitaet untersucht: Dem Ozean-Atmosphaere gekoppelten allgemeinen Zirkulationsmodell ECHAM-1/LSG und dem Klimasystemmodell mittlerer Komplexitaet CLIMBER-2. Inbesondere wurde die Rolle der Vegetation in der letzten interglazialen Periode und ihre Bedeutung fuer eine konsistente Simulation des mittelholozaenischen Klimas untersucht (EU-Projekt ASPEN: Air-Sea Wave Processes in Climate Change Models - 'Klimavariationen in historischen Zeiten'). Der Vergleich der Ergebnisse beider Modelle zeigt eine gute Uebereinstimmung der meisten der grossskaligen Eigenschaften, allerdings zeigen sich
Energy Technology Data Exchange (ETDEWEB)
Montoya, M L [GKSS-Forschungszentrum Geesthacht GmbH (Germany). Inst. fuer Hydrophysik
1999-07-01
Climatic conditions during the lst interglacial (125,000 years before present) are investigated with two climate models of different complexity: The atmosphere-ocean general circulation model ECHAM-1/LSG and the climate system model of intermediate complexity CLIMBER-2. In particular the role of vegetation at the last interglacial maximum, and its importance for a consistent simulation of the Mid-Holocene climate, has been investigated (EU project ASPEN: Air-Sea Wave Processes in Climate Change Models). Comparison of the results of the two models reveals a broad agreement in most large-scale features. Nevertheless, discrepancies are also detected. Essentially, the models differ in their ocean circulation responses. Profiting of the fast turnaround time of CLIMBER-2, a number of sensitivity experiments have been performed to try to explain the possible reasons for these differences, and to analyze additional effects not included in the previous simulations. In particular, the role of vegetation at the last interglacial maximum has been investigated. Comparison of the simulated responses against CLIMAP reconstructed SSTs for Marine Isotope Stage 5e shows a satisfactory agreement within the data uncertainties. (orig.) [German] Die klimatischen Bedingungen waehrend der letzten interglazialen Periode (vor 125 000 Jahren) werden anhand zweier Klimamodelle unterschiedlicher Komplexitaet untersucht: Dem Ozean-Atmosphaere gekoppelten allgemeinen Zirkulationsmodell ECHAM-1/LSG und dem Klimasystemmodell mittlerer Komplexitaet CLIMBER-2. Inbesondere wurde die Rolle der Vegetation in der letzten interglazialen Periode und ihre Bedeutung fuer eine konsistente Simulation des mittelholozaenischen Klimas untersucht (EU-Projekt ASPEN: Air-Sea Wave Processes in Climate Change Models - 'Klimavariationen in historischen Zeiten'). Der Vergleich der Ergebnisse beider Modelle zeigt eine gute Uebereinstimmung der meisten der grossskaligen Eigenschaften, allerdings zeigen sich auch
International Nuclear Information System (INIS)
Bertolotto, D.
2011-11-01
The current doctoral research is focused on the development and validation of a coupled computational tool, to combine the advantages of computational fluid dynamics (CFD) in analyzing complex flow fields and of state-of-the-art system codes employed for nuclear power plant (NPP) simulations. Such a tool can considerably enhance the analysis of NPP transient behavior, e.g. in the case of pressurized water reactor (PWR) accident scenarios such as Main Steam Line Break (MSLB) and boron dilution, in which strong coolant flow asymmetries and multi-dimensional mixing effects strongly influence the reactivity of the reactor core, as described in Chap. 1. To start with, a literature review on code coupling is presented in Chap. 2, together with the corresponding ongoing projects in the international community. Special reference is made to the framework in which this research has been carried out, i.e. the Paul Scherrer Institute's (PSI) project STARS (Steady-state and Transient Analysis Research for the Swiss reactors). In particular, the codes chosen for the coupling, i.e. the CFD code ANSYS CFX V11.0 and the system code US-NRC TRACE V5.0, are part of the STARS codes system. Their main features are also described in Chap. 2. The development of the coupled tool, named CFX/TRACE from the names of the two constitutive codes, has proven to be a complex and broad-based task, and therefore constraints had to be put on the target requirements, while keeping in mind a certain modularity to allow future extensions to be made with minimal efforts. After careful consideration, the coupling was defined to be on-line, parallel and with non-overlapping domains connected by an interface, which was developed through the Parallel Virtual Machines (PVM) software, as described in Chap. 3. Moreover, two numerical coupling schemes were implemented and tested: a sequential explicit scheme and a sequential semi-implicit scheme. Finally, it was decided that the coupling would be single
International Nuclear Information System (INIS)
Han, Y.P.; Cui, Z.W.; Gouesbet, G.
2012-01-01
An efficient numerical method based on the surface integral equations is introduced to simulate the scattering of Gaussian beam by complex particles that consist of an arbitrarily shaped host particle and multiple internal inclusions of arbitrary shape. In particular, the incident focused Gaussian beam is described by the Davis fifth-order approximate expressions in combination with rotation defined by Euler angles. The established surface integral equations are discretized with the method of moments, where the unknown equivalent electric and magnetic currents induced on the surfaces of the host particle and the internal inclusions are expanded using the Rao-Wilton-Glisson (RWG) basis functions. The resultant matrix equations are solved by using the parallel conjugate gradient method. The proposed numerical method is validated and its capability illustrated in several characteristic examples.
Managing the complexity of critical infrastructures a modelling and simulation approach
Rosato, Vittorio; Kyriakides, Elias; Rome, Erich
2016-01-01
This book is open access under a CC BY 4.0 license. This book summarizes work being pursued in the context of the CIPRNet (Critical Infrastructure Preparedness and Resilience Research Network) research project, co-funded by the European Union under the Seventh Framework Programme (FP7). The project is intended to provide concrete and on-going support to the Critical Infrastructure Protection (CIP) research communities, enhancing their preparedness for CI-related emergencies, while also providing expertise and technologies for other stakeholders to promote their understanding and mitigation of the consequences of CI disruptions, leading to enhanced resilience. The book collects the tutorial material developed by the authors for several courses on the modelling, simulation and analysis of CIs, representing extensive and integrated CIP expertise. It will help CI stakeholders, CI operators and civil protection authorities understand the complex system of CIs, and help them adapt to these changes and threats in or...
International Nuclear Information System (INIS)
Ha, Jun Su; Seong, Poong Hyun
2005-01-01
In literature, there are a lot of studies based on EEG signals during cognitive activities of human-beings but most of them dealt with simple cognitive activities such as transforming letters into Morse code, subtraction, reading, semantic memory search, visual search, memorizing a set of words and so on. In this work, EEG signals were analyzed during complex diagnostic tasks in NPP simulator-based environment. Investigated are the theta, alpha, beta, and gamma band EEG powers during the diagnostic tasks. The experimental design and procedure are represented in section 2 and the results are shown in section 3. Finally some considerations are discussed and the direction for the further work is proposed in section 4
Numerical simulation of complex part manufactured by selective laser melting process
Van Belle, Laurent
2017-10-01
Selective Laser Melting (SLM) process belonging to the family of the Additive Manufacturing (AM) technologies, enable to build parts layer by layer, from metallic powder and a CAD model. Physical phenomena that occur in the process have the same issues as conventional welding. Thermal gradients generate significant residual stresses and distortions in the parts. Moreover, the large and complex parts to manufacturing, accentuate the undesirable effects. Therefore, it is essential for manufacturers to offer a better understanding of the process and to ensure production reliability of parts with high added value. This paper focuses on the simulation of manufacturing turbine by SLM process in order to calculate residual stresses and distortions. Numerical results will be presented.
Energy Technology Data Exchange (ETDEWEB)
Ha, Jun Su; Seong, Poong Hyun [Korea Advanced Institute of Science and Technology, Taejon (Korea, Republic of)
2005-07-01
In literature, there are a lot of studies based on EEG signals during cognitive activities of human-beings but most of them dealt with simple cognitive activities such as transforming letters into Morse code, subtraction, reading, semantic memory search, visual search, memorizing a set of words and so on. In this work, EEG signals were analyzed during complex diagnostic tasks in NPP simulator-based environment. Investigated are the theta, alpha, beta, and gamma band EEG powers during the diagnostic tasks. The experimental design and procedure are represented in section 2 and the results are shown in section 3. Finally some considerations are discussed and the direction for the further work is proposed in section 4.
Nagata, Keitro; Nishimura, Jun; Shimasaki, Shinji
2018-03-01
We study QCD at finite density and low temperature by using the complex Langevin method. We employ the gauge cooling to control the unitarity norm and intro-duce a deformation parameter in the Dirac operator to avoid the singular-drift problem. The reliability of the obtained results are judged by the probability distribution of the magnitude of the drift term. By making extrapolations with respect to the deformation parameter using only the reliable results, we obtain results for the original system. We perform simulations on a 43 × 8 lattice and show that our method works well even in the region where the reweighing method fails due to the severe sign problem. As a result we observe a delayed onset of the baryon number density as compared with the phase-quenched model, which is a clear sign of the Silver Blaze phenomenon.
Monnier, Angélique; Loevenbruck, Anne; Gailler, Audrey; Hébert, Hélène
2016-04-01
The 11 March 2011 Tohoku-Oki event, whether earthquake or tsunami, is exceptionally well documented. A wide range of onshore and offshore data has been recorded from seismic, geodetic, ocean-bottom pressure and sea level sensors. Along with these numerous observations, advance in inversion technique and computing facilities have led to many source studies. Rupture parameters inversion such as slip distribution and rupture history permit to estimate the complex coseismic seafloor deformation. From the numerous published seismic source studies, the most relevant coseismic source models are tested. The comparison of the predicted signals generated using both static and cinematic ruptures to the offshore and coastal measurements help determine which source model should be used to obtain the more consistent coastal tsunami simulations. This work is funded by the TANDEM project, reference ANR-11-RSNR-0023-01 of the French Programme Investissements d'Avenir (PIA 2014-2018).
DEFF Research Database (Denmark)
Lei, Tian; Nielsen, Kaspar Kirstein; Engelbrecht, Kurt
2014-01-01
Compared to a conventional vapor compression refrigera-tion system, a magnetocaloric refrigerator has many advantages, such as potentially high efficiency, low vibration and avoidance of refrigerants that deplete the ozone layer and cause the green-house effect. As a main component of the active...... magnetic re-generative refrigerator, the regenerator plays an important role in the cooling performance and efficiency of the whole system. However, the regenerator design is constrained by several exter-nal factors, such as the geometry of the magnetic field source and flow resistance. In this work, novel...... regenerators with complex flow arrange-ments, providing high performance at lower pressure drop, are investigated. Correspondingly a one dimensional model is pre-sented and comparative studies between novel and conventional regenerators are carried out by simulation. The effect of regen-erator geometries...
Interactive ultrasonic field simulations for complex non-destructive testing configurations
International Nuclear Information System (INIS)
Bhatia, Navnina
2016-01-01
Cone tomography is a well established inspection technique for industrial inspection purposes. The generation of scattering noise is inherent to the physical phenomena involved, and occurs both inside the material and the detector. This leads to the apparition of various blurring effects in 2D projections and to reconstruction errors when this effect is not properly taken into account. This works proposes an evolution of the scattering kernel superposition method, aiming at correcting these scattering effect directly in the 2D projections, before the reconstruction process. It consists in fitting analytical kernels that are used to generate realistic scattering contributions, which are in turn subtracted from the 2D projections. The proposed method has been tested using experimental data in cases involving complex materials and different levels of energy. Finally, a joint use of simulated and experimental data is described in the last chapter, in order to enhance the scattering kernels estimation. (author) [fr
Jarrett, Angela M.; Hormuth, David A.; Barnes, Stephanie L.; Feng, Xinzeng; Huang, Wei; Yankeelov, Thomas E.
2018-05-01
Clinical methods for assessing tumor response to therapy are largely rudimentary, monitoring only temporal changes in tumor size. Our goal is to predict the response of breast tumors to therapy using a mathematical model that utilizes magnetic resonance imaging (MRI) data obtained non-invasively from individual patients. We extended a previously established, mechanically coupled, reaction-diffusion model for predicting tumor response initialized with patient-specific diffusion weighted MRI (DW-MRI) data by including the effects of chemotherapy drug delivery, which is estimated using dynamic contrast-enhanced (DCE-) MRI data. The extended, drug incorporated, model is initialized using patient-specific DW-MRI and DCE-MRI data. Data sets from five breast cancer patients were used—obtained before, after one cycle, and at mid-point of neoadjuvant chemotherapy. The DCE-MRI data was used to estimate spatiotemporal variations in tumor perfusion with the extended Kety–Tofts model. The physiological parameters derived from DCE-MRI were used to model changes in delivery of therapy drugs within the tumor for incorporation in the extended model. We simulated the original model and the extended model in both 2D and 3D and compare the results for this five-patient cohort. Preliminary results show reductions in the error of model predicted tumor cellularity and size compared to the experimentally-measured results for the third MRI scan when therapy was incorporated. Comparing the two models for agreement between the predicted total cellularity and the calculated total cellularity (from the DW-MRI data) reveals an increased concordance correlation coefficient from 0.81 to 0.98 for the 2D analysis and 0.85 to 0.99 for the 3D analysis (p < 0.01 for each) when the extended model was used in place of the original model. This study demonstrates the plausibility of using DCE-MRI data as a means to estimate drug delivery on a patient-specific basis in predictive models and
On the required complexity of vehicle dynamic models for use in simulation-based highway design.
Brown, Alexander; Brennan, Sean
2014-06-01
This paper presents the results of a comprehensive project whose goal is to identify roadway design practices that maximize the margin of safety between the friction supply and friction demand. This study is motivated by the concern for increased accident rates on curves with steep downgrades, geometries that contain features that interact in all three dimensions - planar curves, grade, and superelevation. This complexity makes the prediction of vehicle skidding quite difficult, particularly for simple simulation models that have historically been used for road geometry design guidance. To obtain estimates of friction margin, this study considers a range of vehicle models, including: a point-mass model used by the American Association of State Highway Transportation Officials (AASHTO) design policy, a steady-state "bicycle model" formulation that considers only per-axle forces, a transient formulation of the bicycle model commonly used in vehicle stability control systems, and finally, a full multi-body simulation (CarSim and TruckSim) regularly used in the automotive industry for high-fidelity vehicle behavior prediction. The presence of skidding--the friction demand exceeding supply--was calculated for each model considering a wide range of vehicles and road situations. The results indicate that the most complicated vehicle models are generally unnecessary for predicting skidding events. However, there are specific maneuvers, namely braking events within lane changes and curves, which consistently predict the worst-case friction margins across all models. This suggests that any vehicle model used for roadway safety analysis should include the effects of combined cornering and braking. The point-mass model typically used by highway design professionals may not be appropriate to predict vehicle behavior on high-speed curves during braking in low-friction situations. However, engineers can use the results of this study to help select the appropriate vehicle dynamic
Borazjani, Iman; Ge, Liang; Sotiropoulos, Fotis
2008-08-01
The sharp-interface CURVIB approach of Ge and Sotiropoulos [L. Ge, F. Sotiropoulos, A numerical method for solving the 3D unsteady incompressible Navier-Stokes equations in curvilinear domains with complex immersed boundaries, Journal of Computational Physics 225 (2007) 1782-1809] is extended to simulate fluid structure interaction (FSI) problems involving complex 3D rigid bodies undergoing large structural displacements. The FSI solver adopts the partitioned FSI solution approach and both loose and strong coupling strategies are implemented. The interfaces between immersed bodies and the fluid are discretized with a Lagrangian grid and tracked with an explicit front-tracking approach. An efficient ray-tracing algorithm is developed to quickly identify the relationship between the background grid and the moving bodies. Numerical experiments are carried out for two FSI problems: vortex induced vibration of elastically mounted cylinders and flow through a bileaflet mechanical heart valve at physiologic conditions. For both cases the computed results are in excellent agreement with benchmark simulations and experimental measurements. The numerical experiments suggest that both the properties of the structure (mass, geometry) and the local flow conditions can play an important role in determining the stability of the FSI algorithm. Under certain conditions the FSI algorithm is unconditionally unstable even when strong coupling FSI is employed. For such cases, however, combining the strong coupling iteration with under-relaxation in conjunction with the Aitken's acceleration technique is shown to effectively resolve the stability problems. A theoretical analysis is presented to explain the findings of the numerical experiments. It is shown that the ratio of the added mass to the mass of the structure as well as the sign of the local time rate of change of the force or moment imparted on the structure by the fluid determine the stability and convergence of the FSI
Simulating Coupling Complexity in Space Plasmas: First Results from a new code
Kryukov, I.; Zank, G. P.; Pogorelov, N. V.; Raeder, J.; Ciardo, G.; Florinski, V. A.; Heerikhuisen, J.; Li, G.; Petrini, F.; Shematovich, V. I.; Winske, D.; Shaikh, D.; Webb, G. M.; Yee, H. M.
2005-12-01
The development of codes that embrace 'coupling complexity' via the self-consistent incorporation of multiple physical scales and multiple physical processes in models has been identified by the NRC Decadal Survey in Solar and Space Physics as a crucial necessary development in simulation/modeling technology for the coming decade. The National Science Foundation, through its Information Technology Research (ITR) Program, is supporting our efforts to develop a new class of computational code for plasmas and neutral gases that integrates multiple scales and multiple physical processes and descriptions. We are developing a highly modular, parallelized, scalable code that incorporates multiple scales by synthesizing 3 simulation technologies: 1) Computational fluid dynamics (hydrodynamics or magneto-hydrodynamics-MHD) for the large-scale plasma; 2) direct Monte Carlo simulation of atoms/neutral gas, and 3) transport code solvers to model highly energetic particle distributions. We are constructing the code so that a fourth simulation technology, hybrid simulations for microscale structures and particle distributions, can be incorporated in future work, but for the present, this aspect will be addressed at a test-particle level. This synthesis we will provide a computational tool that will advance our understanding of the physics of neutral and charged gases enormously. Besides making major advances in basic plasma physics and neutral gas problems, this project will address 3 Grand Challenge space physics problems that reflect our research interests: 1) To develop a temporal global heliospheric model which includes the interaction of solar and interstellar plasma with neutral populations (hydrogen, helium, etc., and dust), test-particle kinetic pickup ion acceleration at the termination shock, anomalous cosmic ray production, interaction with galactic cosmic rays, while incorporating the time variability of the solar wind and the solar cycle. 2) To develop a coronal
Borazjani, Iman; Ge, Liang; Le, Trung; Sotiropoulos, Fotis
2013-01-01
We develop an overset-curvilinear immersed boundary (overset-CURVIB) method in a general non-inertial frame of reference to simulate a wide range of challenging biological flow problems. The method incorporates overset-curvilinear grids to efficiently handle multi-connected geometries and increase the resolution locally near immersed boundaries. Complex bodies undergoing arbitrarily large deformations may be embedded within the overset-curvilinear background grid and treated as sharp interfaces using the curvilinear immersed boundary (CURVIB) method (Ge and Sotiropoulos, Journal of Computational Physics, 2007). The incompressible flow equations are formulated in a general non-inertial frame of reference to enhance the overall versatility and efficiency of the numerical approach. Efficient search algorithms to identify areas requiring blanking, donor cells, and interpolation coefficients for constructing the boundary conditions at grid interfaces of the overset grid are developed and implemented using efficient parallel computing communication strategies to transfer information among sub-domains. The governing equations are discretized using a second-order accurate finite-volume approach and integrated in time via an efficient fractional-step method. Various strategies for ensuring globally conservative interpolation at grid interfaces suitable for incompressible flow fractional step methods are implemented and evaluated. The method is verified and validated against experimental data, and its capabilities are demonstrated by simulating the flow past multiple aquatic swimmers and the systolic flow in an anatomic left ventricle with a mechanical heart valve implanted in the aortic position. PMID:23833331
International Nuclear Information System (INIS)
Zahn, Dirk
2004-01-01
The rate-determining step of acid catalyzed peptide hydrolysis is the nucleophilic attack of a water molecule to the carbon atom of the amide group. Therein the addition of the hydroxyl group to the amide carbon atom involves the association of a water molecule transferring one of its protons to an adjacent water molecule. The protonation of the amide nitrogen atom follows as a separate reaction step. Since the nucleophilic attack involves the breaking and formation of several bonds, the underlying reaction coordinate is rather complex. We investigate this reaction step from path sampling Car-Parrinello molecular dynamics simulations. This approach does not require the predefinition of reaction coordinates and is thus particularly suited for investigating reaction mechanisms. From our simulations the most relevant components of the reaction coordinate are elaborated. Though the C···O distance of the oxygen atom of the water molecule performing the nucleophilic attack and the corresponding amide carbon atom is a descriptor of the reaction progress, a complete picture of the reaction coordinate must include all three molecules taking part in the reaction. Moreover, the proton transfer is found to depend on favorable solvent configurations. Thus, also the arrangement of non-reacting, i.e. solvent water molecules needs to be considered in the reaction coordinate
Interactive ultrasonic field simulations for complex non-destructive testing configurations
International Nuclear Information System (INIS)
Chouh, Hamza
2016-01-01
In order to fulfill increasing reliability and safety requirements, non-destructive testing techniques are constantly evolving and so does their complexity. Consequently, simulation is an essential part of their design. We developed a tool for the simulation of the ultrasonic field radiated by any planar probes into non-destructive testing configurations involving meshed geometries without prominent edges, isotropic and anisotropic, homogeneous and heterogeneous materials, and wave trajectories that can include reflections and transmissions. We approximate the ultrasonic wave fronts by using polynomial interpolators that are local to ultrasonic ray pencils. They are obtained using a surface research algorithm based on pencil tracing and successive subdivisions. Their interpolators enable the computation of the necessary quantities for the impulse responses on each point of a sampling of the transducer surface that fulfills the Shannon criterion. By doing so, we can compute a global impulse response which, when convolved with the excitation signal of the transducer, results in the ultrasonic field. The usage of task parallelism and of SIMD instructions on the most computationally expensive steps yields an important performance boost. Finally, we developed a tool for progressive visualization of field images. It benefits from an image reconstruction technique and schedules field computations in order to accelerate convergence towards the final image. (author) [fr
Cox, T J; Rutherford, J C; Kerr, S C; Smeaton, D C; Palliser, C C
2013-09-30
Nitrogen loads to several New Zealand lakes are dominated by nonpoint runoff from pastoral farmland which adversely affects lake water quality. A 'cap and trade' scheme is being considered to help meet targets set for nitrogen loads to Lake Rotorua, and a numerical model, NTRADER, has been developed to simulate and compare alternative schemes. NTRADER models both the geophysics of nitrogen generation and transport, including groundwater lag times, and the economics of 'cap and trade' schemes. It integrates the output from several existing models, including a farm-scale nitrogen leaching and abatement model, a farm-scale management economic model, and a catchment-scale nitrogen transport model. This paper details modeling methods and compares possible trading program design features for the Lake Rotorua catchment. Model simulations demonstrate how a cap and trade program could be used to effectively achieve challenging environmental goals in the targeted catchment. However, results also show that, due to complex hydrogeology, satisfactory environmental outcomes may be not achieved unless groundwater lag times are incorporated into the regulatory scheme. One way to do this, as demonstrated here, would be to explicitly include lag times in the cap and trade program. The utility of the model is further demonstrated by quantifying relative differences in abatement costs across potential regulatory schemes. Copyright © 2013 Elsevier Ltd. All rights reserved.
Development of complex simulation suite 'VEB' and application area expansion - 15326
International Nuclear Information System (INIS)
Obraztsov, E.; Kapista, D.; Kremnev, I.; Korokhov, T.; Kukhtevich, V.; Bezlepkin, V.
2015-01-01
Complex simulation suite 'Virtual Unit of NPP' (CSS 'VEB') is a set of connected software tools and computer codes that allow the simulation of various physical processes occurring in a power nuclear reactor (initially VVER - pressurized water reactor). A coupled computational model developed by means of CSS 'VEB' is based on a specific design and called an NPP Virtual Power Unit (VPU). And in November 2012 a pilot version of the Leningrad NPP-2 VPU (NPP-2006 design with water-cooled power reactor) successfully passed acceptance tests. The paper presents further development of CSS 'VEB' and application area expansion both on new tasks such as VPU calculations for the Probability Safety Analysis (PSA) and all modeling of other NPP types, like sodium-cooled reactor (that means a possibility to create a VPU not only for NPP with PWR). In the first part of this paper we will recall the basic idea and concept of CSS 'VEB' and VPU. Then we will describe the main components of CSS 'VEB' and their improvements. In the last part we will briefly describe the broadening of VPU uses
POD evaluation using simulation: A phased array UT case on a complex geometry part
Dominguez, Nicolas; Reverdy, Frederic; Jenson, Frederic
2014-02-01
The use of Probability of Detection (POD) for NDT performances demonstration is a key link in products lifecycle management. The POD approach is to apply the given NDT procedure on a series of known flaws to estimate the probability to detect with respect to the flaw size. A POD is relevant if and only if NDT operations are carried out within the range of variability authorized by the procedure. Such experimental campaigns require collection of large enough datasets to cover the range of variability with sufficient occurrences to build a reliable POD statistics, leading to expensive costs to get POD curves. In the last decade research activities have been led in the USA with the MAPOD group and later in Europe with the SISTAE and PICASSO projects based on the idea to use models and simulation tools to feed POD estimations. This paper proposes an example of application of POD using simulation on the inspection procedure of a complex -full 3D- geometry part using phased arrays ultrasonic testing. It illustrates the methodology and the associated tools developed in the CIVA software. The paper finally provides elements of further progress in the domain.
A Thorax Simulator for Complex Dynamic Bioimpedance Measurements With Textile Electrodes.
Ulbrich, Mark; Muhlsteff, Jens; Teichmann, Daniel; Leonhardt, Steffen; Walter, Marian
2015-06-01
Bioimpedance measurements on the human thorax are suitable for assessment of body composition or hemodynamic parameters, such as stroke volume; they are non-invasive, easy in application and inexpensive. When targeting personal healthcare scenarios, the technology can be integrated into textiles to increase ease, comfort and coverage of measurements. Bioimpedance is generally measured using two electrodes injecting low alternating currents (0.5-10 mA) and two additional electrodes to measure the corresponding voltage drop. The impedance is measured either spectroscopically (bioimpedance spectroscopy, BIS) between 5 kHz and 1 MHz or continuously at a fixed frequency around 100 kHz (impedance cardiography, ICG). A thorax simulator is being developed for testing and calibration of bioimpedance devices and other new developments. For the first time, it is possible to mimic the complete time-variant properties of the thorax during an impedance measurement. This includes the dynamic real part and dynamic imaginary part of the impedance with a peak-to-peak value of 0.2 Ω and an adjustable base impedance (24.6 Ω ≥ Z0 ≥ 51.6 Ω). Another novelty is adjustable complex electrode-skin contact impedances for up to 8 electrodes to evaluate bioimpedance devices in combination with textile electrodes. In addition, an electrocardiographic signal is provided for cardiographic measurements which is used in ICG devices. This provides the possibility to generate physiologic impedance changes, and in combination with an ECG, all parameters of interest such as stroke volume (SV), pre-ejection period (PEP) or extracellular resistance (Re) can be simulated. The speed of all dynamic signals can be altered. The simulator was successfully tested with commercially available BIS and ICG devices and the preset signals are measured with high correlation (r = 0.996).
Linares, Jorge; Eddine Allal, Salah; Dahoo, Pierre Richard; Garcia, Yann
2017-12-01
The spin-crossover (SCO) phenomenon is related to the ability of a transition metal to change its spin state vs. a given perturbation. For an iron(II) SCO complexes the reversible changes involve the diamagnetic low-spin (S = 0) and the paramagnetic high-spin (HS S = 2) states [1,2,3]. In this contribution we simulate the HS Fraction (nHS) for different set values of temperature and pressure for a device using two SCO complexes with weak elastic interactions. We improve the calculation given by Linares et al. [4], taking also into account different volume (VHS, VLS) changes of the SCO. We perform all the calculation in the frame work of an Ising-like model solved in the mean-field approximation. The two SCO show in the case of “weak elastic interactions”, gradual spin transitions such that both temperature and pressure values can be obtained from the optical observation in the light of calculations discussed in this article.
Theory and simulation of cavity quantum electro-dynamics in multi-partite quantum complex systems
Energy Technology Data Exchange (ETDEWEB)
Alidoosty Shahraki, Moslem; Khorasani, Sina; Aram, Mohammad Hasan [Sharif University of Technology, School of Electrical Engineering, Tehran (Iran, Islamic Republic of)
2014-05-15
The cavity quantum electrodynamics of various complex systems is here analyzed using a general versatile code developed in this research. Such quantum multi-partite systems normally consist of an arbitrary number of quantum dots in interaction with an arbitrary number of cavity modes. As an example, a nine-partition system is simulated under different coupling regimes, consisting of eight emitters interacting with one cavity mode. Two-level emitters (e.g. quantum dots) are assumed to have an arrangement in the form of a linear chain, defining the mutual dipole-dipole interactions. It was observed that plotting the system trajectory in the phase space reveals a chaotic behavior in the so-called ultrastrong-coupling regime. This result is mathematically confirmed by detailed calculation of the Kolmogorov entropy, as a measure of chaotic behavior. In order to study the computational complexity of our code, various multi-partite systems consisting of one to eight quantum dots in interaction with one cavity mode were solved individually. Computation run times and the allocated memory for each system were measured. (orig.)
Simulated two-dimensional electronic spectroscopy of the eight-bacteriochlorophyll FMO complex
Energy Technology Data Exchange (ETDEWEB)
Yeh, Shu-Hao [Department of Chemistry and Birck Nanotechnology Center, Purdue University, West Lafayette, Indiana 47907 (United States); Kais, Sabre, E-mail: kais@purdue.edu [Department of Chemistry and Birck Nanotechnology Center, Purdue University, West Lafayette, Indiana 47907 (United States); Qatar Environment and Energy Research Institute, Qatar Foundation, Doha (Qatar)
2014-12-21
The Fenna-Matthews-Olson (FMO) protein-pigment complex acts as a molecular wire conducting energy between the outer antenna system and the reaction center; it is an important photosynthetic system to study the transfer of excitonic energy. Recent crystallographic studies report the existence of an additional (eighth) bacteriochlorophyll a (BChl a) in some of the FMO monomers. To understand the functionality of this eighth BChl, we simulated the two-dimensional electronic spectra of both the 7-site (apo form) and the 8-site (holo form) variant of the FMO complex from green sulfur bacteria, Prosthecochloris aestuarii. By comparing the spectrum, it was found that the eighth BChl can affect two different excitonic energy transfer pathways: (1) it is directly involved in the first apo form pathway (6 → 3 → 1) by passing the excitonic energy to exciton 6; and (2) it facilitates an increase in the excitonic wave function overlap between excitons 4 and 5 in the second pathway (7 → 4,5 → 2 → 1) and thus increases the possible downward sampling routes across the BChls.
Directory of Open Access Journals (Sweden)
M. A. Cremasco
2009-03-01
Full Text Available A laboratory-scale simulated moving bed (SMB was designed and tested for the separation of paclitaxel, a powerful anti-cancer agent known as Taxol@, from impurities of a plant tissue culture (PTC broth. The innovative strategy of a pseudo-binary model, where mixtures A and B were treated as single solutes A and B, was used in the linear standing wave analysis to fix the SMB operating parameters for a multicomponent and complex system. Linear standing wave design was used to specify the zone flow rates and the switching time for the laboratory-scale SMB unit, with two steps of separation. The SMB consists of four packed columns, where each column is 12.5 cm in length and 1.5 cm in diameter. Two sequential separation steps were used to recover paclitaxel from a small feed batch (less than one liter. Placlitaxel was recovered from the complex plant tissue culture broth in 82% yield and 72% purity.
Quantifying Configuration-Sampling Error in Langevin Simulations of Complex Molecular Systems
Directory of Open Access Journals (Sweden)
Josh Fass
2018-04-01
Full Text Available While Langevin integrators are popular in the study of equilibrium properties of complex systems, it is challenging to estimate the timestep-induced discretization error: the degree to which the sampled phase-space or configuration-space probability density departs from the desired target density due to the use of a finite integration timestep. Sivak et al., introduced a convenient approach to approximating a natural measure of error between the sampled density and the target equilibrium density, the Kullback-Leibler (KL divergence, in phase space, but did not specifically address the issue of configuration-space properties, which are much more commonly of interest in molecular simulations. Here, we introduce a variant of this near-equilibrium estimator capable of measuring the error in the configuration-space marginal density, validating it against a complex but exact nested Monte Carlo estimator to show that it reproduces the KL divergence with high fidelity. To illustrate its utility, we employ this new near-equilibrium estimator to assess a claim that a recently proposed Langevin integrator introduces extremely small configuration-space density errors up to the stability limit at no extra computational expense. Finally, we show how this approach to quantifying sampling bias can be applied to a wide variety of stochastic integrators by following a straightforward procedure to compute the appropriate shadow work, and describe how it can be extended to quantify the error in arbitrary marginal or conditional distributions of interest.
Cleland, Jennifer; Walker, Kenneth G; Gale, Michael; Nicol, Laura G
2016-08-01
The focus of simulation-based education (SBE) research has been limited to outcome and effectiveness studies. The effect of social and cultural influences on SBE is unclear and empirical work is lacking. Our objective in this study was to explore and understand the complexity of context and social factors at a surgical boot camp (BC). A rapid ethnographic study, employing the theoretical lenses of complexity and activity theory and Bourdieu's concept of 'capital', to better understand the socio-cultural influences acting upon, and during, two surgical BCs, and their implications for SBE. Over two 4-day BCs held in Scotland, UK, an observer and two preceptors conducted 81 hours of observations, 14 field interviews and 11 formal interviews with faculty members (n = 10, including the lead faculty member, session leaders and junior faculty members) and participants (n = 19 core surgical trainees and early-stage residents). Data collection and inductive analysis for emergent themes proceeded iteratively. This paper focuses on three analytical themes. First, the complexity of the surgical training system and wider health care education context, and how this influenced the development of the BC. Second, participants' views of the BC as a vehicle not just for learning skills but for gaining 'insider information' on how best to progress in surgical training. Finally, the explicit aim of faculty members to use the Scottish Surgical Bootcamp to welcome trainees and residents into the world of surgery, and how this occurred. To the best of our knowledge, this is the first empirical study of a surgical BC that takes a socio-cultural approach to exploring and understanding context, complexities, uncertainties and learning associated with one example of SBE. Our findings suggest that a BC is as much about social and cultural processes as it is about individual, cognitive and acquisitive learning. Acknowledging this explicitly will help those planning similar enterprises and
Energy Technology Data Exchange (ETDEWEB)
Milind Deo; Chung-Kan Huang; Huabing Wang
2008-08-31
Black-oil, compositional and thermal simulators have been developed to address different physical processes in reservoir simulation. A number of different types of discretization methods have also been proposed to address issues related to representing the complex reservoir geometry. These methods are more significant for fractured reservoirs where the geometry can be particularly challenging. In this project, a general modular framework for reservoir simulation was developed, wherein the physical models were efficiently decoupled from the discretization methods. This made it possible to couple any discretization method with different physical models. Oil characterization methods are becoming increasingly sophisticated, and it is possible to construct geologically constrained models of faulted/fractured reservoirs. Discrete Fracture Network (DFN) simulation provides the option of performing multiphase calculations on spatially explicit, geologically feasible fracture sets. Multiphase DFN simulations of and sensitivity studies on a wide variety of fracture networks created using fracture creation/simulation programs was undertaken in the first part of this project. This involved creating interfaces to seamlessly convert the fracture characterization information into simulator input, grid the complex geometry, perform the simulations, and analyze and visualize results. Benchmarking and comparison with conventional simulators was also a component of this work. After demonstration of the fact that multiphase simulations can be carried out on complex fracture networks, quantitative effects of the heterogeneity of fracture properties were evaluated. Reservoirs are populated with fractures of several different scales and properties. A multiscale fracture modeling study was undertaken and the effects of heterogeneity and storage on water displacement dynamics in fractured basements were investigated. In gravity-dominated systems, more oil could be recovered at a given pore
International Nuclear Information System (INIS)
Trebotich, David
2007-01-01
We have developed a simulation capability to model multiscale flow and transport in complex biological systems based on algorithms and software infrastructure developed under the SciDAC APDEC CET. The foundation of this work is a new hybrid fluid-particle method for modeling polymer fluids in irregular microscale geometries that enables long-time simulation of validation experiments. Both continuum viscoelastic and discrete particle representations have been used to model the constitutive behavior of polymer fluids. Complex flow environment geometries are represented on Cartesian grids using an implicit function. Direct simulation of flow in the irregular geometry is then possible using embedded boundary/volume-of-fluid methods without loss of geometric detail. This capability has been used to simulate biological flows in a variety of application geometries including biomedical microdevices, anatomical structures and porous media
Energy Technology Data Exchange (ETDEWEB)
Duru, Kenneth, E-mail: kduru@stanford.edu [Department of Geophysics, Stanford University, Stanford, CA (United States); Dunham, Eric M. [Department of Geophysics, Stanford University, Stanford, CA (United States); Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA (United States)
2016-01-15
Dynamic propagation of shear ruptures on a frictional interface in an elastic solid is a useful idealization of natural earthquakes. The conditions relating discontinuities in particle velocities across fault zones and tractions acting on the fault are often expressed as nonlinear friction laws. The corresponding initial boundary value problems are both numerically and computationally challenging. In addition, seismic waves generated by earthquake ruptures must be propagated for many wavelengths away from the fault. Therefore, reliable and efficient numerical simulations require both provably stable and high order accurate numerical methods. We present a high order accurate finite difference method for: a) enforcing nonlinear friction laws, in a consistent and provably stable manner, suitable for efficient explicit time integration; b) dynamic propagation of earthquake ruptures along nonplanar faults; and c) accurate propagation of seismic waves in heterogeneous media with free surface topography. We solve the first order form of the 3D elastic wave equation on a boundary-conforming curvilinear mesh, in terms of particle velocities and stresses that are collocated in space and time, using summation-by-parts (SBP) finite difference operators in space. Boundary and interface conditions are imposed weakly using penalties. By deriving semi-discrete energy estimates analogous to the continuous energy estimates we prove numerical stability. The finite difference stencils used in this paper are sixth order accurate in the interior and third order accurate close to the boundaries. However, the method is applicable to any spatial operator with a diagonal norm satisfying the SBP property. Time stepping is performed with a 4th order accurate explicit low storage Runge–Kutta scheme, thus yielding a globally fourth order accurate method in both space and time. We show numerical simulations on band limited self-similar fractal faults revealing the complexity of rupture
Simulation of recording the microwave holograms of complex objects by the near range radars
Directory of Open Access Journals (Sweden)
V. V. Razevig
2014-01-01
Full Text Available Radar is an object-detection technology that uses radio waves to determine the presence, range, altitude, direction, or speed of objects. In the recent time, there is an increasingly arising interest to the near range microwave imaging that allows detection of the shape and, in some cases, the inner structure of the investigated objects.For design engineering and efficiency evaluation of the cutting-edge radars as well as for testing the developed recovery algorithms a set of microwave holograms of various objects obtained under different conditions is needed. Microwave holograms cannot be obtained only on the basis of the experimental researches related to the measurements of electromagnetic scattering by the real objects since such experiments are time consuming and quite expensive. Therefore, to simulate electromagnetic scattering processes via objects examination is quite a challenge.This investigation goal is to develop a computer simulation method to record the microwave holograms of complex objects by the near range radars.To specify the shape of the investigated objects, Autodesk 3ds Max (3D computer graphics program for making 3D animations, models, and images is used. At a second stage the surface of the created object is described by a set of triangular facets. While calculating the reflected field, a final representation of the object as a set of point reflectors is used. Thus, the model of single scattering, is used without taking into consideration re-reflection and cross-influence of reflectors.Methods are also described to form the focused images of the microwave holograms that allow us to obtain a function describing object reflectivity, by which in most cases an object shape can be easily recognized.A comparison of computer-simulated holograms with experimental data proves the model adequacy.The model can be used to find a dependence of the plane resolution on used frequency, step of scanning, and distance to the object and a
DEFF Research Database (Denmark)
Loumann Krogh, Charlotte; Konge, Lars; Bjurström, Johanna Margareta
2013-01-01
Virtual-reality (VR) simulation provides a safe and effective learning environment prior to practicing on patients. However, existing bronchoscopy simulators are expensive and not easily portable.......Virtual-reality (VR) simulation provides a safe and effective learning environment prior to practicing on patients. However, existing bronchoscopy simulators are expensive and not easily portable....
Energy Technology Data Exchange (ETDEWEB)
Burgwinkel, Paul; Vreydal, Daniel; Eltaliawi, Gamil; Vijayakumar, Nandhakumar [RWTH Aachen (DE). Inst. fuer Maschinentechnik der Rohstoffindustrie (IMR)
2010-09-15
For the first time the Co-simulation method was successfully used for full representation of a large belt conveyor for an open cast mine in a simulation model at the Institute for Mechanical Engineering in the Raw Materials Industry at Rhineland-Westphalia Technological University in Aachen. The aim of this project was the development of an electro-mechanical simulation model, which represents all components of a large belt conveyor from the drive motor to the conveyor belt in one simulation model and thus makes the interactions between the individual assemblies verifiable by calculations. With the aid of the developed model it was possible to determine critical operating speeds of the represented large belt conveyor and derive suitable measures to combat undesirable resonance states in the drive assembly. Furthermore it was possible to clarify the advantage of the full numerical representation of an electromechanical drive system. (orig.)
International Nuclear Information System (INIS)
Li Di; Wang Geng; Chen Yang; Li Lin; Shrivastav, Gaurav; Oak, Stimit; Tasch, Al; Banerjee, Sanjay; Obradovic, Borna
2001-01-01
A physically-based three-dimensional Monte Carlo simulator has been developed within UT-MARLOWE, which is capable of simulating ion implantation into multi-material systems and arbitrary topography. Introducing the third dimension can result in a severe CPU time penalty. In order to minimize this penalty, a three-dimensional trajectory replication algorithm has been developed, implemented and verified. More than two orders of magnitude savings of CPU time have been observed. An unbalanced Octree structure was used to decompose three-dimensional structures. It effectively simplifies the structure, offers a good balance between modeling accuracy and computational efficiency, and allows arbitrary precision of mapping the Octree onto desired structure. Using the well-established and validated physical models in UT-MARLOWE 5.0, this simulator has been extensively verified by comparing the integrated one-dimensional simulation results with secondary ion mass spectroscopy (SIMS). Two options, the typical case and the worst scenario, have been selected to simulate ion implantation into poly-silicon under various scenarios using this simulator: implantation into a random, amorphous network, and implantation into the worst-case channeling condition, into (1 1 0) orientated wafers
Some Fundamental Issues of Mathematical Simulation in Biology
Razzhevaikin, V. N.
2018-02-01
Some directions of simulation in biology leading to original formulations of mathematical problems are overviewed. Two of them are discussed in detail: the correct solvability of first-order linear equations with unbounded coefficients and the construction of a reaction-diffusion equation with nonlinear diffusion for a model of genetic wave propagation.
International Nuclear Information System (INIS)
Faulin, Javier; Juan, Angel A.; Serrat, Carles; Bargueno, Vicente
2008-01-01
In this paper, we propose the use of discrete-event simulation (DES) as an efficient methodology to obtain estimates of both survival and availability functions in time-dependent real systems-such as telecommunication networks or distributed computer systems. We discuss the use of DES in reliability and availability studies, not only as an alternative to the use of analytical and probabilistic methods, but also as a complementary way to: (i) achieve a better understanding of the system internal behavior and (ii) find out the relevance of each component under reliability/availability considerations. Specifically, this paper describes a general methodology and two DES algorithms, called SAEDES, which can be used to analyze a wide range of time-dependent complex systems, including those presenting multiple states, dependencies among failure/repair times or non-perfect maintenance policies. These algorithms can provide valuable information, specially during the design stages, where different scenarios can be compared in order to select a system design offering adequate reliability and availability levels. Two case studies are discussed, using a C/C++ implementation of the SAEDES algorithms, to show some potential applications of our approach
Mechanical and physical simulation of complex 3-D bulk forming processes with Forge3
International Nuclear Information System (INIS)
Chenot, J-L.; Chastel, Y.
2000-01-01
To-day there is a growing need to predict numerically not only the mechanical parameters, but also the final microstructure of the work-piece. On the other hand, the use of simulation codes to analyze complex laboratory experiments can be viewed as a powerful way to improve the analysis of physical data. We outline basic methods for developing a finite element model of unsteady metal forming processes. At first the thermal and mechanical equations are recalled with several integral formulations. The most important issues are discussed, including time integration, evolving contact with rigid or deformable tools, meshing, remeshing, and parallel computing. Physical coupling is presented with the two possible approaches: introduction of internal parameters describing the evolution of microstructure and coupling with constitutive equations; multi-scale computation illustrated by the texture prediction. Finally it is shown that the inverse approach can be successfully applied to improve parameters identification from data acquisition of laboratory tests, or possibly from industrial experiments. This methodology can be utilized for: constitutive modeling, friction behavior, or even for internal parameters laws describing physical evolution. (author)
Energy Technology Data Exchange (ETDEWEB)
Skraaning, Gyrd Jr.
2004-03-15
This report is a reprint of a dr.philos. thesis written by Gyrd Skraaning Jr. The text was submitted and accepted by the Norwegian University of Science and Technology in 2003 (ISBN 82-471-5237-1). The thesis suggests a nonlinear model of the theoretical relationship between experimental control and realism, claiming that high degrees of realism and experimental control can be obtained simultaneously if the experimental methods are utilized strategically and developed further. This is in opposition to the conventional opinion that realism and experimental control are mutually excluding objectives. The thesis debates the impact of the operating task on human performance during simulator studies in HAMMLAB, and suggests how task variation can be experimentally controlled. In a within subject design, every subject is tested under all experimental conditions, and the presentation order of the conditions is counterbalanced to compensate for order effects. In realistic settings, it is essential that the experimental design imposes few artificial constrains on the research environment. At the same time, the design should be able to uncover experimental effects in situations where the number of participants is low. Within-subject design represents a reasonable compromise between these aspirations. In this respect, an alternative counterbalancing method is proposed (dis-ORDER). A theoretical analysis of the human performance concept and a discussion about performance measurement in complex operating environments, are followed by a debate on the shortcomings of traditional performance indicators. Two specialized operator performance assessment techniques are then presented and evaluated (OPAS and ORT). (Author)
Simulations of Turbulent Flow Over Complex Terrain Using an Immersed-Boundary Method
DeLeon, Rey; Sandusky, Micah; Senocak, Inanc
2018-02-01
We present an immersed-boundary method to simulate high-Reynolds-number turbulent flow over the complex terrain of Askervein and Bolund Hills under neutrally-stratified conditions. We reconstruct both the velocity and the eddy-viscosity fields in the terrain-normal direction to produce turbulent stresses as would be expected from the application of a surface-parametrization scheme based on Monin-Obukhov similarity theory. We find that it is essential to be consistent in the underlying assumptions for the velocity reconstruction and the eddy-viscosity relation to produce good results. To this end, we reconstruct the tangential component of the velocity field using a logarithmic velocity profile and adopt the mixing-length model in the near-surface turbulence model. We use a linear interpolation to reconstruct the normal component of the velocity to enforce the impermeability condition. Our approach works well for both the Askervein and Bolund Hills when the flow is attached to the surface, but shows slight disagreement in regions of flow recirculation, despite capturing the flow reversal.
Energy Technology Data Exchange (ETDEWEB)
Faulin, Javier [Department of Statistics and Operations Research, Los Magnolios Building, First Floor, Campus Arrosadia, Public University of Navarre, 31006 Pamplona, Navarre (Spain)], E-mail: javier.faulin@unavarra.es; Juan, Angel A. [Department of Applied Mathematics I, Av. Doctor Maranon 44-50, Technical University of Catalonia, 08028 Barcelona (Spain)], E-mail: angel.alejandro.juan@upc.edu; Serrat, Carles [Department of Applied Mathematics I, Av. Doctor Maranon 44-50, Technical University of Catalonia, 08028 Barcelona (Spain)], E-mail: carles.serrat@upc.edu; Bargueno, Vicente [Department of Applied Mathematics I, ETS Ingenieros Industriales, Universidad Nacional de Educacion a Distancia, 28080 Madrid (Spain)], E-mail: vbargueno@ind.uned.es
2008-11-15
In this paper, we propose the use of discrete-event simulation (DES) as an efficient methodology to obtain estimates of both survival and availability functions in time-dependent real systems-such as telecommunication networks or distributed computer systems. We discuss the use of DES in reliability and availability studies, not only as an alternative to the use of analytical and probabilistic methods, but also as a complementary way to: (i) achieve a better understanding of the system internal behavior and (ii) find out the relevance of each component under reliability/availability considerations. Specifically, this paper describes a general methodology and two DES algorithms, called SAEDES, which can be used to analyze a wide range of time-dependent complex systems, including those presenting multiple states, dependencies among failure/repair times or non-perfect maintenance policies. These algorithms can provide valuable information, specially during the design stages, where different scenarios can be compared in order to select a system design offering adequate reliability and availability levels. Two case studies are discussed, using a C/C++ implementation of the SAEDES algorithms, to show some potential applications of our approach.
ADVANCED COMPUTATIONALMETHODS FOR COMPLEX SIMULATION OF THERMAL PROCESSES IN POWER ENGINEERING
Directory of Open Access Journals (Sweden)
Risto V. Filkoski
2007-04-01
Full Text Available The overall frame and principal steps of complex numerical modelling of thermal processes in power boiler furnaces on pulverised coal with tangential disposition of the burners are presented in the paper. Computational fluid dynamics (CFD technique is used as a tool to perform comprehensive thermal analysis in two test cases. The methodology for creation of three-dimensional models of boiler furnaces is briefly described. Standard steady k- model is employed for description of the turbulent flow. The coupling of continuity and momentum is achieved by the SIMPLEC method. Coal combustion is modelled by the mixture fraction/probability density function approach for the reaction chemistry, with equilibrium assumption applied for description of the system chemistry. Thermal radiation is computed by means of the simplified P-N model, based on expansion of the radiation intensity into an orthogonal series of spherical harmonics.Comparison between the simulation predictions and available site measurements leads to a conclusion that the model produces realistic insight into the furnace processes. Qualitative agreement of the results indicates reasonability of the calculations and validates the employed sub-models. The described test cases and other experiences with CFD modelling stress the advantages over a purely field data study, such as the ability to quickly and cheaply analyse a variety of design options without actually modifying the object and the availability of significantly more data to interpret the results.
Simulations of Turbulent Flow Over Complex Terrain Using an Immersed-Boundary Method
DeLeon, Rey; Sandusky, Micah; Senocak, Inanc
2018-06-01
We present an immersed-boundary method to simulate high-Reynolds-number turbulent flow over the complex terrain of Askervein and Bolund Hills under neutrally-stratified conditions. We reconstruct both the velocity and the eddy-viscosity fields in the terrain-normal direction to produce turbulent stresses as would be expected from the application of a surface-parametrization scheme based on Monin-Obukhov similarity theory. We find that it is essential to be consistent in the underlying assumptions for the velocity reconstruction and the eddy-viscosity relation to produce good results. To this end, we reconstruct the tangential component of the velocity field using a logarithmic velocity profile and adopt the mixing-length model in the near-surface turbulence model. We use a linear interpolation to reconstruct the normal component of the velocity to enforce the impermeability condition. Our approach works well for both the Askervein and Bolund Hills when the flow is attached to the surface, but shows slight disagreement in regions of flow recirculation, despite capturing the flow reversal.
International Nuclear Information System (INIS)
Skraaning, Gyrd Jr.
2004-03-01
This report is a reprint of a dr.philos. thesis written by Gyrd Skraaning Jr. The text was submitted and accepted by the Norwegian University of Science and Technology in 2003 (ISBN 82-471-5237-1). The thesis suggests a nonlinear model of the theoretical relationship between experimental control and realism, claiming that high degrees of realism and experimental control can be obtained simultaneously if the experimental methods are utilized strategically and developed further. This is in opposition to the conventional opinion that realism and experimental control are mutually excluding objectives. The thesis debates the impact of the operating task on human performance during simulator studies in HAMMLAB, and suggests how task variation can be experimentally controlled. In a within subject design, every subject is tested under all experimental conditions, and the presentation order of the conditions is counterbalanced to compensate for order effects. In realistic settings, it is essential that the experimental design imposes few artificial constrains on the research environment. At the same time, the design should be able to uncover experimental effects in situations where the number of participants is low. Within-subject design represents a reasonable compromise between these aspirations. In this respect, an alternative counterbalancing method is proposed (dis-ORDER). A theoretical analysis of the human performance concept and a discussion about performance measurement in complex operating environments, are followed by a debate on the shortcomings of traditional performance indicators. Two specialized operator performance assessment techniques are then presented and evaluated (OPAS and ORT). (Author)
Vijaykumar, Adithya; Ouldridge, Thomas E.; ten Wolde, Pieter Rein; Bolhuis, Peter G.
2017-03-01
The modeling of complex reaction-diffusion processes in, for instance, cellular biochemical networks or self-assembling soft matter can be tremendously sped up by employing a multiscale algorithm which combines the mesoscopic Green's Function Reaction Dynamics (GFRD) method with explicit stochastic Brownian, Langevin, or deterministic molecular dynamics to treat reactants at the microscopic scale [A. Vijaykumar, P. G. Bolhuis, and P. R. ten Wolde, J. Chem. Phys. 143, 214102 (2015)]. Here we extend this multiscale MD-GFRD approach to include the orientational dynamics that is crucial to describe the anisotropic interactions often prevalent in biomolecular systems. We present the novel algorithm focusing on Brownian dynamics only, although the methodology is generic. We illustrate the novel algorithm using a simple patchy particle model. After validation of the algorithm, we discuss its performance. The rotational Brownian dynamics MD-GFRD multiscale method will open up the possibility for large scale simulations of protein signalling networks.
Schreyer, W.; Kikawa, T.; Losekamm, M. J.; Paul, S.; Picker, R.
2017-06-01
Modern precision experiments trapping low-energy particles require detailed simulations of particle trajectories and spin precession to determine systematic measurement limitations and apparatus deficiencies. We developed PENTrack, a tool that allows to simulate trajectories of ultracold neutrons and their decay products-protons and electrons-and the precession of their spins in complex geometries and electromagnetic fields. The interaction of ultracold neutrons with matter is implemented with the Fermi-potential formalism and diffuse scattering using Lambert and microroughness models. The results of several benchmark simulations agree with STARucn v1.2, uncovered several flaws in Geant4 v10.2.2, and agree with experimental data. Experiment geometry and electromagnetic fields can be imported from commercial computer-aided-design and finite-element software. All simulation parameters are defined in simple text files allowing quick changes. The simulation code is written in C++ and is freely available at github.com/wschreyer/PENTrack.git.
Energy Technology Data Exchange (ETDEWEB)
Schreyer, W., E-mail: w.schreyer@tum.de [Technical University of Munich, James-Franck-Str. 1, 85748 Garching (Germany); Kikawa, T. [TRIUMF, 4004 Wesbrook Mall, Vancouver (Canada); Losekamm, M.J.; Paul, S. [Technical University of Munich, James-Franck-Str. 1, 85748 Garching (Germany); Picker, R. [TRIUMF, 4004 Wesbrook Mall, Vancouver (Canada); Simon Fraser University, 8888 University Drive, Burnaby (Canada)
2017-06-21
Modern precision experiments trapping low-energy particles require detailed simulations of particle trajectories and spin precession to determine systematic measurement limitations and apparatus deficiencies. We developed PENTrack, a tool that allows to simulate trajectories of ultracold neutrons and their decay products—protons and electrons—and the precession of their spins in complex geometries and electromagnetic fields. The interaction of ultracold neutrons with matter is implemented with the Fermi-potential formalism and diffuse scattering using Lambert and microroughness models. The results of several benchmark simulations agree with STARucn v1.2, uncovered several flaws in Geant4 v10.2.2, and agree with experimental data. Experiment geometry and electromagnetic fields can be imported from commercial computer-aided-design and finite-element software. All simulation parameters are defined in simple text files allowing quick changes. The simulation code is written in C++ and is freely available at (github.com/wschreyer/PENTrack.git).
DEFF Research Database (Denmark)
Kaszuba, K.; Postila, P. A.; Cramariuc, O.
2013-01-01
studied in large-scale classical molecular dynamics (MD) simulations. In part, this is due to lack of suitable force field parameters, centered atomic point charges in particular, for the complex's prosthetic redox centers. Accurate redox center charges are needed to depict realistically the inter-molecular...... interactions at different redox stages of the cyt bc(1) complex. Accordingly, here we present high-precision atomic point charges for the metal centers of the cyt bc(1) complex of Rhodobacter capsulatus derived from extensive density functional theory calculations, fitted using the restrained electrostatic...
Molecular dynamics simulations of ter-pyridine, BTP, and their complexes with La3+, Eu3+ and Lu3+
International Nuclear Information System (INIS)
Guilbaud, P.; Dognon, J.P.
2000-01-01
This poster presents molecular dynamics simulations performed to study ter-pyridine and bis-triazinyl-pyridine with lanthanide cations for the gas phase and for water solution. Different counter-ions have been tested in order to assess their influence on complexes structures and stabilities in both phases. For stable complexes, Gibbs free energy calculations have been achieved to estimate the selectivity of these complexes towards the lanthanide cations. Finally, some tests have been done adding a polarization term in the potential energy in order to have a more precise description of interaction energies. (authors)
Chang, T.; Pieterse, K.; Broeren, M.A.C.; Kooijman, H.; Spek, A.L.; Hilbers, P.A.J.; Meijer, E.W.
2007-01-01
The multiple monovalent binding of adamantyl-urea poly(propyleneimine) dendrimers with carboxylic acid-urea guests was investigated using molecular dynamics simulations and X-ray crystallography to better understand the structure and behavior of the dynamic multivalent complex in solution. The
Hagedorn Wonder, Amy
Limited opportunities exist for prelicensure nursing students to observe the interprofessional process required to resolve complex ethical cases in practice. Therefore, a mock hospital ethics committee (MHEC) was assembled to teach the application of ethics in practice through simulation. The MHEC meeting is an example of how nursing education and practice can partner to create meaningful learning experiences.
Harting, J.D.R.; Venturoli, M.; Coveney, P.V.
2004-01-01
Well–designed lattice Boltzmann codes exploit the essentially embarrassingly parallel features of the algorithm and so can be run with considerable efficiency on modern supercomputers. Such scalable codes permit us to simulate the behaviour of increasingly large quantities of complex condensed
The Complex Outgassing of Comets and the Resulting Coma, a Direct Simulation Monte-Carlo Approach
Fougere, Nicolas
During its journey, when a comet gets within a few astronomical units of the Sun, solar heating liberates gases and dust from its icy nucleus forming a rarefied cometary atmosphere, the so-called coma. This tenuous atmosphere can expand to distances up to millions of kilometers representing orders of magnitude larger than the nucleus size. Most of the practical cases of coma studies involve the consideration of rarefied gas flows under non-LTE conditions where the hydrodynamics approach is not valid. Then, the use of kinetic methods is required to properly study the physics of the cometary coma. The Direct Simulation Monte-Carlo (DSMC) method is the method of choice to solve the Boltzmann equation, giving the opportunity to study the cometary atmosphere from the inner coma where collisions dominate and is in thermodynamic equilibrium to the outer coma where densities are lower and free flow conditions are verified. While previous studies of the coma used direct sublimation from the nucleus for spherically symmetric 1D models, or 2D models with a day/night asymmetry, recent observations of comets showed the existence of local small source areas such as jets, and extended sources via sublimating icy grains, that must be included into cometary models for a realistic representation of the physics of the coma. In this work, we present, for the first time, 1D, 2D, and 3D models that can take into account the full effects of conditions with more complex sources of gas with jets and/or icy grains. Moreover, an innovative work in a full 3D description of the cometary coma using a kinetic method with a realistic nucleus and outgassing is demonstrated. While most of the physical models used in this study had already been developed, they are included in one self-consistent coma model for the first time. The inclusion of complex cometary outgassing processes represents the state-of-the-art of cometary coma modeling. This provides invaluable information about the coma by
2005-01-01
Tech-X Corporation releases simulation code for solving complex problems in plasma physics : VORPAL code provides a robust environment for simulating plasma processes in high-energy physics, IC fabrications and material processing applications
Greiner, Maximilian; Sonnleitner, Bettina; Mailänder, Markus; Briesen, Heiko
2014-02-01
Additional benefits of foods are an increasing factor in the consumer's purchase. To produce foods with the properties the consumer demands, understanding the micro- and nanostructure is becoming more important in food research today. We present molecular dynamics (MD) simulations as a tool to study complex and multi-component food systems on the example of chocolate conching. The process of conching is chosen because of the interesting challenges it provides: the components (fats, emulsifiers and carbohydrates) contain diverse functional groups, are naturally fluctuating in their chemical composition, and have a high number of internal degrees of freedom. Further, slow diffusion in the non-aqueous medium is expected. All of these challenges are typical to food systems in general. Simulation results show the suitability of present force fields to correctly model the liquid and crystal density of cocoa butter and sucrose, respectively. Amphiphilic properties of emulsifiers are observed by micelle formation in water. For non-aqueous media, pulling simulations reveal high energy barriers for motion in the viscous cocoa butter. The work for detachment of an emulsifier from the sucrose crystal is calculated and matched with detachment of the head and tail groups separately. Hydrogen bonding is shown to be the dominant interaction between the emulsifier and the crystal surface. Thus, MD simulations are suited to model the interaction between the emulsifier and sugar crystal interface in non-aqueous media, revealing detailed information about the structuring and interactions on a molecular level. With interaction parameters being available for a wide variety of chemical groups, MD simulations are a valuable tool to understand complex and multi-component food systems in general. MD simulations provide a substantial benefit to researchers to verify their hypothesis in dynamic simulations with an atomistic resolution. Rapid rise of computational resources successively
Energy Technology Data Exchange (ETDEWEB)
Garcia Velarde, M
1977-07-01
Thermo convective instabilities in horizontal fluid layers are discussed with emphasis on the Rayleigh-Bernard model problem. Steady solutions and time-dependent phenomena (relaxation oscillations and transition to turbulence) are studied within the nonlinear Boussinesq-Oberbeck approximation. Homogeneous steady solutions, limit cycles, and inhomogeneous (ordered) spatial structures are also studied in simple reaction-diffusion systems. Lastly, the non-periodic attractor that appears at large Rayleigh numbers in the truncated Boussinesq-Oberbeck model of Lorenz, is constructed, and a discussion of turbulent behavior is given. (Author) 105 refs.
International Nuclear Information System (INIS)
Garcia Velarde, M.
1977-01-01
Thermoconvective instabilities in horizontal fluid layers are discussed with emphasis on the Rayleigh-Benard model problem. Steady solutions and time-dependent phenomena (relaxation oscillations and transition to turbulence) are studied within the nonlinear Boussinesq-Oberbeck approximation. Homogeneous steady solutions, limit cycles, and inhomogeneous (ordered) spatial structures are also studied in simple reaction-diffusion systems. Lastly, the non-periodic attractor that appears at large Rayleigh numbers in the truncated Boussinesq-Oberbeck model of Lorenz, is constructed, and a discussion of turbulent behavior is given. (author) [es
International Nuclear Information System (INIS)
Garcia Velarde, M.
1977-01-01
Thermo convective instabilities in horizontal fluid layers are discussed with emphasis on the Rayleigh-Bernard model problem. Steady solutions and time-dependent phenomena (relaxation oscillations and transition to turbulence) are studied within the nonlinear Boussinesq-Oberbeck approximation. Homogeneous steady solutions, limit cycles, and inhomogeneous (ordered) spatial structures are also studied in simple reaction-diffusion systems. Lastly, the non-periodic attractor that appears at large Rayleigh numbers in the truncated Boussinesq-Oberbeck model of Lorenz, is constructed, and a discussion of turbulent behavior is given. (Author) 105 refs
Brodsky, Yu. I.
2015-01-01
The work is devoted to the application of Bourbaki's structure theory to substantiate the synthesis of simulation models of complex multicomponent systems, where every component may be a complex system itself. An application of the Bourbaki's structure theory offers a new approach to the design and computer implementation of simulation models of complex multicomponent systems—model synthesis and model-oriented programming. It differs from the traditional object-oriented approach. The central concept of this new approach and at the same time, the basic building block for the construction of more complex structures is the concept of models-components. A model-component endowed with a more complicated structure than, for example, the object in the object-oriented analysis. This structure provides to the model-component an independent behavior-the ability of standard responds to standard requests of its internal and external environment. At the same time, the computer implementation of model-component's behavior is invariant under the integration of models-components into complexes. This fact allows one firstly to construct fractal models of any complexity, and secondly to implement a computational process of such constructions uniformly-by a single universal program. In addition, the proposed paradigm allows one to exclude imperative programming and to generate computer code with a high degree of parallelism.
Simulating evolution of protein complexes through gene duplication and co-option.
Haarsma, Loren; Nelesen, Serita; VanAndel, Ethan; Lamine, James; VandeHaar, Peter
2016-06-21
We present a model of the evolution of protein complexes with novel functions through gene duplication, mutation, and co-option. Under a wide variety of input parameters, digital organisms evolve complexes of 2-5 bound proteins which have novel functions but whose component proteins are not independently functional. Evolution of complexes with novel functions happens more quickly as gene duplication rates increase, point mutation rates increase, protein complex functional probability increases, protein complex functional strength increases, and protein family size decreases. Evolution of complexity is inhibited when the metabolic costs of making proteins exceeds the fitness gain of having functional proteins, or when point mutation rates get so large the functional proteins undergo deleterious mutations faster than new functional complexes can evolve. Copyright © 2016 Elsevier Ltd. All rights reserved.
Molecular dynamic simulation of the self-assembly of DAP12-NKG2C activating immunoreceptor complex.
Directory of Open Access Journals (Sweden)
Peng Wei
Full Text Available The DAP12-NKG2C activating immunoreceptor complex is one of the multisubunit transmembrane protein complexes in which ligand-binding receptor chains assemble with dimeric signal-transducing modules through non-covalent associations in their transmembrane (TM domains. In this work, both coarse grained and atomistic molecular dynamic simulation methods were applied to investigate the self-assembly dynamics of the transmembrane domains of the DAP12-NKG2C activating immunoreceptor complex. Through simulating the dynamics of DAP12-NKG2C TM heterotrimer and point mutations, we demonstrated that a five-polar-residue motif including: 2 Asps and 2 Thrs in DAP12 dimer, as well as 1 Lys in NKG2C TM plays an important role in the assembly structure of the DAP12-NKG2C TM heterotrimer. Furthermore, we provided clear evidences to exclude the possibility that another NKG2C could stably associate with the DAP12-NKG2C heterotrimer. Based on the simulation results, we proposed a revised model for the self-assembly of DAP12-NKG2C activating immunoreceptor complex, along with a plausible explanation for the association of only one NKG2C with a DAP12 dimer.
Kiracofe, Daniel; Melcher, John; Raman, Arvind
2012-01-01
Dynamic atomic force microscopy (dAFM) continues to grow in popularity among scientists in many different fields, and research on new methods and operating modes continues to expand the resolution, capabilities, and types of samples that can be studied. But many promising increases in capability are accompanied by increases in complexity. Indeed, interpreting modern dAFM data can be challenging, especially on complicated material systems, or in liquid environments where the behavior is often contrary to what is known in air or vacuum environments. Mathematical simulations have proven to be an effective tool in providing physical insight into these non-intuitive systems. In this article we describe recent developments in the VEDA (virtual environment for dynamic AFM) simulator, which is a suite of freely available, open-source simulation tools that are delivered through the cloud computing cyber-infrastructure of nanoHUB (www.nanohub.org). Here we describe three major developments. First, simulations in liquid environments are improved by enhancements in the modeling of cantilever dynamics, excitation methods, and solvation shell forces. Second, VEDA is now able to simulate many new advanced modes of operation (bimodal, phase-modulation, frequency-modulation, etc.). Finally, nineteen different tip-sample models are available to simulate the surface physics of a wide variety different material systems including capillary, specific adhesion, van der Waals, electrostatic, viscoelasticity, and hydration forces. These features are demonstrated through example simulations and validated against experimental data, in order to provide insight into practical problems in dynamic AFM.
Efficient Radiation Simulation in Complex Geometries with Applications to Planetary Entry, Phase I
National Aeronautics and Space Administration — NASA aerocapture missions require an accurate evaluation of radiative thermal transport in order to simulate the aerothermal environment around space vehicles....
Energy Technology Data Exchange (ETDEWEB)
Kuhn, Tilmann E.; Herkel, Sebastian [Fraunhofer Institute for Solar Energy Systems ISE, Heidenhofstr. 2, 79110 Freiburg (Germany); Frontini, Francesco [Fraunhofer Institute for Solar Energy Systems ISE, Heidenhofstr. 2, 79110 Freiburg (Germany); Politecnico di Milano, Dipartimento BEST, Via Bonardi 9, 20133 Milano (Italy); Strachan, Paul; Kokogiannakis, Georgios [ESRU, Dept. of Mechanical Eng., University of Strathclyde, Glasgow G1 1XJ (United Kingdom)
2011-01-15
This paper describes a new general method for building simulation programs which is intended to be used for the modelling of complex facades. The term 'complex facades' is used to designate facades with venetian blinds, prismatic layers, light re-directing surfaces, etc. In all these cases, the facade properties have a complex angular dependence. In addition to this, such facades very often have non-airtight layers and/or imperfect components (e.g. non-ideal sharp edges, non-flat surfaces,..). Therefore building planners often had to neglect some of the innovative features and to use 'work-arounds' in order to approximate the properties of complex facades in building simulation programs. A well-defined methodology for these cases was missing. This paper presents such a general methodology. The main advantage of the new method is that it only uses measureable quantities of the transparent or translucent part of the facade as a whole. This is the main difference in comparison with state of the art modelling based on the characteristics of the individual subcomponents, which is often impossible due to non-existing heat- and/or light-transfer models within the complex facade. It is shown that the new method can significantly increase the accuracy of heating/cooling loads and room temperatures. (author)
Directory of Open Access Journals (Sweden)
Hofmann Bjørn
2009-07-01
Full Text Available Abstract Background It is important to demonstrate learning outcomes of simulation in technology based practices, such as in advanced health care. Although many studies show skills improvement and self-reported change to practice, there are few studies demonstrating patient outcome and societal efficiency. The objective of the study is to investigate if and why simulation can be effective and efficient in a hi-tech health care setting. This is important in order to decide whether and how to design simulation scenarios and outcome studies. Methods Core theoretical insights in Science and Technology Studies (STS are applied to analyze the field of simulation in hi-tech health care education. In particular, a process-oriented framework where technology is characterized by its devices, methods and its organizational setting is applied. Results The analysis shows how advanced simulation can address core characteristics of technology beyond the knowledge of technology's functions. Simulation's ability to address skilful device handling as well as purposive aspects of technology provides a potential for effective and efficient learning. However, as technology is also constituted by organizational aspects, such as technology status, disease status, and resource constraints, the success of simulation depends on whether these aspects can be integrated in the simulation setting as well. This represents a challenge for future development of simulation and for demonstrating its effectiveness and efficiency. Conclusion Assessing the outcome of simulation in education in hi-tech health care settings is worthwhile if core characteristics of medical technology are addressed. This challenges the traditional technical versus non-technical divide in simulation, as organizational aspects appear to be part of technology's core characteristics.
Hofmann, Bjørn
2009-07-23
It is important to demonstrate learning outcomes of simulation in technology based practices, such as in advanced health care. Although many studies show skills improvement and self-reported change to practice, there are few studies demonstrating patient outcome and societal efficiency. The objective of the study is to investigate if and why simulation can be effective and efficient in a hi-tech health care setting. This is important in order to decide whether and how to design simulation scenarios and outcome studies. Core theoretical insights in Science and Technology Studies (STS) are applied to analyze the field of simulation in hi-tech health care education. In particular, a process-oriented framework where technology is characterized by its devices, methods and its organizational setting is applied. The analysis shows how advanced simulation can address core characteristics of technology beyond the knowledge of technology's functions. Simulation's ability to address skilful device handling as well as purposive aspects of technology provides a potential for effective and efficient learning. However, as technology is also constituted by organizational aspects, such as technology status, disease status, and resource constraints, the success of simulation depends on whether these aspects can be integrated in the simulation setting as well. This represents a challenge for future development of simulation and for demonstrating its effectiveness and efficiency. Assessing the outcome of simulation in education in hi-tech health care settings is worthwhile if core characteristics of medical technology are addressed. This challenges the traditional technical versus non-technical divide in simulation, as organizational aspects appear to be part of technology's core characteristics.
A Mathematical Model for Dynamic Simulation of Anaerobic Digestion of Complex Substrates
DEFF Research Database (Denmark)
Angelidaki, Irini; Ellegaard, L.; Ahring, Birgitte Kiær
1993-01-01
of pH and temperature characteristics in order to accurately simulate free ammonia concentration. Free ammonia and acetate constitute the primary modulating factors in the model. The model has been applied for the simulation of digestion of cattle manure in continuously stirred tank reactors (CSTRs...
Teaching Supply Chain Management Complexities: A SCOR Model Based Classroom Simulation
Webb, G. Scott; Thomas, Stephanie P.; Liao-Troth, Sara
2014-01-01
The SCOR (Supply Chain Operations Reference) Model Supply Chain Classroom Simulation is an in-class experiential learning activity that helps students develop a holistic understanding of the processes and challenges of supply chain management. The simulation has broader learning objectives than other supply chain related activities such as the…
Directory of Open Access Journals (Sweden)
G. Arul Elango
2016-09-01
Full Text Available The need for GPS data simulators have become important due to the tremendous growth in the design of versatile GPS receivers. Commercial hardware and software based GPS simulators are expensive and time consuming. In this work, a low cost simple novel GPS L1 signal simulator is designed for testing and evaluating the performance of software GPS receiver in a laboratory environment. A typical real time paradigm, similar to actual satellite derived GPS signal is created on a computer generated scenario. In this paper, a GPS software simulator is proposed that may offer a lot of analysis and testing flexibility to the researchers and developers as it is totally software based primarily running on a laptop/personal computer without the requirement of any hardware. The proposed GPS simulator allows provision for re-configurability and test repeatability and is developed in VC++ platform to minimize the simulation time. It also incorporates Rayleigh multipath channel fading model under non-line of sight (NLOS conditions. In this work, to efficiently design the simulator, several Rayleigh fading models viz. Inverse Discrete Fourier Transform (IDFT, Filtering White Gaussian Noise (FWFN and modified Sum of Sinusoidal (SOS simulators are tested and compared in terms of accuracy of its first and second order statistical metrics, execution time and the later one is found to be as the best appropriate Rayleigh multipath model suitable for incorporating with GPS simulator. The fading model written in ‘MATLAB’ engine has been linked with software GPS simulator module enable to test GPS receiver’s functionality in different fading environments.
International Nuclear Information System (INIS)
Vögele, Martin; Holm, Christian; Smiatek, Jens
2015-01-01
We present simulations of aqueous polyelectrolyte complexes with new MARTINI models for the charged polymers poly(styrene sulfonate) and poly(diallyldimethylammonium). Our coarse-grained polyelectrolyte models allow us to study large length and long time scales with regard to chemical details and thermodynamic properties. The results are compared to the outcomes of previous atomistic molecular dynamics simulations and verify that electrostatic properties are reproduced by our MARTINI coarse-grained approach with reasonable accuracy. Structural similarity between the atomistic and the coarse-grained results is indicated by a comparison between the pair radial distribution functions and the cumulative number of surrounding particles. Our coarse-grained models are able to quantitatively reproduce previous findings like the correct charge compensation mechanism and a reduced dielectric constant of water. These results can be interpreted as the underlying reason for the stability of polyelectrolyte multilayers and complexes and validate the robustness of the proposed models
Directory of Open Access Journals (Sweden)
Krzysztof Małecki
2017-12-01
Full Text Available A complex system is a set of mutually interacting elements for which it is possible to construct a mathematical model. This article focuses on the cellular automata theory and the graph theory in order to compare various types of cellular automata and to analyse applications of graph structures together with cellular automata. It proposes a graph cellular automaton with a variable configuration of cells and relation-based neighbourhoods (r–GCA. The developed mechanism enables modelling of phenomena found in complex systems (e.g., transport networks, urban logistics, social networks taking into account the interaction between the existing objects. As an implementation example, modelling of moving vehicles has been made and r–GCA was compared to the other cellular automata models simulating the road traffic and used in the computer simulation process.
DEFF Research Database (Denmark)
Poyry, S.; Cramariuc, O.; Postila, P. A.
2013-01-01
by both ensuring the structural integrity of the protein complex and also by taking part in the proton uptake. Yet, the atom-scale understanding of these highly charged four-tail lipids in the cyt bc(1) function has remained quite unclear. We consider this issue through atomistic molecular dynamics...... the description of the role of the surrounding lipid environment: in addition to the specific CL-protein interactions, we observe the protein domains on the positive side of the membrane to settle against the lipids. Altogether, the simulations discussed in this article provide novel views into the dynamics...... simulations that are applied to the entire cyt bc(1) dimer of the purple photosynthetic bacterium Rhodobacter capsulatus embedded in a lipid bilayer. We find CLs to spontaneously diffuse to the dimer interface to the immediate vicinity of the higher potential heme b groups of the complex's catalytic Q...
Energy Technology Data Exchange (ETDEWEB)
Vögele, Martin [Institute for Computational Physics, University of Stuttgart, Stuttgart (Germany); Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt a. M. (Germany); Holm, Christian; Smiatek, Jens, E-mail: smiatek@icp.uni-stuttgart.de [Institute for Computational Physics, University of Stuttgart, Stuttgart (Germany)
2015-12-28
We present simulations of aqueous polyelectrolyte complexes with new MARTINI models for the charged polymers poly(styrene sulfonate) and poly(diallyldimethylammonium). Our coarse-grained polyelectrolyte models allow us to study large length and long time scales with regard to chemical details and thermodynamic properties. The results are compared to the outcomes of previous atomistic molecular dynamics simulations and verify that electrostatic properties are reproduced by our MARTINI coarse-grained approach with reasonable accuracy. Structural similarity between the atomistic and the coarse-grained results is indicated by a comparison between the pair radial distribution functions and the cumulative number of surrounding particles. Our coarse-grained models are able to quantitatively reproduce previous findings like the correct charge compensation mechanism and a reduced dielectric constant of water. These results can be interpreted as the underlying reason for the stability of polyelectrolyte multilayers and complexes and validate the robustness of the proposed models.