WorldWideScience

Sample records for random-walk-based stochastic modeling

  1. A model for a correlated random walk based on the ordered extension of pseudopodia.

    Directory of Open Access Journals (Sweden)

    Peter J M Van Haastert

    Full Text Available Cell migration in the absence of external cues is well described by a correlated random walk. Most single cells move by extending protrusions called pseudopodia. To deduce how cells walk, we have analyzed the formation of pseudopodia by Dictyostelium cells. We have observed that the formation of pseudopodia is highly ordered with two types of pseudopodia: First, de novo formation of pseudopodia at random positions on the cell body, and therefore in random directions. Second, pseudopod splitting near the tip of the current pseudopod in alternating right/left directions, leading to a persistent zig-zag trajectory. Here we analyzed the probability frequency distributions of the angles between pseudopodia and used this information to design a stochastic model for cell movement. Monte Carlo simulations show that the critical elements are the ratio of persistent splitting pseudopodia relative to random de novo pseudopodia, the Left/Right alternation, the angle between pseudopodia and the variance of this angle. Experiments confirm predictions of the model, showing reduced persistence in mutants that are defective in pseudopod splitting and in mutants with an irregular cell surface.

  2. Stochastic modeling

    CERN Document Server

    Lanchier, Nicolas

    2017-01-01

    Three coherent parts form the material covered in this text, portions of which have not been widely covered in traditional textbooks. In this coverage the reader is quickly introduced to several different topics enriched with 175 exercises which focus on real-world problems. Exercises range from the classics of probability theory to more exotic research-oriented problems based on numerical simulations. Intended for graduate students in mathematics and applied sciences, the text provides the tools and training needed to write and use programs for research purposes. The first part of the text begins with a brief review of measure theory and revisits the main concepts of probability theory, from random variables to the standard limit theorems. The second part covers traditional material on stochastic processes, including martingales, discrete-time Markov chains, Poisson processes, and continuous-time Markov chains. The theory developed is illustrated by a variety of examples surrounding applications such as the ...

  3. Random walk-based similarity measure method for patterns in complex object

    Directory of Open Access Journals (Sweden)

    Liu Shihu

    2017-04-01

    Full Text Available This paper discusses the similarity of the patterns in complex objects. The complex object is composed both of the attribute information of patterns and the relational information between patterns. Bearing in mind the specificity of complex object, a random walk-based similarity measurement method for patterns is constructed. In this method, the reachability of any two patterns with respect to the relational information is fully studied, and in the case of similarity of patterns with respect to the relational information can be calculated. On this bases, an integrated similarity measurement method is proposed, and algorithms 1 and 2 show the performed calculation procedure. One can find that this method makes full use of the attribute information and relational information. Finally, a synthetic example shows that our proposed similarity measurement method is validated.

  4. Stochastic neuron models

    CERN Document Server

    Greenwood, Priscilla E

    2016-01-01

    This book describes a large number of open problems in the theory of stochastic neural systems, with the aim of enticing probabilists to work on them. This includes problems arising from stochastic models of individual neurons as well as those arising from stochastic models of the activities of small and large networks of interconnected neurons. The necessary neuroscience background to these problems is outlined within the text, so readers can grasp the context in which they arise. This book will be useful for graduate students and instructors providing material and references for applying probability to stochastic neuron modeling. Methods and results are presented, but the emphasis is on questions where additional stochastic analysis may contribute neuroscience insight. An extensive bibliography is included. Dr. Priscilla E. Greenwood is a Professor Emerita in the Department of Mathematics at the University of British Columbia. Dr. Lawrence M. Ward is a Professor in the Department of Psychology and the Brain...

  5. Stochastic Models of Evolution

    Science.gov (United States)

    Bezruchko, Boris P.; Smirnov, Dmitry A.

    To continue the discussion of randomness given in Sect. 2.2.1, we briefly touch on stochastic models of temporal evolution (random processes). They can be specified either via explicit definition of their statistical properties (probability density functions, correlation functions, etc., Sects. 4.1, 4.2 and 4.3) or via stochastic difference or differential equations. Some of the most widely known equations, their properties and applications are discussed in Sects. 4.4 and 4.5.

  6. A random walk-based segmentation framework for 3D ultrasound images of the prostate.

    Science.gov (United States)

    Ma, Ling; Guo, Rongrong; Tian, Zhiqiang; Fei, Baowei

    2017-10-01

    Accurate segmentation of the prostate on ultrasound images has many applications in prostate cancer diagnosis and therapy. Transrectal ultrasound (TRUS) has been routinely used to guide prostate biopsy. This manuscript proposes a semiautomatic segmentation method for the prostate on three-dimensional (3D) TRUS images. The proposed segmentation method uses a context-classification-based random walk algorithm. Because context information reflects patient-specific characteristics and prostate changes in the adjacent slices, and classification information reflects population-based prior knowledge, we combine the context and classification information at the same time in order to define the applicable population and patient-specific knowledge so as to more accurately determine the seed points for the random walk algorithm. The method is initialized with the user drawing the prostate and non-prostate circles on the mid-gland slice and then automatically segments the prostate on other slices. To achieve reliable classification, we use a new adaptive k-means algorithm to cluster the training data and train multiple decision-tree classifiers. According to the patient-specific characteristics, the most suitable classifier is selected and combined with the context information in order to locate the seed points. By providing accuracy locations of the seed points, the random walk algorithm improves segmentation performance. We evaluate the proposed segmentation approach on a set of 3D TRUS volumes of prostate patients. The experimental results show that our method achieved a Dice similarity coefficient of 91.0% ± 1.6% as compared to manual segmentation by clinically experienced radiologist. The random walk-based segmentation framework, which combines patient-specific characteristics and population information, is effective for segmenting the prostate on ultrasound images. The segmentation method can have various applications in ultrasound-guided prostate procedures. © 2017

  7. Stochastic Control - External Models

    DEFF Research Database (Denmark)

    Poulsen, Niels Kjølstad

    2005-01-01

    This note is devoted to control of stochastic systems described in discrete time. We are concerned with external descriptions or transfer function model, where we have a dynamic model for the input output relation only (i.e.. no direct internal information). The methods are based on LTI systems...... a section on that topic can be found in appendix....

  8. Stochasticity Modeling in Memristors

    KAUST Repository

    Naous, Rawan

    2015-10-26

    Diverse models have been proposed over the past years to explain the exhibiting behavior of memristors, the fourth fundamental circuit element. The models varied in complexity ranging from a description of physical mechanisms to a more generalized mathematical modeling. Nonetheless, stochasticity, a widespread observed phenomenon, has been immensely overlooked from the modeling perspective. This inherent variability within the operation of the memristor is a vital feature for the integration of this nonlinear device into the stochastic electronics realm of study. In this paper, experimentally observed innate stochasticity is modeled in a circuit compatible format. The model proposed is generic and could be incorporated into variants of threshold-based memristor models in which apparent variations in the output hysteresis convey the switching threshold shift. Further application as a noise injection alternative paves the way for novel approaches in the fields of neuromorphic engineering circuits design. On the other hand, extra caution needs to be paid to variability intolerant digital designs based on non-deterministic memristor logic.

  9. Stochastic modelling of turbulence

    DEFF Research Database (Denmark)

    Sørensen, Emil Hedevang Lohse

    This thesis addresses stochastic modelling of turbulence with applications to wind energy in mind. The primary tool is ambit processes, a recently developed class of computationally tractable stochastic processes based on integration with respect to Lévy bases. The subject of ambit processes...... is still undergoing rapid development. Turbulence and wind energy are vast and complicated subjects. Turbulence has structures across a wide range of length and time scales, structures which cannot be captured by a Gaussian process that relies on only second order properties. Concerning wind energy, a wind...... turbine operates in the turbulent atmospheric boundary layer. In this respect, three regimes are of particular interest: modelling the turbulent wind before it interacts with the wind turbine (e.g. to be used in load simulations), modelling of the interaction of the wind with the wind turbine (e...

  10. Identifiability in stochastic models

    CERN Document Server

    1992-01-01

    The problem of identifiability is basic to all statistical methods and data analysis, occurring in such diverse areas as Reliability Theory, Survival Analysis, and Econometrics, where stochastic modeling is widely used. Mathematics dealing with identifiability per se is closely related to the so-called branch of ""characterization problems"" in Probability Theory. This book brings together relevant material on identifiability as it occurs in these diverse fields.

  11. Applied stochastic modelling

    CERN Document Server

    Morgan, Byron JT; Tanner, Martin Abba; Carlin, Bradley P

    2008-01-01

    Introduction and Examples Introduction Examples of data sets Basic Model Fitting Introduction Maximum-likelihood estimation for a geometric model Maximum-likelihood for the beta-geometric model Modelling polyspermy Which model? What is a model for? Mechanistic models Function Optimisation Introduction MATLAB: graphs and finite differences Deterministic search methods Stochastic search methods Accuracy and a hybrid approach Basic Likelihood ToolsIntroduction Estimating standard errors and correlations Looking at surfaces: profile log-likelihoods Confidence regions from profiles Hypothesis testing in model selectionScore and Wald tests Classical goodness of fit Model selection biasGeneral Principles Introduction Parameterisation Parameter redundancy Boundary estimates Regression and influence The EM algorithm Alternative methods of model fitting Non-regular problemsSimulation Techniques Introduction Simulating random variables Integral estimation Verification Monte Carlo inference Estimating sampling distributi...

  12. Stochastic Modeling Of Biochemical Reactions

    Science.gov (United States)

    2006-11-01

    STOCHASTIC MODELING OF BIOCHEMICAL REACTIONS Abhyudai Singh and João Pedro Hespanha* Department of Electrical and Computer Engineering University of...procedure for con- structing approximate stochastic models for chemical reactions used for modeling biochemical processes such as gene regulatory networks... biochemical reactions , the modeling tools developed in this paper can be applied to a very general class of stochastic systems, in particular

  13. Stochastic modelling in disability insurance

    OpenAIRE

    Löfdahl, Björn

    2013-01-01

    This thesis consists of two papers related to the stochastic modellingof disability insurance. In the first paper, we propose a stochastic semi-Markovian framework for disability modelling in a multi-period discrete-time setting. The logistic transforms of disability inception and recovery probabilities are modelled by means of stochastic risk factors and basis functions, using counting processes and generalized linear models. The model for disability inception also takes IBNR claims into con...

  14. Stochastic Climate Theory and Modelling

    CERN Document Server

    Franzke, Christian L E; Berner, Judith; Williams, Paul D; Lucarini, Valerio

    2014-01-01

    Stochastic methods are a crucial area in contemporary climate research and are increasingly being used in comprehensive weather and climate prediction models as well as reduced order climate models. Stochastic methods are used as subgrid-scale parameterizations as well as for model error representation, uncertainty quantification, data assimilation and ensemble prediction. The need to use stochastic approaches in weather and climate models arises because we still cannot resolve all necessary processes and scales in comprehensive numerical weather and climate prediction models. In many practical applications one is mainly interested in the largest and potentially predictable scales and not necessarily in the small and fast scales. For instance, reduced order models can simulate and predict large scale modes. Statistical mechanics and dynamical systems theory suggest that in reduced order models the impact of unresolved degrees of freedom can be represented by suitable combinations of deterministic and stochast...

  15. Rainfall Stochastic models

    Science.gov (United States)

    Campo, M. A.; Lopez, J. J.; Rebole, J. P.

    2012-04-01

    This work was carried out in north of Spain. San Sebastian A meteorological station, where there are available precipitation records every ten minutes was selected. Precipitation data covers from October of 1927 to September of 1997. Pulse models describe the temporal process of rainfall as a succession of rainy cells, main storm, whose origins are distributed in time according to a Poisson process and a secondary process that generates a random number of cells of rain within each storm. Among different pulse models, the Bartlett-Lewis was used. On the other hand, alternative renewal processes and Markov chains describe the way in which the process will evolve in the future depending only on the current state. Therefore they are nor dependant on past events. Two basic processes are considered when describing the occurrence of rain: the alternation of wet and dry periods and temporal distribution of rainfall in each rain event, which determines the rainwater collected in each of the intervals that make up the rain. This allows the introduction of alternative renewal processes and Markov chains of three states, where interstorm time is given by either of the two dry states, short or long. Thus, the stochastic model of Markov chains tries to reproduce the basis of pulse models: the succession of storms, each one composed for a series of rain, separated by a short interval of time without theoretical complexity of these. In a first step, we analyzed all variables involved in the sequential process of the rain: rain event duration, event duration of non-rain, average rainfall intensity in rain events, and finally, temporal distribution of rainfall within the rain event. Additionally, for pulse Bartlett-Lewis model calibration, main descriptive statistics were calculated for each month, considering the process of seasonal rainfall in each month. In a second step, both models were calibrated. Finally, synthetic series were simulated with calibration parameters; series

  16. Stochastic models: theory and simulation.

    Energy Technology Data Exchange (ETDEWEB)

    Field, Richard V., Jr.

    2008-03-01

    Many problems in applied science and engineering involve physical phenomena that behave randomly in time and/or space. Examples are diverse and include turbulent flow over an aircraft wing, Earth climatology, material microstructure, and the financial markets. Mathematical models for these random phenomena are referred to as stochastic processes and/or random fields, and Monte Carlo simulation is the only general-purpose tool for solving problems of this type. The use of Monte Carlo simulation requires methods and algorithms to generate samples of the appropriate stochastic model; these samples then become inputs and/or boundary conditions to established deterministic simulation codes. While numerous algorithms and tools currently exist to generate samples of simple random variables and vectors, no cohesive simulation tool yet exists for generating samples of stochastic processes and/or random fields. There are two objectives of this report. First, we provide some theoretical background on stochastic processes and random fields that can be used to model phenomena that are random in space and/or time. Second, we provide simple algorithms that can be used to generate independent samples of general stochastic models. The theory and simulation of random variables and vectors is also reviewed for completeness.

  17. Stochastic model in microwave propagation

    Energy Technology Data Exchange (ETDEWEB)

    Ranfagni, A. [“Nello Carrara” Institute of Applied Physics, CNR Florence Research Area, Via Madonna del Piano 10, 50019 Sesto Fiorentino (Italy); Mugnai, D., E-mail: d.mugnai@ifac.cnr.it [“Nello Carrara” Institute of Applied Physics, CNR Florence Research Area, Via Madonna del Piano 10, 50019 Sesto Fiorentino (Italy)

    2011-11-28

    Further experimental results of delay time in microwave propagation are reported in the presence of a lossy medium (wood). The measurements show that the presence of a lossy medium makes the propagation slightly superluminal. The results are interpreted on the basis of a stochastic (or path integral) model, showing how this model is able to describe each kind of physical system in which multi-path trajectories are present. -- Highlights: ► We present new experimental results on electromagnetic “anomalous” propagation. ► We apply a path integral theoretical model to wave propagation. ► Stochastic processes and multi-path trajectories in propagation are considered.

  18. Stochastic models of cell motility

    DEFF Research Database (Denmark)

    Gradinaru, Cristian

    2012-01-01

    Cell motility and migration are central to the development and maintenance of multicellular organisms, and errors during this process can lead to major diseases. Consequently, the mechanisms and phenomenology of cell motility are currently under intense study. In recent years, a new...... interdisciplinary field focusing on the study of biological processes at the nanoscale level, with a range of technological applications in medicine and biological research, has emerged. The work presented in this thesis is at the interface of cell biology, image processing, and stochastic modeling. The stochastic...... models introduced here are based on persistent random motion, which I apply to real-life studies of cell motility on flat and nanostructured surfaces. These models aim to predict the time-dependent position of cell centroids in a stochastic manner, and conversely determine directly from experimental...

  19. Stochastic Modelling of River Geometry

    DEFF Research Database (Denmark)

    Sørensen, John Dalsgaard; Schaarup-Jensen, K.

    1996-01-01

    Numerical hydrodynamic river models are used in a large number of applications to estimate critical events for rivers. These estimates are subject to a number of uncertainties. In this paper, the problem to evaluate these estimates using probabilistic methods is considered. Stochastic models for ...... for river geometries are formulated and a coupling between hydraulic computational methods and numerical reliability methods is presented....

  20. Stochastic Modelling of Hydrologic Systems

    DEFF Research Database (Denmark)

    Jonsdottir, Harpa

    2007-01-01

    In this PhD project several stochastic modelling methods are studied and applied on various subjects in hydrology. The research was prepared at Informatics and Mathematical Modelling at the Technical University of Denmark. The thesis is divided into two parts. The first part contains an introduct......In this PhD project several stochastic modelling methods are studied and applied on various subjects in hydrology. The research was prepared at Informatics and Mathematical Modelling at the Technical University of Denmark. The thesis is divided into two parts. The first part contains...... an introduction and an overview of the papers published. Then an introduction to basic concepts in hydrology along with a description of hydrological data is given. Finally an introduction to stochastic modelling is given. The second part contains the research papers. In the research papers the stochastic methods...... are described, as at the time of publication these methods represent new contribution to hydrology. The second part also contains additional description of software used and a brief introduction to stiff systems. The system in one of the papers is stiff....

  1. Path Loss Models Based on Stochastic Rays

    OpenAIRE

    Hu, Luoquan; Yu, Han; Chen, Yifan

    2007-01-01

    In this paper, two-dimensional percolation lattices are applied to describe wireless propagation environment, and stochastic rays are employed to model the trajectories of radio waves. We first derive the probability that a stochastic ray undergoes certain number of collisions at a specific spatial location. Three classes of stochastic rays with different constraint conditions are considered: stochastic rays of random walks, and generic stochastic rays with two different anomalous levels. Sub...

  2. Stochastic Volatility and DSGE Models

    DEFF Research Database (Denmark)

    Andreasen, Martin Møller

    This paper argues that a specification of stochastic volatility commonly used to analyze the Great Moderation in DSGE models may not be appropriate, because the level of a process with this specification does not have conditional or unconditional moments. This is unfortunate because agents may...

  3. Stochastic modeling of soil salinity

    NARCIS (Netherlands)

    Suweis, S.; Rinaldo, A.; Zee, van der S.E.A.T.M.; Daly, E.; Maritan, A.

    2010-01-01

    A minimalist stochastic model of primary soil salinity is proposed, in which the rate of soil salinization is determined by the balance between dry and wet salt deposition and the intermittent leaching events caused by rainfall events. The long term probability density functions of salt mass and

  4. Stochastic Models of Polymer Systems

    Science.gov (United States)

    2016-01-01

    information about the behavior of the algorithm. At the same time, we were also able to formulate various acceleration techniques in precise math terms...peer-reviewed journals : Number of Papers published in non peer-reviewed journals : Final Report: Stochastic Models of Polymer Systems Report Title...the algorithm. At the same time, we were also able to formulate various acceleration techniques in precise math terms (e.g. formulate them as

  5. Stochastic Modeling of Soil Salinity

    CERN Document Server

    Suweis, S; Van der Zee, S E A T M; Daly, E; Maritan, A; Porporato, A; 10.1029/2010GL042495

    2012-01-01

    A minimalist stochastic model of primary soil salinity is proposed, in which the rate of soil salinization is determined by the balance between dry and wet salt deposition and the intermittent leaching events caused by rainfall events. The long term probability density functions of salt mass and concentration are found by reducing the coupled soil moisture and salt mass balance equation to a single stochastic differential equation driven by multiplicative Poisson noise. The novel analytical solutions provide insight on the interplay of the main soil, plant and climate parameters responsible for long-term soil salinization. In particular, they show the existence of two distinct regimes, one where the mean salt mass remains nearly constant (or decreases) with increasing rainfall frequency, and another where mean salt content increases markedly with increasing rainfall frequency. As a result, relatively small reductions of rainfall in drier climates may entail dramatic shifts in long-term soil salinization trend...

  6. Stochastic modeling and analysis of telecoms networks

    CERN Document Server

    Decreusefond, Laurent

    2012-01-01

    This book addresses the stochastic modeling of telecommunication networks, introducing the main mathematical tools for that purpose, such as Markov processes, real and spatial point processes and stochastic recursions, and presenting a wide list of results on stability, performances and comparison of systems.The authors propose a comprehensive mathematical construction of the foundations of stochastic network theory: Markov chains, continuous time Markov chains are extensively studied using an original martingale-based approach. A complete presentation of stochastic recursions from an

  7. Stochastic Still Water Response Model

    DEFF Research Database (Denmark)

    Friis-Hansen, Peter; Ditlevsen, Ove Dalager

    2002-01-01

    In this study a stochastic field model for the still water loading is formulated where the statistics (mean value, standard deviation, and correlation) of the sectional forces are obtained by integration of the load field over the relevant part of the ship structure. The objective of the model...... water bending moment is compared to statistics from available regression formulas. It is found that the suggested model predicts a coefficient of variation of the maximum still water bending moment that is a factor of two to three times lower than that obtained by use of the regression formula. It turns...

  8. Stochastic predictive control with adaptive model maintenance

    OpenAIRE

    Bavdekar, VA; Ehlinger, V; Gidon, D; Mesbah, A.

    2016-01-01

    © 2016 IEEE. The closed-loop performance of model-based controllers often degrades over time due to increased model uncertainty. Some form of model maintenance must be performed to regularly adapt the system model using closed-loop data. This paper addresses the problem of control-oriented model adaptation in the context of predictive control of stochastic linear systems. A stochastic predictive control approach is presented that integrates stochastic optimal control with control-oriented inp...

  9. Stochastic modeling analysis and simulation

    CERN Document Server

    Nelson, Barry L

    1995-01-01

    A coherent introduction to the techniques for modeling dynamic stochastic systems, this volume also offers a guide to the mathematical, numerical, and simulation tools of systems analysis. Suitable for advanced undergraduates and graduate-level industrial engineers and management science majors, it proposes modeling systems in terms of their simulation, regardless of whether simulation is employed for analysis. Beginning with a view of the conditions that permit a mathematical-numerical analysis, the text explores Poisson and renewal processes, Markov chains in discrete and continuous time, se

  10. Stochastic models for atmospheric dispersion

    DEFF Research Database (Denmark)

    Ditlevsen, Ove Dalager

    2003-01-01

    Simple stochastic differential equation models have been applied by several researchers to describe the dispersion of tracer particles in the planetary atmospheric boundary layer and to form the basis for computer simulations of particle paths. To obtain the drift coefficient, empirical vertical...... velocity distributions that depend on height above the ground both with respect to standard deviation and skewness are substituted into the stationary Fokker/Planck equation. The particle position distribution is taken to be uniform *the well/mixed condition( and also a given dispersion coefficient...

  11. Stochastic Model of Microtubule Dynamics

    Science.gov (United States)

    Hryniv, Ostap; Martínez Esteban, Antonio

    2017-10-01

    We introduce a continuous time stochastic process on strings made of two types of particle, whose dynamics mimics that of microtubules in a living cell. The long term behaviour of the system is described in terms of the velocity v of the string end. We show that v is an analytic function of its parameters and study its monotonicity properties. We give a complete characterisation of the phase diagram of the model and derive several criteria of the growth (v>0) and the shrinking (v<0) regimes of the dynamics.

  12. Stochastic models, estimation, and control

    CERN Document Server

    Maybeck, Peter S

    1982-01-01

    This volume builds upon the foundations set in Volumes 1 and 2. Chapter 13 introduces the basic concepts of stochastic control and dynamic programming as the fundamental means of synthesizing optimal stochastic control laws.

  13. Nonparametric weighted stochastic block models

    Science.gov (United States)

    Peixoto, Tiago P.

    2018-01-01

    We present a Bayesian formulation of weighted stochastic block models that can be used to infer the large-scale modular structure of weighted networks, including their hierarchical organization. Our method is nonparametric, and thus does not require the prior knowledge of the number of groups or other dimensions of the model, which are instead inferred from data. We give a comprehensive treatment of different kinds of edge weights (i.e., continuous or discrete, signed or unsigned, bounded or unbounded), as well as arbitrary weight transformations, and describe an unsupervised model selection approach to choose the best network description. We illustrate the application of our method to a variety of empirical weighted networks, such as global migrations, voting patterns in congress, and neural connections in the human brain.

  14. Stochastic Subspace Modelling of Turbulence

    DEFF Research Database (Denmark)

    Sichani, Mahdi Teimouri; Pedersen, B. J.; Nielsen, Søren R.K.

    2009-01-01

    Turbulence of the incoming wind field is of paramount importance to the dynamic response of civil engineering structures. Hence reliable stochastic models of the turbulence should be available from which time series can be generated for dynamic response and structural safety analysis. In the paper...... an empirical cross spectral density function for the along-wind turbulence component over the wind field area is taken as the starting point. The spectrum is spatially discretized in terms of a Hermitian cross-spectral density matrix for the turbulence state vector which turns out not to be positive definite...... positive definite cross-spectral density matrix a frequency response matrix is constructed which determines the turbulence vector as a linear filtration of Gaussian white noise. Finally, an accurate state space modelling method is proposed which allows selection of an appropriate model order...

  15. CAM Stochastic Volatility Model for Option Pricing

    Directory of Open Access Journals (Sweden)

    Wanwan Huang

    2016-01-01

    Full Text Available The coupled additive and multiplicative (CAM noises model is a stochastic volatility model for derivative pricing. Unlike the other stochastic volatility models in the literature, the CAM model uses two Brownian motions, one multiplicative and one additive, to model the volatility process. We provide empirical evidence that suggests a nontrivial relationship between the kurtosis and skewness of asset prices and that the CAM model is able to capture this relationship, whereas the traditional stochastic volatility models cannot. We introduce a control variate method and Monte Carlo estimators for some of the sensitivities (Greeks of the model. We also derive an approximation for the characteristic function of the model.

  16. Consistent Stochastic Modelling of Meteocean Design Parameters

    DEFF Research Database (Denmark)

    Sørensen, John Dalsgaard; Sterndorff, M. J.

    2000-01-01

    height from neighboring directional sectors. Numerical examples are presented where the models are calibrated using the Maximum Likelihood method to data from the central part of the North Sea. The calibration of the directional distributions is made such that the stochastic model for the omnidirectional...... maximum wave height is statistically consistent with the directional distribution functions. Finally, it is shown how the stochastic models can be used to estimate characteristic values and in reliability assessment of offshore structures....... velocity, and water level is presented. The stochastic model includes statistical uncertainty and dependency between the four stochastic variables. Further, a new stochastic model for annual maximum directional significant wave heights is presented. The model includes dependency between the maximum wave...

  17. Statistical Model Checking for Stochastic Hybrid Systems

    DEFF Research Database (Denmark)

    David, Alexandre; Du, Dehui; Larsen, Kim Guldstrand

    2012-01-01

    This paper presents novel extensions and applications of the UPPAAL-SMC model checker. The extensions allow for statistical model checking of stochastic hybrid systems. We show how our race-based stochastic semantics extends to networks of hybrid systems, and indicate the integration technique...

  18. Stochastic modeling of soil salinity

    Science.gov (United States)

    Suweis, S.; Porporato, A. M.; Daly, E.; van der Zee, S.; Maritan, A.; Rinaldo, A.

    2010-12-01

    A minimalist stochastic model of primary soil salinity is proposed, in which the rate of soil salinization is determined by the balance between dry and wet salt deposition and the intermittent leaching events caused by rainfall events. The equations for the probability density functions of salt mass and concentration are found by reducing the coupled soil moisture and salt mass balance equations to a single stochastic differential equation (generalized Langevin equation) driven by multiplicative Poisson noise. Generalized Langevin equations with multiplicative white Poisson noise pose the usual Ito (I) or Stratonovich (S) prescription dilemma. Different interpretations lead to different results and then choosing between the I and S prescriptions is crucial to describe correctly the dynamics of the model systems. We show how this choice can be determined by physical information about the timescales involved in the process. We also show that when the multiplicative noise is at most linear in the random variable one prescription can be made equivalent to the other by a suitable transformation in the jump probability distribution. We then apply these results to the generalized Langevin equation that drives the salt mass dynamics. The stationary analytical solutions for the probability density functions of salt mass and concentration provide insight on the interplay of the main soil, plant and climate parameters responsible for long term soil salinization. In particular, they show the existence of two distinct regimes, one where the mean salt mass remains nearly constant (or decreases) with increasing rainfall frequency, and another where mean salt content increases markedly with increasing rainfall frequency. As a result, relatively small reductions of rainfall in drier climates may entail dramatic shifts in longterm soil salinization trends, with significant consequences, e.g. for climate change impacts on rain fed agriculture.

  19. Modelling freeway networks by hybrid stochastic models

    OpenAIRE

    Boel, R.; Mihaylova, L.

    2004-01-01

    Traffic flow on freeways is a nonlinear, many-particle phenomenon, with complex interactions between the vehicles. This paper presents a stochastic hybrid model of freeway traffic at a time scale and at a level of detail suitable for on-line flow estimation, for routing and ramp metering control. The model describes the evolution of continuous and discrete state variables. The freeway is considered as a network of components, each component representing a different section of the network. The...

  20. Stochastic Modelling and Analysis of Warehouse Operations

    NARCIS (Netherlands)

    Y. Gong (Yeming)

    2009-01-01

    textabstractThis thesis has studied stochastic models and analysis of warehouse operations. After an overview of stochastic research in warehouse operations, we explore the following topics. Firstly, we search optimal batch sizes in a parallel-aisle warehouse with online order arrivals. We employ a

  1. Temperature stochastic modeling and weather derivatives pricing ...

    African Journals Online (AJOL)

    ... over a sufficient period to apply a stochastic process that describes the evolution of the temperature. A numerical example of a swap contract pricing is presented, using an approximation formula as well as Monte Carlo simulations. Keywords: Weather derivatives, temperature stochastic model, Monte Carlo simulation.

  2. Towards Model Checking Stochastic Process Algebra

    NARCIS (Netherlands)

    Hermanns, H.; Grieskamp, W.; Santen, T.; Katoen, Joost P.; Stoddart, B.; Meyer-Kayser, J.; Siegle, M.

    2000-01-01

    Stochastic process algebras have been proven useful because they allow behaviour-oriented performance and reliability modelling. As opposed to traditional performance modelling techniques, the behaviour- oriented style supports composition and abstraction in a natural way. However, analysis of

  3. Stochastic models of intracellular transport

    Science.gov (United States)

    Bressloff, Paul C.; Newby, Jay M.

    2013-01-01

    The interior of a living cell is a crowded, heterogenuous, fluctuating environment. Hence, a major challenge in modeling intracellular transport is to analyze stochastic processes within complex environments. Broadly speaking, there are two basic mechanisms for intracellular transport: passive diffusion and motor-driven active transport. Diffusive transport can be formulated in terms of the motion of an overdamped Brownian particle. On the other hand, active transport requires chemical energy, usually in the form of adenosine triphosphate hydrolysis, and can be direction specific, allowing biomolecules to be transported long distances; this is particularly important in neurons due to their complex geometry. In this review a wide range of analytical methods and models of intracellular transport is presented. In the case of diffusive transport, narrow escape problems, diffusion to a small target, confined and single-file diffusion, homogenization theory, and fractional diffusion are considered. In the case of active transport, Brownian ratchets, random walk models, exclusion processes, random intermittent search processes, quasi-steady-state reduction methods, and mean-field approximations are considered. Applications include receptor trafficking, axonal transport, membrane diffusion, nuclear transport, protein-DNA interactions, virus trafficking, and the self-organization of subcellular structures.

  4. Stochastic models of intracellular transport

    KAUST Repository

    Bressloff, Paul C.

    2013-01-09

    The interior of a living cell is a crowded, heterogenuous, fluctuating environment. Hence, a major challenge in modeling intracellular transport is to analyze stochastic processes within complex environments. Broadly speaking, there are two basic mechanisms for intracellular transport: passive diffusion and motor-driven active transport. Diffusive transport can be formulated in terms of the motion of an overdamped Brownian particle. On the other hand, active transport requires chemical energy, usually in the form of adenosine triphosphate hydrolysis, and can be direction specific, allowing biomolecules to be transported long distances; this is particularly important in neurons due to their complex geometry. In this review a wide range of analytical methods and models of intracellular transport is presented. In the case of diffusive transport, narrow escape problems, diffusion to a small target, confined and single-file diffusion, homogenization theory, and fractional diffusion are considered. In the case of active transport, Brownian ratchets, random walk models, exclusion processes, random intermittent search processes, quasi-steady-state reduction methods, and mean-field approximations are considered. Applications include receptor trafficking, axonal transport, membrane diffusion, nuclear transport, protein-DNA interactions, virus trafficking, and the self-organization of subcellular structures. © 2013 American Physical Society.

  5. Stochastic biomathematical models with applications to neuronal modeling

    CERN Document Server

    Batzel, Jerry; Ditlevsen, Susanne

    2013-01-01

    Stochastic biomathematical models are becoming increasingly important as new light is shed on the role of noise in living systems. In certain biological systems, stochastic effects may even enhance a signal, thus providing a biological motivation for the noise observed in living systems. Recent advances in stochastic analysis and increasing computing power facilitate the analysis of more biophysically realistic models, and this book provides researchers in computational neuroscience and stochastic systems with an overview of recent developments. Key concepts are developed in chapters written by experts in their respective fields. Topics include: one-dimensional homogeneous diffusions and their boundary behavior, large deviation theory and its application in stochastic neurobiological models, a review of mathematical methods for stochastic neuronal integrate-and-fire models, stochastic partial differential equation models in neurobiology, and stochastic modeling of spreading cortical depression.

  6. Stochastic Modeling of Soil Salinity

    Science.gov (United States)

    Suweis, Samir; Rinaldo, Andrea; van der Zee, Sjoerd E. A. T. M.; Maritan, Amos; Porporato, Amilcare

    2010-05-01

    Large areas of cultivated land worldwide are affected by soil salinity. Estimates report that 10% of arable land in over 100 countries, and nine million km2 are salt affected, especially in arid and semi-arid regions. High salinity causes both ion specific and osmotic stress effects, with important consequences for plant production and quality. Salt accumulation in the root zone may be due to natural factors (primary salinization) or due to irrigation (secondary salinization). Simple (e.g., vertically averaged over the soil depth) coupled soil moisture and salt balance equations have been used in the past. Despite their approximations, these models have the advantage of parsimony, thus allowing a direct analysis of the interplay of the main processes. They also provide the ideal starting point to include external, random hydro-climatic fluctuations in the analysis of long-term salinization trends. We propose a minimalist stochastic model of primary soil salinity, in which the rate of soil salinization is determined by the balance between dry and wet salt deposition and the intermittent leaching events caused by rainfall events. The long term probability density functions of salt mass and concentration are found by reducing the coupled soil moisture and salt mass balance equation to a stochastic differential equation driven by multiplicative Poisson noise. The novel analytical solutions provide insight on the interplay of the main soil, plant and climate parameters responsible for long-term soil salinization. In fact, soil salinity statistics are obtained as a function of climate, soil and vegetation parameters. These, in turn, can be combined with soil moisture statistics to obtain a full characterization of soil salt concentrations and the ensuing risk of primary salinization. In particular, the solutions show the existence of two quite distinct regimes, the first one where the mean salt mass remains nearly constant with increasing rainfall frequency, and the

  7. Stochasticity and determinism in models of hematopoiesis.

    Science.gov (United States)

    Kimmel, Marek

    2014-01-01

    This chapter represents a novel view of modeling in hematopoiesis, synthesizing both deterministic and stochastic approaches. Whereas the stochastic models work in situations where chance dominates, for example when the number of cells is small, or under random mutations, the deterministic models are more important for large-scale, normal hematopoiesis. New types of models are on the horizon. These models attempt to account for distributed environments such as hematopoietic niches and their impact on dynamics. Mixed effects of such structures and chance events are largely unknown and constitute both a challenge and promise for modeling. Our discussion is presented under the separate headings of deterministic and stochastic modeling; however, the connections between both are frequently mentioned. Four case studies are included to elucidate important examples. We also include a primer of deterministic and stochastic dynamics for the reader's use.

  8. MODELLING OF A STOCHASTIC CONTINUOUS SYSTEM

    Directory of Open Access Journals (Sweden)

    Martin Albertyn

    2012-01-01

    Full Text Available The key objective is to develop a method which can be utilized to model a stochastic continuous system. A system from the "real world" is used as the basis for the simulation modelling technique that is presented. The conceptualization phase indicates that the model has to incorporate stochastic and deterministic elements. A method is developed that utilizes the discrete simulation ability of a stochastic package (ARENA, in conjunction with a deterministic package (FORTRAN, to model the continuous system. (Software packages tend to specialize in either stochastic, or deterministic modelling. The length of the iteration time interval and adequate sample size are investigated. The method is authenticated by the verification and validation ofthe defined model. Two scenarios are modelled and the results are discussed . Conclusions are presented and strengths and weaknesses of this method are considered and discussed .

  9. Stochastic transition model for pedestrian dynamics

    CERN Document Server

    Schultz, Michael

    2012-01-01

    The proposed stochastic model for pedestrian dynamics is based on existing approaches using cellular automata, combined with substantial extensions, to compensate the deficiencies resulting of the discrete grid structure. This agent motion model is extended by both a grid-based path planning and mid-range agent interaction component. The stochastic model proves its capabilities for a quantitative reproduction of the characteristic shape of the common fundamental diagram of pedestrian dynamics. Moreover, effects of self-organizing behavior are successfully reproduced. The stochastic cellular automata approach is found to be adequate with respect to uncertainties in human motion patterns, a feature previously held by artificial noise terms alone.

  10. Modeling and analysis of stochastic systems

    CERN Document Server

    Kulkarni, Vidyadhar G

    2011-01-01

    Based on the author's more than 25 years of teaching experience, Modeling and Analysis of Stochastic Systems, Second Edition covers the most important classes of stochastic processes used in the modeling of diverse systems, from supply chains and inventory systems to genetics and biological systems. For each class of stochastic process, the text includes its definition, characterization, applications, transient and limiting behavior, first passage times, and cost/reward models. Along with reorganizing the material, this edition revises and adds new exercises and examples. New to the second edi

  11. Modelling and application of stochastic processes

    CERN Document Server

    1986-01-01

    The subject of modelling and application of stochastic processes is too vast to be exhausted in a single volume. In this book, attention is focused on a small subset of this vast subject. The primary emphasis is on realization and approximation of stochastic systems. Recently there has been considerable interest in the stochastic realization problem, and hence, an attempt has been made here to collect in one place some of the more recent approaches and algorithms for solving the stochastic realiza­ tion problem. Various different approaches for realizing linear minimum-phase systems, linear nonminimum-phase systems, and bilinear systems are presented. These approaches range from time-domain methods to spectral-domain methods. An overview of the chapter contents briefly describes these approaches. Also, in most of these chapters special attention is given to the problem of developing numerically ef­ ficient algorithms for obtaining reduced-order (approximate) stochastic realizations. On the application side,...

  12. A stochastic SIS epidemic model with vaccination

    Science.gov (United States)

    Cao, Boqiang; Shan, Meijing; Zhang, Qimin; Wang, Weiming

    2017-11-01

    In this paper, we investigate the basic features of an SIS type infectious disease model with varying population size and vaccinations in presence of environment noise. By applying the Markov semigroup theory, we propose a stochastic reproduction number R0s which can be seen as a threshold parameter to utilize in identifying the stochastic extinction and persistence: If R0s 1, under some mild extra conditions, the SDE model has an endemic stationary distribution which results in the stochastic persistence of the infectious disease. The most interesting finding is that large environmental noise can suppress the outbreak of the disease.

  13. Moment Closure for the Stochastic Logistic Model

    National Research Council Canada - National Science Library

    Singh, Abhyudai; Hespanha, Joao P

    2006-01-01

    ..., which we refer to as the moment closure function. In this paper, a systematic procedure for constructing moment closure functions of arbitrary order is presented for the stochastic logistic model...

  14. Computer Aided Continuous Time Stochastic Process Modelling

    DEFF Research Database (Denmark)

    Kristensen, N.R.; Madsen, Henrik; Jørgensen, Sten Bay

    2001-01-01

    A grey-box approach to process modelling that combines deterministic and stochastic modelling is advocated for identification of models for model-based control of batch and semi-batch processes. A computer-aided tool designed for supporting decision-making within the corresponding modelling cycle...

  15. Model checking mobile stochastic logic.

    NARCIS (Netherlands)

    De Nicola, Rocco; Katoen, Joost P.; Latella, Diego; Loreti, Michele; Massink, Mieke

    2007-01-01

    The Temporal Mobile Stochastic Logic (MOSL) has been introduced in previous work by the authors for formulating properties of systems specified in STOKLAIM, a Markovian extension of KLAIM. The main purpose of MOSL is to address key functional aspects of global computing such as distribution

  16. A Stochastic Diffusion Model of Climate Change

    CERN Document Server

    Pelletier, J D

    1995-01-01

    We present a model for variations in atmospheric temperature from time scales of one day to one million years based on a stochastic diffusion (random walk) model of the turbulent transport of heat energy vertically in a coupled atmosphere-ocean model. The predictions of the model are supported by station records and paleoclimatic proxy data of temperature variations.

  17. Stochastic differential equations used to model conjugation

    DEFF Research Database (Denmark)

    Philipsen, Kirsten Riber; Christiansen, Lasse Engbo

    Stochastic differential equations (SDEs) are used to model horizontal transfer of antibiotic resis- tance by conjugation. The model describes the concentration of donor, recipient, transconjugants and substrate. The strength of the SDE model over the traditional ODE models is that the noise can...

  18. Stochastic Modeling of Traffic Air Pollution

    DEFF Research Database (Denmark)

    Thoft-Christensen, Palle

    2014-01-01

    In this paper, modeling of traffic air pollution is discussed with special reference to infrastructures. A number of subjects related to health effects of air pollution and the different types of pollutants are briefly presented. A simple model for estimating the social cost of traffic related air...... and using simple Monte Carlo techniques to obtain a stochastic estimate of the costs of traffic air pollution for infrastructures....... pollution is derived. Several authors have published papers on this very complicated subject, but no stochastic modelling procedure have obtained general acceptance. The subject is discussed basis of a deterministic model. However, it is straightforward to modify this model to include uncertain parameters...

  19. Stochastic differential equation model to Prendiville processes

    Science.gov (United States)

    Granita, Bahar, Arifah

    2015-10-01

    The Prendiville process is another variation of the logistic model which assumes linearly decreasing population growth rate. It is a continuous time Markov chain (CTMC) taking integer values in the finite interval. The continuous time Markov chain can be approximated by stochastic differential equation (SDE). This paper discusses the stochastic differential equation of Prendiville process. The work started with the forward Kolmogorov equation in continuous time Markov chain of Prendiville process. Then it was formulated in the form of a central-difference approximation. The approximation was then used in Fokker-Planck equation in relation to the stochastic differential equation of the Prendiville process. The explicit solution of the Prendiville process was obtained from the stochastic differential equation. Therefore, the mean and variance function of the Prendiville process could be easily found from the explicit solution.

  20. Sequential neural models with stochastic layers

    DEFF Research Database (Denmark)

    Fraccaro, Marco; Sønderby, Søren Kaae; Paquet, Ulrich

    2016-01-01

    How can we efficiently propagate uncertainty in a latent state representation with recurrent neural networks? This paper introduces stochastic recurrent neural networks which glue a deterministic recurrent neural network and a state space model together to form a stochastic and sequential neural ...... the uncertainty in a latent path, like a state space model, we improve the state of the art results on the Blizzard and TIMIT speech modeling data sets by a large margin, while achieving comparable performances to competing methods on polyphonic music modeling....

  1. Stochastic volatility models and Kelvin waves

    Science.gov (United States)

    Lipton, Alex; Sepp, Artur

    2008-08-01

    We use stochastic volatility models to describe the evolution of an asset price, its instantaneous volatility and its realized volatility. In particular, we concentrate on the Stein and Stein model (SSM) (1991) for the stochastic asset volatility and the Heston model (HM) (1993) for the stochastic asset variance. By construction, the volatility is not sign definite in SSM and is non-negative in HM. It is well known that both models produce closed-form expressions for the prices of vanilla option via the Lewis-Lipton formula. However, the numerical pricing of exotic options by means of the finite difference and Monte Carlo methods is much more complex for HM than for SSM. Until now, this complexity was considered to be an acceptable price to pay for ensuring that the asset volatility is non-negative. We argue that having negative stochastic volatility is a psychological rather than financial or mathematical problem, and advocate using SSM rather than HM in most applications. We extend SSM by adding volatility jumps and obtain a closed-form expression for the density of the asset price and its realized volatility. We also show that the current method of choice for solving pricing problems with stochastic volatility (via the affine ansatz for the Fourier-transformed density function) can be traced back to the Kelvin method designed in the 19th century for studying wave motion problems arising in fluid dynamics.

  2. Stochastic stability and instability of model ecosystems

    Science.gov (United States)

    Ladde, G. S.; Siljak, D. D.

    1975-01-01

    In this work, we initiate a stability study of multispecies communities in stochastic environment by using Ito's differential equations as community models. By applying the direct method of Liapunov, we obtain sufficient conditions for stability and instability in the mean of the equilibrium populations. The conditions are expressed in terms of the dominant diagonal property of community matrices, which is a suitable mechanism for resolving the central problem of 'complexity vs stability' in model ecosystems. As a by-product of this analysis we exhibit important structural properties of the stochastic density-dependent models, and establish tolerance of community stability to a broad class of nonlinear time-varying perturbations.

  3. Fuzzy stochastic inventory model for deteriorating item

    Directory of Open Access Journals (Sweden)

    Waliv Rahul H.

    2017-01-01

    Full Text Available A multi item profit maximization inventory model is developed in fuzzy stochastic environment. Demand is taken as Stock dependent demand. Available storage space is assumed to be imprecise and vague in nature. Impreciseness has been expressed by linear membership function. Purchasing cost and investment constraint are considered to be random and their randomness is expressed by normal distribution. The model has been formulated as a fuzzy stochastic programming problem and reduced to corresponding equivalent fuzzy linear programming problem. The model has been solved by using fuzzy linear programming technique and illustrated numerically.

  4. Weather Derivatives and Stochastic Modelling of Temperature

    Directory of Open Access Journals (Sweden)

    Fred Espen Benth

    2011-01-01

    Full Text Available We propose a continuous-time autoregressive model for the temperature dynamics with volatility being the product of a seasonal function and a stochastic process. We use the Barndorff-Nielsen and Shephard model for the stochastic volatility. The proposed temperature dynamics is flexible enough to model temperature data accurately, and at the same time being analytically tractable. Futures prices for commonly traded contracts at the Chicago Mercantile Exchange on indices like cooling- and heating-degree days and cumulative average temperatures are computed, as well as option prices on them.

  5. Stochastic Modelling Of The Repairable System

    Directory of Open Access Journals (Sweden)

    Andrzejczak Karol

    2015-11-01

    Full Text Available All reliability models consisting of random time factors form stochastic processes. In this paper we recall the definitions of the most common point processes which are used for modelling of repairable systems. Particularly this paper presents stochastic processes as examples of reliability systems for the support of the maintenance related decisions. We consider the simplest one-unit system with a negligible repair or replacement time, i.e., the unit is operating and is repaired or replaced at failure, where the time required for repair and replacement is negligible. When the repair or replacement is completed, the unit becomes as good as new and resumes operation. The stochastic modelling of recoverable systems constitutes an excellent method of supporting maintenance related decision-making processes and enables their more rational use.

  6. Some recent developments in stochastic volatility modelling

    DEFF Research Database (Denmark)

    Barndorff-Nielsen, Ole Eiler; Nicolato, Elisa; Shephard, N.

    2002-01-01

    This paper reviews and puts in context some of our recent work on stochastic volatility (SV) modelling for financial economics. Here our main focus is on: (i) the relationship between subordination and SV, (ii) OU based volatility models, (iii) exact option pricing, (iv) realized power variation ...

  7. Stochastic models for turbulent reacting flows

    Energy Technology Data Exchange (ETDEWEB)

    Kerstein, A. [Sandia National Laboratories, Livermore, CA (United States)

    1993-12-01

    The goal of this program is to develop and apply stochastic models of various processes occurring within turbulent reacting flows in order to identify the fundamental mechanisms governing these flows, to support experimental studies of these flows, and to further the development of comprehensive turbulent reacting flow models.

  8. Stochastic Modeling Of Wind Turbine Drivetrain Components

    DEFF Research Database (Denmark)

    Rafsanjani, Hesam Mirzaei; Sørensen, John Dalsgaard

    2014-01-01

    are needed for initial defects and damage accumulation. In this paper, stochastic models are formulated considering some of the failure modes observed in these components. The models are based on theoretical considerations, manufacturing uncertainties, size effects of different scales. It is illustrated how...

  9. Stochastic Differential Equations in Artificial Pancreas Modelling

    DEFF Research Database (Denmark)

    Duun-Henriksen, Anne Katrine

    . However, uncertainty in the model occurs due to the nature of physiological systems and due to the presence of unknown disturbances. An attractive approach to deal with this uncertainty is to use stochastic differential equations (SDEs). In a model based on SDEs, the noise is separated into two terms: 1...

  10. Compositional Modelling of Stochastic Hybrid Systems

    NARCIS (Netherlands)

    Strubbe, S.N.

    2005-01-01

    In this thesis we present a modelling framework for compositional modelling of stochastic hybrid systems. Hybrid systems consist of a combination of continuous and discrete dynamics. The state space of a hybrid system is hybrid in the sense that it consists of a continuous component and a discrete

  11. Modelling Cow Behaviour Using Stochastic Automata

    DEFF Research Database (Denmark)

    Jónsson, Ragnar Ingi

    This report covers an initial study on the modelling of cow behaviour using stochastic automata with the aim of detecting lameness. Lameness in cows is a serious problem that needs to be dealt with because it results in less profitable production units and in reduced quality of life for the affec......This report covers an initial study on the modelling of cow behaviour using stochastic automata with the aim of detecting lameness. Lameness in cows is a serious problem that needs to be dealt with because it results in less profitable production units and in reduced quality of life...

  12. An Enhanced Model for Stochastic Coordination

    Directory of Open Access Journals (Sweden)

    Nuno Oliveira

    2016-10-01

    Full Text Available Applications developed over the cloud coordinate several, often anonymous, computational resources, distributed over different execution nodes, within flexible architectures. Coordination models able to represent quantitative data provide a powerful basis for their analysis and validation. This paper extends IMCreo, a semantic model for Stochastic reo based on interactive Markov chains, to enhance its scalability, by regarding each channel and node, as well as interface components, as independent stochastic processes that may (or may not synchronise with the rest of the coordination circuit.

  13. Modeling stochasticity in biochemical reaction networks

    Science.gov (United States)

    Constantino, P. H.; Vlysidis, M.; Smadbeck, P.; Kaznessis, Y. N.

    2016-03-01

    Small biomolecular systems are inherently stochastic. Indeed, fluctuations of molecular species are substantial in living organisms and may result in significant variation in cellular phenotypes. The chemical master equation (CME) is the most detailed mathematical model that can describe stochastic behaviors. However, because of its complexity the CME has been solved for only few, very small reaction networks. As a result, the contribution of CME-based approaches to biology has been very limited. In this review we discuss the approach of solving CME by a set of differential equations of probability moments, called moment equations. We present different approaches to produce and to solve these equations, emphasizing the use of factorial moments and the zero information entropy closure scheme. We also provide information on the stability analysis of stochastic systems. Finally, we speculate on the utility of CME-based modeling formalisms, especially in the context of synthetic biology efforts.

  14. Stochastic linear programming models, theory, and computation

    CERN Document Server

    Kall, Peter

    2011-01-01

    This new edition of Stochastic Linear Programming: Models, Theory and Computation has been brought completely up to date, either dealing with or at least referring to new material on models and methods, including DEA with stochastic outputs modeled via constraints on special risk functions (generalizing chance constraints, ICC’s and CVaR constraints), material on Sharpe-ratio, and Asset Liability Management models involving CVaR in a multi-stage setup. To facilitate use as a text, exercises are included throughout the book, and web access is provided to a student version of the authors’ SLP-IOR software. Additionally, the authors have updated the Guide to Available Software, and they have included newer algorithms and modeling systems for SLP. The book is thus suitable as a text for advanced courses in stochastic optimization, and as a reference to the field. From Reviews of the First Edition: "The book presents a comprehensive study of stochastic linear optimization problems and their applications. … T...

  15. Normal Forms for Reduced Stochastic Climate Models

    Science.gov (United States)

    Franzke, C.; Majda, A.; Crommelin, D.

    2009-04-01

    The systematic development of reduced low-dimensional stochastic climate models from observations or comprehensive high-dimensional climate models is an important topic for low-frequency variability, climate sensitivity, and improved extended range forecasting. Here techniques from applied mathematics are utilized to systematically derive normal forms for reduced stochastic climate models for low-frequency variables. The use of a few Empirical Orthogonal Functions (EOF) depending on observational data to span the low-frequency subspace requires the assessment of dyad interactions besides the more familiar triads in the interaction between the low- and high-frequency subspaces of the dynamics. It will be shown that the dyad and multiplicative triad interactions combine with the climatological linear operator interactions to simultaneously produce both strong nonlinear dissipation and Correlated Additive and Multiplicative (CAM) stochastic noise. For a single low-frequency variable the dyad interactions and climatological linear operator alone produce a normal form with CAM noise from advection of the large-scales by the small scales and simultaneously strong cubic damping. This normal form should prove useful for developing systematic regression fitting strategies for stochastic models of climate data. The validity of the one and two dimensional normal forms will be presented. Also the analytical PDF form for one-dimensional reduced models will be derived. This PDF can exhibit power-law decay only over a limited range and its ultimate decay is determined by the cubic damping. This cubic damping produces a Gaussian tail.

  16. Stochastic dynamical models for ecological regime shifts

    DEFF Research Database (Denmark)

    Møller, Jan Kloppenborg; Carstensen, Jacob; Madsen, Henrik

    Ecosystems are influenced by a variety of known and unknown drivers. Unknown drivers should be modeled as noise and it is therefore important to analyze how noise influences the deterministic skeleton of system equations. The deterministic skeleton of stochastic dynamical models contains the phys...... definition and stability of regimes become less subtle. Ecological regime shifts and their modeling must be viewed in a probabilistic manner, particularly if such model results are to be used in ecosystem management....

  17. Electricity price modeling with stochastic time change

    NARCIS (Netherlands)

    Borovkova, Svetlana; Schmeck, Maren Diane

    2017-01-01

    In this paper, we develop a novel approach to electricity price modeling, based on the powerful technique of stochastic time change. This technique allows us to incorporate the characteristic features of electricity prices (such as seasonal volatility, time varying mean reversion and seasonally

  18. Positive recurrent of stochastic coral reefs model

    Science.gov (United States)

    Huang, Zaitang

    2017-11-01

    In this work, we discuss permanence and ergodicity of a stochastic coral reefs model. One of the distinctive features of our results is that our results enables characterization of the support of a unique invariant probability measure by Lie groups and geometric control theory. It is proved that the densities either converges to an invariant density or converges weakly to a singular measure.

  19. A Stochastic Dynamic Model of Computer Viruses

    Directory of Open Access Journals (Sweden)

    Chunming Zhang

    2012-01-01

    Full Text Available A stochastic computer virus spread model is proposed and its dynamic behavior is fully investigated. Specifically, we prove the existence and uniqueness of positive solutions, and the stability of the virus-free equilibrium and viral equilibrium by constructing Lyapunov functions and applying Ito's formula. Some numerical simulations are finally given to illustrate our main results.

  20. Vulnerability in a Stochastic Dynamic Model

    NARCIS (Netherlands)

    Elbers, Chris; Gunning, Jan Willem

    2003-01-01

    Most measures of vulnerability are a-theoretic and essentially static. In this paper we use a stochastic Ramsey model to find a household's optimal welfare and we measure vulnerability as the shortfall from the welfare attained if the household consumed permanently at the poverty line. The results

  1. Stochastic biophysical modeling of irradiated cells

    CERN Document Server

    Fornalski, Krzysztof Wojciech

    2014-01-01

    The paper presents a computational stochastic model of virtual cells irradiation, based on Quasi-Markov Chain Monte Carlo method and using biophysical input. The model is based on a stochastic tree of probabilities for each cell of the entire colony. Biophysics of the cells is described by probabilities and probability distributions provided as the input. The adaptation of nucleation and catastrophe theories, well known in physics, yields sigmoidal relationships for carcinogenic risk as a function of the irradiation. Adaptive response and bystander effect, incorporated into the model, improves its application. The results show that behavior of virtual cells can be successfully modeled, e.g. cancer transformation, creation of mutations, radioadaptation or radiotherapy. The used methodology makes the model universal and practical for simulations of general processes. Potential biophysical curves and relationships are also widely discussed in the paper. However, the presented theoretical model does not describe ...

  2. Stochastic models in reliability and maintenance

    CERN Document Server

    2002-01-01

    Our daily lives can be maintained by the high-technology systems. Computer systems are typical examples of such systems. We can enjoy our modern lives by using many computer systems. Much more importantly, we have to maintain such systems without failure, but cannot predict when such systems will fail and how to fix such systems without delay. A stochastic process is a set of outcomes of a random experiment indexed by time, and is one of the key tools needed to analyze the future behavior quantitatively. Reliability and maintainability technologies are of great interest and importance to the maintenance of such systems. Many mathematical models have been and will be proposed to describe reliability and maintainability systems by using the stochastic processes. The theme of this book is "Stochastic Models in Reliability and Main­ tainability. " This book consists of 12 chapters on the theme above from the different viewpoints of stochastic modeling. Chapter 1 is devoted to "Renewal Processes," under which cla...

  3. Evaluation of stochastic reservoir operation optimization models

    Science.gov (United States)

    Celeste, Alcigeimes B.; Billib, Max

    2009-09-01

    This paper investigates the performance of seven stochastic models used to define optimal reservoir operating policies. The models are based on implicit (ISO) and explicit stochastic optimization (ESO) as well as on the parameterization-simulation-optimization (PSO) approach. The ISO models include multiple regression, two-dimensional surface modeling and a neuro-fuzzy strategy. The ESO model is the well-known and widely used stochastic dynamic programming (SDP) technique. The PSO models comprise a variant of the standard operating policy (SOP), reservoir zoning, and a two-dimensional hedging rule. The models are applied to the operation of a single reservoir damming an intermittent river in northeastern Brazil. The standard operating policy is also included in the comparison and operational results provided by deterministic optimization based on perfect forecasts are used as a benchmark. In general, the ISO and PSO models performed better than SDP and the SOP. In addition, the proposed ISO-based surface modeling procedure and the PSO-based two-dimensional hedging rule showed superior overall performance as compared with the neuro-fuzzy approach.

  4. Stochastic discrete model of karstic networks

    Science.gov (United States)

    Jaquet, O.; Siegel, P.; Klubertanz, G.; Benabderrhamane, H.

    Karst aquifers are characterised by an extreme spatial heterogeneity that strongly influences their hydraulic behaviour and the transport of pollutants. These aquifers are particularly vulnerable to contamination because of their highly permeable networks of conduits. A stochastic model is proposed for the simulation of the geometry of karstic networks at a regional scale. The model integrates the relevant physical processes governing the formation of karstic networks. The discrete simulation of karstic networks is performed with a modified lattice-gas cellular automaton for a representative description of the karstic aquifer geometry. Consequently, more reliable modelling results can be obtained for the management and the protection of karst aquifers. The stochastic model was applied jointly with groundwater modelling techniques to a regional karst aquifer in France for the purpose of resolving surface pollution issues.

  5. Dynamic optimization deterministic and stochastic models

    CERN Document Server

    Hinderer, Karl; Stieglitz, Michael

    2016-01-01

    This book explores discrete-time dynamic optimization and provides a detailed introduction to both deterministic and stochastic models. Covering problems with finite and infinite horizon, as well as Markov renewal programs, Bayesian control models and partially observable processes, the book focuses on the precise modelling of applications in a variety of areas, including operations research, computer science, mathematics, statistics, engineering, economics and finance. Dynamic Optimization is a carefully presented textbook which starts with discrete-time deterministic dynamic optimization problems, providing readers with the tools for sequential decision-making, before proceeding to the more complicated stochastic models. The authors present complete and simple proofs and illustrate the main results with numerous examples and exercises (without solutions). With relevant material covered in four appendices, this book is completely self-contained.

  6. Model predictive control classical, robust and stochastic

    CERN Document Server

    Kouvaritakis, Basil

    2016-01-01

    For the first time, a textbook that brings together classical predictive control with treatment of up-to-date robust and stochastic techniques. Model Predictive Control describes the development of tractable algorithms for uncertain, stochastic, constrained systems. The starting point is classical predictive control and the appropriate formulation of performance objectives and constraints to provide guarantees of closed-loop stability and performance. Moving on to robust predictive control, the text explains how similar guarantees may be obtained for cases in which the model describing the system dynamics is subject to additive disturbances and parametric uncertainties. Open- and closed-loop optimization are considered and the state of the art in computationally tractable methods based on uncertainty tubes presented for systems with additive model uncertainty. Finally, the tube framework is also applied to model predictive control problems involving hard or probabilistic constraints for the cases of multiplic...

  7. Moment Closure for the Stochastic Logistic Model

    Science.gov (United States)

    2006-01-16

    Arlington VA 22202-4302. Respondents should be aware that notwithstanding any other provision of law , no person shall be subject to a penalty for failing...model with analysis using cumulant truncation. Enviromental and Ecological Statistics 9, 237–258. Matis, J. H., Kiffe, T. R., Parthasarathy, P. R., 1998...On the cumulant of population size for the stochastic power law logisitc model. Theoretical Population Biology 53, 16–29. Nasell, I., 2001

  8. Stochastic models for atomic clocks

    Science.gov (United States)

    Barnes, J. A.; Jones, R. H.; Tryon, P. V.; Allan, D. W.

    1983-01-01

    For the atomic clocks used in the National Bureau of Standards Time Scales, an adequate model is the superposition of white FM, random walk FM, and linear frequency drift for times longer than about one minute. The model was tested on several clocks using maximum likelihood techniques for parameter estimation and the residuals were acceptably random. Conventional diagnostics indicate that additional model elements contribute no significant improvement to the model even at the expense of the added model complexity.

  9. Stochastic dynamic models and Chebyshev splines

    Science.gov (United States)

    Fan, Ruzong; Zhu, Bin; Wang, Yuedong

    2015-01-01

    In this article, we establish a connection between a stochastic dynamic model (SDM) driven by a linear stochastic differential equation (SDE) and a Chebyshev spline, which enables researchers to borrow strength across fields both theoretically and numerically. We construct a differential operator for the penalty function and develop a reproducing kernel Hilbert space (RKHS) induced by the SDM and the Chebyshev spline. The general form of the linear SDE allows us to extend the well-known connection between an integrated Brownian motion and a polynomial spline to a connection between more complex diffusion processes and Chebyshev splines. One interesting special case is connection between an integrated Ornstein–Uhlenbeck process and an exponential spline. We use two real data sets to illustrate the integrated Ornstein–Uhlenbeck process model and exponential spline model and show their estimates are almost identical. PMID:26045632

  10. Stochastic Modelling of Energy Systems

    DEFF Research Database (Denmark)

    Andersen, Klaus Kaae

    2001-01-01

    of statistical methods and physical interpretation is exploited in the modelling procedure, from the design of experiments to parameter estimation and model validation. The presented models are mainly formulated as state space models in continuous time with discrete time observation equations. The state......In this thesis dynamic models of typical components in Danish heating systems are considered. Emphasis is made on describing and evaluating mathematical methods for identification of such models, and on presentation of component models for practical applications. The thesis consists of seven...... research papers (case studies) together with a summary report. Each case study takes it's starting point in typical heating system components and both, the applied mathematical modelling methods and the application aspects, are considered. The summary report gives an introduction to the scope...

  11. Brain-inspired Stochastic Models and Implementations

    KAUST Repository

    Al-Shedivat, Maruan

    2015-05-12

    One of the approaches to building artificial intelligence (AI) is to decipher the princi- ples of the brain function and to employ similar mechanisms for solving cognitive tasks, such as visual perception or natural language understanding, using machines. The recent breakthrough, named deep learning, demonstrated that large multi-layer networks of arti- ficial neural-like computing units attain remarkable performance on some of these tasks. Nevertheless, such artificial networks remain to be very loosely inspired by the brain, which rich structures and mechanisms may further suggest new algorithms or even new paradigms of computation. In this thesis, we explore brain-inspired probabilistic mechanisms, such as neural and synaptic stochasticity, in the context of generative models. The two questions we ask here are: (i) what kind of models can describe a neural learning system built of stochastic components? and (ii) how can we implement such systems e ̆ciently? To give specific answers, we consider two well known models and the corresponding neural architectures: the Naive Bayes model implemented with a winner-take-all spiking neural network and the Boltzmann machine implemented in a spiking or non-spiking fashion. We propose and analyze an e ̆cient neuromorphic implementation of the stochastic neu- ral firing mechanism and study the e ̄ects of synaptic unreliability on learning generative energy-based models implemented with neural networks.

  12. Modelling conjugation with stochastic differential equations

    DEFF Research Database (Denmark)

    Philipsen, Kirsten Riber; Christiansen, Lasse Engbo; Hasman, Henrik

    2010-01-01

    Conjugation is an important mechanism involved in the transfer of resistance between bacteria. In this article a stochastic differential equation based model consisting of a continuous time state equation and a discrete time measurement equation is introduced to model growth and conjugation of two...... Enterococcus faecium strains in a rich exhaustible media. The model contains a new expression for a substrate dependent conjugation rate. A maximum likelihood based method is used to estimate the model parameters. Different models including different noise structure for the system and observations are compared...

  13. Modeling and Prediction Using Stochastic Differential Equations

    DEFF Research Database (Denmark)

    Juhl, Rune; Møller, Jan Kloppenborg; Jørgensen, John Bagterp

    2016-01-01

    Pharmacokinetic/pharmakodynamic (PK/PD) modeling for a single subject is most often performed using nonlinear models based on deterministic ordinary differential equations (ODEs), and the variation between subjects in a population of subjects is described using a population (mixed effects) setup...... deterministic and can predict the future perfectly. A more realistic approach would be to allow for randomness in the model due to e.g., the model be too simple or errors in input. We describe a modeling and prediction setup which better reflects reality and suggests stochastic differential equations (SDEs...

  14. Fuzzy Stochastic Optimization Theory, Models and Applications

    CERN Document Server

    Wang, Shuming

    2012-01-01

    Covering in detail both theoretical and practical perspectives, this book is a self-contained and systematic depiction of current fuzzy stochastic optimization that deploys the fuzzy random variable as a core mathematical tool to model the integrated fuzzy random uncertainty. It proceeds in an orderly fashion from the requisite theoretical aspects of the fuzzy random variable to fuzzy stochastic optimization models and their real-life case studies.   The volume reflects the fact that randomness and fuzziness (or vagueness) are two major sources of uncertainty in the real world, with significant implications in a number of settings. In industrial engineering, management and economics, the chances are high that decision makers will be confronted with information that is simultaneously probabilistically uncertain and fuzzily imprecise, and optimization in the form of a decision must be made in an environment that is doubly uncertain, characterized by a co-occurrence of randomness and fuzziness. This book begins...

  15. Stochastic Model Checking of the Stochastic Quality Calculus

    DEFF Research Database (Denmark)

    Nielson, Flemming; Nielson, Hanne Riis; Zeng, Kebin

    2015-01-01

    The Quality Calculus uses quality binders for input to express strategies for continuing the computation even when the desired input has not been received. The Stochastic Quality Calculus adds generally distributed delays for output actions and real-time constraints on the quality binders for input...

  16. A stochastic model of human gait dynamics

    Science.gov (United States)

    Ashkenazy, Yosef; M. Hausdorff, Jeffrey; Ch. Ivanov, Plamen; Eugene Stanley, H.

    2002-12-01

    We present a stochastic model of gait rhythm dynamics, based on transitions between different “neural centers”, that reproduces distinctive statistical properties of normal human walking. By tuning one model parameter, the transition (hopping) range, the model can describe alterations in gait dynamics from childhood to adulthood-including a decrease in the correlation and volatility exponents with maturation. The model also generates time series with multifractal spectra whose broadness depends only on this parameter. Moreover, we find that the volatility exponent increases monotonically as a function of the width of the multifractal spectrum, suggesting the possibility of a change in multifractality with maturation.

  17. A stochastic model for the financial market with discontinuous prices

    Directory of Open Access Journals (Sweden)

    Leda D. Minkova

    1996-01-01

    Full Text Available This paper models some situations occurring in the financial market. The asset prices evolve according to a stochastic integral equation driven by a Gaussian martingale. A portfolio process is constrained in such a way that the wealth process covers some obligation. A solution to a linear stochastic integral equation is obtained in a class of cadlag stochastic processes.

  18. Stochastic Models of Solid Particles Grinding

    Directory of Open Access Journals (Sweden)

    G. A. Zueva

    2010-01-01

    Full Text Available Solid particle grinding is considered as a Markov process. Mathematical models of disintegration kinetics are classified on the basis of the class of Markov process that they belong to. A mathematical description of the disintegration kinetics of polydisperse particles by milling in a shock-loading grinder is proposed on the basis of the theory of Markov processes taking into account the operational conditions in the device. The proposed stochastic model calculates the particle size distribution of the material at any instant in any place in the grinder. The experimental data is in accordance with the predicted values according to the proposed model.

  19. A stochastic evolutionary model for survival dynamics

    Science.gov (United States)

    Fenner, Trevor; Levene, Mark; Loizou, George

    2014-09-01

    The recent interest in human dynamics has led researchers to investigate the stochastic processes that explain human behaviour in different contexts. Here we propose a generative model to capture the essential dynamics of survival analysis, traditionally employed in clinical trials and reliability analysis in engineering. In our model, the only implicit assumption made is that the longer an actor has been in the system, the more likely it is to have failed. We derive a power-law distribution for the process and provide preliminary empirical evidence for the validity of the model from two well-known survival analysis data sets.

  20. Stochastic Optimization of Wind Turbine Power Factor Using Stochastic Model of Wind Power

    DEFF Research Database (Denmark)

    Chen, Peiyuan; Siano, Pierluigi; Bak-Jensen, Birgitte

    2010-01-01

    . The optimization algorithm utilizes the stochastic models of wind power generation (WPG) and load demand to take into account their stochastic variation. The stochastic model of WPG is developed on the basis of a limited autoregressive integrated moving average (LARIMA) model by introducing a crosscorrelation......This paper proposes a stochastic optimization algorithm that aims to minimize the expectation of the system power losses by controlling wind turbine (WT) power factors. This objective of the optimization is subject to the probability constraints of bus voltage and line current requirements...... structure to the LARIMA model. The proposed stochastic optimization is carried out on a 69-bus distribution system. Simulation results confirm that, under various combinations of WPG and load demand, the system power losses are considerably reduced with the optimal setting of WT power factor as compared...

  1. Modeling stochastic frontier based on vine copulas

    Science.gov (United States)

    Constantino, Michel; Candido, Osvaldo; Tabak, Benjamin M.; da Costa, Reginaldo Brito

    2017-11-01

    This article models a production function and analyzes the technical efficiency of listed companies in the United States, Germany and England between 2005 and 2012 based on the vine copula approach. Traditional estimates of the stochastic frontier assume that data is multivariate normally distributed and there is no source of asymmetry. The proposed method based on vine copulas allow us to explore different types of asymmetry and multivariate distribution. Using data on product, capital and labor, we measure the relative efficiency of the vine production function and estimate the coefficient used in the stochastic frontier literature for comparison purposes. This production vine copula predicts the value added by firms with given capital and labor in a probabilistic way. It thereby stands in sharp contrast to the production function, where the output of firms is completely deterministic. The results show that, on average, S&P500 companies are more efficient than companies listed in England and Germany, which presented similar average efficiency coefficients. For comparative purposes, the traditional stochastic frontier was estimated and the results showed discrepancies between the coefficients obtained by the application of the two methods, traditional and frontier-vine, opening new paths of non-linear research.

  2. Modelling Evolutionary Algorithms with Stochastic Differential Equations.

    Science.gov (United States)

    Heredia, Jorge Pérez

    2017-11-20

    There has been renewed interest in modelling the behaviour of evolutionary algorithms (EAs) by more traditional mathematical objects, such as ordinary differential equations or Markov chains. The advantage is that the analysis becomes greatly facilitated due to the existence of well established methods. However, this typically comes at the cost of disregarding information about the process. Here, we introduce the use of stochastic differential equations (SDEs) for the study of EAs. SDEs can produce simple analytical results for the dynamics of stochastic processes, unlike Markov chains which can produce rigorous but unwieldy expressions about the dynamics. On the other hand, unlike ordinary differential equations (ODEs), they do not discard information about the stochasticity of the process. We show that these are especially suitable for the analysis of fixed budget scenarios and present analogues of the additive and multiplicative drift theorems from runtime analysis. In addition, we derive a new more general multiplicative drift theorem that also covers non-elitist EAs. This theorem simultaneously allows for positive and negative results, providing information on the algorithm's progress even when the problem cannot be optimised efficiently. Finally, we provide results for some well-known heuristics namely Random Walk (RW), Random Local Search (RLS), the (1+1) EA, the Metropolis algorithm (MA) and the Strong Selection Weak Mutation (SSWM) algorithm.

  3. Models of the stochastic activity of neurones

    CERN Document Server

    Holden, Arun Vivian

    1976-01-01

    These notes have grown from a series of seminars given at Leeds between 1972 and 1975. They represent an attempt to gather together the different kinds of model which have been proposed to account for the stochastic activity of neurones, and to provide an introduction to this area of mathematical biology. A striking feature of the electrical activity of the nervous system is that it appears stochastic: this is apparent at all levels of recording, ranging from intracellular recordings to the electroencephalogram. The chapters start with fluctuations in membrane potential, proceed through single unit and synaptic activity and end with the behaviour of large aggregates of neurones: L have chgaen this seque~~e\\/~~';uggest that the interesting behaviourr~f :the nervous system - its individuality, variability and dynamic forms - may in part result from the stochastic behaviour of its components. I would like to thank Dr. Julio Rubio for reading and commenting on the drafts, Mrs. Doris Beighton for producing the fin...

  4. Predicting extinction rates in stochastic epidemic models

    Science.gov (United States)

    Schwartz, Ira B.; Billings, Lora; Dykman, Mark; Landsman, Alexandra

    2009-01-01

    We investigate the stochastic extinction processes in a class of epidemic models. Motivated by the process of natural disease extinction in epidemics, we examine the rate of extinction as a function of disease spread. We show that the effective entropic barrier for extinction in a susceptible-infected-susceptible epidemic model displays scaling with the distance to the bifurcation point, with an unusual critical exponent. We make a direct comparison between predictions and numerical simulations. We also consider the effect of non-Gaussian vaccine schedules, and show numerically how the extinction process may be enhanced when the vaccine schedules are Poisson distributed.

  5. Stochastic model for market stocks with floors

    Science.gov (United States)

    Villarroel, Javier

    2007-08-01

    We present a model to describe the stochastic evolution of stocks that show a strong resistance at some level and generalize to this situation the evolution based upon geometric Brownian motion. If volatility and drift are related in a certain way we show that our model can be integrated in an exact way. The related problem of how to prize general securities that pay dividends at a continuous rate and earn a terminal payoff at maturity T is solved via the martingale probability approach.

  6. Scalable inference for stochastic block models

    KAUST Repository

    Peng, Chengbin

    2017-12-08

    Community detection in graphs is widely used in social and biological networks, and the stochastic block model is a powerful probabilistic tool for describing graphs with community structures. However, in the era of "big data," traditional inference algorithms for such a model are increasingly limited due to their high time complexity and poor scalability. In this paper, we propose a multi-stage maximum likelihood approach to recover the latent parameters of the stochastic block model, in time linear with respect to the number of edges. We also propose a parallel algorithm based on message passing. Our algorithm can overlap communication and computation, providing speedup without compromising accuracy as the number of processors grows. For example, to process a real-world graph with about 1.3 million nodes and 10 million edges, our algorithm requires about 6 seconds on 64 cores of a contemporary commodity Linux cluster. Experiments demonstrate that the algorithm can produce high quality results on both benchmark and real-world graphs. An example of finding more meaningful communities is illustrated consequently in comparison with a popular modularity maximization algorithm.

  7. Stochastic Model of TCP SYN Attacks

    Directory of Open Access Journals (Sweden)

    Simona Ramanauskaitė

    2011-08-01

    Full Text Available A great proportion of essential services are moving into internet space making the threat of DoS attacks even more actual. To estimate the real risk of some kind of denial of service (DoS attack in real world is difficult, but mathematical and software models make this task easier. In this paper we overview the ways of implementing DoS attack models and offer a stochastic model of SYN flooding attack. It allows evaluating the potential threat of SYN flooding attacks, taking into account both the legitimate system flow as well as the possible attack power. At the same time we can assess the effect of such parameters as buffer capacity, open connection storage in the buffer or filte­ring efficiency on the success of different SYN flooding attacks. This model can be used for other type of memory depletion denial of service attacks.Article in Lithuanian

  8. Infinite-degree-corrected stochastic block model

    DEFF Research Database (Denmark)

    Herlau, Tue; Schmidt, Mikkel Nørgaard; Mørup, Morten

    2014-01-01

    , Phys. Rev. E 83, 016107 (2011)] incorporates a node degree correction to model degree heterogeneity within each group. Although this demonstrably leads to better performance on several networks, it is not obvious whether modeling node degree is always appropriate or necessary. We formulate the degree...... corrected stochastic block model as a nonparametric Bayesian model, incorporating a parameter to control the amount of degree correction that can then be inferred from data. Additionally, our formulation yields principled ways of inferring the number of groups as well as predicting missing links...... in the network that can be used to quantify the model’s predictive performance. On synthetic data we demonstrate that including the degree correction yields better performance on both recovering the true group structure and predicting missing links when degree heterogeneity is present, whereas performance...

  9. Physical and stochastic models of earthquake clustering

    Science.gov (United States)

    Console, Rodolfo; Murru, Maura; Catalli, Flaminia

    2006-04-01

    The phenomenon of earthquake clustering, i.e., the increase of occurrence probability for seismic events close in space and time to other previous earthquakes, has been modeled both by statistical and physical processes. From a statistical viewpoint the so-called epidemic model (ETAS) introduced by Ogata in 1988 and its variations have become fairly well known in the seismological community. Tests on real seismicity and comparison with a plain time-independent Poissonian model through likelihood-based methods have reliably proved their validity. On the other hand, in the last decade many papers have been published on the so-called Coulomb stress change principle, based on the theory of elasticity, showing qualitatively that an increase of the Coulomb stress in a given area is usually associated with an increase of seismic activity. More specifically, the rate-and-state theory developed by Dieterich in the '90s has been able to give a physical justification to the phenomenon known as Omori law. According to this law, a mainshock is followed by a series of aftershocks whose frequency decreases in time as an inverse power law. In this study we give an outline of the above-mentioned stochastic and physical models, and build up an approach by which these models can be merged in a single algorithm and statistically tested. The application to the seismicity of Japan from 1970 to 2003 shows that the new model incorporating the physical concept of the rate-and-state theory performs not worse than the purely stochastic model with two free parameters only. The numerical results obtained in these applications are related to physical characters of the model as the stress change produced by an earthquake close to its edges and to the A and σ parameters of the rate-and-state constitutive law.

  10. Modelling Chinese Smart Grid : A stochastic model checking case study

    Energy Technology Data Exchange (ETDEWEB)

    Yuksel, E.; Nielson, H.R.; Nielson, F. (Technical Univ. of Denmark. DTU Informatics, Kgs. Lyngby (Denmark)); Zhu, H. (East China Normal Univ. (China)); Huang, H. (Wuxi SensingNet Industrialization Research Institute (China))

    2012-07-01

    In this document, we consider a specific Chinese Smart Grid implementation and try to address the verification problem for certain quantitative properties including performance and battery consumption. We employ stochastic model checking approach and present our modelling and analysis study using PRISM model checker. (Author)

  11. Survey of Bayesian Models for Modelling of Stochastic Temporal Processes

    Energy Technology Data Exchange (ETDEWEB)

    Ng, B

    2006-10-12

    This survey gives an overview of popular generative models used in the modeling of stochastic temporal systems. In particular, this survey is organized into two parts. The first part discusses the discrete-time representations of dynamic Bayesian networks and dynamic relational probabilistic models, while the second part discusses the continuous-time representation of continuous-time Bayesian networks.

  12. Stochastic modeling of thermal fatigue crack growth

    CERN Document Server

    Radu, Vasile

    2015-01-01

    The book describes a systematic stochastic modeling approach for assessing thermal-fatigue crack-growth in mixing tees, based on the power spectral density of temperature fluctuation at the inner pipe surface. It shows the development of a frequency-temperature response function in the framework of single-input, single-output (SISO) methodology from random noise/signal theory under sinusoidal input. The frequency response of stress intensity factor (SIF) is obtained by a polynomial fitting procedure of thermal stress profiles at various instants of time. The method, which takes into account the variability of material properties, and has been implemented in a real-world application, estimates the probabilities of failure by considering a limit state function and Monte Carlo analysis, which are based on the proposed stochastic model. Written in a comprehensive and accessible style, this book presents a new and effective method for assessing thermal fatigue crack, and it is intended as a concise and practice-or...

  13. Double diffusivity model under stochastic forcing

    Science.gov (United States)

    Chattopadhyay, Amit K.; Aifantis, Elias C.

    2017-05-01

    The "double diffusivity" model was proposed in the late 1970s, and reworked in the early 1980s, as a continuum counterpart to existing discrete models of diffusion corresponding to high diffusivity paths, such as grain boundaries and dislocation lines. It was later rejuvenated in the 1990s to interpret experimental results on diffusion in polycrystalline and nanocrystalline specimens where grain boundaries and triple grain boundary junctions act as high diffusivity paths. Technically, the model pans out as a system of coupled Fick-type diffusion equations to represent "regular" and "high" diffusivity paths with "source terms" accounting for the mass exchange between the two paths. The model remit was extended by analogy to describe flow in porous media with double porosity, as well as to model heat conduction in media with two nonequilibrium local temperature baths, e.g., ion and electron baths. Uncoupling of the two partial differential equations leads to a higher-ordered diffusion equation, solutions of which could be obtained in terms of classical diffusion equation solutions. Similar equations could also be derived within an "internal length" gradient (ILG) mechanics formulation applied to diffusion problems, i.e., by introducing nonlocal effects, together with inertia and viscosity, in a mechanics based formulation of diffusion theory. While being remarkably successful in studies related to various aspects of transport in inhomogeneous media with deterministic microstructures and nanostructures, its implications in the presence of stochasticity have not yet been considered. This issue becomes particularly important in the case of diffusion in nanopolycrystals whose deterministic ILG-based theoretical calculations predict a relaxation time that is only about one-tenth of the actual experimentally verified time scale. This article provides the "missing link" in this estimation by adding a vital element in the ILG structure, that of stochasticity, that takes into

  14. Stochastic inverse problems: Models and metrics

    Science.gov (United States)

    Sabbagh, Elias H.; Sabbagh, Harold A.; Murphy, R. Kim; Aldrin, John C.; Annis, Charles; Knopp, Jeremy S.

    2015-03-01

    In past work, we introduced model-based inverse methods, and applied them to problems in which the anomaly could be reasonably modeled by simple canonical shapes, such as rectangular solids. In these cases the parameters to be inverted would be length, width and height, as well as the occasional probe lift-off or rotation. We are now developing a formulation that allows more flexibility in modeling complex flaws. The idea consists of expanding the flaw in a sequence of basis functions, and then solving for the expansion coefficients of this sequence, which are modeled as independent random variables, uniformly distributed over their range of values. There are a number of applications of such modeling: 1. Connected cracks and multiple half-moons, which we have noted in a POD set. Ideally we would like to distinguish connected cracks from one long shallow crack. 2. Cracks of irregular profile and shape which have appeared in cold work holes during bolt-hole eddy-current inspection. One side of such cracks is much deeper than other. 3. L or C shaped crack profiles at the surface, examples of which have been seen in bolt-hole cracks. By formulating problems in a stochastic sense, we are able to leverage the stochastic global optimization algorithms in NLSE, which is resident in VIC-3D®, to answer questions of global minimization and to compute confidence bounds using the sensitivity coefficient that we get from NLSE. We will also address the issue of surrogate functions which are used during the inversion process, and how they contribute to the quality of the estimation of the bounds.

  15. Stochastic inverse problems: Models and metrics

    Energy Technology Data Exchange (ETDEWEB)

    Sabbagh, Elias H.; Sabbagh, Harold A.; Murphy, R. Kim [Victor Technologies, LLC, Bloomington, IN 47407-7706 (United States); Aldrin, John C. [Computational Tools, Gurnee, IL 60031 (United States); Annis, Charles [Statistical Engineering, Palm Beach Gardens, FL 33418 (United States); Knopp, Jeremy S. [Air Force Research Laboratory (AFRL/RXCA), Wright Patterson AFB, OH 45433-7817 (United States)

    2015-03-31

    In past work, we introduced model-based inverse methods, and applied them to problems in which the anomaly could be reasonably modeled by simple canonical shapes, such as rectangular solids. In these cases the parameters to be inverted would be length, width and height, as well as the occasional probe lift-off or rotation. We are now developing a formulation that allows more flexibility in modeling complex flaws. The idea consists of expanding the flaw in a sequence of basis functions, and then solving for the expansion coefficients of this sequence, which are modeled as independent random variables, uniformly distributed over their range of values. There are a number of applications of such modeling: 1. Connected cracks and multiple half-moons, which we have noted in a POD set. Ideally we would like to distinguish connected cracks from one long shallow crack. 2. Cracks of irregular profile and shape which have appeared in cold work holes during bolt-hole eddy-current inspection. One side of such cracks is much deeper than other. 3. L or C shaped crack profiles at the surface, examples of which have been seen in bolt-hole cracks. By formulating problems in a stochastic sense, we are able to leverage the stochastic global optimization algorithms in NLSE, which is resident in VIC-3D®, to answer questions of global minimization and to compute confidence bounds using the sensitivity coefficient that we get from NLSE. We will also address the issue of surrogate functions which are used during the inversion process, and how they contribute to the quality of the estimation of the bounds.

  16. Stochastic computations in cortical microcircuit models.

    Directory of Open Access Journals (Sweden)

    Stefan Habenschuss

    Full Text Available Experimental data from neuroscience suggest that a substantial amount of knowledge is stored in the brain in the form of probability distributions over network states and trajectories of network states. We provide a theoretical foundation for this hypothesis by showing that even very detailed models for cortical microcircuits, with data-based diverse nonlinear neurons and synapses, have a stationary distribution of network states and trajectories of network states to which they converge exponentially fast from any initial state. We demonstrate that this convergence holds in spite of the non-reversibility of the stochastic dynamics of cortical microcircuits. We further show that, in the presence of background network oscillations, separate stationary distributions emerge for different phases of the oscillation, in accordance with experimentally reported phase-specific codes. We complement these theoretical results by computer simulations that investigate resulting computation times for typical probabilistic inference tasks on these internally stored distributions, such as marginalization or marginal maximum-a-posteriori estimation. Furthermore, we show that the inherent stochastic dynamics of generic cortical microcircuits enables them to quickly generate approximate solutions to difficult constraint satisfaction problems, where stored knowledge and current inputs jointly constrain possible solutions. This provides a powerful new computing paradigm for networks of spiking neurons, that also throws new light on how networks of neurons in the brain could carry out complex computational tasks such as prediction, imagination, memory recall and problem solving.

  17. Stochastic computations in cortical microcircuit models.

    Science.gov (United States)

    Habenschuss, Stefan; Jonke, Zeno; Maass, Wolfgang

    2013-01-01

    Experimental data from neuroscience suggest that a substantial amount of knowledge is stored in the brain in the form of probability distributions over network states and trajectories of network states. We provide a theoretical foundation for this hypothesis by showing that even very detailed models for cortical microcircuits, with data-based diverse nonlinear neurons and synapses, have a stationary distribution of network states and trajectories of network states to which they converge exponentially fast from any initial state. We demonstrate that this convergence holds in spite of the non-reversibility of the stochastic dynamics of cortical microcircuits. We further show that, in the presence of background network oscillations, separate stationary distributions emerge for different phases of the oscillation, in accordance with experimentally reported phase-specific codes. We complement these theoretical results by computer simulations that investigate resulting computation times for typical probabilistic inference tasks on these internally stored distributions, such as marginalization or marginal maximum-a-posteriori estimation. Furthermore, we show that the inherent stochastic dynamics of generic cortical microcircuits enables them to quickly generate approximate solutions to difficult constraint satisfaction problems, where stored knowledge and current inputs jointly constrain possible solutions. This provides a powerful new computing paradigm for networks of spiking neurons, that also throws new light on how networks of neurons in the brain could carry out complex computational tasks such as prediction, imagination, memory recall and problem solving.

  18. Optimal information diffusion in stochastic block models

    CERN Document Server

    Curato, Gianbiagio

    2016-01-01

    We use the linear threshold model to study the diffusion of information on a network generated by the stochastic block model. We focus our analysis on a two community structure where the initial set of informed nodes lies only in one of the two communities and we look for optimal network structures, i.e. those maximizing the asymptotic extent of the diffusion. We find that, constraining the mean degree and the fraction of initially informed nodes, the optimal structure can be assortative (modular), core-periphery, or even disassortative. We then look for minimal cost structures, i.e. those such that a minimal fraction of initially informed nodes is needed to trigger a global cascade. We find that the optimal networks are assortative but with a structure very close to a core-periphery graph, i.e. a very dense community linked to a much more sparsely connected periphery.

  19. A stochastic model of river discharge fluctuations

    Science.gov (United States)

    Livina, V.; Ashkenazy, Y.; Kizner, Z.; Strygin, V.; Bunde, A.; Havlin, S.

    2003-12-01

    We study the daily river flow fluctuations of 30 international rivers. Using the detrended fluctuation analysis, we study the correlations in the magnitudes of river flow increments (volatilities), and find power-law correlations in volatilities for time scales less than 1 year; these correlations almost disappear for time scales larger than 1 year. Using surrogate data test for nonlinearity, we show that correlations in the magnitudes of river flow fluctuations are a measure for nonlinearity. We propose a simple nonlinear stochastic model for river flow fluctuations that reproduces the main scaling properties of the river flow series as well as the correlations and periodicities in the magnitudes of river flow increments. According to our model, the source of nonlinearity observed in the data is an interaction between a long-term correlated process and the river discharge itself.

  20. Stochastic models for surface diffusion of molecules

    Energy Technology Data Exchange (ETDEWEB)

    Shea, Patrick, E-mail: patrick.shea@dal.ca; Kreuzer, Hans Jürgen [Department of Physics and Atmospheric Science, Dalhousie University, Halifax, Nova Scotia B3H 3J5 (Canada)

    2014-07-28

    We derive a stochastic model for the surface diffusion of molecules, starting from the classical equations of motion for an N-atom molecule on a surface. The equation of motion becomes a generalized Langevin equation for the center of mass of the molecule, with a non-Markovian friction kernel. In the Markov approximation, a standard Langevin equation is recovered, and the effect of the molecular vibrations on the diffusion is seen to lead to an increase in the friction for center of mass motion. This effective friction has a simple form that depends on the curvature of the lowest energy diffusion path in the 3N-dimensional coordinate space. We also find that so long as the intramolecular forces are sufficiently strong, memory effects are usually not significant and the Markov approximation can be employed, resulting in a simple one-dimensional model that can account for the effect of the dynamics of the molecular vibrations on the diffusive motion.

  1. On Scaling Modes and Balancing Stochastic, Discretization, and Modeling Error

    Science.gov (United States)

    Brown, J.

    2015-12-01

    We consider accuracy-cost tradeoffs and the problem of finding Pareto optimal configurations for stochastic forward and inverse problems. As the target accuracy is changed, we should use different physical models, stochastic models, discretizations, and solution algorithms. In this spectrum, we see different scientifically-relevant scaling modes, thus different opportunities and limitations on parallel computers and emerging architectures.

  2. Review of "Stochastic Modelling for Systems Biology" by Darren Wilkinson

    Directory of Open Access Journals (Sweden)

    Bullinger Eric

    2006-12-01

    Full Text Available Abstract "Stochastic Modelling for Systems Biology" by Darren Wilkinson introduces the peculiarities of stochastic modelling in biology. This book is particularly suited to as a textbook or for self-study, and for readers with a theoretical background.

  3. A stochastic modeling of recurrent measles epidemic | Kassem ...

    African Journals Online (AJOL)

    A simple stochastic mathematical model is developed and investigated for the dynamics of measles epidemic. The model, which is a multi-dimensional diffusion process, includes susceptible individuals, latent (exposed), infected and removed individuals. Stochastic effects are assumed to arise in the process of infection of ...

  4. Model of stochastic self-oscillation in Gunn diode oscillators

    Energy Technology Data Exchange (ETDEWEB)

    Bocharov, E.P.; Korostelev, G.N.; Khripunov, M.V.

    1987-07-01

    The applicability of the two-mode nonlinear model of decay stochasticity for explanation of the transition from monochromatic self-oscillation to developed stochasticity in the Gunn diode oscillator is demonstrated. Numerical realizations of the basic regimes corresponding to various cases of consideration of the weak nonlinearity of the falling portion of the current-voltage characteristic are presented. A comparative analysis of calculation results of time realizations and experimentally observed oscillograms of stochastic regimes is performed.

  5. Survival analysis of stochastic competitive models in a polluted environment and stochastic competitive exclusion principle.

    Science.gov (United States)

    Liu, Meng; Wang, Ke; Wu, Qiong

    2011-09-01

    Stochastic competitive models with pollution and without pollution are proposed and studied. For the first system with pollution, sufficient criteria for extinction, nonpersistence in the mean, weak persistence in the mean, strong persistence in the mean, and stochastic permanence are established. The threshold between weak persistence in the mean and extinction for each population is obtained. It is found that stochastic disturbance is favorable for the survival of one species and is unfavorable for the survival of the other species. For the second system with pollution, sufficient conditions for extinction and weak persistence are obtained. For the model without pollution, a partial stochastic competitive exclusion principle is derived. © Society for Mathematical Biology 2010

  6. Stochastic modelling of cardiac cell structure.

    Science.gov (United States)

    Theakston, Elizabeth; Walker, Cameron; O'Sullivan, Michael; Rajagopal, Vijay

    2010-01-01

    Anatomically realistic and biophysically based computational models of the heart have provided valuable insights into cardiac function in health and disease. Nevertheless, these models typically use a "black-box" approach to describe the cellular level processes that underlie the heart beat. We are developing techniques to stochastically generate three-dimensional models of mammalian ventricular myocytes that exhibit salient characteristics of the spatial organisation of key cellular organelles in cardiac cell excitation and contraction. Such anatomically detailed models will facilitate a deeper understanding of cardiac function at multiple scales. This paper presents an important first step towards understanding and modelling the spatial distribution of two key organelles in cardiac cell contraction - myofibrils and mitochondria. The sarcolemma, myofibrils and mitochondria were segmented from transmission electron micrographs of ventricular cells from a healthy wistar rat. The centroids of the myofibrils and mitochondria were calculated, and various spatial statistical techniques for characterising the centroid distribution and inter-point interactions were investigated and implemented using the R spatstat package. Techniques for modelling the observed spatial patterns were also investigated, and preliminary results indicate that the Strauss Hard-core model best captures the interaction observed. We intend to confirm these results with larger sample of cells.

  7. Spatial Stochastic Point Models for Reservoir Characterization

    Energy Technology Data Exchange (ETDEWEB)

    Syversveen, Anne Randi

    1997-12-31

    The main part of this thesis discusses stochastic modelling of geology in petroleum reservoirs. A marked point model is defined for objects against a background in a two-dimensional vertical cross section of the reservoir. The model handles conditioning on observations from more than one well for each object and contains interaction between objects, and the objects have the correct length distribution when penetrated by wells. The model is developed in a Bayesian setting. The model and the simulation algorithm are demonstrated by means of an example with simulated data. The thesis also deals with object recognition in image analysis, in a Bayesian framework, and with a special type of spatial Cox processes called log-Gaussian Cox processes. In these processes, the logarithm of the intensity function is a Gaussian process. The class of log-Gaussian Cox processes provides flexible models for clustering. The distribution of such a process is completely characterized by the intensity and the pair correlation function of the Cox process. 170 refs., 37 figs., 5 tabs.

  8. Stochastic time models of syllable structure.

    Science.gov (United States)

    Shaw, Jason A; Gafos, Adamantios I

    2015-01-01

    Drawing on phonology research within the generative linguistics tradition, stochastic methods, and notions from complex systems, we develop a modelling paradigm linking phonological structure, expressed in terms of syllables, to speech movement data acquired with 3D electromagnetic articulography and X-ray microbeam methods. The essential variable in the models is syllable structure. When mapped to discrete coordination topologies, syllabic organization imposes systematic patterns of variability on the temporal dynamics of speech articulation. We simulated these dynamics under different syllabic parses and evaluated simulations against experimental data from Arabic and English, two languages claimed to parse similar strings of segments into different syllabic structures. Model simulations replicated several key experimental results, including the fallibility of past phonetic heuristics for syllable structure, and exposed the range of conditions under which such heuristics remain valid. More importantly, the modelling approach consistently diagnosed syllable structure proving resilient to multiple sources of variability in experimental data including measurement variability, speaker variability, and contextual variability. Prospects for extensions of our modelling paradigm to acoustic data are also discussed.

  9. Stochastic Time Models of Syllable Structure

    Science.gov (United States)

    Shaw, Jason A.; Gafos, Adamantios I.

    2015-01-01

    Drawing on phonology research within the generative linguistics tradition, stochastic methods, and notions from complex systems, we develop a modelling paradigm linking phonological structure, expressed in terms of syllables, to speech movement data acquired with 3D electromagnetic articulography and X-ray microbeam methods. The essential variable in the models is syllable structure. When mapped to discrete coordination topologies, syllabic organization imposes systematic patterns of variability on the temporal dynamics of speech articulation. We simulated these dynamics under different syllabic parses and evaluated simulations against experimental data from Arabic and English, two languages claimed to parse similar strings of segments into different syllabic structures. Model simulations replicated several key experimental results, including the fallibility of past phonetic heuristics for syllable structure, and exposed the range of conditions under which such heuristics remain valid. More importantly, the modelling approach consistently diagnosed syllable structure proving resilient to multiple sources of variability in experimental data including measurement variability, speaker variability, and contextual variability. Prospects for extensions of our modelling paradigm to acoustic data are also discussed. PMID:25996153

  10. Stochastic modeling of sunshine number data

    Science.gov (United States)

    Brabec, Marek; Paulescu, Marius; Badescu, Viorel

    2013-11-01

    In this paper, we will present a unified statistical modeling framework for estimation and forecasting sunshine number (SSN) data. Sunshine number has been proposed earlier to describe sunshine time series in qualitative terms (Theor Appl Climatol 72 (2002) 127-136) and since then, it was shown to be useful not only for theoretical purposes but also for practical considerations, e.g. those related to the development of photovoltaic energy production. Statistical modeling and prediction of SSN as a binary time series has been challenging problem, however. Our statistical model for SSN time series is based on an underlying stochastic process formulation of Markov chain type. We will show how its transition probabilities can be efficiently estimated within logistic regression framework. In fact, our logistic Markovian model can be relatively easily fitted via maximum likelihood approach. This is optimal in many respects and it also enables us to use formalized statistical inference theory to obtain not only the point estimates of transition probabilities and their functions of interest, but also related uncertainties, as well as to test of various hypotheses of practical interest, etc. It is straightforward to deal with non-homogeneous transition probabilities in this framework. Very importantly from both physical and practical points of view, logistic Markov model class allows us to test hypotheses about how SSN dependents on various external covariates (e.g. elevation angle, solar time, etc.) and about details of the dynamic model (order and functional shape of the Markov kernel, etc.). Therefore, using generalized additive model approach (GAM), we can fit and compare models of various complexity which insist on keeping physical interpretation of the statistical model and its parts. After introducing the Markovian model and general approach for identification of its parameters, we will illustrate its use and performance on high resolution SSN data from the Solar

  11. Stochastic modeling of sunshine number data

    Energy Technology Data Exchange (ETDEWEB)

    Brabec, Marek, E-mail: mbrabec@cs.cas.cz [Department of Nonlinear Modeling, Institute of Computer Science, Academy of Sciences of the Czech Republic, Pod Vodarenskou vezi 2, 182 07 Prague 8 (Czech Republic); Paulescu, Marius [Physics Department, West University of Timisoara, V. Parvan 4, 300223 Timisoara (Romania); Badescu, Viorel [Candida Oancea Institute, Polytechnic University of Bucharest, Spl. Independentei 313, 060042 Bucharest (Romania)

    2013-11-13

    In this paper, we will present a unified statistical modeling framework for estimation and forecasting sunshine number (SSN) data. Sunshine number has been proposed earlier to describe sunshine time series in qualitative terms (Theor Appl Climatol 72 (2002) 127-136) and since then, it was shown to be useful not only for theoretical purposes but also for practical considerations, e.g. those related to the development of photovoltaic energy production. Statistical modeling and prediction of SSN as a binary time series has been challenging problem, however. Our statistical model for SSN time series is based on an underlying stochastic process formulation of Markov chain type. We will show how its transition probabilities can be efficiently estimated within logistic regression framework. In fact, our logistic Markovian model can be relatively easily fitted via maximum likelihood approach. This is optimal in many respects and it also enables us to use formalized statistical inference theory to obtain not only the point estimates of transition probabilities and their functions of interest, but also related uncertainties, as well as to test of various hypotheses of practical interest, etc. It is straightforward to deal with non-homogeneous transition probabilities in this framework. Very importantly from both physical and practical points of view, logistic Markov model class allows us to test hypotheses about how SSN dependents on various external covariates (e.g. elevation angle, solar time, etc.) and about details of the dynamic model (order and functional shape of the Markov kernel, etc.). Therefore, using generalized additive model approach (GAM), we can fit and compare models of various complexity which insist on keeping physical interpretation of the statistical model and its parts. After introducing the Markovian model and general approach for identification of its parameters, we will illustrate its use and performance on high resolution SSN data from the Solar

  12. The multivariate supOU stochastic volatility model

    DEFF Research Database (Denmark)

    Barndorff-Nielsen, Ole; Stelzer, Robert

    structure of the volatility, the log returns, as well as their "squares" are discussed in detail. Moreover, we give several examples in which long memory effects occur and study how the model as well as the simple Ornstein-Uhlenbeck type stochastic volatility model behave under linear transformations....... In particular, the models are shown to be preserved under invertible linear transformations. Finally, we discuss how (sup)OU stochastic volatility models can be combined with a factor modelling approach....

  13. Simultaneous perturbation stochastic approximation for tidal models

    KAUST Repository

    Altaf, M.U.

    2011-05-12

    The Dutch continental shelf model (DCSM) is a shallow sea model of entire continental shelf which is used operationally in the Netherlands to forecast the storm surges in the North Sea. The forecasts are necessary to support the decision of the timely closure of the moveable storm surge barriers to protect the land. In this study, an automated model calibration method, simultaneous perturbation stochastic approximation (SPSA) is implemented for tidal calibration of the DCSM. The method uses objective function evaluations to obtain the gradient approximations. The gradient approximation for the central difference method uses only two objective function evaluation independent of the number of parameters being optimized. The calibration parameter in this study is the model bathymetry. A number of calibration experiments is performed. The effectiveness of the algorithm is evaluated in terms of the accuracy of the final results as well as the computational costs required to produce these results. In doing so, comparison is made with a traditional steepest descent method and also with a newly developed proper orthogonal decompositionbased calibration method. The main findings are: (1) The SPSA method gives comparable results to steepest descent method with little computational cost. (2) The SPSA method with little computational cost can be used to estimate large number of parameters.

  14. A stochastic model for early placental development.

    KAUST Repository

    Cotter, Simon L

    2014-08-01

    In the human, placental structure is closely related to placental function and consequent pregnancy outcome. Studies have noted abnormal placental shape in small-for-gestational-age infants which extends to increased lifetime risk of cardiovascular disease. The origins and determinants of placental shape are incompletely understood and are difficult to study in vivo. In this paper, we model the early development of the human placenta, based on the hypothesis that this is driven by a chemoattractant effect emanating from proximal spiral arteries in the decidua. We derive and explore a two-dimensional stochastic model, and investigate the effects of loss of spiral arteries in regions near to the cord insertion on the shape of the placenta. This model demonstrates that disruption of spiral arteries can exert profound effects on placental shape, particularly if this is close to the cord insertion. Thus, placental shape reflects the underlying maternal vascular bed. Abnormal placental shape may reflect an abnormal uterine environment, predisposing to pregnancy complications. Through statistical analysis of model placentas, we are able to characterize the probability that a given placenta grew in a disrupted environment, and even able to distinguish between different disruptions.

  15. A stochastic model for retinocollicular map development

    Directory of Open Access Journals (Sweden)

    Tsigankov Dmitry N

    2004-08-01

    Full Text Available Abstract Background We examine results of gain-of-function experiments on retinocollicular maps in knock-in mice [Brown et al. (2000 Cell 102:77]. In wild-type mice the temporal-nasal axis of retina is mapped to the rostral-caudal axis of superior colliculus. The established map is single-valued, which implies that each point in retina maps to a unique termination zone in superior colliculus. In homozygous Isl2/EphA3 knock-in mice the map is double-valued, which means that each point on retina maps to two termination zones in superior colliculus. This is because about 50 percent of cells in retina express Isl2, and two types of projections, wild-type and Isl2/EphA3 positive, form two branches of the map. In heterozygous Isl2/EphA3 knock-ins the map is intermediate between the homozygous and wild-type: it is single-valued in temporal and double-valued in the nasal parts of retina. In this study we address possible reasons for such a bifurcation of the map. Results We study the map formation using stochastic model based on Markov chains. In our model the map undergoes a series of reconstructions with probabilities dependent upon a set of chemical cues. Our model suggests that the map in heterozygotes is single-valued in temporal region of retina for two reasons. First, the inhomogeneous gradient of endogenous receptor in retina makes the impact of exogenous receptor less significant in temporal retina. Second, the gradient of ephrin in the corresponding region of superior colliculus is smaller, which reduces the chemical signal-to-noise ratio. We predict that if gradient of ephrin is reduced by a genetic manipulation, the single-valued region of the map should extend to a larger portion of temporal retina, i.e. the point of transition between single-and doulble-valued maps should move to a more nasal position in Isl2-EphA3 heterozygotes. Conclusions We present a theoretical model for retinocollicular map development, which can account for

  16. On the small-time behavior of stochastic logistic models

    Directory of Open Access Journals (Sweden)

    Dung Tien Nguyen

    2017-09-01

    Full Text Available In this paper we investigate the small-time behaviors of the solution to  a stochastic logistic model. The obtained results allow us to estimate the number of individuals in the population and can be used to study stochastic prey-predator systems.

  17. Stochastic modeling of virus capsid assembly pathways

    Science.gov (United States)

    Schwartz, Russell

    2009-03-01

    Virus capsids have become a key model system for understanding self-assembly due to their high complexity, robust and efficient assembly processes, and experimental tractability. Our ability to directly examine and manipulate capsid assembly kinetics in detail nonetheless remains limited, creating a need for computer models that can infer experimentally inaccessible features of the assembly process and explore the effects of hypothetical manipulations on assembly trajectories. We have developed novel algorithms for stochastic simulation of capsid assembly [1,2] that allow us to model capsid assembly over broad parameter spaces [3]. We apply these methods to study the nature of assembly pathway control in virus capsids as well as their sensitivity to assembly conditions and possible experimental interventions. [4pt] [1] F. Jamalyaria, R. Rohlfs, and R. Schwartz. J Comp Phys 204, 100 (2005). [0pt] [2] N. Misra and R. Schwartz. J Chem Phys 129, in press (2008). [0pt] [3] B. Sweeney, T. Zhang, and R. Schwartz. Biophys J 94, 772 (2008).

  18. Constructing stochastic models from deterministic process equations by propensity adjustment.

    Science.gov (United States)

    Wu, Jialiang; Vidakovic, Brani; Voit, Eberhard O

    2011-11-08

    Gillespie's stochastic simulation algorithm (SSA) for chemical reactions admits three kinds of elementary processes, namely, mass action reactions of 0th, 1st or 2nd order. All other types of reaction processes, for instance those containing non-integer kinetic orders or following other types of kinetic laws, are assumed to be convertible to one of the three elementary kinds, so that SSA can validly be applied. However, the conversion to elementary reactions is often difficult, if not impossible. Within deterministic contexts, a strategy of model reduction is often used. Such a reduction simplifies the actual system of reactions by merging or approximating intermediate steps and omitting reactants such as transient complexes. It would be valuable to adopt a similar reduction strategy to stochastic modelling. Indeed, efforts have been devoted to manipulating the chemical master equation (CME) in order to achieve a proper propensity function for a reduced stochastic system. However, manipulations of CME are almost always complicated, and successes have been limited to relative simple cases. We propose a rather general strategy for converting a deterministic process model into a corresponding stochastic model and characterize the mathematical connections between the two. The deterministic framework is assumed to be a generalized mass action system and the stochastic analogue is in the format of the chemical master equation. The analysis identifies situations: where a direct conversion is valid; where internal noise affecting the system needs to be taken into account; and where the propensity function must be mathematically adjusted. The conversion from deterministic to stochastic models is illustrated with several representative examples, including reversible reactions with feedback controls, Michaelis-Menten enzyme kinetics, a genetic regulatory motif, and stochastic focusing. The construction of a stochastic model for a biochemical network requires the utilization

  19. Constructing stochastic models from deterministic process equations by propensity adjustment

    Directory of Open Access Journals (Sweden)

    Wu Jialiang

    2011-11-01

    Full Text Available Abstract Background Gillespie's stochastic simulation algorithm (SSA for chemical reactions admits three kinds of elementary processes, namely, mass action reactions of 0th, 1st or 2nd order. All other types of reaction processes, for instance those containing non-integer kinetic orders or following other types of kinetic laws, are assumed to be convertible to one of the three elementary kinds, so that SSA can validly be applied. However, the conversion to elementary reactions is often difficult, if not impossible. Within deterministic contexts, a strategy of model reduction is often used. Such a reduction simplifies the actual system of reactions by merging or approximating intermediate steps and omitting reactants such as transient complexes. It would be valuable to adopt a similar reduction strategy to stochastic modelling. Indeed, efforts have been devoted to manipulating the chemical master equation (CME in order to achieve a proper propensity function for a reduced stochastic system. However, manipulations of CME are almost always complicated, and successes have been limited to relative simple cases. Results We propose a rather general strategy for converting a deterministic process model into a corresponding stochastic model and characterize the mathematical connections between the two. The deterministic framework is assumed to be a generalized mass action system and the stochastic analogue is in the format of the chemical master equation. The analysis identifies situations: where a direct conversion is valid; where internal noise affecting the system needs to be taken into account; and where the propensity function must be mathematically adjusted. The conversion from deterministic to stochastic models is illustrated with several representative examples, including reversible reactions with feedback controls, Michaelis-Menten enzyme kinetics, a genetic regulatory motif, and stochastic focusing. Conclusions The construction of a stochastic

  20. Constructing stochastic models from deterministic process equations by propensity adjustment

    Science.gov (United States)

    2011-01-01

    Background Gillespie's stochastic simulation algorithm (SSA) for chemical reactions admits three kinds of elementary processes, namely, mass action reactions of 0th, 1st or 2nd order. All other types of reaction processes, for instance those containing non-integer kinetic orders or following other types of kinetic laws, are assumed to be convertible to one of the three elementary kinds, so that SSA can validly be applied. However, the conversion to elementary reactions is often difficult, if not impossible. Within deterministic contexts, a strategy of model reduction is often used. Such a reduction simplifies the actual system of reactions by merging or approximating intermediate steps and omitting reactants such as transient complexes. It would be valuable to adopt a similar reduction strategy to stochastic modelling. Indeed, efforts have been devoted to manipulating the chemical master equation (CME) in order to achieve a proper propensity function for a reduced stochastic system. However, manipulations of CME are almost always complicated, and successes have been limited to relative simple cases. Results We propose a rather general strategy for converting a deterministic process model into a corresponding stochastic model and characterize the mathematical connections between the two. The deterministic framework is assumed to be a generalized mass action system and the stochastic analogue is in the format of the chemical master equation. The analysis identifies situations: where a direct conversion is valid; where internal noise affecting the system needs to be taken into account; and where the propensity function must be mathematically adjusted. The conversion from deterministic to stochastic models is illustrated with several representative examples, including reversible reactions with feedback controls, Michaelis-Menten enzyme kinetics, a genetic regulatory motif, and stochastic focusing. Conclusions The construction of a stochastic model for a biochemical

  1. A hierarchical stochastic model for bistable perception.

    Directory of Open Access Journals (Sweden)

    Stefan Albert

    2017-11-01

    Full Text Available Viewing of ambiguous stimuli can lead to bistable perception alternating between the possible percepts. During continuous presentation of ambiguous stimuli, percept changes occur as single events, whereas during intermittent presentation of ambiguous stimuli, percept changes occur at more or less regular intervals either as single events or bursts. Response patterns can be highly variable and have been reported to show systematic differences between patients with schizophrenia and healthy controls. Existing models of bistable perception often use detailed assumptions and large parameter sets which make parameter estimation challenging. Here we propose a parsimonious stochastic model that provides a link between empirical data analysis of the observed response patterns and detailed models of underlying neuronal processes. Firstly, we use a Hidden Markov Model (HMM for the times between percept changes, which assumes one single state in continuous presentation and a stable and an unstable state in intermittent presentation. The HMM captures the observed differences between patients with schizophrenia and healthy controls, but remains descriptive. Therefore, we secondly propose a hierarchical Brownian model (HBM, which produces similar response patterns but also provides a relation to potential underlying mechanisms. The main idea is that neuronal activity is described as an activity difference between two competing neuronal populations reflected in Brownian motions with drift. This differential activity generates switching between the two conflicting percepts and between stable and unstable states with similar mechanisms on different neuronal levels. With only a small number of parameters, the HBM can be fitted closely to a high variety of response patterns and captures group differences between healthy controls and patients with schizophrenia. At the same time, it provides a link to mechanistic models of bistable perception, linking the group

  2. Prediction horizon effects on stochastic modelling hints for neural networks

    Energy Technology Data Exchange (ETDEWEB)

    Drossu, R.; Obradovic, Z. [Washington State Univ., Pullman, WA (United States)

    1995-12-31

    The objective of this paper is to investigate the relationship between stochastic models and neural network (NN) approaches to time series modelling. Experiments on a complex real life prediction problem (entertainment video traffic) indicate that prior knowledge can be obtained through stochastic analysis both with respect to an appropriate NN architecture as well as to an appropriate sampling rate, in the case of a prediction horizon larger than one. An improvement of the obtained NN predictor is also proposed through a bias removal post-processing, resulting in much better performance than the best stochastic model.

  3. Coevolution Maintains Diversity in the Stochastic "Kill the Winner" Model

    Science.gov (United States)

    Xue, Chi; Goldenfeld, Nigel

    2017-12-01

    The "kill the winner" hypothesis is an attempt to address the problem of diversity in biology. It argues that host-specific predators control the population of each prey, preventing a winner from emerging and thus maintaining the coexistence of all species in the system. We develop a stochastic model for the kill the winner paradigm and show that the stable coexistence state of the deterministic kill the winner model is destroyed by demographic stochasticity, through a cascade of extinction events. We formulate an individual-level stochastic model in which predator-prey coevolution promotes the high diversity of the ecosystem by generating a persistent population flux of species.

  4. On changes of measure in stochastic volatility models

    Directory of Open Access Journals (Sweden)

    Bernard Wong

    2006-01-01

    models. This had led many researchers to “assume the condition away,” even though the condition is not innocuous, and nonsensical results can occur if it is in fact not satisfied. We provide an applicable theorem to check the conditions for a general class of Markovian stochastic volatility models. As an example we will also provide a detailed analysis of the Stein and Stein and Heston stochastic volatility models.

  5. Determining Reduced Order Models for Optimal Stochastic Reduced Order Models

    Energy Technology Data Exchange (ETDEWEB)

    Bonney, Matthew S. [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Brake, Matthew R.W. [Sandia National Lab. (SNL-CA), Livermore, CA (United States)

    2015-08-01

    The use of parameterized reduced order models(PROMs) within the stochastic reduced order model (SROM) framework is a logical progression for both methods. In this report, five different parameterized reduced order models are selected and critiqued against the other models along with truth model for the example of the Brake-Reuss beam. The models are: a Taylor series using finite difference, a proper orthogonal decomposition of the the output, a Craig-Bampton representation of the model, a method that uses Hyper-Dual numbers to determine the sensitivities, and a Meta-Model method that uses the Hyper-Dual results and constructs a polynomial curve to better represent the output data. The methods are compared against a parameter sweep and a distribution propagation where the first four statistical moments are used as a comparison. Each method produces very accurate results with the Craig-Bampton reduction having the least accurate results. The models are also compared based on time requirements for the evaluation of each model where the Meta- Model requires the least amount of time for computation by a significant amount. Each of the five models provided accurate results in a reasonable time frame. The determination of which model to use is dependent on the availability of the high-fidelity model and how many evaluations can be performed. Analysis of the output distribution is examined by using a large Monte-Carlo simulation along with a reduced simulation using Latin Hypercube and the stochastic reduced order model sampling technique. Both techniques produced accurate results. The stochastic reduced order modeling technique produced less error when compared to an exhaustive sampling for the majority of methods.

  6. Multivariate Markov processes for stochastic systems with delays: application to the stochastic Gompertz model with delay.

    Science.gov (United States)

    Frank, T D

    2002-07-01

    Using the method of steps, we describe stochastic processes with delays in terms of Markov diffusion processes. Thus, multivariate Langevin equations and Fokker-Planck equations are derived for stochastic delay differential equations. Natural, periodic, and reflective boundary conditions are discussed. Both Ito and Stratonovich calculus are used. In particular, our Fokker-Planck approach recovers the generalized delay Fokker-Planck equation proposed by Guillouzic et al. The results obtained are applied to a model for population growth: the Gompertz model with delay and multiplicative white noise.

  7. Applications of Little's Law to stochastic models of gene expression

    CERN Document Server

    Elgart, Vlad; Kulkarni, Rahul V

    2010-01-01

    The intrinsic stochasticity of gene expression can lead to large variations in protein levels across a population of cells. To explain this variability, different sources of mRNA fluctuations ('Poisson' and 'Telegraph' processes) have been proposed in stochastic models of gene expression. Both Poisson and Telegraph scenario models explain experimental observations of noise in protein levels in terms of 'bursts' of protein expression. Correspondingly, there is considerable interest in establishing relations between burst and steady-state protein distributions for general stochastic models of gene expression. In this work, we address this issue by considering a mapping between stochastic models of gene expression and problems of interest in queueing theory. By applying a general theorem from queueing theory, Little's Law, we derive exact relations which connect burst and steady-state distribution means for models with arbitrary waiting-time distributions for arrival and degradation of mRNAs and proteins. The de...

  8. Stochastic modeling of the diffusion coefficient for concrete

    DEFF Research Database (Denmark)

    Thoft-Christensen, Palle

    . A deterministic relationship between the diffusion coefficient and the w/c ratio and the temperature is used for the stochastic modelling. The w/c ratio and the temperature are modelled by log-normally and normally distributed stochastic variables, respectively. It is then shown by Monte Carlo simulation...... that the diffusion coefficient D may be modelled by a normally distributed stochastic variable. The sensitivities of D with regard to the mean values and the standard deviations are evaluated.......In the paper, a new stochastic modelling of the diffusion coefficient D is presented. The modelling is based on a physical understanding of the diffusion process and on some recent experimental results. The diffusion coefficient D is strongly dependent on the w/c ratio and the temperature...

  9. Markov Chain Models for the Stochastic Modeling of Pitting Corrosion

    Directory of Open Access Journals (Sweden)

    A. Valor

    2013-01-01

    Full Text Available The stochastic nature of pitting corrosion of metallic structures has been widely recognized. It is assumed that this kind of deterioration retains no memory of the past, so only the current state of the damage influences its future development. This characteristic allows pitting corrosion to be categorized as a Markov process. In this paper, two different models of pitting corrosion, developed using Markov chains, are presented. Firstly, a continuous-time, nonhomogeneous linear growth (pure birth Markov process is used to model external pitting corrosion in underground pipelines. A closed-form solution of the system of Kolmogorov's forward equations is used to describe the transition probability function in a discrete pit depth space. The transition probability function is identified by correlating the stochastic pit depth mean with the empirical deterministic mean. In the second model, the distribution of maximum pit depths in a pitting experiment is successfully modeled after the combination of two stochastic processes: pit initiation and pit growth. Pit generation is modeled as a nonhomogeneous Poisson process, in which induction time is simulated as the realization of a Weibull process. Pit growth is simulated using a nonhomogeneous Markov process. An analytical solution of Kolmogorov's system of equations is also found for the transition probabilities from the first Markov state. Extreme value statistics is employed to find the distribution of maximum pit depths.

  10. Digital simulation and modeling of nonlinear stochastic systems

    Energy Technology Data Exchange (ETDEWEB)

    Richardson, J M; Rowland, J R

    1981-04-01

    Digitally generated solutions of nonlinear stochastic systems are not unique but depend critically on the numerical integration algorithm used. Some theoretical and practical implications of this dependence are examined. The Ito-Stratonovich controversy concerning the solution of nonlinear stochastic systems is shown to be more than a theoretical debate on maintaining Markov properties as opposed to utilizing the computational rules of ordinary calculus. The theoretical arguments give rise to practical considerations in the formation and solution of discrete models from continuous stochastic systems. Well-known numerical integration algorithms are shown not only to provide different solutions for the same stochastic system but also to correspond to different stochastic integral definitions. These correspondences are proved by considering first and second moments of solutions that result from different integration algorithms and then comparing the moments to those arising from various stochastic integral definitions. This algorithm-dependence of solutions is in sharp contrast to the deterministic and linear stochastic cases in which unique solutions are determined by any convergent numerical algorithm. Consequences of the relationship between stochastic system solutions and simulation procedures are presented for a nonlinear filtering example. Monte Carlo simulations and statistical tests are applied to the example to illustrate the determining role which computational procedures play in generating solutions.

  11. Global Stochastic Properties of Dynamic Models and their Linear Approximations

    NARCIS (Netherlands)

    A.M. Babus (Ana Maria); C.G. de Vries (Casper)

    2010-01-01

    textabstractThe dynamic properties of micro based stochastic macro models are often analyzed through a linearization around the associated deterministic steady state. Recent literature has investigated the error made by such a deterministic approximation. Complementary to this literature we

  12. Constructing Stochastic Models for Dipole Fluctuations from Paleomagnetic Observations

    OpenAIRE

    Buffett, Bruce; Puranam, Abhijit

    2017-01-01

    Records of relative paleointensity are subject to several sources of error. Temporal averaging due to gradual acquisition of magnetization removes high-frequency fluctuations, whereas random errors introduce fluctuations at high frequency. Both sources of error limit our ability to construct stochastic models from paleomagnetic observations. We partially circumvent these difficulties by recognizing that the largest affects occur at high frequency. To illustrate we construct a stochastic model...

  13. Population stochastic modelling (PSM)-An R package for mixed-effects models based on stochastic differential equations

    DEFF Research Database (Denmark)

    Klim, Søren; Mortensen, Stig Bousgaard; Kristensen, Niels Rode

    2009-01-01

    The extension from ordinary to stochastic differential equations (SDEs) in pharmacokinetic and pharmacodynamic (PK/PD) modelling is an emerging field and has been motivated in a number of articles [N.R. Kristensen, H. Madsen, S.H. Ingwersen, Using stochastic differential equations for PK/PD model......)) (2005) 1247-1258; R.V. Overgaard, N. Jonsson, C.W. Tornoe, H. Madsen, Non-linear mixed-effects models with stochastic differential equations: implementation of an estimation algorithm, J. Pharmacokinet. Pharmacodyn. 32 (February(1)) (2005) 85-107; U. Picchini, S. Ditlevsen, A. De Gaetano, Maximum...... likelihood estimation of a time-inhomogeneous stochastic differential model of glucose dynamics, Math. Med. Biol. 25 (June(2)) (2008) 141-155]. PK/PD models are traditionally based ordinary differential equations (ODES) with an observation link that incorporates noise. This state-space formulation only...

  14. Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent.

    Science.gov (United States)

    Wang, Yuanfeng; Christley, Scott; Mjolsness, Eric; Xie, Xiaohui

    2010-07-21

    Stochastic effects can be important for the behavior of processes involving small population numbers, so the study of stochastic models has become an important topic in the burgeoning field of computational systems biology. However analysis techniques for stochastic models have tended to lag behind their deterministic cousins due to the heavier computational demands of the statistical approaches for fitting the models to experimental data. There is a continuing need for more effective and efficient algorithms. In this article we focus on the parameter inference problem for stochastic kinetic models of biochemical reactions given discrete time-course observations of either some or all of the molecular species. We propose an algorithm for inference of kinetic rate parameters based upon maximum likelihood using stochastic gradient descent (SGD). We derive a general formula for the gradient of the likelihood function given discrete time-course observations. The formula applies to any explicit functional form of the kinetic rate laws such as mass-action, Michaelis-Menten, etc. Our algorithm estimates the gradient of the likelihood function by reversible jump Markov chain Monte Carlo sampling (RJMCMC), and then gradient descent method is employed to obtain the maximum likelihood estimation of parameter values. Furthermore, we utilize flux balance analysis and show how to automatically construct reversible jump samplers for arbitrary biochemical reaction models. We provide RJMCMC sampling algorithms for both fully observed and partially observed time-course observation data. Our methods are illustrated with two examples: a birth-death model and an auto-regulatory gene network. We find good agreement of the inferred parameters with the actual parameters in both models. The SGD method proposed in the paper presents a general framework of inferring parameters for stochastic kinetic models. The method is computationally efficient and is effective for both partially and fully

  15. Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent

    Directory of Open Access Journals (Sweden)

    Christley Scott

    2010-07-01

    Full Text Available Abstract Background Stochastic effects can be important for the behavior of processes involving small population numbers, so the study of stochastic models has become an important topic in the burgeoning field of computational systems biology. However analysis techniques for stochastic models have tended to lag behind their deterministic cousins due to the heavier computational demands of the statistical approaches for fitting the models to experimental data. There is a continuing need for more effective and efficient algorithms. In this article we focus on the parameter inference problem for stochastic kinetic models of biochemical reactions given discrete time-course observations of either some or all of the molecular species. Results We propose an algorithm for inference of kinetic rate parameters based upon maximum likelihood using stochastic gradient descent (SGD. We derive a general formula for the gradient of the likelihood function given discrete time-course observations. The formula applies to any explicit functional form of the kinetic rate laws such as mass-action, Michaelis-Menten, etc. Our algorithm estimates the gradient of the likelihood function by reversible jump Markov chain Monte Carlo sampling (RJMCMC, and then gradient descent method is employed to obtain the maximum likelihood estimation of parameter values. Furthermore, we utilize flux balance analysis and show how to automatically construct reversible jump samplers for arbitrary biochemical reaction models. We provide RJMCMC sampling algorithms for both fully observed and partially observed time-course observation data. Our methods are illustrated with two examples: a birth-death model and an auto-regulatory gene network. We find good agreement of the inferred parameters with the actual parameters in both models. Conclusions The SGD method proposed in the paper presents a general framework of inferring parameters for stochastic kinetic models. The method is

  16. Computational stochastic model of ions implantation

    Energy Technology Data Exchange (ETDEWEB)

    Zmievskaya, Galina I., E-mail: zmi@gmail.ru; Bondareva, Anna L., E-mail: bal310775@yandex.ru [M.V. Keldysh Institute of Applied Mathematics RAS, 4,Miusskaya sq., 125047 Moscow (Russian Federation); Levchenko, Tatiana V., E-mail: tatlevchenko@mail.ru [VNII Geosystem Russian Federal Center, Varshavskoye roadway, 8, Moscow (Russian Federation); Maino, Giuseppe, E-mail: giuseppe.maino@enea.it [Scuola di Lettere e BeniCulturali, University di Bologna, sede di Ravenna, via Mariani 5, 48100 Ravenna (Italy)

    2015-03-10

    Implantation flux ions into crystal leads to phase transition /PT/ 1-st kind. Damaging lattice is associated with processes clustering vacancies and gaseous bubbles as well their brownian motion. System of stochastic differential equations /SDEs/ Ito for evolution stochastic dynamical variables corresponds to the superposition Wiener processes. The kinetic equations in partial derivatives /KE/, Kolmogorov-Feller and Einstein-Smolukhovskii, were formulated for nucleation into lattice of weakly soluble gases. According theory, coefficients of stochastic and kinetic equations uniquely related. Radiation stimulated phase transition are characterized by kinetic distribution functions /DFs/ of implanted clusters versus their sizes and depth of gas penetration into lattice. Macroscopic parameters of kinetics such as the porosity and stress calculated in thin layers metal/dielectric due to Xe{sup ++} irradiation are attracted as example. Predictions of porosity, important for validation accumulation stresses in surfaces, can be applied at restoring of objects the cultural heritage.

  17. Sensitivity, robustness, and identifiability in stochastic chemical kinetics models.

    Science.gov (United States)

    Komorowski, Michał; Costa, Maria J; Rand, David A; Stumpf, Michael P H

    2011-05-24

    We present a novel and simple method to numerically calculate Fisher information matrices for stochastic chemical kinetics models. The linear noise approximation is used to derive model equations and a likelihood function that leads to an efficient computational algorithm. Our approach reduces the problem of calculating the Fisher information matrix to solving a set of ordinary differential equations. This is the first method to compute Fisher information for stochastic chemical kinetics models without the need for Monte Carlo simulations. This methodology is then used to study sensitivity, robustness, and parameter identifiability in stochastic chemical kinetics models. We show that significant differences exist between stochastic and deterministic models as well as between stochastic models with time-series and time-point measurements. We demonstrate that these discrepancies arise from the variability in molecule numbers, correlations between species, and temporal correlations and show how this approach can be used in the analysis and design of experiments probing stochastic processes at the cellular level. The algorithm has been implemented as a Matlab package and is available from the authors upon request.

  18. Constructing stochastic models for dipole fluctuations from paleomagnetic observations

    Science.gov (United States)

    Buffett, Bruce; Puranam, Abhijit

    2017-11-01

    Records of relative paleointensity are subject to several sources of error. Temporal averaging due to gradual acquisition of magnetization removes high-frequency fluctuations, whereas random errors introduce fluctuations at high frequency. Both sources of error limit our ability to construct stochastic models from paleomagnetic observations. We partially circumvent these difficulties by recognizing that the largest affects occur at high frequency. To illustrate we construct a stochastic model from two recent inversions of paleomagnetic observations for the axial dipole moment. An estimate of the noise term in the stochastic model is recovered from a high-resolution inversion (CALS10k.2), while the drift term is estimated from the low-frequency part of the power spectrum for a long, but lower-resolution inversion (PADM2M). Realizations of the resulting stochastic model yield a composite, broadband power spectrum that agrees well with the spectra from both PADM2M and CALS10k.2. A simple generalization of the stochastic model permits predictions for the mean rate of magnetic reversals. We show that the reversal rate depends on the time-averaged dipole moment, the variance of the dipole moment and a slow timescale that characterizes the adjustment of the dipole toward the time-averaged value. Predictions of the stochastic model give a mean rate of 4.2 Myr-1, which is in good agreement with observations from marine magnetic anomalies.

  19. On the Stochastic Dynamics of a Social Epidemics Model

    Directory of Open Access Journals (Sweden)

    Xun-Yang Wang

    2017-01-01

    Full Text Available Alcohol abuse is a major social problem, which has caused a lot of damages or hidden dangers to the individual and the society. In this paper, with random factors of alcoholism considered in mortality rate of compartment populations, we formulate a stochastic alcoholism model according to compartment theory of infectious disease. Based on this model, we investigate the long-term stochastic dynamics behaviors of two equilibria of the corresponding deterministic model and point out the effect of random disturbance on the stability of the system. We find that when R0≤1, we get the estimation between the trajectory of stochastic system and E0=(Π/μs,0,0,0 in the average in time with respect to the disturbance intensity, while when R0>1, stochastic system is ergodic and has the unique stationary distribution. Finally, we carry out numerical simulations to support the corresponding theoretical results.

  20. Biochemical Network Stochastic Simulator (BioNetS: software for stochastic modeling of biochemical networks

    Directory of Open Access Journals (Sweden)

    Elston Timothy C

    2004-03-01

    Full Text Available Abstract Background Intrinsic fluctuations due to the stochastic nature of biochemical reactions can have large effects on the response of biochemical networks. This is particularly true for pathways that involve transcriptional regulation, where generally there are two copies of each gene and the number of messenger RNA (mRNA molecules can be small. Therefore, there is a need for computational tools for developing and investigating stochastic models of biochemical networks. Results We have developed the software package Biochemical Network Stochastic Simulator (BioNetS for efficientlyand accurately simulating stochastic models of biochemical networks. BioNetS has a graphical user interface that allows models to be entered in a straightforward manner, and allows the user to specify the type of random variable (discrete or continuous for each chemical species in the network. The discrete variables are simulated using an efficient implementation of the Gillespie algorithm. For the continuous random variables, BioNetS constructs and numerically solvesthe appropriate chemical Langevin equations. The software package has been developed to scale efficiently with network size, thereby allowing large systems to be studied. BioNetS runs as a BioSpice agent and can be downloaded from http://www.biospice.org. BioNetS also can be run as a stand alone package. All the required files are accessible from http://x.amath.unc.edu/BioNetS. Conclusions We have developed BioNetS to be a reliable tool for studying the stochastic dynamics of large biochemical networks. Important features of BioNetS are its ability to handle hybrid models that consist of both continuous and discrete random variables and its ability to model cell growth and division. We have verified the accuracy and efficiency of the numerical methods by considering several test systems.

  1. Multivariate moment closure techniques for stochastic kinetic models

    Energy Technology Data Exchange (ETDEWEB)

    Lakatos, Eszter, E-mail: e.lakatos13@imperial.ac.uk; Ale, Angelique; Kirk, Paul D. W.; Stumpf, Michael P. H., E-mail: m.stumpf@imperial.ac.uk [Department of Life Sciences, Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London SW7 2AZ (United Kingdom)

    2015-09-07

    Stochastic effects dominate many chemical and biochemical processes. Their analysis, however, can be computationally prohibitively expensive and a range of approximation schemes have been proposed to lighten the computational burden. These, notably the increasingly popular linear noise approximation and the more general moment expansion methods, perform well for many dynamical regimes, especially linear systems. At higher levels of nonlinearity, it comes to an interplay between the nonlinearities and the stochastic dynamics, which is much harder to capture correctly by such approximations to the true stochastic processes. Moment-closure approaches promise to address this problem by capturing higher-order terms of the temporally evolving probability distribution. Here, we develop a set of multivariate moment-closures that allows us to describe the stochastic dynamics of nonlinear systems. Multivariate closure captures the way that correlations between different molecular species, induced by the reaction dynamics, interact with stochastic effects. We use multivariate Gaussian, gamma, and lognormal closure and illustrate their use in the context of two models that have proved challenging to the previous attempts at approximating stochastic dynamics: oscillations in p53 and Hes1. In addition, we consider a larger system, Erk-mediated mitogen-activated protein kinases signalling, where conventional stochastic simulation approaches incur unacceptably high computational costs.

  2. Multivariate moment closure techniques for stochastic kinetic models

    Science.gov (United States)

    Lakatos, Eszter; Ale, Angelique; Kirk, Paul D. W.; Stumpf, Michael P. H.

    2015-09-01

    Stochastic effects dominate many chemical and biochemical processes. Their analysis, however, can be computationally prohibitively expensive and a range of approximation schemes have been proposed to lighten the computational burden. These, notably the increasingly popular linear noise approximation and the more general moment expansion methods, perform well for many dynamical regimes, especially linear systems. At higher levels of nonlinearity, it comes to an interplay between the nonlinearities and the stochastic dynamics, which is much harder to capture correctly by such approximations to the true stochastic processes. Moment-closure approaches promise to address this problem by capturing higher-order terms of the temporally evolving probability distribution. Here, we develop a set of multivariate moment-closures that allows us to describe the stochastic dynamics of nonlinear systems. Multivariate closure captures the way that correlations between different molecular species, induced by the reaction dynamics, interact with stochastic effects. We use multivariate Gaussian, gamma, and lognormal closure and illustrate their use in the context of two models that have proved challenging to the previous attempts at approximating stochastic dynamics: oscillations in p53 and Hes1. In addition, we consider a larger system, Erk-mediated mitogen-activated protein kinases signalling, where conventional stochastic simulation approaches incur unacceptably high computational costs.

  3. Tsunamis: stochastic models of occurrence and generation mechanisms

    Science.gov (United States)

    Geist, Eric L.; Oglesby, David D.

    2014-01-01

    The devastating consequences of the 2004 Indian Ocean and 2011 Japan tsunamis have led to increased research into many different aspects of the tsunami phenomenon. In this entry, we review research related to the observed complexity and uncertainty associated with tsunami generation, propagation, and occurrence described and analyzed using a variety of stochastic methods. In each case, seismogenic tsunamis are primarily considered. Stochastic models are developed from the physical theories that govern tsunami evolution combined with empirical models fitted to seismic and tsunami observations, as well as tsunami catalogs. These stochastic methods are key to providing probabilistic forecasts and hazard assessments for tsunamis. The stochastic methods described here are similar to those described for earthquakes (Vere-Jones 2013) and volcanoes (Bebbington 2013) in this encyclopedia.

  4. Stochastic bifurcation in a model of love with colored noise

    Science.gov (United States)

    Yue, Xiaokui; Dai, Honghua; Yuan, Jianping

    2015-07-01

    In this paper, we wish to examine the stochastic bifurcation induced by multiplicative Gaussian colored noise in a dynamical model of love where the random factor is used to describe the complexity and unpredictability of psychological systems. First, the dynamics in deterministic love-triangle model are considered briefly including equilibrium points and their stability, chaotic behaviors and chaotic attractors. Then, the influences of Gaussian colored noise with different parameters are explored such as the phase plots, top Lyapunov exponents, stationary probability density function (PDF) and stochastic bifurcation. The stochastic P-bifurcation through a qualitative change of the stationary PDF will be observed and bifurcation diagram on parameter plane of correlation time and noise intensity is presented to find the bifurcation behaviors in detail. Finally, the top Lyapunov exponent is computed to determine the D-bifurcation when the noise intensity achieves to a critical value. By comparison, we find there is no connection between two kinds of stochastic bifurcation.

  5. Stochastic von Bertalanffy models, with applications to fish recruitment.

    Science.gov (United States)

    Lv, Qiming; Pitchford, Jonathan W

    2007-02-21

    We consider three individual-based models describing growth in stochastic environments. Stochastic differential equations (SDEs) with identical von Bertalanffy deterministic parts are formulated, with a stochastic term which decreases, remains constant, or increases with organism size, respectively. Probability density functions for hitting times are evaluated in the context of fish growth and mortality. Solving the hitting time problem analytically or numerically shows that stochasticity can have a large positive impact on fish recruitment probability. It is also demonstrated that the observed mean growth rate of surviving individuals always exceeds the mean population growth rate, which itself exceeds the growth rate of the equivalent deterministic model. The consequences of these results in more general biological situations are discussed.

  6. Low-complexity stochastic modeling of spatially evolving flows

    Science.gov (United States)

    Zare, Armin; Ran, Wei; Hack, M. J. Philipp; Jovanovic, Mihailo

    2016-11-01

    Low-complexity approximations of the Navier-Stokes (NS) equations are commonly used for analysis and control of turbulent flows. In particular, stochastically-forced linearized models have been successfully employed to capture structural and statistical features observed in experiments and direct simulations. In this work, we utilize stochastically-forced linearized NS equations and their parabolized equivalents to study the dynamics of flow fluctuations in transitional and turbulent boundary layers. We exploit the streamwise causality of the parabolized model to efficiently propagate statistics of stochastic disturbances into statistics of velocity fluctuations. Our study provides insight into interactions of slowly-varying base flow with streamwise streaks, oblique modes, and Tollmien-Schlichting waves. It also offers a systematic, computationally efficient framework for quantifying the influence of stochastic excitation sources (e.g., free-stream turbulence and surface roughness) on velocity fluctuations in weakly non-parallel flows.

  7. The stochastic modelling of kleptoparasitism using a Markov process.

    Science.gov (United States)

    Broom, Mark; Crowe, Mary L; Fitzgerald, Meghan R; Rychtár, Jan

    2010-05-21

    Kleptoparasitism, the stealing of food items from other animals, is a common behaviour observed across a huge variety of species, and has been subjected to significant modelling effort. Most such modelling has been deterministic, effectively assuming an infinite population, although recently some important stochastic models have been developed. In particular the model of Yates and Broom (Stochastic models of kleptoparasitism. J. Theor. Biol. 248 (2007), 480-489) introduced a stochastic version following the original model of Ruxton and Moody (The ideal free distribution with kleptoparasitism. J. Theor. Biol. 186 (1997), 449-458), and whilst they generated results of interest, they did not solve the model explicitly. In this paper, building on methods used already by van der Meer and Smallegange (A stochastic version of the Beddington-DeAngelis functional response: Modelling interference for a finite number of predators. J. Animal Ecol. 78 (2009) 134-142) we give an exact solution to the distribution of the population over the states for the Yates and Broom model and investigate the effects of some key biological parameters, especially for small populations where stochastic models can be expected to differ most from their deterministic equivalents. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

  8. Analysis of stochastic effects in Kaldor-type business cycle discrete model

    Science.gov (United States)

    Bashkirtseva, Irina; Ryashko, Lev; Sysolyatina, Anna

    2016-07-01

    We study nonlinear stochastic phenomena in the discrete Kaldor model of business cycles. A numerical parametric analysis of stochastically forced attractors (equilibria, closed invariant curves, discrete cycles) of this model is performed using the stochastic sensitivity functions technique. A spatial arrangement of random states in stochastic attractors is modeled by confidence domains. The phenomenon of noise-induced transitions ;chaos-order; is discussed.

  9. Parameter estimation in stochastic rainfall-runoff models

    DEFF Research Database (Denmark)

    Jonsdottir, Harpa; Madsen, Henrik; Palsson, Olafur Petur

    2006-01-01

    A parameter estimation method for stochastic rainfall-runoff models is presented. The model considered in the paper is a conceptual stochastic model, formulated in continuous-discrete state space form. The model is small and a fully automatic optimization is, therefore, possible for estimating all...... the parameter values are optimal for simulation or prediction. The data originates from Iceland and the model is designed for Icelandic conditions, including a snow routine for mountainous areas. The model demands only two input data series, precipitation and temperature and one output data series...

  10. Stochastic resonance in neuron models: endogenous stimulation revisited.

    Science.gov (United States)

    Plesser, H E; Geisel, T

    2001-03-01

    The paradigm of stochastic resonance (SR)-the idea that signal detection and transmission may benefit from noise-has met with great interest in both physics and the neurosciences. We investigate here the consequences of reducing the dynamics of a periodically driven neuron to a renewal process (stimulation with reset or endogenous stimulation). This greatly simplifies the mathematical analysis, but we show that stochastic resonance as reported earlier occurs in this model only as a consequence of the reduced dynamics.

  11. A stochastic large deformation model for computational anatomy

    DEFF Research Database (Denmark)

    Arnaudon, Alexis; Holm, Darryl D.; Pai, Akshay Sadananda Uppinakudru

    2017-01-01

    In the study of shapes of human organs using computational anatomy, variations are found to arise from inter-subject anatomical differences, disease-specific effects, and measurement noise. This paper introduces a stochastic model for incorporating random variations into the Large Deformation...... registering the landmarks, by applying bridge sampling using a stochastically perturbed version of the large deformation gradient flow algorithm. The method and the estimation algorithms are experimentally validated on synthetic examples and shape data of human corpora callosa....

  12. Stochastic differential equation model for cerebellar granule cell excitability.

    Directory of Open Access Journals (Sweden)

    Antti Saarinen

    2008-02-01

    Full Text Available Neurons in the brain express intrinsic dynamic behavior which is known to be stochastic in nature. A crucial question in building models of neuronal excitability is how to be able to mimic the dynamic behavior of the biological counterpart accurately and how to perform simulations in the fastest possible way. The well-established Hodgkin-Huxley formalism has formed to a large extent the basis for building biophysically and anatomically detailed models of neurons. However, the deterministic Hodgkin-Huxley formalism does not take into account the stochastic behavior of voltage-dependent ion channels. Ion channel stochasticity is shown to be important in adjusting the transmembrane voltage dynamics at or close to the threshold of action potential firing, at the very least in small neurons. In order to achieve a better understanding of the dynamic behavior of a neuron, a new modeling and simulation approach based on stochastic differential equations and Brownian motion is developed. The basis of the work is a deterministic one-compartmental multi-conductance model of the cerebellar granule cell. This model includes six different types of voltage-dependent conductances described by Hodgkin-Huxley formalism and simple calcium dynamics. A new model for the granule cell is developed by incorporating stochasticity inherently present in the ion channel function into the gating variables of conductances. With the new stochastic model, the irregular electrophysiological activity of an in vitro granule cell is reproduced accurately, with the same parameter values for which the membrane potential of the original deterministic model exhibits regular behavior. The irregular electrophysiological activity includes experimentally observed random subthreshold oscillations, occasional spontaneous spikes, and clusters of action potentials. As a conclusion, the new stochastic differential equation model of the cerebellar granule cell excitability is found to expand

  13. Inference for adaptive Time series Models: Stochastic Volatility and Conditionally

    NARCIS (Netherlands)

    Bos, C.S.; Shephard, N.

    2006-01-01

    In this paper we model the Gaussian errors in the standard Gaussian linear state space model as stochastic volatility processes. We show that conventional MCMC algorithms for this class of models are ineffective, but that the problem can be alleviated by reparameterizing the model. Instead of

  14. Stochastic models to simulate paratuberculosis in dairy herds

    DEFF Research Database (Denmark)

    Nielsen, S.S.; Weber, M.F.; Kudahl, Anne Margrethe Braad

    2011-01-01

    Stochastic simulation models are widely accepted as a means of assessing the impact of changes in daily management and the control of different diseases, such as paratuberculosis, in dairy herds. This paper summarises and discusses the assumptions of four stochastic simulation models and their use...... the models are somewhat different in their underlying principles and do put slightly different values on the different strategies, their overall findings are similar. Therefore, simulation models may be useful in planning paratuberculosis strategies in dairy herds, although as with all models caution...

  15. Probabilistic models for stochastic elliptic partial differential equations

    Science.gov (United States)

    Grigoriu, Mircea

    2010-11-01

    Mathematical requirements that the random coefficients of stochastic elliptical partial differential equations must satisfy such that they have unique solutions have been studied extensively. Yet, additional constraints that these coefficients must satisfy to provide realistic representations for physical quantities, referred to as physical requirements, have not been examined systematically. It is shown that current models for random coefficients constructed solely by mathematical considerations can violate physical constraints and, consequently, be of limited practical use. We develop alternative models for the random coefficients of stochastic differential equations that satisfy both mathematical and physical constraints. Theoretical arguments are presented to show potential limitations of current models and establish properties of the models developed in this study. Numerical examples are used to illustrate the construction of the proposed models, assess the performance of these models, and demonstrate the sensitivity of the solutions of stochastic differential equations to probabilistic characteristics of their random coefficients.

  16. Stochastic stage-structured modeling of the adaptive immune system

    Energy Technology Data Exchange (ETDEWEB)

    Chao, D. L. (Dennis L.); Davenport, M. P. (Miles P.); Forrest, S. (Stephanie); Perelson, Alan S.,

    2003-01-01

    We have constructed a computer model of the cytotoxic T lymphocyte (CTL) response to antigen and the maintenance of immunological memory. Because immune responses often begin with small numbers of cells and there is great variation among individual immune systems, we have chosen to implement a stochastic model that captures the life cycle of T cells more faithfully than deterministic models. Past models of the immune response have been differential equation based, which do not capture stochastic effects, or agent-based, which are computationally expensive. We use a stochastic stage-structured approach that has many of the advantages of agent-based modeling but is more efficient. Our model can provide insights into the effect infections have on the CTL repertoire and the response to subsequent infections.

  17. Stochastic model of forecasting spare parts demand

    Directory of Open Access Journals (Sweden)

    Ivan S. Milojević

    2012-01-01

    Full Text Available If demand is known for the whole planning period (complete information, then this type of demand or a supply system is deterministic. In the simplest cases, the demand per time unit is constant. If demand levels change over time following a precisely determined and pre-known principle, this type of demand is also classified as deterministic. This quality of demand is very rare. In most cases demand is the product of a process, for example TMS maintenance, whose progression cannot be predicted due to a number of factors influencing the process and causing random demand changes. In this case, a supply system must function according to the complete information and with a certain degree of uncertainty. In cases when demand may be defined by some of the laws of the probability theory, we are talking about stochastic demand and a stochastic supply system. Demand can be described by mathematical expectation, mathematical expectation and standard deviation, probability distribution or as a random process. However, there is usually a need for the most complex description, i.e. the complex random process because both intensity of demand and the probability distribution change during the observed intervals. The level of temporal (dynamic series is traditionally considered as a complex phenomenon consisting of four components: - basic tendency of phenomenon development - cyclical impact (long-term, 'ancient' - seasonal effects - random fluctuations. The basic tendency of phenomenon development means a long-term evolution of phenomena. A function that expresses the trajectory of changes of the basic tendency of a phenomenon development in the form of the equation is called a trend. Often, the trend involves time regression; i.e. the coefficients of the proposed functions are often determined by the least squares method. To roughly determine the coefficients of the proposed function, the sum of three and three-point methods are also used. After checking the

  18. Impacts of Stochastic Modeling on GPS-derived ZTD Estimations

    CERN Document Server

    Jin, Shuanggen

    2010-01-01

    GPS-derived ZTD (Zenith Tropospheric Delay) plays a key role in near real-time weather forecasting, especially in improving the precision of Numerical Weather Prediction (NWP) models. The ZTD is usually estimated using the first-order Gauss-Markov process with a fairly large correlation, and under the assumption that all the GPS measurements, carrier phases or pseudo-ranges, have the same accuracy. However, these assumptions are unrealistic. This paper aims to investigate the impact of several stochastic modeling methods on GPS-derived ZTD estimations using Australian IGS data. The results show that the accuracy of GPS-derived ZTD can be improved using a suitable stochastic model for the GPS measurements. The stochastic model using satellite elevation angle-based cosine function is better than other investigated stochastic models. It is noted that, when different stochastic modeling strategies are used, the variations in estimated ZTD can reach as much as 1cm. This improvement of ZTD estimation is certainly c...

  19. Electricity Market Stochastic Dynamic Model and Its Mean Stability Analysis

    Directory of Open Access Journals (Sweden)

    Zhanhui Lu

    2014-01-01

    Full Text Available Based on the deterministic dynamic model of electricity market proposed by Alvarado, a stochastic electricity market model, considering the random nature of demand sides, is presented in this paper on the assumption that generator cost function and consumer utility function are quadratic functions. The stochastic electricity market model is a generalization of the deterministic dynamic model. Using the theory of stochastic differential equations, stochastic process theory, and eigenvalue techniques, the determining conditions of the mean stability for this electricity market model under small Gauss type random excitation are provided and testified theoretically. That is, if the demand elasticity of suppliers is nonnegative and the demand elasticity of consumers is negative, then the stochastic electricity market model is mean stable. It implies that the stability can be judged directly by initial data without any computation. Taking deterministic electricity market data combined with small Gauss type random excitation as numerical samples to interpret random phenomena from a statistical perspective, the results indicate the conclusions above are correct, valid, and practical.

  20. Stochastic S-system modeling of gene regulatory network.

    Science.gov (United States)

    Chowdhury, Ahsan Raja; Chetty, Madhu; Evans, Rob

    2015-10-01

    Microarray gene expression data can provide insights into biological processes at a system-wide level and is commonly used for reverse engineering gene regulatory networks (GRN). Due to the amalgamation of noise from different sources, microarray expression profiles become inherently noisy leading to significant impact on the GRN reconstruction process. Microarray replicates (both biological and technical), generated to increase the reliability of data obtained under noisy conditions, have limited influence in enhancing the accuracy of reconstruction . Therefore, instead of the conventional GRN modeling approaches which are deterministic, stochastic techniques are becoming increasingly necessary for inferring GRN from noisy microarray data. In this paper, we propose a new stochastic GRN model by investigating incorporation of various standard noise measurements in the deterministic S-system model. Experimental evaluations performed for varying sizes of synthetic network, representing different stochastic processes, demonstrate the effect of noise on the accuracy of genetic network modeling and the significance of stochastic modeling for GRN reconstruction . The proposed stochastic model is subsequently applied to infer the regulations among genes in two real life networks: (1) the well-studied IRMA network, a real-life in-vivo synthetic network constructed within the Saccharomyces cerevisiae yeast, and (2) the SOS DNA repair network in Escherichia coli.

  1. INFERENCE AND SENSITIVITY IN STOCHASTIC WIND POWER FORECAST MODELS.

    KAUST Repository

    Elkantassi, Soumaya

    2017-10-03

    Reliable forecasting of wind power generation is crucial to optimal control of costs in generation of electricity with respect to the electricity demand. Here, we propose and analyze stochastic wind power forecast models described by parametrized stochastic differential equations, which introduce appropriate fluctuations in numerical forecast outputs. We use an approximate maximum likelihood method to infer the model parameters taking into account the time correlated sets of data. Furthermore, we study the validity and sensitivity of the parameters for each model. We applied our models to Uruguayan wind power production as determined by historical data and corresponding numerical forecasts for the period of March 1 to May 31, 2016.

  2. Methods and models in mathematical biology deterministic and stochastic approaches

    CERN Document Server

    Müller, Johannes

    2015-01-01

    This book developed from classes in mathematical biology taught by the authors over several years at the Technische Universität München. The main themes are modeling principles, mathematical principles for the analysis of these models, and model-based analysis of data. The key topics of modern biomathematics are covered: ecology, epidemiology, biochemistry, regulatory networks, neuronal networks, and population genetics. A variety of mathematical methods are introduced, ranging from ordinary and partial differential equations to stochastic graph theory and  branching processes. A special emphasis is placed on the interplay between stochastic and deterministic models.

  3. Stochastic evolutions of dynamic traffic flow modeling and applications

    CERN Document Server

    Chen, Xiqun (Michael); Shi, Qixin

    2015-01-01

    This book reveals the underlying mechanisms of complexity and stochastic evolutions of traffic flows. Using Eulerian and Lagrangian measurements, the authors propose lognormal headway/spacing/velocity distributions and subsequently develop a Markov car-following model to describe drivers’ random choices concerning headways/spacings, putting forward a stochastic fundamental diagram model for wide scattering flow-density points. In the context of highway onramp bottlenecks, the authors present a traffic flow breakdown probability model and spatial-temporal queuing model to improve the stability and reliability of road traffic flows. This book is intended for researchers and graduate students in the fields of transportation engineering and civil engineering.

  4. Stochastic models of the Social Security trust funds.

    Science.gov (United States)

    Burdick, Clark; Manchester, Joyce

    Each year in March, the Board of Trustees of the Social Security trust funds reports on the current and projected financial condition of the Social Security programs. Those programs, which pay monthly benefits to retired workers and their families, to the survivors of deceased workers, and to disabled workers and their families, are financed through the Old-Age, Survivors, and Disability Insurance (OASDI) Trust Funds. In their 2003 report, the Trustees present, for the first time, results from a stochastic model of the combined OASDI trust funds. Stochastic modeling is an important new tool for Social Security policy analysis and offers the promise of valuable new insights into the financial status of the OASDI trust funds and the effects of policy changes. The results presented in this article demonstrate that several stochastic models deliver broadly consistent results even though they use very different approaches and assumptions. However, they also show that the variation in trust fund outcomes differs as the approach and assumptions are varied. Which approach and assumptions are best suited for Social Security policy analysis remains an open question. Further research is needed before the promise of stochastic modeling is fully realized. For example, neither parameter uncertainty nor variability in ultimate assumption values is recognized explicitly in the analyses. Despite this caveat, stochastic modeling results are already shedding new light on the range and distribution of trust fund outcomes that might occur in the future.

  5. Stochastic magnetic measurement model for relative position and orientation estimation

    NARCIS (Netherlands)

    Schepers, H. Martin; Veltink, Petrus H.

    2010-01-01

    This study presents a stochastic magnetic measurement model that can be used to estimate relative position and orientation. The model predicts the magnetic field generated by a single source coil at the location of the sensor. The model was used in a fusion filter that predicts the change of

  6. A stochastic dynamic programming model for stream water quality ...

    Indian Academy of Sciences (India)

    This paper deals with development of a seasonal fraction-removal policy model for waste load allocation in streams addressing uncertainties due to randomness and fuzziness. A stochastic dynamic programming (SDP) model is developed to arrive at the steady-state seasonal fraction-removal policy. A fuzzy decision model ...

  7. A market model for stochastic smile: a conditional density approach

    NARCIS (Netherlands)

    Zilber, A.

    2005-01-01

    The purpose of this paper is to introduce a new approach that allows to construct no-arbitrage market models of for implied volatility surfaces (in other words, stochastic smile models). That is to say, the idea presented here allows us to model prices of liquidly traded vanilla options as separate

  8. Stochastic models for some meteorological outcomes in Niger Delta ...

    African Journals Online (AJOL)

    In this paper, stochastic models based on autoregressive integrated moving average models of various orders and its seasonalized versions are presented, with a view to identifying the optimal model for some meteorological outcomes in some cities in Niger Delta region of Nigeria, using Normalized Bayesian Information ...

  9. Stochastic Modeling and Deterministic Limit of Catalytic Surface Processes

    DEFF Research Database (Denmark)

    Starke, Jens; Reichert, Christian; Eiswirth, Markus

    2007-01-01

    Three levels of modeling, microscopic, mesoscopic and macroscopic are discussed for the CO oxidation on low-index platinum single crystal surfaces. The introduced models on the microscopic and mesoscopic level are stochastic while the model on the macroscopic level is deterministic. It can be der...

  10. Effects of Stochastic Traffic Flow Model on Expected System Performance

    Science.gov (United States)

    2012-12-01

    feasible. 2.2.2 Brownian Bridge Stochastic Path Model Like the linear model, the Brownian bridge ( Karlin and Taylor 1981) model uses the idea of...IEEE Computer Vision and Pattern Recog- nition Workshop, Piscataway, New Jersey: Institute of Electrical and Electronics Engineers, Inc. Karlin , S

  11. Introduction to modeling and analysis of stochastic systems

    CERN Document Server

    Kulkarni, V G

    2011-01-01

    This is an introductory-level text on stochastic modeling. It is suited for undergraduate students in engineering, operations research, statistics, mathematics, actuarial science, business management, computer science, and public policy. It employs a large number of examples to teach the students to use stochastic models of real-life systems to predict their performance, and use this analysis to design better systems. The book is devoted to the study of important classes of stochastic processes: discrete and continuous time Markov processes, Poisson processes, renewal and regenerative processes, semi-Markov processes, queueing models, and diffusion processes. The book systematically studies the short-term and the long-term behavior, cost/reward models, and first passage times. All the material is illustrated with many examples, and case studies. The book provides a concise review of probability in the appendix. The book emphasizes numerical answers to the problems. A collection of MATLAB programs to accompany...

  12. Distributed parallel computing in stochastic modeling of groundwater systems.

    Science.gov (United States)

    Dong, Yanhui; Li, Guomin; Xu, Haizhen

    2013-03-01

    Stochastic modeling is a rapidly evolving, popular approach to the study of the uncertainty and heterogeneity of groundwater systems. However, the use of Monte Carlo-type simulations to solve practical groundwater problems often encounters computational bottlenecks that hinder the acquisition of meaningful results. To improve the computational efficiency, a system that combines stochastic model generation with MODFLOW-related programs and distributed parallel processing is investigated. The distributed computing framework, called the Java Parallel Processing Framework, is integrated into the system to allow the batch processing of stochastic models in distributed and parallel systems. As an example, the system is applied to the stochastic delineation of well capture zones in the Pinggu Basin in Beijing. Through the use of 50 processing threads on a cluster with 10 multicore nodes, the execution times of 500 realizations are reduced to 3% compared with those of a serial execution. Through this application, the system demonstrates its potential in solving difficult computational problems in practical stochastic modeling. © 2012, The Author(s). Groundwater © 2012, National Ground Water Association.

  13. Model-based clustering in networks with Stochastic Community Finding

    OpenAIRE

    McDaid, Aaron F.; Murphy, Brendan Thomas; Friel, Nial; Hurley, Neil J.

    2012-01-01

    In the model-based clustering of networks, blockmodelling may be used to identify roles in the network. We identify a special case of the Stochastic Block Model (SBM) where we constrain the cluster-cluster interactions such that the density inside the clusters of nodes is expected to be greater than the density between clusters. This corresponds to the intuition behind community-finding methods, where nodes tend to clustered together if they link to each other. We call this model Stochastic C...

  14. On the Robustness of Temporal Properties for Stochastic Models

    Directory of Open Access Journals (Sweden)

    Ezio Bartocci

    2013-08-01

    Full Text Available Stochastic models such as Continuous-Time Markov Chains (CTMC and Stochastic Hybrid Automata (SHA are powerful formalisms to model and to reason about the dynamics of biological systems, due to their ability to capture the stochasticity inherent in biological processes. A classical question in formal modelling with clear relevance to biological modelling is the model checking problem. i.e. calculate the probability that a behaviour, expressed for instance in terms of a certain temporal logic formula, may occur in a given stochastic process. However, one may not only be interested in the notion of satisfiability, but also in the capacity of a system to mantain a particular emergent behaviour unaffected by the perturbations, caused e.g. from extrinsic noise, or by possible small changes in the model parameters. To address this issue, researchers from the verification community have recently proposed several notions of robustness for temporal logic providing suitable definitions of distance between a trajectory of a (deterministic dynamical system and the boundaries of the set of trajectories satisfying the property of interest. The contributions of this paper are twofold. First, we extend the notion of robustness to stochastic systems, showing that this naturally leads to a distribution of robustness scores. By discussing two examples, we show how to approximate the distribution of the robustness score and its key indicators: the average robustness and the conditional average robustness. Secondly, we show how to combine these indicators with the satisfaction probability to address the system design problem, where the goal is to optimize some control parameters of a stochastic model in order to best maximize robustness of the desired specifications.

  15. The critical domain size of stochastic population models.

    Science.gov (United States)

    Reimer, Jody R; Bonsall, Michael B; Maini, Philip K

    2017-02-01

    Identifying the critical domain size necessary for a population to persist is an important question in ecology. Both demographic and environmental stochasticity impact a population's ability to persist. Here we explore ways of including this variability. We study populations with distinct dispersal and sedentary stages, which have traditionally been modelled using a deterministic integrodifference equation (IDE) framework. Individual-based models (IBMs) are the most intuitive stochastic analogues to IDEs but yield few analytic insights. We explore two alternate approaches; one is a scaling up to the population level using the Central Limit Theorem, and the other a variation on both Galton-Watson branching processes and branching processes in random environments. These branching process models closely approximate the IBM and yield insight into the factors determining the critical domain size for a given population subject to stochasticity.

  16. Slow update stochastic simulation algorithms for modeling complex biochemical networks.

    Science.gov (United States)

    Ghosh, Debraj; De, Rajat K

    2017-10-30

    The stochastic simulation algorithm (SSA) based modeling is a well recognized approach to predict the stochastic behavior of biological networks. The stochastic simulation of large complex biochemical networks is a challenge as it takes a large amount of time for simulation due to high update cost. In order to reduce the propensity update cost, we proposed two algorithms: slow update exact stochastic simulation algorithm (SUESSA) and slow update exact sorting stochastic simulation algorithm (SUESSSA). We applied cache-based linear search (CBLS) in these two algorithms for improving the search operation for finding reactions to be executed. Data structure used for incorporating CBLS is very simple and the cost of maintaining this during propensity update operation is very low. Hence, time taken during propensity updates, for simulating strongly coupled networks, is very fast; which leads to reduction of total simulation time. SUESSA and SUESSSA are not only restricted to elementary reactions, they support higher order reactions too. We used linear chain model and colloidal aggregation model to perform a comparative analysis of the performances of our methods with the existing algorithms. We also compared the performances of our methods with the existing ones, for large biochemical networks including B cell receptor and FcϵRI signaling networks. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Modelling fibrinolysis: a 3D stochastic multiscale model.

    Science.gov (United States)

    Bannish, Brittany E; Keener, James P; Fogelson, Aaron L

    2014-03-01

    Fibrinolysis, the proteolytic degradation of the fibrin fibres that stabilize blood clots, is initiated when tissue-type plasminogen activator (tPA) activates plasminogen to plasmin, the main fibrinolytic enzyme. Many experiments have shown that coarse clots made of thick fibres lyse more quickly than fine clots made of thin fibres, despite the fact that individual thick fibres lyse more slowly than individual thin fibres. The generally accepted explanation for this is that a coarse clot with fewer fibres to transect will be degraded faster than a fine clot with a higher fibre density. Other experiments show the opposite result. The standard mathematical tool for investigating fibrinolysis has been deterministic reaction-diffusion models, but due to low tPA concentrations, stochastic models may be more appropriate. We develop a 3D stochastic multiscale model of fibrinolysis. A microscale model representing a fibre cross section and containing detailed biochemical reactions provides information about single fibre lysis times, the number of plasmin molecules that can be activated by a single tPA molecule and the length of time tPA stays bound to a given fibre cross section. Data from the microscale model are used in a macroscale model of the full fibrin clot, from which we obtain lysis front velocities and tPA distributions. We find that the fibre number impacts lysis speed, but so does the number of tPA molecules relative to the surface area of the clot exposed to those molecules. Depending on the values of these two quantities (tPA number and surface area), for given kinetic parameters, the model predicts coarse clots lyse faster or slower than fine clots, thus providing a possible explanation for the divergent experimental observations.

  18. Deterministic and Stochastic Modelling of Ocean Surface Waves

    NARCIS (Netherlands)

    Smit, P.B.

    2014-01-01

    Predicting the mean wave statistics in the nearshore, for instance the significant wave height, has predominantly been the domain of operational stochastic wave models based on the radiative transport (or energy balance) equation. Although reasonably successful in the nearshore, these models were

  19. Powering stochastic reliability models by discrete event simulation

    DEFF Research Database (Denmark)

    Kozine, Igor; Wang, Xiaoyun

    2012-01-01

    it difficult to find a solution to the problem. The power of modern computers and recent developments in discrete-event simulation (DES) software enable to diminish some of the drawbacks of stochastic models. In this paper we describe the insights we have gained based on using both Markov and DES models...

  20. Stochastic Modelling of the Diffusion Coefficient for Concrete

    DEFF Research Database (Denmark)

    Thoft-Christensen, Palle

    In the paper, a new stochastic modelling of the diffusion coefficient D is presented. The modelling is based on physical understanding of the diffusion process and on some recent experimental results. The diffusion coefficients D is strongly dependent on the w/c ratio and the temperature....

  1. Reflected stochastic differential equation models for constrained animal movement

    Science.gov (United States)

    Hanks, Ephraim M.; Hooten, Mevin B.; Johnson, Devin S.

    2017-01-01

    Movement for many animal species is constrained in space by barriers such as rivers, shorelines, or impassable cliffs. We develop an approach for modeling animal movement constrained in space by considering a class of constrained stochastic processes, reflected stochastic differential equations. Our approach generalizes existing methods for modeling unconstrained animal movement. We present methods for simulation and inference based on augmenting the constrained movement path with a latent unconstrained path and illustrate this augmentation with a simulation example and an analysis of telemetry data from a Steller sea lion (Eumatopias jubatus) in southeast Alaska.

  2. Stochastic models to simulate paratuberculosis in dairy herds

    DEFF Research Database (Denmark)

    Nielsen, Søren Saxmose; Weber, M.F.; Kudahl, Anne Margrethe Braad

    2011-01-01

    Stochastic simulation models are widely accepted as a means of assessing the impact of changes in daily management and the control of different diseases, such as paratuberculosis, in dairy herds. This paper summarises and discusses the assumptions of four stochastic simulation models and their use...... in the design of certification, surveillance, and control strategies for paratuberculosis in cattle herds. A detailed comparison is made between the Dutch JohneSSim and the Danish PTB-Simherd, using the same context of a set of control strategies in a typical Dutch/Danish herd. The conclusion is that while...

  3. Fuzzy stochastic neural network model for structural system identification

    Science.gov (United States)

    Jiang, Xiaomo; Mahadevan, Sankaran; Yuan, Yong

    2017-01-01

    This paper presents a dynamic fuzzy stochastic neural network model for nonparametric system identification using ambient vibration data. The model is developed to handle two types of imprecision in the sensed data: fuzzy information and measurement uncertainties. The dimension of the input vector is determined by using the false nearest neighbor approach. A Bayesian information criterion is applied to obtain the optimum number of stochastic neurons in the model. A fuzzy C-means clustering algorithm is employed as a data mining tool to divide the sensed data into clusters with common features. The fuzzy stochastic model is created by combining the fuzzy clusters of input vectors with the radial basis activation functions in the stochastic neural network. A natural gradient method is developed based on the Kullback-Leibler distance criterion for quick convergence of the model training. The model is validated using a power density pseudospectrum approach and a Bayesian hypothesis testing-based metric. The proposed methodology is investigated with numerically simulated data from a Markov Chain model and a two-story planar frame, and experimentally sensed data from ambient vibration data of a benchmark structure.

  4. The stochastic model of pitting corrosion of metals

    Science.gov (United States)

    You, Y. H.; Wang, B. R.; Hu, H. Y.

    2017-12-01

    Considering that pitting corrosion is a stochastic process, the purpose of this paper is to use stochastic theory to investigate the growth process of pitting corrosion of metals. Based on the mechanism of pit growth and nonequilibrium statistical theory, the time evolution equations of pit depth and corrosion rate are obtained, and the probability density function can be derived by solving Fock-Plank Equation. Subsequently, the failure probability or reliability of metals is calculated based on the weakest link model of pitting corrosion. Finally, the stochastic model is used on the aircraft aluminum alloy LD2. Furthermore, this methodology can be applied to analyze the reliability and predict the pitting life of metals.

  5. Model Selection for Integrated Pest Management with Stochasticity.

    Science.gov (United States)

    Akman, Olcay; Comar, Timothy D; Hrozencik, Daniel

    2017-12-11

    In [X. Song and Z. Xiang, 2006. The prey-dependent consumption two-prey one-predator models with stage structure for the predator and impulsive effects. Journal of Theoretical Biology, 242, 683-698.], an integrated pest management model with periodically varying climatic conditions was introduced. In order to address a wider range of environmental effects, the authors here have embarked upon a series of studies resulting in a more flexible modeling approach. In [O. Akman, T.D. Comar, and D. Hrozencik, 2013. Integrated pest management with a stochastic birth rate for prey species. Frontiers in Neuroscience: Systems Biology7:141. doi: 10.3389/fnins.2013.00141], the impact of randomly changing environmental conditions is examined by incorporating stochasticity into the birth pulse of the prey species. In [O. Akman, D. Cairns, T.D. Comar, and D. Hrozencik, 2014. Integrated Pest Management with a Mixed Birth Rate for Prey Species, Letters in Biomathematics, 1. http://www.lettersinbiomath.org.], the authors introduce a class of models via a mixture of two birth-pulse terms and determined conditions for the global and local asymptotic stability of the pest eradication solution. With this work, the authors unify the stochastic and mixture model components to create further flexibility in modeling the impacts of random environmental changes on an integrated pest management system. In particular, we first determine the conditions under which solutions of our deterministic mixture model are permanent. We then analyze the stochastic model to find the optimal value of the mixing parameter that minimizes the variance in the efficacy of the pesticide. Additionally, we perform a sensitivity analysis to show that the corresponding pesticide efficacy determined by this optimization technique is indeed robust. Through numerical simulations we show that permanence can be preserved in our stochastic model. Our study of the stochastic version of the model indicates that our results on

  6. Stochastic Climate Forcing for Ice-Sheet Models

    Science.gov (United States)

    Nuterman, Roman; Jochum, Markus

    2017-04-01

    Climate oscillations from glacial periods, with large parts of the continents covered with ice, to warm interglacials like the present one, are observed in various paleoclimatic records over the past few million years. According to Milankovitch theory, which is commonly assumed, these glacial cycles are linked to changes in insolation due to periodic changes of external earth-orbital forcing. However, this relationship is far from understood, because the insolation variations are so small that enhancing feedbacks must be at play. Moreover, there are several shortcomings in the Milankovitch theory: first, the duration of the glacial cycles changed at the so-called Mid-Pleistocene transition from 41,000 years to approximately 100,000 years and second, the interglacial of 400,000 years ago should not have happened. Thus, the current phasing and magnitude of the glacial cycles are far from being well understood and the external perturbation might only play a minor role in comparison to internal stochastic variations or internal oscillations. Although modern Ice-Sheet Models (ISM) are able to simulate evolution of ice-sheets at the entire glacial or interglacial time scales, the state-of-the-art Earth System Models (ESM) are too computationally expensive for such long integrations. Therefore, a constant climate forcing is usually used in the ice-sheet models. However, this approach does not take into account the stochastic nature of climate. At the same time, ESM models provide valuable information on natural climate variability, which then can be used for building stochastic climate models able to generate both continuous and discrete climate variables with stochastic atmospheric processes. In this study, we present a stochastic climate model, built from large sets of Community Earth System Model (CESM) integrations with both internal and external climate forcing, and able to generate synthetic climate forcing (such as temperature and precipitation fields) of any

  7. Stochastic lattice model of synaptic membrane protein domains

    Science.gov (United States)

    Li, Yiwei; Kahraman, Osman; Haselwandter, Christoph A.

    2017-05-01

    Neurotransmitter receptor molecules, concentrated in synaptic membrane domains along with scaffolds and other kinds of proteins, are crucial for signal transmission across chemical synapses. In common with other membrane protein domains, synaptic domains are characterized by low protein copy numbers and protein crowding, with rapid stochastic turnover of individual molecules. We study here in detail a stochastic lattice model of the receptor-scaffold reaction-diffusion dynamics at synaptic domains that was found previously to capture, at the mean-field level, the self-assembly, stability, and characteristic size of synaptic domains observed in experiments. We show that our stochastic lattice model yields quantitative agreement with mean-field models of nonlinear diffusion in crowded membranes. Through a combination of analytic and numerical solutions of the master equation governing the reaction dynamics at synaptic domains, together with kinetic Monte Carlo simulations, we find substantial discrepancies between mean-field and stochastic models for the reaction dynamics at synaptic domains. Based on the reaction and diffusion properties of synaptic receptors and scaffolds suggested by previous experiments and mean-field calculations, we show that the stochastic reaction-diffusion dynamics of synaptic receptors and scaffolds provide a simple physical mechanism for collective fluctuations in synaptic domains, the molecular turnover observed at synaptic domains, key features of the observed single-molecule trajectories, and spatial heterogeneity in the effective rates at which receptors and scaffolds are recycled at the cell membrane. Our work sheds light on the physical mechanisms and principles linking the collective properties of membrane protein domains to the stochastic dynamics that rule their molecular components.

  8. Stochastic Modeling of Radioactive Material Releases

    Energy Technology Data Exchange (ETDEWEB)

    Andrus, Jason [Idaho National Lab. (INL), Idaho Falls, ID (United States); Pope, Chad [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2015-09-01

    Nonreactor nuclear facilities operated under the approval authority of the U.S. Department of Energy use unmitigated hazard evaluations to determine if potential radiological doses associated with design basis events challenge or exceed dose evaluation guidelines. Unmitigated design basis events that sufficiently challenge dose evaluation guidelines or exceed the guidelines for members of the public or workers, merit selection of safety structures, systems, or components or other controls to prevent or mitigate the hazard. Idaho State University, in collaboration with Idaho National Laboratory, has developed a portable and simple to use software application called SODA (Stochastic Objective Decision-Aide) that stochastically calculates the radiation dose associated with hypothetical radiological material release scenarios. Rather than producing a point estimate of the dose, SODA produces a dose distribution result to allow a deeper understanding of the dose potential. SODA allows users to select the distribution type and parameter values for all of the input variables used to perform the dose calculation. SODA then randomly samples each distribution input variable and calculates the overall resulting dose distribution. In cases where an input variable distribution is unknown, a traditional single point value can be used. SODA was developed using the MATLAB coding framework. The software application has a graphical user input. SODA can be installed on both Windows and Mac computers and does not require MATLAB to function. SODA provides improved risk understanding leading to better informed decision making associated with establishing nuclear facility material-at-risk limits and safety structure, system, or component selection. It is important to note that SODA does not replace or compete with codes such as MACCS or RSAC, rather it is viewed as an easy to use supplemental tool to help improve risk understanding and support better informed decisions. The work was

  9. Tracking stochastic resonance curves using an assisted reference model

    Energy Technology Data Exchange (ETDEWEB)

    Calderón Ramírez, Mario; Rico Martínez, Ramiro [Departamento de Ingeniería Química, Instituto Tecnológico de Celaya, Av. Tecnológico y A. García Cubas S/N, Celaya, Guanajuato, 38010 (Mexico); Ramírez Álvarez, Elizeth [Nonequilibrium Chemical Physics, Physik-Department, TU-München, James-Franck-Str. 1, 85748 Garching bei München (Germany); Parmananda, P. [Department of Physics, Indian Institute of Technology Bombay, Powai, Mumbai 400 076 (India)

    2015-06-15

    The optimal noise amplitude for Stochastic Resonance (SR) is located employing an Artificial Neural Network (ANN) reference model with a nonlinear predictive capability. A modified Kalman Filter (KF) was coupled to this reference model in order to compensate for semi-quantitative forecast errors. Three manifestations of stochastic resonance, namely, Periodic Stochastic Resonance (PSR), Aperiodic Stochastic Resonance (ASR), and finally Coherence Resonance (CR) were considered. Using noise amplitude as the control parameter, for the case of PSR and ASR, the cross-correlation curve between the sub-threshold input signal and the system response is tracked. However, using the same parameter the Normalized Variance curve is tracked for the case of CR. The goal of the present work is to track these curves and converge to their respective extremal points. The ANN reference model strategy captures and subsequently predicts the nonlinear features of the model system while the KF compensates for the perturbations inherent to the superimposed noise. This technique, implemented in the FitzHugh-Nagumo model, enabled us to track the resonance curves and eventually locate their optimal (extremal) values. This would yield the optimal value of noise for the three manifestations of the SR phenomena.

  10. Tracking stochastic resonance curves using an assisted reference model.

    Science.gov (United States)

    Calderón Ramírez, Mario; Rico Martínez, Ramiro; Ramírez Álvarez, Elizeth; Parmananda, P

    2015-06-01

    The optimal noise amplitude for Stochastic Resonance (SR) is located employing an Artificial Neural Network (ANN) reference model with a nonlinear predictive capability. A modified Kalman Filter (KF) was coupled to this reference model in order to compensate for semi-quantitative forecast errors. Three manifestations of stochastic resonance, namely, Periodic Stochastic Resonance (PSR), Aperiodic Stochastic Resonance (ASR), and finally Coherence Resonance (CR) were considered. Using noise amplitude as the control parameter, for the case of PSR and ASR, the cross-correlation curve between the sub-threshold input signal and the system response is tracked. However, using the same parameter the Normalized Variance curve is tracked for the case of CR. The goal of the present work is to track these curves and converge to their respective extremal points. The ANN reference model strategy captures and subsequently predicts the nonlinear features of the model system while the KF compensates for the perturbations inherent to the superimposed noise. This technique, implemented in the FitzHugh-Nagumo model, enabled us to track the resonance curves and eventually locate their optimal (extremal) values. This would yield the optimal value of noise for the three manifestations of the SR phenomena.

  11. Stochastic Model of Maturation and Vesicular Exchange in Cellular Organelles

    CERN Document Server

    Vagne, Quentin

    2016-01-01

    The dynamical organization of membrane-bound organelles along intracellular transport pathways relies on vesicular exchange between organelles and on biochemical maturation of the organelle content by specific enzymes. The relative importance of each mechanism in controlling organelle dynamics remains controversial, in particular for transport through the Golgi apparatus. Using a stochastic model, we show that full maturation of membrane-bound compartments can be seen as the stochastic escape from a steady-state in which export is dominated by vesicular exchange. We show that full maturation can contribute a significant fraction of the total out-flux for small organelles such as endosomes and Golgi cisternae.

  12. Stochastic geometry, spatial statistics and random fields models and algorithms

    CERN Document Server

    2015-01-01

    Providing a graduate level introduction to various aspects of stochastic geometry, spatial statistics and random fields, this volume places a special emphasis on fundamental classes of models and algorithms as well as on their applications, for example in materials science, biology and genetics. This book has a strong focus on simulations and includes extensive codes in Matlab and R, which are widely used in the mathematical community. It can be regarded as a continuation of the recent volume 2068 of Lecture Notes in Mathematics, where other issues of stochastic geometry, spatial statistics and random fields were considered, with a focus on asymptotic methods.

  13. Nonlinear stochastic Markov processes and modeling uncertainty in populations.

    Science.gov (United States)

    Banks, H Thomas; Hu, Shuhua

    2012-01-01

    We consider an alternative approach to the use of nonlinear stochastic Markov processes (which have a Fokker-Planck or Forward Kolmogorov representation for density) in modeling uncertainty in populations. These alternate formulations, which involve imposing probabilistic structures on a family of deterministic dynamical systems, are shown to yield pointwise equivalent population densities. Moreover, these alternate formulations lead to fast efficient calculations in inverse problems as well as in forward simulations. Here we derive a class of stochastic formulations for which such an alternate representation is readily found.

  14. Stochastic models for competing species with a shared pathogen.

    Science.gov (United States)

    Allen, Linda J S; Bokil, Vrushali A

    2012-07-01

    The presence of a pathogen among multiple competing species has important ecological implications. For example, a pathogen may change the competitive outcome, resulting in replacement of a native species by a non-native species. Alternately, if a pathogen becomes established, there may be a drastic reduction in species numbers. Stochastic variability in the birth, death and pathogen transmission processes plays an important role in determining the success of species or pathogen invasion. We investigate these phenomena while studying the dynamics of deterministic and stochastic models for n competing species with a shared pathogen. The deterministic model is a system of ordinary differential equations for n competing species in which a single shared pathogen is transmitted among the n species. There is no immunity from infection, individuals either die or recover and become immediately susceptible, an SIS disease model. Analytical results about pathogen persistence or extinction are summarized for the deterministic model for two and three species and new results about stability of the infection-free state and invasion by one species of a system of n-1 species are obtained. New stochastic models are derived in the form of continuous-time Markov chains and stochastic differential equations. Branching process theory is applied to the continuous-time Markov chain model to estimate probabilities for pathogen extinction or species invasion. Finally, numerical simulations are conducted to explore the effect of disease on two-species competition, to illustrate some of the analytical results and to highlight some of the differences in the stochastic and deterministic models.

  15. Hierarchical stochastic model of terrain subsidence during tunnel excavation

    Science.gov (United States)

    Janda, Tomáš; Šejnoha, Jiří; Šejnoha, Michal

    2017-09-01

    In this contribution the Bayesian statistical method is applied to assess the expected probability distribution of the terrain subsidence in the course of tunnel excavation. The approach utilizes a number of simplifying assumptions regarding the system kinematics to arrive at a very simple model with just a few degrees of freedom. This deterministic model together with the intrinsic uncertainties of its parameters and measurement inaccuracies are used to formulate the stochastic model which defines a distribution of the predicted values of terrain subsidence. Assuming the measured data to be fixed, the stochastic model thus defines the likelihood function of the model parameters which is directly used for updating their prior distribution. This way the model parameters can be incrementally updated with each excavation step and the prediction of the model refined.

  16. Optimal investment models with stochastic volatility: the time ...

    African Journals Online (AJOL)

    In a recent paper by Pham [11] a multidimensional model with stochastic volatility and portfolio constraints has been proposed, solving a class of investment problems. One feature which is common with these problems is that the resultant Hamilton-Jacobi-Bellman (HJB) partial differential equation (PDE) is highly nonlinear.

  17. Lecture notes on stochastic models in systems biology

    OpenAIRE

    Swain, Peter S

    2016-01-01

    These notes provide a short, focused introduction to modelling stochastic gene expression, including a derivation of the master equation, the recovery of deterministic dynamics, birth-and-death processes, and Langevin theory. The notes were last updated around 2010 and written for lectures given at summer schools held at McGill University's Centre for Non-linear Dynamics in 2004, 2006, and 2008.

  18. Stochastic models in risk theory and management accounting

    NARCIS (Netherlands)

    Brekelmans, R.C.M.

    2000-01-01

    This thesis deals with stochastic models in two fields: risk theory and management accounting. Firstly, two extensions of the classical risk process are analyzed. A method is developed that computes bounds of the probability of ruin for the classical risk rocess extended with a constant interest

  19. Time Ordering in Frontal Lobe Patients: A Stochastic Model Approach

    Science.gov (United States)

    Magherini, Anna; Saetti, Maria Cristina; Berta, Emilia; Botti, Claudio; Faglioni, Pietro

    2005-01-01

    Frontal lobe patients reproduced a sequence of capital letters or abstract shapes. Immediate and delayed reproduction trials allowed the analysis of short- and long-term memory for time order by means of suitable Markov chain stochastic models. Patients were as proficient as healthy subjects on the immediate reproduction trial, thus showing spared…

  20. Application of stochastic frontier approach model to assess technical ...

    African Journals Online (AJOL)

    Application of stochastic frontier approach model to assess technical efficiency in Kenya's maize production. ... primary school education would enhance maize productivity. Thus, if hybrid seeds, tractor services and agricultural credit ... efficiency would increase. Key words: Socio-economic factors, farm characteristics, maize ...

  1. Application of a stochastic modelling framework to characterize the ...

    Indian Academy of Sciences (India)

    Application of a stochastic modelling framework to characterize the influence of ... Oxidation is described with a power law (parabolic) approach to quantify the rate of growth of all the three oxide scales. .... activation energy, R is the universal gas constant and T is the absolute temperature. For the case of parabolic oxidation, ...

  2. Efficient, Almost Exact Simulation of the Heston Stochastic Volatility Model

    NARCIS (Netherlands)

    van Haastrecht, A.; Pelsser, A

    2010-01-01

    We deal with discretization schemes for the simulation of the Heston stochastic volatility model. These simulation methods yield a popular and flexible pricing alternative for pricing and managing a book of exotic derivatives which cannot be valued using closed-form expressions. For the Heston

  3. Stochastic Modelling and Optimization of Complex Infrastructure Systems

    DEFF Research Database (Denmark)

    Thoft-Christensen, Palle

    In this paper it is shown that recent progress in stochastic modelling and optimization in combination with advanced computer systems has now made it possible to improve the design and the maintenance strategies for infrastructure systems. The paper concentrates on highway networks and single large...

  4. Estimating Stochastic Volatility Models using Prediction-based Estimating Functions

    DEFF Research Database (Denmark)

    Lunde, Asger; Brix, Anne Floor

    In this paper prediction-based estimating functions (PBEFs), introduced in Sørensen (2000), are reviewed and PBEFs for the Heston (1993) stochastic volatility model are derived. The finite sample performance of the PBEF based estimator is investigated in a Monte Carlo study, and compared...

  5. A note on the assumed distributions in stochastic frontier models

    NARCIS (Netherlands)

    Meesters, Aljar

    2014-01-01

    Stochastic frontier models all need an assumption on the distributional form of the (in)efficiency component. Generally this efficiency component is assumed to be half normally, truncated normally, or exponentially distributed. This paper shows that the exponential distribution is, just like the

  6. Stochastic finite-fault modelling of strong earthquakes in Narmada ...

    Indian Academy of Sciences (India)

    In the present study, the prevailing seismotectonic conditions specified by parameters associated with source, path and site conditions are appraised. Stochastic finite-fault models are formulated for each scenario earthquake. The simulated peak ground accelerations for the rock sites from the possible mean maximum ...

  7. Estimating and Forecasting Generalized Fractional Long Memory Stochastic Volatility Models

    NARCIS (Netherlands)

    S. Peiris (Shelton); M. Asai (Manabu); M.J. McAleer (Michael)

    2016-01-01

    textabstractIn recent years fractionally differenced processes have received a great deal of attention due to its flexibility in financial applications with long memory. This paper considers a class of models generated by Gegenbauer polynomials, incorporating the long memory in stochastic volatility

  8. Numerical Tools for the Bayesian Analysis of Stochastic Frontier Models

    NARCIS (Netherlands)

    Osiewalski, J.; Steel, M.F.J.

    1996-01-01

    In this paper we describe the use of modern numerical integration methods for making posterior inferences in composed error stochastic frontier models for panel data or individual cross-sections.Two Monte Carlo methods have been used in practical applications.We survey these two methods in some

  9. Optimal Tax Reduction by Depreciation : A Stochastic Model

    NARCIS (Netherlands)

    Berg, M.; De Waegenaere, A.M.B.; Wielhouwer, J.L.

    1996-01-01

    This paper focuses on the choice of a depreciation method, when trying to minimize the expected value of the present value of future tax payments.In a quite general model that allows for stochastic future cash- ows and a tax structure with tax brackets, we determine the optimal choice between the

  10. Developing a Dynamic Stochastic General Equilibrium Model for the ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    The Dynamic Stochastic General Equilibrium (DSGE) modelling framework is an approach that combines a rational and dynamic view of economic agents. The DSGE framework proposed for this ... The framework provides a coherent structure to analyze economic fluctuations. In recent years, research has shown that ...

  11. A stochastic large deformation model for computational anatomy

    DEFF Research Database (Denmark)

    Arnaudon, Alexis; Holm, Darryl D.; Pai, Akshay Sadananda Uppinakudru

    2017-01-01

    In the study of shapes of human organs using computational anatomy, variations are found to arise from inter-subject anatomical differences, disease-specific effects, and measurement noise. This paper introduces a stochastic model for incorporating random variations into the Large Deformation...

  12. Stochastic volatility and stochastic leverage

    DEFF Research Database (Denmark)

    Veraart, Almut; Veraart, Luitgard A. M.

    This paper proposes the new concept of stochastic leverage in stochastic volatility models. Stochastic leverage refers to a stochastic process which replaces the classical constant correlation parameter between the asset return and the stochastic volatility process. We provide a systematic...... treatment of stochastic leverage and propose to model the stochastic leverage effect explicitly, e.g. by means of a linear transformation of a Jacobi process. Such models are both analytically tractable and allow for a direct economic interpretation. In particular, we propose two new stochastic volatility...... models which allow for a stochastic leverage effect: the generalised Heston model and the generalised Barndorff-Nielsen & Shephard model. We investigate the impact of a stochastic leverage effect in the risk neutral world by focusing on implied volatilities generated by option prices derived from our new...

  13. Epigenetics and Evolution: Transposons and the Stochastic Epigenetic Modification Model

    OpenAIRE

    Sergio Branciamore; Andrei S. Rodin; Grigoriy Gogoshin; Arthur D. Riggs

    2015-01-01

    In addition to genetic variation, epigenetic variation and transposons can greatly affect the evolutionary fitnesses landscape and gene expression. Previously we proposed a mathematical treatment of a general epigenetic variation model that we called Stochastic Epigenetic Modification (SEM) model. In this study we follow up with a special case, the Transposon Silencing Model (TSM), with, once again, emphasis on quantitative treatment. We have investigated the evolutionary effects of epigeneti...

  14. Use of a linearization approximation facilitating stochastic model building

    OpenAIRE

    Svensson, Elin M.; Karlsson, Mats O.

    2014-01-01

    The objective of this work was to facilitate the development of nonlinear mixed effects models by establishing a diagnostic method for evaluation of stochastic model components. The random effects investigated were between subject, between occasion and residual variability. The method was based on a first-order conditional estimates linear approximation and evaluated on three real datasets with previously developed population pharmacokinetic models. The results were assessed based on the agre...

  15. Population stochastic modelling (PSM)--an R package for mixed-effects models based on stochastic differential equations.

    Science.gov (United States)

    Klim, Søren; Mortensen, Stig Bousgaard; Kristensen, Niels Rode; Overgaard, Rune Viig; Madsen, Henrik

    2009-06-01

    The extension from ordinary to stochastic differential equations (SDEs) in pharmacokinetic and pharmacodynamic (PK/PD) modelling is an emerging field and has been motivated in a number of articles [N.R. Kristensen, H. Madsen, S.H. Ingwersen, Using stochastic differential equations for PK/PD model development, J. Pharmacokinet. Pharmacodyn. 32 (February(1)) (2005) 109-141; C.W. Tornøe, R.V. Overgaard, H. Agersø, H.A. Nielsen, H. Madsen, E.N. Jonsson, Stochastic differential equations in NONMEM: implementation, application, and comparison with ordinary differential equations, Pharm. Res. 22 (August(8)) (2005) 1247-1258; R.V. Overgaard, N. Jonsson, C.W. Tornøe, H. Madsen, Non-linear mixed-effects models with stochastic differential equations: implementation of an estimation algorithm, J. Pharmacokinet. Pharmacodyn. 32 (February(1)) (2005) 85-107; U. Picchini, S. Ditlevsen, A. De Gaetano, Maximum likelihood estimation of a time-inhomogeneous stochastic differential model of glucose dynamics, Math. Med. Biol. 25 (June(2)) (2008) 141-155]. PK/PD models are traditionally based ordinary differential equations (ODEs) with an observation link that incorporates noise. This state-space formulation only allows for observation noise and not for system noise. Extending to SDEs allows for a Wiener noise component in the system equations. This additional noise component enables handling of autocorrelated residuals originating from natural variation or systematic model error. Autocorrelated residuals are often partly ignored in PK/PD modelling although violating the hypothesis for many standard statistical tests. This article presents a package for the statistical program R that is able to handle SDEs in a mixed-effects setting. The estimation method implemented is the FOCE(1) approximation to the population likelihood which is generated from the individual likelihoods that are approximated using the Extended Kalman Filter's one-step predictions.

  16. Mixed Poisson distributions in exact solutions of stochastic autoregulation models.

    Science.gov (United States)

    Iyer-Biswas, Srividya; Jayaprakash, C

    2014-11-01

    In this paper we study the interplay between stochastic gene expression and system design using simple stochastic models of autoactivation and autoinhibition. Using the Poisson representation, a technique whose particular usefulness in the context of nonlinear gene regulation models we elucidate, we find exact results for these feedback models in the steady state. Further, we exploit this representation to analyze the parameter spaces of each model, determine which dimensionless combinations of rates are the shape determinants for each distribution, and thus demarcate where in the parameter space qualitatively different behaviors arise. These behaviors include power-law-tailed distributions, bimodal distributions, and sub-Poisson distributions. We also show how these distribution shapes change when the strength of the feedback is tuned. Using our results, we reexamine how well the autoinhibition and autoactivation models serve their conventionally assumed roles as paradigms for noise suppression and noise exploitation, respectively.

  17. Modeling atmospheric deposition using a stochastic transport model

    Energy Technology Data Exchange (ETDEWEB)

    Buckley, R.L.

    1999-12-17

    An advanced stochastic transport model has been modified to include the removal mechanisms of dry and wet deposition. Time-dependent wind and turbulence fields are generated with a prognostic mesoscale numerical model and are used to advect and disperse individually released particles that are each assigned a mass. These particles are subjected to mass reduction in two ways depending on their physical location. Particles near the surface experience a decrease in mass using the concept of a dry deposition velocity, while the mass of particles located within areas of precipitation are depleted using a scavenging coefficient. Two levels of complexity are incorporated into the particle model. The simple case assumes constant values of dry deposition velocity and scavenging coefficient, while the more complex case varies the values according to meteorology, surface conditions, release material, and precipitation intensity. Instantaneous and cumulative dry and wet deposition are determined from the mass loss due to these physical mechanisms. A useful means of validating the model results is with data available from a recent accidental release of Cesium-137 from a steel-processing furnace in Algeciras, Spain in May, 1998. This paper describes the deposition modeling technique, as well as a comparison of simulated concentration and deposition with measurements taken for the Algeciras release.

  18. Application of Stochastic Partial Differential Equations to Reservoir Property Modelling

    KAUST Repository

    Potsepaev, R.

    2010-09-06

    Existing algorithms of geostatistics for stochastic modelling of reservoir parameters require a mapping (the \\'uvt-transform\\') into the parametric space and reconstruction of a stratigraphic co-ordinate system. The parametric space can be considered to represent a pre-deformed and pre-faulted depositional environment. Existing approximations of this mapping in many cases cause significant distortions to the correlation distances. In this work we propose a coordinate free approach for modelling stochastic textures through the application of stochastic partial differential equations. By avoiding the construction of a uvt-transform and stratigraphic coordinates, one can generate realizations directly in the physical space in the presence of deformations and faults. In particular the solution of the modified Helmholtz equation driven by Gaussian white noise is a zero mean Gaussian stationary random field with exponential correlation function (in 3-D). This equation can be used to generate realizations in parametric space. In order to sample in physical space we introduce a stochastic elliptic PDE with tensor coefficients, where the tensor is related to correlation anisotropy and its variation is physical space.

  19. Beyond multifractional Brownian motion: new stochastic models for geophysical modelling

    Directory of Open Access Journals (Sweden)

    J. Lévy Véhel

    2013-09-01

    Full Text Available Multifractional Brownian motion (mBm has proved to be a useful tool in various areas of geophysical modelling. Although a versatile model, mBm is of course not always an adequate one. We present in this work several other stochastic processes which could potentially be useful in geophysics. The first alternative type is that of self-regulating processes: these are models where the local regularity is a function of the amplitude, in contrast to mBm where it is tuned exogenously. We demonstrate the relevance of such models for digital elevation maps and for temperature records. We also briefly describe two other types of alternative processes, which are the counterparts of mBm and of self-regulating processes when the intensity of local jumps is considered in lieu of local regularity: multistable processes allow one to prescribe the local intensity of jumps in space/time, while this intensity is governed by the amplitude for self-stabilizing processes.

  20. Beyond multifractional Brownian motion: new stochastic models for geophysical modelling

    Science.gov (United States)

    Lévy Véhel, J.

    2013-09-01

    Multifractional Brownian motion (mBm) has proved to be a useful tool in various areas of geophysical modelling. Although a versatile model, mBm is of course not always an adequate one. We present in this work several other stochastic processes which could potentially be useful in geophysics. The first alternative type is that of self-regulating processes: these are models where the local regularity is a function of the amplitude, in contrast to mBm where it is tuned exogenously. We demonstrate the relevance of such models for digital elevation maps and for temperature records. We also briefly describe two other types of alternative processes, which are the counterparts of mBm and of self-regulating processes when the intensity of local jumps is considered in lieu of local regularity: multistable processes allow one to prescribe the local intensity of jumps in space/time, while this intensity is governed by the amplitude for self-stabilizing processes.

  1. Modeling bacterial population growth from stochastic single-cell dynamics.

    Science.gov (United States)

    Alonso, Antonio A; Molina, Ignacio; Theodoropoulos, Constantinos

    2014-09-01

    A few bacterial cells may be sufficient to produce a food-borne illness outbreak, provided that they are capable of adapting and proliferating on a food matrix. This is why any quantitative health risk assessment policy must incorporate methods to accurately predict the growth of bacterial populations from a small number of pathogens. In this aim, mathematical models have become a powerful tool. Unfortunately, at low cell concentrations, standard deterministic models fail to predict the fate of the population, essentially because the heterogeneity between individuals becomes relevant. In this work, a stochastic differential equation (SDE) model is proposed to describe variability within single-cell growth and division and to simulate population growth from a given initial number of individuals. We provide evidence of the model ability to explain the observed distributions of times to division, including the lag time produced by the adaptation to the environment, by comparing model predictions with experiments from the literature for Escherichia coli, Listeria innocua, and Salmonella enterica. The model is shown to accurately predict experimental growth population dynamics for both small and large microbial populations. The use of stochastic models for the estimation of parameters to successfully fit experimental data is a particularly challenging problem. For instance, if Monte Carlo methods are employed to model the required distributions of times to division, the parameter estimation problem can become numerically intractable. We overcame this limitation by converting the stochastic description to a partial differential equation (backward Kolmogorov) instead, which relates to the distribution of division times. Contrary to previous stochastic formulations based on random parameters, the present model is capable of explaining the variability observed in populations that result from the growth of a small number of initial cells as well as the lack of it compared to

  2. A stochastic model of neurogenesis controlled by a single factor.

    Science.gov (United States)

    Barton, A; Fendrik, A J; Rotondo, E

    2014-08-21

    The researches on cortical neurogenesis reveal that asymmetric division plays a key role in controlling the balance between the self-renewal of stem cells and the beginning of the neural differentiation. In such a process a neural stem cell divides by mitosis, originating a postmitotic neuron and other pluripotent stem cell available for subsequent differentiation events. In addition, studies of cell lineage trees of cultured neural progenitors reveal tree shapes and subtrees recurrent, consistent with a stochastic model of division symmetrical/asymmetrical. These considerations have led us to develop a stochastic model of neurogenesis in order to explore the possibility that this is controlled primarily by a single factor (i.e. the concentration of mNumb in the cell). We contrast the predictions of our model with experimental data and compare it with other models of neurogenesis. Copyright © 2014 Elsevier Ltd. All rights reserved.

  3. Predicting population extinction or disease outbreaks with stochastic models

    Directory of Open Access Journals (Sweden)

    Linda J. S. Allen

    2017-01-01

    Full Text Available Models of exponential growth, logistic growth and epidemics are common applications in undergraduate differential equation courses. The corresponding stochastic models are not part of these courses, although when population sizes are small their behaviour is often more realistic and distinctly different from deterministic models. For example, the randomness associated with births and deaths may lead to population extinction even in an exponentially growing population. Some background in continuous-time Markov chains and applications to populations, epidemics and cancer are presented with a goal to introduce this topic into the undergraduate mathematics curriculum that will encourage further investigation into problems on conservation, infectious diseases and cancer therapy. MATLAB programs for graphing sample paths of stochastic models are provided in the Appendix.

  4. Quantitative sociodynamics stochastic methods and models of social interaction processes

    CERN Document Server

    Helbing, Dirk

    1995-01-01

    Quantitative Sociodynamics presents a general strategy for interdisciplinary model building and its application to a quantitative description of behavioural changes based on social interaction processes. Originally, the crucial methods for the modeling of complex systems (stochastic methods and nonlinear dynamics) were developed in physics but they have very often proved their explanatory power in chemistry, biology, economics and the social sciences. Quantitative Sociodynamics provides a unified and comprehensive overview of the different stochastic methods, their interrelations and properties. In addition, it introduces the most important concepts from nonlinear dynamics (synergetics, chaos theory). The applicability of these fascinating concepts to social phenomena is carefully discussed. By incorporating decision-theoretical approaches a very fundamental dynamic model is obtained which seems to open new perspectives in the social sciences. It includes many established models as special cases, e.g. the log...

  5. Dynamic two state stochastic models for ecological regime shifts

    DEFF Research Database (Denmark)

    Møller, Jan Kloppenborg; Carstensen, Niels Jacob; Madsen, Henrik

    2009-01-01

    A simple non-linear stochastic two state, discrete-time model is presented. The interaction between benthic and pelagic vegetation in aquatic ecosystems subject to changing external nutrient loading is described by the nonlinear functions. The dynamical behavior of the deterministic part...... of the model illustrates that hysteresis effect and regime shifts can be obtained for a limited range of parameter values only. The effect of multiplicative noise components entering at different levels of the model is presented and discussed. Including noise leads to very different results on the stability...... of regimes, depending on how the noise propagates through the system. The dynamical properties of a system should therefore be described through propagation of the state distributions rather than the state means and consequently, stochastic models should be compared in a probabilistic framework....

  6. Nonlinear Stochastic Modelling of Antimicrobial resistance in Bacterial Populations

    DEFF Research Database (Denmark)

    Philipsen, Kirsten Riber

    This thesis applies mathematical modelling and statistical methods to investigate the dynamics and mechanisms of bacterial evolution. More specifically it is concerned with the evolution of antibiotic resistance in bacteria populations, which is an increasing problem for the treatment of infections...... in humans and animals. To prevent the evolution and spread of resistance, there is a need for further understanding of its dynamics. A grey-box modelling approach based on stochastic differential equations is the main and innovative method applied to study bacterial systems in this thesis. Through...... for bacterial growth in an environment with multiple substrates. Models based on stochastic differential equations are also used in studies of mutation and conjugation. Mutation and conjugation are important mechanisms for the development of resistance. Earlier models for conjugation have described systems...

  7. Stochastic Dynamics and Critical Phenomena in Permafrost Models

    Science.gov (United States)

    Sudakov, I.

    2016-12-01

    There is an estimated 400 PgC of CH4 stored as frozen gas hydrates under boreal permafrost, and it is thought that permafrost melting could release a considerable amount of CH4 to the atmosphere. Methane emissions from tundra permafrost lakes are a significant positive feedback to the atmosphere in a changing climate. The evolution of tundra lakes on the surface of boreal permafrost is a complex stochastic process that is important in climate modeling. We propose a model (based on the Fokker-Planck equation) describing the stochastic dynamics of tundra lakes. We use this model to compute the methane emission generated by tundra permafrost lakes. This model facilitates investigation of critical phenomena in Earth's cryosphere, and methane emission from permafrost in particular.

  8. Quantitative Sociodynamics Stochastic Methods and Models of Social Interaction Processes

    CERN Document Server

    Helbing, Dirk

    2010-01-01

    This new edition of Quantitative Sociodynamics presents a general strategy for interdisciplinary model building and its application to a quantitative description of behavioral changes based on social interaction processes. Originally, the crucial methods for the modeling of complex systems (stochastic methods and nonlinear dynamics) were developed in physics and mathematics, but they have very often proven their explanatory power in chemistry, biology, economics and the social sciences as well. Quantitative Sociodynamics provides a unified and comprehensive overview of the different stochastic methods, their interrelations and properties. In addition, it introduces important concepts from nonlinear dynamics (e.g. synergetics, chaos theory). The applicability of these fascinating concepts to social phenomena is carefully discussed. By incorporating decision-theoretical approaches, a fundamental dynamic model is obtained, which opens new perspectives in the social sciences. It includes many established models a...

  9. Stochastic Differential Equation-Based Flexible Software Reliability Growth Model

    Directory of Open Access Journals (Sweden)

    P. K. Kapur

    2009-01-01

    Full Text Available Several software reliability growth models (SRGMs have been developed by software developers in tracking and measuring the growth of reliability. As the size of software system is large and the number of faults detected during the testing phase becomes large, so the change of the number of faults that are detected and removed through each debugging becomes sufficiently small compared with the initial fault content at the beginning of the testing phase. In such a situation, we can model the software fault detection process as a stochastic process with continuous state space. In this paper, we propose a new software reliability growth model based on Itô type of stochastic differential equation. We consider an SDE-based generalized Erlang model with logistic error detection function. The model is estimated and validated on real-life data sets cited in literature to show its flexibility. The proposed model integrated with the concept of stochastic differential equation performs comparatively better than the existing NHPP-based models.

  10. Dynamical behavior of a stochastic SVIR epidemic model with vaccination

    Science.gov (United States)

    Zhang, Xinhong; Jiang, Daqing; Hayat, Tasawar; Ahmad, Bashir

    2017-10-01

    In this paper, we investigate the dynamical behavior of SVIR models in random environments. Firstly, we show that if R0s 1, the disease will be prevail. Moreover, this system admits a unique stationary distribution and it is ergodic when R˜0s > 1. Results show that environmental white noise is helpful for disease control. Secondly, we give sufficient conditions for the existence of nontrivial periodic solutions to stochastic SVIR model with periodic parameters. Finally, numerical simulations validate the analytical results.

  11. Stochastic Local Interaction (SLI) Model: Interfacing Machine Learning and Geostatistics

    OpenAIRE

    Hristopulos, Dionissios T.

    2015-01-01

    Machine learning and geostatistics are powerful mathematical frameworks for modeling spatial data. Both approaches, however, suffer from poor scaling of the required computational resources for large data applications. We present the Stochastic Local Interaction (SLI) model, which employs a local representation to improve computational efficiency. SLI combines geostatistics and machine learning with ideas from statistical physics and computational geometry. It is based on a joint probability ...

  12. Stochastic Models Predict User Behavior in Social Media

    OpenAIRE

    Hogg, Tad; Lerman, Kristina; Smith, Laura M.

    2013-01-01

    User response to contributed content in online social media depends on many factors. These include how the site lays out new content, how frequently the user visits the site, how many friends the user follows, how active these friends are, as well as how interesting or useful the content is to the user. We present a stochastic modeling framework that relates a user's behavior to details of the site's user interface and user activity and describe a procedure for estimating model parameters fro...

  13. The Stochastic Ising Model with the Mixed Boundary Conditions

    Directory of Open Access Journals (Sweden)

    Wang Jun

    2009-01-01

    Full Text Available Abstract We estimate the spectral gap of the two-dimensional stochastic Ising model for four classes of mixed boundary conditions. On a finite square, in the absence of an external field, two-sided estimates on the spectral gap for the first class of (weak positive boundary conditions are given. Further, at inverse temperatures , we will show lower bounds of the spectral gap of the Ising model for the other three classes mixed boundary conditions.

  14. Stochastic Online Learning in Dynamic Networks under Unknown Models

    Science.gov (United States)

    2016-08-02

    Stochastic Online Learning in Dynamic Networks under Unknown Models This research aims to develop fundamental theories and practical algorithms for...12211 Research Triangle Park, NC 27709-2211 Online learning , multi-armed bandit, dynamic networks REPORT DOCUMENTATION PAGE 11. SPONSOR/MONITOR’S... Online Learning in Dynamic Networks under Unknown Models Report Title This research aims to develop fundamental theories and practical algorithms for

  15. Approximate Model Checking of Stochastic COWS

    NARCIS (Netherlands)

    Quaglia, Paola; Schivo, Stefano

    2010-01-01

    Given the description of a model and a probabilistic formula, approximate model checking is a verification technique based on statistical reasoning that allows answering whether or not the model satisfies the formula. Only a subset of the properties that can be analyzed by exact model checking can

  16. Stochastic physical ecohydrologic-based model for estimating irrigation requirement

    Science.gov (United States)

    Alizadeh, H.; Mousavi, S. J.

    2012-04-01

    Climate uncertainty affects both natural and managed hydrological systems. Therefore, methods which could take this kind of uncertainty into account are of primal importance for management of ecosystems, especially agricultural ecosystems. One of the famous problems in these ecosystems is crop water requirement estimation under climatic uncertainty. Both deterministic physically-based methods and stochastic time series modeling have been utilized in the literature. Like other fields of hydroclimatic sciences, there is a vast area in irrigation process modeling for developing approaches integrating physics of the process and statistics aspects. This study is about deriving closed-form expressions for probability density function (p.d.f.) of irrigation water requirement using a stochastic physically-based model, which considers important aspects of plant, soil, atmosphere and irrigation technique and policy in a coherent framework. An ecohydrologic stochastic model, building upon the stochastic differential equation of soil moisture dynamics at root zone, is employed as a basis for deriving the expressions considering temporal stochasticity of rainfall. Due to distinguished nature of stochastic processes of micro and traditional irrigation applications, two different methodologies have been used. Micro-irrigation application has been modeled through dichotomic process. Chapman-Kolomogrov equation of time integral of the dichotomic process for transient condition has been solved to derive analytical expressions for probability density function of seasonal irrigation requirement. For traditional irrigation, irrigation application during growing season has been modeled using a marked point process. Using the renewal theory, probability mass function of seasonal irrigation requirement, which is a discrete-value quantity, has been analytically derived. The methodology deals with estimation of statistical properties of the total water requirement in a growing season that

  17. Performance of stochastic Runge-Kutta Methods in approximating the solution of stochastic model in biological system

    Science.gov (United States)

    Amalina Nisa Ariffin, Noor; Rosli, Norhayati; Syahidatul Ayuni Mazlan, Mazma; Samsudin, Adam

    2017-09-01

    Recently, modelling the biological systems by using stochastic differential equations (SDEs) are becoming an interest among researchers. In SDEs the random fluctuations are taking into account, which resulting to the complexity of finding the exact solution of SDEs and contribute to the increasing number of research focusing in finding the best numerical approach to solve the systems of SDEs. This paper will examine the performance of 4-stage stochastic Runge-Kutta (SRK4) and specific stochastic Runge-Kutta (SRKS) methods with order 1.5 in approximating the solution of stochastic model in biological system. A comparative study of SRK4 and SRKS method will be presented in this paper. The non-linear biological model will be used to examine the performance of both methods and the result of numerical experiment will be discussed.

  18. A Jump-Diffusion Model with Stochastic Volatility and Durations

    DEFF Research Database (Denmark)

    Wei, Wei; Pelletier, Denis

    Market microstructure theories suggest that the durations between transactions carry information about volatility. This paper puts forward a model featuring stochastic volatility, stochastic conditional duration, and jumps to analyze high frequency returns and durations. Durations affect price...... jumps in two ways: as exogenous sampling intervals, and through the interaction with volatility. We adopt a bivariate Ornstein-Ulenbeck process to model intraday volatility and conditional duration. We develop a MCMC algorithm for the inference on irregularly spaced multivariate processes with jumps....... The algorithm provides smoothed estimates of the latent variables such as spot volatility, conditional duration, jump times, and jump sizes. We apply this model to IBM data and find that volatility and conditional duration are interdependent. We also find that jumps play an important role in return variation...

  19. Dynamics of a stochastic tuberculosis model with constant recruitment and varying total population size

    Science.gov (United States)

    Liu, Qun; Jiang, Daqing; Shi, Ningzhong; Hayat, Tasawar; Alsaedi, Ahmed

    2017-03-01

    In this paper, we develop a mathematical model for a tuberculosis model with constant recruitment and varying total population size by incorporating stochastic perturbations. By constructing suitable stochastic Lyapunov functions, we establish sufficient conditions for the existence of an ergodic stationary distribution as well as extinction of the disease to the stochastic system.

  20. Modelling of stochastic hybrid systems with applications to accident risk assessment

    OpenAIRE

    Krystul, J.

    2006-01-01

    Stochastic dynamical modelling of accident risk is of high interest for the safe design of complex safety-critical systems and operations, such as in nuclear and chemical industries, and advanced air traffic management. In comparison with statistical analysis of collected data, stochastic dynamical modelling approach has the advantage of enabling the use of stochastic analysis and advanced Monte Carlo simulation approaches.

  1. Stochastic population dynamic models as probability networks

    Science.gov (United States)

    M.E. and D.C. Lee. Borsuk

    2009-01-01

    The dynamics of a population and its response to environmental change depend on the balance of birth, death and age-at-maturity, and there have been many attempts to mathematically model populations based on these characteristics. Historically, most of these models were deterministic, meaning that the results were strictly determined by the equations of the model and...

  2. Radio Channel Modelling Using Stochastic Propagation Graphs

    DEFF Research Database (Denmark)

    Pedersen, Troels; Fleury, Bernard Henri

    2007-01-01

    In this contribution the radio channel model proposed in [1] is extended to include multiple transmitters and receivers. The propagation environment is modelled using random graphs where vertices of a graph represent scatterers and edges model the wave propagation between scatterers. Furthermore...

  3. Spatial stochastic regression modelling of urban land use

    Science.gov (United States)

    Arshad, S. H. M.; Jaafar, J.; Abiden, M. Z. Z.; Latif, Z. A.; Rasam, A. R. A.

    2014-02-01

    Urbanization is very closely linked to industrialization, commercialization or overall economic growth and development. This results in innumerable benefits of the quantity and quality of the urban environment and lifestyle but on the other hand contributes to unbounded development, urban sprawl, overcrowding and decreasing standard of living. Regulation and observation of urban development activities is crucial. The understanding of urban systems that promotes urban growth are also essential for the purpose of policy making, formulating development strategies as well as development plan preparation. This study aims to compare two different stochastic regression modeling techniques for spatial structure models of urban growth in the same specific study area. Both techniques will utilize the same datasets and their results will be analyzed. The work starts by producing an urban growth model by using stochastic regression modeling techniques namely the Ordinary Least Square (OLS) and Geographically Weighted Regression (GWR). The two techniques are compared to and it is found that, GWR seems to be a more significant stochastic regression model compared to OLS, it gives a smaller AICc (Akaike's Information Corrected Criterion) value and its output is more spatially explainable.

  4. A stochastic transcriptional switch model for single cell imaging data.

    Science.gov (United States)

    Hey, Kirsty L; Momiji, Hiroshi; Featherstone, Karen; Davis, Julian R E; White, Michael R H; Rand, David A; Finkenstädt, Bärbel

    2015-10-01

    Gene expression is made up of inherently stochastic processes within single cells and can be modeled through stochastic reaction networks (SRNs). In particular, SRNs capture the features of intrinsic variability arising from intracellular biochemical processes. We extend current models for gene expression to allow the transcriptional process within an SRN to follow a random step or switch function which may be estimated using reversible jump Markov chain Monte Carlo (MCMC). This stochastic switch model provides a generic framework to capture many different dynamic features observed in single cell gene expression. Inference for such SRNs is challenging due to the intractability of the transition densities. We derive a model-specific birth-death approximation and study its use for inference in comparison with the linear noise approximation where both approximations are considered within the unifying framework of state-space models. The methodology is applied to synthetic as well as experimental single cell imaging data measuring expression of the human prolactin gene in pituitary cells. © The Author 2015. Published by Oxford University Press.

  5. Stochastic modeling of central apnea events in preterm infants.

    Science.gov (United States)

    Clark, Matthew T; Delos, John B; Lake, Douglas E; Lee, Hoshik; Fairchild, Karen D; Kattwinkel, John; Moorman, J Randall

    2016-04-01

    A near-ubiquitous pathology in very low birth weight infants is neonatal apnea, breathing pauses with slowing of the heart and falling blood oxygen. Events of substantial duration occasionally occur after an infant is discharged from the neonatal intensive care unit (NICU). It is not known whether apneas result from a predictable process or from a stochastic process, but the observation that they occur in seemingly random clusters justifies the use of stochastic models. We use a hidden-Markov model to analyze the distribution of durations of apneas and the distribution of times between apneas. The model suggests the presence of four breathing states, ranging from very stable (with an average lifetime of 12 h) to very unstable (with an average lifetime of 10 s). Although the states themselves are not visible, the mathematical analysis gives estimates of the transition rates among these states. We have obtained these transition rates, and shown how they change with post-menstrual age; as expected, the residence time in the more stable breathing states increases with age. We also extrapolated the model to predict the frequency of very prolonged apnea during the first year of life. This paradigm-stochastic modeling of cardiorespiratory control in neonatal infants to estimate risk for severe clinical events-may be a first step toward personalized risk assessment for life threatening apnea events after NICU discharge.

  6. Stochastic model updating utilizing Bayesian approach and Gaussian process model

    Science.gov (United States)

    Wan, Hua-Ping; Ren, Wei-Xin

    2016-03-01

    Stochastic model updating (SMU) has been increasingly applied in quantifying structural parameter uncertainty from responses variability. SMU for parameter uncertainty quantification refers to the problem of inverse uncertainty quantification (IUQ), which is a nontrivial task. Inverse problem solved with optimization usually brings about the issues of gradient computation, ill-conditionedness, and non-uniqueness. Moreover, the uncertainty present in response makes the inverse problem more complicated. In this study, Bayesian approach is adopted in SMU for parameter uncertainty quantification. The prominent strength of Bayesian approach for IUQ problem is that it solves IUQ problem in a straightforward manner, which enables it to avoid the previous issues. However, when applied to engineering structures that are modeled with a high-resolution finite element model (FEM), Bayesian approach is still computationally expensive since the commonly used Markov chain Monte Carlo (MCMC) method for Bayesian inference requires a large number of model runs to guarantee the convergence. Herein we reduce computational cost in two aspects. On the one hand, the fast-running Gaussian process model (GPM) is utilized to approximate the time-consuming high-resolution FEM. On the other hand, the advanced MCMC method using delayed rejection adaptive Metropolis (DRAM) algorithm that incorporates local adaptive strategy with global adaptive strategy is employed for Bayesian inference. In addition, we propose the use of the powerful variance-based global sensitivity analysis (GSA) in parameter selection to exclude non-influential parameters from calibration parameters, which yields a reduced-order model and thus further alleviates the computational burden. A simulated aluminum plate and a real-world complex cable-stayed pedestrian bridge are presented to illustrate the proposed framework and verify its feasibility.

  7. Performance modeling, stochastic networks, and statistical multiplexing

    CERN Document Server

    Mazumdar, Ravi R

    2013-01-01

    This monograph presents a concise mathematical approach for modeling and analyzing the performance of communication networks with the aim of introducing an appropriate mathematical framework for modeling and analysis as well as understanding the phenomenon of statistical multiplexing. The models, techniques, and results presented form the core of traffic engineering methods used to design, control and allocate resources in communication networks.The novelty of the monograph is the fresh approach and insights provided by a sample-path methodology for queueing models that highlights the importan

  8. Introduction to stochastic models in biology

    DEFF Research Database (Denmark)

    Ditlevsen, Susanne; Samson, Adeline

    2013-01-01

    This chapter is concerned with continuous time processes, which are often modeled as a system of ordinary differential equations (ODEs). These models assume that the observed dynamics are driven exclusively by internal, deterministic mechanisms. However, real biological systems will always be exp...

  9. Stochastic population and epidemic models persistence and extinction

    CERN Document Server

    Allen, Linda J S

    2015-01-01

    This monograph provides a summary of the basic theory of branching processes for single-type and multi-type processes. Classic examples of population and epidemic models illustrate the probability of population or epidemic extinction obtained from the theory of branching processes. The first chapter develops the branching process theory, while in the second chapter two applications to population and epidemic processes of single-type branching process theory are explored. The last two chapters present multi-type branching process applications to epidemic models, and then continuous-time and continuous-state branching processes with applications. In addition, several MATLAB programs for simulating stochastic sample paths  are provided in an Appendix. These notes originated as part of a lecture series on Stochastics in Biological Systems at the Mathematical Biosciences Institute in Ohio, USA. Professor Linda Allen is a Paul Whitfield Horn Professor of Mathematics in the Department of Mathematics and Statistics ...

  10. A field test of a simple stochastic radiative transfer model

    Energy Technology Data Exchange (ETDEWEB)

    Byrne, N. [Science Applications International Corp., San Diego, CA (United States)

    1995-09-01

    The problem of determining the effect of clouds on the radiative energy balance of the globe is of well-recognized importance. One can in principle solve the problem for any given configuration of clouds using numerical techniques. This knowledge is not useful however, because of the amount of input data and computer resources required. Besides, we need only the average of the resulting solution over the grid scale of a general circulation model (GCM). Therefore, we are interested in estimating the average of the solutions of such fine-grained problems using only coarse grained data, a science or art called stochastic radiation transfer. Results of the described field test indicate that the stochastic description is a somewhat better fit to the data than is a fractional cloud cover model, but more data are needed. 1 ref., 3 figs.

  11. Modeling and stochastic analysis of dynamic mechanisms of the perception

    Science.gov (United States)

    Pisarchik, A.; Bashkirtseva, I.; Ryashko, L.

    2017-10-01

    Modern studies in physiology and cognitive neuroscience consider a noise as an important constructive factor of the brain functionality. Under the adequate noise, the brain can rapidly access different ordered states, and provide decision-making by preventing deadlocks. Bistable dynamic models are often used for the study of the underlying mechanisms of the visual perception. In the present paper, we consider a bistable energy model subject to both additive and parametric noise. Using the catastrophe theory formalism and stochastic sensitivity functions technique, we analyze a response of the equilibria to noise, and study noise-induced transitions between equilibria. We demonstrate and analyse the effect of hysteresis squeezing when the intensity of noise is increased. Stochastic bifurcations connected with the suppression of oscillations by parametric noises are discussed.

  12. Stochastic species abundance models involving special copulas

    Science.gov (United States)

    Huillet, Thierry E.

    2018-01-01

    Copulas offer a very general tool to describe the dependence structure of random variables supported by the hypercube. Inspired by problems of species abundances in Biology, we study three distinct toy models where copulas play a key role. In a first one, a Marshall-Olkin copula arises in a species extinction model with catastrophe. In a second one, a quasi-copula problem arises in a flagged species abundance model. In a third model, we study completely random species abundance models in the hypercube as those, not of product type, with uniform margins and singular. These can be understood from a singular copula supported by an inflated simplex. An exchangeable singular Dirichlet copula is also introduced, together with its induced completely random species abundance vector.

  13. An extension of clarke's model with stochastic amplitude flip processes

    KAUST Repository

    Hoel, Hakon

    2014-07-01

    Stochastic modeling is an essential tool for studying statistical properties of wireless channels. In multipath fading channel (MFC) models, the signal reception is modeled by a sum of wave path contributions, and Clarke\\'s model is an important example of such which has been widely accepted in many wireless applications. However, since Clarke\\'s model is temporally deterministic, Feng and Field noted that it does not model real wireless channels with time-varying randomness well. Here, we extend Clarke\\'s model to a novel time-varying stochastic MFC model with scatterers randomly flipping on and off. Statistical properties of the MFC model are analyzed and shown to fit well with real signal measurements, and a limit Gaussian process is derived from the model when the number of active wave paths tends to infinity. A second focus of this work is a comparison study of the error and computational cost of generating signal realizations from the MFC model and from its limit Gaussian process. By rigorous analysis and numerical studies, we show that in many settings, signal realizations are generated more efficiently by Gaussian process algorithms than by the MFC model\\'s algorithm. Numerical examples that strengthen these observations are also presented. © 2014 IEEE.

  14. A stochastic modeling of isotope exchange reactions in glutamine synthetase

    Science.gov (United States)

    Kazmiruk, N. V.; Boronovskiy, S. E.; Nartsissov, Ya R.

    2017-11-01

    The model presented in this work allows simulation of isotopic exchange reactions at chemical equilibrium catalyzed by a glutamine synthetase. To simulate the functioning of the enzyme the algorithm based on the stochastic approach was applied. The dependence of exchange rates for 14C and 32P on metabolite concentration was estimated. The simulation results confirmed the hypothesis of the ascertained validity for preferred order random binding mechanism. Corresponding values of K0.5 were also obtained.

  15. Stochastic Modeling and Analysis of Energy Commodity Spot Price Processes

    Science.gov (United States)

    2014-06-27

    have been developed in economics. Elloit et al [37] developed a model for pricing variance swaps and volatility swaps under a continuous-time Markov...Wissenschaften, Bände 121, 122. Academic Press, New York. Springer, Berlin [37] Elloitt, R., Siu, T., chan, L. , (2007) Pricing volatility swaps under Heston’s...nomics, University of Chicago. [48] Heston S. 1993. A closed form solution for options with stochastic volatility with applications to Bond and Currency

  16. stochastic modeling and analysis of 3g mobile communication systems

    OpenAIRE

    Thümmler, Axel

    2003-01-01

    Third-generation (3G) mobile communication systems are currently one of the key communication technologies in research and development due to the high market demand for advanced wireless communication. The current evolution is primarily characterized by a transition from circuit-switched voice-oriented networks to integrated multi-service all IP networks. To effectively design complex mobile communication systems, the design process should be accompanied by stochastic modeling and quantitativ...

  17. Constructing stochastic models for dipole fluctuations from paleomagnetic observations

    OpenAIRE

    Buffett, B; Puranam, A

    2017-01-01

    © 2017 Elsevier B.V. Records of relative paleointensity are subject to several sources of error. Temporal averaging due to gradual acquisition of magnetization removes high-frequency fluctuations, whereas random errors introduce fluctuations at high frequency. Both sources of error limit our ability to construct stochastic models from paleomagnetic observations. We partially circumvent these difficulties by recognizing that the largest affects occur at high frequency. To illustrate we constru...

  18. Martingale property for the Scott correlated stochastic volatility model

    OpenAIRE

    Akdim, Khadija; Eddahbi, M'hamed; Haddadi, Mouna

    2016-01-01

    In this paper, we study the martingale property for a Scott correlated stochastic volatility model, when the correlation coefficient between the Brownian motion driving the volatility and the one driving the asset price process is arbitrary. For this study we verify the martingale property by using the necessary and sufficient conditions given by Bernard \\emph{et al.} \\cite{Bernard}. Our main results are to prove that the price process is a true and uniformly integrable martingale if and only...

  19. Stochastic Models of Molecule Formation on Dust

    Science.gov (United States)

    Charnley, Steven; Wirstroem, Eva

    2011-01-01

    We will present new theoretical models for the formation of molecules on dust. The growth of ice mantles and their layered structure is accounted for and compared directly to observations through simulation of the expected ice absorption spectra

  20. Radio Channel Modelling Using Stochastic Propagation Graphs

    OpenAIRE

    Pedersen, Troels; Fleury, Bernard Henri

    2007-01-01

    In this contribution the radio channel model proposedin [1] is extended to include multiple transmitters and receivers.The propagation environment is modelled using randomgraphs where vertices of a graph represent scatterers and edgesmodel the wave propagation between scatterers. Furthermore,we develop a closed form analytical expression for the transfermatrix of the propagation graph. It is shown by simulation thatimpulse response and the delay-power spectrum of the graphexhibit exponentiall...

  1. Stochastic and Centrifuge Modelling of Jointed Rock

    Science.gov (United States)

    1990-08-31

    Whitman D. Veneziano 0. Reyes G. Iglesia J. S. Lee I Sponsored by U.S. Air Force Air Force Office of Scientific Research Boiling Air Force Base Air...1b Maxmu Tensile Prnia StesVcos fSeie * t 30󈨏 Preextin- Frcue and -ne a Wine Crck Subec toUix.Cmrsie* tesi Vetia Direction- Noe Hg eniesteslee i oe...German sponsors, enhanced our modelling the model approach and led to a paper, "Trapdoor Experiments With Simulated Jointed Rock", Iglesia , et al., by

  2. Stochastic modeling of a serial killer

    OpenAIRE

    Simkin, M. V.; Roychowdhury, V. P.

    2014-01-01

    We analyze the time pattern of the activity of a serial killer, who during twelve years had murdered 53 people. The plot of the cumulative number of murders as a function of time is of "Devil's staircase" type. The distribution of the intervals between murders (step length) follows a power law with the exponent of 1.4. We propose a model according to which the serial killer commits murders when neuronal excitation in his brain exceeds certain threshold. We model this neural activity as a bran...

  3. Time-Weighted Balanced Stochastic Model Reduction

    DEFF Research Database (Denmark)

    Tahavori, Maryamsadat; Shaker, Hamid Reza

    2011-01-01

    A new relative error model reduction technique for linear time invariant (LTI) systems is proposed in this paper. Both continuous and discrete time systems can be reduced within this framework. The proposed model reduction method is mainly based upon time-weighted balanced truncation and a recently...... developed inner-outer factorization technique. Compared to the other analogous counterparts, the proposed method shows to provide more accurate results in terms of time weighted norms, when applied to different practical examples. The results are further illustrated by a numerical example....

  4. Stochastic modelling of dynamical systems in biology

    NARCIS (Netherlands)

    Pellin, Danilo

    2017-01-01

    In this thesis two relevant biological problems will be addressed from a statistical modelling perspective. The first regards the study of hematopoiesis, a still not well understood biological process rarely observable in humans due to technical and ethical reasons. Hematopoiesis is responsible for

  5. STOCHASTIC MODELING OF INFLATION IN NIGERIA

    African Journals Online (AJOL)

    2006-04-04

    Apr 4, 2006 ... In this paper, we adopt a time series approach in modeling inflation in Nig'eria using a four-decade data (1960- 1999) on consumer price index.. Logarithmic transformation was used to stabilize the variation in the data. On the whole four decades, a quadratic trend was obtained. This is also true with the ...

  6. Uncertainty modelling of atmospheric dispersion by stochastic ...

    Indian Academy of Sciences (India)

    The parameters associated to a environmental dispersion model may include different kinds of variability, imprecision and uncertainty. More often, it is seen that available information is interpreted in probabilistic sense. Probability theory is a well-established theory to measure such kind of variability. However, not all ...

  7. Can Household Benefit from Stochastic Programming Models?

    DEFF Research Database (Denmark)

    Rasmussen, Kourosh Marjani; Madsen, Claus A.; Poulsen, Rolf

    2014-01-01

    slightly outperform a passive benchmark on average and are less risky than pure adjustable rate loans, we find considerable gains from using the model-based strategies. Using a strategy that minimizes conditional-value-at-risk lowers average effective yearly interest rate over a 10-year horizon by 0.3–0...

  8. Detecting Character Dependencies in Stochastic Models of Evolution.

    Science.gov (United States)

    Chakrabarty, Deeparnab; Kannan, Sampath; Tian, Kevin

    2016-03-01

    Stochastic models of biological evolution generally assume that different characters (runs of the stochastic process) are independent and identically distributed. In this article we determine the asymptotic complexity of detecting dependence for some fairly general models of evolution, but simple models of dependence. A key difference from much of the previous work is that our algorithms work without knowledge of the tree topology. Specifically, we consider various stochastic models of evolution ranging from the common ones used by biologists (such as Cavender-Farris-Neyman and Jukes-Cantor models) to very general ones where evolution of different characters can be governed by different transition matrices on each edge of the evolutionary tree (phylogeny). We also consider several models of dependence between two characters. In the most specific model, on each edge of the phylogeny the joint distribution of the dependent characters undergoes a perturbation of a fixed magnitude, in a fixed direction from what it would be if the characters were evolving independently. More general dependence models don't require such a strong "signal." Instead they only require that on each edge, the perturbation of the joint distribution has a significant component in a specific direction. Our main results are nearly tight bounds on the induced or operator norm of the transition matrices that would allow us to detect dependence efficiently for most models of evolution and dependence that we consider. We make essential use of a new concentration result for multistate random variables of a Markov random field on arbitrary trivalent trees: We show that the random variable counting the number of leaves in any particular state has variance that is subquadratic in the number of leaves.

  9. A Fractional Order Recovery SIR Model from a Stochastic Process.

    Science.gov (United States)

    Angstmann, C N; Henry, B I; McGann, A V

    2016-03-01

    Over the past several decades, there has been a proliferation of epidemiological models with ordinary derivatives replaced by fractional derivatives in an ad hoc manner. These models may be mathematically interesting, but their relevance is uncertain. Here we develop an SIR model for an epidemic, including vital dynamics, from an underlying stochastic process. We show how fractional differential operators arise naturally in these models whenever the recovery time from the disease is power-law distributed. This can provide a model for a chronic disease process where individuals who are infected for a long time are unlikely to recover. The fractional order recovery model is shown to be consistent with the Kermack-McKendrick age-structured SIR model, and it reduces to the Hethcote-Tudor integral equation SIR model. The derivation from a stochastic process is extended to discrete time, providing a stable numerical method for solving the model equations. We have carried out simulations of the fractional order recovery model showing convergence to equilibrium states. The number of infecteds in the endemic equilibrium state increases as the fractional order of the derivative tends to zero.

  10. Neural network connectivity and response latency modelled by stochastic processes

    DEFF Research Database (Denmark)

    Tamborrino, Massimiliano

    is connected to thousands of other neurons. The rst question is: how to model neural networks through stochastic processes? A multivariate Ornstein-Uhlenbeck process, obtained as a diffusion approximation of a jump process, is the proposed answer. Obviously, dependencies between neurons imply dependencies......Stochastic processes and their rst passage times have been widely used to describe the membrane potential dynamics of single neurons and to reproduce neuronal spikes, respectively.However, cerebral cortex in human brains is estimated to contain 10-20 billions of neurons and each of them...... between their spike times. Therefore, the second question is: how to detect neural network connectivity from simultaneously recorded spike trains? Answering this question corresponds to investigate the joint distribution of sequences of rst passage times. A non-parametric method based on copulas...

  11. Stochasticity in the signalling network of a model microbe

    Science.gov (United States)

    Bischofs, Ilka; Foley, Jonathan; Battenberg, Eric; Fontaine-Bodin, Lisa; Price, Gavin; Wolf, Denise; Arkin, Adam

    2007-03-01

    The soil dwelling bacterium Bacillus subtilis is an excellent model organism for studying stochastic stress response induction in an isoclonal population. Subjected to the same stressor cells undergo different cell fates, including sporulation, competence, degradative enzyme synthesis and motility. For example, under conditions of nutrient deprivation and high cell density only a portion of the cell population forms an endospore. Here we use a combined experimental and theoretical approach to study stochastic sporulation induction in Bacillus subtilis. Using several fluorescent reporter strains we apply time lapse fluorescent microscopy in combination with quantitative image analysis to study cell fate progression on a single cell basis and elucidate key noise generators in the underlying cellular network.

  12. Stochastic sensitivity of a bistable energy model for visual perception

    Science.gov (United States)

    Pisarchik, Alexander N.; Bashkirtseva, Irina; Ryashko, Lev

    2017-01-01

    Modern trends in physiology, psychology and cognitive neuroscience suggest that noise is an essential component of brain functionality and self-organization. With adequate noise the brain as a complex dynamical system can easily access different ordered states and improve signal detection for decision-making by preventing deadlocks. Using a stochastic sensitivity function approach, we analyze how sensitive equilibrium points are to Gaussian noise in a bistable energy model often used for qualitative description of visual perception. The probability distribution of noise-induced transitions between two coexisting percepts is calculated at different noise intensity and system stability. Stochastic squeezing of the hysteresis range and its transition from positive (bistable regime) to negative (intermittency regime) are demonstrated as the noise intensity increases. The hysteresis is more sensitive to noise in the system with higher stability.

  13. A stochastic model for tumor heterogeneity

    CERN Document Server

    Simone, Giuseppina

    2015-01-01

    Phenotype variations define heterogeneity of biological and molecular systems, which play a crucial role in several mechanisms. Heterogeneity has been demonstrated in tumor cells. Here, samples from blood of patients affected from colon tumor were analyzed and fished with a microfluidic assay based on galactose active moieties, and incubated, for culturing, in SCID mice. Following the experimental investigation, a model based on Markov theory was implemented and discussed to explain the equilibrium existing between phenotypes of subpopulations of cells sorted using the microfluidic assay. The model in combination with the experimental results had many implications for tumor heterogeneity. It displayed interconversion of phenotypes, as observed after experiments. The interconversion generates of metastatic cells and implies that targeting the CTCs will be not an efficient method to prevent tumor recurrence. Most importantly, understanding the transitions between cell phenotypes in cell population can boost the...

  14. Stochastic modeling of a serial killer.

    Science.gov (United States)

    Simkin, M V; Roychowdhury, V P

    2014-08-21

    We analyze the time pattern of the activity of a serial killer, who during 12 years had murdered 53 people. The plot of the cumulative number of murders as a function of time is of "Devil's staircase" type. The distribution of the intervals between murders (step length) follows a power law with the exponent of 1.4. We propose a model according to which the serial killer commits murders when neuronal excitation in his brain exceeds certain threshold. We model this neural activity as a branching process, which in turn is approximated by a random walk. As the distribution of the random walk return times is a power law with the exponent 1.5, the distribution of the inter-murder intervals is thus explained. We illustrate analytical results by numerical simulation. Time pattern activity data from two other serial killers further substantiate our analysis. Copyright © 2014 Elsevier Ltd. All rights reserved.

  15. Stochastic modelling for financial bubbles and policy

    OpenAIRE

    Fry, John

    2015-01-01

    In this paper, we draw upon the close relationship between statistical physics and mathematical finance to develop a suite of models for financial bubbles and crashes. By modifying previous approaches, we are able to derive novel analytical formulae for evaluation problems and for the expected timing of future change points. In particular, we help to explain why previous approaches have systematically overstated the timing of changes in market regime. The list of potential empirical applicati...

  16. Stochastic Parametrisations and Regime Behaviour of Atmospheric Models

    Science.gov (United States)

    Arnold, Hannah; Moroz, Irene; Palmer, Tim

    2013-04-01

    The presence of regimes is a characteristic of non-linear, chaotic systems (Lorenz, 2006). In the atmosphere, regimes emerge as familiar circulation patterns such as the El-Nino Southern Oscillation (ENSO), the North Atlantic Oscillation (NAO) and Scandinavian Blocking events. In recent years there has been much interest in the problem of identifying and studying atmospheric regimes (Solomon et al, 2007). In particular, how do these regimes respond to an external forcing such as anthropogenic greenhouse gas emissions? The importance of regimes in observed trends over the past 50-100 years indicates that in order to predict anthropogenic climate change, our climate models must be able to represent accurately natural circulation regimes, their statistics and variability. It is well established that representing model uncertainty as well as initial condition uncertainty is important for reliable weather forecasts (Palmer, 2001). In particular, stochastic parametrisation schemes have been shown to improve the skill of weather forecast models (e.g. Berner et al., 2009; Frenkel et al., 2012; Palmer et al., 2009). It is possible that including stochastic physics as a representation of model uncertainty could also be beneficial in climate modelling, enabling the simulator to explore larger regions of the climate attractor including other flow regimes. An alternative representation of model uncertainty is a perturbed parameter scheme, whereby physical parameters in subgrid parametrisation schemes are perturbed about their optimal value. Perturbing parameters gives a greater control over the ensemble than multi-model or multiparametrisation ensembles, and has been used as a representation of model uncertainty in climate prediction (Stainforth et al., 2005; Rougier et al., 2009). We investigate the effect of including representations of model uncertainty on the regime behaviour of a simulator. A simple chaotic model of the atmosphere, the Lorenz '96 system, is used to study

  17. Stochastic wind turbine modeling for individual pitch control

    DEFF Research Database (Denmark)

    Thomsen, Sven Creutz; Niemann, Hans Henrik; Poulsen, Niels Kjølstad

    2009-01-01

    By pitching the blades of a wind turbine individually it is possible to attenuate the asymmetric loads caused by a non-uniform wind field - this is denoted individual pitch control. In this work we investigate how to set up a simplified stochastic and deterministic description of the wind...... and a simplified description of the aerodynamics with sufficient detail to design model-based individual pitch controllers. Combined with a simplified model of the wind turbine, we exemplify how to use the model elements to systematically design an individual pitch controller. The design is investigated...

  18. Uncertainty quantification and stochastic modeling with Matlab

    CERN Document Server

    Souza de Cursi, Eduardo

    2015-01-01

    Uncertainty Quantification (UQ) is a relatively new research area which describes the methods and approaches used to supply quantitative descriptions of the effects of uncertainty, variability and errors in simulation problems and models. It is rapidly becoming a field of increasing importance, with many real-world applications within statistics, mathematics, probability and engineering, but also within the natural sciences. Literature on the topic has up until now been largely based on polynomial chaos, which raises difficulties when considering different types of approximation and does no

  19. Stochastic modelling for financial bubbles and policy

    Directory of Open Access Journals (Sweden)

    John Fry

    2015-12-01

    Full Text Available In this paper, we draw upon the close relationship between statistical physics and mathematical finance to develop a suite of models for financial bubbles and crashes. By modifying previous approaches, we are able to derive novel analytical formulae for evaluation problems and for the expected timing of future change points. In particular, we help to explain why previous approaches have systematically overstated the timing of changes in market regime. The list of potential empirical applications is deep and wide ranging, and includes contemporary housing bubbles, the Eurozone crisis and the Crash of 2008.

  20. Stochastic Modelling of Past Volcanic Crises

    Science.gov (United States)

    Woo, Gordon

    2017-04-01

    It is customary to have continuous monitoring of volcanoes showing signs of unrest that might lead to an eruption threatening local populations. Despite scientific progress in estimating the probability of an eruption occurring, the concept of continuously tracking eruption probability remains a future aspiration for volcano risk analysts. During some recent major volcanic crises, attempts have been made to estimate the eruption probability in real time to support government decision-making. These include the possibility of an eruption of Katla linked with the eruption of Eyjafjallajökull in 2010, and the Santorini crisis of 2011-2012. However, once a crisis fades, interest in analyzing the probability that there might have been an eruption tends to wane. There is an inherent outcome bias well known to psychologists: if disaster was avoided, there is perceived to be little purpose in exploring scenarios where a disaster might have happened. Yet the better that previous periods of unrest are understood and modelled, the better that the risk associated with future periods of unrest will be quantified. Scenarios are counterfactual histories of the future. The task of quantifying the probability of an eruption for a past period of unrest should not be merely a statistical calculation, but should serve to elucidate and refine geophysical models of the eruptive processes. This is achieved by using a Bayesian Belief Network approach, in which monitoring observations are used to draw inferences on the underlying causal factors. Specifically, risk analysts are interested in identifying what dynamical perturbations might have tipped an unrest period in history over towards an eruption, and assessing what was the likelihood of such perturbations. Furthermore, in what ways might a historical volcano crisis have turned for the worse? Such important counterfactual questions are addressed in this paper.

  1. Stochastic Earthquake Rupture Modeling Using Nonparametric Co-Regionalization

    Science.gov (United States)

    Lee, Kyungbook; Song, Seok Goo

    2017-09-01

    Accurate predictions of the intensity and variability of ground motions are essential in simulation-based seismic hazard assessment. Advanced simulation-based ground motion prediction methods have been proposed to complement the empirical approach, which suffers from the lack of observed ground motion data, especially in the near-source region for large events. It is important to quantify the variability of the earthquake rupture process for future events and to produce a number of rupture scenario models to capture the variability in simulation-based ground motion predictions. In this study, we improved the previously developed stochastic earthquake rupture modeling method by applying the nonparametric co-regionalization, which was proposed in geostatistics, to the correlation models estimated from dynamically derived earthquake rupture models. The nonparametric approach adopted in this study is computationally efficient and, therefore, enables us to simulate numerous rupture scenarios, including large events ( M > 7.0). It also gives us an opportunity to check the shape of true input correlation models in stochastic modeling after being deformed for permissibility. We expect that this type of modeling will improve our ability to simulate a wide range of rupture scenario models and thereby predict ground motions and perform seismic hazard assessment more accurately.

  2. Developing stochastic models for spatial inference: bacterial chemotaxis.

    Directory of Open Access Journals (Sweden)

    Yoon-Dong Yu

    Full Text Available BACKGROUND: Biological systems are inherently inhomogeneous and spatial effects play a significant role in processes such as pattern formation. At the cellular level proteins are often localised either through static attachment or via a dynamic equilibrium. As well as spatial heterogeneity many cellular processes exhibit stochastic fluctuations and so to make inferences about the location of molecules there is a need for spatial stochastic models. A test case for spatial models has been bacterial chemotaxis which has been studied extensively as a model of signal transduction. RESULTS: By creating specific models of a cellular system that incorporate the spatial distributions of molecules we have shown how the fit between simulated and experimental data can be used to make inferences about localisation, in the case of bacterial chemotaxis. This method allows the robust comparison of different spatial models through alternative model parameterisations. CONCLUSIONS: By using detailed statistical analysis we can reliably infer the parameters for the spatial models, and also to evaluate alternative models. The statistical methods employed in this case are particularly powerful as they reduce the need for a large number of simulation replicates. The technique is also particularly useful when only limited molecular level data is available or where molecular data is not quantitative.

  3. Stochastic representations of seismic anisotropy: transversely isotropic effective media models

    Science.gov (United States)

    Song, Xin; Jordan, Thomas H.

    2017-06-01

    We apply Jordan's self-consistent, second-order Born theory to compute the effective stiffness tensor for spatially stationary, stochastic models of 3-D elastic heterogeneity. The effects of local anisotropy can be separated from spatially extended geometric anisotropy by factoring the covariance of the moduli into a one-point variance tensor and a two-point correlation function. The latter is incorporated into the rescaled Kneer tensor, which is contracted against the one-point variance tensor to yield a second-order perturbation to the Voigt average. The theory can handle heterogeneity with orthotropic stochastic symmetry, but the calculations presented here are restricted to media with transversely isotropic (TI) statistics. We thoroughly investigate TI stochastic media that are locally isotropic. If the heterogeneity aspect ratio η is unity, the effective medium is isotropic, and the main effect of the scattering is to reduce the moduli. The two limiting regimes are a 2-D vertical stochastic bundle (η → 0), where the P and S anisotropy ratios are negative, and a 1-D horizontal stochastic laminate (η → ∞), where they are positive. The effective-medium equations for the latter yield the second-order approximation to Backus's exact solution, demonstrating the connection between Backus theory and self-consistent effective-media theory. Comparisons of the exact and second-order results for non-Gaussian laminates indicate that the approximation should be adequate for moduli heterogeneities less than about 30 per cent and thus valid for most seismological purposes. We apply the locally isotropic theory to data from the Los Angeles Basin to illustrate how it can be used to explain shallow seismic anisotropy. To assess the relative contributions of geometric and local anisotropy to the effective anisotropy, we consider a rotational model for stochastic anisotropic variability proposed by Jordan. In this model, the axis of a hexagonally symmetric stiffness

  4. Stochastic juvenile--adult models with application to a green tree frog population.

    Science.gov (United States)

    Ackleh, Azmy S; Deng, Keng; Huang, Qihua

    2011-01-01

    We derive several stochastic models from a deterministic population model that describes the dynamics of age-structured juveniles coupled with size-structured adults. Numerical simulation results of the stochastic models are compared with the solution of the deterministic model. These models are then used to understand the effect of demographic stochasticity on the dynamics of an urban green tree frog (Hyla cinerea) population.

  5. A validation study of a stochastic model of human interaction

    Science.gov (United States)

    Burchfield, Mitchel Talmadge

    The purpose of this dissertation is to validate a stochastic model of human interactions which is part of a developmentalism paradigm. Incorporating elements of ancient and contemporary philosophy and science, developmentalism defines human development as a progression of increasing competence and utilizes compatible theories of developmental psychology, cognitive psychology, educational psychology, social psychology, curriculum development, neurology, psychophysics, and physics. To validate a stochastic model of human interactions, the study addressed four research questions: (a) Does attitude vary over time? (b) What are the distributional assumptions underlying attitudes? (c) Does the stochastic model, {-}N{intlimitssbsp{-infty}{infty}}varphi(chi,tau)\\ Psi(tau)dtau, have utility for the study of attitudinal distributions and dynamics? (d) Are the Maxwell-Boltzmann, Fermi-Dirac, and Bose-Einstein theories applicable to human groups? Approximately 25,000 attitude observations were made using the Semantic Differential Scale. Positions of individuals varied over time and the logistic model predicted observed distributions with correlations between 0.98 and 1.0, with estimated standard errors significantly less than the magnitudes of the parameters. The results bring into question the applicability of Fisherian research designs (Fisher, 1922, 1928, 1938) for behavioral research based on the apparent failure of two fundamental assumptions-the noninteractive nature of the objects being studied and normal distribution of attributes. The findings indicate that individual belief structures are representable in terms of a psychological space which has the same or similar properties as physical space. The psychological space not only has dimension, but individuals interact by force equations similar to those described in theoretical physics models. Nonlinear regression techniques were used to estimate Fermi-Dirac parameters from the data. The model explained a high degree

  6. Modelling the heat dynamics of buildings using stochastic

    DEFF Research Database (Denmark)

    Andersen, Klaus Kaae; Madsen, Henrik

    2000-01-01

    This paper describes the continuous time modelling of the heat dynamics of a building. The considered building is a residential like test house divided into two test rooms with a water based central heating. Each test room is divided into thermal zones in order to describe both short and long term...... variations. Besides modelling the heat transfer between thermal zones, attention is put on modelling the heat input from radiators and solar radiation. The applied modelling procedure is based on collected building performance data and statistical methods. The statistical methods are used in parameter...... estimation and model validation, while physical knowledge is used in forming the model structure. The suggested lumped parameter model is thus based on thermodynamics and formulated as a system of stochastic differential equations. Due to the continuous time formulation the parameters of the model...

  7. On the deterministic and stochastic use of hydrologic models

    Science.gov (United States)

    Farmer, William H.; Vogel, Richard M.

    2016-01-01

    Environmental simulation models, such as precipitation-runoff watershed models, are increasingly used in a deterministic manner for environmental and water resources design, planning, and management. In operational hydrology, simulated responses are now routinely used to plan, design, and manage a very wide class of water resource systems. However, all such models are calibrated to existing data sets and retain some residual error. This residual, typically unknown in practice, is often ignored, implicitly trusting simulated responses as if they are deterministic quantities. In general, ignoring the residuals will result in simulated responses with distributional properties that do not mimic those of the observed responses. This discrepancy has major implications for the operational use of environmental simulation models as is shown here. Both a simple linear model and a distributed-parameter precipitation-runoff model are used to document the expected bias in the distributional properties of simulated responses when the residuals are ignored. The systematic reintroduction of residuals into simulated responses in a manner that produces stochastic output is shown to improve the distributional properties of the simulated responses. Every effort should be made to understand the distributional behavior of simulation residuals and to use environmental simulation models in a stochastic manner.

  8. The stochastic resonance for the incidence function model of metapopulation

    Science.gov (United States)

    Li, Jiang-Cheng; Dong, Zhi-Wei; Zhou, Ruo-Wei; Li, Yun-Xian; Qian, Zhen-Wei

    2017-06-01

    A stochastic model with endogenous and exogenous periodicities is proposed in this paper on the basis of metapopulation dynamics to model the crop yield losses due to pests and diseases. The rationale is that crop yield losses occur because the physiology of the growing crop is negatively affected by pests and diseases in a dynamic way over time as crop both grows and develops. Metapopulation dynamics can thus be used to model the resultant crop yield losses. The stochastic metapopulation process is described by using the Simplified Incidence Function model (IFM). Compared to the original IFMs, endogenous and exogenous periodicities are considered in the proposed model to handle the cyclical patterns observed in pest infestations, diseases epidemics, and exogenous affecting factors such as temperature and rainfalls. Agricultural loss data in China are used to fit the proposed model. Experimental results demonstrate that: (1) Model with endogenous and exogenous periodicities is a better fit; (2) When the internal system fluctuations and external environmental fluctuations are negatively correlated, EIL or the cost of loss is monotonically increasing; when the internal system fluctuations and external environmental fluctuations are positively correlated, an outbreak of pests and diseases might occur; (3) If the internal system fluctuations and external environmental fluctuations are positively correlated, an optimal patch size can be identified which will greatly weaken the effects of external environmental influence and hence inhibit pest infestations and disease epidemics.

  9. Use of a linearization approximation facilitating stochastic model building.

    Science.gov (United States)

    Svensson, Elin M; Karlsson, Mats O

    2014-04-01

    The objective of this work was to facilitate the development of nonlinear mixed effects models by establishing a diagnostic method for evaluation of stochastic model components. The random effects investigated were between subject, between occasion and residual variability. The method was based on a first-order conditional estimates linear approximation and evaluated on three real datasets with previously developed population pharmacokinetic models. The results were assessed based on the agreement in difference in objective function value between a basic model and extended models for the standard nonlinear and linearized approach respectively. The linearization was found to accurately identify significant extensions of the model's stochastic components with notably decreased runtimes as compared to the standard nonlinear analysis. The observed gain in runtimes varied between four to more than 50-fold and the largest gains were seen for models with originally long runtimes. This method may be especially useful as a screening tool to detect correlations between random effects since it substantially quickens the estimation of large variance-covariance blocks. To expedite the application of this diagnostic tool, the linearization procedure has been automated and implemented in the software package PsN.

  10. Optimizing ZigBee Security using Stochastic Model Checking

    DEFF Research Database (Denmark)

    Yuksel, Ender; Nielson, Hanne Riis; Nielson, Flemming

    ZigBee is a fairly new but promising wireless sensor network standard that offers the advantages of simple and low resource communication. Nevertheless, security is of great concern to ZigBee, and enhancements are prescribed in the latest ZigBee specication: ZigBee-2007. In this technical report......, we identify an important gap in the specification on key updates, and present a methodology for determining optimal key update policies and security parameters. We exploit the stochastic model checking approach using the probabilistic model checker PRISM, and assess the security needs for realistic...

  11. Dynamic analysis of a stochastic rumor propagation model

    Science.gov (United States)

    Jia, Fangju; Lv, Guangying

    2018-01-01

    The rapid development of the Internet, especially the emergence of the social networks, leads rumor propagation into a new media era. In this paper, we are concerned with a stochastic rumor propagation model. Sufficient conditions for extinction and persistence in the mean of the rumor are established. The threshold between persistence in the mean and extinction of the rumor is obtained. Compared with the corresponding deterministic model, the threshold affected by the white noise is smaller than the basic reproduction number R0 of the deterministic system.

  12. Modelling of nonlinear shoaling based on stochastic evolution equations

    DEFF Research Database (Denmark)

    Kofoed-Hansen, Henrik; Rasmussen, Jørgen Hvenekær

    1998-01-01

    A one-dimensional stochastic model is derived to simulate the transformation of wave spectra in shallow water including generation of bound sub- and super-harmonics, near-resonant triad wave interaction and wave breaking. Boussinesq type equations with improved linear dispersion characteristics...... are recast into evolution equations for the complex amplitudes, and serve as the underlying deterministic model. Next, a set of evolution equations for the cumulants is derived. By formally introducing the well-known Gaussian closure hypothesis, nonlinear evolution equations for the power spectrum...

  13. Generation of a stochastic precipitation model for the tropical climate

    Science.gov (United States)

    Ng, Jing Lin; Abd Aziz, Samsuzana; Huang, Yuk Feng; Wayayok, Aimrun; Rowshon, MK

    2017-06-01

    A tropical country like Malaysia is characterized by intense localized precipitation with temperatures remaining relatively constant throughout the year. A stochastic modeling of precipitation in the flood-prone Kelantan River Basin is particularly challenging due to the high intermittency of precipitation events of the northeast monsoons. There is an urgent need to have long series of precipitation in modeling the hydrological responses. A single-site stochastic precipitation model that includes precipitation occurrence and an intensity model was developed, calibrated, and validated for the Kelantan River Basin. The simulation process was carried out separately for each station without considering the spatial correlation of precipitation. The Markov chains up to the fifth-order and six distributions were considered. The daily precipitation data of 17 rainfall stations for the study period of 1954-2013 were selected. The results suggested that second- and third-order Markov chains were suitable for simulating monthly and yearly precipitation occurrences, respectively. The fifth-order Markov chain resulted in overestimation of precipitation occurrences. For the mean, distribution, and standard deviation of precipitation amounts, the exponential, gamma, log-normal, skew normal, mixed exponential, and generalized Pareto distributions performed superiorly. However, for the extremes of precipitation, the exponential and log-normal distributions were better while the skew normal and generalized Pareto distributions tend to show underestimations. The log-normal distribution was chosen as the best distribution to simulate precipitation amounts. Overall, the stochastic precipitation model developed is considered a convenient tool to simulate the characteristics of precipitation in the Kelantan River Basin.

  14. A stochastic phase-field model determined from molecular dynamics

    KAUST Repository

    von Schwerin, Erik

    2010-03-17

    The dynamics of dendritic growth of a crystal in an undercooled melt is determined by macroscopic diffusion-convection of heat and by capillary forces acting on the nanometer scale of the solid-liquid interface width. Its modelling is useful for instance in processing techniques based on casting. The phase-field method is widely used to study evolution of such microstructural phase transformations on a continuum level; it couples the energy equation to a phenomenological Allen-Cahn/Ginzburg-Landau equation modelling the dynamics of an order parameter determining the solid and liquid phases, including also stochastic fluctuations to obtain the qualitatively correct result of dendritic side branching. This work presents a method to determine stochastic phase-field models from atomistic formulations by coarse-graining molecular dynamics. It has three steps: (1) a precise quantitative atomistic definition of the phase-field variable, based on the local potential energy; (2) derivation of its coarse-grained dynamics model, from microscopic Smoluchowski molecular dynamics (that is Brownian or over damped Langevin dynamics); and (3) numerical computation of the coarse-grained model functions. The coarse-grained model approximates Gibbs ensemble averages of the atomistic phase-field, by choosing coarse-grained drift and diffusion functions that minimize the approximation error of observables in this ensemble average. © EDP Sciences, SMAI, 2010.

  15. Combining Deterministic structures and stochastic heterogeneity for transport modeling

    Science.gov (United States)

    Zech, Alraune; Attinger, Sabine; Dietrich, Peter; Teutsch, Georg

    2017-04-01

    Contaminant transport in highly heterogeneous aquifers is extremely challenging and subject of current scientific debate. Tracer plumes often show non-symmetric but highly skewed plume shapes. Predicting such transport behavior using the classical advection-dispersion-equation (ADE) in combination with a stochastic description of aquifer properties requires a dense measurement network. This is in contrast to the available information for most aquifers. A new conceptual aquifer structure model is presented which combines large-scale deterministic information and the stochastic approach for incorporating sub-scale heterogeneity. The conceptual model is designed to allow for a goal-oriented, site specific transport analysis making use of as few data as possible. Thereby the basic idea is to reproduce highly skewed tracer plumes in heterogeneous media by incorporating deterministic contrasts and effects of connectivity instead of using unimodal heterogeneous models with high variances. The conceptual model consists of deterministic blocks of mean hydraulic conductivity which might be measured by pumping tests indicating values differing in orders of magnitudes. A sub-scale heterogeneity is introduced within every block. This heterogeneity can be modeled as bimodal or log-normal distributed. The impact of input parameters, structure and conductivity contrasts is investigated in a systematic manor. Furthermore, some first successful implementation of the model was achieved for the well known MADE site.

  16. stpm: an R package for stochastic process model.

    Science.gov (United States)

    Zhbannikov, Ilya Y; Arbeev, Konstantin; Akushevich, Igor; Stallard, Eric; Yashin, Anatoliy I

    2017-02-23

    The Stochastic Process Model (SPM) represents a general framework for modeling the joint evolution of repeatedly measured variables and time-to-event outcomes observed in longitudinal studies, i.e., SPM relates the stochastic dynamics of variables (e.g., physiological or biological measures) with the probabilities of end points (e.g., death or system failure). SPM is applicable for analyses of longitudinal data in many research areas; however, there are no publicly available software tools that implement this methodology. We developed an R package stpm for the SPM-methodology. The package estimates several versions of SPM currently available in the literature including discrete- and continuous-time multidimensional models and a one-dimensional model with time-dependent parameters. Also, the package provides tools for simulation and projection of individual trajectories and hazard functions. In this paper, we present the first software implementation of the SPM-methodology by providing an R package stpm, which was verified through extensive simulation and validation studies. Future work includes further improvements of the model. Clinical and academic researchers will benefit from using the presented model and software. The R package stpm is available as open source software from the following links: https://cran.r-project.org/package=stpm (stable version) or https://github.com/izhbannikov/spm (developer version).

  17. Sampling from stochastic reservoir models constrained by production data

    Energy Technology Data Exchange (ETDEWEB)

    Hegstad, Bjoern Kaare

    1997-12-31

    When a petroleum reservoir is evaluated, it is important to forecast future production of oil and gas and to assess forecast uncertainty. This is done by defining a stochastic model for the reservoir characteristics, generating realizations from this model and applying a fluid flow simulator to the realizations. The reservoir characteristics define the geometry of the reservoir, initial saturation, petrophysical properties etc. This thesis discusses how to generate realizations constrained by production data, that is to say, the realizations should reproduce the observed production history of the petroleum reservoir within the uncertainty of these data. The topics discussed are: (1) Theoretical framework, (2) History matching, forecasting and forecasting uncertainty, (3) A three-dimensional test case, (4) Modelling transmissibility multipliers by Markov random fields, (5) Up scaling, (6) The link between model parameters, well observations and production history in a simple test case, (7) Sampling the posterior using optimization in a hierarchical model, (8) A comparison of Rejection Sampling and Metropolis-Hastings algorithm, (9) Stochastic simulation and conditioning by annealing in reservoir description, and (10) Uncertainty assessment in history matching and forecasting. 139 refs., 85 figs., 1 tab.

  18. Modelling biochemical reaction systems by stochastic differential equations with reflection.

    Science.gov (United States)

    Niu, Yuanling; Burrage, Kevin; Chen, Luonan

    2016-05-07

    In this paper, we gave a new framework for modelling and simulating biochemical reaction systems by stochastic differential equations with reflection not in a heuristic way but in a mathematical way. The model is computationally efficient compared with the discrete-state Markov chain approach, and it ensures that both analytic and numerical solutions remain in a biologically plausible region. Specifically, our model mathematically ensures that species numbers lie in the domain D, which is a physical constraint for biochemical reactions, in contrast to the previous models. The domain D is actually obtained according to the structure of the corresponding chemical Langevin equations, i.e., the boundary is inherent in the biochemical reaction system. A variant of projection method was employed to solve the reflected stochastic differential equation model, and it includes three simple steps, i.e., Euler-Maruyama method was applied to the equations first, and then check whether or not the point lies within the domain D, and if not perform an orthogonal projection. It is found that the projection onto the closure D¯ is the solution to a convex quadratic programming problem. Thus, existing methods for the convex quadratic programming problem can be employed for the orthogonal projection map. Numerical tests on several important problems in biological systems confirmed the efficiency and accuracy of this approach. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. Deterministic modelling and stochastic simulation of biochemical pathways using MATLAB.

    Science.gov (United States)

    Ullah, M; Schmidt, H; Cho, K H; Wolkenhauer, O

    2006-03-01

    The analysis of complex biochemical networks is conducted in two popular conceptual frameworks for modelling. The deterministic approach requires the solution of ordinary differential equations (ODEs, reaction rate equations) with concentrations as continuous state variables. The stochastic approach involves the simulation of differential-difference equations (chemical master equations, CMEs) with probabilities as variables. This is to generate counts of molecules for chemical species as realisations of random variables drawn from the probability distribution described by the CMEs. Although there are numerous tools available, many of them free, the modelling and simulation environment MATLAB is widely used in the physical and engineering sciences. We describe a collection of MATLAB functions to construct and solve ODEs for deterministic simulation and to implement realisations of CMEs for stochastic simulation using advanced MATLAB coding (Release 14). The program was successfully applied to pathway models from the literature for both cases. The results were compared to implementations using alternative tools for dynamic modelling and simulation of biochemical networks. The aim is to provide a concise set of MATLAB functions that encourage the experimentation with systems biology models. All the script files are available from www.sbi.uni-rostock.de/ publications_matlab-paper.html.

  20. A stochastic surplus production model in continuous time

    DEFF Research Database (Denmark)

    Pedersen, Martin Wæver; Berg, Casper Willestofte

    2017-01-01

    Surplus production modelling has a long history as a method for managing data-limited fish stocks. Recent advancements have cast surplus production models as state-space models that separate random variability of stock dynamics from error in observed indices of biomass. We present a stochastic......-space model formulation include the ability to provide estimates of exploitable biomass and fishing mortality at any point in time from data sampled at arbitrary and possibly irregular intervals. We show in a simulation that the ability to analyse subannual data can increase the effective sample size...... estimation and incorporation of seasonality. We argue that including all known sources of uncertainty, propagation of that uncertainty to reference points and checking of model assumptions using residuals are critical prerequisites to rigorous fish stock management based on surplus production models....

  1. Clustering network layers with the strata multilayer stochastic block model.

    Science.gov (United States)

    Stanley, Natalie; Shai, Saray; Taylor, Dane; Mucha, Peter J

    2016-01-01

    Multilayer networks are a useful data structure for simultaneously capturing multiple types of relationships between a set of nodes. In such networks, each relational definition gives rise to a layer. While each layer provides its own set of information, community structure across layers can be collectively utilized to discover and quantify underlying relational patterns between nodes. To concisely extract information from a multilayer network, we propose to identify and combine sets of layers with meaningful similarities in community structure. In this paper, we describe the "strata multilayer stochastic block model" (sMLSBM), a probabilistic model for multilayer community structure. The central extension of the model is that there exist groups of layers, called "strata", which are defined such that all layers in a given stratum have community structure described by a common stochastic block model (SBM). That is, layers in a stratum exhibit similar node-to-community assignments and SBM probability parameters. Fitting the sMLSBM to a multilayer network provides a joint clustering that yields node-to-community and layer-to-stratum assignments, which cooperatively aid one another during inference. We describe an algorithm for separating layers into their appropriate strata and an inference technique for estimating the SBM parameters for each stratum. We demonstrate our method using synthetic networks and a multilayer network inferred from data collected in the Human Microbiome Project.

  2. A stochastic model dissects cell states in biological transition processes.

    Science.gov (United States)

    Armond, Jonathan W; Saha, Krishanu; Rana, Anas A; Oates, Chris J; Jaenisch, Rudolf; Nicodemi, Mario; Mukherjee, Sach

    2014-01-17

    Many biological processes, including differentiation, reprogramming, and disease transformations, involve transitions of cells through distinct states. Direct, unbiased investigation of cell states and their transitions is challenging due to several factors, including limitations of single-cell assays. Here we present a stochastic model of cellular transitions that allows underlying single-cell information, including cell-state-specific parameters and rates governing transitions between states, to be estimated from genome-wide, population-averaged time-course data. The key novelty of our approach lies in specifying latent stochastic models at the single-cell level, and then aggregating these models to give a likelihood that links parameters at the single-cell level to observables at the population level. We apply our approach in the context of reprogramming to pluripotency. This yields new insights, including profiles of two intermediate cell states, that are supported by independent single-cell studies. Our model provides a general conceptual framework for the study of cell transitions, including epigenetic transformations.

  3. Stochastic fire-diffuse-fire model with realistic cluster dynamics

    Science.gov (United States)

    Calabrese, Ana; Fraiman, Daniel; Zysman, Daniel; Ponce Dawson, Silvina

    2010-09-01

    Living organisms use waves that propagate through excitable media to transport information. Ca2+ waves are a paradigmatic example of this type of processes. A large hierarchy of Ca2+ signals that range from localized release events to global waves has been observed in Xenopus laevis oocytes. In these cells, Ca2+ release occurs trough inositol 1,4,5-trisphosphate receptors (IP3Rs) which are organized in clusters of channels located on the membrane of the endoplasmic reticulum. In this article we construct a stochastic model for a cluster of IP3R ’s that replicates the experimental observations reported in [D. Fraiman , Biophys. J. 90, 3897 (2006)10.1529/biophysj.105.075911]. We then couple this phenomenological cluster model with a reaction-diffusion equation, so as to have a discrete stochastic model for calcium dynamics. The model we propose describes the transition regimes between isolated release and steadily propagating waves as the IP3 concentration is increased.

  4. A stochastic model dissects cell states in biological transition processes

    Science.gov (United States)

    Armond, Jonathan W.; Saha, Krishanu; Rana, Anas A.; Oates, Chris J.; Jaenisch, Rudolf; Nicodemi, Mario; Mukherjee, Sach

    2014-01-01

    Many biological processes, including differentiation, reprogramming, and disease transformations, involve transitions of cells through distinct states. Direct, unbiased investigation of cell states and their transitions is challenging due to several factors, including limitations of single-cell assays. Here we present a stochastic model of cellular transitions that allows underlying single-cell information, including cell-state-specific parameters and rates governing transitions between states, to be estimated from genome-wide, population-averaged time-course data. The key novelty of our approach lies in specifying latent stochastic models at the single-cell level, and then aggregating these models to give a likelihood that links parameters at the single-cell level to observables at the population level. We apply our approach in the context of reprogramming to pluripotency. This yields new insights, including profiles of two intermediate cell states, that are supported by independent single-cell studies. Our model provides a general conceptual framework for the study of cell transitions, including epigenetic transformations.

  5. Particle model for optical noisy image recovery via stochastic resonance

    Science.gov (United States)

    Zhang, Yongbin; Liu, Hongjun; Huang, Nan; Wang, Zhaolu; Han, Jing

    2017-10-01

    We propose a particle model for investigating the optical noisy image recovery via stochastic resonance. The light propagating in nonlinear media is regarded as moving particles, which are used for analyzing the nonlinear coupling of signal and noise. Owing to nonlinearity, a signal seeds a potential to reinforce itself at the expense of noise. The applied electric field, noise intensity, and correlation length are important parameters that influence the recovery effects. The noise-hidden image with the signal-to-noise intensity ratio of 1:30 is successfully restored and an optimal cross-correlation gain of 6.1 is theoretically obtained.

  6. Classification in postural style based on stochastic process modeling.

    Science.gov (United States)

    Denis, Christophe

    2014-01-01

    We address the statistical challenge of classifying subjects as hemiplegic, vestibular or normal based on complex trajectories obtained through two experimental protocols designed to evaluate potential deficits in postural control. The classification procedure involves a dimension reduction step where the complex trajectories are summarized by finite-dimensional summary measures based on a stochastic process model for a real-valued trajectory. This allows us to retrieve from the trajectories information relative to their temporal dynamic. A leave-one-out evaluation yields a 79% performance of correct classification for a total of n=70 subjects, with 22 hemiplegic (31%), 16 vestibular (23%) and 32 normal (46%) subjects.

  7. Investment timing decisions in a stochastic duopoly model

    Energy Technology Data Exchange (ETDEWEB)

    Marseguerra, Giovanni [Istituto di Econometria e CRANEC, Universita Cattolica del Sacro Cuore di Milan (Italy)]. E-mail: giovanni.marseguerra@unicatt.it; Cortelezzi, Flavia [Dipartimento di Diritto ed Economia delle Persone e delle Imprese, Universita dell' Insubria (Italy)]. E-mail: flavia.cortelezzi@uninsubria.it; Dominioni, Armando [CORE-Catholique de Louvain la Neuve (Belgium)]. E-mail: dominioni@core.ucl.ac.be

    2006-08-15

    We investigate the role of strategic considerations on the optimal timing of investment when firms compete for a new market (e.g., the provision of an innovative product) under demand uncertainty. Within a continuous time model of stochastic oligopoly, we show that strategic considerations are likely to be of limited impact when the new product is radically innovative whilst the fear of a rival's entry may deeply affect firms' decisions whenever innovation is to some extent limited. The welfare analysis shows surprisingly that the desirability of the different market structures considered does not depend on the fixed entry cost.

  8. Mapping of the stochastic Lotka-Volterra model to models of population genetics and game theory

    Science.gov (United States)

    Constable, George W. A.; McKane, Alan J.

    2017-08-01

    The relationship between the M -species stochastic Lotka-Volterra competition (SLVC) model and the M -allele Moran model of population genetics is explored via timescale separation arguments. When selection for species is weak and the population size is large but finite, precise conditions are determined for the stochastic dynamics of the SLVC model to be mappable to the neutral Moran model, the Moran model with frequency-independent selection, and the Moran model with frequency-dependent selection (equivalently a game-theoretic formulation of the Moran model). We demonstrate how these mappings can be used to calculate extinction probabilities and the times until a species' extinction in the SLVC model.

  9. A stochastic pocket model for aluminum agglomeration in solid propellants

    Energy Technology Data Exchange (ETDEWEB)

    Gallier, Stany [SNPE Materiaux Energetiques, Vert le Petit (France)

    2009-04-15

    A new model is derived to estimate the size and fraction of aluminum agglomerates at the surface of a burning propellant. The basic idea relies on well-known pocket models in which aluminum is supposed to aggregate and melt within pocket volumes imposed by largest oxidizer particles. The proposed model essentially relaxes simple assumptions of previous pocket models on propellant structure by accounting for an actual microstructure obtained by packing. The use of statistical tools from stochastic geometry enables to determine a statistical pocket size volume and hence agglomerate diameter and agglomeration fraction. Application to several AP/Al propellants gives encouraging results that are shown to be superior to former pocket models. (Abstract Copyright [2009], Wiley Periodicals, Inc.)

  10. Hierarchical Stochastic Simulation Algorithm for SBML Models of Genetic Circuits

    Directory of Open Access Journals (Sweden)

    Leandro eWatanabe

    2014-11-01

    Full Text Available This paper describes a hierarchical stochastic simulation algorithm which has been implemented within iBioSim, a tool used to model, analyze, and visualize genetic circuits. Many biological analysis tools flatten out hierarchy before simulation, but there are many disadvantages associated with this approach. First, the memory required to represent the model can quickly expand in the process. Second, the flattening process is computationally expensive. Finally, when modeling a dynamic cellular population within iBioSim, inlining the hierarchy of the model is inefficient since models must grow dynamically over time. This paper discusses a new approach to handle hierarchy on the fly to make the tool faster and more memory-efficient. This approach yields significant performance improvements as compared to the former flat analysis method.

  11. A stochastic model for the analysis of maximum daily temperature

    Science.gov (United States)

    Sirangelo, B.; Caloiero, T.; Coscarelli, R.; Ferrari, E.

    2017-10-01

    In this paper, a stochastic model for the analysis of the daily maximum temperature is proposed. First, a deseasonalization procedure based on the truncated Fourier expansion is adopted. Then, the Johnson transformation functions were applied for the data normalization. Finally, the fractionally autoregressive integrated moving average model was used to reproduce both short- and long-memory behavior of the temperature series. The model was applied to the data of the Cosenza gauge (Calabria region) and verified on other four gauges of southern Italy. Through a Monte Carlo simulation procedure based on the proposed model, 105 years of daily maximum temperature have been generated. Among the possible applications of the model, the occurrence probabilities of the annual maximum values have been evaluated. Moreover, the procedure was applied for the estimation of the return periods of long sequences of days with maximum temperature above prefixed thresholds.

  12. The BDS Triple Frequency Pseudo-range Correlated Stochastic Model of Single Station Modeling Method

    Directory of Open Access Journals (Sweden)

    HUANG Lingyong

    2017-05-01

    Full Text Available In order to provide a reliable pseudo-range stochastic model, a method is studied to estimate the BDS triple-frequency pseudo-range related stochastic model based on three BDS triple-frequency pseudo-range minus carrier (GIF combinations using the data of a single station. In this algorithm, the low order polynomial fitting method is used to fit the GIF combination in order to eliminate the error and other constants except non pseudo noise at first. And then, multiple linear regression analysis method is used to model the stochastic function of three linearly independent GIF combinations. Finally the related stochastic model of the original BDS triple-frequency pseudo-range observations is obtained by linear transformation. The BDS triple-frequency data verification results show that this algorithm can get a single station related stochastic model of BDS triple-frequency pseudo-range observation, and it is advantageous to provide accurate stochastic model for navigation and positioning and integrity monitoring.

  13. A review on stochastic models and analysis of warehouse operations

    National Research Council Canada - National Science Library

    Gong, Yeming; de Koster, René B. M

    2011-01-01

    This paper provides an overview of stochastic research in warehouse operations. We identify uncertainty sources of warehousing systems and systematically present typical warehouse operations from a stochastic system viewpoint...

  14. Stochastic Constraint Programming

    OpenAIRE

    Walsh, Toby

    2009-01-01

    To model combinatorial decision problems involving uncertainty and probability, we introduce stochastic constraint programming. Stochastic constraint programs contain both decision variables (which we can set) and stochastic variables (which follow a probability distribution). They combine together the best features of traditional constraint satisfaction, stochastic integer programming, and stochastic satisfiability. We give a semantics for stochastic constraint programs, and propose a number...

  15. A spatial stochastic programming model for timber and core area management under risk of fires

    Science.gov (United States)

    Yu Wei; Michael Bevers; Dung Nguyen; Erin Belval

    2014-01-01

    Previous stochastic models in harvest scheduling seldom address explicit spatial management concerns under the influence of natural disturbances. We employ multistage stochastic programming models to explore the challenges and advantages of building spatial optimization models that account for the influences of random stand-replacing fires. Our exploratory test models...

  16. Measurement and stochastic modeling of kidney puncture forces.

    Science.gov (United States)

    van Gerwen, D J; Dankelman, J; van den Dobbelsteen, J J

    2014-03-01

    The development of needle insertion robots and training simulators requires knowledge of the forces that arise when a needle is inserted into soft-tissue. The present study aims to construct stochastic models of the force required to puncture a kidney using a trocar needle, based on measurements. To this end, a total of sixty insertions were performed into porcine kidneys (ex vivo), at constant speed, using a linear motion stage. Axial force was measured at the needle hub and an ultrasound probe moved with the needle to enable identification of anatomical structures. Two force peaks were observed for each tissue layer punctured, one caused by the tip and one by the edge of the cannula. Based on ultrasound data these double-peaks were classified into four groups, related to kidney capsule and internal structures. Group size varied from 7 to 55 double-peaks. Force peaks in each group were evaluated in terms of peak force and drop in force for both tip and cannula, and stochastic models were constructed that describe the multivariate distribution of these metrics. Peak forces in the capsule and internal structures ranged up to 2 N and 8 N, respectively. The resulting models can be used to simulate kidney puncture events in a variety of applications.

  17. Efficient Stochastic Inversion Using Adjoint Models and Kernel-PCA

    Energy Technology Data Exchange (ETDEWEB)

    Thimmisetty, Charanraj A. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Center for Applied Scientific Computing; Zhao, Wenju [Florida State Univ., Tallahassee, FL (United States). Dept. of Scientific Computing; Chen, Xiao [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Center for Applied Scientific Computing; Tong, Charles H. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Center for Applied Scientific Computing; White, Joshua A. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Atmospheric, Earth and Energy Division

    2017-10-18

    Performing stochastic inversion on a computationally expensive forward simulation model with a high-dimensional uncertain parameter space (e.g. a spatial random field) is computationally prohibitive even when gradient information can be computed efficiently. Moreover, the ‘nonlinear’ mapping from parameters to observables generally gives rise to non-Gaussian posteriors even with Gaussian priors, thus hampering the use of efficient inversion algorithms designed for models with Gaussian assumptions. In this paper, we propose a novel Bayesian stochastic inversion methodology, which is characterized by a tight coupling between the gradient-based Langevin Markov Chain Monte Carlo (LMCMC) method and a kernel principal component analysis (KPCA). This approach addresses the ‘curse-of-dimensionality’ via KPCA to identify a low-dimensional feature space within the high-dimensional and nonlinearly correlated parameter space. In addition, non-Gaussian posterior distributions are estimated via an efficient LMCMC method on the projected low-dimensional feature space. We will demonstrate this computational framework by integrating and adapting our recent data-driven statistics-on-manifolds constructions and reduction-through-projection techniques to a linear elasticity model.

  18. Modelling Real World Using Stochastic Processes and Filtration

    Directory of Open Access Journals (Sweden)

    Jaeger Peter

    2016-03-01

    Full Text Available First we give an implementation in Mizar [2] basic important definitions of stochastic finance, i.e. filtration ([9], pp. 183 and 185, adapted stochastic process ([9], p. 185 and predictable stochastic process ([6], p. 224. Second we give some concrete formalization and verification to real world examples.

  19. Stochastic persistence and stationary distribution in an SIS epidemic model with media coverage

    Science.gov (United States)

    Guo, Wenjuan; Cai, Yongli; Zhang, Qimin; Wang, Weiming

    2018-02-01

    This paper aims to study an SIS epidemic model with media coverage from a general deterministic model to a stochastic differential equation with environment fluctuation. Mathematically, we use the Markov semigroup theory to prove that the basic reproduction number R0s can be used to control the dynamics of stochastic system. Epidemiologically, we show that environment fluctuation can inhibit the occurrence of the disease, namely, in the case of disease persistence for the deterministic model, the disease still dies out with probability one for the stochastic model. So to a great extent the stochastic perturbation under media coverage affects the outbreak of the disease.

  20. Comparing stochastic differential equations and agent-based modelling and simulation for early-stage cancer

    National Research Council Canada - National Science Library

    Figueredo, Grazziela P; Siebers, Peer-Olaf; Owen, Markus R; Reps, Jenna; Aickelin, Uwe

    2014-01-01

    .... It does not suffer from some limitations of ordinary differential equation models, such as the lack of stochasticity, representation of individual behaviours rather than aggregates and individual memory...

  1. Large scale stochastic spatio-temporal modelling with PCRaster

    Science.gov (United States)

    Karssenberg, Derek; Drost, Niels; Schmitz, Oliver; de Jong, Kor; Bierkens, Marc F. P.

    2013-04-01

    PCRaster is a software framework for building spatio-temporal models of land surface processes (http://www.pcraster.eu). Building blocks of models are spatial operations on raster maps, including a large suite of operations for water and sediment routing. These operations are available to model builders as Python functions. The software comes with Python framework classes providing control flow for spatio-temporal modelling, Monte Carlo simulation, and data assimilation (Ensemble Kalman Filter and Particle Filter). Models are built by combining the spatial operations in these framework classes. This approach enables modellers without specialist programming experience to construct large, rather complicated models, as many technical details of modelling (e.g., data storage, solving spatial operations, data assimilation algorithms) are taken care of by the PCRaster toolbox. Exploratory modelling is supported by routines for prompt, interactive visualisation of stochastic spatio-temporal data generated by the models. The high computational requirements for stochastic spatio-temporal modelling, and an increasing demand to run models over large areas at high resolution, e.g. in global hydrological modelling, require an optimal use of available, heterogeneous computing resources by the modelling framework. Current work in the context of the eWaterCycle project is on a parallel implementation of the modelling engine, capable of running on a high-performance computing infrastructure such as clusters and supercomputers. Model runs will be distributed over multiple compute nodes and multiple processors (GPUs and CPUs). Parallelization will be done by parallel execution of Monte Carlo realizations and sub regions of the modelling domain. In our approach we use multiple levels of parallelism, improving scalability considerably. On the node level we will use OpenCL, the industry standard for low-level high performance computing kernels. To combine multiple nodes we will use

  2. A stochastic model of ant trail following with two pheromones

    CERN Document Server

    Malíčková, Miriam; Boďová, Katarína

    2015-01-01

    Colonies of ants are systems of interacting living organisms in which interactions between individuals and their environment can produce a reliable performance of a complex tasks without the need for centralised control. Particularly remarkable is the process of formation of refined paths between the nest and food sources that is essential for successful foraging. We have designed a simple stochastic off-lattice model of ant foraging in the absence of direct communication. The motion of ants is governed by two components - a random change in direction of motion that improves ability to explore the environment (facilitating food discovery), and a non-random global indirect interaction component based on pheromone signalling. Using numerical simulations we have studied the model behaviour in different parameter regimes and tested the ability of our model ants to adapt to changes in the external environment. The simulated behaviour of ants in the model recapitulated the experimentally observed behaviours of real...

  3. Stochastic hybrid model of spontaneous dendritic NMDA spikes.

    Science.gov (United States)

    Bressloff, Paul C; Newby, Jay M

    2014-02-01

    Following recent advances in imaging techniques and methods of dendritic stimulation, active voltage spikes have been observed in thin dendritic branches of excitatory pyramidal neurons, where the majority of synapses occur. The generation of these dendritic spikes involves both Na(+) ion channels and M-methyl-D-aspartate receptor (NMDAR) channels. During strong stimulation of a thin dendrite, the resulting high levels of glutamate, the main excitatory neurotransmitter in the central nervous system and an NMDA agonist, modify the current-voltage (I-V) characteristics of an NMDAR so that it behaves like a voltage-gated Na(+) channel. Hence, the NMDARs can fire a regenerative dendritic spike, just as Na(+) channels support the initiation of an action potential following membrane depolarization. However, the duration of the dendritic spike is of the order 100 ms rather than 1 ms, since it involves slow unbinding of glutamate from NMDARs rather than activation of hyperpolarizing K(+) channels. It has been suggested that dendritic NMDA spikes may play an important role in dendritic computations and provide a cellular substrate for short-term memory. In this paper, we consider a stochastic, conductance-based model of dendritic NMDA spikes, in which the noise originates from the stochastic opening and closing of a finite number of Na(+) and NMDA receptor ion channels. The resulting model takes the form of a stochastic hybrid system, in which membrane voltage evolves according to a piecewise deterministic dynamics that is coupled to a jump Markov process describing the opening and closing of the ion channels. We formulate the noise-induced initiation and termination of a dendritic spike in terms of a first-passage time problem, under the assumption that glutamate unbinding is negligible, which we then solve using a combination of WKB methods and singular perturbation theory. Using a stochastic phase-plane analysis we then extend our analysis to take proper account of the

  4. Stochastic dynamics modeling solute transport in porous media modeling solute transport in porous media

    CERN Document Server

    Kulasiri, Don

    2002-01-01

    Most of the natural and biological phenomena such as solute transport in porous media exhibit variability which can not be modeled by using deterministic approaches. There is evidence in natural phenomena to suggest that some of the observations can not be explained by using the models which give deterministic solutions. Stochastic processes have a rich repository of objects which can be used to express the randomness inherent in the system and the evolution of the system over time. The attractiveness of the stochastic differential equations (SDE) and stochastic partial differential equations (SPDE) come from the fact that we can integrate the variability of the system along with the scientific knowledge pertaining to the system. One of the aims of this book is to explaim some useufl concepts in stochastic dynamics so that the scientists and engineers with a background in undergraduate differential calculus could appreciate the applicability and appropriateness of these developments in mathematics. The ideas ...

  5. Stochastic Modeling and Optimization in a Microgrid: A Survey

    Directory of Open Access Journals (Sweden)

    Hao Liang

    2014-03-01

    Full Text Available The future smart grid is expected to be an interconnected network of small-scale and self-contained microgrids, in addition to a large-scale electric power backbone. By utilizing microsources, such as renewable energy sources and combined heat and power plants, microgrids can supply electrical and heat loads in local areas in an economic and environment friendly way. To better adopt the intermittent and weather-dependent renewable power generation, energy storage devices, such as batteries, heat buffers and plug-in electric vehicles (PEVs with vehicle-to-grid systems can be integrated in microgrids. However, significant technical challenges arise in the planning, operation and control of microgrids, due to the randomness in renewable power generation, the buffering effect of energy storage devices and the high mobility of PEVs. The two-way communication functionalities of the future smart grid provide an opportunity to address these challenges, by offering the communication links for microgrid status information collection. However, how to utilize stochastic modeling and optimization tools for efficient, reliable and economic planning, operation and control of microgrids remains an open issue. In this paper, we investigate the key features of microgrids and provide a comprehensive literature survey on the stochastic modeling and optimization tools for a microgrid. Future research directions are also identified.

  6. Extinction pathways and outbreak vulnerability in a stochastic Ebola model.

    Science.gov (United States)

    Nieddu, Garrett T; Billings, Lora; Kaufman, James H; Forgoston, Eric; Bianco, Simone

    2017-02-01

    A zoonotic disease is a disease that can be passed from animals to humans. Zoonotic viruses may adapt to a human host eventually becoming endemic in humans, but before doing so punctuated outbreaks of the zoonotic virus may be observed. The Ebola virus disease (EVD) is an example of such a disease. The animal population in which the disease agent is able to reproduce in sufficient number to be able to transmit to a susceptible human host is called a reservoir. There is little work devoted to understanding stochastic population dynamics in the presence of a reservoir, specifically the phenomena of disease extinction and reintroduction. Here, we build a stochastic EVD model and explicitly consider the impacts of an animal reservoir on the disease persistence. Our modelling approach enables the analysis of invasion and fade-out dynamics, including the efficacy of possible intervention strategies. We investigate outbreak vulnerability and the probability of local extinction and quantify the effective basic reproduction number. We also consider the effects of dynamic population size. Our results provide an improved understanding of outbreak and extinction dynamics in zoonotic diseases, such as EVD. © 2017 The Author(s).

  7. Outbreak and Extinction Dynamics in a Stochastic Ebola Model

    Science.gov (United States)

    Nieddu, Garrett; Bianco, Simone; Billings, Lora; Forgoston, Eric; Kaufman, James

    A zoonotic disease is a disease that can be passed between animals and humans. In many cases zoonotic diseases can persist in the animal population even if there are no infections in the human population. In this case we call the infected animal population the reservoir for the disease. Ebola virus disease (EVD) and SARS are both notable examples of such diseases. There is little work devoted to understanding stochastic disease extinction and reintroduction in the presence of a reservoir. Here we build a stochastic model for EVD and explicitly consider the presence of an animal reservoir. Using a master equation approach and a WKB ansatz, we determine the associated Hamiltonian of the system. Hamilton's equations are then used to numerically compute the 12-dimensional optimal path to extinction, which is then used to estimate mean extinction times. We also numerically investigate the behavior of the model for dynamic population size. Our results provide an improved understanding of outbreak and extinction dynamics in diseases like EVD.

  8. Aggregation patterns from nonlocal interactions: Discrete stochastic and continuum modeling

    KAUST Repository

    Hackett-Jones, Emily J.

    2012-04-17

    Conservation equations governed by a nonlocal interaction potential generate aggregates from an initial uniform distribution of particles. We address the evolution and formation of these aggregating steady states when the interaction potential has both attractive and repulsive singularities. Currently, no existence theory for such potentials is available. We develop and compare two complementary solution methods, a continuous pseudoinverse method and a discrete stochastic lattice approach, and formally show a connection between the two. Interesting aggregation patterns involving multiple peaks for a simple doubly singular attractive-repulsive potential are determined. For a swarming Morse potential, characteristic slow-fast dynamics in the scaled inverse energy is observed in the evolution to steady state in both the continuous and discrete approaches. The discrete approach is found to be remarkably robust to modifications in movement rules, related to the potential function. The comparable evolution dynamics and steady states of the discrete model with the continuum model suggest that the discrete stochastic approach is a promising way of probing aggregation patterns arising from two- and three-dimensional nonlocal interaction conservation equations. © 2012 American Physical Society.

  9. Stochastic cellular automata model for stock market dynamics.

    Science.gov (United States)

    Bartolozzi, M; Thomas, A W

    2004-04-01

    In the present work we introduce a stochastic cellular automata model in order to simulate the dynamics of the stock market. A direct percolation method is used to create a hierarchy of clusters of active traders on a two-dimensional grid. Active traders are characterized by the decision to buy, sigma(i) (t)=+1, or sell, sigma(i) (t)=-1, a stock at a certain discrete time step. The remaining cells are inactive, sigma(i) (t)=0. The trading dynamics is then determined by the stochastic interaction between traders belonging to the same cluster. Extreme, intermittent events, such as crashes or bubbles, are triggered by a phase transition in the state of the bigger clusters present on the grid, where almost all the active traders come to share the same spin orientation. Most of the stylized aspects of the financial market time series, including multifractal proprieties, are reproduced by the model. A direct comparison is made with the daily closures of the S&P 500 index.

  10. Stochastic cellular automata model for stock market dynamics

    Science.gov (United States)

    Bartolozzi, M.; Thomas, A. W.

    2004-04-01

    In the present work we introduce a stochastic cellular automata model in order to simulate the dynamics of the stock market. A direct percolation method is used to create a hierarchy of clusters of active traders on a two-dimensional grid. Active traders are characterized by the decision to buy, σi (t)=+1 , or sell, σi (t)=-1 , a stock at a certain discrete time step. The remaining cells are inactive, σi (t)=0 . The trading dynamics is then determined by the stochastic interaction between traders belonging to the same cluster. Extreme, intermittent events, such as crashes or bubbles, are triggered by a phase transition in the state of the bigger clusters present on the grid, where almost all the active traders come to share the same spin orientation. Most of the stylized aspects of the financial market time series, including multifractal proprieties, are reproduced by the model. A direct comparison is made with the daily closures of the S&P500 index.

  11. Stochastic effects in a discretized kinetic model of economic exchange

    Science.gov (United States)

    Bertotti, M. L.; Chattopadhyay, A. K.; Modanese, G.

    2017-04-01

    Linear stochastic models and discretized kinetic theory are two complementary analytical techniques used for the investigation of complex systems of economic interactions. The former employ Langevin equations, with an emphasis on stock trade; the latter is based on systems of ordinary differential equations and is better suited for the description of binary interactions, taxation and welfare redistribution. We propose a new framework which establishes a connection between the two approaches by introducing random fluctuations into the kinetic model based on Langevin and Fokker-Planck formalisms. Numerical simulations of the resulting model indicate positive correlations between the Gini index and the total wealth, that suggest a growing inequality with increasing income. Further analysis shows, in the presence of a conserved total wealth, a simultaneous decrease in inequality as social mobility increases, in conformity with economic data.

  12. A stochastic model of supercoiling-dependent transcription

    CERN Document Server

    Brackley, C A; Bentivogli, A; Corles, S; Gilber, N; Gonnella, G; Marenduzzo, D

    2016-01-01

    We propose a stochastic model for gene transcription coupled to DNA supercoiling, where we incorporate the experimental observation that polymerases create supercoiling as they unwind the DNA helix, and that these enzymes bind more favourably to regions where the genome is unwound. Within this model, we show that when the transcriptionally induced flux of supercoiling increases, there is a sharp crossover from a regime where torsional stresses relax quickly and gene transcription is random, to one where gene expression is highly correlated and tightly regulated by supercoiling. In the latter regime, the model displays transcriptional bursts, waves of supercoiling, and up-regulation of divergent or bidirectional genes. It also predicts that topological enzymes which relax twist and writhe should provide a pathway to down-regulate transcription. This article has been accepted for publication in Physical Review Letters, May 2016.

  13. Developing a new stochastic competitive model regarding inventory and price

    Science.gov (United States)

    Rashid, Reza; Bozorgi-Amiri, Ali; Seyedhoseini, S. M.

    2015-01-01

    Within the competition in today's business environment, the design of supply chains becomes more complex than before. This paper deals with the retailer's location problem when customers choose their vendors, and inventory costs have been considered for retailers. In a competitive location problem, price and location of facilities affect demands of customers; consequently, simultaneous optimization of the location and inventory system is needed. To prepare a realistic model, demand and lead time have been assumed as stochastic parameters, and queuing theory has been used to develop a comprehensive mathematical model. Due to complexity of the problem, a branch and bound algorithm has been developed, and its performance has been validated in several numerical examples, which indicated effectiveness of the algorithm. Also, a real case has been prepared to demonstrate performance of the model for real world.

  14. Stochastic continuous time neurite branching models with tree and segment dependent rates

    NARCIS (Netherlands)

    van Elburg, Ronald A. J.

    2011-01-01

    In this paper we introduce a continuous time stochastic neurite branching model closely related to the discrete time stochastic BES-model. The discrete time BES-model is underlying current attempts to simulate cortical development, but is difficult to analyze. The new continuous time formulation

  15. Insights into pre-reversal paleosecular variation from stochastic models

    Directory of Open Access Journals (Sweden)

    Klaudio ePeqini

    2015-09-01

    Full Text Available To provide insights on the paleosecular variation of the geomagnetic field and the mechanism of reversals, long time series of the dipolar magnetic moment are generated by two different stochastic models, known as the domino model and the inhomogeneous Lebovitz disk dynamo model, with initial values taken from the from paleomagnetic data. The former model considers mutual interactions of N macrospins embedded in a uniformly rotating medium, where random forcing and dissipation act on each macrospin. With an appropriate set of the model’s parameters values, the series generated by this model have similar statistical behaviour to the time series of the SHA.DIF.14K model. The latter model is an extension of the classical two-disk Rikitake model, considering N dynamo elements with appropriate interactions between them.We varied the parameters set of both models aiming at generating suitable time series with behaviour similar to the long time series of recent secular variation (SV. Such series are then extended to the near future, obtaining reversals in both cases of models. The analysis of the time series generated by simulating the models show that the reversals appears after a persistent period of low intensity geomagnetic field, as it is occurring in the present times.

  16. Epigenetics and Evolution: Transposons and the Stochastic Epigenetic Modification Model

    Directory of Open Access Journals (Sweden)

    Sergio Branciamore

    2015-04-01

    Full Text Available In addition to genetic variation, epigenetic variation and transposons can greatly affect the evolutionary fitnesses landscape and gene expression. Previously we proposed a mathematical treatment of a general epigenetic variation model that we called Stochastic Epigenetic Modification (SEM model. In this study we follow up with a special case, the Transposon Silencing Model (TSM, with, once again, emphasis on quantitative treatment. We have investigated the evolutionary effects of epigenetic changes due to transposon (T insertions; in particular, we have considered a typical gene locus A and postulated that (i the expression level of gene A depends on the epigenetic state (active or inactive of a cis- located transposon element T, (ii stochastic variability in the epigenetic silencing of T occurs only in a short window of opportunity during development, (iii the epigenetic state is then stable during further development, and (iv the epigenetic memory is fully reset at each generation. We develop the model using two complementary approaches: a standard analytical population genetics framework (di usion equations and Monte-Carlo simulations. Both approaches led to similar estimates for the probability of fixation and time of fixation of locus TA with initial frequency P in a randomly mating diploid population of effective size Ne. We have ascertained the e ect that ρ, the probability of transposon Modification during the developmental window, has on the population (species. One of our principal conclusions is that as ρ increases, the pattern of fixation of the combined TA locus goes from "neutral" to "dominant" to "over-dominant". We observe that, under realistic values of ρ, epigenetic Modifications can provide an e cient mechanism for more rapid fixation of transposons and cis-located gene alleles. The results obtained suggest that epigenetic silencing, even if strictly transient (being reset at each generation, can still have signi cant

  17. Stochastic Polynomial Dynamic Models of the Yeast Cell Cycle

    Science.gov (United States)

    Mitra, Indranil; Dimitrova, Elena; Jarrah, Abdul S.

    2010-03-01

    In the last decade a new holistic approach for tackling biological problems, systems biology, which takes into account the study of the interactions between the components of a biological system to predict function and behavior has emerged. The reverse-engineering of biochemical networks from experimental data have increasingly become important in systems biology. Based on Boolean networks, we propose a time-discrete stochastic framework for the reverse engineering of the yeast cell cycle regulatory network from experimental data. With a suitable choice of state set, we have used powerful tools from computational algebra, that underlie the reverse-engineering algorithm, avoiding costly enumeration strategies. Stochasticity is introduced by choosing at each update step a random coordinate function for each variable, chosen from a probability space of update functions. The algorithm is based on a combinatorial structure known as the Gr"obner fans of a polynomial ideal which identifies the underlying network structure and dynamics. The model depicts a correct dynamics of the yeast cell cycle network and reproduces the time sequence of expression patterns along the biological cell cycle. Our findings indicate that the methodolgy has high chance of success when applied to large and complex systems to determine the dynamical properties of corresponding networks.

  18. Stochastic models for spike trains of single neurons

    CERN Document Server

    Sampath, G

    1977-01-01

    1 Some basic neurophysiology 4 The neuron 1. 1 4 1. 1. 1 The axon 7 1. 1. 2 The synapse 9 12 1. 1. 3 The soma 1. 1. 4 The dendrites 13 13 1. 2 Types of neurons 2 Signals in the nervous system 14 2. 1 Action potentials as point events - point processes in the nervous system 15 18 2. 2 Spontaneous activi~ in neurons 3 Stochastic modelling of single neuron spike trains 19 3. 1 Characteristics of a neuron spike train 19 3. 2 The mathematical neuron 23 4 Superposition models 26 4. 1 superposition of renewal processes 26 4. 2 Superposition of stationary point processe- limiting behaviour 34 4. 2. 1 Palm functions 35 4. 2. 2 Asymptotic behaviour of n stationary point processes superposed 36 4. 3 Superposition models of neuron spike trains 37 4. 3. 1 Model 4. 1 39 4. 3. 2 Model 4. 2 - A superposition model with 40 two input channels 40 4. 3. 3 Model 4. 3 4. 4 Discussion 41 43 5 Deletion models 5. 1 Deletion models with 1nd~endent interaction of excitatory and inhibitory sequences 44 VI 5. 1. 1 Model 5. 1 The basic de...

  19. Model of an excitatory synapse based on stochastic processes.

    Science.gov (United States)

    L'Espérance, Pierre-Yves; Labib, Richard

    2013-09-01

    We present a mathematical model of a biological synapse based on stochastic processes to establish the temporal behavior of the postsynaptic potential following a quantal synaptic transmission. This potential form is the basis of the neural code. We suppose that the release of neurotransmitters in the synaptic cleft follows a Poisson process, and that they diffuse according to integrated Ornstein-Uhlenbeck processes in 3-D with random initial positions and velocities. The diffusion occurs in an isotropic environment between two infinite parallel planes representing the pre- and postsynaptic membrane. We state that the presynaptic membrane is perfectly reflecting and that the other is perfectly absorbing. The activation of the receptors polarizes the postsynaptic membrane according to a parallel RC circuit scheme. We present the results obtained by simulations according to a Gillespie algorithm and we show that our model exhibits realistic postsynaptic behaviors from a simple quantal occurrence.

  20. Stochastic modeling of reinforced concrete structures exposed to chloride attack

    DEFF Research Database (Denmark)

    Sørensen, John Dalsgaard; Frier, Christian

    2004-01-01

    For many reinforced concrete structures corrosion of reinforcement is an important problem since it can result in expensive maintenance and repair actions. Further, a significant reduction of the load-bearing capacity can occur. One mode of corrosion initiation is that the chloride content around...... the reinforcement exceeds a critical threshold value. In the present paper a stochastic model is described by which the chloride content in a reinforced concrete structure can be estimated. The chloride ingress is modeled by a 2-dimensional diffusion process and the diffusion coefficient, surface chloride....... The distribution of the time to initiation of corrosion is estimated by simulation. As an example a bridge pier in a marine environment is considered....

  1. Stochastic Modeling of Reinforced Concrete Structures Exposed to Chloride Attack

    DEFF Research Database (Denmark)

    Sørensen, John Dalsgaard; Frier, Christian

    2003-01-01

    For many reinforced concrete structures corrosion of reinforcement is an important problem since it can result in expensive maintenance and repair actions. Further, a significant reduction of the load-bearing capacity can occur. One mode of corrosion initiation is that the chloride content around...... the reinforcement exceeds a critical threshold value. In the present paper a stochastic model is described by which the chloride content in a reinforced concrete structure can be estimated. The chloride ingress is modeled by a 2-dimensional diffusion process and the diffusion coefficient, surface chloride....... The distribution of the time to initiation of corrosion is estimated by simulation. As an example a bridge pier in a marine environment is considered....

  2. Critical behavior of a stochastic anisotropic Bak-Sneppen model

    Science.gov (United States)

    Han, Jihui; Li, Wei; Su, Zhu; Deng, Webing

    2017-11-01

    In this paper we present our study on the critical behavior of a stochastic anisotropic Bak-Sneppen (saBS) model, in which a parameter α is introduced to describe the interaction strength among nearest species. We estimate the threshold fitness f c and the critical exponent τ r by numerically integrating a master equation for the distribution of avalanche spatial sizes. Other critical exponents are then evaluated from previously known scaling relations. The numerical results are in good agreement with the counterparts yielded by the Monte Carlo simulations. Our results indicate that all saBS models with nonzero interaction strength exhibit self-organized criticality, and fall into the same universality class, by sharing the universal critical exponents.

  3. Stochastic Local Interaction (SLI) model: Bridging machine learning and geostatistics

    Science.gov (United States)

    Hristopulos, Dionissios T.

    2015-12-01

    Machine learning and geostatistics are powerful mathematical frameworks for modeling spatial data. Both approaches, however, suffer from poor scaling of the required computational resources for large data applications. We present the Stochastic Local Interaction (SLI) model, which employs a local representation to improve computational efficiency. SLI combines geostatistics and machine learning with ideas from statistical physics and computational geometry. It is based on a joint probability density function defined by an energy functional which involves local interactions implemented by means of kernel functions with adaptive local kernel bandwidths. SLI is expressed in terms of an explicit, typically sparse, precision (inverse covariance) matrix. This representation leads to a semi-analytical expression for interpolation (prediction), which is valid in any number of dimensions and avoids the computationally costly covariance matrix inversion.

  4. Stochastic group selection model for the evolution of altruism

    CERN Document Server

    Silva, A T C; Silva, Ana T. C.

    1999-01-01

    We study numerically and analytically a stochastic group selection model in which a population of asexually reproducing individuals, each of which can be either altruist or non-altruist, is subdivided into $M$ reproductively isolated groups (demes) of size $N$. The cost associated with being altruistic is modelled by assigning the fitness $1- \\tau$, with $\\tau \\in [0,1]$, to the altruists and the fitness 1 to the non-altruists. In the case that the altruistic disadvantage $\\tau$ is not too large, we show that the finite $M$ fluctuations are small and practically do not alter the deterministic results obtained for $M \\to \\infty$. However, for large $\\tau$ these fluctuations greatly increase the instability of the altruistic demes to mutations. These results may be relevant to the dynamics of parasite-host systems and, in particular, to explain the importance of mutation in the evolution of parasite virulence.

  5. Stochastic group selection model for the evolution of altruism

    Science.gov (United States)

    Silva, Ana T. C.; Fontanari, J. F.

    We study numerically and analytically a stochastic group selection model in which a population of asexually reproducing individuals, each of which can be either altruist or non-altruist, is subdivided into M reproductively isolated groups (demes) of size N. The cost associated with being altruistic is modelled by assigning the fitness 1- τ, with τ∈[0,1], to the altruists and the fitness 1 to the non-altruists. In the case that the altruistic disadvantage τ is not too large, we show that the finite M fluctuations are small and practically do not alter the deterministic results obtained for M→∞. However, for large τ these fluctuations greatly increase the instability of the altruistic demes to mutations. These results may be relevant to the dynamics of parasite-host systems and, in particular, to explain the importance of mutation in the evolution of parasite virulence.

  6. A Stochastic Model for Evolution of Altruistic Genes

    Science.gov (United States)

    Donato, Roberta

    1996-04-01

    We study numerically a stochastic model for evolution and maintenance of a population which reproduces asexually under selective pressure and is divided into smaller groups of variable size. An altruistic trait is defined as lowering the fitness of the carrier, but the survival probability of all the members of a group with a large enough number of altruists is enhanced. Numerical results show that there is a transition in the average proportion of altruists versus the relative advantage conferred by the presence of altruists to all the members of the group. At the transition the distribution of altruistic frequence in the groups is not trivial, and average deme size reaches a minimum. We found also an error-threshold in mutation rate analogous to the quasi-species model of M. Eigen.

  7. Individualism in plant populations: using stochastic differential equations to model individual neighbourhood-dependent plant growth.

    Science.gov (United States)

    Lv, Qiming; Schneider, Manuel K; Pitchford, Jonathan W

    2008-08-01

    We study individual plant growth and size hierarchy formation in an experimental population of Arabidopsis thaliana, within an integrated analysis that explicitly accounts for size-dependent growth, size- and space-dependent competition, and environmental stochasticity. It is shown that a Gompertz-type stochastic differential equation (SDE) model, involving asymmetric competition kernels and a stochastic term which decreases with the logarithm of plant weight, efficiently describes individual plant growth, competition, and variability in the studied population. The model is evaluated within a Bayesian framework and compared to its deterministic counterpart, and to several simplified stochastic models, using distributional validation. We show that stochasticity is an important determinant of size hierarchy and that SDE models outperform the deterministic model if and only if structural components of competition (asymmetry; size- and space-dependence) are accounted for. Implications of these results are discussed in the context of plant ecology and in more general modelling situations.

  8. Stochastic and deterministic model of microbial heat inactivation.

    Science.gov (United States)

    Corradini, Maria G; Normand, Mark D; Peleg, Micha

    2010-03-01

    Microbial inactivation is described by a model based on the changing survival probabilities of individual cells or spores. It is presented in a stochastic and discrete form for small groups, and as a continuous deterministic model for larger populations. If the underlying mortality probability function remains constant throughout the treatment, the model generates first-order ("log-linear") inactivation kinetics. Otherwise, it produces survival patterns that include Weibullian ("power-law") with upward or downward concavity, tailing with a residual survival level, complete elimination, flat "shoulder" with linear or curvilinear continuation, and sigmoid curves. In both forms, the same algorithm or model equation applies to isothermal and dynamic heat treatments alike. Constructing the model does not require assuming a kinetic order or knowledge of the inactivation mechanism. The general features of its underlying mortality probability function can be deduced from the experimental survival curve's shape. Once identified, the function's coefficients, the survival parameters, can be estimated directly from the experimental survival ratios by regression. The model is testable in principle but matching the estimated mortality or inactivation probabilities with those of the actual cells or spores can be a technical challenge. The model is not intended to replace current models to calculate sterility. Its main value, apart from connecting the various inactivation patterns to underlying probabilities at the cellular level, might be in simulating the irregular survival patterns of small groups of cells and spores. In principle, it can also be used for nonthermal methods of microbial inactivation and their combination with heat.

  9. Stochastic Technology Choice Model for Consequential Life Cycle Assessment.

    Science.gov (United States)

    Kätelhön, Arne; Bardow, André; Suh, Sangwon

    2016-12-06

    Discussions on Consequential Life Cycle Assessment (CLCA) have relied largely on partial or general equilibrium models. Such models are useful for integrating market effects into CLCA, but also have well-recognized limitations such as the poor granularity of the sectoral definition and the assumption of perfect oversight by all economic agents. Building on the Rectangular-Choice-of-Technology (RCOT) model, this study proposes a new modeling approach for CLCA, the Technology Choice Model (TCM). In this approach, the RCOT model is adapted for its use in CLCA and extended to incorporate parameter uncertainties and suboptimal decisions due to market imperfections and information asymmetry in a stochastic setting. In a case study on rice production, we demonstrate that the proposed approach allows modeling of complex production technology mixes and their expected environmental outcomes under uncertainty, at a high level of detail. Incorporating the effect of production constraints, uncertainty, and suboptimal decisions by economic agents significantly affects technology mixes and associated greenhouse gas (GHG) emissions of the system under study. The case study also shows the model's ability to determine both the average and marginal environmental impacts of a product in response to changes in the quantity of final demand.

  10. Stochastic radiative transfer model for mixture of discontinuous vegetation canopies

    Energy Technology Data Exchange (ETDEWEB)

    Shabanov, Nikolay V. [Department of Geography, Boston University, 675 Commonwealth Avenue, Boston, MA 02215 (United States)]. E-mail: shabanov@bu.edu; Huang, D. [Brookhaven National Laboratory, Environmental Sciences Department, P.O. Box 5000, Upton, NY 11973 (United States); Knjazikhin, Y. [Department of Geography, Boston University, 675 Commonwealth Avenue, Boston, MA 02215 (United States); Dickinson, R.E. [School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA 30332 (United States); Myneni, Ranga B. [Department of Geography, Boston University, 675 Commonwealth Avenue, Boston, MA 02215 (United States)

    2007-09-15

    Modeling of the radiation regime of a mixture of vegetation species is a fundamental problem of the Earth's land remote sensing and climate applications. The major existing approaches, including the linear mixture model and the turbid medium (TM) mixture radiative transfer model, provide only an approximate solution to this problem. In this study, we developed the stochastic mixture radiative transfer (SMRT) model, a mathematically exact tool to evaluate radiation regime in a natural canopy with spatially varying optical properties, that is, canopy, which exhibits a structured mixture of vegetation species and gaps. The model solves for the radiation quantities, direct input to the remote sensing/climate applications: mean radiation fluxes over whole mixture and over individual species. The canopy structure is parameterized in the SMRT model in terms of two stochastic moments: the probability of finding species and the conditional pair-correlation of species. The second moment is responsible for the 3D radiation effects, namely, radiation streaming through gaps without interaction with vegetation and variation of the radiation fluxes between different species. We performed analytical and numerical analysis of the radiation effects, simulated with the SMRT model for the three cases of canopy structure: (a) non-ordered mixture of species and gaps (TM); (b) ordered mixture of species without gaps; and (c) ordered mixture of species with gaps. The analysis indicates that the variation of radiation fluxes between different species is proportional to the variation of species optical properties (leaf albedo, density of foliage, etc.) Gaps introduce significant disturbance to the radiation regime in the canopy as their optical properties constitute major contrast to those of any vegetation species. The SMRT model resolves deficiencies of the major existing mixture models: ignorance of species radiation coupling via multiple scattering of photons (the linear mixture

  11. On cross-currency models with stochastic volatility and correlated interest rates

    NARCIS (Netherlands)

    Grzelak, L.A.; Oosterlee, C.W.

    2010-01-01

    We construct multi-currency models with stochastic volatility and correlated stochastic interest rates with a full matrix of correlations. We first deal with a foreign exchange (FX) model of Heston-type, in which the domestic and foreign interest rates are generated by the short-rate process of

  12. Can Centre Surround Model Explain the Enhancement of Visual Perception through Stochastic Resonance?

    CERN Document Server

    Kundu, Ajanta

    2010-01-01

    We demonstrate the ability of centre surround model for simulating the enhancement of contrast sensitivity through stochastic resonance observed in psychophysical experiments. We also show that this model could be used to simulate the contrast sensitivity function through stochastic resonance. The quality of the fit of measured contrast sensitivity function to the simulated data is very good.

  13. Dynamics of a stochastic HIV-1 infection model with logistic growth

    Science.gov (United States)

    Jiang, Daqing; Liu, Qun; Shi, Ningzhong; Hayat, Tasawar; Alsaedi, Ahmed; Xia, Peiyan

    2017-03-01

    This paper is concerned with a stochastic HIV-1 infection model with logistic growth. Firstly, by constructing suitable stochastic Lyapunov functions, we establish sufficient conditions for the existence of ergodic stationary distribution of the solution to the HIV-1 infection model. Then we obtain sufficient conditions for extinction of the infection. The stationary distribution shows that the infection can become persistent in vivo.

  14. Efficient Bayesian inference in stochastic chemical kinetic models using graphical processing units

    OpenAIRE

    Niemi, Jarad; Wheeler, Matthew

    2011-01-01

    A goal of systems biology is to understand the dynamics of intracellular systems. Stochastic chemical kinetic models are often utilized to accurately capture the stochastic nature of these systems due to low numbers of molecules. Collecting system data allows for estimation of stochastic chemical kinetic rate parameters. We describe a well-known, but typically impractical data augmentation Markov chain Monte Carlo algorithm for estimating these parameters. The impracticality is due to the use...

  15. Modelling and Analysis of Smart Grid: A Stochastic Model Checking Case Study

    DEFF Research Database (Denmark)

    Yuksel, Ender; Zhu, Huibiao; Nielson, Hanne Riis

    2012-01-01

    Cyber-physical systems integrate information and communication technology functions to the physical elements of a system for monitoring and controlling purposes. The conversion of traditional power grid into a smart grid, a fundamental example of a cyber-physical system, raises a number of issues...... consumption. We employ stochastic model checking approach and present our modelling and analysis study using PRISM model checker....

  16. Application of a Theorem in Stochastic Models of Elections

    Directory of Open Access Journals (Sweden)

    Norman Schofield

    2010-01-01

    Full Text Available Previous empirical research has developed stochastic electoral models for Israel, Turkey, and other polities. The work suggests that convergence to an electoral center (often predicted by electoral models is a nongeneric phenomenon. In an attempt to explain nonconvergence, a formal model based on intrinsic valence is presented. This theory showed that there are necessary and sufficient conditions for convergence. The necessary condition is that a convergence coefficient c is bounded above by the dimension w of the policy space, while a sufficient condition is that the coefficient is bounded above by 1. This coefficient is defined in terms of the difference in exogenous valences, the “spatial coefficient”, and the electoral variance. The theoretical model is then applied to empirical analyses of elections in the United States and Britain. These empirical models include sociodemographic valence and electoral perceptions of character trait. It is shown that the model implies convergence to positions close to the electoral origin. To explain party divergence, the model is then extended to incorporate activist valences. This extension gives a first-order balance condition that allows the party to calculate the optimal marginal condition to maximize vote share. We argue that the equilibrium positions of presidential candidates in US elections and by party leaders in British elections are principally due to the influence of activists, rather than the centripetal effect of the electorate.

  17. Modeling Stochastic Route Choice Behaviors with Equivalent Impedance

    Directory of Open Access Journals (Sweden)

    Jun Li

    2015-01-01

    Full Text Available A Logit-based route choice model is proposed to address the overlapping and scaling problems in the traditional multinomial Logit model. The nonoverlapping links are defined as a subnetwork, and its equivalent impedance is explicitly calculated in order to simply network analyzing. The overlapping links are repeatedly merged into subnetworks with Logit-based equivalent travel costs. The choice set at each intersection comprises only the virtual equivalent route without overlapping. In order to capture heterogeneity in perception errors of different sizes of networks, different scale parameters are assigned to subnetworks and they are linked to the topological relationships to avoid estimation burden. The proposed model provides an alternative method to model the stochastic route choice behaviors without the overlapping and scaling problems, and it still maintains the simple and closed-form expression from the MNL model. A link-based loading algorithm based on Dial’s algorithm is proposed to obviate route enumeration and it is suitable to be applied on large-scale networks. Finally a comparison between the proposed model and other route choice models is given by numerical examples.

  18. Stochastic Model Predictive Control with Applications in Smart Energy Systems

    DEFF Research Database (Denmark)

    Sokoler, Leo Emil; Edlund, Kristian; Mølbak, Tommy

    2012-01-01

    to cover more than 50% of the total consumption by 2050. Energy systems based on significant amounts of renewable energy sources are subject to uncertainties. To accommodate the need for model predictive control (MPC) of such systems, the effect of the stochastic effects on the constraints must...... function). This is convenient for energy systems, since some constraints are very important to satisfy with a high probability, whereas violation of others are less prone to have a large economic penalty. In MPC applications the control action is obtained by solving an optimization problem at each sampling......, we show that tailored interior point algorithms are well suited to handle this type of problems. Namely, by utilizing structure-exploiting methods, we implement a special-purpose solver for control of smart energy systems. The solver is compared against general-purpose implementations. As a case...

  19. Neural network connectivity and response latency modelled by stochastic processes

    DEFF Research Database (Denmark)

    Tamborrino, Massimiliano

    is connected to thousands of other neurons. The rst question is: how to model neural networks through stochastic processes? A multivariate Ornstein-Uhlenbeck process, obtained as a diffusion approximation of a jump process, is the proposed answer. Obviously, dependencies between neurons imply dependencies...... between their spike times. Therefore, the second question is: how to detect neural network connectivity from simultaneously recorded spike trains? Answering this question corresponds to investigate the joint distribution of sequences of rst passage times. A non-parametric method based on copulas...... generation of pikes. When a stimulus is applied to the network, the spontaneous rings may prevail and hamper detection of the effects of the stimulus. Therefore, the spontaneous rings cannot be ignored and the response latency has to be detected on top of a background signal. Everything becomes more dicult...

  20. Stochastic Modeling Approach to the Incubation Time of Prionic Diseases

    Science.gov (United States)

    Ferreira, A. S.; da Silva, M. A.; Cressoni, J. C.

    2003-05-01

    Transmissible spongiform encephalopathies are neurodegenerative diseases for which prions are the attributed pathogenic agents. A widely accepted theory assumes that prion replication is due to a direct interaction between the pathologic (PrPSc) form and the host-encoded (PrPC) conformation, in a kind of autocatalytic process. Here we show that the overall features of the incubation time of prion diseases are readily obtained if the prion reaction is described by a simple mean-field model. An analytical expression for the incubation time distribution then follows by associating the rate constant to a stochastic variable log normally distributed. The incubation time distribution is then also shown to be log normal and fits the observed BSE (bovine spongiform encephalopathy) data very well. Computer simulation results also yield the correct BSE incubation time distribution at low PrPC densities.

  1. Maximum caliber inference and the stochastic Ising model

    Science.gov (United States)

    Cafaro, Carlo; Ali, Sean Alan

    2016-11-01

    We investigate the maximum caliber variational principle as an inference algorithm used to predict dynamical properties of complex nonequilibrium, stationary, statistical systems in the presence of incomplete information. Specifically, we maximize the path entropy over discrete time step trajectories subject to normalization, stationarity, and detailed balance constraints together with a path-dependent dynamical information constraint reflecting a given average global behavior of the complex system. A general expression for the transition probability values associated with the stationary random Markov processes describing the nonequilibrium stationary system is computed. By virtue of our analysis, we uncover that a convenient choice of the dynamical information constraint together with a perturbative asymptotic expansion with respect to its corresponding Lagrange multiplier of the general expression for the transition probability leads to a formal overlap with the well-known Glauber hyperbolic tangent rule for the transition probability for the stochastic Ising model in the limit of very high temperatures of the heat reservoir.

  2. Cancer growth dynamics: stochastic models and noise induced effects

    Science.gov (United States)

    Spagnolo, B.; Fiasconaro, A.; Pizzolato, N.; Valenti, D.; Adorno, D. Persano; Caldara, P.; Ochab-Marcinek, A.; Gudowska-Nowak, E.

    2009-04-01

    In the framework of the Michaelis-Menten (MM) reaction kinetics, we analyze the cancer growth dynamics in the presence of the immune response. We found the coexistence of noise enhanced stability (NES) and resonant activation (RA) phenomena which act in an opposite way with respect to the extinction of the tumor. The role of the stochastic resonance (SR) in the case of weak cancer therapy has been analyzed. The evolutionary dynamics of a system of cancerous cells in a model of chronic myeloid leukemia (CML) is investigated by a Monte Carlo approach. We analyzed the effects of a targeted therapy on the evolutionary dynamics of normal, first-mutant and cancerous cell populations. We show how the patient response to the therapy changes when an high value of the mutation rate from healthy to cancerous cells is present. Our results are in agreement with clinical observations.

  3. A Method for Systematic Improvement of Stochastic Grey-Box Models

    DEFF Research Database (Denmark)

    Kristensen, Niels Rode; Madsen, Henrik; Jørgensen, Sten Bay

    2004-01-01

    A systematic framework for improving the quality of continuous time models of dynamic systems based on experimental data is presented. The framework is based on an interplay between stochastic differential equation modelling, statistical tests and nonparametric modelling and provides features...

  4. Handbook of EOQ inventory problems stochastic and deterministic models and applications

    CERN Document Server

    Choi, Tsan-Ming

    2013-01-01

    This book explores deterministic and stochastic EOQ-model based problems and applications, presenting technical analyses of single-echelon EOQ model based inventory problems, and applications of the EOQ model for multi-echelon supply chain inventory analysis.

  5. A Stochastic Programming Model for Fuel Treatment Management

    Directory of Open Access Journals (Sweden)

    Mohannad Kabli

    2015-06-01

    Full Text Available This work considers a two-stage stochastic integer programming (SIP approach for optimizing fuel treatment planning under uncertainty in weather and fire occurrence for rural forests. Given a set of areas for potentially performing fuel treatment, the problem is to decide the best treatment option for each area under uncertainty in future weather and fire occurrence. A two-stage SIP model is devised whose objective is to minimize the here-and-now cost of fuel treatment in the first-stage, plus the expected future costs due to uncertain impact from potential fires in the second-stage calculated as ecosystem services losses. The model considers four fuel treatment options: no treatment, mechanical thinning, prescribed fire, and grazing. Several constraints such as budgetary and labor constraints are included in the model and a standard fire behavior model is used to estimate some of the parameters of the model such as fuel levels at the beginning of the fire season. The SIP model was applied to data for a study area in East Texas with 15 treatment areas under different weather scenarios. The results of the study show, for example, that unless the expected ecosystem services values for an area outweigh fuel treatment costs, no treatment is the best choice for the area. Thus the valuation of the area together with the probability of fire occurrence and behavior strongly drive fuel treatment choices.

  6. High-dimensional nonlinear diffusion stochastic processes modelling for engineering applications

    CERN Document Server

    Mamontov, Yevgeny

    2001-01-01

    This book is the first one devoted to high-dimensional (or large-scale) diffusion stochastic processes (DSPs) with nonlinear coefficients. These processes are closely associated with nonlinear Ito's stochastic ordinary differential equations (ISODEs) and with the space-discretized versions of nonlinear Ito's stochastic partial integro-differential equations. The latter models include Ito's stochastic partial differential equations (ISPDEs). The book presents the new analytical treatment which can serve as the basis of a combined, analytical-numerical approach to greater computational efficienc

  7. Stochastic Analysis 2010

    CERN Document Server

    Crisan, Dan

    2011-01-01

    "Stochastic Analysis" aims to provide mathematical tools to describe and model high dimensional random systems. Such tools arise in the study of Stochastic Differential Equations and Stochastic Partial Differential Equations, Infinite Dimensional Stochastic Geometry, Random Media and Interacting Particle Systems, Super-processes, Stochastic Filtering, Mathematical Finance, etc. Stochastic Analysis has emerged as a core area of late 20th century Mathematics and is currently undergoing a rapid scientific development. The special volume "Stochastic Analysis 2010" provides a sa

  8. A Spatial Clustering Approach for Stochastic Fracture Network Modelling

    Science.gov (United States)

    Seifollahi, S.; Dowd, P. A.; Xu, C.; Fadakar, A. Y.

    2014-07-01

    Fracture network modelling plays an important role in many application areas in which the behaviour of a rock mass is of interest. These areas include mining, civil, petroleum, water and environmental engineering and geothermal systems modelling. The aim is to model the fractured rock to assess fluid flow or the stability of rock blocks. One important step in fracture network modelling is to estimate the number of fractures and the properties of individual fractures such as their size and orientation. Due to the lack of data and the complexity of the problem, there are significant uncertainties associated with fracture network modelling in practice. Our primary interest is the modelling of fracture networks in geothermal systems and, in this paper, we propose a general stochastic approach to fracture network modelling for this application. We focus on using the seismic point cloud detected during the fracture stimulation of a hot dry rock reservoir to create an enhanced geothermal system; these seismic points are the conditioning data in the modelling process. The seismic points can be used to estimate the geographical extent of the reservoir, the amount of fracturing and the detailed geometries of fractures within the reservoir. The objective is to determine a fracture model from the conditioning data by minimizing the sum of the distances of the points from the fitted fracture model. Fractures are represented as line segments connecting two points in two-dimensional applications or as ellipses in three-dimensional (3D) cases. The novelty of our model is twofold: (1) it comprises a comprehensive fracture modification scheme based on simulated annealing and (2) it introduces new spatial approaches, a goodness-of-fit measure for the fitted fracture model, a measure for fracture similarity and a clustering technique for proposing a locally optimal solution for fracture parameters. We use a simulated dataset to demonstrate the application of the proposed approach

  9. Modeling of uncertain spectra through stochastic autoregressive systems

    Science.gov (United States)

    Wang, Yiwei; Wang, X. Q.; Mignolet, Marc P.; Yang, Shuchi; Chen, P. C.

    2016-03-01

    The focus of this investigation is on the formulation and validation of a modeling strategy of the uncertainty that may exist on the specification of the power spectral density of scalar stationary processes and on the spectral matrices of vector ones. These processes may, for example, be forces on a structure originating from natural phenomena which are coarsely modeled (i.e., with epistemic uncertainty) or are specified by parameters unknown (i.e., with aleatoric uncertainty) in the application considered. The propagation of the uncertainty, e.g., to the response of the structure, may be carried out provided that a stochastic model of the uncertainty in the power spectral density/matrix is available from which admissible samples can be efficiently generated. Such a stochastic model will be developed here through an autoregressive-based parameterization of the specified baseline power spectral density/matrix and of its random samples. Autoregressive (AR) models are particularly well suited for this parametrization since their spectra are known to converge to a broad class of spectra (all non-pathological spectra) as the AR order increases. Note that the characterization of these models is not achieved directly in terms of their coefficients but rather in terms of their reflection coefficients which lie (or their eigenvalues in the vector process case) in the domain [0,1) as a necessary and sufficient condition for stability. Maximum entropy concepts are then employed to formulate the distribution of the reflection coefficients in both scalar and vector process case leading to a small set of hyperparameters of the uncertain model. Depending on the information available, these hyperparameters could either be varied in a parametric study format to assess the effects of uncertainty or could be identified, e.g., in a maximum likelihood format, from observed data. The validation and assessment of these concepts is finally achieved on several examples including the

  10. Controlled Nonlinear Stochastic Delay Equations: Part I: Modeling and Approximations

    Energy Technology Data Exchange (ETDEWEB)

    Kushner, Harold J., E-mail: hjk@dam.brown.edu [Brown University, Applied Math (United States)

    2012-08-15

    This two-part paper deals with 'foundational' issues that have not been previously considered in the modeling and numerical optimization of nonlinear stochastic delay systems. There are new classes of models, such as those with nonlinear functions of several controls (such as products), each with is own delay, controlled random Poisson measure driving terms, admissions control with delayed retrials, and others. There are two basic and interconnected themes for these models. The first, dealt with in this part, concerns the definition of admissible control. The classical definition of an admissible control as a nonanticipative relaxed control is inadequate for these models and needs to be extended. This is needed for the convergence proofs of numerical approximations for optimal controls as well as to have a well-defined model. It is shown that the new classes of admissible controls do not enlarge the range of the value functions, is closed (together with the associated paths) under weak convergence, and is approximatable by ordinary controls. The second theme, dealt with in Part II, concerns transportation equation representations, and their role in the development of numerical algorithms with much reduced memory and computational requirements.

  11. Stochastic model for the vocabulary growth in natural languages

    CERN Document Server

    Gerlach, Martin

    2013-01-01

    We propose a stochastic model for the number of different words in a given database which incorporates the dependence on the database size and historical changes. The main feature of our model is the existence of two different classes of words: (i) a finite number of core-words which have higher frequency and do not affect the probability of a new word to be used; and (ii) the remaining virtually infinite number of noncore-words which have lower frequency and once used reduce the probability of a new word to be used in the future. Our model relies on a careful analysis of the google-ngram database of books published in the last centuries and its main consequence is the generalization of Zipf's and Heaps' law to two scaling regimes. We confirm that these generalizations yield the best simple description of the data among generic descriptive models and that the two free parameters depend only on the language but not on the database. From the point of view of our model the main change on historical time scales i...

  12. Bayesian analysis of botanical epidemics using stochastic compartmental models.

    Science.gov (United States)

    Gibson, G J; Kleczkowski, A; Gilligan, C A

    2004-08-17

    A stochastic model for an epidemic, incorporating susceptible, latent, and infectious states, is developed. The model represents primary and secondary infection rates and a time-varying host susceptibility with applications to a wide range of epidemiological systems. A Markov chain Monte Carlo algorithm is presented that allows the model to be fitted to experimental observations within a Bayesian framework. The approach allows the uncertainty in unobserved aspects of the process to be represented in the parameter posterior densities. The methods are applied to experimental observations of damping-off of radish (Raphanus sativus) caused by the fungal pathogen Rhizoctonia solani, in the presence and absence of the antagonistic fungus Trichoderma viride, a biological control agent that has previously been shown to affect the rate of primary infection by using a maximum-likelihood estimate for a simpler model with no allowance for a latent period. Using the Bayesian analysis, we are able to estimate the latent period from population data, even when there is uncertainty in discriminating infectious from latently infected individuals in data collection. We also show that the inference that T. viride can control primary, but not secondary, infection is robust to inclusion of the latent period in the model, although the absolute values of the parameters change. Some refinements and potential difficulties with the Bayesian approach in this context, when prior information on parameters is lacking, are discussed along with broader applications of the methods to a wide range of epidemiological systems.

  13. Stochastic Dynamics on Hypergraphs and the Spatial Majority Rule Model

    Science.gov (United States)

    Lanchier, N.; Neufer, J.

    2013-04-01

    This article starts by introducing a new theoretical framework to model spatial systems which is obtained from the framework of interacting particle systems by replacing the traditional graphical structure that defines the network of interactions with a structure of hypergraph. This new perspective is more appropriate to define stochastic spatial processes in which large blocks of vertices may flip simultaneously, which is then applied to define a spatial version of the Galam's majority rule model. In our spatial model, each vertex of the lattice has one of two possible competing opinions, say opinion 0 and opinion 1, as in the popular voter model. Hyperedges are updated at rate one, which results in all the vertices in the hyperedge changing simultaneously their opinion to the majority opinion of the hyperedge. In the case of a tie in hyperedges with even size, a bias is introduced in favor of type 1, which is motivated by the principle of social inertia. Our analytical results along with simulations and heuristic arguments suggest that, in any spatial dimensions and when the set of hyperedges consists of the collection of all n×⋯× n blocks of the lattice, opinion 1 wins when n is even while the system clusters when n is odd, which contrasts with results about the voter model in high dimensions for which opinions coexist. This is fully proved in one dimension while the rest of our analysis focuses on the cases when n=2 and n=3 in two dimensions.

  14. Stochastic Model for the Vocabulary Growth in Natural Languages

    Science.gov (United States)

    Gerlach, Martin; Altmann, Eduardo G.

    2013-04-01

    We propose a stochastic model for the number of different words in a given database which incorporates the dependence on the database size and historical changes. The main feature of our model is the existence of two different classes of words: (i) a finite number of core words, which have higher frequency and do not affect the probability of a new word to be used, and (ii) the remaining virtually infinite number of noncore words, which have lower frequency and, once used, reduce the probability of a new word to be used in the future. Our model relies on a careful analysis of the Google Ngram database of books published in the last centuries, and its main consequence is the generalization of Zipf’s and Heaps’ law to two-scaling regimes. We confirm that these generalizations yield the best simple description of the data among generic descriptive models and that the two free parameters depend only on the language but not on the database. From the point of view of our model, the main change on historical time scales is the composition of the specific words included in the finite list of core words, which we observe to decay exponentially in time with a rate of approximately 30 words per year for English.

  15. Stochastic Model for the Vocabulary Growth in Natural Languages

    Directory of Open Access Journals (Sweden)

    Martin Gerlach

    2013-05-01

    Full Text Available We propose a stochastic model for the number of different words in a given database which incorporates the dependence on the database size and historical changes. The main feature of our model is the existence of two different classes of words: (i a finite number of core words, which have higher frequency and do not affect the probability of a new word to be used, and (ii the remaining virtually infinite number of noncore words, which have lower frequency and, once used, reduce the probability of a new word to be used in the future. Our model relies on a careful analysis of the Google Ngram database of books published in the last centuries, and its main consequence is the generalization of Zipf’s and Heaps’ law to two-scaling regimes. We confirm that these generalizations yield the best simple description of the data among generic descriptive models and that the two free parameters depend only on the language but not on the database. From the point of view of our model, the main change on historical time scales is the composition of the specific words included in the finite list of core words, which we observe to decay exponentially in time with a rate of approximately 30 words per year for English.

  16. Stochastic inverse modelling of hydraulic conductivity fields taking into account independent stochastic structures: A 3D case study

    Science.gov (United States)

    Llopis-Albert, C.; Capilla, J. E.

    2010-09-01

    SummaryMajor factors affecting groundwater flow through fractured rocks include the geometry of each fracture, its properties and the fracture-network connectivity together with the porosity and conductivity of the rock matrix. When modelling fractured rocks this is translated into attaining a characterization of the hydraulic conductivity ( K) as adequately as possible, despite its high heterogeneity. This links with the main goal of this paper, which is to present an improvement of a stochastic inverse model, named as Gradual Conditioning (GC) method, to better characterise K in a fractured rock medium by considering different K stochastic structures, belonging to independent K statistical populations (SP) of fracture families and the rock matrix, each one with its own statistical properties. The new methodology is carried out by applying independent deformations to each SP during the conditioning process for constraining stochastic simulations to data. This allows that the statistical properties of each SPs tend to be preserved during the iterative optimization process. It is worthwhile mentioning that so far, no other stochastic inverse modelling technique, with the whole capabilities implemented in the GC method, is able to work with a domain covered by several different stochastic structures taking into account the independence of different populations. The GC method is based on a procedure that gradually changes an initial K field, which is conditioned only to K data, to approximate the reproduction of other types of information, i.e., piezometric head and solute concentration data. The approach is applied to the Äspö Hard Rock Laboratory (HRL) in Sweden, where, since the middle nineties, many experiments have been carried out to increase confidence in alternative radionuclide transport modelling approaches. Because the description of fracture locations and the distribution of hydrodynamic parameters within them are not accurate enough, we address the

  17. Symbolic Model Checking of Stochastic Systems: Theory and Implementation

    NARCIS (Netherlands)

    Kuntz, G.W.M.; Siegle, Markus; Valmari, Antti

    2006-01-01

    This paper presents IM-SPDL, a stochastic extension of the modal logic PDL, which supports the specification of complex performance and dependability requirements. The logic is interpreted over extended stochastic labelled transition systems (ESLTS), i.e. transition systems containing both immediate

  18. Stochastic Modeling and Analysis of Power System with Renewable Generation

    DEFF Research Database (Denmark)

    Chen, Peiyuan

    be achieved through a probabilistic analysis that takes into account the stochastic behavior of wind power generation (WPG) and load demand. Such a probabilistic analysis may help network operators to cut down the cost associated with system planning. Thus, the objective of this thesis is to develop......Unlike traditional fossil-fuel based power generation, renewable generation such as wind power relies on uncontrollable prime sources such as wind speed. Wind speed varies stochastically, which to a large extent determines the stochastic behavior of power generation from wind farms....... With the increasing number of wind turbines (WTs) connected to distribution systems, network operators are concerned about how such a stochastic generation affects power losses of the network. Furthermore, the operators need to estimate how much and when the stochastic generation can reduce the loading of substation...

  19. Exercise effects in a virtual type 1 diabetes patient: Using stochastic differential equations for model extension

    DEFF Research Database (Denmark)

    Duun-Henriksen, Anne Katrine; Schmidt, S.; Nørgaard, K.

    2013-01-01

    physical activity. Exercise constitutes a substantial challenge to closed-loop control of T1D. The effects are many and depend on intensity and duration and may be delayed by several hours. In this study, we use a model for the glucoregulatory system based on the minimal model and a previously published...... extension incorporating exercise effects on insulin and glucose dynamics. Our model is constructed as a stochastic state space model consisting of a set of stochastic differential equations (SDEs). In a stochastic state space model, the residual error is split into random measurement error...

  20. Reservoir modelling of heterolithic tidal deposits : Sensitivity analysis of an object-based stochastic model

    NARCIS (Netherlands)

    Geel, C.R.; Donselaar, M.E.

    2007-01-01

    Object-based stochastic modelling techniques are routinely employed to generate multiple realisations of the spatial distribution of sediment properties in settings where data density is insufficient to construct a unique deterministic facies architecture model. Challenge is to limit the wide range

  1. Stochastic model of Tsc1 lesions in mouse brain.

    Directory of Open Access Journals (Sweden)

    Shilpa Prabhakar

    Full Text Available Tuberous sclerosis complex (TSC is an autosomal dominant disorder due to mutations in either TSC1 or TSC2 that affects many organs with hamartomas and tumors. TSC-associated brain lesions include subependymal nodules, subependymal giant cell astrocytomas and tubers. Neurologic manifestations in TSC comprise a high frequency of mental retardation and developmental disorders including autism, as well as epilepsy. Here, we describe a new mouse model of TSC brain lesions in which complete loss of Tsc1 is achieved in multiple brain cell types in a stochastic pattern. Injection of an adeno-associated virus vector encoding Cre recombinase into the cerebral ventricles of mice homozygous for a Tsc1 conditional allele on the day of birth led to reduced survival, and pathologic findings of enlarged neurons, cortical heterotopias, subependymal nodules, and hydrocephalus. The severity of clinical and pathologic findings as well as survival was shown to be dependent upon the dose and serotype of Cre virus injected. Although several other models of TSC brain disease exist, this model is unique in that the pathology reflects a variety of TSC-associated lesions involving different numbers and types of cells. This model provides a valuable and unique addition for therapeutic assessment.

  2. A stochastic discrete optimization model for designing container terminal facilities

    Science.gov (United States)

    Zukhruf, Febri; Frazila, Russ Bona; Burhani, Jzolanda Tsavalista

    2017-11-01

    As uncertainty essentially affect the total transportation cost, it remains important in the container terminal that incorporates several modes and transshipments process. This paper then presents a stochastic discrete optimization model for designing the container terminal, which involves the decision of facilities improvement action. The container terminal operation model is constructed by accounting the variation of demand and facilities performance. In addition, for illustrating the conflicting issue that practically raises in the terminal operation, the model also takes into account the possible increment delay of facilities due to the increasing number of equipment, especially the container truck. Those variations expectantly reflect the uncertainty issue in the container terminal operation. A Monte Carlo simulation is invoked to propagate the variations by following the observed distribution. The problem is constructed within the framework of the combinatorial optimization problem for investigating the optimal decision of facilities improvement. A new variant of glow-worm swarm optimization (GSO) is thus proposed for solving the optimization, which is rarely explored in the transportation field. The model applicability is tested by considering the actual characteristics of the container terminal.

  3. A continuous stochastic model for non-equilibrium dense gases

    Science.gov (United States)

    Sadr, M.; Gorji, M. H.

    2017-12-01

    While accurate simulations of dense gas flows far from the equilibrium can be achieved by direct simulation adapted to the Enskog equation, the significant computational demand required for collisions appears as a major constraint. In order to cope with that, an efficient yet accurate solution algorithm based on the Fokker-Planck approximation of the Enskog equation is devised in this paper; the approximation is very much associated with the Fokker-Planck model derived from the Boltzmann equation by Jenny et al. ["A solution algorithm for the fluid dynamic equations based on a stochastic model for molecular motion," J. Comput. Phys. 229, 1077-1098 (2010)] and Gorji et al. ["Fokker-Planck model for computational studies of monatomic rarefied gas flows," J. Fluid Mech. 680, 574-601 (2011)]. The idea behind these Fokker-Planck descriptions is to project the dynamics of discrete collisions implied by the molecular encounters into a set of continuous Markovian processes subject to the drift and diffusion. Thereby, the evolution of particles representing the governing stochastic process becomes independent from each other and thus very efficient numerical schemes can be constructed. By close inspection of the Enskog operator, it is observed that the dense gas effects contribute further to the advection of molecular quantities. That motivates a modelling approach where the dense gas corrections can be cast in the extra advection of particles. Therefore, the corresponding Fokker-Planck approximation is derived such that the evolution in the physical space accounts for the dense effects present in the pressure, stress tensor, and heat fluxes. Hence the consistency between the devised Fokker-Planck approximation and the Enskog operator is shown for the velocity moments up to the heat fluxes. For validation studies, a homogeneous gas inside a box besides Fourier, Couette, and lid-driven cavity flow setups is considered. The results based on the Fokker-Planck model are

  4. ARIMA-Based Time Series Model of Stochastic Wind Power Generation

    DEFF Research Database (Denmark)

    Chen, Peiyuan; Pedersen, Troels; Bak-Jensen, Birgitte

    2010-01-01

    This paper proposes a stochastic wind power model based on an autoregressive integrated moving average (ARIMA) process. The model takes into account the nonstationarity and physical limits of stochastic wind power generation. The model is constructed based on wind power measurement of one year from...... the Nysted offshore wind farm in Denmark. The proposed limited-ARIMA (LARIMA) model introduces a limiter and characterizes the stochastic wind power generation by mean level, temporal correlation and driving noise. The model is validated against the measurement in terms of temporal correlation...... and probability distribution. The LARIMA model outperforms a first-order transition matrix based discrete Markov model in terms of temporal correlation, probability distribution and model parameter number. The proposed LARIMA model is further extended to include the monthly variation of the stochastic wind power...

  5. Stochastic Parameterization: Towards a new view of Weather and Climate Models

    NARCIS (Netherlands)

    D.T. Crommelin (Daan); not CWI et al

    2017-01-01

    htmlabstractThe last decade has seen the success of stochastic parameterizations in short-term, medium-range and seasonal ensembles: operational weather centers now routinely use stochastic parameterization schemes to better represent model inadequacy and improve the quantification of forecast

  6. Modelling of stochastic hybrid systems with applications to accident risk assessment

    NARCIS (Netherlands)

    Krystul, J.

    2006-01-01

    Stochastic dynamical modelling of accident risk is of high interest for the safe design of complex safety-critical systems and operations, such as in nuclear and chemical industries, and advanced air traffic management. In comparison with statistical analysis of collected data, stochastic dynamical

  7. Modelling anisotropic covariance using stochastic development and sub-Riemannian frame bundle geometry

    DEFF Research Database (Denmark)

    Sommer, Stefan Horst; Svane, Anne Marie

    2017-01-01

    We discuss the geometric foundation behind the use of stochastic processes in the frame bundle of a smooth manifold to build stochastic models with applications in statistical analysis of non-linear data. The transition densities for the projection to the manifold of Brownian motions developed in...

  8. Variational formulation for Black-Scholes equations in stochastic volatility models

    Science.gov (United States)

    Gyulov, Tihomir B.; Valkov, Radoslav L.

    2012-11-01

    In this note we prove existence and uniqueness of weak solutions to a boundary value problem arising from stochastic volatility models in financial mathematics. Our settings are variational in weighted Sobolev spaces. Nevertheless, as it will become apparent our variational formulation agrees well with the stochastic part of the problem.

  9. Stochastic order in dichotomous item response models for fixed, adaptive, and multidimensional tests

    NARCIS (Netherlands)

    van der Linden, Willem J.

    Dichotomous IRT models can be viewed as families of stochastically ordered distributions of responses to test items. This paper explores several properties of such distributions. In particular, it is examined under what conditions stochastic order in families of conditional distributions is

  10. On the modelling of nested risk-neutral stochastic processes with applications in insurance

    NARCIS (Netherlands)

    S.N. Singor (Stefan); A. Boer; J.S.C. Alberts; C.W. Oosterlee (Cornelis)

    2017-01-01

    textabstractWe propose a modelling framework for risk-neutral stochastic processes nested in a real-world stochastic process. The framework is important for insurers that deal with the valuation of embedded options and in particular at future points in time. We make use of the class of State Space

  11. Hybrid approaches for multiple-species stochastic reaction–diffusion models

    Energy Technology Data Exchange (ETDEWEB)

    Spill, Fabian, E-mail: fspill@bu.edu [Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, MA 02215 (United States); Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 (United States); Guerrero, Pilar [Department of Mathematics, University College London, Gower Street, London WC1E 6BT (United Kingdom); Alarcon, Tomas [Centre de Recerca Matematica, Campus de Bellaterra, Edifici C, 08193 Bellaterra (Barcelona) (Spain); Departament de Matemàtiques, Universitat Atonòma de Barcelona, 08193 Bellaterra (Barcelona) (Spain); Maini, Philip K. [Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford OX2 6GG (United Kingdom); Byrne, Helen [Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford OX2 6GG (United Kingdom); Computational Biology Group, Department of Computer Science, University of Oxford, Oxford OX1 3QD (United Kingdom)

    2015-10-15

    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. - Highlights: • A novel hybrid stochastic/deterministic reaction–diffusion simulation method is given. • Can massively speed up stochastic simulations while preserving stochastic effects. • Can handle multiple reacting species. • Can handle moving boundaries.

  12. Stochastic model simulation using Kronecker product analysis and Zassenhaus formula approximation.

    Science.gov (United States)

    Caglar, Mehmet Umut; Pal, Ranadip

    2013-01-01

    Probabilistic Models are regularly applied in Genetic Regulatory Network modeling to capture the stochastic behavior observed in the generation of biological entities such as mRNA or proteins. Several approaches including Stochastic Master Equations and Probabilistic Boolean Networks have been proposed to model the stochastic behavior in genetic regulatory networks. It is generally accepted that Stochastic Master Equation is a fundamental model that can describe the system being investigated in fine detail, but the application of this model is computationally enormously expensive. On the other hand, Probabilistic Boolean Network captures only the coarse-scale stochastic properties of the system without modeling the detailed interactions. We propose a new approximation of the stochastic master equation model that is able to capture the finer details of the modeled system including bistabilities and oscillatory behavior, and yet has a significantly lower computational complexity. In this new method, we represent the system using tensors and derive an identity to exploit the sparse connectivity of regulatory targets for complexity reduction. The algorithm involves an approximation based on Zassenhaus formula to represent the exponential of a sum of matrices as product of matrices. We derive upper bounds on the expected error of the proposed model distribution as compared to the stochastic master equation model distribution. Simulation results of the application of the model to four different biological benchmark systems illustrate performance comparable to detailed stochastic master equation models but with considerably lower computational complexity. The results also demonstrate the reduced complexity of the new approach as compared to commonly used Stochastic Simulation Algorithm for equivalent accuracy.

  13. Escape problem under stochastic volatility: the Heston model.

    Science.gov (United States)

    Masoliver, Jaume; Perelló, Josep

    2008-11-01

    We solve the escape problem for the Heston random diffusion model from a finite interval of span L . We obtain exact expressions for the survival probability (which amounts to solving the complete escape problem) as well as for the mean exit time. We also average the volatility in order to work out the problem for the return alone regardless of volatility. We consider these results in terms of the dimensionless normal level of volatility-a ratio of the three parameters that appear in the Heston model-and analyze their form in several asymptotic limits. Thus, for instance, we show that the mean exit time grows quadratically with large spans while for small spans the growth is systematically slower, depending on the value of the normal level. We compare our results with those of the Wiener process and show that the assumption of stochastic volatility, in an apparently paradoxical way, increases survival and prolongs the escape time. We finally observe that the model is able to describe the main exit-time statistics of the Dow-Jones daily index.

  14. Unified Stochastic Geometry Model for MIMO Cellular Networks with Retransmissions

    KAUST Repository

    Afify, Laila H.

    2016-10-11

    This paper presents a unified mathematical paradigm, based on stochastic geometry, for downlink cellular networks with multiple-input-multiple-output (MIMO) base stations (BSs). The developed paradigm accounts for signal retransmission upon decoding errors, in which the temporal correlation among the signal-to-interference-plus-noise-ratio (SINR) of the original and retransmitted signals is captured. In addition to modeling the effect of retransmission on the network performance, the developed mathematical model presents twofold analysis unification for MIMO cellular networks literature. First, it integrates the tangible decoding error probability and the abstracted (i.e., modulation scheme and receiver type agnostic) outage probability analysis, which are largely disjoint in the literature. Second, it unifies the analysis for different MIMO configurations. The unified MIMO analysis is achieved by abstracting unnecessary information conveyed within the interfering signals by Gaussian signaling approximation along with an equivalent SISO representation for the per-data stream SINR in MIMO cellular networks. We show that the proposed unification simplifies the analysis without sacrificing the model accuracy. To this end, we discuss the diversity-multiplexing tradeoff imposed by different MIMO schemes and shed light on the diversity loss due to the temporal correlation among the SINRs of the original and retransmitted signals. Finally, several design insights are highlighted.

  15. On a stochastic leaky integrate-and-fire neuronal model.

    Science.gov (United States)

    Buonocore, A; Caputo, L; Pirozzi, E; Ricciardi, L M

    2010-10-01

    The leaky integrate-and-fire neuronal model proposed in Stevens and Zador (1998), in which time constant and resting potential are postulated to be time dependent, is revisited within a stochastic framework in which the membrane potential is mathematically described as a gauss-diffusion process. The first-passage-time probability density, miming in such a context the firing probability density, is evaluated by either the Volterra integral equation of Buonocore, Nobile, and Ricciardi ( 1987 ) or, when possible, by the asymptotics of Giorno, Nobile, and Ricciardi (1990). The model examined here represents an extension of the classic leaky integrate-and-fire one based on the Ornstein-Uhlenbeck process in that it is in principle compatible with the inclusion of some other physiological characteristics such as relative refractoriness. It also allows finer tuning possibilities in view of its accounting for certain qualitative as well as quantitative features, such as the behavior of the time course of the membrane potential prior to firings and the computation of experimentally measurable statistical descriptors of the firing time: mean, median, coefficient of variation, and skewness. Finally, implementations of this model are provided in connection with certain experimental evidence discussed in the literature.

  16. A Stochastic Unit Commitment Model for a Local CHP Plant

    DEFF Research Database (Denmark)

    Ravn, Hans V.; Riisom, Jannik; Schaumburg-Müller, Camilla

    2005-01-01

    Local CHP development in Denmark has during the 90’s been characterised by large growth primarily due to government subsidies in the form of feed-in tariffs. In line with the liberalisation process in the EU, Danish local CHPs of a certain size must operate on market terms from 2005. This paper p...... the spot prices of the years 2001-2003, both with and without the immersion heater included in the model, and the results are compared to the full information case.......Local CHP development in Denmark has during the 90’s been characterised by large growth primarily due to government subsidies in the form of feed-in tariffs. In line with the liberalisation process in the EU, Danish local CHPs of a certain size must operate on market terms from 2005. This paper...... presents a stochastic unit commitment model for a single local CHP plant (consisting of CHP unit, boiler, and heat storage facility) which takes into account varying spot prices. Further, additional technology is implemented in the model in the form of an immersion heater. Simulations are conducted using...

  17. Stochastic model for gene transcription on Drosophila melanogaster embryos

    Science.gov (United States)

    Prata, Guilherme N.; Hornos, José Eduardo M.; Ramos, Alexandre F.

    2016-02-01

    We examine immunostaining experimental data for the formation of stripe 2 of even-skipped (eve) transcripts on D. melanogaster embryos. An estimate of the factor converting immunofluorescence intensity units into molecular numbers is given. The analysis of the eve dynamics at the region of stripe 2 suggests that the promoter site of the gene has two distinct regimes: an earlier phase when it is predominantly activated until a critical time when it becomes mainly repressed. That suggests proposing a stochastic binary model for gene transcription on D. melanogaster embryos. Our model has two random variables: the transcripts number and the state of the source of mRNAs given as active or repressed. We are able to reproduce available experimental data for the average number of transcripts. An analysis of the random fluctuations on the number of eves and their consequences on the spatial precision of stripe 2 is presented. We show that the position of the anterior or posterior borders fluctuate around their average position by ˜1 % of the embryo length, which is similar to what is found experimentally. The fitting of data by such a simple model suggests that it can be useful to understand the functions of randomness during developmental processes.

  18. Patterns of mesenchymal condensation in a multiscale, discrete stochastic model.

    Directory of Open Access Journals (Sweden)

    Scott Christley

    2007-04-01

    Full Text Available Cells of the embryonic vertebrate limb in high-density culture undergo chondrogenic pattern formation, which results in the production of regularly spaced "islands" of cartilage similar to the cartilage primordia of the developing limb skeleton. The first step in this process, in vitro and in vivo, is the generation of "cell condensations," in which the precartilage cells become more tightly packed at the sites at which cartilage will form. In this paper we describe a discrete, stochastic model for the behavior of limb bud precartilage mesenchymal cells in vitro. The model uses a biologically motivated reaction-diffusion process and cell-matrix adhesion (haptotaxis as the bases of chondrogenic pattern formation, whereby the biochemically distinct condensing cells, as well as the size, number, and arrangement of the multicellular condensations, are generated in a self-organizing fashion. Improving on an earlier lattice-gas representation of the same process, it is multiscale (i.e., cell and molecular dynamics occur on distinct scales, and the cells are represented as spatially extended objects that can change their shape. The authors calibrate the model using experimental data and study sensitivity to changes in key parameters. The simulations have disclosed two distinct dynamic regimes for pattern self-organization involving transient or stationary inductive patterns of morphogens. The authors discuss these modes of pattern formation in relation to available experimental evidence for the in vitro system, as well as their implications for understanding limb skeletal patterning during embryonic development.

  19. Reverse stochastic resonance in a hippocampal CA1 neuron model.

    Science.gov (United States)

    Durand, Dominique M; Kawaguchi, Minato; Mino, Hiroyuki

    2013-01-01

    Stochastic resonance (SR) is a ubiquitous and counter- intuitive phenomenon whereby the addition of noise to a non-linear system can improve the detection of sub-threshold signals. The "signal" is normally periodic or deterministic whereas the "noise" is normally stochastic. However, in neural systems, signals are often stochastic. Moreover, periodic signals are applied near neurons to control neural excitability (i.e. deep brain stimulation). We therefore tested the hypothesis that a quasi-periodic signal applied to a neural network could enhance the detection of a stochastic neural signal (reverse stochastic resonance). Using computational methods, a CA1 hippocampal neuron was simulated and a Poisson distributed subthreshold synaptic input ("signal") was applied to the synaptic terminals. A periodic or quasi periodic pulse train at various frequencies ("noise") was applied to an extracellular electrode located near the neuron. The mutual information and information transfer rate between the output and input of the neuron were calculated. The results display the signature of stochastic resonance with information transfer reaching a maximum value for increasing power (or frequency) of the "noise". This result shows that periodic signals applied extracellularly can improve the detection of subthreshold stochastic neural signals. The optimum frequency (110 Hz) is similar to that used in patients with Parkinson's suggesting that this phenomenon could play a role in the therapeutic effect of high frequency stimulation.

  20. SMART (Stochastic Model Acquisition with ReinforcemenT) learning agents: A preliminary report

    OpenAIRE

    Child, C. H. T.; Stathis, K.

    2005-01-01

    We present a framework for building agents that learn using SMART, a system that combines stochastic model acquisition with reinforcement learning to enable an agent to model its environment through experience and subsequently form action selection policies using the acquired model. We extend an existing algorithm for automatic creation of stochastic strips operators [9] as a preliminary method of environment modelling. We then define the process of generation of future states using these ope...

  1. Parameter discovery in stochastic biological models using simulated annealing and statistical model checking.

    Science.gov (United States)

    Hussain, Faraz; Jha, Sumit K; Jha, Susmit; Langmead, Christopher J

    2014-01-01

    Stochastic models are increasingly used to study the behaviour of biochemical systems. While the structure of such models is often readily available from first principles, unknown quantitative features of the model are incorporated into the model as parameters. Algorithmic discovery of parameter values from experimentally observed facts remains a challenge for the computational systems biology community. We present a new parameter discovery algorithm that uses simulated annealing, sequential hypothesis testing, and statistical model checking to learn the parameters in a stochastic model. We apply our technique to a model of glucose and insulin metabolism used for in-silico validation of artificial pancreata and demonstrate its effectiveness by developing parallel CUDA-based implementation for parameter synthesis in this model.

  2. Fish Processed Production Planning Using Integer Stochastic Programming Model

    Science.gov (United States)

    Firmansyah, Mawengkang, Herman

    2011-06-01

    Fish and its processed products are the most affordable source of animal protein in the diet of most people in Indonesia. The goal in production planning is to meet customer demand over a fixed time horizon divided into planning periods by optimizing the trade-off between economic objectives such as production cost and customer satisfaction level. The major decisions are production and inventory levels for each product and the number of workforce in each planning period. In this paper we consider the management of small scale traditional business at North Sumatera Province which performs processing fish into several local seafood products. The inherent uncertainty of data (e.g. demand, fish availability), together with the sequential evolution of data over time leads the production planning problem to a nonlinear mixed-integer stochastic programming model. We use scenario generation based approach and feasible neighborhood search for solving the model. The results which show the amount of each fish processed product and the number of workforce needed in each horizon planning are presented.

  3. Hierarchic stochastic modelling applied to intracellular Ca(2+ signals.

    Directory of Open Access Journals (Sweden)

    Gregor Moenke

    Full Text Available Important biological processes like cell signalling and gene expression have noisy components and are very complex at the same time. Mathematical analysis of such systems has often been limited to the study of isolated subsystems, or approximations are used that are difficult to justify. Here we extend a recently published method (Thurley and Falcke, PNAS 2011 which is formulated in observable system configurations instead of molecular transitions. This reduces the number of system states by several orders of magnitude and avoids fitting of kinetic parameters. The method is applied to Ca(2+ signalling. Ca(2+ is a ubiquitous second messenger transmitting information by stochastic sequences of concentration spikes, which arise by coupling of subcellular Ca(2+ release events (puffs. We derive analytical expressions for a mechanistic Ca(2+ model, based on recent data from live cell imaging, and calculate Ca(2+ spike statistics in dependence on cellular parameters like stimulus strength or number of Ca(2+ channels. The new approach substantiates a generic Ca(2+ model, which is a very convenient way to simulate Ca(2+ spike sequences with correct spiking statistics.

  4. A stochastic model for EEG microstate sequence analysis.

    Science.gov (United States)

    Gärtner, Matthias; Brodbeck, Verena; Laufs, Helmut; Schneider, Gaby

    2015-01-01

    The analysis of spontaneous resting state neuronal activity is assumed to give insight into the brain function. One noninvasive technique to study resting state activity is electroencephalography (EEG) with a subsequent microstate analysis. This technique reduces the recorded EEG signal to a sequence of prototypical topographical maps, which is hypothesized to capture important spatio-temporal properties of the signal. In a statistical EEG microstate analysis of healthy subjects in wakefulness and three stages of sleep, we observed a simple structure in the microstate transition matrix. It can be described with a first order Markov chain in which the transition probability from the current state (i.e., map) to a different map does not depend on the current map. The resulting transition matrix shows a high agreement with the observed transition matrix, requiring only about 2% of mass transport (1/2 L1-distance). In the second part, we introduce an extended framework in which the simple Markov chain is used to make inferences on a potential underlying time continuous process. This process cannot be directly observed and is therefore usually estimated from discrete sampling points of the EEG signal given by the local maxima of the global field power. Therefore, we propose a simple stochastic model called sampled marked intervals (SMI) model that relates the observed sequence of microstates to an assumed underlying process of background intervals and thus, complements approaches that focus on the analysis of observable microstate sequences. Copyright © 2014 Elsevier Inc. All rights reserved.

  5. Stochastic Modelling as a Tool for Seismic Signals Segmentation

    Directory of Open Access Journals (Sweden)

    Daniel Kucharczyk

    2016-01-01

    Full Text Available In order to model nonstationary real-world processes one can find appropriate theoretical model with properties following the analyzed data. However in this case many trajectories of the analyzed process are required. Alternatively, one can extract parts of the signal that have homogenous structure via segmentation. The proper segmentation can lead to extraction of important features of analyzed phenomena that cannot be described without the segmentation. There is no one universal method that can be applied for all of the phenomena; thus novel methods should be invented for specific cases. They might address specific character of the signal in different domains (time, frequency, time-frequency, etc.. In this paper we propose two novel segmentation methods that take under consideration the stochastic properties of the analyzed signals in time domain. Our research is motivated by the analysis of vibration signals acquired in an underground mine. In such signals we observe seismic events which appear after the mining activity, like blasting, provoked relaxation of rock, and some unexpected events, like natural rock burst. The proposed segmentation procedures allow for extraction of such parts of the analyzed signals which are related to mentioned events.

  6. The threshold of a stochastic avian-human influenza epidemic model with psychological effect

    Science.gov (United States)

    Zhang, Fengrong; Zhang, Xinhong

    2018-02-01

    In this paper, a stochastic avian-human influenza epidemic model with psychological effect in human population and saturation effect within avian population is investigated. This model describes the transmission of avian influenza among avian population and human population in random environments. For stochastic avian-only system, persistence in the mean and extinction of the infected avian population are studied. For the avian-human influenza epidemic system, sufficient conditions for the existence of an ergodic stationary distribution are obtained. Furthermore, a threshold of this stochastic model which determines the outcome of the disease is obtained. Finally, numerical simulations are given to support the theoretical results.

  7. On the connection between morphological and stochastic permeability models of porous media

    Science.gov (United States)

    Hristopulos, D. T.

    2003-04-01

    We present a theoretical framework that connects morphological and stochastic models of the fluid permeability in porous media. Morphological models relate fluid permeability to properties of the pore space geometry, such as the porosity and specific interfacial area. On the other hand, stochastic theories of flow and transport are based on statistical representations of the fluid permeability obtained from the analysis of permeability data, which do not make a direct connection with the pore morphology. Using the local porosity theory, we develop a link between the morphological and stochastic permeability models, and we show how statistical properties follow from the small-scale variability of the morphology.

  8. A stochastic model for predicting the mortality of breast cancer.

    Science.gov (United States)

    Lee, Sandra; Zelen, Marvin

    2006-01-01

    Consider a cohort of women, identified by year of birth, some of whom will eventually be diagnosed with breast cancer. A stochastic model is developed for predicting the U.S. breast cancer mortality that depends on advances in therapy and dissemination of mammographic screening. The predicted mortality can be compared with the same cohort having usual care with no screening program and absence of modern therapy, or a cohort in which only a proportion participate in a screening program and have modern therapy. The model envisions that a woman may be in four health states: i.e., 1) no disease or breast cancer that cannot be diagnosed (S0), 2) preclinical state (Sp), 3) clinical state (Sc), and 4) disease-specific death (Sd). The preclinical disease refers to breast cancer that is asymptomatic but that may be diagnosed with a special exam. The clinical state refers to symptomatic disease diagnosed under usual care. One of the basic assumptions of the model is that the disease is progressive; i.e., the transitions for the first three states are S0-->Sp-->Sc. The other basic assumption is that any reduction in mortality associated with earlier diagnosis is due to a stage shift in diagnosis; i.e., early diagnosis results in a larger proportion of earlier stage patients. The model is used to predict changes in female breast cancer mortality in the U.S. women for 1975-2000. The model is general and may predict mortality for other chronic diseases that satisfy the two basic assumptions.

  9. A Stochastic Tick-Borne Disease Model: Exploring the Probability of Pathogen Persistence.

    Science.gov (United States)

    Maliyoni, Milliward; Chirove, Faraimunashe; Gaff, Holly D; Govinder, Keshlan S

    2017-07-13

    We formulate and analyse a stochastic epidemic model for the transmission dynamics of a tick-borne disease in a single population using a continuous-time Markov chain approach. The stochastic model is based on an existing deterministic metapopulation tick-borne disease model. We compare the disease dynamics of the deterministic and stochastic models in order to determine the effect of randomness in tick-borne disease dynamics. The probability of disease extinction and that of a major outbreak are computed and approximated using the multitype Galton-Watson branching process and numerical simulations, respectively. Analytical and numerical results show some significant differences in model predictions between the stochastic and deterministic models. In particular, we find that a disease outbreak is more likely if the disease is introduced by infected deer as opposed to infected ticks. These insights demonstrate the importance of host movement in the expansion of tick-borne diseases into new geographic areas.

  10. Model Checking for a Class of Performance Properties of Fluid Stochastic Models

    NARCIS (Netherlands)

    Bujorianu, L.M.; Bujorianu, M.C.; Horváth, A.; Telek, M.

    2006-01-01

    Recently, there is an explosive development of fluid approa- ches to computer and distributed systems. These approaches are inherently stochastic and generate continuous state space models. Usually, the performance measures for these systems are defined using probabilities of reaching certain sets

  11. A 5G Hybrid Channel Model Considering Rays and Geometric Stochastic Propagation Graph

    DEFF Research Database (Denmark)

    Steinböck, Gerhard; Karstensen, Anders; Kyösti, Pekka

    2016-01-01

    We consider a ray-tracing tool, in particular the METIS map based model for deterministic simulation of the channel impulse response. The ray-tracing tool is extended by adding a geometric stochastic propagation graph to model additional stochastic paths and the dense multipath components observed...... concept of a hybrid model that allows to simulate computationally efficient deterministic paths and the dense multipath components in a spatially consistent way....

  12. Stability of the Stochastic Model for Power Markets with Interval Parameters

    Directory of Open Access Journals (Sweden)

    Zhanhui Lu

    2016-01-01

    Full Text Available Pertaining to the random nature of demand sides and the range of demand elasticity with suppliers and consumers, a stochastic model for power markets with interval parameters is described to illustrate uncertain external disturbances, which is a generalization of the Alvarado dynamic model, stochastic model, and interval model. The interval stochastic stability criteria of the provided model are investigated by the theory of economics, interval dynamical system, and the theory stability of stochastic differential equations. The conclusions indicate that the demand elasticity stable interval can be calculated and the random excitation intensity does not impact the system stability. Some numerical examples are given to show the applicability and validity of the obtained results from a statistical perspective.

  13. Bayesian parameter inference for stochastic biochemical network models using particle Markov chain Monte Carlo.

    Science.gov (United States)

    Golightly, Andrew; Wilkinson, Darren J

    2011-12-06

    Computational systems biology is concerned with the development of detailed mechanistic models of biological processes. Such models are often stochastic and analytically intractable, containing uncertain parameters that must be estimated from time course data. In this article, we consider the task of inferring the parameters of a stochastic kinetic model defined as a Markov (jump) process. Inference for the parameters of complex nonlinear multivariate stochastic process models is a challenging problem, but we find here that algorithms based on particle Markov chain Monte Carlo turn out to be a very effective computationally intensive approach to the problem. Approximations to the inferential model based on stochastic differential equations (SDEs) are considered, as well as improvements to the inference scheme that exploit the SDE structure. We apply the methodology to a Lotka-Volterra system and a prokaryotic auto-regulatory network.

  14. Longitudinal functional principal component modelling via Stochastic Approximation Monte Carlo

    KAUST Repository

    Martinez, Josue G.

    2010-06-01

    The authors consider the analysis of hierarchical longitudinal functional data based upon a functional principal components approach. In contrast to standard frequentist approaches to selecting the number of principal components, the authors do model averaging using a Bayesian formulation. A relatively straightforward reversible jump Markov Chain Monte Carlo formulation has poor mixing properties and in simulated data often becomes trapped at the wrong number of principal components. In order to overcome this, the authors show how to apply Stochastic Approximation Monte Carlo (SAMC) to this problem, a method that has the potential to explore the entire space and does not become trapped in local extrema. The combination of reversible jump methods and SAMC in hierarchical longitudinal functional data is simplified by a polar coordinate representation of the principal components. The approach is easy to implement and does well in simulated data in determining the distribution of the number of principal components, and in terms of its frequentist estimation properties. Empirical applications are also presented.

  15. Stochastic model of microcredit interest rate in Morocco

    Directory of Open Access Journals (Sweden)

    Ghita Bennouna

    2016-11-01

    Full Text Available Access to microcredit can have a beneficial effect on the well-being of low-income households excluded from the traditional banking system. It allows this population to receive affordable financial services to help them to meet their needs and to improve their living conditions. However to provide access to credit, microfinance institutions should ensure not only their social mission but also commercial and financial mission to enable the institution to perpetuate and become self-sufficient. To this end, MFIs (microfinance institutions must apply an interest rate that covers their costs and risk, while generating profits, Also microentrepreneurs need, to this end, to ensure the profitability of their activities. This paper presents the microfinance sector in Morocco. It focuses then on the interest rate applied by the Moroccan microfinance institutions; it provides also a comparative study between Morocco and other comparable countries in terms of interest rates charged to borrowers. Finally, this article presents a stochastic model of the interest rate in microcredit built in random loan repayment periods and on a real example of the program of loans of microfinance institution in Morocco

  16. Multistage Stochastic Programming Models for Pharmaceutical Clinical Trial Planning

    Directory of Open Access Journals (Sweden)

    Zuo Zeng

    2017-11-01

    Full Text Available Clinical trial planning of candidate drugs is an important task for pharmaceutical companies. In this paper, we propose two new multistage stochastic programming formulations (CM1 and CM2 to determine the optimal clinical trial plan under uncertainty. Decisions of a clinical trial plan include which clinical trials to start and their start times. Its objective is to maximize expected net present value of the entire clinical trial plan. Outcome of a clinical trial is uncertain, i.e., whether a potential drug successfully completes a clinical trial is not known until the clinical trial is completed. This uncertainty is modeled using an endogenous uncertain parameter in CM1 and CM2. The main difference between CM1 and CM2 is an additional binary variable, which tracks both start and end time points of clinical trials in CM2. We compare the sizes and solution times of CM1 and CM2 with each other and with a previously developed formulation (CM3 using different instances of clinical trial planning problem. The results reveal that the solution times of CM1 and CM2 are similar to each other and are up to two orders of magnitude shorter compared to CM3 for all instances considered. In general, the root relaxation problems of CM1 and CM2 took shorter to solve, CM1 and CM2 yielded tight initial gaps, and the solver required fewer branches for convergence to the optimum for CM1 and CM2.

  17. OPTIMAL TRAINING POLICY FOR PROMOTION - STOCHASTIC MODELS OF MANPOWER SYSTEMS

    Directory of Open Access Journals (Sweden)

    V.S.S. Yadavalli

    2012-01-01

    Full Text Available In this paper, the optimal planning of manpower training programmes in a manpower system with two grades is discussed. The planning of manpower training within a given organization involves a trade-off between training costs and expected return. These planning problems are examined through models that reflect the random nature of manpower movement in two grades. To be specific, the system consists of two grades, grade 1 and grade 2. Any number of persons in grade 2 can be sent for training and after the completion of training, they will stay in grade 2 and will be given promotion as and when vacancies arise in grade 1. Vacancies arise in grade 1 only by wastage. A person in grade 1 can leave the system with probability p. Vacancies are filled with persons in grade 2 who have completed the training. It is assumed that there is a perfect passing rate and that the sizes of both grades are fixed. Assuming that the planning horizon is finite and is T, the underlying stochastic process is identified as a finite state Markov chain and using dynamic programming, a policy is evolved to determine how many persons should be sent for training at any time k so as to minimize the total expected cost for the entire planning period T.

  18. Stochastic model for detection of signals in noise

    Science.gov (United States)

    Klein, Stanley A.; Levi, Dennis M.

    2010-01-01

    Fifty years ago Birdsall, Tanner, and colleagues made rapid progress in developing signal detection theory into a powerful psychophysical tool. One of their major insights was the utility of adding external noise to the signals of interest. These methods have been enhanced in recent years by the addition of multipass and classification-image methods for opening up the black box. There remain a number of as yet unresolved issues. In particular, Birdsall developed a theorem that large amounts of external input noise can linearize nonlinear systems, and Tanner conjectured, with mathematical backup, that what had been previously thought of as a nonlinear system could actually be a linear system with uncertainty. Recent findings, both experimental and theoretical, have validated Birdsall’s theorem and Tanner’s conjecture. However, there have also been experimental and theoretical findings with the opposite outcome. In this paper we present new data and simulations in an attempt to sort out these issues. Our simulations and experiments plus data from others show that Birdsall’s theorem is quite robust. We argue that uncertainty can serve as an explanation for violations of Birdsall’s linearization by noise and also for reports of stochastic resonance. In addition, we modify present models to better handle detection of signals with both noise and pedestal backgrounds. PMID:19884912

  19. Inexact Multistage Stochastic Chance Constrained Programming Model for Water Resources Management under Uncertainties

    Directory of Open Access Journals (Sweden)

    Hong Zhang

    2017-01-01

    Full Text Available In order to formulate water allocation schemes under uncertainties in the water resources management systems, an inexact multistage stochastic chance constrained programming (IMSCCP model is proposed. The model integrates stochastic chance constrained programming, multistage stochastic programming, and inexact stochastic programming within a general optimization framework to handle the uncertainties occurring in both constraints and objective. These uncertainties are expressed as probability distributions, interval with multiply distributed stochastic boundaries, dynamic features of the long-term water allocation plans, and so on. Compared with the existing inexact multistage stochastic programming, the IMSCCP can be used to assess more system risks and handle more complicated uncertainties in water resources management systems. The IMSCCP model is applied to a hypothetical case study of water resources management. In order to construct an approximate solution for the model, a hybrid algorithm, which incorporates stochastic simulation, back propagation neural network, and genetic algorithm, is proposed. The results show that the optimal value represents the maximal net system benefit achieved with a given confidence level under chance constraints, and the solutions provide optimal water allocation schemes to multiple users over a multiperiod planning horizon.

  20. Quantitative modelling and analysis of a Chinese smart grid: a stochastic model checking case study

    DEFF Research Database (Denmark)

    Yuksel, Ender; Nielson, Hanne Riis; Nielson, Flemming

    2014-01-01

    that require novel methods and applications. One of the important issues in this context is the verification of certain quantitative properties of the system. In this paper, we consider a specific Chinese smart grid implementation as a case study and address the verification problem for performance and energy...... consumption.We employ stochastic model checking approach and present our modelling and analysis study using PRISM model checker....

  1. Meso-Scale Stochastic Model for Flow and Transport in Porous Media

    Science.gov (United States)

    Tartakovsky, A. M.; Tartakovsky, D. M.; Meakin, P.

    2008-12-01

    In a homogeneous porous medium, dispersive mixing is the result of a combination of molecular diffusion (diffusive mixing) and spreading due to variations in the fluid velocity (advective mixing). In traditional Darcy(continuum)-scale models this combination is treated as a Fickian diffusion process with a macro-scale effective diffusion coefficient (the dispersion coefficient). However, dispersive mixing is very different from purely diffusive mixing and there is ample evidence that the advection-dispersion equations significantly over-predict the extent of reactions in mixing induced chemical transformations. We have developed a new meso-scale stochastic Lagrangian particle model that treats advective mixing and diffusive mixing separately. We assume that fluid flow in homogeneous porous media is governed by a stochastic Langevin equation that is obtained by adding white noise fluctuations to the momentum conservation equation. The noise represents the random interactions between the fluid and the disordered porous medium, which forces fluid flow paths to deviate from the smooth flow paths predicted by the Darcy scale continuum flow equations. The molecular diffusion of solutes carried by the fluid is governed by the classical advection-diffusion equation, which becomes stochastic due to random advection. The stochastic meso-scale model and deterministic advection-dispersion theory were used to simulate the reactive mixing of two solutions injected in parallel into a flow domain. IN the stochastic model, the transport equations were numerically solved using smoothed particle hydrodynamics (SPH), a Lagrangian particle method that has been previously applied to both deterministic and stochastic transport problems. Comparison of the two solutions revealed that the Langevin model gives better estimates of concentrations than the Darcy scale advection-dispersion model, and that the Darcy scale model significantly overestimates the amount of product in mixing induced

  2. Avalanches in a stochastic model of spiking neurons.

    Directory of Open Access Journals (Sweden)

    Marc Benayoun

    Full Text Available Neuronal avalanches are a form of spontaneous activity widely observed in cortical slices and other types of nervous tissue, both in vivo and in vitro. They are characterized by irregular, isolated population bursts when many neurons fire together, where the number of spikes per burst obeys a power law distribution. We simulate, using the Gillespie algorithm, a model of neuronal avalanches based on stochastic single neurons. The network consists of excitatory and inhibitory neurons, first with all-to-all connectivity and later with random sparse connectivity. Analyzing our model using the system size expansion, we show that the model obeys the standard Wilson-Cowan equations for large network sizes ( neurons. When excitation and inhibition are closely balanced, networks of thousands of neurons exhibit irregular synchronous activity, including the characteristic power law distribution of avalanche size. We show that these avalanches are due to the balanced network having weakly stable functionally feedforward dynamics, which amplifies some small fluctuations into the large population bursts. Balanced networks are thought to underlie a variety of observed network behaviours and have useful computational properties, such as responding quickly to changes in input. Thus, the appearance of avalanches in such functionally feedforward networks indicates that avalanches may be a simple consequence of a widely present network structure, when neuron dynamics are noisy. An important implication is that a network need not be "critical" for the production of avalanches, so experimentally observed power laws in burst size may be a signature of noisy functionally feedforward structure rather than of, for example, self-organized criticality.

  3. Comparison of the Stochastic Models for Double-Differenced GPS Measurements

    Directory of Open Access Journals (Sweden)

    Dudy Darmawan

    2004-11-01

    Full Text Available Double-differenced GPS carrier phase measurements are commonly used in GPS precise positioning applications and processed with algorithms based on the least-squares (LS principle. In order to apply the LS principle, one needs to define properly both the functional and stochastic models. Whilst the functional model for precise GPS positioning is sufficiently well known, realistic stochastic modeling is still a difficult task to accomplish in practice. Incorrect stochastic models for double-differenced GPS measurements will lead to unreliable estimates for ambiguity resolution and, eventually, it will bias positioning results. The common assumption when we construct the stochastic model is that all raw GPS measurements are independent and have the same variances. In fact, this is not realistic, since due to varying noise levels measurements obtained from different GPS satellites cannot have the same accuracy. A realistic stochastic modeling should be able to capture the ordinary noises in the observables. In order to specify a realistic stochastic model for precise relative GPS positioning applications, in this paper the performance of three stochastic models namely the commonly used model or the standard model, the outer product of residual data vector model and Minimum Norm Quadratic Unbiased Estimation (MINQUE are examined and effects of each the proposed model on statistic for ambiguity search and positioning accuracy are compared. The results indicate that the MINQUE model tends to perform better than the other models. Using the MINQUE model, the reliability of the ambiguity resolution and the statistics of the baseline components can be improved. It may suggest that the MINQUE model, which is based on modern statistical theory, is capable of capturing the ordinary noises.

  4. Using copulas for modeling stochastic dependence in power system uncertainty analysis

    NARCIS (Netherlands)

    Papaefthymiou, G.; Kurowicka, D.

    2009-01-01

    The increasing penetration of renewable generation in power systems necessitates the modeling of this stochastic system infeed in operation and planning studies. The system analysis leads to multivariate uncertainty analysis problems, involving non-Normal correlated random variables. In this

  5. Large Deviations for Stochastic Models of Two-Dimensional Second Grade Fluids

    Energy Technology Data Exchange (ETDEWEB)

    Zhai, Jianliang, E-mail: zhaijl@ustc.edu.cn [University of Science and Technology of China, School of Mathematical Sciences (China); Zhang, Tusheng, E-mail: Tusheng.Zhang@manchester.ac.uk [University of Manchester, School of Mathematics (United Kingdom)

    2017-06-15

    In this paper, we establish a large deviation principle for stochastic models of incompressible second grade fluids. The weak convergence method introduced by Budhiraja and Dupuis (Probab Math Statist 20:39–61, 2000) plays an important role.

  6. Multivariate Stochastic Processes Compatible With "Aspect" Models of Similarity and Choice.

    Science.gov (United States)

    Marley, A. A. J.

    1981-01-01

    The multivariate stochastic processes associated with the Marshall-Olkin multivariate exponential distribution are shown to be able to generate several models of similarity or preference data in the literature. (JKS)

  7. A scalable community detection algorithm for large graphs using stochastic block models

    KAUST Repository

    Peng, Chengbin

    2017-11-24

    Community detection in graphs is widely used in social and biological networks, and the stochastic block model is a powerful probabilistic tool for describing graphs with community structures. However, in the era of

  8. Persistence and distribution of a stochastic susceptible-infected-removed epidemic model with varying population size

    Science.gov (United States)

    Chen, Lihong; Wei, Fengying

    2017-10-01

    In this paper, the dynamics of a stochastic susceptible-infected-removed model in a population with varying size is investigated. We firstly show that the stochastic epidemic model has a unique global positive solution with any positive initial value. Then we verify that random perturbations lead to extinction when some conditions are being valid. Moreover, we prove that the solution of the stochastic epidemic model is persistent in the mean by building up a suitable Lyapunov function and using generalized Itô's formula. Further, the stochastic epidemic model admits a stationary distribution around the endemic equilibrium when parameters satisfy some sufficient conditions. To end this contribution and to check the validity of the main results, numerical simulations are separately carried out to illustrate these results.

  9. Rules of thumb for conservation of metapopulations based on a stochastic winking-patch model

    NARCIS (Netherlands)

    Etienne, R.S.; Heesterbeek, J.A.P.

    2001-01-01

    From a theoretical viewpoint, nature management basically has two options to prolong metapopulation persistence: decreasing local extinction probabilities and increasing colonization probabilities. This article focuses on those options with a stochastic, single-species metapopulation model. We found

  10. A stochastic multi-agent optimization model for energy infrastructure planning under uncertainty and competition.

    Science.gov (United States)

    2017-07-04

    This paper presents a stochastic multi-agent optimization model that supports energy infrastruc- : ture planning under uncertainty. The interdependence between dierent decision entities in the : system is captured in an energy supply chain network, w...

  11. Rejection-free stochastic simulation of BNGL-encoded models

    Energy Technology Data Exchange (ETDEWEB)

    Hlavacek, William S [Los Alamos National Laboratory; Monine, Michael I [Los Alamos National Laboratory; Colvin, Joshua [TRANSLATIONAL GENOM; Posner, Richard G [NORTHERN ARIZONA UNIV.; Von Hoff, Daniel D [TRANSLATIONAL GENOMICS RESEARCH INSTIT.

    2009-01-01

    Formal rules encoded using the BioNetGen language (BNGL) can be used to represent the system-level dynamics of molecular interactions. Rules allow one to compactly and implicitly specify the reaction network implied by a set of molecules and their interactions. Typically, the reaction network implied by a set of rules is large, which makes generation of the underlying rule-defined network expensive. Moreover, the cost of conventional simulation methods typically depends on network size. Together these factors have limited application of the rule-based modeling approach. To overcome this limitation, several methods have recently been developed for determining the reaction dynamics implied by rules while avoiding the expensive step of network generation. The cost of these 'network-free' simulation methods is independent of the number of reactions implied by rules. Software implementing such methods is needed for the analysis of rule-based models of biochemical systems. Here, we present a software tool called RuleMonkey that implements a network-free stochastic simulation method for rule-based models. The method is rejection free, unlike other network-free methods that introduce null events (i.e., steps in the simulation procedure that do not change the state of the reaction system being simulated), and the software is capable of simulating models encoded in BNGL, a general-purpose model-specification language. We verify that RuleMonkey produces correct simulation results, and we compare its performance against DYNSTOC, another BNGL-compliant general-purpose simulator for rule-based models, as well as various problem-specific codes that implement network-free simulation methods. RuleMonkey enables the simulation of models defined by rule sets that imply large-scale reaction networks. It is faster than DYNSTOC for stiff problems, although it requires the use of more computer memory. RuleMonkey is freely available for non-commercial use as a stand

  12. A Stochastic Model for Short-Term Probabilistic Forecast of Solar Photo-Voltaic Power

    OpenAIRE

    Ramakrishna, Raksha; Scaglione, Anna; Vittal, Vijay

    2017-01-01

    In this paper, a stochastic model with regime switching is developed for solar photo-voltaic (PV) power in order to provide short-term probabilistic forecasts. The proposed model for solar PV power is physics inspired and explicitly incorporates the stochasticity due to clouds using different parameters addressing the attenuation in power.Based on the statistical behavior of parameters, a simple regime-switching process between the three classes of sunny, overcast and partly cloudy is propose...

  13. Dynamics for a class of stochastic SIS epidemic models with nonlinear incidence and periodic coefficients

    Science.gov (United States)

    Rifhat, Ramziya; Wang, Lei; Teng, Zhidong

    2017-09-01

    In this paper, we investigate the dynamics of a class of periodic stochastic SIS epidemic models with general nonlinear incidence f(S , I) . Some sufficient conditions on the permanence in the mean and extinction of positive solutions with probability one are established. By using the Khasminskii's boundary periodic Markov processes, the existence of stochastic nontrivial periodic solution for the models is also obtained. The numerical simulations are given to illustrate the main theoretical results and some interesting conjectures are presented.

  14. Microgrid Reliability Modeling and Battery Scheduling Using Stochastic Linear Programming

    Energy Technology Data Exchange (ETDEWEB)

    Cardoso, Goncalo; Stadler, Michael; Siddiqui, Afzal; Marnay, Chris; DeForest, Nicholas; Barbosa-Povoa, Ana; Ferrao, Paulo

    2013-05-23

    This paper describes the introduction of stochastic linear programming into Operations DER-CAM, a tool used to obtain optimal operating schedules for a given microgrid under local economic and environmental conditions. This application follows previous work on optimal scheduling of a lithium-iron-phosphate battery given the output uncertainty of a 1 MW molten carbonate fuel cell. Both are in the Santa Rita Jail microgrid, located in Dublin, California. This fuel cell has proven unreliable, partially justifying the consideration of storage options. Several stochastic DER-CAM runs are executed to compare different scenarios to values obtained by a deterministic approach. Results indicate that using a stochastic approach provides a conservative yet more lucrative battery schedule. Lower expected energy bills result, given fuel cell outages, in potential savings exceeding 6percent.

  15. Impact of a refined airborne LiDAR stochastic model for natural hazard applications

    Science.gov (United States)

    Glennie, C. L.; Bolkas, D.; Fotopoulos, G.

    2016-12-01

    Airborne Light Detection and Ranging (LiDAR) is often employed to derive multi-temporal Digital Elevation Models (DEMs), that are used to estimate vertical displacement resulting from natural hazards such as landslides, rockfalls and erosion. Vertical displacements are estimated by computing the difference between two DEMs separated by a specified time period and applying a threshold to remove the inherent noise. Thus, reliable information about the accuracy of DEMs is essential. The assessment of airborne LiDAR errors is typically based on (i) independent ground control points (ii) forward error propagation utilizing the LiDAR geo-referencing equation. The latter approach is dependent on the stochastic model information of the LiDAR measurements. Furthermore, it provides the user with point-by-point accuracy estimation. In this study, a refined stochastic model is obtained through variance component estimation (VCE) for a dataset in Houston, Texas. Results show that initial stochastic information was optimistic by 35% for both horizontal coordinates and ellipsoidal heights. To assess the impact of a refined stochastic model, surface displacement simulations are evaluated. The simulations include scenarios with topographic slopes that vary from 10º to 60º, and vertical displacement of ±1 to ±5 m. Results highlight the cases where a reliable stochastic model is important. A refined stochastic model can be used in practical applications for determining appropriate noise thresholds in vertical displacement, improve quantitative analysis, and enhance relevant decision-making.

  16. Robust nonlinear autoregressive moving average model parameter estimation using stochastic recurrent artificial neural networks

    DEFF Research Database (Denmark)

    Chon, K H; Hoyer, D; Armoundas, A A

    1999-01-01

    error is obtained by subtracting the corrupt signal of the estimated ARMA model obtained via the deterministic estimation step from the system output response. We present computer simulation examples to show the efficacy of the proposed stochastic recurrent neural network approach in obtaining accurate......In this study, we introduce a new approach for estimating linear and nonlinear stochastic autoregressive moving average (ARMA) model parameters, given a corrupt signal, using artificial recurrent neural networks. This new approach is a two-step approach in which the parameters of the deterministic...... part of the stochastic ARMA model are first estimated via a three-layer artificial neural network (deterministic estimation step) and then reestimated using the prediction error as one of the inputs to the artificial neural networks in an iterative algorithm (stochastic estimation step). The prediction...

  17. GERMcode: A Stochastic Model for Space Radiation Risk Assessment

    Science.gov (United States)

    Kim, Myung-Hee Y.; Ponomarev, Artem L.; Cucinotta, Francis A.

    2012-01-01

    A new computer model, the GCR Event-based Risk Model code (GERMcode), was developed to describe biophysical events from high-energy protons and high charge and energy (HZE) particles that have been studied at the NASA Space Radiation Laboratory (NSRL) for the purpose of simulating space radiation biological effects. In the GERMcode, the biophysical description of the passage of HZE particles in tissue and shielding materials is made with a stochastic approach that includes both particle track structure and nuclear interactions. The GERMcode accounts for the major nuclear interaction processes of importance for describing heavy ion beams, including nuclear fragmentation, elastic scattering, and knockout-cascade processes by using the quantum multiple scattering fragmentation (QMSFRG) model. The QMSFRG model has been shown to be in excellent agreement with available experimental data for nuclear fragmentation cross sections. For NSRL applications, the GERMcode evaluates a set of biophysical properties, such as the Poisson distribution of particles or delta-ray hits for a given cellular area and particle dose, the radial dose on tissue, and the frequency distribution of energy deposition in a DNA volume. By utilizing the ProE/Fishbowl ray-tracing analysis, the GERMcode will be used as a bi-directional radiation transport model for future spacecraft shielding analysis in support of Mars mission risk assessments. Recent radiobiological experiments suggest the need for new approaches to risk assessment that include time-dependent biological events due to the signaling times for activation and relaxation of biological processes in cells and tissue. Thus, the tracking of the temporal and spatial distribution of events in tissue is a major goal of the GERMcode in support of the simulation of biological processes important in GCR risk assessments. In order to validate our approach, basic radiobiological responses such as cell survival curves, mutation, chromosomal

  18. Optimal Stochastic Modeling and Control of Flexible Structures

    Science.gov (United States)

    1988-09-01

    Multivariate Stationary Gaussian Processes," SIAM J-control and Optimization, Vol. 23, No. 6, Nov. 1985. 1.14. George Adomian , Stochastic Systems...Systems Whose Coefficients are Functions of Param- eters," IEEE Trans. on Automatic Control, Vol. AC-29, No. 1, Jan. 1984. 1.52. G. Adomian and L.h...Automation and Remote Control, No. 2, February, No. 3, March, pp. 5-19, 1984. 2.3. George Adomian , Stochastic Systems, Academic Press, N.Y., 1983. 2.4. Peter S

  19. Models for interrupted monitoring of a stochastic process

    Science.gov (United States)

    Palmer, E.

    1977-01-01

    As computers are added to the cockpit, the pilot's job is changing from of manually flying the aircraft, to one of supervising computers which are doing navigation, guidance and energy management calculations as well as automatically flying the aircraft. In this supervisorial role the pilot must divide his attention between monitoring the aircraft's performance and giving commands to the computer. Normative strategies are developed for tasks where the pilot must interrupt his monitoring of a stochastic process in order to attend to other duties. Results are given as to how characteristics of the stochastic process and the other tasks affect the optimal strategies.

  20. Cluster dynamics modelling of materials: A new hybrid deterministic/stochastic coupling approach

    Science.gov (United States)

    Terrier, Pierre; Athènes, Manuel; Jourdan, Thomas; Adjanor, Gilles; Stoltz, Gabriel

    2017-12-01

    Deterministic simulations of the rate equations governing cluster dynamics in materials are limited by the number of equations to integrate. Stochastic simulations are limited by the high frequency of certain events. We propose a coupling method combining deterministic and stochastic approaches. It allows handling different time scale phenomena for cluster dynamics. This method, based on a splitting of the dynamics, is generic and we highlight two different hybrid deterministic/stochastic methods. These coupling schemes are highly parallelizable and specifically designed to treat large size cluster problems. The proof of concept is made on a simple model of vacancy clustering under thermal ageing.

  1. Asymptotic behavior of a stochastic delayed HIV-1 infection model with nonlinear incidence

    Science.gov (United States)

    Liu, Qun; Jiang, Daqing; Hayat, Tasawar; Ahmad, Bashir

    2017-11-01

    In this paper, a stochastic delayed HIV-1 infection model with nonlinear incidence is proposed and investigated. First of all, we prove that there is a unique global positive solution as desired in any population dynamics. Then by constructing some suitable Lyapunov functions, we show that if the basic reproduction number R0 ≤ 1, then the solution of the stochastic system oscillates around the infection-free equilibrium E0, while if R0 > 1, then the solution of the stochastic system fluctuates around the infective equilibrium E∗. Sufficient conditions of these results are established. Finally, we give some examples and a series of numerical simulations to illustrate the analytical results.

  2. Stochastic resonance induced by Lévy noise in a tumor growth model with periodic treatment

    Science.gov (United States)

    Xu, Wei; Hao, Mengli; Gu, Xudong; Yang, Guidong

    2014-05-01

    In this paper, the stochastic resonance phenomenon in a tumor growth model under subthreshold periodic therapy and Lévy noise excitation is investigated. The possible reoccurrence of tumor due to stochastic resonance is discussed. The signal-to-noise ratio (SNR) is calculated numerically to measure the stochastic resonance. It is found that smaller stability index is better for avoiding tumor reappearance. Besides, the effect of the skewness parameter on the tumor regrowth is related to the stability index. Furthermore, increasing the intensity of periodic treatment does not always facilitate tumor therapy. These results are beneficial to the optimization of periodic tumor therapy.

  3. Optically levitated nanoparticle as a model system for stochastic bistable dynamics

    Science.gov (United States)

    Ricci, F.; Rica, R. A.; Spasenović, M.; Gieseler, J.; Rondin, L.; Novotny, L.; Quidant, R.

    2017-05-01

    Nano-mechanical resonators have gained an increasing importance in nanotechnology owing to their contributions to both fundamental and applied science. Yet, their small dimensions and mass raises some challenges as their dynamics gets dominated by nonlinearities that degrade their performance, for instance in sensing applications. Here, we report on the precise control of the nonlinear and stochastic bistable dynamics of a levitated nanoparticle in high vacuum. We demonstrate how it can lead to efficient signal amplification schemes, including stochastic resonance. This work contributes to showing the use of levitated nanoparticles as a model system for stochastic bistable dynamics, with applications to a wide variety of fields.

  4. Addressing model uncertainty through stochastic parameter perturbations within the High Resolution Rapid Refresh (HRRR) ensemble

    Science.gov (United States)

    Wolff, J.; Jankov, I.; Beck, J.; Carson, L.; Frimel, J.; Harrold, M.; Jiang, H.

    2016-12-01

    It is well known that global and regional numerical weather prediction ensemble systems are under-dispersive, producing unreliable and overconfident ensemble forecasts. Typical approaches to alleviate this problem include the use of multiple dynamic cores, multiple physics suite configurations, or a combination of the two. While these approaches may produce desirable results, they have practical and theoretical deficiencies and are more difficult and costly to maintain. An active area of research that promotes a more unified and sustainable system for addressing the deficiencies in ensemble modeling is the use of stochastic physics to represent model-related uncertainty. Stochastic approaches include Stochastic Parameter Perturbations (SPP), Stochastic Kinetic Energy Backscatter (SKEB), Stochastic Perturbation of Physics Tendencies (SPPT), or some combination of all three. The focus of this study is to assess the model performance within a convection-permitting ensemble at 3-km grid spacing across the Contiguous United States (CONUS) when using stochastic approaches. For this purpose, the test utilized a single physics suite configuration based on the operational High-Resolution Rapid Refresh (HRRR) model, with ensemble members produced by employing stochastic methods. Parameter perturbations were employed in the Rapid Update Cycle (RUC) land surface model and Mellor-Yamada-Nakanishi-Niino (MYNN) planetary boundary layer scheme. Results will be presented in terms of bias, error, spread, skill, accuracy, reliability, and sharpness using the Model Evaluation Tools (MET) verification package. Due to the high level of complexity of running a frequently updating (hourly), high spatial resolution (3 km), large domain (CONUS) ensemble system, extensive high performance computing (HPC) resources were needed to meet this objective. Supercomputing resources were provided through the National Center for Atmospheric Research (NCAR) Strategic Capability (NSC) project support

  5. Design starch: stochastic modeling of starch granule biogenesis.

    Science.gov (United States)

    Raguin, Adélaïde; Ebenhöh, Oliver

    2017-08-15

    Starch is the most widespread and abundant storage carbohydrate in plants and the main source of carbohydrate in the human diet. Owing to its remarkable properties and commercial applications, starch is still of growing interest. Its unique granular structure made of intercalated layers of amylopectin and amylose has been unraveled thanks to recent progress in microscopic imaging, but the origin of such periodicity is still under debate. Both amylose and amylopectin are made of linear chains of α-1,4-bound glucose residues, with branch points formed by α-1,6 linkages. The net difference in the distribution of chain lengths and the branching pattern of amylose (mainly linear), compared with amylopectin (racemose structure), leads to different physico-chemical properties. Amylose is an amorphous and soluble polysaccharide, whereas amylopectin is insoluble and exhibits a highly organized structure of densely packed double helices formed between neighboring linear chains. Contrarily to starch degradation that has been investigated since the early 20th century, starch production is still poorly understood. Most enzymes involved in starch growth (elongation, branching, debranching, and partial hydrolysis) are now identified. However, their specific action, their interplay (cooperative or competitive), and their kinetic properties are still largely unknown. After reviewing recent results on starch structure and starch growth and degradation enzymatic activity, we discuss recent results and current challenges for growing polysaccharides on granular surface. Finally, we highlight the importance of novel stochastic models to support the analysis of recent and complex experimental results, and to address how macroscopic properties emerge from enzymatic activity and structural rearrangements. © 2017 The Author(s).

  6. Stochastic Models for Laser Propagation in Atmospheric Turbulence.

    Science.gov (United States)

    Leland, Robert Patton

    In this dissertation, stochastic models for laser propagation in atmospheric turbulence are considered. A review of the existing literature on laser propagation in the atmosphere and white noise theory is presented, with a view toward relating the white noise integral and Ito integral approaches. The laser beam intensity is considered as the solution to a random Schroedinger equation, or forward scattering equation. This model is formulated in a Hilbert space context as an abstract bilinear system with a multiplicative white noise input, as in the literature. The model is also modeled in the Banach space of Fresnel class functions to allow the plane wave case and the application of path integrals. Approximate solutions to the Schroedinger equation of the Trotter-Kato product form are shown to converge for each white noise sample path. The product forms are shown to be physical random variables, allowing an Ito integral representation. The corresponding Ito integrals are shown to converge in mean square, providing a white noise basis for the Stratonovich correction term associated with this equation. Product form solutions for Ornstein -Uhlenbeck process inputs were shown to converge in mean square as the input bandwidth was expanded. A digital simulation of laser propagation in strong turbulence was used to study properties of the beam. Empirical distributions for the irradiance function were estimated from simulated data, and the log-normal and Rice-Nakagami distributions predicted by the classical perturbation methods were seen to be inadequate. A gamma distribution fit the simulated irradiance distribution well in the vicinity of the boresight. Statistics of the beam were seen to converge rapidly as the bandwidth of an Ornstein-Uhlenbeck process was expanded to its white noise limit. Individual trajectories of the beam were presented to illustrate the distortion and bending of the beam due to turbulence. Feynman path integrals were used to calculate an

  7. Exploring behaviors of stochastic differential equation models of biological systems using change of measures

    Directory of Open Access Journals (Sweden)

    Jha Sumit

    2012-04-01

    Full Text Available Abstract Stochastic Differential Equations (SDE are often used to model the stochastic dynamics of biological systems. Unfortunately, rare but biologically interesting behaviors (e.g., oncogenesis can be difficult to observe in stochastic models. Consequently, the analysis of behaviors of SDE models using numerical simulations can be challenging. We introduce a method for solving the following problem: given a SDE model and a high-level behavioral specification about the dynamics of the model, algorithmically decide whether the model satisfies the specification. While there are a number of techniques for addressing this problem for discrete-state stochastic models, the analysis of SDE and other continuous-state models has received less attention. Our proposed solution uses a combination of Bayesian sequential hypothesis testing, non-identically distributed samples, and Girsanov's theorem for change of measures to examine rare behaviors. We use our algorithm to analyze two SDE models of tumor dynamics. Our use of non-identically distributed samples sampling contributes to the state of the art in statistical verification and model checking of stochastic models by providing an effective means for exposing rare events in SDEs, while retaining the ability to compute bounds on the probability that those events occur.

  8. ENISI SDE: A New Web-Based Tool for Modeling Stochastic Processes.

    Science.gov (United States)

    Mei, Yongguo; Carbo, Adria; Hoops, Stefan; Hontecillas, Raquel; Bassaganya-Riera, Josep

    2015-01-01

    Modeling and simulations approaches have been widely used in computational biology, mathematics, bioinformatics and engineering to represent complex existing knowledge and to effectively generate novel hypotheses. While deterministic modeling strategies are widely used in computational biology, stochastic modeling techniques are not as popular due to a lack of user-friendly tools. This paper presents ENISI SDE, a novel web-based modeling tool with stochastic differential equations. ENISI SDE provides user-friendly web user interfaces to facilitate adoption by immunologists and computational biologists. This work provides three major contributions: (1) discussion of SDE as a generic approach for stochastic modeling in computational biology; (2) development of ENISI SDE, a web-based user-friendly SDE modeling tool that highly resembles regular ODE-based modeling; (3) applying ENISI SDE modeling tool through a use case for studying stochastic sources of cell heterogeneity in the context of CD4+ T cell differentiation. The CD4+ T cell differential ODE model has been published [8] and can be downloaded from biomodels.net. The case study reproduces a biological phenomenon that is not captured by the previously published ODE model and shows the effectiveness of SDE as a stochastic modeling approach in biology in general and immunology in particular and the power of ENISI SDE.

  9. Stochastic modeling of oligodendrocyte generation in cell culture: model validation with time-lapse data

    Directory of Open Access Journals (Sweden)

    Noble Mark

    2006-05-01

    Full Text Available Abstract Background The purpose of this paper is two-fold. The first objective is to validate the assumptions behind a stochastic model developed earlier by these authors to describe oligodendrocyte generation in cell culture. The second is to generate time-lapse data that may help biomathematicians to build stochastic models of cell proliferation and differentiation under other experimental scenarios. Results Using time-lapse video recording it is possible to follow the individual evolutions of different cells within each clone. This experimental technique is very laborious and cannot replace model-based quantitative inference from clonal data. However, it is unrivalled in validating the structure of a stochastic model intended to describe cell proliferation and differentiation at the clonal level. In this paper, such data are reported and analyzed for oligodendrocyte precursor cells cultured in vitro. Conclusion The results strongly support the validity of the most basic assumptions underpinning the previously proposed model of oligodendrocyte development in cell culture. However, there are some discrepancies; the most important is that the contribution of progenitor cell death to cell kinetics in this experimental system has been underestimated.

  10. Stochastic Greybox Modeling for Control of an Alternating Activated Sludge Process

    DEFF Research Database (Denmark)

    Halvgaard, Rasmus Fogtmann; Vezzaro, Luca; Grum, M.

    We present a stochastic greybox model of a BioDenitro WWTP that can be used for short time horizon Model Predictive Control. The model is based on a simplified ASM1 model and takes model uncertainty in to account. It estimates unmeasured state variables in the system, e.g. the inlet concentration...

  11. Analyzing Properties of Stochastic Business Processes By Model Checking

    DEFF Research Database (Denmark)

    Herbert, Luke Thomas; Sharp, Robin

    2013-01-01

    This chapter presents an approach to precise formal analysis of business processes with stochastic properties. The method presented here allows for both qualitative and quantitative properties to be individually analyzed at design time without requiring a full specification. This provides an effe...

  12. Stochastic resonance in neuron models : Endogenous stimulation revisited

    NARCIS (Netherlands)

    Plesser, HE; Geisel, T

    The paradigm of stochastic resonance (SR)-the idea that signal detection and transmission may benefit from noise-has met with great interest in both physics and the neurosciences. We investigate here the consequences of reducing the dynamics of a periodically driven neuron to a renewal process

  13. Effects of stochastic population fluctuations in two models of biological macroevolution

    Science.gov (United States)

    Murase, Yohsuke; Shimada, Takashi; Ito, Nobuyasu; Rikvold, Per Arne

    Two mathematical models of macroevolution are studied. These models have population dynamics at the species level, and mutations and extinction of species are also included. The population dynamics are updated by difference equations with stochastic noise terms that characterize population fluctuations. The effects of the stochastic population fluctuations on diversity and total population sizes on evolutionary time scales are studied. In one model, species can make either predator-prey, mutualistic, or competitive interactions, while the other model allows only predator-prey interactions. When the noise in the population dynamics is strong enough, both models show intermittent behavior and their power spectral densities show approximate 1/f fluctuations. In the noiseless limit, the two models have different power spectral densities. For the predator-prey model, 1/f2 fluctuations appears, indicating random-walk like behavior, while the other model still shows 1/f noise. These results indicate that stochastic population fluctuations may significantly affect long-time evolutionary dynamics.

  14. Ekofisk chalk: core measurements, stochastic reconstruction, network modeling and simulation

    Energy Technology Data Exchange (ETDEWEB)

    Talukdar, Saifullah

    2002-07-01

    This dissertation deals with (1) experimental measurements on petrophysical, reservoir engineering and morphological properties of Ekofisk chalk, (2) numerical simulation of core flood experiments to analyze and improve relative permeability data, (3) stochastic reconstruction of chalk samples from limited morphological information, (4) extraction of pore space parameters from the reconstructed samples, development of network model using pore space information, and computation of petrophysical and reservoir engineering properties from network model, and (5) development of 2D and 3D idealized fractured reservoir models and verification of the applicability of several widely used conventional up scaling techniques in fractured reservoir simulation. Experiments have been conducted on eight Ekofisk chalk samples and porosity, absolute permeability, formation factor, and oil-water relative permeability, capillary pressure and resistivity index are measured at laboratory conditions. Mercury porosimetry data and backscatter scanning electron microscope images have also been acquired for the samples. A numerical simulation technique involving history matching of the production profiles is employed to improve the relative permeability curves and to analyze hysteresis of the Ekofisk chalk samples. The technique was found to be a powerful tool to supplement the uncertainties in experimental measurements. Porosity and correlation statistics obtained from backscatter scanning electron microscope images are used to reconstruct microstructures of chalk and particulate media. The reconstruction technique involves a simulated annealing algorithm, which can be constrained by an arbitrary number of morphological parameters. This flexibility of the algorithm is exploited to successfully reconstruct particulate media and chalk samples using more than one correlation functions. A technique based on conditional simulated annealing has been introduced for exact reproduction of vuggy

  15. Asymptotic Behavior of a Chemostat Model with Stochastic Perturbation on the Dilution Rate

    Directory of Open Access Journals (Sweden)

    Chaoqun Xu

    2013-01-01

    Full Text Available We present a stochastic simple chemostat model in which the dilution rate was influenced by white noise. The long time behavior of the system is studied. Mainly, we show how the solution spirals around the washout equilibrium and the positive equilibrium of deterministic system under different conditions. Furthermore, the sufficient conditions for persistence in the mean of the stochastic system and washout of the microorganism are obtained. Numerical simulations are carried out to support our results.

  16. Stochastic transient of a noise-perturbed Haken-Zwanzig model

    Science.gov (United States)

    Leung, H. K.; Lai, B. C.

    1993-05-01

    A bivariate nonlinear model perturbed by external white noises is investigated stochastically. Attention is concentrated on the transient properties before the nonequilibrium phase is achieved. Effects of both additive and multiplicative noises are found to weaken stability and to slow down transient processes. The critical exponent describing this slowing-down phenomenon near a noise-induced instability is estimated for various types of noises. Results derived with two versions of stochastic calculus are compared systematically.

  17. Stochastic Optimization Model to STudy the Operational Impacts of High Wind Penetrations in Ireland

    DEFF Research Database (Denmark)

    Meibom, Peter; Barth, R.; Hasche, B.

    2011-01-01

    A stochastic mixed integer linear optimization scheduling model minimizing system operation costs and treating load and wind power production as stochastic inputs is presented. The schedules are updated in a rolling manner as more up-to-date information becomes available. This is a fundamental ch...... of future high wind penetrations for the island of Ireland. Results show that at least 6000 MW of wind (34% of energy demand) can be integrated into the island of Ireland without significant curtailment and reliability problems....

  18. Stochastic differential equation model for linear growth birth and death processes with immigration and emigration

    Science.gov (United States)

    Granita, Bahar, A.

    2015-03-01

    This paper discusses on linear birth and death with immigration and emigration (BIDE) process to stochastic differential equation (SDE) model. Forward Kolmogorov equation in continuous time Markov chain (CTMC) with a central-difference approximation was used to find Fokker-Planckequation corresponding to a diffusion process having the stochastic differential equation of BIDE process. The exact solution, mean and variance function of BIDE process was found.

  19. Stochastic differential equation model for linear growth birth and death processes with immigration and emigration

    Energy Technology Data Exchange (ETDEWEB)

    Granita, E-mail: granitafc@gmail.com [Dept. Mathematical Education, State Islamic University of Sultan Syarif Kasim Riau, 28293 Indonesia and Dept. of Mathematical Science, Universiti Teknologi Malaysia, 81310,Johor (Malaysia); Bahar, A. [Dept. of Mathematical Science, Universiti Teknologi Malaysia, 81310,Johor Malaysia and UTM Center for Industrial and Applied Mathematics (UTM-CIAM) (Malaysia)

    2015-03-09

    This paper discusses on linear birth and death with immigration and emigration (BIDE) process to stochastic differential equation (SDE) model. Forward Kolmogorov equation in continuous time Markov chain (CTMC) with a central-difference approximation was used to find Fokker-Planckequation corresponding to a diffusion process having the stochastic differential equation of BIDE process. The exact solution, mean and variance function of BIDE process was found.

  20. Stochastic linear dynamical programming in order to apply it in energy modelling

    Energy Technology Data Exchange (ETDEWEB)

    El Hachem, S.

    1995-11-01

    This thesis contributes to the development of new algorithms for the computation of stochastic dynamic problem and its mini-maxi variant for the case of imperfect knowledge on random data. The proposed algorithms are scenarios aggregation type. It also contributes to integrate these algorithms in a decision support approach and to discuss the stochastic modeling of two energy problems: the refining and the portfolio gas contracts. (author). 112 refs., 5 tabs.

  1. Estimation of stochastic volatility by using Ornstein-Uhlenbeck type models

    Science.gov (United States)

    Mariani, Maria C.; Bhuiyan, Md Al Masum; Tweneboah, Osei K.

    2018-02-01

    In this study, we develop a technique for estimating the stochastic volatility (SV) of a financial time series by using Ornstein-Uhlenbeck type models. Using the daily closing prices from developed and emergent stock markets, we conclude that the incorporation of stochastic volatility into the time varying parameter estimation significantly improves the forecasting performance via Maximum Likelihood Estimation. Furthermore, our estimation algorithm is feasible with large data sets and have good convergence properties.

  2. Effects of Risk Aversion on Market Outcomes: A Stochastic Two-Stage Equilibrium Model

    DEFF Research Database (Denmark)

    Kazempour, Jalal; Pinson, Pierre

    2016-01-01

    This paper evaluates how different risk preferences of electricity producers alter the market-clearing outcomes. Toward this goal, we propose a stochastic equilibrium model for electricity markets with two settlements, i.e., day-ahead and balancing, in which a number of conventional and stochastic...... by its optimality conditions, resulting in a mixed complementarity problem. Numerical results from a case study based on the IEEE one-area reliability test system are derived and discussed....

  3. Drift Scale Modeling: Study of Unsaturated Flow into a Drift Using a Stochastic Continuum Model

    Energy Technology Data Exchange (ETDEWEB)

    Birkholzer, J.T.; Tsang, C.F.; Tsang, Y.W.; Wang, J.S

    1996-09-01

    Unsaturated flow in heterogeneous fractured porous rock was simulated using a stochastic continuum model (SCM). In this model, both the more conductive fractures and the less permeable matrix are generated within the framework of a single continuum stochastic approach, based on non-parametric indicator statistics. High-permeable fracture zones are distinguished from low-permeable matrix zones in that they have assigned a long range correlation structure in prescribed directions. The SCM was applied to study small-scale flow in the vicinity of an access tunnel, which is currently being drilled in the unsaturated fractured tuff formations at Yucca Mountain, Nevada. Extensive underground testing is underway in this tunnel to investigate the suitability of Yucca Mountain as an underground nuclear waste repository. Different flow scenarios were studied in the present paper, considering the flow conditions before and after the tunnel emplacement, and assuming steady-state net infiltration as well as episodic pulse infiltration. Although the capability of the stochastic continuum model has not yet been fully explored, it has been demonstrated that the SCM is a good alternative model feasible of describing heterogeneous flow processes in unsaturated fractured tuff at Yucca Mountain.

  4. Evaluation of Stochastic Rainfall Models in Capturing Climate Variability for Future Drought and Flood Risk Assessment

    Science.gov (United States)

    Chowdhury, A. F. M. K.; Lockart, N.; Willgoose, G. R.; Kuczera, G. A.; Kiem, A.; Nadeeka, P. M.

    2016-12-01

    One of the key objectives of stochastic rainfall modelling is to capture the full variability of climate system for future drought and flood risk assessment. However, it is not clear how well these models can capture the future climate variability when they are calibrated to Global/Regional Climate Model data (GCM/RCM) as these datasets are usually available for very short future period/s (e.g. 20 years). This study has assessed the ability of two stochastic daily rainfall models to capture climate variability by calibrating them to a dynamically downscaled RCM dataset in an east Australian catchment for 1990-2010, 2020-2040, and 2060-2080 epochs. The two stochastic models are: (1) a hierarchical Markov Chain (MC) model, which we developed in a previous study and (2) a semi-parametric MC model developed by Mehrotra and Sharma (2007). Our hierarchical model uses stochastic parameters of MC and Gamma distribution, while the semi-parametric model uses a modified MC process with memory of past periods and kernel density estimation. This study has generated multiple realizations of rainfall series by using parameters of each model calibrated to the RCM dataset for each epoch. The generated rainfall series are used to generate synthetic streamflow by using a SimHyd hydrology model. Assessing the synthetic rainfall and streamflow series, this study has found that both stochastic models can incorporate a range of variability in rainfall as well as streamflow generation for both current and future periods. However, the hierarchical model tends to overestimate the multiyear variability of wet spell lengths (therefore, is less likely to simulate long periods of drought and flood), while the semi-parametric model tends to overestimate the mean annual rainfall depths and streamflow volumes (hence, simulated droughts are likely to be less severe). Sensitivity of these limitations of both stochastic models in terms of future drought and flood risk assessment will be discussed.

  5. Modelling the cancer growth process by Stochastic Differential Equations with the effect of Chondroitin Sulfate (CS) as anticancer therapeutics

    Science.gov (United States)

    Syahidatul Ayuni Mazlan, Mazma; Rosli, Norhayati; Jauhari Arief Ichwan, Solachuddin; Suhaity Azmi, Nina

    2017-09-01

    A stochastic model is introduced to describe the growth of cancer affected by anti-cancer therapeutics of Chondroitin Sulfate (CS). The parameters values of the stochastic model are estimated via maximum likelihood function. The numerical method of Euler-Maruyama will be employed to solve the model numerically. The efficiency of the stochastic model is measured by comparing the simulated result with the experimental data.

  6. Dynamics between cancer cell subpopulations reveals a model coordinating with both hierarchical and stochastic concepts.

    Science.gov (United States)

    Wang, Weikang; Quan, Yi; Fu, Qibin; Liu, Yu; Liang, Ying; Wu, Jingwen; Yang, Gen; Luo, Chunxiong; Ouyang, Qi; Wang, Yugang

    2014-01-01

    Tumors are often heterogeneous in which tumor cells of different phenotypes have distinct properties. For scientific and clinical interests, it is of fundamental importance to understand their properties and the dynamic variations among different phenotypes, specifically under radio- and/or chemo-therapy. Currently there are two controversial models describing tumor heterogeneity, the cancer stem cell (CSC) model and the stochastic model. To clarify the controversy, we measured probabilities of different division types and transitions of cells via in situ immunofluorescence. Based on the experiment data, we constructed a model that combines the CSC with the stochastic concepts, showing the existence of both distinctive CSC subpopulations and the stochastic transitions from NSCCs to CSCs. The results showed that the dynamic variations between CSCs and non-stem cancer cells (NSCCs) can be simulated with the model. Further studies also showed that the model can be used to describe the dynamics of the two subpopulations after radiation treatment. More importantly, analysis demonstrated that the experimental detectable equilibrium CSC proportion can be achieved only when the stochastic transitions from NSCCs to CSCs occur, indicating that tumor heterogeneity may exist in a model coordinating with both the CSC and the stochastic concepts. The mathematic model based on experimental parameters may contribute to a better understanding of the tumor heterogeneity, and provide references on the dynamics of CSC subpopulation during radiotherapy.

  7. Dynamics between cancer cell subpopulations reveals a model coordinating with both hierarchical and stochastic concepts.

    Directory of Open Access Journals (Sweden)

    Weikang Wang

    Full Text Available Tumors are often heterogeneous in which tumor cells of different phenotypes have distinct properties. For scientific and clinical interests, it is of fundamental importance to understand their properties and the dynamic variations among different phenotypes, specifically under radio- and/or chemo-therapy. Currently there are two controversial models describing tumor heterogeneity, the cancer stem cell (CSC model and the stochastic model. To clarify the controversy, we measured probabilities of different division types and transitions of cells via in situ immunofluorescence. Based on the experiment data, we constructed a model that combines the CSC with the stochastic concepts, showing the existence of both distinctive CSC subpopulations and the stochastic transitions from NSCCs to CSCs. The results showed that the dynamic variations between CSCs and non-stem cancer cells (NSCCs can be simulated with the model. Further studies also showed that the model can be used to describe the dynamics of the two subpopulations after radiation treatment. More importantly, analysis demonstrated that the experimental detectable equilibrium CSC proportion can be achieved only when the stochastic transitions from NSCCs to CSCs occur, indicating that tumor heterogeneity may exist in a model coordinating with both the CSC and the stochastic concepts. The mathematic model based on experimental parameters may contribute to a better understanding of the tumor heterogeneity, and provide references on the dynamics of CSC subpopulation during radiotherapy.

  8. Stochastic Ordering Using the Latent Trait and the Sum Score in Polytomous IRT Models.

    Science.gov (United States)

    Hemker, Bas T.; Sijtsma, Klaas; Molenaar, Ivo W.; Junker, Brian W.

    1997-01-01

    Stochastic ordering properties are investigated for a broad class of item response theory (IRT) models for which the monotone likelihood ratio does not hold. A taxonomy is given for nonparametric and parametric models for polytomous models based on the hierarchical relationship between the models. (SLD)

  9. Hybrid approaches for multiple-species stochastic reaction-diffusion models

    Science.gov (United States)

    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.

  10. Hybrid approaches for multiple-species stochastic reaction-diffusion models.

    KAUST Repository

    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.

  11. A Stochastic-Variational Model for Soft Mumford-Shah Segmentation

    Directory of Open Access Journals (Sweden)

    2006-01-01

    Full Text Available In contemporary image and vision analysis, stochastic approaches demonstrate great flexibility in representing and modeling complex phenomena, while variational-PDE methods gain enormous computational advantages over Monte Carlo or other stochastic algorithms. In combination, the two can lead to much more powerful novel models and efficient algorithms. In the current work, we propose a stochastic-variational model for soft (or fuzzy Mumford-Shah segmentation of mixture image patterns. Unlike the classical hard Mumford-Shah segmentation, the new model allows each pixel to belong to each image pattern with some probability. Soft segmentation could lead to hard segmentation, and hence is more general. The modeling procedure, mathematical analysis on the existence of optimal solutions, and computational implementation of the new model are explored in detail, and numerical examples of both synthetic and natural images are presented.

  12. Development of a stochastic dynamical model for hermetic compressor's components with experimental investigation

    Science.gov (United States)

    Fontanela, F.; Silva, O. M.; Lenzi, A.; Ritto, T. G.

    2016-08-01

    The analysis of household compressor's components is typically evaluated by using mathematical-mechanical models, and many decisions are taken based on simulations. However, such an investigation is usually performed in a deterministic framework, which cannot consider manufacturing variabilities and epistemic uncertainties. In this paper, a stochastic structural model that considers data and model uncertainties is developed for a discharge pipe connected to a hermetic compressor's shell. An experimental test rig is constructed to test each part separately, and an identification strategy is proposed to fit the stochastic model to experimental results. Finally, the impact of the uncertainties in each structural component on the dynamical responses of the whole system is investigated. It turns out that: (1) the proposed stochastic dynamical model presented very good results when compared to the experimental responses, and (2) uncertainties in the discharge pipe model play an important role in the coupled system dynamics.

  13. Stochastic processes

    CERN Document Server

    Parzen, Emanuel

    1962-01-01

    Well-written and accessible, this classic introduction to stochastic processes and related mathematics is appropriate for advanced undergraduate students of mathematics with a knowledge of calculus and continuous probability theory. The treatment offers examples of the wide variety of empirical phenomena for which stochastic processes provide mathematical models, and it develops the methods of probability model-building.Chapter 1 presents precise definitions of the notions of a random variable and a stochastic process and introduces the Wiener and Poisson processes. Subsequent chapters examine

  14. An introduction to continuous-time stochastic processes theory, models, and applications to finance, biology, and medicine

    CERN Document Server

    Capasso, Vincenzo

    2015-01-01

    This textbook, now in its third edition, offers a rigorous and self-contained introduction to the theory of continuous-time stochastic processes, stochastic integrals, and stochastic differential equations. Expertly balancing theory and applications, the work features concrete examples of modeling real-world problems from biology, medicine, industrial applications, finance, and insurance using stochastic methods. No previous knowledge of stochastic processes is required. Key topics include: * Markov processes * Stochastic differential equations * Arbitrage-free markets and financial derivatives * Insurance risk * Population dynamics, and epidemics * Agent-based models New to the Third Edition: * Infinitely divisible distributions * Random measures * Levy processes * Fractional Brownian motion * Ergodic theory * Karhunen-Loeve expansion * Additional applications * Additional  exercises * Smoluchowski  approximation of  Langevin systems An Introduction to Continuous-Time Stochastic Processes, Third Editio...

  15. Persistence and extinction of a stochastic single-specie model under regime switching in a polluted environment.

    Science.gov (United States)

    Liu, Meng; Wang, Ke

    2010-06-07

    A new single-species model disturbed by both white noise and colored noise in a polluted environment is developed and analyzed. Sufficient criteria for extinction, stochastic nonpersistence in the mean, stochastic weak persistence in the mean, stochastic strong persistence in the mean and stochastic permanence of the species are established. The threshold between stochastic weak persistence in the mean and extinction is obtained. The results show that both white and colored environmental noises have sufficient effect to the survival results. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

  16. Application of an NLME-Stochastic Deconvolution Approach to Level A IVIVC Modeling.

    Science.gov (United States)

    Kakhi, Maziar; Suarez-Sharp, Sandra; Shepard, Terry; Chittenden, Jason

    2017-07-01

    Stochastic deconvolution is a parameter estimation method that calculates drug absorption using a nonlinear mixed-effects model in which the random effects associated with absorption represent a Wiener process. The present work compares (1) stochastic deconvolution and (2) numerical deconvolution, using clinical pharmacokinetic (PK) data generated for an in vitro-in vivo correlation (IVIVC) study of extended release (ER) formulations of a Biopharmaceutics Classification System class III drug substance. The preliminary analysis found that numerical and stochastic deconvolution yielded superimposable fraction absorbed (Fabs) versus time profiles when supplied with exactly the same externally determined unit impulse response parameters. In a separate analysis, a full population-PK/stochastic deconvolution was applied to the clinical PK data. Scenarios were considered in which immediate release (IR) data were either retained or excluded to inform parameter estimation. The resulting Fabs profiles were then used to model level A IVIVCs. All the considered stochastic deconvolution scenarios, and numerical deconvolution, yielded on average similar results with respect to the IVIVC validation. These results could be achieved with stochastic deconvolution without recourse to IR data. Unlike numerical deconvolution, this also implies that in crossover studies where certain individuals do not receive an IR treatment, their ER data alone can still be included as part of the IVIVC analysis. Published by Elsevier Inc.

  17. Comparison of a deterministic model, a stochastic multifractal model and radar rainfall data

    Science.gov (United States)

    Gires, Auguste; Schertzer, Daniel; Tchiguirinskaia, Ioulia; Lovejoy, Shaun

    2010-05-01

    Two primary approaches to model rainfall are the stochastic approaches, which aim at mimicking the rain phenomenology, and the deterministic approaches. The latter mainly rely on geophysical fluid dynamics equations, in particular the Navier-Stokes equations. Solving these equations require simplifying assumptions such as parameterization and scale truncations. In the present case, we used Meso-NH model, which is a meteorological non-hydrostatic mesoscale model developed by Meteo-France/CNRM and Laboratoire d'Aérologie (Toulouse, France). Multiplicative cascade models, which are physically based models involving huge ratios of scales and intensities, allow to bridge the gap between the two previously mentioned methods. In this study, we considered a multifractal space-time cascade model, whose space-time anisotropy is defined with the help of a unique scaling exponent. We worked in the framework of universal multifractals in which the scaling variability and the extremes of the rain are quantified with the help of three parameters. The rainfall outputs of the Meso-NH model and the radar data were analyzed in the framework of the stochastic model. We selected a case study corresponding to a heavy rainfall event in the south of France. Both data sets exhibit a similar qualitative multifractal behavior in accordance with the framework of a unified space-time scaling model. Quantitatively, the estimates of the multifractal parameters suggest that the deterministic model under-represent the natural variability of the rainfall field.

  18. Stochastic partial differential equations a modeling, white noise functional approach

    CERN Document Server

    Holden, Helge; Ubøe, Jan; Zhang, Tusheng

    1996-01-01

    This book is based on research that, to a large extent, started around 1990, when a research project on fluid flow in stochastic reservoirs was initiated by a group including some of us with the support of VISTA, a research coopera­ tion between the Norwegian Academy of Science and Letters and Den norske stats oljeselskap A.S. (Statoil). The purpose of the project was to use stochastic partial differential equations (SPDEs) to describe the flow of fluid in a medium where some of the parameters, e.g., the permeability, were stochastic or "noisy". We soon realized that the theory of SPDEs at the time was insufficient to handle such equations. Therefore it became our aim to develop a new mathematically rigorous theory that satisfied the following conditions. 1) The theory should be physically meaningful and realistic, and the corre­ sponding solutions should make sense physically and should be useful in applications. 2) The theory should be general enough to handle many of the interesting SPDEs that occur in r...

  19. A mathematical model for the product mixing and lot-sizing problem by considering stochastic demand

    Directory of Open Access Journals (Sweden)

    Dionicio Neira Rodado

    2016-11-01

    Full Text Available The product-mix planning and the lot size decisions are some of the most fundamental research themes for the operations research community. The fact that markets have become more unpredictable has increaed the importance of these issues, rapidly. Currently, directors need to work with product-mix planning and lot size decision models by introducing stochastic variables related to the demands, lead times, etc. However, some real mathematical models involving stochastic variables are not capable of obtaining good solutions within short commuting times. Several heuristics and metaheuristics have been developed to deal with lot decisions problems, in order to obtain high quality results within short commuting times. Nevertheless, the search for an efficient model by considering product mix and deal size with stochastic demand is a prominent research area. This paper aims to develop a general model for the product-mix, and lot size decision within a stochastic demand environment, by introducing the Economic Value Added (EVA as the objective function of a product portfolio selection. The proposed stochastic model has been solved by using a Sample Average Approximation (SAA scheme. The proposed model obtains high quality results within acceptable computing times.

  20. Probabilistic Forecast of Wind Power Generation by Stochastic Differential Equation Models

    KAUST Repository

    Elkantassi, Soumaya

    2017-04-01

    Reliable forecasting of wind power generation is crucial to optimal control of costs in generation of electricity with respect to the electricity demand. Here, we propose and analyze stochastic wind power forecast models described by parametrized stochastic differential equations, which introduce appropriate fluctuations in numerical forecast outputs. We use an approximate maximum likelihood method to infer the model parameters taking into account the time correlated sets of data. Furthermore, we study the validity and sensitivity of the parameters for each model. We applied our models to Uruguayan wind power production as determined by historical data and corresponding numerical forecasts for the period of March 1 to May 31, 2016.