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Juan Carlos Nuño

Bio: Juan Carlos Nuño is an academic researcher from Technical University of Madrid. The author has contributed to research in topics: Population & Visibility (geometry). The author has an hindex of 11, co-authored 37 publications receiving 2049 citations.

Papers
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Journal ArticleDOI
TL;DR: A simple and fast computational method, the visibility algorithm, that converts a time series into a graph, which inherits several properties of the series in its structure, enhancing the fact that power law degree distributions are related to fractality.
Abstract: In this work we present a simple and fast computational method, the visibility algorithm, that converts a time series into a graph. The constructed graph inherits several properties of the series in its structure. Thereby, periodic series convert into regular graphs, and random series do so into random graphs. Moreover, fractal series convert into scale-free networks, enhancing the fact that power law degree distributions are related to fractality, something highly discussed recently. Some remarkable examples and analytical tools are outlined to test the method's reliability. Many different measures, recently developed in the complex network theory, could by means of this new approach characterize time series from a new point of view.

1,320 citations

Journal ArticleDOI
01 Mar 1999
TL;DR: Algorithms for computing the convex basis and elementary modes developed earlier are briefly reviewed, and a newly developed algorithm for detecting all enzyme subsets in a given network is presented.
Abstract: Motivation: To reconstruct metabolic pathways from biochemical and/or genome sequence data, the stoichiometric and thermodynamic feasibility of the pathways has to be tested. This is achieved by characterizing the admissible region of flux distributions in steady state. This region is spanned by what can be called a convex basis. The concept of 'elementary flux modes' provides a mathematical tool to define all metabolic routes that are feasible in a given metabolic network. In addition, we define 'enzyme subsets' to be groups of enzymes that operate together in fixed flux proportions in all steady states of the system. Results: Algorithms for computing the convex basis and elementary modes developed earlier are briefly reviewed. A newly developed algorithm for detecting all enzyme subsets in a given network is presented. All of these algorithms have been implemented in a novel computer program named METATOOL, whose features are outlined here. The algorithms are illustrated by an example taken from sugar metabolism. Availability: METATOOL is available from ftp://bmsdarwin.brookes.ac.uk/pub/software/ibmpc/metatool. Supplementary information: http://www.biologie.hu-berlin.de/biophysics/Theory/tpfeiffer/metatool.html.

388 citations

Journal ArticleDOI
01 May 2009-EPL
TL;DR: In this paper, it was shown that the exponent of the power law degree distribution depends linearly on the Hurst parameter, H, and that the degree distribution is a function of H. The authors also proposed a new methodology to quantify long-range dependence in fractional Gaussian noises and generic f−β noises.
Abstract: Fractional Brownian motion (fBm) has been used as a theoretical framework to study real-time series appearing in diverse scientific fields. Because of its intrinsic nonstationarity and long-range dependence, its characterization via the Hurst parameter, H, requires sophisticated techniques that often yield ambiguous results. In this work we show that fBm series map into a scale-free visibility graph whose degree distribution is a function of H. Concretely, it is shown that the exponent of the power law degree distribution depends linearly on H. This also applies to fractional Gaussian noises (fGn) and generic f−β noises. Taking advantage of these facts, we propose a brand new methodology to quantify long-range dependence in these series. Its reliability is confirmed with extensive numerical simulations and analytical developments. Finally, we illustrate this method quantifying the persistent behavior of human gait dynamics.

347 citations

Journal ArticleDOI
TL;DR: This work presents an alternative approach to compute in a more efficient way the optimal design of glycolysis interacting with an external ATP-consuming reaction, based on the laws of evolution by natural selection, and may be viewed as a particular version of evolutionary algorithms.

43 citations

Journal ArticleDOI
TL;DR: In this article, a quantitative model describing the interaction of three sociological species, termed as owners, criminals and security guards, was proposed, and a system of three ordinary differential equations to account for the time evolution of X(t), Y(t) and Z(t).
Abstract: This paper is concerned with a quantitative model describing the interaction of three sociological species, termed as owners, criminals and security guards, and denoted by X, Y and Z respectively. In our model, Y is a predator of the species X, and so is Z with respect to Y. Moreover, Z can also be thought of as a predator of X, since this last population is required to bear the costs of maintaining Z. We propose a system of three ordinary differential equations to account for the time evolution of X(t), Y(t) and Z(t) according to our previous assumptions. Out of the various parameters that appear in that system, we select two of them, denoted by H, and h, which are related with the efficiency of the security forces as a control parameter in our discussion. To begin with, we consider the case of large and constant owners population, which allows us to reduce (3)-(5) to a bidimensional system for Y(t) and Z(t). As a preliminary step, this situation is first discussed under the additional assumption that Y(t) + Z(t) is constant. A bifurcation study is then performed in terms of H and h, which shows the key role played by the rate of casualties in Y and Z, that results particularly in a possible onset of histability. When the previous restriction is dropped, we observe the appearance of oscillatory behaviours in the full two-dimensional system. We finally provide a exploratory study of the complete model (3)-(5), where a number of bifurcations appear as parameter H changes, and the corresponding solutions behaviours are described.

39 citations


Cited by
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28 Jul 2005
TL;DR: PfPMP1)与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作�ly.
Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1(PfPMP1)与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员,通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

18,940 citations

Book
01 Jan 2001
TL;DR: This chapter discusses Decision-Theoretic Foundations, Game Theory, Rationality, and Intelligence, and the Decision-Analytic Approach to Games, which aims to clarify the role of rationality in decision-making.
Abstract: Preface 1. Decision-Theoretic Foundations 1.1 Game Theory, Rationality, and Intelligence 1.2 Basic Concepts of Decision Theory 1.3 Axioms 1.4 The Expected-Utility Maximization Theorem 1.5 Equivalent Representations 1.6 Bayesian Conditional-Probability Systems 1.7 Limitations of the Bayesian Model 1.8 Domination 1.9 Proofs of the Domination Theorems Exercises 2. Basic Models 2.1 Games in Extensive Form 2.2 Strategic Form and the Normal Representation 2.3 Equivalence of Strategic-Form Games 2.4 Reduced Normal Representations 2.5 Elimination of Dominated Strategies 2.6 Multiagent Representations 2.7 Common Knowledge 2.8 Bayesian Games 2.9 Modeling Games with Incomplete Information Exercises 3. Equilibria of Strategic-Form Games 3.1 Domination and Ratonalizability 3.2 Nash Equilibrium 3.3 Computing Nash Equilibria 3.4 Significance of Nash Equilibria 3.5 The Focal-Point Effect 3.6 The Decision-Analytic Approach to Games 3.7 Evolution. Resistance. and Risk Dominance 3.8 Two-Person Zero-Sum Games 3.9 Bayesian Equilibria 3.10 Purification of Randomized Strategies in Equilibria 3.11 Auctions 3.12 Proof of Existence of Equilibrium 3.13 Infinite Strategy Sets Exercises 4. Sequential Equilibria of Extensive-Form Games 4.1 Mixed Strategies and Behavioral Strategies 4.2 Equilibria in Behavioral Strategies 4.3 Sequential Rationality at Information States with Positive Probability 4.4 Consistent Beliefs and Sequential Rationality at All Information States 4.5 Computing Sequential Equilibria 4.6 Subgame-Perfect Equilibria 4.7 Games with Perfect Information 4.8 Adding Chance Events with Small Probability 4.9 Forward Induction 4.10 Voting and Binary Agendas 4.11 Technical Proofs Exercises 5. Refinements of Equilibrium in Strategic Form 5.1 Introduction 5.2 Perfect Equilibria 5.3 Existence of Perfect and Sequential Equilibria 5.4 Proper Equilibria 5.5 Persistent Equilibria 5.6 Stable Sets 01 Equilibria 5.7 Generic Properties 5.8 Conclusions Exercises 6. Games with Communication 6.1 Contracts and Correlated Strategies 6.2 Correlated Equilibria 6.3 Bayesian Games with Communication 6.4 Bayesian Collective-Choice Problems and Bayesian Bargaining Problems 6.5 Trading Problems with Linear Utility 6.6 General Participation Constraints for Bayesian Games with Contracts 6.7 Sender-Receiver Games 6.8 Acceptable and Predominant Correlated Equilibria 6.9 Communication in Extensive-Form and Multistage Games Exercises Bibliographic Note 7. Repeated Games 7.1 The Repeated Prisoners Dilemma 7.2 A General Model of Repeated Garnet 7.3 Stationary Equilibria of Repeated Games with Complete State Information and Discounting 7.4 Repeated Games with Standard Information: Examples 7.5 General Feasibility Theorems for Standard Repeated Games 7.6 Finitely Repeated Games and the Role of Initial Doubt 7.7 Imperfect Observability of Moves 7.8 Repeated Wines in Large Decentralized Groups 7.9 Repeated Games with Incomplete Information 7.10 Continuous Time 7.11 Evolutionary Simulation of Repeated Games Exercises 8. Bargaining and Cooperation in Two-Person Games 8.1 Noncooperative Foundations of Cooperative Game Theory 8.2 Two-Person Bargaining Problems and the Nash Bargaining Solution 8.3 Interpersonal Comparisons of Weighted Utility 8.4 Transferable Utility 8.5 Rational Threats 8.6 Other Bargaining Solutions 8.7 An Alternating-Offer Bargaining Game 8.8 An Alternating-Offer Game with Incomplete Information 8.9 A Discrete Alternating-Offer Game 8.10 Renegotiation Exercises 9. Coalitions in Cooperative Games 9.1 Introduction to Coalitional Analysis 9.2 Characteristic Functions with Transferable Utility 9.3 The Core 9.4 The Shapkey Value 9.5 Values with Cooperation Structures 9.6 Other Solution Concepts 9.7 Colational Games with Nontransferable Utility 9.8 Cores without Transferable Utility 9.9 Values without Transferable Utility Exercises Bibliographic Note 10. Cooperation under Uncertainty 10.1 Introduction 10.2 Concepts of Efficiency 10.3 An Example 10.4 Ex Post Inefficiency and Subsequent Oilers 10.5 Computing Incentive-Efficient Mechanisms 10.6 Inscrutability and Durability 10.7 Mechanism Selection by an Informed Principal 10.8 Neutral Bargaining Solutions 10.9 Dynamic Matching Processes with Incomplete Information Exercises Bibliography Index

3,569 citations

Journal ArticleDOI
Oliver Fiehn1
TL;DR: In this review, the differences among metabolite target analysis, metabolite profiling, and metabolic fingerprinting are clarified, and terms are defined.
Abstract: Metabolites are the end products of cellular regulatory processes, and their levels can be regarded as the ultimate response of biological systems to genetic or environmental changes. In parallel to the terms ‘transcriptome’ and ‘proteome’, the set of metabolites synthesized by a biological system constitute its ‘metabolome’. Yet, unlike other functional genomics approaches, the unbiased simultaneous identification and quantification of plant metabolomes has been largely neglected. Until recently, most analyses were restricted to profiling selected classes of compounds, or to fingerprinting metabolic changes without sufficient analytical resolution to determine metabolite levels and identities individually. As a prerequisite for metabolomic analysis, careful consideration of the methods employed for tissue extraction, sample preparation, data acquisition, and data mining must be taken. In this review, the differences among metabolite target analysis, metabolite profiling, and metabolic fingerprinting are clarified, and terms are defined. Current approaches are examined, and potential applications are summarized with a special emphasis on data mining and mathematical modelling of metabolism.

3,547 citations

Journal ArticleDOI
TL;DR: COPASI is presented, a platform-independent and user-friendly biochemical simulator that offers several unique features, and numerical issues with these features are discussed; in particular, the criteria to switch between stochastic and deterministic simulation methods, hybrid deterministic-stochastic methods, and the importance of random number generator numerical resolution in Stochastic simulation.
Abstract: Motivation: Simulation and modeling is becoming a standard approach to understand complex biochemical processes. Therefore, there is a big need for software tools that allow access to diverse simulation and modeling methods as well as support for the usage of these methods. Results: Here, we present COPASI, a platform-independent and user-friendly biochemical simulator that offers several unique features. We discuss numerical issues with these features; in particular, the criteria to switch between stochastic and deterministic simulation methods, hybrid deterministic--stochastic methods, and the importance of random number generator numerical resolution in stochastic simulation. Availability: The complete software is available in binary (executable) for MS Windows, OS X, Linux (Intel) and Sun Solaris (SPARC), as well as the full source code under an open source license from http://www.copasi.org. Contact: mendes@vbi.vt.edu

2,351 citations