Implicit methods for qualitative modeling of gene regulatory networks.

Advancements in high-throughput technologies to measure increasingly complex biological phenomena at the genomic level are rapidly changing the face of biological research from the single-gene single-protein experimental approach to studying the behavior of a gene in the context of the entire genome (and proteome). This shift in research methodologies has resulted in a new field of network biology that deals with modeling cellular behavior in terms of network structures such as signaling pathways and gene regulatory networks. In these networks, different biological entities such as genes, proteins, and metabolites interact with each other, giving rise to a dynamical system. Even though there exists a mature field of dynamical systems theory to model such network structures, some technical challenges are unique to biology such as the inability to measure precise kinetic information on gene-gene or gene-protein interactions and the need to model increasingly large networks comprising thousands of nodes. These challenges have renewed interest in developing new computational techniques for modeling complex biological systems. This chapter presents a modeling framework based on Boolean algebra and finite-state machines that are reminiscent of the approach used for digital circuit synthesis and simulation in the field of very-large-scale integration (VLSI). The proposed formalism enables a common mathematical framework to develop computational techniques for modeling different aspects of the regulatory networks such as steady-state behavior, stochasticity, and gene perturbation experiments.

Notas del primer seminario de integrabilidad de la Universitat Politècnica de Catalunya

Estas notas corresponden a las exposiciones presentadas en el \emph{Primer Seminario de Integrabilidad}, dentro de lo que se denomina \emph{Aula de Sistemas Din\'amicos}. Durante este evento se realizaron seis conferencias, todas presentadas por miembros del grupo de Sistemas Din\'amicos de la UPC. El programa desarrollado fue el siguiente:\\\begin{center}AULA DE SISTEMAS DIN\'AMICOS\end{center}\begin{center}\texttt{http://www.ma1.upc.es/recerca/seminaris/aulasd-cat.html}\end{center}\begin{center}SEMINARIO DE INTEGRABILIDAD\end{center}\begin{center}Martes 29 y Mi\'ercoles 30 de marzo de 2005\\Facultad de Matem\'aticas y Estad\'{\i}stica, UPC\\Aula: Seminario 1\end{center}\bigskip\begin{center}PROGRAMA Y RES\'UMENES\end{center}{\bf Martes 29 de marzo}\begin{itemize}\item15:30. Juan J. Morales-Ruiz. \emph{El problema de laintegrabilidad en Sistemas Din\'amicos}\medskip {\bf Resumen.} En esta presentaci\'on se pretende dar unaidea de conjunto, pero sin entrar en detalles, sobre las diversasnociones de integrabilidad, asociadas a nombres de matem\'aticostan ilustres como Liouville, Galois-Picard-Vessiot, Lie, Darboux,Kowalevskaya, Painlev\'e, Poincar\'e, Kolchin, Lax, etc. Adem\'astambi\'en mencionaremos la revoluci\'on que supuso en los a\~nossesenta del siglo pasado el descubrimiento de Gardner, Green,Kruskal y Miura sobre un nuevo m\'etodo para resolver en algunoscasos determinadas ecuaciones en derivadas parciales. \medskip\item16:00. David G\'omez-Ullate. \emph{Superintegrabilidad, pares deLax y modelos de $N-$cuerpos en el plano}\medskip{\bf Resumen.} Introduciremos algunas t\'ecnicas cl\'asicas paraconstruir modelos de N-cuerpos integrables, como los pares de Laxo la din\'amica de los ceros de un polinomio. Revisaremos lanoci\'on de integrabilidad Liouville y superintegrabilidad, ydiscutiremos un nuevo m\'etodo debido a F. Calogero para contruirmodelos de N-cuerpos en el plano con muchas \'orbitasperi\'odicas. La exposici\'on se acompa\~nar\'a de animaciones delmovimiento de los cuerpos, y se plantear\'an algunos problemasabiertos.\medskip\item17:00. Pausa\medskip\item17:30. Yuri Fedorov. \emph{An\'alisis de Kovalevskaya--Painlev\'ey Sistemas Algebraicamente Integrables}\medskip{\bf Resumen.} Muchos sistemas integrables poseen una propiedadremarcable: todas sus soluciones son funciones meromorfas deltiempo como una variable compleja. Tal comportamiento, que serefiere como propiedad de Kovalevskaya-Painleve (KP) y que se usafrecuentemente como una ensayo de integrabilidad, no es accidentaly tiene unas ra\'{\i}ces geom\'etricas profundas. En esta charladescribiremos una clase de tales sistemas (conocidos como lossistemas algebraicamente integrables) y subrayaremos suspropiedades geom\'etricas principales que permiten predecir laestructura de las soluciones complejas y adem\'as encontrarlasexpl\'{\i}citamente. Eso lo ilustraremos con algunos sistemas dela mec\'anica cl\'asica. Tambi\'en mencionaremos unasgeneralizaciones \'utiles de la noci\'on de integrabilidadalgebraica y de la propiedad KP.\end{itemize}\medskip{\bf Mi\'ercoles 30 de marzo}\begin{itemize}\item 15:30. Rafael Ram\'{\i}rez-Ros. \emph{El m\'etodo de Poincar\'e}\medskip{\bf Resumen.} Dado un sistema Hamiltoniano aut\'onomo cercano acompletamente integrable Poincar\'e prob\'o que, en general, noexiste ninguna integral primera adicional uniforme en elpar\'ametro de perturbaci\'on salvo el propio Hamiltoniano.Esbozaremos las ideas principales del m\'etodo de prueba ycomentaremos algunas extensiones y generalizaciones.\newpage\item16:30. Chara Pantazi. \emph{El M\'etodo de Darboux}\medskip{\bf Resumen.} Darboux, en 1878, present\'o su m\'etodo paraconstruir integrales primeras de campos vectoriales polinomialesutilizando sus curvas invariantes algebraicas. En estaexposici\'on presentaremos algunas extensiones del m\'etodocl\'asico de Darboux y tambi\'en algunas aplicaciones.\medskip\item17:30. Pausa\medskip\item18:00. Juan J. Morales-Ruiz. \emph{M\'etodos recientes paradetectar la no integrabilidad}\medskip{\bf Resumen.} En 1982 Ziglin utiliza la estructura de laecuaci\'on en variaciones de Poincar\'e (sobre una curva integralparticular) como una herramienta fundamental para detectar la nointegrabilidad de un sistema Hamiltoniano. En esta charla sepretende dar una idea de esta aproximaci\'on a la nointegrabilidad, junto con t\'ecnicas m\'as recientes queinvolucran la teor\'{\i}a de Galois de ecuaciones diferencialeslineales, haciendo \'enfasis en los ejemplos m\'as que en lateor\'{\i}a general. Ilustraremos estos m\'etodos con resultadossobre la no integrabilidad de algunos problemas de $N$ cuerpos enMec\'anica Celeste.\end{itemize}

Cyclicity versus center problem

We prove that there are one-parameter families of planar differential equations for which the center problem has a trivial solution and on the other hand the cyclicity of the weak focus is arbitrarily high. We illustrate this phenomenon in several examples for which this cyclicity is computed.

A survey on the inverse integrating factor

The relation between limit cycles of planar differential systems and the inverse integrating factor was first shown in an article of Giacomini, Llibre and Viano appeared in 1996. From that moment on, many research articles are devoted to the study of the properties of the inverse integrating factor and its relationwith limit cycles and their bifurcations. This paper is a summary of all the results about this topic. We include a list of references together with the corresponding related results aiming at being as much exhaustive as possible. The paper is, nonetheless, self-contained in such a way that all the main results on the inverse integrating factor are stated and a complete overview of the subject is given. Each section contains a different issue to which the inverse integrating factor plays a role: the integrability problem, relation with Lie symmetries, the center problem, vanishing set of an inverse integrating factor, bifurcation of limit cycles from either a period annulus or from a monodromic ω-limit set and some generalizations.

A parameterization method for the computation of invariant tori and their whiskers in quasi-periodic maps: explorations and mechanisms for the breakdown of hyperbolicity

In two previous papers [J. Differential Equations, 228 (2006), pp. 530 579; Discrete Contin. Dyn. Syst. Ser. B, 6 (2006), pp. 1261 1300] we have developed fast algorithms for the computations of invariant tori in quasi‐periodic systems and developed theorems that assess their accuracy. In this paper, we study the results of implementing these algorithms and study their performance in actual implementations. More importantly, we note that, due to the speed of the algorithms and the theoretical developments about their reliability, we can compute with confidence invariant objects close to the breakdown of their hyperbolicity properties. This allows us to identify a mechanism of loss of hyperbolicity and measure some of its quantitative regularities. We find that some systems lose hyperbolicity because the stable and unstable bundles approach each other but the Lyapunov multipliers remain away from 1. We find empirically that, close to the breakdown, the distances between the invariant bundles and the Lyapunov multipliers which are natural measures of hyperbolicity depend on the parameters, with power laws with universal exponents. We also observe that, even if the rigorous justifications in [J. Differential Equations, 228 (2006), pp. 530-579] are developed only for hyperbolic tori, the algorithms work also for elliptic tori in Hamiltonian systems. We can continue these tori and also compute some bifurcations at resonance which may lead to the existence of hyperbolic tori with nonorientable bundles. We compute manifolds tangent to nonorientable bundles.

Sierpinski curve Julia sets for quadratic rational maps

We investigate under which dynamical conditions the Julia set of a quadratic rational map is a Sierpiński curve.

On the computation of reducible invariant tori on a parallel computer

We present an algorithm for the computation of reducible invariant tori of discrete dynamical systems that is suitable for tori of dimensions larger than 1. It is based on a quadratically convergent scheme that approximates, at the same time, the Fourier series of the torus, its Floquet transformation, and its Floquet matrix. The Floquet matrix describes the linearization of the dynamics around the torus and, hence, its linear stability. The algorithm presents a high degree of parallelism, and the computational effort grows linearly with the number of Fourier modes needed to represent the solution. For these reasons it is a very good option to compute quasi-periodic solutions with several basic frequencies. The paper includes some examples (flows) to show the efficiency of the method in a parallel computer. In these flows we compute invariant tori of dimensions up to 5, by taking suitable sections.

Fluctuation-Driven Neural Dynamics Reproduce Drosophila Locomotor Patterns.

The neural mechanisms determining the timing of even simple actions, such as when to walk or rest, are largely mysterious. One intriguing, but untested, hypothesis posits a role for ongoing activity fluctuations in neurons of central action selection circuits that drive animal behavior from moment to moment. To examine how fluctuating activity can contribute to action timing, we paired high-resolution measurements of freely walking Drosophila melanogaster with data-driven neural network modeling and dynamical systems analysis. We generated fluctuation-driven network models whose outputs-locomotor bouts-matched those measured from sensory-deprived Drosophila. From these models, we identified those that could also reproduce a second, unrelated dataset: the complex time-course of odor-evoked walking for genetically diverse Drosophila strains. Dynamical models that best reproduced both Drosophila basal and odor-evoked locomotor patterns exhibited specific characteristics. First, ongoing fluctuations were required. In a stochastic resonance-like manner, these fluctuations allowed neural activity to escape stable equilibria and to exceed a threshold for locomotion. Second, odor-induced shifts of equilibria in these models caused a depression in locomotor frequency following olfactory stimulation. Our models predict that activity fluctuations in action selection circuits cause behavioral output to more closely match sensory drive and may therefore enhance navigation in complex sensory environments. Together these data reveal how simple neural dynamics, when coupled with activity fluctuations, can give rise to complex patterns of animal behavior.

Persistent random walk model for transport trough thin slabs

We present a model for transport in multiply scattering media based on a three-dimensional generalization of the persistent random walk. The model assumes that photons move along directions that are parallel to the axes. Although this hypothesis is not realistic, it allows us to solve exactly the problem of multiple scattering propagation in a thin slab. Among other quantities, the transmission probability and the mean transmission time can be calculated exactly. Besides being completely solvable, the model could be used as a benchmark for approximation schemes to multiple light scattering.

Aspectos relacionados à utilização da equação logística quadrática em processos eletroquímicos

The concepts of dissipation and feedback are contained in the behavior of many natural dynamical systems. They have been used to predict the evolution of populations leading to the formulation of the quadratic logistic equation (QLE). More recently, the QLE has been used to provide a better understanding of physicochemical systems with promising results. Many physical, chemical and biological dynamic phenomena can be understood on the basis of the QLE and this work describes the main aspects of this equation and some recent applications, with emphasis on electrochemical systems. Also, it is illustrated the concept of potential energy as a convenient way of describing the stability of the fixed points of the QLE.

Chaotic dynamics of electric-field domains in periodically driven superlattices

Self-sustained time-dependent current oscillations under dc voltage bias have been observed in recent experiments on n-doped semiconductor superlattices with sequential resonant tunneling. The current oscillations are caused by the motion and recycling of the domain wall separating low- and high-electric-field regions of the superlattice, as the analysis of a discrete drift model shows and experimental evidence supports. Numerical simulation shows that different nonlinear dynamical regimes of the domain wall appear when an external microwave signal is superimposed on the dc bias and its driving frequency and driving amplitude vary. On the frequency-amplitude parameter plane, there are regions of entrainment and quasiperiodicity forming Arnold tongues. Chaos is demonstrated to appear at the boundaries of the tongues and in the regions where they overlap. Coexistence of up to four electric-field domains randomly nucleated in space is detected under ac+dc driving.

SQualTrack: A Tool for Robust Fault Detection

One of the techniques used to detect faults in dynamic systems is analytical redundancy. An important difficulty in applying this technique to real systems is dealing with the uncertainties associated with the system itself and with the measurements. In this paper, this uncertainty is taken into account by the use of intervals for the parameters of the model and for the measurements. The method that is proposed in this paper checks the consistency between the system's behavior, obtained from the measurements, and the model's behavior; if they are inconsistent, then there is a fault. The problem of detecting faults is stated as a quantified real constraint satisfaction problem, which can be solved using the modal interval analysis (MIA). MIA is used because it provides powerful tools to extend the calculations over real functions to intervals. To improve the results of the detection of the faults, the simultaneous use of several sliding time windows is proposed. The result of implementing this method is semiqualitative tracking (SQualTrack), a fault-detection tool that is robust in the sense that it does not generate false alarms, i.e., if there are false alarms, they indicate either that the interval model does not represent the system adequately or that the interval measurements do not represent the true values of the variables adequately. SQualTrack is currently being used to detect faults in real processes. Some of these applications using real data have been developed within the European project advanced decision support system for chemical/petrochemical manufacturing processes and are also described in this paper

Small and Large Scale Dynamics in the Milky Way

This thesis contains dynamical analysis on four different scales: the Solar system, the Sun itself, the Solar neighbourhood, and the central region of the Milky Way galaxy. All of these topics have been handled through methods of potential theory and statistics. The central topic of the thesis is the orbits of stars in the Milky Way. An introduction into the general structure of the Milky Way is presented, with an emphasis on the evolution of the observed value for the scale-length of the Milky Way disc and the observations of two separate bars in the Milky Way. The basics of potential theory are also presented, as well as a developed potential model for the Milky Way. An implementation of the backwards restricted integration method is shown, rounding off the basic principles used in the dynamical studies of this thesis. The thesis looks at the orbit of the Sun, and its impact on the Oort cloud comets (Paper IV), showing that there is a clear link between these two dynamical systems. The statistical atypicalness of the orbit of the Sun is questioned (Paper I), concluding that there is some statistical typicalness to the orbit of the Sun, although it is not very significant. This does depend slightly on whether one includes a bar, or not, as a bar has a clear effect on the dynamical features seen in the Solar neighbourhood (Paper III). This method can be used to find the possible properties of a bar. Finally, we look at the effect of a bar on a statistical system in the Milky Way, seeing that there are not only interesting effects depending on the mass and size of the bar, but also how bars can capture disc stars (Paper II).

Lagrangian multipliers for coast-arcs of optimum space trajectories

Some properties of generalized canonical systems - special dynamical systems described by a Hamiltonian function linear in the adjoint variables - are applied in determining the solution of the two-dimensional coast-arc problem in an inverse-square gravity field. A complete closed-form solution for Lagrangian multipliers - adjoint variables - is obtained by means of such properties for elliptic, circular, parabolic and hyperbolic motions. Classic orbital elements are taken as constants of integration of this solution in the case of elliptic, parabolic and hyperbolic motions. For circular motion, a set of nonsingular orbital elements is introduced as constants of integration in order to eliminate the singularity of the solution.