Reduction of dynamical biochemical reaction networks in computational biology

Biochemical networks are used in computational biology, to model the static and dynamical details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as combinatorial explosion are strong obstacles against analyzing the dynamics of large models of this type. Multi-scaleness is another property of these networks, that can be used to get past some of these obstacles. Networks with many well separated time scales, can be reduced to simpler networks, in a way that depends only on the orders of magnitude and not on the exact values of the kinetic parameters. The main idea used for such robust simplifications of networks is the concept of dominance among model elements, allowing hierarchical organization of these elements according to their effects on the network dynamics. This concept finds a natural formulation in tropical geometry. We revisit, in the light of these new ideas, the main approaches to model reduction of reaction networks, such as quasi-steady state and quasi-equilibrium approximations, and provide practical recipes for model reduction of linear and nonlinear networks. We also discuss the application of model reduction to backward pruning machine learning techniques

On Nonnormal Asymptotic Behavior of Optimal Solutions of Stochastic Programming Problems: The Parametric Case

Under incomplete information about the parameters of the true distribution of the random coefficients, the optimal solutions to stochastic programs can be only approximated. This paper extends the previous results of the author to the case when strict complementarity conditions need not be assumed

Information geometric methods for complexity

Research on the use of information geometry (IG) in modern physics has witnessed significant advances recently. In this review article, we report on the utilization of IG methods to define measures of complexity in both classical and, whenever available, quantum physical settings. A paradigmatic example of a dramatic change in complexity is given by phase transitions (PTs). Hence we review both global and local aspects of PTs described in terms of the scalar curvature of the parameter manifold and the components of the metric tensor, respectively. We also report on the behavior of geodesic paths on the parameter manifold used to gain insight into the dynamics of PTs. Going further, we survey measures of complexity arising in the geometric framework. In particular, we quantify complexity of networks in terms of the Riemannian volume of the parameter space of a statistical manifold associated with a given network. We are also concerned with complexity measures that account for the interactions of a given number of parts of a system that cannot be described in terms of a smaller number of parts of the system. Finally, we investigate complexity measures of entropic motion on curved statistical manifolds that arise from a probabilistic description of physical systems in the presence of limited information. The Kullback-Leibler divergence, the distance to an exponential family and volumes of curved parameter manifolds, are examples of essential IG notions exploited in our discussion of complexity. We conclude by discussing strengths, limits, and possible future applications of IG methods to the physics of complexity.Comment: review article, 60 pages, no figure

Trajectory optimization for the National Aerospace Plane

The primary objective of this research is to develop an efficient and robust trajectory optimization tool for the optimal ascent problem of the National Aerospace Plane (NASP). This report is organized in the following order to summarize the complete work: Section two states the formulation and models of the trajectory optimization problem. An inverse dynamics approach to the problem is introduced in Section three. Optimal trajectories corresponding to various conditions and performance parameters are presented in Section four. A midcourse nonlinear feedback controller is developed in Section five. Section six demonstrates the performance of the inverse dynamics approach and midcourse controller during disturbances. Section seven discusses rocket assisted ascent which may be beneficial when orbital altitude is high. Finally, Section eight recommends areas of future research