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From one cell to another, from one individual to another, and from one species to another, the content of DNA molecules is often similar. The organization of these molecules, however, differs dramatically, and the mutations that affect this organization are known as genome rearrangements. Combinatorial methods are used to reconstruct putative rearrangement scenarios in order to explain the evolutionary history of a set of species, often formalizing the evolutionary events that can explain the multiple combinations of observed genomes as combinatorial optimization problems. This book offers a comprehensive survey of this rapidly expanding application of combinatorial optimization. It can be used as a reference for experienced researchers or as an introductory text for a broader audience. Genome rearrangement problems have proved so interesting from a combinatorial point of view that the field now belongs as much to mathematics as to biology. The book takes a mathematically oriented approach, but provides biological background when necessary. It presents a series of models, beginning with the simplest (which is progressively extended by dropping restrictions), each constructing a genome rearrangement problem. The book also discusses an important generalization of the basic problem known as the median problem, surveys attempts to reconstruct the relationships between genomes with phylogenetic trees, and offers a collection of summaries and appendixes with additional information.

This book bridges optimal control theory and economics, discussing ordinary differential equations (ODEs), optimal control, game theory, and mechanism design in one volume. Technically rigorous and largely self-contained, it provides an introduction to the use of optimal control theory for deterministic continuous-time systems in economics. The theory of ordinary differential equations is the backbone of the theory developed in the book, and Chapter 2 offers a detailed review of basic concepts in the theory of ODEs, including the solution of systems of linear ODEs, state-space analysis, potential functions, and stability analysis. Following this, the book covers the main results of optimal control theory, in particular necessary and sufficient optimality conditions; game theory, with an emphasis on differential games; and the application of control-theoretic concepts to the design of economic mechanisms. Appendices provide a mathematical review and full solutions to all end-of-chapter problems. The material is presented at three levels: single-person decision making; games, in which a group of decision makers interact strategically; and mechanism design, which is concerned with a designer’s creation of an environment in which players interact to maximize the designer’s objective. The book focuses on applications; the problems are an integral part of the text.

Research in systems biology requires the collaboration of researchers from diverse backgrounds, including biology, computer science, mathematics, statistics, physics, and biochemistry. These collaborations, necessary because of the enormous breadth of background needed for research in this field, can be hindered by differing understandings of the limitations and applicability of techniques and concerns from different disciplines. The emerging area of systems level modeling in cellular biology has lacked a critical and thorough overview. The book provides the necessary critical comparison of concepts and approaches, with an emphasis on their possible applications. It presents key concepts and their theoretical background, including the concepts of robustness and modularity and their exploitation to study biological systems; the best-known modeling approaches, and their advantages and disadvantages; lessons from the application of mathematical models to the study of cellular biology; and available modeling tools and datasets, along with their computational limitations.