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Simple Mathematical Models of Gene Regulatory Dynamics
This is a short and self-contained introduction to the field of mathematical modeling of gene-networks in bacteria. As an entry point to the field, we focus on the analysis of simple gene-network dynamics. The notes commence with an introduction to the deterministic modeling of gene-networks, with extensive reference to applicable results coming from dynamical systems theory. The second part of the notes treats extensively several approaches to the study of gene-network dynamics in the presence of noise—either arising from low numbers of molecules involved, or due to noise external to the regulatory process. The third and final part of the notes gives a detailed treatment of three well stu...
Current Challenges in Modeling Cellular Metabolism
Mathematical and computational models play an essential role in understanding the cellular metabolism. They are used as platforms to integrate current knowledge on a biological system and to systematically test and predict the effect of manipulations to such systems. The recent advances in genome sequencing techniques have facilitated the reconstruction of genome-scale metabolic networks for a wide variety of organisms from microbes to human cells. These models have been successfully used in multiple biotechnological applications. Despite these advancements, modeling cellular metabolism still presents many challenges. The aim of this Research Topic is not only to expose and consolidate the s...
Computing the Continuous Discretely
This richly illustrated textbook explores the amazing interaction between combinatorics, geometry, number theory, and analysis which arises in the interplay between polyhedra and lattices. Highly accessible to advanced undergraduates, as well as beginning graduate students, this second edition is perfect for a capstone course, and adds two new chapters, many new exercises, and updated open problems. For scientists, this text can be utilized as a self-contained tooling device. The topics include a friendly invitation to Ehrhart’s theory of counting lattice points in polytopes, finite Fourier analysis, the Frobenius coin-exchange problem, Dedekind sums, solid angles, Euler–Maclaurin summat...
Boolean Networks as Predictive Models of Emergent Biological Behaviors
Interacting biological systems at all organizational levels display emergent behavior. Modeling these systems is made challenging by the number and variety of biological components and interactions – from molecules in gene regulatory networks to species in ecological networks – and the often-incomplete state of system knowledge, such as the unknown values of kinetic parameters for biochemical reactions. Boolean networks have emerged as a powerful tool for modeling these systems. This Element provides a methodological overview of Boolean network models of biological systems. After a brief introduction, the authors describe the process of building, analyzing, and validating a Boolean model. They then present the use of the model to make predictions about the system's response to perturbations and about how to control its behavior. The Element emphasizes the interplay between structural and dynamical properties of Boolean networks and illustrates them in three case studies from disparate levels of biological organization.
Integer Programming and Combinatorial Optimization
This book constitutes the refereed proceedings of the 12th International Conference on Integer Programming and Combinatorial Optimization, IPCO 2007, held in Ithaca, NY, USA, in June 2007. Among the topics addressed in the 36 revised full papers are approximation algorithms, algorithmic game theory, computational biology, integer programming, polyhedral combinatorics, scheduling theory and scheduling algorithms, as well as semidefinite programs.
Approximation, Complex Analysis, and Potential Theory
Hermann Weyl considered value distribution theory to be the greatest mathematical achievement of the first half of the 20th century. The present lectures show that this beautiful theory is still growing. An important tool is complex approximation and some of the lectures are devoted to this topic. Harmonic approximation started to flourish astonishingly rapidly towards the end of the 20th century, and the latest development, including approximation manifolds, are presented here. Since de Branges confirmed the Bieberbach conjecture, the primary problem in geometric function theory is to find the precise value of the Bloch constant. After more than half a century without progress, a breakthrough was recently achieved and is presented. Other topics are also presented, including Jensen measures. A valuable introduction to currently active areas of complex analysis and potential theory. Can be read with profit by both students of analysis and research mathematicians.
Complex Analysis and Potential Theory
This is the proceedings volume of an international conference entitled Complex Analysis and Potential Theory, which was held to honor the important contributions of two influential analysts, Kohur N. GowriSankaran and Paul M. Gauthier, in June 2011 at the Centre de Recherches Mathematiques (CRM) in Montreal. More than fifty mathematicians from fifteen countries participated in the conference. The twenty-four surveys and research articles contained in this book are based on the lectures given by some of the most established specialists in the fields. They reflect the wide breadth of research interests of the two honorees: from potential theory on trees to approximation on Riemann surfaces, fr...
Convex Optimization & Euclidean Distance Geometry
The study of Euclidean distance matrices (EDMs) fundamentally asks what can be known geometrically given onlydistance information between points in Euclidean space. Each point may represent simply locationor, abstractly, any entity expressible as a vector in finite-dimensional Euclidean space.The answer to the question posed is that very much can be known about the points;the mathematics of this combined study of geometry and optimization is rich and deep.Throughout we cite beacons of historical accomplishment.The application of EDMs has already proven invaluable in discerning biological molecular conformation.The emerging practice of localization in wireless sensor networks, the global posi...
