Böcker i Theoretical Biology-serien

This book helps the reader make use of the mathematical models of biological phenomena starting from the basics of programming and computer simulation. Computer simulations based on a mathematical model enable us to find a novel biological mechanism and predict an unknown biological phenomenon. Mathematical biology could further expand the progress of modern life sciences. Although many biologists are interested in mathematical biology, they do not have experience in mathematics and computer science. An educational course that combines biology, mathematics, and computer science is very rare to date. Published books for mathematical biology usually explain the theories of established mathematical models, but they do not provide a practical explanation for how to solve the differential equations included in the models, or to establish such a model that fits with a phenomenon of interest. MATLAB is an ideal programming platform for the beginners of computer science. This book starts from the very basics about how to write a programming code for MATLAB (or Octave), explains how to solve ordinary and partial differential equations, and how to apply mathematical models to various biological phenomena such as diabetes, infectious diseases, and heartbeats. Some of them are original models, newly developed for this book. Because MATLAB codes are embedded and explained throughout the book, it will be easy to catch up with the text. In the final chapter, the book focuses on the mathematical model of the proneural wave, a phenomenon that guarantees the sequential differentiation of neurons in the brain. This model was published as a paper from the author¿s lab (Sato et al., PNAS 113, E5153, 2016), and was intensively explained in the book chapter ¿Notch Signaling in Embryology and Cancer¿, published by Springer in 2020. This book provides the reader who has a biological background with invaluable opportunities to learn and practice mathematical biology.

This book shows that evolutionary game theory can unravel how mutual cooperation, trust, and credit in a group emerge in organizations and institutions. Some organizations and institutions, such as insurance unions, credit unions, and banks, originated from very simple mutual-aid groups. Members in these early-stage mutual-aid groups help each other, making rules to promote cooperation, and suppressing free riders. Then, they come to ¿trust¿ not only each other but also the group they belong to, itself. The division of labor occurs when the society comes to have diversity and complexity in a larger group, and the division of labor also requires mutual cooperation and trust among different social roles. In a larger group, people cannot directly interact with each other, and the reputation of  unknown people helps other decide who is a trustworthy person. However, if gossip spreads untruths about a reputation, trust and cooperation are destroyed. Therefore, how to suppress untrue gossip is also important for trust and cooperation in a larger group. If trustworthiness and credibility can be established, these groups are successfully sustainable. Some develop and evolve and then mature into larger organizations and institutions. Finally, these organizations and institutions become what they are now. Therefore, not only cooperation but also trust and credit are keys to understanding these organizations and institutions.The evolution of cooperation, a topic of research in evolutionary ecology and evolutionary game theory, can be applied to understanding how to make institutions and organizations sustainable, trustworthy, and credible. It provides us with the idea that evolutionary game theory is a good mathematical tool to analyze trust and credit. This kind of research can be applied to current hot topics such as microfinance and the sustainable use of ecosystems.

This textbook provides an introduction to the mathematical models of population dynamics in mathematical biology. The focus of this book is on the biological meaning/translation of mathematical structures in mathematical models, rather than simply explaining mathematical details and literacies to analyze a model. In some recent usages of the mathematical model simply with computer numerical calculations, the model includes some inappropriate mathematical structure concerning the reasonability of modeling for the biological problem under investigation. For students and researchers who study or use mathematical models, it is important and helpful to understand what mathematical setup could be regarded as reasonable for the model with respect to the relation between the biological factors involved in the assumptions and the mathematical structure of the model.Topics covered in this book are; modeling with geometric progression, density effect in population dynamics, deriving continuous time models from discrete time models, basic modeling for birth-death stochastic processes, continuous time models, modeling interspecific reaction for the continuous time population dynamics model, competition and prey-predator dynamics, modeling for population dynamics with a heterogeneous structure of population, qualitative analysis on the discrete time dynamical system, necessary knowledge about fundamental mathematical theories to understand the dynamical nature of continuous time models. The book includes popular topics in ecology and mathematical biology, as well as classic theoretical topics.By understanding the biological meaning of modeling for simple models, readers will be able to derive a specific mathematical model for a biological problem by reasonable modeling. The contents of this book is made accessible for readers without strong Mathematical background.

This book describes the dynamics of biological cells and their mathematical modeling. The topics cover the dynamics of RNA polymerases in transcription, construction of vascular networks in angiogenesis, and synchronization of cardiomyocytes. Statistical analysis of single cell dynamics and classification of proteins by mathematical modeling are also presented. The book provides the most up-to-date information on both experimental results and mathematical models that can be used to analyze cellular dynamics. Novel experimental results and approaches to understand them will be appealing to the readers. Each chapter contains 1) an introductory description of the phenomenon, 2) explanations about the mathematical technique to analyze it, 3) new experimental results, 4) mathematical modeling and its application to the phenomenon. Elementary introductions for the biological phenomenon and mathematical approach to them are especially useful for beginners. The importance of collaboration between mathematics and biological sciences has been increasing and providing new outcomes. This book gives good examples of the fruitful collaboration between mathematics and biological sciences. 

This book describes the shape formation of living organisms using mathematical models. Genes are deeply related to the shape of living organisms, and elucidation of a pathway of shape formation from genes is one of the fundamental problems in biology. Mathematical cell models are indispensable tools to elucidate this problem.  The book introduces two mathematical cell models, the cell center model and the vertex model, with their applications. The cell center model is applied to elucidate the formation of neat cell arrangements in epidermis, cell patterns consisting of heterogeneous-sized cells, capillary networks, and the branching patterns of blood vessels. The vertex model is applied to elucidate the wound healing mechanisms of the epithelium and ordered pattern formation involving apoptosis. Pattern formation with differential cell adhesion is also described. The vertex model is then extended from a two-dimensional (2D) to a three-dimensional (3D) model. A cell aggregate involving a large cavity is described to explain the development of the mammalian blastocyst or the formation of an epithelial vesicle. Epithelial tissues and the polarity formation process of the epithelium are also explained. The vertex model also recapitulates active remodeling of tissues and describes the twisting of tissue that contributes to understanding the cardiac loop formation of the embryonic tube. The book showcases that mathematical cell models are indispensable tools to understand the shape formation of living organisms. Successful contribution of the mathematical cell models means that the remodeling of collective cells is self-construction. Examining the successive iterations of self-constructions leads to understanding the remarkable and mysterious morphogenesis that occurs during the development of living organisms.  The intended readers of this book are not only theoretical or mathematical biologists, but also experimental and general biologists, including undergraduate and postgraduate students who are interested in the relationship between genes and morphogenesis. 

This book presents new theoretical perspectives on ecological community dynamics and in so doing casts fresh light on the enduring complexity-stability debate.

This book presents a unique fusion of two different research topics. Although the combination is simple and straightforward, the book describes the emergence of rather intricate behavior, provoking the interest of readers for further developments and applications of related topics.

This book covers recent developments in epidemic process models and related data on temporally varying networks.