Monte Carlo Methods For Applied Scientists by Ivan T. Dimov
(World Scientific Publishing Company) Stochastic optimization refers
to the minimization (or maximization) of a function in the presence
of randomness in the optimization process. The randomness may be
present as either noise in measurements or Monte Carlo randomness in
the search procedure, or both. The study of random geometric
structures. Stochastic geometry leads to modelling and analysis
tools such as Monte Carlo methods.
Common methods of stochastic optimization include direct search
methods (such as the NelderMead method), stochastic approximation,
stochastic programming, and miscellaneous methods such as simulated
annealing and genetic algorithms.
The Monte Carlo method is inherently parallel and the extensive and rapid development in parallel computers, computational clusters and grids has resulted in renewed and increasing interest in this method. At the same time there has been an expansion in the application areas and the method is now widely used in many important areas of science including nuclear and semiconductor physics, statistical mechanics and heat and mass transfer.
This book attempts to bridge the gap between theory and practice concentrating on modern algorithmic implementation on parallel architecture machines. Although a suitable text for final year postgraduate mathematicians and computational scientists it is principally aimed at the applied scientists: only a small amount of mathematical knowledge is assumed and theorem proving is kept to a minimum, with the main focus being on parallel algorithms development often to applied industrial problems.
A selection of algorithms developed both for serial and parallel machines are provided.
The primary motivation for new developments in Monte Carlo methods is the fact that they are widely used for those problems for which deterministic algorithms hopelessly break down. An important reason for this is that Monte Carlo methods do not require additional regularity of the problem's initial data. The main problem with the deterministic algorithms is that they normally need some additional approximation procedure, requiring additional regularity. Monte Carlo algorithms do not need such procedures. Nevertheless, if one can exploit the existing smoothness of the input data then normally Monte Carlo methods have a better convergence rate than the deterministic methods. At the same time, dealing with Monte Carlo algorithms one has to accept the fact that the result of the computation can be close to the true value only with a certain probability. Such a setting may not be acceptable if one needs a guaranteed accuracy or strictly reliable results. But in most cases it is reasonable to accept an error estimate with a probability smaller than 1. In fact, we shall see that this is a price paid by Monte Carlo methods to increase their convergence rate. The better convergence rate for Monte Carlo algorithms is reached with a given probability, so the advantage of Monte Carlo algorithms is a matter of definition of the probability error.
The second important motivation is that Monte Carlo is efficient in dealing with large and very large computational problems: multidimensional integration, very large linear algebra problems, integrodifferential equations of high dimensions, boundaryvalue problems for differential equations in domains with complicated boundaries, simulation of turbulent flows, studying of chaotic structures, etc.. At the same time it is important to study applicability and acceleration analysis of Monte Carlo algorithms both theoretically and experimentally. Obviously the performance analysis of algorithms for people dealing with largescale problems is a very important issue.
The third motivation for new developments of Monte Carlo methods is that they are very efficient when parallel processors or parallel computers are available. The reason for this is because Monte Carlo algorithms are inherently parallel and have minimum dependency. In addition, they are also naturally vectorizable when powerful vector processors are used. At the same time, the problem of parallelization of the Monte Carlo algorithms is not a trivial task because different kinds of parallelization can be used. To find the most efficient parallelization in order to obtain high speedup of the algorithm is an extremely important practical problem in scientific computing. Another very important issue is the scalability of the algorithms. Scalability is a desirable property of algorithms that indicates their ability to handle growing amounts of computational work on systems with increasing number of processing nodes. With the latest developments of distributed and Grid computing during last ten years there is a serious motivation to prepare scalable largescale Monte Carlo computational models as Grid applications.
One of most surprising findings is the absence of a systematic guide to Monte Carlo methods for applied scientists. This book differs from other existing Monte Carlo books by focusing on performance analysis of the algorithms and demonstrating some existing large scale applications in semiconductor device modeling. The reader will find description of some basic Monte Carlo algorithms as well as numerical results of implementations. Nevertheless, I found it important to give some known fundamental facts about Monte Carlo methods to help readers who want to know a little bit more about the theory. I also decided to include some exercises specially created for students participating in the course of "Stochastic Methods and Algorithms for Computational Science" at the University of Reading, UK. My experience working with students studying stochastic methods shows that the exercises chosen help in understanding the nature of Monte Carlo methods.
This book is primary addressed to applied scientists and students from Computer Science, Physics, Biology and Environmental Sciences dealing with Monte Carlo methods.
Monte Carlo methods are a powerful tool in many fields of mathematics, physics and engineering. It is known that the algorithms based on this method give statistical estimates for any linear functional of the solution by performing random sampling of a certain random variable (r.v.) whose mathematical expectation is the desired functional.
Definition 1.1. Monte Carlo methods are methods of approximation of the solution to problems of computational mathematics, by using random processes for each such problem, with the parameters of the process equal to the solution of the problem. The method can guarantee that the error of Monte Carlo approximation is smaller than a given value with a certain probability.
So, Monte Carlo methods always produce an approximation of the solution, but one can control the accuracy of this solution in terms of the probability error. The Las Vegas method is a randomized method which also uses
r.v. or random processes, but it always produces the correct result (not an approximation). The computational problem in Monte Carlo algorithms becomes one of calculating repeated realizations of the r.v. and of combining them into an appropriate statistical estimator of the functional J(u) or solution. One can consider Las Vegas algorithms as a class of Monte Carlo algorithms if one allows P = 1 (in this case RN = 0) in Definition 1.2. For most problems of computational mathematics it is reasonable to accept an error estimate with a probability smaller than 1.
The year 1949 is generally regarded as the official birthday of the Monte Carlo method when the paper of Metropolis and Ulam was published, although some authors point to earlier dates.
Ermakov notes that a solution of a problem by the Monte Carlo method is contained in the Old Testament. In 1777 G. Compte de Buffon posed the following problem: suppose we have a floor made of parallel strips of wood, each the same width, and we drop a needle onto the floor. What is the probability that the needle will lie across a line between two strips? The problem in more mathematical terms is: given a needle of length I dropped on a plane ruled with parallel lines t units apart, what is the probability P that the needle will cross a line?; Kalos and Whitlock (1986)]). He found that P = 2//(7t). In 1886 Marquis PierreSimon de Laplace showed that the number 71 can be approximated by repeatedly throwing a needle onto a lined sheet of paper and counting the number of intersected lines. The development and intensive applications of the method is connected with the names of J. von Neumann, E. Fermi, G. Kahn and S. M. Ulam, who worked at Los Alamos (USA) for forty years on the Manhattan project 1. A legend says that the method was named in honor of Ulam's uncle, who was a gambler, at the suggestion of Metropolis.
The development of modern computers, and particularly parallel computing systems, provided fast and specialized generators of random numbers and gave a new momentum to the development of Monte Carlo algorithms.
Any method which solves a problem by generating suitable random numbers and observing that fraction of the numbers obeying some property or properties. The method is useful for obtaining numerical solutions to problems which are too complicated to solve analytically. It was named by S. Ulam, who in 1949 became the first mathematician to dignify this approach with a name, in honor of a relative having a propensity to gamble. Nicolas Metropolis also made important contributions to the development of such methods.
The most common application of the Monte Carlo method is Monte Carlo integration. In order to integrate a function over a complicated domain , Monte Carlo integration picks random points over some simple domain which is a superset of , checks whether each point is within , and estimates the area of (volume, dimensional content, etc.) as the area of multiplied by the fraction of points falling within . Monte Carlo integration is implemented in Mathematica as NIntegrate [f, ..., Method>MonteCarlo].
Picking randomly distributed points , , ..., in a multidimensional volume to determine the integral of a function in this volume gives a result

(1) 
where



(2) 



(3) 
QuasiMonte Carlo integration is a method of numerical integration that operates in the same way as Monte Carlo integration, but instead uses sequences of quasirandom numbers to compute the integral. Quasirandom numbers are generated algorithmically by computer, and are similar to pseudorandom numbers while having the additional important property of being deterministically chosen based on equidistributed sequences in order to minimize errors.
Monte Carlo methods are connected with computer simulation, and there is a distinction between simulation (where the system investigated and the mathematical model are both stochastic in nature, as in the simulation of a supermarket), and Monte Carlo simulation (where the modeled system is deterministic and the model used is stochastic) as in the case of Monte Carlo integration.
There are many algorithms using this essential idea for solving a wide range of problems. The Monte Carlo algorithms are currently widely used for those problems for which the deterministic algorithms hopelessly break down: highdimensional integration, integral and integrodifferential equations of high dimensions, boundaryvalue problems for differential equations in domains with complicated boundaries, simulation of turbulent flows, studying of chaotic structures, etc..
An important advantage of Monte Carlo algorithms is that they permit the direct determination of an unknown functional of the solution, in a given number of operations equivalent to the number of operations needed to calculate the solution at only one point of the domain. This is very important for some problems of applied science. Often, one does not need to know the solution on the whole domain in which the problem is defined.
The Structural Stabilization of Polymers: Fractal Models by G. V.
Kozlov, G. E. Zaikov (New Concepts in Polymer Science: VSP
International (Brill) This monograph deals with the structural aspects of
transport processes of gases, physical ageing and thermooxidative degradation
of polymers in detail. Fractal analysis, cluster models of the polymer
structure's amorphous state as well as irreversible aggregation models are used
as main structural models. It is shown that the polymer structure is often a
more important parameter than its chemical construction. Another significant
aspect is the structural role in polymer melts oxidation.
The basis for understanding of structural stabilization gives anomalous
diffusion of oxidant molecules on the fractal structure for both solid state
polymers and polymeric melts. The important part of this problem is structure
connectivity characterized by its spectral dimension. Therefore branched
(crosslinked) polymers have smaller diffusivity in comparison with linear
polymers. Fractal mathematics is used throughout to sharpen measures and tighten
explanations. The volume could have used an Englishlanguage editor.
More
Elementorganic Monomers: Technology, Properties, Applications by L. M. Khananashvili, O. V. Mukbaniani, G. E. Zaikov (New Concepts in Polymer Science: Brill Academic Publishers) The chemical industry in our country and abroad is rapidly developing. It is only natural that the young industry of elementorganic monomers, oligomers and polymers should develop at the same rate. The numerous valuable and sometimes unique properties of these substances account for their wide application in various industries, households, medicine and cuttingedge technologies. That is why contemporary industry produces more than 500 types of silicone monomers, oligomers and polymers, to say nothing of other elementorganic compounds. The synthesis of these elementorganic compounds is based on many different reactions. More
Numerical Modeling of Water Waves, Second Edition, includes CDROM by Charles L. Mader (CRC Press) is a wellwritten, comprehensive treatise of the evolving science of computer modeling of waves. In a very skillful and methodical manner, the Dr. Charles Mader provides new insights on the subject and updates the reader with what is being done with stateoftheart, highperformance computers which allow for the adaptation of new codes that can result in even more accurate simulations of waves generated from a variety of source mechanisms  whether generated by earthquakes, landslides, explosions, or the impact of asteroids. The book is an outstanding work of scholarship and a valuable reference for any researcher involved or interested in the numerical modeling of waves.
Numerical Modeling of Water Waves discusses the numerical methods for modeling water waves and their applications. This book describes methods developed primarily at the Los Alamos National Laboratory within the last forty years. It explains data on basic fluid dynamics associated with water waves and also addresses advanced techniques for modeling. It provides numerical modeling of the largest historical tsunami wave recorded. Also included is a CDROM with FORTRAN codes of numerical methods for water wave modeling, and tsunami wave generation, propagation and flooding. Includes animations of many of the solved problems using these codes.
This second edition of Numerical Modeling of Water Waves describes the technological revolution that has occurred in numerical modeling of water waves during the last decade. A CDROM with many of the FORTRAN codes of the numerical methods for solving water wave problems and computer animations of the problems that have been solved using the codes is included with the book. Several PowerPoint presentations describing the modeling results are on the CDROM. It will be called the NMWW CDROM in the rest of the book.
The objective of this book is to describe the numerical methods for modeling water waves that have been developed primarily at the Los Alamos National Laboratory over the last four decades and to describe some examples of the applications of these methods. Some of the applications of the numerical modeling methods were performed while the author was working at the Joint Institute for Marine and Atmospheric Research at the University of Hawaii, some as Mader Consulting Co. research projects, and the rest as a Fellow of the Los Alamos National Laboratory.
Although the two and threedimensional numerical methods for modeling water waves had been available in the 1980's for several decades, they had seldom been used. A major obstacle to their use was the need for access to large and expensive computers. By the 1980's, inexpensive personal computers were adequate for many applications of these numerical methods.
In this book, the basic fluid dynamics associated with water waves are described. The common water wave theories are reviewed in Chapter 1. A computer code called WAVE for personal computers that calculates the wave properties for Airy, thirdorder Stokes, and Laitone solitary gravity waves is available on the NMWW CDROM.
The incompressible fluid dynamics model used for shallow water, long waves is described in Chapter 2. A computer code for personal computers using the shallow water model is called SWAN and is available on the NMWW CDROM. The SWAN code is used to model the 1946, 1960 and 1964 earthquake generated Hilo, Hawaii tsunamis, the 1964 Crescent City, California tsunami and the 1994 underwater landslide generated Skagway, Alaska tsunami.
The twodimensional incompressible NavierStokes model used for solving water wave problems is described in Chapter 3. A computer code for personal computers using the twodimensional NavierStokes model is called ZUNI and is available on the NMWW CDROM. The ZUNI code is used to model tsunami wave propagation and flooding. It is also used to model the effect of underwater barriers on tsunami waves.
The threedimensional incompressible NavierStokes model for solving water wave problems of any type is described in Chapter 4. The equations used in the computer code called SOLA3D are described and the FORTRAN code is`on the NMWW CDROM. The SOLA3D code is used to model the 1975 Hawaiian tsunami and the 1994 Skagway tsunami by water surface cavities generated by underwater landslides.
It is surprising that most academic and government modelers of water waves have chosen to use shallow water or other incompressible models of limited validity for modeling water waves and not use the incompressible NavierStokes model since the first edition of this book was published. The severe limitations of the shallow water model are described in Chapter 5.
The generation of water waves by volcanic explosions, conventional or nuclear explosions, projectile and asteroid impacts require the use of the compressible NavierStokes model. The numerical models and codes for solving such problems have recently become available as part of the Accelerated Strategic Computer Initiative program. A computer code for solving one, two and three dimensional compressible problems called SAGE, NOBEL or RAGE is described in Chapter 6 and some of its remarkable capabilities are presented. These include modeling of the KT Chicxulub asteroid impact and the modeling of the largest historical tsunami which occurred July 8, 1958, at Lituya Bay, Alaska. The modeling of the Lituya Bay impact landslide generated tsunami and the flooding to 520 meters altitude is described.
A color videotape (VTC–86–4) lecture featuring computer generated films of many of the applications discussed in this book is available from the Los Alamos National Laboratory library. Several web sites have been established that contain additional information and computer movies of the problems described in this book. The major sites are http://www.mccohi.org and httpi/tl4web.lanl.gov/Staff/clm/tsunami.mve/tsunami.html.
Finite
Mathematics and Its Applications, Eighth Edition by
Larry Joel Goldstein, David I. Schneider, Martha J. Siegel, T. E. Graedel
(Prentice Hall) This work is the eighth edition of our text for the traditional
finite mathematics course taught to first and secondyear college students,
especially those majoring in business and the social and biological sciences.
Finite mathematics courses exhibit tremendous diversity with respect to both
content and approach. Therefore, in revising this book, we incorporated a wide
range of topics from which an instructor may design a curriculum, as well as a
high degree of flexibility in the order in which the topics may be presented.
For the mathematics of finance, we even allow for flexibility in the approach of
the presentation.
This
edition maintains a popular studentoriented approach throughout and, in
particular, through the use of the following features:
Realistic
applications illustrate the uses of finite mathematics in other disciplines. The
reader may survey the variety of applications by referring to the Index of
Applications located on the front endpapers. Wherever possible, the authors
attempt to use applications to motivate the mathematics. For example, the
concept of linear programming is introduced via a discussion of production
options for a factory with a labor limitation.
They
include many more worked examples than is customary in textbooks. Furthermore,
they include computational details to enhance comprehension by students whose
basic skills are weak.
More than
2700 exercises comprise about onequarter of the book, the most important part
of the text in our opinion. The exercises at the ends of the sections are
usually arranged in the order in which the text proceeds, so that homework
assignments may be easily made after only part of a section is discussed.
Interesting applications and more challenging problems tend to be located near
the ends of the exercise sets. Supplementary exercises at the end of each
chapter amplify the other exercise sets and provide cumulative exercises that
require skills acquired from earlier chapters. Answers to the oddnumbered
exercises from the sections and answers to all the supplementary and chapter
test exercises are included at the back of the book.
The
practice problems are a popular and useful feature of the book. They are
carefully selected exercises located at the end of each section, just before the
exercise set. Complete solutions follow the exercise set. The practice problems
often focus on points that are potentially confusing or are likely to be
overlooked. The authors recommend that the reader seriously attempt to do the
practice problems and study their solutions before moving on to the exercises.
Although
the use of technology is optional for this text, many of the topics can be
enhanced with graphing calculators, electronic spreadsheets, and mathematical
software. Whenever relevant, we explicitly show the student how to use graphing
calculators and electronic spreadsheets effectively to assist in understanding
the fundamental concepts of the course. In addition, the text contains
appendices on the fundamentals of using graphing calculators and electronic
spreadsheets. The powerful mathematical software "Explorations in Finite
Mathematics" is packaged with each Student Solutions Manual. Many sections of
the book contain specially designed technology exercises intended to be solved
with one of these technologies.
In our
discussions of graphing calculators, we specifically refer to the TI83 since
this is the most popular graphing calculator. Therefore, most students will
have a book customized to their calculator. Students with other graphing
calculators can consult their guidebooks to learn how to make adjustments. Had
the calculator material been written generically, every student would have to
make adjustments. For the same reasons, the discussions of electronic
spreadsheets refer to Microsoft Excel.
We have
included questions similar to those found on CPA, GMAT, and GRE Economics exams
to illustrate further the relevance of the material in the course. These
multiplechoice questions are identified with the notation PE (which stands for
"professional exams").
Near the
end of each chapter is a set of questions that help the student recall the key
ideas of the chapter and focus on the relevance of these concepts.
Each
chapter contains a detailed summary of the important definitions and results
from the chapter serving as a handy study tool for the student. Each chapter has
a sample test that can be used by the student to help determine if he or she has
mastered the important concepts of the chapter. The answers to the chapter test
are given at the back of the book.
Most
chapters have extended projects that can be used as inclass or outofclass
group projects, or special assignments. These projects develop interesting
applications or enhance key concepts of the chapters.
Among the
changes in this edition, the following are the most significant:
Personal financial decisions section. A section has been added to the end of
Chapter 10 that considers financial decisions that students often have to
make shortly after graduating from college. The section discusses IRAs,
consumer loans, and mortgages. The differences between traditional and Roth
IRAs are discussed along with the advantages of starting them early. The
common addon method for computing the finance charges for a consumer loan
is presented and analyzed. The section shows how to compare mortgages
having different upfront fees by calculating their APRs, which must be
provided by the lender, and their effective mortgage rates, which are used
by mortgage analysts to compare mortgages.
Electronic spreadsheets. An appendix titled "Spreadsheet Fundamentals" has
been added. In addition, relevant material on the use of spreadsheets is
presented alongside appropriate topics in the book.
A new
chapter project for the Mathematics of Finance chapter provides useful
insights into the effects of interest.
The
discussion of sensitivity analysis of linear programming problems has been
expanded.
Additional exercises and updated data. We have added many new exercises
(including about twodozen similar to those appearing in professional exams,
such as the GMAT) and have updated the realworld data appearing in
exercises and examples.
Because
of great variation in student preparation, we keep formal prerequisites to a
minimum. We assume only one year of high school algebra. Furthermore, we
review, as needed, those topics that are typically weak spots for students.
This
edition has more material than can be covered in most onesemester courses.
Therefore, the instructor can structure the course to the students' needs and
interests. The book divides naturally into four parts. The first part consists
of linear mathematics: linear equations, matrices, and linear programming
(Chapters 14); the second part is devoted to probability and statistics
(Chapters 57); the third part covers topics utilizing the ideas of the other
parts (Chapters 810); and the fourth part explores key topics from discrete
mathematics that are sometimes included in the modern finite mathematics
curriculum (Chapters 1113). We prefer to begin with linear mathematics since it
makes for a smooth transition from high school mathematics and leads quickly to
interesting applications, especially linear programming. Our preference
notwithstanding, the instructor may begin this book with Chapter 5 ("Sets and
Counting") and then do either the linear mathematics or the probability and
statistics.
Mathematics for Chemistry & Physics by George Turrell (Academic Press) This book has been written in an attempt to provide students with the mathematical basis of chemistry and physics. Many of the subjects chosen are those that I wish that I had known when I was a student. It was just at that time that the no‑mans‑land between these two domains ‑ chemistry and physics ‑ was established by the "Harvard School", certainly attributable to E. Bright Wilson, Jr., J. H. van Vleck and the others of that epoch…
That chemistry and physics are brought together by mathematics is the "raison d'être" of the present volume. The first three chapters are essentially a review of elementary calculus. After that there are three chapters devoted to differential equations and vector analysis. The remainder of the book is at a somewhat higher level. It is a presentation of group theory and some applications, approximation methods in quantum chemistry, integral transforms and numerical methods.
This is not a fundamental mathematics book, nor is it intended to serve a textbook for a specific course, but rather as a reference for students in chemistry and physics at all university levels. Although it is not computer based, I have made many references to current applications ‑ in particular to try to convince students that they should know more about what goes on behind the screen when they do one of their computer experiments. As an example, most students in the sciences now use a program for the fast Fourier transform. How many of them have any knowledge of the basic mathematics involved?
The lecture notes that I have written over many years in several countries have provided a basis for this book. More recently, I have distributed an early version to students at the third and fourth years at the University of Lille. It has been well received and found to be very useful. I hope that in its present form the book will be equally of value to students throughout their university studies.
An Introduction to Stochastic Processes with Applications to Biology by
Linda J. S. Allen (Prentice Hall) My goal in writing this
book is to provide an introduction to the basic theory of stochastic processes
and to some of the many biological applications of stochastic processes. The
mathematical and biological background required is kept to a minimum so that
the topics are accessible to students and scientists in biology, mathematics,
and engineering. Many of the biological applications are from the areas of
population dynamics and epidemiology due to personal preference and expertise
and because these applications can be readily understood.
Interdisciplinary areas such as mathematical biology, biostatistics, and
bioengineering are growing rapidly. Modeling and analysis of biological
phenomena require techniques and tools from various disciplines. Many recent
books have addressed the need for a better understanding of the underlying
theory of modeling in biology. However, much more attention has been paid to the
area of deterministic modeling in biology than to stochastic modeling, and this
book helps to fill the gap.
The topics
in this book are covered in a onesemester graduate course offered by the
Department of Mathematics and Statistics at Texas Tech University. This book is
intended for an introductory course in stochastic processes. The targeted
audiences for this book are advanced undergraduate students and beginning
graduate students in mathematics, statistics, biology, or engineering. The level
of material in this book requires only a basic background in probability
theory, linear algebra, and analysis. Measure theory is not required. Exercises
at the end of each chapter help reinforce concepts discussed in each chapter. To
better visualize and understand the dynamics of various stochastic processes,
students are encouraged to use the MATLAB programs provided in the Appendices.
These programs can be modified for other types of processes or adapted to other
programming languages. In addition, research on current stochastic biological
models in the literature can be assigned as individual or group research
projects.
The book is
organized according to the following three types of stochastic processes:
discrete time Markov chains, continuous time Markov chains and continuous time
and state Markov processes. Because many biological phenomena can be modeled by
one or more of these three modeling approaches, there may be different
stochastic models for the same biological phenomena, e.g.. logistic growth and
epidemics. Biological applications are presented in each chapter. Some chapters
and sections are devoted entirely to the discussion of biological applications
and their analysis (e.g.., Chapter 7).
In Chapter
1, topics from probability theory are briefly reviewed which are particularly
relevant to stochastic processes. In Chapters 2 and 3, the theory and biological
applications of discrete time Markov chains are discussed, including the
classical gambler's ruin problem, birth and death processes and epidemic
processes. In Chapter 4, the topic of branching process is discussed, a
discrete time Markov chain important to applications in biology and medicine. An
application to an agestructured population is discussed in Chapter 4. Chapters
5, 6, and 7 present the theory and biological applications of continuous time
Markov chains. Chapter 6 concentrates on birth and death processes and in
Chapter 7 there are applications to epidemic, competition, predation and
population genetics processes. The last chapter, Chapter 8, is a brief
introduction to continuous time and continuous state, Markov processes; that
is, diffusion processes and stochastic differential equations. Chapter 8 is a
nonmeasure theoretic introduction to stochastic differential equations. These
eight chapters can be covered in a onesemester course. One may be selective
about the particular applications covered, particularly in Chapters 3, 7, and
8. In addition, Section 1.6 on the simple birth process and Section 2.10 on the
random walk in two and three dimensions are optional.
Numerous
applications of stochastic processes important in areas outside of biology,
including finance, economics, physics, chemistry, and engineering, can be found
in the references. This book stresses biological applications and therefore,
some topics in stochastic processes important to these other areas are omitted
or discussed very briefly. For example, martingales are not discussed and
queueing theory is only briefly discussed in Chapter 6.
Throughout
this book, the emphasis is placed on Markov processes due to their rich
structure and the numerous biological models satisfying the Markov property.
However, there are also many biological applications where the Markov
restriction does not apply. A stochastic process is discussed in Section 7.2,
which is a nonMarkovian, agedependent process belonging to a class of
stochastic processes known as regenerative processes. It is important to note
that in some applications the Markov restriction is not necessary, e.g.., first
passage time in Chapter 2 and the waiting time distribution in Chapter 5. This
latter theory can be discussed in the more general context of renewal theory.
insert content here