Mathematical and theoretical biology is an interdisciplinary academic research field with a range of applications in biology, medicine and biotechnology.^{[1]} The field may be referred to as mathematical biology or biomathematics to stress the mathematical side, or as theoretical biology to stress the biological side.^{[2]} It includes at least four major subfields: biological mathematical modeling, relational biology/complex systems biology (CSB), bioinformatics and computational biomodeling/biocomputing.^{[citation needed]}
Mathematical biology aims at the mathematical representation, treatment and modeling of biological processes, using a variety of applied mathematical techniques and tools. It has both theoretical and practical applications in biological, biomedical and biotechnology research. For example, in cell biology, protein interactions are often represented as "cartoon" models, which, although easy to visualize, do not accurately describe the systems studied. In order to do this, precise mathematical models are required. By describing the systems in a quantitative manner, their behavior can be better simulated, and hence properties can be predicted that might not be evident to the experimenter.
Contents 
Applying mathematics to biology has a long history, but only recently has there been an explosion of interest in the field. Some reasons for this include:
Several areas of specialized research in mathematical and theoretical biology^{[3]}^{[4]}^{[5]}^{[6]}^{[7]} as well as external links to related projects in various universities are concisely presented in the following subsections, including also a large number of appropriate validating references from a list of several thousands of published authors contributing to this field. Many of the included examples are characterised by highly complex, nonlinear, and supercomplex mechanisms, as it is being increasingly recognised that the result of such interactions may only be understood through a combination of mathematical, logical, physical/chemical, molecular and computational models. Due to the wide diversity of specific knowledge involved, biomathematical research is often done in collaboration between mathematicians, biomathematicians, theoretical biologists, physicists, biophysicists, biochemists, bioengineers, engineers, biologists, physiologists, research physicians, biomedical researchers, oncologists, molecular biologists, geneticists, embryologists, zoologists, chemists, etc.
A monograph on this topic summarizes an extensive amount of published research in this area up to 1987,^{[8]} including subsections in the following areas: computer modeling in biology and medicine, arterial system models, neuron models, biochemical and oscillation networks, quantum automata, quantum computers in molecular biology and genetics, cancer modelling, neural nets, genetic networks, abstract relational biology, metabolicreplication systems, category theory^{[9]} applications in biology and medicine,^{[10]} automata theory,cellular automata, tessallation models^{[11]}^{[12]} and complete selfreproduction, chaotic systems in organisms, relational biology and organismic theories.^{[13]}^{[14]} This published report also includes 390 references to peerreviewed articles by a large number of authors.^{[3]}^{[15]}^{[16]}
Modeling cell and molecular biology
This area has received a boost due to the growing importance of molecular biology.^{[6]}
Modelling physiological systems
Molecular set theory was introduced by Anthony Bartholomay, and its applications were developed in mathematical biology and especially in Mathematical Medicine.^{[26]} Molecular set theory (MST) is a mathematical formulation of the widesense chemical kinetics of biomolecular reactions in terms of sets of molecules and their chemical transformations represented by settheoretical mappings between molecular sets. In a more general sense, MST is the theory of molecular categories defined as categories of molecular sets and their chemical transformations represented as settheoretical mappings of molecular sets. The theory has also contributed to biostatistics and the formulation of clinical biochemistry problems in mathematical formulations of pathological, biochemical changes of interest to Physiology, Clinical Biochemistry and Medicine.^{[26]}^{[27]}
Population dynamics has traditionally been the dominant field of mathematical biology. Work in this area dates back to the 19th century. The Lotka–Volterra predatorprey equations are a famous example. In the past 30 years, population dynamics has been complemented by evolutionary game theory, developed first by John Maynard Smith. Under these dynamics, evolutionary biology concepts may take a deterministic mathematical form. Population dynamics overlap with another active area of research in mathematical biology: mathematical epidemiology, the study of infectious disease affecting populations. Various models of the spread of infections have been proposed and analyzed, and provide important results that may be applied to health policy decisions.
A model of a biological system is converted into a system of equations, although the word 'model' is often used synonymously with the system of corresponding equations. The solution of the equations, by either analytical or numerical means, describes how the biological system behaves either over time or at equilibrium. There are many different types of equations and the type of behavior that can occur is dependent on both the model and the equations used. The model often makes assumptions about the system. The equations may also make assumptions about the nature of what may occur.
The earlier stages of mathematical biology were dominated by mathematical biophysics, described as the application of mathematics in biophysics, often involving specific physical/mathematical models of biosystems and their components or compartments.
The following is a list of mathematical descriptions and their assumptions.
A fixed mapping between an initial state and a final state. Starting from an initial condition and moving forward in time, a deterministic process will always generate the same trajectory and no two trajectories cross in state space.
A random mapping between an initial state and a final state, making the state of the system a random variable with a corresponding probability distribution.
One classic work in this area is Alan Turing's paper on morphogenesis entitled The Chemical Basis of Morphogenesis, published in 1952 in the Philosophical Transactions of the Royal Society.
Phylogenetics is an area that deals with the reconstruction and analysis of phylogenetic (evolutionary) trees and networks based on inherited characteristics^{[33]}
The eukaryotic cell cycle is very complex and is one of the most studied topics, since its misregulation leads to cancers. It is possibly a good example of a mathematical model as it deals with simple calculus but gives valid results. Two research groups ^{[34]}^{[35]} have produced several models of the cell cycle simulating several organisms. They have recently produced a generic eukaryotic cell cycle model which can represent a particular eukaryote depending on the values of the parameters, demonstrating that the idiosyncrasies of the individual cell cycles are due to different protein concentrations and affinities, while the underlying mechanisms are conserved (CsikaszNagy et al., 2006).
By means of a system of ordinary differential equations these models show the change in time (dynamical system) of the protein inside a single typical cell; this type of model is called a deterministic process (whereas a model describing a statistical distribution of protein concentrations in a population of cells is called a stochastic process).
To obtain these equations an iterative series of steps must be done: first the several models and observations are combined to form a consensus diagram and the appropriate kinetic laws are chosen to write the differential equations, such as rate kinetics for stoichiometric reactions, MichaelisMenten kinetics for enzyme substrate reactions and Goldbeter–Koshland kinetics for ultrasensitive transcription factors, afterwards the parameters of the equations (rate constants, enzyme efficiency coefficients and Michealis constants) must be fitted to match observations; when they cannot be fitted the kinetic equation is revised and when that is not possible the wiring diagram is modified. The parameters are fitted and validated using observations of both wild type and mutants, such as protein halflife and cell size.
In order to fit the parameters the differential equations need to be studied. This can be done either by simulation or by analysis.
In a simulation, given a starting vector (list of the values of the variables), the progression of the system is calculated by solving the equations at each timeframe in small increments.
In analysis, the proprieties of the equations are used to investigate the behavior of the system depending of the values of the parameters and variables. A system of differential equations can be represented as a vector field, where each vector described the change (in concentration of two or more protein) determining where and how fast the trajectory (simulation) is heading. Vector fields can have several special points: a stable point, called a sink, that attracts in all directions (forcing the concentrations to be at a certain value), an unstable point, either a source or a saddle point which repels (forcing the concentrations to change away from a certain value), and a limit cycle, a closed trajectory towards which several trajectories spiral towards (making the concentrations oscillate).
A better representation which can handle the large number of variables and parameters is called a bifurcation diagram(Bifurcation theory): the presence of these special steadystate points at certain values of a parameter (e.g. mass) is represented by a point and once the parameter passes a certain value, a qualitative change occurs, called a bifurcation, in which the nature of the space changes, with profound consequences for the protein concentrations: the cell cycle has phases (partially corresponding to G1 and G2) in which mass, via a stable point, controls cyclin levels, and phases (S and M phases) in which the concentrations change independently, but once the phase has changed at a bifurcation event (Cell cycle checkpoint), the system cannot go back to the previous levels since at the current mass the vector field is profoundly different and the mass cannot be reversed back through the bifurcation event, making a checkpoint irreversible. In particular the S and M checkpoints are regulated by means of special bifurcations called a Hopf bifurcation and an infinite period bifurcation.

Mathematical biology is also called theoretical biology,^{[1]} and sometimes biomathematics. It includes at least four major subfields: biological mathematical modeling, relational biology/complex systems biology (CSB), bioinformatics and computational biomodeling/biocomputing. It is an interdisciplinary academic research field with a wide range of applications in biology, medicine^{[2]} and biotechnology.^{[3]}
Mathematical biology aims at the mathematical representation, treatment and modeling of biological processes, using a variety of applied mathematical techniques and tools. It has both theoretical and practical applications in biological, biomedical and biotechnology research. For example, in cell biology, protein interactions are often represented as "cartoon" models, which, although easy to visualize, do not accurately describe the systems studied. In order to do this, precise mathematical models are required. By describing the systems in a quantitative manner, their behavior can be better simulated, and hence properties can be predicted that might not be evident to the experimenter.
Contents 
Applying mathematics to biology has a long history, but only recently has there been an explosion of interest in the field. Some reasons for this include:
Several areas of specialized research in mathematical and theoretical biology^{[4]}^{[5]}^{[6]}^{[7]}^{[8]}^{[9]} as well as external links to related projects in various universities are concisely presented in the following subsections, including also a large number of appropriate validating references from a list of several thousands of published authors contributing to this field. Many of the included examples are characterised by highly complex, nonlinear, and supercomplex mechanisms, as it is being increasingly recognised that the result of such interactions may only be understood through a combination of mathematical, logical, physical/chemical, molecular and computational models. Due to the wide diversity of specific knowledge involved, biomathematical research is often done in collaboration between mathematicians, biomathematicians, theoretical biologists, physicists, biophysicists, biochemists, bioengineers, engineers, biologists, physiologists, research physicians, biomedical researchers,oncologists, molecular biologists, geneticists, embryologists, zoologists, chemists, etc.
A monograph on this topic summarizes an extensive amount of published research in this area up to 1987,^{[10]} including subsections in the following areas: computer modeling in biology and medicine, arterial system models, neuron models, biochemical and oscillation networks, quantum automata, quantum computers in molecular biology and genetics, cancer modelling, neural nets, genetic networks, abstract relational biology, metabolicreplication systems, category theory^{[11]} applications in biology and medicine,^{[12]} automata theory,cellular automata, tessallation models^{[13]}^{[14]} and complete selfreproduction, chaotic systems in organisms, relational biology and organismic theories.^{[15]}^{[16]} This published report also includes 390 references to peerreviewed articles by a large number of authors.^{[17]}^{[18]}^{[19]}
Modeling cell and molecular biology
This area has received a boost due to the growing importance of molecular biology.^{[20]}
Modelling physiological systems
Molecular set theory was introduced by Anthony Bartholomay, and its applications were developed in mathematical biology and especially in Mathematical Medicine.^{[30]} Molecular set theory (MST) is a mathematical formulation of the widesense chemical kinetics of biomolecular reactions in terms of sets of molecules and their chemical transformations represented by settheoretical mappings between molecular sets. In a more general sense, MST is the theory of molecular categories defined as categories of molecular sets and their chemical transformations represented as settheoretical mappings of molecular sets. The theory has also contributed to biostatistics and the formulation of clinical biochemistry problems in mathematical formulations of pathological, biochemical changes of interest to Physiology, Clinical Biochemistry and Medicine.^{[31]}^{[32]}
Population dynamics has traditionally been the dominant field of mathematical biology. Work in this area dates back to the 19th century. The Lotka–Volterra predatorprey equations are a famous example. In the past 30 years, population dynamics has been complemented by evolutionary game theory, developed first by John Maynard Smith. Under these dynamics, evolutionary biology concepts may take a deterministic mathematical form. Population dynamics overlap with another active area of research in mathematical biology: mathematical epidemiology, the study of infectious disease affecting populations. Various models of viral spread have been proposed and analyzed, and provide important results that may be applied to health policy decisions.
A model of a biological system is converted into a system of equations, although the word 'model' is often used synonymously with the system of corresponding equations. The solution of the equations, by either analytical or numerical means, describes how the biological system behaves either over time or at equilibrium. There are many different types of equations and the type of behavior that can occur is dependent on both the model and the equations used. The model often makes assumptions about the system. The equations may also make assumptions about the nature of what may occur.
The earlier stages of mathematical biology were dominated by mathematical biophysics, described as the application of mathematics in biophysics, often involving specific physical/mathematical models of biosystems and their components or compartments.
The following is a list of mathematical descriptions and their assumptions.
A fixed mapping between an initial state and a final state. Starting from an initial condition and moving forward in time, a deterministic process will always generate the same trajectory and no two trajectories cross in state space.
A random mapping between an initial state and a final state, making the state of the system a random variable with a corresponding probability distribution.
One classic work in this area is Alan Turing's paper on morphogenesis entitled The Chemical Basis of Morphogenesis, published in 1952 in the Philosophical Transactions of the Royal Society.
Phylogenetics is an area of mathematical biology that deals with the reconstruction and analysis of phylogenetic (evolutionary) trees and networks based on inherited characteristics.Template:Fact The main mathematical concepts are trees, Xtrees and maximum parsimony trees.Template:Fact
The eukaryotic cell cycle is very complex and is one of the most studied topics, since its misregulation leads to cancers.
It is possibly a good example of a mathematical model as it deals with simple calculus but gives valid results. Two research groups ^{[38]}^{[39]} have produced several models of the cell cycle simulating several organisms. They have recently produced a generic eukaryotic cell cycle model which can represent a particular eukaryote depending on the values of the parameters, demonstrating that the idiosyncrasies of the individual cell cycles are due to different protein concentrations and affinities, while the underlying mechanisms are conserved (CsikaszNagy et al., 2006).
By means of a system of ordinary differential equations these models show the change in time (dynamical system) of the protein inside a single typical cell; this type of model is called a deterministic process (whereas a model describing a statistical distribution of protein concentrations in a population of cells is called a stochastic process).
To obtain these equations an iterative series of steps must be done: first the several models and observations are combined to form a consensus diagram and the appropriate kinetic laws are chosen to write the differential equations, such as rate kinetics for stoichiometric reactions, MichaelisMenten kinetics for enzyme substrate reactions and Goldbeter–Koshland kinetics for ultrasensitive transcription factors, afterwards the parameters of the equations (rate constants, enzyme efficiency coefficients and Michealis constants) must be fitted to match observations; when they cannot be fitted the kinetic equation is revised and when that is not possible the wiring diagram is modified. The parameters are fitted and validated using observations of both wild type and mutants, such as protein halflife and cell size.
In order to fit the parameters the differential equations need to be studied. This can be done either by simulation or by analysis.
In a simulation, given a starting vector (list of the values of the variables), the progression of the system is calculated by solving the equations at each timeframe in small increments.
In analysis, the proprieties of the equations are used to investigate the behavior of the system depending of the values of the parameters and variables. A system of differential equations can be represented as a vector field, where each vector described the change (in concentration of two or more protein) determining where and how fast the trajectory (simulation) is heading. Vector fields can have several special points: a stable point, called a sink, that attracts in all directions (forcing the concentrations to be at a certain value), an unstable point, either a source or a saddle point which repels (forcing the concentrations to change away from a certain value), and a limit cycle, a closed trajectory towards which several trajectories spiral towards (making the concentrations oscillate).
A better representation which can handle the large number of variables and parameters is called a bifurcation diagram(Bifurcation theory): the presence of these special steadystate points at certain values of a parameter (e.g. mass) is represented by a point and once the parameter passes a certain value, a qualitative change occurs, called a bifurcation, in which the nature of the space changes, with profound consequences for the protein concentrations: the cell cycle has phases (partially corresponding to G1 and G2) in which mass, via a stable point, controls cyclin levels, and phases (S and M phases) in which the concentrations change independently, but once the phase has changed at a bifurcation event (Cell cycle checkpoint), the system cannot go back to the previous levels since at the current mass the vector field is profoundly different and the mass cannot be reversed back through the bifurcation event, making a checkpoint irreversible. In particular the S and M checkpoints are regulated by means of special bifurcations called a Hopf bifurcation and an infinite period bifurcation.

