Overview

Transport of mass, into, out of, and within biological systems (including single cells, multicellular organisms, and even ecological systems) is fundamental to their operation. The subject of transport phenomena is treated in great depth in classic texts [10], as well as in books focused on biological systems [62]. Here we explore a number of examples that allow us to see how fundamental transport phenomena are accounted for in a wide range of biological systems. Specifically, we develop and apply basic frameworks for simulating transport in the following sorts of systems:

• Well-mixed systems. The defining characteristic of these systems is that they are fluid systems (often aqueous solutions in biological application) with the solutes of interest distributed homogeneously (i.e., well mixed) over the timescales of interest. An example of a well-mixed system is the aquarium studied in the previous chapter. Other examples are chemical reaction systems inside cells or compartments within cells when spatial gradients of the intracellular reactants do not significantly influence the behaviors that are simulated. Models of well-mixed systems (or models that adopt the well-mixed assumption) do not explicitly account for the spatial distribution of the variables simulated. For biochemical systems this means that, at any given time, concentrations are constant throughout a compartment. The kinetics of such systems are typically described by ordinary differential equations, as in the examples of Section 2.1 of this chapter and in Chapter 3.