Describes simple mathematical models for bacterial growth and death and how to experimentally measure growth curves.

Describes passive and active liquid crystals including defect textures and order parameters.

Introduces some simple reaction-diffusion equations to describe pattern formation in bacterial cells and biofilms including anomalous wave fronts, Turing patterns and the French flag model.

Considers how to track cells and molecules. Introduces tracking algorithms and statistical tools to analyse the resultant data.

Introduces models for biofilms including agent-based models, Vicsek models and cellular automata.

For analytical simplicity, most research to date on RT and RM instabilities has focused on planar geometries. Such a simplified design is very helpful in easing the diagnostic requirements for laboratory experiments. However, in our limited observations of Chapter 15, we have already witnessed that other geometric configurations may alter the mixing layer growth significantly. In a variety of important applications, one must deal with imploding/exploding flows, the prime examples of which are inertial confinement fusion implosions (convergent geometry) and supernova explosions (divergent geometry). In these configurations, the flows are radially accelerated/decelerated. In contrast to planar geometry, where only RM growth is expected to occur, converging/diverging shock-accelerated interfaces can be RT unstable as they geometrically contract or expand. In the experiments and analytical modeling in this chapter, the amplitude growth depends on the convergence history in a complicated way.

The structure of diatomic molecules is discussed in this chapter. The electronic structure of diatomic molecules is then discussed in detail. The coupling of the orbital and spin angular momenta of electrons and the angular momentum associated with nuclear rotation are discussed, with an emphasis on Hund’s cases (a) and (b). The rotational wavefunctions for diatomic molecules in the limits of Hund’s cases (a) and (b) and in the case intermediate between Hund’s cases (a) and (b) are then discussed in detail. For molecules that are of importance in combustion diagnostics, such as OH, CH, CN, and NO, the electronic levels are intermediate between Hund’s cases (a) and (b). We use Hund’s case (a) as the basis wavefunctions, and linear combinations of these wavefunctions are used to represent wavefunctions for electronic levels intermediate between cases (a) and (b). The choice of case (a) wavefunctions as the basis set is typical in the literature although case (b) wavefunctions can also be used as a basis set.

Describes a range of physical techniques that can be applied to bacterial biophysics including sample culture, flow cytometry, microscopy, photonics, NMR, mass spectrometry and electrophoresis.

Introduces the physical action of antibiotics and antiseptics including penetration through biofilms, persister cells, surface activity, physical sterilization and antibiofilm molecules.

Raman scattering spectroscopy is widely used in analytical chemistry, for structural analysis of materials and molecules and, most importantly for our purposes, as a gas-phase diagnostic technique. Raman scattering is a two-photon scattering process, and the mathematical treatment of Raman scattering is very similar to the mathematical treatment of two-photon absorption. Many of the molecules of interest for quantitative gas-phase spectroscopy are diatomic molecules with non-degenerate 1Σ ground electronic levels, including N2, CO, and H2. In this chapter, the theory of Raman scattering is developed based on Placzek polarizability theory and using irreducible spherical tensor analysis. Herman–Wallis effects are discussed in detail. The chapter concludes with detailed examples of Raman scattering signal calculations.