bluuebunny/crossref_metadata_2025 huggingface dataset:
Writing an abstract
Authors: Aysha Divan
Published: September 2023

This chapter aims to develop the ability to write concise and comprehensive abstracts of research findings. It explains that an abstract is a short paragraph which summarizes concisely the content of the work. The chapter also emphasizes that abstracts form part of many types of scientific communications including research papers reporting original work, review articles, dissertations and theses, research proposals, and conference proceedings. The chapter looks at the purpose and essential features of abstracts and includes annotated examples of abstracts. It also offers tips on how to write a good abstract and provides a checklist for reviewing an abstract.
Recording and managing information
Authors: Aysha Divan
Published: September 2023

This chapter focuses on recording and managing the large amounts of information that will build up during the course of a study programme. It provides guidance on writing good experimental notes of research work. Records of experimental work are typically maintained as a hard copy in bound notebooks. Experimental notebooks are likely to consist of a combination of hard copy notebooks and electronic stores of data. The chapter emphasizes the need to organize this information carefully so that experimental records are comprehensible to another scientist looking through the work. It then offers some guidance on how to manage an e-mail account efficiently. E-mail is an extremely useful tool for sending and receiving messages between individuals or between groups of people easily and quickly. Lastly, the chapter provides guidance on how to organize and manage electronic and hard copy information.
The Theory of Disperse Systems
Authors: Moynihan Humphrey A. , Crean Abina M.
Published: September 2023

This chapter focuses on the theory of disperse systems. Various types of disperse system can be formed depending on the state of the disperse phase and the continuous phase. The chapter then looks at the drug distribution in pharmaceutical disperse systems. Drug molecules usually partition between the disperse phase and the continuous phase and can be present in both phases, but the concentration of drug is usually much greater in one phase. Disperse systems can be classified as molecular, colloidal, and coarse dispersions, according to the properties exhibited. Dispersed entities move in dispersions due to Brownian motion, diffusion, and sedimentation. Viscosity describes the resistance of a liquid to flow and the higher the viscosity of a liquid the greater the resistance of the liquid to flow when shear stress is applied. Increases in interfacial tension and interfacial contact area increase interfacial free energy and can destabilize disperse systems.
Drug Partitioning and Transport Across Biological Barriers
Authors: Moynihan Humphrey A. , Crean Abina M.
Published: September 2023

This chapter addresses drug partitioning and transport across biological barriers. In order to exert a therapeutic response, drug molecules must interact with target receptors. Drug transport across biological barriers is influenced by the partitioning of the drug molecule between aqueous and lipid phases. Factors that influence the type of journey the drug molecules experience include the following: the ability of drug molecules to partition into biological fluids and tissues, the site of the target receptor, the route of administration, and the delivery system used to deliver the drug. The chapter then introduces drug–target receptor interactions, highlighting factors influencing the partitioning of drug molecules and describing the biological barriers drug molecules encounter during delivery. It explores the main transport mechanisms by which drug molecules are transported across these biological barriers.
What this book is about and who should read it
Authors: Keeler James , Wothers Peter
Published: September 2023

This chapter introduces the concept of chemical reactions. It mentions how the Second Law of Thermodynamics does not really help explain the science behind chemical reactions in detail. The chapter lists the interactions which lead to the formation of chemical bonds: electrostatic interactions and covalent interactions. Moreover, it previews the topics to be discussed in latter chapters. The chapter describes the people who would benefit from reading the book, such as university students and teachers. It notes the abbreviations and systematic names for compounds that will also be used across the title.
α-Amino protection
Authors: Jones John
Published: September 2023

This chapter focuses on the protection of α-amino groups in the context of peptide synthesis that suppresses nucleophilic reactivity by draining its electron density away into an appropriate substituent. It points out how the protection of α-amino must be achieved at the outset and have no adverse effects on the structure being assembled without jeopardizing the chiral integrity of nearby chiral centres. It also considers acetylation, which satisfies the fundamental requirement of suppressing nucleophilic reactivity and is considered hydrolytically reversible. The chapter analyzes severe conditions required for hydrolytic deacetylation that can be eased by building in the potential for mild intramolecular deprotection. It details the development of α-amino-protecting groups which involved an extended investigation of variations on a number of themes.
Organic reactions
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter evaluates organic reactions. It looks at the behaviour of organic molecules: why some react together and some do not, and how to understand reactivity in terms of charges, orbitals, and the movement of electrons. The chapter also introduces a device for representing the detailed movement of electrons—the mechanism of the reaction—called the curly arrow. The best reactions are ones in which the energies of the interacting orbitals are similar in energy. What does this mean for nucleophiles and electrophiles? In general, filled orbitals tend to be low in energy. Conversely, empty orbitals tend to be high in energy. As such, the best interaction is likely to be between the highest in energy of all the filled orbitals—the ‘highest occupied molecular orbital’ or HOMO for short—and the lowest in energy of all of the unfilled orbitals—the ‘lowest unoccupied molecular orbital’ or LUMO.
Equilibria, rates, and mechanisms
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter studies a number of thermodynamic principles, looking at equilibria, rates, and mechanisms. At any one particular temperature, the equilibrium constant is just that: constant. This provides a means of forcing the equilibrium to favour the products (or reactants) since the ratio between them must remain constant. One way to make esters in the laboratory is to use a large excess of the alcohol and remove water continually from the system as it is formed, for example by distilling it out. This means that in the equilibrium mixture there is a tiny quantity of water, lots of the ester, lots of the alcohol, and very little of the carboxylic acid; in other words, we convert the carboxylic acid into the ester. The acid catalyst does not alter the position of the equilibrium; it simply speeds up the rate of the reaction, allowing equilibrium to be reached more quickly.
Conformational analysis
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter examines conformational analysis. Even though no two molecules have exactly the same shape at any one time, they are still all the same chemical compound—they have all the same atoms attached in the same way. The different shapes of molecules of the same compound are called different conformations. To get from one conformation to another, we can rotate about as many single bonds as we like. The one thing we cannot do is to break any bonds. Some pairs of structures can only be interconverted by breaking a bond. This means that they have different configurations—configurations can be interconverted only by breaking bonds. The chapter then considers the conformations of ethane, propane, and butane. It also looks at cyclohexane.
Elimination reactions
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter investigates elimination reactions. The elimination reaction of t-butyl bromide happens because the nucleophile is basic. The hydroxide is behaving as a base because it is attacking the hydrogen atom, instead of the carbon atom it would attack in a substitution reaction. The hydrogen atom is not acidic, but proton removal can occur because bromide is a good leaving group. As the hydroxide attacks, the bromide is forced to leave, taking with it the negative charge. Two molecules—t-butyl bromide and hydroxide—are involved in the rate-determining step of the reaction. This means that the concentrations of both appear in the rate equation, which is therefore second-order and this mechanism for elimination is termed E2. The other mechanism for elimination is termed E1. The difference between the two reactions is the strength of the base.
Formation and reactions of enols and enolates
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter focuses on the formation and reactions of enols and enolates. Carbonyl compounds have two opposed sides to their characters. They can be nucleophilic as well: electrophilic attack on aldehydes, ketones, and acid derivatives is a useful reaction too. How can the same class of compound be subject to both nucleophilic and electrophilic attack? The resolution of this paradox is the subject of the chapter, showing that most carbonyl compounds exist in two forms: one electrophilic and one nucleophilic. The electrophilic form is the carbonyl compound itself and the nucleophilic form is called the enol. The chapter then considers tautomerism, enolization, and enol ethers.
Radical reactions
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter highlights radical reactions. This is the most important way of making radicals: unpairing a pair of electrons by homolysis, making two new radicals. Temperatures of over 200°C will homolyse most bonds; on the other hand, some weak bonds will undergo homolysis at temperatures little above room temperature. Light is a possible energy source for the homolysis of bonds too. There are a number of compounds whose homolysis is particularly important to chemists. They all have weak σ bonds, and generate radicals that can be put to some chemical use. The chapter looks at electron spin resonance, radical–radical reactions, radical chain reactions, the chlorination of alkanes, and allylic bromination.
Linear motion and the harmonic oscillator
Authors: Atkins Peter , Friedman Ronald
Published: September 2023

This chapter expresses the whole of quantum mechanics in terms of a small set of postulates, which embraces the behaviour of all known forms of matter. It introduces the postulates and illustrates how they are used, including how to apply them to problems of chemical interest, such as atomic and molecular structure and the properties of molecules. It also establishes the full significance of the Hψ=Eψequation and provides a foundation for its application. The chapter includes the solutions of the Schrödinger equation for a particle and the operator, which is a symbol for an instruction to carry out some action on a function. The principal mathematical difference between classical mechanics and quantum mechanics is that whereas in the former physical observables are represented by functions, in quantum mechanics they are represented by mathematical operators.
Techniques of approximation
Authors: Atkins Peter , Friedman Ronald
Published: September 2023

This chapter assesses the mathematical theory of symmetry, which is one of the most remarkable in quantum mechanics. Not only does it simplify calculations, but it also reveals unexpected connections between apparently disparate phenomena. It considers angular momentum as a part of group theory and as properties of the harmonic oscillator. The chapter talks about the conservation of energy and of momentum that can be discussed in terms of group theory, which is used to classify the fundamental particles and the selection rules that govern what spectroscopic transitions are allowed. Integrals occur throughout quantum chemistry, for they include expectation values, overlap integrals, and matrix elements.
Atomic spectra and atomic structure
Authors: Atkins Peter , Friedman Ronald
Published: September 2023

This chapter explores the point at which the hope of finding exact solutions is set aside, starting with looking for methods of approximation. It cites the problems of quantum chemistry that cannot be solved exactly, such as the problem for which the Schrödinger equation can be solved exactly. As soon as the shape of the potential is distorted from the forms already considered, or more than two particles interact with one another, the equation cannot be solved exactly. The chapter highlights several ways of making progress, such as being guided to a form for the wavefunction by using principles of classical mechanics and taking note of the small magnitude of Planck's constant. Another way is to guess the shape of the wavefunction of the system and make use of self-consistent field procedures, which is an iterative method for solving the Schrödinger equation for systems.
O-Linked glycosylation
Authors: Taylor Maureen E. , Drickamer Kurt
Published: September 2023

This chapter examines O-linked glycosylation, considering two groups of glycoproteins: mucins and proteoglycans. O-linked glycans are extremely diverse in both structure and function, and the full extent of this diversity has not yet been established. The groups of O-linked glycans are built on different protein–glycan linkages, in which GalNAc, fucose, GlcNAc, mannose, xylose, or galactose can be attached to serine, threonine, or hydroxylysine residues. Terminal structures on some of the O-linked glycans are similar or identical to structures on N-linked glycans, suggesting that there may be a functional overlap between these types of glycosylation. Indeed, enzymes involved in the synthesis of these structures may be shared, indicating that they have co-evolved to display similar terminal elaborations that can be involved in various recognition events. However, O-linked glycans have also evolved to serve unique functions, many of which remain to be explored.
Conformations of oligosaccharides
Authors: Taylor Maureen E. , Drickamer Kurt
Published: September 2023

This chapter assesses the conformation of oligosaccharides. A major goal in glycobiology is to relate structures of glycans to their functions. Glycans with different covalent structures take up different conformations in the same way that proteins with different sequences have distinct tertiary structures or folds. Sequences of proteins dictate their three-dimensional structures, and these structures determine their functions. Similar rules probably apply in the case of oligosaccharides. However, principles relating structure to function have not been easy to establish, partly because of our limited knowledge of the conformations that glycans assume. The chapter summarizes what is known about the three-dimensional structure of N-linked oligosaccharides.
Adsorption and the thermodynamics of surfaces
Authors: Barnes Geoffrey , Gentle Ian
Published: September 2023

This chapter provides a loose interpretation of adsorption, which is the tendency for one component of a system to have a higher or lower concentration at the interface than it has in the adjacent bulk phases. It highlights an example wherein it observes a decrease in pressure when a gas is adsorbed onto a solid, or a decrease in solute concentration when a solution is shaken with a solid powder. It also points out how adsorption can be inferred from other information, such as a change in the surface tension of the solution. The chapter talks about the three regions of a system containing an interface: bulk phase α, bulk phase β, and the interface σ. It looks at the surface phase approach wherein a distinct surface phase is defined by two mathematical boundaries, one on either side of and parallel to the interface.
The gas-liquid interface: adsorption; films and foams; aerosols
Authors: Barnes Geoffrey , Gentle Ian
Published: September 2023

This chapter describes some of the most obvious and dramatic effects of adsorption that can be seen at the air-solution interface. It talks about liquid drops that change their shape, foams that can be formed on liquids that otherwise will not foam, and the rise of liquids in capillaries that is reduced. It also analyses the enhanced spreading of liquids over solid surfaces, the reduction of the ability of light winds to ruffle the surface of water in a pond, and soils that are wetted more readily by water. The chapter deals with the measurement of adsorption by analysis of the surface or by change in bulk phase concentration that is usually not feasible as the area of a gas-liquid interface is usually small and sample collection is often difficult. It explains how adsorption is normally determined from surface tension data using the Gibbs equation.
The gas–solid interface: adsorption; catalysis
Authors: Barnes Geoffrey , Gentle Ian
Published: September 2023

This chapter illustrates a solid surface in contact with a gas that usually attracts an adsorbed layer of gas molecules. It also discusses the spontaneous occurrence of adsorption wherein the free energy change is negative. It also refers to a decrease in entropy as the gas loses degrees of freedom, ensuring that the enthalpy change is negative and large enough to outweigh the entropy term. The chapter highlights the important role the adsorption of gases plays in heterogeneous catalysis, wherein there is a weakening or breaking of chemical bonds that occurs upon adsorption and makes some solid surfaces effective catalysts for gas phase reactions. It reviews the use of gas adsorption for the characterization of porous materials.
Electrons in molecules: diatomics
Authors: Keeler James , Wothers Peter
Published: September 2023

This chapter evaluates the bonding in diatomics. Molecular orbitals are constructed from a linear combination of atomic orbitals (AOs). The combination of two atomic orbitals gives two molecular orbitals: a bonding molecular orbital which places electron density between the atoms and contributes to the formation of a bond; and an antibonding molecular orbital which pushes electron density away from the internuclear region and does not favour bond formation. The chapter begins by looking at homonuclear diatomics, which are those in which both atoms are the same, such as H2 and N2. It then considers heteronuclear diatomics, in which the two atoms are different, such as HF and CO. Photoelectron spectroscopy provides an experimental way of probing the energies and other characteristics of molecular orbitals.
Organic chemistry 1: functional groups
Authors: Keeler James , Wothers Peter
Published: September 2023

This chapter studies functional groups, which can be classified according to the number of bonds a given carbon has to elements of greater electronegativity. The functional group level is the number of these bonds. Reactions can be classified according to the change in functional group level. The outcome of a reaction can be rationalized by considering where the highest energy electrons are to be found, and what low energy vacant molecular orbitals are available. Within a particular functional group level, there is often a general order of reactivity for different functional groups. Ultimately, transformations from one functional group to another may take place via different mechanisms depending on the particular reagents and reaction conditions.
The rates of reactions
Authors: Keeler James , Wothers Peter
Published: September 2023

This chapter reviews the rate at which a chemical reaction proceeds. The experimentally determined rate law gives the dependence of the rate on the concentrations of the reactants. Rate constants have a strong temperature dependence given by the Arrhenius law. However, there is an energy barrier to most reactions. Complex reactions proceed by a series of elementary steps, called a mechanism. The kinetics of complex reactions can sometimes be simplified using the pre equilibrium or steady-state approximations. In a multi-step reaction, one step can often be identified as the rate limiting (or rate-determining) step. The chapter then looks at sequential reactions, the reactions of complex mechanisms, and chain reactions.
How did evolution get started?
Authors: Bromham Lindell , Cardillo Marcel
Published: September 2023

This chapter discusses how evolution started on earth. For evolution to occur, there must be a population of replicators able to copy themselves with near-perfect accuracy, with occasional variations that provide the potential for natural selection to improve copying ability. The capacity for heritable information can be increased by combining previously independent replicators into coordinated systems that rely on each other for replication. The major transitions in evolution are macroevolutionary events that led to increases in informational capacity, permitting the evolution of diversity and complexity over time. The chapter then looks at the use of experiments and models in considering the origin of life. While models and experiments are general tools employed in many different scientific fields, there is another method for testing ideas that is particular to evolution. The evolutionary comparative method uses comparisons between the end products of evolution to make inferences about evolutionary process and history.
Were dinosaurs evolutionary failures?
Authors: Bromham Lindell , Cardillo Marcel
Published: September 2023

This chapter focuses on dinosaurs as a case study for examining the macroevolutionary processes of adaptive radiation and mass extinction. Considering the rise of dinosaurs allows us to examine the role of both key adaptations and chance in diversification, while considering their fall prompts us to examine our ability to resolve events and determine cause and effect in deep time. The study of fossils sheds light on physiology, locomotion, behaviour, and ecology of extinct species. The diversification of dinosaurs may have been driven by key adaptations, such as upright gait and fast metabolism, which allowed them to exploit a wide range of niches, or it may have been triggered by opportunity through the extinction of other reptile groups. Given that vertebrate fossils are rare, and biased in terms of location, taxa, and time period, there is some uncertainty over the timing and nature of dinosaur extinctions.
Why are there so many species in the tropics?
Authors: Bromham Lindell , Cardillo Marcel
Published: September 2023

This chapter discusses tropical diversity. Biodiversity varies enormously from region to region. Probably the most impressive geographical pattern of biodiversity is the decline in species richness from the tropics towards high latitudes. However, even the most fundamental questions about why this pattern exists are not fully answered. Proposed explanations for the latitudinal diversity gradient (LDG) can be classified into historical (based on the accumulation of diversity through time) and ecological (based on current environmental conditions). An underlying assumption of historical explanations is non-equilibrium diversification: diversity is still increasing through evolutionary time. Meanwhile, ecological explanations assume equilibrium dynamics: diversity has levelled off to a 'carrying capacity'. Fossil and phylogenetic data provide complementary approaches to testing hypotheses about large-scale geographical patterns in diversity, each with its own strengths and weaknesses.
What is the future of biodiversity?
Authors: Bromham Lindell , Cardillo Marcel
Published: September 2023

This chapter examines extinction and biodiversity loss. Extinction is one of the key processes that have shaped the history of life and the development of biodiversity. Currently, species declines and extinctions appear to be happening much more rapidly than at any time in geological history as a result of the way human activity is modifying the world's natural systems. There is widespread international consensus that action is needed to prevent further extinctions and mitigate ongoing loss of biodiversity. To develop effective strategies for conservation, we need to understand how biodiversity is distributed (phylogenetically and spatially), we need objective methods to quantify the speed and extent of biodiversity loss, and we need an understanding of the processes that cause the loss of biodiversity. In developing this kind of big-picture view of conservation, we can make use of some of the tools and knowledge gained from the study of macroevolution and macroecology.
Protozoa
Authors: Playfair John H.L. , Bancroft Gregory J.
Published: September 2023

This chapter begins with defining protozoa as single-celled eucaryotes of amazing diversity and sophistication. It considers the environment of protozoa, their medical importance, and how they are generally classified. The chapter then shifts to detail the life cycle of the malaria parasite, Plasmodium. It also describes the Leishmania parasite, which is taken up by macrophages where it survives and replicates as an amastigote (no tail), and the species of Trypanosoma, which belongs to the same order as Leishmania and resemble them in appearance. Next, the chapter investigates other life cycles of protozoan parasites such as toxoplasma, amoebae, giardia, cryptosporidium, and trichomonas. It then displays a variety of drugs that are available to kill protozoa, many of them quite toxic to the host and prone to the development of resistance.
Disease: virulence and susceptibility
Authors: Playfair John H.L. , Bancroft Gregory J.
Published: September 2023

This chapter addresses elements in the pathogen that predispose to disease. These are collectively known as virulence factors. The chapter begins by displaying the two main categories of virulence factors: pathogen mechanisms directly or indirectly causing host damage, and pathogen mechanisms aimed at escaping host protective mechanisms, including immunity. The chapter also studies the host gene expression, genome sequencing, and deep sequencing. It then shifts to examine how genetic differences on the host side contribute to the occurrence and severity of the disease. Next, the chapter looks at the two situations in which disease is caused directly by the pathogen: pathogens that destroy cells (cytopathic), predominantly viruses, and pathogens that release toxins, predominantly bacteria. It then reviews some common complications of intestinal infection such as diarrhoea and vomiting.
T cells and the MHC
Authors: Playfair John H.L. , Bancroft Gregory J.
Published: September 2023

This chapter analyzes the common feature of T-cells and a special set of molecules known as major histocompatibility complex (MHC) proteins. The chapter studies the major distinction of T-cells between cytotoxic and helper cells. The T-cell receptor, or TCR, cannot be discussed without also discussing MHC molecules. The chapter then demonstrates how TCR and MHC act together in protein recognition. The chapter also emphasizes the CD1 molecules when presenting non-protein molecules, then expounds the meaning of MHC in more detail. Next, the chapter investigates how to convert an intracellular virus or other pathogen into a series of small peptides in the groove of the MHC molecules on the cell surface. These take place in the antigen-presenting cells (APCs), which may be dendritic cells (the most important for activating resting T-cells), macrophages, or B lymphocytes. The chapter then considers superantigens, γδ T-cells, and NKT-cells.
Disease due to adaptive immunity I: hypersensitivity
Authors: Playfair John H.L. , Bancroft Gregory J.
Published: September 2023

This chapter uncovers the unwelcome side effects of 'normal' responses against perfectly ordinary non-self antigens. It classifies these effects and displays the causes of hypersensitivity. The chapter begins with describing the most common type of immunopathology, since about one person in six suffers from some kind of allergy: type I (allergic) hypersensitivity. It then examines the ability of IgG antibody to destroy cells by causing them to be either phagocytosed or lysed by complement (IgM will do the latter too), causing the type II (cytotoxic) hypersensitivity. Next, the chapter explicates the cause of type III (immune complex-mediated) hypersensitivity. Here, too, IgG antibody is involved, but the damage is actually initiated by soluble complexes of antigen and antibody. It also considers the harmful aspects of cell-mediated immune responses, the principal one being excessive granuloma formation.
Control of infectious disease: public health measures
Authors: Playfair John H.L. , Bancroft Gregory J.
Published: September 2023

This chapter points out the importance of public health measures in controlling disease and its spread. It argues that the control of infectious disease was a matter of both scientific understanding and political will. The chapter also assesses the impact of the general improvement in health, accompanied by better nutrition and food handling, better housing, and housing regulations to the public. It then recounts some success stories that have nothing to do with vaccines or drugs. Next, the chapter presents some examples that highlight the public health approach. About half of the public health measures listed in the chapter are directed at insect or larger animal vectors. The chapter emphasizes that with vector-borne diseases, control or elimination of the vector may sometimes be the most practical approach.
Fungal disease and immunity
Authors: Playfair John H.L. , Bancroft Gregory J.
Published: September 2023

This chapter illustrates the three main patterns of fungal diseases: (1) filamentous moulds infecting the superficial and subcutaneous tissues, (2) a dimorphic group causing systemic infections; and (3) secondary infections caused by a number of important opportunists which have come to the fore with the increase in immunocompromised patients. It opens with a discussion on primary superficial and subcutaneous infections, focusing on tinea (ringworm) which is more common in children. The chapter also elaborates on the dimorphic fungi Histoplasma, Blastomyces, and Coccidioides. It then examines the evidence for protective immunity and predominant opportunistic fungal infection. Ultimately, the chapter considers the antifungal vaccine and treatment.
Protozoal disease and immunity
Authors: Playfair John H.L. , Bancroft Gregory J.
Published: September 2023

This chapter highlights the common features of protozoal pathogens. It emphasizes that the diseases they cause are extremely chronic, with spontaneous recovery a very rare event and only partial immunity at best. The chapter then discusses the complications of malaria, and outlines a number of factors for the continued survival of parasites in patients with high levels of antibody and activated T-cells. The chapter also demonstrates the potential target antigens for malarial immunity and vaccination and its treatment. Ultimately, the chapter reviews the critical element in leishmaniasis. It also examines the cases of African trypanosomiasis and South American trypanosomiasis, and considers the case of toxoplasmosis and the infection of amoebiasis.
Emerging and future infectious diseases
Authors: Playfair John H.L. , Bancroft Gregory J.
Published: September 2023

This chapter assesses major changes in infectious immunology that have occurred within living memory. It begins with elaborating the newly identified pathogens and newly acquired zoonoses. The chapter also outlines the reasons why the number of immunocompromised individuals in the population during the last 50 years has increased tremendously. It also illustrates the changes in virulence, highlighting influenza as the classic example. The chapter also discusses the artificial creation of new pathogens and attenuated vaccines. It then shifts to examine the widespread use of antibiotics and its enormous effect on the world of pathogens. Finally, the chapter looks at the importance of vaccine uptake and public health. It also investigates the implications of travel and immigration and climate change.
Extracting information from the wavefunction
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Postulate III: quantum mechanical operators 47

Brief illustration 6.1: The kinetic energy operator in two dimensions 49

Postulate IV: eigenvalues and eigenfunctions 50

Example 6.1: Identifying an eigenfunction 50

Brief illustration 6.2: The wavefunction as an eigenfunction 51

Checklist of concepts 52...
Translational motion in one dimension
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Free motion 73

Brief illustration 9.1: The wavefunction of a freely moving particle 74

Confined motion: the particle in a box 74

The acceptable solutions 75

Brief illustration 9.2: The energy of a particle in a box 76

The properties...
Vibrational motion
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The energy levels 93

Brief illustration 12.1: The vibrational energy separation in a diatomic molecule 94

The wavefunctions 94

Example 12.1: Confirming that a wavefunction is a solution of the Schrödinger equation 95

Example 12.2: Normalizing a harmonic oscillator wavefunction 96

Example...
Transitions
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Time-dependent perturbation theory 140

The general procedure 140

Example 16.1: Using time-dependent perturbation theory for a slowly switched perturbation 140

Oscillating perturbations and spectroscopic transitions 142

Example 16.2: Analysing spectroscopic transitions of a harmonic oscillator 142

The energy of time-varying...
Many-electron atoms
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The orbital approximation 169

Brief illustration 19.1: Atomic configurations 170

Factors affecting electronic structure 170

Spin 170

Brief illustration 19.2: Spin 171

The Pauli principle 171

Brief illustration 19.3: The Pauli principle 172

Penetration and shielding 172

Example 19.1:...
Applications of symmetry
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Vanishing integrals 291

Integrals over the product of two functions 292

Example 33.1: Deciding if an integral must be zero 1 292

Decomposition of a direct product 293

Brief illustration 33.1: Decomposition of a direct product 293

Integrals over products...
Real gases
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Molecular interactions in gases 321

Brief illustration 36.1: Interactions in gases 321

The virial equation of state 321

Brief illustration 36.2: The virial equation of state 322

The van der Waals equation 323

The development of the equation 323

Example...
Electronic spectroscopy
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The electronic spectra of diatomic molecules 423

Term symbols 423

Brief illustration 45.1: Multiplicity of a term 423

Brief illustration 45.2: Term symbol of O2 1 424

Brief illustration 45.3: Term symbol of O2 2 424

Brief illustration 45.4: Term...
Electron paramagnetic resonance
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The g-value 487

Brief illustration 50.1: The g-value of a radical 487

Hyperfine structure 488

The effects of nuclear spin 488

Example 50.1: Predicting the hyperfine structure of an EPR spectrum 489

The McConnell equation 490

Brief illustration...
The First Law
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Work, heat, and energy 542

Brief illustration 55.1: Combustions in adiabatic and diathermic containers 542

Internal energy 543

Brief illustration 55.2: The internal energy of a gas 543

Brief illustration 55.3: Contributions to ΔU 544

Expansion work 544

The...
Internal energy
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Changes in internal energy 570

The effect of changing temperature and volume 570

Brief illustration 58.1: Changes in internal energy 571

Changes at constant pressure 571

Example 58.1: Calculating the expansion coefficient of a gas 572

The molecular basis of...
Standard Gibbs energies
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Gibbs energies of formation 633

Brief illustration 65.1: The reaction Gibbs energy 634

Example 65.1: Calculating a standard Gibbs energy of formation from partition functions 634

Ions in solution 635

The convention 635

Brief illustration 65.2: Standard Gibbs energies of ions...
Combining the First and Second Laws
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The fundamental equation 638

Properties of the internal energy 639

The Maxwell relations 639

Brief illustration 66.1: The Maxwell relations 639

The thermodynamic equation of state 640

Example 66.1: Deriving a thermodynamic relation 640

Properties of the Gibbs energy...
Phase diagrams: two-component systems
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Liquid–vapour systems 664

Pressure–composition diagrams 664

Brief illustration 68.1: The lever rule 665

Temperature–composition diagrams 665

Brief illustration 68.2: Azeotropes 667

Liquid–liquid systems 667

Example 68.1: Interpreting a liquid–liquid phase diagram 668

Liquid–solid systems 668

Brief illustration 68.3: A...
Transport properties of gases
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The phenomenological equations 767

Brief illustration 79.1: Energy flux 769

The transport parameters 769

The diffusion coefficient 769

Brief illustration 79.2: The diffusion coefficient 770

Thermal conductivity 770

Brief illustration 79.3: The thermal conductivity 771

Viscosity 771

Brief illustration...
Transition-state theory
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The Eyring equation 848

The formulation of the equation 848

The rate of decay of the activated complex 848

Brief illustration 89.1: The decay rate 850

The concentration of the activated complex 850

Brief illustration 89.2: The discarded mode 850...
The dynamics of molecular collisions
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Molecular beams 857

Techniques 857

Experimental results 858

Brief illustration 90.1: The role of the impact parameter 859

Reactive collisions 860

Probes of reactive collisions 860

State-to-state reaction dynamics 861

Brief illustration 90.2: The state-to-state rate constant 861...
Electrophoresis
Authors: Campbell Iain D.
Published: September 2023

Introduction

Migration rates of molecules through a matrix depend on their charge, size, and shape. Electrophoresis exploits the differential mobility of molecular ions in an applied electric field. The method is relatively simple and inexpensive, with good resolving power, so it has become...
Diffraction
Authors: Campbell Iain D.
Published: September 2023

Introduction

The scattering of electromagnetic radiation by mole­cules in solution was discussed in Chapter 4.1. As we will see in this chapter, scattering of short wavelength radiation by an ordered array of scatterers (e.g. crystals or fibers) can yield much more...
Infrared and Raman spectroscopy
Authors: Campbell Iain D.
Published: September 2023

Introduction

Molecules are said to undergo vibrational motion when their bonds stretch or bend. The energy of most molecular vibrations corresponds to the infrared (IR) region of the electromagnetic spectrum. Vibrations may be detected directly by measuring an IR spectrum or indirectly by...
Mammalian metabolic pathways
Authors: Cox Lynne S. , Harris David A. , Pears Catherine J.
Published: September 2023

This chapter addresses the mammalian metabolic pathways. It begins by explaining catabolism and anabolism. Catabolism is the breakdown of organic molecules to release energy in a usable form of ATP. ATP acts as an energy 'currency' in the cell and it is not stored in the cell. Meanwhile, anabolism is the biosynthesis of complex molecules using energy, usually in form of ATP. The chapter then looks at glucose breakdown and synthesis; the tricarboxylic acid (TCA) cycle; and oxidative phosphorylation. It also considers the breakdown and synthesis of glycogen, lipid, ketone body, and amino acid. Finally, the chapter examines the pentose phosphate pathway, as well as lactate and ethanol metabolism.
Integration of mammalian metabolism
Authors: Cox Lynne S. , Harris David A. , Pears Catherine J.
Published: September 2023

This chapter explores the integration of mammalian metabolism. All metabolic pathways are coordinated to meet the needs of the whole body as they vary with changes in exercise and nutrition. The chapter then looks at the key organs, metabolites, and hormones in metabolic integration. It also considers the key aspects of fuel utilization. Finally, the chapter highlights the principles of hormone signalling in metabolism. There are two main classes of receptors: G-protein-coupled receptors (GPCR) and receptor tyrosine kinases (RTKs). Receptor activation stimulates production of second messengers — diffusible molecules inside the cell which transmit the signal to intracellular components. Often a cascade of protein kinases amplifies the effect of a few activated receptor molecules by phosphorylating downstream target proteins.
Training for Anaerobic Events and Team Sports
Authors: MacDougall Duncan , Sale Digby
Published: September 2023

This chapter reviews a wide range of sports that require maximal efforts over a period as brief as two seconds or less or as long as two minutes. It looks at the relative contribution of energy-delivery pathways that depends upon the duration of the event. It also analyszes explosive events such as throwing, jumping, or weightlifting, which require maximal power output over only a few seconds and are derived from resting muscle stores of adenosine triphosphate (ATP) and from hydrolysis of phosphocreatine (PCr). The chapter illustrates team sports that typically require bursts of maximal effort separated by lower-intensity intervals or stoppages in play for rule infractions. It mentions ice hockey or soccer, wherein the intense activity may be sustained for up to 60 seconds without a stoppage in play or a slowing in tempo.
Training for Strength, Power, and Speed
Authors: MacDougall Duncan , Sale Digby
Published: September 2023

This chapter discusses training principles that increase performance by stimulating both muscular and neural adaptations. It examines the role of specificity in adaptations and its importance in the design of training programs and highlights training that results in an increase in the muscle cross-sectional area (CSA) and strength. It also explores muscle-fiber hypertrophy that increased muscle size, which is primarily the result of increased muscle-fiber size that is expressed as fiber area. The chapter points out that the main contributor to increased fiber size is an increase in the size and number of myofibrils. It refers to the increase in the number of filaments and the number of myosin cross-bridges in cross-section that results in increased force-generating capacity.
Peaking, Tapering, and Overtraining
Authors: MacDougall Duncan , Sale Digby
Published: September 2023

This chapter focuses on training given on a set of physiological adaptations, wherein training stimulus is reduced once maximal adaptation has occurred and a different form of training is introduced. It explains how peaking occurs when an athlete completes a training program incorporating the correct sequencing of different forms of training. It also defines overtraining as the condition that arises when the magnitude of the training stimulus chronically exceeds the athlete's capacity to adapt to it. The chapter talks about the suppressive effect of overtraining on certain components of the immune system. This makes the athlete less resistant to infection and common illnesses, such as upper-respiratory-tract infections (URTI). It explains how the recognition of the early indications that an athlete may be approaching the overtrained state is a major challenge for a coach.
Stretching and Flexibility
Authors: MacDougall Duncan , Sale Digby
Published: September 2023

This chapter discusses muscle stretching exercises performed by most athletes, which make up part of their warm-up before training sessions and competition. It analyszes regular stretch training that athletes do to increase their flexibility, which can be defined as the maximum range of movement achievable without injury at a joint or series of joints. It also talks about a high level of flexibility that is important in many types of performance. The chapter reviews issues of whether pre-activity stretching prevents injury or enhances or hinders performance and highlights be methods of flexibility training. It considers the different types of stretching and their effect on the muscle-tendon unit.
Mass spectrometry, chemical, and thermal analysis techniques
Authors: Weller Mark T. , Young Nigel A.
Published: September 2023

This chapter describes the methods that can be used to determine the elemental composition of a compound. In mass spectrometry, gaseous ions are produced from a compound and then analysed to determine their mass-to-charge ratio. As one of the gaseous species produced in the mass spectrometer is often the molecular ion, which is simply the charged molecule of the compound under investigation, the relative molecular mass (RMM) of the compound is directly measured. Meanwhile, the CHN analysis undertakes the automated determination of carbon, hydrogen, and nitrogen contents. The chapter then looks at atomic absorption spectroscopy, flame emission spectroscopy, and flame photometry. It also considers thermal analysis, which concerns the change in a property of a sample induced by heating.
The alkaline and alkaline earth metals
Authors: Rehder Dieter
Published: September 2023

This chapter focuses on Alkaline metal ions (sodium and potassium ions) and alkaline earth metal ions (magnesium and calcium ions), which play important roles in a plethora of physiological processes. It discusses the mechanisms that are responsible for steering and control of the ion concentrations in the extracellular space and the cytosolic cell compartments. It describes the four main transportation routes for alkaline and alkaline earth metal ions and tackles ion channels — the membrane-bound proteins which are gated by chemical, mechanical, electric, or light stimuli. The chapter also explains the concept of exchange kinetics. Furthermore, it looks at the biomineralization of calcium with special reference to its impact on the stabilization of bone structures through the formation of hydroxyapatite.