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Analytical centrifugation  

Introduction Hand-driven centrifuges were used in the middle ages to separate milk products. Today, a variety of preparative centrifuges, ranging from small desktop to large scale devices, are in routine use in almost all molecular biology laboratories. We focus here on the analytical ultracentrifuge (AUC),...

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Atomic and molecular orbitals, their energy states, and transitions  

The aim of this tutorial is to introduce ideas about the shapes and energies of the wave functions that describe the distribution of electrons in atoms and molecules. This is important for understanding many of the properties described elsewhere, especially Section 5, which is concerned...

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Biological molecules  

The aim of this tutorial is to remind readers about some of the molecules of life, their nomenclature and some of their properties. Nucleic acids are made from linear chains of nucleotides (Figure T1A). Phosphate groups bridge the 3’and 5’positions of...

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Iain D. Campbell

Biophysical Techniques starts off by introducing the topics that come under the umbrella of biophysical techniques. It then considers molecular principles in the biophysical sphere. It looks at transport and heat. Then it considers scattering, refraction, and diffraction. The text also looks at electronic and vibrational spectroscopy. Next, it moves on to magnetic resonance. Microscopy and single molecule studies are also examined in detail. Finally, computational biology is presented as a topic to end with.

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Calorimetry  

Introduction Calorimetry (Latin calor = heat) measures the heat produced by chemical reactions or physical changes. Joseph Black (1728–1799) is usually said to be the founder of the method but Antoine Lavoisier (1743– 1794) designed a calorimeter to measure the metabolic heat...

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Chromatography  

Introduction Chromatography refers to a broad range of methods that separate and analyze mixtures of molecules. The components to be separated are distributed between two phases: a stationary phase and a mobile phase which percolates through the stationary phase. Chromatography literally...

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Computational biology  

Introduction Computational biology is the application of computational methods to all levels of exploration; molecules to ecosystems. This is huge area of research that can be subdivided in various ways. The computer is, of course, also an indispensible tool in every branch of biophysics discussed...

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Diffraction  

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...

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Diffusion, osmosis, viscosity, and friction  

Introduction The cell contains large numbers of ions, metabolites, and macromolecules. The various macromolecules have unique properties, including mass, size, shape, and charge, that influence the way they move in response to flow and an applied driving force. Variation in movement is the basis of...

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Dipoles, dipole-dipole interactions, and spectral effects  

Dipoles, dipole moments, and their interactions are very important for explaining many properties of molecules that are considered in this book, including non-covalent interactions and spectra. This tutorial sets out some of the key points about dipoles and their interactions. An electric dipole...

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Electrical circuits  

The aim of this tutorial is to introduce some basic ideas and nomenclature for electrical circuits. These concepts are helpful for understanding aspects of Chapters 3.4 and 3.6 . Some of the nomenclature used in this field is illustrated in Figure T4A; this...

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Electromagnetic radiation  

The aim of this tutorial is to convey the basic properties of electromagnetic radiation: these concepts are essential for understanding Sections 4, 5, 6, and 7 in this book. Electromagnetic waves James Clerk Maxwell (1831-1879) combined the laws of electricity and magnetism with those...

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Electron paramagnetic resonance  

Introduction Electron paramagnetic resonance (EPR) was first observed by Yevgeny Zavoisky in 1944. Also known as electron spin resonance (ESR), the method detects unpaired electrons. Unpaired electrons are relatively rare in biological systems but they occur in important processes—for example, free radicals in photosynthesis. EPR...

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Electrophoresis  

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...

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Electrophysiology  

Introduction Electrophysiology is the study of the electrical properties of biological cells and tissues. Valuable information can be obtained by measuring voltages and currents in a wide range of systems, ranging from single ion channels to beating hearts. Measurement of the electrical activity of neurons...

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Fluorescence  

Introduction Fluorescence occurs when light is emitted from an excited state. A molecular group that fluoresces is called a fluorophore. Naturally occurring fluorophores in biology include tryptophan, the Y-base of t-RNA, NADH, and chlorophyll. A wide range of synthetic fluorescent probes, dyes, and...

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Fourier series, Fourier transforms, and convolution  

The aim of this tutorial is to introduce some mathematical concepts that are essential for understanding many parts of this book. The Fourier transform is very important for understanding material in Sections 4, 5, 6, and 7. In 1807, Joseph Fourier introduced the idea...

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Infrared and Raman spectroscopy  

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...

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Introduction  

This chapter talks about the identification of molecules, the measurement of their concentrations and interaction partners, and the definition of their structure and location in the cell. It reviews extraordinarily powerful sets of physical and mathematical tools that can be used to study molecules. It also analyses molecular assemblies which need appropriate dynamic and energetic properties and the correct location and structure in order to function properly. The chapter describes diverse, powerful, and complementary biophysical tools, which exploit developments in technology and apply insights from the laws of physics and chemistry to all aspects of molecular and cellular biology. It reviews the key role of biophysical techniques in the exploration of other properties of cellular components.

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Introduction to absorption and emission spectra  

Introduction The development and application of spectroscopy has had an enormous influence on our understanding of the world; from microscopic atomic structure (nm) to the macroscopic (light year scale!) universe. William Wollaston discovered the existence of dark lines in the solar spectrum in 1801. A...