Note: Cover -- Half-title -- Series information -- Title page -- Copyright information -- Table of contents -- List of contributors -- About the Editors -- Preface -- Part I Introduction -- 1 The Principles of Fluorescence -- 1.1 Luminescence -- 1.2 The Relevance of Quantum Mechanics and Electronic Theory -- 1.2.1 Wave-Particle Duality and Quantization of Energy and Matter -- 1.2.1.1 Subatomic Particles -- 1.2.1.2 Quantized Matter and Energy -- 1.2.1.3 Copenhagen Interpretation -- 1.2.2 Chemical Bonding and Molecular Orbitals -- 1.2.2.1 Sigma Bonds (s Bonds) -- 1.2.2.2 Pi Bonds (p Bonds) -- 1.2.2.3 Antibonding Orbitals -- 1.2.2.4 Nonbonded Electrons -- 1.3 Understanding the Fluorescence Process -- 1.3.1 Electronic Transitions -- 1.3.1.1 Spin Multiplicity -- 1.3.1.2 Absorption -- 1.3.1.3 Franck-Condon Principle -- 1.3.2 Nonradiative Decay -- 1.3.2.1 Vibrational Relaxation -- 1.3.2.2 Internal Conversion and Intersystem Crossing -- 1.3.3 Radiative Decay -- 1.3.4 Fluorescence -- 1.3.4.1 Stokes Shift -- 1.3.4.2 Fluorescence Decay Kinetics -- 1.3.4.3 Fluorescence Efficiency (Quantum Yield) -- 1.3.4.4 Fluorescence Quenching -- 1.3.4.5 Influence of Molecular Structure on Fluorescence -- 1.3.4.6 The Effect of pH -- 1.3.4.7 Effects of Solvents on Fluorescence Emission -- 1.3.4.8 The Heavy Atom Effect -- 1.3.4.9 Fluorescence Spectra -- 1.3.4.10 Scattering of Radiation -- 1.3.4.11 Normalization of Fluorescence Intensities -- References -- 2 Fluorescence and Dissolved Organic Matter: A Chemist's Perspective -- 2.1 Introduction -- 2.2 Theory -- 2.2.1 Absorption -- 2.2.2 Fluorescence -- 2.3 DOM Fluorescence -- 2.4 Fluorophores of Interest -- 2.4.1 Amino Acids and Proteins -- 2.4.2 Simple Phenols -- 2.4.3 Indoles -- 2.4.4 Phenylpropanes -- 2.4.5 Oxygen Ring Compounds -- 2.4.6 Lignin -- 2.4.7 Quinones -- 2.4.8 Alkaloids -- 2.5 Factors Influencing DOM Fluorescence. , 2.5.1 Quenching -- 2.5.2 pH Effects -- 2.5.3 Interactions with Metals -- 2.5.4 Charge Transfer Interactions -- 2.6 Conclusions -- Acknowledgments -- References -- 3 Aquatic Organic Matter Fluorescence -- 3.1 Introduction -- 3.1.1 Peak Nomenclature -- 3.1.2 Humic-like EEM Components -- 3.1.3 Other EEM Components -- 3.1.4 Reconciling PARAFAC Model EEM Components -- 3.2 Fluorescence in Seawater -- 3.2.1 Introduction -- 3.2.2 CDOM in Coastal Ocean and Estuaries -- 3.2.3 CDOM in Open Ocean Waters -- 3.3 Fluorescence in Freshwater -- 3.3.1 Temporal Variation in DOM Source and Dynamics -- 3.3.2 Anthropogenic and Land Use Impacts on DOM -- 3.3.3 Transformations and Reactivity -- 3.3.4 Rainwater DOM Fluorescence -- 3.3.5 Dissolved Organic Carbon vs. Fluorescence Relationships -- 3.4 Fluorescence in Groundwater -- 3.4.1 Introduction -- 3.4.2 Groundwater NOM Fluorescence Characteristics -- 3.4.3 Groundwater Anthropogenic Organic Matter Characteristics -- 3.5 Fluorescence of Wastewater and Drinking Water -- 3.5.1 Wastewater Fluorescence -- 3.5.2 Drinking Water Fluorescence -- References -- Part II Instrumentation and Sampling -- 4 Sampling Design for Organic Matter Fluorescence Analysis -- 4.1 Introduction -- 4.2 Sample Collection -- 4.2.1 Contamination Sources -- 4.2.2 Blanks and Replicate Samples -- 4.2.3 Equipment Cleaning -- 4.2.4 Water Samplers -- 4.3 Sample Preservation -- 4.3.1 Filtration Techniques -- 4.3.2 Effects of Filtration on Fluorescence -- 4.4 Storage -- 4.4.1 General Comments -- 4.4.2 Refrigeration and Freezing -- 4.4.3 Poisoning - Acidification -- 4.5 Summary and Future Needs -- Acknowledgments -- References -- 5 Optical Spectroscopy Instrumentation Design, Quality Assurance, and Control: Bench-Top Fluorimetry -- 5.1 Introduction -- 5.2 Methods of Optical Spectroscopy -- 5.2.1 Absorption Spectroscopy -- 5.2.2 Optical Emission Spectroscopy. , 5.2.3 Scattering -- 5.2.4 Photoluminescence (Fluorescence and Phosphorescence) -- 5.3 The Fluorescence Spectrometer -- 5.3.1 The Ideal Fluorescence Spectrometer System -- 5.3.2 Basic Spectrofluorimeter Design -- 5.4 Measuring Fluorescence -- 5.4.1 Defining the Sensing Volume and Inner Filter Effects -- 5.4.2 Continuum Light Sources -- 5.4.3 Monochromators and Filters -- 5.4.4 Polarization Effects -- 5.4.5 Detectors -- 5.4.6 Measurement Systems: Data Acquisition Electronics and Software -- 5.4.7 Data Collection, Display, and Analysis Software -- 5.4.8 Instrument Performance Validation -- 5.4.9 Linearity, Signal to Noise, and Dynamic Range -- 5.4.10 Speed and Sensitivity -- 5.4.11 Wavelength Accuracy -- 5.4.12 Bandpass Selection -- 5.4.13 Stray Light -- 5.4.14 Cuvettes, Cleaning and Handling -- 5.4.15 Solvents and Contaminants -- 5.4.16 Background Signals: Rayleigh and Raman Scattering -- 5.4.17 Spectral Irradiance of the Excitation Channel -- 5.4.18 Correcting Excitation Signal Channels -- 5.4.19 Correcting Emission Signal Channels -- 5.4.20 Quantum Yield -- 5.4.21 Measuring Quantum Yields: The Three-Measurement Technique -- 5.4.22 Fluorescence Units - What Are They? -- References -- 6 Experimental Design and Quality Assurance: In Situ Fluorescence Instrumentation -- 6.1 Introduction -- 6.2 Historical Perspective of In Situ Sensors -- 6.2.1 Chlorophyll Field Sensors: Precursors to In Situ DOM Fluorometers -- 6.2.2 Evolution of DOM Field Sensors -- 6.3 Instrument Design Types -- 6.3.1 Sensor Configurations -- 6.3.2 Light Sources and Detectors -- 6.3.3 Optical Filters -- 6.3.4 Optical Configurations -- 6.3.5 Data Output -- 6.4 Calibration and Correction Procedures -- 6.4.1 Temperature Correction -- 6.4.2 Blank Subtraction -- 6.4.3 Standards and Intensity Calibration -- 6.4.4 Correction for Inner Filter Effects -- 6.4.5 Dynamic Range. , 6.5 Environmental Considerations -- 6.5.1 Factors of Concern -- 6.5.1.1 Particles -- 6.5.1.2 Bubbles -- 6.5.1.3 Dynamic Range -- 6.5.1.4 Temperature Effects -- 6.5.1.5 Biofouling -- 6.5.1.6 Understanding NOM Sources Within Environments -- 6.5.2 Sensor Choices for Specific Environments -- 6.5.2.1 Optically Dilute Systems -- 6.5.2.2 Optically Thick Systems -- 6.5.2.3 Turbid Systems -- 6.5.2.4 Energetically Flashy Environments -- 6.6 Revolutionizing NOM Studies via High-Resolution Fluorescence Measurements -- 6.6.1 Deployment Platforms -- 6.6.1.1 Spatial Resolution -- 6.6.1.2 Temporal Resolution -- 6.6.2 Importance of Scale -- 6.6.2.1 Neponset River Estuary in Boston Harbor- Small Temporal and Spatial Scales -- 6.6.2.2 Hudson River Estuary - Large Spatial and Small Temporal Scales -- 6.6.2.3 Mississippi Bight Region - Large Spatial and Temporal Scales -- 6.7 Remotely Sensed NOM Measurements -- 6.7.1 Fluorescent CDOM and Validation of Remote Sensing Products -- 6.7.2 Active Remote Sensors -- 6.7.3 Fluorescence of CDOM and Passive Sensors -- 6.7.4 Remote Sensing Summary -- 6.8 Summary -- Acknowledgments -- References -- Part III Environmental Effects -- 7 Physicochemical Effects on Dissolved Organic Matter Fluorescence in Natural Waters -- 7.1 Introduction -- 7.2 The Quenching of DOM Fluorescence -- 7.3 Effects of Molecular Weight and Fluorophore Size -- 7.4 Effect of Temperature -- 7.5 Effect of pH -- 7.6 Effect of Metals -- 7.7 Effect of Salinity (Ionic Strength) -- 7.8 Effect of Particles -- 7.9 Effect of Sunlight -- 7.10 Summary and Future Directions -- Acknowledgments -- References -- 8 Biological Origins and Fate of Fluorescent Dissolved Organic Matter in Aquatic Environments -- 8.1 Introduction -- 8.2. Sources -- 8.2.1 Allochthonous versus autochthonous -- 8.2.2 Terrestrial Organic Matter -- 8.2.3 Aquatic Organic Matter. , 8.3 Microbial Degradation of Fluorescent Dissolved Organic Matter -- 8.3.1 Bioavailability of FDOM -- 8.3.1.1 Amino Acid-like Fluorescence -- 8.3.1.2 Humic-like Fluorescence -- 8.3.2 Interactions between Photochemical and Microbial Degradation -- 8.4 Future Research -- Acknowledgments -- References -- Part IV Interpretation and Classification -- 9 Fluorescence Indices and Their Interpretation -- 9.1 Introduction -- 9.2 Overview of Common Fluorescence Indices -- 9.2.1 A "Humification Index" to Track Chemical Properties Developed by Kalbitz and Colleagues (HIX< -- sub> -- SYN< -- /sub> -- ) -- 9.2.2 Zsolnay's Humification Index to Identify Soil Organic Matter Properties (HIX< -- sub> -- EM< -- /sub> -- ) -- 9.2.3 Freshness Index to Identify Microbial Material in Marine DOM (the "ß/a" and "BIX" Index) -- 9.2.4 Fluorescence Index to identify Precursor Material in Freshwater DOM (FI) -- 9.2.5 The "Peak T/Peak C Ratio" to Identify Sewage Impact on Rivers -- 9.2.6 Redox Index as an Indicator of the Oxidation State of Quinone-Like Moieties -- 9.3 Applications of Fluorescence Indices -- 9.3.1 Using Fluorescence Indices to Identify Environmental Controls on Soil Organic Matter -- 9.3.2 The Development of a Fluorescence Index to Measure Organic Matter Humification Preserved in Cave Stalagmites -- 9.3.3 Understanding Controls on DOM Source and Quality in Surface Waters -- 9.3.4 Understanding DOM Changes in Estuaries -- 9.4 Spectroscopic Challenges toward Using the Indices -- 9.4.1 Instrument-Specific Effects and Proper EEM Correction -- 9.4.2 Concentration Issues and the Inner-Filter Effect -- 9.4.3 pH Effect on Fluorescence -- 9.5 Conclusions -- Acknowledgments -- References -- 10 Chemometric Analysis of Organic Matter Fluorescence -- 10.1 Introduction -- 10.2 Multivariate and Multiway Data Sets -- 10.3 Preprocessing of Data Matrices and Arrays. , 10.4 Exploratory Data Analysis.

Note: Intro -- Speleothem Science -- Contents -- Preface -- Acknowledgements -- I: Scientific and geologica lcontext -- CHAPTER 1: Introduction to speleothems and systems -- 1.1 What is all the fuss about? -- 1.1.1 What types of speleothem areuseful for generating climate archives? -- 1.1.2 Where do speleothems occur? -- 1.1.3 How do they form? -- 1.1.4 How do we date them? -- 1.1.5 What are the proxies for past environments and climates? -- 1.1.6 How do speleothems compare with other archives? -- 1.1.7 What next for speleothem science? -- 1.2 How is this book organized? -- 1.3 Concepts and approaches of system science -- Box 1.1 Box models and feedback -- 1.4 The speleothem factory within the karst system -- 1.4.1 Long-term change -- 1.4.2 Annual-scale behaviour -- 1.4.3 Decadal- to multi-millennial-scale changes -- CHAPTER 2: Carbonate and karst cave geology -- 2.1 Carbonates in the Earth system over geological time -- 2.2 Lithologies of carbonate hostrocks -- 2.2.1 Carbonate facies -- 2.2.2 The architecture of carbonate host rocks: sequence stratigraphy -- 2.2.3 Impure and geologically complex host rocks -- 2.2.4 Carbonate porosity -- 2.3 Carbonate diagenesis and eogenetic karst -- 2.3.1 Early diagenesis in marine waters and brines -- 2.3.2 Vadose diagenetic processes -- 2.3.3 Meteoric phreatic diagenesis -- 2.3.4 Eogenetic karst development -- 2.3.5 Burial diagenesis -- 2.4 Speleogenesis in mesogenetic and telogenetic karst (with contributions from John Gunn and David J Lowe) -- 2.4.1 Chronologies of cavedevelopment -- 2.4.2 Geometry of cave passages and systems -- 2.4.3 Localization of caves: the inception horizon hypothesis -- 2.4.4 Mesogenetic caves -- 2.4.5 Modelling the development of conduits and networks -- 2.5 Cave infilling -- 2.5.1 Mechanisms of cave infill and their relative power -- 2.5.2 Dating the infills. , 2.5.3 Physical sedimentology -- 2.5.4 Archaeological issues -- 2.5.5 The long-term prognosis -- 2.6 Conclusion -- CHAPTER 3: Surface environments: climate, soil and vegetation -- 3.1 The modern climate system -- 3.1.1 The global energy budget -- 3.1.2 Global patterns of temperature, rainfall and evapotranspiration -- 3.1.3 The general circulation of the atmosphere -- 3.1.4 Ocean circulation and land-ocean interactions -- Box 3.1 Climate indices -- Box 3.2 Back trajectory analysis -- 3.2 Water isotopes in the atmosphere -- 3.2.1 Variation in stable isotopes owing to evaporation and Rayleigh condensation -- 3.2.2 Other factors responsible for variations in isotopic composition -- 3.2.3 Isotopic variations in space within the annual cycle -- 3.2.4 Inter-annual isotopic variations -- 3.3 Soils of karst regions -- 3.3.1 Processes of soil formation -- 3.3.2 Soil development through time -- 3.3.3 Concluding views on karst soils -- 3.4 Vegetation of karst regions -- 3.5 Synthesis: inputsto the incubator -- II: Transfer processes in karst -- CHAPTER 4: The speleothem incubator -- 4.1 Introduction to speleophysiology -- 4.2 Physical parameters and f luid behaviour -- 4.2.1 Measurement of parameters -- 4.2.2 Static parameters in air -- 4.2.3 Dynamic f luid behaviour: laminar versus turbulent f low -- 4.2.4 Dynamic f luid behaviour: advective versus diffusive transport -- 4.3 Water movement -- 4.4 Air circulation -- 4.4.1 Physical causes -- Cave breathing -- Wind-induced f low -- Chimney circulation -- Convection -- Water-induced f low -- 4.4.2 Radon studies as indicators of rates of air-exchange -- 4.4.3 Carbon dioxide and its variability -- 4.4.4 Generalizing seasonality and its implications for speleothems -- 4.5 Heat f lux (authored by David Domínguez-Villar) -- 4.5.1 Sources and mechanisms of heat transfer into caves -- Geothermal heat f lux. , Surface heat f lux -- Heat transferred by the atmosphere -- Heat transferred from water -- Heat transferred from the rock -- 4.5.2 Thermal equilibrium in caves -- 4.6 Synthesis: cave climatologies -- CHAPTER 5: Inorganic water chemistry -- 5.1 Sampling protocols for water chemistry -- Box 5.1 Aqueous chemistry definitions -- 5.2 The carbonate system -- 5.3 Weathering, trace elements and isotopes -- 5.3.1 Overview of element sourcesand sinks -- 5.3.2 Calcite dissolution as an exemplar of weathering processes -- 5.3.3 Mineral weathering -- 5.3.4 Isotope studies -- 5.3.5 Colloidally bound elements -- Box 5.2 Ion behaviour and complexation -- 5.4 Carbon isotopes -- Box 5.3 Stable isotopes and their fractionation -- 5.5 Evolution of cave water chemistry: modelling sources and environmental signals -- 5.5.1 Forward modelling -- 5.5.2 Backward modelling -- CHAPTER 6: Biogeochemistry of karstic environments -- 6.1 Introduction -- 6.2 Organic macromolecules -- 6.2.1 Fluorescent organic matter -- Box 6.1 Organic macromolecules in speleothems -- 6.2.2 Lipid and lignin macromolecules -- Box 6.2 Colloids and gels: interactions between organic matter and inorganic stalagmite proxies (lead author Adam Hartland) -- 6.2.3 Ribosomal DNA -- 6.3 Pollen and spores -- 6.3.1 Pollen -- 6.3.2 Spores -- 6.4 Cave faunal remains -- 6.5 Synthesis and research gaps -- Box 6.3 Vegetation and soil cycling of inorganic proxies: evidence from sulphur isotopes -- III: Speleothem properties -- CHAPTER 7: The architecture of speleothems -- 7.1 Introduction -- 7.2 Theoretical models of stalagmite growth and of stalagmite and stalactite shapes -- 7.2.1 Theories of speleothem growth rate -- 7.2.2 Models of stalagmite shapes -- 7.2.3 Models of stalactite shapes -- 7.3 Geometrical classificationof speleothems -- 7.3.1 Soda-straw stalactites -- 7.3.2 Non-'soda-straw' stalactites. , 7.3.3 'Minimum-diameter' stalagmites -- 7.3.4 Non-'minimum-diameter' stalagmites -- 7.3.5 Flowstones -- 7.3.6 Other speleothem forms -- Box 7.1 Speleoseismicity in the Mechara karst, southeastern Ethiopia (authored by Asfawossen Asrat) -- 7.4 Mineralogy and petrology -- 7.4.1 Mineralogy: aragonite versus calcite -- 7.4.2 Crystal fabrics -- Nucleation -- Crystal morphology -- Impingement growth -- Stalagmite fabrics -- 7.4.3 Laminae -- 7.4.4 Growth phases and hiatuses -- 7.5 Synthesis -- CHAPTER 8: Geochemistry of speleothems -- 8.1 Analysis and the sources of uncertainty -- 8.1.1 What's the research question? -- 8.1.2 Analytical specificity -- 8.1.3 The geometry of the growth surface and spatial precision -- 8.1.4 Analytical precision and accuracy -- 8.2 The growth interface -- 8.2.1 Nanostructure of the growth surface -- 8.2.2 Organic molecules -- 8.2.3 Biological activity at the growth interface -- 8.3 Trace element partitioning -- 8.3.1 Thermodynamic and mixed empirical-thermodynamic approaches -- 8.3.2 Limitations of the partition coefficient concept -- 8.4 Oxygen and carbon isotope fractionation -- 8.4.1 Fluid inclusions -- 8.4.2 Can an equilibrium composition be defined? -- 8.4.3 Kinetic effects during CaCO3 precipitation -- pH and growth rate effects -- The Hendy test -- Modelling fractionation along speleothem surfaces -- 8.4.4 Clumped isotope geothermometry (Δ47 value) -- 8.5 Evolution of dripwater and speleothem chemistry along water f lowlines -- 8.6 Process models of variability over time -- 8.6.1 Stadial- to glacial-length episodes -- 8.6.2 Sub-millennial variation -- 8.6.3 Annual cycles -- CHAPTER 9: Dating of speleothems -- 9.1 Introduction -- 9.2 Dating techniques -- 9.2.1 Interval dating -- 9.2.2 14C -- 9.2.3 U-Th -- 9.2.4 U-Pb -- 9.2.5 Other techniques -- 9.3 Age-distance models -- 9.4 Conclusions -- IV: Palaeoenvironments. , CHAPTER 10: The instrumental era: calibration and validation of proxy-environment relationships -- 10.1 Available instrumental and derived series -- 10.1.1 Directly measured data -- 10.1.2 Interpolated data products -- 10.1.3 Reanalysis data -- 10.1.4 Climate indices -- 10.2 Methodologies -- 10.2.1 Overview of methodologies used in other f ields -- Linear-regression-based techniques -- Compositing records -- Forward modelling -- Pseudoproxies -- 10.2.2 Appropriate methodologies for speleothem calibration -- Linear-regression-based approaches -- Compositing -- Forward modelling -- Pseudoproxies -- 10.3 Case studies of calibrated speleothem proxies -- 10.3.1 Annual lamina thickness -- 10.3.2 δ18O -- 10.3.3 Other proxies -- 10.4 Questions raised and future directions -- CHAPTER 11: The Holocene epoch: testing the climate and environmental proxies -- 11.1 A brief overview of the Holocene -- 11.1.1 The Early Holocene -- 11.1.2 The Mid-Holocene -- 11.1.3 Late Holocene -- 11.2 The past millennium -- 11.2.1 Instrumentally calibrated speleothem climate reconstructions -- 11.2.2 Multi-proxy reconstructions and model-proxy comparisons -- 11.3 Holocene environmental changes: speleothem responses -- 11.3.1 The period of remnant ice sheets in the Early Holocene -- The last Mediterranean sapropel -- The '8.2 ka event' -- 11.3.2 Orbital forcing over the Mid- to Late Holocene -- 11.3.3 Evidence for multi-decadal and multi-centennial climate variability -- Box 11.1 Times-series analysis of speleothems -- 11.3.4 Speleothem evidence of Holocene soil and vegetation change -- 11.4 Questions raised and future directions -- CHAPTER 12: The Pleistocene and beyond -- 12.1 Pleistocene proxy records (ice-age climate f luctuations defined and drawn) -- 12.1.1 Subaqueous speleothem records: Devils Hole, USA -- 12.1.2 Composite speleothem records: Soreq Cave, Israel. , 12.1.3 Palaeoclimate hotspots: the Asian monsoon and the nature of glacial terminations.