bluuebunny/crossref_metadata_2025 huggingface dataset:
Applications of Stable Isotopes in Archaeological Geology
Authors: Herz Norman , Garrison Ervan G.
Published: November 2020

Isotopic ratios of elements in natural materials on the earth either have been constant in time and space or have varied as a result of radioactive decay or geochemical fractionation. Elements which show variations in isotopic abundances in different samples and the reasons for these variations have helped resolve many geological and archaeological problems. Radioactive decay has provided absolute dating clocks: for archaeology, the most useful systems have been associated with 14C, 40Ar, and U-disequilibrium series. Variations in isotopic ratios of the stable elements H, C, O, N, S, Sr, and Pb have helped solve problems of provenance, paleoenvironments, and paleodiets. The rationale for isotopic variations of individual elements will determine the types of applications to archaeological geology. The most important applications are the determinations of artifact signatures, paleodiet, and paleoenvironment. Isotopic fractionation of light elements by physical, chemical, and biological processes is controlled by those thermodynamic properties which are determined by atomic weight and electronic configuration. Thermodynamic properties of molecules that are mass and temperature dependent include energy, which decreases with decreasing temperature, and vibrational frequency, which varies inversely in proportion to the square root of the reduced mass. Easily measurable isotopic separation is generally restricted to the lighter elements, that is, with atomic weights less than 40. Because isotopic fractionation is mass dependent, the separation is greater for elements with the greater mass difference between isotopes. The greatest separation is expected for hydrogen (mass 1) versus deuterium (mass 2); the other light elements commonly have isotopic differences closer to 10%. Thus, the lighter isotopes have higher vibrational energy and their chemical bonds are more easily broken. The different reactivity of lighter versus heavier isotopes of an element is responsible for their separation during geochemical and biological processes. Thermodynamic behavior has been considered a principal cause for variations, not in isotopic abundances of the heavier elements Sr and Pb, but rather in abundances of their parent radionuclides: Rb for Sr and U and Th for Pb. Recently, however, P. Budd and others suggested that under nonequilibrium conditions, fractionation could theoretically take place among the lead isotopes.
Sodom and Gomorrah Event
Authors: Emery K. O. , Neev David
Published: November 2020

About 7800 B.P. after the first effects of warmings and droughts associated with the Atlantic Interval, many people of the Mideast moved into river floodplains where suitable agricultural soils and freshwater were available. Prominent examples are in Mesopotamia, the Nile Valley, and along the Jordan-Dead Sea rift. The extremely dry climates occasionally improved because of small fluctuations within the Chalcolithic and a larger one during Early Bronze II, when there was a 250-year wet interval. These climatic changes explain the settling, flourishing, and abandonment by the Ghassulians about 6000 B.C. and of the city of Arad, 4900 to 4650 B.P. at the fringe of the desert (R. Amiran and Gophna, 1989, n. 18; D. Amiran, 1991; Gilead, 1993). During the Early Bronze ages overall the climatic conditions in the Dead Sea region were not appreciably different from those at present, as attested by fossil flora found in excavations at Bab edh-Dhr’a and Numeira (McCreery, 1980). High yields of agriculture in fertile irrigated areas were an incentive to settle in the Plain of Sodom. This settling gradually intensified within the fertile plains of the Jordan-Dead Sea region as well as in Canaan through Early Bronze I and II but weakened toward the end of Early Bronze III. This is indicated by the pattern of settlements that developed from individual villages to city-states with satellite villages—mostly because of economic and social motivations— which later were changed into fortified communities (Esse, 1989). A gradual increase in fortification of Early Bronze settlements along the Dead Sea and Jordan Valley basins and the position of some of them along the narrow elevated step-faulted strip of the east foothills (Zori, 1962;Ben-Arieh, 1965; Rast, 1987 and personal communication, 1989) indicate increased need for defense by settlers against raids and invasions. These evidences of stress probably resulted from gradual climatic drying and warming. Investments in defense facilities were worthwhile if increased productivity was tempting enough. Such areas could have been found not only along the east foothills but also at the foot of the Amazyahu fault escarpment and in the delta of Nahal Zohar north of Mount Sedom if fresh or slightly brackish water was available there during the Early Bronze age.
Synopsis
Authors: Emery K. O. , Neev David
Published: November 2020

The two large lakes named Samra and Lisan existed in the Dead Sea graben from 350,000 to 120,000B.p. and 60,000 to 12,000B.p. Their sediments tentatively are correlated with the European Riss and Würm glacial epochs. Thick marls are the chief sediments in the deep water north basin. Rocksalt deposition dominated within the troughs of both north and south basins throughout the intervening Riss-Würm Interglacial stage. Lithology of Lisan Formation (Würm) in that basin indicates rapid and extreme fluctuations of level. Eight major climatic cycles are recorded during Würm glaciation when the level fluctuated between -180 m m.s.l. and probably lower than -400 m m.s.l. Rocksalt was deposited within both basins during warm dry phases of the Lisan stage. At the present state of knowledge no specific tectonic or volcanic activities can be tied to these climatic events. The Holocene Period was similar lithologically to that of the Lisan Formation and transition between them was gradual. Primarily the difference between the two was change in relative time span between alternate wet and dry phases. Dry phases of Holocene gradually became longer while wet ones with Dead Sea transgressions became shorter. Tectonic regimes during the first part—the Natufian age to Early Bronze III, 12,000 to 4400 B.P.—seem to have been milder than later ones, end of Early Bronze III to the present. The severe earthquake that destroyed Sodom and Gomorrah in 4350 B.P. was followed by a 300-year long subphase of gradually warming climate that became extremely dry during the latter part of the Intermediate Bronze age. Climatic Wet Phase III began about 3900 B.P. It was the longest, about 800 years, and most intense wet phase of Holocene and it probably was associated with volcanism. No abrupt cultural or demographic changes are known during transition from Epi-Paleolithic or Geometric Kebaran from the last glacial phase of the Pleistocene Period through Natufian to the early part of Holocene Pre-Pottery Neolithic. The reason for this stability is not clear especially because average temperatures of global oceans during the latest Pleistocene glaciation were appreciably lower than those during Early Holocene (Emiliani, 1978).
Spectroscopy of Matter
Authors: Thomas Michael E.
Published: November 2020

It is critical to understand the nature of the propagation medium in terms of the available resonances which couple to the electromagnetic field. The detailed specification of the complex index of refraction as a function of frequency is the subject of spectroscopy. Since propagation media cover all phases of matter, the spectroscopy of gases, solids, and liquids is introduced in this chapter. Topics are not exhaustively covered, but rather with sufficient depth to support the practical applications that will come later. The chapter begins with a formal review of topics covered in stationary-state quantum mechanics necessary for the development of spectroscopy. The next section develops models to calculate spectral line positions, which are necessary to characterize a spectral line. The full development of spectral line parameters is not only the goal of this chapter but the next two as well. The remaining sections address the essential elements of the spectroscopy of gases, solids and liquids. Both classical and quantum models are used. Time-independent quantum mechanics allows the description of the quantized energy level structure of matter. This is the central topic of this chapter. Time-dependent quantum mechanics is necessary for the development of a theory covering transitions between stationary-state energy levels and is the topic of Chapter 5. The classical concept of light is that of an oscillating continuous wave field, as presented in the first two chapters. This is consistent with the classical electrodynamics based on Maxwell’s equations. However, the work by Planck on blackbody radiation and Einstein on the photoelectric effect showed that optical fields also have a quantized or particle-like nature. Planck, in 1900, suggested that the energy of light, E, be quantized according to . . . E = h f [J] (3.1) . . . where f is frequency (sec−1) and h is Planck’s constant (h = 6.6260755(40) × 10−34 J-sec). This allowed a theoretical description of blackbody radiation for the first time. However, it was Einstein, who, a few years later, made Eq. 3.1 more credible by applying it to explain the photoelectric effect.
Electrodynamics II: Microscopic Interaction of Light and Matter
Authors: Thomas Michael E.
Published: November 2020

Although the primarily phenomenological theory of absorption and refraction of light by matter, based on classical models as presented in Chapter 4, is very useful, it is incomplete and often inadequate. A more complete and accurate picture of electrodynamics is given by the theory of quantum optics, and that is the topic of this chapter. The models developed in this chapter are more detailed and therefore more complicated than the phenomenological models of Chapter 4. The most robust models, which are applied in Part II, are presented in this chapter. The quantum models accurately represent experimental data and allow extrapolation and interpolation of such data. Many practical computer based models concerning optical propagation are based on this theory. The theory of elastic scatter as presented in Chapter 4 is consistent with quantum optics and is not presented again. (However, inelastic scatter must address the quantum nature of the scattering medium.) Quantum optics is not completely covered in this chapter. Entire textbooks are devoted to this diverse and comprehensive topic covering optics (see Refs. 5.1–5.3). The emphasis of this book is on absorption and reflection spectroscopy. Now details of internal structure of the medium impacting light–matter interaction are examined. The classical oscillator model is upgraded by semiclassical radiation theory and a quantum oscillator model is developed. Semiclassical radiation theory is based on a quantized medium coupled to a classical field. It is often applied to laser theory, where near-line-center stimulated emission dominates. The quantum oscillator model again utilizes the quantized medium and classical field, but with more attention to detailed balance between absorption and emission. It satisfies causality and the fundamental symmetry relationships established in Chapter 2. These quantum optics models are more complete formalisms and provide solutions to the shortcomings of classical electrodynamics. Of particular interest to propagation in gaseous media is the line shape in the far wing. To achieve long path lengths, propagation near line center of a resonance must be avoided. Line shape models in quantum optics accurately represent much of the frequency and temperature dependence observed in experimental data.
Wealth of Nature
Authors: Worster Donald
Published: November 2020

Hailed as "one of the most eminent environmental historians of the West" by Alan Brinkley in The New York Times Book Review, Donald Worster has been a leader in reshaping the study of American history. Winner of the prestigious Bancroft Prize for his book Dust Bowl, Worster has helped bring humanity's interaction with nature to the forefront of historical thinking. Now, in The Wealth of Nature, he offers a series of thoughtful, eloquent essays which lay out his views on environmental history, tying the study of the past to today's agenda for change. The Wealth of Nature captures the fruit of what Worster calls "my own intellectual turning to the land." History, he writes, represents a dialogue between humanity and nature--though it is usually reported as if it were simple dictation. Worster takes as his point of departure the approach expressed early on by Aldo Leopold, who stresses the importance of nature in determining human history; Leopold pointed out that the spread of bluegrass in Kentucky, for instance, created new pastures and fed the rush of American settlers across the Appalachians, which affected the contest between Britain, France, and the U.S. for control of the area. Worster's own work offers an even more subtly textured understanding, noting in this example, for instance, that bluegrass itself was an import from the Old World which supplanted native vegetation--a form of "environmental imperialism." He ranges across such areas as agriculture, water development, and other questions, examining them as environmental issues, showing how they have affected--and continue to affect--human settlement. Environmental history, he argues, is not simply the history of rural and wilderness areas; cities clearly have a tremendous impact on the land, on which they depend for their existence. He argues for a comprehensive approach to understanding our past as well as our present in environmental terms. "Nostalgia runs all through this society," Worster writes, "fortunately, for it may be our only hope of salvation." These reflective and engaging essays capture the fascination of environmental history--and the beauty of nature lost or endangered--underscoring the importance of intelligent action in the present.
An End to Ecstasy
Authors: Worster Donald
Published: November 2020

Back in the halcyon days of 1951, when the United States was entering its golden years of wealth and power and proclaiming that this was the American Century, there seemed no limit to what we could do with nature. Were some climates too hot? We could air-condition them. Were some too cold? We could thaw them out or raise tomatoes under glass. Were some too dry? We could, through hydraulic engineering, make them over into a veritable Eden of delights. In that year a Time magazine reporter traveled to the arid West to write about “the endless frontier” being won there by the engineers of the Bureau of Reclamation. They promised to develop enough water to redeem fifty million acres from aridity, enough acres to feed the equivalent of a whole new nation the size of France or Germany. And the engineers were not in the least reluctant to say what pleasure they got out of the work: “We enjoy pushing rivers around,” they told the reporter. Whether the pushing had any real direction, any clear sense of ends, was secondary; they (and by extension, we Americans) were a people who enjoyed dominating nature and we would look for rationales later. In a spirit of what the magazine called “engineering ecstasy,” almost every river in the western part of the country came under control and was made to raise alfalfa, fruit, and cotton. Our agricultural base shifted abruptly westward into the desert, and eastern and midwestern farmers suffered substantial damage to their fortunes. By the last agricultural census, the West counted over 45 million irrigated acres, producing one-fourth of the nation’s annual farm market sales. Though it irrigated only a small percentage of that acreage, the Bureau of Reclamation was unexcelled among water pushers for ambition and scale. It was the Bureau that had erected some of the biggest dams ever: Hoover, Grand Coulee, Shasta, Glen Canyon, Teton, Navajo, Flaming Gorge, etc., the clearest, brightest expressions we had of our national drive to conquer the land. But the big dams were more than that.
The Environmentalists’ Dilemma
Authors: Norton Bryan G.
Published: November 2020

The poignancy of the dilemma facing advocates of environmental protection was dramatized for me in an encounter with a little girl. It was a sleepy, summer-beach Saturday and I was walking on a sandbar just off my favorite remnant of unspoiled beach on the north tip of Longboat Key, Florida. The little girl clambered up the ledge onto the sandbar, trying not to lose a dozen fresh sand dollars she cradled against her pushed-out and Dan-skinned stomach. I guessed she was about eight. Thirty yards away, in knee-deep water, her mother and older sister were strip mining sand dollars—they walked back and forth through the colony, systematically scuffing their feet just under the soft sand on the bottom of the lagoon and bending over to retrieve each disk as it was dislodged. Their treasure was held until collected by the eight-year-old transporter, whose feet were too small to serve as plowshares. Gathering the sand dollars at the point of excavation, she relayed them to the sand bar where a considerable pile was accumulating near the family’s beached powerboat. Many months earlier, I had noted how the fickle current through Longboat Inlet had begun to dump sand in a large crescent spit out into the Gulf of Mexico, forming a waist-deep lagoon. Next came a profusion of shore birds and the colony of sand dollars that multiplied in the protected water, and then came the little girl and her family in their powerboat. I was startled by the level of industrial organization; even the little girl executed her task with square-jawed efficiency. I engaged her as she emerged onto the sand bar. “You know, they’re alive,” I said. “We can put ‘em in Clorox at home and they’ll turn white.” I asked whether they needed so many. She said, “My Momma makes ‘em outta things.” I persisted: “How many does she need to make things?” “We can get a nickel apiece for the extras at the craft store.” I sighed and walked away. Our brief conversation had ended in ideological impasse. But I was troubled.
Rainfall
Authors: Hoyt Douglas V. , Shatten Kenneth H.
Published: November 2020

This chapter examines rainfall and associated phenomena and their possible relationship to solar activity. Rainfall can be measured directly using rain gauges or estimated by monitoring lake levels and river flows. Satellite and radar rainfall measurements have become increasingly important. Historical documentation on drought, or the absence of rain, also reveals empirical relationships. Both rainfall and evaporation show marked variations with latitude and geography. First, we examine these rainfall-associated variations and estimate how they might change with solar activity. Second, we cover empirical studies of rainfall, lake levels, river flows, and droughts. The sun bathes the Earth’s equator with enormous amounts of surface energy. Much of this absorbed radiant energy evaporates water, causes atmospheric convection, and is later released to space as thermal radiation. Steady-state energy escapes, so tropical temperatures do not rise without limit. Some absorbed energy is transported poleward by winds from the point of absorption. Intense convection near the equator leads to a large updraft known as the intratropical convergence zone (ITCZ), a band of lofty, high-precipitation clouds producing the largest rainfall of any region on Earth. Solar energy in the ITCZ is carried to high elevations where it diverges and moves poleward. It is unable to travel all the way to the poles, so instead creates a large atmospheric circulation cell known as the Hadley cell. The Hadley cell has an upward motion near the equator and downward motions at about 30° north and south latitude. These downflow regions produce clear air with few clouds and create areas of minimum rainfall called deserts. These regions of upflow and downflow are connected by poleward flows in the upper atmosphere and equatorward flows in the lower atmosphere, forming a complete circulation pattern. Outside the Hadley cell are temperate and polar regions. The temperate regions have more rainfall than the deserts, while the cold polar regions have even less precipitation. Figure 6.1 shows the three regions with relative maximum rainfall. The mean evaporation has a much simpler latitudinal variation that tends to follow the surface temperature. Figure 6.1 shows this variation as a parabolicshaped dotted line.
Biota
Authors: Hoyt Douglas V. , Shatten Kenneth H.
Published: November 2020

We now consider insect populations, circumpolar mammal populations, seaweed density, agricultural yields, and similar topics. Good reasons exist to link such biological phenomena to solar activity. For one thing, if such meteorological parameters as temperature and precipitation vary with solar activity, life forms sensitive to small changes in these parameters may show dramatic responses. We will examine various claims from the 100 to 200 articles that either provide support for or criticize these types of ideas. The topics generally start at the lower levels of the food chain (i.e., insects) and proceed to the upper levels (i.e., predatory mammals), concluding with agricultural and economic studies. Insect populations are sensitive climate indicators. Paleontologists have used fossilized insects (see, for example, Coope, 1977) to show that very rapid changes in climate can occur in only a few years. Certain species of insects can tolerate only narrow ranges of temperature or precipitation. If meteorological variables alter that range, a new species of insect will replace the old. Insects occupy one of the lower rungs of the food chain, so fluctuations in their numbers may cause corresponding fluctuations in such predators as birds or spiders. Therefore, correlating insect populations with solar activity is a worthwhile venture. In his doctoral treatise, “Über die Beziehungen der Sonnenfleckenperiode zu meteorologischen Erscheinungen” published in 1877, F. G. Hahn argues that locusts will probably appear in temperate regions only during unusually hot and dry years. Hahn shows that European locusts appear preferentially between the years of sunspot minimums up to the next sunspot maximum, an average of about 4 years. For the 7 years from the sunspot maximum to the next sunspot minimum, locusts are scarcer. Since sunspot minimums produced relatively warm temperatures for the years 1800–1862, this suggests that the sun influences European locust populations. E. D. Archibald, who in his later years was a very ardent advocate of sun/climate relationships, extended Hahn’s findings. In a letter to Nature in 1878, Archibald showed that locusts appeared in Europe in 1613, 1690, and 1748–1749. According to Wolf, these dates occur 1 to 3 years after a sunspot minimum, which is consistent with Hahn’s findings.
Solar and Climate Changes
Authors: Hoyt Douglas V. , Shatten Kenneth H.
Published: November 2020

Until now we have considered only 11-year variations in solar activity and climate. The sun also varies on longer time scales. Since these variations seem to parallel a number of climatic changes, the sun may contribute to climatic changes on time scales of decades to centuries. We now examine several solar indices that vary in parallel with Earth’s climate change. There exist plausible arguments that these indices are proxy indicators of the sun’s radiative output, but there is no proof. We now present the strongest correlations we have seen for a sun/climate connection. First, as it is the most widely publicized index, we consider the mean level of solar activity. In 1801 Herschel first proposed a relationship between climate and the level of solar activity. Second, we examine solar cycle lengths, which have been studied sporadically since 1905. Third, we look at two closely related indices—sunspot structure and sunspot decay rates. Fourth, we consider variations in the solar rotation rate. Lastly, we examine some major solar and climatic events of the last thousand years to see if any indications of solar influence are evident on climate. Although we present the solar-induced changes as arising from total-irradiance variations, as discussed earlier spectral-irradiance changes may be the primary driver. When Rudolf Wolf reconstructed solar activity based on historical observations of sunspots, he found an 11-year cycle going back to at least 1700. In 1853 Wolf also claimed that there is an 83-year sunspot cycle. This longer term variation becomes evident simply by smoothing the data, as in Socher’s 1939 example. Wolf’s original discovery of an 83-year cycle was forgotten, but the long cycle was rediscovered by H. H. Turner, W. Schmidt, H. H. Clayton, and probably others. After W. Gleissberg also discovered this 80- to 90-year cycle around 1938, he published so much material on the subject that ever since it has been called the Gleissberg cycle. All these rediscoveries of the same phenomenon indicate that the 80- to 90-year cycle may be real but not strictly periodic. Rather, the cycle may be a “persistency” with an 80- to 90-year period. During this period solar activity is quite powerful but fails to exhibit a single sharp spectral peak.
Liquids, Solutions, and Interfaces
Authors: Fawcett W. Ronald
Published: November 2020

Fifty years ago solution chemistry occupied a major fraction of physical chemistry textbooks, and dealt mainly with classical thermodynamics, phase equilibria, and non-equilibrium phenomena, especially those related to electrochemistry. Much has happened in the intervening period, with tremendous advances in theory and the development of important new experimental techniques. This book brings the reader through the developments from classical macroscopic descriptions to more modern microscopic details.
Charge Transfer Equilibria at Interfaces
Authors: Fawcett W. Ronald
Published: November 2020

Processes in which charge is transferred from one phase to another at an interface make up an important class of interfacial reactions. Well-known examples are the reactions which occur at the electrodes of an electrochemical cell. These are electron transfer reactions, oxidation taking place at one electrode and reduction at the other. The early study of electrochemical cells provided valuable thermodynamic information about the redox processes occurring in them. When an electrochemical cell is a source of energy, for example, a battery, chemical energy is converted to electrical energy. When electrical energy is driven into an electrochemical cell from an external source, electrode reactions producing products of commercial interest are possible. Thus the general subject discussed here is of considerable practical importance. Another important class of interfacial charge transfer processes occurs at the membrane | solution interface. Some solute species can move into the membrane phase, whereas others cannot. When ions are involved in membrane selectivity, a potential drop is established at the interface. Ion transfer processes at membranes are extremely important in living organisms and form the basis for the functioning of the nervous system. Membranes are also involved in ion selective electrodes such as the ubiquitous pH electrode. These electrodes are often used in modern analytical techniques based on potentiometry. In the present chapter, the relationship between the electrode potential and the activity of the solution components in the cell is examined in detail. The connection between the Galvani potential difference at the electrode solution interface and the electrode potential on the standard redox scale is discussed. This leads to an examination of the extrathermodynamic assumption which allows one to define an absolute electrode potential. Ion transfer processes at the membrane | solution interface are then examined. Diffusion potentials within the membrane and the Donnan potentials at the interface are illustrated for both liquid and solid state membranes. Specific ion electrodes are described, and their various modes of sensing ion activities in an analyte solution discussed. The structure and type of membrane used are considered with respect to its selectivity to a particular ion over other ions.
Simple Insights from the Beginnings of Magnetic Resonance in Molecular Biology
Authors: Jardetzky Oleg
Published: November 2020

Birthday symposia inevitably provide an opportunity for reflection. Noting that greater minds than mine have offered an apology for their life (St. Augustine, 1853 edition; St. Thomas Aquinas; John Henry cardinal Newman, 1864), I shall attempt to answer the question: What have been the lasting contributions of my generation - the generation that began its work before Richard Ernst’s epoch making development of 2D NMR, and the equally momentous development of high field spectrometers, pioneered by Harry Weaver at Varian, Rex Richards at Oxford and Gunther Laukien at Bruker, revolutionized the technology and put biological applications within everyone’s reach? I offer these insights in the spirit that to fully understand a subject one must understand its history. The essence of scientific endeavor is to see something no one has seen before - or understand something no one had understood before. If there had been such a contribution, it was to understand what biological questions could be asked by NMR and to develop prototype experiments showing how. Difficult as it is to imagine this today when such understanding is taken for granted, the now obvious just wasn’t obvious then. Quite the contrary: well considered expert opinion of the day held the undertaking to be of very dubious merit. Linus Pauling, with whom it was my great fortune to spend my postdoctoral year, was never much interested in nuclear magnetic resonance (and did not think much of its promise for biological applications, as he clearly pointed out at this symposium). But, Linus Pauling firmly believed in giving the young the freedom to explore, and so the first crude interpretation of a protein NMR spectrum, taken a few weeks earlier by Martin Saunders, Arnold Wishnia and J. G. Kirkwoodat Yale, was based on the first amino acid and peptide spectra we had taken at Caltech. When I got my first faculty job at Harvard, and wanted to apply for an NMR spectrometer, it was not quite as easy.
NMR Approaches To Understanding Protein Specificity
Authors: Roberts G.C. K. , Lian L.-Y.
Published: November 2020

The biological functions of proteins all depend on their highly specific interactions with other molecules, and the understanding of the molecular basis of the specificity of these interactions is an important part of the effort to understand protein structure-function relationships. NMR spectroscopy can provide information on many different aspects of protein-ligand interactions, ranging from the determination of the complete structure of a protein-ligand complex to focussing on selected features of the interactions between the ligand and protein by using “reporter groups” on the ligand or the protein. It has two particular advantages: the ability to study the complex in solution, and the ability to provide not only structural, but also dynamic, kinetic and thermodynamic information on ligand binding. Early analyses of ligand binding (Jardetzky and Roberts, 1981) focused on measurements of relaxation times, chemical shifts and coupling constants, which gave relatively limited, although valuable, structural information. More recently, it has become possible to obtain much more detailed information, due to the extensive use of nuclear Overhauser effect measurements and isotope-labeled proteins and ligands; a number of reviews of this area are available (Feeney and Birdsall, 1993; Lian et al, 1994; Wand and Short, 1994; Petros and Fesik, 1994; Wemmer and Williams, 1994). In this article, we describe some recent work from our laboratory which illustrates the use of NMR spectroscopy to obtain structural and mechanistic information on relatively large enzyme-substrate and proteinprotein complexes. A number of species of pathogenic bacteria, notably Streptococci and Staphylococci, have proteins on their surface that bind immurioglobulins (reviewed in Boyle (1990)). Protein A from S. aureus and protein G from species of Streptococci are widely used as imrnunological tools and are the most extensively studied of these antibody-binding proteins. A detailed understanding of the binding mechanisms of these proteins is important, not only for providing us with the structural basis for their functions, but also as a contribution toward understanding the general rules of protein-protein interactions.
Physical Processes
Authors: Krishnamurti T. N. , Bedi H. S. , Hardiker V. M.
Published: November 2020

In this chapter we present some of the physical processes that are used in numerical weather prediction modeling. Grid-point models, based on finite differences, and spectral models both generally treat the physical processes in the same manner. The vertical columns above the horizontal grid points (the transform grid for the spectral models) are the ones along which estimates of the effects of the physical processes are made. In this chapter we present a treatment of the planetary boundary layer, including a discussion on the surface similarity theory. Also covered is the cumulus parameterization problem in terms of the Kuo scheme and the Arakawa- Schubert sheme. Large-scale condensation and radiative transfer in clear and cloudy skies are the final topics reviewed. There are at least three types of fluxes that one deals with, namely momentum, sensible heat, and moisture. Furthermore, one needs to examine separately the land and ocean regions. In this section we present the socalled bulk aerodynamic methods as well as the similarity analysis approach for the estimation of the surface fluxes. The radiation code in a numerical weather prediction model is usually coupled to the calculation of the surface energy balance. This will be covered later in Section 8.5.6. This surface energy balance is usually carried out over land areas, where one balances the net radiation against the surface fluxes of heat and moisture for the determination of soil temperature. Over oceans, the sea-surface temperatures are prescribed where the surface energy balance is implicit. Thus it is quite apparent that what one does in the parameterization of the planetary boundary layer has to be integrated with the radiative parameterization in a consistent manner.
Spectral Energetics
Authors: Krishnamurti T. N. , Bedi H. S. , Hardiker V. M.
Published: November 2020

In this chapter we present spectral energetics. This is a useful tool for the interpretation of model output. It can be used to interpret both short term weather evolution and climate time scales. These same procedures can be used with both real atmospheric data and model output. A comparison of energetics histories can be very useful for the assessment of model performance. In the first section of this chapter we derive the equations for atmospheric energetics. In the following section, a method for the representation of these equations in the Fourier domain is introduced, and the equations are derived in the one-dimensional (zonal) wavenumber domain. In the last section, we view the problem in two-dimensional wavenumber domain and derive expressions for barotropic energy exchanges and baroclinic energy conversions in this framework. Some sample results of the energetics in two-dimensional wavenumber domain are also presented in this section. In this section we consider a system of basic equations in spherical coordinates and derive the relevant energy equations for the zonally averaged flow and the eddy flow. These derivations are essentially based on the work of Saltzman (1957).
Activity Coefficients
Authors: Bethke Craig M.
Published: November 2020

Among the most vexing tasks for geochemical modelers, especially when they work with concentrated solutions, is estimating values for the activity coefficients of electrolyte species. To understand in a qualitative sense why activity coefficients in electrolyte solutions vary, we can imagine how solution concentration affects species activities. In the solution, electrical attraction draws anions around cations and cations around anions. We might think of a dilute solution as an imperfect crystal of loosely packed, hydrated ions that, within a matrix of solvent water, is constantly rearranging itself by Brownian motion. A solution of uncharged, nonpolar species, by contrast, would be nearly random in structure. The electrolyte solution is lower in free energy G than it would be if the species did not interact electrically because of the energy liberated by moving ions of opposite charge together while separating those of like charge. The chemical potentials of the species, for the same reason, are smaller than they would be in the absence of electrostatic forces.
Geochemical Buffers
Authors: Bethke Craig M.
Published: November 2020

Buffers are reactions that at least temporarily resist change to some aspect of a
Fluid’s chemistry. A pH buffer, for example, holds pH to an approximately
constant value, opposing processes that would otherwise drive the solution acid
or alkaline.
Strain History and Polar Decomposition
Authors: Oertel Gerhard
Published: November 2020

The effect of two consecutive strains (only two states enter into the calculation of a strain, the states before and after, independently of the actual strain path) can be calculated by premultiplying the transformation matrix of the first strain (its stretch tensor) with that of the second. Unless the two strains are coaxial (their principal directions coincide), however, the resulting cumulative transformation matrix represents not only a strain but also a rigid-body rotation; in that case the matrix is asymmetric. The method of polar decomposition allows one to interpret the combined transformation as if it had come about either by a strain followed by a rotation (right polar decomposition) or by a rotation followed by a strain (left polar decomposition). Let 𝔸 and 𝔹 be two stretch tensors, or transformation matrices, representing each a strain without rotation; and let the strain 𝔹 follow the strain 𝔸. Then the combined transformation matrix 𝔽 is: . . . 𝔹𝔸 = 𝔽 = ℝ𝕌= 𝕍ℝ, (8.1) . . . where 𝔽 results from premultiplication of the earlier stretch 𝔸 with the later 𝔹, where ℝ𝕌 is the “right” and 𝕍ℝ the “left” decomposition of 𝔽, where 𝕌 and 𝕍 are two distinct stretch tensors, and where ℝ is the transformation matrix for a rotation (elements of rotation matrices are indicated by the symbol aij elsewhere in this book). 𝔽 is asymmetric and ℝ differs from the identity matrix (δij) except when 𝔸 and 𝔹 are coaxial. 𝕌 and 𝕍 have the same principal stretches and differ by orientation only. In Problems 120 to 122, false approaches in the search for an appropriate decomposition of an asymmetric transformation were recognized by yielding impossible values for a rotation. Application of eq. (8.1) makes such a trial-and-error approach unnecessary.
Organic Synthesis Engineering
Authors: Doraiswamy L. K.
Published: November 2020

This book will formally launch "organic synthesis engineering" as a distinctive field in the armory of the reaction engineer. Its main theme revolves around two developments: catalysis and the role of process intensification in enhancing overall productivity. Each of these two subjects are becoming increasingly useful in organic synthesis engineering, especially in the production of medium and small volume chemicals and enhancing reaction rates by extending laboratory techniques, such as ultrasound, phase transfer catalysts, membrane reactor, and microwaves, to industrial scale production. This volume describes the applications of catalysis in organic synthesis and outlines different techniques of reaction rate and/or selectivity enhancement against a background of reaction engineering principles for both homogeneous and heterogeneous systems.
Estimation of Properties of Organic Compounds
Authors: Doraiswamy L. K.
Published: November 2020

A primary requirement of any reactor design or process development computation is knowledge of the major properties of the compounds involved. Although most of these can be obtained from the literature, there is still a need to estimate them from correlations. The main difficulty is the large number of correlations proposed for a given property and the need to select the best from among them. No single correlation works with equally high precision under all conditions. On the other hand, correlations that can be used with acceptable levels of precision over a wide range of conditions are also available for a number of properties. The slight sacrifice of accuracy is often more than compensated for by the ease and generality of application of these methods. Our emphasis here will be on such correlations. For a detailed treatment, reference should be made to books devoted exclusively to properties estimation. The book by Reid, Prausnitz, and Poling (1987), along with its earlier versions by Reid and Sherwood (1958, 1966) and Reid, Prausnitz, and Sherwood (1977), and the works of Janz (1958), Hansch and Leo (1979), and Lyman, Reehl, and Rosenblatt (1982) are noteworthy. The following methods selected for a few properties are based in part on the recommendations contained in these treatises. The two most important bases for formulating correlations for estimating the properties of organic compounds (indeed of any compound) are the law of corresponding states (LCS), and the method of group contributions (GC). LCS is based on the concept that all substances exhibit identical properties under conditions equally removed from their critical states. The “equally removed” state for any property is usually expressed as the ratio of its value at that state to the value at the critical state and is referred to as the reduced property. Thus Tr — T/TC, Pr = P/PC, Vr = V/Vc and ηr = η/ ηc are the reduced temperature, pressure, volume, and viscosity, respectively. If the simple ideal gas law PV/RgT — Z, where Z is the compressibility, can be recast in terms of reduced properties as PrVt/RgTr = Z/ZC, then the PVT behavior of all fluids can be represented as Pr versus Tr plots for different values of Zr.
Biphasic Reaction Engineering
Authors: Doraiswamy L. K.
Published: November 2020

The chemical equilibria of many industrially important organic reactions in aqueous solutions are often displaced in the direction of the reactants, leading to very low conversions. Therefore, there is a need for an environmentally friendly strategy that will shift the equilibria toward the products, resulting in enhanced conversions. A particularly effective technique is to add a second phase, appropriately termed biphasing. In general, biphasing is the intentional addition of an immiscible phase to a reaction mixture to increase the yield of the desired product or to facilitate separation of product from (say) catalyst. Much of the effort till recently has been on adding a water-immiscible organic solvent in enzyme-catalyzed organic reactions in the aqueous phase. Although strictly the term biphasing should apply only to soluble catalysts, thus preserving the purity of its definition, in practice it also includes insoluble catalysts such as immobilized enzymes (which would constitute a third phase). Biphasing received an exciting stimulus around 1984 when it was used to overcome the inherent and perhaps the most telling deficiency of homogeneous catalysis. By biphasing with an aqueous phase (unlike in enzymatic catalysis where the biphasing liquid is an organic solvent), the catalyst was fully retained in that phase, whereas the product (and unused reactant) remained in the organic phase. The consequent easy separation of catalyst from product added a new dimension to homogeneous catalysis that gives it a decided edge over its heterogeneous counterpart for many reactions. Yet another dimension to biphasing was added in the last decade when it was found that both phases could be aqueous. This variant of traditional biphasing has many obvious advantages. Although still in its infancy, its enormous potential is not difficult to visualize. The chief advantages and disadvantages of biphasing are listed in Table 18.1. We begin our treatment of biphasing by developing the theoretical foundation for predicting an apparent or effective equilibrium constant for a biphasic reaction. This will be done specifically for enzyme-catalyzed reactions, but it can be extended to straight organic synthesis. Several important aspects of these biphasic systems, such as solvent selection and the role of mass transfer, will be discussed.
Use of Partial Molar Volumes of Model Compounds in the Interpretation of High-Pressure Effects on Proteins
Authors: Prehoda Kenneth E. , Markley John L.
Published: November 2020

The transfer of liquid hydrocarbons into water is accompanied by a large decrease in volume at 25 °C and atmospheric pressure, with typical values for ΔV°tr of — 2.0 ml mol methylene−1. Considering the large amount of apolar surface that is exposed when a globular protein unfolds, the hydrocarbon transfer results imply that the change in volume accompanying the unfolding process (ΔV°obs) should be highly negative under these conditions. However, experimental data on the pressure denaturation of proteins typically yield relatively small values of ΔV°obs at atmospheric pressure and 25 °C. We analyze this apparent inconsistency in terms of a simple thermodynamic dissection of the partial molar volume. This approach allows the volume effects that result from solute-solvent interactions to be determined from experimental partial molar volumes. The use of absolute quantities (partial molar volumes) circumvents assumptions associated with the use of results from transfer experiments. An important finding is that hydration of apolar species is less dense than bulk water. This discovery leads to the conclusion that the contribution to ΔV°obs for protein unfolding from the hydration of apolar surfaces is highly positive, contrary to predictions based on transfer data. Further, hydration of polar surfaces makes a positive contribution to ΔV°obs. The large, positive term from the differential hydration of the folded and unfolded states is compensated by the difference in free volume of the protein in the two states. This finding provides a new framework for interpreting pressure effects on macromolecules. The full characterization of a macromolecular system requires knowledge of the effect of pressure on the system. The thermodynamic information obtained from using pressure as a perturbation is a volume change for the particular reaction being studied. The observed volume change, ΔV°obs, for protein unfolding may provide insight into the mechanisms that determine the three-dimensional structure of the folded state. Pressure denaturation experiments have been demonstrated for a number of proteins, including ribonuclease A (Gill & Glogovsky, 1965; Brandts et al., 1970), chymotrypsinogen (Hawley, 1971), metmyoglobin (Zipp & Kauzmann, 1973), and, more recently, lysozyme (Samarasinghe et al., 1992) and staphylococcal nuclease (Royer et al., 1993).