bluuebunny/crossref_metadata_2025 huggingface dataset:
Optical Electromagnetics I
Authors: Thomas Michael E.
Published: November 2020

In this chapter, the optical spectrum is defined and subdivided into many sub-bands, which are traditionally determined by transparency in various media. Propagation of the electromagnetic field in vacuum, as based on Maxwell’s equations, and basic notions of geometrical and physical optics, are covered. The theoretical and conceptual foundation of the remaining chapters is established in this chapter and the next. Optical electromagnetic propagation is generally and often accurately described by classical geometrical optics or ray optics. When diffraction or wave interference is of concern, then the more complete field of physical optics is used. Geometrical optics requires precise knowledge of the spatial and spectral dependence of the index of refraction. This requires electrodynamics, which is most appropriately described by quantum optics. These topics are covered in the first five chapters. The definitions of the optical spectrum and the various models for describing propagation are introduced in the following. The optical electromagnetic field covers the range of frequencies from microwaves to the ultraviolet (UV) or wavelengths from 10 cm to 100 nm. This is a very liberal definition covering six orders of magnitude, yet the description of propagation is very similar over this entire band, and distinct from radio-wave propagation and x-ray propagation. A listing of the nomenclature for the different spectral bands within the range of optical wavelengths is given in Table 1.1. Other commonly used units of spectral measure such as wave number, frequency, and energy are also listed in the table. These various quantities are related to wavelength by the following formulas: where c is the speed of light (c = 2.99792458 × 108 m/sec), λ is wavelength, f is frequency in hertz, E is energy, h is Planck’s constant (h = 6.6260755(40) × 10−34 J sec), and ν is frequency in wave numbers (the number of wavelengths per centimeter). Although wavelength is commonly used by applied scientists and engineers, frequency is the most appropriate unit for the theoretical description of light–matter interactions. Because of the importance of spectroscopy in the discussion of optical propagation, the spectroscopic unit of wave number will be consistently used.
Optical Propagation in Gases and the Atmosphere of the Earth
Authors: Thomas Michael E.
Published: November 2020

Propagation within the atmosphere is an important consideration concerning the performance of many electro-optical systems. An electro-optical system can be described as containing three basic components: source, detector, and propagation medium. Because of the quality of source and detection systems today, often the limiting factor in overall system performance is the propagation medium. Thus a thorough discussion of the atmosphere and various mechanisms of attenuation is required. Absorption, scattering, and turbulence are the dominant mechanisms of signal loss and distortion. This chapter covers gaseous absorption and scattering in the atmosphere of the earth. Turbulence is not covered, and the reader is referred to other texts (see Chapter 1, Refs. 1.10 and 1.11). The atmosphere surrounds and protects the earth in the form of a gaseous blanket that acts as the transition between the solid surface of the earth and the near-vacuum of the outer solar atmosphere. It acts as a shield against harmful particle radiation, meteors, and high-energy photons. The dynamics of the atmosphere drive the weather on the surface. It provides for life itself as part of the earth’s biosphere. Thus optical propagation in this medium has many important characteristics and consequences. These include meteorological optics, infrared and visible astronomy, remote sensing, and electro-optical systems performance in general. Therefore, it is appropriate to begin this chapter with an introduction to the nature of the atmosphere. The atmosphere is composed of gases and suspended particles or aerosols at various temperatures and concentrations as a function of altitude and azimuth. The variations in altitude show a marked structure. Six main horizontal layers form the stratified structure of the atmosphere, as shown in Fig. 7.1. The lowest is the troposphere, which extends from ground level to approximately 11 km (36,000 ft or 7 mi.). The temperature in this layer generally decreases with increasing altitude at the rate of 6.5 K/km. However, variations can exist on this rate, which creates interesting refractive effects. The pressure varies from one atmosphere at sea level to a few tenths of an atmosphere at the top of this layer.
Optical Propagation in Water
Authors: Thomas Michael E.
Published: November 2020

From a basic physics perspective, liquids are the least understood state of matter. Yet this medium plays an important role in the process of life on this planet. The human body is largely composed of liquids, and three-quarters of the surface of the earth is covered by seawater. The main liquid of interest in this chapter, and to the applied scientist and engineer, is water. The importance of understanding the optical properties of water cannot be overemphasized. The chapter appropriately begins with a discussion of the optical properties of pure water, since it is the main ingredient in seawater and in biomedical fluids. Pure water is an insulator with a strong dipole moment and an effective electronic band edge in the ultraviolet near 0.16 μm (62,500 cm−1). Absorption near the band edge shows similar structure to that observed in solids. Water has extensive infrared vibrational bands just as in the gas phase. Dipoles in a liquid can partially rotate in response to the polarization of the incident microscopic field, and Debye relaxation bands occur in the microwave region. A permittivity model for Debye relaxation was presented in Chapter 4 by Eq. 4.60. This is an important mechanism that describes the optical properties of liquids at far-infrared and microwave frequencies.
Foundational Work in Integrated Dialog Processing
Authors: Smith Ronnie W. , Hipp D. Richard
Published: November 2020

Building a working spoken natural language dialog system is a complex challenge. It requires the integration of solutions to many of the important subproblems of natural language processing. This chapter discusses the foundations for a theory of integrated dialog processing, highlighting previous research efforts. The traditional approach in AI for problem solving has been the planning of a complete solution. We claim that the interactive environment, especially one with variable initiative, renders such a strategy inadequate. A user with the initiative may not perform the task steps in the same order as those planned by the computer. They may even perform a different set of steps. Furthermore, there is always the possibility of miscommunication. Regardless of the source of complexity, the previously developed solution plan may be rendered unusable and must be redeveloped. This is noted by Korf [Kor87]: . . . Ideally, the term planning applies to problem solving in a real-world environment where the agent may not have complete information about the world or cannot completely predict the effects of its actions. In that case, the agent goes through several iterations of planning a solution, executing the plan, and then replanning based on the perceived result of the solution. Most of the literature on planning, however, deals with problem solving with perfect information and prediction. . . . Wilkins [W1184] also acknowledges this problem: . . . In real-world domains, things do not always proceed as planned. Therefore, it is desirable to develop better execution-monitoring techniques and better capabilities to replan when things do not go as expected. This may involve planning for tests to verify that things are indeed going as expected.... The problem of replanning is also critical. In complex domains it becomes increasingly important to use as much as possible of the old plan, rather than to start all over when things go wrong. . . . Consequently, Wilkins adopts the strategy of producing a complete plan and revising it rather than reasoning in an incremental fashion.
Performance of the Speech Recognizer and Parser
Authors: Smith Ronnie W. , Hipp D. Richard
Published: November 2020

The results of the experiments reported in the previous chapter were independently analyzed in order to measure the accuracy of the speech recognizer and parser. A summary of the key results of this analysis follows. • On average, one out of every three words emitted by the speech recognizer was in error. • On average, three out of every four sentences contained one or more speech recognition errors. • In spite of the high speech recognition error rate, the meanings of the spoken utterances were correctly deduced 83% of the time. • Finally, and perhaps most surprisingly, it was found that dialog expectation was helpful only as a tie-breaker in deducing the correct meaning of spoken utterances. . . . The remainder of this chapter describes the analysis in detail. The performance measurements of the speech recognizer and parser were computed from transcripts of 2804 individual utterances2 taken from the second and third sessions of the 8 experimental subjects. No information from the pilot subjects or from the first session with each subject was used in this analysis. Information about each utterance was collected and converted to a standardized, machine-readable format. The information that was collected follows. • The sequence of words actually spoken by the user. These were manually entered by the experimenters based on the audio recordings of the experiment. • The sequence of words recognized by the speech recognizer. This information was recorded automatically during the experiments. • The set of up to K minimum matching strings between elements of the hypothesis set and dialog expectations, together with an utterance cost and an expectation cost for each. (See section 5.8.5). • The final output of the parser. • The text spoken by the dialog controller immediately prior to the user’s utterance, and notes concerning the user’s utterance which were entered by the person who transcribed the utterance from the audio tapes. This information was used to assist in manually judging the correctness of each parse. . . . After the above information was collected and carefully audited to remove errors, the following additional features of each utterance were computed through a combination of automatic and manual processing.
History as Natural History
Authors: Worster Donald
Published: November 2020

Forty years ago a wise, visionary man, the Wisconsin wildlife biologist and conservationist Aldo Leopold, called for “an ecological interpretation of history,” by which he meant using the ideas and research of the emerging field of ecology to help explain why the past developed the way it did. At that time ecology was still in its scientific infancy, but its promise was bright and the need for its insights was beginning to be apparent to a growing number of leaders in science, politics, and society. It has taken a while for historians to heed Leopold’s advice, but at last the field of environmental history has begun to take shape and its practitioners are trying to build on his initiative. Leopold’s own suggestion of how an ecologically informed history might proceed had to do with the frontier lands of Kentucky, pivotal in the westward movement of the nation. In the period of the revolutionary war it was uncertain who would possess and control those lands: the native Indians, the French or English empires, or the colonial settlers? And then rather quickly the struggle was resolved in favor of the Americans, who brought along their plows and livestock to take possession. It was more than their prowess as fighters, their determination as conquerors, or their virtue in the eyes of God that allowed those agricultural settlers to win the competition; the land itself had something to contribute to their success. Leopold pointed out that growing along the Kentucky bottomlands, the places most accessible to newcomers, were formidable canebrakes, where the canes rose as high as fifteen feet and posed an insuperable barrier to the plow. But fortunately for the Americans, when the cane was burned or grazed out, the magic of bluegrass sprouted in its place. Grass replaced cane in what ecologists call the pattern of secondary ecological succession, which occurs when vegetation is disturbed but the soil is not destroyed, as when a fire sweeps across a prairie or a hurricane levels a forest; succession refers to the fact that a new assortment of species enters and replaces what was there before.
A Sense of Soil
Authors: Worster Donald
Published: November 2020

Last year marked the fiftieth anniversary of a landmark event in American agricultural and conservation history, and few seem to be aware of the fact. In April 1935, Congress passed the Soil Erosion Act, the first effort in the United States to establish a nationwide, comprehensive program to preserve the very earth on which farming and rural life depend. That act committed the nation to a permanent program of research and action to stop “the wastage of soil and moisture resources on farm, grazing, and forest lands.” Describing erosion as “a menace to the national welfare,” it promised action on private as well as public lands, even to the point of condemning and purchasing private properties when inducements to good practices proved ineffective. And the act established within the Department of Agriculture a new agency, the Soil Conservation Service (SCS), to carry out the work. Now, after fifty years, it is appropriate to ask what cultural forces produced this 1935 commitment and to speculate about what our attitude, our commitment, is today. What have we as a people done with our soil since the act was passed? What have we learned about preserving the soil and what have we forgotten? The South, soil-conscious and erosion-plagued beyond other regions, played an extraordinary role in preparing the way for the 1935 act. It furnished both lessons in consequences and leaders for reform. From an earlier period, a succession of southern leaders had warned of the dangers of soil depletion and erosion. Thomas Jefferson, for example, wrote in 1819 of a land carelessness that, if not ended, would force planters to abandon their Virginia fields and “run away to Alibama (sic), as so many of our countrymen are doing, who find it easier to resolve on quitting their country, than to change the practices in husbandry to which they have been brought up.” After him, men like Edmund Ruffin preached the gospel of lime, of “calcareous manure,” up and down the land, earnestly calling for stability, conservation, and a permanent agriculture for the region.
The Kingdom, the Power, and the Water
Authors: Worster Donald
Published: November 2020

Among the truly outstanding books written in this century about the American frontier—and the shelf of such books is rather small—is Great Basin Kingdom by Leonard J. Arrington, published in 1958. When it appeared, it had only a few rivals either in scholarship or ideas. There was Henry Nash Smith’s work on the West as symbol and myth, Bernard DeVoto’s vigorous account of explorers and imperialists, Paul Morgan’s saga of the Rio Grande valley, Wallace Stegner’s biography of John Wesley Powell, and Walter Prescott Webb’s sweeping survey of Europeans on the global frontier. All of those books appeared in the 1950s within a few years of each other. All were well researched and brilliantly written, in many cases by accomplished novelists whose talents in creating plot and character recruited a wide audience for frontier and western history. Arrington’s study of the Mormon frontier was different from the others in that it was the work of an economic and social historian who was interested in how institutions took shape in one small part of the West and how they differed from those in other parts of the region and in the East. Like the other historians, he gave his story a compelling plot and filled it with arresting, complex characters; but for him the chief interest was how a vague, half-articulated set of ideas had migrated to Utah and taken shape there as a thriving, distinctive economic order. Better than any of his contemporaries, moreover, and better than most of his successors, he understood how powerful the drives of capitalism had been in developing the West, how thoroughly those drives had entered into the region’s overall sense of purpose, and how fiercely the battle had been waged, at least in Utah, to prevent that from happening. As romance, his story may not have been able to compete with DeVoto’s lusty adventurers or Morgan’s brown-robed padres preaching among the Indians, but in its implications it may have been the most important story of all. Arrington’s thesis was that nineteenth-century Mormon Utah was at once an intensely materialistic society, intent on achieving wealth, and a determinedly anti-capitalistic one.
The Shaky Ground of Sustainable Development
Authors: Worster Donald
Published: November 2020

The first thing to know when starting to climb a hill is where the summit lies. The second is that there are no completely painless ways to get there. Failing to know those things may lead one up a deceptively easy path that never reaches the top but meanders off into a dead-end, frustrating the climber and wasting energy. The currently popular slogan of “sustainable development” threatens to become such a road. Though appealing at first view, it appeals particularly to people who are disheartened by the long, arduous hike they see ahead of them or who don’t really have a clear notion of what the principal goal of environmental politics ought to be. After much milling about in a confused, contentious mood, they have discovered what looks like a broad easy path where all kinds of people can walk along together, and they hurry toward it, unaware that it may be going in the wrong direction. When contemporary environmentalism first emerged in the 1960s and ′70s, and before its goals became obscured by political compromising and diffusion, the destination was more obvious and the route more clear. The goal was to save the living world around us, millions of species of plants and animals, including humans, from destruction by our technology, population, and appetites. The only way to do that, it was easy enough to see, was to think the radical thought that there must be limits to growth in three areas—limits to population, limits to technology, and limits to appetite and greed. Underlying that insight was a growing awareness that the progressive, secular, and materialist philosophy on which modern life rests, indeed on which Western civilization has rested for the past three hundred years, is deeply flawed and ultimately destructive to ourselves and the whole fabric of life on the planet. The only true, certain way to the environmental goal, therefore, was to challenge that philosophy at its foundation and find a new one based on material simplicity and spiritual richness—to find other ends to life than production and consumption.
Conservationists and Preservationists Today
Authors: Norton Bryan G.
Published: November 2020

Aldo Leopold died in 1948, of a heart attack suffered while fighting a brushfire that threatened the pines he and his family had planted at the shack. By dint of his strong personality, scientific curiosity, and near-universal respect from professional colleagues and nonprofessional wilderness advocates alike, Leopold had personified the search for a unified vision to guide human use of the land and offered a unifying model for conservationists. His death, at the height of his intellectual and leadership powers, left the movement effectively rudderless. The country was at the time being swept away by the postwar economic boom and a new period of unrestrained economic growth pushed environmental concerns off the political agenda. Stephen Rauschenbush, writing in 1952, said, “Conservation is in danger of becoming a lost cause” and provided a list of five “forces and events that had battered away at the old ideal.” Grant McConnell similarly described the conservation movement in 1954 as “small, divided and frequently uncertain.” Wise-use conservationists and land preservationists appeared in the eyes of their opponents, McConnell lamented, as “but the representatives of particular interest groups and . . . hence no better than those whom they accuse.” But the same economic growth that placed conservationists on the defensive in the late 1940s and 1950s created a new demographic situation, including a baby boom that resulted eventually in a large surge in the youthful segment of the population. Increasing incomes allowed discretionary spending on amenities. Outdoor recreation became more popular and vacation homes near the shore or in the mountains proliferated as more families chose to spend time in areas with natural amenities. Environmental historian Samuel Hays explains the resulting shift as focusing interest and concern increasingly on the quality of life. New social, economic, and demographic factors created a context in which the older conservationist concerns about efficient development and use of material resources—concerns with production—were replaced, in the postwar era, with increasing concern with the consumption side of the picture. These changes created a new constituency for environmental groups.
The Pressures of Growth
Authors: Norton Bryan G.
Published: November 2020

Critics of environmentalism have often charged that the movement is “elitist.” By this is meant, among other complaints, that environmentalists are mainly members of the middle and upper classes who have achieved a comfortable level of economic well-being and who want to “lock up” natural resources, discourage economic growth, and withhold upwardly mobile job opportunities from less privileged economic groups in the society. Environmentalists, of course, dispute this criticism, arguing that it is unsupported by any reasonable interpretation of either environmentalists’ goals or the socioeconomic data. Nevertheless, the criticism strikes a sensitive nerve. It is interesting that the charge is directed at environmentalists, a majority of whom are liberals or progressives, both from the right, which claims environmental regulations choke off economic opportunities, and from the left, which argues that skirmishes over resource policy represent just one more episode in the ongoing war between the classes. What is undeniable is that the growth issue is the most difficult one facing environmentalists today. Here is a real dilemma. If environmentalists embrace economic growth in America, they apparently embrace endless sprawl, boom towns, high energy use, degradation of watersheds and wetlands, more chemicals—evils without end. If they oppose growth, however, they appear to favor unemployment, reduced wages, and economic stagnation. About growth, the dilemma encourages ambivalence and waffling: In 1977, the Rockefeller Brothers Fund published The Unfinished Agenda: The Citizen’s Guide to Environmental Issues, which emphasized a need for “a major transformation in human values” and argued that the United States has “enjoyed a development that is no longer possible for most [nations].” The United States must, the report urges, aid in “the transition from abundance to scarcity” and provide examples of how, “in a ‘Conserver Society,’ quality of life can be preserved (and, for many, increased) in an era of scarcity.” In the years since the Reagan antiregulatory revolution, however, environmentalists have also emphasized the importance of economic growth in achieving environmental goals. In a 1985 agenda document (environmentalists love to compose agendas), the Group of Ten (chief executive officers of ten leading environmental organizations) said: “Continued economic growth is essential.
Pollution Control
Authors: Norton Bryan G.
Published: November 2020

When active environmentalists were asked in a questionnaire, “Has there been an author who has most deeply affected your thinking about environmental issues?” respondents mentioned Rachel Carson about three times as often as any other writer. Carson’s book Silent Spring has been described as the primary catalyst in transforming the largely moribund conservation movement of the 1950s into the modern environmental movement of the 1960s and 1970s. Carson’s work precipitated the shift from first-generation environmental problems of land and resource protection to second-generation problems, especially pollution, which were more pervasive, less immediately apparent, and in many ways more insidiously threatening to members of the general population. The rise of pollution problems to the forefront of public policy concerns required a new vernacular, a new way of speaking about environmental threats and solutions. Rachel Carson, it is said, succeeded in one place where Leopold had failed; she injected ecological concepts and ideas into broader public policy discussions. Her graphic writing style, as well as her considerable status as a successful author, succeeded in transforming public discussions of environmental problems into a more ecological context by emphasizing the ways in which persistent chemicals move through natural systems and into human bodies. Immense economic stakes were involved in the pesticide issue; production of DDT, for example, quintupled between 1945 and 1962, as chemical manufacturers’ sales climbed from just over $10 billion to almost $33 billion. The publication of Silent Spring caused a huge public controversy; that controversy has set the parameters, as well as the tone, for much of the subsequent debate regarding environmental regulation and environmental policy. Carson began her attack on the indiscriminate use of pesticides with “A Fable for Tomorrow,” in which she described an imaginary town in the heart of America. She first described an idyllic scene of humans living in harmony with their surroundings, including woods and hedgerows inhabited by countless birds, and streams swimming with fish. But “then a strange blight crept over the area and everything began to change.” Domestic animals died. Humans became ill.
Land Use Policy
Authors: Norton Bryan G.
Published: November 2020

Albert Hochbaum, whom we met in Chapter 3, was Leopold’s student and friend; Director of the Delta Duck Station in Manitoba, Canada; and a part-time collaborator on A Sand County Almanac. He also had an admirable talent for succinctly hitting the nail on the head. He summed up Leopold’s message in four words. “The lesson you wish to put across is the lesson that must be taught,” he said, “preservation of the natural.” So much for succinctness; the difficult problem, of course, is to explain what is meant by “preservation” and by “natural.” Thomas McNamee, writing forty years later, uses the same basic approach: “I believe that the true object of conservation is nature,” he says. “What is nature?” The answer cannot help but be complicated, he notes, because “our conception of nature springs from the darkest depths of our culture’s unconscious sense of life itself, and ancient irrational urges and fears give the concept its power.’” But that is only half of the story: “At the same time,” he says, “nature must also have an objective, rational, manageable, thinkable value.” And thus we have the paradox of modern land use theory: Americans love nature; our values were formed in nature’s womb, a huge, wonderful, and horrible wild place. Our values are freedom and independence, “split rail values,” as Leopold called them. But our activities, as builders and consumers, transform our environment into something not-wild; we manipulate and control and artificialize nature; we make it not-nature. As the song says, you always hurt the one you love. But the paradox has also an optimistic face: As we have built and consumed, we have become wealthy by exploiting nature. Wildness has become valuable, objectively, according even to economists, because our wealthy society is now willing to pay to preserve nature. But here is the bitter pill to swallow: We all must admit that, at least in some sense, “nature” preservation is a sham—we’ve gone too far to “free” nature, as we might free a wild animal, release it from captivity.
Intertemporal Ethics
Authors: Norton Bryan G.
Published: November 2020

“What good is a world view, anyway?” we might well ask, if environmentalists are allowed to put them on and take them off like hats. This is serious business; after all—it’s no fashion show—the future of the planet is at stake. We have noted that environmentalists lack a fully developed world view, a complete conceptual, theoretical, and evaluative framework for interpreting the world. Environmentalists have generally, as David did in facing Goliath, gone into battle against the powerful forces of exploitation, which are well armed with a reductionistic world view, with just slingshots and pebbles. But environmentalists have done remarkably well, given the apparently uneven distribution of intellectual armaments. The hit-and-run tactics of guerilla warfare have obvious benefits. Playing fast and loose with metaphysical and moral principles, environmentalists have gained considerable political clout by employing that value which seems particularly appropriate for a given issue, or by emphasizing a particular world view that will be effective in reaching a coveted constituency. But guerilla warfare has important costs as well. Environmentalists can appear to outsiders as disorganized and fractious, especially if one listens to their rhetoric, rather than observing their political actions. Further, the fragmentation of environmentalists’ world views has real costs internal to the movement because it results in failures of communication and mistrust, even among individuals and groups that are pursuing identical or nearly identical policies. For example, while committees formed by the Group of Ten could reach a detailed consensus on policy in all areas of environmental concern, they were unable to present the document as endorsed by their respective organizations because some organizations wished not to be publicly associated with others because of differing attitudes toward hunting. The most important cost of world view fragmentation among environmentalists, however, exists not in the past or in the present, but in the future. Environmentalists have failed to articulate a positive vision for the future; they cannot explain in terms comprehensible to each other or to the public at large what is their positive dream. As is sometimes said, environmentalists are always “against something.”
Observations of the Sun
Authors: Hoyt Douglas V. , Shatten Kenneth H.
Published: November 2020

Our sun is a typical “second generation,” or G2, star nearly 4.5 billion years old. The sun is composed of 92.1% hydrogen and 7.8% helium gas, as well as 0.1% of such all-important heavy elements as oxygen, carbon, nitrogen, silicon, magnesium, neon, iron, sulfur, and so forth in decreasing amounts (see Appendix 3). The heavy elements are generated from nucleosynthetic processes in stars, novae, and supernovae after the original formation of the Universe. This has led to the popular statement that we are, literally, the “children of the stars” because our bodies are composed of the elements formed inside stars. From astronomical studies of stellar structure, we know that, since its beginnings, the sun’s luminosity has gradually increased by about 30%. This startling conclusion has raised the so-called faint young sun climate problem: if the sun were even a few percent fainter in the past, then Earth could have been covered by ice. In this frozen state, it might not have warmed because the ice would reflect most of the incoming solar radiation back into space. Although volcanic aerosols covering the ice, early oceans moderating the climate, and other theories have been suggested to circumvent the “faint young sun” problem, how Earth escaped the ice catastrophe remains uncertain. How can the sun generate vast amounts of energy for billions of years and still keep shining? Before nuclear physics, scientists believed the sun generated energy by means of slow gravitational collapse. Still, this process would only let the sun shine about 30 million years before its energy was depleted. To shine longer, the sun requires another energy source. We now believe that a chain of nuclear reactions occurs inside the sun, with four hydrogen nuclei fusing into one helium nucleus at the sun’s center. Because the four hydrogen nuclei have more mass than the one helium nucleus, the resulting mass deficit is converted into energy according to Einstein’s famous formula E = mc2. The energy, produced near the sun’s center, creates a central temperature of about 15 million degrees Kelvin (°K).
Cyclomania
Authors: Hoyt Douglas V. , Shatten Kenneth H.
Published: November 2020

In his 1874 book Contributions to Solar Physics, Sir Norman Lockyer writes the following: . . . Surely in meteorology, as in astronomy, the thing to hunt down is a cycle, and if that is not to be found in the temperate zone, then go to frigid zones, or the torrid zones and look for it, and if found, then above all things, and in whatever manner, lay hold of, study it, record it, and see what it means. If there is no cycle, then despair for a time if you will, but yet plant firmly your science on a physical basis, as Dr. Balfour Stewart long ago suggested, before, to the infinite detriment of English science, he left the Meteorological Observatory at Kew; and having got such a basis as this, wait for results. In the absence of these methods, statements of what is happening to a blackened bulb in vacuo, or its companion exposed to the sky, is, for research purposes, work of the tenth order of importance. . . . As Lockyer notes, looking for cycles is certainly an attractive prospect. If found, a cycle will help with predictions, and successful predictions are a central goal of scientific studies. Cycle hunting is also a relatively straightforward procedure, with several well-developed techniques. Cycle hunting has become even easier with the advent of computers. By feeding a stream of data into an algorithm to detect cycles, one is likely to find cycles even in a series of random numbers. Hence the danger that a cycle, if detected, may prove to be only a random fluctuation. Will the cycle persist with more data, or will it simply disappear? For ardent cycle hunters, and the sun/climate field has attracted its fair share, these questions are hardly a deterrent. The lure seems to be finding something of seeming importance with minimal effort. From a practical point of view, a cycle may be considered important only if it can be plotted. If sophisticated analyses are required to detect the cycle, the cycle probably has only secondary importance. While these criteria are not the usual mathematical criteria for significance, they are a practical, down-to-earth guide to what is important.
Choice of Problems in the Early Days of Biological NMR Spectroscopy
Authors: Cohn M.
Published: November 2020

It was a mere ten years after the discovery of NMR that Oleg Jardetzky under the mentorship of the physical chemist John Wertz (Wertz and Jardetzky, 1956) began using 23Na NMR with the aim of studying Na+ transport in biological systems as suggested by William Lipscomb. Jardetzky found that Na+ NMR provided a unique method for following the binding of Na+ in weak complexes. Advantage was taken of the sensitivity of quadrupolar nuclei to their chemical environment as reflected in their relaxation rates which could be readily observed at a field of 7,030 gauss available at the time (Jardetzky and Wertz, 1956). From the very first, Jardetzky limited his choice to those problems that could be investigated uniquely or most effectively by NMR Spectroscopy. One of Jardetzky’s principal goals was to elucidate, at least in part, the threedimensional structures of biological macromolecules in aqueous solution, a distant goal in the late 1950’s. He realized that before attempting to tackle the structure of these complex molecules, proteins and nucleic acids, by NMR it was essential to initially characterize the spectra of their components, amino acids andnucleosides. In 1957, he published a note in the Journal of Chemical Physics (Takedaand Jardetzky, 1957) on a few amino acids, not only reporting the chemical shifts of all the protons but also showing that in a dipeptide, for example, glycylglycine, the two CH2 groups are non-equivalent. In 1958, he published an NMR paper, a systematic study of the proton NMR spectra of amino acids, in the Journal of Biological Chemistry (Jardetzky and Jardetzky, 1958), thus introducing many facets of NMR Spectroscopy to the biochemical community. This seminal paper included: l) the chemical shifts of the protons of 22 amino acids and their dependence on pH, concentration and ionic strength and 2) the effect of rate processes on the NMR spectrum as exemplified by the exchange of the guanidino protons of arginine with water. Increased structural information from peptide NMR spectroscopy attracted many investigators to this area of research.
NMR and Mutagenesis Investigations of a Model Cis: Trans Peptide tsomerization Reaction: Xaa116-Pro117of Staphylococcal Nuclease and its Role in Protein Stability and Folding
Authors: Hinck A.P. , Walkenhorst W.F.
Published: November 2020

The slow rates of peptide bond isomerization in imino acids and the substantial population of the cis peptide bond isomer in Xaa-Pro linkages in peptides were first recognized in NMR studies of proline-containing model compounds (Maia et al., 1971). The important role of this isomerization in protein stability and folding (reviewed by Kim and Baldwin, 1982, 1990; Schmid, 1993) were recognized several years later (Brandts et al., 1975) and the biological relevance of this process was substantiated by the discovery of a ubiquitous enzyme that catalyzes Xaa-Pro peptide bond isomerization (Fischer et al., 1984, 1989; Takahashi et al., 1989). The strict evolutionary conservation of some prolyl residues and the observation that the kinetics of interconversion between alternative functional forms of some systems is consistent with the time scale of proline isomerization suggest that proline isomerization may play a wide role in protein structure and function. Suggestive examples include the sodium pump of Escherichia coli, the disulfide isomerase/thioredoxin class of enzymes, concanavalin A, and bovine prothrornbin fragment I (Brown et al., 1977; Marsh et al, 1979; Dunker, 1982; Brandland Deber, 1986; Langsetmo et al, 1989). NMR spectroscopy is one of the most suitable tools for studying this isomerization reaction. The rates generally are slow on the time scale of NMR chemical shifts but, in favorable cases, are comparable to longitudinal relaxation rates so that the isomerization process can be investigated by chemical exchange spectroscopy. NMR data obtained on calbindin D9k (Chazin et al., 1989), insulin (Higgins et al., 1988), and staphylococcal nuclease (nuclease) as discussed below have shown that each exists in solution under native conditions as a mixture of slowly exchanging conformers. The fact that dynamic molecular heterogeneity in nuclease was first observed in the laboratory of Oleg Jardetzky, as manifested by splitting of the histidyl 1H ε1 resonance from His46 in one-dimensional 1H NMR spectra recorded at 100 MHz (Markley et al., 1970), makes this topic particularly appropriate to a volume celebrating his scientific contributions.
Computing the Structure of Large Complexes: Modeling the 16S Ribosoma RNA
Authors: Chen R. , Fink D.
Published: November 2020

Ribosomes are the sites of messenger RNA (mRNA) translation to protein, and thus are crucial to the normal functioning of all cells. These ribonucleoprotein particles are composed of a small (30S) subunit and a large (50S) subunit. The 30S subunit, in turn, is composed of a strand of RNA (16S rRNA) and 21 proteins ranging in molecular weight from 9 kD to 61 kD. Studies have demonstrated that ribosomal RNA is necessary for normal ribosome function and protein production (Dahlberg, 1989; Noller, 1991). In particular, 16S rRNA is essential for normal assembly and function of the 30S subunit, which is responsible for translation initiation (Hardestyand Kramer, 1985). Elucidating the structure of 16S rRNA could greatly aid our understanding of the molecular mechanisms for protein translation, and such basic structural information could ultimately have wide-ranging importance in fields such as pharmacology and drug design. Because of the difficulties associated with X-ray analysis of large complexes such as the ribosome (Eisenstein et al., 1991), high-resolution structural data for the 16S rRNA remain sparse. However, neutron diffraction studies have determined the relative positions of the 30S proteins (Capel et al., 1988), which, along with the reported 16S rRNA-protein interactions (Noller, 1991, Noller et al., unpublished; Brimacombe, 1991), enable low-resolution structural models—showing how the RNA associates with the protein components—to be built. Several studies have sought to take advantage of these structural data for the 308 subunit. Stern et al. have used interactive model building to produce a three-dimensional 16S rRNA structure (Stern et al., 1988). This method can produce viable models, but is hindered somewhat by subjectivity intrinsic to the process and by the nonexhaustive nature of its conformation search. Hubbard and Hearst have used distance geometry techniques to model the RNA structure, but did not incorporate neutron diffraction data on the protein positions (Hubbard and Hearst, 1991). Malhotra and Harvey have used an energy minimization technique to produce a set of possible conformations for 16S rRNA; their study, however, depends on electron microscopic studies on the molecule to provide initial information on surface topology (Malhotra, 1994).
Determination by 1H NMR of a Slow Conformational Transition and Hydration Change in the Consensus TATAAT Prsbnow Box
Authors: Milhé C.
Published: November 2020

The conformational dynamics and hydration of a DNA 14-mer containing the consensus Pribnow box sequence TATAAT have been measured using rotating frame T1 measurements and NOESY and ROESY in water. The H2 proton resonances of adenines show fast intermediate exchange behavior which can be attributed to a conformational transition that affects the distances between H2 protons of neighboring adenine residues, both sequential and cross-strand. The relaxation rate constant of the transition was measured at 4000s-1 at 25°C. Bound water close to the H2 proton of adenines was observed with residence times of >lns. At low temperature (5°C), the Pribnow box is in a closed state in which hydration water in the minor groove is tightly bound. At higher temperatures, the conformation opens up as judged by the increase in separation between sequential H2 protons of adenines and water exchanges freely from the minor groove. The conformational transition and the altered hydration pattern may be related to promoter function. The control of gene expression in procaryotes depends on the specific recognition by RNA polymerase of a six base-pair sequence (consensus: TTGACA) located at -35 from the transcription site, and a second one, named the Pribnow box (consensus: TATAAT) at about 10 base-pairs upstream the initiation site (Rosenberg and Court, 1979). It has been shown (Hawley and McClure, 1983) that strong promoters exhibit a high degree of homology with the consensus sequences, separated by an optimum consensus spacer length of 17 base pairs. The strength of a promoter depends on, among other thing, the rate of the initiation of transcription. This rate depends on the product between the thermodynamic and kinetic constants KB and k2 (McClure, 1980). The initial binding of RNA polymerase to the promoter results in the formation of a transcriptionally inactive ‘closed’ complex, characterized by the association constant KB. Isomerization to the active ‘open’ complex then occurs, and is characterized by the first order rate constant k2. Hence, the frequency of transcription initiation depends both on the strength of the polymerase-promoter interaction, and the ease with which this complex can isomerize to the productive state. Both of these events are likely to depend on the physical properties of the promoter.
Lower-Order Spectral Model
Authors: Krishnamurti T. N. , Bedi H. S. , Hardiker V. M.
Published: November 2020

This system was first developed by Lorenz (1960b). It is an elegant system that provides an introduction to the concepts of spectral modeling, based on the use of double Fourier series representations of the basic equations in a doubly periodic domain. Here we examine the barotropic vorticity equation.
Initialization Procedures
Authors: Krishnamurti T. N. , Bedi H. S. , Hardiker V. M.
Published: November 2020

In this chapter we describe two of the most commonly used initialization procedures. These are the dynamic normal mode initialization and the physical initialization methods. Historically, initialization for primitive equation models started from a hierarchy of static initialization methods. These include balancing the mass and the wind fields using a linear or nonlinear balance equation (Charney 1955; Phillips 1960), variational techniques for such adjustments satisfying the constraints of the model equations (Sasaki 1958), and dynamic initialization involving forward and backward integration of the model over a number of cycles to suppress high frequency gravity oscillations before the start of the integration (Miyakoda and Moyer 1968; Nitta and Hovermale 1969; Temperton 1976). A description of these classical methods can be found in textbooks such as Haltiner and Williams (1980). Basically, these methods invoke a balanced relationship between the mass and motion fields. However, it was soon realized that significant departures from the balance laws do occur over the tropics and the upperlevel jet stream region. It was also noted that such departures can be functions of the heat sources and sinks and dynamic instabilities of the atmosphere. The procedure called nonlinear normal mode initialization with physics overcomes some of these difficulties. Physical initialization is a powerful method that permits the incorporation of realistic rainfall distribution in the model’s initial state. This is an elegant and successful initialization procedure based on selective damping of the normal modes of the atmosphere, where the high-frequency gravity modes are suppressed while the slow-moving Rossby modes are left untouched. Williamson (1976) used the normal modes of a shallow water model for initialization by setting the initial amplitudes of the high frequency gravity modes equal to zero. Machenhauer (1977) and Baer (1977) developed the procedure for nonlinear normal mode initialization (NMI), which takes into account the nonlinearities in the model equations. Kitade (1983) incorporated the effect of physical processes in this initialization procedure. We describe here the normal mode initialization procedure. Essentially following Kasahara and Puri (1981), we first derive the equations for vertical and horizontal modes of the linearized form of the model equations.