bluuebunny/crossref_metadata_2025 huggingface dataset:
Temperature
Authors: Hoyt Douglas V. , Shatten Kenneth H.
Published: November 2020

How the bulk of the sun’s energy variations, which arise from the solar-irradiance changes, contribute to terrestrial changes will be the subject of this and the next few chapters. Although it’s a simplification, the hypothesis that only the largest solar activity–related energy contributors to the Earth’s atmosphere need to be considered allows us to ignore such far-flung ideas as the influence of sector boundary crossings, cosmic rays, and other less energetic phenomena. If the Foukal and Lean model of solar irradiance is a close approximation of known solar behavior on the 11-year time scale, what are the climatic consequences of these variations? We can ignore all the other proposed solar cycles ranging from 6 to 7 days to hundreds or thousands of years. Although some of these other proposed solar cycles may be real, we will not indulge in cyclomania here. North and his colleagues in 1983 developed a theoretical energy-balance model with a geographical distribution of land and ocean. Testing the model to see how well it reproduced the observed annual cycle of temperatures revealed satisfactory agreement, so North et al. subjected their model to other cyclic solar forcings. Figure 5.1 shows a 10-year cycle imposed on the Earth. Climatologists were not too surprised by the conclusions, as the solar-irradiance and temperature changes are nearly in phase because Earth’s time constant (about 3–5 years) is less than the imposed cycle time. The response over the land is greater than that over the oceans because the land holds less heat than water does and responds more strongly. The amplitude of the temperature variations is very small, no larger than about 0.11 °C. The maximum response is also centered near Arabia. Not everyone agrees that Earth’s temperature response to solar cycle changes will follow the scenario shown in Figure 5.1. In the last chapter, we described a novel approach suggesting the possibility of a larger response to solar activity than North’s and similar models provide. Kim in 1994 argues that tropical ocean waters, about 30° north or south of the equator, are the center of response to solar variations, (personal communication).
The Role of NMR Spectroscopy in Understanding How Proteins Fold
Authors: Dobson C.M.
Published: November 2020

Proteins are synthesized within the cell on ribosomes. Although there is debate as to the beginnings of folding, it is clear that the major events in the folding process of a protein occur following departure from the ribosome. Folding may involve a series of auxiliary proteins, including molecular chaperones, and for extracellular proteins may occur in part following secretion from the cell itself (Ellis, 1994). Nevertheless, many proteins also fold efficiently and correctly in isolation, for example, following transfer from a denaturing medium to a medium in which the native state is thermodynamically stable (Anfinsen, 1973). It seems most unlikely, given the improbability that folding could occur in a finite time on a random search basis (Levinthal, 1968), that the principles behind the folding process differ fundamentally in the two situations (in vivo and in vitro). Studies of the molecular basis of protein folding are therefore appropriately initiated in vitro, where physical techniques capable of providing detailed structural information can be used most readily and where folding of molecules can be examined in isolation (Evans and Radford, 1994). It has long been recognized that NMR spectroscopy, with its ability to define protein structure and dynamics in solution, is ideally suited as a technique for studying the structural transitions that take place during folding. The rapidity of folding of small proteins under most conditions, however, has until recently limited its direct application in ‘real time’ kinetic studies. Early applications of NMR in folding studies therefore included investigations of the equilibrium between folded and unfolded states, and a search for stable intermediate species (Jardetzky et al., 1972). This approach has in fact become very important in recent years with the discovery that a wide range of stable partially structured states can be generated under carefully chosen conditions, and with the development of heteronuclear NMR techniques that make possible their detailed characterisation (Dobson, 1994). The most famous of these partially folded states are known as ‘molten globules’, compact species with extensive secondary structure but Sacking persistent tertiary interactions; these are of particular interest as they appeal to be closely linked to intermediates observed in kinetic refolding experiments (Ptitsyn, 1995).
Multilevel Global Spectral Model
Authors: Krishnamurti T. N. , Bedi H. S. , Hardiker V. M.
Published: November 2020

Since the 1970s, the spectral method has become an increasingly popular technique for global numerical weather prediction. Global numerical models formulated using the spectral technique are used worldwide for both research and operational purposes. The success of the spectral technique can be attributed to the spectral transform technique developed independently by Eliasen et al. (1970) and Orszag (1970), and later refined by Bourke (1972). Prior to the introduction of the transform technique, the nonlinear terms were computed using a very tedious process called the interaction coefficients method. This method required large amounts of computer resources as well as enormous bookkeeping. The transform technique facilitates the computation of the nonlinear terms, as discussed later in Section 7.4. Furthermore, the Galerkin method discussed in Chapter 4 is widely used in most spectral models and provides us with alias-free computation of the nonlinear terms. The transform technique enables the current spectral models to be competitive in terms of computational overhead with respect to their grid-point counterparts. The transform technique is also well-suited for incorporating the terms dealing with physics in the prediction scheme. There are a number of advantages to using the spectral technique over the conventional grid-point method. However, we will not get into this discussion here. It should be noted that the model truncation limit specifies the scale of the shortest wavelength that can be resolved by the model. In the following section, we discuss the two most widely used truncations in a spectral model.
Uniqueness
Authors: Bethke Craig M.
Published: November 2020

A practical question that arises in quantitative modeling is whether the results of a modeling study are unique. In other words, is it possible to arrive at results that differ, at least slightly, from the original ones but nonetheless satisfy the governing equations and honor the input constraints? In the broadest sense, of course, no model is unique (see, for example, Oreskes et al., 1994). A geochemical modeler could conceptualize the problem differently, choose a different compilation of thermodynamic data, include more or fewer species and minerals in the calculation, or employ a different method of estimating activity coefficients. The modeler might allow a mineral to form at equilibrium with the fluid or require it to precipitate according to any of a number of published kinetic rate laws and rate constants, and so on. Since a model is a simplified version of reality that is useful as a tool (Chapter 2), it follows that there is no“correct” model, only a model that is most useful for a given purpose. A more precise question (Bethke, 1992) is the subject of this chapter: in geochemical modeling is there but a single root to the set of governing equations that honors a given set of input constraints? We might call such a property mathematical uniqueness, to differentiate it from the broader aspects of uniqueness. The property of mathematical uniqueness is important because once the software has discovered a root to a problem, the modeler may abandon any search for further solutions. There is no concern that the choice of a starting point for iteration has affected the answer. In the absence of a demonstration of uniqueness, on the other hand, the modeler cannot be completely certain that another solution, perhaps a more realistic or useful one, remains undiscovered. Geochemists, following early theoretical work in other fields, have long considered the multicomponent equilibrium problem (as defined in Chapter 3) to be mathematically unique. In fact, however, this assumption is not correct. Although relatively uncommon, there are examples of geochemical models in which more than one root of the governing equations satisfy the modeling constraints equally well. In this chapter, we consider the question of uniqueness and pose three simple problems in geochemical modeling that have nonunique solutions.
Stable Isotopes
Authors: Bethke Craig M.
Published: November 2020

Stable isotopes serve as naturally occurring tracers that can provide much information about how chemical reactions proceed in nature, such as which reactants are consumed and at what temperatures reactions occur. The stable isotopes of several of the lighter elements are sufficiently abundant and fractionate strongly enough to be of special usefulness. Foremost in importance are hydrogen, carbon, oxygen, and sulfur. The strong conceptual link between stable isotopes and chemical reaction makes it possible to integrate isotope fractionation into reaction modeling, allowing us to predict not only the mineralogical and chemical consequences of a reaction process, but also the isotopic compositions of the reaction products. By tracing the distribution of isotopes in our calculations, we can better test our reaction models against observation and perhaps better understand how isotopes fractionate in nature. Bowers and Taylor (1985) were the first to incorporate isotope fractionation into a reaction model. They used a modified version of EQ3/EQ6 (Wolery, 1979) to study the convection of hydrothermal fluids through the oceanic crust, along midocean ridges. Their calculation method is based on evaluating mass balance equations, as described in this chapter. As originally derived, however, the mass balance model has an important (and well acknowledged) limitation: implicit in its formulation is the assumption that fluid and minerals in the modeled system remain in isotopic equilibrium over the reaction path. This assumption is equivalent to assuming that isotope exchange between fluid and minerals occurs rapidly enough to maintain equilibrium compositions. We know, however, that isotope exchange in nature tends to be a slow process, especially at low temperature (e.g., O’Neil, 1987). This knowledge comes from experimental study (e.g., Cole and Ohmoto, 1986) as well as from the simple observation that, unless they have reacted together, groundwaters and minerals are seldom observed to be in isotopic equilibrium with each other. In fact, if exchange were a rapid process, it would be very difficult to interpret the origin of geologic materials from their isotopic compositions: the information would literally diffuse away. Lee and Bethke (1996) presented an alternative technique, also based on mass balance equations, in which the reaction modeler can segregate minerals from isotopic exchange. By segregating the minerals, the model traces the effects of the isotope fractionation that would result from dissolution and precipitation reactions alone.
Evaporation
Authors: Bethke Craig M.
Published: November 2020

The process of evaporation, including transpiration (evaporation from plants), returns to the atmosphere more than half of the water reaching the Earth’s land surface; thus, it plays an important role in controlling the chemistry of surface water and groundwater, especially in relatively arid climates. Geochemists study the evaporation process to understand the evolution of water in desert playas and lakes as well as the origins of evaporite deposits. They also investigate environmental aspects of evaporation (e.g., Appelo and Postma, 1993), such as its effects on the chemistry of rainfall and, in areas where crops are irrigated, the quality of groundwater and runoff. To model the chemical effects of evaporation, we construct a reaction path in which H2O is removed from a solution, thereby progressively concentrating the solutes. We also must account in the model for the exchange of gases such as CO2 and O2 between fluid and atmosphere. In this chapter we construct simulations of this sort, modeling the chemical evolution of water from saline alkaline lakes and the reactions that occur as seawater evaporates to desiccation. We choose as a first example the evaporation of spring water from the Sierra Nevada mountains of California and Nevada, USA, as modeled by Garrels and Mackenzie (1967). Their hand calculation, the first reaction path traced in geochemistry (see Chapter 1), provided the inspiration for Helgeson’s (1968 and later) development of computerized methods for reaction modeling. Garrels and Mackenzie wanted to test whether simple evaporation of groundwater discharging from the mountains, which is the product of the reaction of rainwater and CO2 with igneous rocks, could produce the water compositions found in the saline alkaline lakes of the adjacent California desert. They began with the mean of analyses of perennial springs from the Sierra Nevada (Table 18.1). The springs are Na-Ca-HCO3 waters, rich in dissolved silica.
Kinetic Reaction Paths
Authors: Bethke Craig M.
Published: November 2020

In calculating most of the reaction paths in this book, we have measured reaction progress with respect to the dimensionless variable ξ. We showed in Chapter 14, however, that by incorporating kinetic rate laws into a reaction model, we can trace reaction paths using time as the reaction coordinate. In this chapter we construct a variety of kinetic reaction paths to explore how this class of models behaves. Our calculations in each case are based on kinetic rate laws determined by laboratory experiment. In considering the calculation results, therefore, it is important to keep in mind the uncertainties entailed in applying laboratory measurements to model reaction processes in nature, as discussed in detail in Section 14.2. In Chapter 14 we considered how quickly quartz dissolves into water at 100°C, using a kinetic rate law determined by Rimstidt and Barnes (1980). In this section we take up the reaction of silica (SiO2) minerals in more detail, this time working at 25°C. We use kinetic data for quartz and cristobalite from the same study, as shown in Table 20.1.
Acid Drainage
Authors: Bethke Craig M.
Published: November 2020

Acid drainage is a persistent environmental problem in many mineralized areas. The problem is especially pronounced in areas that host or have hosted mining activity (e.g., Lind and Hem, 1993), but it also occurs naturally in unmined areas. The acid drainage results from the weathering of sulfide minerals that oxidize to produce hydrogen ions and contribute dissolved metals to solution. These acidic waters are toxic to plant and animal life, including fish and aquatic insects. Streams affected by acid drainage may be rendered nearly lifeless, their stream beds coated with unsightly yellow and red precipitates of oxy-hydroxide minerals. In some cases, the heavy metals in acid drainage threaten water supplies and irrigation projects. Where acid drainage is well developed and extensive, the costs of remediation can be high. In the Summitville, Colorado district (USA), for example, efforts to limit the contamination of fertile irrigated farmlands in the nearby San Luis Valley and protect aquatic life in the Alamosa River will cost an estimated $100 million or more (Plumlee, 1994a). Not all mine drainage, however, is acidic or rich in dissolved metals (e.g., Ficklin et al., 1992; Mayo et al., 1992; Plumlee et al., 1992). Drainage from mining districts in the Colorado Mineral Belt ranges in pH from 1.7 to greater than 8 and contains total metal concentrations ranging from as low as about 0.1 mg/kg to more than 1000 mg/kg. The primary controls on drainage pH and metal content seem to be (1) the exposure of sulfide minerals to weathering, (2) the availability of atmospheric oxygen, and (3) the ability of nonsulfide minerals to buffer acidity. In this chapter we construct geochemical models to consider how the availability of oxygen and the buffering of host rocks affect the pH and composition of acid drainage. We then look at processes that can attenuate the dissolved metal content of drainage waters. Acid drainage results from the reaction of sulfide minerals with oxygen in the presence of water. As we show in this section, water in the absence of a supply of oxygen gas becomes saturated with respect to a sulfide mineral after only a small amount of the mineral has dissolved.
Experiments in Environment Integration
Authors: Brown Alan W. , Carney David J. , Morris Edwin J. , Smith Dennis B. , Zarrella Paul F.
Published: November 2020

In assembling a CASE environment from a collection of commercial off-theshelf (COTS) tools, tool users must find ways to connect the tools such that they provide adequate support for their particular software development approach. This task takes place in the context of limited knowledge of the tools, limited access to the source or internal structures of the tools, limited resources with which to perform and maintain the tool connections, and evolving understanding of the needs of the tool users. This places severe restrictions on what can be attempted in terms of tool interconnection. Environment framework technologies (e.g., ECMA PCTE, ATIS, BMS, ToolTalk, or CORBA) claim to provide a set of common integration services that aid in the tool integration process. There have been numerous discussions about the value, maturity, and complexity of these framework technologies. Such discussions are characterized by three points: general agreement that framework technology per se is a valuable goal to pursue; moderate disagreement as to whether the current level of framework technology is a sufficient basis for production quality CASE environments; and considerable disagreement about which of the current technologies are the most likely to mature and succeed. Notable about these discussions, however, is that there has not been extensive use of the technologies in question. This stems from several sources: their expense, their unfamiliarity and complexity to current tool users, and a widespread concern about their immaturity. This lack of use is perhaps understandable, but it has had the additional effect that partisans of one or another technology have made assertions based on little factual information about the relative merits of the technology in question. To expand our own expertise in tool integration and framework technologies, and to answer the question, “What tool integrations are possible for third-party tool users given the current state of COTS tools and integration technology?” we performed a set of experiments involving the integration of a collection of common COTS tools with environment framework technologies in support of a typical development scenario. Our selection of these tools and technologies was based on common availability and application to the development scenario(s) of interest.
Birds
Authors: Young Bruce E. , McDonald David B.
Published: November 2020

Birds have been a major focus of study in Monteverde. The first biologists to study in Monteverde were ornithologists William Buskirk and George Powell, who arrived in 1970 on the recommendation of F. Gary Stiles. They were attracted by the low stature of the cloud forest, which made research on mixed-species flocks more tractable than in tall lowland forests. The number of publications since then (110 as of 1996) and the number of different first authors of those publications (31) attest to the extent to which Monteverde birds have been studied. Sixteen Ph.D. students have written dissertations based largely on data collected on the birds of Monteverde. In comparison, other well-known tropical study sites such as La Selva in Costa Rica or Manú in Peru have supported less graduate work on birds (five and four dissertations, respectively). Two major strengths of the Monteverde bird research are autecological studies and birdplant interaction studies. Although autecological studies may be declining because of changing scientific fashion (Levey and Stiles 1994), studies on single species or small groups of species have abounded at Monteverde. We know much about certain species but have little information about the bird community as a whole. Most studies of avian community ecology in Monteverde have been in the context of interactions with plants. Monteverde’s avifauna is attractive to ornithologists for five reasons: (1) Unusual behaviors: From the perspective of temperate ornithologists, many species of birds in Monteverde exhibit bizarre behaviors. For example, dual-male duets and dances by male Long-tailed Manakins are phenomena that are virtually unique in the animal kingdom (McDonald and Potts 1994; Fig. 6.1; see McDonald, “Cooperation Between Male Longtailed Manakins,”). Similarly, the March- July chorus of Three-wattled Bellbirds, heard for kilometers in every direction, draws attention to this species. Many who walk into a pasture in the dairy community have been mobbed by Brown Jays and wondered about their communal social behavior (Lawton and Guindon 1981, Lawton and Lawton 1985). These vocal species literally cry out to be studied.
An Introduction to Nonlinear Chemical Dynamics
Authors: Epstein Irving R. , Pojman John A.
Published: November 2020

Just a few decades ago, chemical oscillations were thought to be exotic reactions of only theoretical interest. Now known to govern an array of physical and biological processes, including the regulation of the heart, these oscillations are being studied by a diverse group across the sciences. This book is the first introduction to nonlinear chemical dynamics written specifically for chemists. It covers oscillating reactions, chaos, and chemical pattern formation, and includes numerous practical suggestions on reactor design, data analysis, and computer simulations. Assuming only an undergraduate knowledge of chemistry, the book is an ideal starting point for research in the field. The book begins with a brief history of nonlinear chemical dynamics and a review of the basic mathematics and chemistry. The authors then provide an extensive overview of nonlinear dynamics, starting with the flow reactor and moving on to a detailed discussion of chemical oscillators. Throughout the authors emphasize the chemical mechanistic basis for self-organization. The overview is followed by a series of chapters on more advanced topics, including complex oscillations, biological systems, polymers, interactions between fields and waves, and Turing patterns. Underscoring the hands-on nature of the material, the book concludes with a series of classroom-tested demonstrations and experiments appropriate for an undergraduate laboratory.
Fundamentals
Authors: Epstein Irving R. , Pojman John A.
Published: November 2020

Before plunging into the meat of our discussions, we will review some basic but necessary ideas. Much of this material will be familiar to many readers, and we encourage you to move quickly through it or to skip it completely if appropriate. If you have not encountered these concepts before, you will find it worthwhile to invest some time here and perhaps to take a look at some of the more detailed references that we shall mention. We begin with a review of chemical kinetics. We then consider how to determine the stability of steady states in an open system using analytical and graphical techniques. Finally, we look at some of the methods used to represent data in nonlinear dynamics. The problems that we are interested in involve the rates of chemical reactions, the study of which forms the basis of chemical kinetics. This is a rich and beautiful subject, worthy of whole volumes. For those interested in a less superficial view than we have room to present here, we recommend several excellent texts on kinetics (Jordan, 1979; Cox, 1994; Espenson, 1995). We review here a minimal set of fundamentals necessary for what comes later.
Synthesis of Chemical Oscillations
Authors: Epstein Irving R. , Pojman John A.
Published: November 2020

There is no doubt that the phenomenon of chemical oscillation—the periodic or nearly periodic temporal variation of concentrations in a reacting system— provided the initial impetus for the development of nonlinear chemical dynamics, and has continued to be the most thoroughly studied of the phenomena that constitute this rich field. In our opening chapter, we alluded to the early skepticism that experimental observations of chemical oscillation engendered. We also noted that the first chemical oscillators were discovered accidentally, by researchers looking for other phenomena. It is relatively easy to understand intuitively why a typical physical oscillator, like a spring, should behave in a periodic fashion. It is considerably more difficult for most of us to see how a chemical reaction might undergo oscillation. As a result, the thought of building a physical oscillator seems far more reasonable than the notion of designing an oscillatory chemical reaction. In this chapter, we will examine how chemical oscillation can arise, in general, and how it is possible to create chemical reactions that are likely to show oscillatory behavior. In the next chapter, we will discuss how to take a chemical oscillator apart and analyze why it oscillates—the question of mechanism. We also look in detail there at the mechanisms of several oscillating reactions. In order to gain some insight into how oscillation might arise in a chemical system, we shall consider a very simple and general model for a reaction involving two concentrations, u and v. Two independent concentration variables is the smallest number that can generate oscillatory behavior in a chemical system. The basic idea, however, is applicable to many-variable systems, because the essential features of the dynamics are often controlled by a small number of variables, and the other variables simply follow the behavior of the key species.
Liquid-Liquid and Solid-Liquid Reactions
Authors: Doraiswamy L. K.
Published: November 2020

Chapter 14 was concerned with gas-liquid reactions, although it was mentioned at the beginning of the chapter that the same principles would apply equally if phase 1 were a liquid or a solid. The premise for such a statement was that phase 1 comes into the picture only to the extent that it supplies the solute A that diffuses into phase 2 and reacts with B in the film, bulk, or both, in that phase only. Because the state of phase 1 is immaterial in such a situation, the theories are equally applicable when the phase is a liquid or a solid. However, an additional factor comes into play when phase 1 is also a liquid. Component B from phase 2 can have a finite solubility in phase 1, diffuse into that phase and react there with A. Thus reaction can occur in both phases. This is equally true when phase 1 is a solid, but the mechanism of diffusion and reaction in a solid is different. It is also possible for a gas and a solid to simultaneously dissolve and react in a liquid, but as three phases are involved here, it is considered in Chapter 17. In this chapter we consider the following two classes of reactions: liquid-liquid and solid-liquid. One encounters reactions belonging to these classes quite frequently in organic chemical technology. We shall give instances of these while dealing with the individual systems. Hydrolysis and saponification of esters and fats (Jeffreys et al., 1961; Donders et al., 1968; Sharma and Nanda, 1968), sulfonation and nitration of aromatic compounds (Albright and Hanson, 1969, 1975; Hanson and Ismail, 1976; Barona and Prengle, 1973), alkylation of isobutane, toluene, and phenols with isobutylene (Jernigan et al., 1965; Mosby and Albright, 1966; Sprow, 1969; Tiwari and Sharma, 1977; Zaldivar et al., 1996), and oximation of cycloyhexanone (Rod, 1974, 1976) are some of the liquid-liquid reactions in which reaction occurs in both phases. The reaction last mentioned between cyclohexanone (which constitutes the organic phase) and aqueous hydroxylamine sulfate (containing ammonium sulfate) to give cyclohexanone oxime comprises the first step in the manufacture of caprolactam, an important reactant in the synthesis of Nylon.
Gas-Liquid and Liquid-Liquid Reactor Design
Authors: Doraiswamy L. K.
Published: November 2020

The design equation for any reactor expresses its output as a function of the input. For a gas-liquid reactor, the output may be expressed as [Output] = f [input] In Chapter 14, we formulated a number of regimes with corresponding conditions and governing rate equations. In the present chapter, we recast the rate equations in a general form that indicates the relative roles of reaction, liquid film diffusion, and gas film diffusion. Then we briefly discuss the design principles of the more common classes of fluid-fluid reactors. Detailed treatments of design may be found in the books of Astarita (1967), Danckwerts (1970), Shah (1979), Levenspiel (1972, 1993), Doraiswamy and Sharma (1984b), Bisio et al. (1985), and Kastanek et al. (1993).
Microphase-Assisted Reaction Engineering
Authors: Doraiswamy L. K.
Published: November 2020

A relatively recent concept in organic reaction engineering is the use of submicron particles to enhance the rate of a reaction. These are usually microparticles of solids, but can also be microdroplets of liquids, or even microbubbles of gases. They can be external agents, participating reactants, or precipitating solids. In this chapter, we cover the role of small particles as a whole, which may be regarded as constituting an additional colloid-like phase normally referred to as the microphase. We begin by classifying the microphase in terms of its mode of action and then proceed to an analysis of the following categories of importance in organic technology: microslurry of (1) catalyst or adsorbing particles in a reactive mixture; (2) solid reactant particles in a continuous phase of the second reactant; and (3) solid particles precipitating from reaction between two dissolved reactants, one of which can be a solid dissolving and reacting simultaneously with the other reactant. The microphase in the first case is externally added, whereas that in the last two cases is a reactant or a product. The field is still developing (with many unproven theories), and hence we restrict the treatment to a simple analysis of selected situations based on reasonable assumptions (thus avoiding often unjustified complexity). A microphase can be described as an assemblage of very small dispersed phase particles with average size (dp) much less than the diffusional length scale of the solute. Usually dp < l0μm, compared to the diffusional length scale which is of the order of 50-60 μm. Although the microphase is a distinct phase, the phase in which it is present is commonly regarded as pseudohomogeneous. In a stricter sense, however, it should be regarded as a microheterogeneous phase. Indeed, several studies have been reported on modeling heterogeneous microphase systems (Holstvoogd et al., 1986, 1988; Yagi and Hikita, 1987). In view of the ability of the particles of such a system, pseudohomogeneous or pseudoheterogeneous, to get inside the fluid film, they can enhance the transport rate of the solute through the film. Experimental observations in typical gas-liquid and slurry systems have clearly demonstrated (see Ramachandran and Sharma, 1969; Uchida et al., 1975; Sada et al., 1977a,b, 1980; Alper et al., 1980; Pal et al., 1982; Bruining et al., 1986; Bhaskarwar et al., 1986; Bhagwat et al., 1987; Mehra et al., 1988; Mehra and Sharma, 1988a; Hagenson et al., 1994) the enhancing role of a microphase made up of fine particles. The case of a second liquid phase acting as a microphase or of a solid product performing a similar function has also been studied and found to enhance the reaction rate (Janakiraman and Sharma, 1985; Mehra and Sharma, 1985, 1988b; Anderson et al., 1998). Mehra et al. (1988) and Mehra (1990a,b, 1996) presented a detailed account of the role of different types of microphases in rate enhancement. In all these cases, either a microphase is separately introduced or one of the reactants or products acts as a microphase.
High-Pressure NMR Studies of the Dissociation of Arc Represser and the Cold Denaturation of Ribonuclease A
Authors: Peng Xiangdong , Silva Jerson L.
Published: November 2020

We begin this article with a brief discussion of the specialized high-resolution NMR instrumentation developed for high-pressure studies of biochemical systems. We then present the potential for the unique information content of high-pressure NMR spectroscopy as illustrated by the results of two NMR studies performed recently in our laboratory. Different denatured states of Arc represser are characterized by one-dimensional (1D) and two-dimensional (2D) NMR. Increasing pressure promotes sequential changes in the structure of Arc represser: from the native dimer through a predissociated state to a denaturated molten globule monomer. A compact state (molten globule) of Arc represser is obtained in the dissociation of Arc represser by pressure, whereas high temperature and urea induce dissociation and unfolding to less structured conformations. The presence of NOEs (Nuclear Overhauser Enhancement) in the β-sheet region in the dissociated state suggests that the intersubunit β-sheet (residues 6–14) in the native dimer is replaced by an intramonomer β-sheet. Changes in 2D NMR spectra prior to dissociation indicate the existence of a predissociated state that may represent an intermediate stage in the folding and subunit association pathway of Arc represser. The cold denaturation study of ribonuclease A has shown that high pressure can be utilized not only to perturb the protein structure in a controlled way but also to lower the freezing point of aqueous protein solutions substantially. As a result, one can access subzero temperatures and carry out cold denaturation studies of proteins. The results of the NMR study of the reversible cold denaturation are compared with the heat and pressure denaturation of bovine pancreatic ribonuclease A. High-resolution NMR spectra of complex molecules in the liquid phase usually exhibit a great deal of structure and yield a wealth of information about the molecule. Therefore, it is not surprising that multinuclear high-resolution Fourier transform NMR spectroscopy at high pressure represents the most promising technique in studies of the pressure effects on biochemical systems (Jonas & Jonas, 1994). The high information content of the various advanced NMR techniques, including 2D NMR techniques such as NOESY, COSY, and ROESY, have yet to be fully exploited in high-pressure NMR experiments.
Exploring Structural, Functional, and Kinetic Aspects of Nucleic Acid–Protein Complexes with Pressure: Nucleosomes and RNA Polymerase
Authors: Villas-Boas Mauro , De Rezende Ana Sepulveda
Published: November 2020

High pressure has provided us with new insights into two complex DNA-protein systems: nucleosomes and RNA polymerase. In spite of their complexity, we can derive new and useful information about them by coupling high pressure with a variety of other physical techniques and functional assays. These studies have shown clearly that multiple conformations of these large–molecular weight DNA-protein assemblies are present simultaneously in solution, although both molecular assemblies are generally considered to be single structures in most in vitro experiments. Considering the variety of different cellular situations encountered by nucleosomes and RNA polymerases, it is perhaps to be expected that evolution would select structures with flexible and multifarious conformations that possesses sufficient stability, rather than static, rigid, singular, and highly stable structures. The molecular organization in the nucleus of a biological cell is extensive and involves intricate protein-protein and protein–nucleic acid interactions that are changing continually during the cell cycle. These dynamic activities in the nucleus are tightly coordinated with many extranuclear events throughout the cell. Highly organized molecular complexes involving multisubunit proteins (and higher order protein assemblies) interacting with the nucleic acid components are the rule rather than the exception in the nucleus (Alberts et al., 1983; Darnell et al., 1990; Lewin, 1994). For instance, chromosomes are organized in a structural hierarchy culminating in the metaphase state in which they are packed tightly together with proteins in a highly specific and economical manner that still largely eludes our understanding; the DNA of a eukaryotic cell is replicated with the help of a complex assembly of proteins; and information coded within the DNA sequence is transcribed with the assistance of multisubunit DNA-binding proteins, some acting as enzymes and others serving mainly as organizational and structural assistants to the catalytic process. Many important features of protein-nucleic acid (DNA and RNA) interactions have been elucidated in the last decade (Pabo & Sauer, 1992; Steitz, 1990), and exciting results have been obtained for singleprotein molecules and dimers binding to DNA. Although we are a long way from understanding these interactions completely, enough aspects are known so that structural predictions are sometimes possible simply from the amino acid sequence.
NMR Studies of the Order and Dynamics of Dipalmitoylphosphatidylchoiine Bilayers as a Function of Pressure
Authors: Jonas Ana , Peng Xiangdong
Published: November 2020

We have used 2H NMR methods to examine the order and dynamics of dipalmitoylphosphatidylcholine (DPPC) in multilamellar and small unilamellar vesicles in water as a function of pressure. Multipulse 2H NMR techniques were used with selectively deuterated DPPC on both chains at positions C-2, C-9, or C-13, to obtain lineshapes, spin-lattice relaxation times (T1), and spin-spin relaxation times (T2) at 50 °C from 1 bar to 5.2 kbar pressure. This pressure range allowed us to explore the phase behavior of DPPC from the liquid crystalline (LC) phase through various gel phases (Gl, Gll, Glll, GX), including the interdigited Gi phase. Pressure has an ordering effect: on all chain segments in all the phases. In the LC phase, the order parameter (SCD) decreases from C-2 > C-9 > C-13, while in the gel phases SCD decreases from C-9 > C-13 > C-2, indicating that in the gel phases the middle segments of the chains are more restricted in their motions than the ends. In the LC phase, T1 and T2 values for all segments decrease with pressure and have an order from C-13 > C-9 > C-2. These results suggest that similar conformational motions and molecular rotational motions occur in the LC state in all segments, but have increased amplitudes and frequencies toward the methyl ends. At the phase transitions, discontinuities and abrupt reversal of the slopes for the T1 or T2 dependences on pressure indicate major changes in motional modes and rates for DPPC molecules in the different structures. In the second part of this study, we have measured the lateral diffusion of DPPC in sonicated vesicles in D2O as a function of pressure. The spin-lattice relaxation rate in the rotating frame T−11p was plotted as a function of the square root of the spin-locking field angular frequency (ω1)1/2, and the lateral diffusion coefficient (D) was calculated from the slope. Pressure effects are observed on lateral diffusion in the LC phase (D = 5.4 − 2 × 10−9 cm2 seconds, from 1 to 300 bar) but are negligible in the GI phase (D ≈ 1.0 × 10−9 cm2 seconds, from 400 to 800 bar).
A Home and School Community
Authors: Pendell Ann Chalmers
Published: November 2020

I put my first child in the OC because I wanted to be part of her school life. When my husband and I chose to adopt her, it was because we wanted the experience of raising her. We didn’t want to shuttle her off to a day care or school for someone else to raise. When Alysha was old enough to attend preschool, I found a parent co-op, and when she was old enough to attend elementary school, I heard about the OC and was glad to be able to continue participating in her education. The OC community became important not only as a support in educating our children but also as a community of families with similar goals—helping our children to get the best education we can provide. Other committed parents provide activities for our kids that the teacher and my husband and I cannot. David and I are both artists and can provide techniques and insights for their creative efforts, but we also want them to be able to work with adults who are dedicated to and enthusiastic about math, science, history, ecology, and other aspects of today’s world. The community extends beyond educating our children at school. For 10 years, our family has gone on OC class camping trips sponsored and planned by parents, exploring places we might have never seen on our own. With our children’s classmates and their families we have hiked, shared food, and shared good experiences and bad, warm and cold, the joy of discovery and of watching our children grow. We have learned about children and how they learn and about how to work with other adults. We have developed deep friendships with other families in our children’s classes and have memories and photo albums full of good family experiences that include our OC community. The children’s learning is enhanced by the caring evident in the OC community. For example, the community supports its members in times of family crisis by providing emotional support and practical support—bringing meals, providing child care, and helping with carpools and other responsibilities.
Learning to Manage Time
Authors: Magarian David
Published: November 2020

One of the most important things I learned at the OC was how to manage my time. I learned this by making my own assignments that I needed to keep up with by myself. In the OC, kids don’t have to do their work every day at a certain time. They learn to keep track of their progress toward deadlines that the teachers help them set. For example, when I worked on math, I would have maybe two weeks to turn in the same amount that I do in my new school (in another state) in two weeks. But I didn’t have to stay on somebody else’s schedule; I chose the time to do it within the two weeks. When I got frustrated with my work or just tired of it, I could take a break, go get a snack, or play a game and then come back to it. After a little bit I always got back into it. To set deadlines, kids get together with the teacher to make a plan for how much should be done by the end of a certain time. The teachers help plan the schedule, but they’re doing it in a suggestive way that still helps kids learn how to manage their own time; it’s not just the teacher’s decision. If a teacher would plan the schedule, kids wouldn’t learn how to manage their own time—they would just do it when they are told. If kids plan to do too much, the teachers suggest doing less, because the deadline needs to be one the kid can meet. When kids set their own deadlines, they feel committed to them because they planned them. Often a teacher helped me when I had trouble getting started on hard activities by asking what I still needed to do and talking with me about how to get going. Once I got going on the activity, even if a co-oper said, “You’ve put in your time, you can go on to something else if you’d like,” usually I would just keep going on it because by that time I would have gotten into it, like a good book that I don’t want to put down.
Teaching by Learning from Children
Authors: Randell Carol
Published: November 2020

In a learning community, a teacher learns a great deal from students about how to chart the direction of the curriculum. Observing the strategies the students are using and listening to what they are saying provides a way to learn from their thinking, which is essential for a teacher to be able to help students make connections and build on prior knowledge. Learning from the students is also essential for teachers to build the framework of their own ideas about what is likely to work with a new group of students. Over the years of teaching, I learn from each group of students how to keep their learning moving in a productive direction. I am guided in thinking about how each new group of children is likely to build their concepts and how I can best aid them by my learning from previous students and my reflections on my own previous strategies for trying to help them. All the talking that we do in the classroom helps me learn about the children’s ideas and make my next decision about how to help lead the process down a productive path. I get a window into what the children are thinking when they explain things to me and each other, and with what I have learned from previous groups, this knowledge helps me know where they’re going and what they need to do next. An example of building instruction by observing and learning from children’s strategies occurred in a second-grade math lesson where the class was trying to determine how many “pogs” (decorative cardboard game pieces) had been purchased by the cafeteria to give away at lunch. We had salvaged from the garbage the 70 punch-out cards that the pogs had come in. Background knowledge that I brought to the situation (in large part from my learning from previous students) was that our problem could be solved in a variety of ways: simple counting, repeated addition, multiplication, using counting tallies, combining groups, or using a calculator. My goal and sometimes challenge is to allow the students to try various approaches and determine which works best at their skill level.
Scattering of X-rays and Neutrons
Authors: Coppens Philip
Published: November 2020

This chapter starts with a discussion of the classical treatment of X-ray scattering, followed by a brief overview of the quantum-mechanical theory in the first Born approximation. The scattering of a periodic arrangement is derived by considering the crystal as a convolution of the unit cell contents and a periodic lattice. The atomic description of the charge density, which is the basis for structure analysis, is introduced. The origin of resonance anomalous scattering is discussed. While its effect must be accounted for before charge densities can be derived from the X-ray scattering amplitudes, resonance scattering itself can give invaluable information on the electronic states of the resonating atoms. The final section of this chapter deals with the scattering of neutrons by atomic nuclei. Nuclear neutron scattering is independent of the distribution of the electrons, and can provide atomic positions and thermal amplitudes unbiased by the bonding effects which are the subject of this book. In the classical theory of scattering (Cohen-Tannoudji et al. 1977, James 1982), atoms are considered to scatter as dipole oscillators with definite natural frequencies. They undergo harmonic vibrations in the electromagnetic field, and emit radiation as a result of the oscillations.