bluuebunny/crossref_metadata_2025 huggingface dataset:
Design of Novel Hemoglobins
Authors: Ho C. , Kim H.-W.
Published: November 2020

Human normal adult hemoglobin (Hb) A, the oxygen carrier of blood, is a tetrameric protein consisting of two α chains of 141 amino acid residues each and two β chains of 146 amino acid residues each. Each Hb chain contains a heme group which is an iron complex of protoporphyrin IX. Under physiological conditions, the heme-iron atoms of Hb remain in the ferrous state. In the absence of oxygen, the four heme-irom atoms in Hb A are in the highspin ferrous state [Fe(II)] with four unpaired electrons each. Each of the four heme-iron atoms in Hb A can combine with an O2 molecule to give oxyhemoglobin (HbO2) in which the iron atom is in a low-spin, diamagnetic ferrous state. The oxygen binding of Hb exhibits sigmoidal behavior, with an overall association constant expression giving a greater than first-power dependence on the concentration of O2. Thus, the oxygenation of Hb is a cooperative process, such that when one O2 is bound, succeeding O2 molecules are bound more readily. Hb is an allosteric protein, i.e., its functional properties are regulated by a number of metabolites [such as hydrogen ions, chloride, carbon dioxide, 2,3-diphosphoglycerate (2,3-DPG)] other than its ligand, O2. It has been used as a model for allosteric proteins, and indeed, hemoglobins of vertebrates are among the most extensively studied allosteric proteins. Their allosteric properties are physiologically important in optimizing O2 transport by erythrocytes. The large number of mutant forms of Hb available provides an array of structural alterations with which to correlate effects on function. For details, see DickersonandGeis (1983), Bunnand Forget (1986), Ho (1992), Ho and Perussi (1994). There are two types of contacts between the α and β subunits of Hb (Perutz, 1970; Dickerson and Geis, 1983). The α1β1 (or α2 β2) contacts, involving B, G, and H helices, and GH corners, are called packing contacts. These contacts remain unchanged and hold the dimer together even when there is a change in the ligation state of the heme.
An Introduction to Finite Differencing
Authors: Krishnamurti T. N. , Bedi H. S. , Hardiker V. M.
Published: November 2020

This chapter on finite differencing appears oddly placed in the early part of a text on spectral modeling. Finite differences are still traditionally used for vertical differencing and for time differencing. Therefore, we feel that an introduction to finite-differencing methods is quite useful. Furthermore, the student reading this chapter has the opportunity to compare these methods with the spectral method which will be developed in later chapters. One may use Taylor’s expansion of a given function about a single point to approximate the derivative(s) at that point. Derivatives in the equation involving a function are replaced by finite difference approximations. The values of the function are known at discrete points in both space and time. The resulting equation is then solved algebraically with appropriate restrictions. Suppose u is a function of x possessing derivatives of all orders in the interval (x — n∆x, x + n∆x). Then we can obtain the values of u at points x ± n∆ x, where n is any integer, in terms of the value of the function and its derivatives at point x, that is, u(x) and its higher derivatives.
Modeling Overview
Authors: Bethke Craig M.
Published: November 2020

A model is a simplified version of reality that is useful as a tool. A successful model strikes a balance between realism and practicality. Properly constructed, a model is neither so simplified that it is unrealistic nor so detailed that it cannot be readily evaluated and applied to the problem of interest. Geologic maps constitute a familiar class of models. To map a sedimentary section, a geologist collects data at certain outcrops. He casts his observations in terms of the local stratigraphy, which is itself a model that simplifies reality by allowing groups of sediments to be lumped together into formations. He then interpolates among his data points (and projects beneath them) to infer positions for formation contacts, faults, and so on across his field area. The final map is detailed enough to show the general arrangement of formations and major structures, but simplified enough, when drawn to scale, that small details do not obscure the overall picture. The map, despite its simplicity, is without argument a useful tool for understanding the area's geology. To be successful, a geochemical model should also portray the important features of the problem of interest without necessarily attempting to reproduce each chemical or mineralogical detail. The first and most critical step in developing a geochemical model is conceptualizing the system or process of interest in a useful manner. By system, we simply mean the portion of the universe that we decide is relevant. The composition of a closed system is fixed, but mass can enter and leave an open system. A system has an extent, which the modeler defines when he sets the amounts of fluid and mineral considered in the calculation. A system's extent might be a droplet of rainfall, the groundwater and sediments contained in a unit volume of an aquifer, or the world's oceans. The “art” of geochemical modeling is conceptualizing the model in a useful way. Figure 2.1 shows schematically the basis for constructing a geochemical model. The heart of the model is the equilibrium system, which remains in some form of chemical equilibrium, as described below, throughout the calculation.
Automatic Reaction Balancing
Authors: Bethke Craig M.
Published: November 2020

Conveniently, perhaps even miraculously, the equations developed in Chapter 4 to accomplish basis swaps can be used to balance chemical reactions automatically. Once the equations have been coded into a computer program, there is no need to balance reactions, compute equilibrium constants, or even determine equilibrium equations by hand. Instead, these procedures can be performed quickly and reliably on a small computer. To balance a reaction, we first choose a species to appear on the reaction’ s left side, and express that species’ composition in terms of a basis B. The basis might be a list of the elements in the species’ stoichiometry, or an arbitrary list of species that combine to form the left-side species. Then we form a second basis B´ composed of species that we want to appear on the reaction’ s right side. To balance the reaction, we calculate the transformation matrix relating basis B´ to B, following the procedures in Chapter 4. The transformation matrix, in turn, gives the balanced reaction and its equilibrium constant. Two methods of balancing reactions are of interest. We can balance reactions in terms of the stoichiometries of the species considered. In this case, the existing basis B is a list of elements and, if charged species are involved, the electron e–. Alternatively, we may use a dataset of balanced reactions, such as the LLNL database. Basis B, in this case, is the one used in the database to write reactions. We will consider each possibility in turn. A straightforward way to balance reactions is to use as the initial basis the stoichiometries of the species involved. If the species’ free energies of formation are known, the reaction’ s equilibrium constant can be determined as well. In the stoichiometric approach, basis B is the list of elements that will appear in the reaction, plus the electron if needed. We write swap reactions and calculate a transformation matrix as described in Section 3.1. The equations in Sections 3.2 and 3.3 give the balanced reaction and associated equilibrium constant.
Hydrothermal Fluids
Authors: Bethke Craig M.
Published: November 2020

Hydrothermal fluids, hot groundwaters that circulate within the Earth’s crust, play central roles in many geological processes, including the genesis of a broad variety of ore deposits, the chemical alteration of rocks and sediments, and the origin of hot springs and geothermal fields. Many studies have been devoted to modeling how hydrothermal fluids react chemically as they encounter wall rocks, cool, boil, and mix with other fluids. Such modeling proliferated in part because hydrothermal fluids are highly reactive and because the reaction products are commonly well preserved, readily studied, and likely to be of economic interest. Further impetus was provided by the development of reliable modeling software in the 1970s, a period of concern over the availability of strategic and critical minerals and of heightened interest in economic geology and the exploitation of geothermal energy. As a result, many of the earliest and most imaginative applications of geochemical modeling, beginning with Helgeson’s (1970) simulation of ore deposition in hydrothermal veins and the alteration of nearby country rock, have addressed the reaction of hydrothermal fluids. For example, Reed (1977) considered the origin of a precious metal district; Garven and Freeze (1984), Sverjensky (1984, 1987), and Anderson and Garven (1987) studied the role of sedimentary brines in forming Mississippi Valley-type and other ore deposits; Wolery (1978), Janecky and Seyfried (1984), Bowers et al. (1985), and Janecky and Shanks (1988) simulated hydrothermal interactions along the midocean ridges; and Drummond and Ohmoto (1985) and Spycher and Reed (1988) modeled how fluid boiling is related to ore deposition. In this chapter, we develop geochemical models of two hydrothermal processes: the formation of fluorite veins in the Albigeois ore district and the origin of “black smokers, ” a name given to hydrothermal vents found along the ocean floor at midocean ridges. As a first case study, we borrow from the modeling work of Rowan (1991), who considered the origin of fluorite (CaF2) veins in the Albigeois district of the southwest Massif Central, France. Production and reserves for the district as a whole total about 7 million metric tons, making it comparable to the more famous deposits of southern Illinois and western Kentucky, USA.
Toward a Better Understanding of Integration
Authors: Brown Alan W. , Carney David J. , Morris Edwin J. , Smith Dennis B. , Zarrella Paul F.
Published: November 2020

The need to provide better automated support for software engineering activities has led people to concentrate attention on the problems of integrating the many different components that can be found in a typical CASE environment. In the previous chapter we reviewed some of the work that has taken place to try to provide a greater shared understanding of the meaning of integration, and to build integrated CASE environments. We have synthesized some of the best aspects of this previous work to develop a model that helps to provide a more comprehensive view of integration, and can be readily applied to different environment needs. The model attempts to provide a set of concepts for understanding a range of integration issues, a vocabulary that can be used to clearly separate different integration aspects, and an organizing framework that helps to relate many of the important issues in CASE tool integration. An attraction of our model of integration is that it also can be used as the basis of a CASE environment architecture in which the integration characteristics of the environment are defined, understood, and amenable to change. In this chapter we describe this model in detail, discuss how it can help in considering the design and construction of a CASE environment, and analyze the kinds of CASE environments that will result from realizing implementations of this model. The previous chapter highlighted a number of shortcomings with previous conceptual models of integration in a CASE environment. The discussion pointed to the need for a better understanding of the issues involved in designing, constructing, and using an integrated software development environment, regardless of the available technology. Here we propose a new conceptual model for understanding integration in a CASE environment that we believe can be used to improve our understanding in this area. In this model we distinguish three levels at which we are concerned with the integration of a CASE environment. The central one consists of the services available to environment end-users. The second level consists of the mechanisms that implement the end-user services.
Data Integration Mechanisms
Authors: Brown Alan W. , Carney David J. , Morris Edwin J. , Smith Dennis B. , Zarrella Paul F.
Published: November 2020

Data integration is a basic need for a CASE environment because individual tools operate on data that are of interest to other tools. For example, many CASE analysis and design tools produce code templates representing the interfaces between system components. These templates are of interest to tools that assist in code generation since they specify an interface between system components that ideally is maintained during the implementation process. Likewise, changes made to these interface descriptions during the implementation process often have an impact on the design of the system as reflected in the analysis and design tool. Many approaches have been developed to facilitate the sharing of data between components of a CASE environment. These approaches differ both in the mechanisms used to provide this support and in the degree of support provided. In this chapter we consider some concepts central to the problem of data integration, discuss the major strategies adopted to provide data integration, and analyze the strengths and weaknesses of these strategies. Finally, we discuss particular mechanisms that reflect these strategies. If environment components are to share data, then two issues must be addressed. First, agreements must be made between components concerning what data are stored, where, and how they are accessed. Second, the components must share a common understanding of the meaning of the data. We refer to the first issue as data persistence, and the second issue as data semantics. These two issues provide the backdrop for our discussion of the principal types of mechanisms for data integration. One type of mechanism focuses on different storage strategies, and the second type of mechanism focuses on semantic agreements. Although we consider each separately, no mechanism exclusively addresses only data persistence or data semantics. In practice, all mechanisms address both data persistence and data semantics to varying degrees. There are two basic strategies that support storage and sharing of persistent data. The first involves data import and export, whereby tools maintain separate databases for their unique data, and sharing is accomplished by some translation from an internal form to an external form to make it available to other tools.
Replacing the Message Service in a CASE Integration Framework
Authors: Brown Alan W. , Carney David J. , Morris Edwin J. , Smith Dennis B. , Zarrella Paul F.
Published: November 2020

In the experiment scenario described in the previous chapter, control integration was accomplished through inter-tool communication via messages. In this approach, tools interact by passing messages (through a message system) requesting services of each other and notifying each other of their actions. This eliminates the need to duplicate functionality among tools, and the need to coordinate and operate via a shared tool database. Many influential vendors have considered this approach as a basis for control integration in CASE environment applications. To this end, Hewlett-Packard, Sun Microsystems, IBM, Unix Systems Laboratories (USL), The Santa Cruz Operation (SCO), and Univel formed the Common Open Software Environment (COSE) alliance. Hewlett-Packard already uses the “control integration via messaging” approach in its SoftBench framework product. Therefore, the original experiment used the message passing capabilities of SoftBench (particularly, the SoftBench Encapsulator and Broadcast Message Server (BMS)) as the primary means of tool-activity synchronization in the scenario. While analyzing the results of the initial set of experiments, we determined that the use of BMS as the message passing component of the experiment framework could (at least in principle) be replaced by an equivalent product such as Sun’s ToolTalk or Digital’s FUSE. This is significant in that one of the premises of the work of the SEI CASE Environments Project, and of the experiments in particular, is that different implementations of similar services can be easily interchanged to provide a degree of interoperability. The ability to interchange control-oriented integration framework mechanisms is an important part of that premise. While it would have been possible to hypothesize about the feasibility of the message service replacement by comparing and contrasting the services and their inherent functionality, it was decided to demonstrate better the practicality of the operation by example. An extension to the experiment was undertaken then, not to see if the message service replacement was theoretically possible, but to examine the process of actually performing (or attempting to perform) the replacement.
Matter Tensors and Coordinate Transformations
Authors: Oertel Gerhard
Published: November 2020

Vectors, the subject of the previous two chapters, may be classified as members of a class of mathematical entities called tensors, insofar as they can be expressed in the form of ordered arrays, or matrices, and insofar as they further conform to conditions to be explored in the present chapter. Tensors can have various ranks, and vectors are tensors of the first rank, which in three-dimensional space have 31 or three components. Much of this, and later, chapters deals with tensors of the second rank which in the same space have 32 or nine components. Tensors of higher (nth) rank do exist and have 3n components, and so do, at least nominally, tensors of zero rank with a single, or 30, component, which makes them scalars. Tensors of the second rank for three dimensions are written as three-by-three matrices with each component marked by two subscripts, which may be either letters or numbers.
Finite Strain
Authors: Oertel Gerhard
Published: November 2020

Before dealing with finite strain, we demonstrate an important property of the determinant of a three by three matrix the rows of which are vectors. The result can be used to calculate the volume of a general parallelepiped (a solid bounded by parallelograms). The following problems also introduce the concept of dual position vectors, an original set, ai, and a final set, xi, where one set is a function of the other. This concept may alternatively be taken to produce two distinct cartesian coordinate systems, a concept used throughout this chapter. The description of a transformation from coordinates ai to xi, is designated as Lagrangian if it is referred to the system of original coordinates ai and as Eulerian if it is referred to the system of final coordinates xi. The origins and orientations of the two coordinate systems are independent of each other. For certain purposes, however, it is useful to let the two coordinate systems coincide in origin and orientation, being distinct only by the fact that they indicate positions before and after some event (such as a deformation).
Minimizing Species Loss: The Imperative of Protection
Authors: Terborgh John , van Schaik Carel P.
Published: November 2020

The major rush of extinctions under way in tropical rain forests is caused by habitat loss, habitat fragmentation, and overexploitation of species useful or threatening to humans. As burgeoning human populations continue to claim an ever greater share of the world’s renewable resources, intensification of land use will make it increasingly difficult to maintain biodiversity outside of strictly protected nature preserves. Further, because many species can maintain themselves only in large expanses of unaltered or lightly disturbed habitat, fully protected areas should remain the cornerstone of any conservation strategy that aims at minimizing the loss of tropical biodiversity. We have identified five principal forces of extinction in a humandominated world: deforestation, habitat fragmentation, overkill, secondary extinction, and introduced species. In this chapter, we briefly review the manner in which each of these processes contributes to extinction, both as isolated forces and in synergism with other forces. Our conclusion is that all five forces of extinction can be minimized by retaining intact natural habitat in the largest possible blocks. As the human population continues to expand, it is inevitable that most land outside strictly protected nature preserves will be subject to increasingly intensive use, resulting in decreased biodiversity. We therefore argue that maintaining biodiversity can best be achieved through development planning at the largest practical spatial scales. Parks should be as large as possible, designed to benefit from passive protection (inaccessibility), and rigorously protected. Only through major strengthening of institutions responsible for park protection can we expect to see tropical biodiversity survive the coming century. The earth is experiencing an extinction crisis because the human population is increasing rapidly and laying claim to an ever larger share of land and resources. Simultaneously, nearly all individual humans fervently desire to increase their level of material well-being. The resulting double impetus for rapid economic expansion generates exponentially increasing demands for most renewable and nonrenewable resources. The world is consequently experiencing a wave of nonsustainable use of most basic, life-supporting resources, including soil, groundwater, forests, grasslands, and fisheries. The earth’s population today is 5.5 billion, and it is increasing by more than 90 million per year.
Tropical Forest Biodiversity Protection: Who Pays and Why
Authors: Kramer Randall A. , Sharma Narendra
Published: November 2020

People value biodiversity found in tropical rain forests for a variety of utilitarian, aesthetic, moral, ecological, and socioeconomic reasons (Botkin and Talbot, 1992). For instance, traditional medicines derived from plant and animal species found in the tropics provide health services to rural and urban populations; about 25 percent of the pharmaceutical products produced in the United States are associated with plants (WRI et al., 1992). Genetic materials extracted from plant and animal species have contributed to the development of commercial agricultural products (e.g., new varieties of wheat, maize, and rice) that are more resistant to pests and diseases. And nature tourism, often associated with protected wildlife habitats, has become an important source of income, generating about $ 12 billion annually in worldwide earnings (Lindberg, 1991). There are important socioeconomic and political considerations in the valuation of biological resources and the protection of biodiversity. First, the benefits that result from biodiversity have spatial and temporal dimensions. The ecological services linked with biodiversity, such as clean air and water, and the use of genetic material and ingredients extracted from plants, animals, and microorganisms, occur at different places and at different times, often beyond the “economic time scale” of individuals. Second, biodiversity has characteristics of a public good locally arid nationally and may be considered a “global environmental good” in an international context. The benefits of public goods flow to all people regardless of whether they have paid for the good, which means that public goods suffer from the problem of “free riders.” In a national context, economists have long focused attention on the difficulty of financing public goods and have generally concluded that such goods will be underprovided by markets. In the international context, the provision and financing of public goods is even more problematic. These characteristics make management of biodiversity institutionally complex and create problems in defining property rights. Third, conservation of biodiversity can create significant nonuse values. By its very existence, biodiversity can generate economic value without requiring actual use and can provide value by leaving open the option of future use.
Introduction
Authors: Nadkarni Nalini M. , Wheelwright Nathaniel T.
Published: November 2020

Monteverde has been variously described as a virgin tropical cloud forest, a Quaker dairy community, an artists’ commune, a haven for those seeking spirituality, a model for tropical rain forest conservation, and a “forest in the clouds” where the sound of the bellbird’s call and images of mist-enshrouded trees long linger in visitors’ minds. The environment of Monteverde is typical of many tropical montane cloud forest regions, but Monteverde provides a unique setting because of its biogeographic, human, and conservation history. This book was created to fulfill three objectives: to compile what we know about Monteverde’s natural history, ecology, and conservation; to identify areas where information is lacking; and to facilitate communication among those who carry out research, education, and conservation. Contributors include a wide range of people with expertise from many different fields, levels of training, and approaches to understanding the natural world, and they have communicated in many modes, ranging from the objective style of scientific prose, statistics, and tables to the more reflective descriptions of personal experiences. In addition to academic scientists, we have invited the voices of farmers, natural history guides, anthropologists, educators, and homemakers, all of whom have important insights into Monteverde’s biology and conservation. In 1951, a band of fewer than fifty North American Quakers bought land and settled in Monteverde (Note that, throughout, when an author refers to another essay in this volume, the essay is cited by author name and a short form of the essay title.) In 1977, visitors to the area were still relatively uncommon. Now, only two decades later, nearly 50,000 visitors walk the trails of Monteverde each year to catch sight of a quetzal or absorb the peaceful outlook of the community. Growth of ecotourism has been phenomenal, eclipsing the small single-family farm as the region’s economic mainstay. New agricultural methods, a changing local, regional, and global economy, and the sheer number of visitors have changed Monteverde and surrounding communities.
Apparatus
Authors: Epstein Irving R. , Pojman John A.
Published: November 2020

In the previous chapter, we developed a set of conceptual and mathematical tools for analyzing the models and experimental data that form the subject matter of nonlinear chemical dynamics. Here, we describe some of the key items of experimental apparatus used to obtain these data so that the reader can better appreciate the results discussed in the following chapters and can learn how to begin his or her own investigations. The first several sections are devoted to measurements of temporal behavior, with emphasis on the techniques used to monitor reactions in time and on the reactors in which these reactions are studied. The final section focuses on the study of spatial patterns and waves in chemical systems. It is possible, by methods that we shall discuss later, to reconstruct the qualitative dynamics of a system from the measurement of only a single variable. However, the more species whose concentrations can be measured, the easier it is to elucidate a mechanism and the more rigorously that mechanism can be tested. The most impressive study of multiple species in a chemical oscillator was carried out by Vidal et al. (1980), who were able, by a combination of techniques, to monitor the concentrations of Ce4 + , Ce3+ , Br2, Br-, bromomalonic acid, O2, and CO2 in the BZ reaction. In the following sections, we will look at the most widely employed techniques: spectroscopic and potentiometric methods. In principle, and occasionally in practice, essentially any technique that can be used to detect changes in concentration can be utilized to monitor the systems that we are interested in. Approaches that have been employed to date include polarography, high-pressure liquid chromatography, and calorimetry. If there are absorbing species, ultraviolet and/or visible (UV/vis) spectroscopy offers rapid response time and high sensitivity for monitoring concentrations, particularly if the species of interest have spectra with relatively little overlap. Measurements can be made in a cuvette placed in a standard UV/vis spectrophotometer, but this configuration has several limitations.
Mixing, Multiple Solutions, and Forced Unsteady-State Operation
Authors: Doraiswamy L. K.
Published: November 2020

Three important (complicating) possibilities were not considered in the treatment of reactors presented in earlier chapters: (1) the residence time of the reactant molecules need not always be fully defined in terms of plug flow or fully mixed flow; (2) the equations describing certain situations can have more than one solution, leading to multiple steady states; and (3) there could be periods of unsteady-state operation with detrimental effects on performance, that is, transients could develop in a reactor. Actually, reactors can operate under conditions where there is an arbitrary distribution of residence times, leading to different degrees of mixing with consequent effects on reactor performance. Also, multiple solutions do exist for equations describing certain situations, and they can have an important bearing on the choice of operating conditions. And, finally, unsteady-state operation is a known feature of the start-up and shutdown periods of continuous reactor operation; it can also be introduced by intentional cycling of reactants. We briefly review these three important aspects of reactors in this chapter. However, because the subjects are highly mathematical, the treatment will be restricted to simple formulations and qualitative discussions that can act as guidelines in predicting reactor performance. All aspects of mixing in chemical reactors are based on the theory of residence time distribution first enunciated by Danckwerts (1953). Therefore, we begin our discussion of mixing with a brief description of this theory. When a steady stream of fluid flows through a vessel, different elements of the fluid spend different amounts of time within it. This distribution of residence times is denoted by a curve which represents, at any given time, the amount of fluid with ages between t and t + dt flowing out in the exit stream.
Sonoorganic Synthesis Engineering
Authors: Doraiswamy L. K.
Published: November 2020

Ultrasonics or ultrasound refers to sound waves beyond the audible range of the human ear. The normal human hearing range is 16-16,000 cycles per second. The accepted terminology for one cycle per second is the Hertz (or Hz), and hence the hearing range is expressed as 16 Hz to 16kHz. Ultrasound is normally considered to lie approximately in the range of 15kHz to 10 MHz, that is, 15 x 103 to 10000 x 103 cycles per second, with acoustic wavelengths of 10 to 0.01 cm. Like any sound wave, ultrasound is propagated through a medium in alternating cycles of compression and stretching or rarefaction. These produce certain effects in the medium that can be usefully exploited. One such application is in the field of synthetic organic chemistry, first reported by Richards and Loomis (1927) and designated sonochemistry. The most appealing feature of sonochemistry is its ability to enhance reaction rates, often to remarkably high levels under environmentally benign conditions. Despite this potential, economic considerations have precluded the use of sonochemical processes. It is noteworthy, however, that a change in perspective appears to be emerging, as evidenced by the fact that a pilot plant is currently being funded by a French company to sonochemically oxidize cyclohexanol to cyclohexanone, and developmental work is underway in Germany to produce 4 tons of Grignard reagent per year (Ondrey et al., 1996). A number of books and reviews covering mostly the chemical aspects of sonochemistry have appeared over the years, for example, Suslick, 1988, 198, 1990a,b; Ley and Low, 1989; Mason, 1986, 1990a,b, 1991; Mason and Lorime 1989; Price, 1992; Bremner, 1994; Low, 1995; Luche, 1998. A recent review Thompson and Doraiswamy (1999) covers both the chemical and engineering aspects of sonochemistry and another by Keil and Swamy (1999) examines the present state of our understanding of sonoreactor design. Sonochemical enhancement of reaction rates is caused by a phenomenon called cavitation. Therefore, we largely confine the treatment in this chapter to the chemical and reaction engineering (scale-up) aspects of cavitation and its associated effects (see Shah et al., 1999, for a detailed treatment). An alternative means of achieving the same result is by mimicking the ultrasonic effect by inducing “hydrodynamic cavitation.”
Resolution of the Ambiguity of van’t Hoff Plots by the Effect of Pressure on the Equilibrium
Authors: Weber Gregorio
Published: November 2020

The change in the Gibbs free energy function, ΔG, of chemical reaction is determined by the difference between the heats respectively released to and absorbed from the environment, and separation of the enthalpy and entropy changes that these changes represent cannot be achieved without specific hypotheses as to their relations. The determination of the enthalpy of reaction by the plot of ΔG/T against 1/T (van’t Hoff plot) implicitly assumes that the enthalpy ΔH and entropy ΔS are temperature independent, and this assumption leads to very large errors when this is not the case and ΔH « TΔS. It is therefore inapplicable to the reactions of molecules, such as proteins, that have thermally activated local motions. The concepts offered previously by the author to relate the entropy and enthalpy changes in protein associations are reviewed briefly and applied to account for the temperature dependence of ΔH and ΔS. It is shown that two different values of the enthalpy computed in that manner correspond to each value of the apparent van’t Hoff enthalpy, but that the choice between the two is easily made by reference to the volume change on reaction. The enthalpies of association of subunit pairs of seven oligomers are all found to be positive and much more uniformly related to the size of the intersubunit surface than those previously assigned by use of the classical van’t Hoff plot.
High-Pressure FTIR Studies of the Secondary Structure of Proteins
Authors: Taniguchi Yoshihiro , Takeda Naohiro
Published: November 2020

Infrared spectra of five globular proteins (bovine pancreas ribonuclease A, horse skeletal muscle myoglobin, bovine pancreas insulin, horse heart cytochrome c, egg white lysozyme) in 5% D2O solutions (pD 7.0) were measured as a function of pressure up to 1470 MPa at 30 °C. According to the second-derivative spectral changes in the observed amide I band of the proteins, which indicate that the α-helix and β-sheet substructures of the secondary structures break dramatically into the random coil conformation, ribonuclease A and myoglobin are denatured reversibly at 850 MPa and 350 MPa, respectively. Lysozyme denatures partially and reversibly at 670 MPa, as shown by decrease in the α-helix and β-turn substructures, but no change occurs in the random coil and β-sheet substructures. The secondary structure of cytochrome c is not disrupted at pressures up to 1470 MPa, and partial transformation of the α-helix of insulin to random coil starts at 960 MPa. Hydrogen-deuterium exchange of protons on the amide groups in the protein interior is increased by external pressure and is associated with the pressure-induced protein conformational changes. A number of studies on the effects of pressure on protein denaturation have been carried out using various high-pressure detection methods: ultraviolet absorbance spectroscopy (Brandts et al., 1970; Hawley, 1971), visible absorbance spectroscopy (Zipp & Kauzmann, 1973), fluorescence intensity spectroscopy (Li et al., 1976), polarization fluorescence spectroscopy (Chryssomallis et al., 1981), and enzyme activity assays (Taniguchi & Suzuki, 1983; Makimoto et al., 1989). These techniques have the great advantage of being applicable to pressure-induced reversible denaturation of proteins to identify the thermodynamic parameters, especially the volume change and compressibility of a protein in solution, because the experiments can be run under dilute conditions at a protein concentration of less than 0.05% w/v. Therefore, these data reflect the intramolecular phenomena of reversible pressure changes and provide the volume changes accompanying the denaturation of proteins, which are due to the difference in partial molal (specific) volume between the native and denatured proteins in solution.
Steady-State Enzyme Kinetics at High Pressure
Authors: Northrop Dexter B.
Published: November 2020

Pressure effects on enzyme-catalyzed reactions were traditionally interpreted within a simplistic kinetic mechanism in which the transition state presented the highest energy barrier, and the chemical transformation of substrate to product was considered to be a singular, rate-limiting step. This was also true of isotope effects on enzyme-catalyzed reactions, but extensive isotopic studies have led to the conclusion that this transition state is rarely the highest barrier. Rather, the release of products (or the conformational change preceding product release) is usually the slowest step, often accompanied by several other partially ratelimiting steps. Thus, our interpretations of pressure effects must be shifted accordingly. Values attributed to AV‡ have been determined for more than 50 enzymes, more of them with a positive sign than negative, and most in the range of 20 to 40 ml mol–1 but these may or may not have anything to do with the activation volume associated with the transition state. Volume changes specifically associated with the binding of ligands to enzymes have been reported as well, including some very large values, as high as ΔV = 85 ml mo–1. Kinetically, these equilibrium pressure effects also originate in conformational changes because water is not very compressible; hence, rates of diffusion to and from enzymes are virtually unaffected by pressure. Much larger changes, as high as ΔV = –391 mi mo–1, have been observed during disaggregation and denaturation of enzymes. Thus, while it is possible for pressure effects to be expressed on every step of an enzymatic reaction, and to cause denaturation as well, making kinetic data from pressure effects hopelessly complex and uninterpretable, it appears likely that the most significant pressure effects will be expressed on conformational changes associated with product dissociations, without much kinetic complexity. This makes sense from another point of view—that the largest volume changes are probably on solvation equilibria during ligand binding and protein folding. Pressure effects on isotope effects have the potential of specifically identifying whether or not a volume change occurs upon attaining the transition state. With the exception of hydrogen tunneling, intrinsic isotope effects are independent of pressure.
The Effects of Increased Viscosity on the Function of Integral Membrane Proteins
Authors: Scarlata Suzanne F.
Published: November 2020

For many years the idea that the activity of integral membrane proteins is regulated by the fluidity of the lipid matrix was popular and appeared to be quite rational. However, as information about the effect of viscosity on the function of different membrane proteins became available, the correlation between the two became increasingly unclear. The purpose of this article is to readdress this issue in light of our recent pressure and temperature studies. This chapter is divided into seven parts: (1) the effect of viscosity on enzyme activity; (2) the effect of viscosity on the local motions of proteins; (3) characterization of membrane viscosity; (4) demonstration of changes in protein-lipid contacts brought about by changes in viscosity; (5) an example of a protein in which the viscosity appears to stabilize a particular conformational state: (6) relations between membrane viscosity and protein function; and (7) conclusions. The effect of viscosity (η) on the rate (k) of a chemical reaction was first given by Kramers (1940): . . . k=A/ηe−Ea/RT (1) . . . In this expression, viscosity will affect the rate of a reaction by limiting the rate of diffusion of reactants. Viscosity will thus modify the frequency factor (A) and should not affect the activation energy. This expression has been applied to aqueous soluble enzymes (for example, Gavish, 1979; Gavish & Werber, 1979; Somogyi et al., 1984), and it appears that, in general, enzymes obey Kramers’s relation, although in some cases the exponent of η is less than one. Viscosity can affect enzymatic rates not only by limiting the diffusion of substrates but also by damping internal motions of the protein chains. It seems reasonable that a high enough viscosities, the protein would be damped sufficiently so that large activation energies will be required for the backbone motions that allow substrates and products to diffuse into and out of the active site. This viscosity-induced increase in activation energy was shown by studies of the reassociation of carbon monoxide and dioxygen to the heme site of myoglobin after flash photodissociation (Austin et al., 1975; Beece et al., 1980).
Acidity
Authors: Kong X. L. , Zhang X. N.
Published: November 2020

For variable charge soils, acidity is a property that is of equal importance as the surface charge. These two properties may affect each other, with the effect of the former on the latter more remarkable than the reverse. In the previous chapters it was shown that pH affects many other properties of the soil by affecting the surface charge. Therefore, soil acidity is more significant than surface charge in some aspects. Owing to a similar reason, the importance of acidity for variable charge soils may exceed that for constant charge soils. Soil acidity generally manifests itself in the form of hydrogen ions. Actually, these hydrogen ions are chiefly the product of the hydrolysis of aluminum ions. Therefore, when examining soil acidity it is necessary to examine the properties of aluminum ions. In the previous chapter the transformation of hydrogen ions into aluminum ions has already been mentioned. In this chapter the relationship between aluminum ions and hydrogen ions will be discussed in greater detail. Another difference between variable charge soils and constant charge soils with respect to acidity is that, not only hydrogen ions, but also hydroxyl ions can participate in chemical reactions between the solid phase and the liquid phase. In constant charge soils the quantity of hydroxyl ions is an induced variable and is determined by the quantity of hydrogen ions in the solution and the ionic product of water. In variable charge soils, on the other hand, the quantity is also determined by the chemical equilibrium of that ion species itself at the solid-solution interface. Thus, hydroxyl ions can, in turn, affect the quantity of hydrogen ions in solution. In this chapter the nature of acidity of variable charge soils will be discussed mainly from these characteristics. In the field of soil chemistry, there has been an interesting history with regard to the nature of soil acidity. Soon after the recognition of the relationship between acid reaction and hydrogen ions in chemistry, this concept of the nature of acidity was introduced into soil science, and the significance of hydrogen ions was invariably associated with it whenever soil acidity was considered.
Ferrous Ions and Manganous Ions
Authors: Bao X. M.
Published: November 2020

It has been seen in the previous chapter that, when organic reducing substances are in contact with soils, iron and manganese oxides of the soil can be reduced, producing ferrous and manganous ions. This reduction process is of particular significance for variable charge soils. This is because the contents of iron and manganese oxides in these soils are higher than those in constant charge soils, and therefore there is the basis for the production of large amounts of ferrous and manganous ions. On the other hand, the low pH of variable charge soils is one of the favorable factors in the reduction of iron and manganese. Hence, the possibility exists for the production of the reduced form of these two elements exists even under well-aerated conditions, provided that the soil contains organic matter. It is for these reasons that iron and manganese can actively participate in chemical reactions in variable charge soils in the form of ions, and they are of great significance in both soil genesis and plant nutrition. As a matter of fact, many reports have shown that the amount of manganous ions in strongly acid soils is so high that the toxicity of manganese may be one of the causes for the poor growth of plants. In this chapter, after the elucidation of the reduction and dissolution of iron and manganese, emphasis of discussions will be placed on the chemical equilibria of the two kinds of ions. Finally, the regimes of the two ions in variable charge soils under field conditions will be described. The solubility of iron oxides in soils is extremely low. The solubility product of Fe(OH)3 is about 10-38. Therefore, the concentration of Fe3+ ions in solution is only 10-8 M even at a pH of 4, if the concentration is determined solely by the solubility of the oxides. Similarly, the quantity of Mn4+ ions due to the dissolution of manganese oxides is also very small. On the other hand, because the solubility products of Fe(OH)2 and Mn(OH)2 are about 10-16 and 10-13, respectively, after reduction, ferrous and manganous (in this chapter the latter is simply referred to as manganese) ions can exist stably in soils.