Naomi E. Chayen, John R. Helliwell, and Edward H. Snell
- Published in print:
- 2010
- Published Online:
- May 2010
- ISBN:
- 9780199213252
- eISBN:
- 9780191707575
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199213252.003.0015
- Subject:
- Physics, Crystallography
Unusual diffraction geometries may seem a curiosity but may stimulate novel avenues of application. Not least they illustrate a diversity of diffraction‐measuring possibilities. Laue diffraction ...
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Unusual diffraction geometries may seem a curiosity but may stimulate novel avenues of application. Not least they illustrate a diversity of diffraction‐measuring possibilities. Laue diffraction including 3‐dimensional detector arrangements is described. The particular congestion of neutron Laue diffraction patterns with big crystals is highlighted. The large‐angle oscillation technique is discussed including the principle with the Ewald sphere construction and practical examples of ‘LOT’ diffraction patterns. Ultra‐fine‐phi‐slicing with perfect or near‐perfect crystals is described. Particular success has been obtained with Laue diffraction where applications to time‐resolved structural intermediates using synchrotron radiation as well as hydrogen and hydration in macromolecular structure are described.Less
Unusual diffraction geometries may seem a curiosity but may stimulate novel avenues of application. Not least they illustrate a diversity of diffraction‐measuring possibilities. Laue diffraction including 3‐dimensional detector arrangements is described. The particular congestion of neutron Laue diffraction patterns with big crystals is highlighted. The large‐angle oscillation technique is discussed including the principle with the Ewald sphere construction and practical examples of ‘LOT’ diffraction patterns. Ultra‐fine‐phi‐slicing with perfect or near‐perfect crystals is described. Particular success has been obtained with Laue diffraction where applications to time‐resolved structural intermediates using synchrotron radiation as well as hydrogen and hydration in macromolecular structure are described.
Naomi E. Chayen, John R. Helliwell, and Edward H. Snell
- Published in print:
- 2010
- Published Online:
- May 2010
- ISBN:
- 9780199213252
- eISBN:
- 9780191707575
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199213252.003.0019
- Subject:
- Physics, Crystallography
Major increases in brightness are anticipated with the upcoming coherent X‐ray lasers. Extrapolation suggests that a single macromolecule ‘sample’ may be sufficient to generate a measurable X‐ray ...
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Major increases in brightness are anticipated with the upcoming coherent X‐ray lasers. Extrapolation suggests that a single macromolecule ‘sample’ may be sufficient to generate a measurable X‐ray diffraction pattern, a continuous Fourier transform of the molecule giving easier phase determination. The practical difficulties are enormous in the recording of such diffraction patterns, not least the so‐called ‘molecule blow‐up problem’ due to the thermal and radiation blast that a single molecule must take. By taking the exposure at a sufficiently small time‐flash, a few femtoseconds, this may be practical. For 3D structure determination multiple sample orientations are needed. A risk is too few photons in the femtosecond pulse that must be used to take data before sample damage occurs. A nanocluster of molecules would be a way of compensating for that and a ‘jet stream’ of these would lead to powder diffraction patterns rather than single‐molecule patterns.Less
Major increases in brightness are anticipated with the upcoming coherent X‐ray lasers. Extrapolation suggests that a single macromolecule ‘sample’ may be sufficient to generate a measurable X‐ray diffraction pattern, a continuous Fourier transform of the molecule giving easier phase determination. The practical difficulties are enormous in the recording of such diffraction patterns, not least the so‐called ‘molecule blow‐up problem’ due to the thermal and radiation blast that a single molecule must take. By taking the exposure at a sufficiently small time‐flash, a few femtoseconds, this may be practical. For 3D structure determination multiple sample orientations are needed. A risk is too few photons in the femtosecond pulse that must be used to take data before sample damage occurs. A nanocluster of molecules would be a way of compensating for that and a ‘jet stream’ of these would lead to powder diffraction patterns rather than single‐molecule patterns.
Naomi E. Chayen, John R. Helliwell, and Edward H. Snell
- Published in print:
- 2010
- Published Online:
- May 2010
- ISBN:
- 9780199213252
- eISBN:
- 9780191707575
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199213252.001.0001
- Subject:
- Physics, Crystallography
Structural crystallography provides key information to understand the mechanism involved for biological processes. The technique requires high‐quality crystals. The book Macromolecular ...
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Structural crystallography provides key information to understand the mechanism involved for biological processes. The technique requires high‐quality crystals. The book Macromolecular crystallization and crystal perfection covers the techniques to get these high quality crystals and then obtain the best structural data from them. We focus on two areas, the crystal and the diffraction experiment. We briefly address crystallization theory and then focus on practical crystallization strategies discussing screening and optimization. Where high quality crystals are not initially obtained, remediation strategies and alternative approaches are discussed. Diffraction is covered from both the X‐ray and neutron viewpoint. A physical analysis of long and short‐range order is used to explain features seen in the diffraction pattern and the causes of those features. Diffraction disorders are discussed. Factors that cause degradation to the diffraction and strategies to mitigate those factors are addressed. We then address beamline and detector optimization as a means to improve the data quality. Crystallization is still a largely empirical process and our final chapters focus on the use of powder methods, where crystals are small, complementary techniques where we have no crystals at all and what the future holds with the advent of fourth generation X‐ray sources. Overall the book is aimed at both more experienced researchers and graduate students. We aim for it to become a reference work for all researchers in these interdisciplinary subjects on these topics.Less
Structural crystallography provides key information to understand the mechanism involved for biological processes. The technique requires high‐quality crystals. The book Macromolecular crystallization and crystal perfection covers the techniques to get these high quality crystals and then obtain the best structural data from them. We focus on two areas, the crystal and the diffraction experiment. We briefly address crystallization theory and then focus on practical crystallization strategies discussing screening and optimization. Where high quality crystals are not initially obtained, remediation strategies and alternative approaches are discussed. Diffraction is covered from both the X‐ray and neutron viewpoint. A physical analysis of long and short‐range order is used to explain features seen in the diffraction pattern and the causes of those features. Diffraction disorders are discussed. Factors that cause degradation to the diffraction and strategies to mitigate those factors are addressed. We then address beamline and detector optimization as a means to improve the data quality. Crystallization is still a largely empirical process and our final chapters focus on the use of powder methods, where crystals are small, complementary techniques where we have no crystals at all and what the future holds with the advent of fourth generation X‐ray sources. Overall the book is aimed at both more experienced researchers and graduate students. We aim for it to become a reference work for all researchers in these interdisciplinary subjects on these topics.
Naomi E. Chayen, John R. Helliwell, and Edward H. Snell
- Published in print:
- 2010
- Published Online:
- May 2010
- ISBN:
- 9780199213252
- eISBN:
- 9780191707575
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199213252.003.0020
- Subject:
- Physics, Crystallography
This chapter summarizes the state‐of‐the‐art in the field and discusses upcoming techniques to solve and to improve the current problems.
This chapter summarizes the state‐of‐the‐art in the field and discusses upcoming techniques to solve and to improve the current problems.
Reinhard B. Neder and Thomas Proffen
- Published in print:
- 2008
- Published Online:
- September 2008
- ISBN:
- 9780199233694
- eISBN:
- 9780191715563
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199233694.001.0001
- Subject:
- Physics, Crystallography
In recent years it has become apparent that merely knowing and understanding the average atomic structure is insufficient for comprehending material properties fully. Deviations from this average ...
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In recent years it has become apparent that merely knowing and understanding the average atomic structure is insufficient for comprehending material properties fully. Deviations from this average structure play an important role regarding these properties. To understand the defect or local structure one has to study diffuse scattering and go beyond the classic interpretation of Bragg intensities. Although there is an increasing interest in analysing disordered materials, as expressed by a number of recent text books, the practical aspects of this analysis are not yet widely known. A detailed step-by-step guide that explains how to simulate disordered materials has been missing. This book covers the full range; from basic steps such as how to build a computer model of the crystal to complex disorder models such as domains, stacking faults, and nanoparticles. It also explains how to use advanced refinement techniques to determine the parameters of a disordered structure. This book provides many examples of the simulation of disordered materials including the input files for DISCUS and explains the concepts and pitfalls encountered when simulating disordered materials.Less
In recent years it has become apparent that merely knowing and understanding the average atomic structure is insufficient for comprehending material properties fully. Deviations from this average structure play an important role regarding these properties. To understand the defect or local structure one has to study diffuse scattering and go beyond the classic interpretation of Bragg intensities. Although there is an increasing interest in analysing disordered materials, as expressed by a number of recent text books, the practical aspects of this analysis are not yet widely known. A detailed step-by-step guide that explains how to simulate disordered materials has been missing. This book covers the full range; from basic steps such as how to build a computer model of the crystal to complex disorder models such as domains, stacking faults, and nanoparticles. It also explains how to use advanced refinement techniques to determine the parameters of a disordered structure. This book provides many examples of the simulation of disordered materials including the input files for DISCUS and explains the concepts and pitfalls encountered when simulating disordered materials.
Sander van Smaalen
- Published in print:
- 2007
- Published Online:
- January 2008
- ISBN:
- 9780198570820
- eISBN:
- 9780191718762
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780198570820.001.0001
- Subject:
- Physics, Crystallography
Aperiodic crystals are crystalline materials with atomic structures that lack translational symmetry. This book gives a comprehensive account of the superspace theory for the description of the ...
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Aperiodic crystals are crystalline materials with atomic structures that lack translational symmetry. This book gives a comprehensive account of the superspace theory for the description of the crystal structures, and symmetries of incommensurately modulated crystals and composite crystals. It also gives a brief introduction to quasicrystals, thus providing the necessary background for understanding the distinctive features of aperiodic crystals, and it provides the tools for the application of quantitative methods from the realms of crystallography, solid state chemistry, and solid state physics to aperiodic crystal structures. The second half of the book is devoted to crystallographic methods of structural analysis of incommensurate crystals. Thorough accounts are given of the diffraction by incommensurate crystals, the choice of parameters in structure refinements, and the use of superspace in analysing crystal structures. The presentation of methods of structure determination includes direct methods, Fourier methods, Patterson function methods, the maximum entropy method (MEM), and charge flipping. So-called t-plots are introduced as a versatile method for the crystal chemical analysis of incommensurately modulated structures and composite crystals.Less
Aperiodic crystals are crystalline materials with atomic structures that lack translational symmetry. This book gives a comprehensive account of the superspace theory for the description of the crystal structures, and symmetries of incommensurately modulated crystals and composite crystals. It also gives a brief introduction to quasicrystals, thus providing the necessary background for understanding the distinctive features of aperiodic crystals, and it provides the tools for the application of quantitative methods from the realms of crystallography, solid state chemistry, and solid state physics to aperiodic crystal structures. The second half of the book is devoted to crystallographic methods of structural analysis of incommensurate crystals. Thorough accounts are given of the diffraction by incommensurate crystals, the choice of parameters in structure refinements, and the use of superspace in analysing crystal structures. The presentation of methods of structure determination includes direct methods, Fourier methods, Patterson function methods, the maximum entropy method (MEM), and charge flipping. So-called t-plots are introduced as a versatile method for the crystal chemical analysis of incommensurately modulated structures and composite crystals.
David Paganin
- Published in print:
- 2006
- Published Online:
- September 2007
- ISBN:
- 9780198567288
- eISBN:
- 9780191717963
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780198567288.001.0001
- Subject:
- Physics, Atomic, Laser, and Optical Physics
This book offers a grounding in the field of coherent X-ray optics, which in the closing years of the 20th century experienced something of a renaissance with the availability of third-generation ...
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This book offers a grounding in the field of coherent X-ray optics, which in the closing years of the 20th century experienced something of a renaissance with the availability of third-generation synchrotron sources. It begins with a treatment of the fundamentals of X-ray diffraction for both coherent and partially coherent radiation, together with the interactions of X-rays with matter. X-ray sources, optical elements, and detectors are then discussed, with an emphasis on their role in coherent X-ray optics. Various aspects of coherent X-ray imaging are then considered, including holography, interferometry, self imaging, phase contrast, and phase retrieval. The foundations of the new field of singular X-ray optics are examined, focusing on the topic of X-ray phase vortices. Most topics in the book are developed from first principles using a chain of logic which ultimately derives from the Maxwell equations, with numerous references to the contemporary and historical research literature.Less
This book offers a grounding in the field of coherent X-ray optics, which in the closing years of the 20th century experienced something of a renaissance with the availability of third-generation synchrotron sources. It begins with a treatment of the fundamentals of X-ray diffraction for both coherent and partially coherent radiation, together with the interactions of X-rays with matter. X-ray sources, optical elements, and detectors are then discussed, with an emphasis on their role in coherent X-ray optics. Various aspects of coherent X-ray imaging are then considered, including holography, interferometry, self imaging, phase contrast, and phase retrieval. The foundations of the new field of singular X-ray optics are examined, focusing on the topic of X-ray phase vortices. Most topics in the book are developed from first principles using a chain of logic which ultimately derives from the Maxwell equations, with numerous references to the contemporary and historical research literature.
Sander Van Smaalen
- Published in print:
- 2007
- Published Online:
- January 2008
- ISBN:
- 9780198570820
- eISBN:
- 9780191718762
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780198570820.003.0009
- Subject:
- Physics, Crystallography
This chapter presents the steps that are required to determine the superspace group of an aperiodic crystal from its diffraction pattern. This includes the analysis of the metric of the reciprocal ...
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This chapter presents the steps that are required to determine the superspace group of an aperiodic crystal from its diffraction pattern. This includes the analysis of the metric of the reciprocal lattice in superspace, the point symmetry of the diffraction pattern, and the reflection conditions.Less
This chapter presents the steps that are required to determine the superspace group of an aperiodic crystal from its diffraction pattern. This includes the analysis of the metric of the reciprocal lattice in superspace, the point symmetry of the diffraction pattern, and the reflection conditions.
Dennis Sherwood and Jon Cooper
- Published in print:
- 2010
- Published Online:
- January 2011
- ISBN:
- 9780199559046
- eISBN:
- 9780191595028
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199559046.001.0001
- Subject:
- Physics, Crystallography
This book presents a complete account of the theory of the diffraction of X-rays by crystals with particular reference to the processes of determining the structures of protein molecules. The book ...
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This book presents a complete account of the theory of the diffraction of X-rays by crystals with particular reference to the processes of determining the structures of protein molecules. The book develops from first principles all relevant mathematics, diffraction, and wave theory. The practical aspects of sample preparation and X-ray data collection using both laboratory and synchrotron sources are covered along with data analysis at both the theoretical and practical levels. The important role played by the Patterson function in structure analysis by both molecular replacement and experimental phasing approaches is covered, as are methods for improving the resulting electron density map. The theoretical basis of methods used in refinement of protein crystal structures are then covered in depth along with the crucial task of defining the binding sites of ligands and drug molecules. The complementary roles of other diffraction methods which reveal further detail of great functional importance in a crystal structure are outlined.Less
This book presents a complete account of the theory of the diffraction of X-rays by crystals with particular reference to the processes of determining the structures of protein molecules. The book develops from first principles all relevant mathematics, diffraction, and wave theory. The practical aspects of sample preparation and X-ray data collection using both laboratory and synchrotron sources are covered along with data analysis at both the theoretical and practical levels. The important role played by the Patterson function in structure analysis by both molecular replacement and experimental phasing approaches is covered, as are methods for improving the resulting electron density map. The theoretical basis of methods used in refinement of protein crystal structures are then covered in depth along with the crucial task of defining the binding sites of ligands and drug molecules. The complementary roles of other diffraction methods which reveal further detail of great functional importance in a crystal structure are outlined.
William Clegg, Alexander J Blake, Jacqueline M Cole, John S O Evans, Peter Main, Simon Parsons, and David J Watkin (eds)
- Published in print:
- 2009
- Published Online:
- September 2009
- ISBN:
- 9780199219469
- eISBN:
- 9780191722516
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199219469.001.0001
- Subject:
- Physics, Crystallography
This book presents a less mathematical approach to X-ray crystal structure determination than is given in some detailed texts and concentrates on practical aspects. The book provides the necessary ...
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This book presents a less mathematical approach to X-ray crystal structure determination than is given in some detailed texts and concentrates on practical aspects. The book provides the necessary conceptual framework for understanding and applying the techniques described, but also gives practical advice on topics such as growing crystals, solving and refining structures, and understanding and using the results. There are also plenty of worked examples and problems provided (with answers), to reinforce the material presented. The book is based on the intensive course run by the Chemical Crystallography Group of the British Crystallographic Association every two years, and the material is drawn from the 2007 and 2009 courses. Much of the material of the first edition in 2001 has been significantly updated and expanded, and some new topics have been added. The approach to several of the topics is somewhat different as a result of changes in the authorship and the course teaching team. These changes reflect developments in the subject.Less
This book presents a less mathematical approach to X-ray crystal structure determination than is given in some detailed texts and concentrates on practical aspects. The book provides the necessary conceptual framework for understanding and applying the techniques described, but also gives practical advice on topics such as growing crystals, solving and refining structures, and understanding and using the results. There are also plenty of worked examples and problems provided (with answers), to reinforce the material presented. The book is based on the intensive course run by the Chemical Crystallography Group of the British Crystallographic Association every two years, and the material is drawn from the 2007 and 2009 courses. Much of the material of the first edition in 2001 has been significantly updated and expanded, and some new topics have been added. The approach to several of the topics is somewhat different as a result of changes in the authorship and the course teaching team. These changes reflect developments in the subject.
Peter Main
- Published in print:
- 2009
- Published Online:
- September 2009
- ISBN:
- 9780199219469
- eISBN:
- 9780191722516
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199219469.003.0001
- Subject:
- Physics, Crystallography
This introductory chapter provides information on some fundamental aspects of crystal structures and their diffraction of X-rays as a basis for the rest of the book. It describes electrons, atoms, ...
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This introductory chapter provides information on some fundamental aspects of crystal structures and their diffraction of X-rays as a basis for the rest of the book. It describes electrons, atoms, molecules, and crystals scatter X-rays, leading to the observed diffraction pattern, and introduces concepts such as the reciprocal lattice, structure factors, Fourier transforms, Bragg's law for the geometry of diffraction, the phase problem encountered in crystallography, and the meaning of resolution and how it is related to the extent of the measured diffraction pattern.Less
This introductory chapter provides information on some fundamental aspects of crystal structures and their diffraction of X-rays as a basis for the rest of the book. It describes electrons, atoms, molecules, and crystals scatter X-rays, leading to the observed diffraction pattern, and introduces concepts such as the reciprocal lattice, structure factors, Fourier transforms, Bragg's law for the geometry of diffraction, the phase problem encountered in crystallography, and the meaning of resolution and how it is related to the extent of the measured diffraction pattern.
Sherin S. Abdel-Meguid, David Jeruzalmi, and Mark R. Sanderson
- Published in print:
- 2007
- Published Online:
- September 2007
- ISBN:
- 9780198520979
- eISBN:
- 9780191706295
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780198520979.003.0004
- Subject:
- Biology, Biochemistry / Molecular Biology
The past decade and a half have witnessed an almost complete revolution in the way that macromolecular diffraction data are recorded. The promise of diffraction data measurements essentially free of ...
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The past decade and a half have witnessed an almost complete revolution in the way that macromolecular diffraction data are recorded. The promise of diffraction data measurements essentially free of the effects of radiation damage has driven a change from older methods requiring crystalline samples to be mounted in thin glass capillaries for measurements at ambient temperatures (or so) to newer, experimental schemes that enable measurements at cryogenic temperatures from crystals mounted in free-standing films. Preparation of macromolecular crystalline samples for measurements at cryogenic temperatures has three separable: cryoprotection, shock-cooling, and cryogenic transfer to the X-ray diffraction camera. This chapter describes each of these in detail.Less
The past decade and a half have witnessed an almost complete revolution in the way that macromolecular diffraction data are recorded. The promise of diffraction data measurements essentially free of the effects of radiation damage has driven a change from older methods requiring crystalline samples to be mounted in thin glass capillaries for measurements at ambient temperatures (or so) to newer, experimental schemes that enable measurements at cryogenic temperatures from crystals mounted in free-standing films. Preparation of macromolecular crystalline samples for measurements at cryogenic temperatures has three separable: cryoprotection, shock-cooling, and cryogenic transfer to the X-ray diffraction camera. This chapter describes each of these in detail.
John Shotter
- Published in print:
- 2010
- Published Online:
- January 2011
- ISBN:
- 9780199594566
- eISBN:
- 9780191595721
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199594566.003.0005
- Subject:
- Business and Management, Organization Studies
What is involved in our adopting a process orientation, in practice, rather than just talking about it in theory? Below, I explore some of the difficulties involved in terms of Wittgenstein's (1980) ...
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What is involved in our adopting a process orientation, in practice, rather than just talking about it in theory? Below, I explore some of the difficulties involved in terms of Wittgenstein's (1980) distinction between difficulties of the intellect—difficulties that can be solved by rational thought—and those of the will—which require our coming to embody new ways of relating or orienting ourselves towards events happening in our surroundings. So although I begin by examining what both Whitehead (1925/1975; 1929/1978) and Bergson (1911) had to say about a process orientation, in theory, now, after Wittgenstein's (1953, 1969) emphasis on the fact that our utterances can only take on determinate meanings within the confines of a “language‐game,” I argue that our talk of various entities can only take on a determinate meaning within a particular language‐entwined practice, and will remain indeterminate outside such practices. And straightaway, in situating us within the realm of practice and practices, this requirement re‐orients us toward the importance of poetic forms of talk, utterances which can “touch” us and “move” us towards adopting expectations and anticipations relevant to going out to meet events happening around us with the right kind of embodied responses, at the ready, so to speak.Less
What is involved in our adopting a process orientation, in practice, rather than just talking about it in theory? Below, I explore some of the difficulties involved in terms of Wittgenstein's (1980) distinction between difficulties of the intellect—difficulties that can be solved by rational thought—and those of the will—which require our coming to embody new ways of relating or orienting ourselves towards events happening in our surroundings. So although I begin by examining what both Whitehead (1925/1975; 1929/1978) and Bergson (1911) had to say about a process orientation, in theory, now, after Wittgenstein's (1953, 1969) emphasis on the fact that our utterances can only take on determinate meanings within the confines of a “language‐game,” I argue that our talk of various entities can only take on a determinate meaning within a particular language‐entwined practice, and will remain indeterminate outside such practices. And straightaway, in situating us within the realm of practice and practices, this requirement re‐orients us toward the importance of poetic forms of talk, utterances which can “touch” us and “move” us towards adopting expectations and anticipations relevant to going out to meet events happening around us with the right kind of embodied responses, at the ready, so to speak.
Naomi E. Chayen, John R. Helliwell, and Edward H. Snell
- Published in print:
- 2010
- Published Online:
- May 2010
- ISBN:
- 9780199213252
- eISBN:
- 9780191707575
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199213252.003.0009
- Subject:
- Physics, Crystallography
Diffraction and practical aspects in the diffraction pattern are described. The characteristics of the structural detail obtainable at different resolutions are then discussed along with implications ...
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Diffraction and practical aspects in the diffraction pattern are described. The characteristics of the structural detail obtainable at different resolutions are then discussed along with implications when resolution is less than desired and how accurate the structural information can be.Less
Diffraction and practical aspects in the diffraction pattern are described. The characteristics of the structural detail obtainable at different resolutions are then discussed along with implications when resolution is less than desired and how accurate the structural information can be.
Yuan Wang and Xiang Zhang
- Published in print:
- 2010
- Published Online:
- September 2010
- ISBN:
- 9780199219698
- eISBN:
- 9780191594229
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199219698.003.0008
- Subject:
- Mathematics, Mathematical Biology
This chapter reviews the recent development of near-field biomolecule imaging systems. Near-field scanning optical microscopy (NSOM) offers a practical means of optical imaging at a resolution well ...
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This chapter reviews the recent development of near-field biomolecule imaging systems. Near-field scanning optical microscopy (NSOM) offers a practical means of optical imaging at a resolution well beyond the diffraction limit of light. Applications are limited, however, due to strong attenuation of transmitted light through the sub-wavelength aperture. A variety of approaches to address this problem, such as apertureless NSOM and plasmonic near-field focusing devices, are covered in this chapter. These approaches provide an enhanced nanoscale imaging tool for cellular visualization, single molecule detection, and many other applications requiring high spatial and temporal resolution.Less
This chapter reviews the recent development of near-field biomolecule imaging systems. Near-field scanning optical microscopy (NSOM) offers a practical means of optical imaging at a resolution well beyond the diffraction limit of light. Applications are limited, however, due to strong attenuation of transmitted light through the sub-wavelength aperture. A variety of approaches to address this problem, such as apertureless NSOM and plasmonic near-field focusing devices, are covered in this chapter. These approaches provide an enhanced nanoscale imaging tool for cellular visualization, single molecule detection, and many other applications requiring high spatial and temporal resolution.
Reinhard B. Neder and Thomas Proffen
- Published in print:
- 2008
- Published Online:
- September 2008
- ISBN:
- 9780199233694
- eISBN:
- 9780191715563
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199233694.003.0004
- Subject:
- Physics, Crystallography
In most cases, simulations of disordered materials are performed to understand experimental observations, in this case diffraction data. This chapter discusses the calculation of several experimental ...
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In most cases, simulations of disordered materials are performed to understand experimental observations, in this case diffraction data. This chapter discusses the calculation of several experimental quantities: single crystal diffuse scattering, powder diffraction, and the atomic pair distribution function (PDF). Since diffraction data are obtained via a Fourier transform, the finite size of the model crystal as well as issues concerning coherence are discussed in detail. The PDF is basically calculated from the atomic structure directly. Different ways to incorporate thermal motion are illustrated.Less
In most cases, simulations of disordered materials are performed to understand experimental observations, in this case diffraction data. This chapter discusses the calculation of several experimental quantities: single crystal diffuse scattering, powder diffraction, and the atomic pair distribution function (PDF). Since diffraction data are obtained via a Fourier transform, the finite size of the model crystal as well as issues concerning coherence are discussed in detail. The PDF is basically calculated from the atomic structure directly. Different ways to incorporate thermal motion are illustrated.
DOUGLAS L. DORSET
- Published in print:
- 2004
- Published Online:
- September 2007
- ISBN:
- 9780198529088
- eISBN:
- 9780191712838
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780198529088.003.0001
- Subject:
- Physics, Crystallography
This chapter introduces the problem of polydispersity for understanding properties of materials containing polymethylene chains. A model has been proposed for the assembly of molecular chains in a ...
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This chapter introduces the problem of polydispersity for understanding properties of materials containing polymethylene chains. A model has been proposed for the assembly of molecular chains in a petroleum waxes that will remain a focal point for later discussions in the book. The energetics of molecular crystalline polymorphism is discussed as are the methods used for the construction and interpretation of binary phase diagrams. Variances to symmetry rules for chain co-solubility proposed by A. I. Kitaigorodskii are presented for further consideration in later chapters.Less
This chapter introduces the problem of polydispersity for understanding properties of materials containing polymethylene chains. A model has been proposed for the assembly of molecular chains in a petroleum waxes that will remain a focal point for later discussions in the book. The energetics of molecular crystalline polymorphism is discussed as are the methods used for the construction and interpretation of binary phase diagrams. Variances to symmetry rules for chain co-solubility proposed by A. I. Kitaigorodskii are presented for further consideration in later chapters.
DOUGLAS L. DORSET
- Published in print:
- 2004
- Published Online:
- September 2007
- ISBN:
- 9780198529088
- eISBN:
- 9780191712838
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780198529088.003.0002
- Subject:
- Physics, Crystallography
This chapter discusses energetic principles important for the close packing of linear polymethylene chains that lead to favoured layer packing arrays, revealing that a hard sphere repulsive model is ...
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This chapter discusses energetic principles important for the close packing of linear polymethylene chains that lead to favoured layer packing arrays, revealing that a hard sphere repulsive model is a good first approximation. The methylene subcell concept is introduced, both from a theoretical basis as well as from observation, based on known crystal structures of representative materials. Convenient methods for identifying methylene subcells, based on powder diffraction, electron diffraction, and infrared spectroscopy, are presented.Less
This chapter discusses energetic principles important for the close packing of linear polymethylene chains that lead to favoured layer packing arrays, revealing that a hard sphere repulsive model is a good first approximation. The methylene subcell concept is introduced, both from a theoretical basis as well as from observation, based on known crystal structures of representative materials. Convenient methods for identifying methylene subcells, based on powder diffraction, electron diffraction, and infrared spectroscopy, are presented.
Naomi E. Chayen
- Published in print:
- 2007
- Published Online:
- September 2007
- ISBN:
- 9780198520979
- eISBN:
- 9780191706295
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780198520979.003.0003
- Subject:
- Biology, Biochemistry / Molecular Biology
The availability of high-quality crystals is crucial to the structure determination of proteins by X-ray diffraction. It is still not understood why some proteins crystallize with ease while others ...
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The availability of high-quality crystals is crucial to the structure determination of proteins by X-ray diffraction. It is still not understood why some proteins crystallize with ease while others stubbornly refuse to produce suitable crystals. Producing high-quality crystals has always been the bottleneck to structure determination and with the advent of structural genomics this problem is becoming increasingly acute. In spite of impressive advances in throughput, the crystallization problem has not been solved and better crystallization techniques need to be designed in order to overcome this hurdle. Finding favourable conditions for crystallization is usually achieved by screening of the protein solution with numerous crystallizing agents in order to find ‘hits’ that indicate which conditions may be suitable for crystal growth. Optimization of the crystallization conditions is done either by fine tuning of the parameters (precipitant, pH, temperature, additives, etc.) involved, or by manipulation of the crystallization phase diagram with the aim of guiding the experiment in the direction that will produce the desired results. This chapter highlights a variety of non-standard experimental methods of screening and optimization techniques with a focus on those that have been automated and can be adapted to high-throughput trials.Less
The availability of high-quality crystals is crucial to the structure determination of proteins by X-ray diffraction. It is still not understood why some proteins crystallize with ease while others stubbornly refuse to produce suitable crystals. Producing high-quality crystals has always been the bottleneck to structure determination and with the advent of structural genomics this problem is becoming increasingly acute. In spite of impressive advances in throughput, the crystallization problem has not been solved and better crystallization techniques need to be designed in order to overcome this hurdle. Finding favourable conditions for crystallization is usually achieved by screening of the protein solution with numerous crystallizing agents in order to find ‘hits’ that indicate which conditions may be suitable for crystal growth. Optimization of the crystallization conditions is done either by fine tuning of the parameters (precipitant, pH, temperature, additives, etc.) involved, or by manipulation of the crystallization phase diagram with the aim of guiding the experiment in the direction that will produce the desired results. This chapter highlights a variety of non-standard experimental methods of screening and optimization techniques with a focus on those that have been automated and can be adapted to high-throughput trials.
H. M. Krishna Murthy
- Published in print:
- 2007
- Published Online:
- September 2007
- ISBN:
- 9780198520979
- eISBN:
- 9780191706295
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780198520979.003.0008
- Subject:
- Biology, Biochemistry / Molecular Biology
From a relatively small beginning, nearly two decades ago, phase calculation using multiple-wavelength anomalous diffraction (MAD) data has become more widespread and generally used. This chapter ...
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From a relatively small beginning, nearly two decades ago, phase calculation using multiple-wavelength anomalous diffraction (MAD) data has become more widespread and generally used. This chapter discusses the most recent developments and experimental details. Topics covered include the theoretical background of MAD phasing and some of the choices that need to be made in the design and implementation of MAD experiments.Less
From a relatively small beginning, nearly two decades ago, phase calculation using multiple-wavelength anomalous diffraction (MAD) data has become more widespread and generally used. This chapter discusses the most recent developments and experimental details. Topics covered include the theoretical background of MAD phasing and some of the choices that need to be made in the design and implementation of MAD experiments.
