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  • Articles  (11,625)
  • American Physical Society  (10,570)
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  • Annual Reviews
  • 2000-2004  (11,625)
  • 2003  (11,625)
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  • 2000-2004  (11,625)
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  • 1
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 47-67 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Optical single transporter recording (OSTR) is an emerging technique for the fluorescence microscopic measurement of transport kinetics in membrane patches. Membranes are attached to transparent microarrays of cylindrical test compartments (TCs) ~0.1-100 mum in diameter and ~10-100 mum in depth. Transport across membrane patches that may contain single transporters or transporter populations is recorded by confocal microscopy. By these means transport of proteins through single nuclear pore complexes has been recorded at rates of 〈1 translocation/s. In addition to the high sensitivity in terms of measurable transport rates OSTR features unprecedented spatial selectivity and parallel processing. This article reviews the conceptual basis of OSTR and its realization. Applications to nuclear transport are summarized. The further development of OSTR is discussed and its extension to a diversity of transporters, including translocases and ATP-binding cassette (ABC) pumps, projected.
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  • 2
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 93-114 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Since mid-1990, with cloning and identification of several families of natural killer (NK) receptors, research on NK cells began to receive appreciable attention. Determination of structures of NK cell surface receptors and their ligand complexes led to a fast growth in our understanding of the activation and ligand recognition by these receptors as well as their function in innate immunity. Functionally, NK cell surface receptors are divided into two groups, the inhibitory and the activating receptors. Structurally, they belong to either the immunoglobulin (Ig)-like receptor superfamily or the C-type lectin-like receptor (CTLR) superfamily. Their ligands are either members of class I major histocompatibility complexes (MHC) or homologs of class I MHC molecules. The inhibitory form of NK receptors provides the protective immunity through recognizing class I MHC molecules with self-peptides on healthy host cells. The activating, or the noninhibitory, NK receptors mediate the killing of tumor or virally infected cells through their specific ligand recognition. The structures of activating and inhibitory NK cell surface receptors and their complexes with the ligands determined to date, including killer immunoglobulin-like receptors (KIRs) and their complexes with HLA molecules, CD94, Ly49A, and its complex with H-2Dd, and NKG2D receptors and their complexes with class I MHC homologs, are reviewed here.
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  • 3
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    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 161-182 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Recent years have witnessed a renaissance of fluorescence microscopy techniques and applications, from live-animal multiphoton confocal microscopy to single-molecule fluorescence spectroscopy and imaging in living cells. These achievements have been made possible not so much because of improvements in microscope design, but rather because of development of new detectors, accessible continuous wave and pulsed laser sources, sophisticated multiparameter analysis on one hand, and the development of new probes and labeling chemistries on the other. This review tracks the lineage of ideas and the evolution of thinking that have led to the actual developments, and presents a comprehensive overview of the field, with emphasis put on our laboratory's interest in single-molecule microscopy and spectroscopy.
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  • 4
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    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 135-159 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The lamba integrase, or tyrosine-based family of site-specific recombinases, plays an important role in a variety of biological processes by inserting, excising, and inverting DNA segments. Flp, encoded by the yeast 2-mum plasmid, is the best-characterized eukaryotic member of this family and is responsible for maintaining the copy number of this plasmid. Over the past several years, structural and biochemical studies have shed light on the details of a common catalytic scheme utilized by these enzymes with interesting variations under different biological contexts. The emergence of new Flp structures and solution data provides insights not only into its unique mechanism of active site assembly and activity regulation but also into the specific contributions of certain protein residues to catalysis.
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  • 5
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    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 285-310 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The past decade has witnessed increasingly detailed insights into the structural mechanism of the bacteriorhodopsin photocycle. Concurrently, there has been much progress within our knowledge pertaining to the lipids of the purple membrane, including the discovery of new lipids and the overall effort to localize and identify each lipid within the purple membrane. Therefore, there is a need to classify this information to generalize the findings. We discuss the properties and roles of haloarchaeal lipids and present the structural data as individual case studies. Lipid-protein interactions are discussed in the context of structure-function relationships. A brief discussion of the possibility that bacteriorhodopsin functions as a light-driven inward hydroxide pump rather than an outward proton pump is also presented.
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  • 6
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    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 375-397 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract G protein-coupled receptors (GPCRs) are integral membrane proteins that respond to environmental signals and initiate signal transduction pathways activating cellular processes. Rhodopsin is a GPCR found in rod cells in retina where it functions as a photopigment. Its molecular structure is known from cryo-electron microscopic and X-ray crystallographic studies, and this has reshaped many structure/function questions important in vision science. In addition, this first GPCR structure has provided a structural template for studies of other GPCRs, including many known drug targets. After presenting an overview of the major structural elements of rhodopsin, recent literature covering the use of the rhodopsin structure in analyzing other GPCRs will be summarized. Use of the rhodopsin structural model to understand the structure and function of other GPCRs provides strong evidence validating the structural model.
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  • 7
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    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 399-424 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The coupling of high-performance mass spectrometry instrumentation with highly efficient chromatographic and electrophoretic separations has enabled rapid qualitative and quantitative analysis of thousands of proteins from minute samples of biological materials. Here, we review recent progress in the development and application of mass spectrometry-based techniques for the qualitative and quantitative analysis of global proteome samples derived from whole cells, tissues, or organisms. Techniques such as multidimensional peptide and protein separations coupled with mass spectrometry, accurate mass measurement of peptides from global proteome digests, and mass spectrometric characterization of intact proteins hold great promise for characterization of highly complex protein mixtures. Advances in chemical tagging and isotope labeling techniques have enabled quantitative analysis of proteomes, and highly specific isolation strategies have been developed aimed at selective analysis of posttranslationally modified proteins.
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  • 8
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    Annual Review of Fluid Mechanics 35 (2003), S. 1-10 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
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  • 9
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    Annual Review of Fluid Mechanics 35 (2003), S. 45-62 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Abstract Drag reduction in wall-bounded flows can be achieved by transverse motions imposed by passive means, e.g., riblets, or by external forcing, such as wall oscillation or transverse traveling-wave excitation. In this article, we review possible physical mechanisms responsible for turbulent drag reduction and corresponding near-wall flow modification.
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  • 10
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    Annual Review of Fluid Mechanics 35 (2003), S. 89-111 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Abstract In this review we describe the aerodynamic problems that must be addressed in order to design a successful small aerial vehicle. The effects of Reynolds number and aspect ratio (AR) on the design and performance of fixed-wing vehicles are described. The boundary-layer behavior on airfoils is especially important in the design of vehicles in this flight regime. The results of a number of experimental boundary-layer studies, including the influence of laminar separation bubbles, are discussed. Several examples of small unmanned aerial vehicles (UAVs) in this regime are described. Also, a brief survey of analytical models for oscillating and flapping-wing propulsion is presented. These range from the earliest examples where quasi-steady, attached flow is assumed, to those that account for the unsteady shed vortex wake as well as flow separation and aeroelastic behavior of a flapping wing. Experiments that complemented the analysis and led to the design of a successful ornithopter are also described.
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  • 11
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    Annual Review of Fluid Mechanics 35 (2003), S. 135-167 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Abstract The issue of the physical mechanism(s) that control the efficiency with which the density field in stably stratified fluid is mixed by turbulent processes has remained enigmatic. Similarly enigmatic has been an explanation of the numerical value of ~0.2, which is observed to characterize this efficiency experimentally. We review recent work on the turbulence transition in stratified parallel flows that demonstrates that this value is not only numerically predictable but also that it is expected to be a nonmonotonic function of the Richardson number that characterizes preturbulent stratification strength. This value of the mixing efficiency appears to be characteristic of the late-time behavior of the turbulent flow that develops after an initially laminar shear flow has undergone the transition to turbulence through an intermediate instability of Kelvin-Helmholtz type.
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  • 12
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    Annual Review of Fluid Mechanics 35 (2003), S. 373-412 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Abstract Recent small-scale turbulence observations allow the mixing regimes in lakes, reservoirs, and other enclosed basins to be categorized into the turbulent surface and bottom boundary layers as well as the comparably quiet interior. The surface layer consists of an energetic wave-affected thin zone at the very top and a law-of-the-wall layer right below, where the classical logarithmic-layer characteristic applies on average. Short-term current and dissipation profiles, however, deviate strongly from any steady state. In contrast, the quasi-steady bottom boundary layer behaves almost perfectly as a logarithmic layer, although periodic seiching modifies the structure in the details. The interior stratified turbulence is extremely weak, even though much of the mechanical energy is contained in baroclinic basin-scale seiching and Kelvin waves or inertial currents (large lakes). The transformation of large-scale motions to turbulence occurs mainly in the bottom boundary and not in the interior, where the local shear remains weak and the Richardson numbers are generally large.
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  • 13
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    Annual Review of Fluid Mechanics 35 (2003), S. 469-496 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Abstract Increasing urbanization and concern about sustainability and quality of life issues have produced considerable interest in flow and dispersion in urban areas. We address this subject at four scales: regional, city, neighborhood, and street. The flow is one over and through a complex array of structures. Most of the local fluid mechanical processes are understood; how these combine and what is the most appropriate framework to study and quantify the result is less clear. Extensive and structured experimental databases have been compiled recently in several laboratories. A number of major field experiments in urban areas have been completed very recently and more are planned. These have aided understanding as well as model development and evaluation.
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  • 14
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    Annual Review of Fluid Mechanics 35 (2003), S. 295-315 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Abstract It is classically assumed that the far field of a round turbulent jet discharging into quiescent fluid has a unique behavior characterized only by its momentum flux. However, there is now considerable evidence that different discharge conditions at the jet nozzle exit can give rise to very different far-field flows. Perhaps the most striking examples of these are the bifurcating and blooming jets produced by appropriate combinations of controlled axial and circumferential excitations at the nozzle exit. With the right excitations, a jet can be made to divide into two separate jets (bifurcating jet), each of which carries half the axial momentum and spreads in a manner similar to a single jet. Trifurcating jets can also be produced. Other excitations can produce blooming jets, in which the jet explodes into a shower of vortex rings, producing a far-field flow that is quite unlike a normal unexcited jet. Bifurcating and blooming jets exhibit much greater mixing than normal jets, suggesting possible applications in flow control. This article summarizes our work on bifurcating and blooming jets, which began with our discovery of them in the early 1980s and continued through the mid- 1990s. One of us (D.E.P.) continued exploration of flow control using excited jets, first at the McDonnell Douglas Corporation, and more recently at the Georgia Institute of Technology. The key to flow control is the manipulation of the large vortical structures in the near field of the jet. Ultimately this work, and that of others, led to full-scale testing of jet engine exhaust mixing control. There it was shown that the jet temperature downstream of the engine can be very significantly reduced by application of well-designed and easily implemented excitation at the engine discharge, thereby solving problems encountered during ground operations. Related jet control work by other investigators is included in this review.
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  • 15
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    Annual Review of Fluid Mechanics 35 (2003), S. 413-440 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Abstract The recent progress in three-dimensional boundary-layer stability and transition is reviewed. The material focuses on the crossflow instability that leads to transition on swept wings and rotating disks. Following a brief overview of instability mechanisms and the crossflow problem, a summary of the important findings of the 1990s is given.
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  • 16
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    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 183-206 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Cyclooxygenases-1 and -2 (COX-1 and COX-2, also known as prostaglandin H2 synthases-1 and -2) catalyze the committed step in prostaglandin synthesis. COX-1 and -2 are of particular interest because they are the major targets of nonsteroidal antiinflammatory drugs (NSAIDs) including aspirin, ibuprofen, and the new COX-2-selective inhibitors. Inhibition of the COXs with NSAIDs acutely reduces inflammation, pain, and fever, and long-term use of these drugs reduces the incidence of fatal thrombotic events, as well as the development of colon cancer and Alzheimer's disease. In this review, we examine how the structures of COXs relate mechanistically to cyclooxygenase and peroxidase catalysis and how alternative fatty acid substrates bind within the COX active site. We further examine how NSAIDs interact with COXs and how differences in the structure of COX-2 result in enhanced selectivity toward COX-2 inhibitors.
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  • 17
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    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 425-443 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Understanding the action of enzymes on an atomistic level is one of the important aims of modern biophysics. This review describes the state of the art in addressing this challenge by simulating enzymatic reactions. It considers different modeling methods including the empirical valence bond (EVB) and more standard molecular orbital quantum mechanics/molecular mechanics (QM/MM) methods. The importance of proper configurational averaging of QM/MM energies is emphasized, pointing out that at present such averages are performed most effectively by the EVB method. It is clarified that all properly conducted simulation studies have identified electrostatic preorganization effects as the source of enzyme catalysis. It is argued that the ability to simulate enzymatic reactions also provides the chance to examine the importance of nonelectrostatic contributions and the validity of the corresponding proposals. In fact, simulation studies have indicated that prominent proposals such as desolvation, steric strain, near attack conformation, entropy traps, and coherent dynamics do not account for a major part of the catalytic power of enzymes. Finally, it is pointed out that although some of the issues are likely to remain controversial for some time, computer modeling approaches can provide a powerful tool for understanding enzyme catalysis.
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  • 18
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    Annual Review of Astronomy and Astrophysics 41 (2003), S. 15-56 
    ISSN: 0066-4146
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
    Notes: The galaxies of the Local Group serve as important laboratories for understanding the physics of massive stars. Here I discuss what is involved in identifying various kinds of massive stars in nearby galaxies: the hydrogen-burning O-type stars and their evolved He-burning evolutionary descendants, the luminous blue variables, red supergiants, and Wolf-Rayet stars. Primarily I review what our knowledge of the massive star population in nearby galaxies has taught us about stellar evolution and star formation. I show that the current generation of stellar evolutionary models do well at matching some of the observed features and provide a look at the sort of new observational data that will provide a benchmark against which new models can be evaluated.
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    Annual Review of Astronomy and Astrophysics 41 (2003), S. 169-189 
    ISSN: 0066-4146
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
    Notes: The first law of theoretical physics, the Newtonian law of gravitation, relies on the concept of action at a distance. The success of this law led to the concept being applied to electricity and magnetism, which were next to be explored in depth. Here the action at a distance had a limited success and ultimately had to be abandoned in favor of the increasingly more popular field theory. Nevertheless, in the 1940s, an attempt was made to revive the concept of action at a distance in a relativistically invariant way by Wheeler & Feynman (1945, 1949). It inspired a series of investigations in both electrodynamics and gravity in which the field concept was not used but the interaction was described as taking place directly between particles. As it impinged very intimately on cosmology, Hoyle was keenly interested in it. This review discusses the work by Hoyle, the author, and others on the development of electrodynamics and gravitation as direct particle theories. In this review, the author discusses how the work was started and went through stages of increasing sophistication, e.g., extending the Wheeler-Feynman electrodynamics to curved spacetime, its consequences in different cosmologies, and the issues arising from its quantization. The resolution of ultraviolet divergences in quantum electrodynamics is also briefly discussed. The parallel development of a Machian theory of gravitation followed the lead from electrodynamics. In both theories one sees a strong link between the large-scale structure of the universe and local physics, as might be expected from an action-at-a-distance framework.
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    Annual Review of Astronomy and Astrophysics 41 (2003), S. 343-390 
    ISSN: 0066-4146
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
    Notes: Targeted laboratory astrophysics measurements are being conducted to address the needs of X-ray astronomy. The measurements are producing large sets of reliable atomic data, which include ionization and recombination cross sections for charge balance calculations, as well as line lists, excitation cross sections, and dielectronic recombination rates for interpreting X-ray line formation. Additional experiments focus on resolving specific puzzles posed by astrophysical observations, as well as on calibrating existing and developing new X-ray line diagnostics. We discuss the types of data produced and illustrate how the laboratory measurements support such missions as ASCA, EUVE, Chandra, XMM, and ASTRO-E2.
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    Annual Review of Astronomy and Astrophysics 41 (2003), S. 517-554 
    ISSN: 0066-4146
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
    Notes: Photoionized clouds are ubiquitous. They define the endpoints of stellar evolution (H II regions and planetary nebulae), constitute the interstellar and intergalactic media, and are found in high redshift quasars and star-forming galaxies. The spectra of these objects are dominated by emission lines that are sensitive to details of the emitting gas. These details include the microscopic atomic processes that cause the gas to glow; the density, composition, and temperature of the gas; and the radiation field of the central continuum source. Large-scale numerical codes that incorporate all the needed physics and predict the observed spectrum have become essential tools in understanding these objects. This article reviews the current status of the numerical simulations of emitting gas, with particular emphasis on photoionized clouds and the underlying simplicity that governs these nebulae; the types of questions that can be addressed by today's codes; and the big questions that remain unanswered.
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    Annual Review of Fluid Mechanics 35 (2003), S. 169-182 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Abstract The modern study of a crowd as a flowing continuum is a recent development. Distinct from a classical fluid because of the property that a crowd has the capacity to think, interesting new physical ideas are involved in its study. An appealing property of a crowd in motion is that the nonlinear, time-dependent, simultaneous equations representing a crowd are conformably mappable. This property makes many interesting applications analytically tractable. In this review examples are given in which the theory has been used to provide possible assistance in the annual Muslim Hajj, to understand the Battle of Agincourt, and, surprisingly, to locate barriers that actually increase the flow of pedestrians above that when there are no barriers present. Modern developments may help prevent some of the approximately two thousand deaths that annually occur in accidents owing to crowding.The field of crowd motion, that is, the field of "thinking fluids," is an intriguing area of research with great promise.
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    Annual Review of Fluid Mechanics 35 (2003), S. 267-293 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Abstract The recent avalanche of research activity in the field of granular matter has yielded much progress. The use of state-of-the-art (and other) computational and experimental methods has led to the discovery of new states and patterns and enabled detailed tests of theories and models. The application of statistical mechanical methods and phenomenology has contributed to the understanding of the microscopic a nd macroscopic properties of granular systems. Some previously open problems seem to be solved. Fluidized granular systems (rapid granular flows), recently referred to as granular gases, are often modeled by hydrodynamic equations of motion, some of which are based on systematic expansions applied to the pertinent Boltzmann equation. The undeniable success of granular hydrodynamics is somewhat surprising in view of the lack of scale separation in these systems and the neglect of certain correlations in most derivations of the hydrodynamic equations. Microstructures have been recognized as key features of granular gases; explanations for their existence have been proposed, and many of their properties elucidated. Granular-gas multistability can often be traced back to microstructure dynamics. In spite of these and other impressive advances, this field still poses serious challenges.
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    Annual Review of Fluid Mechanics 35 (2003), S. 317-340 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Abstract Recent advances in achieving textbook multigrid efficiency for fluid simulations are presented. Textbook multigrid efficiency is defined as attaining the solution to the governing system of equations in a computational work that is a small multiple of the operation counts associated with discretizing the system. Strategies are reviewed to attain this efficiency by exploiting the factorizability properties inherent to a range of fluid simulations, including the compressible Navier-Stokes equations. Factorizability is used to separate the elliptic and hyperbolic factors contributing to the target system; each of the factors can then be treated individually and optimally. Boundary regions and discontinuities are addressed with separate (local) treatments. New formulations and recent calculations demonstrating the attainment of textbook efficiency for aerodynamic simulations are shown.
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    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 1-25 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Mass spectrometry has provided a powerful method for monitoring hydrogen exchange of protein backbone amides with deuterium from solvent. In comparison to popular NMR approaches, mass spectrometry has the advantages of higher sensitivity, wider coverage of sequence, and the ability to analyze larger proteins. Proteolytic fragmentation of proteins following the exchange reaction provides moderate structural resolution, in some cases enabling measurements from single amides. The technique has provided new insight into protein-protein and protein-ligand interfaces, as well as conformational changes during protein folding or denaturation. In addition, recent studies illustrate the utility of hydrogen exchange mass spectrometry toward detecting protein motions relevant to allostery, covalent modifications, and enzyme function.
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    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 27-45 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Cations are bound to nucleic acids in a solvated state. High-resolution X-ray diffraction studies of oligonucleotides provide a detailed view of Mg2+, and occasionally other ions bound to DNA. In a survey of several such structures, certain general observations emerge. First, cations bind preferentially to the guanine base in the major groove or to phosphate group oxygen atoms. Second, cations interact with DNA most frequently via water molecules in their primary solvation shell, direct ion-DNA contacts being only rarely observed. Thus, the solvated ions should be viewed as hydrogen bond donors in addition to point charges. Finally, ion interaction sites are readily exchangeable: The same site may be occupied by any ion, including spermine, as well as by a water molecule.
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    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 69-92 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Although protein function is thought to depend on flexibility, precisely how the dynamics of the molecule and its environment contribute to catalytic mechanisms is unclear. We review experimental and computational work relating to enzyme dynamics and function, including the role of solvent. The evidence suggests that fast motions on the 100 ps timescale, and any motions coupled to these, are not required for enzyme function. Proteins where the function is electron transfer, proton tunneling, or ligand binding may have different dynamical dependencies from those for enzymes, and enzymes with large turnover numbers may have different dynamical dependencies from those that turn over more slowly. The timescale differences between the fastest anharmonic fluctuations and the barrier-crossing rate point to the need to develop methods to resolve the range of motions present in enzymes on different time- and lengthscales.
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    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 115-133 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The OB-fold domain is a compact structural motif frequently used for nucleic acid recognition. Structural comparison of all OB-fold/nucleic acid complexes solved to date confirms the low degree of sequence similarity among members of this family while highlighting several structural sequence determinants common to most of these OB-folds. Loops connecting the secondary structural elements in the OB-fold core are extremely variable in length and in functional detail. However, certain features of ligand binding are conserved among OB-fold complexes, including the location of the binding surface, the polarity of the nucleic acid with respect to the OB-fold, and particular nucleic acid-protein interactions commonly used for recognition of single-stranded and unusually structured nucleic acids. Intriguingly, the observation of shared nucleic acid polarity may shed light on the longstanding question concerning OB-fold origins, indicating that it is unlikely that members of this family arose via convergent evolution.
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    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 469-492 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The observation of liquid-liquid immiscibility in cholesterol-phospholipid mixtures in monolayers and bilayers has opened a broad field of research into their physical chemistry. Some mixtures exhibit multiple immiscibilities. This unusual property has led to a thermodynamic model of "condensed complexes." These complexes are the consequence of an exothermic, reversible reaction between cholesterol and phospholipids. In this quantitative model the complexes are sometimes concentrated in a separate liquid phase. The phase separation into a complex-rich phase depends on membrane composition and intensive variables such as temperature. The properties of defined cholesterol-phospholipid mixtures provide a conceptual foundation for the exploration of a number of aspects of the biophysics and biochemistry of animal cell membranes.
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    Annual Review of Astronomy and Astrophysics 41 (2003), S. 1-14 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
    Notes: Astrophysics has been an important part of my personal and scientific life three times. The first was in 1938 when I did work on stellar energy production. The second was a joyful period nearly 30 years later when that work was rewarded with the Nobel Prize in physics. And the third has lasted over the time since my retirement in 1975 during which Gerry Brown and I have had a very satisfactory collaboration exploring various aspects of supernovae and, more recently, binary pairs.
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    Annual Review of Astronomy and Astrophysics 41 (2003), S. 117-167 
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    Notes: Blueshifted absorption lines in the UV and X-ray spectra of active galaxies reveal the presence of massive outflows of ionized gas from their nuclei. The "intrinsic" UV and X-ray absorbers show large global covering factors of the central continuum source, and the inferred mass loss rates are comparable to the mass accretion rates. Many absorbers show variable ionic column densities, which are attributed to a combination of variable ionizing flux and motion of gas into and out of the line of sight. Detailed studies of the intrinsic absorbers, with the assistance of monitoring observations and photoionization models, provide constraints on their kinematics, physical conditions, and locations relative to the central continuum source, which range from the inner nucleus (~0.01 pc) to the galactic disk or halo (~10 kpc). Dynamical models that make use of thermal winds, radiation pressure, and/or hydromagnetic flows have reached a level of sophistication that permits comparisons with the observational constraints.
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    Annual Review of Astronomy and Astrophysics 41 (2003), S. 465-515 
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    Notes: Old, cool white dwarfs convey valuable information about the early history of our Galaxy. They have been used to determine the age of the galactic disk, several open clusters, and a globular cluster. We review the current understanding of the physics of cool white dwarfs, including their mass distribution, chemical evolution, magnetism, and cooling. We also examine the role of white dwarfs as tracers of various stellar populations, both in terms of observational searches and theoretical models.
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    Annual Review of Astronomy and Astrophysics 41 (2003), S. 429-463 
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    Notes: Giant planets have now been discovered around other stars, and it is only a matter of time until Earth-sized planets are detected. Whether any of these planets are suitable for life depends on their volatile abundances, especially water, and on their climates. Only planets within the liquid-water habitable zone (HZ) can support life on their surfaces and, thus, can be analyzed remotely to determine whether they are inhabited. Fortunately, current models predict that HZs are relatively wide around main-sequence stars not too different from our sun. This conclusion is based on studies of how our own planet has evolved over time. Earth's climate has remained conducive to life for the past 3.5 billion years or more, despite a large increase in solar luminosity, probably because of previous higher concentrations of CO2 and/or CH4. Both these gases are involved in negative feedback loops that help to stabilize the climate. In addition to these topics, we also briefly discuss the rise of atmospheric O2 and O3, along with their possible significance as indicators of life on other planets.
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    Annual Review of Astronomy and Astrophysics 41 (2003), S. 57-115 
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    Notes: Stellar clusters are born embedded within giant molecular clouds (GMCs) and during their formation and early evolution are often only visible at infrared wavelengths, being heavily obscured by dust. Over the past 15 years advances in infrared detection capabilities have enabled the first systematic studies of embedded clusters in galactic molecular clouds. In this article we review the current state of empirical knowledge concerning these extremely young protocluster systems. From a survey of the literature we compile the first extensive catalog of galactic embedded clusters. We use the catalog to construct the mass function and estimate the birthrate for embedded clusters within ~2 kpc of the sun. We find that the embedded cluster birthrate exceeds that of visible open clusters by an order of magnitude or more indicating a high infant mortality rate for protocluster systems. Less than 4-7% of embedded clusters survive emergence from molecular clouds to become bound clusters of Pleiades age. The vast majority (90%) of stars that form in embedded clusters form in rich clusters of 100 or more members with masses in excess of 50 Mo. Moreover, observations of nearby cloud complexes indicate that embedded clusters account for a significant (70-90%) fraction of all stars formed in GMCs. We review the role of embedded clusters in investigating the nature of the initial mass function (IMF) that, in one nearby example, has been measured over the entire range of stellar and substellar mass, from OB stars to substellar objects near the deuterium burning limit. We also review the role embedded clusters play in the investigation of circumstellar disk evolution and the important constraints they provide for understanding the origin of planetary systems. Finally, we discuss current ideas concerning the origin and dynamical evolution of embedded clusters and the implications for the formation of bound open clusters.
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    Annual Review of Astronomy and Astrophysics 41 (2003), S. 391-427 
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    Notes: In this contribution, a review is presented on the ample data obtained on post-AGB stars, both on the central stars and their circumstellar material. The fast evolutionary phase is characterized by a rapid change in the properties of the objects, but the variety is so large that there is yet no clear consensus on how the detailed studies of individual objects are linked together by evolutionary channels. The absence of strong molecular veiling in the photospheres of the central stars, together with a spread in intrinsic metallicity make post-AGB stars very useful in constraining AGB chemical evolutionary models. We discuss the surprisingly wide variety of chemical signatures observed. The onset in the creation process of the panoply of structures and shapes observed in planetary nebulae occurs during the short post-AGB evolution, but the physical nature of the processes involved is still badly understood. In the rapidly growing field of circumstellar mineralogy, post-AGB stars have their story to tell and also the molecular envelope changes significantly due to dilution and hardening of the stellar radiation. The real-time evolution of some objects suffering a late thermal flash is reviewed and their possible link to other hydrogen-deficient objects is discussed. Any review on stellar evolution has a section on binaries and this contribution is no exception because binaries make up a significant fraction of the post-AGB stars known to date.
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    Annual Review of Fluid Mechanics 35 (2003), S. 11-21 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Abstract Full-scale icing experiments and, therefore, certification time and cost can be significantly reduced by developing calculation methods to evaluate the aircraft and system performance for a wide range of icing conditions. This article summarizes calculation methods for icing that include ice accretion, ice system performance, and icing effects on aircraft.
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    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 207-235 
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    Notes: Abstract Structural and thermodynamic characterizations of a variety of intra- and intermolecular interactions stabilizing/destabilizing protein systems represent a major part of multidisciplinary efforts aimed at solving the problems of protein folding and binding. To this end, volumetric techniques have been successfully used to gain insights into protein hydration and intraglobular packing. Despite the fact that the use of volumetric measurements in protein-related studies dates back to the 1950s, such measurements still represent a relatively untapped yet potentially informative means for tackling the problems of protein folding and binding. This notion has been further emphasized by recent advances in the development of highly sensitive volumetric instrumentation that has led to intensifying volumetric investigations of protein systems. This paper reviews the volumetric properties of proteins and their low-molecular-weight analogs, in particular, discussing the recent progress in the use of volumetric data for studying conformational transitions of proteins as well as protein-ligand, protein-protein, and protein-nucleic acid interactions.
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    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 237-256 
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    Notes: Abstract This review focuses on cofactor-ligand and protein-protein interactions within the photosystem I reaction center. The topics include a description of the electron transfer cofactors, the mode of binding of the cofactors to protein-bound ligands, and a description of intraprotein contacts that ultimately allow photosystem I to be assembled (in cyanobacteria) from 96 chlorophylls, 22 carotenoids, 2 phylloquinones, 3 [4Fe-4S] clusters, and 12 polypeptides. During the 15 years that have elapsed from the first report of crystals to the atomic-resolution X-ray crystal structure, cofactor-ligand interactions and protein-protein interactions were systematically being explored by spectroscopic and genetic methods. This article charts the interplay between these disciplines and assesses how good the early insights were in light of the current structure of photosystem I.
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    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 257-283 
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    Notes: Abstract Lipid raft microdomains were conceived as part of a mechanism for the intracellular trafficking of lipids and lipid-anchored proteins. The raft hypothesis is based on the behavior of defined lipid mixtures in liposomes and other model membranes. Experiments in these well-characterized systems led to operational definitions for lipid rafts in cell membranes. These definitions, detergent solubility to define components of rafts, and sensitivity to cholesterol deprivation to define raft functions implicated sphingolipid- and cholesterol-rich lipid rafts in many cell functions. Despite extensive work, the basis for raft formation in cell membranes and the size of rafts and their stability are all uncertain. Recent work converges on very small rafts 〈10 nm in diameter that may enlarge and stabilize when their constituents are cross-linked.
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    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 335-373 
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    Notes: Abstract Molecular docking is an invaluable tool in modern drug discovery. This review focuses on methodological developments relevant to the field of molecular docking. The forces important in molecular recognition are reviewed and followed by a discussion of how different scoring functions account for these forces. More recent applications of computational chemistry tools involve library design and database screening. Last, we summarize several critical methodological issues that must be addressed in future developments.
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    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 311-334 
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    Notes: Abstract Acetylcholine binding protein (AChBP) has recently been identified from molluskan glial cells. Glial cells secrete it into cholinergic synapses, where it plays a role in modulating synaptic transmission. This novel mechanism resembles glia-dependent modulation of glutamate synapses, with several key differences. AChBP is a homolog of the ligand binding domain of the pentameric ligand-gated ion-channels. The crystal structure of AChBP provides the first high-resolution structure for this family of Cys-loop receptors. Nicotinic acetylcholine receptors and related ion-channels such as GABAA, serotonin 5HT3, and glycine can be interpreted in the light of the 2.7 A AChBP structure. The structural template provides critical details of the binding site and helps create models for toxin binding, mutational effects, and molecular gating.
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    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 445-468 
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    Notes: Abstract Active transport of cations is achieved by a large family of ATP-dependent ion pumps, known as P-type ATPases. Various members of this family have been targets of structural and functional investigations for over four decades. Recently, atomic structures have been determined for Ca2+-ATPase by X-ray crystallography, which not only reveal the architecture of these molecules but also offer the opportunity to understand the structural mechanisms by which the energy of ATP is coupled to calcium transport across the membrane. This energy coupling is accomplished by large-scale conformational changes. The transmembrane domain undergoes plastic deformations under the influence of calcium binding at the transport site. Cytoplasmic domains undergo dramatic rigid-body movements that deliver substrates to the catalytic site and that establish new domain interfaces. By comparing various structures and correlating functional data, we can now begin to associate the chemical changes constituting the reaction cycle with structural changes in these domains.
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    Annual Review of Astronomy and Astrophysics 41 (2003), S. 191-239 
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    Topics: Physics
    Notes: We review the origin, evolution, and physical nature of hot gas in elliptical galaxies and associated galaxy groups. Unanticipated recent X-ray observations with Chandra and XMM indicate much less cooling than previously expected. Consequently, many long-held assumptions must be reexamined or discarded and new approaches must be explored. Chief among these are the role of heating by active galactic nuclei, the influence of radio lobes on the hot gas, details of the cooling process, possible relation between the hot and colder gas in elliptical galaxies, and the complexities of stellar enrichment of the hot gas.
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    Annual Review of Astronomy and Astrophysics 41 (2003), S. 241-289 
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    Topics: Physics
    Notes: This review surveys the observed properties of interstellar dust grains: the wavelength-dependent extinction of starlight, including absorption features, from UV to infrared; optical luminescence; infrared emission; microwave emission; optical, UV, and X-ray scattering by dust; and polarization of starlight and of infrared emission. The relationship between presolar grains in meteorites and the interstellar grain population is discussed. Candidate grain materials and abundance constraints are considered. A dust model consisting of amorphous silicate grains, graphite grains, and polycyclic aromatic hydrocarbons is compared with observed emission and scattering. Some issues concerning evolution of interstellar dust are discussed.
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    Annual Review of Astronomy and Astrophysics 41 (2003), S. 555-597 
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    Topics: Physics
    Notes: The status of our current understanding of angular momentum transport in accretion disks is reviewed. The last decade has seen a dramatic increase both in the recognition of key physical processes and in our ability to carry through direct numerical simulations of turbulent flow. Magnetic fields have at once powerful and subtle influences on the behavior of (sufficiently) ionized gas, rendering them directly unstable to free energy gradients. Outwardly descreasing angular velocity profiles are unstable. The breakdown of Keplerian rotation into MHD turbulence may be studied in some numerical detail, and key transport coefficients may be evaluated. Chandra observations of the Galactic Center support the existence of low luminosity accretion, which may ultimately prove amenable to global three-dimensional numerical simulation.
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    Annual Review of Astronomy and Astrophysics 41 (2003), S. 599-643 
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    Topics: Physics
    Notes: Helioseismology has transformed our knowledge of the Sun's rotation. Earlier studies revealed the Sun's surface rotation, but now a detailed observational picture has been built up of the internal rotation of our nearest star. Unlike the predictions of stellar-evolution models, the radiative interior is found to rotate roughly uniformly. The rotation within the convection zone is also very different from prior expectations, which had been that the rotation rate would depend primarily on the distance from the rotation axis. Layers of rotational shear have been discovered at the base of the convection zone and in the subphotospheric layers. Studies of the time variation of rotation have uncovered zonal-flow bands, extending through a substantial fraction of the convection zone, which migrate over the course of the solar cycle, and there are hints of other temporal variations and of a jet-like structure. At the same time, building on earlier work with mean-field models, researchers have made great progress in supercomputer simulations of the intricate interplay between turbulent convection and rotation in the Sun's interior. Such studies are beginning to transform our understanding of how rotation organizes itself in a stellar interior.
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    Annual Review of Astronomy and Astrophysics 41 (2003), S. 291-342 
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    Topics: Physics
    Notes: The launches of the Chandra X-Ray Observatory in June 1999 and the XMM-Newton Observatory in December 1999 opened a new era in X-ray astronomy. Both of these missions incorporate novel diffraction grating spectrometers that are providing the first high-resolution X-ray spectra of most classes of astrophysical sources. The spectra obtained to date exhibit a wealth of discrete detail, yielding sensitive constraints on physical conditions in the emitting plasmas. We review the essential characteristics of these instruments, the basics of X-ray spectral formation in cosmic sources, and the exciting new results that have emerged from Chandra and XMM-Newton grating observations of a wide variety of astrophysical systems.
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    Annual Review of Astronomy and Astrophysics 41 (2003), S. 645-668 
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    Topics: Physics
    Notes: Weak gravitational lensing provides a unique method to map directly the distribution of dark matter in the universe and to measure cosmological parameters. This cosmic-shear technique is based on the measurement of the weak distortions that lensing induces in the shape of background galaxies as photons travel through large-scale structures. This technique is now widely used to measure the mass distribution of galaxy clusters and has recently been detected in random regions of the sky. In this review, we present the theory and observational status of cosmic shear. We describe the principles of weak lensing and the predictions for the shear statistics in favored cosmological models. Next, we review the current measurements of cosmic shear and show how they constrain cosmological parameters. We then describe the prospects offered by upcoming and future cosmic-shear surveys as well as the technical challenges that have to be met for the promises of cosmic shear to be fully realized.
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    Annual Review of Fluid Mechanics 35 (2003), S. 23-43 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Abstract The more violent impacts of water waves on walls create velocities and pressures having magnitudes much larger than those associated with the propagation of ordinary waves under gravity. Insight into these effects has been gained by irrotational-flow computations and by investigating the role of entrained and trapped air in wave impacts. This review focuses on the results of theoretical work, making particular note of the value of considering pressure impulse, and highlights the aspects that are poorly understood.
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    Annual Review of Fluid Mechanics 35 (2003), S. 63-88 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Abstract This paper reviews recent advances in our understanding of the origin and hierarchy of organized flow structures in fluidized beds, distinction between bubbling and nonbubbling systems, and stages of bubble evolution. Experimental data and theory suggest that, at high particle concentrations, the particle-phase pressure arising from flow-induced velocity fluctuations decreases with increasing concentration of particles. This, in turn, implies that nonhydrodynamic stresses must be present to impart stability to a uniformly fluidized bed at very high particle concentrations. There is ample evidence to support an argument that, in commonly encountered gas-fluidized beds, yield stresses associated with enduring particle networks are present in the window of stable bed expansion, where the particles are essentially immobile until bubbling commences. However, some recent data on gas-fluidized beds of agglomerates of cohesive particles suggest that there exists a window of bed expansion where the bed does manifest a smooth appearance to the naked eye and the particles are mobile; at higher gas velocities the bed bubbles visibly. The mechanics of such beds remain to be fully explained.
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    Annual Review of Fluid Mechanics 35 (2003), S. 113-133 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Abstract A review is given of the stability of complex fluids subject to homogeneous states of shearing, a research field that is scarcely two decades old. For the benefit of fluid mechanicians, a brief, somewhat historical overview is presented of material instability in elastoplastic solids, where one finds a considerable body of experiment and a rich source of theoretical concepts including Hadamard instability, strain localization, and nonlocal constitutive models. A survey is then given of recent theoretical and experimental studies of instability with shear banding in various complex fluids, including micellar solutions, particulate suspensions, and rapidly sheared granular media. Various stability analyses are encapsulated in a mathematical dynamical-systems model for constitutive equations of the rate-type, and a general linear-stability theory is given for viscoelastic fluids in unbounded homogeneous shear flows. A general form of (Kelvin) wave-vector stretching is shown to play a key role in the growth of Fourier modes, as illustrated by recent computations for granular shear flow. The Fourier description also provides an explicit representation of higher-gradient (nonlocal) effects as higher-order powers of wave number.
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    Annual Review of Fluid Mechanics 35 (2003), S. 183-227 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Abstract Turbulence is ubiquitous in atmospheric clouds, which have enormous turbulence Reynolds numbers owing to the large range of spatial scales present. Indeed, the ratio of energy-containing and dissipative length scales is on the order of 105 for a typical convective cloud, with a corresponding large-eddy Reynolds number on the order of 106 to 107. A characteristic trait of high-Reynolds-number turbulence is strong intermittency in energy dissipation, Lagrangian acceleration, and scalar gradients at small scales. Microscale properties of clouds are determined to a great extent by thermodynamic and fluid-mechanical interactions between droplets and the surrounding air, all of which take place at small spatial scales. Furthermore, these microscale properties of clouds affect the efficiency with which clouds produce rain as well as the nature of their interaction with atmospheric radiation and chemical species. It is expected, therefore, that fine-scale turbulence is of direct importance to the evolution of, for example, the droplet size distribution in a cloud. In general, there are two levels of interaction that are considered in this review: (a) the growth of cloud droplets by condensation and (b) the growth of large drops through the collision and coalescence of cloud droplets. Recent research suggests that the influence of fine-scale turbulence on the condensation process may be limited, although several possible mechanisms have not been studied in detail in the laboratory or the field. There is a growing consensus, however, that the collision rate and collision efficiency of cloud droplets can be increased by turbulence-particle interactions. Adding strength to this notion is the growing experimental evidence for droplet clustering at centimeter scales and below, most likely due to strong fluid accelerations in turbulent clouds. Both types of interaction, condensation and collision-coalescence, remain open areas of research with many possible implications for the physics of atmospheric clouds.
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    Annual Review of Fluid Mechanics 35 (2003), S. 229-265 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Abstract This review describes some of the important developments in the numerical investigation of transition to turbulence in wall-bounded and free shear flows during the past decade. The evolution of numerical techniques and models as well as the advances in our theoretical understanding of the physics of laminar-turbulent transition that were achieved using these tools are described. For wall-bounded flows, particular emphasis is placed on investigations studying various scenarios of "bypass transition" in flows that are asymptotically stable. A brief review of investigations into receptivity and control of transitional flows is included.
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    Annual Review of Fluid Mechanics 35 (2003), S. 341-372 
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    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Abstract We provide an overview of level set methods, introduced by Osher and Sethian, for computing the solution to fluid-interface problems. These are computational techniques that rely on an implicit formulation of the interface, represented through a time-dependent initial-value partial-differential equation. We discuss the essential ideas behind the techniques, the coupling of these techniques to finite-difference methods for incompressible and compressible flow, and a collection of applications including two-phase flow, ship hydrodynamics, and ink-jet-printhead design.
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    Annual Review of Fluid Mechanics 35 (2003), S. 441-468 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Abstract We review the most important theoretical and numerical results obtained in the realm of shell models for the energy-turbulent cascade. We mainly focus here on those results that had or will have some impact on the fluid-dynamics community. In particular, we address the problem of small-scale intermittency by discussing energy-helicity interactions, energy-dissipation multifractality, and universality of intermittency, i.e., independence of anomalous scaling exponents from large-scale forcing and boundary conditions. A multifractal-based description of multiscale and multitime correlation functions in turbulence is also presented. Finally, we also briefly review the analytical difficulties, and hopes, of calculating anomalous exponents.
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    Annual Review of Earth and Planetary Sciences 31 (2003), S. 555-577 
    ISSN: 0084-6597
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Geosciences , Physics
    Notes: Abstract We present preliminary evidence for a ~10,000-year earthquake record from two major fault systems based on sediment cores collected along the continental margins of western North America. New stratigraphic evidence from Cascadia demonstrates that 13 earthquakes ruptured the entire margin from Vancouver Island to at least the California border since the eruption of the Mazama ash 7700 years ago. The 13 events above this prominent stratigraphic marker have an average repeat time of 600 years, and the youngest event ~300 years ago coincides with the coastal record. We also extend the record of past earthquakes to the base of the Holocene (at least 9800 years ago), during which 18 events correlate along the same region. The sequence of Holocene events in Cascadia appears to contain a repeating pattern of events, a tantalizing first look at what may be the long-term behavior of a major fault system. The northern California margin cores show a cyclic record of turbidite beds that may represent Holocene earthquakes on the northern segment of the San Andreas Fault. Preliminary results are in reasonably good agreement with onshore paleoseismic data that indicate an age for the penultimate event in the mid-1600s at several sites and the most likely age for the third event of ~AD 1300.
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    Annual Review of Earth and Planetary Sciences 31 (2003), S. 399-427 
    ISSN: 0084-6597
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Geosciences , Physics
    Notes: Abstract Considerable progress has been made over the past decade in understanding the static rheological properties of granitic magmas in the continental crust. Changes in H2O content, CO2 content, and oxidation state of the interstitial melt phase have been identified as important compositional factors governing the rheodynamic behavior of the solid/fluid mixture. Although the strengths of granitic magmas over the crystallization interval are still poorly constrained, theoretical investigations suggest that during magma ascent, yield strengths of the order of 9 kPa are required to completely retard the upward flow in meter-wide conduits. In low Bagnold number magma suspensions with moderate crystal contents (solidosities 0.1 〈=phi〈= 0.3), viscous fluctuations may lead to flow differentiation by shear-enhanced diffusion. AMS and microstructural studies support the idea that granite plutons are intruded as crystal-poor liquids (phi〈= 50%), with fabric and foliation development restricted to the final stages of emplacement. If so, then these fabrics contain no information on the ascent (vertical transport) history of the magma. Deformation of a magmatic mush during pluton emplacement can enhance significantly the pressure gradient in the melt, resulting in a range of local macroscopic flow structures, including layering, crystal alignment, and other mechanical instabilities such as shear zones. As the suspension viscosity varies with stress rate, it is not clear how the timing of proposed rheological transitions formulated from simple equations for static magma suspensions applies to mixtures undergoing shear. New theories of magmas as multiphase flows are required if the full complexity of granitic magma rheology is to be resolved.
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    Annual Review of Earth and Planetary Sciences 31 (2003), S. 579-594 
    ISSN: 0084-6597
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Geosciences , Physics
    Notes: Abstract Is El Nino one phase of a continual, self-sustaining natural mode of the coupled ocean-atmosphere that has La Nina as the complementary phase? Or is El Nino a temporary departure from "normal" conditions "triggered" by a random disturbance such as a burst of westerly winds? A growing body of evidence-stability analyses, studies of the energetics, simulations that reproduce the statistics of sea surface temperature variations in the eastern equatorial Pacific-indicates that reality corresponds to a compromise between these two possibilities: The observed Southern Oscillation between El Nino and La Nina corresponds to a weakly damped mode that is sustained by random disturbances. This means that the predictability of El Nino is limited by the continual presence of "noise" so that forecasts should be probabilistic. The Southern Oscillation is also subject to decadal modulations. How it will be influenced by global warming is a matter of considerable uncertainty.
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    Annual Review of Earth and Planetary Sciences 31 (2003), S. 275-301 
    ISSN: 0084-6597
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Geosciences , Physics
    Notes: Abstract Fossil deposits that preserve soft-bodied organisms provide critical evidence of the history of life. Usually, only more decay resistant materials, e.g., cuticles, survive as organic remains as a result of selective preservation and subsequent diagenesis to more resistant biopolymers. Permineralization, the permeation of tissues by mineralizing fluids, may preserve remarkable detail, particularly of plants. However, evidence of more labile tissues, e.g., muscle, normally requires the replication of their morphology by rapid in situ growth of minerals, i.e., authigenic mineralization. This process relies on the steep geochemical gradients generated by decay microbes. The minerals involved, and the level of detail preserved (which may be subcellular), depend on a number of factors, including the nature of microbial activity and amount of decay, availability of ions, and the type of organism that is fossilized. Understanding these controls is essential to determining the conditions that favor exceptional preservation.
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    Annual Review of Earth and Planetary Sciences 31 (2003), S. 329-356 
    ISSN: 0084-6597
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Geosciences , Physics
    Notes: Abstract The anthropogenic production of greenhouse gases and their consequent effects on global climate have garnered international attention for years. A remaining challenge facing scientists is to unambiguously quantify both sources and sinks of targeted gases. Microbiological metabolism accounts for the largest source of nitrous oxide (N2O), mostly due to global conversion of land for agriculture and massive usage of nitrogen-based fertilizers. A most powerful method for characterizing the sources of N2O lies in its multi-isotope signature. This review summarizes mechanisms that lead to biological N2O production and how discriminate placement of 15N into molecules of N2O occurs. Through direct measurements and atmospheric modeling, we can now place a constraint on the isotopic composition of biological sources of N2O and trace its fate in the atmosphere. This powerful interdisciplinary combination of biology and atmospheric chemistry is rapidly advancing the closure of the global N2O budget.
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    Annual Review of Earth and Planetary Sciences 31 (2003), S. 525-554 
    ISSN: 0084-6597
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Geosciences , Physics
    Notes: Abstract Decades of seabed mapping, reflection profiling, and seabed sampling reveal that throughout the past two million years the Black Sea was predominantly a freshwater lake interrupted only briefly by saltwater invasions coincident with global sea level highstand. When the exterior ocean lay below the relatively shallow sill of the Bosporus outlet, the Black Sea operated in two modes. As in the neighboring Caspian Sea, a cold climate mode corresponded with an expanded lake and a warm climate mode with a shrunken lake. Thus, during much of the cold glacial Quaternary, the expanded Black Sea's lake spilled into to the Marmara Sea and from there to the Mediterranean. However, in the warm climate mode, after receiving a vast volume of ice sheet meltwater, the shoreline of the shrinking lake contracted to the outer shelf and on a few occasions even beyond the shelf edge. If the confluence of a falling interior lake and a rising global ocean persisted to the moment when the rising ocean penetrated across the dividing sill, it would set the stage for catastrophic flooding. Although recently challenged, the flood hypothesis for the connecting event best fits the full set of observations.
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    Annual Review of Earth and Planetary Sciences 31 (2003), S. 135-174 
    ISSN: 0084-6597
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Geosciences , Physics
    Notes: Abstract Accretion models for the Earth and terrestrial planets are based on the distribution of siderophile (iron-loving) elements between metal and silicate. Extensive experimental studies of the partitioning of these elements between metallic liquid and silicate melt have led to a better understanding and a more sophisticated application to planetary problems. Siderophile element metal/silicate partition coefficients are a function of temperature, pressure, oxygen fugacity, and metal and silicate composition. Quantification of these effects for a limited subset of siderophile elements has led to the idea that early Earth had a 700-km or deeper magma ocean. This new understanding of siderophile element partitioning has also led to applications to the kinetics of metal-silicate equilibrium, links to the timing of core formation, and a better understanding of core formation and metal-silicate equilibrium in the Moon and Mars. Key issues for future consideration include the role of water in early Earth, consideration of the core as a reservoir for noble gases and/or traditionally lithophile elements, siderophile element concentrations in the deep mantle, oxygen fugacity at high pressures, and further evaluation of the need for a late accretional veneer. The strongest approach to improving accretion models for the terrestrial planets is one that combines geochemistry, geophysics, and planetary dynamics.
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    Annual Review of Earth and Planetary Sciences 31 (2003), S. 303-328 
    ISSN: 0084-6597
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Geosciences , Physics
    Notes: Abstract We review the present status of global mantle tomography and discuss two main classes of models that have been developed in the past 10 years: P velocity models based on large datasets of travel times from the International Seismological Centre bulletins, often referred to as "high resolution" models, and S velocity models based on a combination of surface wave and hand picked body wave travel times, or waveforms, referred to as "long wavelength" models. We discuss their respective strengths and weaknesses, as well as progress in the resolution of other physical parameters, such as anisotropy, anelasticity, density, and bulk sound velocity using tomographic approaches. We present the view that future improvements in global seismic tomography require the utilization of the rich information contained in complete broadband seismic waveforms. This is presently within our reach owing to theoretical progress as well as the increase in computational power in recent years.
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    Annual Review of Earth and Planetary Sciences 31 (2003), S. 429-467 
    ISSN: 0084-6597
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Geosciences , Physics
    Notes: Abstract For over 300 years, the monsoon has been viewed as a gigantic land-sea breeze. It is shown in this paper that satellite and conventional observations support an alternative hypothesis, which considers the monsoon as a manifestation of seasonal migration of the intertropical convergence zone (ITCZ). With the focus on the Indian monsoon, the mean seasonal pattern is described, and why it is difficult to simulate it is discussed. Some facets of the intraseasonal variation, such as active-weak cycles; break monsoon; and a special feature of intraseasonal variation over the region, namely, poleward propagations of the ITCZ at intervals of 2-6 weeks, are considered. Vertical moist stability is shown to be a key parameter in the variation of monthly convection over ocean and land as well as poleward propagations. Special features of the Bay of Bengal and the monsoon brought out by observations during a national observational experiment in 1999 are briefly described.
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    Annual Review of Earth and Planetary Sciences 31 (2003), S. 105-134 
    ISSN: 0084-6597
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Geosciences , Physics
    Notes: Abstract Theoretical calculations, based on both the chemical and isotopic composition of sedimentary rocks, indicate that atmospheric O2 has varied appreciably over Phanerozoic time, with a notable excursion during the Permo-Carboniferous reaching levels as high as 35% O2. This agrees with measurements of the carbon isotopic composition of fossil plants together with experiments and calculations on the effect of O2 on photosynthetic carbon isotope fractionation. The principal cause of the excursion was the rise of large vascular land plants and the consequent increased global burial of organic matter. Higher levels of O2 are consistent with the presence of Permo-Carboniferous giant insects, and preliminary experiments indicate that insect body size can increase with elevated O2. Higher O2 also may have caused more extensive, possibly catastrophic, wildfires. To check this, realistic burning experiments are needed to examine the effects of elevated O2 on fire behavior.
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    Annual Review of Earth and Planetary Sciences 31 (2003), S. 249-273 
    ISSN: 0084-6597
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Geosciences , Physics
    Notes: Abstract Plants and animals exploit the soil for food and shelter and, in the process, affect it in many different ways. For example, uprooted trees may break up bedrock, transport soil downslope, increase the heterogeneity of soil respiration rates, and inhibit soil horizonation. In this contribution, we review previously published papers that provide insights into the process of bioturbation. We focus particularly on studies that allow us to place bioturbation within a quantitative framework that links the form of hillslopes with the processes of sediment transport and soil production. Using geometrical relationships and data from others' work, we derive simple sediment flux equations for tree throw and root growth and decay.
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    Annual Review of Earth and Planetary Sciences 31 (2003), S. 1-74 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Annual Review of Earth and Planetary Sciences 31 (2003), S. 75-104 
    ISSN: 0084-6597
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Geosciences , Physics
    Notes: Abstract Tropical cyclones encompass virtually every subdiscipline of geophysical fluid dynamics, including cumulus convection, boundary layers, thermodynamic cycles, surface wave dynamics, upper ocean wind-driven circulations, barotropic instability, Rossby waves, and air-sea interaction. After briefly reviewing what is known about the structure, behavior, and climatology of these fascinating storms, the author provides an overview of their physics, focusing on the unique and poorly understood nature of the air-sea interface, and discusses several of the most interesting avenues of ongoing research.
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    Annual Review of Earth and Planetary Sciences 31 (2003), S. 213-248 
    ISSN: 0084-6597
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Geosciences , Physics
    Notes: Abstract Neither geologists nor biologists have a definition that is capable of classifying Madagascar unambiguously as an island or a continent; nor can they incorporate Malagasy natural history into a single model rooted in Africa or Asia. Madagascar is a microcosm of the larger continents, with a rock record that spans more than 3000 million years (Ma), during which it has been united episodically with, and divorced from, Asian and African connections. This is reflected in its Precambrian history of deep crustal tectonics and a Phanerozoic history of biodiversity that fluctuated between cosmopolitanism and parochialism. Both vicariance and dispersal events over the past 90 Ma have blended a unique endemism on Madagascar, now in decline following rapid extinctions that started about 2000 years ago.
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    Annual Review of Earth and Planetary Sciences 31 (2003), S. 469-523 
    ISSN: 0084-6597
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Geosciences , Physics
    Notes: Abstract Mantle plumes are recognized by domal uplift, triple junction rifting, and especially the presence of a large igneous province (LIP), dominated in the Phanerozoic by flood basalts, and in the Proterozoic by the exposed plumbing system of dykes, sills, and layered intrusions. In the Archean, greenstone belts that contain komatiites have been linked to plumes. In addition, some carbonatites and kimberlites may originate from plumes that have stalled beneath thick lithosphere. Geochemistry and isotopes can be used to test and characterize the plume origin of LIPs. Seismic tomography and geochemistry of crustal and subcrustal xenoliths in kimberlites can identify fossil plumes. More speculatively, plumes (or clusters of plumes) have been linked with variation in the isotopic composition of marine carbonates, sea-level rise, iron formations, anoxia events, extinctions, continental breakup, juvenile crust production, magnetic superchrons, and meteorite impacts. The central region of a plume is located using the focus of a radiating dyke swarm, the distribution of komatiites and picrites, etc. The outer boundary of a plume head circumscribes the main flood basalt distribution and approximately coincides with the edge of domal uplift that causes shoaling and offlap in regional sedimentation.
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    Annual Review of Earth and Planetary Sciences 31 (2003), S. 175-211 
    ISSN: 0084-6597
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Geosciences , Physics
    Notes: Abstract Galileo's explorations have revealed a remarkable variety of eruptive styles among Io's diverse volcanoes. Activity at hundreds of volcanic centers ranges from dormant through sporadic to continuous over the 20-year period of spacecraft observation. High temperature volcanism is common on Io, suggesting that the lavas are made up of mafic to ultramafic silicates rather than sulfur compounds. Io's largest plumes are driven by SO2 and sulfur-rich gasses vented from the silicate interior that produce prominent red pyroclastic deposits. Red deposits flag the source regions of many other ongoing or very recent eruptions. Smaller plumes are produced near the margins of active lava flows by explosive volatilization of the underlying or surrounding SO2. These plumes produce SO2 snowflakes that mantle existing topography. Io's volcanism drives significant variations in the atmosphere and plasma torus, yet most of the heat loss occurs through lava flows and by the quiet overturning of lava lakes without large-scale explosive activity. Although only a handful of Io's volcanoes have been directly observed to produce explosive eruptions, volcanic resurfacing is efficient enough to erase even small craters from Io's youthful surface.
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    Annual Review of Earth and Planetary Sciences 31 (2003), S. 357-397 
    ISSN: 0084-6597
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Geosciences , Physics
    Notes: Abstract A review of crocodylian phylogeny reveals a more complex history than might have been anticipated from a direct reading of the fossil record without consideration of phylogenetic relationships. The three main extant crocodylian lineages-Gavialoidea, Alligatoroidea, Crocodyloidea-are known from fossils in the Late Cretaceous, and the group is found nearly worldwide during the Cenozoic. Some groups have distributions that are best explained by the crossing of marine barriers during the Tertiary. Early Tertiary crocodylian faunas are phylogenetically composite, and clades tend to be morphologically uniform and geographically widespread. Later in the Tertiary, Old World crocodylian faunas are more endemic. Crocodylian phylogeneticists face numerous challenges, the most important being the phylogenetic relationships and time of divergence of the two living gharials (Gavialis gangeticus and Tomistoma schlegelii), the relationships among living true crocodiles (Crocodylus), and the relationships among caimans.
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    Annual Review of Physical Chemistry 54 (2003), S. 57-87 
    ISSN: 0066-426X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Physics
    Notes: Abstract The current state of understanding of molecular resonance energy transfer (RET) and recent developments in the field are reviewed. The development of more general theoretical approaches has uncovered some new principles underlying RET processes. This review brings many of these important new concepts together into a generalization of Forster's original theory. The conclusions of studies investigating the various approximations in Forster theory are summarized. Areas of present and future activity are discussed. The review covers Forster theory for donor-acceptor pairs and electronic coupling for singlet-singlet, triplet-triplet, and superexchange-mediated energy transfer. This includes the transition density picture of Coulombic coupling as well as electronic coupling between molecular aggregates (excitons). Spectral overlaps and ensemble energy transfer rates in disordered aggregates, the role of dielectric properties of the medium, weak versus strong coupling, and new models for energy transfer in complex molecular assemblies are also described.
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    Annual Review of Physical Chemistry 54 (2003), S. 245-275 
    ISSN: 0066-426X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Physics
    Notes: Abstract The master equation provides a quantitative description of the interaction between collisional energy transfer and chemical reaction for dissociation, isomerization, and association processes. The approach is outlined for both irreversible and reversible dissociation, isomerization, and association reactions. There is increasing interest, especially in combustion, in association reactions that involve several linked potential wells, with the possibility of isomerization, collisional stabilization, and dissociation along several product channels. A major aim of the application of the master equation to such systems is the linking of the eigenvalues obtained by its solution to the rate coefficients for the phenomenological chemical reactions that describe the system and that are used in combustion models. The approach is illustrated by reference to the reactions C2H5 + O2, H + SO2, and the dissociation and isomerization of alkyl radicals.
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    Annual Review of Physical Chemistry 54 (2003), S. 425-463 
    ISSN: 0066-426X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Physics
    Notes: Abstract The simplest two-dimensional (2D) spectra show how excitation with one (variable) frequency affects the spectrum at all other frequencies, thus revealing the molecular connections between transitions. Femtosecond 2D Fourier transform (2D FT) spectra are more flexible and share some of the remarkable properties of their conceptual parent, 2D FT nuclear magnetic resonance. When 2D FT spectra are experimentally separated into real absorptive and imaginary refractive parts, the time resolution and frequency resolution can both reach the uncertainty limit set for each resonance by the sample itself. Coherent four-level contributions to the signal provide new molecular phase information, such as relative signs of transition dipoles. The nonlinear response can be picked apart by selecting a single coherence pathway (e.g., specifying the relative signs of energy level difference frequencies during different time intervals as in the photon echo). Because molecules are frozen on the femtosecond timescale, femtosecond 2D FT experiments can separate a distribution of instantaneous molecular environments and intramolecular geometries as inhomogeneous broadening. This review provides an introduction to two-dimensional Fourier transform experiments exploiting second- and third-order vibrational and electronic nonlinearities.
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    Annual Review of Physical Chemistry 54 (2003), S. 331-366 
    ISSN: 0066-426X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Physics
    Notes: Abstract Noble metal particles have long fascinated scientists because of their intense color, which led to their application in stained glass windows as early as the Middle Ages. The recent resurrection of colloidal and cluster chemistry has brought about the strive for new materials that allow a bottoms-up approach of building improved and new devices with nanoparticles or artificial atoms. In this review, we discuss some of the properties of individual and some assembled metallic nanoparticles with a focus on their interaction with cw and pulsed laser light of different energies. The potential application of the plasmon resonance as sensors is discussed.
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    Annual Review of Physical Chemistry 54 (2003), S. 215-244 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Physics
    Notes: Abstract We discuss experiments on the dynamics of photodissociation that employ methods to select the energy, sometimes quantum states, of the reactant and to determine the quantum states and energy, sometimes also the orientation and alignment, of products. A summary of new advances of experimental methods is followed by applications to photodissociation of various types. Representative examples of simple bond fission, molecular elimination, and three-body dissociation with determined electronic states-sometimes the orientation of their angular momentum-of product atoms or distributions of electronic and internal states of product molecules illustrate the detailed information and insight that one can derive from such experiments. Photodissociation of van der Waals complexes, ions, species adsorbed on surfaces, and species in solution is excluded from this review.
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    Annual Review of Physical Chemistry 54 (2003), S. 277-305 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Physics
    Notes: Abstract Optical diagnostics are used to probe the plasma or neutral gas above the substrate, particles in the gas or on the surface, the film surface and reactor walls, the film itself, and the substrate during thin film processing. The development and application of optical probes are highlighted, in particular for analyzing plasma/gas phase intermediates and products and film composition, and performing metrology, thermometry, and endpoint detection and control. Probing etching (particularly plasma etching) and deposition (particularly epitaxy) are emphasized.
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    Annual Review of Physical Chemistry 54 (2003), S. 1-28 
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    Annual Review of Physical Chemistry 54 (2003), S. 121-140 
    ISSN: 0066-426X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Physics
    Notes: Abstract Carbonaceous compounds comprise a substantial fraction of atmospheric particulate matter (PM). Particulate organic material can be emitted directly into the atmosphere or formed in the atmosphere when the oxidation products of certain volatile organic compounds condense. Such products have lower volatilities than their parent molecules as a result of the fact that adding oxygen and/or nitrogen to organic molecules reduces volatility. Formation of secondary organic PM is often described in terms of a fractional mass yield, which relates how much PM is produced when a certain amount of a parent gaseous organic is oxidized. The theory of secondary organic PM formation is outlined, including the role of water, which is ubiquitous in the atmosphere. Available experimental studies on secondary organic PM formation and molecular products are summarized.
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    Annual Review of Physical Chemistry 54 (2003), S. 493-529 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Physics
    Notes: Abstract This review discusses recent quantum scattering calculations on bimolecular chemical reactions in the gas phase. This theory provides detailed and accurate predictions on the dynamics and kinetics of reactions containing three atoms. In addition, the method can now be applied to reactions involving polyatomic molecules. Results obtained with both time-independent and time-dependent quantum dynamical methods are described. The review emphasises the recent development in time-dependent wave packet theories and the applications of reduced dimensionality approaches for treating polyatomic reactions. Calculations on over 40 different reactions are described.
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    Annual Review of Physical Chemistry 54 (2003), S. 173-213 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Physics
    Notes: Abstract This review provides a historical context for our understanding of the hydration shell surrounding halide ions and illustrates how the cluster systems can be used, in combination with theory, to elucidate the behavior of water molecules in direct contact with the anion. We discuss how vibrational predissociation spectroscopy, carried out with weakly bound argon atoms, has been employed to deduce the morphology of the small water networks attached to anions in the primary steps of hydration. We emphasize the importance of charge-transfer in the binary interaction, and discuss how this process affects the structures of the larger networks. Finally, we survey how the negatively charged water clusters (H2O)n- are providing a molecular-level perspective on how diffuse excess electrons interact with the water networks.
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    Annual Review of Physical Chemistry 54 (2003), S. 397-424 
    ISSN: 0066-426X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Physics
    Notes: Abstract Angle-resolved photoelectron spectroscopy has been performed for more than 70 years in various guises, but recently its potential to help solve in detail problems in the photoionization dynamics and intramolecular dynamics of gas-phase molecules has been recognized. One key development has been the design of experiments in appropriate geometries to extract information that pertains to the molecular frame, another has been the development of imaging spectrometers, and a third is the use of ultrafast lasers to cause photoionization. In this review, which is aimed at experimentalists, simple expressions for photoelectron angular distributions (PADs) in various experimental geometries are given and their applications explained.
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    Annual Review of Physical Chemistry 54 (2003), S. 89-119 
    ISSN: 0066-426X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Physics
    Notes: Abstract Femtosecond time-resolved photoelectron spectroscopy is emerging as a useful technique for investigating excited state dynamics in isolated polyatomic molecules. The sensitivity of photoelectron spectroscopy to both electronic configurations and vibrational dynamics makes it well suited to the study of ultrafast nonadiabatic processes. We review the conceptual interpretation of wavepacket dynamics experiments, emphasizing the role of the final state. We discuss the advantages of the molecular ionization continuum as the final state in polyatomic wavepacket experiments and show how the electronic structure of the continuum can be used to disentangle electronic from vibrational dynamics. We illustrate these methods with examples from diatomic wavepacket dynamics, internal conversion in polyenes and polyaromatic hydrocarbons, excited state intramolecular proton transfer, and azobenzene photoiosomerization dynamics.
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  • 85
    ISSN: 0066-426X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Physics
    Notes: Abstract Proteins directly control the nucleation and growth of biominerals, but the details of molecular recognition at the protein-biomineral interface remain poorly understood. The elucidation of recognition mechanisms at this interface may provide design principles for advanced materials development in medical and ceramic composites technologies. Here, we describe both the theory and practice of double-quantum solid-state NMR (ssNMR) structure-determination techniques, as they are used to determine the secondary structures of surface-adsorbed peptides and proteins. In particular, we have used ssNMR dipolar techniques to provide the first high-resolution structural and dynamic characterization of a hydrated biomineralization protein, salivary statherin, adsorbed to its biologically relevant hydroxyapatite (HAP) surface. Here, we also review NMR data on peptides designed to adsorb from aqueous solutions onto highly porous hydrophobic surfaces with specific helical secondary structures. The adsorption or covalent attachment of biological macromolecules onto polymer materials to improve their biocompatibility has been pursued using a variety of approaches, but key to understanding their efficacy is the verification of the structure and dynamics of the immobilized biomolecules using double-quantum ssNMR spectroscopy.
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    Annual Review of Physical Chemistry 54 (2003), S. 29-56 
    ISSN: 0066-426X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Physics
    Notes: Abstract Anisotropic etchants selectively reveal a specific crystallographic plane. Although prized industrially, these etchants are poorly understood because they target specific defect sites on a surface. New methods, which rely on a combination of scanning tunneling microscopy, kinetic Monte Carlo simulations, and infrared spectroscopy, have been developed to quantify these reactions. By correlating the measured reaction rates with the structure of the defects, information about reaction mechanisms can be obtained. These techniques have also been extended to allow for the quantification of impurity reactions such as the reaction of dissolved O2, and of nonetching additives, such as alcohols. A complementary macroscopic technique, which utilizes microfabricated arrays of miscut surfaces to measure orientation-dependent kinetics, is also described.
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    Annual Review of Physical Chemistry 54 (2003), S. 141-172 
    ISSN: 0066-426X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Physics
    Notes: Abstract The electronic structure of conjugated polymers is of current interest because of the wide range of potential applications for such materials in optoelectronic devices. It is increasingly clear that the electronic properties of conjugated polymers depend sensitively on the physical conformation of the polymer chains and the way the chains pack together in films. This article reviews the evidence that interchain electronic species do form in conjugated polymer films, and that their number and chemical nature depend on processing conditions; the chain conformation, degree of interchain contact, and rate of energy transfer can be controlled by factors such as choice of solvent, polymer concentration, thermal annealing, presence of electrically charged side groups, and encapsulation of the polymer chains in mesoporous silica. Taken together, the results reconcile many contradictions in the literature and provide a prescription for the optimization of conjugated polymer film morphology for device applications.
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    Annual Review of Physical Chemistry 54 (2003), S. 307-330 
    ISSN: 0066-426X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Physics
    Notes: Abstract The fascinating advances in single atom/molecule manipulation with a scanning tunneling microscope (STM) tip allow scientists to fabricate atomic-scale structures or to probe chemical and physical properties of matters at an atomic level. Owing to these advances, it has become possible for the basic chemical reaction steps, such as dissociation, diffusion, adsorption, readsorption, and bond-formation processes, to be performed by using the STM tip. Complete sequences of chemical reactions are able to induce at a single-molecule level. New molecules can be constructed from the basic molecular building blocks on a one-molecule-at-a-time basis by using a variety of STM manipulation schemes in a systematic step-by-step manner. These achievements open up entirely new opportunities in nanochemistry and nanochemical technology. In this review, various STM manipulation techniques useful in the single-molecule reaction process are reviewed, and their impact on the future of nanoscience and technology are discussed.
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    Annual Review of Physical Chemistry 54 (2003), S. 367-396 
    ISSN: 0066-426X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Physics
    Notes: Abstract The problem of the binding of an excess electron to polar molecules and their clusters has long fascinated researchers. Although excess electrons bound to such species tend to be very extended spatially and to have little spatial overlap with the valence electrons of the neutral molecules, inclusion of electron correlation effects is essential for quantitatively describing the electron binding. The major electron correlation contribution may be viewed as a dispersion interaction between the excess electron and the electrons of the molecule or cluster. Recent work using a one-electron Drude model to describe excess electrons interacting with polar molecules is reviewed.
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    Annual Review of Physical Chemistry 54 (2003), S. 465-492 
    ISSN: 0066-426X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Physics
    Notes: Abstract The use of a combination of tunneling and optical spectroscopy to investigate the size and shape-dependent level structure and single-electron charging phenomena in semiconductor nanocrystals is reviewed. The artificial atom character of semiconductor nanocrystal quantum dots is manifested in both the discrete level structure and in the charging multiplicity of the single-electron tunneling data, revealing s and p atomic-like states. Such states can be directly imaged using scanning tunneling microscopy, providing the extent and symmetry of the envelope wavefunctions. A detailed description of the effect of the tunneling geometry on the single-electron tunneling spectra is presented. Correlation of the optical and tunneling data allows for the assignment of the level spectrum. The generality of this powerful combination is further demonstrated in the study of quantum rods that manifest the transition from zero-dimensional quantum dots to one-dimensional quantum wires.
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  • 91
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    Nature 426 (2003), S. 812-816 
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] The discrete nature of crystal lattices plays a role in virtually every material property. But it is only when the size of entities hosted by a crystal becomes comparable to the lattice period—as occurs for dislocations, vortices in superconductors and domain walls—that this ...
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    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Pathogens that are transmitted between wildlife, livestock and humans present major challenges for the protection of human and animal health, the economic sustainability of agriculture, and the conservation of wildlife. Mycobacterium bovis, the aetiological agent of bovine tuberculosis (TB), is ...
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    Nature 426 (2003), S. 826-829 
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] The oceans are a global reservoir and redistribution agent for several important constituents of the Earth's climate system, among them heat, fresh water and carbon dioxide. Whereas these constituents are actively exchanged with the atmosphere, salt is a component that is approximately ...
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    Nature 426 (2003), S. 797-802 
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] A key pacemaker of ice ages on the Earth is climatic forcing due to variations in planetary orbital parameters. Recent Mars exploration has revealed dusty, water-ice-rich mantling deposits that are layered, metres thick and latitude dependent, occurring in both hemispheres from mid-latitudes to the ...
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    Source: Nature Archives 1869 - 2009
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    Notes: [Auszug] Silica waveguides with diameters larger than the wavelength of transmitted light are widely used in optical communications, sensors and other applications. Minimizing the width of the waveguides is desirable for photonic device applications, but the fabrication of low-loss optical waveguides ...
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    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Synthesis and sorting of lipids are essential for membrane biogenesis; however, the mechanisms underlying the transport of membrane lipids remain little understood. Ceramide is synthesized at the endoplasmic reticulum and translocated to the Golgi compartment for conversion to sphingomyelin. The ...
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    Nature 426 (2003), S. 841-845 
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] The induction of associative synaptic plasticity in the mammalian central nervous system classically depends on coincident presynaptic and postsynaptic activity. According to this principle, associative homosynaptic long-term potentiation (LTP) of excitatory synaptic transmission can be induced ...
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    Nature 426 (2003), S. 584-584 
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Nature 424, 309–312 (2003). The support of the University of Liverpool, where some of the work was carried out (by M.M.M., P.M. and T.G.), is ...
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    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] The electronic transport properties of conventional three-dimensional metals are successfully described by Fermi-liquid theory. But when the dimensionality of such a system is reduced to one, the Fermi-liquid state becomes unstable to Coulomb interactions, and the conduction electrons should ...
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    Nature 426 (2003), S. 563-566 
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Protein coats deform flat lipid membranes into buds and capture membrane proteins to form transport vesicles. The assembly/disassembly cycle of the COPI coat on Golgi membranes is coupled to the GTP/GDP cycle of the small G protein Arf1. At the heart of this coupling is the specific interaction ...
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