ALBERT

Notes: This paper reviews the current state of the art in accidental explosion modeling using methods based on computational fluid dynamics (CFD) in the petrochemical process industries. We discuss the problem in terms of its industrial importance and its technical difficulty, which stems mainly from the large range of length and timescales that must be represented. Explicit representation of all scales is not feasible due to limitations of computational cost, and modeling of unresolved physical features is required. We also discuss geometry modeling using the porosity/distributed resistance (PDR) method and review relevant combustion modeling. We describe an advanced CFD approach using unstructured adaptive gridding and discuss its usefulness in the context of results obtained for both two dimensional and three dimensional simulations of gas explosion phenomena in complex geometries.

Notes: Early concepts in shock wave drag reduction enabled modern aeronautical systems, and continuing research progress in this arena is crucial for significant improvements in long haul transports and various military platforms and weapons. The research area is rich in concepts/approaches, but many of these have not progressed into the realm of application. This is due in part to a lack of knowledge on the part of the fluids research community concerning the multidisciplinary "real-world" design space/metrics and a consequent lack of the requisite breadth and depth of research information required to evaluate/apply the concept. The article reviews the extant wave drag reduction approaches that are (a) well understood/applied, (b) under active study/indicate considerable promise, and (c) those in the nascent stage only.

Notes: Almost all vessels carrying fluids within the body are flexible, and interactions between an internal flow and wall deformation often underlie a vessel's biological function or dysfunction. Such interactions can involve a rich range of fluid-mechanical phenomena, including nonlinear pressure-drop/flow-rate relations, self-excited oscillations of single-phase flow at high Reynolds number and capillary-elastic instabilities of two-phase flow at low Reynolds number. We review recent advances in understanding the fundamental mechanics of flexible-tube flows, and discuss physiological applications spanning the cardiovascular system (involving wave propagation and flow-induced instabilities of blood vessels), the respiratory system (involving phonation, the closure and reopening of liquid-lined airways, and Marangoni flows on flexible surfaces), and elsewhere in the body (involving active peristaltic transport driven by fluid-structure/muscle interactions).

Notes: We review the use of ray models for internal waves, particularly formulations for calculating wave amplitudes along the ray. These are expressed in spatial, wave number, and phase-space coordinates. The choice of formulation affects not only the difficulty of the calculations for rays and caustics but also the degree to which the waves satisfy slowly varying assumptions. We describe several examples taken from atmospheric and oceanic applications that illustrate the variety of options for ray models.

Notes: The characterization of blood flow is important for understanding the function of the cardiovascular system under normal and diseased conditions, designing cardiovascular devices, and diagnosing and treating congenital and acquired cardiovascular disease. Experimental methods, especially magnetic resonance imaging techniques can be used to noninvasively quantify blood flow for diagnosing cardiovascular disease, researching disease mechanisms, and validating assumptions and predictions of mathematical models. Computational methods can be used to simulate blood flow and vessel dynamics, test hypotheses of disease formation under controlled conditions, and evaluate devices that have not yet been built and treatments that have not yet been implemented. In this article we review experimental and computational methods for quantifying blood flow velocity and pressure fields in human arteries. We place particular emphasis on providing an introduction to the physics and applications of magnetic resonance imaging, and surveying lumped parameter, one-dimensional, and three-dimensional numerical methods used to model blood flow.

Notes: We review the experimental evidence on turbulent flows over rough walls. Two parameters are important: the roughness Reynolds number ks+ , which measures the effect of the roughness on the buffer layer, and the ratio of the boundary layer thickness to the roughness height, which determines whether a logarithmic layer survives. The behavior of transitionally rough surfaces with low ks+ depends a lot on their geometry. Riblets and other drag-reducing cases belong to this regime. In flows with delta/k 〈 50, the effect of the roughness extends across the boundary layer, and is also variable. There is little left of the original wall-flow dynamics in these flows, which can perhaps be better described as flows over obstacles. We also review the evidence for the phenomenon of d-roughness. The theoretical arguments are sound, but the experimental evidence is inconclusive. Finally, we discuss some ideas on how rough walls can be modeled without the detailed computation of the flow around the roughness elements themselves.

Notes: We review artificial boundary conditions (BCs) for simulation of inflow, outflow, and far-field (radiation) problems, with an emphasis on techniques suitable for compressible turbulent shear flows. BCs based on linearization near the boundary are usually appropriate for inflow and radiation problems. A variety of accurate techniques have been developed for this case, but some robustness and implementation issues remain. At an outflow boundary, the linearized BCs are usually not accurate enough. Various ad hoc models have been proposed for the nonlinear case, including absorbing layers and fringe methods. We discuss these techniques and suggest directions for future modeling efforts.

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.

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.

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.

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.

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.

Notes: DNA secondary structure plays an important role in biology, genotyping diagnostics, a variety of molecular biology techniques, in vitro-selected DNA catalysts, nanotechnology, and DNA-based computing. Accurate prediction of DNA secondary structure and hybridization using dynamic programming algorithms requires a database of thermodynamic parameters for several motifs including Watson-Crick base pairs, internal mismatches, terminal mismatches, terminal dangling ends, hairpins, bulges, internal loops, and multibranched loops. To make the database useful for predictions under a variety of salt conditions, empirical equations for monovalent and magnesium dependence of thermodynamics have been developed. Bimolecular hybridization is often inhibited by competing unimolecular folding of a target or probe DNA. Powerful numerical methods have been developed to solve multistate-coupled equilibria in bimolecular and higher-order complexes. This review presents the current parameter set available for making accurate DNA structure predictions and also points to future directions for improvement.

Notes: Phosphoserine/threonine-binding domains integrate intracellular signal transduction events by forming multiprotein complexes with substrates of protein serine/threonine kinases. These phosphorylation-dependent molecular recognition events are responsible for coordinating the precise temporal and spatial response of cells to a wide range of stimuli, particularly those involved in cell cycle control and the response to DNA damage. The known families of phosphoserine/threonine-binding modules include 14-3-3 proteins, WW domains, FHA domains, WD40 repeats, and the Polo-box domains of Polo-like kinases. Peptide-library experiments reveal the optimal sequence motifs recognized by these domains, and facilitate high-resolution structural studies elucidating the mechanisms of phospho-dependent binding and the molecular basis for domain function within intricate signaling networks. Information emerging from these studies is critical for the design of novel experimental and therapeutic tools aimed at altering signal transduction cascades in normal and diseased cells.

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.

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.

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.

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.

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.

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.

Notes: Planets form in the circumstellar disks of young stars. We review the basic physical processes by which solid bodies accrete each other and alter each others' random velocities, and we provide order-of-magnitude derivations for the rates of these processes. We discuss and exercise the two-groups approximation, a simple yet powerful technique for solving the evolution equations for protoplanet growth. We describe orderly, runaway, neutral, and oligarchic growth. We also delineate the conditions under which each occurs. We refute a popular misconception by showing that the outer planets formed quickly by accreting small bodies. Then we address the final stages of planet formation. Oligarchy ends when the surface density of the oligarchs becomes comparable to that of the small bodies. Dynamical friction is no longer able to balance viscous stirring and the oligarchs' random velocities increase. In the inner-planet system, oligarchs collide and coalesce. In the outer-planet system, some of the oligarchs are ejected. In both the inner- and outer-planet systems, this stage ends once the number of big bodies has been reduced to the point that their mutual interactions no longer produce large-scale chaos. Subsequently, dynamical friction by the residual small bodies circularizes and flattens their orbits. The final stage of planet formation involves the clean up of the residual small bodies. Clean up has been poorly explored.

Notes: The Universe is in transition. At early times, galactic evolution was dominated by hierarchical clustering and merging, processes that are violent and rapid. In the far future, evolution will mostly be secular-the slow rearrangement of energy and mass that results from interactions involving collective phenomena such as bars, oval disks, spiral structure, and triaxial dark halos. Both processes are important now. This review discusses internal secular evolution, concentrating on one important consequence, the buildup of dense central components in disk galaxies that look like classical, merger-built bulges but that were made slowly out of disk gas. We call these pseudobulges. We begin with an "existence proof"-a review of how bars rearrange disk gas into outer rings, inner rings, and stuff dumped onto the center. The results of numerical simulations correspond closely to the morphology of barred galaxies. In the simulations, gas is transported to small radii, where it reaches high densities and plausibly feeds star formation. In the observations, many barred and oval galaxies have dense central concentrations of gas and star formation. Optical colors and spectra often imply young stellar populations. So the formation of pseudobulges is well supported by theory and observations. It is embedded in a broader evolution picture that accounts for much of the richness observed in galaxy structure. If secular processes built dense central components that masquerade as bulges, how can we distinguish them from merger-built bulges? Observations show that pseudobulges retain a memory of their disky origin. That is, they have one or more characteristics of disks: (a) flatter shapes than those of classical bulges, (b) correspondingly large ratios of ordered to random velocities, (c) small velocity dispersions sigma with respect to the Faber-Jackson correlation between sigma and bulge lumi nosity, (d) spiral structure or nuclear bars in the "bulge" part of the light profile, (e) nearly exponential brightness profiles, and ( f ) starbursts. All these structures occur preferentially in barred and oval galaxies, where secular evolution should be most rapid. So the cleanest examples of pseudobulges are recognizable. Are their formation timescales plausible? We use measurements of central gas densities and star-formation rates to show that pseudobulges of the observed densities form on timescales of a few billion years. Thus a large variety of observational and theoretical results lead to a new picture of galaxy evolution that complements hierarchical clustering and merging. Secular evolution consists of more than the aging of stellar populations. Every galaxy is dynamically evolving.

Notes: Interstellar turbulence has implications for the dispersal and mixing of the elements, cloud chemistry, cosmic ray scattering, and radio wave propagation through the ionized medium. This review discusses the observations and theory of these effects. Metallicity fluctuations are summarized, and the theory of turbulent transport of passive tracers is reviewed. Modeling methods, turbulent concentration of dust grains, and the turbulent washout of radial abundance gradients are discussed. Interstellar chemistry is affected by turbulent transport of various species between environments with different physical properties and by turbulent heating in shocks, vortical dissipation regions, and local regions of enhanced ambipolar diffusion. Cosmic rays are scattered and accelerated in turbulent magnetic waves and shocks, and they generate turbulence on the scale of their gyroradii. Radio wave scintillation is an important diagnostic for small-scale turbulence in the ionized medium, giving information about the power spectrum and amplitude of fluctuations. The theory of diffraction and refraction as well as the main observations and scintillation regions are reviewed.

Notes: Impulsive reconnection dynamics is characterized not only by fast growth but also by a sudden change in the time derivative of the growth rate. I review recent developments in the theory and simulation of forced impulsive reconnection based on the equations of resistive and Hall magnetohydrodynamics (MHD). Impulsive reconnection can be realized in resistive as well as Hall MHD by the imposition of suitable boundary conditions. However, compared with resistive MHD, Hall MHD reconnection is distinguished by qualitatively different magnetic field and electron and ion signatures in the reconnection layer. Furthermore, nonlinear reconnection rates in Hall MHD are weakly dependent on the Lundquist number. I discuss applications of the physics of impulsive reconnection to substorms in the Earth's magnetotail and solar flares.

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.

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.

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.

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.

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.

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.

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.

Notes: Is it by design or by default that water molecules are observed at the interfaces of some protein-DNA complexes? Both experimental and theoretical studies on the thermodynamics of protein-DNA binding overwhelmingly support the extended hydrophobic view that water release from interfaces favors binding. Structural and energy analyses indicate that the waters that remain at the interfaces of protein-DNA complexes ensure liquid-state packing densities, screen the electrostatic repulsions between like charges (which seems to be by design), and in a few cases act as linkers between complementary charges on the biomolecules (which may well be by default). This review presents a survey of the current literature on water in protein-DNA complexes and a critique of various interpretations of the data in the context of the role of water in protein-DNA binding and principles of protein-DNA recognition in general.

Notes: Two current frontiers in EPR research are high-field ( nu0 〉 70 GHz, B0 〉 2.5 T ) electron paramagnetic resonance (EPR) and high-field electron-nuclear double resonance (ENDOR). This review focuses on recent advances in high-field ENDOR and its applications to the study of proteins containing native paramagnetic sites. It concentrates on two aspects; the first concerns the determination of the location of protons and is related to the site geometry, and the second focuses on the spin density distribution within the site, which is inherent to the electronic structure. Both spin density and proton locations can be derived from ligand hyperfine couplings determined by ENDOR measurements. A brief description of the experimental methods is presented along with a discussion of the advantages and disadvantages of high-field ENDOR compared with conventional X-band (~ 9.5 GHz) experiments. Specific examples of both protein single crystals and frozen solutions are then presented. These include the determination of the coordinates of water ligand protons in the Mn(II) site of concanavalin A, the detection of hydrogen bonds in a quinone radical in the bacterial photosynthetic reaction center as well as in the tyrosyl radical in ribonuclease reductase, and the study of the spin distribution in copper proteins. The copper proteins discussed are the type I copper of azurin and the binuclear CuA center in a number of proteins. The last part of the review presents a brief discussion of the interpretation of hyperfine couplings using quantum chemical calculations, primarily density functional theory (DFT) methods. Such methods are becoming an integral part of the data analysis tools, as they can facilitate signal assignment and provide the ultimate relation between the experimental hyperfine couplings and the electronic wave function.

Notes: Most reactions on DNA are carried out by multimeric protein complexes that interact with two or more sites in the DNA and thus loop out the DNA between the sites. The enzymes that catalyze these reactions usually have no activity until they interact with both sites. This review examines the mechanisms for the assembly of protein complexes spanning two DNA sites and the resultant triggering of enzyme activity. There are two main routes for bringing together distant DNA sites in an enzyme complex: either the proteins bind concurrently to both sites and capture the intervening DNA in a loop, or they translocate the DNA between one site and another into an expanding loop, by an energy-dependent translocation mechanism. Both capture and translocation mechanisms are discussed here, with reference to the various types of restriction endonuclease that interact with two recognition sites before cleaving DNA.

Notes: Medical genetics so far has identified ~16,000 missense mutations leading to single amino acid changes in protein sequences that are linked to human disease. A majority of these mutations affect folding or trafficking, rather than specifically affecting protein function. Many disease-linked mutations occur in integral membrane proteins, a class of proteins about whose folding we know very little. We examine the phenomenon of disease-linked misassembly of membrane proteins and describe model systems currently being used to study the delicate balance between proper folding and misassembly. We review a mechanism by which cells recognize membrane proteins with a high potential to misfold before they actually do, and which targets these culprits for degradation. Serious disease phenotypes can result from loss of protein function and from misfolded proteins that the cells cannot degrade, leading to accumulation of toxic aggregates. Misassembly may be averted by small-molecule drugs that bind and stabilize the native state. Where there is danger there should be prudent haste. Quick! Pilgrim, be quick and tarry not in the place of danger. -Charles Spurgeon, sermon at Newington, 1889

Notes: The phenomenon of allostery is conventionally described for small symmetrical oligomeric proteins such as hemoglobin. Here we review experimental evidence from a variety of systems-including bacterial chemotaxis receptors, muscle ryanodine receptors, and actin filaments-showing that conformational changes can also propagate through extended lattices of protein molecules. We explore the statistical mechanics of idealized linear and two-dimensional arrays of allosteric proteins and show that, as in the analogous Ising models, arrays of closely packed units can show large-scale integrated behavior. We also discuss proteins that undergo conformational changes driven by the hydrolysis of ATP and give examples in which these changes propagate through linear chains of molecules. We suggest that conformational spread could provide the basis of a solid-state "circuitry" in a living cell, able to integrate biochemical and biophysical events over hundreds of protein molecules.

Notes: Systems biology research is currently dominated by integrative, multidisciplinary approaches. Although important, these strategies lack an overarching systems perspective such as those used in engineering. We describe here the Axiomatic Design approach to system analysis and illustrate its utility in the study of biological systems. Axiomatic Design relates functions at all levels to the behavior of biological molecules and uses a Design Matrix to understand these relationships. Such an analysis reveals that robustness in many biological systems is achieved through the maintenance of functional independence of numerous subsystems. When the interlinking (coupling) of systems is required, biological systems impose a functional period in order to maximize successful operation of the system. Ultimately, the application of Axiomatic Design methods to the study of biological systems will aid in handling cross-scale models, identifying control points, and predicting system-wide effects of pharmacological agents.

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.

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.

Notes: Observations of interstellar gas-phase and solid-state species in the 2.4-200 mum range obtained with the spectrometers on board the Infrared Space Observatory (ISO) are reviewed. Lines and bands caused by ices, polycyclic aromatic hydrocarbons, silicates, and gas-phase atoms and molecules (in particular H2, CO, H2O, OH, and CO2) are summarized and their diagnostic capabilities illustrated. The results are discussed in the context of the physical and chemical evolution of star-forming regions, including photon-dominated regions, shocks, protostellar envelopes, and disks around young stars.

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.

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.

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.

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.

Notes: I was born in 1914 in Amsterdam. I grew up there, filling my teenage years with activities as an amateur astronomer. I later studied at Leiden University and volunteered at Leiden Observatory. From 1938 to 1945, I was assistant at the Kapteyn Institute in Groningen, including during the war years 1940-1945, returning to Leiden in October 1945. After prolonged stays at Yerkes Observatory in 1947-1948 and 1952, and participation in Leiden's astrometric Kenya expedition in 1949-1950, I became associate professor at Yerkes Observatory in the fall of 1953. In 1957, I returned to the Kapteyn Institute and soon became involved in the creation of ESO, of which I became scientific director in 1968 and director general from 1970 to 1974. In 1975, I joined Leiden Observatory again, staying until my retirement in 1981, and since then I have enjoyed the hospitality of the Kapteyn Institute. I was president of the IAU from 1976 to 1979. From 1982 to 1989, I was chairman of the Scientific Programs Selection Committee for the European Space Agency's satellite, Hipparcos. My principal research interests have been in galactic structure and star formation, with emphasis on stellar associations. In addition to my astronomical interests, I have researched and published on Dutch village history.

Notes: Abundance variations within globular clusters (GCs), and of GC stars with respect to field stars, are important diagnostics of a variety of physical phenomena, related to the evolution of individual stars, mass transfer in binary systems, and chemical evolution in high density environments. The broad astrophysical implications of GCs as building blocks of our knowledge of the Universe make a full understanding of their history and evolution basic in a variety of astrophysical fields. We review the current status of the research in this field, comparing the abundances in GCs with those obtained for field stars, discussing in depth the evidence for H-burning at high temperatures in GC stars, describing the process of self-enrichment in GCs with particular reference to the case of the most massive Galactic GC (omega Cen), and discussing various classes of cluster stars with abundance anomalies. Whereas the overall pattern might appear very complex at first sight, exciting new scenarios are opening where the interplay between GC dynamical and chemical properties are closely linked with each other.

Notes: Important physical processes on the Sun, and especially in sunspots, occur on spatial scales at or below the limiting resolution of current solar telescopes. Over the past decade, using a number of new techniques, high-resolution observations have begun to reveal the complex thermal and magnetic structure of a sunspot, along with associated flows and oscillations. During this time remarkable advances in computing power have allowed significant progress in our theoretical understanding of the dynamical processes, such as magnetoconvection, taking place within a sunspot. In this review we summarize the latest observational results and theoretical interpretations of the fine structure in sunspots. A number of projects underway to build new solar telescopes or upgrade existing ones, along with several promising new theoretical ideas, ensure that there will be significant advances in sunspot research over the coming decade.

Notes: The giant impact theory is the leading hypothesis for the origin of the Moon. This review focuses on dynamical aspects of an impact-induced lunar formation, in particular those areas that have advanced considerably in the past decade, including (a) late-stage terrestrial accretion, (b) giant impact simulations, (c) protolunar disk evolution and lunar accretion, and (d) the origin of the initial lunar inclination. In all, recent developments now provide a reasonably consistent dynamical account of the origin of the Moon through a late giant impact with Earth, and suggest that the impact-generation of satellites is likely to be a common process in late-stage solid planet formation.

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.

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.

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.

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.

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.

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.

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.

Notes: After early work by Newton, the eighteenth and early nineteenth century French mathematicians Laplace, Lagrange, Poisson, and Cauchy made real theoretical advances in the linear theory of water waves; in Germany, Gerstner considered nonlinear waves, and the brothers Weber performed fine experiments. Later in Britain during 1837-1847, Russell, Green, Kelland, Airy, and Earnshaw all made substantial contributions, setting the scene for subsequent work by Stokes and others.

Notes: Coating is the process of applying thin liquid layers to a substrate, often a moving web. Complex coating processes can be approached through examination of their fluid mechanical components. The flow elements reviewed in this article include the boundary layer along a moving wall, the dynamic wetting line, withdrawal from a pool, flow metered by a narrow channel, die flow, flow on an incline, the freely falling liquid curtain, premetered coating with a small gap, and flow after coating. Although some flow elements are well studied and understood, others require additional investigation. Genuinely predictive modeling of complex coating processes is not yet possible and coating practice remains largely empirical. Nonetheless, coating science is sufficiently advanced that physical insights and mathematical models greatly benefit design and practice.

Notes: Since Leibovich's comprehensive review of Langmuir circulation in 1983 there have been substantial advances in modeling (notably the construction of Large Eddy Simulation models) and in observations using novel techniques that together have led to a radical change in understanding the phenomena. It is now regarded as one of the several turbulent processes driven by wind and waves in the upper layers of large bodies of water, influential in producing and maintaining the uniform surface mixed layer and in driving dispersion.

Notes: Online, continuous, two-phase flow measurement is often necessary, particularly in the oil and gas industry. In this article, we describe some of the commercially most important techniques for gas-liquid, gas-solid, liquid-solid, and liquid-liquid flows, and provide associated illustrative sketches and regime maps. These techniques involve Venturi pressure drop, Coriolis, electromagnetic, and cross-correlation flow meters, gamma-ray absorption and gradio-manometer densitometers, and local electrical and fiber-optic sensors, for which we describe the principles of operation and interpretation. References are given to more comprehensive texts and papers; these are representative rather than exhaustive. It is emphasized that empirical calibration is the norm and that detailed fluid-mechanical analysis has so far played little part in instrument design and operation.

Notes: This paper is a short and nonexhaustive survey of some recent developments in optimal shape design (OSD) for fluids. OSD is an interesting field both mathematically and for industrial applications. Existence, sensitivity, and compatibility of discretizations are important theoretical issues. Efficient algorithmic implementations with low complexity are also critical. In this paper we discuss topological optimization, algorithmic differentiation, gradient smoothers, Computer Aided Design (CAD)-free platforms and shock differentiation; all these are applied to a multicriterion optimization for a supersonic business jet.

Notes: The coexistence in the deep ocean of a finite, stable stratification, a strong meridional overturning circulation, and mesoscale eddies raises complex questions concerning the circulation energetics. In particular, small-scale mixing processes are necessary to resupply the potential energy removed in the interior by the overturning and eddy-generating process. A number of lines of evidence, none complete, suggest that the oceanic general circulation, far from being a heat engine, is almost wholly governed by the forcing of the wind field and secondarily by deep water tides. In detail however, the budget of mechanical energy input into the ocean is poorly constrained. The now inescapable conclusion that over most of the ocean significant "vertical" mixing is confined to topographically complex boundary areas implies a potentially radically different interior circulation than is possible with uniform mixing. Whether ocean circulation models, either simple box or full numerical ones, neither explicitly accounting for the energy input into the system nor providing for spatial variability in the mixing, have any physical relevance under changed climate conditions is at issue.

Notes: Microfluidic devices for manipulating fluids are widespread and finding uses in many scientific and industrial contexts. Their design often requires unusual geometries and the interplay of multiple physical effects such as pressure gradients, electrokinetics, and capillarity. These circumstances lead to interesting variants of well-studied fluid dynamical problems and some new fluid responses. We provide an overview of flows in microdevices with focus on electrokinetics, mixing and dispersion, and multiphase flows. We highlight topics important for the description of the fluid dynamics: driving forces, geometry, and the chemical characteristics of surfaces.

Notes: Shock wave research was traditionally developed as an element of high-speed gas dynamics supporting supersonic flights and atmospheric reentry of space vehicles. However, recently its scope has expanded to the comprehensive interpretation of shock wave phenomena in nature and the artificial world. In particular, many aspects of volcanoes's explosive eruptions are closely related to shock wave dynamics. One hypothesis proposes that during asteroid impact events that took place millions of years ago underwater shock waves played a decisive role in mass extinction of marine creatures. Shock waves have been successfully applied to medical therapy. Extracorporeal shock wave lithotripsy (ESWL) was a wonderful success in noninvasive removal of urinary tract stones. Recently, shock wave therapy was further developed for the revascularization of cerebral embolism, drug delivery, and other interesting therapeutic methods. This review provides an overview of the state-of-the-art interdisciplinary applications of shock wave research to geophysics and medicine.

Notes: This review summarizes fundamental results and discoveries concerning vortex-induced vibration (VIV), that have been made over the last two decades, many of which are related to the push to explore very low mass and damping, and to new computational and experimental techniques that were hitherto not available. We bring together new concepts and phenomena generic to VIV systems, and pay special attention to the vortex dynamics and energy transfer that give rise to modes of vibration, the importance of mass and damping, the concept of a critical mass, the relationship between force and vorticity, and the concept of "effective elasticity," among other points. We present new vortex wake modes, generally in the framework of a map of vortex modes compiled from forced vibration studies, some of which cause free vibration. Some discussion focuses on topics of current debate, such as the decomposition of force, the relevance of the paradigm flow of an elastically mounted cylinder to more complex systems, and the relationship between forced and free vibration.

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.

Notes: The nation has over 40,000 metric tonnes (MT) of nuclear waste destined for disposal in a geologic repository at Yucca Mountain. In this review, we highlight some of the important geoscience issues associated with the project and place them in the context of the process by which a final decision on Yucca Mountain will be made. The issues include understanding how water could infiltrate the repository, corrode the canisters, dissolve the waste, and transport it to the biosphere during a 10,000-year compliance period in a region, the Basin and Range province, that is known for seismic and volcanic activity. Although the site is considered to be "dry," a considerable amount of water is present as pore waters and as structural water in zeolites. The geochemical environment is oxidizing, and the present repository design will maintain temperatures at greater than 100oC for thousands of years. Geoscientists in this project are challenged to make unprecedented predictions about coupled thermal, hydrologic, mechanical, and geochemical processes governing the future behavior of the repository and to conduct research in a regulatory and legal environment that requires a quantitative analysis of repository performance.

Notes: The migration of the Mendocino triple junction through central and northern California over the past 25-30 million years has led to a profound change in plate interactions along coastal California. The tectonic consequences of the abrupt change from subduction plate interactions north of the triple junction to the development of the San Andreas transform system south of the triple junction can be seen in the geologic record and geophysical observations. The primary driver of this tectonism is a coupling among the subducting Juan de Fuca (Gorda), North American, and Pacific plates that migrates with the triple junction. This coupling leads to ephemeral thickening of the overlying North American crust, associated uplift and subsequent subsidence, and a distinctive sequence of fault development and volcanism.

Notes: Bedrock rivers set much of the relief structure of active orogens and dictate rates and patterns of denudation. Quantitative understanding of the role of climate-driven denudation in the evolution of unglaciated orogens depends first and foremost on knowledge of fluvial erosion processes and the factors that control incision rate. The results of intense research in the past decade are reviewed here, with the aim of highlighting remaining unknowns and suggesting fruitful avenues for further research. This review considers in turn (a) the occurrence and morphology of bedrock channels and their relation to tectonic setting; (b) the physical processes of fluvial incision into rock; and (c) models of river incision, their implications, and the field and laboratory data needed to test, refine, and extend them.

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.

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.

Notes: Computer models are used to mimic the early evolution of ancient vascular plants (tracheophytes). These models have three components: (a) an N-dimensional domain of all mathematically conceivable ancient morphologies (a morphospace); (b) a numerical assessment of the ability (fitness) of each morphology to intercept light, maintain mechanical stability, conserve water, and produce and disperse spores; and (c) an algorithm that searches the morphospace for successively more fit variants (an adaptive walk). Beginning with the most ancient known plant form, evolution is simulated by locating neighboring morphologies that progressively perform one or more tasks more efficiently. The resulting simulated adaptive walks indicate that early tracheophyte evolution involved optimizing the performance of many tasks simultaneously rather than maximizing the performance of one or only a few tasks individually, and that the requirement for optimization accelerated the tempo of morphological evolution in the Silurian and Devonian.

Notes: Models of processes in the alpine snow cover fundamentally depend on the spatial distribution of the surface energy balance over areas where topographic variability causes huge differences in the incoming solar radiation and in snow depth because of redistribution by wind. At a spatial scale commensurate with that of the terrain, we want to know which areas are covered by snow, and we want to estimate the snow's spectral albedo, along with other properties such as grain size, contaminants, temperature, liquid water content, and depth or water equivalent. From multispectral and hyperspectral remote sensing at wavelengths from 0.4-15 mum, the retrievable properties include snow-covered area, albedo, grain size, liquid water very near the surface, and temperature. Spectral mixture analysis allows the retrieval of the subpixel variability of snow-covered area, along with the snow's albedo. Remaining research challenges include the remote sensing of absorbing impurities; accounting for variability in the bidirectional-reflectance distribution function and the variability of grain size with depth; retrieving snow cover in forested regions; reconciling field measurements of emissivity with snow properties; and adapting the algorithms to frequent, large-scale processing.

Notes: We examine the genetics of marine diversification along the West Coast of North America in relation to the Late Neogene geology and climate of the region. Trophically important components of the diverse West Coast fauna, including kelp, alcid birds (e.g., auks, puffins), salmon, rockfish, abalone, and Cancer crabs, appear to have radiated during peaks of upwelling primarily in the Late Miocene and in some cases secondarily in the Pleistocene. Phylogeographic barriers associated with Mio-Pliocene estuaries of the mid-California coast, the Pliocene opening of the Gulf of California, tectonic and eustatic evolution of the California Bight, as well as the influence of Pleistocene and Holocene climate change on genetic structure are assessed in a geologic context. Comparisons to East Coast and western freshwater systems, as well as upwelling systems around the globe, provide perspective for the survey.

Notes: Measurements of cosmogenic nuclides, predominately 10Be, allow new insights into the ways in which and the rates at which sediment is generated, transported, and deposited over timescales ranging from 103 to 106 years. Samples from rock exposures are used to estimate erosion rates at points on the landscape, whereas samples of fluvial sediment provide estimates of basin-scale rates of denudation integrated over 〈1 to 〉104 km2. Nuclide data show that hilltop, bare rock outcrops erode more slowly than basins as a whole, suggesting the potential for relief to increase over time as well-drained outcrops grow higher. More elaborate experiments and interpretive models provide insight into the distribution of hillslope processes, including the bedrock-to-soil conversion rate, which appears to increase under shallow soil cover and then decrease under deeper soils. Changes in average nuclide activity down slopes can be used to estimate grain speed over millennia, suggesting, for example, that sediment on desert piedmonts moves, on average, decimeters to meters per year. In other cases, changes in nuclide activity down river networks or along shorelines can be interpreted with mixing models to indicate sediment sources. Sediment deposition rates in otherwise undateable deposits can now be estimated by analyzing samples collected from depth profiles. Over the past decade, the analysis and interpretation of cosmogenic nuclides has given geomorphologists an unprecedented opportunity to measure rates and infer the distribution of geomorphic processes across Earth's varied landscapes. Long-standing models of landscape change can now be tested quantitatively.

Notes: Avulsion is the natural process by which flow diverts out of an established river channel into a new permanent course on the adjacent floodplain. Avulsions are primarily features of aggrading floodplains. Their recurrence interval varies widely among the few modern rivers for which such data exist, ranging from as low as 28 years for the Kosi River (India) to up to 1400 years for the Mississippi. Avulsions cause loss of life, property damage, destabilization of shipping and irrigation channels, and even coastal erosion as sediment is temporarily sequestered on the floodplain. They are also the main process that builds alluvial stratigraphy. Their causes remain relatively unknown, but stability analyses of bifurcating channels suggest that thresholds in the relative energy slope and Shields parameter of the bifurcating channel system are key factors.

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.

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.

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.

Notes: The Cordilleran orogen of western North America is a segment of the Circum-Pacific orogenic belt where subduction of oceanic lithosphere has been underway along a great circle of the globe since breakup of the supercontinent Pangea began in Triassic time. Early stages of Cordilleran evolution involved Neoproterozoic rifting of the supercontinent Rodinia to trigger miogeoclinal sedimentation along a passive continental margin until Late Devonian time, and overthrusting of oceanic allochthons across the miogeoclinal belt from Late Devonian to Early Triassic time. Subsequent evolution of the Cordilleran arc-trench system was punctuated by tectonic accretion of intraoceanic island arcs that further expanded the Cordilleran continental margin during mid-Mesozoic time, and later produced a Cretaceous batholith belt along the Cordilleran trend. Cenozoic interaction with intra-Pacific seafloor spreading systems fostered transform faulting along the Cordilleran continental margin and promoted incipient rupture of continental crust within the adjacent continental block.

Notes: Wrinkle ridges accommodate very low amounts of shortening strain around immense volcanic constructs and within impact basins on Mars. They originate from stresses distributed uniformly throughout the brittle lithosphere and are consistently located in stratified deposits, including lava flows and sediment. Most recent models interpret wrinkle ridges as the surface manifestation of folding above underlying blind thrusts that accommodate similarly low strain and likely penetrate tens of kilometers into the brittle crust. Alternative models suggest shortening accommodated by some wrinkle ridges is confined to only the upper few kilometers of the crust. The interpretation of the geometry of blind thrusts on Mars appears to be quite varied and remains controversial, although some models suggest they may ultimately flatten into the brittle-ductile transition in the middle to lower crust. Small-scale crenulations superposed on ridges are interpreted as produced by high-level back thrusts nucleating at a weak layer in the upper crust, or by flexural slip faults that facilitate bending of layered materials. Wrinkle ridges are related to their structural cousins, lobate scarps that accommodate shortening in older Noachian cratered highlands as surface fault ruptures. Wrinkle ridges thus form when displacement across upwardly propagating blind thrusts is consumed by folding of layered material near the surface. Conversely, lobate scarps are formed by blind thrusts that are not impeded by folding of overlying layered deposits. Broad, low-amplitude arches associated with ridges on the Tharsis rise also accommodate shortening, but their relationship to adjacent or superposed ridges remains enigmatic. The evenly spaced nature of wrinkle ridges that appears to vary systematically between the ridged plains and northern lowlands may be related to the depth of the brittle-ductile transition, which is respectively located in the middle crust and upper mantle in these regions.

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.

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.

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.

Notes: The history of the theory and experimental evidence that the natural catalytic and reactive qualities of transition metal sulfides are linked to primitive metabolism is reviewed. In the late 1980s, a hypothesis arose that proposed that transition metal sulfides (in particular pyrrhotite and pyrite) might play a significant role promoting abiotic organic chemistry. As an outgrowth of this hypothesis, elaborate theories were presented, including proposals for earliest life being structurally distinct from extant prokaryotic life. During the 1990s and into the twenty-first century, experimental evidence has emerged that supports certain aspects of these theories; in other cases, the experiments reveal chemistry that diverges significantly from that which was proposed theoretically. In either case, however, there is clear evidence that transition metal sulfide minerals exhibit catalytic qualities for the promotion of reactions that have obvious metabolic utility and, therefore, could have provided the primitive Earth with valuable biochemical intermediates.

Notes: Accumulation rates of terrestrial sediment have increased in the past few million years both on and adjacent to continents, although not everywhere. Apparently, erosion has increased in elevated terrain regardless of when last tectonically active or what the present-day climate. In many regions, sediment coarsened abruptly in late Pliocene time. Sparser data suggest increased sedimentation rates at ~15 Ma, approximately when oxygen isotopes in benthic foraminifera imply high-latitude cooling. If climate change effected accelerated erosion, understanding how it did so remains the challenge. Some obvious candidates, such as lowered sea level leading to erosion of continental shelves or increased glaciation, account for increased sedimentation in some, but not all, areas. Perhaps stable climates that varied slowly allowed geomorphic processes to maintain a state of equilibrium with little erosion until ~3-4 Ma, when large oscillations in climate with periods of 20,000-40,000 years developed and denied the landscape the chance to reach equilibrium.

Notes: Visible and near-infrared spectra of reflected sunlight from asteroid surfaces exhibit features that hold the promise for identifying surface mineralogy. However, the very surfaces that are observed by remote-sensing are also subject to impingement by micrometeoroids and solar wind particles, which are believed to play the dominant role in space weathering, which is the time-dependent modification of an asteroid's reflectance spectrum. Such space weathering has confused the interpretations of telescopic spectra of asteroids, especially concerning the possible association of common ordinary chondritic meteorites with so-called S-type asteroids. Recent spacecraft studies of asteroids (especially of Eros by NEAR-Shoemaker) have documented aspects of space weathering processes, but we still do not understand the physics of space weathering well enough to confidently assay mineralogy of diverse asteroids by remote-sensing. A review of the intellectual history of this topic reveals the complexity of interdisciplinary research on far-away astronomical bodies.

Notes: Manganese(IV) oxides produced through microbial activity, i.e., biogenic Mn oxides or Mn biooxides, are believed to be the most abundant and highly reactive Mn oxide phases in the environment. They mediate redox reactions with organic and inorganic compounds and sequester a variety of metals. The major pathway for bacterial Mn(II) oxidation is enzymatic, and although bacteria that oxidize Mn(II) are phylogenetically diverse, they require a multicopper oxidase-like enzyme to oxidize Mn(II). The oxidation of Mn(II) to Mn(IV) occurs via a soluble or enzyme-complexed Mn(III) intermediate. The primary Mn(IV) biooxide formed is a phyllomanganate most similar to delta-MnO2 or acid birnessite. Metal sequestration by the Mn biooxides occurs predominantly at vacant layer octahedral sites.

Notes: The existence of gravitational radiation is a direct prediction of Einstein's theory of general relativity, published in 1916. The observation of gravitational radiation will open a new astronomical window on the universe, allowing the study of dynamic strong-field gravity, as well as many other astrophysical objects and processes impossible to observe with electromagnetic radiation. The relative weakness of the gravitational force makes detection extremely challenging; nevertheless, sustained advances in detection technology have made the observation of gravitational radiation probable in the near future. In this article, we review the theoretical and experimental status of this emerging field.

Notes: The Gerasimov-Drell-Hearn sum rule is one of several dispersive sum rules that connect the Compton scattering amplitudes to the inclusive photoproduction cross sections of the target under investigation. Being based on such universal principles as causality, unitarity, and gauge invariance, these sum rules provide a unique testing ground to study the internal degrees of freedom that hold the system together. The present article reviews these sum rules for the spin-dependent cross sections of the nucleon by presenting an overview of recent experiments and theoretical approaches. The generalization from real to virtual photons provides a microscope of variable resolution: At small virtuality of the photon, the data sample information about the long-range phenomena, which are described by effective degrees of freedom (Goldstone bosons and collective resonances), whereas the primary degrees of freedom (quarks and gluons) become visible at the larger virtualities. Through a rich body of new data and several theoretical developments, a unified picture of virtual Compton scattering emerges, which ranges from coherent to incoherent processes, and from the generalized spin polarizabilities on the low-energy side to higher twist effects in deep-inelastic lepton scattering.

Notes: A career devoted to the study of weak interactions and fundamental symmetries is summarized. Subjects include the induced pseudoscalar coupling in muon capture, the hypothesis of a superweak interaction, the oscillation of neutrinos in matter, and a parameterization of the CKM matrix of particular importance for B physics. Also discussed are the origin of the Aspen Center for Physics and activities related to the dangers of nuclear weapons.

Notes: Quantum chromodynamics (QCD), which describes hadrons and their interactions, is a non-Abelian gauge theory. The salient property of QCD is color confinement, quantitative understanding of which still remains a challenge. Major contributions to understanding quantum dynamics of non-Abelian fields are due to V.N. Gribov, both in the framework of pure gluodynamics (Gribov copies, Gribov horizon) and in the quest for confinement in the presence of light quarks (supercritical confinement scenario). We discuss Gribov's approach to the confinement problem and review some recent developments that are motivated, directly or indirectly, by his ideas.

Notes: Recent applications of neutron reflectometry to the study of wet interfaces are described. An outline is given of the basic principles that allow the techniques to determine composition and structure in a variety of situations. These are the adsorption of surfactant molecules at air/liquid and solid/liquid interfaces, the shape of the segment-density profiles of different types of polymer, including block copolymers and polyelectrolytes, adsorption in mixed surfactant and polymer/surfactant systems, and interfacial systems of biophysical interest.

Notes: Charge transport at conjugated polymer interfaces with metals and inorganic semiconductors is reviewed. Experiments on the equilibrium properties and DC current-voltage behavior of four specific classes of interfaces-metal-doped conjugated polymer, inorganic semiconductor-doped conjugated polymer, metal-intrinsic conjugated polymer, and metal-intrinsic conjugated polymer/electrolyte-are discussed. To facilitate this discussion, classic models of equilibration at ideal interfaces between electronic conductors and free-electron transport are introduced and their limitations discussed. Particular emphasis is placed on the charge distributions and interfacial potential profiles expected at various types of electroactive interfaces.

Notes: Recent progress in the development of semiclassical methods to describe quantum effects in molecular dynamics is reviewed. Focusing on rigorous semiclassical methods that are based on the initial-value representation of the semiclassical propagator, we discuss several promising schemes that have been developed in the past few years to extend the applicability of semiclassical approaches to complex molecular systems. In particular, integral-filtering techniques and forward-backward methods are surveyed. Furthermore, recently proposed approaches that allow the semiclassical description of nonadiabatic molecular dynamics are discussed. The potential and efficiency of these methods is illustrated by selected applications.

Notes: Time-dependent density functional theory (TDDFT) can be viewed as an exact reformulation of time-dependent quantum mechanics, where the fundamental variable is no longer the many-body wave function but the density. This time-dependent density is determined by solving an auxiliary set of noninteracting Schrodinger equations, the Kohn-Sham equations. The nontrivial part of the many-body interaction is contained in the so-called exchange-correlation potential, for which reasonably good approximations exist. Within TDDFT two regimes can be distinguished: (a) If the external time-dependent potential is "small," the complete numerical solution of the time-dependent Kohn-Sham equations can be avoided by the use of linear response theory. This is the case, e.g., for the calculation of photoabsorption spectra. (b) For a "strong" external potential, a full solution of the time-dependent Kohn-Sham equations is in order. This situation is encountered, for instance, when matter interacts with intense laser fields. In this review we give an overview of TDDFT from its theoretical foundations to several applications both in the linear and in the nonlinear regime.

Notes: The review describes the studies of the magneto-optical properties of II-VI and III-V semiconductor nanocrystals (NCs) capped with organic or inorganic epitaxial shells. The investigations focused on the chemical identification of localization sites (core, shell, or interface) of photogenerated carriers in spherical NCs and elucidated the influence of the surface/interface quality on the optical properties of the materials. Optically detected magnetic resonance (ODMR) spectroscopy was used for the study of the proposed physical properties. The ODMR method provides the means to identify the surface/interface sites and correlate them with specific optical transition. In addition, this method reveals information about the spin multiplicity of band edge and trapped states and the electron-hole exchange interaction, determines the spectroscopic g-factors, distinguishes between the radiative and nonradiative characteristic of a trapping site, and evaluates the spin-lattice relaxation times.

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.

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.