ALBERT

Notes: Residual dipolar couplings (RDCs) have recently emerged as a new tool in nuclear magnetic resonance (NMR) with which to study macromolecular structure and function in a solution environment. RDCs are complementary to the more conventional use of NOEs to provide structural information. While NOEs are local-distance restraints, RDCs provide long-range orientational information. RDCs are now widely utilized in structure calculations. Increasingly, they are being used in novel applications to address complex issues in structural biology such as the accurate determination of the global structure of oligonucleotides and the relative orientation of protein domains. This review briefly describes the theory and methods for obtaining RDCs and then describes the range of biological applications where RDCs have been used.

Notes: Views of how cell membranes are organized are presently changing. The lipid bilayer that constitutes these membranes is no longer understood to be a homogeneous fluid. Instead, lipid assemblies, termed rafts, have been introduced to provide fluid platforms that segregate membrane components and dynamically compartmentalize membranes. These assemblies are thought to be composed mainly of sphingolipids and cholesterol in the outer leaflet, somehow connected to domains of unknown composition in the inner leaflet. Specific classes of proteins are associated with the rafts. This review critically analyzes what is known of phase behavior and liquid-liquid immiscibility in model systems and compares these data with what is known of domain formation in cell membranes.

Notes: Turbulence affects the structure and motions of nearly all temperature and density regimes in the interstellar gas. This two-part review summarizes the observations, theory, and simulations of interstellar turbulence and their implications for many fields of astrophysics. The first part begins with diagnostics for turbulence that have been applied to the cool interstellar medium and highlights their main results. The energy sources for interstellar turbulence are then summarized along with numerical estimates for their power input. Supernovae and superbubbles dominate the total power, but many other sources spanning a large range of scales, from swing-amplified gravitational instabilities to cosmic ray streaming, all contribute in some way. Turbulence theory is considered in detail, including the basic fluid equations, solenoidal and compressible modes, global inviscid quadratic invariants, scaling arguments for the power spectrum, phenomenological models for the scaling of higher-order structure functions, the direction and locality of energy transfer and cascade, velocity probability distributions, and turbulent pressure. We emphasize expected differences between incompressible and compressible turbulence. Theories of magnetic turbulence on scales smaller than the collision mean free path are included, as are theories of magnetohydrodynamic turbulence and their various proposals for power spectra. Numerical simulations of interstellar turbulence are reviewed. Models have reproduced the basic features of the observed scaling relations, predicted fast decay rates for supersonic MHD turbulence, and derived probability distribution functions for density. Thermal instabilities and thermal phases have a new interpretation in a supersonically turbulent medium. Large-scale models with various combinations of self-gravity, magnetic fields, supernovae, and star formation are beginning to resemble the observed interstellar medium in morphology and statistical properties. The role of self-gravity in turbulent gas evolution is clarified, leading to new paradigms for the formation of star clusters, the stellar mass function, the origin of stellar rotation and binary stars, and the effects of magnetic fields. The review ends with a reflection on the progress that has been made in our understanding of the interstellar medium and offers a list of outstanding problems.

Notes: Observation of cooling neutron stars can potentially provide information about the states of matter at supernuclear densities. We review physical properties important for cooling such as neutrino emission processes and superfluidity in the stellar interior, surface envelopes of light elements owing to accretion of matter, and strong surface magnetic fields. The neutrino processes include the modified Urca process and the direct Urca process for nucleons and exotic states of matter, such as a pion condensate, kaon condensate, or quark matter. The dependence of theoretical cooling curves on physical input and observations of thermal radiation from isolated neutron stars are described. The comparison of observation and theory leads to a unified interpretation in terms of three characteristic types of neutron stars: high-mass stars, which cool primarily by some version of the direct Urca process; low-mass stars, which cool via slower processes; and medium-mass stars, which have an intermediate behavior. The related problem of thermal states of transiently accreting neutron stars with deep crustal burning of accreted matter is discussed in connection with observations of soft X-ray transients. Observations imply that some stars cool more rapidly than can be explained on the basis of nonsuperfluid neutron star models cooling via the modified Urca process, whereas other star cool less rapidly. We describe possible theoretical models that are consistent with observations.

Notes: We review recent theoretical results on the formation of the first stars in the universe, and emphasize related open questions. In particular, we discuss the initial conditions for Population III star formation, as given by variants of the cold dark matter cosmology. Numerical simulations have investigated the collapse and the fragmentation of metal-free gas, showing that the first stars were predominantly very massive. The exact determination of the stellar masses, and the precise form of the primordial initial mass function, is still hampered by our limited understanding of the accretion physics and the protostellar feedback effects. We address the importance of heavy elements in bringing about the transition from an early star formation mode dominated by massive stars to the familiar mode dominated by low-mass stars at later times. We show how complementary observations, both at high redshifts and in our local cosmic neighborhood, can be utilized to probe the first epoch of star formation.

Notes: Until the late 1990s the rich Hyades and the sparse UMa clusters were the only coeval, comoving concentrations of stars known within 60 pc of Earth. Both are hundreds of millions of years old. Then beginning in the late 1990s the TW Hydrae Association, the Tucana/Horologium Association, the beta Pictoris Moving Group, and the AB Doradus Moving Group were identified within ~60 pc of Earth, and the eta Chamaeleontis cluster was found at 97 pc. These young groups (ages 8-50 Myr), along with other nearby, young stars, will enable imaging and spectroscopic studies of the origin and early evolution of planetary systems.

Notes: GRS 1915+105-the first stellar-scale, highly relativistic jet source identified-is a key system for our understanding of the disc-jet coupling in accreting black hole systems. Comprehending the coupling between inflow and outflow in this source not only is important for X-ray binary systems but has a broader relevance for studies of active galactic nuclei and gamma-ray bursts. In this paper, we present a detailed review of the observational properties of the system, as established in the decade since its discovery. We attempt to place it in context by a detailed comparison with other sources, and construct a simple model for the disc-jet coupling, which may be more widely applicable to accreting black hole systems.

Notes: The effect of force on the thermodynamics and kinetics of reactions is described. The key parameters are the difference in end-to-end distance between reactant and product for thermodynamics, and the distance to the transition state for kinetics. I focus the review on experimental results on force unfolding of RNA. Methods to measure Gibbs free energies and kinetics for reversible and irreversible reactions are described. The use of the worm-like-chain model to calculate the effects of force on thermodynamics and kinetics is illustrated with simple models. The main purpose of the review is to describe the simple experiments that have been done so far, and to encourage more people to enter a field that is new and full of opportunities.

Notes: The structural elucidation of clear but distant homologs of actin and tubulin in bacteria and GFP labeling of these proteins promises to reinvigorate the field of prokaryotic cell biology. FtsZ (the tubulin homolog) and MreB/ParM (the actin homologs) are indispensable for cellular tasks that require the cell to accurately position molecules, similar to the function of the eukaryotic cytoskeleton. FtsZ is the organizing molecule of bacterial cell division and forms a filamentous ring around the middle of the cell. Many molecules, including MinCDE, SulA, ZipA, and FtsA, assist with this process directly. Recently, genes much more similar to tubulin than to FtsZ have been identified in Verrucomicrobia. MreB forms helices underneath the inner membrane and probably defines the shape of the cell by positioning transmembrane and periplasmic cell wall-synthesizing enzymes. Currently, no interacting proteins are known for MreB and its relatives that help these proteins polymerize or depolymerize at certain times and places inside the cell. It is anticipated that MreB-interacting proteins exist in analogy to the large number of actin binding proteins in eukaryotes. ParM (a plasmid-borne actin homolog) is directly involved in pushing certain single-copy plasmids to the opposite poles by ParR/parC-assisted polymerization into double-helical filaments, much like the filaments formed by actin, F-actin. Mollicutes seem to have developed special systems for cell shape determination and motility, such as the fibril protein in Spiroplasma.

Notes: Molecular motions are widely regarded as contributing factors in many aspects of protein function. The enzyme dihydrofolate reductase (DHFR), and particularly that from Escherichia coli, has become an important system for investigating the linkage between protein dynamics and catalytic function, both because of the location and timescales of the motions observed and because of the availability of a large amount of structural and mechanistic data that provides a detailed context within which the motions can be interpreted. Changes in protein dynamics in response to ligand binding, conformational change, and mutagenesis have been probed using numerous experimental and theoretical approaches, including X-ray crystallography, fluorescence, nuclear magnetic resonance (NMR), molecular dynamics simulations, and hybrid quantum/classical dynamics methods. These studies provide a detailed map of changes in conformation and dynamics throughout the catalytic cycle of DHFR and give new insights into the role of protein motions in the catalytic activity of this enzyme.

Notes: The genomics revolution has provided a deluge of new targets for drug discovery. To facilitate the drug discovery process, many researchers are turning to fragment-based approaches to find lead molecules more efficiently. One such method, Tethering1, allows for the identification of small-molecule fragments that bind to specific regions of a protein target. These fragments can then be elaborated, combined with other molecules, or combined with one another to provide high-affinity drug leads. In this review we describe the background and theory behind Tethering and discuss its use in identifying novel inhibitors for protein targets including interleukin-2 (IL-2), thymidylate synthase (TS), protein tyrosine phosphatase 1B (PTP-1B), and caspases.

Notes: Recent work is extending the methodology of X-ray crystallography to the structure determination of noncrystalline specimens. The phase problem is solved using the oversampling method, which takes advantage of "continuous" diffraction patterns from noncrystalline specimens. Here we review the principle of this newly developed technique and discuss the ongoing experiments of imaging nonperiodic objects, such as cells and cellular structures, using coherent and bright X rays produced by third-generation synchrotron sources. In the longer run, the technique may be applicable to image single biomolecules using anticipated X-ray free electron lasers. Here, computer simulations have so far demonstrated two important steps: (a) by using an extremely intense femtosecond X-ray pulse, a diffraction pattern can be recorded from a macromolecule before radiation damage manifests itself; and (b) the phase information can be retrieved in an ab initio fashion from a set of calculated noisy diffraction patterns of single protein molecules.

Notes: Topoisomerases are enzymes that use DNA strand scission, manipulation, and rejoining activities to directly modulate DNA topology. These actions provide a powerful means to effect changes in DNA supercoiling levels, and allow some topoisomerases to both unknot and decatenate chromosomes. Since their initial discovery over three decades ago, researchers have amassed a rich store of information on the cellular roles and regulation of topoisomerases, and have delineated general models for their chemical and physical mechanisms. Topoisomerases are now known to be necessary for the survival of cellular organisms and many viruses and are rich clinical targets for anticancer and antimicrobial treatments. In recent years, crystal structures have been obtained for each of the four types of topoisomerases in a number of distinct conformational and substrate-bound states. In addition, sophisticated biophysical methods have been utilized to study details of topoisomerase reaction dynamics and enzymology. A synthesis of these approaches has provided researchers with new physical insights into how topoisomerases employ chemistry and allostery to direct the large-scale molecular motions needed to pass DNA strands through each other.

Notes: Emerging methods in cryo-electron microscopy allow determination of the three-dimensional architectures of objects ranging in size from small proteins to large eukaryotic cells, spanning a size range of more than 12 orders of magnitude. Advances in determining structures by "single particle" microscopy and by "electron tomography" provide exciting opportunities to describe the structures of subcellular assemblies that are either too large or too heterogeneous to be investigated by conventional crystallographic methods. Here, we review selected aspects of progress in structure determination by cryo-electron microscopy at molecular resolution, with a particular emphasis on topics at the interface of single particle and tomographic approaches. The rapid pace of development in this field suggests that comprehensive descriptions of the structures of whole cells and organelles in terms of the spatial arrangements of their molecular components may soon become routine.

Notes: F1-ATPase is a rotary motor made of a single protein molecule. Its rotation is driven by free energy obtained by ATP hydrolysis. In vivo, another motor, Fo, presumably rotates the F1 motor in the reverse direction, reversing also the chemical reaction in F1 to let it synthesize ATP. Here we attempt to answer two related questions, How is free energy obtained by ATP hydrolysis converted to the mechanical work of rotation, and how is mechanical work done on F1 converted to free energy to produce ATP? After summarizing single-molecule observations of F1 rotation, we introduce a toy model and discuss its free-energy diagrams to possibly answer the above questions. We also discuss the efficiency of molecular motors in general.

Notes: Mass spectrometry provides key tools for the analysis of proteins. New types of mass spectrometers that provide enhanced capability to discover protein identities and perform improved proteomic experiments are discussed. Handling the complex mixtures of peptides and proteins generated from protein complexes and whole cells requires multidimensional separations; several forms of separation are discussed. Applications of mass spectrometry-based approaches for contemporary proteomic analyses are described.

Notes: Nucleic acids are characterized by a vast structural variability. Secondary structural conformations include the main polymorphs A, B, and Z, cruciforms, intrinsic curvature, and multistranded motifs. DNA secondary motifs are stabilized and regulated by the primary base sequence, contextual effects, environmental factors, as well as by high-order DNA packaging modes. The high-order modes are, in turn, affected by secondary structures and by the environment. This review is concerned with the flow of structural information among the hierarchical structural levels of DNA molecules, the intricate interplay between the various factors that affect these levels, and the regulation and physiological significance of DNA high-order structures.

Notes: Meteorites and interplanetary dust particles contain presolar stardust grains: solid samples of stars that can be studied in the laboratory. The stellar origin of the grains is indicated by enormous isotopic ratio variations compared with Solar System materials, explainable only by nuclear reactions occurring in stars. Known presolar phases include diamond, SiC, graphite, Si3N4, Al2O3, MgAl2O4, CaAl12O19, TiO2, Mg(Cr,Al)2O4, and most recently, silicates. Subgrains of refractory carbides (e.g., TiC), and Fe-Ni metal have also been observed within individual presolar graphite grains. We review the astrophysical implications of these grains for the sciences of nucleosynthesis, stellar evolution, grain condensation, and the chemical and dynamic evolution of the Galaxy. Unique scientific information derives primarily from the high precision (in some cases 〈1%) of the measured isotopic ratios of large numbers of elements in single stardust grains. Stardust science is just now reaching maturity and will play an increasingly important role in nucleosynthesis applications.

Notes: This chapter reviews the properties of faint IR-selected field galaxies and the extremely red color-selected populations in particular. These populations are a mix of passively evolving stellar systems and heavily obscured star-forming galaxies. The star-forming component appears to constitute 20-50% of the population depending on the magnitude and color cuts employed. The remaining objects are a mix of passively evolving ellipticals and early-type disk galaxies. The passively evolving red galaxies are strongly clustered in space and are likely the high-mass high-luminosity end of the elliptical galaxy progenitor population at redshifts between one and two. These galaxies have masses and space densities that appear to be in conflict with late-forming hierarchical galaxy-formation models. The red galaxies appear to be a population that is distinct from the moderately star-forming Lyman-Break galaxies but may be related to the starburst population at z 〉 2 seen in deep submillimeter surveys.

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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: The 100 kyr quasiperiodic variation of continental ice cover, which has been a persistent feature of climate system evolution throughout the most recent 900 kyr of Earth history, has occurred as a consequence of changes in the seasonal insolation regime forced by the influence of gravitational n-body effects in the Solar System on the geometry of Earth's orbit around the Sun. The impacts of the changing surface ice load upon both Earth's shape and gravitational field, as well as upon sea-level history, have come to be measurable using a variety of geological and geophysical techniques. These observations are invertible to obtain useful information on both the internal viscoelastic structure of the solid Earth and on the detailed spatiotemporal characteristics of glaciation history. This review focuses upon the most recent advances that have been achieved in each of these areas, advances that have proven to be central to the construction of the refined model of the global process of glacial isostatic adjustment, denoted ICE-5G (VM2). A significant test of this new global model will be provided by the global measurement of the time dependence of the gravity field of the planet that will be delivered by the GRACE satellite system that is now in space.

Notes: This review describes the changes in the understanding of turbulence and mixing in the upper layers of the ocean, the abyssal ocean, and in continental shelf seas that have come in the past 25 years, largely through advances in instruments and methodology.

Notes: This article reviews the standard-model prediction for the anomalous magnetic moment of the muon and describes recent updates of QED, electroweak, and hadronic contributions. Comparison of theory and experiment suggests a 2.4 difference if e+e hadrons data are used to evaluate the main hadronic effects, but a smaller discrepancy if hadronic decay data are employed. Implications of a deviation for "new physics" contributions, along with an outlook for future improvements in theory and experiment, are briefly discussed.

Notes: This review explains why generalized parton distributions and the related quantum phase-space distributions are useful in exploring the quark and gluon structure of the proton and neutron. It starts with the physics of form factors and parton distributions. Then quantum phase-space distributions and their offspring are discussed. The properties of generalized parton distributions are described. In particular, I elucidate the relation to the spin structure of the nucleon. Finally, various methods to determine the new distributions are explained.

Notes: We summarize residual background sources encountered in experiments conducted deep underground. Physical mechanisms of production and methods of estimation for the dominant sources are considered, and comparisons of the calculations with underground measurements are discussed. Principal background sources discussed include primary interactions of cosmic rays, mechanisms of neutron production by cosmic rays and low energy backgrounds from neutrons, primordial and anthropogenic radionuclides, and secondary radioactivity from spallation.

Notes: We review the experimental and theoretical status of elastic electron scattering and elastic low-energy photon scattering (with both real and virtual photons) from the nucleon. As a consequence of new experimental facilities and new theoretical insights, these subjects are advancing with unprecedented precision. These reactions provide many important insights into the spatial distributions and correlations of quarks in the nucleon.

Notes: Modern analog analysis, the comparison of Quaternary fossil pollen assemblages with modern assemblages, has long been a mainstay of paleoecological and paleoclimatic inference. The logic of analogical inference involves a comparative element (comparison of modern and fossil assemblages to select matches and assess goodness of fit) and a causal element (assumption that the relationships between modern vegetation and derivative pollen assemblages are matched by those between ancient vegetation and fossil pollen assemblages). An array of numerical and statistical tools have been developed to ensure objective, consistent, and quantitative assessments of similarity between pollen assemblages. Divergent or convergent relationships between vegetation and pollen assemblages can arise from a variety of sources, composing a potential source of error in analog analysis, but such errors can be anticipated and minimized. Pollen assemblages lacking modern analogs are well documented for the late-glacial period (17,000-10,000 years BP) in eastern North America and other regions. Simulated climates for this period also lacked modern analogs owing to increased seasonality of insolation, lowered CO2, and persistent ice sheets. Most pollen assemblages from the last glacial maximum (23,000-20,000 years BP) in eastern North America have modern analogs, but macrofossil and other evidence suggest that the vegetation may have lacked modern analogs, owing to unique climate realizations and perhaps direct effects of lowered CO2. Better understanding of the nature of past no-analog vegetation, and the underlying causes, will address important issues in ecology and evolutionary biology and help anticipate biotic responses to the no-analog greenhouse world of the near-future.

Notes: A large extraterrestrial object striking Earth at cosmic velocity melts and vaporizes silicate materials, which can condense into highly spheroidal, sand-size particles that get deposited hundreds to thousands of kilometers from the point of impact. These particles, known as impact spherules, have been detected in great abundance in a relatively small number of thin, discrete layers ranging in age from less than a million years to 3.47 billion years. Unaltered impact spherules consist entirely of glass (microtektites) or a combination of glass and crystals grown in flight (microkrystites). Impact spherule layers form very rapidly and can be very extensive, even global in extent [e.g., the Cretaceous-Tertiary (K/T) boundary layer], so they form excellent time-stratigraphic markers. Because they are always found in a stratigraphic context, spherule layers are probably superior to terrestrial craters and related structures for assessing the environmental and biotic effects of large impacts. A record of impacts whose craters have since been obliterated, most notably those in pre-Mesozoic oceanic crust, could survive in the form of spherule layers. Secular changes in surface environments and/or the nature of the impactors striking Earth through its history could also be reflected in differences in spherules and spherule layers as a function of geologic age. In this paper, we briefly review what spherules and spherule layers are and the processes that create them, then speculate about what might be learned through wider identification of and more extensive study of impact spherule layers.

Notes: The fossil record preserves a wide range of events that might be used to build timescales and correlate strata from place to place. The events include the originations and extinctions of species, the occurrence of distinctive faunal assemblages, magnetic field reversals, changes in ocean chemistry, and volcanic ash falls. The fundamental task is to determine the global sequence of all these events. Modern computer algorithms can build high-resolution timescales by sequencing and calibrating thousands of such events from hundreds of localities. Each successful sequencing algorithm can be understood in terms of a simple two-dimensional visual device. Graphic correlation, permutable sequences, permutable matrices, and slotting devices are each suited to a different data problem, such as contradictory evidence of sequence, a lack of information about sequence, or uncertain correspondence of events. Algorithms based upon permutable sequences and evolutionary programming heuristics have the flexibility to optimize sequences with a wide variety of event types and data problems; they are slower than the more narrowly tailored methods. All methods will be challenged to keep pace with the amount of biostratigraphic information that is accumulating in the latest generation of shared databases. Currently, it is possible to sequence sufficiently large numbers of events to imagine a potential resolution of 10,000 to 50,000 years over time spans on the order of 50 to 100 million years. The actual resolving power is less because the solutions to these sequencing problems are not unique. Multiple equally good solutions typically emerge and, to extract a consensus sequence with which all solutions agree, some runs of events must be collapsed into unresolvable clusters. Nevertheless, quantitative methods have been shown to improve resolution up to tenfold over traditional methods that discard many potentially useful events.

Notes: Lattice quantum chromodynamics provides first-principles calculations for hadrons containing heavy quarkscharm and bottom quarks. Their mass spectra, decay rates, and some hadronic matrix elements can be calculated on the lattice in a model-independent manner. In this review, we introduce the effective theories that treat heavy quarks on the lattice. We summarize results on the heavy quarkonium spectrum, which verify the validity of the effective theory approach. We then discuss applications to B physics, which is the main target of the lattice theory of heavy quarks. We review progress in lattice calculations of the B meson decay constant, the B parameter, semileptonic decay form factors, and other important quantities.

Notes: We discuss the physics motivations for building a 500 GeV-1 TeV electron-positron linear collider. The state-of-the-art collider technologies and the physics-driven machine parameters are discussed. Some of the phenomena well suited to study at a linear collider are described, including Higgs bosons, supersymmetry, other extensions to the standard model, and cosmology.

Notes: The hep process is a weak-interaction reaction, 3He + p 4He + e+ + e , which occurs in the sun. There is renewed interest in hep owing to current experimental efforts to extract from the observed solar neutrino spectrum information on nonstandard physics in the neutrino sector. hep produces highest-energy solar neutrinos, although their flux is quite modest. This implies that the hep neutrinos can at some level influence the solar neutrino spectrum near its upper end. Therefore, a precise interpretation of the observed solar neutrino spectrum requires an accurate estimate of the hep rate. This is an interesting but challenging task. We describe the difficulties involved and how the recent theoretical developments in nuclear physics have enabled us to largely overcome these difficulties. A historical survey of hep calculations is followed by an overview of the latest developments. We compare the results obtained in the conventional nuclear physics approach and those obtained in a newly developed effective field theory approach. We also discuss the current status of the experiments relevant to hep.

Notes: Trace analysis of radionuclides is an essential and versatile tool in modern science and technology. Because of their ideal geophysical and geochemical properties, long-lived noble gas radionuclidesparticularly 39Ar (t1/2 = 269 y), 81Kr (t1/2 = 2.3 105 y), and 85Kr (t1/2 = 10.8 y)have long been recognized to have a wide range of important applications in Earth sciences. In recent years, significant progress in the development of practical analytical methods has led to applications of these isotopes in the hydrosphere (tracing the flow of groundwater and ocean water). In this article, we introduce the applications of these isotopes and review three leading analytical methods: low-level counting (LLC), accelerator mass spectrometry (AMS) and atom trap trace analysis (ATTA).

Notes: This article reviews the astrophysics and cosmological evidence for nonbaryonic dark matter (DM). It covers historical, current, and future experiments that look for direct evidence of particle DM. In addition, it surveys the underlying particle theories that provide some guidance about expected event rates, and the future prospects for the discovery of DM. A number of recent theoretical papers, making calculations in SUSY-based frameworks, show a spread of many (〉5) orders of magnitude in the possible interaction rates for models consistent with existing cosmological and accelerator bounds. Within this decade, it seems likely that DM searches will be successful, or at the very least rule out a broad class of the currently most favored DM models.

Notes: One can extract unique information about the nuclear interaction from the study of the heaviest elements. They exist solely on the basis of quantum effects, which create a barrier against spontaneous fission. The important questions concern the end of the periodic table and the location of the next closed nucleon shells. Considerable progress was achieved during the past few years in structure studies in this region. This was made possible by the development of detector systems for decay and in-beam studies using recoil separators and heavy ion fusion reactions. We concentrate on these developments and on recent results from structure studies in the region from einsteinium to dubnium. We present recent data on the elements 110 (darmstadtium), 111, and 112, and discuss claims for the synthesis of even heavier elements. We discuss the implications of these studies for predicting the location of the next spherical shells and give a brief outlook on the future.

Notes: The E821 Experiment at the Brookhaven Alternating Gradient Synchrotron has measured the muon anomalous magnetic moment a to a relative precision of 0.5 parts per million. This effort required a new beamline, a super-ferric muon storage ring with a highly uniform magnetic field, a precision magnetic field measurement system, and electromagnetic calorimeters to record the electrons from muon decay, which carry the essential spin precession frequency information. Data obtained over five years resulted in more than nine billion analyzed events, in nearly equal samples of both muon charges. The experimental results a + = 11 659 203(8) 1010 and a = 11 659 214(9) 1010 are consistent with each other, as predicted by the CPT invariance theorem. The combined result a +- = 11 659 208(6) 1010 is 0.9-2.4 standard deviations higher than predicted by theory; the range depends on the method employed to obtain the hadronic vacuum polarization term in the standard-model calculation. We review the experimental design, physical realization, and analysis procedures and compare the results to the theoretical prediction.

Notes: Over the past three decades, surface-enhanced Raman spectroscopy (SERS) has gone through a tortuous pathway to develop into a powerful surface diagnostic technique for in situ investigation of surface adsorption and reactions on electrodes. This review presents the recent progress achieved mainly in our laboratory on the improvement of detection sensitivities as well as spectral, temporal, and spatial resolutions. Various surface roughening procedures for electrodes of different metals coupled with maximum use of a high-sensitivity confocal Raman microscope enable us to obtain good-quality SER spectra on the electrode surfaces made from net Pt, Ni, Co, Fe, Pd, Rh, Ru, and their alloys that were traditionally considered to be non-SERS active. A novel technique called potential-averaged SERS (PASERS) has been developed for the quantitative study of electrochemical sorption. Applications are exemplified on extensively studied areas such as coadsorption, electrocatalysis, corrosion, and fuel cells, and several advantages of in situ electrochemical SERS are demonstrated. Finally, further developments in this field are briefly discussed with emphasis on the emerging methodology.

Notes: We review recent developments in single-molecule spectroscopy and microscopy. New optical methods provide access to the absorption, emission, or excitation spectra of single nano-objects and can determine either the positions of these objects with subwavelength accuracy or the full three-dimensional orientation of their transition dipole moments. Recent work aims at using single molecules as nanoparts or nanoelements in a variety of molecular-scale devices, from triggered sources of single photons to single-molecular switches. A prominent new direction explores the various interactions between molecules within individual multichromophoric systems obtained by chemical synthesis. These systems are the models for natural self-assembled systems such as the light-harvesting proteins of bacteria and green plants, which are currently studied on a single-molecule basis. Another important class of multichromophoric systems are conjugated polymers. The combination of microscopy with time- and frequency-resolved spectroscopy is opening a wide field of new and exciting applications to individual nano-objects.

Notes: Nonadiabatic effects play an important role in many areas of physics and chemistry. The coupling between electrons and nuclei may, for example, lead to the formation of a conical intersection between potential energy surfaces, which provides an efficient pathway for radiationless decay between electronic states. At such intersections the Born-Oppenheimer approximation breaks down, and unexpected dynamical processes result, which can be observed spectroscopically. We review the basic theory required to understand and describe conical, and related, intersections. A simple model is presented, which can be used to classify the different types of intersections known. An example is also given using wavepacket dynamics simulations to demonstrate the prototypical features of how a molecular system passes through a conical intersection.

Notes: Molecular beam scattering experiments provide a way to disentangle the elementary steps involved in energy transfer and chemical reactions between gases and liquids. After surveying the history and recent progress in this field, we review studies of the kinematics of gas-liquid collisions and proton exchange of HCl, DCl, and HBr with supercooled sulfuric acid and liquid glycerol. These experiments help to clarify the role of the surface region in controlling trapping and interfacial- and bulk-phase reactions.

Notes: Single-molecule spectroscopy (SMS) is a powerful experimental technique used to investigate a wide range of physical, chemical, and biophysical phenomena. The merit of SMS is that it does not require ensemble averaging, which is found in standard spectroscopic techniques. Thus SMS yields insight into complex fluctuation phenomena that cannot be observed using standard ensemble techniques. We investigate theoretical aspects of SMS, emphasizing (a) dynamical fluctuations (e.g., spectral diffusion, photon-counting statistics, antibunching, quantum jumps, triplet blinking, and nonergodic blinking) and (b) single-molecule fluctuations in disordered systems, specifically distribution of line shapes of single molecules in low-temperature glasses. Special emphasis is given to single-molecule systems that reveal surprising connections to Levy statistics (i.e., blinking of quantum dots and single molecules in glasses). We compare theory with experiment and mention open problems. Our work demonstrates that the theory of SMS is a complementary field of research for describing optical spectroscopy in the condensed phase.