ALBERT

Notes: Abstract Early NMR structural studies of serum lipoproteins were based on 1H, 13C, 31P, and 2H studies of lipid components. From the early studies information on composition, lipid chain dynamics and order parameters, and monolayer organization resulted. More recently, selective or complete isotopic labeling techniques, combined with multidimensional NMR spectroscopy, have resulted in structural information of apoprotein fragments. Finally, use of heteronuclear three- and four-dimensional experiments have yielded solution structures and protein-lipid interactions of intact apolipoproteins C-I, C-II, and A-I.

Notes: Abstract During the course of their biological function, proteins undergo different types of structural rearrangements ranging from local to large-scale conformational changes. These changes are usually triggered by their interactions with small-molecular-weight ligands or other macromolecules. Because binding interactions occur at specific sites and involve only a small number of residues, a chain of cooperative interactions is necessary for the propagation of binding signals to distal locations within the protein structure. This process requires an uneven structural distribution of protein stability and cooperativity as revealed by NMR-detected hydrogen/deuterium exchange experiments under native conditions. The distribution of stabilizing interactions does not only provide the architectural foundation to the three-dimensional structure of a protein, but it also provides the required framework for functional cooperativity. In this review, the statistical thermodynamic linkage between protein stability, functional cooperativity, and ligand binding is discussed.

Notes: Abstract Active transport requires the alternation of substrate uptake and release with a switch in the access of the substrate binding site to the two sides of the membrane. Both the transfer and switch aspects of the photocycle have been subjects of magnetic resonance studies in bacteriorhodopsin. The results for ion transfer indicate that the Schiff base of the chromophore is hydrogen bonded before, during, and after its deprotonation. This suggests that the initial complex counterion of the Schiff base decomposes in such a way that the Schiff base carries its immediate hydrogen-bonding partner with it as it rotates during the first half of the photocycle. If so, bacteriorhodopsin acts as an inward-directed hydroxide pump rather than as an outward-directed proton pump. The studies of the access switch explore both protein-based and chromophore-based mechanisms. Combined with evidence from functional studies of mutants and other forms of spectroscopy, the results suggest that maintaining access to the extracellular side of the protein after photoisomerization involves twisting of the chromophore and that the decisive switch in access to the cytoplasmic side results from relaxation of the chromophore when the constraints on the Schiff base are released by decomposition of the complex counterion.

Notes: Abstract We review the physical properties of phosphatidylinositol 4,5-bisphosphate (PIP2) that determine both its specific interactions with protein domains of known structure and its nonspecific electrostatic sequestration by unstructured domains. Several investigators have postulated the existence of distinct pools of PIP2 within the cell to account for the myriad functions of this lipid. Recent experimental work indicates certain regions of the plasma membrane-membrane ruffles and nascent phagosomes-do indeed concentrate PIP2. We consider two mechanisms that could account for this phenomenon: local synthesis and electrostatic sequestration. We conclude by considering the hypothesis that proteins such as MARCKS bind a significant fraction of the PIP2 in a cell, helping to sequester it in lateral membrane domains, then release this lipid in response to local signals such as an increased concentration of Ca++/calmodulin or activation of protein kinase C.

Notes: Abstract The first crystal structures of intact T cell receptors (TCRs) bound to class I peptide-MHC (pMHCs) antigens were determined in 1996. Since then, further structures of class I TCR/pMHC complexes have explored the degree of structural variability in the TCR-pMHC system and the structural basis for positive and negative selection. The recent determination of class II and allogeneic class I TCR/pMHC structures, as well as those of accessory molecules (e.g., CD3), has pushed our knowledge of TCR/pMHC interactions into new realms, shedding light on clinical pathologies, such as graft rejection and graft-versus-host disease. Furthermore, the determination of coreceptor structures lays the foundation for a more comprehensive structural description of the supramolecular TCR signaling events and those assemblies that arise in the immunological synapse. While these telling photodocumentaries of the TCR/pMHC interaction are composed mainly from static crystal structures, a full description of the biological snapshots in T cell signaling requires additional analytical methods that record the dynamics of the process. To this end, surface plasmon resonance (SPR), isothermal titration calorimetry (ITC), and ultracentrifugation (UC) have furnished both affinities and kinetics of the TCR/pMHC association. In the past year, structural, biochemical, and molecular biological data describing TCR/pMHC interactions have sublimely coalesced into a burgeoning well of understanding that promises to deliver further insights into T cell recognition. The coming years will, through a more intimate union of structural and kinetic data, allow many pressing questions to be addressed, such as how TCR/pMHC ligation is affected by coreceptor binding and what is the mechanism of TCR signaling in both early and late stages of T cell engagement with antigen-presenting cells.

Notes: Abstract The structures of an increasing number of channels and other alpha-helical membrane proteins have been determined recently, including the KcsA potassium channel, the MscL mechanosensitive channel, and the AQP1 and GlpF members of the aquaporin family. In this chapter, the orientation and packing characteristics of bilayer-spanning helices are surveyed in integral membrane proteins. In the case of channels, alpha-helices create the sealed barrier that separates the hydrocarbon region of the bilayer from the permeation pathway for solutes. The helices surrounding the permeation pathway tend to be rather steeply tilted relative to the membrane normal and are consistently arranged in a right-handed bundle. The helical framework further provides a supporting scaffold for nonmembrane-spanning structures associated with channel selectivity. Although structural details remain scarce, the conformational changes associated with gating transitions between closed and open states of channels are reviewed, emphasizing the potential roles of helix-helix interactions in this process.

Notes: Abstract Using luminescent lanthanides, instead of conventional fluorophores, as donor molecules in resonance energy transfer measurements offers many technical advantages and opens up a wide range of new applications. Advantages include farther measurable distances (~100 A) with greater accuracy, insensitivity to incomplete labeling, and the ability to use generic relatively large labels, when necessary. Applications highlighted include the study of ion channels in living cells, protein-protein interaction in cells, DNA-protein complexes, and high-throughput screening assays to measure peptide dimerization associated with DNA transcription factors and ligand-receptor interactions.

Notes: Abstract Cryo-electron microscopy (cryo-EM) of biological molecules in single-particle (i.e., unordered, nonaggregated) form is a new approach to the study of molecular assemblies, which are often too large and flexible to be amenable to X-ray crystallography. New insights into biological function on the molecular level are expected from cryo-EM applied to the study of such complexes "trapped" at different stages of their conformational changes and dynamical interactions. Important molecular machines involved in the fundamental processes of transcription, mRNA splicing, and translation are examples for successful applications of the new technique, combined with structural knowledge gained by conventional techniques of structure determination, such as X-ray crystallography and NMR.

Notes: Abstract The recent report of the crystal structure of rhodopsin provides insights concerning structure-activity relationships in visual pigments and related G protein-coupled receptors (GPCRs). The seven transmembrane helices of rhodopsin are interrupted or kinked at multiple sites. An extensive network of interhelical interactions stabilizes the ground state of the receptor. The ligand-binding pocket of rhodopsin is remarkably compact, and several chromophore-protein interactions were not predicted from mutagenesis or spectroscopic studies. The helix movement model of receptor activation, which likely applies to all GPCRs of the rhodopsin family, is supported by several structural elements that suggest how light-induced conformational changes in the ligand-binding pocket are transmitted to the cytoplasmic surface. The cytoplasmic domain of the receptor includes a helical domain extending from the seventh transmembrane segment parallel to the bilayer surface. The cytoplasmic surface appears to be approximately large enough to bind to the transducin heterotrimer in a one-to-one complex. The structural basis for several unique biophysical properties of rhodopsin, including its extremely low dark noise level and high quantum efficiency, can now be addressed using a combination of structural biology and various spectroscopic methods. Future high-resolution structural studies of rhodopsin and other GPCRs will form the basis to elucidate the detailed molecular mechanism of GPCR-mediated signal transduction.

Notes: Abstract Integrins are a structurally elaborate family of heterodimers that mediate divalent cation-dependent cell adhesion in a wide range of biological contexts. The inserted (I) domain binds ligand in the subset of integrins in which it is present. Its structure has been determined in two alternative conformations, termed open and closed. In striking similarity to signaling G proteins, rearrangement of a Mg2+-binding site is linked to large conformational movements in distant backbone regions. Mutations have been used to stabilize either the closed or open structures. These show that the snapshots of the open conformation seen only in the presence of a ligand or a ligand mimetic represent a high-affinity, ligand-binding conformation, whereas those of the closed conformation correspond to a low-affinity conformation. The C-terminal alpha-helix moves 10 A down the side of the domain in the open conformation. Locking in the conformation of the preceding loop is sufficient to increase affinity for ligand 9000-fold. This C-terminal "bell-rope" provides a mechanism for linkage to conformational movements in other domains. The transition from the closed to open conformation has been implicated in fast (〈1 s) regulation of integrin affinity in response to activation signals from inside the cell. Recent integrin structures and functional studies reveal interactions between beta-propeller, I, and I-like domains in the headpiece, and a critical role for integrin EGF domains in the stalk region. These studies suggest that the headpiece of the integrin faces down toward the membrane in the inactive conformation and extends upward in a "switchblade"-like opening motion upon activation. These long-range structural rearrangements of the entire integrin molecule involving multiple interdomain contacts appear closely linked to conformational changes in the I domain, which result in increased affinity and competence for ligand binding.

Notes: Abstract The Kuiper Belt consists of a large number of small, solid bodies in heliocentric orbit beyond Neptune. Discovered as recently as 1992, the Kuiper Belt objects (KBOs) are thought to hold the keys to understanding the early solar system, as well as the origin of outer solar system objects, such as the short-period comets and the Pluto-Charon binary. The KBOs are probably best viewed as aged relics of the Sun's accretion disk. Dynamical structures in the Kuiper Belt provide evidence for processes operative in the earliest days of the solar system, including a phase of planetary migration and a clearing phase, in which substantial mass was lost from the disk. Dust is produced to this day by collisions between KBOs. In its youth, the Kuiper Belt may have compared to the dust rings observed now around such stars as GG Tau and HR 4796A. This review presents the basic physical parameters of the KBOs and makes connections with the disks observed around nearby stars.

Notes: Abstract Cosmic microwave background (CMB) temperature anisotropies have and will continue to revolutionize our understanding of cosmology. The recent discovery of the previously predicted acoustic peaks in the power spectrum has established a working cosmological model: a critical density universe consisting of mainly dark matter and dark energy, which formed its structure through gravitational instability from quantum fluctuations during an inflationary epoch. Future observations should test this model and measure its key cosmological parameters with unprecedented precision. The phenomenology and cosmological implications of the acoustic peaks are developed in detail. Beyond the peaks, the yet to be detected secondary anisotropies and polarization present opportunities to study the physics of inflation and the dark energy. The analysis techniques devised to extract cosmological information from voluminous CMB data sets are outlined, given their increasing importance in experimental cosmology as a whole.

Notes: Abstract Considerable progress has been made over the past decade in the study of the evolutionary trends of the population of galaxy clusters in the Universe. In this review we focus on observations in the X-ray band. X-ray surveys with the ROSAT satellite, supplemented by follow-up studies with ASCA and Beppo-SAX, have allowed an assessment of the evolution of the space density of clusters out to z= 1 and the evolution of the physical properties of the intracluster medium out to z= 0.5. With the advent of Chandra and Newton-XMM and their unprecedented sensitivity and angular resolution, these studies have been extended beyond redshift unity and have revealed the complexity of the thermodynamical structure of clusters. The properties of the intracluster gas are significantly affected by nongravitational processes including star formation and Active Galactic Nuclei (AGN) activity. Convincing evidence has emerged for modest evolution of both the bulk of the X-ray cluster population and their thermodynamical properties since redshift unity. Such an observational scenario is consistent with hierarchical models of structure formation in a flat low-density universe with Omegam= 0.3 and sigma8= 0.7-0.8 for the normalization of the power spectrum. Basic methodologies for construction of X-ray-selected cluster samples are reviewed, and implications of cluster evolution for cosmological models are discussed.

Notes: Abstract Giant planet research has moved from the study of a handful of solar system objects to that of a class of bodies with dozens of known members. Since the original 1995 discovery of the first extrasolar giant planets (EGPs), the total number of known examples has increased to ~80 (circa November 2001). Current theoretical studies of giant planets emphasize predicted observable properties, such as luminosity, effective temperature, radius, external gravity field, atmospheric composition, and emergent spectra as a function of mass and age. This review focuses on the general theory of hydrogen-rich giant planets; smaller giant planets with the mass and composition of Uranus and Neptune are not covered. We discuss the status of the theory of the nonideal thermodynamics of hydrogen and hydrogen-helium mixtures under the conditions found in giant-planet interiors, and the experimental constraints on it. We provide an overview of observations of extrasolar giant planets and our own giant planets by which the theory can be validated.

Notes: Abstract Magnetic fields in the intercluster medium have been measured using a variety of techniques, including studies of synchrotron relic and halo radio sources within clusters, studies of inverse Compton X-ray emission from clusters, surveys of Faraday rotation measures of polarized radio sources both within and behind clusters, and studies of cluster cold fronts in X-ray images. These measurements imply that most cluster atmospheres are substantially magnetized, with typical field strengths of order 1 muGauss with high areal filling factors out to Mpc radii. There is likely to be considerable variation in field strengths and topologies both within and between clusters, especially when comparing dynamically relaxed clusters to those that have recently undergone a merger. In some locations, such as the cores of cooling flow clusters, the magnetic fields reach levels of 10-40 muG and may be dynamically important. In all clusters the magnetic fields have a significant effect on energy transport in the intracluster medium. We also review current theories on the origin of cluster magnetic fields.

Notes: Abstract David Crighton, a greatly admired figure in fluid mechanics, Head of the Department of Applied Mathematics and Theoretical Physics at Cambridge, and Master of Jesus College, Cambridge, died at the peak of his career. He had made important contributions to the theory of waves generated by unsteady flow. Crighton's work was always characterized by the application of rigorous mathematical approximations to fluid mechanical idealizations of practically relevant problems. At the time of his death, he was certainly the most influential British applied mathematical figure, and his former collaborators and students form a strong school that continues his special style of mathematical application. Rigorous analysis of well-posed aeroacoustical problems was transformed by David Crighton.

Notes: Abstract Cavitation in vortical structures is a common, albeit complex, problem in engineering applications. Cavitating vortical structures can be found on the blade surfaces, in the clearance passages, and at the hubs of various types of turbomachinery. Cavitating microvortices at the trailing edge of attached sheet cavitation can be highly erosive. Cavitating hub vortices in the draft tubes of hydroturbines can cause major surges and power swings. There is also mounting evidence that vortex cavitation is a dominant factor in the inception process in a broad range of turbulent flows. Most research has focused on the inception process, with limited attention paid to developed vortex cavitation. Wave-like disturbances on the surfaces of vapor cores are an important feature. Vortex core instabilities in microvortices are found to be important factors in the erosion mechanisms associated with sheet/cloud cavitation. Under certain circumstances, intense sound at discrete frequencies can result from a coupling between tip vortex disturbances and oscillating sheet cavitation. Vortex breakdown phenomena that have some commonalities are also noted, as are some differences with vortex breakdown in fully wetted flow. Simple vortex models can sometimes be used to describe the cavitation process in complex turbulent flows such as bluff body wakes and in plug valves. Although a vortex model for cavitation in jets does not exist, the mechanism of inception appears to be related to the process of vortex pairing. The pairing process can produce negative peaks in pressure that can exceed the rms value by a factor of ten, sometimes exceeding the dynamic pressure by a factor of two. A new and important issue is that cavitation is not only induced in vortical structures but is also a mechanism for vorticity generation.

Notes: Abstract Microstructure in an immiscible polymer blend consists of the size, shape, and orientation of the phases. Blends exhibit many interesting behaviors, including enhanced elasticity at small strains, drop-size hysteresis, enhanced shear thinning, and stress relaxation curves whose shapes are sensitive to deformation history. These behaviors are directly related to changes in the microstructure, which result from phase deformation, coalescence, retraction, and different types of breakup. These phenomena are reviewed, together with models that describe them. Rheological measurements can probe the microstructure because microstructure contributes directly to stress through interfacial tension. Rheo-optical experiments also provide important insights. Droplet theories explain most of the phenomena for Newtonian phases at low concentrations. Behaviors at high volume fractions or with strongly non-Newtonian phases are less well understood.

Notes: Abstract Recent advances in the computational modeling of molecular conformational and orientational effects in the flow of viscoelastic fluids are described. These advances involve the coupling of molecular models for the underlying microstructure of macromolecules with the macroscopic equations of change. The kinetic theory for polymeric liquids is described along with the most useful micromechanical models for computing the fluid flow of polymeric liquids. Three levels of description are covered for the computation of molecular orientation effects: methods for molecular models for which closed-form, continuum-like evolution equations for average quantities describing molecular conformations can be obtained, hybrid methods that involve coupling direct solution of the Fokker-Planck equation describing the distribution function for molecular orientations with the equations of change, and hybrid methods that couple stochastic simulations of individual molecule trajectories with the macroscopic equations of change. Illustrative results for rheometric flows (flows with homogeneous, fixed kinematics) and complex flows are given.

Notes: Abstract The El Nino variability in the equatorial Tropical Pacific is characterized by sea-surface temperature anomalies and associated changes in the atmospheric circulation. Through an enormous monitoring effort over the last decades, the relevant time scales and spatial patterns are fairly well documented. In the meantime, a hierarchy of models has been developed to understand the physics of this phenomenon and to make predictions of future variability. In this review, the robust and relevant details of the observations, the fluid mechanical "building blocks," the theory of the deterministic part of the variability, and the impact of small-scale ("noise") and remote ("external") processes are evaluated.

Notes: Abstract We determined the high-resolution structures of large and small ribosomal subunits from mesophilic and thermophilic bacteria and compared them with those of the thermophilic ribosome and the halophilic large subunit. We confirmed that the elements involved in intersubunit contacts and in substrate binding are inherently flexible and that a common ribosomal strategy is to utilize this conformational variability for optimizing its functional efficiency and minimizing nonproductive interactions. Under close-to-physiological conditions, these elements maintain well-ordered characteristic conformations. In unbound subunits, the features creating intersubunit bridges within associated ribosomes lie on the interface surface, and the features that bind factors and substrates reach toward the binding site only when conditions are ripe.

Notes: Abstract Chromatin fibers are dynamic macromolecular assemblages that are intimately involved in nuclear function. This review focuses on recent advances centered on the molecular mechanisms and determinants of chromatin fiber dynamics in solution. Major points of emphasis are the functions of the core histone tail domains, linker histones, and a new class of proteins that assemble supramolecular chromatin structures. The discussion of important structural issues is set against a background of possible functional significance.

Notes: Abstract The review deals with recent advances in magnetic resonance spectroscopy (hf EPR and NMR) of paramagnetic metal centers in biological macromolecules. In the first half of our chapter, we present an overview of recent technical developments in the NMR of paramagnetic bio-macromolecules. These are illustrated by a variety of examples deriving mainly from the spectroscopy of metalloproteins and their complexes. The second half focuses on recent developments in high-frequency EPR spectroscopy and the application of the technique to copper, iron, and manganese proteins. Special attention is given to the work on single crystals of copper proteins.

Notes: Abstract Fungal pathogens of plants or animals invade their hosts either by secretion of lytic enzymes, exerting force, or by a combination of both. Although many fungi are thought to rely mostly on lysis of the host tissue, some plant pathogenic fungi differentiate complex infection cells that develop enormous turgor pressure, which in turn is translated into force used for invasion. In order to understand mechanisms of fungal infection in detail, methods have been developed that indirectly or directly measure turgor pressure and force. In this article, these methods are described and critically discussed, and their importance in analysis of fungal infection are outlined.

Notes: Abstract The field of computational cell biology has emerged within the past 5 years because of the need to apply disciplined computational approaches to build and test complex hypotheses on the interacting structural, physical, and chemical features that underlie intracellular processes. To meet this need, newly developed software tools allow cell biologists and biophysicists to build models and generate simulations from them. The construction of general-purpose computational approaches is especially challenging if the spatial complexity of cellular systems is to be explicitly treated. This review surveys some of the existing efforts in this field with special emphasis on a system being developed in the authors' laboratory, Virtual Cell. The theories behind both stochastic and deterministic simulations are discussed. Examples of respective applications to cell biological problems in RNA trafficking and neuronal calcium dynamics are provided to illustrate these ideas.

Notes: Abstract I fled with my parents from Hitler's Austria to Australia and studied physics at Sydney University. I obtained my Ph.D. in quantum electrodynamics with Rudolf Peierls at Birmingham University and came to Cornell to work with Hans Bethe. I have stayed at Cornell ever since, and I have essentially had only a single job in my whole life, but have switched fields quite often. I worked in nuclear astrophysics and in late-stellar evolution, estimated the Initial Mass Function for star formation and the metal enrichment of the interstellar medium. I suggested black hole accretion as the energy source for quasars, worked on molecule formation on dust grain surfaces, and was involved in 21-cm studies of gas clouds and disk galaxies. I collaborated with my wife on the neurobiology of the neuromuscular junction and with one of my daughters on the epidemiology of tuberculosis.

Notes: Abstract Although we have a general understanding of the manner in which individual stars form, our understanding of how binary stars form is far from complete. This is in large part due to the fact that the star formation process happens very quickly and in regions of the Galaxy that are difficult to study observationally. We review the theoretical models that have been developed in an effort to explain how binaries form. Several proposed mechanisms appear to be quite promising, but none is completely satisfactory.

Notes: Abstract Radio astronomy has provided evidence for the presence of ionized atmospheres around almost all classes of nondegenerate stars. Magnetically confined coronae dominate in the cool half of the Hertzsprung-Russell diagram. Their radio emission is predominantly of nonthermal origin and has been identified as gyrosynchrotron radiation from mildly relativistic electrons, apart from some coherent emission mechanisms. Ionized winds are found in hot stars and in red giants. They are detected through their thermal, optically thick radiation, but synchrotron emission has been found in many systems as well. The latter is emitted presumably by shock-accelerated electrons in weak magnetic fields in the outer wind regions. Radio emission is also frequently detected in pre-main sequence stars and protostars and has recently been discovered in brown dwarfs. This review summarizes the radio view of the atmospheres of nondegenerate stars, focusing on energy release physics in cool coronal stars, wind phenomenology in hot stars and cool giants, and emission observed from young and forming stars. Eines habe ich in einem langen Leben gelernt, namlich, dass unsere ganze Wissenschaft, an den Dingen gemessen, von kindlicher Primitivitat ist-und doch ist es das Kostlichste, was wir haben. One thing I have learned in a long life: that all our science, measured against reality, is primitive and childlike-and yet it is the most precious thing we have. A. Einstein 1951, in a letter to H. Muhsam, Einstein Archive 36-610

Notes: Abstract Study of radio supernovae over the past 20 years includes two dozen detected objects and more than 100 upper limits. From this work it is possible to identify classes of radio properties, demonstrate conformance to and deviations from existing models, estimate the density and structure of the circumstellar material and, by inference, the evolution of the presupernova stellar wind, and reveal the last stages of stellar evolution before explosion. It is also possible to detect ionized hydrogen along the line of sight, to demonstrate binary properties of the stellar system, and to show clumpiness of the circumstellar material. More speculatively, it may be possible to provide distance estimates to radio supernovae. Over the past four years the afterglow of gamma-ray bursters has occasionally been detected in the radio, as well in other wavelengths bands. In particular, the interesting and unusual gamma-ray burst GRB980425, thought to be related to SN1998bw, is a possible link between supernovae and gamma-ray bursters. Analyzing the extensive radio emission data avaliable for SN1998bw, one can describe its time evolution within the well-established framework available for the analysis of radio emission from supernovae. This allows relatively detailed description of a number of physical properties of the object. The radio emission can best be explained as the interaction of a mildly relativistic (Gamma~ 1.6) shock with a dense preexplosion stellar wind-established circumstellar medium that is highly structured both azimuthally, in clumps or filaments, and radially, with observed density enhancements. Because of its unusual characteristics for a Type Ib/c supernova, the relation of SN1998bw to GRB980425 is strengthened and suggests that at least some classes of GRBs originate in massive star explosions. Thus, employing the formalism for describing the radio emission from supernovae and following the link through SN1998bw/GRB980425, it is possible to model the gross properties of the radio and optical/infrared emission from the half-dozen GRBs with extensive radio observations. From this we conclude that at least some members of the "slow-soft" class of GRBs can be attributed to the explosion of a massive star in a dense, highly structured circumstellar medium that was presumably established by the preexplosion stellar system.

Notes: Abstract The Sunyaev-Zel'dovich effect (SZE) provides a unique way to map the large-scale structure of the universe as traced by massive clusters of galaxies. As a spectral distortion of the cosmic microwave background, the SZE is insensitive to the redshift of the galaxy cluster, making it well-suited for studies of clusters at all redshifts, and especially at reasonably high redshifts (z〉 1) where the abundance of clusters is critically dependent on the underlying cosmology. Recent high signal-to-noise detections of the SZE have enabled interesting constraints on the Hubble constant and on the matter density of the universe using small samples of galaxy clusters. Upcoming SZE surveys are expected to find hundreds to thousands of new galaxy clusters, with a mass selection function that is remarkably uniform with redshift. In this review we provide an overview of the SZE and its use for cosmological studies, with emphasis on the cosmology that can, in principle, be extracted from SZE survey yields. We discuss the observational and theoretical challenges that must be met before precise cosmological constraints can be extracted from the survey yields.

Notes: Abstract This essay is based on the G.K. Batchelor Memorial Lecture that I delivered in May 2000 at the Institute for Theoretical Physics (ITP), Santa Barbara, where two parallel programs on Turbulence and Astrophysical Turbulence were in progress. It focuses on George Batchelor's major contributions to the theory of turbulence, particularly during the postwar years when the emphasis was on the statistical theory of homogeneous turbulence. In all, his contributions span the period 1946-1992 and are for the most part concerned with the Kolmogorov theory of the small scales of motion, the decay of homogeneous turbulence, turbulent diffusion of a passive scalar field, magnetohydrodynamic turbulence, rapid distortion theory, two-dimensional turbulence, and buoyancy-driven turbulence.

Notes: Abstract Turbulent flows driven by thermal buoyancy are featured by phenomena that pose a special challenge to conventional one-point closure models. Inherent unsteadiness, energy nonequilibrium, counter-gradient diffusion, strong pressure fluctuations, and lack of universal scaling, all believed to be associated with distinct large-scale coherent eddy structures, are hardly tractable by Reynolds-type averaging. Second-moment closures, though inadequate for providing information on eddy structure, offer better prospects than eddy-viscosity models for capturing at least some of the phenomena. For some configurations (e.g., with heating from below), unsteady computational solutions of ensemble-averaged equations, using a one-point closure as the subscale model, may be unavoidable for accurate prediction of flow details and wall heat transfer. This article reviews the rationale and some specific modeling issues related to buoyant flows within the realm of one-point closures. The inadequacy of isotropic eddy-diffusivity models is discussed first, followed by the rationale of the second-moment modeling and its term-by-term scrutiny based on direct numerical simulations (DNS). Algebraic models based on a rational truncation of the differential second-moment closure are proposed as the minimum closure level for complex flows. These closures are also recommended as subscale models for transient statistical modeling (T-RANS) and very large eddy simulations (VLES). Examples of applications illustrate some recent achievements.

Notes: Abstract Remote observations of a surface ship wake using synthetic aperture radar (SAR) show distinct features such as a dark trailing centerline region, bright V-images aligned at some angle to the ship's path, and, sometimes, either the transverse or the diverging waves of the Kelvin-wave pattern. The dark region of relatively low radar backscatter is usually associated with a region that is relatively lacking in short wave components, whereas the bright line feature suggests a region of enhanced radar return within the apparent angular confines of the ship's usual Kelvin-wave pattern. This review provides a survey of remotely sensed wake images, the systems that have collected these images, and an overview of the theory of Kelvin wakes-a primary source of the phenomena that cause the dark centerline and bright V-images-with example predictions. The review concludes with a survey of the phenomena that cause the dark centerline returns and some example predictions of the radar reflectivity across these dark centerline returns.

Notes: Abstract We review the mechanisms of steepening and breaking for internal gravity waves in a continuous density stratification. After discussing the instability of a plane wave of arbitrary amplitude in an infinite medium at rest, we consider the steepening effects of wave reflection on a sloping boundary and propagation in a shear flow. The final process of breaking into small-scale turbulence is then presented. The influence of those processes upon the fluid medium by mean flow changes is discussed. The specific properties of wave turbulence, induced by wave-wave interactions and breaking, are illustrated by comparative studies of oceanic and atmospheric observations, as well as laboratory and numerical experiments. We then review the different attempts at a statistical description of internal gravity wave fields, whether weakly or strongly interacting.

Notes: Abstract Genome sequencing and structural genomics projects are providing new insights into the evolutionary history ofprote in domains. As methods for sequence and structure comparison improve, more distantly related domains are shown to be homologous. Thus there is a need for domain families to be classified within a hierarchy similar to Linnaeus' Systema Naturae, the classification of species. With such a hierarchy in mind, we discuss the evolution of domains, their combination into proteins, and evidence as to the likely origin of protein domains. We also discuss when and how analysis of domains can be used to understand details of protein function. Unconventional features of domain evolution such as intragenomic competition, domain insertion, horizontal gene transfer, and convergent evolution are seen as analogs of organismal evolutionary events. These parallels illustrate how the concept of domains can be applied to provide insights into evolutionary biology.

Notes: Abstract Nearly twenty years after the first high-resolution crystal structures of specific protein-DNA complexes were determined, the stereo-chemical basis for protein-DNA recognition remains an active area of investigation. One outstanding question is, how are proteins able to detect noncontacted sequences in their binding sites? The papillomavirus E2 proteins represent a particularly suitable group of proteins in which to examine the mechanisms of "indirect readout." Coordinated structural and thermodynamic studies of the E2-DNA interaction conducted over the past five years are summarized in this review. The data support a model in which the electrostatic properties of the individual E2 proteins correlate with their affinities for intrinsically flexible or rigidly prebent DNA targets.

Notes: Abstract The formation and evolution of galaxies is one of the great outstanding problems of astrophysics. Within the broad context of hierachical structure formation, we have only a crude picture of how galaxies like our own came into existence. A detailed physical picture where individual stellar populations can be associated with (tagged to) elements of the protocloud is far beyond our current understanding. Important clues have begun to emerge from both the Galaxy (near-field cosmology) and the high redshift universe (far-field cosmology). Here we focus on the fossil evidence provided by the Galaxy. Detailed studies of the Galaxy lie at the core of understanding the complex processes involved in baryon dissipation. This is a necessary first step toward achieving a successful theory of galaxy formation.

Notes: Abstract In this paper we review the properties of Lyman-break galaxies, namely starburst galaxies at high redshifts, approximately in the range 2.5 〈z〈 5, identified by the colors of their far ultraviolet spectral energy distribution around the 912 A Lyman continuum discontinuity. The properties of forming galaxies in the young universe are very important to constrain the history of galaxy evolution and the formation of the Hubble sequence, and until recently, they have remained largely unexplored. The Lyman-break technique has broken an impasse in the exploration of galaxies at high redshift that lasted for about two decades, and within a few years has yielded large and well-controlled samples of star-forming, but otherwise normal, galaxies at z〉 2.5, including ~1000 spectroscopic redshifts and another few thousands of robust candidates. This dataset has allowed us an unprecedented look at fundamental properties of galaxies at 20% of the Hubble time or less. In this paper, we discuss the nature of the Lyman-break galaxies and their properties, including star-formation rate, stellar and total mass, chemical abundance, morphology, and interstellar medium (ISM) kinematics, and outline their contribution to the stellar content of the universe and their connection to the galaxies observed in the present-day universe. We also discuss what the properties of these galaxies, in particular their spatial clustering, imply about the mechanisms of galaxy formation and about the relationship between the underlying distribution of dark matter and the activity of star formation.

Notes: Abstract Some applications of the study of outdoor acoustics and sets of data for sound-level spectra obtained close to the ground are described. Measurements and models of ground effects arising from the interaction between sound traveling directly from source to receiver and sound reflected from the ground are emphasized. Details are given concerning the influences of porosity, layering, small-scale surface roughness, and tall vegetation. Areas of related current and future research are outlined.

Notes: Abstract A Lagrangian description of turbulence has unique physical advantages that are especially important in studies of mixing and dispersion. We focus on fundamental aspects, using mainly data from direct numerical simulations capable of great detail and precision when specific accuracy requirements are met. Differences between time evolution in Eulerian and Lagrangian frames illustrate the dominance of advective transport. We examine basic results in Kolmogorov similarity, giving an estimate of an inertial-range universal constant and the grid resolution and Reynolds number needed to attain the requisite scaling range of time lags. The Lagrangian statistics of passive scalars are discussed in view of current efforts in model development, with differential diffusion between multiple scalars being characterized by shorter timescales. We also note the need for new data in more complex flows and in other applications where a Lagrangian viewpoint is especially useful.

Notes: Abstract In this review we describe the discovery and development of understanding of the so-called elliptical instability. This is the name given to the linear instability mechanism that tends to break up regions of elliptical streamlines in a rotating flow. The instability is discussed in the three different contexts-an unbounded strained vortex, a localized strained vortex, and a triaxial ellipsoid-where it was originally discovered and then rediscovered. These make it clear that the instability is one of parametric resonance where a normal mode, or pair of normal modes, of the undistorted rotating flow resonates with the underlying strain field. The effects of additional physics on the instability process are examined before its nonlinear evolution is discussed. Various applications of the instability in nature are then reviewed.

Notes: Abstract Filament-stretching rheometers are devices for measuring the extensional viscosity of moderately viscous non-Newtonian fluids such as polymer solutions. In these devices, a cylindrical liquid bridge is initially formed between two circular end-plates. The plates are then moved apart in a prescribed manner such that the fluid sample is subjected to a strong extensional deformation. Asymptotic analysis and numerical computation show that the resulting kinematics closely approximate those of an ideal homogeneous uniaxial elongation. The evolution in the tensile stress (measured mechanically) and the molecular conformation (measured optically) can be followed as functions of the rate of stretching and the total strain imposed. The resulting rheological measurements are a sensitive discriminant of molecularly based constitutive equations proposed for complex fluids. The dynamical response of the elongating filament is also coupled to the extensional rheology of the polymeric test fluid, and this can lead to complex viscoelastic-flow instabilities such as filament necking and rupture or elastic peeling from the rigid end-plates.

Notes: Abstract The evolution of a synthetic (zero-net mass flux) jet and the flow mechanisms of its interaction with a cross flow are reviewed. An isolated synthetic jet is produced by the interactions of a train of vortices that are typically formed by alternating momentary ejection and suction of fluid across an orifice such that the net mass flux is zero. A unique feature of these jets is that they are formed entirely from the working fluid of the flow system in which they are deployed and, thus, can transfer linear momentum to the flow system without net mass injection across the flow boundary. Synthetic jets can be produced over a broad range of length and timescale, and their unique attributes make them attractive fluidic actuators for a number of flow control applications. The interaction of synthetic jets with an external cross flow over the surface in which they are mounted can displace the local streamlines and induce an apparent or virtual change in the shape of the surface, thereby effecting flow changes on length scales that are one to two orders of magnitude larger than the characteristic scale of the jets. This control approach emphasizes an actuation frequency that is high enough so that the interaction domain between the actuator and the cross flow is virtually invariant on the global timescale of the flow, and therefore, global effects such as changes in aerodynamic forces are effectively decoupled from the operating frequency of the actuators.

Notes: Abstract Flow cytometers make homogeneous real-time measurements of ligand-receptor interactions and, simultaneously, the physiological responses of cells. Their multiparameter capabilities are also useful in resolving multicomponent assemblies or in developing multiplexed assays. Recent advances suggest that these approaches can be extended in several important ways. Sample delivery in the millisecond time domain is applicable to the analysis of complex binding kinetics and reaction mechanisms. The homogeneous discrimination of free components and particle-based assemblies can be extended into the micromolar concentration range. Measurements can be made of molecular assemblies among proteins, DNA, RNA, lipids, and carbohydrates on beads. The topography and assembly of components within cells can be evaluated with resonance energy transfer. Temperature dependence can be evaluated with Peltier temperature control. Many assembly endpoints can be assessed through new tools for high-throughput flow cytometry using plate-based assay formats and small volume samples.

Notes: Abstract This review discusses three main topics: evolution to the ultra-compact (UC) state; the properties of UC HII regions and their environments; and UC HII regions as probes of Galactic structure. The evolution to UC HII regions begins in giant molecular clouds that provide the natal material for prestellar cores that evolve into hot cores, the precursors of UC HII regions. The properties of each evolutionary phase are reviewed, with particular emphasis on those of hot cores. The observed properties of UC HII regions and their environments are summarized with emphasis on the physical processes that may produce the observed properties. The final section summarizes the use of UC HII regions as probes of Galactic structure: in particular, the Galactic population and distribution of newly formed massive stars, the location of spiral arms, and the average galactocentric temperature and abundance gradients.

Notes: Abstract The gamma ray burst phenomenon is reviewed from a theoretical point of view, with emphasis on the fireball shock scenario of the prompt emission and the longer wavelength afterglow. Recent progress and issues are discussed, including spectral-temporal evolution, localizations, jets, spectral lines, environmental and cosmological aspects, as well as some prospects for future experiments in both electromagnetic and nonelectromagnetic channels.

Notes: Abstract Modified Newtonian dynamics (MOND) is an empirically motivated modification of Newtonian gravity or inertia suggested by Milgrom as an alternative to cosmic dark matter. The basic idea is that at accelerations below ao= 10-8 cm/s2=cHo/6 the effective gravitational attraction approaches , where gn is the usual Newtonian acceleration. This simple algorithm yields flat rotation curves for spiral galaxies and a mass-rotation velocity relation of the form MV4 that forms the basis for the observed luminosity-rotation velocity relation-the Tully-Fisher law. We review the phenomenological success of MOND on scales ranging from dwarf spheroidal galaxies to superclusters and demonstrate that the evidence for dark matter can be equally well interpreted as evidence for MOND. We discuss the possible physical basis for an acceleration-based modification of Newtonian dynamics as well as the extention of MOND to cosmology and structure formation.

Notes: Abstract We review the state of observational and theoretical studies of the shaping of planetary nebulae (PNe) and protoplanetary nebulae (pPNe). In the past decade, high-resolution studies of PNe have revealed a bewildering array of morphologies with elaborate symmetries. Recent imaging studies of pPNe exhibit an even richer array of shapes. The variety of shapes, sometimes multiaxial symmetries, carefully arranged systems of low-ionization knots and jets, and the often Hubble-flow kinematics of PNe and pPNe indicate that there remains much to understand about the last stages of stellar evolution. In many cases, the basic symmetries and shapes of these objects develop on extremely short timescales, seemingly at the end of AGB evolution when the mode of mass loss abruptly and radically changes. No single explanation fits all of the observations. The shaping process may be related to external torques of a close or merging binary companion or the emergence of magnetic fields embedded in dense outflowing stellar winds. We suspect that a number of shaping processes may operate with different strengths and at different stages of the evolution of any individual object.

Notes: Abstract The coupling of fluid dynamics and biology at the level of the cell is an intensive area of investigation because of its critical role in normal physiology and disease. Microcirculatory flow has been a focus for years, owing to the complexity of cell-cell or cell-glycocalyx interactions. Noncirculating cells, particularly those that comprise the walls of the circulatory system, experience and respond biologically to fluid dynamic stresses. In this article, we review the more recent studies of circulating cells, with an emphasis on the role of the glycocalyx on red-cell motion in small capillaries and on the deformation of leukocytes passing through the microcirculation. We also discuss flows in the vicinity of noncirculating cells, the influence of fluid dynamic shear stress on cell biology, and diffusion in the lipid bi-layer, all in the context of the important fluid-dynamic phenomena.

Notes: Abstract Recent progress in modeling and simulation of the flow of nematic liquid crystals is presented. The Leslie-Ericksen (LE) theory has been successful in elucidating the flow of low molar-mass nematics. The theoretical framework for the flow of polymeric nematic liquid crystals is still evolving; extensions of the Doi theory capture qualitative features of the flow of polymeric nematics in simple geometries, but these theories have not been shown to predict texture development in flow. Mesoscopic theories for textured materials based on spatial averaging capture only some qualitative features of nonrectilinear liquid-crystalline polymer flow. Interfacial effects in liquid-crystalline systems have begun to receive attention in the context of interfacial viscoelasticity and the dynamics of dispersed liquid-crystalline polymers in immiscible blends.

Notes: Abstract We examine situations in which two droplets of the same liquid may come into apparent contact without coalescing or in which a droplet that normally wets a surface may deform against it without actually wetting it. The focus of this review is on cases driven by hydrodynamic lubrication, the lubricant provided either by surface motion or by evaporation.

Notes: Abstract The current understanding of boundary-layer receptivity to external acoustic and vortical disturbances is reviewed. Recent advances in theoretical modeling, numerical simulations, and experiments are discussed. It is shown that aspects of the theory have been validated and that the mechanisms by which freestream disturbances provide the initial conditions for unstable waves are better understood. Challenges remain, however, particularly with respect to freestream turbulence.

Notes: Abstract Because the cost of large-eddy simulations (LES) of wall-bounded flows that resolve all the important eddies depends strongly on the Reynolds number, methods to bypass the wall layer are required to perform high-Reynolds-number LES at a reasonable cost. In this paper the available methodologies are reviewed, and their ranges of applicability are highlighted. Various unresolved issues in wall-layer modeling are presented, mostly in the context of engineering applications.

Notes: Abstract The Richtmyer-Meshkov instability arises when a shock wave interacts with an interface separating two different fluids. It combines compressible phenomena, such as shock interaction and refraction, with hydrodynamic instability, including nonlinear growth and subsequent transition to turbulence, across a wide range of Mach numbers. This review focuses on the basic physical processes underlying the onset and development of the Richtmyer-Meshkov instability in simple geometries. It examines the principal theoretical results along with their experimental and numerical validation. It also discusses the different experimental approaches and techniques and how they can be used to resolve outstanding issues in this field.

Notes: Abstract Molecular and paleontological data provide independent means of estimating when groups of organisms evolved in the geological past, but neither approach can be considered straightforward. The single most fundamental obstacle to developing an accurate estimate of times of origination from gene sequence data is variation in rates of molecular evolution, both through time and among lineages. Although various techniques have been proposed to circumvent this problem, none unambiguously allow the components of time and rate to be separated. Furthermore, problems of establishing accurate calibration points, correctly rooted phylogenies, and accurate estimates of branch length remain formidable. Conversely, paleontological dates fix only the latest possible time of divergence, and so probabilistic methods are required to set a lower boundary on origination dates. Realistic confidence intervals that take preservational biases into account are only just becoming available. Although molecular and paleontological approaches to dating often agree reasonably well, there are two notable areas of disagreement; when mammal and bird orders originated and when the major phyla originated. The discrepancy in dating bird/mammal ordinal origins probably reflects a global rock-record bias. Paleontological sampling in the Late Cretaceous is still too restricted geographically to draw any firm conclusions about the existence of a pre-Tertiary record for modern orders of bird or mammal from anywhere other than North America. Dating the time of origin of phyla is more complicated, and is confounded by both preservational biases and problems of molecular clock estimation.

Notes: Abstract The subducted lithosphere is composed of a complex pattern of chemical systems that undergo continuous and discontinuous phase transformation, through pressure and temperature variations. Volatile recycling plays a major geodynamic role in triggering mass transfer, melting, and volcanism. Although buoyancy forces are controlled by modal amounts of the most abundant phases, usually volatile-free, petrogenesis and chemical differentiation are controlled by the occurrence of minor phases, most of them volatile-bearing. Devolatilization of the subducted lithosphere is a continuous process distributed over more than 300 km of the slab-mantle interface. Melting of the subducted crust, if any, along sufficiently hot P-T paths, is governed by fluid-absent reactions, even though the difference between fluid and melt vanishes at pressures above the second critical end point. The density distribution at a depth of 660 km suggests episodic penetration in space and time of subducted slabs into the lower mantle and sinking down to the D" region at the core-mantle boundary.

Notes: Abstract Pluto and Charon, once thought to be a singular system in an odd orbit at the edge of the solar system, are now known as members of a vast population of icy bodies beyond Neptune. Models for the occurrence of the odd orbit and formation of these bodies in the context of the total population are reviewed. Pluto's orbital characteristics, coupled with the existence of volatiles on the surface, suggest that large-scale seasonal change should occur on the surface. Models of seasonal variability are discussed, past and current observations are examined for evidence of variability, and a straw-man model of seasonal changes is proposed. Finally, recent observations of the surface composition of Charon are discussed and compared with observations of other similarly sized icy bodies in the outer Solar System.

Notes: Abstract The legacy of the LEP program encompasses an extensive investigation of the electroweak interaction and the most comprehensive search to date for the origin of spontaneous symmetry breaking. The results comprise a large variety of theoretical models challenged by dedicated searches and a persistent search for the standard-model Higgs boson. The direct search for the standard-model Higgs boson confronted an excess of signal-like events in the final year. This observation reaches a significance of approximately two standard deviations for a Higgs boson mass of 115.6 GeV/c2, a value consistent with the mass range indicated by electroweak precision measurements. The definitive confirmation of the standard-model Higgs boson search and the continued investigation for a Higgs sector at higher masses await new data from the Tevatron and LHC colliders.

Notes: Abstract We review the effective field theories (EFTs) developed for few-nucleon systems. These EFTs are controlled expansions in momenta, where certain (leading-order) interactions are summed to all orders. At low energies, an EFT with only contact interactions allows a detailed analysis of renormalization in a nonperturbative context and uncovers novel asymptotic behavior. Manifestly model-independent calculations can be carried out to high orders, leading to high precision. At higher energies, an EFT that includes pion fields justifies and extends the traditional framework of phenomenological potentials. The correct treatment of QCD symmetries ensures a connection with lattice QCD. Several tests and prospects of these EFTs are discussed.

Notes: Abstract The observed properties of extrasolar planets and planetary systems are reviewed, including discussion of the mass, period, and eccentricity distributions; the presence of multiple systems; and the properties of the host stars. In all cases, the data refer to systems with ages in the Ga range. Some of the properties primarily reflect the formation mechanism, while others are determined by postformation dynamical evolutionary processes. The problem addressed here is the extraction of information relevant to the identification of the formation mechanism. The presumed formation sites, namely disks around young stars, therefore, must provide clues at times much closer to the actual formation time. The properties of such disks are briefly reviewed. The amount of material and its distribution in the disks provide a framework for the development of a model for planet formation. The strengths of, as well as the problems with, the two major planet formation mechanisms-gravitational instability and core accretion-gas capture-are then described. It is concluded that most of the known planetary systems are best explained by the accretion process. The timescales for the persistence of disks and for the formation time by this process are similar, and the mass range of the observed planets, up to approximately 10 Jupiter masses, is naturally explained. The mass range of 5-15 Jupiter masses probably represents an overlapping transition region, with planetary formation processes dominating below that range and star formation processes dominating above it.

Notes: Abstract The past seven years have seen significant advances in computational simulations of convection and magnetic field generation in the Earth's core. Although dynamically self-consistent models of the geodynamo have simulated magnetic fields that appear in some ways quite similar to the geomagnetic field, none are able to run in an Earth-like parameter regime because of the considerable spatial resolution that is required. Here we discuss some of the subtle compromises that have been made in current models and propose a grand challenge for the future, requiring significant improvements in numerical methods and spatial resolution.

Notes: Abstract Geological investigations of major fault scarps ("tectonic windows") and DSDP/ODP Drill Holes provide direct views of the uppermost oceanic crust generated at fast- to intermediate-rate spreading centers. These areas reveal a consistent upper crustal structural geometry with basaltic lava flows defining a pattern of downward increasing ("inward") dip toward the spreading center at which they formed and dikes in the lavas and underlying sheeted dike complex showing a similar degree of "outward" dip. Widespread fracturing, faulting, and hydrothermal metamorphism accompanied magmatic construction. These geological relationships can be interpreted in terms of dramatic, asymmetrical, subaxial subsidence of upper crustal rock units that diminishes across the very narrow (few kilometers wide) zone of lava accumulation and dike intrusion at the ridge axis. This type of crustal structure is in accord with some existing models of spreading but augments these idealized views with more realistic geological complexity.

Notes: Abstract Observations of the geochemical diversity of mid-oceanic ridge and ocean-island basalts have traditionally been attributed to the existence of large-scale mantle heterogeneity. In particular, the layered convection model has provided an important conceptual basis for discussing the chemical evolution of the Earth. In this model, a long-term boundary is assumed between a well-mixed and depleted upper mantle and a heterogeneous and more primitive lower mantle. The existence of high 3He/4He in ocean-island sources has been used to argue for the preservation of a primitive component in the deep mantle. Nevertheless, a primitive deep layer is difficult to reconcile with the abundant lithophile isotopic evidence for recycling of oceanic crust and the lack of preservation of primitive mantle. In addition, the widespread acceptance of geophysical evidence for whole mantle flow has made straightforward application of the layered convection model problematic. Model calculations show that whole mantle convection with present day heat flow and surface velocities is sufficiently vigorous to mix large-scale heterogeneity to an extent that is incompatible with the geochemical observations. Several concepts have been proposed in recent years to resolve the apparent conflicts between the various observational constraints and theoretical interpretations. The suggestions include the presence of deeper layering, preservation of highly viscous blobs, core mantle interaction, and strong temporal variations in mantle dynamics. Although these models generally appear to solve parts of the puzzle, at present no single model is able to account for all of the major observations. The reconciliation of conflicting evidence awaits improvements in observational and experimental techniques integrated with better model testing of hypotheses for the generation and destruction of mantle heterogeneity.

Notes: Abstract The motivation, present status, and future plans of the search for betabeta(0nu) decay are reviewed. Recent observations of neutrino oscillations encourage the hope that betabeta(0nu) decay corresponding to the neutrino mass scale suggested by oscillations, mnu= 50 meV, actually exists. The challenges to achieve the sensitivity corresponding to this mass scale, and plans to overcome them, are described.

Notes: Abstract The possibility that spacetime extends beyond the familiar 3 + 1 dimensions has intrigued physicists for a century. The consequences of a dimensionally richer spacetime would be profound. Recently, new theories with higher-dimensional spacetimes have been developed to resolve the hierarchy problem in particle physics. The distinct predictions of these scenarios allow experiment to probe the existence of extra dimensions in new ways. We review the conceptual framework of these scenarios, their implications in collider and short-range gravity experiments, and their astrophysical and cosmological effects, as well as the constraints placed on them by current data.

Notes: Abstract This article describes the physics capabilities of a future facility that would provide extremely intense and clean neutrino beams. This facility, called a neutrino factory, consists of a muon storage ring with long straight sections, pointed at experimental areas both near and far. Given the expected intensity of muons stored in the rings, this facility could give the lepton sector what decades of precision kaon and B experiments have given the quark sector. One would measure with unprecedented precision the parameters of the leptonic mixing matrix, explore the neutrino mass pattern, and ultimately search for CP violation in the leptonic sector. In addition, the high fluxes at a neutrino factory would open up a whole new field in precision neutrino scattering physics close to the ring itself.

Notes: Abstract This article reviews the concepts and methods of transition path sampling. These methods allow computational studies of rare events without requiring prior knowledge of mechanisms, reaction coordinates, and transition states. Based upon a statistical mechanics of trajectory space, they provide a perspective with which time dependent phenomena, even for systems driven far from equilibrium, can be examined with the same types of importance sampling tools that in the past have been applied so successfully to static equilibrium properties.

Notes: Abstract This article reviews a new and general theory of nonuniform fluids that naturally incorporates molecular scale information into the classical van der Waals theory of slowly varying interfaces. The method optimally combines two standard approximations, molecular (mean) field theory to describe interface formation and linear response (or Gaussian fluctuation) theory to describe local structure. Accurate results have been found in many different applications in nonuniform simple fluids and these ideas may have important implications for the theory of hydrophobic interactions in water.

Notes: Abstract Until the early 1990s, numerical simulations of Solar System dynamics were done using accurate but slow integrators. The typical timescales were on the order of a million years, apart from exceptions achieved by considering averaged equations or using specifically designed supercomputers. In the last decade, new numerical integration methods for Solar System dynamics have been introduced. The mixed variable symplectic method (Wisdom & Holman 1991) has permitted the study, in the absence of close encounters, of the evolution of planets and small bodies on timescales comparable to the age of the Solar System. The regularized mixed variable scheme (Levison & Duncan 1994) has allowed the compilation of statistics on the evolution of thousands of near-Earth asteroids and comets, from their source regions to their dynamical elimination. The Symba and the Mercury codes (Duncan et al. 1998, Chambers 1999), which treat close encounters between massive bodies in a symplectic way, have permitted the simulations of planetary accretion and of the early phase of the highly chaotic evolution of the Solar System. This paper reviews the most exciting results obtained with these new integrators. Emphasis is given to the conceptual steps that these works represent in our understanding of Solar System dynamics.

Notes: Abstract In the last decades, insights from the fields of ecology, geomorphology, and hydrology have been applied to the question of the streamflows necessary for environmental maintenance. For instance, determining the streamflow needed for spawning by salmon or trout requires ascertaining how much water, for how long, and at what time it will be needed? And what flows are necessary for the sustenance of streamside vegetation? Answers to these and similar questions have been sought to minimize environmental degradation in the development or relicensing of water projects, in restoring riverine ecosystems, and in balancing multiple uses for limited water resources. In this contribution, the varieties of environmental maintenance flows applied to rivers are described, as are their fundamental principles. These environmental maintenance flows include flows to maintain aesthetics and recreation, streambed sediment size and its mobility, the channel, its features and continuity, and the floodplain, its wetness regime, and riparian vegetation.

Notes: Abstract The Prelude began with the origin of Metazoa, perhaps between 720 and 660 million years ago (mya), and ended with the geologically abrupt appearance of crown bilaterian phyla that began between 530 and 520 mya. The origin and early evolution of phyla cannot be tracked by fossils during this interval, but molecular phylogenetics permits reconstruction of their branching topology, whereas molecular developmental evidence supports hypotheses for the evolution of the metzoan genome during the rise of complex bodyplans. A flexible architecture of genetic regulation was in place even before the appearance of crown sponges, permitting increases in gene expression events as bodyplan complexity rose. Neoproterozoic bilaterians were chiefly small-bodied but likely diverse, whereas in the earliest Cambrian, between 543 and approximately 530-520 mya, bodies that were complex by marine invertebrate standards evolved in association with body-size increases.

Notes: Abstract The recent recognition of a potentially vast, unexplored hot microbial biosphere associated with active volcanism along the global mid-ocean ridge network has fundamentally shifted concepts of how planets and life coevolve. Many processes intrinsic to the dynamics of the spreading center volcanic system provide partial or complete nutritional fluxes that support diverse microbial communities that thrive under extreme conditions on and beneath the seafloor. Mantle melting, volcanism, and fluid-rock reactions transport volatiles from the asthenosphere to the hydrosphere. Volcanic heat and exothermic reactions drive circulation of nutrient-rich fluids from which chemosynthetic organisms gain metabolic energy. In turn, many of these organisms symbiotically support macrofaunal communities that populate the vents. Long-term seafloor observatories will allow exploration of linkages between volcanism and this newly discovered biosphere. Such approaches may provide essential new information about our own planet while providing critically needed insights into how we can explore other planets for life.

Notes: Abstract We review the current status of determinations of the b-quark mass, mb. We describe the theoretical tools required for determining mb, with particular emphasis on effective field theories both in the continuum and on the lattice. We present several definitions of mb and highlight their advantages and disadvantages. Finally, we discuss the determinations of mb from systems, b-flavored hadrons, and high-energy processes, with careful attention to the corresponding theoretical uncertainties.

Notes: Abstract We review selected geological processes to which numerical modeling has been applied, with the aim of describing some of the general approaches and applications of the modeling. All of these examples involve multiphase fluid flow, in some cases coupled with heat transport and phase changes. First, we describe modeling approaches to a human-made geological system-a potential underground radioactive waste repository. Next, we describe recent advances in modeling two-phase flow through random heterogeneous porous media. We review recent modeling studies of fluid processes in magmatic systems, especially focusing on melting and crystallization induced by magma chambers. Finally, several research directions are suggested, including improving our understanding of the linkage between small-scale and field-scale processes, coupling across regimes (e.g., surface water and ground water), and further developments in the modeling of stochastic geological processes.

Notes: Abstract Soil moisture is spatially and temporally highly variable, and it influences a range of environmental processes in a nonlinear manner. This leads to scale effects that need to be understood for improved prediction of moisture dependent processes. We provide some introductory material on soil moisture, and then review results from the literature relevant to a variety of scaling techniques applicable to soil moisture. This review concentrates on spatial scaling with brief reference to results on temporal scaling. Scaling techniques are divided into behavioral techniques and process-based techniques. We discuss the statistical distribution of soil moisture, spatial correlation of soil moisture at scales from tens of meters to thousands of kilometers and related interpolation and regularization techniques, and the use of auxiliary variables such as terrain indices. Issues related to spatially distributed deterministic modeling of soil moisture are also briefly reviewed.

Notes: Abstract Imaging using seismic reflection data has undergone tremendous advances over the past few years. The advances have been fostered in part by the availability of faster computers that have made more reliable algorithms for migration imaging feasible. The conventional approach to migration imaging, ray-based Kirchhoff migration, has been improved by the use of multiple-valued traveltime tables, ray amplitudes, and ray phases that can be calculated from various ray-tracing implementations. Wave-equation imaging, based on implementations of solutions of the wave equation, one-way wave equation, and approximations to the Lippmann-Schwinger equation, has become tractable. Wave-equation methods take account of wave phenomena such as focusing, defocusing, and diffraction that are important in many geological environments where imaging is used for petroleum exploration. There have also been applications of various types of migration imaging in basic studies of Earth structure. Such studies have been made to investigate deep Earth structure and large-scale lithospheric structure using waveforms from teleseisms as sources.

Notes: Abstract Developments in plant physiology since the 1980s have led to the realization that fossil plants archive both the isotopic composition of atmospheric CO2 and its concentration, both critical integrators of carbon cycle processes through geologic time. These two carbon cycle signals can be read by analyzing the stable carbon isotope composition (delta13C) of fossilized terrestrial organic matter and by determining the stomatal characters of well-preserved fossil leaves, respectively. We critically evaluate the use of fossil plants in this way at abrupt climatic boundaries associated with mass extinctions and during times of extreme global warmth. Particular emphasis is placed on evaluating the potential to extract a quantitative estimate of the delta13C of atmospheric CO2 because of the key role it plays in understanding the carbon cycle. We critically discuss the use of stomatal index and stomatal ratios for reconstructing atmospheric CO2 levels, especially the need for adequate replication, and present a newly derived CO2 record for the Mesozoic that supports levels calculated from geochemical modeling of the long-term carbon cycle. Several suggestions for future research using stable carbon isotope analyses of fossil terrestrial organic matter and stomatal measurements are highlighted.

Notes: Abstract Pion-nucleus interactions have been extensively investigated in the past three decades with the meson factories at LAMPF, TRIUMF, and PSI. This article gives a pedagogical review of the advances and discusses open questions as well as issues related to current research.

Notes: Abstract By the 1950s, Europe was recovering from the human and material destruction of World War II. The fundamental rebirth of particle physics in this period was especially due to the development and diffusion of the nuclear emulsion technique, which was suitable for international collaboration. Research groups emerging from the catastrophe of the war had little more than their enthusiasm to contribute at the forefront of physics research, but by using the nuclear emulsion technique, they were able to disclose phenomena whose existence no one had suspected.

Notes: Abstract Atmospheric neutrinos produced by cosmic-ray interactions in the atmosphere are of interest for several reasons. As a beam for studies of neutrino oscillations, they cover a range of parameter space hitherto unexplored by accelerator neutrino beams. The atmospheric neutrinos also constitute an important background and calibration beam for neutrino astronomy and for the search for proton decay and other rare processes. We review the literature on calculations of atmospheric neutrinos over the full range of energy, with particular attention to the aspects important for neutrino oscillations. Our goal is to assess how well the properties of atmospheric neutrinos are known at present.

Notes: Abstract Positron emission tomography (PET) is a molecular imaging technology for examining the molecular basis of normal biological functions of cells and their failure in disease. PET's molecular diagnostics of the biology of disease are often more accurate than lesion-based diagnosis by structural imaging techniques such as x-ray films, x-ray computed tomography, and magnetic resonance imaging. PET provides the means to examine the pharmacokinetics and biodistribution of drugs in living mammals, from the mouse to the human patient. PET includes three major technical components: the PET scanner, cyclotron-based electronic generators for producing labeled probes, and biological assays using tracer principles. This chapter examines these components, provides a brief history of the development of PET technologies, and discusses applications of PET.

Notes: Abstract This review discusses the design and initial operation of the Relativistic Heavy Ion Collider (RHIC), noting the novel features of a heavy ion collider that are distinct from conventional hadron colliders. These features reflect the experimental requirements of operation with a variety of ion species over a wide energy range, including collisions between ions of unequal energies and polarized protons. Other unique aspects of RHIC include intrabeam scattering, interaction-region error compensation, and transition crossing with a slow ramp rate. The RHIC facility has just completed the second physics run after beam commissioning in 2000.

Notes: Abstract Linear optical spectroscopies have long been used to study the behavior of liquids. Laser technology has progressed to the point that it has become possible to perform nonlinear optical experiments that probe higher-order correlation functions in liquids, opening a new window into our understanding of the microscopic details of solution-phase processes. Here we review advances that have been made in recent years in employing higher-order electronic and vibrational spectroscopies to study liquid-state dynamics and structure.

Notes: Abstract The molecular Hamiltonian represents one of the most basic concepts in spectroscopy and molecular reaction dynamics. Its derivation is notoriously difficult owing to the use of a rotating reference frame which, in turn, is necessary to define the concept of vibration and rotation. In this article, we review the construction of the molecular Hamiltonian in normal mode and in internal coordinates. For normal mode coordinates, the Watson Hamiltonian including its modification for linear molecules is derived using an approach based on classical mechanics and the Podolsky transformation. The method is subsequently used to derive the molecular Hamiltonian in terms of Jacobi and valence coordinates. Results are presented for the triatomic system and for the extension toward N-atom systems with N 〉= 3.

Notes: Abstract Recent applications of density functional theory base ab initio molecular dynamics in chemical relevant systems are reviewed. The emphasis is on the dynamical aspect in the study of structures, reaction mechanisms, and electronic properties in both the molecular and condensed phases. Examples were chosen from fluxional molecules, solution reactions, and biological systems to illustrate the broad potential applications and unique information that can be obtained from ab initio molecular dynamics calculations. Recent advances in the development of efficient numerical algorithms for the prediction of spectroscopic properties are highlighted.

Notes: Abstract Recent experimental advances have uncovered many of the diverse reaction pathways following an energetic collision between a molecular ion and a solid surface. Hyperthermal translational energies (5-500 eV) are sufficient to activate a number of chemical transformations in the near-surface region, including charge transfer, dissociation, abstraction, and deposition. State-of-the-art scattering studies probe the consumption and disposal of energy and the effects of approach geometry and surface electronic structure on the operative reaction mechanisms. These fundamental investigations provide insight relevant to the fabrication of microelectronics devices, the interaction of space vehicles with the earth's atmosphere, and the development of analytical techniques in mass spectrometry.

Notes: Abstract The powerful computational resources available to scientists today, together with recent improvements in electronic structure calculation algorithms, are providing important new tools for researchers in the fields of surface science and catalysis. In this review, we discuss first principles calculations that are now capable of providing qualitative and, in many cases, quantitative insights into surface chemistry. The calculations can aid in the establishment of chemisorption trends across the transition metals, in the characterization of reaction pathways on individual metals, and in the design of novel catalysts. First principles studies provide an excellent fundamental complement to experimental investigations of the above phenomena and can often allow the elucidation of important mechanistic details that would be difficult, if not impossible, to determine from experiments alone.

Notes: Abstract This review discusses methods for the incorporation of quantum mechanical effects into enzyme kinetics simulations in which the enzyme is an explicit part of the model. We emphasize three aspects: (a) use of quantum mechanical electronic structure methods such as molecular orbital theory and density functional theory, usually in conjunction with molecular mechanics; (b) treating vibrational motions quantum mechanically, either in an instantaneous harmonic approximation, or by path integrals, or by a three-dimensional wave function coupled to classical nuclear motion; (c) incorporation of multidimensional tunneling approximations into reaction rate calculations.

Notes: Abstract Recent studies of state-resolved angular distributions show the participation of reactive scattering resonances in the simplest chemical reaction. This review is intended for those who wish to learn about the state-of-the-art in the study of the H + H2 reaction family that has made this breakthrough possible. This review is also intended for those who wish to gain insight into the nature of reactive scattering resonances. Following a tour across several fields of physics and chemistry where the concept of resonance has been crucial for the understanding of new phenomena, we offer an operational definition and taxonomy of reactive scattering resonances. We introduce simple intuitive models to illustrate each resonance type. We focus next on the last decade of H + H2 reaction dynamics. Emphasis is placed on the various experimental approaches that have been applied to the search for resonance behavior in the H + H2 reaction family. We conclude by sketching the road ahead in the study of H + H2 reactive scattering resonances.

Notes: Abstract This paper reviews the molecular theory of hydrophobic effects relevant to biomolecular structure and assembly in aqueous solution. Recent progress has resulted in simple, validated molecular statistical thermodynamic theories and clarification of confusing theories of decades ago. Current work is resolving effects of wider variations of thermodynamic state, e.g., pressure denaturation of soluble proteins, and more exotic questions such as effects of surface chemistry in treating stability of macromolecular structures in aqueous solution.

Notes: Abstract This review presents a case study of the direct, real-time observation of a surface photochemical reaction, namely the frustrated photodesorption of alkali atoms from noble metal surfaces. Charge transfer excitation of an electron from the metal substrate into an unoccupied resonance of the alkali atom instantaneously turns on the repulsive Coulomb force inducing the nuclear motion of both the adsorbate and substrate atoms. The incipient nuclear wave packet dynamics are documented for the case of Cs/Cu(111) through the accompanying change in the surface electronic structure. The intimate view of atoms attempting to escape the surface bond highlights the unique role of the substrate in the electronic and nuclear dynamics that ultimately determine the product yields. Moreover, slow dephasing of the coherent polarization is exploited to demonstrate the control of nuclear wave packets through the phase of the excitation light.

Notes: Abstract Recent developments in scanning tunneling microscopy studies of the electronic properties of single-walled carbon nanotubes are reviewed. A broad range of topics focused on the unique electronic properties of nanotubes are discussed, including (a) the underlying theoretical description of the electronic properties of nanotubes; (b) the roles of finite curvature and broken symmetries in perturbing electronic properties; (c) the unique one-dimensional energy dispersion in nanotubes; (d) the nature of end states; (e) quantum size effects in short tubes; (f) the interactions between local spins and carriers in metallic systems (the Kondo effect); and (g) the atomic structure and electronic properties of intramolecular junctions. The implications of these studies for understanding fundamental one-dimensional physics and future nanotube device applications are discussed.

Notes: Abstract The use of photoelectron angular distributions (PADs) as a probe in short-pulse, pump-probe scenarios is reviewed. We focus on concepts, on the insight that can be gained through theoretical analysis, on applications, and on future opportunities. Time-resolved PADs are sensitive to both the time-evolving rotational composition of wavepackets and their time-evolving electronic symmetry. The former feature renders this observable a potential probe of molecular structure, intensity effects, and rotational perturbations. The latter feature renders the PAD a potential probe of radiationless transitions.

Notes: Abstract The aggregation of monomers into polymers, whether by covalent or noncovalent interactions, is often reversible and frequently occurs with the entropy and enthalpy of the aggregation sharing the same sign. In such a case, the aggregation goes forward or reverses, depending on such variables as temperature and composition, rather like a phase transition. We explore the physical chemistry of three such systems: an organic monomer (alpha-methylstyrene), an inorganic monomer (sulfur), and a biopolymer (actin). We compare the available theories and experiments and list issues still open.

Notes: The Watson-Crick double helix of DNA was first revealed in 1953. Since then a wide range of physical chemical methods have been applied to DNA and to its more versatile relative RNA to determine their structures and functions. My major goal is to predict the folded structure of any RNA from its sequence. We have used bulk and single-molecule measurements of thermodynamics and kinetics, plus various spectroscopic methods (UV absorption, optical rotation, circular dichroism, circular intensity differential scattering, fluorescence, NMR) to approach this goal.

Notes: Abstract The recent developments of vacuum ultraviolet (VUV) laser and third generation synchrotron radiation sources, together with the introduction of pulsed field ionization (PFI) schemes for photoion-photoelectron detection, have had a profound impact on the field of VUV spectroscopy and chemistry. Owing to the mediation of near-resonant autoionizing states, rovibronic states of ions with negligible Franck-Condon factors for direct photoionization can be examined by VUV-PFI measurements with rotational resolutions. The VUV-PFI spectra thus obtained have provided definitive ionization energies (IEs) for many small molecules. The recent synchrotron-based PFI-photoelectron-photoion coincidence experiments have demonstrated that dissociative photoionization thresholds for a range of molecules can be determined to the same precision as in PFI-photoelectron measurements. Combining appropriate dissociation thresholds and IEs measured in PFI studies, thermochemical data for many neutrals and cations can be determined with unprecedented precision. The further development of two-color excitation-ionization schemes promises to expand the scope of spectroscopic and chemical applications using the photoionization-photoelectron method.

Notes: Abstract Electron transfer between a molecular resonance and a metal surface is a ubiquitous process in many chemical disciplines, ranging from molecular electronics to surface photochemistry. This problem has been probed recently by two-photon photoemission spectroscopy. The first photon excites an electron from an occupied metal state to an unoccupied molecular resonance. Subsequent evolution of the excited electronic wavefunction is probed in energy, momentum, and time domains by the absorption of a second photon, which ionizes the electron for detection. These experiments reveal the important roles of molecule-metal wavefunction mixing, intermolecular band formation, polarization, and localization in interfacial electron transfer.