ALBERT

Notes: Toroidal DNA condensates have attracted the attention of biophysicists, biochemists, and polymer physicists for more than thirty years. In the biological community, the quest to understand DNA toroid formation has been motivated by its relevance to gene packing in certain viruses and by the potential use of DNA toroids in artificial gene delivery (e.g., gene therapy). In the physical sciences, DNA toroids are appreciated as a superb model system for studying particle formation by the collapse of a semiflexible, polyelectrolyte polymer. This review focuses on experimental studies from the past few years that have significantly increased our understanding of DNA toroid structure and the mechanism of their formation. Highlights include structural studies that show the DNA strands within toroids to be packed in an ideal hexagonal lattice, and also in regions with a nonhexagonal lattice that are required by the topological constraints associated with winding DNA into a toroid. Recent studies of DNA toroid formation have also revealed that toroid size limits result from a complex interplay between kinetic and thermodynamic factors that govern both toroid nucleation and growth. The work discussed in this review indicates that it will ultimately be possible to obtain substantial control over DNA toroid dimensions.

Notes: With genome sequencing nearing completion for the model organisms used in biomedical research, there is a rapidly growing appreciation that proteomics, the study of covalent modification to proteins, and transcriptional regulation will likely dominate the research headlines in the next decade. Protein methylation plays a central role in both of these fields, as several different residues (Arg, Lys, Gln) are methylated in cells and methylation plays a central role in the "histone code" that regulates chromatin structure and impacts transcription. In some cases, a single lysine can be mono-, di-, or trimethylated, with different functional consequences for each of the three forms. This review describes structural aspects of methylation of histone lysine residues by two enzyme families with entirely different structural scaffolding (the SET proteins and Dot1p) and methylation of protein arginine residues by PRMTs.

Notes: Potassium (K+) channels are tetrameric membrane-spanning proteins that provide a selective pore for the conductance of K+ across the cell membranes. These channels are most remarkable in their ability to discriminate K+ from Na+ by more than a thousandfold and conduct at a throughput rate near diffusion limit. The recent progress in the structural characterization of K+ channel provides us with a unique opportunity to understand their function at the atomic level. With their ability to go beyond static structures, molecular dynamics simulations based on atomic models can play an important role in shaping our view of how ion channels carry out their function. The purpose of this review is to summarize the most important findings from experiments and computations and to highlight a number of fundamental mechanistic questions about ion conduction and selectivity that will require further work.

Notes: Proteins have become accessible targets for chemical synthesis. The basic strategy is to use native chemical ligation, Staudinger ligation, or other orthogonal chemical reactions to couple synthetic peptides. The ligation reactions are compatible with a variety of solvents and proceed in solution or on a solid support. Chemical synthesis enables a level of control on protein composition that greatly exceeds that attainable with ribosome-mediated biosynthesis. Accordingly, the chemical synthesis of proteins is providing previously unattainable insight into the structure and function of proteins.

Notes: A powerful approach to understanding protein enzyme catalysis is to examine the structural context of essential amino acid side chains whose deletion or modification negatively impacts catalysis. In principle, this approach can be even more powerful for RNA enzymes, given the wide variety and subtlety of functionally modified nucleotides now available. Numerous recent success stories confirm the utility of this approach to understanding ribozyme function. An anomaly, however, is the hammerhead ribozyme, for which the structural and functional data do not agree well, preventing a unifying view of its catalytic mechanism from emerging. To delineate the hammerhead structure-function comparison, we have evaluated and distilled the large body of biochemical data into a consensus set of functional groups unambiguously required for hammerhead catalysis. By examining the context of these functional groups within available structures, we have established a concise set of disagreements between the structural and functional data. The number and relative distribution of these inconsistencies throughout the hammerhead reaffirms that an extensive conformational rearrangement from the fold observed in the crystal structure must be necessary for cleavage to occur. The nature and energetic driving force of this conformational isomerization are discussed.

Notes: The development of single-molecule detection and manipulation has allowed us to monitor the behavior of individual biological molecules and molecular complexes in real time. This approach significantly expands our capability to characterize complex dynamics of biological processes, allowing transient intermediate states and parallel kinetic pathways to be directly observed. Exploring this capability to elucidate complex dynamics, recent single-molecule experiments on RNA folding and catalysis have improved our understanding of the folding energy landscape of RNA and allowed us to better dissect complex RNA catalytic reactions, including translation by the ribosome.

Notes: Water plays a central role in the structures and properties of biomoleculesĐ??proteins, nucleic acids, and membranesĐ??and in their interactions with ligands and drugs. Over the past half century, our understanding of water has been advanced significantly owing to theoretical and computational modeling. However, like the blind men and the elephant, different models describe different aspects of water's behavior. The trend in water modeling has been toward finer-scale properties and increasing structural detail, at increasing computational expense. Recently, our labs and others have moved in the opposite direction, toward simpler physical models, focusing on more global propertiesĐ??water's thermodynamics, phase diagram, and solvation properties, for exampleĐ??and toward less computational expense. Simplified models can guide a better understanding of water in ways that complement what we learn from more complex models. One ultimate goal is more tractable models for computer simulations of biomolecules. This review gives a perspective from simple models on how the physical properties of waterĐ??as a pure liquid and as a solventĐ??derive from the geometric and hydrogen bonding properties of water.

Notes: Structural data on protein-DNA complexes provide clues for understanding the mechanism of protein-DNA recognition. Although the structures of a large number of protein-DNA complexes are known, the mechanisms underlying their specific binding are still only poorly understood. Analysis of these structures has shown that there is no simple one-to-one correspondence between bases and amino acids within protein-DNA complexes; nevertheless, the observed patterns of interaction carry important information on the mechanisms of protein-DNA recognition. In this review, we show how the patterns of interaction, either observed in known structures or derived from computer simulations, confer recognition specificity, and how they can be used to examine the relationship between structure and specificity and to predict target DNA sequences used by regulatory proteins.

Notes: The objective of this review is to critically assess the different approaches developed in recent years to understand the dynamics of open flows such as mixing layers, jets, wakes, separation bubbles, boundary layers, and so on. These complex flows develop in extended domains in which fluid particles are continuously advected downstream. They behave either as noise amplifiers or as oscillators, both of which exhibit strong nonlinearities ( Huerre & Monkewitz 1990 ). The local approach is inherently weakly nonparallel and it assumes that the basic flow varies on a long length scale compared to the wavelength of the instability waves. The dynamics of the flow is then considered as a superposition of linear or nonlinear instability waves that, at leading order, behave at each streamwise station as if the flow were homogeneous in the streamwise direction. In the fully global context, the basic flow and the instabilities do not have to be characterized by widely separated length scales, and the dynamics is then viewed as the result of the interactions between Global modes living in the entire physical domain with the streamwise direction as an eigendirection. This second approach is more and more resorted to as a result of increased computational capability. The earlier review of Huerre & Monkewitz (1990) emphasized how local linear theory can account for the noise amplifier behavior as well as for the onset of a Global mode. The present survey first adopts the opposite point of view by demonstrating how fully global theory accounts for the noise amplifier behavior of open flows. From such a perspective, there is strong emphasis on the very peculiar nonorthogonality of linear Global modes, which in turn allows a novel interpretation of recent numerical simulations and experimental observations. The nonorthogonality of linear Global modes also imposes severe constraints on the extension of linear global theory to the fully nonlinear re??gime. When the flow is weakly nonparallel, this limitation is so severe that the linear Global mode theory is of little help. It is then much more appropriate to develop a fully nonlinear formulation involving the presence of a front separating the base state region from the bifurcated state region.

Notes: We review the fluid mechanics and rheology of dense suspensions, emphasizing investigations of microstructure and total stress. "Dense" or "highly concentrated" suspensions are those in which the average particle separation distance is less than the particle radius. For these suspensions, multiple-body interactions as well as two-body lubrication play a significant role and the rheology is non-Newtonian. We include investigations of multimodal suspensions, but not those of suspensions with dominant nonhydrodynamic interactions. We consider results from both physical experiments and computer simulations and explore scaling theories and the development of constitutive equations.

Notes: George Gabriel Stokes died just over 100 years ago, and it has been more than 150 years since he published his great 1847 paper on water waves. The work of Stokes' precursors, which informed his early publications of 1842Đ??50, is described in the previous volume of the Annual Review of Fluid Mechanics ( Craik 2004 ). Here I examine Stokes' papers and letters concerning water waves.

Notes: Chaotic advection and, more generally, ideas from dynamical systems, have been fruitfully applied to a diverse, and varied, collection of mixing and transport problems arising in engineering applications over the past 20 years. Indeed, the "dynamical systems approach" was developed, and tested, to the point where it can now be considered a standard tool for understanding mixing and transport issues in many disciplines. This success for engineering-type flows motivated an effort to apply this approach to transport and mixing problems in geophysical flows. However, there are fundamental difficulties arising in this endeavor that must be properly understood and overcome. Central to this approach is that the starting point for analysis is a velocity field (i.e., the "dynamical system"). In many engineering applications this can be obtained sufficiently accurately, either analytically or computationally, so that it describes particle trajectories for the actual flow. However, in geophysical flows (and we concentrate here almost exclusively on oceanographic flows), the wide range of dynamically significant time and length scales makes the justification of any velocity field, in the sense of reproducing particle trajectories for the actual flow, a much more difficult matter. Nevertheless, the case for this approach is compelling due to the advances in observational capabilities in oceanography (e.g., drifter deployments, remote sensing capabilities, satellite imagery, etc.), which reveal space-time structures that are highly suggestive of the structures one visualizes in the global, geometrical study of dynamical systems theory. This has been pursued in recent years through a combination of laboratory studies, kinematic models, and dynamically consistent models that have all been compared with observational data. During the course of these studies it has become apparent that a new type of dynamical system is necessary to consider in these studies (i.e., a finite time, aperiodically time-dependent velocity field defined as a data set), which requires the development of new analytical and computational tools, as well as the necessity to discard some of the standard ideas and results from dynamical systems theory. In this article we review a number of the key developments to date in this young, but rapidly developing, area at the interface between geophysical fluid dynamics and applied and computational mathematics. We also describe the wealth of new directions for research that this approach unlocks.

Notes: The gas-lift technique comprises the injection of gas bubbles in vertical oil wells to increase production. It is based on a reduction of the tubing gravitational pressure gradient. Several fluid-flow phenomena influencing such vertical gas-liquid flows are discussed. These effects include the radial distribution of void fraction and of gas and liquid velocity, flow regime changes, and system stability problems. Associated consequences for gas-lift performance and related optimization approaches are also discussed.

Notes: What mechanisms of flow control do animals use to enhance hydrodynamic performance? Animals are capable of manipulating flow around the body and appendages both passively and actively. Passive mechanisms rely on structural and morphological components of the body (i.e., humpback whale tubercles, riblets). Active flow control mechanisms use appendage or body musculature to directly generate wake flow structures or stiffen fins against external hydrodynamic loads. Fish can actively control fin curvature, displacement, and area. The vortex wake shed by the tail differs between eel-like fishes and fishes with a discrete narrowing of the body in front of the tail, and three-dimensional effects may play a major role in determining wake structure in most fishes.

Notes: Over the past four decades, the combination of in situ and remote sensing observations has demonstrated that long nonlinear internal solitary-like waves are ubiquitous features of coastal oceans. The following provides an overview of the properties of steady internal solitary waves and the transient processes of wave generation and evolution, primarily from the point of view of weakly nonlinear theory, of which the Korteweg-de Vries equation is the most frequently used example. However, the oceanographically important processes of wave instability and breaking, generally inaccessible with these models, are also discussed. Furthermore, observations often show strongly nonlinear waves whose properties can only be explained with fully nonlinear models.

Notes: Electrophoretic separation of a mixture of chemical species is a fundamental technique of great usefulness in biology, health care, and forensics. In capillary electrophoresis (which has evolved from its predecessor, slab-gel electrophoresis), the sample migrates through a single microcapillary instead of through the network of pores in a gel. A fundamental design problem is to minimize dispersion in the separation direction. Molecular diffusion is inevitable and sets a theoretical limit on the best separation that can be achieved. But in practice, there are a number of effects arising out of the interplay between fluid flow, chemistry, thermal effects, and electric fields that result in enhanced dispersion. This paper reviews the subject of fluid flow in such capillary microchannels and examines the various causes of enhanced dispersion that limit the efficiency of separation.

Notes: Race car performance depends on elements such as the engine, tires, suspension, road, aerodynamics, and of course the driver. In recent years, however, vehicle aerodynamics gained increased attention, mainly due to the utilization of the negative lift (downforce) principle, yielding several important performance improvements. This review briefly explains the significance of the aerodynamic downforce and how it improves race car performance. After this short introduction various methods to generate downforce such as inverted wings, diffusers, and vortex generators are discussed. Due to the complex geometry of these vehicles, the aerodynamic interaction between the various body components is significant, resulting in vortex flows and lifting surface shapes unlike traditional airplane wings. Typical design tools such as wind tunnel testing, computational fluid dynamics, and track testing, and their relevance to race car development, are discussed as well. In spite of the tremendous progress of these design tools (due to better instrumentation, communication, and computational power), the fluid dynamic phenomenon is still highly nonlinear, and predicting the effect of a particular modification is not always trouble free. Several examples covering a wide range of vehicle shapes (e.g., from stock cars to open-wheel race cars) are presented to demonstrate this nonlinear nature of the flow field.

Notes: Large-eddy simulation (LES) of turbulent combustion is a relatively new research field. Much research has been carried out over the past years, but to realize the full predictive potential of combustion LES, many fundamental questions still have to be addressed, and common practices of LES of nonreacting flows revisited. The focus of the present review is to highlight the fundamental differences between Reynolds-averaged Navier-Stokes (RANS) and LES combustion models for nonpremixed and premixed turbulent combustion, to identify some of the open questions and modeling issues for LES, and to provide future perspectives.

Notes: Progress in experimental and theoretical biology is likely to provide us with the opportunity to assemble detailed predictive models of mammalian cells. Using a functional format to describe the organization of mammalian cells, we describe current approaches for developing qualitative and quantitative models using data from a variety of experimental sources. Recent developments and applications of graph theory to biological networks are reviewed. The use of these qualitative models to identify the topology of regulatory motifs and functional modules is discussed. Cellular homeostasis and plasticity are interpreted within the framework of balance between regulatory motifs and interactions between modules. From this analysis we identify the need for detailed quantitative models on the basis of the representation of the chemistry underlying the cellular process. The use of deterministic, stochastic, and hybrid models to represent cellular processes is reviewed, and an initial integrated approach for the development of large-scale predictive models of a mammalian cell is presented.

Notes: Efficiently and accurately solving the equations governing fluid flow in oil reservoirs is very challenging because of the complex geological environment and the intricate properties of crude oil and gas at high pressure. We present these challenges and review successful and promising solution approaches. We discuss in detail the modeling of fluid flow in reservoirs with strongly varying rock properties. This requires subgrid-scale models that accurately represent the flow physics due to fine-scale fluctuations. A second focus is on the complex multiphase, multicomponent systems that describe miscible gas injection processes for enhanced oil recovery and CO2 sequestration.

Notes: Mammalian fertilization requires the coordinated activity of motile spermatozoa, muscular contractions of the uterus and oviduct, as well as ciliary beating. These elastic structures generate forces that drive fluid motion, but their configurations are, in turn, determined by the fluid dynamics. We review the basic fluid mechanical aspects of reproduction, including flagellar/ciliary beating and peristalsis. We report on recent biological studies that have shed light on the relative importance of the mechanical ingredients of reproduction. In particular, we examine sperm motility in the reproductive tract, ovum pickup and transport in the oviduct, as well as sperm-egg interactions. We review recent advances in understanding the internal mechanics of cilia and flagella, flagellar surface interaction, sperm motility in complex fluids, and the role of fluid dynamics in embryo transfer. We outline promising computational fluid dynamics frameworks that may be used to investigate these complex, fluid-structure interactions.

Notes: This article provides a critical review of computational techniques for flow-noise prediction and the underlying theories. Hybrid approaches, in which the turbulent noise source field is computed and/or modeled separately from the far-field calculation, are afforded particular attention. Numerical methods and modern flow simulation techniques are discussed in terms of their suitability and accuracy for flow-noise calculations. Other topics highlighted include some important formulation and computational issues in the application of aeroacoustic theories, generalized acoustic analogies with better accounts of flow-sound interaction, and recent computational investigations of noise-control strategies. The review ends with an analysis of major challenges and key areas for improvement in order to advance the state of the art of computational aeroacoustics.

Notes: The challenges in understanding hypersonic flight are discussed and critical hypersonic aerothermodynamics issues are reviewed. The ability of current analytical methods, numerical methods, ground testing capabilities, and flight testing approaches to predict hypersonic flow are evaluated. The areas where aerothermodynamic shortcomings restrict our ability to design and analyze hypersonic vehicles are discussed, and prospects for future capabilities are reviewed. Considerable work still needs to be done before our understanding of hypersonic flow will allow for the accurate prediction of vehicle flight characteristics throughout the flight envelope from launch to orbital insertion.

Notes: We review mathematical models of confined bubbles, emphasizing physical mechanisms as expressed in simple geometries. Molecular interactions between liquid, gas, and the confining solid are all important and are described through the disjoining pressure concept. Methods for finding static shapes are considered. The static solution is a springboard for discussing pressure-driven and surface-tension-driven flows, both of which involve viscous effects and macroscopic films entrained near apparent contact lines. We next discuss vapor bubbles produced by thermal effects. Vaporization localized near contact lines and condensation distributed in colder parts of the interface lead to steady vapor bubbles. Their size is determined through global constraints. Unsteady vapor bubbles are discussed and we end with thoughts on open problems.

Notes: The review deals with drop impacts on thin liquid layers and dry surfaces. The impacts resulting in crown formation are referred to as splashing. Crowns and their propagation are discussed in detail, as well as some additional kindred, albeit nonsplashing, phenomena like drop spreading and deposition, receding (recoil), jetting, fingering, and rebound. The review begins with an explanation of various practical motivations feeding the interest in the fascinating phenomena of drop impact, and the above-mentioned topics are then considered in their experimental, theoretical, and computational aspects.

Notes: Recent advancements in single-molecule tracking methods with nanometer-level precision now allow researchers to observe the movement, recruitment, and activation of single molecules in the plasma membrane in living cells. In particular, on the basis of the observations by high-speed single-particle tracking at a frame rate of 40,000 frames s1, the partitioning of the fluid plasma membrane into submicron compartments throughout the cell membrane and the hop diffusion of virtually all the molecules have been proposed. This could explain why the diffusion coefficients in the plasma membrane are considerably smaller than those in artificial membranes, and why the diffusion coefficient is reduced upon molecular complex formation (oligomerization-induced trapping). In this review, we first describe the high-speed single-molecule tracking methods, and then we critically review a new model of a partitioned fluid plasma membrane and the involvement of the actin-based membrane-skeleton "fences" and anchored-transmembrane protein "pickets" in the formation of compartment boundaries.

Notes: The recent development of new techniques to manipulate single DNA molecules has opened new opportunities for the study of the enzymes that control DNA topology: the type I and II topoisomerases. These single-molecule assays provide a unique way to study the uncoiling of single supercoiled DNA molecules and the unlinking of two intertwined DNAs. They allow for a detailed characterization of the activity of topoisomerases, including the processivity, the chiral discrimination, and the dependence of their enzymatic rate on ATP concentration, degree of supercoiling, and the tension in the molecule. These results shed new light on the mechanism of these enzymes and their function in vivo.

Notes: Simulation of protein folding has come a long way in five years. Notably, new quantitative comparisons with experiments for small, rapidly folding proteins have become possible. As the only way to validate simulation methodology, this achievement marks a significant advance. Here, we detail these recent achievements and ask whether simulations have indeed rendered quantitative predictions in several areas, including protein folding kinetics, thermodynamics, and physics-based methods for structure prediction. We conclude by looking to the future of such comparisons between simulations and experiments.

Notes: Research in the past decade has revealed that many cytosolic proteins are recruited to different cellular membranes to form protein-protein and lipid-protein interactions during cell signaling and membrane trafficking. Membrane recruitment of these peripheral proteins is mediated by a growing number of modular membrane-targeting domains, including C1, C2, PH, FYVE, PX, ENTH, ANTH, BAR, FERM, and tubby domains, that recognize specific lipid molecules in the membranes. Structural studies of these membrane-targeting domains demonstrate how they specifically recognize their cognate lipid ligands. However, the mechanisms by which these domains and their host proteins are recruited to and interact with various cell membranes are only beginning to unravel with recent computational studies, in vitro membrane binding studies using model membranes, and cellular translocation studies using fluorescent protein-tagged proteins. This review summarizes the recent progress in our understanding of how the kinetics and energetics of membrane-protein interactions are regulated during the cellular membrane targeting and activation of peripheral proteins.

Notes: Early work and recent advances in feedback control of combustion oscillations are described. The physics of combustion oscillations, most commonly caused by a coupling between acoustic waves and unsteady heat release, are discussed, and the concept of using feedback control to interrupt these interactions is introduced. Factors affecting practical implementation of feedback control, including sensors, actuators, and controller design are described, and the historical development of control strategy for combustion oscillations is reviewed. Finally, demonstrations of feedback control on full-scale combustion systems are described, and it is concluded that there is potential to apply more systematic controller designs at full scale.

Notes: Flow simulations are one of the archetypal multiscale problems. Simulations of turbulent and unsteady separated flows have to resolve a multitude of interacting scales, whereas molecular phenomena determine the structure of shocks and the validity of the no-slip boundary condition. Particle simulations of continuum and molecular phenomena can be formulated by following the motion of interacting particles that carry the physical properties of the flow. In this article we review Lagrangian, multiresolution, particle methods such as vortex methods and smooth particle hydrodynamics for the simulation of continuous flows and molecular dynamics for the simulation of flows at the atomistic scale. We review hybrid molecular-continuum simulations with an emphasis on the computational aspects of the problem. We identify the common computational characteristics of particle methods and discuss their properties that enable the formulation of a systematic framework for multiscale flow simulations.

Notes: Gravity-driven bubbly flows are a specific class of flows, where all action is provided by gravity. An industrial example is formed by the so-called bubble column: a vertical cylinder filled with liquid through which bubbles flow that are introduced at the bottom of the cylinder. On the bubble scale, gravity gives rise to buoyancy of individual bubbles. On larger scales, gravity acts on nonuniformities in the spatial bubble distribution present in the bubbly mixture. The gravity-induced flow and flow structures can increase the inhomogeneity of the bubble distribution, leading to a turbulent flow. In this flow, specific scales are identified: a large-scale circulation with the liquid flowing upward in the center of the column and downward close to the wall. On the intermediate scale there are vortical structures; eddies of liquid, with a size on the order of the diameter of the column, that stir the liquid and radially transport the bubbles. On the small scale there is the local stirring of the bubbles. We describe the ideas developed over time and identify some open questions. We discuss the experimental findings on the turbulence generated, the stability of the flow, axial dispersion, and the similarities between bubble columns and air lifts. Especially for higher gas fractions, many questions still lack accurate answers. The lateral lift force in bubble swarms and the structure of the turbulence in the bubbly mixture are important examples of inadequately understood physical phenomena, providing many challenges for fundamental and applied research on bubbly flows.

Notes: Development and optimization of multifunctional devices for fluidic manipulation of films, drops, and bubbles require detailed understanding of interfacial phenomena and microhydrodynamic flows. Systems are distinguished by a large surface to volume ratio and flow at small Reynolds, capillary, and Bond numbers are strongly influenced by boundary effects and therefore amenable to control by a variety of surface treatments and surface forces. We review the principles underlying common techniques for actuation of droplets and films on homogeneous, chemically patterned, and topologically textured surfaces by modulation of normal or shear stresses.

Notes: "What force does an insect wing generate?" Finding answers to this enduring question is an essential step toward our understanding of interactions of moving objects with fluids that enable most living species such as insects, birds, and fish to travel efficiently and us to follow similar suit with sails, oars, and airfoils. We give a brief history of research in insect flight and discuss recent findings in unsteady aerodynamics of flapping flight at intermediate range Reynolds numbers ( 10Đ??104 ). In particular, we examine the unsteady mechanisms in uniform and accelerated motions, forward and hovering flight, as well as passive flight of free-falling objects. The results obtained by "taking the insects apart" helped us to resolve previous puzzles about the force estimates in hovering insects, to ellucidate basic mechanisms essential to flapping flight, and to gain insights about the efficieny of flight.

Notes: We review recent advances in understanding, modeling, and controlling oscillations in the flow past a cavity. The fundamental mechanisms underlying cavity flow oscillations have been known for at least 40 years, but suppressing these oscillations in a reliable and robust way is still a challenge today. Interest in controlling the flow past a cavity is motivated by aerospace applications, but in addition, cavity flows provide an attractive canonical problem for exploring general flow control techniques. The focus is on recent advances in modeling these flows, and in controlling them, using both open-loop and closed-loop techniques. A relatively new perspective is that cavity oscillations may not always be self-sustained, but under some flow conditions may be lightly damped resonances, sustained by external disturbances such as boundary layer turbulence. Areas in which our understanding is incomplete, and which deserve further study, are discussed, in particular the effects of high-frequency open-loop forcing, fundamental limitations of feedback control for a given configuration of sensors and actuators, and the development of a feedback design methodology that respects the limited range of validity of the available dynamical models.

Notes: When the free surfaces of most solids approach their bulk melting temperatures from below, the molecular structure of the material gives way to a disordered structure with some attributes of both the solid and liquid phases. When the temperature is sufficiently close to that of bulk transition, the surface melts and literally flows as a viscous fluid. This phenomenon, called interfacial premelting, lies at the heart of the microscopic theory of melting of solid matter, and captures the interest of condensed matter physicists and physical chemists alike. The process is ubiquitous and responsible for a wide range of consequences in materials with biological, geophysical, and technological significance. Because such systems are often exposed to spatial or temporal variations in thermodynamic forcing, there are a host of fluid mechanical phenomena that result from this underlying melting behavior. The fluid dynamics of unfrozen surfaces holds clues for understanding the bulk behavior of polycrystalline materials, from Earth's mantle to the stratosphere and beyond. In this review we focus on the fluid dynamical consequences of the premelting of solids.

Notes: We consider the hydrodynamics of creatures capable of sustaining themselves on the water surface by means other than flotation. Particular attention is given to classifying water walkers according to their principal means of weight support and lateral propulsion. The various propulsion mechanisms are rationalized through consideration of energetics, hydrodynamic forces applied, or momentum transferred by the driving stroke. We review previous research in this area and suggest directions for future work. Special attention is given to introductory discussions of problems not previously treated in the fluid mechanics literature, with hopes of attracting physicists, applied mathematicians, and engineers to this relatively unexplored area of fluid mechanics.

Notes: The conformation of the ligand in complex with a macromolecular target can be studied by nuclear magnetic resonance (NMR) in solution for both tightly and weakly forming complexes. In the weak binding regime (koff 〉 104 Hz), the structure of the bound ligand is accessible also for very large complexes (〉100 kDa), which are not amenable to NMR studies in the tight binding regime. Here I review the state-of-the-art NMR methodology used for screening ligands and for the structural investigation of bound ligand conformations, in both tight and weak binding regimes. The advantages and disadvantages of each approach are critically described. The NMR methodology used to investigate transiently forming complexes has expanded considerably in the past few years, opening new possibilities for a detailed description of ligand-target interactions. Novel methods for the determination of the bound ligand conformation, in particular transferred cross-correlated relaxation, are thoroughly reviewed, and their advantages with respect to established methodology are discussed, using the epothilone-tubulin complex as a primary example.

Notes: The problem of how ions influence the folding of RNA into specific tertiary structures is being addressed from both thermodynamic (by how much do different salts affect the free energy change of folding) and structural (how are ions arranged on or near an RNA and what kinds of environments do they occupy) points of view. The challenge is to link these different approaches in a theoretical framework that relates the energetics of ion-RNA interactions to the spatial distribution of ions. This review distinguishes three different kinds of ion environments that differ in the extent of direct ion-RNA contacts and the degree to which the ion hydration is perturbed, and summarizes the current understanding of the way each environment relates to the overall energetics of RNA folding.

Notes: Molecular interactions are the language that molecules use to communicate recognition, binding, and regulation, events central to biological control mechanisms. Traditionally, such interactions involve direct, atom-to-atom, noncovalent contacts, or indirect contacts bridged by relatively fixed solvent molecules. Here we discuss a third class of molecular communication that, to date, has received less experimental attention, namely solvent-mediated communication between noncontacting macromolecules. This form of communication can be understood in terms of fundamental, well-established principles (coupled equilibria and linkage thermodynamics) that govern interactions between individual polymers and their solutions. In contrast to simple solutions used in laboratory studies, biological systems contain a multitude of nominally noninteracting biopolymers within the same solution environment. The exquisite control of biological function requires some form of communication between many of these solution components, even in the absence of direct and/or indirect contacts. Such communication must be considered when describing potential mechanisms of biological regulation.

Notes: Despite the central importance of peripheral membrane proteins to cellular signaling and metabolic pathways, the structures of protein-membrane interfaces remain largely inaccessible to high-resolution structural methods. In recent years a number of laboratories have contributed to the development of an electron paramagnetic resonance (EPR) power saturation approach that utilizes site-directed spin labeling to determine the key geometric parameters of membrane-docked proteins, including their penetration depths and angular orientations relative to the membrane surface. Representative applications to Ca2+-activated, membrane-docking C2 domains are described.

Notes: This article reviews our current understanding of the physical mechanisms governing the movement of a tropical cyclone. In a barotropic framework, a tropical cyclone is basically "steered" by the surrounding flow but its movement is modified by the Coriolis force (referred to as the beta effect) and the horizontal vorticity gradient of the surrounding flow. In the presence of vertical wind shear and latent heat release, a tropical cyclone tends to move toward an area with a maximum in the time tendency of potential vorticity, which is mainly contributed by two processes: (a) advection that depends on the structures of the vortex and the environment surrounding the vortex in terms of their flow speed and vorticity gradient (including the beta effect), and (b) heating that results from a coupling between the latent heat released in the clouds and the vertical wind shear.

Notes: The large-scale dynamics of the extratropical stratosphere are reviewed. The role of Rossby waves and vortex dynamics in shaping the winter stratospheric circulation and the dynamics of the longitudinal mean flow are first discussed separately. The important effects of two-way interaction between waves and mean flow are then described, with emphasis on how mechanisms discovered in simple models can be followed through to models that are closer to the real stratosphere. A final topic is the possible effect of the stratosphere on the troposphere, with emphasis on dynamical mechanisms for such an effect.

Notes: The flow in turbomachines is unsteady due to the relative motion of the rows of blades. In the low-pressure turbine, the wakes from the upstream bladerows provide the dominant source of unsteadiness. Because much of the blade-surface boundary-layer flow is laminar, one of the most important consequences of this unsteadiness is the interaction of the wakes with the suction-side boundary layer of a downstream blade. This is important because the blade suctionĐ??side boundary layers are responsible for most of the loss of efficiency and because the combined effects of random (wake turbulence) and periodic disturbances (wake velocity defect and pressure fields) cause the otherwise laminar boundary layer to undergo transition and eventually become turbulent. This article summarizes the process of wake-induced boundary-layer transition in low-pressure turbines and the loss generation processes that result. Particular emphasis is placed on how the effects of wakes may be exploited to control loss generation and how this has enabled successful development of ultra-high-lift low-pressure turbines.

Notes: We review major experimental and theoretical studies on microcirculation and hemorheology, focusing on mechanics of blood flow and the vascular wall. We discuss flow of the blood formed elements [red blood cells (RBCs), white blood cells or leukocytes (WBCs) and platelets] in individual arterioles, capillaries, and venules, and in microvascular networks. We also review mechanical and rheological properties of the formed elements and their interactions with the vascular wall. We discuss short-term and long-term regulation of the microvasculature; the modes of regulation include metabolic, myogenic, and shear-stress-dependent mechanisms as well as vascular adaptation such as angiogenesis and vascular remodeling.

Notes: His contemporaries saw R.T. Jones as one of the notably creative aerodynamicists of the twentieth century. This essay reviews his remarkable life and career, including his years as a farm-country boy, college dropout, and fledgling airplane designer in Missouri, his time as an elevator operator and self-directed student in Washington, D.C., and his long professional career as an aerodynamicist at the Langley and Ames Aeronautical Laboratories and Stanford University. The focus in his career is on his fundamental discovery of the benefits of sweepback for the wings of high-speed airplanes. This includes speculation about his highly intuitive thought processes in arriving at his creative ideas. I also give an account of his work on blood flow and the mechanical heart, his avocational accomplishments as a maker of telescopes and violins, and his philosophical interest in human affairs.

Notes: Wind tunnels have wide-ranging functionality, including many applications beyond aeronautics, and historically have been the major source of information for technological aerodynamics/aeronautical applications. There are a myriad of scaling issues/differences from flight to wind tunnel, and their study and impacts are uneven and a function of the particular type of extant flow phenomena. Typically, the most serious discrepancies are associated with flow separation. The tremendous ongoing increases in numerical simulation capability are changing and in many aspects have changed the function of the wind tunnel from a (scaled) "predictor" to a source of computational calibration/validation information with the computation then utilized as the flight prediction/scaling tool. Numerical simulations can increasingly include the influences of the various scaling issues. This wind tunnel role change has been occurring for decades as computational capability improves in all aspects. Additional issues driving this trend are the increasing cost (and time) disparity between physical experiments and computations, and increasingly stringent accuracy requirements.

Notes: Brooke Benjamin's original theories of fluid mechanical phenomena changed our basic understanding of cavitation bubbles, surface and internal waves, gravity currents, instabilities of shear flow over flexible surfaces, and swirling flows. For some types of finite-amplitude wave phenomena, he generated integral constraints and derived new partial differential equations; by establishing their general properties he showed how they have wide application. He developed a complementary approach based on functional analysis that was quite new to fluid mechanics. He demonstrated methods for deriving, without detailed calculation, the essential features of nonlinear and indeterminate flow problems that are otherwise intractable.

Notes: The fluid mechanics of artificial blood pumps has been studied since the early 1970s in an attempt to understand and mitigate hemolysis and thrombus formation by the device. Pulsatile pumps are characterized by inlet jets that set up a rotational "washing" pattern during filling. Strong regurgitant jets through the closed artificial heart valves have Reynolds stresses on the order of 10,000 dynes/cm2 and are the most likely cause of red blood cell damage and platelet activation. Although the flow in the pump chamber appears benign, low wall shear stresses throughout the pump cycle can lead to thrombus formation at the wall of the smaller pumps (10Đ??50 cc). The local fluid mechanics is critical. There is a need to rapidly measure or calculate the wall shear stress throughout the device so that the results may be easily incorporated into the design process.

Notes: Homeland security involves many applications of fluid mechanics and offers many opportunities for research and development. This review explores a wide selection of fluids topics in counterterrorism and suggests future directions. Broad topics range from preparedness and deterrence of impending terrorist attacks to detection, response, and recovery. Specific topics include aircraft hardening, blast mitigation, sensors and sampling, explosive detection, microfluidics and labs-on-a-chip, chemical plume dispersal in urban settings, and building ventilation. Also discussed are vapor plumes and standoff detection, nonlethal weapons, airborne disease spread, personal protective equipment, and decontamination. Involvement in these applications requires fluid dynamicists to think across the traditional boundaries of the field and to work with related disciplines, especially chemistry, biology, aerosol science, and atmospheric science.

Notes: Various forms of atmospheric moist convection are reviewed through a consideration of three prevalent regimes: stratocumulus; trade-wind; and deep, precipitating, maritime convection. These regimes are chosen because they are structural components of the general circulation of the atmosphere and because they highlight distinguishing features of this polymorphous phenomenon. In particular, the ways in which varied forms of moist convection communicate with remote parts of the flow through mechanisms other than the rearrangement of fluid parcels are emphasized. These include radiative, gravity wave, and/or microphysical (precipitation) processes. For each regime, basic aspects of its phenomenology are presented along with theoretical frameworks that have arisen to help rationalize the phenomenology. Recent developments suggest that the increased capacity for numerical simulation and increasingly refined remote sensing capabilities bodes well for major advances in the coming years.

Notes: Recent developments in volcanic seismology include new techniques to improve earthquake locations that have changed clouds of earthquakes to lines (faults) for high-frequency events and small volumes for low-frequency (LF) events. Spatial mapping of the b-value shows regions of normal b and high b anomalies at depths of 3-4 and 7-10 km. Increases in b precede some eruptions. LF events and very-long-period (VLP) events have been recorded at many volcanoes, and models are becoming increasingly sophisticated. Deep long-period (LP) events are fairly common, but may represent several processes. Acoustic sensors have greatly improved the study of volcanic explosions. Volcanic tremor is stronger for fissure eruptions, phreatic eruptions, and higher gas contents. Path and site effects can be extreme at volcanoes. Seismicity at volcanoes is triggered by large earthquakes, although mechanisms are still uncertain. A number of volcanoes have significant deformation with very little seismicity. Tomography has benefited from improved techniques and better instrumental arrays.

Notes: Contrary to Earth, the interior of terrestrial planets is poorly known. This is mainly related to the lack of seismic data and of planetary seismic networks on these planets. So far, despite several attempts, only the Apollo Seismic Network has returned seismic information from the Moon. But even in this case, very few seismic signals were recorded after a propagation path through the deep interior and core owing to a hemispheric distribution of the stations on the near side and to a probably strongly attenuating lower mantle. This review presents the main results achieved by the analysis of the Apollo seismic data and the associated constraints on the internal structure of the Moon. It then presents the current knowledge on the Martian interior, the seismic activity of the planet, and possible source of seismic noise. This information can be used for preparing future Martian seismic network missions. A short review on existing space-qualified instruments and on possible seismic missions toward other telluric bodies, such as Venus, the giant planets' satellites, or small bodies, is then given.

Notes: We know that giant planets played a crucial role in the making of our Solar System. The discovery of giant planets orbiting other stars is a formidable opportunity to learn more about these objects, what their composition is, how various processes influence their structure and evolution, and most importantly how they form. Jupiter, Saturn, Uranus, and Neptune can be studied in detail, mostly from close spacecraft flybys. We can infer that they are all enriched in heavy elements compared to the Sun, with the relative global enrichments increasing with distance to the Sun. We can also infer that they possess dense cores of varied masses. The intercomparison of presently characterized extrasolar giant planets shows that they are also mainly made of hydrogen and helium, but that they either have significantly different amounts of heavy elements, have had different orbital evolutions, or both. Hence, many questions remain and need to be answered to make significant progress on the origins of planets.

Notes: The influence of surface orography on patterns of precipitation gives rise to some of the most pronounced climate gradients on Earth, and plays a fundamental role in the interaction between the atmosphere and the rest of the Earth System on a wide variety of time scales. The physical mechanisms involved comprise a rich set of interactions encompassing fluid dynamics, thermodynamics, and micron-scale cloud processes, as well as being dependent on the larger-scale patterns of the atmospheric general circulation. Investigations into orographic precipitation have pursued three parallel tracks of inquiry: observations, theory, and modeling. Significant advances have been made in each over the last few decades, and these are summarized and synthesized here. While many aspects of the basic mechanisms responsible for orographic precipitation have been understood, important issues remain unresolved. The sheer number of contributing processes, together with their convoluted interactions, make the quantitative prediction of precipitation in complex terrain a very hard task. However, while prediction of precipitation amounts for any given event may be difficult, various lines of evidence suggest that the patterns of orgraphic precipitation, even on scales of a few kilometers, are much more robust.

Notes: The bulk of the Đ♯50-km-thick Martian crust formed at Đ♯4.5 Gyr B.P., perhaps from a magma ocean. This crust is probably a basaltic andesite or andesite and is enriched in incompatible and heat-producing elements. Later additions of denser basalt to the crust were volumetrically minor, but resurfaced significant portions of the Northern hemisphere. A significant fraction of the total thickness of the crust was magnetized prior to 4 Gyr B.P., with the magnetization later selectively removed by large impacts. Early large impacts also modified the hemispheric contrast in crustal thickness (the dichotomy), which was possibly caused by long-wavelength mantle convection. Subsequent Noachian modification of the crust included further impacts, significant fluvial erosion, and volcanism associated with the formation of the Tharsis rise. Remaining outstanding questions include the origin of the dichotomy and the nature of the magnetic anomalies.

Notes: Processes operating beneath glaciers can have a greater influence on flow dynamics than those operating within them. The variety and complexity of these processes, which involve interactions among ice, water, and geological solids, resist efforts to establish simple truths and can lead to surprising outcomes. Thermal conditions at the ice-bed interface (melting or nonmelting) and the mechanical properties of the glacier substrate (soft or hard) determine which processes can be activated. The warm-soft case supports the greatest variety of processes and is the most important for fast-flow dynamics and for the mobilization of subglacial sediment. Process interactions can lead to oscillations and spatio-temporal switching behavior in glaciers and ice sheets as well as to the generation of subglacial landforms.

Notes: The Ediacara biota (575Đ??542 Ma) marks the first appearance of large, architecturally complex organisms in Earth history. Present evidence suggests that the Ediacara biota included a mixture of stem- and crown-group radial animals, stem-group bilaterian animals, "failed experiments" in animal evolution, and perhaps representatives of other eukaryotic kingdoms. These soft-bodied organisms were preserved under (or rarely within) event beds of sand or volcanic ash, and four distinct preservational styles (Flinders-, Fermeuse-, Conception-, and Nama-style) profoundly affected the types of organisms and features that could be preserved. Even the earliest Ediacaran communities (575Đ??565 Ma) show vertical and lateral niche subdivision of the sessile, benthic, filter-feeding organisms, which is strikingly like that of Phanerozoic and modern communities. Later biological and ecological innovations include mobility (〉555 Ma), calcification (550 Ma), and predation (〈549 Ma). The Ediacara biota abruptly disappeared 542 million years ago, probably as a consequence of mass extinction andor biological interactions with the rapidly evolving animals of the Cambrian explosion.

Notes: Contrary to Earth, the interior of terrestrial planets is poorly known. This is mainly related to the lack of seismic data and of planetary seismic networks on these planets. So far, despite several attempts, only the Apollo Seismic Network has returned seismic information from the Moon. But even in this case, very few seismic signals were recorded after a propagation path through the deep interior and core owing to a hemispheric distribution of the stations on the near side and to a probably strongly attenuating lower mantle. This review presents the main results achieved by the analysis of the Apollo seismic data and the associated constraints on the internal structure of the Moon. It then presents the current knowledge on the Martian interior, the seismic activity of the planet, and possible source of seismic noise. This information can be used for preparing future Martian seismic network missions. A short review on existing space-qualified instruments and on possible seismic missions toward other telluric bodies, such as Venus, the giant planets' satellites, or small bodies, is then given.

Notes: Processes operating beneath glaciers can have a greater influence on flow dynamics than those operating within them. The variety and complexity of these processes, which involve interactions among ice, water, and geological solids, resist efforts to establish simple truths and can lead to surprising outcomes. Thermal conditions at the ice-bed interface (melting or nonmelting) and the mechanical properties of the glacier substrate (soft or hard) determine which processes can be activated. The warm-soft case supports the greatest variety of processes and is the most important for fast-flow dynamics and for the mobilization of subglacial sediment. Process interactions can lead to oscillations and spatio-temporal switching behavior in glaciers and ice sheets as well as to the generation of subglacial landforms.

Notes: Microbes are recognized as important components of the Earth system, playing key roles in controlling the composition of the atmosphere and surface waters, forming the basis of the marine food web, and the cycling of chemicals in the ocean. A revolution in microbial ecology has occurred in the past 15Đ??20 years with the advent of rapid methods for discovering and sequencing the genes of uncultivated microbes from natural environments. Initially based on sequences from the 16S rRNA gene, this revolution made it possible to identify microorganisms without first cultivating them, to discover and characterize the immense previously unsuspected diversity of the microbial world, and to reconstruct the evolutionary relationships among microbes. Subsequent focus on functional genes, those that encode enzymes that catalyze biogeochemical transformations, and current work on larger DNA fragments and entire genomes make it possible to link microbial diversity to ecosystem function. These approaches have yielded insights into the regulation of microbial activity and proof of the microbial role in biogeochemical processes previously unknown. Questions raised by the molecular revolution, which are now the focus of microbial ecology research, include the significance of microbial diversity and redundancy to biogeochemical processes and ecosystem function.

Notes: This paper reviews the Precambrian history of atmospheric oxygen, beginning with a brief discussion of the possible nature and magnitude of life before the evolution of oxygenic photosynthesis. This is followed by a summary of the various lines of evidence constraining oxygen levels through time, resulting in a suggested history of atmospheric oxygen concentrations. Also reviewed are the various processes regulating oxygen concentrations, and several models of Precambrian oxygen evolution are presented. A sparse geologic record, combined with uncertainties as to its interpretation, yields only a fragmentary and imprecise reading of atmospheric oxygen evolution. Nevertheless, oxygen levels have increased through time, but not monotonically, with major and fascinating swings to both lower and higher levels.

Notes: Real-time seismology refers to a practice in which seismic data are collected and analyzed quickly after a significant seismic event, so that the results can be effectively used for postearthquake emergency response and early warning. As the technology of seismic instrumentation, telemetry, computers, and data storage facility advances, the real-time seismology for rapid postearthquake notification is essentially established. Research for early warning is still underway. Two approaches are possible: (a) regional warning and (b) on-site (or site-specific) warning. In (a), the traditional seismological method is used to locate an earthquake, determine the magnitude, and estimate the ground motion at other sites. In (b), the beginning of the ground motion (mainly P wave) observed at a site is used to predict the ensuing ground motion at the same site. An effective approach to on-site warning is discussed in light of earthquake rupture physics.

Notes: Stable cratons and stable continental platforms are salient features of the Earth. Mantle xenoliths provide detailed data on deep structure. Cratonal lithosphere is about 200 km thick. It formed in the Archean by processes analogous to modern tectonics and has been stable beneath the larger cratons since that time. Its high viscosity, high yield strength, and chemical buoyancy protected it from being entrained by underlying stagnant lid convection and by subduction. Chemically buoyant mantle does not underlie platforms. Platform lithosphere has gradually thickened with time as convection waned as the Earth's interior cooled. The thermal contraction associated with this thickening causes platforms to subside relative to cratons. At present, the thickness of platform lithosphere is comparable to that of cratonal lithosphere.

Notes: Earthquake triggering is the process by which stress changes associated with an earthquake can induce or retard seismic activity in the surrounding region or trigger other earthquakes at great distances. Calculations of static Coulomb stress changes associated with earthquake slip have proven to be a powerful tool in explaining many seismic observations, including aftershock distributions, earthquake sequences, and the quiescence of broad, normally active regions following large earthquakes. Delayed earthquake triggering, which can range from seconds to decades, can be explained by a variety of time-dependent stress transfer mechanisms, such as viscous relaxation, poroelastic rebound, or afterslip, or by reductions in fault friction, such as predicted by rate and state constitutive relations. Rapid remote triggering of earthquakes at great distances (from several fault lengths to 1000s of km) is best explained by the passage of transient (dynamic) seismic waves, which either immediately induce Coulomb-type failure or initiate a secondary mechanism that induces delayed triggering. The passage of seismic waves may also play a significant role in the triggering of near-field earthquakes.

Notes: The mathematical modeling of landform evolution consists of two components: the processes represented (i.e., considered dominant) in the model and the (typically computer) model representation of these processes. This review discusses the current debates surrounding processes represented in landform evolution. The potential impact on both evolving landforms and computer model structure is discussed. Issues specifically discussed include (a) the fundamental nature of mass conservation and the role of detachment- and transport-limited processes in mass conservation equations, (b) the interaction between detachment- and transport-limitation in channels, (c) the role of hillslope erosion and soil properties and their interaction with channel processes, (d) the interactions with tectonics when applying these models at large scale, (e) depositional structures and implications for paleo-climatic interpretation, (f) engineering applications of these models, and (g) numerical issues in the computer implementations. This review is not a model comparison. However, many applications are at the boundaries of computer capabilities so a comparison of existing models is provided.

Notes: The Earth has a radiogenic W-isotopic composition compared to chondrites, demonstrating that it formed while 182Hf (half-life 9 Myr) was extant in Earth and decaying to 182W. This implies that Earth underwent early and rapid accretion and core formation, with most of the accumulation occurring in Đ♯10 Myr, and concluding approximately 30 Myr after the origin of the Solar System. The Hf-W data for lunar samples can be reconciled with a major Moon-forming impact that terminated the terrestrial accretion process Đ♯30 Myr after the origin of the Solar System. The suggestion that the proto-Earth to impactor mass ratio was 7:3 and occurred during accretion is inconsistent with the W isotope data. The W isotope data is satisfactorily modeled with a Mars-sized impactor on proto-Earth (proto-Earth to impactor ratio of 9:1) to form the Moon at Đ♯30 Myr.

Notes: The influence of surface orography on patterns of precipitation gives rise to some of the most pronounced climate gradients on Earth, and plays a fundamental role in the interaction between the atmosphere and the rest of the Earth System on a wide variety of time scales. The physical mechanisms involved comprise a rich set of interactions encompassing fluid dynamics, thermodynamics, and micron-scale cloud processes, as well as being dependent on the larger-scale patterns of the atmospheric general circulation. Investigations into orographic precipitation have pursued three parallel tracks of inquiry: observations, theory, and modeling. Significant advances have been made in each over the last few decades, and these are summarized and synthesized here. While many aspects of the basic mechanisms responsible for orographic precipitation have been understood, important issues remain unresolved. The sheer number of contributing processes, together with their convoluted interactions, make the quantitative prediction of precipitation in complex terrain a very hard task. However, while prediction of precipitation amounts for any given event may be difficult, various lines of evidence suggest that the patterns of orgraphic precipitation, even on scales of a few kilometers, are much more robust.

Notes: Real-time seismology refers to a practice in which seismic data are collected and analyzed quickly after a significant seismic event, so that the results can be effectively used for postearthquake emergency response and early warning. As the technology of seismic instrumentation, telemetry, computers, and data storage facility advances, the real-time seismology for rapid postearthquake notification is essentially established. Research for early warning is still underway. Two approaches are possible: (a) regional warning and (b) on-site (or site-specific) warning. In (a), the traditional seismological method is used to locate an earthquake, determine the magnitude, and estimate the ground motion at other sites. In (b), the beginning of the ground motion (mainly P wave) observed at a site is used to predict the ensuing ground motion at the same site. An effective approach to on-site warning is discussed in light of earthquake rupture physics.

Notes: Stable cratons and stable continental platforms are salient features of the Earth. Mantle xenoliths provide detailed data on deep structure. Cratonal lithosphere is about 200 km thick. It formed in the Archean by processes analogous to modern tectonics and has been stable beneath the larger cratons since that time. Its high viscosity, high yield strength, and chemical buoyancy protected it from being entrained by underlying stagnant lid convection and by subduction. Chemically buoyant mantle does not underlie platforms. Platform lithosphere has gradually thickened with time as convection waned as the Earth's interior cooled. The thermal contraction associated with this thickening causes platforms to subside relative to cratons. At present, the thickness of platform lithosphere is comparable to that of cratonal lithosphere.

Notes: The Ediacara biota (575Đ??542 Ma) marks the first appearance of large, architecturally complex organisms in Earth history. Present evidence suggests that the Ediacara biota included a mixture of stem- and crown-group radial animals, stem-group bilaterian animals, "failed experiments" in animal evolution, and perhaps representatives of other eukaryotic kingdoms. These soft-bodied organisms were preserved under (or rarely within) event beds of sand or volcanic ash, and four distinct preservational styles (Flinders-, Fermeuse-, Conception-, and Nama-style) profoundly affected the types of organisms and features that could be preserved. Even the earliest Ediacaran communities (575-565 Ma) show vertical and lateral niche subdivision of the sessile, benthic, filter-feeding organisms, which is strikingly like that of Phanerozoic and modern communities. Later biological and ecological innovations include mobility (〉555 Ma), calcification (550 Ma), and predation (〈549 Ma). The Ediacara biota abruptly disappeared 542 million years ago, probably as a consequence of mass extinction andor biological interactions with the rapidly evolving animals of the Cambrian explosion.

Notes: The Earth has a radiogenic W-isotopic composition compared to chondrites, demonstrating that it formed while 182Hf (half-life 9 Myr) was extant in Earth and decaying to 182W. This implies that Earth underwent early and rapid accretion and core formation, with most of the accumulation occurring in Đ♯10 Myr, and concluding approximately Đ♯30 Myr after the origin of the Solar System. The Hf-W data for lunar samples can be reconciled with a major Moon-forming impact that terminated the terrestrial accretion process 30 Myr after the origin of the Solar System. The suggestion that the proto-Earth to impactor mass ratio was 7:3 and occurred during accretion is inconsistent with the W isotope data. The W isotope data is satisfactorily modeled with a Mars-sized impactor on proto-Earth (proto-Earth to impactor ratio of 9:1) to form the Moon at Đ♯30 Myr.

Notes: This paper reviews the Precambrian history of atmospheric oxygen, beginning with a brief discussion of the possible nature and magnitude of life before the evolution of oxygenic photosynthesis. This is followed by a summary of the various lines of evidence constraining oxygen levels through time, resulting in a suggested history of atmospheric oxygen concentrations. Also reviewed are the various processes regulating oxygen concentrations, and several models of Precambrian oxygen evolution are presented. A sparse geologic record, combined with uncertainties as to its interpretation, yields only a fragmentary and imprecise reading of atmospheric oxygen evolution. Nevertheless, oxygen levels have increased through time, but not monotonically, with major and fascinating swings to both lower and higher levels.

Notes: Weather and climate predictions are uncertain, because both forecast initial conditions and the computational representation of the known equations of motion are uncertain. Ensemble prediction systems provide the means to estimate the flow-dependent growth of uncertainty during a forecast. Sources of uncertainty must therefore be represented in such systems. In this paper, methods used to represent model uncertainty are discussed. It is argued that multimodel and related ensembles are vastly superior to corresponding single-model ensembles, but do not provide a comprehensive representation of model uncertainty. A relatively new paradigm is discussed, whereby unresolved processes are represented by computationally efficient stochastic-dynamic schemes.

Notes: Recent fossil discoveries from Early Cretaceous rocks of Liaoning Province, China, have provided a wealth of spectacular specimens. Included in these are the remains of several different kinds of small theropod dinosaurs, many of which are extremely closely related to modern birds. Unique preservation conditions allowed soft tissues of some of these specimens to be preserved. Many dinosaur specimens that preserve feathers and other types of integumentary coverings have been recovered. These fossils show a progression of integumentary types from simple fibers to feathers of modern aspect. The distribution of these features on the bodies of these animals is surprising in that some show large tail plumes, whereas others show the presence of wing-like structures on both fore and hind limbs. The phylogenetic distribution of feather types is highly congruent with models of feather evolution developed from developmental biology.

Notes: Ichthyosaurs were a group of Mesozoic marine reptiles that evolved fish-shaped body outlines. They are unique in several anatomical characters, including the possession of enormous eyeballs sometimes exceeding 25 cm and an enlarged manus with sometimes up to 20 bones in a single digit, or 10 digits per manus. They are also unique in that their biology has been studied from the perspective of physical constraints, which allowed estimation of such characteristics as optimal cruising speed, visual sensitivity, and even possible basal metabolic rate ranges. These functional inferences, although based on physical principles, obviously contain errors arising from the limitations of fossilized data, but are necessarily stronger than the commonly made inferences based on superficial correlations among quantities without mechanical or optical explanations for why such correlations exist.

Notes: We know that giant planets played a crucial role in the making of our Solar System. The discovery of giant planets orbiting other stars is a formidable opportunity to learn more about these objects, what their composition is, how various processes influence their structure and evolution, and most importantly how they form. Jupiter, Saturn, Uranus, and Neptune can be studied in detail, mostly from close spacecraft flybys. We can infer that they are all enriched in heavy elements compared to the Sun, with the relative global enrichments increasing with distance to the Sun. We can also infer that they possess dense cores of varied masses. The intercomparison of presently characterized extrasolar giant planets shows that they are also mainly made of hydrogen and helium, but that they either have significantly different amounts of heavy elements, have had different orbital evolutions, or both. Hence, many questions remain and need to be answered to make significant progress on the origins of planets. Pourquoi l'azur muet et l'espace insondable? Pourquoi les astres d'or fourmillant comme un sable? Arthur RimbaudĐ??Soleil et chair

Notes: Moving highly-charged ions carry strong electromagnetic fields that act as a beam of photons. In collisions at large impact parameters, hadronic interactions are not possible, and the ions interact through photon-ion and photon-photon collisions known as ultra-peripheral collisions (UPCs). Hadron colliders like the Relativistic Heavy Ion Collider (RHIC), the Tevatron, and the Large Hadron Collider (LHC) produce photonuclear and two-photon interactions at luminosities and energies beyond that accessible elsewhere; the LHC will reach a ??p energy ten times that of the Hadron-Electron Ring Accelerator (HERA). Reactions as diverse as the production of anti-hydrogen, photoproduction of the ??0, transmutation of lead into bismuth, and excitation of collective nuclear resonances have already been studied. At the LHC, UPCs can study many types of new physics processes.

Notes: Analyses of two-particle correlations have provided the chief means for determining spatio-temporal characteristics of relativistic heavy ion collisions. We discuss the theoretical formalism behind these studies and the experimental methods used in carrying them out. Recent results from RHIC are put into context in a systematic review of correlation measurements performed over the past two decades. The current understanding of these results is discussed in terms of model comparisons and overall trends.

Notes: We summarize the lessons learned from studies of hard scattering processes in high-energy electron-proton collisions at HERA and antiproton-proton collisions at the Tevatron, with the aim of predicting new strong interaction phenomena observable in next-generation experiments at the Large Hadron Collider (LHC). Processes reviewed include inclusive deep-inelastic scattering (DIS) at small x, exclusive and diffractive processes in DIS and hadron-hadron scattering, as well as color transparency and nuclear shadowing effects. A unified treatment of these processes is outlined on the basis of factorization theorems of quantum chromodynamics, and using the correspondence between the "parton" picture in the infinite-momentum frame and the "dipole" picture of high-energy processes in the target rest frame. The crucial role of the three dimensional quark and gluon structure of the nucleon is emphasized. A new dynamical effect predicted at high energies is the unitarity, or black disk, limit (BDL) in the interaction of small dipoles with hadronic matter, owing to the increase of the gluon density at small x. This effect is marginally visible in diffractive DIS at HERA and will lead to the complete disappearance of Bjorken scaling at higher energies. In hadron-hadron scattering at LHC energies and beyond (cosmic ray physics), the BDL will be a standard feature of the dynamics, with implications for (a) hadron production at forward and central rapidities in central proton-proton and proton-nucleus collisions, in particular events with heavy particle production (Higgs), (b) proton-proton elastic scattering, and (c) heavy-ion collisions. We also outline the possibilities for studies of diffractive processes and photon-induced reactions (ultraperipheral collisions) at LHC, as well as possible measurements with a future electron-ion collider.

Notes: We explore in some detail the hypothesis that the generation of a primordial lepton-antilepton asymmetry (Leptogenesis) early on in the history of the Universe is the root cause for the origin of matter. After explaining the theoretical conditions for producing a matter-antimatter asymmetry in the Universe we detail how, through sphaleron processes, it is possible to transmute a lepton asymmetryĐ??or, more precisely, a (B Đ?? L)-asymmetryĐ??into a baryon asymmetry. Because Leptogenesis depends in detail on properties of the neutrino spectrum, we review briefly existing experimental information on neutrinos as well as the seesaw mechanism, which offers a theoretical understanding of why neutrinos are so light. The bulk of the review is devoted to a discussion of thermal Leptogenesis, and we show that for the neutrino spectrum suggested by oscillation experiments, one obtains the observed value for the baryon to photon density ratio in the Universe, independently of any initial boundary conditions. In the latter part of the review we consider how well Leptogenesis fits with particle physics models of dark matter. Although axionic dark matter and Leptogenesis can be very naturally linked, there is a potential clash between Leptogenesis and models of supersymmetric dark matter because the high temperature needed for Leptogenesis leads to an overproduction of gravitinos, which alter the standard predictions of Big Bang Nucleosynthesis. This problem can be resolved, but it constrains the supersymmetric spectrum at low energies and the nature of the lightest supersymmetric particle (LSP). Finally, as an illustration of possible other options for the origin of matter, we discuss the possibility that Leptogenesis may occur as a result of non-thermal processes.

Notes: Time-resolved infrared (IR) and Raman spectroscopy elucidates molecular structure evolution during ultrafast chemical reactions. Following vibrational marker modes in real time provides direct insight into the structural dynamics, as is evidenced in studies on intramolecular hydrogen transfer, bimolecular proton transfer, electron transfer, hydrogen bonding during solvation dynamics, bond fission in organometallic compounds and heme proteins, cis-trans isomerization in retinal proteins, and transformations in photochromic switch pairs. Femtosecond IR spectroscopy monitors the site-specific interactions in hydrogen bonds. Conversion between excited electronic states can be followed for intramolecular electron transfer by inspection of the fingerprint IR- or Raman-active vibrations in conjunction with quantum chemical calculations. Excess internal vibrational energy, generated either by optical excitation or by internal conversion from the electronic excited state to the ground state, is observable through transient frequency shifts of IR-active vibrations and through nonequilibrium populations as deduced by Raman resonances.

Notes: We review prototype studies in the area of quantum control with femtosecond lasers. We restrict this discussion to atoms and diatomics under gas-phase collision-free conditions to allow for a comparison between theory and experiment. Both the perturbative regime and the nonperturbative regime of the light-matter interaction are addressed. To that end, atomic/molecular beam techniques are combined together with femtosecond laser techniques and energy-resolved photoelectron spectroscopy and ion detection. Highly detailed information on the laser-induced quantum dynamics is extracted with the help of kinetic energy-resolved photoelectron spectroscopy.

Notes: Transport spectroscopy, a technique based on current-voltage measurements of individual nanostructures in a three-terminal transistor geometry, has emerged as a powerful new tool to investigate the electronic properties of chemically derived nanostructures. In this review, we discuss the utility of this approach using the recent studies of single-nanotube transistors as an example. Specifically, we discuss how transport measurements can be used to gain detailed insight into the electronic motion in metallic single-walled carbon nanotubes in several distinct regimes, depending on the coupling strength of the contacts to the nanotubes. Measurements of nanotube devices in these different conductance regimes have enabled a detailed analysis of the transport properties, including the experimental determination of all Hartree-Fock parameters that govern the electronic structure of metallic nanotubes and the demonstration of Fabry-Perot resonators based on the interference of electron waves.

Notes: Significant advances in laser technology have led to an increasing interest in the time evolution of Rydberg wavepackets as a means to understanding, and ultimately controlling, quantum phenomena. Rydberg wavepackets in molecules are particularly interesting as they possess many of the dynamical complications of large molecules, such as nonadiabatic coupling between the various degrees of freedom, yet they remain tractable experimentally and theoretically. This review explains in detail how the method of interfering wavepackets can be applied to observe and control Rydberg wavepackets in molecules; it discusses the achievements to date and the possibilities for the future.

Notes: Molecular structures during chemical processes are crucial for predicting molecular reactivity and reaction mechanisms. Using a laser pulse as an internal clock for starting fundamental chemical processes, molecular structural dynamics can be characterized by coherent vibrational motions and by incoherent transitions between different intermediate states. Recent developments in pulsed X-ray facilities allow structural determination of discrete excited states and reaction intermediates using laser-initiated time-resolved X-ray absorption spectroscopy (LITR-XAS). Moreover, femtosecond X-ray sources have begun making significant contributions in monitoring coherent molecular motions. This review summarizes recent developments in the field, including technical and scientific challenges as well as several examples involving excited state molecular structure and electronic configuration determinations. Future applications of this technique with high time resolution will enable visualization of fundamental chemical events in many systems and further our understanding in photochemistry.

Notes: Orogenic collapse is a process that transfers gravitational potential energy from regions of high potential energy to regions of lower potential energy. This transfer is classically considered to be accomplished by extension in the orogenic core and by synchronous shortening in foreland regions of the orogen. Not all extensional features in collisional mountain belts need, however, reflect orogenic collapse. Normal faulting, thrust faulting, and strike-slip faulting are all active in different parts of the Alps today and reflect complex local responses to ongoing Europe-Adria convergence. The Western Alps is the only area today where extension and shortening radial to orogen trend occur synchronously and where orogenic collapse may be an important process. Elsewhere in the Alps, normal faults are oriented at a high angle to orogen trend and were primarily active in Oligocene and Miocene time. Most present-day activity in the Central and Eastern Alps is on strike-slip faults that are accommodating lateral extrusion of material rather than orogenic collapse.

Notes: The bulk of the Đ♯50-km-thick Martian crust formed at Đ♯4.5 Gyr B.P., perhaps from a magma ocean. This crust is probably a basaltic andesite or andesite and is enriched in incompatible and heat-producing elements. Later additions of denser basalt to the crust were volumetrically minor, but resurfaced significant portions of the Northern hemisphere. A significant fraction of the total thickness of the crust was magnetized prior to 4 Gyr B.P., with the magnetization later selectively removed by large impacts. Early large impacts also modified the hemispheric contrast in crustal thickness (the dichotomy), which was possibly caused by long-wavelength mantle convection. Subsequent Noachian modification of the crust included further impacts, significant fluvial erosion, and volcanism associated with the formation of the Tharsis rise. Remaining outstanding questions include the origin of the dichotomy and the nature of the magnetic anomalies.

Notes: Weather and climate predictions are uncertain, because both forecast initial conditions and the computational representation of the known equations of motion are uncertain. Ensemble prediction systems provide the means to estimate the flow-dependent growth of uncertainty during a forecast. Sources of uncertainty must therefore be represented in such systems. In this paper, methods used to represent model uncertainty are discussed. It is argued that multimodel and related ensembles are vastly superior to corresponding single-model ensembles, but do not provide a comprehensive representation of model uncertainty. A relatively new paradigm is discussed, whereby unresolved processes are represented by computationally efficient stochastic-dynamic schemes.

Notes: Dedicated to the memory of three pioneers, I??hsan Ketin, Srr Erinc?? and Melih Tokay, and a recent student, Aykut Barka, who burnt himself out in pursuit of the mysteries of the North Anatolian Fault. The North Anatolian Fault (NAF) is a 1200-km-long dextral strike-slip fault zone that formed by progressive strain localization in a generally westerly widening right-lateral keirogen in northern Turkey mostly along an interface juxtaposing subduction-accretion material to its south and older and stiffer continental basements to its north. The NAF formed approximately 13 to 11 Ma ago in the east and propagated westward. It reached the Sea of Marmara no earlier than 200 ka ago, although shear-related deformation in a broad zone there had already commenced in the late Miocene. The fault zone has a very distinct morphological expression and is seismically active. Since the seventeenth century, it has shown cyclical seismic behavior, with century-long cycles beginning in the east and progressing westward. For earlier times, the record is less clear but does indicate a lively seismicity. The twentieth century record has been successfully interpreted in terms of a Coulomb failure model, whereby every earthquake concentrates the shear stress at the western tips of the broken segments leading to westward migration of large earthquakes. The August 17 and November 12, 1999, events have loaded the Marmara segment of the fault, mapped since the 1999 earthquakes, and a major, M Đ$ 7.6 event is expected in the next half century with an approximately 50% probability on this segment. Currently, the strain in the Sea of Marmara region is highly asymmetric, with greater strain to the south of the Northern Strand. This is conditioned by the geology, and it is believed that this is generally the case for the entire North Anatolian Fault Zone. What is now needed is a more detailed geological mapping base with detailed paleontology and magnetic stratigraphy in the shear-related basins and more paleomagnetic observations to establish shear-related rotations.

Notes: Airborne geophysics has been used to identify more than 100 lakes beneath the ice sheets of Antarctica. The largest, Lake Vostok, is more than 250 km in length and 1 km deep. Subglacial lakes occur because the ice base is kept warm by geothermal heating, and generated meltwater collects in topographic hollows. For lake water to be in equilibrium with the ice sheet, its roof must slope ten times more than the ice sheet surface. This slope causes differential temperatures and melting/freezing rates across the lake ceiling, which excites water circulation. The exploration of subglacial lakes has two goals: to find and understand the life that may inhabit these unique environments and to measure the climate records that occur in sediments on lake floors. The technological developments required for in situ measurements mean, however, that direct studies of subglacial lakes may take several years to happen.

Notes: Microbes are recognized as important components of the Earth system, playing key roles in controlling the composition of the atmosphere and surface waters, forming the basis of the marine food web, and the cycling of chemicals in the ocean. A revolution in microbial ecology has occurred in the past 15Đ??20 years with the advent of rapid methods for discovering and sequencing the genes of uncultivated microbes from natural environments. Initially based on sequences from the 16S rRNA gene, this revolution made it possible to identify microorganisms without first cultivating them, to discover and characterize the immense previously unsuspected diversity of the microbial world, and to reconstruct the evolutionary relationships among microbes. Subsequent focus on functional genes, those that encode enzymes that catalyze biogeochemical transformations, and current work on larger DNA fragments and entire genomes make it possible to link microbial diversity to ecosystem function. These approaches have yielded insights into the regulation of microbial activity and proof of the microbial role in biogeochemical processes previously unknown. Questions raised by the molecular revolution, which are now the focus of microbial ecology research, include the significance of microbial diversity and redundancy to biogeochemical processes and ecosystem function.

Notes: Recent developments in volcanic seismology include new techniques to improve earthquake locations that have changed clouds of earthquakes to lines (faults) for high-frequency events and small volumes for low-frequency (LF) events. Spatial mapping of the b-value shows regions of normal b and high b anomalies at depths of 3Đ??4 and 7Đ??10 km. Increases in b precede some eruptions. LF events and very-long-period (VLP) events have been recorded at many volcanoes, and models are becoming increasingly sophisticated. Deep long-period (LP) events are fairly common, but may represent several processes. Acoustic sensors have greatly improved the study of volcanic explosions. Volcanic tremor is stronger for fissure eruptions, phreatic eruptions, and higher gas contents. Path and site effects can be extreme at volcanoes. Seismicity at volcanoes is triggered by large earthquakes, although mechanisms are still uncertain. A number of volcanoes have significant deformation with very little seismicity. Tomography has benefited from improved techniques and better instrumental arrays.

Notes: Various forms of atmospheric moist convection are reviewed through a consideration of three prevalent regimes: stratocumulus; trade-wind; and deep, precipitating, maritime convection. These regimes are chosen because they are structural components of the general circulation of the atmosphere and because they highlight distinguishing features of this polymorphous phenomenon. In particular, the ways in which varied forms of moist convection communicate with remote parts of the flow through mechanisms other than the rearrangement of fluid parcels are emphasized. These include radiative, gravity wave, and/or microphysical (precipitation) processes. For each regime, basic aspects of its phenomenology are presented along with theoretical frameworks that have arisen to help rationalize the phenomenology. Recent developments suggest that the increased capacity for numerical simulation and increasingly refined remote sensing capabilities bodes well for major advances in the coming years.

Notes: We provide a pedagogical introduction to a recently studied class of phenomenologically interesting string models known as Intersecting D-Brane Models. The gauge fields of the Standard Model are localized on D-branes wrapping certain compact cycles on an underlying geometry, whose intersections can give rise to chiral fermions. We address the basic issues and also provide an overview of the recent activity in this field. This article is intended to serve non-experts with explanations of the fundamental aspects of string phenomenology and also to provide some orientation for both experts and non-experts in this active field.

Notes: The North Anatolian Fault (NAF) is a 1200-km-long dextral strike-slip fault zone that formed by progressive strain localization in a generally westerly widening right-lateral keirogen in northern Turkey mostly along an interface juxtaposing subduction-accretion material to its south and older and stiffer continental basements to its north. The NAF formed approximately 13 to 11 Ma ago in the east and propagated westward. It reached the Sea of Marmara no earlier than 200 ka ago, although shear-related deformation in a broad zone there had already commenced in the late Miocene. The fault zone has a very distinct morphological expression and is seismically active. Since the seventeenth century, it has shown cyclical seismic behavior, with century-long cycles beginning in the east and progressing westward. For earlier times, the record is less clear but does indicate a lively seismicity. The twentieth century record has been successfully interpreted in terms of a Coulomb failure model, whereby every earthquake concentrates the shear stress at the western tips of the broken segments leading to westward migration of large earthquakes. The August 17 and November 12, 1999, events have loaded the Marmara segment of the fault, mapped since the 1999 earthquakes, and a major, MĐ$7.6 event is expected in the next half century with an approximately 50% probability on this segment. Currently, the strain in the Sea of Marmara region is highly asymmetric, with greater strain to the south of the Northern Strand. This is conditioned by the geology, and it is believed that this is generally the case for the entire North Anatolian Fault Zone. What is now needed is a more detailed geological mapping base with detailed paleontology and magnetic stratigraphy in the shear-related basins and more paleomagnetic observations to establish shear-related rotations.

Notes: Airborne geophysics has been used to identify more than 100 lakes beneath the ice sheets of Antarctica. The largest, Lake Vostok, is more than 250 km in length and 1 km deep. Subglacial lakes occur because the ice base is kept warm by geothermal heating, and generated meltwater collects in topographic hollows. For lake water to be in equilibrium with the ice sheet, its roof must slope ten times more than the ice sheet surface. This slope causes differential temperatures and melting/freezing rates across the lake ceiling, which excites water circulation. The exploration of subglacial lakes has two goals: to find and understand the life that may inhabit these unique environments and to measure the climate records that occur in sediments on lake floors. The technological developments required for in situ measurements mean, however, that direct studies of subglacial lakes may take several years to happen.