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  • Elsevier  (208,070)
  • American Physical Society  (34,711)
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  • 1
    Publication Date: 2017-04-04
    Description: We describe a numerical simulation of both concentrated and dilute gravity-driven pyroclastic flows on a digital topographic model of the Campi Flegrei volcanic field. Families of numerical flows are generated by sampling a multi-dimensional matrix of vent coordinates, flow properties and dynamical parameters within a wide range of values. Hazard maps are constructed from the data base of simulated flows, using a mixed deterministic^statistical approach. The set of probable vents covers the area of recent eruptions. Results show the key role of topography in controlling the flow dispersion. The maximum hazard appears to be the NE sector of the caldera. Flows in the eastern sector, including the city of Naples, are shown to be efficiently hindered by the Posillipo and Camaldoli hills at the caldera borders, thus reducing the hazard. The results represent the first physically based estimate of hazard from pyroclastic flows in this densely populated area, and can be used for civil defence purposes.
    Description: Published
    Description: 1-14
    Description: partially_open
    Keywords: Campi flegrei ; calderas ; pyroclastic flows ; hazard maps ; 05. General::05.01. Computational geophysics::05.01.04. Statistical analysis ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions ; 04. Solid Earth::04.08. Volcanology::04.08.08. Volcanic risk
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  • 2
    Publication Date: 2017-04-04
    Description: Hydrothermal fluids and sediments from subaerial and shallow submarine sites at Vulcano Island, Italy were investigated for relations between the thermophilic microbial communities, as analysed by fluorescence in situ hybridization, and their geochemical environment, as assessed by photometry, chromatography, and in situ microsensor measurements. Mixing between hydrothermal fluids and seawater in the sediment pore space was reflected in the chemical composition of the emitted fluids, in depth profiles of pore water oxygen and sulfide concentrations, and in the structure of the benthic microbial community. Organic compounds did not accumulate in the vent fluids (b10 AM fatty acids) or in the sediments (b0.1% Corg), suggesting that efficient utilization supported microbial populations on the order of 104 cells per ml fluid and 108 cells per cm3 sediment. Groups of thermophiles that typically gain metabolic energy from the fermentation of organic matter (Thermococcales, Thermotoga/Thermosipho spp., and Bacillus sp.)were detected in significant abundances at all study sites. Also abundant were thermophiles capable of oxidizing organic acids with oxygen, nitrate, or sulfate. Aerobic thermophiles (Aquificales and Thermus sp.) were more abundant at oxic sites than at anoxic sites. Increasingly oxygenated habitats were associated with decreasing abundance of anaerobic (hyper)thermophiles belonging to the order Archaeoglobales.
    Description: Published
    Description: 169– 182
    Description: partially_open
    Keywords: Biogeochemistry ; Hydrothermal system ; Marine sediment ; Microbial ecology ; Microsensor ; Thermophiles ; 03. Hydrosphere::03.04. Chemical and biological::03.04.04. Ecosystems ; 03. Hydrosphere::03.04. Chemical and biological::03.04.06. Hydrothermal systems
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  • 3
    Publication Date: 2017-04-04
    Description: We present regional centroid-moment tensor (RCMT) solutions for 168 moderate-magnitude earthquakes that occurred in the European-Mediterranean region during 2001 and 2002. Events with moment magnitudes as low as 4.0 were successfully analyzed, although this low threshold is only achievable in regions with the best azimuthal coverage and with stations at a few hundred kilometers distance. Earthquakes with focal depths from 10 to more than 200 km were analyzed. Comparison with standard Harvard CMTs, when available, shows good agreement. The solutions shown in this paper represent an addition to the European-Mediterranean RCMT catalog that we are maintaining. The RCMT catalog now spans 6 years, from 1997 to 2002, and contains 420 solutions. We also outline the main seismic sequences that occurred in the European-Mediterranean region during 2001–2002.
    Description: MedNet Data Centre ORFEUS-MEREDIAN GEOFON IRIS
    Description: Published
    Description: 127-147
    Description: reserved
    Keywords: Seismicity ; Seismic moment tensors ; European-Mediterranean region ; 05. General::05.02. Data dissemination::05.02.02. Seismological data
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  • 4
    Publication Date: 2017-04-04
    Description: In this paper we describe evidence of strong tectonic deformation affecting two aqueducts of Roman age (II–III century A.D.). The channels are located approximately 20 km northeast of Rome along the ancient Via Tiburtina. Brittle and ductile deformation affects these two structures, including extensional joint systems, NE-oriented faults, and horizontal distortion. This deformation is consistent with rightlateral movement on major N-striking faults, and represents the first evidence that tectonic deformation took place in historical times in the vicinity of Rome, with local strike–slip movement superimposed on a regional extensional fault system.
    Description: Published
    Description: 679–690
    Description: reserved
    Keywords: Strike–slip tectonics ; Active tectonics ; Geo-archaeology ; Rome ; Italy ; 04. Solid Earth::04.07. Tectonophysics::04.07.07. Tectonics
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 5
    Publication Date: 2017-04-04
    Description: A Conjugated Toop-Samis-Flood-Grjotheim (CTSFG) model is developed by combining the framework of the Toop-Samis polymeric approach with the Flood-Grjotheim theoretical treatment of silicate melts and slags. Electrically equivalent ion fractions are computed over the appropriate matrixes (anionic and cationic) in a Temkin notation for fused salts, and are used to weigh the contribution of the various disproportionation reactions of type: M2/pO(melt)+ 1/2S(gas)+M2/pS(melt)+1/2O2(gas) M2/po(melt)+1/2S2(gas)+3/2O2(gas)-M2/pSO4(melt)v being the charge of the generic Mp-1 cation. The extension of the anionic matrix is calculated in the framework of a previously developed polymeric model (Ottonello et al., 2001), based on a parameterization of Lux-Flood acid-base properties of melt components. Model activities follow the Raoultian behavior implicit in the Temkin notation, without the needs of introducing adjustable parameters. The CTSFG model is based on a large amount of data available in literature and exhibits a satisfactory heuristic capability, with virtually no compositional limits, as long as the structural role given to each oxide holds. The model may be employed to compute gas-melt equilibria involving sulfur and allows computing sulfide and sulfate contents of silicate melts whenever the fugacity of a gaseous sulfur species and oxygen are known. Alternatively, the model calculates the oxidation state of the system (i.e., oxygen fugacity), whenever an analytical determination of either sulfide/sulfate or ferrous/ferric ratios in the melt is provided. Calculated sulfide and sulfate capacities allow the estimates of sulfur abundance in various melts of geological interest, both under anhydrous and hydrous conditions or, alternatively, of fS2, given fO2 and the bulk sulfur content. In this case, fSO2 and fH2S may be eventually computed along the water-sulfur-melt boundary provided fH2O is known.
    Description: Published
    Description: 801-823
    Description: partially_open
    Keywords: sulfur ; silicate melts ; 04. Solid Earth::04.04. Geology::04.04.05. Mineralogy and petrology ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.03. Magmas ; 04. Solid Earth::04.08. Volcanology::04.08.04. Thermodynamics
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  • 6
    Publication Date: 2017-04-04
    Description: The aim of this paper is to describe the theoretical fundamentals, the main features and some geophysical applications of a software (STRAINGPS) suitably implemented to estimate the strain tensor from repeated GPS surveys of deformation control networks. Current softwares developed for geophysical applications generally estimate or compute bi-dimensional strain, since this is the most requested use. On the contrary, this software allows for a three-dimensional (3D) estimate of the strain tensor and does not need a subdivision of the network in triangles. It accounts for all the significant coordinate differences (or velocities) coming from repeated surveys and estimates the strain tensor components by the least squares method, starting from the hypothesis of one homogeneous strain field. Moreover, some tests to control both model adequacy and detecting outliers are performed, allowing a subdivision of the field into sub-domains with homogeneous strain field. We applied this software to three real geophysical situations. The first concerns the geodynamic (long term) induced deformation at regional scale, by estimating extensional strain rate ((0.22 ± 0.06) × 10−7) per year in central-southern Italy across the Apennines chain; the second is co-seismic strain by the assessment of the strike slip style of the Molise (central-southern Italy) earthquakes (31 October and 1 November 2002); the last regards the subsidence induced strain in the Travale-Radicondoli (central Italy) exploitation area. © 2004 Elsevier Ltd. All rights reserved.
    Description: Published
    Description: 1-18
    Description: reserved
    Keywords: GPS observations ; 04. Solid Earth::04.02. Exploration geophysics::04.02.05. Downhole, radioactivity, remote sensing, and other methods
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  • 7
    Publication Date: 2017-04-04
    Description: The deep structures of the Central–Southern Apennines are analysed on the basis of the regional component of gravity anomalies, obtained applying a stripping technique. This procedure allows the accurate removal of the gravimetric effect of the three-dimensional shallow (within the first 10 km) geological bodies from the observed Bouguer anomaly. The resulting anomaly map differs quite significantly from the Bouguer anomaly map, providing new constraints on the nature of the deeper part of the crust and on the upper mantle. The stripping reveals that the regional gravity lows are shifted westward in comparison with Bouguer anomaly lows. Moreover, the gravimetric pattern indicates a lack of cylindrism for the deep structures of the Apennine Chain, which in the study area can be roughly divided into three main segments. The observed differences between the gravity anomalies pattern of the Central Apennines and that of the Southern Apennines are marked. The integration of gravimetric results with other geophysical data suggests that: (i) a ramp-dominated style for the buried Apulia (Adria) units and part of the underlying basement is compatible with gravimetric data and (ii) most of the regional gravity anomalies in the Central Apennines seem to originate within the lower crust.
    Description: Published
    Description: 73-91
    Description: open
    Keywords: Bouguer anomalies ; Rock density ; Stripping technique ; Deep crust ; Southern Italy ; 04. Solid Earth::04.02. Exploration geophysics::04.02.02. Gravity methods
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  • 8
    Publication Date: 2017-04-04
    Description: We argue that the recent discovery of the non-Poissonian statistics of the seismic main-shocks is a special case of a more general approach to the detection of the distribution of the time increments between one crucial but invisible event and the next. We make the conjecture that the proposed approach can be applied to the analysis of terrorist network with significant benefits for the Intelligence Community.
    Description: Published
    Description: 77-85
    Description: partially_open
    Keywords: crucial events ; against terrorism ; 05. General::05.01. Computational geophysics::05.01.02. Cellular automata, fuzzy logic, genetic alghoritms, neural networks ; 05. General::05.01. Computational geophysics::05.01.04. Statistical analysis
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  • 9
    Publication Date: 2017-04-04
    Description: On October 31, 2002 a ML=5.4 earthquake occurred in southern Italy, at the margin between the Apenninic thrust belt (to the west) and the Adriatic plate (to the east). In this area, neither historical event nor seismogenic fault is reported in the literature. In spite of its moderate magnitude, the earthquake caused severe damage in cities close to the epicenter and 27 people, out of a total of 29 casualties, were killed by the collapse of a primary school in S. Giuliano di Puglia. By inverting broadband regional waveforms, we computed moment tensor solutions for 15 events, as small as ML=3.5 (Mw=3.7). The obtained focal mechanisms show pure strike-slip geometry, mainly with focal planes oriented to NS (sinistral) and EW (dextral). In several solutions focal planes are rotated counterclockwise, in particular for later events, occurring west of the mainshock. From the relocated aftershock distribution, we found that the mainshock ruptured along an EW plane, and the fault mechanisms of some aftershocks were not consistent with the mainshock fault plane. The observed stress field, resulting from the stress tensor inversion, shows a maximum principal stress axis with an east–west trend (N83°W), whereas the minimum stress direction is almost N–S. Considering both the aftershock distribution and moment tensor solutions, it appears that several pre-existing faults were activated rather than a single planar fault associated with the mainshock. The finite fault analysis shows a very simple slip distribution with a slow rupture velocity of 1.1 km/s, that could explain the occurrence of a second mainshock about 30 h after. Finally, we attempt to interpret how the Molise sequence is related to the normal faulting system to the west (along the Apennines) and the dextral strike-slip Mattinata fault to the east.
    Description: Published
    Description: 141-154
    Description: reserved
    Keywords: waveform modeling ; source parameters ; stress field ; southern Apennines ; 04. Solid Earth::04.06. Seismology::04.06.99. General or miscellaneous
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  • 10
    Publication Date: 2017-04-04
    Description: Despite its impact in understanding oceanic crust formation and eruptive styles of related volcanism, magma dynamics at midocean ridges are poorly known. Here, we propose a new method to assess ascent rates of mid-ocean ridge basalt (MORB) magmas,as well as their pre- and sin-eruptive dynamics. It is based on the idea that a rising magma can reach a variable degree of both CO2 supersaturation in melt and kinetic fractionation among noble gases in vesicles in relation to its ascent rate through the crust. To quantify the relationship, we have used a model of multicomponent bubble growth in MORB melts, developed by extending the single-component model of Proussevitch and Sahagian [A.A. Proussevitch, D.L. Sahagian, Dynamics and energetics of bubble growth in magmas: analytical formulation and numerical modeling, J. Geophys. Res. 103 (1998), 18223–18251.] to CO2–He–Ar gas mixtures. After proper parameterization, we have applied it to published suites of data having the required features (glasses from Pito Seamount and mid-Atlantic ridges). Our results highlight that the investigated MORB magmas display very different ranges of ascent rates: slow rises of popping rock forming-magmas that cross the crust (0.01–0.5 m/s), slightly faster rates of energetic effusions (0.1–1 m/s), up to rates of 1–10 m/s which fall on the edge between lava effusion and Hawaiian activity. Inside a single plumbing system, very dissimilar magma dynamics highlight the large differences in compressive stress of the oceanic crust on a small scale. Constraints on how the systems of ridges work, as well as the characteristics of the magmatic source, can also be obtained. Our model shows how measurements of both the dissolved gas concentration in melt and the volatile composition of vesicles in the same sample are crucial in recognizing the kinetic effects and definitively assessing magma dynamics. An effort should be made to correctly set the studied samples in the sequence of volcanic submarine deposits where they are collected. Enhanced knowledge of a number of physical properties of gas-bearing MOR magmas is also required, mainly noble gas diffusivities, to describe multicomponent bubble growth at a higher confidence level.
    Description: Published
    Description: 138-158
    Description: partially_open
    Keywords: Bubble growth ; MORB ; Noble gas ; Kinetic fractionation ; Modeling ; 04. Solid Earth::04.04. Geology::04.04.07. Rock geochemistry ; 04. Solid Earth::04.04. Geology::04.04.12. Fluid Geochemistry ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.03. Magmas ; 04. Solid Earth::04.08. Volcanology::04.08.04. Thermodynamics
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  • 11
    Publication Date: 2017-04-04
    Description: The cataclysmic 18 May 1980 eruption at Mount St. Helens was preceded by intense seismic activity marking the mechanical response of the volcanic edifice to interior pressurisation. This seismicity is analysed to yield the temporal change in the seismic scaling exponent, D, inferred from the seismic b-value, that in-turn is related to the seismic moment of an earthquake. Time evolution of D preceding the eruption onset reveals: (1) a major decrease in D occurring over only a few days at the end of March; (2) a steady but stepped decrease in D (steps ~5–10 days) occurring from the end of March to early May; (3) a sharp decrease in D in early May; and (4) steady low values of D occurring 2–3 days before the eruption onset. This response is interpreted as major ruptures, formed at the end of March, arresting and participating in, but not triggering the ultimate failure of the flank. Rather, the rate of interior fracturing slowed in the 2 months preceding the 18 May 1980 major blast, and the triggering of failure is consistent with interior gas overpressurisation. The occurrence of two swarms of low frequency seismic events and the high values of the harmonic tremor indicate the action of interior pressurisation on a cycle of 20–25 days. Solutions are applied to represent the harmonic interior pressurisation of the edifice by gas exsolving from the volcano core. The transient radial migration of overpressured gas may reduce the apparent strength of the edifice, and ultimately trigger failure of the flank. Importantly, this mechanism is capable of triggering flank failure both after multiple core pressurisation cycles have been sustained, and as core pressures are low and diminishing—and may be a minimum. These twin attributes are both apparent in the seismic record for Mount St. Helens, used as a proxy for the unrecorded timing and magnitude of gas pressurisation at the volcano core.
    Description: Published
    Description: 155-168
    Description: partially_open
    Keywords: seismicity ; scaling exponents ; haronic inflation ; pressurisation mechanics ; 04. Solid Earth::04.01. Earth Interior::04.01.04. Mineral physics and properties of rocks ; 04. Solid Earth::04.08. Volcanology::04.08.02. Experimental volcanism ; 04. Solid Earth::04.08. Volcanology::04.08.05. Volcanic rocks
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  • 12
    Publication Date: 2017-04-04
    Description: Thermally anomalous fluids released in seismic areas in Slovenia were the subjects of geochemical monitoring. Thermal waters were surveyed from the seismically active area of Poso$cje (Bled and Zatolmin; NW Slovenia) and from Rogaska Slatina in eastern Slovenia. Continuous monitoring of geochemical parameters (radon concentration, electrical conductivity, and water temperature) was performed with discrete gas sampling for their 3He/4He ratio. The observed values were correlated with meteorological parameters (rainfall, barometric pressure and air temperature) and with seismic activity. Only a few earthquakes occurred in the vicinity of the measuring sites during the monitoring period. Nevertheless, changes in radon concentration, water temperature, electrical conductivity and helium isotopic ratio were detected at the three thermal springs in the periods preceding the earthquakes. A close correlation was also observed of both water temperature and electrical conductivity with the Earth tide, making the observations in the selected sites a promising tool for addressing the widely debated question of earthquake prediction.
    Description: Ministry of Education,Science and Sport of Slovenia
    Description: Published
    Description: 919–930
    Description: partially_open
    Keywords: Seismicity ; Thermal waters ; Geochemistry ; 03. Hydrosphere::03.02. Hydrology::03.02.02. Hydrological processes: interaction, transport, dynamics ; 03. Hydrosphere::03.02. Hydrology::03.02.03. Groundwater processes ; 03. Hydrosphere::03.02. Hydrology::03.02.04. Measurements and monitoring
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  • 13
    Publication Date: 2017-04-04
    Description: Thermal springs with a maximum measured temperature of 89°C discharge hot water and gas from a depth of 11 m, 400 m offshore of Punta Pantoque, located in the northern part of Bahìa de Banderas, near Puerto Vallarta, Mexico. The composition of all water samples collected from the sea bottom is close to that of sea water. Nevertheless, it was possible to estimate the thermal endmember composition by extrapolating the sulfate concentration to zero. This endmember is similar in chemical composition both to waters of the Rio Purificacion and La Tuna thermal springs, located to the South along the Pacific coast of the Jalisco Block, and to pore waters from the deep-sea drilling cores from some accretionary complexes. Gas composition as well as isotopic composition of He and carbon from CO2, CH4 and C2H6 suggests an essentially thermo-biogenic origin for the gas and the presence of a high proportion of radiogenic, crustal helium. Isotopic composition of He in the Punta de Mita gas (0.4 Ra) is the lowest ever measured in Mexican hydrothermal gases. These findings do not support the idea that there exists a direct connection between the Punta de Mita springs and the last volcanic events which occurred in this area at V3 Ma. Rather, this hydrothermal activity is related to deep active faulting and the existence of a deep regional aquifer or local aquifers of connate waters underlying the granites of the Jalisco Block.
    Description: Published
    Description: 329-338
    Description: partially_open
    Keywords: submarine springs ; hydrothermal systems ; geothermometry ; He-isotopes ; formation waters ; Jalisco Block ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
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  • 14
    Publication Date: 2017-04-04
    Description: Normal faults within orogenic belts can be pre-, syn- or post-orogenic features. We studied the Gubbio normal fault (central Italy), which is an example of a pre-orogenic fault reactivated in a post-orogenic stage. The Gubbio Fault is a 22-km-long fault bordering a Quaternary basin and part of an active faults system in the Umbria–Marche region (Central Italy). The interpretation of a set of seismic profiles enables us to reconstruct the fault geometry in detail and to measure displacement and throw distributions along the fault strike. Seismic data indicate that the Gubbio Fault represents an example of multiple reactivation: at least a portion of the fault was active in the Miocene and only a part of the total displacement was achieved in the Quaternary. The reconstruction of the fault geometry at depth shows that the fault is characterised by listric geometry. The fault is also characterised by a bend along strike and structure contours show that this geometry is maintained at depth. As the fault is commonly addressed as presently active, the maximum fault dimensions are correlated to the maximum expected earthquake, and the presence of the fault bend is discussed as a possible barrier to seismic ruptures propagation.
    Description: Published
    Description: (2233–2249)
    Description: reserved
    Keywords: Listric normal faults ; Fault reactivation ; Seismic profiles ; Displacement distribution ; Earthquakes ; 04. Solid Earth::04.06. Seismology::04.06.01. Earthquake faults: properties and evolution
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  • 15
    Publication Date: 2017-04-04
    Description: The Phlegraean Fields caldera is an active volcanic system where episodes of ground deformation are accompanied by significant changes in geochemical and geophysical parameters monitored at the surface. These changes derive from a complex interaction between magmatic system and hydrothermal fluid circulation. We calculate the gravity changes associated with the variable density of hydrothermal fluids. We simulate the multi-phase and multi-component fluid circulation triggered by a pulsating magma degassing, periodically increasing the discharge of CO2-enriched fluids into the shallow hydrothermal system. The simulated evolution of the hydrothermal system successfully reproduces the observed composition of gas discharged at the surface. At the same time, results indicate that changes in average fluid density generate a detectable gravity signal that is of the same order of magnitude of the observed changes. This contribution to gravity changes can explain the peculiar behavior of gravity data collected at Solfatara, where surface hydrothermal phenomena are present. Simultaneous fitting of two independent sets of monitoring data (gas composition and gravity changes) confirms the conceptual model proposed for the hydrothermal system at Solfatara, and it provides new insights for the interpretation of gravity data.
    Description: Published
    Description: 328–338
    Description: partially_open
    Keywords: Phlegraean Fields ; Models ; Gas composition ; Gravity ; Hydrothermal circulation ; Monitoring ; 04. Solid Earth::04.03. Geodesy::04.03.05. Gravity variations ; 04. Solid Earth::04.03. Geodesy::04.03.06. Measurements and monitoring ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
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  • 16
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    Elsevier
    In:  Taran Y. A., Inguaggiato S., Marin M., and Yurova L. M. (2002) Geochemistry of fluids from submarine hot springs at Punta de Mita, Nayarit, Mexico. J. Volcanol. Geoth. Res. 115, 329-338.
    Publication Date: 2017-04-04
    Description: We thank R.M. Prol-Ledesma for her comment on the paper by Taran et al. (2002a) and the new data presented on the water composition of the Punta de Mita (PM) submarine springs. Prol-Ledesma (2003) comments refer to a supposedly wrong citation, superficial description of the geological background, incorrect method of water sampling, wrong approach for the estimation of the end-member composition, irrelevant discussion on the origin of fluids and, lastly, the using of someone else’s ideas and conclusions. In addition, she claims that our data on the fluid chemistry of the springs are not the first (original)ones. The Comment is supported by numerous references to publications by Prol-Ledesma et al. The text below follows the rubrics in the Comment.
    Description: Published
    Description: 319-322
    Description: partially_open
    Keywords: submarine springs ; hydrothermal systems ; geothermometry ; He-isotopes ; formation waters ; Jalisco Block ; 04. Solid Earth::04.04. Geology::04.04.12. Fluid Geochemistry ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
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  • 17
    Publication Date: 2020-01-08
    Description: Despite recent advances by means of experiments and high-resolution surveys and the growing understanding of the physical processes before and during volcanic eruptions, duration and type of eruptive activity still remain highly unpredictable. This uncertainty hinders appropriate hazard and associated risk assessment tremendously. In an effort to counter this problem, experimentally generated pyroclasts have been studied by fractal statistics with the aim of evaluating possible relationships between eruption energy and fragmentation efficiency. Rapid decompression experiments have been performed on three differently porous sample sets of the 1990–1995 eruption of Unzen volcano (Japan) at 850 °C and at initial pressure values above the respective fragmentation threshold [U. Kueppers, B. Scheu, O. Spieler, D. B. Dingwell, Fragmentation efficiency of explosive volcanic eruptions: a study of experimentally generated pyroclasts. J. Volcanol. Geotherm. Res. 153 (2006) 125–135.,O. Spieler, B. Kennedy, U. Kueppers, D.B. Dingwell, B. Scheu, J. Taddeucci, The fragmentation threshold of pyroclastic rocks. EPSL 226 (2004) 139–148.]. The size distribution of generated pyroclasts has been studied by fractal fragmentation theory and the fractal dimension of fragmentation (Df), a value quantifying the intensity of fragmentation, has been measured for each sample. Results showthat size distribution of pyroclastic fragments follows a fractal law(i.e. power-law) in the investigated range of fragment sizes, indicating that fragmentation of experimental samples reflects a scale-invariant mechanism. In addition, Df is correlated positively with the potential energy for fragmentation (PEF) while showing a strong influence of the open porosity of the samples. Results obtained in this work indicate that fractal fragmentation theory may allow for quantifying fragmentation processes during explosive volcanic eruptions by calculating the fractal dimension of the size distribution of pyroclasts. It emerges fromthis study that fractal dimension may be utilised as a proxy for estimating the explosivity of volcanic eruptions by analysing their natural pyroclastic deposits.
    Description: Published
    Description: 800-807
    Description: open
    Keywords: volcanic fragmentation ; simulation of eruptions ; explosive energy ; pyroclasts ; fragment size distribution ; fractal fragmentation theory ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 18
    Publication Date: 2020-01-08
    Description: Products of magma fragmentation can pose a severe threat to health, infrastructure, environment, and aviation. Systematic evaluation of the mechanisms and the consequences of volcanic fragmentation is very difficult as the adjacent processes cannot be observed directly and their deposits undergo transport-related sorting. However, enhanced knowledge is required for hazard assessment and risk mitigation. Laboratory experiments on natural samples allow the precise characterization of the generated pyroclasts and open the possibility for substantial advances in the quantification of fragmentation processes. They hold the promise of precise characterization and quantification of fragmentation efficiency and its dependence on changing material properties and the physical conditions at fragmentation. We performed a series of rapid decompression experiments on three sets of natural samples from Unzen volcano, Japan. The analysis comprised grain-size analysis and surface area measurements. The grain-size analysis is performed by dry sieving for particles larger than 250 Am and wet laser refraction for smaller particles. For all three sets of samples, the grain-size of the most abundant fraction decreases and the weight fraction of newly generated ash particles (up to 40 wt.%) increases with experimental pressure/potential energy for fragmentation. This energy can be estimated from the volume of the gas fraction and the applied pressure. The surface area was determined through Argon adsorption. The fragmentation efficiency is described by the degree of fineparticle generation. Results show that the fragmentation efficiency and the generated surface correlate positively with the applied energy.
    Description: Published
    Description: 125-135
    Description: partially_open
    Keywords: experimental volcanology ; fragmentation efficiency ; particle analysis ; ash ; magma ; porosity ; Unzen volcano ; 04. Solid Earth::04.08. Volcanology::04.08.02. Experimental volcanism
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    Publication Date: 2020-01-08
    Description: For an improvement in the quality of conduit flow and dome-related explosive eruption models, knowledge of the preeruption or precollapse density of the rocks involved is necessary. As close investigation is impossible during eruption, the best substitute comes from quantitative investigation of the eruption deposits. The porosity of volcanic rocks is of primary importance for the eruptive behaviour and, accordingly, a key-parameter for realistic models of dome stability and conduit flow. Fortunately, this physical property may be accurately determined via density measurements. We developed a robust, battery-powered device for rapid and reliable density measurements of dry rock samples in the field. The density of the samples (sealed in plastic bags at 250 mbar) is determined using the Archimedean principle. We have tested the device on the deposits of the 1990–1995 eruption of Unzen volcano, Japan. Short setup and operation times allow up to 60 measurements per day under fieldwork conditions. The rapid accumulation of correspondingly large data sets has allowed us to acquire the first statistically significant data set of clast density distribution in block-and-ash flow deposits. More than 1100 samples with a total weight of 2.2 tons were measured. The data set demonstrates that the deposits of the last eruptive episode at Unzen display a bimodal density distribution, with peaks at 2.0F0.1 and 2.3F0.1 g/cm3, corresponding to open porosity values of 20 and 8 vol.%, respectively. We use this data set to link the results of laboratory-based fragmentation experiments to field studies at recently active lava domes.
    Description: Published
    Description: 65-75
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    Keywords: field-based density measurements ; dome ; Unzen volcano ; explosive eruption ; block-and-ash flow ; fragmentation behaviour ; volcanology ; 04. Solid Earth::04.08. Volcanology::04.08.07. Instruments and techniques
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    Publication Date: 2020-01-08
    Description: In response to rapid decompression, porous magma may fragment explosively. This occurs when the melt can no longer withstand forces exerted upon it due to the overpressure in included bubbles. This occurs at a critical pressure difference between the bubbles and the surrounding magma. In this study we have investigated this pressure threshold necessary for the fragmentation of magma. Here we present the first comprehensive, high temperature experimental quantification of the fragmentation threshold of volcanic rocks varying widely in porosity, permeability, crystallinity, and chemical composition. We exposed samples to increasing pressure differentials in a high temperature shock tube apparatus until fragmentation was initiated. Experimentally, we define the fragmentation threshold as the minimum pressure differential that leads to complete fragmentation of the pressurized porous rock sample. Our results show that the fragmentation threshold is strongly dependent on porosity; high porosity samples fragment at lower pressure differentials than low porosity samples. The fragmentation threshold is inversely proportional to the porosity. Of the other factors, permeability likely affects the fragmentation threshold at high porosity values, whereas chemical composition, crystallinity and bubble size distribution appear to have minor effects. The relationship for fragmentation threshold presented here can be used to predict the minimum pressure differential necessary for the initiation or cessation of the explosive fragmentation of porous magma.
    Description: Published
    Description: 139-148
    Description: partially_open
    Keywords: fragmentation ; threshold ; experimental ; volcanology ; magma ; eruption ; porosity ; decompression ; 04. Solid Earth::04.08. Volcanology::04.08.02. Experimental volcanism
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  • 21
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    Publication Date: 2022-05-25
    Description: Author Posting. © Annual Reviews, 2006. This article is posted here by permission of Annual Reviews for personal use, not for redistribution. The definitive version was published in Annual Review of Fluid Mechanics 38 (2006): 395-425, doi:10.1146/annurev.fluid.38.050304.092129.
    Description: 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.
    Description: KRH acknowledges support from NSF and ONR and an Independent Study Award from the Woods Hole Oceanographic Institution. WKM acknowledges support from NSF and ONR, which has made his work in this area possible, in close collaboration with former graduate students at Scripps Institution of Oceanography and MIT.
    Keywords: Solitary waves ; Nonlinear waves ; Stratified flow ; Physical Oceanography
    Repository Name: Woods Hole Open Access Server
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    Publication Date: 2022-05-25
    Description: Author Posting. © The Authors, 2006. This article is posted here by permission of American Physical Society for personal use, not for redistribution. The definitive version was published in Physical Review Letters 96 (2006): 018305, doi:10.1103/PhysRevLett.96.018305.
    Description: We study the liquid-crystalline phase behavior of a concentrated suspension of helical flagella isolated from Salmonella typhimurium. Flagella are prepared with different polymorphic states, some of which have a pronounced helical character while others assume a rodlike shape. We show that the static phase behavior and dynamics of chiral helices are very different when compared to simpler achiral hard rods. With increasing concentration, helical flagella undergo an entropy-driven first order phase transition to a liquid-crystalline state having a novel chiral symmetry.
    Description: M. S. and R. O. are supported by NIH Grant No. EB002583.
    Keywords: Entropy ; Molecular biophysics ; Liquid crystal phase transformations ; Symmetry ; Chirality
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 1-44 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 177-206 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Early NMR structural studies of serum lipoproteins were based on 1H, 13C, 31P, and 2H studies of lipid components. From the early studies information on composition, lipid chain dynamics and order parameters, and monolayer organization resulted. More recently, selective or complete isotopic labeling techniques, combined with multidimensional NMR spectroscopy, have resulted in structural information of apoprotein fragments. Finally, use of heteronuclear three- and four-dimensional experiments have yielded solution structures and protein-lipid interactions of intact apolipoproteins C-I, C-II, and A-I.
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    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 235-256 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract During the course of their biological function, proteins undergo different types of structural rearrangements ranging from local to large-scale conformational changes. These changes are usually triggered by their interactions with small-molecular-weight ligands or other macromolecules. Because binding interactions occur at specific sites and involve only a small number of residues, a chain of cooperative interactions is necessary for the propagation of binding signals to distal locations within the protein structure. This process requires an uneven structural distribution of protein stability and cooperativity as revealed by NMR-detected hydrogen/deuterium exchange experiments under native conditions. The distribution of stabilizing interactions does not only provide the architectural foundation to the three-dimensional structure of a protein, but it also provides the required framework for functional cooperativity. In this review, the statistical thermodynamic linkage between protein stability, functional cooperativity, and ligand binding is discussed.
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    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 73-95 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Active transport requires the alternation of substrate uptake and release with a switch in the access of the substrate binding site to the two sides of the membrane. Both the transfer and switch aspects of the photocycle have been subjects of magnetic resonance studies in bacteriorhodopsin. The results for ion transfer indicate that the Schiff base of the chromophore is hydrogen bonded before, during, and after its deprotonation. This suggests that the initial complex counterion of the Schiff base decomposes in such a way that the Schiff base carries its immediate hydrogen-bonding partner with it as it rotates during the first half of the photocycle. If so, bacteriorhodopsin acts as an inward-directed hydroxide pump rather than as an outward-directed proton pump. The studies of the access switch explore both protein-based and chromophore-based mechanisms. Combined with evidence from functional studies of mutants and other forms of spectroscopy, the results suggest that maintaining access to the extracellular side of the protein after photoisomerization involves twisting of the chromophore and that the decisive switch in access to the cytoplasmic side results from relaxation of the chromophore when the constraints on the Schiff base are released by decomposition of the complex counterion.
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    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 151-175 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract We review the physical properties of phosphatidylinositol 4,5-bisphosphate (PIP2) that determine both its specific interactions with protein domains of known structure and its nonspecific electrostatic sequestration by unstructured domains. Several investigators have postulated the existence of distinct pools of PIP2 within the cell to account for the myriad functions of this lipid. Recent experimental work indicates certain regions of the plasma membrane-membrane ruffles and nascent phagosomes-do indeed concentrate PIP2. We consider two mechanisms that could account for this phenomenon: local synthesis and electrostatic sequestration. We conclude by considering the hypothesis that proteins such as MARCKS bind a significant fraction of the PIP2 in a cell, helping to sequester it in lateral membrane domains, then release this lipid in response to local signals such as an increased concentration of Ca++/calmodulin or activation of protein kinase C.
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    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 121-149 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The first crystal structures of intact T cell receptors (TCRs) bound to class I peptide-MHC (pMHCs) antigens were determined in 1996. Since then, further structures of class I TCR/pMHC complexes have explored the degree of structural variability in the TCR-pMHC system and the structural basis for positive and negative selection. The recent determination of class II and allogeneic class I TCR/pMHC structures, as well as those of accessory molecules (e.g., CD3), has pushed our knowledge of TCR/pMHC interactions into new realms, shedding light on clinical pathologies, such as graft rejection and graft-versus-host disease. Furthermore, the determination of coreceptor structures lays the foundation for a more comprehensive structural description of the supramolecular TCR signaling events and those assemblies that arise in the immunological synapse. While these telling photodocumentaries of the TCR/pMHC interaction are composed mainly from static crystal structures, a full description of the biological snapshots in T cell signaling requires additional analytical methods that record the dynamics of the process. To this end, surface plasmon resonance (SPR), isothermal titration calorimetry (ITC), and ultracentrifugation (UC) have furnished both affinities and kinetics of the TCR/pMHC association. In the past year, structural, biochemical, and molecular biological data describing TCR/pMHC interactions have sublimely coalesced into a burgeoning well of understanding that promises to deliver further insights into T cell recognition. The coming years will, through a more intimate union of structural and kinetic data, allow many pressing questions to be addressed, such as how TCR/pMHC ligation is affected by coreceptor binding and what is the mechanism of TCR signaling in both early and late stages of T cell engagement with antigen-presenting cells.
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    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 207-233 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The structures of an increasing number of channels and other alpha-helical membrane proteins have been determined recently, including the KcsA potassium channel, the MscL mechanosensitive channel, and the AQP1 and GlpF members of the aquaporin family. In this chapter, the orientation and packing characteristics of bilayer-spanning helices are surveyed in integral membrane proteins. In the case of channels, alpha-helices create the sealed barrier that separates the hydrocarbon region of the bilayer from the permeation pathway for solutes. The helices surrounding the permeation pathway tend to be rather steeply tilted relative to the membrane normal and are consistently arranged in a right-handed bundle. The helical framework further provides a supporting scaffold for nonmembrane-spanning structures associated with channel selectivity. Although structural details remain scarce, the conformational changes associated with gating transitions between closed and open states of channels are reviewed, emphasizing the potential roles of helix-helix interactions in this process.
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    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 275-302 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Using luminescent lanthanides, instead of conventional fluorophores, as donor molecules in resonance energy transfer measurements offers many technical advantages and opens up a wide range of new applications. Advantages include farther measurable distances (~100 A) with greater accuracy, insensitivity to incomplete labeling, and the ability to use generic relatively large labels, when necessary. Applications highlighted include the study of ion channels in living cells, protein-protein interaction in cells, DNA-protein complexes, and high-throughput screening assays to measure peptide dimerization associated with DNA transcription factors and ligand-receptor interactions.
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    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 303-319 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Cryo-electron microscopy (cryo-EM) of biological molecules in single-particle (i.e., unordered, nonaggregated) form is a new approach to the study of molecular assemblies, which are often too large and flexible to be amenable to X-ray crystallography. New insights into biological function on the molecular level are expected from cryo-EM applied to the study of such complexes "trapped" at different stages of their conformational changes and dynamical interactions. Important molecular machines involved in the fundamental processes of transcription, mRNA splicing, and translation are examples for successful applications of the new technique, combined with structural knowledge gained by conventional techniques of structure determination, such as X-ray crystallography and NMR.
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    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 443-484 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The recent report of the crystal structure of rhodopsin provides insights concerning structure-activity relationships in visual pigments and related G protein-coupled receptors (GPCRs). The seven transmembrane helices of rhodopsin are interrupted or kinked at multiple sites. An extensive network of interhelical interactions stabilizes the ground state of the receptor. The ligand-binding pocket of rhodopsin is remarkably compact, and several chromophore-protein interactions were not predicted from mutagenesis or spectroscopic studies. The helix movement model of receptor activation, which likely applies to all GPCRs of the rhodopsin family, is supported by several structural elements that suggest how light-induced conformational changes in the ligand-binding pocket are transmitted to the cytoplasmic surface. The cytoplasmic domain of the receptor includes a helical domain extending from the seventh transmembrane segment parallel to the bilayer surface. The cytoplasmic surface appears to be approximately large enough to bind to the transducin heterotrimer in a one-to-one complex. The structural basis for several unique biophysical properties of rhodopsin, including its extremely low dark noise level and high quantum efficiency, can now be addressed using a combination of structural biology and various spectroscopic methods. Future high-resolution structural studies of rhodopsin and other GPCRs will form the basis to elucidate the detailed molecular mechanism of GPCR-mediated signal transduction.
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    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 485-516 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Integrins are a structurally elaborate family of heterodimers that mediate divalent cation-dependent cell adhesion in a wide range of biological contexts. The inserted (I) domain binds ligand in the subset of integrins in which it is present. Its structure has been determined in two alternative conformations, termed open and closed. In striking similarity to signaling G proteins, rearrangement of a Mg2+-binding site is linked to large conformational movements in distant backbone regions. Mutations have been used to stabilize either the closed or open structures. These show that the snapshots of the open conformation seen only in the presence of a ligand or a ligand mimetic represent a high-affinity, ligand-binding conformation, whereas those of the closed conformation correspond to a low-affinity conformation. The C-terminal alpha-helix moves 10 A down the side of the domain in the open conformation. Locking in the conformation of the preceding loop is sufficient to increase affinity for ligand 9000-fold. This C-terminal "bell-rope" provides a mechanism for linkage to conformational movements in other domains. The transition from the closed to open conformation has been implicated in fast (〈1 s) regulation of integrin affinity in response to activation signals from inside the cell. Recent integrin structures and functional studies reveal interactions between beta-propeller, I, and I-like domains in the headpiece, and a critical role for integrin EGF domains in the stalk region. These studies suggest that the headpiece of the integrin faces down toward the membrane in the inactive conformation and extends upward in a "switchblade"-like opening motion upon activation. These long-range structural rearrangements of the entire integrin molecule involving multiple interdomain contacts appear closely linked to conformational changes in the I domain, which result in increased affinity and competence for ligand binding.
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    Annual Review of Cell and Developmental Biology 18 (2002), S. 25-51 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract The amyloid precursor protein and the proteases cleaving this protein are important players in the pathogenesis of Alzheimer's disease via the generation of the amyloid peptide. Physiologically, the amyloid precursor protein is implied in axonal vesicular trafficking and the proteases are implicated in developmentally important signaling pathways, most significantly those involving regulated intramembrane proteolysis or RIP. We discuss the cell biology behind the amyloid and tangle hypothesis for Alzheimer's disease, drawing on the many links to the fields of cell biology and developmental biology that have been established in the recent years.
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    Annual Review of Cell and Developmental Biology 18 (2002), S. 107-133 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract The type III mechanism of protein secretion is a pathogenic strategy shared by a number of gram-negative pathogens of plants and animals that has evolved in order to inject virulence proteins into the cytosol of target eukaryotic cells. The pathogens of the Yersinia genus represent a model system where much progress has been made in understanding this secretion pathway. Herein, we review what has been recently learned in yersiniae about the various environmental signals that induce type III secretion, how the synthesis of secretion substrates is regulated, and how such a diverse group of proteins is recognized as a substrate for secretion.
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    Annual Review of Cell and Developmental Biology 18 (2002), S. 135-161 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Notes: Abstract The host cytoskeleton plays important roles in the entry, replication, and egress of viruses. An assortment of viruses hijack cellular motor proteins to move on microtubules toward the cell interior during the entry process; others reverse this transport during egress to move assembling virus particles toward the plasma membrane. Polymerization of actin filaments is sometimes used to propel viruses from cell to cell, while many viruses induce the destruction of select cytoskeletal filaments apparently to effect efficient egress. Indeed, the tactics used by any given virus to achieve its infectious life cycle are certain to involve multiple cytoskeletal interactions. Understanding these interactions, and their orchestration during viral infections, is providing unexpected insights into basic virology, viral pathogenesis, and the biology of the cytoskeleton.
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    Annual Review of Cell and Developmental Biology 18 (2002), S. 193-219 
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    Notes: Abstract Spindle microtubules interact with mitotic chromosomes, binding to their kinetochores to generate forces that are important for accurate chromosome segregation. Motor enzymes localized both at kinetochores and spindle poles help to form the biologically significant attachments between spindle fibers and their cargo, but microtubule-associated proteins without motor activity contribute to these junctions in important ways. This review examines the molecules necessary for chromosome-microtubule interaction in a range of well-studied organisms, using biological diversity to identify the factors that are essential for organized chromosome movement. We conclude that microtubule dynamics and the proteins that control them are likely to be more important for mitosis than the current enthusiasm for motor enzymes would suggest.
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    Annual Review of Cell and Developmental Biology 18 (2002), S. 221-245 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract Chlamydiae, bacterial obligate intracellular pathogens, are the etiologic agents of several human diseases. A large part of the chlamydial intracellular survival strategy involves the formation of a unique organelle called the inclusion that provides a protected site within which they replicate. The chlamydial inclusion is effectively isolated from endocytic pathways but is fusogenic with a subset of exocytic vesicles that deliver sphingomyelin from the Golgi apparatus to the plasma membrane. A combination of host and parasite functions contribute to the biogenesis of this compartment. Establishment of the mature inclusion is accompanied by the insertion of multiple chlamydial proteins, suggesting that chlamydiae actively modify the inclusion to define its interactions with the eukaryotic host cell. Despite being sequestered within a membrane-bound vacuole, chlamydiae clearly communicate with and manipulate the host cell from within this privileged intracellular niche.
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    Annual Review of Cell and Developmental Biology 18 (2002), S. 463-493 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract Epithelial morphogenesis comprises the various processes by which epithelia contribute to organ formation and body shape. These complex and diverse events play a central role in animal development and regeneration. Recently, the characterization of some of the molecular mechanisms involved in epithelial morphogenesis has provided an abundance of new information on the role and regulation of the cytoskeleton, cell-cell adhesion, and cell-matrix adhesion in these processes. In this review, we discuss our current understanding of the molecular mechanisms driving cell shape changes, cell intercalation, fusion of epithelia, ingression, egression, and cell migration. Our discussion is mostly focused on results from Drosophila and mammalian tissue culture but also draws on the insights gained from other organisms.
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    Annual Review of Cell and Developmental Biology 18 (2002), S. 379-420 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract Golgi inheritance proceeds via sequential biogenesis and partitioning phases. Although little is known about Golgi growth and replication (biogenesis), ultrastructural and fluorescence analyses have provided a detailed, though still controversial, perspective of Golgi partitioning during mitosis in mammalian cells. Partitioning requires the fragmentation of the juxtanuclear ribbon of interconnected Golgi stacks into a multitude of tubulovesicular clusters. This process is choreographed by a cohort of mitotic kinases and an inhibition of heterotypic and homotypic Golgi membrane-fusion events. Our model posits that accurate partitioning occurs early in mitosis by the equilibration of Golgi components on either side of the metaphase plate. Disseminated Golgi components then coalesce to regenerate Golgi stacks during telophase. Semi-intact cell and cell-free assays have accurately recreated these processes and allowed their molecular dissection. This review attempts to integrate recent findings to depict a more coherent, synthetic molecular picture of mitotic Golgi fragmentation and reassembly. Of particular importance is the emerging concept of a highly regulated and dynamic Golgi structural matrix or template that interfaces with cargo receptors, Golgi enzymes, Rab-GTPases, and SNAREs to tightly couple biosynthetic transport to Golgi architecture. This structural framework may be instructive for Golgi biogenesis and may encode sufficient information to ensure accurate Golgi inheritance, thereby helping to resolve some of the current discrepancies between different workers.
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    Annual Review of Astronomy and Astrophysics 11 (1973), S. 29-50 
    ISSN: 0066-4146
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    Annual Review of Astronomy and Astrophysics 11 (1973), S. 135-154 
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    Annual Review of Astronomy and Astrophysics 11 (1973), S. 219-238 
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    Annual Review of Astronomy and Astrophysics 11 (1973), S. 363-386 
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    Annual Review of Astronomy and Astrophysics 40 (2002), S. 63-101 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
    Notes: Abstract The Kuiper Belt consists of a large number of small, solid bodies in heliocentric orbit beyond Neptune. Discovered as recently as 1992, the Kuiper Belt objects (KBOs) are thought to hold the keys to understanding the early solar system, as well as the origin of outer solar system objects, such as the short-period comets and the Pluto-Charon binary. The KBOs are probably best viewed as aged relics of the Sun's accretion disk. Dynamical structures in the Kuiper Belt provide evidence for processes operative in the earliest days of the solar system, including a phase of planetary migration and a clearing phase, in which substantial mass was lost from the disk. Dust is produced to this day by collisions between KBOs. In its youth, the Kuiper Belt may have compared to the dust rings observed now around such stars as GG Tau and HR 4796A. This review presents the basic physical parameters of the KBOs and makes connections with the disks observed around nearby stars.
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    Annual Review of Astronomy and Astrophysics 40 (2002), S. 171-216 
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    Topics: Physics
    Notes: Abstract Cosmic microwave background (CMB) temperature anisotropies have and will continue to revolutionize our understanding of cosmology. The recent discovery of the previously predicted acoustic peaks in the power spectrum has established a working cosmological model: a critical density universe consisting of mainly dark matter and dark energy, which formed its structure through gravitational instability from quantum fluctuations during an inflationary epoch. Future observations should test this model and measure its key cosmological parameters with unprecedented precision. The phenomenology and cosmological implications of the acoustic peaks are developed in detail. Beyond the peaks, the yet to be detected secondary anisotropies and polarization present opportunities to study the physics of inflation and the dark energy. The analysis techniques devised to extract cosmological information from voluminous CMB data sets are outlined, given their increasing importance in experimental cosmology as a whole.
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    Annual Review of Astronomy and Astrophysics 40 (2002), S. 539-577 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
    Notes: Abstract Considerable progress has been made over the past decade in the study of the evolutionary trends of the population of galaxy clusters in the Universe. In this review we focus on observations in the X-ray band. X-ray surveys with the ROSAT satellite, supplemented by follow-up studies with ASCA and Beppo-SAX, have allowed an assessment of the evolution of the space density of clusters out to z= 1 and the evolution of the physical properties of the intracluster medium out to z= 0.5. With the advent of Chandra and Newton-XMM and their unprecedented sensitivity and angular resolution, these studies have been extended beyond redshift unity and have revealed the complexity of the thermodynamical structure of clusters. The properties of the intracluster gas are significantly affected by nongravitational processes including star formation and Active Galactic Nuclei (AGN) activity. Convincing evidence has emerged for modest evolution of both the bulk of the X-ray cluster population and their thermodynamical properties since redshift unity. Such an observational scenario is consistent with hierarchical models of structure formation in a flat low-density universe with Omegam= 0.3 and sigma8= 0.7-0.8 for the normalization of the power spectrum. Basic methodologies for construction of X-ray-selected cluster samples are reviewed, and implications of cluster evolution for cosmological models are discussed.
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    Annual Review of Astronomy and Astrophysics 40 (2002), S. 103-136 
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    Topics: Physics
    Notes: Abstract Giant planet research has moved from the study of a handful of solar system objects to that of a class of bodies with dozens of known members. Since the original 1995 discovery of the first extrasolar giant planets (EGPs), the total number of known examples has increased to ~80 (circa November 2001). Current theoretical studies of giant planets emphasize predicted observable properties, such as luminosity, effective temperature, radius, external gravity field, atmospheric composition, and emergent spectra as a function of mass and age. This review focuses on the general theory of hydrogen-rich giant planets; smaller giant planets with the mass and composition of Uranus and Neptune are not covered. We discuss the status of the theory of the nonideal thermodynamics of hydrogen and hydrogen-helium mixtures under the conditions found in giant-planet interiors, and the experimental constraints on it. We provide an overview of observations of extrasolar giant planets and our own giant planets by which the theory can be validated.
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    Annual Review of Astronomy and Astrophysics 40 (2002), S. 319-348 
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    Notes: Abstract Magnetic fields in the intercluster medium have been measured using a variety of techniques, including studies of synchrotron relic and halo radio sources within clusters, studies of inverse Compton X-ray emission from clusters, surveys of Faraday rotation measures of polarized radio sources both within and behind clusters, and studies of cluster cold fronts in X-ray images. These measurements imply that most cluster atmospheres are substantially magnetized, with typical field strengths of order 1 muGauss with high areal filling factors out to Mpc radii. There is likely to be considerable variation in field strengths and topologies both within and between clusters, especially when comparing dynamically relaxed clusters to those that have recently undergone a merger. In some locations, such as the cores of cooling flow clusters, the magnetic fields reach levels of 10-40 muG and may be dynamically important. In all clusters the magnetic fields have a significant effect on energy transport in the intracluster medium. We also review current theories on the origin of cluster magnetic fields.
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    Annual Review of Fluid Mechanics 34 (2002), S. 37-49 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Abstract David Crighton, a greatly admired figure in fluid mechanics, Head of the Department of Applied Mathematics and Theoretical Physics at Cambridge, and Master of Jesus College, Cambridge, died at the peak of his career. He had made important contributions to the theory of waves generated by unsteady flow. Crighton's work was always characterized by the application of rigorous mathematical approximations to fluid mechanical idealizations of practically relevant problems. At the time of his death, he was certainly the most influential British applied mathematical figure, and his former collaborators and students form a strong school that continues his special style of mathematical application. Rigorous analysis of well-posed aeroacoustical problems was transformed by David Crighton.
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    Annual Review of Fluid Mechanics 34 (2002), S. 143-175 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Abstract Cavitation in vortical structures is a common, albeit complex, problem in engineering applications. Cavitating vortical structures can be found on the blade surfaces, in the clearance passages, and at the hubs of various types of turbomachinery. Cavitating microvortices at the trailing edge of attached sheet cavitation can be highly erosive. Cavitating hub vortices in the draft tubes of hydroturbines can cause major surges and power swings. There is also mounting evidence that vortex cavitation is a dominant factor in the inception process in a broad range of turbulent flows. Most research has focused on the inception process, with limited attention paid to developed vortex cavitation. Wave-like disturbances on the surfaces of vapor cores are an important feature. Vortex core instabilities in microvortices are found to be important factors in the erosion mechanisms associated with sheet/cloud cavitation. Under certain circumstances, intense sound at discrete frequencies can result from a coupling between tip vortex disturbances and oscillating sheet cavitation. Vortex breakdown phenomena that have some commonalities are also noted, as are some differences with vortex breakdown in fully wetted flow. Simple vortex models can sometimes be used to describe the cavitation process in complex turbulent flows such as bluff body wakes and in plug valves. Although a vortex model for cavitation in jets does not exist, the mechanism of inception appears to be related to the process of vortex pairing. The pairing process can produce negative peaks in pressure that can exceed the rms value by a factor of ten, sometimes exceeding the dynamic pressure by a factor of two. A new and important issue is that cavitation is not only induced in vortical structures but is also a mechanism for vorticity generation.
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    Annual Review of Fluid Mechanics 34 (2002), S. 177-210 
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    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Abstract Microstructure in an immiscible polymer blend consists of the size, shape, and orientation of the phases. Blends exhibit many interesting behaviors, including enhanced elasticity at small strains, drop-size hysteresis, enhanced shear thinning, and stress relaxation curves whose shapes are sensitive to deformation history. These behaviors are directly related to changes in the microstructure, which result from phase deformation, coalescence, retraction, and different types of breakup. These phenomena are reviewed, together with models that describe them. Rheological measurements can probe the microstructure because microstructure contributes directly to stress through interfacial tension. Rheo-optical experiments also provide important insights. Droplet theories explain most of the phenomena for Newtonian phases at low concentrations. Behaviors at high volume fractions or with strongly non-Newtonian phases are less well understood.
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    Annual Review of Fluid Mechanics 34 (2002), S. 417-444 
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    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Abstract Recent advances in the computational modeling of molecular conformational and orientational effects in the flow of viscoelastic fluids are described. These advances involve the coupling of molecular models for the underlying microstructure of macromolecules with the macroscopic equations of change. The kinetic theory for polymeric liquids is described along with the most useful micromechanical models for computing the fluid flow of polymeric liquids. Three levels of description are covered for the computation of molecular orientation effects: methods for molecular models for which closed-form, continuum-like evolution equations for average quantities describing molecular conformations can be obtained, hybrid methods that involve coupling direct solution of the Fokker-Planck equation describing the distribution function for molecular orientations with the equations of change, and hybrid methods that couple stochastic simulations of individual molecule trajectories with the macroscopic equations of change. Illustrative results for rheometric flows (flows with homogeneous, fixed kinematics) and complex flows are given.
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    Annual Review of Fluid Mechanics 34 (2002), S. 531-558 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Abstract The El Nino variability in the equatorial Tropical Pacific is characterized by sea-surface temperature anomalies and associated changes in the atmospheric circulation. Through an enormous monitoring effort over the last decades, the relevant time scales and spatial patterns are fairly well documented. In the meantime, a hierarchy of models has been developed to understand the physics of this phenomenon and to make predictions of future variability. In this review, the robust and relevant details of the observations, the fluid mechanical "building blocks," the theory of the deterministic part of the variability, and the impact of small-scale ("noise") and remote ("external") processes are evaluated.
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    Annual Review of Fluid Mechanics 38 (2006), S. 225-249 
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    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    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.
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    Annual Review of Fluid Mechanics 38 (2006), S. 193-224 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: 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.
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    Annual Review of Fluid Mechanics 38 (2006), S. 395-425 
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    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    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.
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    Annual Review of Fluid Mechanics 38 (2006), S. 309-338 
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    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    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.
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    Annual Review of Fluid Mechanics 38 (2006), S. 27-63 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: 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.
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    Annual Review of Fluid Mechanics 38 (2006), S. 453-482 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: 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.
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    Annual Review of Fluid Mechanics 5 (1973), S. 31-58 
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    Annual Review of Fluid Mechanics 5 (1973), S. 59-78 
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    Annual Review of Fluid Mechanics 5 (1973), S. 161-184 
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    Annual Review of Fluid Mechanics 5 (1973), S. 185-212 
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    Annual Review of Fluid Mechanics 5 (1973), S. 247-280 
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    Annual Review of Fluid Mechanics 5 (1973), S. 281-300 
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    Annual Review of Fluid Mechanics 5 (1973), S. 339-360 
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    Annual Review of Fluid Mechanics 5 (1973), S. 383-404 
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    Annual Review of Genetics 36 (2002), S. 557-615 
    ISSN: 0066-4197
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Abstract Cryptococcus neoformans is a pathogenic fungus that primarily afflicts immunocompromised patients, infecting the central nervous system to cause meningoencephalitis that is uniformly fatal if untreated. C. neoformans is a basidiomycetous fungus with a defined sexual cycle that has been linked to differentiation and virulence. Recent advances in classical and molecular genetic approaches have allowed molecular descriptions of the pathways that control cell type and virulence. An ongoing genome sequencing project promises to reveal much about the evolution of this human fungal pathogen into three distinct varieties or species. C. neoformans shares features with both model ascomycetous yeasts (Saccharomyces cerevisiae, Schizosaccharomyces pombe) and basidiomycetous pathogens and mushrooms (Ustilago maydis, Coprinus cinereus, Schizophyllum commune), yet ongoing studies reveal unique features associated with virulence and the arrangement of the mating type locus. These advances have catapulted C. neoformans to center stage as a model of both fungal pathogenesis and the interesting approaches to life that the kingdom of fungi has adopted.
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    Annual Review of Genetics 36 (2002), S. 521-556 
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    Topics: Biology
    Notes: Abstract An unusual feature of the Diptera is that homologous chromosomes are intimately synapsed in somatic cells. At a number of loci in Drosophila, this pairing can significantly influence gene expression. Such influences were first detected within the bithorax complex (BX-C) by E.B. Lewis, who coined the term transvection to describe them. Most cases of transvection involve the action of enhancers in trans. At several loci deletion of the promoter greatly increases this action in trans, suggesting that enhancers are normally tethered in cis by the promoter region. Transvection can also occur by the action of silencers in trans or by the spreading of position effect variegation from rearrangements having heterochromatic breakpoints to paired unrearranged chromosomes. Although not demonstrated, other cases of transvection may involve the production of joint RNAs by trans-splicing. Several cases of transvection require Zeste, a DNA-binding protein that is thought to facilitate homolog interactions by self-aggregation. Genes showing transvection can differ greatly in their response to pairing disruption. In several cases, transvection appears to require intimate synapsis of homologs. However, in at least one case (transvection of the iab-5,6,7 region of the BX-C), transvection is independent of synapsis within and surrounding the interacting gene. The latter example suggests that transvection could well occur in organisms that lack somatic pairing. In support of this, transvection-like phenomena have been described in a number of different organisms, including plants, fungi, and mammals.
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    Annual Review of Genetics 36 (2002), S. 617-656 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Abstract DNA checkpoints play a significant role in cancer pathology, perhaps most notably in maintaining genome stability. This review summarizes the genetic and molecular mechanisms of checkpoint activation in response to DNA damage. The major checkpoint proteins common to all eukaryotes are identified and discussed, together with how the checkpoint proteins interact to induce arrest within each cell cycle phase. Also discussed are the molecular signals that activate checkpoint responses, including single-strand DNA, double-strand breaks, and aberrant replication forks. We address the connection between checkpoint proteins and damage repair mechanisms, how cells recover from an arrest response, and additional roles that checkpoint proteins play in DNA metabolism. Finally, the connection between checkpoint gene mutation and genomic instability is considered.
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    Annual Review of Genetics 36 (2002), S. 687-720 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Abstract Long-term potentiation (LTP) is the predominant experimental model for the synaptic plasticity mechanisms thought to underlie learning and memory. This review is focused on the contributions of genetics to the understanding of the role of LTP in learning and memory. These studies have used a combination of genetics, molecular biology, neurophysiology, and psychology to demonstrate that molecular mechanisms of synaptic plasticity are critical for learning and memory. Because of the large scope of this literature, we focus primarily on genetic studies of hippocampal-dependent learning. Altogether, these findings not only demonstrate a role for plasticity in learning, they also lay down the foundations for the new field of molecular and cellular cognition.
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    Annual Review of Genetics 36 (2002), S. 657-686 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Abstract The compilation of a dense gene map and eventually a whole genome sequence (WGS) of the domestic cat holds considerable value for human genome annotation, for veterinary medicine, and for insight into the evolution of genome organization among mammals. Human association and veterinary studies of the cat, its domestic breeds, and its charismatic wild relatives of the family Felidae have rendered the species a powerful model for human hereditary diseases, for infectious disease agents, for adaptive evolutionary divergence, for conservation genetics, and for forensic applications. Here we review the advantages, rationale, and present strategy of a feline genome project, and we describe the disease models, comparative genomics, and biological applications posed by the full resolution of the cat's genome.
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    Annual Review of Genetics 36 (2002), S. 721-750 
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    Topics: Biology
    Notes: Abstract A moment estimator of theta, the coancestry coefficient for alleles within a population, was described by Weir & Cockerham in 1984 (100) and is still widely cited. The estimate is used by population geneticists to characterize population structure, by ecologists to estimate migration rates, by animal breeders to describe genetic variation, and by forensic scientists to quantify the strength of matching DNA profiles. This review extends the work of Weir & Cockerham by allowing different levels of coancestry for different populations, and by allowing non-zero coancestries between pairs of populations. All estimates are relative to the average value of theta between pairs of populations. Moment estimates for within- and between-population theta values are likely to have large sampling variances, although these may be reduced by combining information over loci. Variances also decrease with the numbers of alleles at a locus, and with the numbers of populations sampled. This review also extends the work of Weir & Cockerham by employing maximum likelihood methods under the assumption that allele frequencies follow the normal distribution over populations. For the case of equal theta values within populations and zero theta values between populations, the maximum likelihood estimate is the same as that given by Robertson & Hill in 1984 (70). The review concludes by relating functions of theta values to times of population divergence under a pure drift model.
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    Annual Review of Genetics 7 (1973), S. 225-237 
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    Annual Review of Genetics 7 (1973), S. 267-287 
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    Annual Review of Genetics 7 (1973), S. 239-265 
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    Annual Review of Genetics 7 (1973), S. 289-324 
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    Annual Review of Genetics 7 (1973), S. 325-341 
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    Annual Review of Genetics 7 (1973), S. 381-433 
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    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 257-273 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract We determined the high-resolution structures of large and small ribosomal subunits from mesophilic and thermophilic bacteria and compared them with those of the thermophilic ribosome and the halophilic large subunit. We confirmed that the elements involved in intersubunit contacts and in substrate binding are inherently flexible and that a common ribosomal strategy is to utilize this conformational variability for optimizing its functional efficiency and minimizing nonproductive interactions. Under close-to-physiological conditions, these elements maintain well-ordered characteristic conformations. In unbound subunits, the features creating intersubunit bridges within associated ribosomes lie on the interface surface, and the features that bind factors and substrates reach toward the binding site only when conditions are ripe.
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    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 361-392 
    ISSN: 1056-8700
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    Topics: Biology , Physics
    Notes: Abstract Chromatin fibers are dynamic macromolecular assemblages that are intimately involved in nuclear function. This review focuses on recent advances centered on the molecular mechanisms and determinants of chromatin fiber dynamics in solution. Major points of emphasis are the functions of the core histone tail domains, linker histones, and a new class of proteins that assemble supramolecular chromatin structures. The discussion of important structural issues is set against a background of possible functional significance.
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    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 393-422 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The review deals with recent advances in magnetic resonance spectroscopy (hf EPR and NMR) of paramagnetic metal centers in biological macromolecules. In the first half of our chapter, we present an overview of recent technical developments in the NMR of paramagnetic bio-macromolecules. These are illustrated by a variety of examples deriving mainly from the spectroscopy of metalloproteins and their complexes. The second half focuses on recent developments in high-frequency EPR spectroscopy and the application of the technique to copper, iron, and manganese proteins. Special attention is given to the work on single crystals of copper proteins.
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    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 321-341 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Fungal pathogens of plants or animals invade their hosts either by secretion of lytic enzymes, exerting force, or by a combination of both. Although many fungi are thought to rely mostly on lysis of the host tissue, some plant pathogenic fungi differentiate complex infection cells that develop enormous turgor pressure, which in turn is translated into force used for invasion. In order to understand mechanisms of fungal infection in detail, methods have been developed that indirectly or directly measure turgor pressure and force. In this article, these methods are described and critically discussed, and their importance in analysis of fungal infection are outlined.
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    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 423-441 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The field of computational cell biology has emerged within the past 5 years because of the need to apply disciplined computational approaches to build and test complex hypotheses on the interacting structural, physical, and chemical features that underlie intracellular processes. To meet this need, newly developed software tools allow cell biologists and biophysicists to build models and generate simulations from them. The construction of general-purpose computational approaches is especially challenging if the spatial complexity of cellular systems is to be explicitly treated. This review surveys some of the existing efforts in this field with special emphasis on a system being developed in the authors' laboratory, Virtual Cell. The theories behind both stochastic and deterministic simulations are discussed. Examples of respective applications to cell biological problems in RNA trafficking and neuronal calcium dynamics are provided to illustrate these ideas.
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    Annual Review of Cell and Developmental Biology 18 (2002), S. 53-80 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract Co-option occurs when natural selection finds new uses for existing traits, including genes, organs, and other body structures. Genes can be co-opted to generate developmental and physiological novelties by changing their patterns of regulation, by changing the functions of the proteins they encode, or both. This often involves gene duplication followed by specialization of the resulting paralogous genes into particular functions. A major role for gene co-option in the evolution of development has long been assumed, and many recent comparative developmental and genomic studies have lent support to this idea. Although there is relatively less known about the molecular basis of co-option events involving developmental pathways, much can be drawn from well-studied examples of the co-option of structural proteins. Here, we summarize several case studies of both structural gene and developmental genetic circuit co-option and discuss how co-option may underlie major episodes of adaptive change in multicellular organisms. We also examine the phenomenon of intraspecific variability in gene expression patterns, which we propose to be one form of material for the co-option process. We integrate this information with recent models of gene family evolution to provide a framework for understanding the origin of co-optive evolution and the mechanisms by which natural selection promotes evolutionary novelty by inventing new uses for the genetic toolkit.
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    Annual Review of Cell and Developmental Biology 18 (2002), S. 81-105 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract In flowering plants, pollen grains germinate to form pollen tubes that transport male gametes (sperm cells) to the egg cell in the embryo sac during sexual reproduction. Pollen tube biology is complex, presenting parallels with axon guidance and moving cell systems in animals. Pollen tube cells elongate on an active extracellular matrix in the style, ultimately guided by stylar and embryo sac signals. A well-documented recognition system occurs between pollen grains and the stigma in sporophytic self-incompatibility, where both receptor kinases in the stigma and their peptide ligands from pollen are now known. Complex mechanisms act to precisely target the sperm cells into the embryo sac. These events initiate double fertilization in which the two sperm cells from one pollen tube fuse to produce distinctly different products: one with the egg to produce the zygote and embryo and the other with the central cell to produce the endosperm.
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    Annual Review of Cell and Developmental Biology 18 (2002), S. 163-192 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract The Arabidopsis genome sequence has revealed that plants contain a much larger complement of receptor kinase genes than other organisms. Early analysis of these genes revealed involvement in a diverse array of developmental and defense functions that included gametophyte development, pollen-pistil interactions, shoot apical meristem equilibrium, hormone perception, and cell morphogenesis. Amino acid sequence motifs and binding studies indicate that the ectodomains are capable of binding, either directly or indirectly, various classes of molecules including proteins, carbohydrates, and steroids. Genetic and biochemical approaches have begun to identify other components of several signal transduction pathways. Some receptor-like kinases (RLKs) appear to function with coreceptors lacking kinase domains, and genome analysis suggests this might be true for many RLKs. The KAPP protein phosphatase functions as a negative regulator of at least two RLK systems, and in vitro studies suggest it could be a common component of more. Whether plant signaling systems display a modularity similar to animal systems remains to be determined. Future efforts will reveal unknown functions of other RLKs and elucidate the relationships among their signaling networks.
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    Annual Review of Cell and Developmental Biology 18 (2002), S. 247-288 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract Eukaryotic cells use actin polymerization to change shape, move, and internalize extracellular materials by phagocytosis and endocytosis, and to form contractile structures. In addition, several pathogens have evolved to use host cell actin assembly for attachment, internalization, and cell-to-cell spread. Although cells possess multiple mechanisms for initiating actin polymerization, attention in the past five years has focused on the regulation of actin nucleation-the formation of new actin filaments from actin monomers. The Arp2/3 complex and the multiple nucleation-promoting factors (NPFs) that regulate its activity comprise the only known cellular actin-nucleating factors and may represent a universal machine, conserved across eukaryotic phyla, that nucleates new actin filaments for various cellular structures with numerous functions. This review focuses on our current understanding of the mechanism of actin nucleation by the Arp2/3 complex and NPFs and how these factors work with other cytoskeletal proteins to generate structurally and functionally diverse actin arrays in cells.
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    Annual Review of Cell and Developmental Biology 18 (2002), S. 289-314 
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    Topics: Biology , Medicine
    Notes: Abstract Membrane fusion is a fundamental biochemical reaction and the final step in all vesicular trafficking events. It is crucial for the transfer of proteins and lipids between different compartments and for exo- and endocytic traffic of signaling molecules and receptors. It leads to the reconstruction of organelles such as the Golgi or the nuclear envelope, which decay into fragments during mitosis. Hence, controlled membrane fusion reactions are indispensible for the compartmental organization of eukaryotic cells; for their communication with the environment via hormones, neurotransmitters, growth factors, and receptors; and for the integration of cells into multicellular organisms. Intracellular pathogenic bacteria, such as Mycobacteria or Salmonellae, have developed means to control fusion reactions in their host cells. They persist in phagosomes whose fusion with lysosomes they actively suppress-a means to ensure survival inside host cells. The past decade has witnessed rapid progress in the elucidation of parts of the molecular machinery involved in these membrane fusion reactions. Whereas some elements of the fusion apparatus are remarkably similar in several compartments, there is an equally striking divergence of others. The purpose of this review is to highlight common features of different fusion reactions and the concepts that emerged from them but also to stress the differences and challenge parts of the current hypotheses. This review covers only the endoplasmic fusion reactions mentioned above, i.e., reactions initiated by contacts of membranes with their cytoplasmic faces. Ectoplasmic fusion events, which depend on an initial contact of the fusion partners via the membrane surfaces exposed to the surrounding medium are not discussed, nor are topics such as the entry of enveloped viruses, formation of syncytia, gamete fusion, or vesicle scission (a fusion reaction that leads to the fission of, e.g., transport vesicles).
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    Annual Review of Cell and Developmental Biology 18 (2002), S. 315-344 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract Bacterial pathogens utilize several strategies to modulate the organization of the actin cytoskeleton. Some bacterial toxins catalyze the covalent modification of actin or the Rho GTPases, which are involved in the control of the actin cytoskeleton. Other bacteria produce toxins that act as guanine nucleotide exchange factors or GTPase-activating proteins to modulate the nucleotide state of the Rho GTPases. This latter group of toxins provides a temporal modulation of the actin cytoskeleton. A third group of bacterial toxins act as adenylate cyclases, which directly elevate intracellular cAMP to supra-physiological levels. Each class of toxins gives the bacterial pathogen a selective advantage in modulating host cell resistance to infection.
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    Annual Review of Cell and Developmental Biology 18 (2002), S. 345-378 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract The mammalian cell continuously adjusts its sterol content by regulating levels of key sterol synthetic enzymes and levels of LDL receptors that mediate uptake of cholesterol-laden particles. Control is brought about by sterol-regulated transcription of relevant genes and by regulated degradation of the committed step enzyme HMG-CoA reductase (HMGR). Current work has revealed that proteolysis is at the heart of each of these mechanistically distinct axes. Transcriptional control is effected by regulated cleavage of the membrane-bound transcription factor sterol regulatory element binding protein (SREBP), and HMGR degradation is brought about by ubiquitin-mediated degradation. In each case, ongoing cell biological processes are being harnessed to bring about regulation. The secretory pathway plays a central role in allowing sterol-mediated control of transcription. The constitutively active endoplasmic reticulum (ER) quality control apparatus is employed to bring about regulated destruction of HMGR. This review describes the methods and results of various studies to understand the mechanisms and molecules involved in these distinct but interrelated aspects of sterol regulation and the intriguing similarities that appear to exist at the levels of protein sequence and cell biology.
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    Annual Review of Materials Research 32 (2002), S. 1-37 
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract Multiferroic magnetoelectrics are materials that are both ferromagnetic and ferroelectric in the same phase. As a result, they have a spontaneous magnetization that can be switched by an applied magnetic field and a spontaneous polarization that can be switched by an applied electric field. In this paper we show that density functional theory has been invaluable both in explaining the properties of known magnetically ordered ferroelectric materials, and in predicting the occurrence of new ones. Density functional calculations have shown that, in general, the transition metal d electrons essential for magnetism reduce the tendency for off-center ferroelectric distortion. Consequently, an additional electronic or structural driving force must be present for ferromagnetism and ferroelectricity to occur simultaneously.
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    Annual Review of Materials Research 32 (2002), S. 271-295 
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract Vacancies and self-interstitial defects in silicon are here investigated by means of semi-empirical quantum molecular dynamics simulations performed within the tight-binding model. We extensively discuss the process of formation and migration of native point defects and investigate their interaction and clustering phenomena. The formation of larger stable structures is further studied by combining tight-binding and Monte Carlo simulations. Tight-binding simulation results provide a global picture for defect-induced microstructure evolution in bulk silicon. These results are consistent with state-of-the-art experimental data and elucidate many relevant atomic-scale mechanisms.
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    Annual Review of Astronomy and Astrophysics 11 (1973), S. 115-134 
    ISSN: 0066-4146
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    Topics: Physics
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    Annual Review of Astronomy and Astrophysics 11 (1973), S. 269-308 
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    Annual Review of Astronomy and Astrophysics 11 (1973), S. 309-362 
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    Annual Review of Astronomy and Astrophysics 40 (2002), S. 1-25 
    ISSN: 0066-4146
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
    Notes: Abstract I fled with my parents from Hitler's Austria to Australia and studied physics at Sydney University. I obtained my Ph.D. in quantum electrodynamics with Rudolf Peierls at Birmingham University and came to Cornell to work with Hans Bethe. I have stayed at Cornell ever since, and I have essentially had only a single job in my whole life, but have switched fields quite often. I worked in nuclear astrophysics and in late-stellar evolution, estimated the Initial Mass Function for star formation and the metal enrichment of the interstellar medium. I suggested black hole accretion as the energy source for quasars, worked on molecule formation on dust grain surfaces, and was involved in 21-cm studies of gas clouds and disk galaxies. I collaborated with my wife on the neurobiology of the neuromuscular junction and with one of my daughters on the epidemiology of tuberculosis.
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    Annual Review of Astronomy and Astrophysics 40 (2002), S. 349-385 
    ISSN: 0066-4146
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
    Notes: Abstract Although we have a general understanding of the manner in which individual stars form, our understanding of how binary stars form is far from complete. This is in large part due to the fact that the star formation process happens very quickly and in regions of the Galaxy that are difficult to study observationally. We review the theoretical models that have been developed in an effort to explain how binaries form. Several proposed mechanisms appear to be quite promising, but none is completely satisfactory.
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    Annual Review of Astronomy and Astrophysics 40 (2002), S. 217-261 
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    Topics: Physics
    Notes: Abstract Radio astronomy has provided evidence for the presence of ionized atmospheres around almost all classes of nondegenerate stars. Magnetically confined coronae dominate in the cool half of the Hertzsprung-Russell diagram. Their radio emission is predominantly of nonthermal origin and has been identified as gyrosynchrotron radiation from mildly relativistic electrons, apart from some coherent emission mechanisms. Ionized winds are found in hot stars and in red giants. They are detected through their thermal, optically thick radiation, but synchrotron emission has been found in many systems as well. The latter is emitted presumably by shock-accelerated electrons in weak magnetic fields in the outer wind regions. Radio emission is also frequently detected in pre-main sequence stars and protostars and has recently been discovered in brown dwarfs. This review summarizes the radio view of the atmospheres of nondegenerate stars, focusing on energy release physics in cool coronal stars, wind phenomenology in hot stars and cool giants, and emission observed from young and forming stars. Eines habe ich in einem langen Leben gelernt, namlich, dass unsere ganze Wissenschaft, an den Dingen gemessen, von kindlicher Primitivitat ist-und doch ist es das Kostlichste, was wir haben. One thing I have learned in a long life: that all our science, measured against reality, is primitive and childlike-and yet it is the most precious thing we have. A. Einstein 1951, in a letter to H. Muhsam, Einstein Archive 36-610
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