bluuebunny/crossref_metadata_2025 huggingface dataset:
Are amyloid diseases caused by protein aggregates that mimic bacterial pore-forming toxins?
Authors: Lashuel Hilal A. , Lansbury Peter T.
Published: September 2006

1. Introduction 2

2. What is the significance of the shared structural properties of disease-associated protein fibrils? 3

2.1 Mechanism of amyloid fibril formation in vitro 6

2.1.1 In vitro fibril formation involves transient population of ordered aggregates of intermediate stability, or protofibrils 6

3. Toxic properties of protofibrils 7

3.1 Protofibrils, rather than fibrils, are likely to be pathogenic 7

3.2 The toxic protofibril may be a mixture of related species 8

3.3 Morphological similarities of protofibrils suggest a common mechanism of toxicity 9

3.4 Are the amyloid diseases a subset of a much larger class of previously unrecognized protofibril diseases? 9

3.5 Fibrils, in the form of aggresomes, may function to sequester toxic protofibrils 9

4. Amyloid pores, a common structural link among protein aggregation neurodegenerative diseases 10

4.1 Mechanistic studies of amyloid fibril formation reveal common features, including pore-like protofibrils 10

4.1.1 Amyloid-β (Aβ) (Alzheimer's disease) 10

4.1.2 α-Synuclein (PD and diffuse Lewy body disease) 12

4.1.3 ABri (familial British dementia) 13

4.1.4 Superoxide dismutase-1 (amyotrophic lateral sclerosis) 13

4.1.5 Prion protein (Creutzfeldt–Jakob disease, bovine spongiform encephalopathy, etc.) 14

4.1.6 Huntingtin (Huntington's disease) 14

4.2 Amyloidogenic proteins that are not linked to disease also from pore-like protofibrils 15

4.3 Amyloid proteins form non-fibrillar aggregates that have properties of protein channels or pores 15

4.3.1 Aβ ‘channels’ 15

4.3.2 α-Synuclein ‘pores’ 16

4.3.3 PrP ‘channels’ 16

4.3.4 Polyglutamine ‘channels’ 17

4.4 Nature uses β-strand-mediated protein oligomerization to construct pore-forming toxins 17

5. Mechanisms of protofibril induced toxicity in protein aggregation diseases 19

5.1 The amyloid pore can explain the age-association and cell-type selectivity of the neurodegenerative diseases 19

5.2 Protofibrils may promote their own accumulation by inhibiting the proteasome 20

6. Testing the amyloid pore hypothesis by attempting to disprove it 21

7. Acknowledgments 22

8. References 22

Protein fibrillization is implicated in the pathogenesis of most, if not all, age-associated neurodegenerative diseases, but the mechanism(s) by which it triggers neuronal death is unknown. Reductionist in vitro studies suggest that the amyloid protofibril may be the toxic species and that it may amplify itself by inhibiting proteasome-dependent protein degradation. Although its pathogenic target has not been identified, the properties of the protofibril suggest that neurons could be killed by unregulated membrane permeabilization, possibly by a type of protofibril referred to here as the ‘amyloid pore’. The purpose of this review is to summarize the existing supportive circumstantial evidence and to stimulate further studies designed to test the validity of this hypothesis.
Small-vessel cerebrovascular disease in older people
Authors: McManus Julie , Stott David J
Published: September 2006

Over recent years, small-vessel cerebrovascular disease has become increasingly recognized as an important contributor to cognitive and functional decline in elderly people.
A theory of rupture pulse on softening interface with application to the Chi‐Chi earthquake
Authors: Linkov Alexander M.
Published: September 2006

The rupture process at the near‐front zone of a propagating crack, being strongly nonlinear and irreversible, a detailed Fourier analysis becomes complicated, often impractical. Meanwhile, a simplified approach, employing formally derived dispersion equation, may serve for obtaining meaningful information. Data on the rupture velocity, the size of the fracture process zone (FPZ), the possibility of exponential growth in time, and also on decaying with the distance from the rupture surface become available. The approach actually presumes that the size of the FPZ defines a dominant wavelength in the Fourier spectrum of a propagating rupture pulse. We verify this suggestion by revisiting the classical problem of a propagating shear crack having a cohesive FPZ with linear softening. It appears that in this particular problem, the simplified approach provides results which remarkably agree with the exact solution. This suggests using the approach for the analysis of the unique data on a rupture pulse obtained in the Chi‐Chi (Taiwan, 20 September 1999) earthquake. We conclude that the approach allows easy interpretation of the observed phenomena. The importance of the softening modulus as an independent characteristic of initiation and propagation of rupture is emphasized.
Forced annular variations in the 20th century Intergovernmental Panel on Climate Change Fourth Assessment Report models
Authors: Miller R. L. , Schmidt G. A. , Shindell D. T.
Published: September 2006

We examine the annular mode within each hemisphere (defined here as the leading empirical orthogonal function and principal component of hemispheric sea level pressure) as simulated by the Intergovernmental Panel on Climate Change Fourth Assessment Report ensembles of coupled ocean‐atmosphere models. The simulated annular patterns exhibit a high spatial correlation with the observed patterns during the late 20th century, though the mode represents too large a percentage of total temporal variability within each hemisphere. In response to increasing concentrations of greenhouse gases and tropospheric sulfate aerosols, the multimodel average exhibits a positive annular trend in both hemispheres, with decreasing sea level pressure (SLP) over the pole and a compensating increase in midlatitudes. In the Northern Hemisphere, the trend agrees in sign but is of smaller amplitude than that observed during recent decades. In the Southern Hemisphere, decreasing stratospheric ozone causes an additional reduction in Antarctic surface pressure during the latter half of the 20th century. While annular trends in the multimodel average are positive, individual model trends vary widely. Not all models predict a decrease in high‐latitude SLP, although no model exhibits an increase. As a test of the models' annular sensitivity, the response to volcanic aerosols in the stratosphere is calculated during the winter following five major tropical eruptions. The observed response exhibits coupling between stratospheric anomalies and annular variations at the surface, similar to the coupling between these levels simulated elsewhere by models in response to increasing GHG concentration. The multimodel average is of the correct sign but significantly smaller in magnitude than the observed annular anomaly. This suggests that the models underestimate the coupling of stratospheric changes to annular variations at the surface and may not simulate the full response to increasing GHGs.
Ability of the land surface model ISBA‐A‐gs to simulate leaf area index at the global scale: Comparison with satellites products
Authors: Gibelin Anne‐Laure , Calvet Jean‐Christophe , Roujean Jean‐Louis , Jarlan Lionel , Los Sietse O.
Published: September 2006

The land surface model (LSM) ISBA‐A‐gs (Interactions between Soil, Biosphere and Atmosphere, CO2‐reactive) is specifically designed to simulate leaf stomatal conductance and leaf area index (LAI) in response to climate, soil properties, and atmospheric carbon dioxide concentration. The model is run at the global scale, forced by the GSWP‐2 meteorological data at a resolution of 1° for the period of 1986–1995. We test the model by comparing the simulated LAI values against three satellite‐derived data sets (ISLSCP Initiative II data, MODIS data and ECOCLIMAP data) and find that the model reproduces the major patterns of spatial and temporal variability in global vegetation. As a result, the mean of the maximum annual LAI estimates of the model falls within the range of the various satellite data sets. Despite no explicit representation of phenology, the model captures the seasonal cycle in LAI well and shows realistic variations in start of the growing season as a function of latitude. The interannual variability is also well reported for numerous regions of the world, particularly where precipitation controls photosynthesis. The comparison also reveals that some processes need to be improved or introduced in the model, in particular the snow dynamics and the treatment of vegetation in cultivated areas, respectively. The overall comparisons demonstrate the potential of ISBA‐A‐gs model to simulate LAI in a realistic fashion at the global scale.
Phase dispersion relation of the 5‐micron hot spot wave from a long‐term study of Jupiter in the visible
Authors: Arregi J. , Rojas J. F. , Sánchez‐Lavega A. , Morgado A.
Published: September 2006

We present a long‐term study at visible wavelengths of the motions and spatial distribution of the hot spots at 7°N of Jupiter. This research involves seven years of observations of the planet between 1979 and 2002 and includes data from Voyagers 1 and 2, Hubble Space Telescope, and a number of ground‐based observatories. Our analysis of the North Equatorial Belt (NEB) dark projections (DPs) velocities and wave numbers shows that a dispersion relationship exists, with the DPs velocity (ranging from 97 to 113 m s−1) slightly increasing with wave number (ranging from 6 to 20, although usually 8–12). We interpret this relationship in terms of a superposition of equatorial Rossby waves traveling along the planet and confined to the upper troposphere. The resulting equivalent depth for the waves on an incompressible fluid is 1–2 km, and they move relative to a background flow with speed 140 m s−1, a result in good agreement with previous analysis of the wave interpretation for hot spot motions as observed in the infrared.
Tropical cyclone triggering of sediment discharge in Taiwan
Authors: Galewsky J. , Stark C. P. , Dadson S. , Wu C.‐C. , Sobel A. H. , Horng M.‐J.
Published: September 2006

The impact of tropical cyclones on precipitation variability and surface processes in Taiwan is studied using suspended sediment and river discharge data along with a meteorological model of tropical cyclone dynamics. The interactions between tropical cyclones and topography produce distinctive, localized patterns of heavy precipitation that can trigger high sediment discharge in Taiwan's rivers. We focus on Typhoon Toraji, which made landfall in Taiwan on 30 July 2001 and was the first major tropical cyclone to affect Taiwan after the 1999 Chichi earthquake. The passage of the tropical cyclone eye over the east coast of Taiwan produced intense rainfall (>100 mm h−1) for a short period (about 2 hours), triggering the highest sediment concentration ever recorded on the Hualien River. Orographic effects localized heavy rainfall (between 10 and 50 mm h−1) over the southwestern slopes of the Central Mountain Range, triggering high sediment discharge on the Kaoping River and flushing landslide debris produced during the Chichi earthquake into the Choshui River. We show that a range of atmospheric processes, with distinctive spatial variability and varying degrees of coupling to topography, interacted with tectonic processes of limited spatial extent to produce the overall sediment discharge from Taiwan during Typhoon Toraji. Landscape evolution models may need to be modified to account for the distinctive patterns of localized rainfall in tropical mountain belts. Furthermore, the links between tropical cyclones and topography suggest the potential for a range of previously unrecognized feedbacks between tectonics and climate in tropical mountain belts.
Adequacy of using surface humidity to estimate atmospheric moisture availability for probable maximum precipitation
Authors: Chen Li‐Chuan , Bradley A. Allen
Published: September 2006

Because of limitations in sampling of atmospheric moisture, surface humidity is used to estimate atmospheric moisture availability for probable maximum precipitation (PMP) estimation. In practice, a pseudoadiabatic moisture profile is assumed to estimate precipitable water from surface 12‐hour persisting dew point. This assumption was evaluated for the central United States using surface and upper air observations. The results show that the pseudoadiabatic assumption systematically overestimates precipitable water for PMP estimation. The overestimation occurs for extreme rainstorms and for climatological maximum conditions because the surface humidity is high but the upper air is drier than predicted by a pseudoadiabatic profile. To better represent the moisture relationship for the central United States, an empirical power law moisture profile was derived from a 23‐year climatology of the monthly maximum precipitable water and monthly maximum 12‐hour persisting dew point. Moisture maximization concepts were then used to recompute PMP estimates for the Chicago area. The results suggest that the pseudoadiabatic assumption overestimates PMP by about 6.9% on average. An analysis of atmospheric conditions for extreme rainstorms also raises concerns regarding the PMP moisture maximization assumption that such storms could occur under maximum atmospheric moisture conditions.
Simulation of groundwater recharge dynamics in partially saturated fractured soils incorporating spatially variable fracture apertures
Authors: Cey Edwin , Rudolph David , Therrien René
Published: September 2006

In this paper, numerical simulations are used to analyze complex flow behavior in partially saturated fractured low‐permeability soils during groundwater recharge. The aim is to develop an understanding of the influence of fracture‐matrix interactions and different physical parameters on flow processes. A three‐dimensional discrete fracture model is used to simulate infiltration into a variably saturated porous block containing a single vertical rough‐walled fracture. The results show that flow system dynamics are considerably more sensitive to matrix properties, namely, hydraulic conductivity and antecedent moisture content, than fracture properties. A high degree of fracture‐matrix interaction restricts preferential flow down the fracture and decreases the influence of fracture roughness. The study results suggest that aperture variability within individual fractures may be neglected when modeling water flow through unsaturated soils. Nevertheless, the fracture plays an important role in water movement and controls the vertical flux of a surface applied tracer.
Sulfur hexafluoride as a transient tracer in the North Pacific Ocean
Authors: Bullister John L. , Wisegarver David P. , Sonnerup Rolf E.
Published: September 2006

The atmospheric concentration of sulfur hexafluoride (SF6) has increased steadily during the past 30 years, making it potentially a valuable transient tracer of oceanic circulation and mixing processes on decadal timescales. Simultaneous measurements of dissolved SF6 with chlorofluorocarbons (CFCs), which have longer atmospheric histories but different growth rates, provides additional information over the use of each tracer alone. Concentrations of dissolved SF6, CFC11 and CFC12 were measured at the Hawaii Ocean Time‐Series (HOT) site in 2005. Concentrations were highest in the upper water column, with pronounced CFC11 and CFC12 maxima at a depth of ∼400 meters. Apparent water mass ages calculated from SF6 concentrations tend to be younger than those calculated from CFC12 concentrations. An isopycnal pipe model is used to estimate the effects of mixing on SF6 and CFC12 derived ages. Combining SF6 and CFC12 ages allows improved estimates of ideal ages and oceanic uptake of anthropogenic CO2.
Tectonic velocities, dynamic topography, and relative sea level
Authors: Husson Laurent , Conrad Clinton P.
Published: September 2006

A simple dynamic model based on boundary layer theory shows that dynamic topography is unlikely to vary significantly in response to short term (≤20 Myr) variations in the mean tectonic velocity. Tectonic velocities essentially mirror variations in mantle viscosity, but are not indicative of substantial modification of dynamic topography, which primarily reflects mass anomalies in the mantle. This implies that relative sea level is unlikely to be affected by “tectonic pulses” and also that observed tilting of cratonic margins cannot result from a pulse of increased tectonic velocities. Thus, relative sea level is primarily controlled by the seafloor age distribution, although long term (≥100 Myrs) changes in tectonic velocity will produce dynamic topography that reinforces sea level changes associated with changing ridge volume.
Impact of nonabsorbing anthropogenic aerosols on clear‐sky atmospheric absorption
Authors: Stier Philip , Seinfeld John H. , Kinne Stefan , Feichter Johann , Boucher Olivier
Published: September 2006

Absorption of solar radiation by atmospheric aerosol has become recognized as important in regional and global climate. Nonabsorbing, hydrophilic aerosols, such as sulfate, potentially affect atmospheric absorption in opposing ways: first, decreasing absorption through aging initially hydrophobic black carbon (BC) to a hydrophilic state, enhancing its removal by wet scavenging, and consequently decreasing BC lifetime and abundance, and second, increasing absorption through enhancement of the BC absorption efficiency by internal mixing as well as through increasing the amount of diffuse solar radiation in the atmosphere. On the basis of General Circulation Model studies with an embedded microphysical aerosol module we systematically demonstrate the significance of these mechanisms both on the global and regional scales. In remote transport regions, the first mechanism prevails, reducing atmospheric absorption, whereas in the vicinity of source regions, despite enhanced wet scavenging, absorption is enhanced owing to the prevalence of the second mechanisms. Our findings imply that the sulfur to BC emission ratio plays a key role in aerosol absorption.
An evaluation of the geomorphically effective event for fluvial processes over long periods
Authors: Huang Xiangjiang , Niemann Jeffrey D.
Published: September 2006

Fluvial processes erode landscapes in response to a wide range of discharges. The importance of a given discharge to the erosion of a basin can be calculated by multiplying the discharge's frequency of occurrence and the erosion rate produced by the discharge. The discharge that contributes the most geomorphic work is called the geomorphically effective event (GEE). In this paper, the behavior of the GEE is examined when a generic stream power model with a threshold is used to describe either the detachment or transport of sediment by flowing water. The results suggest that the return period of the GEE depends primarily on the threshold value when the exponent on discharge is less than 2. Otherwise, it depends primarily on the exponent. The GEE usually cannot be substituted for the probability density function of discharge because it produces a different long‐term erosion rate. Furthermore, the return period of the GEE can vary spatially in a basin. For example, the return period can be different between locations where the fluvial process is dominant and subdominant if the threshold is nonzero. For a detachment‐limited model the return period of the GEE is different upstream and downstream of knickpoints, and for a transport‐limited model the return period is different along channel profiles even at steady state. Spatial variation in streamflow generation also produces spatial variations in the return period of the GEE.
Small molecules with antimicrobial activity against E. coli and P. aeruginosa identified by high‐throughput screening
Authors: De La Fuente R , Sonawane N D , Arumainayagam D , Verkman A S
Published: September 2006

Background and purpose:

New antimicrobials are needed because of the emergence of organisms that are resistant to available antimicrobials. The purpose of this study was to evaluate a high‐throughput screening approach to identify antibacterials against two common disease‐causing bacteria, and to determine the frequency, novelty, and potency of compounds with antibacterial activity.

Experimental approach:

A high‐throughput, turbidometric assay of bacterial growth in a 96‐well plate format was used to screen a diverse collection of 150,000 small molecules for antibacterial activity against E. coli and P. aeruginosa. The statistical Z′‐factor for the assay was 0.7.

Key results:

Screening for inhibition of E. coli growth gave a ‘hit’ rate (>60% inhibition at 12.5 μM) of 0.025%, which was more than 5‐fold reduced for P. aeruginosa. The most potent antibacterials (EC50<0.5 μM) were of the nitrofuran class followed by naphthalimide, salicylanilide, bipyridinium and quinoazolinediamine chemical classes. Screening of >250 analogs of the most potent antibacterial classes established structure‐activity data sets.

Conclusions and Implications:

Our results validate and demonstrate the utility of a growth‐based phenotype screen for rapid identification of small‐molecule antibacterials. The favourable efficacy and structure‐activity data for several of the antibacterial classes suggests their potential development for clinical use.

British Journal of Pharmacology (2006) 149, 551–559. doi:10.1038/sj.bjp.0706873
Cholinergic regulation of epithelial ion transport in the mammalian intestine
Authors: Hirota C L , McKay D M
Published: September 2006

Acetylcholine (ACh) is critical in controlling epithelial ion transport and hence water movements for gut hydration. Here we review the mechanism of cholinergic control of epithelial ion transport across the mammalian intestine. The cholinergic nervous system affects basal ion flux and can evoke increased active ion transport events. Most studies rely on measuring increases in short‐circuit current (ISC= active ion transport) evoked by adding ACh or cholinomimetics to intestinal tissue mounted in Ussing chambers. Despite subtle species and gut regional differences, most data indicate that, under normal circumstances, the effect of ACh on intestinal ion transport is mainly an increase in Cl‐secretion due to interaction with epithelial M3muscarinic ACh receptors (mAChRs) and, to a lesser extent, neuronal M1mAChRs; however, AChR pharmacology has been plagued by a lack of good receptor subtype‐selective compounds. Mice lacking M3mAChRs display intact cholinergically‐mediated intestinal ion transport, suggesting a possible compensatory mechanism. Inflamed tissues often display perturbations in the enteric cholinergic system and reduced intestinal ion transport responses to cholinomimetics. The mechanism(s) underlying this hyporesponsiveness are not fully defined. Inflammation‐evoked loss of mAChR‐mediated control of epithelial ion transport in the mouse reveals a role for neuronal nicotinic AChRs, representing a hitherto unappreciated braking system to limit ACh‐evoked Cl‐secretion. We suggest that: i) pharmacological analyses should be supported by the use of more selective compounds and supplemented with molecular biology techniques targeting specific ACh receptors and signalling molecules, and ii) assessment of ion transport in normal tissue must be complemented with investigations of tissues from patients or animals with intestinal disease to reveal control mechanisms that may go undetected by focusing on healthy tissue only.

British Journal of Pharmacology(2006)149, 463–479. doi:10.1038/sj.bjp.0706889
Regional vascular responses to ATP and ATP analogues in the rabbit kidneyin vivo: roles for adenosine receptors and prostanoids
Authors: Eppel G A , Ventura S , Evans R G
Published: September 2006

Background and purpose:

Our knowledge of the effects of P2‐receptor activation on renal vascular tone comes mostly fromin vitromodels. We aimed to characterise the pharmacology of ATP in the renal circulationin vivo.

Experimental approach:

In pentobarbitone anaesthetized rabbits, we examined total renal and medullary vascular responses to ATP (0.2 and 0.8 mg kg‐1), β,γ‐methylene ATP (β,γ‐mATP, 7 and 170 μg kg‐1), α,β‐mATP (0.2 and 2 μg kg‐1) and adenosine (2 and 6 μg kg‐1) using transit‐time ultrasound and laser Doppler flowmetry, respectively. We also determined whether adenosine receptors, NO or prostanoids contribute to the actions of the purinoceptor agonists.

Key results:

Renal arterial boluses of ATP, β,γ‐mATP, and adenosine produced biphasic changes; ischaemia followed by hyperaemia, in total renal and medullary blood flow. α,β‐mATP induced only ischaemia. The adenosine receptor antagonist 8‐(p‐sulphophenyl)theophylline reduced the responses to adenosine and the hyperaemic responses to ATP and β,γ‐mATP only. NO synthase inhibition (Nω‐nitro‐L‐arginine) did not significantly alter responses to the P2 receptor agonists. Subsequent cyclooxygenase inhibition (ibuprofen) reduced the ATP‐ and β,γ‐mATP‐induced increases in renal blood flow. All other responses remained unchanged.

Conclusions and implications:

In the rabbit kidneyin vivo, α,β‐mATP sensitive receptors mediate vasoconstriction. β,γ‐mATP and ATP induce vasodilation at least partly through adenosine receptors. ATP induced renal vasodilatation is independent of NO and partly dependent on prostanoids in the bulk of the kidney, but not in the vasculature controlling medullary blood flow.

British Journal of Pharmacology(2006)149, 523–531. doi:10.1038/sj.bjp.0706901
Spectroscopic studies of fractal aggregates of silver nanospheres undergoing local restructuring
Authors: Karpov Sergei V. , Gerasimov Valeriy S. , Isaev Ivan L. , Markel Vadim A.
Published: September 2006

We present an experimental spectroscopic study of large random colloidal aggregates of silver nanoparticles undergoing local restructuring. We argue that such well-known phenomena as strong fluctuation of local electromagnetic fields, appearance of “hot spots” and enhancement of nonlinear optical responses depend on the local structure on the scales of several nanosphere diameters, rather than the large-scale fractal geometry of the sample.
The molecular origins of nonlinear response in solute energy relaxation: The example of high-energy rotational relaxation
Authors: Tao Guohua , Stratt Richard M.
Published: September 2006

A key step in solution-phase chemical reactions is often the removal of excess internal energy from the product. Yet, the way one typically studies this process is to follow the relaxation of a solute that has been excited into some distribution of excited states quite different from that produced by any reaction of interest. That the effects of these different excitations can frequently be ignored is a consequence of the near universality of linear-response behavior, the idea that relaxation dynamics is determined by the solvent fluctuations (which may not be all that different for different kinds of solute excitation). Nonetheless, there are some clear examples of linear-response breakdowns seen in solute relaxation, including a recent theoretical and experimental study of rapidly rotating diatomics in liquids. In this paper we use this rotational relaxation example to carry out a theoretical exploration of the conditions that lead to linear-response failure. Some features common to all of the linear-response breakdowns studied to date, including our example, are that the initial solute preparation is far from equilibrium, that the subsequent relaxation promotes a significant rearrangement of the liquid structure, and that the nonequilibrium response is nonstationary. However, we show that none of these phenomena is enough to guarantee a nonlinear response. One also needs a sufficient separation between the solute time scale and that of the solvent geometry evolution. We illustrate these points by demonstrating precisely how our relaxation rate is tied to our liquid-structural evolution, how we can quantitatively account for the initial nonstationarity of our effective rotational friction, and how one can tune our rotational relaxation into and out of linear response.
Depolarized light scattering versus optical Kerr effect spectroscopy of supercooled liquids: Comparative analysis
Authors: Brodin Alexander , Rössler Ernst A.
Published: September 2006

Recently, heterodyne-detected optical Kerr effect (HD-OKE) spectroscopy was used to study dynamics of supercooled molecular liquids. The studies revealed an apparently new physical phenomenon that had not been reported before from the related depolarized light scattering (DLS), namely, an intermediate power law (nearly logarithmic decay) of the response functions [H. Cang et al., J. Chem. Phys. 118, 2800 (2003)]. Conceptually, HD-OKE and DLS data reflect optical anisotropy fluctuations mainly due to molecular reorientation dynamics in time and frequency domains, respectively. The above-mentioned effects are revealed in the mesoscopic range ≲1GHz (≳100ps), where no direct comparison of the techniques was reported. In this Communication, we attempt such a comparison of exemplifying HD-OKE literature data of the glass-forming salol (phenyl salicylate), benzophenone, and liquid-crystal forming 4-cyano-4′-pentylbiphenyl with DLS data of the same systems that we measured down to ca. 200MHz by a combined tandem Fabry-Pérot interferometer plus tandem-grating-monochromator technique. Generally, we find a satisfactory agreement, albeit in some cases with subtle differences at frequencies ≳10GHz. We conclude that, in the mesoscopic dynamic range, HD-OKE and DLS studies provide consistent and comparable information, and therefore their conclusions must agree. We argue that the intermediate power law of HD-OKE is in essence a manifestation of the excess wing of the corresponding frequency-domain data, known long since from broadband dielectric spectroscopy and anticipated from DLS studies of supercooled liquids.
On suq(1,1)-models of quantum oscillator
Authors: Atakishiyev M. N. , Atakishiyev N. M. , Klimyk A. U.
Published: September 2006

Models of the quantum oscillator, based on the discrete series representations of the quantum algebra suq(1,1), are constructed. The position and momentum operators in these models are twisted generators J2 and J1 for such suq(1,1)-representations, respectively. As in the case of the standard harmonic oscillator in quantum mechanics, the position and momentum operators here have continuous simple spectra. These spectra cover a finite interval on the real line, which depends on a value of q. Eigenfunctions of these operators are explicitly found. It is shown that the Macfarlane–Biedenharn q-oscillator is a limit case of the oscillators under discussion. The q=1 limit case, in which spectra of the position and momentum operators cover the whole real line, is also considered in detail.
On Fay identity
Authors: Michev Iordan P.
Published: September 2006

In the first part of this paper we consider the transformation of the cubic identities for general Korteweg–de Vries (KdV) tau functions from [Mishev, J. Math. Phys. 40, 2419–2428 (1999)] to the specific identities for trigonometric KdV tau functions. Afterwards, we consider the Fay identity as a functional equation and provide a wide set of solutions of this equation. The main result of this paper is Theorem 3.4, where we generalize the identities from Mishev. An open problem is the transformation of the cubic identities from Mishev to the specific identities for elliptic KdV tau functions.
Effect of quantum partial charges on the structure and dynamics of water in single-walled carbon nanotubes
Authors: Won Chang Y. , Joseph Sony , Aluru N. R.
Published: September 2006

In this work, using quantum partial charges, computed from 6–31G**∕B3LYP density functional theory, in molecular dynamics simulations, we found that water inside (6,6) and (10,0) single-walled carbon nanotubes with similar diameters but with different chiralities has remarkably different structural and dynamical properties. Density functional calculations indicate that tubes with different chiralities have significantly different partial charges at the ends of tubes. The partial charges at the ends of a (10,0) tube are around 4.5 times higher than those of a (6,6) tube. Molecular dynamics simulations with the partial charges show different water dipole orientations. In the (10,0) tube, dipole vectors of water molecules at the end of the tube point towards the water reservoir resulting in the formation of an L defect in the center region. This is not observed in the (6,6) tube where dipole vectors of all the water molecules inside the tube point towards either the top or the bottom water reservoir. The water diffusion coefficient is found to increase in the presence of the partial charges. Water in the partially charged (10,0) tube has a lower diffusion coefficient compared to that of in the partially charged (6,6) tube.
Coexistence of ferroelectricity and ferromagnetism in tantalum clusters
Authors: Fa Wei , Luo Chuanfu , Dong Jinming
Published: September 2006

The atomic and electronic structures of TaN (N=2–23) clusters have been determined in the framework of pseudopotential density-functional calculations, based upon an unbiased global search with guided simulated annealing to an empirical potential. It is found that the ground-state structures of TaN are very similar to those of NbN, showing no preference for the icosahedral growth. Also, a size- and structure-dependent ferroelectricity is found in these tantalum clusters. More importantly, it is found that the ferroelectricity and ferromagnetism can coexist in the homogeneous transition-metal cluster, offering a possibility to obtain a new type of “multiferroic” materials composed of the clusters. Finally, the far-infrared spectroscopy is suggested to be an efficient tool to distinguish the ferroelectric clusters.
On the impact of vessel size on the threshold of bubble collapse
Authors: Sassaroli E. , Hynynen K.
Published: September 2006

A series of experiments involving microbubbles in narrow tubes is presented. The threshold for bubble collapse has been investigated as a function of the applied pressure and tube diameter. The threshold has been found to be dependent not only on the applied pressure amplitude but also on the tube size with an increase for smaller tubes. The data have been interpreted in terms of a simple damped harmonic oscillator model. The motivation of this study lies in the possibility of obtaining a better understanding of microbubble behavior in blood vessels in order to optimize applications of microbubbles in medical ultrasound.
Structure, dynamics, and electronic properties of lithium disilicate melt and glass
Authors: Du Jincheng , Corrales L. Rene
Published: September 2006

Ab initio molecular dynamics simulations within the framework of density functional theory have been performed to study the structural, dynamic, and electronic properties of lithium disilicate melt and the glass derived from quenching the melt. It is found that lithium ions have a much higher diffusion coefficient and show different diffusion mechanisms than the network forming silicon and oxygen ions in the melt. The simulated lithium disilicate glass structure has 100% four coordinated silicon, close to theoretical nonbridging oxygen to bridging oxygen ratio (2:3), and Qn distributions of 20.8%, 58.4%, and 20.8% for n=2,3,4, respectively. In the melt there are considerable amounts (10%–15%) of silicon coordination defects; however, the average silicon coordination number remains about 4, similar to that in the glass. The lithium ion coordination number increases from 3.7 in the glass to 4.4 in the melt mainly due to the increase of bridging oxygen in the first coordination shell. The bond length and bond angle distributions, vibrational density of states, and static structure factors of the simulated glass were determined where the latter was found to be in good agreement with experimental measurement. Atomic charges were obtained based on Bader and Hirshfeld population analyses [Atoms in Molecule: A Quantum Theory (Oxford University Press, Oxford, 1990); Theor. Chim. Acta 44, 129 (1977)]. The average Bader charges found in lithium disilicate glass were −1.729, 3.419, and 0.915 for oxygen, silicon, and lithium, respectively. The corresponding Hirshfeld charges were −0.307, 0.550, and 0.229. The electronic densities of states of the melt and glass were calculated and compared with those of crystalline lithium disilicate.
New evaluation of reconstructed spatial distribution function from radial distribution functions
Authors: Yokogawa Daisuke , Sato Hirofumi , Sakaki Shigeyoshi
Published: September 2006

Although three dimensional (3D) solvation structure is much more informative than one dimensional structure, its evaluation is difficult experimentally and theoretically. In our previous Communication [Yokogawa et al., J. Chem. Phys. 123, 211102 (2005)], we proposed a new method to present reconstructed spatial distribution function (RC-SDF) from a set of radial distribution functions (RDFs). In this article, we successfully extended the method more accurately with new basis sets. This new method was applied to two liquid solvation structures, methanol and dimethyl sulfoxide, as examples. Their RC-SDFs evaluated here clearly show that the former solvation structure is well defined while the latter one is broad, which agrees well with the SDFs calculated directly from molecular dynamics simulations. These results indicate that the method can reproduce well these 3D solvation structures in reasonable computational cost.
Vertically aligned tin-doped indium oxide nanowire arrays: Epitaxial growth and electron field emission properties
Authors: Wan Q. , Feng P. , Wang T. H.
Published: September 2006

Vertically aligned tin-doped indium oxide (ITO) single-crystalline nanowire arrays are epitaxially grown on ITO/yttrium stabilized zirconia substrates by vapor transport method. Vacuum electron field emission properties of the aligned ITO nanowires are investigated. The turn-on electrical field at a current density of 1μA∕cm2 is about 2.0V∕μm, and the lowest vacuum for an obvious emission is 1×10−1Pa. The good performance of field emission is attributed to the vertically aligned morphology, which has a stronger local electric field due to their orientation parallel to the electric-field direction.
C 1 s and O1s photoelectron satellite spectra of CO with symmetry-dependent vibrational excitations
Authors: Ehara M. , Kuramoto K. , Nakatsuji H. , Hoshino M. , Tanaka T. , Kitajima M. , Tanaka H. , De Fanis A. , Tamenori Y. , Ueda K.
Published: September 2006

The photoelectron shake-up satellite spectra that accompany the C1s and O1s main lines of carbon monoxide have been studied by a combination of high-resolution x-ray photoelectron spectroscopy and accurate ab initio calculations. The symmetry-adapted cluster-expansion configuration-interaction general-R method satisfactorily reproduces the satellite spectra over a wide energy region, and the quantitative assignments are proposed for the 16 and 12 satellite bands for C1s and O1s spectra, respectively. Satellite peaks above the π−1π* transitions are mainly assigned to the Rydberg excitations accompanying the inner-shell ionization. Many shake-up states, which interact strongly with three-electron processes such as π−2π*2 and n−2π*2, are calculated in the low-energy region, while the continuous Rydberg excitations are obtained with small intensities in the higher-energy region. The vibrational structures of low-lying shake-up states have been examined for both C1s and O1s ionizations. The vibrational structures appear in the low-lying C1s satellite states, and the symmetry-dependent angular distributions for the satellite emission have enabled the Σ and Π symmetries to be resolved. On the other hand, the potential curves of the low-lying O1s shake-up states are predicted to be weakly bound or repulsive.
Electron mobility in dilute GaAs bismide and nitride alloys measured by time-resolved terahertz spectroscopy
Authors: Cooke D. G. , Hegmann F. A. , Young E. C. , Tiedje T.
Published: September 2006

We report time-resolved terahertz spectroscopy measurements of the electronic transport properties of dilute GaAs bismide and nitride alloys. The electron mobility for GaAs1−yBiy (y=0.84%) extracted from Drude fits to the transient complex conductivity was ∼2800cm2∕Vs at a carrier density of 2.7×1018cm−3, close to the mobility of 3300cm2∕Vs measured for GaAs at a similar carrier density. The electron mobility did not decrease significantly for Bi concentrations up to 1.4%. In contrast, the GaNxAs1−x (x=0.84%) and GaNxAs1−x−yBiy (x=0.85%, y=1.4%) films exhibited non-Drude behavior with a highly reduced electron mobility and suppressed conductivity at low frequencies indicative of carrier localization.
Isomerization dynamics and thermodynamics of ionic argon clusters
Authors: Calvo F. , Gadéa F. X. , Lombardi A. , Aquilanti V.
Published: September 2006

The dynamics and thermodynamics of small Arn+ clusters, n=3, 6, and 9, are investigated using molecular dynamics (MD) and exchange Monte Carlo (MC) simulations. A diatomic-in-molecule Hamiltonian provides an accurate model for the electronic ground state potential energy surface. The microcanonical caloric curves calculated from MD and MC methods are shown to agree with each other, provided that the rigorous conservation of angular momentum is accounted for in the phase space density of the MC simulations. The previously proposed projective partition of the kinetic energy is used to assist MD simulations in interpreting the cluster dynamics in terms of inertial, internal, and external modes. The thermal behavior is correlated with the nature of the charged core in the cluster by computing a dedicated charge localization order parameter. We also perform systematic quenches to establish a connection with the various isomers. We find that the Ar3+ cluster is very stable in its linear ground state geometry up to about 300K, and then isomerizes to a T-shaped isomer in which a quasineutral atom lies around a charged dimer. In Ar6+ and Ar9+, the covalent trimer core is solvated by neutral atoms, and the weakly bound solvent shell melts at much lower energies, occasionally leading to a tetramer or pentamer core with weakly charged extremities. At high energies the core itself becomes metastable and the cluster transforms into Ar2+ solvated by a fluid of neutral argon atoms.
Polymer transistors fabricated by painting of metallic nanoparticles
Authors: Li S. P. , Russell D. M. , Newsome C. J. , Kugler T. , Shimoda T.
Published: September 2006

In this letter the authors describe the fabrication of high performance polymer thin film transistors using an aqueous based silver colloid to form source and drain electrodes patterned by brush painting. The electrode dimensions were controlled by a surface energy pattern defined by soft contact printing of a self-assembled monolayer 1H,1H,2H,2H-perfluorodecyl-trichlorosilane on a SiO2 surface which acted as a dewetting layer for the painted silver particle suspension. Another self-assembled monolayer of 1H,1H,2H,2H-perfluorodecanethiol was also used to increase the work function of the patterned silver electrodes in order to decrease the barrier for charge injection into the polymer semiconductor. The field-effect mobility of the thin film transistors fabricated by this method approached 0.02cm2V−1s−1 with an on/off current ratio of 105. The relative high mobility may be influenced by the ordering of the poly(3-hexylthiophene) semiconductor layer by the self-assembled monolayer used to define the source and drain electrodes.
Charging effect on current conduction in aluminum nitride thin films containing Al nanocrystals
Authors: Liu Y. , Chen T. P. , Lau H. W. , Wong J. I. , Ding L. , Zhang S. , Fung S.
Published: September 2006

The presence of Al nanocrystals (nc-Al) in AlN thin films is found to enhance the current conduction of the thin film system greatly due to the formation of tunneling paths of nc-Al arrays, and the nc-Al∕AlN system shows a quasi-two-dimensional transport following a power law. However, charge trapping in nc-Al reduces the current conduction because of the increase in the tunneling resistance and/or the breaking of some tunneling paths due to Coulomb blockade effect. The current conduction also evolves with a trend towards one-dimensional transport due to the breaking of some transverse tunneling paths as a result of the charge trapping.
Microlithography of electron gases formed at interfaces in oxide heterostructures
Authors: Schneider C. W. , Thiel S. , Hammerl G. , Richter C. , Mannhart J.
Published: September 2006

Submicron wide structures of conducting quasi-two-dimensional electron gases generated at SrTiO3∕LaAlO3 interfaces have successfully been patterned by modulating the thickness of the LaAlO3 layers with unit cell resolution. This technique allows the authors to structure the electron gases without exposing them to the environment and without incorporating other materials at the edges. The structured electron gases have resistances of ≈200Ω∕◻ (4.2K) and mobilities of ≈700cm2∕Vs (4.2K), while the resistances of the areas patterned to be insulating exceed 1010Ω∕◻.
Direct determination of Mn occupations in Ga1−xMnxN dilute magnetic semiconductors by x-ray absorption near-edge structure spectroscopy
Authors: Wei Shiqiang , Yan Wensheng , Sun Zhihu , Liu Qinghua , Zhong Wenjie , Zhang Xinyi , Oyanagi Hiroyuki , Wu Ziyu
Published: September 2006

X-ray absorption near-edge structure (XANES) spectroscopy is used to study the features of occupation sites of Mn dopants in the Ga1−xMnxN dilute magnetic semiconductors (DMSs) with zinc-blende structure. Theoretical XANES spectra are calculated for representative structure models of Mn atoms in the GaN lattice. It is shown that the substitutional Mn in GaN is characterized by a preedge peak at 2.0eV and a postedge multiple-scattering peak at 29.1eV. The peaks shift in position and drop in intensity dramatically for the interstitial MnI and MnGa–MnI dimer, and then disappear completely for Mn clusters. The experimental spectrum of Ga0.990Mn0.010N is almost reproduced by the calculated XANES spectrum of GaMnN with substitutional Mn.
Inherent nanoscale bend of crystal lattice in Fe-doped calcium copper titanate
Authors: Chung Sung-Yoon , Choi Si-Young , Yamamoto Takahisa , Ikuhara Yuichi
Published: September 2006

Utilizing high-resolution electron microscopy and image simulation, it is demonstrated that some of the crystal lattices of Fe-doped CaCu3Ti4O12 are intrinsically bent at the nanometer scale. A comparison between experimentally obtained and simulated images indicates that the bending angle is of a few milliradians, which is remarkable in a brittle oxide. Despite such lattice distortion, much of the lattice strain induced by the distortion appears to be released at the domain walls where a number of misfit dislocations are present.
Electrical detection of deoxyribonucleic acid hybridization with AlGaN∕GaN high electron mobility transistors
Authors: Kang B. S. , Pearton S. J. , Chen J. J. , Ren F. , Johnson J. W. , Therrien R. J. , Rajagopal P. , Roberts J. C. , Piner E. L. , Linthicum K. J.
Published: September 2006

Au-gated AlGaN∕GaN high electron mobility transistor (HEMT) structures were functionalized in the gate region with label-free 3′-thiol-modified oligonucleotides. This serves as a binding layer to the AlGaN surface for hybridization of matched target deoxyribonucleic acid (DNA). X-ray photoelectron spectroscopy shows the immobilization of thiol-modified DNA covalently bonded with gold on the gated region. Hybridization between probe DNA and matched or mismatched target DNA on the Au-gated HEMT was detected by electrical measurements. The HEMT drain-source current showed a clear decrease of 115μA as this matched target DNA was introduced to the probe DNA on the surface, showing the promise of the DNA sequence detection approach for biological sensing.