bluuebunny/crossref_metadata_2025 huggingface dataset:
Self-consistent mean-field model based on molecular dynamics: Application to lipid-cholesterol bilayers
Authors: Khelashvili George A. , Pandit Sagar A. , Scott H. L.
Published: July 2005

We have developed a dynamic self-consistent mean-field model, based on molecular-dynamics simulations, to study lipid-cholesterol bilayers. In this model the lipid bilayer is represented as a two-dimensional lattice field in the lipid chain order parameters, while cholesterol molecules are represented by hard rods. The motion of rods in the system is continuous and is not confined to lattice cells. The statistical mechanics of chain ordering is described by a mean field derived from an extension of a model due to Marčelja. The time evolution of the system is governed by stochastic equations. The ensemble of chain configurations required in partition sums, and the energies of interaction, are taken from atomistic level molecular-dynamics simulations of lipid bilayers. The model allows us to simulate systems 500nm in lateral size for 20μs time scales, or greater. We have applied the model to dipalmitoyl-phosphatidylcholine–cholesterol (Chol) bilayers at 50°C for Chol concentrations between 2% and 33%. At low concentrations of Chol (2%–4%), the model predicts the formation of isolated clusters of Chol surrounded by relatively ordered lipid chains, randomly dispersed in the disordered bilayer. With increasing Chol composition, regions of Chol-induced order begin to overlap. Starting from about 11% Chol this ordering effect becomes system wide and regions unaffected by Chol are no longer detectable. From the analysis of properties of the model we conclude that the change in lipid chain order with increasing Chol concentration is continuous over the 20-μs scale of the simulations. We also conclude that at 50°C no large-scale Chol-rich and Chol-depleted coexisting phase-separated regions form at any concentration. At no point in any of the simulations do we observe a higher degree of lateral organization, such as Chol-based superlattice structures.
Absolute free energy calculations by thermodynamic integration in four spatial dimensions
Authors: Rodinger Tomas , Howell P. Lynne , Pomès Régis
Published: July 2005

An optimized technique for calculating the excess chemical potential of small molecules in dense liquids and the binding affinity of molecular ligands to biomolecules is reported. In this method, a molecular species is coupled to the system of interest via a nonphysical fourth spatial dimension w through which insertion or extraction can be carried out [R. Pomès, E. Eisenmesser, C. B. Post et al., J. Chem. Phys. 111, 3387 (1999)]. Molecular simulations are used to compute the potential of mean force (PMF) acting on the solute molecule in the fourth dimension. The excess chemical potential of that molecule is obtained as the difference in the PMF between fully coupled and fully decoupled systems. The simplicity, efficiency, and generality of the method are demonstrated for the calculation of the hydration free energies of water and methanol as well as sodium, cesium, and chloride ions. A significant advantage over other methods is that the 4D-PMF approach provides a single effective and general route for decoupling all nonbonded interactions (i.e., both Lennard-Jones and Coulombic) at once for both neutral and charged solutes. Direct calculation of the mean force from thermodynamic integration is shown to be more computationally efficient than calculating the PMF from umbrella sampling. Statistical error analysis suggests a simple strategy for optimizing sampling. The detailed analysis of systematic errors arising from the truncation of Coulombic interactions in a solvent droplet of finite size leads to straightforward corrections to ionic hydration free energies.
Diffusion-influenced excited-state reversible transfer reactions, A*+B⇌C*+D, with two different lifetimes: Theories and simulations
Authors: Park Soohyung , Shin Kook Joe , Popov Alexander V. , Agmon Noam
Published: July 2005

We report accurate Brownian simulation results for the kinetics of the pseudo-first-order diffusion-influenced excited-state reversible transfer reaction A*+B⇌C*+D with two different lifetimes using two different propagation algorithms. The results are used to test approximate solutions for this many-particle problem. Available theories fail when one of the two reactions or (decay) rate constants is large. To remedy this situation, we develop two uniform approximations, which are based on introducing a generalized Smoluchowski term into the relaxation-time approximation. The best of these is the extended unified theory of reversible target reactions, which reduces correctly in all limits and exhibits superior agreement with simulations.
Investigation of composition fluctuations in GaN:Mg using optical transmission spectroscopy, near-field scanning optical microscopy, and scanning Kelvin probe microscopy
Authors: Han B. , Wessels B. W. , Ulmer M. P.
Published: July 2005

Composition fluctuations in GaN:Mg have been investigated by optical transmission spectroscopy, near-field scanning optical microscopy (NSOM), and scanning Kelvin probe microscopy (SKPM). An Urbach tail is observed in the optical transmission spectrum of heavily Mg-doped GaN, with the magnitude of Urbach energy increasing with increasing compositional/potential fluctuations. From the relationship between the Urbach energy and the potential fluctuation magnitude, the spatial size of the compositional fluctuations in GaN:Mg (with the average Mg concentration of ∼4×1019cm−3) is calculated to be 220nm. The nanoscale compositional fluctuations are determined by NSOM and SKPM. A spatial variation of the transmission mode NSOM intensity is observed with a characteristic wavelength of ∼300nm, which is attributed to the inhomogeneous distribution of Mg. The normalized root-mean-square (rms) fluctuation of the transmission mode NSOM intensity for heavily Mg-doped GaN is a factor of 5 greater than that for undoped GaN. Similar microstructure patterns are observed in the NSOM and surface potential images of GaN:Mg as probed by SKPM. The variation of local surface potential (on the order of 100mV) is attributed to the same compositional fluctuations of Mg, which changes the local surface work function. The local Mg concentrations are calculated from the SKPM image. For GaN:Mg with the Mg concentration of 4×1019cm−3, a rms value of 5.4×1019cm−3 of the compositional fluctuations has been observed.
Two-Gaussian excitations model for the glass transition
Authors: Matyushov Dmitry V. , Angell C. A.
Published: July 2005

We develop a modified “two-state” model with Gaussian widths for the site energies of both ground and excited states, consistent with expectations for a disordered system. The thermodynamic properties of the system are analyzed in configuration space and found to bridge the gap between simple two-state models (“logarithmic” model in configuration space) and the random energy model (“Gaussian” model in configuration space). The Kauzmann singularity given by the random energy model remains for very fragile liquids but is suppressed or eliminated for stronger liquids. The sharp form of constant-volume heat capacity found by recent simulations for binary mixed Lennard-Jones and soft-sphere systems is reproduced by the model, as is the excess entropy and heat capacity of a variety of laboratory systems, strong and fragile. The ideal glass in all cases has a narrow Gaussian, almost invariant among molecular and atomic glassformers, while the excited-state Gaussian depends on the system and its width plays a role in the thermodynamic fragility. The model predicts the possibility of first-order phase transitions for fragile liquids. The analysis of laboratory data for toluene and o-terphenyl indicates that fragile liquids resolve the Kauzmann paradox by a first-order transition from supercooled liquid to ideal-glass state at a temperature between Tg and Kauzmann temperature extrapolated from experimental data. We stress the importance of the temperature dependence of the energy landscape, predicted by the fluctuation-dissipation theorem, in analyzing the liquid thermodynamics.
Investigation of the poly[2-methoxy-5-(2′-ethyl-hexyloxy)-1,4-phenylene vinylene]∕indium tin oxide interface using photoemission spectroscopy
Authors: Lägel B. , Beerbom M. M. , Doran B. V. , Lägel M. , Cascio A. , Schlaf R.
Published: July 2005

The interface between the luminescent polymer poly [2-methoxy-5-(2′-ethyl-hexyloxy)-1,4-phenylene vinylene] (MEH-PPV) and sputter-cleaned indium tin oxide (ITO) was investigated using photoemission spectroscopy in combination with in situ thin film deposition. MEH-PPV was deposited in high vacuum directly from toluene solution on the ITO substrate using a home-built electrospray thin-film deposition system. The deposition was carried out in multiple steps without breaking the vacuum. In between deposition steps the sample was characterized with x-ray and ultraviolet photoemission spectroscopy. The evaluation of the spectra sequence allowed the determination of the orbital lineup (charge injection barriers) at the interface, as well as the MEH-PPV growth mode at the interface.
Melting temperature of ice Ih calculated from coexisting solid-liquid phases
Authors: Wang J. , Yoo S. , Bai J. , Morris James R. , Zeng X. C.
Published: July 2005

We carried out molecular-dynamics simulations by using the two-phase coexistence method with the constant pressure, particle number, and enthalpy ensemble to compute the melting temperature of proton-disordered hexagonal ice Ih at 1-bar pressure. Four models of water were considered, including the widely used TIP4P [W. L. Jorgensen, J. Chandrasekha, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys.79, 926 (1983)] and TIP5P [M. W. Mahoney and W. L. Jorgensen J. Chem. Phys.112, 8910 (2000)] models, as well as recently improved TIP4P and TIP5P models for use with Ewald techniques—the TIP4P-Ew [W. Horn, W. C. Swope, J. W. Pitera, J. C. Madura, T. J. Dick, G. L. Hura, and T. Head-Gordon, J. Chem. Phys.120, 9665 (2004)] and TIP5P-Ew [S. W. Rick, J. Chem. Phys.120, 6085 (2004)] models. The calculated melting temperature at 1bar is Tm=229±1K for the TIP4P and Tm=272.0±0.6K for the TIP5P ice Ih, both are consistent with previous simulations based on free-energy methods. For the TIP4P-Ew and TIP5P-Ew models, the calculated melting temperature is Tm=257.0±1.1K and Tm=253.9±1.1K, respectively.
Hydration forces between silica surfaces: Experimental data and predictions from different theories
Authors: Valle-Delgado J. J. , Molina-Bolívar J. A. , Galisteo-González F. , Gálvez-Ruiz M. J. , Feiler A. , Rutland M. W.
Published: July 2005

Silica is a very interesting system that has been thoroughly studied in the last decades. One of the most outstanding characteristics of silica suspensions is their stability in solutions at high salt concentrations. In addition to that, measurements of direct-interaction forces between silica surfaces, obtained by different authors by means of surface force apparatus or atomic force microscope (AFM), reveal the existence of a strong repulsive interaction at short distances (below 2nm) that decays exponentially. These results cannot be explained in terms of the classical Derjaguin, Landau, Verwey, and Overbeek (DLVO) theory, which only considers two types of forces: the electrical double-layer repulsion and the London–van der Waals attraction. Although there is a controversy about the origin of the short-range repulsive force, the existence of a structured layer of water molecules at the silica surface is the most accepted explanation for it. The overlap of structured water layers of different surfaces leads to repulsive forces, which are known as hydration forces. This assumption is based on the very hydrophilic nature of silica. Different theories have been developed in order to reproduce the exponentially decaying behavior (as a function of the separation distance) of the hydration forces. Different mechanisms for the formation of the structured water layer around the silica surfaces are considered by each theory. By the aid of an AFM and the colloid probe technique, the interaction forces between silica surfaces have been measured directly at different pH values and salt concentrations. The results confirm the presence of the short-range repulsion at any experimental condition (even at high salt concentration). A comparison between the experimental data and theoretical fits obtained from different theories has been performed in order to elucidate the nature of this non-DLVO repulsive force.
Growth stresses and cracking in GaN films on (111) Si grown by metalorganic chemical vapor deposition. II. Graded AlGaN buffer layers
Authors: Raghavan Srinivasan , Redwing Joan
Published: July 2005

Growth stress and critical thickness for cracking on cooling in GaN films deposited by metalorganic chemical vapor deposition on (111) Si using graded AlGaN (from AlN to GaN) buffer layers, 0.1–2μm thick, were examined. During the growth of the graded buffer layers, the incremental growth stress was observed to change from tension (∼+1to+1.5GPa) to compression (∼−1to−1.7GPa). An interruption in the composition grading during the compressive segment, followed by continued growth of the AlGaN composition at the interruption, resulted in the eventual transition to a tensile stress in films as thick as 0.75μm. A similar stress evolution, a reduction in the value of the initial compressive stress with thickness, was observed during the growth of 1-μm-thick GaN layers on 2-μm-thick graded AlGaN buffer layers. Such stress evolution, at thickness far beyond coalescence, cannot be explained by initial grain coalescence stresses alone. A combination of compressive stress generation due to the change in AlGaN composition and tensile stress generation due to the lateral increase in grain size with thickness are used to explain these results. In the GaN layer, the thickness at which the compressive-to-tensile stress transition takes place increases and the magnitude of the final stress decreases with an increase in the thickness of the graded AlGaN buffer layer. X-ray diffraction results show that this is due to increasing accommodation of the tensile stress generating microstructural changes within the thickness of the AlGaN buffer layer, thus reducing the level of tensile stress in the subsequent GaN layer. A 1-μm-thick graded AlGaN buffer layer enabled the growth of a 1-μm-thick GaN layer that is crack-free after dicing at room temperature.
Apparatus for high temperatures and intermediate pressures, for in situ nuclear magnetic resonance of hydrogen storage systems
Authors: Baker D. B. , Conradi Mark S.
Published: July 2005

An apparatus is described for hydrogen nuclear magnetic resonance (NMR) in an electromagnet for temperatures up to 1300 K and pressures to 55 atm. A crucial feature for studies of transition-metal hydrides and complex hydrides of light metals is the ability to add or remove hydrogen or other gases at operating conditions, enabling in situ NMR. The sample is held in a long, closed-end ceramic tube; the tube is supported against rupture by a greater external pressure of (typically) argon gas. An electrical heater heats only the sample end of the tube; the pressurized argon is ultimately held by the inner wall of the cooling water jacket. Potential modifications are discussed for operation in a high-field solenoid and with tuning components near the coil, among other improvements.
Investigation of the precipitation kinetics and changes of magnetic anisotropy of iron particles in ion-irradiated silica gel films by means of electron-spin resonance
Authors: Pivin J. C. , Esnouf S. , Singh F. , Avasthi D. K.
Published: July 2005

This paper reports the effect of the density of ion-induced electronic excitations on the nucleation of Fe particles in a silicon-based gel and on the magnetic ordering in SiO2:Fe composites with a volume fraction of metal of a few percent derived from the same gel. The nucleation occurs for a critical value of the energy density deposited by ions in electronic excitation. The dependence of the nucleation yield on the ion fluence ϕ is determined by the product of the electronic energy loss Se and the number n of ion impacts on a same area a which are necessary for reaching locally this critical energy density. Irradiation-induced changes in the magnetic anisotropy of composite films, previously formed by heat treatment of the same gel, depend more drastically on the order of magnitude of Se. When the latter is high enough for damaging the matrix, a tilt of the easy magnetization axis is observed.
On nonhomogeneous Bose condensation
Authors: Pulé Joseph V. , Verbeure André F. , Zagrebnov Valentin A.
Published: July 2005

We prove, in great generality, that in a system of bosons, whenever Bose condensation in a nonzero mode occurs then there is also spontaneous breaking of translation symmetry. In particular the proof holds for realistic Bose systems with two-body superstable interaction. This generalizes an old result proving that the occurrence of Bose-Einstein condensation in the zero mode implies spontaneous breaking of gauge invariance.
Orthogonal shape/intrinsic anisotropy toggle-mode magnetoresistance random access memory
Authors: Wang S.-Y. , Fujiwara H.
Published: July 2005

Magnetization response to in-plane applied fields has been studied, using Stoner-Wohlfarth model, on the bilayer systems of synthetic antiferromagnet having an anisotropy configuration in which the induced intrinsic uniaxial anisotropy is set either parallel or orthogonal to the shape anisotropy. It has been found that the toggle-mode magnetoresistance random access memory operation is possible even when the shape anisotropy exceeds the intrinsic anisotropy to some extent due to the anisotropic effect of the magnetostatic coupling and that the minimum operating field and maximum relative operating field margin are attained when the two anisotropy compensate each other. The optimal operating fields increase with the increase of the absolute value of the total anisotropy constant. However, the tolerance of total anisotropy constant in the positive direction is greater than in the negative direction if zero total anisotropy is chosen to be optimal.
Magnetic levitation using magnesium diboride
Authors: Zeisberger M. , Gawalek W. , Giunchi G.
Published: July 2005

We have investigated the levitation properties of magnesium diboride. The samples were prepared from magnesium and boron using the reactive liquid infiltration method. The precursor, which is made by pressing boron powder is infiltrated by liquid magnesium, resulting in a reaction to magnesium diboride. Cylindrical samples with diameters of up to 5cm were prepared. With these samples we measured the levitation force acting on a SmCo permanent magnet in the temperature range of 15–40K, obtained using a closed cycle refrigerator. For temperatures below 37K we observed a force which increases with decreasing temperature. Below 25K the force is nearly constant and its absolute value corresponds to a completely shielded superconductor. One of the samples was used to build a rotating bearing. We accelerated this bearing up to 14000rpm and measured the rotation speed as a function of time under free rotation.
Structural, electrical, optical, and mechanical characterizations of decorative ZrOxNy thin films
Authors: Carvalho P. , Vaz F. , Rebouta L. , Cunha L. , Tavares C. J. , Moura C. , Alves E. , Cavaleiro A. , Goudeau Ph. , Le Bourhis E. , Rivière J. P. , Pierson J. F. , Banakh O.
Published: July 2005

The main objective of this work is the preparation of decorative zirconium oxynitride, ZrOxNy, thin films by dc reactive magnetron sputtering. Film properties were analyzed as a function of the reactive gas flow and were correlated with the observed structural changes. Measurements showed a systematic decrease in the deposition rate with the increase of the reactive gas flow and revealed three distinct modes: (i) a metallic mode, (ii) a transition mode (subdivided into three zones), and (iii) an oxide mode. The measurements of target potential were also consistent with these changes, revealing a systematic increase from 314to337V. Structural characterization uncovered different behaviors within each of the different zones, with a strong dependence of film texture on the oxygen content. These structural changes were also confirmed by resistivity measurements, whose values ranged from 250to400μΩcm for low gas flows and up to 106μΩcm for the highest flow rates. Color measurements in the films revealed a change from bright yellow at low reactive gas flows to red brownish at intermediate flows and dark blue for the films prepared at the highest flows. Hardness measurements gave higher values for the region where larger grain sizes were found, showing that the grain growth hardening effect is one of the main parameters that can help explain the observed behavior. Also the peak intensity ratio and the residual stress states were found to be important factors for explaining this behavior.
Effect of ion attachment on mechanical dissipation of a resonator
Authors: Ono Takahito , Esashi Masayoshi
Published: July 2005

The influence of adsorbates on the surface-related mechanical dissipation of a silicon resonator was investigated. Different ion species were attached on a silicon resonator with a native oxide, and the quality factor (Q factor) and resonant frequency changes were observed by in situ measurement. It was found that water ion attachment creates OH terminations and results in a similar Q factor to that after exposure to the atmosphere. Nitrogen ions created very active sites for surface mechanical dissipation. In contrast, exposure to hydrogen ions increased the Q factor by a factor of 2. Hydrogen ions caused the dissipation sites on the surface to become inactive or less active for surface-related mechanical dissipation.
Development of a high velocity accessory for atomic force microscopy-based friction measurements
Authors: Tocha Ewa , Stefański Tomasz , Schönherr Holger , Vancso G. Julius
Published: July 2005

A high velocity accessory for friction force microscopy measurements for velocities up to the mm/s range was developed for a commercial stand-alone atomic force microscope (AFM). The accessory consists of a shear piezo element, which rapidly displaces the sample in the lateral direction, perpendicular to the main axis of the AFM cantilever. Friction forces, which are acquired via conventional optical beam deflection detection, can thus be measured as a function of velocity and load in controlled environment (0–40% relative humidity and 0–40°C). Using the accessory, a broad range of velocities up to several mm/s can be accessed independent of the lateral scan size up to a maximum scan size of 1000nm. The velocity dependence of friction forces and coefficients was measured on organic [poly(methylmethacrylate)], as well as inorganic [oxidized Si(100)] samples to demonstrate the feasibility and underline the importance of high velocity nanotribology using this accessory.
Telemetry system driven by radiation power for use in gravitational wave detectors
Authors: Zhao Yi , Zhao Chunnong , Ju Li , Small Michael , Blair David G.
Published: July 2005

To prevent electrical wiring from mechanically short circuiting in the high performance vibration isolators for gravitational wave detection, we designed a telemetry system. The system provides wireless signal transmission and radiation power supplies. A consideration of heat dissipation of in-vacuum electronic components is presented. The preliminary experiments demonstrated that the telemetry system is feasible.
Tuning of the metal-insulator transition in La0.75Sr0.25MnO3∕PrBa2Cu3O7−δ superlattices
Authors: Haberkorn N. , Guimpel J.
Published: July 2005

We have investigated the magnetotransport and magnetic properties of La0.75Sr0.25MnO3∕PrBa2Cu3O7−δ superlattices. Magnetic hysteresis loops show the expected ferromagnetic behavior, although the saturation magnetization is smaller than the expected value based on nominal layer thickness. We find that the electric transport on the superlattices can be qualitatively described using a simple layers-in-parallel model. We also find that the temperature at which the peak of the resistivity curve is located, and in consequence the temperature at which the maximum of the magnetoresistance curve are observed, are a function of layer thickness. The superlattices show an appreciable magnetoresistance for low temperatures, which may be consequence of a spin canted or weak antiferromagnetic manganite phase stabilized at the interfaces.
Water use of wheat, barley, canola, and lucerne in the high rainfall zone of south-western Australia
Authors: Zhang Heping , Turner Neil C. , Poole Michael L.
Published: July 2005

Water use of wheat (Triticum aestivum L.), barley (Hordeum vulgare L.), canola (Brassica napus L.), and lucerne (Medicago sativa L.) was measured on a duplex soil in the high rainfall zone (HRZ) of south-western Australia from 2001 to 2003. Rainfall exceeded evapotranspiration in all years, resulting in transient perched watertables, subsurface waterlogging in 2002 and 2003, and loss of water by deep drainage and lateral flow in all years. There was no significant difference in water use among wheat, barley, and canola. Lucerne used water at a similar rate to annual crops during the winter and spring, but continued to extract 80−100 mm more water than the annual crops over the summer and autumn fallow period. This resulted in about 50 mm less drainage past the root-zone than for annual crops in the second and third years after the establishment of the lucerne. Crop water use was fully met by rainfall from sowing to anthesis and a significant amount of water (120−220 mm) was used during the post-anthesis period, resulting in a ratio of pre- to post-anthesis water use (ETa : ETpa) of 1 : 1 to 2 : 1. These ratios were lower than the indicative value of 2 : 1 for limited water supply for grain filling. High water use during the post-anthesis period was attributed to high available soil water at anthesis, a large rooting depth (≥1.4 m), a high proportion (15%) of roots in the clay subsoil, and regular rainfall during grain filling. The pattern of seasonal water use by crops suggested that high dry matter at anthesis did not prematurely exhaust soil water for grain filling and that it is unlikely to affect dry matter accumulation during grain filling and final grain yield under these conditions.
Investigating diversity in human plasma proteins
Authors: Nedelkov Dobrin , Kiernan Urban A. , Niederkofler Eric E. , Tubbs Kemmons A. , Nelson Randall W.
Published: July 2005

Plasma proteins represent an important part of the human proteome. Although recent proteomics research efforts focus largely on determining the overall number of proteins circulating in plasma, it is equally important to delineate protein variations among individuals, because they can signal the onset of diseases and be used as biological markers in diagnostics. To date, there has been no systematic proteomics effort to characterize the breadth of structural modifications in individual proteins in the general population. In this work, we have undertaken a population proteomics study to define gene- and protein-level diversity that is encountered in the general population. Twenty-five plasma proteins from a cohort of 96 healthy individuals were investigated through affinity-based mass spectrometric assays. A total of 76 structural forms/variants were observed for the 25 proteins within the samples cohort. Posttranslational modifications were detected in 18 proteins, and point mutations were observed in 4 proteins. The frequency of occurrence of these variations was wide-ranged, with some modifications being observed in only one sample, and others detected in all 96 samples. Even though a relatively small cohort of individuals was investigated, the results from this study illustrate the extent of protein diversity in the human population and can be of immediate aid in clinical proteomics/biomarker studies by laying a basal-level statistical foundation from which protein diversity relating to disease can be evaluated.
Self-assembled graphitic nanotubes with one-handed helical arrays of a chiral amphiphilic molecular graphene
Authors: Jin Wusong , Fukushima Takanori , Niki Makiko , Kosaka Atsuko , Ishii Noriyuki , Aida Takuzo
Published: July 2005

Self-assembly of a Gemini-shaped, chiral amphiphilic hexa-
peri
-hexabenzocoronene having two chiral oxyalkylene side chains, along with two lipophilic side chains, yields graphitic nanotubes with one-handed helical chirality. The nanotubes are characterized by an extremely high aspect ratio of >1,000 and have a uniform diameter of 20 nm and a wall thickness of 3 nm. The nanotubes with right- and left-handed helical senses were obtained from the (
S
)- and (
R
)-enantiomers of the amphiphile, respectively, due to an efficient translation of point chirality into supramolecular helical chirality. The (
S
)- and (
R
)-enantiomers coassemble at varying mole ratios to give nanotubes, whose circular dichroism profiles are almost unchanged over a wide range of the enantiomeric excess of the amphiphile (100–20%). The high level of chirality amplification thus observed indicates a long-range cooperativity in the self-assembling process. In sharp contrast, a hexabenzocoronene amphiphile with chiral lipophilic side chains did not form nanotubular assemblies. The present work demonstrates the majority rule in noncovalent systems and also may provide a synthetic strategy toward realization of molecular solenoids.
The gene associated with trichorhinophalangeal syndrome in humans is overexpressed in breast cancer
Authors: Radvanyi Laszlo , Singh-Sandhu Devender , Gallichan Scott , Lovitt Corey , Pedyczak Artur , Mallo Gustavo , Gish Kurt , Kwok Kevin , Hanna Wedad , Zubovits Judith , Armes Jane , Venter Deon , Hakimi Jalil , Shortreed Jean , Donovan Melinda , Parrington Mark , Dunn Pamela , Oomen Ray , Tartaglia James , Berinstein Neil L.
Published: July 2005

A comprehensive differential gene expression screen on a panel of 54 breast tumors and >200 normal tissue samples using DNA microarrays revealed 15 genes specifically overexpressed in breast cancer. One of the most prevalent genes found was trichorhinophalangeal syndrome type 1 (TRPS-1), a gene previously shown to be associated with three rare autosomal dominant genetic disorders known as the trichorhinophalangeal syndromes. A number of corroborating methodologies, includingin situhybridization, e-Northern analysis using ORF EST (ORESTES) and Unigene EST abundance analysis, immunoblot and immunofluorescence analysis of breast tumor cell lines, and immunohistochemistry, confirmed the microarray findings. Immunohistochemistry analysis found TRPS-1 protein expressed in >90% of early- and late-stage breast cancer, including ductal carcinomain situand invasive ductal, lobular, and papillary carcinomas. The TRPS-1 gene is also immunogenic with processed and presented peptides activating T cells found after vaccination of HLA-A2.1 transgenic mouse. Human T cell lines from HLA-A*0201+female donors exhibiting TRPS-1-specific cytotoxic T lymphocyte activity could also be generated.
Evolutionary cycles of cooperation and defection
Authors: Imhof Lorens A. , Fudenberg Drew , Nowak Martin A.
Published: July 2005

The main obstacle for the evolution of cooperation is that natural selection favors defection in most settings. In the repeated prisoner's dilemma, two individuals interact several times, and, in each round, they have a choice between cooperation and defection. We analyze the evolutionary dynamics of three simple strategies for the repeated prisoner's dilemma: always defect (ALLD), always cooperate (ALLC), and tit-for-tat (TFT). We study mutation–selection dynamics in finite populations. Despite ALLD being the only strict Nash equilibrium, we observe evolutionary oscillations among all three strategies. The population cycles from ALLD to TFT to ALLC and back to ALLD. Most surprisingly, the time average of these oscillations can be entirely concentrated on TFT. In contrast to the classical expectation, which is informed by deterministic evolutionary game theory of infinitely large populations, stochastic evolution of finite populations need not choose the strict Nash equilibrium and can therefore favor cooperation over defection.
Noise-induced stability in dryland plant ecosystems
Authors: D'Odorico Paolo , Laio Francesco , Ridolfi Luca
Published: July 2005

Dryland plant ecosystems tend to exhibit bistable dynamics with two preferential configurations of bare and vegetated soils. Climate fluctuations are usually believed to act as a source of disturbance on these ecosystems and to reduce their stability and resilience. In contrast, this work shows that random interannual fluctuations of precipitation may lead to the emergence of an intermediate statistically stable condition between the two stable states of the deterministic dynamics of vegetation. As a result, there is an enhancement of ecosystem resilience and a decrease in the likelihood of catastrophic shifts to the desert state.
Human POT1 disrupts telomeric G-quadruplexes allowing telomerase extension
in vitro
Authors: Zaug Arthur J. , Podell Elaine R. , Cech Thomas R.
Published: July 2005

The POT1 (protection of telomeres 1) protein binds the ssDNA overhangs at the ends of chromosomes in diverse eukaryotes. POT1 is essential for chromosome end-protection, as best demonstrated in fission yeast. In human cells, hPOT1 is also involved in telomere-length regulation. We now show that telomeric oligonucleotides, such as d[GGG(TTAGGG)
3
], which form intramolecular G-quadruplexes through Hoogsteen base-pairing, serve as only marginal primers for extension by recombinant human telomerase; telomerase stalls after every nucleotide addition. Addition of hPOT1 to the reaction restores the normal processive elongation pattern seen with primers that cannot form G-quadruplexes. hPOT1 does not act catalytically but, instead, forms a stoichiometric complex with the DNA, freeing its 3′ tail. An antisense oligonucleotide, which base-pairs near the 5′ end of the telomeric sequence, leaving a telomerase-extendible 3′ tail, duplicates the effect of hPOT1 on activation of G-quadruplex primers. Thus, hPOT1 may function simply by trapping the unfolded forms of these telomeric primers in an equilibrium population. We propose an additional role for hPOT1 in telomere maintenance: disrupting G-quadruplex structures in telomeric DNA, thereby allowing proper elongation by telomerase.
Automated projection spectroscopy (APSY)
Authors: Hiller Sebastian , Fiorito Francesco , Wüthrich Kurt , Wider Gerhard
Published: July 2005

This work presents the automated projection spectroscopy (APSY) method for the recording of discrete sets of
j
projections from
N
-dimensional (
N
≥ 3) NMR experiments at operator-selected projection angles and automatic identification of the correlation cross peaks. The result from APSY is the fully automated generation of the complete or nearly complete peak list for the
N
-dimensional NMR spectrum from a geometric analysis of the
j
experimentally recorded, low-dimensional projections. In the present implementation of APSY, two-dimensional projections of the
N
-dimensional spectrum are recorded by using techniques developed for projection–reconstruction spectroscopy [Kupče,E.& Freeman, R. (2004)
J. Am. Chem. Soc.
126, 6429–6440]. All projections are peak-picked with the available automated routine
atnos
. The previously undescribed algorithm GAPRO (geometric analysis of projections) uses vector algebra to identify subgroups of peaks in different projections that arise from the same resonance in the
N
-dimensional spectrum, and from these subgroups it calculates the peak positions in the
N
-dimensional frequency space. Unambiguous identification thus can be achieved for all cross peaks that are not overlapped with other peaks in at least one of the
N
dimensions. Because of the correlation between the positions of corresponding peaks in multiple projections, uncorrelated noise is efficiently suppressed, so that APSY should be quite widely applicable for correlation spectra of biological macromolecules, which have intrinsically low peak density in the
N
-dimensional spectral space.
Magnetic isotope effect of magnesium in phosphoglycerate kinase phosphorylation
Authors: Buchachenko Anatoly L. , Kouznetsov Dmitri A. , Orlova Marina A. , Markarian Artyom A.
Published: July 2005

Phosphoglycerate kinase (PGK) is found to be controlled by a
25
Mg
2+
-related magnetic isotope effect. Mg
2+
nuclear spin selectivity manifests itself in PGK-directed ADP phosphorylation, which has been clearly proven by comparison of ATP synthesis rates estimated in reaction mixtures with different Mg isotopy parameters. Both pure
25
Mg
2+
(nuclear spin 5/2, magnetic moment +0.85) and
24
Mg
2+
(spinless, nonmagnetic nucleus) species as well as their mixtures were used in experiments. In the presence of
25
Mg
2+
, ATP production is 2.6 times higher compared with the yield of ATP reached in
24
Mg
2+
-containing PGK-based catalytic systems. The chemical mechanism of this phenomenon is discussed. A key element of the mechanism proposed is a nonradical pair formation in which
25
Mg
+
radical cation and phosphate oxyradical are involved.
The structure of phospholamban pentamer reveals a channel-like architecture in membranes
Authors: Oxenoid Kirill , Chou James J.
Published: July 2005

Contraction and relaxation of heart muscle cells is regulated by cycling of calcium between cytoplasm and sarcoplasmic reticulum. Human phospholamban (PLN), expressed in the sarcoplasmic reticulum membrane as a 30-kDa homopentamer, controls cellular calcium levels by a mechanism that depends on its phosphorylation. Since PLN was discovered ≈30 years ago, extensive studies have aimed to explain how it influences calcium pumps and to determine whether it acts as an ion channel. We have determined by solution NMR methods the atomic resolution structure of an unphosphorylated PLN pentamer in dodecylphosphocholine micelles. The unusual bellflower-like assembly is held together by leucine/isoleucine zipper motifs along the membrane-spanning helices. The structure reveals a channel-forming architecture that could allow passage of small ions. The central pore gradually widens toward the cytoplasmic end as the transmembrane helices twist around each other and bend outward. The dynamic N-terminal amphipathic helices point away from the membrane, perhaps facilitating recognition and inhibition of the calcium pump.
Genome-wide expression profiling of human blood reveals biomarkers for Huntington's disease
Authors: Borovecki F. , Lovrecic L. , Zhou J. , Jeong H. , Then F. , Rosas H. D. , Hersch S. M. , Hogarth P. , Bouzou B. , Jensen R. V. , Krainc D.
Published: July 2005

Huntington's disease (HD) is an autosomal dominant disorder caused by an expansion of glutamine repeats in ubiquitously distributed huntingtin protein. Recent studies have shown that mutant huntingtin interferes with the function of widely expressed transcription factors, suggesting that gene expression may be altered in a variety of tissues in HD, including peripheral blood. Affymetrix and Amersham Biosciences oligonucleotide microarrays were used to analyze global gene expression in blood samples of HD patients and matched controls. We identified 322 mRNAs that showed significantly altered expression in HD blood samples, compared with controls (
P
< 0.0005), on two different microarray platforms. A subset of up-regulated mRNAs selected from this group was able to distinguish controls, presymptomatic individuals carrying the HD mutation, and symptomatic HD patients. In addition, early presymptomatic subjects showed gene expression profiles similar to those of controls, whereas late presymptomatic subjects showed altered expression that resembled that of symptomatic HD patients. These elevated mRNAs were significantly reduced in HD patients involved in a dose-finding study of the histone deacetylase inhibitor sodium phenylbutyrate. Furthermore, expression of the marker genes was significantly up-regulated in postmortem HD caudate, suggesting that alterations in blood mRNAs may reflect disease mechanisms observed in HD brain. In conclusion, we identified changes in blood mRNAs that clearly distinguish HD patients from controls. These alterations in mRNA expression correlate with disease progression and response to experimental treatment. Such markers may provide clues to the state of HD and may be of predictive value in clinical trials.
Knockout mice reveal a tumor suppressor function for Testin
Authors: Drusco Alessandra , Zanesi Nicola , Roldo Claudia , Trapasso Francesco , Farber John L. , Fong Louise Y. , Croce Carlo M.
Published: July 2005

The Testin (TES) gene was previously identified as a putative human tumor suppressor gene at 7q31.2, a region that is frequently deleted in hematopoietic malignancies, as well as in epithelial tumors. To determine whether TES acts as a tumor suppressorin vivo, we generated a Tes knockout mouse and then used it in an established model of carcinogen-induced gastric cancer. In mice a zinc-deficient (ZD) diet enhances cellular proliferation in the forestomach and susceptibility toN-nitrosomethylbenzylamine (NMBA)-induced carcinogenesis. Five-week-old Tes wild-type (+/+), heterozygous (+/-), and homozygous (-/-) mice were divided into four groups: mice fed a zinc-sufficient diet (ZS); mice fed a ZD diet; ZS fed plus NMBA-treated mice (ZS+NMBA), and ZD fed plus NMBA-treated mice (ZD+NMBA). After 4 weeks, the ZS+NMBA and ZD+NMBA groups were treated with three intragastric doses of NMBA. Animals were killed 8 weeks after NMBA administration: 25% of +/+ mice developed benign lesions; 88% of +/- showed multiple papillomas, atypical glandular metaplasia, and squamous cell carcinomasl; and 81% of -/- mice displayed very large papillomas, squamous cell carcinomas, and adenocarcinomas. A statistically significant difference in tumor incidence was found between +/- versus +/+ and -/- versus +/+ (P< 0.0001). These data suggest that Tes functions as a tumor suppressor genein vivo.
Obesity alters gut microbial ecology
Authors: Ley Ruth E. , Bäckhed Fredrik , Turnbaugh Peter , Lozupone Catherine A. , Knight Robin D. , Gordon Jeffrey I.
Published: July 2005

We have analyzed 5,088 bacterial 16S rRNA gene sequences from the distal intestinal (cecal) microbiota of genetically obese
ob
/
ob
mice, lean
ob
/+ and wild-type siblings, and their
ob
/+ mothers, all fed the same polysaccharide-rich diet. Although the majority of mouse gut species are unique, the mouse and human microbiota(s) are similar at the division (superkingdom) level, with Firmicutes and Bacteroidetes dominating. Microbial-community composition is inherited from mothers. However, compared with lean mice and regardless of kinship,
ob
/
ob
animals have a 50% reduction in the abundance of Bacteroidetes and a proportional increase in Firmicutes. These changes, which are division-wide, indicate that, in this model, obesity affects the diversity of the gut microbiota and suggest that intentional manipulation of community structure may be useful for regulating energy balance in obese individuals.
Microsatellites and 16S sequences corroborate phenotypic evidence of trans-Andean variation in the parasitoid Microctonus hyperodae (Hymenoptera: Braconidae)
Authors: Winder L.M. , Phillips C.B. , Lenney-Williams C. , Cane R.P. , Paterson K. , Vink C.J. , Goldson S.L.
Published: July 2005

Eight South American geographical populations of the parasitoid Microctonus hyperodae Loan were collected in South America (Argentina, Brazil, Chile and Uruguay) and released in New Zealand for biological control of the weevil Listronotus bonariensis (Kuschel), a pest of pasture grasses and cereals. DNA sequencing (16S, COI, 28S, ITS1, β-tubulin), RAPD, AFLP, microsatellite, SSCP and RFLP analyses were used to seek markers for discriminating between the South American populations. All of the South American populations were more homogeneous than expected. However, variation in microsatellites and 16S gene sequences corroborated morphological, allozyme and other phenotypic evidence of trans-Andes variation between the populations. The Chilean populations were the most genetically variable, while the variation present on the eastern side of the Andes mountains was a subset of that observed in Chile.
The separation of two hymenopteran parasitoids, Tersilochus obscurator and Tersilochus microgaster (Ichneumonidae), of stem-mining pests of winter oilseed rape using DNA, morphometric and ecological data
Authors: Barari H. , Ferguson A.W. , Piper R.W. , Smith E. , Quicke D.L.J. , Williams I.H.
Published: July 2005

Tersilochus obscurator Aubert and Tersilochus microgaster (Szépligeti) are larval endoparasitoids of economically-important stem-mining pests of winter oilseed rape (Brassica napus L.) in Europe. They are difficult to separate morphologically. Their hosts are Ceutorhynchus pallidactylus (Marsham) and Psylliodes chrysocephala Linnaeus, respectively. The parasitoids' taxonomic status, identification, host range and phenology were studied using genetic, morphometric and ecological data. The study used 527 female parasitoids from the UK and Germany, either field-collected in emergence traps or reared from field-collected host larvae. Two morphometric characters, the ovipositor sheath to first metasomal tergite ratio and the percentage of the mesopleuron spanned by the sternaulus, were measured. A 440 bp section of mitochondrial DNA cytochrome oxidase subunit I (COI) gene was sequenced from 35 parasitoids reared from C. pallidactylus, 20 reared from P. chrysocephala and individuals from two outgroups, Tersilochus heterocerus Thomson and Phradis interstitialis Thomson. Distinct and invariable COI sequences corresponded exclusively to each parasitoid group, confirming that T. obscurator and T. microgaster are discrete species. Measurements of host-reared and COI-sequenced specimens indicated that the ranges of both morphometric characters overlapped between species. Using these ranges as criteria, all but 3.6% of UK specimens and 2% of German specimens were identifiable to species without reference to host or phenology. There were differences in emergence phenology in the UK, adult T. microgaster emerging from winter diapause by 29 March 2000, T. obscurator emerging between 12 April and 24 May 2000. The value of molecular techniques in the identification of closely-related parasitoid species is discussed.
Effect of host quality ofCallosobruchus maculatus(Coleoptera: Bruchidae) on performance of the egg parasitoidUscana lariophaga(Hymenoptera: Trichogrammatidae)
Authors: Spitzen J. , van Huis A.
Published: July 2005

Development and reproductive success of the solitary egg parasitoidUscana lariophagaSteffan were examined after development in eggs of the bruchid storage pestCallosobruchus maculatusFabricius reared at either low or high densities on cowpea seeds and laid at day 1 and 4 of maternal life. Both bruchid larval competition and maternal age negatively affected egg size, but the latter more than the former.Uscana lariophagareared in small hosts developed slower, were smaller and produced fewer eggs compared to parasitoids reared in large hosts. Fecundity of the parasitoid was heavily influenced by host egg size. This was reflected in the values for the intrinsic rate of increase ofU. lariophaga, which differed for wasps that developed in host eggs laid by bruchid females of different age. Wasps allocated marginally more female offspring to larger hosts.