bluuebunny/crossref_metadata_2025 huggingface dataset:
Thermodynamics of folding and association of lattice-model proteins
Authors: Cellmer Troy , Bratko Dusan , Prausnitz John M. , Blanch Harvey
Published: May 2005

Closely related to the “protein folding problem” is the issue of protein misfolding and aggregation. Protein aggregation has been associated with the pathologies of nearly 20 human diseases and presents serious difficulties during the manufacture of pharmaceutical proteins. Computational studies of multiprotein systems have recently emerged as a powerful complement to experimental efforts aimed at understanding the mechanisms of protein aggregation. We describe the thermodynamics of systems containing two lattice-model 64-mers. A parallel tempering algorithm abates problems associated with glassy systems and the weighted histogram analysis method improves statistical quality. The presence of a second chain has a substantial effect on single-chain conformational preferences. The melting temperature is substantially reduced, and the increase in the population of unfolded states is correlated with an increase in interactions between chains. The transition from two native chains to a non-native aggregate is entropically favorable. Non-native aggregates receive ∼25% of their stabilizing energy from intraprotein contacts not found in the lowest-energy structure. Contact maps show that for non-native dimers, nearly 50% of the most probable interprotein contacts involve pairs of residues that form native contacts, suggesting that a domain-swapping mechanism is involved in self-association.
Ab initio intermolecular potential energy surface, bound states, and microwave spectra for the van der Waals complex Ne–HCCCN
Authors: Zhou Yanzi , Xie Daiqian
Published: May 2005

We report two ab initio intermolecular potential energy surfaces for Ne–HCCCN using a supermolecular method. The calculations were performed at the fourth-order Møller-Plesset (MP4) and the coupled cluster singles-and-doubles with noniterative inclusion of connected triples [CCSD(T)] levels with the full counterpoise correction for the basis set superposition error and a large basis set including bond functions. The complex was found to have a planar T-shaped structure minimum and a linear minimum with the Ne atom facing the H atom. The two-dimensional discrete variable representation method was employed to calculate the rovibrational bound states. In addition, the microwave spectra including intensities for the ground vibrational state were predicted. The results show that the spectrum is dominated by b-type (ΔKa=±1) transitions with very weak a-type (ΔKa=0) transitions. The calculated results at the CCSD(T) potential are in good agreement with those at MP4 potential.
Luminescence spectroscopy of matrix-isolated zP6 state atomic manganese
Authors: Collier Martin A. , McCaffrey John G.
Published: May 2005

The relaxation of electronically excited atomic manganese isolated in solid rare gas matrices is observed from recorded emission spectra, to be strongly site specific. zP6 state excitation of Mn atoms isolated in the red absorption site in Ar and Kr produces narrow aD4 and aD6 state emissions while blue-site excitation produces zP6 state fluorescence and broadened aD4 and aD6 emissions. Mn∕Xe exhibits only a single thermally stable site whose emission at 620nm is similar to the broad aD6 bands produced with blue-site excitation in Ar and Kr. Thus in Ar(Kr), excitation of the red site at 393(400)nm produces narrow line emissions at 427.5 (427.8) and 590(585.7)nm. From their spectral positions, linewidths, and long decay times, these emission bands are assigned to the aD7∕24 and aD9∕26 states, respectively. Excitation of the blue site at 380(385.5)nm produces broad emission at 413(416)nm which, because of its nanosecond radiative lifetime, is assigned to resonance zP6→aS6 fluorescence. Emission bands at 438 (440) and 625(626.8)nm, also produced with blue-site excitation, are broader than their red-site equivalents at 427.5 and 590nm (427.8 and 585.7nm in Kr) but from their millisecond and microsecond decay times are assigned to the aD4 and aD6 states. The line features observed in high resolution scans of the red-site emission at 427.5 and 427.8nm in Mn∕Ar and Mn∕Kr, respectively, have been analyzed with the Wp optical line shape function and identified as resolved phonon structure originating from very weak (S=0.4) electron-phonon coupling. The presence of considerable hot-phonon emission (even in 12K spectra) and the existence of crystal field splittings of 35 and 45cm−1 on the excited aD7∕24 level in Ar and Kr matrices have been identified in Wp line shape fits. The measured matrix lifetimes for the narrow red-site aD6 state emissions (0.29 and 0.65ms) in Ar and Kr are much shorter than the calculated (3s) gas phase value. With the lifetime of the metastable aD9∕26 state shortened by four orders of magnitude in the solid rare gases, it is clear that the probability of the “forbidden” aD6→aS6 atomic transition is greatly enhanced in the solid state. A novel feature identified in the present work is the large width and shifted D4 and D6 emissions produced for Mn atoms isolated in the blue sites of Ar and Kr. In contrast, these states produce narrow, unshifted (gas-phase-like) D4 and D6 state emissions from the red site.
Examination of membrane fusion by dissipative particle dynamics simulation and comparison with continuum elastic models
Authors: Li Da-Wei , Liu Xiang Yang
Published: May 2005

A dissipative particle dynamics model is applied to probe the lipidic membrane fusion. This model is verified by reproducing the lipid phase behavior. The classical stalk model has been visited and modified. The tilt deformation of the lipids and the noncircular shape of the stalk are supported. The stalk is shown to undergo asymmetric expansion to form the trans-monolayers contact (TMC). Unlike previous models, an energy barrier between the stalk and the TMC has been identified, implying that the TMC should be a metastable formation. This shows good agreement with the fusion experiments. Two typical elastic continuum models are compared with our result and possible modifications to the two elastic models are suggested. The effect of spontaneous curvature of lipid on selection of fusion pathway is also examined. It is observed that a bent stalk with pore or an inverted micellar intermediate will have more chance to occur than traditional stalk when the spontaneous curvature of the lipid becomes more negative.
Improved procedure on the microscopic approach to determine colloidal stability
Authors: Sun Zhiwei , Xu Shenghua , Liu Jie , Li Yinmei , Lou Liren , Xie Jingchang
Published: May 2005

We present an improved procedure on the approach to determine the stability of polystyrene spheres at microscopic particle levels by means of artificially induced particle collisions with the aid of optical tweezers [J. Chem. Phys. 119, 2399 (2003)]. The basic consideration on this new development is that the major contribution to the sticking probability for a particle pair caught into the optical trap for a short period is from its single collision; therefore, if the trapping duration for the pair is taken to be short, the accumulated sticking probability will be a good approximation for the single collision. The experimental procedure associated with this approximation does not resort to exactly controlling the short trapping duration or request the trapping duration correction as previously reported, and therefore it is more practical and applicable for a broader range of the stability ratio. The experimental results under different electrolyte concentrations by the new procedure are consistent with those from the turbidity measurements.
Density-functional theory calculations of XH3-decorated SiC nanotubes (X={C,Si}): Structures, energetics, and electronic structures
Authors: Li Feng , Xia Yue-Yuan , Zhao Ming-Wen , Liu Xiang-Dong , Huang Bo-Da , Yang Zhao-Hua , Ji Yan-Ju , Song Chen
Published: May 2005

We have investigated the structures, energetics, and electronic structures of XH3-radical-decorated silicon carbide nanotubes (SiCNTs), where X={C,Si}, using density-functional theory. Our results show that all the XH3 radicals can be chemically adsorbed on Si sites or C sites on the tube wall, with the adsorption energies ranging from −2.01 to −2.90eV for a (5,5) SiCNT. The modification in electronic structures of these decorated SiCNTs highly depends on the adsorption site rather than the XH3 species. The electronic structures of XH3-decorated SiCNTs demonstrate characteristics of n-type semiconductors for XH3 adsorbed on a C atom, whereas p-type semiconductors can be achieved by XH3 adsorption on a Si atom.
Induced anisotropy of Ar2: A state-of-the-art semiempirical model
Authors: Chrysos M. , Dixneuf S.
Published: May 2005

We report a semiempirical induced anisotropy model for Ar2 that optimally reproduces highly accurate experimental induced scattering band shapes over a large domain of frequency detunings. We believe that our model, which was derived (after an extensive compilation of the data) by using a systematic methodology and a novel reliable multiparameter equation solver (presented here), is the best induced anisotropy ever proposed. The applicability of our methodology to any induced band shape and its economical implementation make it a promising device for accessing various incremental properties for weakly interacting systems of an arbitrary complexity.
Ab initio investigation of the autoionization process Ar*(4sP23,P3)+Hg→(Ar–Hg)++e−: Potential energy curves and autoionization widths, ionization cross sections, and electron energy spectra
Authors: Thiel Linda , Hotop Hartmut , Meyer Wilfried
Published: May 2005

Multireference configuration interaction (MRCI) calculations have been performed for the Ar*(4sP2,03)+Hg collision complex. Feshbach projection based on orbital occupancy defines the entrance channel resonance states and provides their potential energy curves as well as resonance-continuum coupling matrix elements, which are turned into an autoionization width function by Stieltjes imaging. Coupled cluster calculations with singles, doubles, and pertubative triples [CCSD(T)] give the exit channel potential of ArHg+. The Hg20+ core is treated by a scalar-relativistic effective core potential, reparametrized to reproduce experimental excitation and ionization energies. Spin-orbit interaction is included for the Ar* open 3p shell. The nuclear motion is treated within the local complex potential approximation. Ionization occurs for 85% (P03) and 98% (P23) of the symmetry allowed close collisions. Calculated ionization cross sections show good agreement with experimental data. The difference potential of the collision complex is remarkably flat down to internuclear separations of 8a0 and leads to very sharp peaks in theoretical electron energy spectra for single collision energies. After accounting for the experimental energy distribution and the resolution function of the spectrometer, a very satisfying agreement with experimental electron energy spectra is found, including subtle differences due to spin-orbit coupling. Theoretical input appears indispensable for an analysis of the measured data in terms of potential energy curves and autoionization width functions.
Theoretical study of the electronic spectroscopy of CO adsorbed on Pt(111)
Authors: Besley Nicholas A.
Published: May 2005

The excited states of CO adsorbed on the Pt(111) surface are studied using a time-dependent density functional theory formalism. To reduce the computational cost, electronic excitations are computed within a reduced single excitation space. Using cluster models of the surface, excitation energies are computed for CO in the on-top, threefold, and bridge binding sites. On adsorption, there is a lowering of the 5σ orbital energy. This leads to a large blueshift in the 5σ→πCO* excitation energy for all adsorption sites. The 1π and 4σ orbital energies are lowered to a lesser extent, and smaller shifts in the corresponding excitation energies are predicted. For the larger clusters, π* excitations at lower energies are observed. These transitions correspond to excitations to virtual orbitals of π* character which lie below the π* orbitals of gas phase CO. These orbitals are associated predominantly with the metal atoms of the cluster. The excitation energies are also found to be sensitive to changes in the adsorption geometry. The electronic spectrum of CO on Pt(111) is simulated and the assignment of the bands observed in experimental electron energy loss spectroscopy discussed.
Instantaneous dynamics and quantum control fields: Principle and numerical applications
Authors: Gräfe S. , Meier C. , Engel V.
Published: May 2005

The relation between laser pulses serving the purpose of controlling elementary molecular processes and the instantaneous dynamics of the perturbed system is investigated. The application of the conditions assuring a controlled change of the expectation value of an observable directly links the internal motion to the external perturbation. Several numerical applications document that the derived control fields are efficient and can be interpreted clearly on physical grounds.
Rapid ion-beam-induced Ostwald ripening in two dimensions
Authors: Berdahl P. , Reade R. P. , Russo R. E.
Published: May 2005

Ion-beam-induced grain coarsening in initially amorphous (Zr,Y)Ox layers is observed by atomic force microscopy. The films were bombarded at room temperature. Grain-boundary grooves indicate that the larger grains have a diameter of about 83nm at 2min, and 131nm at 5min. Up to 5min, the grain size evolves with time as tβ, with β=0.5±0.2. Based on a new parametrization of ion-induced grain-boundary translation, we derive a theoretical estimate of β=3∕7, consistent with our measurement. By 7.5min, many of the grain-boundary grooves are shallow and indistinct, suggesting that the surviving grains are mutually well aligned. Such rapid grain growth at room temperature is unusual and is enabled by the ion bombardment. Similar grain growth processes are expected during ion-beam-assisted deposition film growth. The status of ion-textured yttria stabilized zirconia films as buffer layers for high-current high-temperature superconducting films is briefly summarized.
Diffusion and viscosity of a calamitic liquid crystal model studied by computer simulation
Authors: Cinacchi Giorgio , De Gaetani Luca , Tani Alessandro
Published: May 2005

We report a molecular dynamics simulation study on an ensemble of rod-like particles, each composed of nine soft spheres held rigidly along a line. We have calculated translational mean square displacements and velocity autocorrelation functions in the fluid phases exhibited by the model, i.e., smectic A, nematic and isotropic. These quantities have then been used to compute diffusion coefficients. In addition, we have calculated viscosities in the nematic and isotropic phases. Despite its crude nature, the model is capable of providing a faithful reproduction of many features of the transport behavior observed in real liquid-crystalline materials. The simulation results have been compared with the predictions of the modified affine transformation theory, finding only a fair agreement.
Effect of Kapitza contact and consideration of tube-end transport on the effective conductivity in nanotube-based composites
Authors: Chen Tungyang , Weng George J. , Liu Wen-Ching
Published: May 2005

Recent studies reported that the theoretical predictions of the effective thermal conductivity of nanotube-based composites by conventional micromechanical models are anomalously higher than those measured experimentally and suggested that the contact resistance on the interface could be the contributing factor to the lower measured value. We explore theoretically whether the large disagreement could be attributed to the effect of Kapitza contact resistance. Our simulations show that the thermal contact resistance on the lateral surfaces of the nanotubes could not be a major factor of this marked disparity. By contrast, the heat transport mechanisms at the ends of the nanotubes could be a significant factor to influence the value. We propose a few simple models to simulate the thermal conductivity at the ends of the nanotubes, similar to two springs in serial and/or in parallel. Under the propositions, we find that the experimental data can be better predicted than the conventional theory and that the tube-end transport is, in general, poor.
Energy dissipation in spiral vortex layers wrapped around a straight vortex tube
Authors: Kawahara Genta
Published: May 2005

Energy dissipation in spiral layers of high azimuthal vorticity around a straight vortex tube is investigated analytically. Asymptotic expressions of local and total viscous dissipation are obtained for the spiral vortex layers. When a vortex tube, which aligns with a uniform shear flow of a shear rate S, starts with a vortex filament of circulation Γ at an initial instant t=0, it wraps and stretches background vorticity lines around itself to form double spiral vortex layers of intense dissipation. The contribution of the spiral layers to total dissipation per unit axial length is evaluated to be 1.29πν2S2(Γ∕2πν)4∕3t at large vortex Reynolds numbers Γ∕ν⪢1, ν being the kinematic viscosity of fluid. There exists the critical time after which the contribution of the spirals to the total dissipation dominates that of the tube. If the tube is tilted at a small angle α in the direction of the uniform shear vorticity, the spirals around the tube are cross axially sheared into different shapes depending on the sign of α, which leads to local reduction (or enhancement) of the energy dissipation in the spirals at α>0 (or <0). The primary effect of the cross-axial shear on the total dissipation is shown to be −14ανS3Γln(Γ∕2πν)t2 at St∣α∣⪡1 for Γ∕ν⪢1. The contribution to turbulent energy dissipation from spiral structures around a tubular vortex at a large-Reynolds-number limit is also discussed based upon recently reported direct numerical simulations and the present analysis.
Electrically programmable photonic crystal slab based on the metal-insulator transition in VO2
Authors: Xiao D. , Kim K. W. , Zavada J. M.
Published: May 2005

The possibility of an electrically programmable photonic crystal is investigated theoretically based on the metal-insulator transition of vanadium dioxide (VO2). Recent experiments indicate that this phase transition of the first order can be controlled via external bias and results in significant changes in the electrical and optical properties of VO2. We propose a slab structure based on VO2 whose dielectric properties are modulated periodically in the in-plane direction by selectively inducing phase transition through a lithographically defined array of gate electrodes. A two-dimensional photonic band calculation predicts the presence of a band gap, clearly illustrating the feasibility of the proposed structure. The electrically controlled nature may enable the VO2- based structure to be programmable at a very high speed.
Single-defect Bragg stacks for high-power narrow-band thermal emission
Authors: Ben-Abdallah Philippe , Ni Bo
Published: May 2005

The radiative properties of single-defect Bragg stacks are investigated in the midinfrared region with the transfer-matrix theory. For a sufficiently small number of layers we find a regime where the structure emits radiation within a narrow range of wavelengths (δλ∕λ⩽0.01) and with an emissivity close to 1 in all directions. A description of the electric-field distribution inside the structure allows us to interpret this behavior in terms of coupling between the localized defect states and surface waves. This result should find broad applications in infrared spectroscopy, chemical sensing, and thermophotovoltaic conversion.
Electromagnetic instability of an axially inhomogeneous plasma
Authors: Smolyakov A. I. , Krasheninnikov S. I. , Tolstikhin O. I.
Published: May 2005

The electromagnetic drift instability leading to the excitation of the Alfvén waves in an axially inhomogeneous plasma is investigated. The instability is driven by the axial shear of the E×B drift velocity maintained by the localized density gradient. Analytical dispersion relation has been derived in the short wavelength (WKB) limit. The eigenvalue problem has also been solved numerically by using the recently developed algebraic method [D. I. Tolstikhin, V. N. Ostrovsky, and H. Nakamura, Phys. Rev. A 58, 2077 (1998)].
Azimuthal instability of radiation in gyrotrons with overmoded resonators
Authors: Dumbrajs O. , Nusinovich G. S.
Published: May 2005

Stability of efficient operation at one of the high-order modes is of great importance for the development of megawatt-level gyrotrons intended for plasma experiments in controlled fusion reactors. Typically such gyrotrons operate at modes with large azimuthal indices, which form a rather dense spectrum of eigenfrequencies. Therefore, instead of considering interaction of electrons with a large number of such modes it is more convenient to analyze the spatial-temporal evolution of an envelope formed by a superposition of these modes with the electrons. In all previous studies of stability of such envelopes it was assumed that some kind of azimuthal nonuniformity is present in the initial condition for the wave envelope. However, the physical reason for this nonuniformity, which is apparently the nonuniformity of the electron emission, was not analyzed. In the present paper, the relation between the emission nonuniformity and resulting nonuniformity of the wave envelope is established. Then, results of numerical simulations are given, which demonstrate various changes in the gyrotron dynamics caused by the azimuthal instability of the wave envelope. These results allow one to determine the maximum azimuthal index of the operating mode and show that this maximum index can depend on the degree of azimuthal nonuniformity of the electron emission.
Optical evidence for a self-propagating molten buried layer in germanium films upon nanosecond laser irradiation
Authors: Vega F. , Chaoui N. , Solis J. , Armengol J. , Afonso C. N.
Published: May 2005

This work describes the phase transitions occurring at the film-substrate interface of amorphous germanium films upon nanosecond laser-pulse-induced melting of the surface. Films with thickness ranging from 50 to 130 nm deposited on glass substrates were studied. Real-time reflectivity measurements with subnanosecond time resolution performed both at the air-film and film-substrate interfaces were used to obtain both surface and in-depth information of the process. In the thicker films (⩾80nm), the enthalpy released upon solidification of a shallow molten surface layer induces a thin buried liquid layer that self-propagates in-depth towards the film-substrate interface. This buried liquid layer propagates with a threshold velocity of 16±1m∕s and causes, eventually, melting at the film-substrate interface. In the thinnest film (50 nm) there is no evidence of the formation of the buried layer. The presence of the self-propagating buried layer for films thicker than 80 nm at low and intermediate laser fluences is discussed in terms of the thermal gradient in the primary melt front and the heat released upon solidification.
Some physical appearances of vector coherent states and coherent states related to degenerate Hamiltonians
Authors: Ali S. Twareque , Bagarello F.
Published: May 2005

In the spirit of some earlier work on the construction of vector coherent states (VCS) over matrix domains, we compute here such states associated to some physical Hamiltonians. In particular, we construct vector coherent states of the Gazeau–Klauder type. As a related problem, we also suggest a way to handle degeneracies in the Hamiltonian for building coherent states. Specific physical Hamiltonians studied include a single photon mode interacting with a pair of fermions, a Hamiltonian involving a single boson and a single fermion, a charged particle in a three-dimensional harmonic force field and the case of a two-dimensional electron placed in a constant magnetic field, orthogonal to the plane which contains the electron. In this last example, which is related to the fractional quantum Hall effect, an interesting modular structure emerges for two underlying von Neumann algebras, related to opposite directions of the magnetic field. This leads to the existence of coherent states built out of Kubo-Martin-Schwinger (KMS) states for the system.
Giant heating of Si nanoparticles by weak laser light: Optical microspectroscopic study and application to particle modification
Authors: Poborchii Vladimir , Tada Tetsuya , Kanayama Toshihiko
Published: May 2005

We show that Si particles 20–30 nm in diameter can be heated up to ∼1500K in atmospheric conditions by illumination with weak (∼1mW) but sharply focused (∼2μm) visible laser light. Crystallization, oxidation, and color change of the particles occur as the result of the light-induced heating of the particles. These effects can be used for modification of the particles and preparation of Si-based luminescent material.
Atomistic analysis of the evolution of boron activation during annealing in crystalline and preamorphized silicon
Authors: Aboy Maria , Pelaz Lourdes , Marqués Luis A. , López Pedro , Barbolla Juan , Duffy R.
Published: May 2005

We use kinetic nonlattice Monte Carlo atomistic simulations to investigate the physical mechanisms for boron cluster formation and dissolution in complementary metal-oxide semiconductor (MOS) processing, and the role of Si interstitials in the different processes. For this purpose, B implants in crystalline Si as well as B implants in preamorphized Si are analyzed. For subamorphizing B implants, a high concentration of Si interstitials overlaps with the B profile and this causes a very quick B deactivation for both low- and high-dose B implants. For B implants in preamorphized silicon, B is activated during the regrowth of the amorphous layer if the B concentration is lower than 1020cm−3 and remains active upon annealing. However, if B concentrations higher than 1020cm−3 are present, as occurs in the formation of extensions in p-channel MOS transistors, B atoms are not completely activated during the regrowth. Moreover, the injection of Si interstitials from the end-of-range defects leads to additional B deactivation in the regrown layer during subsequent annealing. If the end-of-range defects overlap with a B profile, even of relatively low concentration, as it occurs for B pockets in n-channel MOS transistors, very quick and local B deactivation occurs in the high Si-interstitial concentration region.
Magneto-optic Kerr effect: Incorporating the nonlinearities of the analyzer into static photometric ellipsometry analysis
Authors: Mikuszeit N. , Pütter S. , Frömter R. , Oepen H. P.
Published: May 2005

A static photometric ellipsometer allows the measurement of the magneto-optic Kerr effect at a very high signal-to-noise ratio. To gain information about the state of magnetization a mathematical description of the optical components is required. This involves the use of trigonometric functions, e.g., within the Müller calculus. As these are transcendental functions the inversion of the formulae defining the final state of polarization is impossible. The commonly applied linearization is only valid for thin samples with small Kerr angles. For large Kerr angles the nonlinearity of the analyzer setup becomes important. The influence of these nonlinearities on static ellipsometry is studied analytically and numerically. A method is developed to reveal the magnetic properties with high accuracy despite of the nonlinearities due to the optical setup. The applicability of the method is demonstrated for the experimental data obtained from an ion-irradiated iron film on silicon, revealing the magnetic behavior of the investigated sample. The encountered effects are of fundamental importance for the full vectorial magnetization analysis when large Kerr signals are obtained in experiments.
Real-time photodisplacement imaging using parallel excitation and parallel heterodyne interferometry
Authors: Nakata Toshihiko , Ninomiya Takanori
Published: May 2005

A parallel photodisplacement technique that achieves real-time imaging of subsurface structures is presented. In this technique, a linear region of photothermal displacement is excited by a line-focused intensity-modulated laser beam and detected with a parallel heterodyne interferometer using a charge-coupled device linear image sensor as a detector. Because of integration and sampling effects of the sensor, the interference light is spatiotemporally multiplexed. To extract the spatially resolved photodisplacement component from the sensor signal, a scheme of phase-shifting light integration combined with a Fourier analysis technique is developed for parallel interferometry. The frequencies of several control signals, including the heterodyne beat signal, modulation signal, and sensor gate signal, are optimized so as to eliminate undesirable components, allowing only the displacement component to be extracted. Two-dimensional subsurface lattice defects in silicon are clearly imaged at a remarkable speed of only 0.26s for an area of 256×256pixels. Thus, the proposed technique allows for real-time imaging more than 10 000 times faster than conventional photoacoustic microscopy.
Thermally induced viscoelastic stresses in multilayer thin films
Authors: Chang Win-Jin , Fang Te-Hua , Lin Chao-Ming
Published: May 2005

This paper presents a viscoelastic analysis of the thermal stress in multilayer thin-film structures. In this analysis the viscoelastic field was calculated utilizing the Laplace transform. The thermal stress equation in the Laplace transform space can be numerically inverted to obtain the time domain. In the case of a single-layer film the stress of the thin film at any time can be obtained analytically. In a bilayer system, the normalized viscoelastic stress of the thin film is affected by the relaxation times, the biaxial moduli ratio, and the ratio of thickness between the film layer and the substrate. The effects of different ratio values of thickness on the normalized viscoelastic stress were analyzed. Viscoelastic stress can also be calculated if the elastic behavior in either the film or the substrate is considered. Furthermore, when both the substrate and film’s relaxation times approach infinity, they begin to exhibit elastic behavior, and then the residual stress in the film can be determined. The residual stress results were shown to be identical to those results obtained by the elastic analysis.
Inertial instability of a liquid film inside a rotating horizontal cylinder
Authors: Benilov E. S. , O’Brien S. B. G.
Published: May 2005

We examine the dynamics of a thin film of viscous fluid on the inside surface of a cylinder with horizontal axis, rotating about this axis. The stability of the film has been previously explored using the leading-order lubrication approximation, under which it was found to be neutrally stable. In the present paper, we examine how the stability of the film is affected by higher-order corrections, such as inertia (described by the material derivatives in the Navier–Stokes equations), surface tension, and the hydrostatic pressure gradient. Assuming that these effects are weak, we derive an asymptotic equation which takes them into account as perturbations. The equation is used to examine the stability of the steady-state distribution of film around the cylinder (rimming flow) with respect to linear disturbances with harmonic dependence on time (normal modes). It is shown that hydrostatic pressure gradient does not affect those at all, and the effect of surface tension is weak—whereas inertia always causes instability. The inertial instability, however, can be inhibited by viscosity, which can make the characteristic time of growth so large that the film would be effectively stable.
Direct force measurements of biomolecular interactions by nanomechanical force gauge
Authors: Jeong Ki-Hun , Keller Chris G. , Lee Luke P.
Published: May 2005

Without using the laser and optical detection method of an atomic force microscope (AFM), direct force measurements of biomolecular interactions in biological solution are accomplished by a nanomechanical force gauge. The device consists of integrated nanoscale single-crystal Si cantilever and reading scales, which allow the direct measurements of biomolecular interactions by reading the deflection of the cantilever with an optical microscope. The spring constant of the cantilevers was calibrated by measuring the resonant frequency under electrostatic force excitation, and the minimum value among the designed devices shows 80pN∕μm. The piconewton regime dissociation force between a biotinylated bead and streptavidins in an aqueous solution was directly measured with this device.
Pressure and relative motion in colloidal suspensions
Authors: Peppin S. S. L. , Elliott J. A. W. , Worster M. G.
Published: May 2005

We examine the nature of relative motion in colloidal suspensions. By distinguishing carefully between the thermodynamic pressure of a mixture, defined by Gibbs, and the pressure measured by Darcy in porous media, we resolve apparent contradictions between the results and interpretations of different experiments. We show that Fick’s and Darcy’s laws, two empirical equations thought to describe different and complementary physical phenomena, are in fact particular limits of a single, unifying thermodynamic equation which can be used more generally to describe transport in colloidal systems. Importantly, this equation relates macroscopically measurable quantities. We use it to provide new interpretations of experiments in ultrafiltration.
Fluid-phase diagrams of binary mixtures from constant pressure integral equations
Authors: Pastore G. , Santin R. , Taraphder S. , Colonna F.
Published: May 2005

A new algorithm for solving integral equations of the theory of liquids at fixed pressure is introduced. Combining this technique with the Lee’s star function approximation for the chemical potentials, we obtain an efficient method to investigate fluid-phase diagrams of binary mixtures. We have tested the capabilities of such technique to study symmetric and asymmetric phase diagrams in nonadditive hard spheres and Lennard-Jones mixtures. We find that the integral equation theories, although approximate, can provide a flexible tool to determine the fluid-phase diagrams whose accuracy is critically dependent on the quality of the closure and of the resulting chemical potentials.
Theory of improved spectral purity in index patterned Fabry-Pérot lasers
Authors: O’Brien S. , O’Reilly E. P.
Published: May 2005

The spectral purity of a ridge waveguide Fabry-Pérot laser can be improved by patterning the effective refractive index seen by an optical mode propagating in the cavity. Here we present a transmission matrix calculation to first order in the effective index step from which we derive the threshold condition as a function of cavity mode index. This approach enables us to solve the inverse problem relating the index pattern along the cavity to the threshold gain modulation in wavenumber space. Quasiperiodic index patterns are constructed, which lead to improved spectral purity at a predetermined wavelength.
Identification of the wind in Rayleigh–Bénard convection
Authors: van Reeuwijk M. , Jonker H. J. J. , Hanjalić K.
Published: May 2005

Using a symmetry-accounting ensemble-averaging method, we have identified the wind in unbounded Rayleigh–Bénard convection. This makes it possible to distinguish the wind from fluctuations and to identify dynamic features of each. We present some results from processing five independent three-dimensional direct numerical simulations of a Γ=4 aspect-ratio domain with periodic side boundaries at Ra=107 and Pr=1. It is found that the wind boundary layer scales linearly very close to the wall and has a logarithmic region further away. Despite the still noticeable molecular effects, the identification of log scaling and significant velocity and temperature fluctuations well within the thermal boundary layer clearly indicate that the boundary layer cannot be classified as laminar.
Room temperature near-ultraviolet emission from In-rich InGaN∕GaN multiple quantum wells
Authors: Kwon Soon-Yong , Baik Sung-Il , Kim Young-Woon , Kim Hee Jin , Ko Dong-Su , Yoon Euijoon , Yoon Jung-Won , Cheong Hyeonsik , Park Yoon-Soo
Published: May 2005

We grew In-rich InGaN∕GaN multiple quantum wells (MQWs) using growth interruption (GI) by metalorganic chemical vapor deposition. The quality of overgrown InGaN∕GaN QW layers in MQWs was largely affected by the crystalline quality and interfacial abruptness of the underlying QW layer. Introduction of 10s GI was very effective in improving the crystalline quality and interfacial abruptness of InGaN QW layers, and we grew a ten periods of 1-nm-thick In-rich InGaN∕GaN MQW with 10s GI and obtained a strong near-ultraviolet (UV) emission (∼390nm) at room temperature. We believe that use of less than 1-nm-thick In-rich InGaN MQW can be a candidate for near-UV source, which might replace the conventional low-indium content (<10%), thicker InGaN QW layer.
Calculation of the linewidth broadening in vertical-cavity surface-emitting lasers due to temperature fluctuations
Authors: Lauer Christian , Amann Markus-Christian
Published: May 2005

We investigate the broadening of the spectral linewidth of vertical-cavity surface-emitting lasers due to the temperature fluctuations occuring in the small resonator volume of these lasers. The present analysis is restricted to the direct impact of temperature changes on the emission wavelength via the temperature dependent refractive index of the semiconductor materials (thermorefractive effect). Our results indicate a significant contribution to the laser linewidth of up to ≈10MHz for small devices. This broadening adds to the Schawlow–Townes–Henry linewidth and thus defines a minimal achievable spectral linewidth.
Optical add-drop multiplexers based on Si-wire waveguides
Authors: Yamada Hirohito , Chu Tao , Ishida Satomi , Arakawa Yasuhiko
Published: May 2005

Ultrasmall optical add-drop multiplexers (OADMs) with Si-wire waveguides were demonstrated. Bragg grating reflectors based on Si-wire waveguides were developed and used as the wavelength-selective mechanism in the OADMs. The dropping wavelength bandwidth of the OADMs was less than 0.7 nm, and the dropping wavelengths could be controlled precisely by adjusting the grating period.
Impact of niobium doping upon the magnetotransport properties of the oxygen-deficient perovskite SrCo1−xNbxO3−δ
Authors: Motohashi T. , Caignaert V. , Pralong V. , Hervieu M. , Maignan A. , Raveau B.
Published: May 2005

The oxygen-deficient perovskite cobaltite SrCo1−xNbxO3−δ was synthesized by direct solid-state reaction and its magnetotransport properties were investigated. This cobaltite exhibits an unusual ferromagnetic behavior with a transition temperature Tm=130to150K and a spin-glass-like behavior below Tm. Importantly, this phase reaches a large magnetoresistance (MR) value, MR≡−(ρH−ρ0)∕ρ0=30% at 5K in 7T. The large MR effect is believed to be related to the disordered magnetic state induced by the Nb-for-Co substitution.
Stress-driven formation of Si nanowires
Authors: Prokes S. M. , Arnold Stephen
Published: May 2005

We present an alternate mechanism for the growth of Si nanowires directly from a silicon substrate, without the use of a metal catalyst, silicon vapor or chemical vapor deposition (CVD) gasses. Since the silicon wires grow directly from the silicon substrate, they do not need to be manipulated or aligned for subsequent applications. Wires in the 20–50 nm diameter range with lengths over 80μm can be easily grown by this technique. The critical parameters in the growth of these nanowires are the surface treatment and the carrier gas used. A model is proposed involving stress-driven wire growth, which is enhanced by surface Si atom diffusion due to the presence of hydrogen gas.
Carbon-doped high-mobility two-dimensional hole gases on (110) faced GaAs
Authors: Schmult S. , Gerl C. , Wurstbauer U. , Mitzkus C. , Wegscheider W.
Published: May 2005

Carbon-doped high-mobility two-dimensional hole gases grown on (110) oriented GaAs substrates have been grown with hole mobilities exceeding 106cm2∕Vs in single heterojunction GaAs∕AlGaAs structures. At these high mobilities, a pronounced mobility anisotropy has been observed. Rashba induced spin-splitting in these asymmetric structures has been found to be independent on the transport direction.
Electro-optic effect in an unbalanced AlGaAs∕GaAs microresonator
Authors: Mitrofanov Oleg , Gasparyan Arman , Pfeiffer Loren N. , West Ken W.
Published: May 2005

An unbalanced Fabry–Pérot resonator is proposed as a miniature electro-optic probe. The resonator allows simultaneous enhancement of the electro-optic effect and the total reflectance at the resonance wavelength. We demonstrate a compact 3.31μm long electro-optic probe based on the unbalanced AlGaAs∕GaAs microresonator.
Mechanism of controlled crack formation in thin-film dielectrics
Authors: Mani Sathya , Saif Taher M.
Published: May 2005

Thin films on substrate may crack due to tensile residual stress taking a mud crack like pattern. The pattern can be controlled by prescribing stress raisers that initiate, and arresters that terminate, cracks at desired locations. Here, we describe the mechanism by which stresses are amplified in plasma-deposited films. Stress raisers in the form of narrow slits or features with sharp corners are reactive ion etched in silicon. Plasma deposition of thin films on these stress raisers causes a nonconformal coverage leading to the formation of narrow voids within the slits. On annealing, the voids amplify the stress and initiate cracks through the thickness of the film.
Diffracted moiré fringes as analysis and alignment tools for multilayer fabrication in soft lithography
Authors: Lee Jae-Hwang , Kim Chang-Hwan , Kim Yong-Sung , Ho Kai-Ming , Constant Kristen , Leung Wai , Oh Cha-Hwan
Published: May 2005

We studied the first-order diffracted moiré fringes of transparent multilayered structures comprised of irregularly deformed periodic patterns. By a comparison study of the diffracted moiré fringe pattern and detailed microscopy of the structure, we show that the diffracted moiré fringe can be used as a nondestructive tool to analyze the alignment of multilayered structures. We demonstrate the alignment method for the case of layer-by-layer microstructures using soft lithography. The alignment method yields high contrast of fringes even when the materials being aligned have very weak contrasts. The imaging method of diffracted moiré fringes is a versatile visual tool for the microfabrication of transparent deformable microstructures in layer-by-layer fashion.
Outdiffusion of La and Al from amorphous LaAlO3 in direct contact with Si (001)
Authors: Sivasubramani P. , Kim M. J. , Gnade B. E. , Wallace R. M. , Edge L. F. , Schlom D. G. , Craft H. S. , Maria J.-P.
Published: May 2005

We have evaluated the thermal stability of Al2O3/LaAlO3/Si (001) stacks with atomic force microscopy, x-ray diffraction, transmission electron microscopy, and secondary ion mass spectrometry using a back side polishing approach. Crystallization of the amorphous LaAlO3 film was found to occur for rapid thermal anneals (RTA) above 935 °C for 20 s, in flowing N2. Penetration of Al and La into the underlying Si (001) is clearly observed for RTA at or above 950 °C for 20 s in flowing N2.
Differential requirement for OBF-1 during antibody-secreting cell differentiation
Authors: Corcoran Lynn M. , Hasbold Jhagvaral , Dietrich Wendy , Hawkins Edwin , Kallies Axel , Nutt Stephen L. , Tarlinton David M. , Matthias Patrick , Hodgkin Philip D.
Published: May 2005

Resting B cells can be cultured to induce antibody-secreting cell (ASC) differentiation in vitro. A quantitative analysis of cell behavior during such a culture allows the influences of different stimuli and gene products to be measured. The application of this analytical system revealed that the OBF-1 transcriptional coactivator, whose loss impairs antibody production in vivo, has two effects on ASC development. Although OBF-1 represses early T cell–dependent (TD) differentiation, it is also critical for the completion of the final stages of ASC development. Under these conditions, the loss of OBF-1 blocks the genetic program of ASC differentiation so that Blimp-1/prdm1 induction fails, and bcl-6, Pax5, and AID are not repressed as in control ASC. Retroviral complementation confirmed that OBF-1 was the critical entity. Surprisingly, when cells were cultured in lipopolysaccharide to mimic T cell–independent conditions, OBF-1–null B cells differentiated normally to ASC. In the OBF-1−/− ASC generated under either culture regimen, antibody production was normal or only modestly reduced, revealing that Ig genes are not directly dependent on OBF-1 for their expression. The differential requirement for OBF-1 in TD ASC generation was confirmed in vivo. These studies define a new regulatory role for OBF-1 in determining the cell-autonomous capacity of B cells to undergo terminal differentiation in response to different immunological signals.
T cell lineage choice and differentiation in the absence of the RNase III enzyme Dicer
Authors: Cobb Bradley S. , Nesterova Tatyana B. , Thompson Elizabeth , Hertweck Arnulf , O'Connor Eric , Godwin Jonathan , Wilson Christopher B. , Brockdorff Neil , Fisher Amanda G. , Smale Stephen T. , Merkenschlager Matthias
Published: May 2005

The ribonuclease III enzyme Dicer is essential for the processing of micro-RNAs (miRNAs) and small interfering RNAs (siRNAs) from double-stranded RNA precursors. miRNAs and siRNAs regulate chromatin structure, gene transcription, mRNA stability, and translation in a wide range of organisms. To provide a model system to explore the role of Dicer-generated RNAs in the differentiation of mammalian cells in vivo, we have generated a conditional Dicer allele. Deletion of Dicer at an early stage of T cell development compromised the survival of αβ lineage cells, whereas the numbers of γδ-expressing thymocytes were not affected. In developing thymocytes, Dicer was not required for the maintenance of transcriptional silencing at pericentromeric satellite sequences (constitutive heterochromatin), the maintenance of DNA methylation and X chromosome inactivation in female cells (facultative heterochromatin), and the stable shutdown of a developmentally regulated gene (developmentally regulated gene silencing). Most remarkably, given that one third of mammalian mRNAs are putative miRNA targets, Dicer seems to be dispensable for CD4/8 lineage commitment, a process in which epigenetic regulation of lineage choice has been well documented. Thus, although Dicer seems to be critical for the development of the early embryo, it may have limited impact on the implementation of some lineage-specific gene expression programs.
Left cells and constructible representations
Authors: Geck Meinolf
Published: May 2005

We consider the partition of a finite Coxeter groupWWinto left cells with respect to a weight functionLL. In the equal parameter case, Lusztig has shown that the representations carried by the left cells are precisely the so-called constructible ones. We show that this holds for generalLL, assuming that the conjectural properties (P1)–(P15) in Lusztig’s book on Hecke algebras with unequal parameters hold forW,LW,L. Our proofs use the idea (Gyoja, Rouquier) that left cell representations are projective in the sense of modular representation theory. This also gives partly new proofs for Lusztig’s result in the equal parameter case.