bluuebunny/crossref_metadata_2025 huggingface dataset:
De novo formation, fusion and fission of mammalian COPII‐coated endoplasmic reticulum exit sites
Authors: Stephens David J
Published: February 2003

Transport between the endoplasmic reticulum (ER) and Golgi is mediated by the sequential action of the COPII and COPI coat complexes. COPII subunits are recruited to the ER membrane where they mediate the selection of cargo for transport to the Golgi, and also membrane deformation and vesicle formation. New ER exit sites can be generated by lateral growth and medial fission (in Pythium sp.) or by de novo formation (in Pichia pastoris) but it is not known how mammalian ER exit sites form. Here, time‐lapse imaging of COPII‐coated structures in live mammalian cells reveals that the number of ER export sites increases greatly during interphase by de novo formation. These results show the fusion of pre‐existing ER export sites and the fission of larger structures. These three mechanisms of de novo formation, fusion and fission probably cooperate to regulate the size of these sites in mammalian cells.
Modification with SUMO
Authors: Verger Alexis , Perdomo José , Crossley Merlin
Published: February 2003

Small ubiquitin‐related modifier (SUMO) is a protein moiety that is ligated to lysine residues in a variety of target proteins. The addition of SUMO can modulate the ability of proteins to interact with their partners, alter their patterns of subcellular localization and control their stability. It is clear that SUMO influences many different biological processes, but recent data suggest that it is particularly important in the regulation of transcription. Indeed, several transcription factors, such as Sp3, c‐Jun, c‐Myb and various nuclear receptors, have recently been shown to be subject to sumoylation and, although this modification can have a positive influence, a growing body of evidence highlights its role in the negative regulation of transcription. This review summarizes recent experiments focusing on sumoylation and transcriptional repression.
The kangaroo genome
Authors: Wakefield Matthew J , Graves Jennifer A Marshall
Published: February 2003

The kangaroo genome is a rich and unique resource for comparative genomics. Marsupial genetics and cytology have made significant contributions to the understanding of gene function and evolution, and increasing the availability of kangaroo DNA sequence information would provide these benefits on a genomic scale. Here we summarize the contributions from cytogenetic and genetic studies of marsupials, describe the genomic resources currently available and those being developed, and explore the benefits of a kangaroo genome project.
Priming the nucleosome: a role for HMGB proteins?
Authors: Travers Andrew A
Published: February 2003

The high‐mobility‐group B (HMGB) chromosomal proteins are characterized by the HMG box, a DNA‐binding domain that both introduces a tight bend into DNA and binds preferentially to a variety of distorted DNA structures. The HMGB proteins seem to act primarily as architectural facilitators in the manipulation of nucleoprotein complexes; for example, in the assembly of complexes involved in recombination and transcription. Recent genetic and biochemical evidence suggests that these proteins can facilitate nucleosome remodelling. One mechanism by which HMGB proteins could prime the nucleosome for migration is to loosen the wrapped DNA and so enhance accessibility to chromatin‐remodelling complexes and possibly also to transcription factors. By constraining a tight loop of untwisted DNA at the edge of a nucleosome, an HMGB protein could induce movements in the contacts between certain core histones that would result in an overall change in nucleosome structure.
Theoretical and experimental aspects of chaos control by time-delayed feedback
Authors: Just Wolfram , Benner Hartmut , Reibold Ekkehard
Published: February 2003

We review recent developments for the control of chaos by time-delayed feedback methods. While such methods are easily applied even in quite complex experimental context the theoretical analysis yields infinite-dimensional differential-difference systems which are hard to tackle. The essential ideas for a general theoretical approach are sketched and the results are compared to electronic circuits and to high power ferromagnetic resonance experiments. Our results show that the control performance can be understood on the basis of experimentally accessible quantities without resort to any model for the internal dynamics.
Frequency and phase synchronization in stochastic systems
Authors: Freund Jan A. , Schimansky-Geier Lutz , Hänggi Peter
Published: February 2003

The phenomenon of frequency and phase synchronization in stochastic systems requires a revision of concepts originally phrased in the context of purely deterministic systems. Various definitions of an instantaneous phase are presented and compared with each other with special attention paid to their robustness with respect to noise. We review the results of an analytic approach describing noise-induced phase synchronization in a thermal two-state system. In this context exact expressions for the mean frequency and the phase diffusivity are obtained that together determine the average length of locking episodes. A recently proposed method to quantify frequency synchronization in noisy potential systems is presented and exemplified by applying it to the periodically driven noisy harmonic oscillator. Since this method is based on a threshold crossing rate pioneered by Rice the related phase velocity is termed the Rice frequency. Finally, we discuss the relation between the phenomenon of stochastic resonance and noise-enhanced phase coherence by applying the developed concepts to the periodically driven bistable Kramers oscillator.
The geometry of chaos synchronization
Authors: Barreto Ernest , Josić Krešimir , Morales Carlos J. , Sander Evelyn , So Paul
Published: February 2003

Chaos synchronization in coupled systems is often characterized by a map φ between the states of the components. In noninvertible systems, or in systems without inherent symmetries, the synchronization set—by which we mean graph(φ)—can be extremely complicated. We identify, describe, and give examples of several different complications that can arise, and we link each to inherent properties of the underlying dynamics. In brief, synchronization sets can in general become nondifferentiable, and in the more severe case of noninvertible dynamics, they might even be multivalued. We suggest two different ways to quantify these features, and we discuss possible failures in detecting chaos synchrony using standard continuity-based methods when these features are present.
Synchronization of reconstructed dynamical systems
Authors: Voss H. U.
Published: February 2003

The problem of constructing synchronizing systems to observed signals is approached from a data driven perspective, in which it is assumed that neither the drive nor the response systems are known explicitly but have to be derived from the observations. The response systems are modeled by utilizing standard methods of nonlinear time series analysis applied to sections of the driving signals. As a result, synchronization is more robust than what might be expected, given that the reconstructed systems are only approximations of the unknown true systems. Successful synchronization also may be accomplished in cases where the driving signals result from nonlinearly transformed chaotic states. The method is readily extended and applied to limited real-time predictions of chaotic signals.
Characterizing direction of coupling from experimental observations
Authors: Bezruchko Boris , Ponomarenko Vladimir , Rosenblum Michael G. , Pikovsky Arkady S.
Published: February 2003

We demonstrate that the direction of coupling of two interacting self-sustained electronic oscillators can be determined from the realizations of their signals. In our experiments, two electronic generators, operating in a periodic or a chaotic state, were subject to symmetrical or unidirectional coupling. In data processing, first the phases have been extracted from the observed signals and then the directionality of coupling was quantitatively estimated from the analysis of mutual dependence of the phase dynamics.
Numerical and experimental investigation of the effect of filtering on chaotic symbolic dynamics
Authors: Zhu Liqiang , Lai Ying-Cheng , Hoppensteadt Frank C. , Bollt Erik M.
Published: February 2003

Motivated by the practical consideration of the measurement of chaotic signals in experiments or the transmission of these signals through a physical medium, we investigate the effect of filtering on chaotic symbolic dynamics. We focus on the linear, time-invariant filters that are used frequently in many applications, and on the two quantities characterizing chaotic symbolic dynamics: topological entropy and bit-error rate. Theoretical consideration suggests that the topological entropy is invariant under filtering. Since computation of this entropy requires that the generating partition for defining the symbolic dynamics be known, in practical situations the computed entropy may change as a filtering parameter is changed. We find, through numerical computations and experiments with a chaotic electronic circuit, that with reasonable care the computed or measured entropy values can be preserved for a wide range of the filtering parameter.
Discrete symmetry’s chains and links between integrable equations
Authors: Yurov A. V.
Published: February 2003

We consider the discrete symmetry’s dressing chains of the nonlinear Schrödinger equation (NLS) and Davey–Stewartson equations (DS). The modified NLS (mNLS) equation and the modified DS (mDS) equations are obtained. The explicitly reversible Bäcklund auto-transformations for the mNLS and mDS equations are constructed. We demonstrate discrete symmetry’s conjugate chains of the KP and DS models. The two-dimensional generalization of the P4 equation is obtained.
Involution analysis of the partial differential equations characterizing Hamiltonian vector fields
Authors: Seiler Werner M.
Published: February 2003

In a recent article, certain underdetermined linear systems of partial differential equations connected with Lie–Poisson structures have been studied. They were constructed via power series solutions of the evolution equation for a given Hamiltonian. We extend the results to arbitrary Poisson manifolds, correct an error in the case of degenerate Poisson structures, and show that these linear systems simply characterize Hamiltonian vector fields. Our basic tool is the formal theory of differential equations with its central concept of an involutive system.
Statistics of defect motion in spatiotemporal chaos in inclined layer convection
Authors: Daniels Karen E. , Bodenschatz Eberhard
Published: February 2003

We report experiments on defect-tracking in the state of undulation chaos observed in thermal convection of an inclined fluid layer. We characterize the ensemble of defect trajectories according to their velocities, relative positions, diffusion, and gain and loss rates. In particular, the defects exhibit incidents of rapid transverse motion which result in power law distributions for a number of quantitative measures. We examine connections between this behavior and Lévy flights and anomalous diffusion. In addition, we describe time-reversal and system size invariance for defect creation and annihilation rates.
Null cubics and Lie quadratics
Authors: Noakes Lyle
Published: February 2003

Riemannian cubics are curves in a Riemannian manifold M satisfying a variational condition. They arise in computer graphics and in trajectory planning problems for rigid body motion, where M is the group SO(3) of rotations of Euclidean three-space E3. Riemannian cubics on a Lie group correspond to Lie quadratics in the Lie algebra. There are only a few cases where closed-form expressions are available for Lie quadratics. The present article is a qualitative analysis of null quadratics in so(3), focusing on long term dynamics and internal symmetries. Conclusions are drawn for asymptotics and symmetries of null cubics in SO(3).
Controlling flow turbulence
Authors: Guan Shuguang , Zhou Y. C. , Wei G. W. , Lai C.-H.
Published: February 2003

This paper investigates the viability and effectiveness of using a technique developed for low-dimensional chaotic systems to control flow turbulence governed by the Navier–Stokes equations. By using a global pinning coupling strategy, we show that turbulence can be controlled to desirable time-varying target states, including a spatially extended periodic state and a turbulent one. Exponential convergence to the target state is found and the exponential rate scales linearly to the coupling strength. The linear scaling law breaks down when localized pinning control is applied. A wavelet multiscale technique is utilized for the characterization of both the effectiveness of the present control strategy and the inverse energy transfer in two-dimensional turbulence.
Scattering of solitons of the Klein–Gordon equation coupled to a classical particle
Authors: Imaikin Valery , Komech Alexander , Markowich Peter A.
Published: February 2003

Long-time asymptotics are established for finite energy solutions of the scalar Klein–Gordon equation coupled to a relativistic classical particle: any “scattering” solution is asymptotically a sum of a soliton and of a dispersive free wave packet as t→±∞. These asymptotics mean the nonlinear scattering of free wave packets by the soliton.
Noisy heteroclinic networks
Authors: Armbruster Dieter , Stone Emily , Kirk Vivien
Published: February 2003

The influence of small noise on the dynamics of heteroclinic networks is studied, with a particular focus on noise-induced switching between cycles in the network. Three different types of switching are found, depending on the details of the underlying deterministic dynamics: random switching between the heteroclinic cycles determined by the linear dynamics near one of the saddle points, noise induced stability of a cycle, and intermittent switching between cycles. All three responses are explained by examining the size of the stable and unstable eigenvalues at the equilibria.
Thermodynamic properties of the 2N-piece relativistic string
Authors: Brevik Iver , Bytsenko Andrei A. , Sollie Roger
Published: February 2003

The thermodynamic free energy F(β) is calculated for a gas consisting of the transverse oscillations of a piecewise uniform bosonic string. The string consists of 2N parts of equal length, of alternating type I and type II material, and is relativistic in the sense that the velocity of sound everywhere equals the velocity of light. The present paper is a continuation of two earlier papers, one dealing with the Casimir energy of a 2N-piece string [I. Brevik and R. Sollie, J. Math. Phys. 38, 2774 (1997)], and another dealing with the thermodynamic properties of a string divided into two (unequal) parts [I. Brevik, A. A. Bytsenko, and H. B. Nielsen, Class. Quantum Grav. 15, 3383 (1998)]. Making use of the Meinardus theorem, we calculate the asymptotics of the level state density, and show that the critical temperatures in the individual parts are equal, for arbitrary space–time dimension D. If D=26, we find β=(2/N)2π/TII, TII being the tension in part II. Thermodynamic interactions of parts related to high genus g is also considered.
Transport of energy in dissipative advection phenomena
Authors: Núñez Manuel
Published: February 2003

A study of the distribution of energy among the different scales is performed for several systems in fluid mechanics, including the Navier–Stokes, magnetohydrodynamics and active scalars equations. It is found that all these systems possess a common structure which enables us to deduce how the energy introduced by the forcing is transferred to the scales present in the flow. It is also shown that in special cases an energy cascade will occur. The limits of this method are also considered.
A boot-strap Poisson–Boltzmann theory for the structure and thermodynamics of charged colloidal solutions
Authors: Petris Simon N. , Chan Derek Y. C. , Linse Per
Published: February 2003

The structural properties and thermodynamics of one- and two-component solutions of charged colloidal particles with explicit counterions have been investigated by Monte Carlo simulation. A boot-strap Poisson–Boltzmann (BSPB) theory has been developed to interpret these results and the accuracy of its predictions is compared with other existing theories. The BSPB was also used to predict the gas–liquid binodal and spinodal curves for a one-component system with colloid charge to counterion-charge ratio Zr=10.
Geometric characterizations of the Lamb equation
Authors: Murugesh S. , Balakrishnan Radha
Published: February 2003

Recently, we developed a unified formalism which shows that an exact solution of an integrable nonlinear evolution equation (belonging to a certain class) can be associated with three distinct moving space curves, which represent the geometric characterizations of the equation concerned. Here, we apply our formalism to the Lamb equation, iqu+qs+q∫s|q|2 ds′=0, and obtain its geometric characterizations by exploiting its mapping to the exactly solvable Belavin–Polyakov equation, mu=m×ms;  m2=1. We show that the Lamb equation supports “envelope solitons” and novel “envelope instantons” as exact solutions. As illustrative examples, the surfaces swept out by the three moving curves that correspond to each of these solutions are derived and displayed pictorially. Possible applications are suggested.
Adjoint operators, gauge invariant perturbations, and covariant symplectic form for black holes in string theory
Authors: Cartas-Fuentevilla R.
Published: February 2003

Using a scheme of adjoint operators, we give a covariant and gauge invariant treatment for the perturbation theory of static charged black holes in string theory, valid for curvature below the Planck scale; conserved quantities and a covariant symplectic form on the phase space are explicitly constructed. Future extensions of the present results are discussed.
Reciprocal transformations of Hamiltonian operators of hydrodynamic type: Nonlocal Hamiltonian formalism for linearly degenerate systems
Authors: Ferapontov E. V. , Pavlov M. V.
Published: February 2003

Reciprocal transformations of Hamiltonian operators of hydrodynamic type are investigated. The transformed operators are generally nonlocal, possessing a number of remarkable algebraic and differential-geometric properties. We apply our results to linearly degenerate semi-Hamiltonian systems in Riemann invariants, a typical example being Rti=(∑m=1nRm−Ri)Rxi, i=1,2,…,n. Since all such systems are linearizable by appropriate (generalized) reciprocal transformations, our formulas provide an infinity of mutually compatible nonlocal Hamiltonian structures, explicitly parametrized by n arbitrary functions of one variable.
Spherically symmetric solutions of a boundary value problem for monopoles
Authors: Marini Antonella , Sadun Lorenzo
Published: February 2003

In this article we study spherically symmetric monopoles, which are critical points for the Yang–Mills–Higgs functional over a disk in three dimensions, with prescribed degree and covariant constant at the boundary. This is a three-dimensional gauge-theory generalization of the Ginzburg-Landau model in two dimensions.
The van der Waals potentials between all the rare gas atoms from He to Rn
Authors: Tang K. T. , Toennies J. P.
Published: February 2003

The interatomic van der Waals potentials for all the possible 21 homogeneous and heterogeneous pairs of rare gas atoms including radon are determined using the Tang–Toennies potential model and a set of previously derived combining rules. The three dispersion coefficients and the two Born–Mayer parameters needed for calculating the potential curves are listed.
An operator method for finding exact solutions to vector Korteweg–de Vries equations
Authors: Huang Sen-Zhong
Published: February 2003

We develop an operator method which helps finding exact solutions to nonlinear evolution equations (NLEs). Our working schema goes as follows: First we translate the given (NLE) into an appropriate operator version (ONLE). Second, we look for solutions to (ONLE) of the form U=(I+L)−1M, where both L and M are operator-valued functions of the space–time variables and the range of M locates in some appropriate Banach algebras which admits a functional φ that preserves the squares [i.e., φ(A2)=φ(A)2]. Finally, a solution u of the given (NLE) can be obtained by setting u≔φ(U). This method is named by the LM method. Using the LM method, we have rederived the famous Cole–Hopf transformation which reduces the nonlinear Burgers equation into the linear heat equation. The main part of this article is to use the LM method to study the vector Korteweg–de Vries (KdV) equations ut=uxxx+3(u2)x settled in finite-dimensional unital Banach algebras 𝒥. It is shown that these vector KdV equations admit soliton solutions. Specially, we have carried out a thorough study of the quaternionic KdV equation (i.e., the vector KdV equation settled in the Hamilton quaternion algebra ℍ) and shown many interesting and surprising aspects of the quaternionic KdV solitons. Two of them read as follows. (a) The paradoxical energy symmetry breaking phenomenon: Two quaternionic KdV solitons with different energies can annihilate each other. (b) The surprising low-dimensional phenomenon: The interaction of any finitely many quaternionic KdV solitons which live in a unital three-dimensional subspace Π of ℍ does not yield any effect to the part outside that subspace Π and thus their interaction behaves as if it were linear although the interaction between quaternionic KdV solitons is really nonlinear. The LM method can be thought as a complement to the famous bilinear operator method of Hirota. Hirota’s method works very powerful for solving scalar equation but has difficulty with vector equations. The LM method helps overcoming this difficulty.
G3-RAD and G3X-RAD: Modified Gaussian-3 (G3) and Gaussian-3X (G3X) procedures for radical thermochemistry
Authors: Henry David J. , Sullivan Michael B. , Radom Leo
Published: February 2003

The G3-RAD, G3X-RAD, G3(MP2)-RAD, and G3X(MP2)-RAD, procedures, designed particularly for the prediction of reliable thermochemistry for free radicals, are formulated and their performance assessed using the G2/97 test set. The principal features of the RAD procedures include (a) the use of B3-LYP geometries and vibrational frequencies (in place of UHF and UMP2), including the scaling of vibrational frequencies so as to reproduce ZPVEs, (b) the use of URCCSD(T) [in place of UQCISD(T)] as the highest-level correlation procedure, and (c) the use of RMP (in place of UMP) to approximate basis-set-extension effects. G3-RAD and G3X-RAD are found to perform well overall with mean absolute deviations (MADs) from experiment of 3.96 and 3.65 kJ mol−1, respectively, compared with 4.26 and 4.02 kJ mol−1 for standard G3 and G3X. G3-RAD and G3X-RAD successfully predict heats of formation with MADs of 3.68 and 3.11 kJ mol−1, respectively (compared with 3.93 and 3.60 kJ mol−1 for standard G3 and G3X), and perform particularly well for radicals with MADs of 2.59 and 2.50 kJ mol−1, respectively (compared with 3.51 and 3.18 kJ mol−1 for standard G3 and G3X). The G3(MP2)-RAD and G3X(MP2)-RAD procedures give acceptable overall performance with mean absolute deviations from experiment of 5.17 and 4.92 kJ mol−1, respectively, compared with 5.44 and 5.23 kJ mol−1 for standard G3(MP2) and G3X(MP2). G3(MP2)-RAD and G3X(MP2)-RAD give improved performance over their standard counterparts for heats of formation (MADs=4.73 and 4.44 kJ mol−1, respectively, versus 4.94 and 4.64 kJ mol−1). G3(MP2)-RAD shows similar performance to G3(MP2) for radical heats of formation (MAD=5.10 versus 5.15 kJ mol−1) while G3X(MP2)-RAD performs significantly better than G3X(MP2) (MAD=4.67 versus 5.19 kJ mol−1).
Interactions and structure of poly(dimethylsiloxane) at silicon dioxide surfaces: Electronic structure and molecular dynamics studies
Authors: Tsige Mesfin , Soddemann Thomas , Rempe Susan B. , Grest Gary S. , Kress Joel D. , Robbins Mark O. , Sides Scott W. , Stevens Mark J. , Webb Edmund
Published: February 2003

Electronic structure studies are used to probe the interactions and molecular dynamics simulations are used to study the structure of thin poly(dimethylsiloxane) (PDMS) films near hydroxylated SiO2 substrates. Results of the electronic structure calculations show that the PDMS end groups, rather than atoms such as oxygen in the PDMS backbone structure, dominate interactions at the interface. Methyl–terminated PDMS binds weakly with the substrate via interactions between H atoms on PDMS methyl groups and O atoms on the substrate hydroxyl groups, while hydroxyl–terminated PDMS binds strongly with the substrate via hydrogen bonding between hydroxyl groups on PDMS and the substrate. To study the effect of temperature and type of substrate on the structural ordering of the PDMS liquid near the solid/liquid and liquid/air interfaces, molecular dynamics simulations for two temperatures (300 and 400 K) are carried out for three hydroxylated SiO2 substrates (α–quartz, β–cristobalite and amorphous SiO2). A direct correlation between the amount of ordering in the liquid near the solid/liquid interface and both the roughness of the substrate and the temperature is found. Furthermore the type of terminal end groups on the PDMS molecule also plays a role in the ordering of the PDMS segments near the interface.
Quiescent and flow-induced transitional behavior of hydroxypropylcellulose solutions
Authors: Grizzuti Nino , Maffettone Pier Luca
Published: February 2003

The flow-induced transition of liquid crystalline polymers (LCPs) is studied by rheological techniques. Aqueous solutions of hydroxypropylcellulose (HPC) in water are adopted as a model LCP system. Nonisothermal oscillatory tests are first used to quantitatively determine the “rheological” phase diagram of the HPC/water system under quiescent conditions. The phase diagram compares well with those obtained by other, more conventional techniques. Superposition of oscillatory and steady shear flow is then used to describe the nonisothermal flow-induced transition. In this case, it is shown that a critical shear stress must be reached to effectively induce the isotropic/mesophase transition. Stress-loop experiments are also used to identify the isothermal flow-induced transition, and to provide information on the transition kinetics.
Size dependent phase stability of carbon nanoparticles: Nanodiamond versus fullerenes
Authors: Barnard A. S. , Russo S. P. , Snook I. K.
Published: February 2003

Over the past 15 years, a number of studies have reported findings comparing the relative stability of diamond and graphite, at the nanoscale. In light of more recent experimental and theoretical results concerning the transformation of nanodiamonds into carbon-onions, it is considered important to extend this body of work to included fullerenes. Presented here is a study of the phase stability of carbon nanoparticles, with particular attention given to the relative stability of nanodiamonds and fullerenes. The structural energies have been calculated using density functional theory within the generalized gradient approximation using the Vienna ab initio simulation package, and used to determine the standard heat of formation for respective carbon phases as a function of the number of carbon atoms. Our results show that in contrast to previously reported studies, nanodiamond is not necessarily the stable phase a the nanoscale, but instead occupies a “window” of stability between ∼1.9 and ∼5.2 nm.
Simple model potential and model wave functions for (Na, K, Rb, Cs)–H molecules
Authors: Patil S. H. , Tang K. T.
Published: February 2003

A simple model potential is used to describe the interaction of a valence electron with the alkali core, which has the correct asymptotic form with the Coulomb and dipolar polarizability terms, and an effective hard-core radius adjusted to give the correct energy for the valence electron. Based on this potential, some simple wave functions are developed to describe the (Na, K, Rb, Cs)–H molecules, which incorporate some important local properties, in particular the cusp property when two charged particles are close to each other. These wave functions provide reliable values for the potential, and a simple physical perspective of their structure.
The spin–flip approach within time-dependent density functional theory: Theory and applications to diradicals
Authors: Shao Yihan , Head-Gordon Martin , Krylov Anna I.
Published: February 2003

An extension of density functional theory to situations with significant nondynamical correlation is presented. The method is based on the spin–flip (SF) approach which is capable of describing multireference wave functions within a single reference formalism as spin–flipping, e.g., α→β, excitations from a high-spin (Ms=1) triplet reference state. An implementation of the spin–flip approach within the Tamm–Dancoff approximation to time-dependent density functional theory (TDDFT) is presented. The new method, SF-TDDFT/TDA or simply SF-DFT, describes target states (i.e., closed- and open-shell singlets, as well as low-spin triplets) by linear response from a reference high-spin triplet (Ms=1) Kohn–Sham state. Contrary to traditional TDDFT, the SF-DFT response equations are solved in a subspace of spin–flipping operators. The method is applied to bond-breaking (ethylene torsional potential), and equilibrium properties of eight diradicals. The results demonstrate significant improvement over traditional Kohn–Sham DFT, particularly for 50/50 hybrid functional.
Design of toy proteins capable of rearranging conformations in a mechanical fashion
Authors: Borovinskiy Alexander L. , Grosberg Alexander Yu.
Published: February 2003

We design toy protein mimicking a machinelike function of an enzyme. Using an insight gained by the study of conformation space of compact lattice polymers, we demonstrate the possibility of a large scale conformational rearrangement which occurs (i) without opening a compact state, and (ii) along a linear (one-dimensional) path. We also demonstrate the possibility to extend sequence design method such that it yields a “collective funnel” landscape in which the toy protein (computationally) folds into the valley with rearrangement path at its bottom. Energies of the states along the path can be designed to be about equal, allowing for diffusion along the path. They can also be designed to provide for a significant bias in one certain direction. Together with a toy ligand molecule, our “enzimatic” machine can perform the entire cycle, including conformational relaxation in one direction upon ligand binding and conformational relaxation in the opposite direction upon ligand release. This model, however schematic, should be useful as a test ground for phenomenological theories of machinelike properties of enzymes.
Charge transfer for the ground state O+(4S) ion in collisions with H2 molecules
Authors: Pichl Lukáš , Li Yan , Liebermann Heinz-Peter , Buenker Robert J. , Kimura Mineo
Published: February 2003

A new theoretical result of the total charge transfer cross section in collisions of O+ ion in the ground state with H2 molecule is reported. The collision energy of the incident O+(4S) ion ranges from 1 eV/u to 10 keV/u, covering the available experimental data. States of A24 and B14 symmetry are included in the calculation. The state-resolved cross sections are obtained by using both the semiclassical and full quantum molecular orbital close coupling method. Based on our results, we propose a possible explanation for the large discrepancies in recent measurements among various experimental groups.
Cumulant approach to the direct calculation of reduced density matrices: A critical analysis
Authors: Nooijen Marcel , Wladyslawski Mark , Hazra Anirban
Published: February 2003

In this paper we address a number of topics regarding the contracted Schrödinger equation (CSE): (i) The cumulant expansion of reduced density matrices (RDMs), and the reduction of the CSE to a connected form. (ii) The comparison of the resulting formalism to coupled cluster theory. (iii) The direct calculation of the two-particle RDM in terms of the cumulants, without explicitly imposing any N-representability conditions. We explore a number of approximations, the most elaborate of which is the 3,5-CSE in which the cumulant expansion is carried out to the three-particle level, and the only approximation made is to equate the four- and five-particle cumulants to zero. Overall the numerical results we present for selected small model systems are found to be disappointing and we provide a critical analysis of the perceived shortcomings of our cumulant approach to the CSE.
An atomistic simulation study of a solid monolayer and trilayer of n-hexane on graphite
Authors: Krishnan M. , Balasubramanian S. , Clarke S.
Published: February 2003

We present all-atom molecular dynamics simulations of n-hexane on the basal plane of graphite at monolayer and trilayer coverages. In keeping with experimental data, we find the presence of ordered adsorbed layers at both coverages. Using a simulation method that does not impose any particular periodicity on the adsorbed layer, we quantitatively compare our results to the results of neutron diffraction experiments and find a structural transition from a uniaxially incommensurate lattice to a fully commensurate structure on increasing the coverage from a monolayer to a trilayer. The zig–zag backbone planes of all the alkane molecules lie parallel to the graphite surface at the trilayer coverage, while a few molecules are observed to attain the perpendicular orientation at monolayer coverage.
Polymer escape through a nanopore
Authors: Muthukumar M.
Published: February 2003

Free energy barrier and mean translocation time, τ, are calculated for the movement of a single Gaussian chain from one sphere to another larger sphere through a narrow pore. The potential interaction between the polymer and pore significantly modifies the entropic barrier landscape of translocation. As the pore length increases, the translocation process undergoes a transition from entropic barrier mechanism to a mechanism dominated by the pore–polymer interaction. This shift in mechanism leads to nonmonotonic dependence of τ on the pore length. Explicit formulas are derived for the dependence of τ on chain length, pore length, sizes of the donor and recipient spheres, strength of pore–polymer interaction, applied voltage, and electrochemical potential gradient for translocation. The calculated results provide guidance for tuning the rate of polymer translocation through narrow pores.
Free-volume theory of the freezing of polydisperse hard-sphere mixtures: Initial preparation, fractionation, and terminal polydispersity
Authors: Xu H. , Baus M.
Published: February 2003

The freezing of hard-sphere mixtures of arbitrary polydispersity is studied within a van der Waals-type free-volume approximation. The present theory is simple enough to allow for a thorough numerical investigation of all the polydispersity effects on the order–disorder transition of hard spheres. Within this context we have studied the influence on the order–disorder transition of the initial preparation, the subsequent fractionation, and the possible terminal polydispersity. It is found that the order–disorder transition occupies a finite domain of the initial density–initial polydispersity plane and the frontier of this domain is determined. Considerable variation within this domain is found with respect to the initial density, while the influence of the specific form of the initial size-distribution is found to be only marginal.
Heterogeneous nucleation and wetting of water thin films on a metal surface: A study by optical second harmonic generation
Authors: Yang Minchul , Dai Hai-Lung
Published: February 2003

The condensation of water thin films on a hydrophobic metal surface, Ag(111), was examined using optical second harmonic generation. Condensation coefficient and the fraction of metal surface area covered with water during film deposition were measured in the temperature range of 145–175 K. It was found that under isothermal condensation conditions, the condensation coefficient decreases abruptly to zero at a temperature several degrees lower than that predicted by zero-order desorption kinetics. This catastrophic failure in water film deposition at these temperatures can be explained by the occurrence of wetting–dewetting transition as a result of three-dimensional cluster formation, i.e., the critical nucleus size becomes too large at these temperatures to allow the formation of the first layer and subsequent growth of water film. Model calculations based on classical nucleation theory which depicts that heterogeneous nucleation is the initial step of water film deposition can be used to quantitatively characterize the critical nucleus size as about 100 and the nucleation rate to be slower than 10−3 ML s−1 at these temperatures.
On the determination of molecular orientation from polarized imaging in second-harmonic microscopy
Authors: Bordo Vladimir G. , Kato Teiji
Published: February 2003

The polarized imaging of a monolayer film in second-harmonic microscopy in oblique incidence geometry has been analyzed theoretically. It has been demonstrated that both azimuthal and tilt angles of molecules in the film can be determined from measurements of relative second harmonic intensities at different orientations of a polarizer or an analyzer.
Nanofocusing parabolic refractive x-ray lenses
Authors: Schroer C. G. , Kuhlmann M. , Hunger U. T. , Günzler T. F. , Kurapova O. , Feste S. , Frehse F. , Lengeler B. , Drakopoulos M. , Somogyi A. , Simionovici A. S. , Snigirev A. , Snigireva I. , Schug C. , Schröder W. H.
Published: February 2003

Parabolic refractive x-ray lenses with short focal distance can generate intensive hard x-ray microbeams with lateral extensions in the 100 nm range even at a short distance from a synchrotron radiation source. We have fabricated planar parabolic lenses made of silicon that have a focal distance in the range of a few millimeters at hard x-ray energies. In a crossed geometry, two lenses were used to generate a microbeam with a lateral size of 380 nm by 210 nm at 25 keV in a distance of 42 m from the synchrotron radiation source. Using diamond as the lens material, microbeams with a lateral size down to 20 nm and below are conceivable in the energy range from 10 to 100 keV.
Electro-optic characteristics of (001)-oriented Ba0.6Sr0.4TiO3 thin films
Authors: Kim Dal-Young , Moon Seung Eon , Kim Eun-Kyung , Lee Su-Jae , Choi Jong-Jin , Kim Hyoun-Ee
Published: February 2003

Ba 0.6 Sr 0.4 TiO 3 thin films were grown on MgO(001) substrates using pulsed-laser deposition. The films were highly oriented along the (001) direction, and showed a high electro-optic response to an external electric field. The quadratic electro-optic coefficient Rc was 1.0×10−14 m2/V2, and the birefringence variation was as large as 0.09. Various electro-optic applications as well as the microwave applications of barium strontium titanate thin films are expected.
Strong green luminescence in quaternary InAlGaN thin films
Authors: Feng Shih-Wei , Cheng Yung-Chen , Chung Yi-Yin , Yang C. C. , Ma Kung-Jeng , Yan Chih-Chiang , Hsu Chen , Lin J. Y. , Jiang H. X.
Published: February 2003

We observed strong green luminescence (around 2.37 eV) in two InAlGaN thin film samples, which were originally prepared for applications in the UV range. Based on the observation of the InN peaks and the extended distributions, corresponding to InGaN compounds, in the x-ray diffraction patterns, such green luminescence was attributed to the formation of indium-rich clusters, which formed localized states, in the quaternary films of low indium content (2%). Carrier trapping of such localized states, particularly when carriers received thermal energy such that they could overcome certain potential barriers around the clusters, resulted in strong green luminescence. The observed optical behaviors, including the blueshift phenomenon of photoluminescence spectral peak position in varying temperature, showed that the green luminescence was quite different from the previously reported yellow luminescence, which resulted from defects.
Strain-induced magnetic stripe domains in La0.7Sr0.3MnO3 thin films
Authors: Dho Joonghoe , Kim Y. N. , Hwang Y. S. , Kim J. C. , Hur N. H.
Published: February 2003

We have investigated magnetic microstructures of magnetoresistive La0.7Sr0.3MnO3 (LSMO) thin films. Magnetic images are strongly dependent on structural strain induced by the substrates. The LSMO film on SrTiO3 dominated by tensile stress effect displays a feather-like pattern, whereas LSMO films on LaAlO3 and NdGaO3 substrates under compressive stress show stripe domains. In particular, the magnetic image of the film on NdGaO3 reveals distinctive straight stripe domain patterns on the order of about 120 nm, suggesting the presence of a sizable out-of-plane magnetization. The ordering of the stripe domains is also sensitive to the field direction.
Insight into the premelting and melting processes of metal nanoparticles through capacitance measurements
Authors: Parravicini G. B. , Stella A. , Tognini P. , Merli P. G. , Migliori A. , Cheyssac P. , Kofman R.
Published: February 2003

We demonstrate that capacitance measurements on metallic nanosystems (specifically Ga nanoparticles embedded in dielectric matrix) yield information to clarify the complex phenomenon of melting, where different mechanisms may interplay. The technique is proved to be extremely powerful to study the role of surfaces and interfaces on a twofold basis: very short (of the order of a few angstroms) penetration depth of the probing electric field and a strict relationship of capacity with entropy. We show that initial disorder starts to take place ≈65 °C before full melting, with evidence of two regimes in the premelting and melting region.
X-ray imaging of surface acoustic waves generated in semiconductor crystals by an external transducer
Authors: Shilo D. , Lakin E. , Zolotoyabko E. , Härtwig J. , Baruchel J.
Published: February 2003

We demonstrate successful x-ray-diffraction imaging of high-frequency (0.29-GHz) surface acoustic waves (SAWs) propagating in semiconductor crystals (Si and GaAs) with no deposited electrodes on top of them. Experiments were performed at the ID19 beamline of the European Synchrotron Radiation Facility (Grenoble). We used the stroboscopic x-ray topography technique, in which x-ray bursts coming from the storage ring are synchronized with the excited acoustic waves. This technique is able to visualize individual acoustic wave fronts of traveling SAWs and their distortions caused by phonon scattering. In order to generate SAW in semiconductor crystals the latter were coupled to LiNbO3-based SAW transducers via contact liquids. The maximum SAW transmission is achieved for evanescent waves under optimized coupling conditions at the liquid/sample interface. The technique developed opens a way to directly study phonon interaction with defects in nonpiezoelectric and weakly piezoelectric crystals.
Unified closed-form model of thermionic-field and field emissions through a triangular potential barrier
Authors: Karmalkar Shreepad , Sathaiya D. Mahaveer
Published: February 2003

We report a simple closed-form model of the total emission through a triangular potential barrier due to thermionic field emission (TFE) and field emission (FE). Such a model has not been derived previously, since the energy distribution function of emitted electrons is not analytically integrable. We overcame this difficulty using a geometrical approximation of the integration operation. Our model so derived reveals the energy location and spread of the emission, which allow estimation of the emission through any fraction of the barrier. It also yields a characteristic field parameter in terms of the barrier height, temperature, and effective mass, which can be used to identify the TFE, FE, and TE regimes of device operation.
Magnetic coupling in Co/Cr2O3/CrO2 “trilayer” films
Authors: Cheng Ruihua , Caruso A. N. , Yuan L. , Liou S.-H. , Dowben P. A.
Published: February 2003

The ferromagnetic coupling between Co and CrO2, through an insulator (Cr2O3) was characterized by in situ magneto-optic Kerr effect. By evaporating 20–60 Å Co thin films on top of epitaxial CrO2 films, a Co/Cr2O3/CrO2 trilayer system can be readily fabricated; this is possible because the native surface layer of CrO2 is Cr2O3. In situ x-ray photoemission studies show that the Co is oxidized at the interface between Co and Cr2O3, so that the system more resembles Co/CoO/Cr2O3/CrO2. The Co thickness and temperature dependence of the magnetic hysteresis loops indicate that magnetic coupling strength increases with increasing Co thickness and decreases with increasing temperature. The magnetic coupling through the insulator barrier may be related to defect states in the insulating barrier layer.
Correlation between threading dislocation density and the refractive index of AlN grown by molecular-beam epitaxy on Si(111)
Authors: Natali F. , Semond F. , Massies J. , Byrne D. , Laügt S. , Tottereau O. , Vennéguès P. , Dogheche E. , Dumont E.
Published: February 2003

We report on the influence of the structural properties on the refractive index of AlN films grown on Si(111) substrates by molecular-beam epitaxy using ammonia. The structural properties are assessed by reflection high-energy electron diffraction, atomic force microscopy, transmission electron microscopy, and x-ray diffraction. Refractive index values are deduced from room-temperature spectroscopic ellipsometry. Optical data analysis is performed using the Kramers-Krönig relation in the transparent spectral region, from 1.6 to 3.2 eV. Evidence is presented showing the influence of strain and dislocation density on the AlN layer refractive index.
Natural transition orbitals
Authors: Martin Richard L.
Published: February 2003

A means of finding a compact orbital representation for the electronic transition density matrix is described. The technique utilizes the corresponding orbital transformation of Amos and Hall and allows a dramatic simplification in the qualitative description of an electronic transition.
Chirality-dependent curvature effect in smallest single-walled carbon nanotubes
Authors: Li Irene L. , Li G. D. , Liu H. J. , Chan C. T. , Tang Z. K.
Published: February 2003

Polarized Raman spectra are measured for 0.4 nm single-walled carbon nanotubes embedded in the zeolite matrix. The polarization dependence of the Raman intensity of the radial breathing mode showed that the carbon nanotubes inside the channels of the zeolite are perfectly aligned. The observed radial breathing mode frequencies deviated from those predicted by the elastic model. The strong curvature effect leads to two features: (i) the radial breathing mode frequencies show obvious softening and (ii) the degree of the softening depends on the tube chirality, which agrees well with the theoretic calculations.