bluuebunny/crossref_metadata_2025 huggingface dataset:
Geometry optimization in redundant internal coordinates
Authors: Pulay P. , Fogarasi G.
Published: July 2002

The gradient geometry-optimization procedure is reformulated in terms of redundant internal coordinates. By replacing the matrix inverse with the generalized inverse, the usual Newton–Raphson–type algorithms can be formulated in exactly the same way for redundant and nonredundant coordinates. Optimization in redundant coordinates is particularly useful for bridged polycyclic compounds and cage structures where it is difficult to define physically reasonable redundancy-free internal coordinates. This procedure, already used for the geometry optimization of porphine, C20N4H14, is illustrated here at the ab initio self-consistent-field level for the four-membered ring azetidine, for bicyclo[2.2.2]octane, and for the four-ring system C16O2H22, the skeleton of taxol.
Self-interaction corrected density functionals and the structure of metal clusters
Authors: Fois Ettore S. , Penman James I. , Madden Paul A.
Published: July 2002

An approach, based upon the Car–Parrinello method, for finding the electronic ground state for a self-interaction corrected density functional theory is described. The influence of the self-interaction correction for the ground-state properties and for predicted equilibrium molecular structures is illustrated with reference to calculations on small clusters of sodium.
Thermodynamics of open nonlinear systems far from equilibrium: The continuously stirred tank reactor
Authors: Yoshida Nobuo
Published: July 2002

A thermodynamic analysis is made of a continuously stirred tank reactor (CSTR) which is fed with ideal gases and in which arbitrary types of chemical reactions take place. For stationary states and oscillatory ones in which limit cycles are established, expressions are derived which describe the change of entropy of the reactor contents relative to the feed in terms of explicit quantities, including the rate of entropy production due to the chemical reactions. This entropy change is shown to be always greater than what would be observed in closed systems under comparable circumstances. It is pointed out that this statement is beyond what the second law of thermodynamics can predict. In previous articles, entropy and entropy production have been found to follow certain systematic trends in some specific models based on the CSTR. That work is compared with the present theory.
Calculated pressure-induced phase transition in MgF2
Authors: Allan N. L. , Hines R. I. , Towler M. D. , Mackrodt W. C.
Published: July 2002

Calculations are reported of the pressure-induced phase transition in MgF2 based on free-energy lattice simulations and ab initio Hartree–Fock calculations. In the athermal limit the predicted transition pressures are 26 and 24 GPa respectively, of which the former is increased to ∼30–40 GPa at 296 K. These compare with an experimental estimate of ∼30 GPa.
Field-induced intensity and Stark shift measurements of the electric dipole moment of ICl in the B 3Π0+ state
Authors: Wang S.-X. , Booth J. L. , Dalby F. W. , Ozier I.
Published: July 2002

The laser-induced fluorescence spectrum in ICl of the (2′–0″) vibrational band in the B 3Π0+–X 1Σ+ electronic system has been measured as a function of the electric field strength up to 32.5 kV/cm. Field-induced intensity measurements on I35Cl have been used to determine the magnitude and sign of the electric dipole moment μB in the B state relative to the magnitude and sign of the moment μX in the X state. From the intensity ratio of the field-induced line Q(0) to the allowed Stark component P(1,0), which has the same upper state, it was found that μB/μX=+(0.888±0.051). The positive sign indicates that the polarity is the same in the B and the X states. Intensity ratio measurements for Q(0) to R(5) and for Q(1) to R(5) yield similar (but less precise) results. In order to test this first application of the method to excited electronic states, Stark shift measurements were carried out on a number of P-branch Stark components. It was found for I35Cl that ‖μB/μX‖=(0.8984±0.0036), in good agreement with the intensity measurements. The corresponding determination for I37Cl is that ‖μB/μX‖=(0.900±0.014). The present results are in agreement with those obtained earlier from studies of the absorption spectrum by Watanabe et al. [Jpn. J. Appl. Phys. 31, 901 (1992)].
Separability properties of reduced and effective density matrices in the equation-of-motion coupled cluster method
Authors: Stanton John F.
Published: July 2002

Certain aspects of final state descriptions provided by the equation-of-motion coupled cluster (EOM-CC) method are analyzed, particularly the asymptotic separability of density matrices. Specific attention is focused on a supermolecule system that consists of two fragments, one of which is in an excited electronic state. For this example, the reduced n-particle density matrix [ρ(n)] associated with EOM-CC theory exhibits unphysical long range behavior due to a lack of bra state multiplicative separability. More satisfactory is the effective density [D(n)] which includes the first order response of ground state correlation. In particular, local components of D(n) reduce to the corresponding monomer quantities in the limit of infinite separation. This feature guarantees that observables calculated by contracting D(n) with local operators are size consistent. However, the situation with respect to physical phenomena associated with nonlocal operators is less clear, as multicenter matrix elements of both ρ(n) and D(n) behave incorrectly for n≥2 in the separated limit. The latter consideration should not be misconstrued as an inherent failure of the EOM-CC approximation, as problems associated with nonlocal parts of the density are already present in the normal coupled cluster treatment of the ground state.
Frequency spectra of two-band fluids and fluid mixtures: Mean spherical approximation and beyond
Authors: Ho/ye J. S. , López-Martín J. L. , Lomba E.
Published: July 2002

In the framework of a recently proposed approximation, we investigate here the frequency spectra of two-band fluids (fluids composed of particles with two independent Drude oscillators embedded) as well as fluid mixtures of particles with one Drude oscillator. Both cases are analyzed in the low density regime where departures from the linear theories are more evident. Our theory, which goes beyond the mean spherical approximation (MSA), reproduces the correct low density spectra while retaining the proper qualitative behavior of the MSA at fluid densities.
Microphase separation in block copolymer/homopolymer blends: Theory and experiment
Authors: Floudas G. , Hadjichristidis N. , Stamm M. , Likhtman A. E. , Semenov A. N.
Published: July 2002

The process of microphase separation in diblock copolymer/homopolymer blends is studied both theoretically and experimentally for an asymmetric diblock copolymer and for homopolymer concentration less than 25%. The degree of polymerization of the added homopolymer (Nh) covered all possible cases; N≈Nh, N>Nh, and N<Nh. SAXS and rheology are employed and provide the order–disorder transition temperature through the discontinuous changes of the structure factor and the storage modulus. The minority phase can solubilize only a small amount of added homopolymer; addition of a higher amount results in the formation of nonequilibrium structures. Theoretical calculations performed in the strong segregation limit provide the period and the critical value of χN for the stability of the disordered phase. The theory predicts that (χN)c always increases with the addition of the majority phase. When the minority phase is added, (χN)c can increase (N≫Nh and N⩾Nh) or decrease (N≪Nh). The experimental results are in good agreement with the theoretical predictions for the two extreme cases; N≫Nh and N≪Nh, but differ when the minority component is added with N⩾Nh. These results demonstrate that the degree of compatibility between the two blocks of the diblock AB can be effectively controlled by adding a small amount of homopolymer A or B.
Molecular dynamics simulations of elementary chemical processes in liquid water using combined density functional and molecular mechanics potentials. II. Charge separation processes
Authors: Strnad M. , Martins-Costa M. T. C. , Millot C. , Tuñón I. , Ruiz-López M. F. , Rivail J. L.
Published: July 2002

A new approach to carry out molecular dynamics simulations of chemical reactions in solution using combined density functional theory/molecular mechanics potentials is presented. We focus our attention on the analysis of reactive trajectories, dynamic solvent effects and transmission coefficient rather than on the evaluation of free energy which is another important topic that will be examined elsewhere. In a previous paper we have described the generalities of this hybrid molecular dynamics method and it has been employed to investigate low energy barrier proton transfer process in water. The study of processes with activation energies larger than a few kT requires the use of specific techniques adapted to “rare events” simulations. We describe here a method that consists in the simulation of short trajectories starting from an equilibrated transition state in solution, the structure of which has been approximately established. This calculation is particularly efficient when carried out with parallel computers since the study of a reactive process is decomposed in a set of short time trajectories that are completely independent. The procedure is close to that used by other authors in the context of classical molecular dynamics but present the advantage of describing the chemical system with rigorous quantum mechanical calculations. It is illustrated through the study of the first reaction step in electrophilic bromination of ethylene in water. This elementary process is representative of many charge separation reactions for which static and dynamic solvent effects play a fundamental role.
A method for accelerating the molecular dynamics simulation of infrequent events
Authors: Voter Arthur F.
Published: July 2002

For infrequent-event systems, transition state theory (TST) is a powerful approach for overcoming the time scale limitations of the molecular dynamics (MD) simulation method, provided one knows the locations of the potential-energy basins (states) and the TST dividing surfaces (or the saddle points) between them. Often, however, the states to which the system will evolve are not known in advance. We present a new, TST-based method for extending the MD time scale that does not require advanced knowledge of the states of the system or the transition states that separate them. The potential is augmented by a bias potential, designed to raise the energy in regions other than at the dividing surfaces. State to state evolution on the biased potential occurs in the proper sequence, but at an accelerated rate with a nonlinear time scale. Time is no longer an independent variable, but becomes a statistically estimated property that converges to the exact result at long times. The long-time dynamical behavior is exact if there are no TST-violating correlated dynamical events, and appears to be a good approximation even when this condition is not met. We show that for strongly coupled (i.e., solid state) systems, appropriate bias potentials can be constructed from properties of the Hessian matrix. This new “hyper-MD” method is demonstrated on two model potentials and for the diffusion of a Ni atom on a Ni(100) terrace for a duration of 20 μs.
Sideband optical–optical double resonance Zeeman spectroscopy. II. Studies of NiH, PdD, and PtH
Authors: McCarthy Michael C. , Kanamori Hideto , Steimle Timothy C. , Li Mingguang , Field Robert W.
Published: July 2002

Sideband optical–optical double resonance Zeeman spectroscopy is applied here to studies of the transition metal hydrides NiH, PdD, and PtH. For both NiH and PtH, in addition to obtaining Zeeman information on the ground and several excited electronic states, extremely small ground state proton hyperfine splittings have been resolved. For PdD, sub-Doppler spectra of the XΩ=0.5 ground state have been recorded even though the upper state in the optical transition is strongly predissociated. For all three radicals, the double-resonance Zeeman studies reveal that the g values in each state deviate from their nominal Hund’s coupling case (a) or (b) value with increasing rotational quantum number J. This Zeeman information, in addition to providing a sensitive confirmation of electronic assignments, also provides direct evidence of electronic state mixing (which is not present in ordinary non-Zeeman spectra) and useful in modeling the interactions between electronic states.
Swelling of colloidal systems
Authors: Kokkoli Efrosini , van Swol Frank
Published: July 2002

The role of solvent–particle and particle–particle interactions on the swelling of colloidal systems has been investigated. A density functional theory (DFT) approach is taken here to describe a colloid–solvent mixture and develop phase diagrams that give a qualitative picture of possible transitions as a function of the bulk conditions (density and temperature) and the degree of surface solvophobicity. The solvophobicity of the surface is taken as a measure of how much the surface dislikes the solvent, and is determined from the contact angle of the solvent on the surface. The results demonstrate that the nature of the surface (solvophobic or solvophobilic) is a key factor in shaping the phase diagrams. For example, when the surface is solvophilic, the dominant phase is the crystalline, where surfaces are spaced by one solvent layer, while when the surface is solvophobic, the system is most often found in the collapsed state (the surfaces are in contact). The shape of the phase diagrams also depends on the particle–particle interaction. When only the repulsive part of the wall–wall interaction is considered, the collapsed phase is observed less frequently and the diagrams are insensitive to the strength of the purely repulsive interaction. In contrast, the strength of the attractive surface–surface potential plays a crucial role in shaping the phase diagrams.
Calculated high-temperature partition function and related thermodynamic data for H216O
Authors: Harris Gregory J. , Viti Serena , Mussa Hamse Y. , Tennyson Jonathan
Published: July 2002

The partition function, Q, of water is calculated by explicit summation of ∼200 000 vibration–rotation levels computed using variational nuclear motion calculations. Temperatures up to 6000 K are studied. Estimates are obtained for the heat capacity (Cp), the Gibbs enthalpy factor (gef), the Helmholtz function (hcf), and the entropy (S) of gas-phase water as a function of temperature. To get converged results at higher temperatures it is necessary to augment the accurate list of energy levels. This is done using estimates for all the vibrational band origins to dissociation and rotational levels calculated using Padé approximants. The widely used method of computing the internal partition function as the product of vibrational and rotational partition functions is tested and found to overestimate the partition function by up to 10%. The present estimates of Q(T), Cp(T), gef(T), hcf(T), and S(T) are probably the most accurate available for water at temperatures, T, above 2000 K. Errors, as a function of temperature, are estimated in each case.
The ethylene 1 1B1u V state revisited
Authors: Müller Thomas , Dallos Michal , Lischka Hans
Published: July 2002

We describe a general procedure to resolve the problem of artifical valence/Rydberg mixing encountered in ab initio CI calculations on the V (1 1B1u) state of ethylene. Davidson and McMurchie realized that the key to this problem are orbitals which adequately represent the V state. A two-step procedure is proposed, in which the first step focuses on generating appropriate molecular orbitals and the second step aims to describe the electron correlation quantitatively. A series of the currently most extensive MCSCF, MR-CISD, and MR-AQCC calculations for basis sets up to quadruple zeta quality and up to 80 million configurations are presented. Size extensivity corrections turn out to be crucial for highly accurate excitation energies. Our best estimate for the N–V state excitation energy of 7.7 eV lies between the experimental absorption maximum of 7.66 eV and a vibrationally corrected value of 7.8 eV. Hence, we do not find it necessary to refer to nonadiabatic effects in order to achieve agreement with the experimental data. The V state is characterized by its spatial extent, measured through the expectation value 〈x2〉, where x is the out-of-plane direction. With 16.5–17.0a02 it has a strong valence character, as compared to ≈90a02 for the 2 1B1u Rydberg state and 11.7a02 for the ground state.
Hydrodynamics of magnetic and dielectric fluids in interaction with the electromagnetic field
Authors: Felderhof B. U. , Kroh H. J.
Published: July 2002

The hydrodynamics of polar fluids and suspensions in interaction with the electromagnetic field is studied in the framework of irreversible thermodynamics. It is shown that the approach developed earlier by de Groot and Mazur can be extended to include intrinsic rotation and a decomposition of polarization and magnetization into slow and fast parts. An expression for the entropy production is derived which leads to phenomenological relaxation equations. For incompressible fluids these reduce to relaxation equations postulated in the literature. If it is assumed that intrinsic rotation decays much faster than the other variables, then a simplified description is possible in which the intrinsic angular momentum does not occur. Several proposed expressions for electromagnetic stress tensor and force density are discussed and shown to be inadequate.
Calculating rovibrational energy levels of a triatomic molecule with a simple Lanczos method
Authors: Sarkar Pranab , Poulin Nicolas , Carrington Tucker
Published: July 2002

We present a simple Lanczos method for calculating rovibrational energy levels of a triatomic molecule from a kinetic energy operator (KEO) with the z axis perpendicular to the molecular plane. We use rotational basis functions which are linear combinations of symmetric top functions so that all matrix elements are real. For some molecules, coupling between rotation and vibration is less important if the z axis is chosen perpendicular to the molecular plane, but the singularities of the z-axis operator are more difficult to deal with than those of the commonly used y-axis operator. The KEO with z axis perpendicular to the plane also reduces the number of sums over vibrational indices required to evaluate Hamiltonian matrix-vector products. Using a new symmetry-adapted basis and the z-axis KEO we calculate rovibrational energy levels of H2O for high J values. Even at J=40 we do not observe the formation of fourfold clusters.
Relativistic regular approximations revisited: An infinite-order relativistic approximation
Authors: Dyall Kenneth G. , van Lenthe Erik
Published: July 2002

The concept of the regular approximation is presented as the neglect of the energy dependence of the exact Foldy–Wouthuysen transformation of the Dirac Hamiltonian. Expansion of the normalization terms leads immediately to the zeroth-order regular approximation (ZORA) and first-order regular approximation (FORA) Hamiltonians as the zeroth- and first-order terms of the expansion. The expansion may be taken to infinite order by using an un-normalized Foldy–Wouthuysen transformation, which results in the ZORA Hamiltonian and a nonunit metric. This infinite-order regular approximation, IORA, has eigenvalues which differ from the Dirac eigenvalues by order E3/c4 for a hydrogen-like system, which is a considerable improvement over the ZORA eigenvalues, and similar to the nonvariational FORA energies. A further perturbation analysis yields a third-order correction to the IORA energies, TIORA. Results are presented for several systems including the neutral U atom. The IORA eigenvalues for all but the 1s spinor of the neutral system are superior even to the scaled ZORA energies, which are exact for the hydrogenic system. The third-order correction reduces the IORA error for the inner orbitals to a very small fraction of the Dirac eigenvalue.
Orientational relaxation of liquid water molecules as an activated process
Authors: Nienhuys Han-Kwang , van Santen Rutger A. , Bakker Huib J.
Published: July 2002

Femtosecond mid-infrared pump–probe spectroscopy is used to study the orientational relaxation of HDO molecules dissolved in liquid D2O. In this technique, the excitation of the O–H stretch vibration is used as a label in order to follow the orientational motion of the HDO molecules. The decay of the anisotropy is nonexponential with a typical time scale of 1 ps and can be described with a model in which the reorientation time depends on frequency and in which the previously observed spectral diffusion is incorporated. From the frequency and temperature dependence of the anisotropy decay, the activation energy for reorientation can be derived. This activation energy is found to increase with increasing hydrogen bond strength.
Physical adsorption of xenon in open single walled carbon nanotubes: Observation of a quasi-one-dimensional confined Xe phase
Authors: Kuznetsova A. , Yates J. T. , Liu J. , Smalley R. E.
Published: July 2002

The adsorption of Xe into carbon single walled nanotubes with both closed and open ends has been investigated using temperature programmed desorption and other surface analytical tools. It has been found that opening the ends of the nanotube by chemical cutting increases both the kinetic rate and the saturation capacity of the nanotubes for Xe at 95 K. Further enhancement in Xe adsorption kinetics and capacity are achieved by treating the nanotubes in vacuum at 1073 K where CO, CO2, CH4, and H2 are evolved. On this basis it is postulated that surface functionalities such as −COOH block entry ports for adsorption at the nanotube ends and at the defect sites on the walls. The thermal destruction of these functionalities leads to enhanced adsorption. The denser phase of Xe inside the saturated nanotubes desorbs by zero-order kinetics (Ed=26.8±0.6 kJ/mol). It is postulated that a quasi-one-dimensional Xe confined phase in equilibrium, with a two-dimensional Xe gas phase on the exterior, provides a phase transition governing the zero-order kinetics desorption process.
On the viability of single atom abstraction in the dissociative chemisorption of O2 on the Al(111) surface
Authors: Neuburger M. L. , Pullman D. P.
Published: July 2002

The dissociative chemisorption of O2 on the Al(111) surface is investigated by means of a Monte Carlo simulation that incorporates two mechanisms that have been proposed for this reaction in the literature: single atom abstraction and two-atom adsorption that generates translationally hot atoms on the surface. A comparison is made to the much-debated STM results of Brune et al. [J. Chem. Phys. 99, 2128 (1993)], in which the oxygen island density (number of islands per binding site) was determined as a function of coverage. Since the two-atom channel has been discussed heavily in the literature, we focus primarily on the abstraction mechanism. We show that atom abstraction in its basic form is incompatible with the STM results; however, we propose two simple modifications that enable atom abstraction to reproduce the STM results. In the first modification, the probability of dissociation is higher at sites next to preexisting O adatoms. In essence, we are proposing that the increased Al–O bond strength at sites next to preexisting O adatoms [Jacobsen et al., Phys. Rev. B 52, 14954 (1995)] stabilizes the transition state for dissociation. If atom abstraction is assumed to be the only operative mechanism, and if its probability increases by a factor of ∼10 next to a site that is occupied versus unoccupied, the STM island density data can be approximately reproduced. In the second modification, the abstracted atom is permitted to make a single hop in the direction of a preexisting, nearby O adatom. The allowance of merely a single, directed hop has a dramatic effect on the coverage dependence of the island density.
Geometric approach to classical improvement of lattice actions
Authors: Mitra P.
Published: July 2002

The classical improvement program in lattice gauge theory is examined from the geometric point of view. Improved actions are derived for pure gauge theories as well as for fermions.
On dissipativity of quantum optical systems
Authors: Andres J.
Published: July 2002

Applying a suitably modified Liapunov–Yoshizawa direct method [T. Yoshizawa, Stability Theory by Liapunov’s Second Method (Math. Soc. Japan, Tokyo, 1966)], a rigorous mathematical proof of dissipativity in the sense of Levinson [N. Rouche, P. Habets, and M. Laloy, Stability Theory by Liapunov’s Direct Method (Springer, Berlin, 1977)] to the majority of effective optical processes has been carried out. The ability of an upper final estimation of the average number of photons is demonstrated (as an example) on the well-known second-harmonic generation process with classical pumping.
Physical condition for elimination of ambiguity in conditionally convergent lattice sums
Authors: Young K.
Published: July 2002

The conditional convergence of the lattice sum defining the Madelung constant gives rise to an ambiguity in its value. It is shown that this ambiguity is related, through a simple and universal integral, to the average charge density on the crystal surface. The physically correct value is obtained by setting the charge density to zero. A simple and universally applicable formula for the Madelung constant is derived as a consequence. It consists of adding up dipole–dipole energies together with a nontrivial correction term.
Building blocks for topology change
Authors: Alty L. J.
Published: July 2002

Topology changing space–times are investigated by breaking them into their constituent parts. It is shown that, for a large class of space–times, topology change between kink zero (e.g., spacelike) surfaces must produce singularities regardless of the existence of closed timelike curves. A relationship between the kink number and causality is also described.
The generalized Gauss–Bonnet–Chern theorem
Authors: Alty L. J.
Published: July 2002

For Riemannian manifolds with boundary, the well-known Gauss–Bonnet–Chern theorem gives an integral formula for the Euler characteristic of the manifold. Here we extend a proof by Avez to show that there is a similar result for manifolds with boundary endowed with a pseudo–Riemannian metric of arbitrary signature. In the case when the metric is Lorentzian there are some applications to general relativity. The generalized Gauss–Bonnet–Chern theorem also provides a formula for the gravitational kink.
Modular groups of quantum fields in thermal states
Authors: Borchers H. J. , Yngvason J.
Published: July 2002

For a quantum field in a thermal equilibrium state we discuss the group generated by time translations and the modular action associated with an algebra invariant under half-sided translations. The modular flows corresponding to the algebras of the forward light cone and a space-like wedge admit a simple geometric description in two-dimensional models that factorize in light-cone coordinates. At large distances from the domain boundary compared to the inverse temperature, the flow pattern is essentially the same as time translations, whereas the zero temperature results are approximately reproduced close to the edge of the wedge and the apex of the cone. For each domain there is also a one-parameter group with a positive generator, for which the thermal state is a ground state. Formally, this may be regarded as a certain converse of the Unruh effect.
Asymptotics of the scattering coefficients for a generalized Schrödinger equation
Authors: Aktosun Tuncay , Klaus Martin
Published: July 2002

The generalized Schrödinger equation d2ψ/dx2+F(k)ψ=[ikP(x)+Q(x)]ψ is considered, where P and Q are integrable potentials with finite first moments and F satisfies certain conditions. The behavior of the scattering coefficients near zeros of F is analyzed. It is shown that in the so-called exceptional case, the values of the scattering coefficients at a zero of F may be affected by P(x). The location of the k-values in the complex plane where the exceptional case can occur is studied. Some examples are provided to illustrate the theory.
The nonlinear development of supersonic instability waves in a mixing layer
Authors: Ragab Saad A. , Sheen S.
Published: July 2002

The nonlinear development of two-dimensional supersonic instability waves in a mixing layer is investigated by solving the full unsteady Navier–Stokes equations. A finite-difference predictor–corrector explicit method is used. The method is second-order accurate in time and fourth-order accurate in space. The results have also been checked using a fourth-order central-difference scheme with a Runge–Kutta time marching. Both confined and unconfined shear layers are simulated. For a fast or a slow mode of instability, in which the flow relative to the wave is subsonic on one side of the shear layer and supersonic on the other side, rolled up vortical structures are observed on the subsonic side only. The development of these structures is enhanced by confining the layer between parallel walls. Contours of a passive scalar show that the core of the rolled up vortex contains fluid predominantly from the subsonic side. Oblique shock waves develop in the side where the relative flow is supersonic. In the unconfined case, shock waves form in the far field as a result of the coalescence of compression waves initiated at the deforming shear layer. In the confined shear layer case, they appear as reflections of compression waves off the side wall. In the case of supersonic relative Mach numbers on both sides of the layer, no vortical roll-up is observed; only a staggered pattern of oblique shock waves is found.
Evidence for a singularity of the three-dimensional, incompressible Euler equations
Authors: Kerr Robert M.
Published: July 2002

Three-dimensional, incompressible Euler calculations of the interaction of perturbed antiparallel vortex tubes using smooth initial profiles in a bounded domain with bounded initial vorticity are discussed. A numerical method that uses symmetries and additional resolution in the direction and location of maximum compression is used to simulate periodic boundary conditions in all directions. For an initial condition that yields singular behavior, the growth of the peak vorticity, the peak axial strain, and the enstrophy production obey (tc−t)−1, and the enstrophy grows logarithmically. The enstrophy growth is associated with the energy spectrum approaching k−3. Self-similar development and equal rates of collapse in all three directions are shown.
Computer simulation study of the effective viscosity in Brinkman’s equation
Authors: Martys N. , Bentz D. P. , Garboczi E. J.
Published: July 2002

Brinkman’s equation is often used to match solutions of Stokes’ equation to solutions of Darcy’s law at free-fluid:porous medium interfaces by the introduction of an effective viscosity parameter, μe. Theoretical predictions of the dependence of μe on the porosity of the porous medium have given conflicting results. A finite difference solution of Stokes’ equation in three dimensions was used to study fluid flow near the interface between a free fluid and a porous medium. It was found that in order to match solutions of Brinkman’s equation to the numerical solutions, the value of μe had to be greater than the free-fluid viscosity. Within numerical precision, the effective viscosity μe was monotonically increasing with decreasing porosity. Good fits to the numerical fluid velocity profiles were obtained for porosities ranging from 50% to 80%.
Motion and arrest of a molten contact line on a cold surface: An experimental study
Authors: Schiaffino Stefano , Sonin Ain A.
Published: July 2002

An experimental study is presented of the behavior of a molten contact line under conditions which simulate what happens when a molten droplet touches a subcooled solid, spreads partly over it, and freezes. We restrict our attention to the case where the solid and melt are of the same material and have approximately the same thermal properties, and reach two conclusions. First, we show that an advancing molten contact line is arrested at an apparent dynamic contact angle, which for a given material depends primarily on the Stefan number based on the temperature difference between the fusion point and the temperature of the solid over which the melt spreads. Second, during much of the spreading prior to contact-line arrest, the relationship between the melt’s apparent dynamic contact angle and the contact-line speed appears to obey the Hoffman–Tanner–Voinov law with the equilibrium contact angle taken as zero.
Observed mechanisms for turbulence attenuation and enhancement in opposition-controlled wall-bounded flows
Authors: Hammond E. P. , Bewley T. R. , Moin P.
Published: July 2002

Opposition control is a simple method used to attenuate near-wall turbulence and reduce drag in wall-bounded turbulent flows [H. Choi, P. Moin, and J. Kim, J. Fluid Mech. 262, 75 (1994)]. This method employs blowing and suction at the wall in opposition to the wall-normal fluid velocity a small distance from the wall. Results from direct numerical simulations of turbulent channel flow indicate that, when the control at the wall is based on detection of the wall-normal velocity in a plane sufficiently close to the wall, the opposition control strategy establishes a “virtual wall,” i.e., a plane that has approximately no through flow, halfway between the detection plane and the wall. As a consequence, drag is reduced about 25%. When the detection plane is at a greater distance from the wall, a virtual wall is not established, and the blowing and suction increase the drag significantly.
Evidence of positive selection acting at the human dopamine receptor D4 gene locus
Authors: Ding Yuan-Chun , Chi Han-Chang , Grady Deborah L. , Morishima Atsuyuki , Kidd Judith R. , Kidd Kenneth K. , Flodman Pamela , Spence M. Anne , Schuck Sabrina , Swanson James M. , Zhang Ya-Ping , Moyzis Robert K.
Published: July 2002

Associations have been reported of the seven-repeat
(7R) allele of the human dopamine receptor D4 (
DRD4
) gene
with both attention-deficit/hyperactivity disorder and the
personality trait of novelty seeking. This polymorphism occurs in a
48-bp tandem repeat in the coding region of
DRD4
,
with the most common allele containing four repeats (4R) and
rarer variants containing 2–11. Here we show by DNA
resequencing/haplotyping of 600
DRD4
alleles,
representing a worldwide population sample, that the origin of 2R–6R
alleles can be explained by simple one-step recombination/mutation
events. In contrast, the 7R allele is not simply related to the other
common alleles, differing by greater than six
recombinations/mutations. Strong linkage disequilibrium was found
between the 7R allele and surrounding
DRD4
polymorphisms,
suggesting that this allele is at least 5–10-fold “younger” than
the common 4R allele. Based on an observed bias toward nonsynonymous
amino acid changes, the unusual DNA sequence organization, and the
strong linkage disequilibrium surrounding the
DRD4
7R allele, we propose that this allele originated as a rare
mutational event that nevertheless increased to high frequency in human
populations by positive selection.
Cloning, expression, and characterization of a nitric oxide synthase protein from
Deinococcus radiodurans
Authors: Adak Subrata , Bilwes Alexandrine M. , Panda Koustubh , Hosfield David , Aulak Kulwant S. , McDonald John F. , Tainer John A. , Getzoff Elizabeth D. , Crane Brian R. , Stuehr Dennis J.
Published: July 2002

We cloned, expressed, and characterized a hemeprotein from
Deinococcus radiodurans
(
D. radiodurans
NO synthase, deiNOS) whose sequence is 34% identical to the oxygenase
domain of mammalian NO synthases (NOSoxys). deiNOS was dimeric,
bound substrate Arg and cofactor tetrahydrobiopterin, and had a normal
heme environment, despite its missing N-terminal structures that in
NOSoxy bind Zn
2+
and tetrahydrobiopterin and help form an
active dimer. The deiNOS heme accepted electrons from a mammalian NOS
reductase and generated NO at rates that met or exceeded NOSoxy.
Activity required bound tetrahydrobiopterin or tetrahydrofolate and was
linked to formation and disappearance of a typical heme-dioxy catalytic
intermediate. Thus, bacterial NOS-like proteins are surprisingly
similar to mammalian NOSs and broaden our perspective of NO
biochemistry and function.
High relatedness and inbreeding at the origin of eusociality in gall-inducing thrips
Authors: Chapman T. W. , Crespi B. J. , Kranz B. D. , Schwarz M. P.
Published: July 2002

Within the haplodiploid eusocial gall-inducing thrips, a species-level phylogeny combined with genetic data for five eusocial species enables an inference of levels of relatedness and inbreeding values for lineages at the origin of eusociality. Character optimization using data from five eusocial species indicates that the lineage or lineages where eusociality is inferred to have originated exhibit relatedness of 0.64–0.92, and FISof 0.33–0.64. The high inbreeding coefficients found in these eusocial thrips have increased relatedness among and within both sexes and have reduced the haplodiploidy-induced relatedness asymmetries [Hamilton, W. D. (1964)J. Theor. Biol.7, 1–52]. These results indicate that unusually high relatedness is associated with the origin of eusociality, and they suggest a role for inbreeding in the evolution of bisexual helping.
Combined effect of tumor necrosis factor-related apoptosis-inducing ligand and ionizing radiation in breast cancer therapy
Authors: Chinnaiyan Arul M. , Prasad Uttara , Shankar Sunita , Hamstra Daniel A. , Shanaiah Murthy , Chenevert Thomas L. , Ross Brian D. , Rehemtulla Alnawaz
Published: July 2002

Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is a potent endogenous activator of the cell death pathway and functions by activating the cell surface death receptors 4 and 5 (DR4 and DR5). TRAIL is nontoxicin vivoand preferentially kills neoplastically transformed cells over normal cells by an undefined mechanism. Radiotherapy is a common treatment for breast cancer as well as many other cancers. Here we demonstrate that ionizing radiation can sensitize breast carcinoma cells to TRAIL-induced apoptosis. This synergistic effect is p53-dependent and may be the result of radiation-induced up-regulation of the TRAIL-receptor DR5. Importantly, TRAIL and ionizing radiation have a synergistic effect in the regression of established breast cancer xenografts. Changes in tumor cellularity and extracellular space were monitoredin vivoby diffusion-weighted magnetic resonance imaging (diffusion MRI), a noninvasive technique to produce quantitative images of the apparent mobility of water within a tissue. Increased water mobility was observed in combined TRAIL- and radiation-treated tumors but not in tumors treated with TRAIL or radiation alone. Histological analysis confirmed the loss of cellularity and increased numbers of apoptotic cells in TRAIL- and radiation-treated tumors. Taken together, our results provide support for combining radiation with TRAIL to improve tumor eradication and suggest that efficacy of apoptosis-inducing cancer therapies may be monitored noninvasively, using diffusion MRI.
Stable suppression of gene expression by RNAi in mammalian cells
Authors: Paddison Patrick J. , Caudy Amy A. , Hannon Gregory J.
Published: July 2002

In a diverse group of organisms including plants,
Caenorhabditis elegans
,
Drosophila
, and trypanosomes, double-stranded RNA (dsRNA) is a potent trigger of gene silencing. In several model systems, this natural response has been developed into a powerful tool for the investigation of gene function. Use of RNA interference (RNAi) as a genetic tool has recently been extended to mammalian cells, being inducible by treatment with small, ≈22-nt RNAs that mimic those produced in the first step of the silencing process. Here, we show that some cultured murine cells specifically silence gene expression upon treatment with long dsRNAs (≈500 nt). This response shows hallmarks of conventional RNAi including silencing at the posttranscriptional level and the endogenous production of ≈22-nt small RNAs. Furthermore, enforced expression of long, hairpin dsRNAs induced stable gene silencing. The ability to create stable “knock-down” cell lines expands the utility of RNAi in mammalian cells by enabling examination of phenotypes that develop over long time periods and lays the groundwork for by using RNAi in phenotype-based, forward genetic selections.
CA1-specific
N
-methyl-
d
-aspartate receptor knockout mice are deficient in solving a nonspatial transverse patterning task
Authors: Rondi-Reig Laure , Libbey Megan , Eichenbaum Howard , Tonegawa Susumu
Published: July 2002

In both humans and animals, the hippocampus is critical to memory
across modalities of information (e.g., spatial and nonspatial memory)
and plays a critical role in the organization and flexible expression
of memories. Recent studies have advanced our understanding of cellular
basis of hippocampal function, showing that
N
-methyl-
d
-aspartate (NMDA) receptors in
area CA1 are required in both the spatial and nonspatial domains of
learning. Here we examined whether CA1 NMDA receptors are specifically
required for the acquisition and flexible expression of nonspatial
memory. Mice lacking CA1 NMDA receptors were impaired in solving a
transverse patterning problem that required the simultaneous
acquisition of three overlapping odor discriminations, and their
impairment was related to an abnormal strategy by which they failed to
adequately sample and compare the critical odor stimuli. By contrast,
they performed normally, and used normal stimulus sampling strategies,
in the concurrent learning of three nonoverlapping concurrent odor
discriminations. These results suggest that CA1 NMDA receptors play a
crucial role in the encoding and flexible expression of stimulus
relations in nonspatial memory.
Alveolar epithelial type I cells contain transport proteins and transport sodium, supporting an active role for type I cells in regulation of lung liquid homeostasis
Authors: Johnson Meshell D. , Widdicombe Jonathan H. , Allen Lennell , Barbry Pascal , Dobbs Leland G.
Published: July 2002

Transport of lung liquid is essential for both normal pulmonary physiologic processes and for resolution of pathologic processes. The large internal surface area of the lung is lined by alveolar epithelial type I (TI) and type II (TII) cells; TI cells line >95% of this surface, TII cells <5%. Fluid transport is regulated by ion transport, with water movement following passively. Current concepts are that TII cells are the main sites of ion transport in the lung. TI cells have been thought to provide only passive barrier, rather than active, functions. Because TI cells line most of the internal surface area of the lung, we hypothesized that TI cells could be important in the regulation of lung liquid homeostasis. We measured both Na
+
and K
+
(Rb
+
) transport in TI cells isolated from adult rat lungs and compared the results to those of concomitant experiments with isolated TII cells. TI cells take up Na
+
in an amiloride-inhibitable fashion, suggesting the presence of Na
+
channels; TI cell Na
+
uptake, per microgram of protein, is ≈2.5 times that of TII cells. Rb
+
uptake in TI cells was ≈3 times that in TII cells and was inhibited by 10
−4
M ouabain, the latter observation suggesting that TI cells exhibit Na
+
-, K
+
-ATPase activity. By immunocytochemical methods, TI cells contain all three subunits (α, β, and γ) of the epithelial sodium channel ENaC and two subunits of Na
+
-, K
+
-ATPase. By Western blot analysis, TI cells contain ≈3 times the amount of αENaC/μg protein of TII cells. Taken together, these studies demonstrate that TI cells not only contain molecular machinery necessary for active ion transport, but also transport ions. These results modify some basic concepts about lung liquid transport, suggesting that TI cells may contribute significantly in maintaining alveolar fluid balance and in resolving airspace edema.
Inference of functional regions in proteins by quantification of evolutionary constraints
Authors: Simon Alexander L. , Stone Eric A. , Sidow Arend
Published: July 2002

Likelihood estimates of local rates of evolution within proteins reveal that selective constraints on structure and function are quantitatively stable over billions of years of divergence. The stability of constraints produces an intramolecular clock that gives each protein a characteristic pattern of evolutionary rates along its sequence. This pattern allows the identification of constrained regions and, because the rate of evolution is a quantitative measure of the strength of the constraint, of their functional importance. We show that results from such analyses, which require only sequence alignments, are consistent with experimental and mutational data. The methodology has significant predictive power and may be used to guide structure–function studies for any protein represented by a modest number of homologs in sequence databases.
Comparative genomics of the restriction-modification systems in
Helicobacter pylori
Authors: Lin Lee-Fong , Posfai Janos , Roberts Richard J. , Kong Huimin
Published: July 2002

Helicobacter pylori
is a Gram-negative
bacterial pathogen with a small genome of 1.64–1.67 Mb. More than 20
putative DNA restriction-modification (R-M) systems, comprising more
than 4% of the total genome, have been identified in the two
completely sequenced
H. pylori
strains, 26695 and J99,
based on sequence similarities. In this study, we have investigated the
biochemical activities of 14 Type II R-M systems in
H.
pylori
26695. Less than 30% of the Type II R-M systems in
26695 are fully functional, similar to the results obtained from strain
J99. Although nearly 90% of the R-M genes are shared by the two
H. pylori
strains, different sets of these R-M genes are
functionally active in each strain. Interestingly, all strain-specific
R-M genes are active, whereas most shared genes are inactive. This
agrees with the notion that strain-specific genes have been acquired
more recently through horizontal transfer from other bacteria and
selected for function. Thus, they are less likely to be impaired by
random mutations. Our results also show that
H. pylori
has extremely diversified R-M systems in different strains, and that
the diversity may be maintained by constantly acquiring new R-M systems
and by inactivating and deleting the old ones.