bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparisons between integral equation theory and molecular dynamics simulations for realistic models of polyethylene liquids
Authors: Curro John G. , Webb Edmund B. , Grest Gary S. , Weinhold Jeffrey D. , Pütz Mathias , McCoy John D.
Published: July 2002

Molecular dynamics (MD) simulations were performed on dense liquids of polyethylene chains of 24 and 66 united atom CH2 units. A series of models was studied ranging in atomistic detail from coarse-grained, freely-jointed, tangent site chains to realistic, overlapping site models subjected to bond angle restrictions and torsional potentials. These same models were also treated with the self-consistent, polymer reference interaction site model (PRISM) theory. The intramolecular and total structure factors, as well as, the intermolecular radial distribution functions g(r) and direct correlation functions C(r) were obtained from theory and simulation. Angular correlation functions were also obtained from the MD simulations. Comparisons between theory and simulation reveal that PRISM theory works well for computing the intermolecular structure of coarse-grained chain models, but systematically underpredicts the extent of intermolecular packing, and overpredicts the compressibility, as more realistic details are introduced into the model. We found that the PRISM theory could be considerably improved by adding a tail function to C(r) beyond the effective hard core diameter. The range of this tail function was determined by requiring the theory to yield the correct compressibility. The intermolecular radial distribution functions from this modified PRISM theory were in excellent agreement with g(r)’s obtained from the simulations.
Spin-free relativistic no-pair ab initio core model potentials and valence basis sets for the transition metal elements Sc to Hg. II
Authors: Rakowitz Frank , Marian Christel M. , Seijo Luis
Published: July 2002

This is the second part of a report on spin-free relativistic no-pair ab initio core model potentials for the transition elements Sc to Hg. In the first part [J. Chem. Phys. 110, 3678 (1999)], we introduced the no-pair ab initio model potential method and supplied model potentials for [Mg], [Zn], and [Cd,4f] cores of first-, second-, and third-row transition metals, respectively. At the Hartree–Fock level excellent agreement between all-electron and model potential results was observed for late transition metal oxides, whereas the performance of the model potentials was slightly less satisfactory for early transition metal oxides. In this paper we will present small-core model potentials corresponding to [Ne], [Ar,3d], and [Kr,4d,4f] cores, respectively. The performance of the model potentials is tested extensively in calculations on the diatomic oxides VO, NbO, TaO, NiO, PdO, and PtO, both at the Hartree–Fock level and when electron correlation is included by means of coupled-pair functional methods. Further we investigate the requirements on valence and intermediate basis sets used to represent the exchange and no-pair operators.
Scanning near-field optical microscopy with aperture probes: Fundamentals and applications
Authors: Hecht Bert , Sick Beate , Wild Urs P. , Deckert Volker , Zenobi Renato , Martin Olivier J. F. , Pohl Dieter W.
Published: July 2002

In this review we describe fundamentals of scanning near-field optical microscopy with aperture probes. After the discussion of instrumentation and probe fabrication, aspects of light propagation in metal-coated, tapered optical fibers are considered. This includes transmission properties and field distributions in the vicinity of subwavelength apertures. Furthermore, the near-field optical image formation mechanism is analyzed with special emphasis on potential sources of artifacts. To underline the prospects of the technique, selected applications including amplitude and phase contrast imaging, fluorescence imaging, and Raman spectroscopy, as well as near-field optical desorption, are presented. These examples demonstrate that scanning near-field optical microscopy is no longer an exotic method but has matured into a valuable tool.
Symmetric diblock copolymer thin films confined between homogeneous and patterned surfaces: Simulations and theory
Authors: Wang Qiang , Nath Shyamal K. , Graham Michael D. , Nealey Paul F. , de Pablo Juan J.
Published: July 2002

We have investigated the ability of a simple phenomenological theory to describe the behavior of symmetric diblock copolymer thin films confined between two hard surfaces. Prior knowledge of the morphology in the confined films is crucial for applying this theory to predict the phase diagram of such systems. Taking advantage of our observations in Monte Carlo simulations, we use the theory to construct phase diagrams for thin films confined between patterned-homogeneous surfaces, and obtain good agreement with our results of simulations. Two conditions are essential for obtaining long-range ordered perpendicular lamellae: a lower stripe-patterned surface with the surface pattern period Ls comparable to the bulk lamellar period L0, and an upper neutral or weakly preferential surface. We have also examined the undulation of perpendicular lamellae between two hard surfaces. For the cases of two homogeneous (preferential) surfaces and patterned-preferential surfaces, our calculations using the phenomenological theory indicate that the amplitudes of the undulation are on the same order of magnitude as observed in our Monte Carlo simulations, and are one order of magnitude larger than previously reported. The theory, however, is unable to capture the shape of the undulation. For the case of patterned-neutral surfaces, we find that an earlier analysis is unable to yield the undulations that would stabilize the perpendicular lamellar morphology. We have addressed this issue and obtained undulations that are consistent with our observations from Monte Carlo simulations.
The Painlevé property and Bäcklund transformations for the sequence of Boussinesq equations
Authors: Weiss John
Published: July 2002

We investigate the sequence of Boussinesq equations by the method of singular manifolds. For the Boussinesq equation, which is known to possess the Painlevé property, a Bäcklund transformation is defined. This Bäcklund transformation, which is formulated in terms of the Schwarzian derivative, obtains the system of modified Boussinesq equations and the resulting Miura-type transformation. The modified Boussinesq equations are found to be invariant under a discrete group of symmetries, acting on the dependent variables. By linearizing the Miura transformation (and modified equations) the Lax pair is readily obtained. Furthermore, by a result of Fokas and Anderson, the recursion operators defining the sequence of (higher-order) Boussinesq equations may be constructed from the Miura transformation. This allows the (recursive) definition of Bäcklund transformations for this sequence of equations. The recursion operator is found to preserve the discrete symmetries of the modified Boussinesq equations. This leads to the conclusion that the sequences of Boussinesq and modified Boussinesq equations identically possess the Painlevé property (are meromorphic). We also find that, by a simple reduction, the sequences of Caudrey–Dodd–Gibbon and Kuperschmidt equations are contained within the Boussinesq sequence. Rational solutions are iteratively constructed for the Boussinesq equation and a criterion is proposed for the existence of rational solutions of general integrable systems.
Duality rotations and type D solutions to Einstein equations with nonlinear electromagnetic sources
Authors: Salazar I. Humberto , García D. Alberto , Plebański Jerzy
Published: July 2002

Within nonlinear electrodynamics of Born–Infeld type allowing for the freedom of duality rotations, explicit type D solutions are constructed. The obtained type D solutions, which generalize the charged Taub–NUT (Newman–Unti–Tamburino) metric with λ, exhaust all solutions within the considered class, under the assumption that the real eigenvectors of the electromagnetic field are aligned along the geodesic and shear-free principal null directions. Various relevant limiting transitions, in particular those of the flat space-time, are studied in some detail.
Inelastic collapse and clumping in a one-dimensional granular medium
Authors: McNamara Sean , Young W. R.
Published: July 2002

The dynamics of a one-dimensional gas of inelastic point particles is investigated. To model inelastic collisions, it is supposed that the relative velocity of two colliding particles is reduced by a factor r, where 0<r<1. The constant r is the coefficient of restitution. Because the collisions are inelastic, particles can collide infinitely often in finite time so that the relative separations and velocities of adjacent particles on the line become zero. The minimal example of this ‘‘inelastic collapse’’ requires r<7−4 7/8 ≊0.0718. With this restriction, three particles condense into a single lump in a finite time: The particle in the middle is sandwiched between the monotonically converging outer particles. When r is greater than 7−4 7/8, more than three particles are needed to trigger inelastic collapse and it is shown that r is close to 1 the minimum number scales as −ln(1−r)/(1−r). The simplest statistical problem is the ‘‘cooling law’’ of a uniformly excited gas confined between inelastic boundaries. A scaling argument suggests that the mean square velocity (the ‘‘granular temperature’’) of the particles decreases like t−2. Numerical simulations show that this scaling is correct only if the total number of particles in the domain is less than the number required to trigger collapse (e.g., roughly 88 if r=0.95). When the number of particles is much greater than this minimum, and before the first collapse, clusters form throughout the medium. Thus a state with uniform particle density is unstable to the formation of aggregates and inelastic collapse is the finite-amplitude expression of this instability.
The effects of static contact angles on standing waves
Authors: Henderson D. , Hammack J. , Kumar P. , Shah D.
Published: July 2002

Damping rates and natural frequencies of the fundamental axisymmetric mode in circular cylinders were measured when the contact angle between the water and the side walls was acute, obtuse, and about π/2. Damping rates decreased with increasing contact angle; natural frequencies increased with increasing contact angle.
The transition in the sedimentation pattern of a particle cloud
Authors: Noh Y. , Fernando H. J. S.
Published: July 2002

Experiments were carried out to study the sedimentation of a two-dimensional particle cloud. When a large number of particles (glass beads) of uniform size are released from a two-dimensional opening into a column of fresh water, the mixture initially descends as a thermal; however, after some time, the particles start settling individually, thus leaving the parent fluid behind. For a given type of particle, the critical depth zc at which this transition occurs, measured from a virtual origin, was found to change as zcws/ν∼(Q/νws)α, with α≂0.3, where ws is the terminal velocity of a single particle, ν is the kinematic viscosity, and Q is the total buoyancy of the released particles per unit length. The descending velocity and the spatial growth of the particle cloud were found to depend on its sedimentation characteristics.
Effect of drifts on the diffusion of runaway electrons in tokamak stochastic magnetic fields
Authors: Myra J. R. , Catto Peter J.
Published: July 2002

The quasilinear diffusion of runaway electrons in tokamak stochastic magnetic fields is examined. Previous models are generalized with respect to the spatial location and coherency of the perturbing magnetic fields, treatment of the radial as well as poloidal drift motion of the electrons, and the role of sidebands that arise from the beating of the electron drift motion with the applied perturbing fields. It is found that drift effects act to reduce the level of quasilinear diffusion by an amount that depends on the poloidal distribution of the magnetic turbulence. The results are employed to estimate the internal magnetic fluctuation levels at the edge during recent experiments on the TEXT tokamak [Phys. Fluids B 3, 2038 (1991)], where the drift modification effects are shown to be small. It is inferred that intrinsic magnetic turbulence controls runaway diffusion, but not the thermal diffusivity of the background electrons.
Stability of miscible displacements in porous media: Rectilinear flow
Authors: Tan C. T. , Homsy G. M.
Published: July 2002

A theoretical treatment of the stability of miscible displacement in a porous medium is presented. For a rectilinear displacement process, since the base state of uniform velocity and a dispersive concentration profile is time dependent, we make the quasi-steady-state approximation that the base state evolves slowly with respect to the growth of disturbances, leading to predictions of the growth rate. Comparison of results with initial value solutions of the partial differential equations shows that, excluding short times, there is good agreement between the two theories. Comparison of the theory with several experiments in the literature indicates that the theory gives a good prediction of the most dangerous wavelength of unstable fingers. An approximate analysis for transversely anisotropic media has elucidated the role of transverse dispersion in controlling the length scale of fingers.
Influence of a strong adverse pressure gradient on the turbulent structure in a boundary layer
Authors: Krogstad Per-Åge , Skåre Per Egil
Published: July 2002

A comparison between the turbulent structures found in a zero pressure gradient boundary layer and a boundary layer subjected to a strong adverse pressure gradient is presented. The pressure gradient reverses the direction of the dominant turbulent diffusion, resulting in considerable turbulent transport towards the wall. Two-point space–time correlations and the invariants show that this reduces the anisotropy in the near wall region and indicate an important reflection of the turbulent motion from the wall back into the outer layer. This is verified by a quadrant analysis [Lu and Willmarth, J. Fluid Mech. 60, 481 (1973)] which demonstrates that the strong events near the wall are totally dominated by motions in the first and fourth quadrants.
Resonant reflection of surface gravity waves by one-dimensional doubly sinusoidal beds
Authors: Rey Vincent , Guazzelli Élisabeth , Mei Chiang C.
Published: July 2002

The interaction between small-amplitude surface waves and a wavy bed described by two sinusoids is considered. Based on the method of multiple scales, an analytical theory for subharmonic Bragg resonances caused by second-order interactions between the surface wave and the seabed is derived. Comparisons with experiments and with a numerical theory are also discussed.
Turbulence in homogeneous shear flows
Authors: Pumir Alain
Published: July 2002

Homogeneous shear flows with an imposed mean velocity U=Syx̂ are studied in a period box of size Lx×Ly×Lz, in the statistically stationary turbulent state. In contrast with unbounded shear flows, the finite size of the system constrains the large-scale dynamics. The Reynolds number, defined by Re≡SL2y/ν varies in the range 2600⩽Re⩽11300. The total kinetic energy and enstrophy in the volume of numerical integration have large peaks, resulting in fluctuations of kinetic energy of order 30%–50%. The mechanism leading to these fluctuations is very reminiscent of the ‘‘streaks’’ responsible for the violent bursts observed in turbulent boundary layers. The large scale anisotropy of the flow, characterized by the two-point correlation tensor 〈uiuj〉 depends on the aspect ratio of the system. The probability distribution functions (PDF) of the components of the velocity are found to be close to Gaussian. The physics of the Reynolds stress tensor, uv, is very similar to what is found experimentally in wall bounded shear flows. The study of the two-point correlation tensor of the vorticity 〈ωiωj〉 suggests that the small scales become isotropic when the Reynolds number increases, as observed in high Reynolds number turbulent boundary layers. However, the skewness of the z component of vorticity is independent of the Reynolds number in this range, suggesting that some small scale anisotropy remains even at very high Reynolds numbers. An analogy is drawn with the problem of turbulent mixing, where a similar anisotropy is observed.
A membraneless experiment for the study of Richtmyer–Meshkov instability of a shock-accelerated gas interface
Authors: Jones M. A. , Jacobs J. W.
Published: July 2002

Previous Richtmyer–Meshkov instability experiments carried out in shock tubes have been hampered by the need to separate the two gases with a thin plastic membrane. As a result, many of these experiments have had poor agreement with the linear stability theory of Richtmyer [Commun. Pure Appl. Math. 23, 297 (1960)]. This limitation has been removed in the present investigation by the use of a novel technique in which the interface is formed by flowing light (N2) and heavy (SF6) gases from opposite ends of a vertical shock tube. Both gases exit the shock tube through slots in the test section walls leaving behind a flat motionless interface which is then given a sinusoidal initial shape by gently oscillating the shock tube at a prescribed frequency in the horizontal direction. A weak shock wave (Ms=1.10), generated in the shock tube, impacts the interface and produces the instability. Photographs of the interface, which is visualized by seeding the heavy gas with a water droplet fog and illuminating it with a strobe light source, provide particularly clear views of the developing instability far into the nonlinear regime. In addition, amplitude measurements obtained from these photographs are found to be in good agreement with Richtmyer’s theory.
Self-diffusion in freely evolving granular gases
Authors: Brey J. Javier , Ruiz-Montero M. J. , Cubero D. , Garcı́a-Rojo R.
Published: July 2002

A self-diffusion equation for a freely evolving gas of inelastic hard disks or spheres is derived starting from the Boltzmann–Lorentz equation, by means of a Chapman–Enskog expansion in the density gradient of the tagged particles. The self-diffusion coefficient depends on the restitution coefficient explicitly, and also implicitly through the temperature of the system. This latter introduces also a time dependence of the coefficient. As in the elastic case, the results are trivially extended to the Enskog equation. The theoretical predictions are compared with numerical solutions of the kinetic equation obtained by the direct simulation Monte Carlo method, and also with molecular dynamics simulations. An excellent agreement is found, providing mutual support to the different approaches.
A vorticity dynamics theory of three-dimensional flow separation
Authors: Wu J. Z. , Tramel R. W. , Zhu F. L. , Yin X. Y.
Published: July 2002

A theory of three-dimensional incompressible flow separation is presented in terms of the on-wall signatures of the flow. Some long-standing controversial issues are revisited and answers given, such as the inconsistency of the separation criteria based on the topological theory and “open separation,” and whether a separation line is an asymptote or envelope of neighboring skin-friction lines. General criteria for identifying an “open” or “closed” flow separation zone and separation line (including the initial point of the latter), steady and unsteady, are obtained, which apply to a generic smooth curved wall at any Reynolds numbers. The criteria are found to be most clearly given in terms of on-wall signatures of vorticity dynamics. These are then specified to steady boundary layer separation at large Reynolds numbers. A scale analysis under mild assumptions leads to a three-dimensional triple-deck structure near a generic boundary layer separation line. Criteria are presented for “separation watch,” which tells that a boundary-layer may soon break away, and for “separation warning,” which identifies the vorticity characteristics in an already formed boundary-layer separation zone and along a boundary-layer separation line. Flow behavior and its dependence on outer flow conditions are examined qualitatively. A numerical example is given which confirms the predictions of the theory.
On the dynamics of turbulent transport near marginal stability
Authors: Diamond P. H. , Hahm T. S.
Published: July 2002

A general methodology for describing the dynamics of transport near marginal stability is formulated. Marginal stability is a special case of the more general phenomenon of self-organized criticality. Simple, one field models of the dynamics of tokamak plasma self-organized criticality have been constructed, and include relevant features such as sheared mean flow and transport bifurcations. In such models, slow mode (i.e., large-scale, low-frequency transport events) correlation times determine the behavior of transport dynamics near marginal stability. To illustrate this, impulse response scaling exponents (z) and turbulent diffusivities (D) have been calculated for the minimal (Burgers’) and sheared flow models. For the minimal model, z=1 (indicating ballistic propagation) and D∼(S20)1/3, where S20 is the noise strength. With an identically structured noise spectrum and flow with shearing rate exceeding the ambient decorrelation rate for the largest-scale transport events, diffusion is recovered with z=2 and D∼(S20)3/5. This indicates a qualitative change in the dynamics, as well as a reduction in losses. These results are consistent with recent findings from dimensionless scaling studies. Several tokamak transport experiments are suggested.
Beyond paradigm: Turbulence, transport, and the origin of the radial electric field in low to high confinement mode transitions in the DIII-D tokamak
Authors: Moyer R. A. , Burrell K. H. , Carlstrom T. N. , Coda S. , Conn R. W. , Doyle E. J. , Gohil P. , Groebner R. J. , Kim J. , Lehmer R. , Peebles W. A. , Porkolab M. , Rettig C. L. , Rhodes T. L. , Seraydarian R. P. , Stockdale R. , Thomas D. M. , Tynan G. R. , Watkins J. G.
Published: July 2002

The paradigm of shear suppression of turbulence as the mechanism for the low to high confinement mode (L to H) transition is examined by quantitative comparison of the predictions of the paradigm with experimental results from the DIII-D tokamak [Plasma Physics and Controlled Fusion Research (International Atomic Energy Agency, Vienna, 1986), p. 159]. The L to H transition trigger is V×B rotation, not the main ion pressure gradient. The radial electric field Er shear increases before the fluctuation suppression, consistent with increasing Er shear as the cause of the turbulence suppression. The spatial dependence of the turbulence reduction is consistent with shear suppression for negative Er shear. For positive Er shear, the turbulence suppression is consistent with the effect of Er curvature for modes for which an Er well is destabilizing. Finally, the transport barrier depends on the phase angle between the density and potential fluctuations inside the Er well, an effect not included in existing L to H transition models.
The science applications of the high-energy density plasmas created on the Nova laser
Authors: Rosen Mordecai D.
Published: July 2002

Since the late 1970s it has been realized that the laser-heated hohlraums envisioned for indirect drive Inertial Confinement Fusion (ICF) could also serve as ‘‘physics factories’’ by providing a high-energy density environment for the study of a wide variety of physics with important applications. In this review we will describe some of these studies, accomplished in the early 1990s using the Nova laser [J. T. Hunt and D. R. Speck, Opt. Eng. 28, 461 (1989)] at the Lawrence Livermore National Laboratory. They include measuring the opacity of Fe, thus confirming that the OPAL low Z opacity code [C. A. Iglesias and F. J. Rogers, Astrophys. J. 443, 460 (1995)] is quantitatively more accurate than ‘‘standard’’ models, with important astrophysical implications such as modeling the Cepheid variables [F. J. Rogers and C. A. Iglesias, Science 263, 50 (1994)]; measuring the Rosseland mean opacity of Au, confirming the correctness of the ‘‘Super Transition Array’’ (STA) high-Z code [Bar Shalom et al., Phys. Rev. A 40, 3183 (1989)] with important implications for ignition targets designed for the National Ignition Facility (NIF); sophisticated Rayleigh–Taylor and other hydrodynamic turbulence experiments and analysis that serve as a test bed for understanding astrophysical observations such as supernova explosions; using laboratory x-ray lasers for probing high-density ICF plasmas as well as biology; and creating near Gbar pressures [Cauble et al. Phys. Rev. Lett. 70, 2102 (1993)]. Expanded opportunities for such research on the NIF will also be described.
Dynamics of laser produced shocks in foam–solid targets
Authors: Benuzzi Alessandra , Koenig Michel , Krishnan Jyothi , Faral Bernard , Nazarov Wigen , Temporal Mauro , Batani Dimitri , Müller Laura , Torsiello Flavia , Hall Tom , Grandjouan Nicolas
Published: July 2002

The influence of foams on laser shocks was studied with ns laser pulses smoothed with phase zone plates and focused onto layered foam–aluminum targets. Foams of 5–200 mg/cm3 density and 60 μm thickness were used. A strong pressure increase was measured with the foam in comparison to focusing the beam directly onto aluminum due to impedance mismatch at the aluminum–foam interface. Below a particular density, the measured pressure decreased as a result of hydrodynamics effects. Results are compared with computer simulations.
Equation of state data experiments for plastic foams using smoothed laser beams
Authors: Koenig Michel , Benuzzi Alessandra , Philippe Franck , Batani Dimitri , Hall Tom , Grandjouan Nicolas , Nazarov Wigen
Published: July 2002

The importance of foams in laser produced plasmas has been recently pointed out in both Inertial Confinement Fusion (ICF) and astrophysics laboratory dedicated experiments. In this paper, Equation of State (EOS) data measurements of plastic porous materials have been experimentally determined using ns laser pulses smoothed with Phase Zone Plates (PZP). Foams of density in the range 20–400 mg/cm3 and thickness about 20 μm were used. A new original scheme for the targets has been designed which allowed, for the first time with laser, EOS data to be obtained for pressures ranging from 0.1 to 2.5 Mbars. Results are discussed and compared with available models.
Electron tunneling into superconducting filaments using mechanically adjustable barriers
Authors: Moreland John , Ekin J. W.
Published: July 2002

A new type of squeezable electron tunneling (SET) junction has been developed for tunneling into superconducting filaments. Stable, mechanically adjustable tunneling barriers between the native surfaces of sputtered Nb films and 30-μm-diam Nb filaments were established in liquid helium at 4 K. The current versus voltage characteristics of these SET junctions were used to determine the superconducting energy gap at the surface of the filaments. Since the filaments were etched from commercial superconducting magnet wire, this type of tunnel junction shows promise as a diagnostic probe of superconducting materials for high-field magnets.
Disappearance of insectivorous birds from tropical forest fragments
Authors: Şekercioḡlu Çaḡan H. , Ehrlich Paul R. , Daily Gretchen C. , Aygen Deniz , Goehring David , Sandí Randi F.
Published: July 2002

Determining the impact of forest disturbance and fragmentation on
tropical biotas is a central goal of conservation biology. Among
tropical forest birds, understory insectivores are particularly
sensitive to habitat disturbance and fragmentation, despite
their relatively small sizes and freedom from hunting pressure. Why
these birds are especially vulnerable to fragmentation is not known.
Our data indicate that the best determinant of the persistence of
understory insectivorous birds in small fragments is the ability
to disperse through deforested countryside habitats. This finding
contradicts our initial hypothesis that the decline of insectivorous
birds in forest fragments is caused by impoverished invertebrate prey
base in fragments. Although we observed significantly fewer
insectivorous birds in smaller fragments, extensive sampling of
invertebrate communities (106,082 individuals) and avian diets (of 735
birds) revealed no important differences between large and small
fragments. Neither habitat specificity nor drier fragment microclimates
seemed critical. Bird species that were less affected by forest
fragmentation were, in general, those that used the deforested
countryside more, and we suggest that the key to their conservation
will be found there.
Cooperation of multiple signaling pathways in CD40-regulated gene expression in B lymphocytes
Authors: Dadgostar Hajir , Zarnegar Brian , Hoffmann Alexander , Qin Xiao-Feng , Truong Uyen , Rao Govinda , Baltimore David , Cheng Genhong
Published: July 2002

CD40/CD40L interaction is essential for multiple biological events in T dependent humoral immune responses, including B cell survival and proliferation, germinal center and memory B cell formation, and antibody isotype switching and affinity maturation. By using high-density microarrays, we examined gene expression in primary mouse B lymphocytes after multiple time points of CD40L stimulation. In addition to genes involved in cell survival and growth, which are also induced by other mitogens such as lipopolysaccharide, CD40L specifically activated genes involved in germinal center formation and T cell costimulatory molecules that facilitate T dependent humoral immunity. Next, by examining the roles of individual CD40-activated signal transduction pathways, we dissected the overall CD40-mediated response into genes independently regulated by the individual pathways or collectively by all pathways. We also found that gene down-regulation is a significant part of the overall response and that the p38 pathway plays an important role in this process, whereas the NF-κB pathway is important for the up-regulation of primary response genes. Our finding of overlapping independent control of gene expression modules by different pathways suggests, in principle, that distinct biological behaviors that depend on distinct gene expression subsets can be manipulated by targeting specific signaling pathways.
A single domestication for maize shown by multilocus microsatellite genotyping
Authors: Matsuoka Yoshihiro , Vigouroux Yves , Goodman Major M. , Sanchez G. Jesus , Buckler Edward , Doebley John
Published: July 2002

There exists extraordinary morphological and genetic diversity among the maize landraces that have been developed by pre-Columbian cultivators. To explain this high level of diversity in maize, several authors have proposed that maize landraces were the products of multiple independent domestications from their wild relative (teosinte). We present phylogenetic analyses based on 264 individual plants, each genotyped at 99 microsatellites, that challenge the multiple-origins hypothesis. Instead, our results indicate that all maize arose from a single domestication in southern Mexico about 9,000 years ago. Our analyses also indicate that the oldest surviving maize types are those of the Mexican highlands with maize spreading from this region over the Americas along two major paths. Our phylogenetic work is consistent with a model based on the archaeological record suggesting that maize diversified in the highlands of Mexico before spreading to the lowlands. We also found only modest evidence for postdomestication gene flow from teosinte into maize.
Melanin-concentrating hormone 1 receptor-deficient mice are lean, hyperactive, and hyperphagic and have altered metabolism
Authors: Marsh Donald J. , Weingarth Drew T. , Novi Dawn E. , Chen Howard Y. , Trumbauer Myrna E. , Chen Airu S. , Guan Xiao-Ming , Jiang Michael M. , Feng Yue , Camacho Ramon E. , Shen Zhu , Frazier Easter G. , Yu Hong , Metzger Joseph M. , Kuca Stephanie J. , Shearman Lauren P. , Gopal-Truter Shobhna , MacNeil Douglas J. , Strack Alison M. , MacIntyre D. Euan , Van der Ploeg Lex H. T. , Qian Su
Published: July 2002

Melanin-concentrating hormone (MCH) is a cyclic 19-aa hypothalamic neuropeptide derived from a larger prohormone precursor of MCH (Pmch), which also encodes neuropeptide EI (NEI) and neuropeptide GE (NGE). Pmch-deficient (
Pmch
−/−
) mice are lean, hypophagic, and have an increased metabolic rate. Transgenic mice overexpressing
Pmch
are hyperphagic and develop mild obesity. Consequently, MCH has been implicated in the regulation of energy homeostasis. The MCH 1 receptor (MCH1R) is one of two recently identified G protein-coupled receptors believed to be responsible for the actions of MCH. We evaluated the physiological role of MCH1R by generating MCH1R-deficient (
Mch1r
−/−
) mice.
Mch1r
−/−
mice have normal body weights, yet are lean and have reduced fat mass. Surprisingly,
Mch1r
−/−
mice are hyperphagic when maintained on regular chow, and their leanness is a consequence of hyperactivity and altered metabolism. Consistent with the hyperactivity,
Mch1r
−/−
mice are less susceptible to diet-induced obesity. Importantly, chronic central infusions of MCH induce hyperphagia and mild obesity in wild-type mice, but not in
Mch1r
−/−
mice. We conclude that MCH1R is a physiologically relevant MCH receptor in mice that plays a role in energy homeostasis through multiple actions on locomotor activity, metabolism, appetite, and neuroendocrine function.
Effect Of DNA-dependent protein kinase on the molecular fate of the rAAV2 genome in skeletal muscle
Authors: Song Sihong , Laipis Philip J. , Berns Kenneth I. , Flotte Terence R.
Published: July 2002

We report here that the DNA-dependent protein kinase (DNA-PK)
affects the molecular fate of the recombinant adeno-associated virus
(rAAV) genome in skeletal muscle. rAAV-human α1-antitrypsin
(rAAV-hAAT) vectors were delivered by intramuscular injection to either
C57BL/6 (DNA-PKcs
+
) or C57BL/6-SCID [severe combined
immunodeficient (SCID), DNA-PKcs
−
] mice. In both strains,
high levels of transgene expression were sustained for up to 1 year
after a single injection. Southern blot analysis showed that rAAV
genomes persisted as linear episomes for more than 1 year in SCID mice,
whereas only circular episomal forms were observed in the C57BL/6
strain. These results indicate that DNA-PK is involved in the formation
of circular rAAV episomes.
A comprehensive two-hybrid analysis to explore the yeast protein interactome
Authors: Ito Takashi , Chiba Tomoko , Ozawa Ritsuko , Yoshida Mikio , Hattori Masahira , Sakaki Yoshiyuki
Published: July 2002

Protein–protein interactions play crucial roles in the execution
of various biological functions. Accordingly, their comprehensive
description would contribute considerably to the functional
interpretation of fully sequenced genomes, which are flooded with novel
genes of unpredictable functions. We previously developed a system to
examine two-hybrid interactions in all possible combinations between
the ≈6,000 proteins of the budding yeast
Saccharomyces
cerevisiae
. Here we have completed the comprehensive analysis
using this system to identify 4,549 two-hybrid interactions among 3,278
proteins. Unexpectedly, these data do not largely overlap with those
obtained by the other project [Uetz, P.,
et al.
(2000)
Nature (London)
403, 623–627] and hence have
substantially expanded our knowledge on the protein interaction space
or interactome of the yeast. Cumulative connection of these binary
interactions generates a single huge network linking the vast majority
of the proteins. Bioinformatics-aided selection of biologically
relevant interactions highlights various intriguing subnetworks. They
include, for instance, the one that had successfully foreseen the
involvement of a novel protein in spindle pole body function as well as
the one that may uncover a hitherto unidentified multiprotein complex
potentially participating in the process of vesicular transport. Our
data would thus significantly expand and improve the protein
interaction map for the exploration of genome functions that eventually
leads to thorough understanding of the cell as a molecular system.
Directed evolution of polymerase function by compartmentalized self-replication
Authors: Ghadessy Farid J. , Ong Jennifer L. , Holliger Philipp
Published: July 2002

We describe compartmentalized self-replication (CSR), a strategy
for the directed evolution of enzymes, especially polymerases. CSR is
based on a simple feedback loop consisting of a polymerase that
replicates only its own encoding gene. Compartmentalization serves to
isolate individual self-replication reactions from each other. In such
a system, adaptive gains directly (and proportionally) translate into
genetic amplification of the encoding gene. CSR has applications in the
evolution of polymerases with novel and useful properties. By using
three cycles of CSR, we obtained variants of
Taq
DNA
polymerase with 11-fold higher thermostability than the wild-type
enzyme or with a >130-fold increased resistance to the potent
inhibitor heparin. Insertion of an extra stage into the CSR cycle
before the polymerase reaction allows its application to enzymes other
than polymerases. We show that nucleoside diphosphate kinase and
Taq
polymerase can form such a cooperative CSR cycle
based on reciprocal catalysis, whereby nucleoside diphosphate kinase
produces the substrates required for the replication of its own gene.
We also find that in CSR the polymerase genes themselves evolve toward
more efficient replication. Thus, polymerase genes and their encoded
polypeptides cooperate to maximize postselection copy number. CSR
should prove useful for the directed evolution of enzymes, particularly
DNA or RNA polymerases, as well as for the design and study of
in vitro
self-replicating systems mimicking
prebiotic evolution and viral replication.
Modular organization of the Friend murine leukemia virus envelope protein underlies the mechanism of infection
Authors: Barnett Anna L. , Davey Robert A. , Cunningham James M.
Published: July 2002

Retrovirus infection is initiated by receptor-dependent fusion of
the envelope to the cell membrane. The modular organization of the
envelope protein of C type retroviruses has been exploited to
investigate how binding of the surface subunit (SU) to receptor
triggers fusion mediated by the transmembrane (TM) subunit. We show
that deletion of the receptor-binding domain (RBD) from SU of Friend
murine leukemia virus (Fr-MLV) abolishes infection that is restored by
supplying RBD as a soluble protein. Infection by this mechanism remains
dependent on receptor expression. When membrane attachment of the virus
lacking RBD is reestablished by inserting the hormone erythropoietin,
infection remains dependent on the RBD/receptor complex. However,
infection increases 50-fold to 5 × 10
5
units/ml on
cells that also express the erythropoietin receptor. Soluble RBD from
Fr-MLV also restores infection by amphotropic and xenotropic MLVs in
which RBD is deleted. These experiments demonstrate that RBD has two
functions: mediating virus attachment and activating the fusion
mechanism. In addition, they indicate that receptor engagement triggers
fusion by promoting a subgroup-independent functional interaction
between RBD and the remainder of SU and/or TM.
Genome-wide analysis of vaccinia virus protein–protein interactions
Authors: McCraith Stephen , Holtzman Ted , Moss Bernard , Fields Stanley
Published: July 2002

To detect interactions between proteins of vaccinia virus, we carried out a comprehensive two-hybrid analysis to assay every pairwise combination. We constructed an array of yeast transformants that contained each of the 266 predicted viral ORFs as Gal4 activation domain hybrid proteins. The array was individually mated to transformants containing each ORF as a Gal4–DNA-binding domain hybrid, and diploids expressing the two-hybrid reporter gene were identified. Of the ≈70,000 combinations, we found 37 protein–protein interactions, including 28 that were previously unknown. In some cases, e.g., late transcription factors, both proteins were known to have related roles although there was no prior evidence of physical associations. For some other interactions, neither protein had a known role. In the majority of cases, however, one of the interacting proteins was known to be involved in DNA replication, transcription, virion structure, or host evasion, thereby providing a clue to the role of the other uncharacterized protein in a specific process.
The neural system that bridges reward and cognition in humans: An fMRI study
Authors: Pochon J. B. , Levy R. , Fossati P. , Lehericy S. , Poline J. B. , Pillon B. , Le Bihan D. , Dubois B.
Published: July 2002

We test the hypothesis that motivational and cognitive processes are linked by a specific neural system to reach maximal efficiency. We studied six normal subjects performing a working memory paradigm (n-back tasks) associated with different levels of monetary reward during an fMRI session. The study showed specific brain activation in relation with changes in both the cognitive loading and the reward associated with task performance. First, the working memory tasks activated a network including the dorsolateral prefrontal cortex [Brodmann area (BA) 9/46] and, in addition, in the lateral frontopolar areas (BA 10), but only in the more demanding condition (3-back task). This result suggests that lateral prefrontal areas are organized in a caudo-rostral continuum in relation with the increase in executive requirement. Second, reward induces an increased activation in the areas already activated by working memory processing and in a supplementary region, the medial frontal pole (BA 10), regardless of the level of cognitive processing. It is postulated that the latter region plays a specific role in monitoring the reward value of ongoing cognitive processes. Third, we detected areas where the signal decreases (ventral-BA 11/47 and subgenual prefrontal cortices) in relation with both the increase of cognitive demand and the reward. The deactivation may represent an emotional gating aimed at inhibiting adverse emotional signals to maximize the level of performance. Taken together, these results suggest a balance between increasing activity in cortical cognitive areas and decreasing activity in the limbic and paralimbic structures during ongoing higher cognitive processing.
Bepridil opens the regulatory N-terminal lobe of cardiac troponin C
Authors: Li Yu , Love Michael L. , Putkey John A. , Cohen Carolyn
Published: July 2002

Cardiac troponin C (cTnC) is the calcium-dependent switch for contraction in heart muscle and a potential target for drugs in the therapy of congestive heart failure. This calmodulin-like protein consists of two lobes connected by a central linker; each lobe contains two EF-hand domains. The regulatory N-terminal lobe of cTnC, unlike that of skeletal troponin C (sTnC), contains only one functional EF-hand and does not open fully upon the binding of Ca
2+
. We have determined the crystal structure of cTnC, with three bound Ca
2+
ions, complexed with the calcium-sensitizer bepridil, to 2.15-Å resolution. In contrast to apo- and 3Ca
2+
-cTnC, the drug-bound complex displays a fully open N-terminal lobe similar to the N-terminal lobes of 4Ca
2+
-sTnC and cTnC bound to a C-terminal fragment of cardiac troponin I (residues 147–163). The closing of the lobe is sterically hindered by one of the three bound bepridils. Our results provide a structural basis for the Ca
2+
-sensitizing effect of bepridil and reveal the details of a distinctive two-stage mechanism for Ca
2+
regulation by troponin C in cardiac muscle.
The current biodiversity extinction event: Scenarios for mitigation and recovery
Authors: Novacek Michael J. , Cleland Elsa E.
Published: July 2002

The current massive degradation of habitat and extinction of species is taking place on a catastrophically short timescale, and their effects will fundamentally reset the future evolution of the planet's biota. The fossil record suggests that recovery of global ecosystems has required millions or even tens of millions of years. Thus, intervention by humans, the very agents of the current environmental crisis, is required for any possibility of short-term recovery or maintenance of the biota. Many current recovery efforts have deficiencies, including insufficient information on the diversity and distribution of species, ecological processes, and magnitude and interaction of threats to biodiversity (pollution, overharvesting, climate change, disruption of biogeochemical cycles, introduced or invasive species, habitat loss and fragmentation through land use, disruption of community structure in habitats, and others). A much greater and more urgently applied investment to address these deficiencies is obviously warranted. Conservation and restoration in human-dominated ecosystems must strengthen connections between human activities, such as agricultural or harvesting practices, and relevant research generated in the biological, earth, and atmospheric sciences. Certain threats to biodiversity require intensive international cooperation and input from the scientific community to mitigate their harmful effects, including climate change and alteration of global biogeochemical cycles. In a world already transformed by human activity, the connection between humans and the ecosystems they depend on must frame any strategy for the recovery of the biota.
Induction of male sterility in plants by metabolic engineering of the carbohydrate supply
Authors: Goetz Marc , Godt Dietmute E. , Guivarc'h Anne , Kahmann Uwe , Chriqui Dominique , Roitsch Thomas
Published: July 2002

Extracellular invertase mediates phloem unloading via an apoplastic
pathway. The gene encoding isoenzyme Nin88 from tobacco was cloned and
shown to be characterized by a specific spatial and temporal expression
pattern. Tissue-specific antisense repression of
Nin88
under control of the corresponding promoter in tobacco results in a
block during early stages of pollen development, thus, causing male
sterility. This result demonstrates a critical role of extracellular
invertase in pollen development and strongly supports the essential
function of extracellular sucrose cleavage for supplying carbohydrates
to sink tissues via the apoplast. The specific interference with phloem
unloading, the sugar status, and metabolic signaling during pollen
formation will be a potentially valuable approach to induce male
sterility in various crop species for hybrid seed production.