bluuebunny/crossref_metadata_2025 huggingface dataset:
Multiple-scattering approach to the vibrational-rotational excitation of molecules by slow electrons
Authors: G F Drukarev  , I Y Yurova
Published: July 2002

The cross sections for vibrational and rotational excitation of H2, Li2, Na2 and K2 by slow electrons are calculated in the adiabatic approximation using a zero range potential model to obtain the amplitude of electron scattering for a 'frozen' molecule. The advantage of the zero range potential model is the possibility of taking into account explicitly the effect of multiple scattering. The results are compared with the available experimental data and other calculations.
On the rotational polarization of diatomic molecules by atomic impact
Authors: P Eckelt  , H J Korsch
Published: July 2002

The collision-induced polarization of the angular momentum of a diatomic molecule is discussed within the framework of the quantum-mechanical spectator model. For purely rotational excitation from the molecular ground state to some final angular momentum j, the distribution over the projections m is investigated at different scattering angles and the differential and total cross sections are studied as functions of m. A simple scheme for the calculation of the most probable m transitions is given. Numerical results are presented for a simplified model of the system N2+Li+.
Differential cross sections for electron scattering by strongly polar molecules
Authors: A S Dickinson
Published: July 2002

A simple model, combining the Born approximation and classical perturbation theory, is derived for small- and moderate-angle scattering ( theta <or=60 degrees ) into all states. Agreement within 33% is obtained with close-coupling and Glauber calculations. Comparable agreement is obtained with the recoil measurements on CsF, CsCl and KI but poor agreement is found with the recent relative measurements on KI by Rudge, Trajmar and Williams (1976). Using a hard-sphere model for wide-angle scattering, simple formulae for the total and momentum-transfer cross sections into all states are derived.
Excited electronic states of H3and their role in the dissociative recombination of H3+
Authors: K C Kulander  , M F Guest
Published: July 2002

Accurate calculations of several electronically excited states of H3which are important in dissociative recombination of H3+are reported. These surfaces allow discussion of the dissociation products. For electron energies above 1 eV the dominant product is expected to be vibrationally excited H2(X1Sigmag+)+H(2s or 2p). The threshold for directly producing H-from ground state H3+is predicted to be 5.8 eV.
Correlation effects in low-energy scattering of electrons by a model negative ion
Authors: M Valley  , R S Berry
Published: July 2002

Presents the results of first-order Bethe-Goldstone (BG) calculations of electron scattering from a two-electron model of a negative ion. The results of the BG calculations are compared to those obtained using several approximate polarisation potentials. The BG calculations appear to contain significant contributions from dynamical effects that are not incorporated in a formulation based on adiabatic (static) polarisation potentials, but that can be represented at least partially if the polarisability is treated as a frequency-dependent function.
The unified theories of line broadening
Authors: R Lee
Published: July 2002

The line broadening theories of Smith et al., Voslamber and Bezzerides are discussed. These theories are related, and then it is shown that all of them depend on the same approximations. The unified theory is then compared to the first order contribution from an expansion formulated by Dufty, and a discussion of the unification is presented.
Some energy curves of ArH+and their use in the study of the scattering of H+by Ar
Authors: V Sidis
Published: July 2002

Calculations on the ground state and some excited states of ArH+in the LCAO-STO-MO-SCF approximation are reported. The ground state interaction potential is then used to study the elastic scattering of protons by argon atoms at low and moderate energies. Partial wave calculations involving the JWKB evaluation of the phase shifts are compared to the available experimental results and subsequently used to improve the well depth obtained in the ab initio calculation. The values U=4.3 eV and Re=1.34 AA are thus found. Qualitative discussions of the approximate excited states lead to the conclusions that the excitation of the argon target, at moderate energies, can take place only via the charge exchange channel-that is, the four lowest monoexcited states of ArH+-at R1approximately=1 AA. This charge exchange channel being itself coupled to the ground state at internuclear distances 1.70 AA<or approximately=Rx<or approximately=1.85 AA. A tentative explanation of the preferential excitation Ar*(3p53d) is given.
Dissociative attachment in NO2and CO2
Authors: R Abouaf  , R Paineau  , F Fiquet-Fayard
Published: July 2002

Ions produced by dissociative attachment in NO2and CO2are studied using a trochoidal monochromator as electron gun. Appearance potentials obtained for O-, O2-and NO-from NO2are respectively 1.61+or-0.05 eV, 4.03+or-0.05 eV, 3.11+or-0.05 eV. These results are, within the experimental errors in good agreement with the (D-A) values presently known. The O-/CO2peak near 4.4 eV shows various structures spaced by 0.12+or-0.02 eV. These structures are connected to the vibrational structure of Co2-above the CO+O-dissociation limit.
Reflectance and electroreflectance of TiO2single crystals. II. Assignment to electronic energy levels
Authors: K Vos
Published: July 2002

For pt.I see ibid., vol.10, no.19, p.3893 (1977). The interband optical properties of TiO2are analysed on the basis of a tight-binding band structure which is calculated by using estimated values for the LCOAO parameters. The major interband transitions giving rise to the pronounced optical structure around 4 eV occur between energy band regions near the Sigma symmetry line of the Brillouin zone. The broad structure of the electroreflectance (ER) is mainly caused by the energy shift of these bands due to the dielectric polarisation. Values for four elements of the polarisation-potential tensor have been deduced from the experimental data which agree with the results of a quantitative model developed for the electro-optic effect. Some features of the ER fine structure are unambiguously identified as Franz-Keldysh oscillations and are designated to specific critical points.
A Mossbauer investigation of Rb2FeF5: A one-dimensional antiferromagnetic system
Authors: G P Gupta  , D P E Dickson  , C E Johnson  , B M Wanklyn
Published: July 2002

Mossbauer spectra of Rb2FeF5show that it undergoes an ordering to a four sublattice antiferromagnetic state at 9.3+or-0.5K. The saturated value of the hyperfine field is 43.0+or-0.5 T, and is the same for both pairs of sublattices. This value is anomalously low for a high-spin ferric ion and corresponds to a zero-point spin reduction of about 28%. At finite temperatures the hyperfine fields at the iron nuclei are appreciably modified by the application of an external magnetic field. This behaviour is a characteristic of one-dimensional antiferromagnets. Relationships for the spin reduction as a function of the magnitude and direction of the external field are developed on the basis of spin wave theory. The measured values of the hyperfine fields are compared with those calculated from these relationships which leads to the ratio J'/J of the intrachain to interchain exchange constants being less than 10-3and the ratio BA/BEof anisotropy to exchange fields being around 4*10-3.
The M4,5N4,5N4,5Auger spectra of Ag, Cd, In and Sn
Authors: A C Parry-Jones  , P Weightman  , P T Andrews
Published: July 2002

High-resolution M4,5N4,5N4,5Auger and M5and valence-band photoelectron spectra of Ag, Cd, In and Sn, measured using X-ray excitation, are combined to yield the magnitude of Ueff, the Coulomb repulsion between two holes on the same atomic site. The extra-atomic relaxation contributions to Auger and photoelectron processes in these elements are determined by comparing the experimental results with atomic structure calculations. The relationship Ueff>>2W, where W is the width of the 4d band, holds for Cd, In and Sn and the M4,5N4,5N4,5Auger spectra of these elements are in good agreement with multiplet structure calculations. Discrepancies between the observed and the calculated M4,5N4,5N4,5spectra of Ag are interpreted in terms of its failure to satisfy the Ueff>>2W condition and the variation of Ueffwith the final-state component of the Auger spectrum. It is suggested that the3F4component is able to decay into the Ag 4d band and is thus substantially broader than the other components of the Auger spectrum.
The temperature dependence of inelastic neutron scattering in rotational tunnelling systems. II. Calculation of the time-dependent correlation functions
Authors: A C Hewson
Published: July 2002

For pt.I see ibid., vol.15, p.3841 (1982). The problem of explaining the temperature dependence observed in the inelastic neutron scattering spectrum of rotational tunnelling systems was considered in an earlier paper and based on a model in which a threefold molecular group in a hindering potential is coupled to a spectrum of phonon modes. An expression was derived for the neutron scattering function in terms of the correlation functions of the standard basis operators of the uncoupled system. Here the authors extends the perturbational approach for the calculation of these correlation functions that was developed earlier to include the effects of line broadening. The temperature dependence of the shifting and broadening of the peaks in the neutron spectrum is then calculated for different assumed forms for the density of the coupled-phonon states. Not enough is known about the coupling to the phonon spectrum for a complete quantitative comparison with experiment for any one system. However, the author shows that the theory can be used to explain the range of the experimentally observed behaviour, and the form of the temperature dependence of the shifting and broadening of the peaks.
The point group crystal field and the superposition model for Re3+ions in CaF2and SrF2
Authors: M F Reid  , P H Butler
Published: July 2002

Point group 3jm symbols are used in crystal-field calculations for Re3+ions in tetragonal CaF2and SrF2sites with F-and H-charge compensation. The point group basis gives a parametrisation that clearly distinguishes Ohand C4vcontributions to the crystal-field Hamiltonian and, since the basis states are close to being eigenstates, the assignment of both Ohand C4virreps to the energy levels is direct. Some ions have well determined parameters that follow a smooth trend, but for other ions the data are sparse or contradictory. Theoretical schemes using interpolated parameters are presented for these ions. The authors show that the superposition model predicts the signs of the crystal-field parameters, and they use the model to calculate coordination angles for several ions in CaF2and SrF2. The results are consistent with published ENDOR data.
Universal dependences of the conductivity of metallic disordered systems on temperature, magnetic field and frequency
Authors: M Kaveh  , N F Mott
Published: July 2002

The authors generalise the Mooij rule (1973) for disordered metals. They find that the temperature dependence of the conductivity sigma of a disordered metal as a function of temperature must change slope due to diffusion effects, and if interaction effects are included, sigma changes its slope three times. The crossover temperature (if it occurs at high temperatures) from positive to negative d sigma /dT due to diffusion effects varies as C5, where C is the average concentration of impurities or scattering centres. Another crossover temperature which separates electron correlation effects from diffusion effects is predicted. This explains the temperature dependence observed for Ge1-xAux. It is also shown that the non-metallic behaviour of the AC conductivity is accounted for by diffusion effects and there is no need to invoke the concept of a pseudogap due to electron interaction. The negative magnetoresistance follows from the theory for diffusion effects in agreement with the perturbation theory of Kawabata (1980).
The low-temperature variation of the elastic constants of lithium hydride and lithium deuteride
Authors: B W James  , H Kheyrandish
Published: July 2002

The adiabatic elastic constants C11, C12and C44of7LiH and7LiD have been obtained from measurements of ultrasonic wave transit times through single crystals over the range 4.2-300K. The temperature variation follows quite closely the approximation Cij(T)=Cij(0)(1-D epsilon ). The anisotropy factor A=C44/(C11-C12) and the deviation ( Delta =C12-C44) from the Cauchy relation have been used to make comparisons with the alkali halides. It has been found that the Gruneisen parameter gamma is approximately constant at 1.2 for both7LiH and7LiD from 50 to 270K. There are signs of anomalous behaviour of the elastic constants in the region of 11K, where a lambda -type heat capacity anomaly has been reported.
Effect of excited-oxygen exposures on spectra and transition density of states for cleaved Si(111) from L1L2,3V and L2,3VV Auger transitions
Authors: R H Brockman  , G J Russell
Published: July 2002

Detailed AES measurements for clean cleaved and excited-oxygen exposed silicon surfaces, at room temperature, are reported. For oxygen exposures in the range 10-7to 10-4Torr s a continuous shift, to a maximum of 2.2 eV was observed in the negative excursion of both the L1L2,3V and L2,3VV (N'(E)) Auger peaks. Higher oxygen doses, up to 10-1Torr s, did not alter the 2.2 eV shift. For exposures >or=10-5Torr s the formation of SiO2was detected. The derived transition density of states curves showed (i) that the 'dangling bond' surface states associated with the clean surface were removed for oxygen exposures >or=10-7Torr s and (ii) that a number of oxygen induced peaks appeared at well defined energies below the vacuum level. For the range of exposures studied, the valence band spectroscopic data reported have been interpreted as showing the simultaneous existence of both atomic and molecular chemisorption states and their coexistence with SiO2formation during the early oxidation stage.
Brillouin scattering and ultrasonic propagation in the nearly cubic antiferromagnet KNiF3
Authors: F Ganot  , C Dugautier  , P Moch  , J Nouet
Published: July 2002

Spin waves, elastic waves and their magnetostrictive coupling in KNiF3are studied as functions of temperature and of applied magnetic field by Brillouin scattering and ultrasonic measurements. The light scattering data provide the magnetic and elastic coefficients; in addition, they enable magnetostrictive coefficients to be evaluated, in the framework of the usual magnetoelastic description and, more fruitfully, of a Landau model describing the antiferromagnetic-paramagnetic phase transition. Various features concerning the size of the magnetic domains and their repartition in the crystals are derived from the authors' experiments. The existing differences between ultrasonic and Brillouin scattering results in the magnetically ordered phase are discussed.
Thermal conductivity of single-crystal NaCl under uniaxial compression
Authors: U Brydsten  , D Gerlich  , G Backstrom
Published: July 2002

The variation of the thermal conductivity of single-crystal NaCl under uniaxial compression is investigated by the dynamic hot-strip method. Over a stress range of 0-1.0 MPa no effect whatsoever is found. The relative change in thermal conductivity under uniaxial compression must be smaller than 1.5*10-9Pa-1, contrary to the result of an earlier investigation.
Methyl Zeeman-tunnel resonance and nuclear spin relaxation in copper acetate
Authors: P Coppens  , L Van Gerven  , S Clough  , A J Horsewill
Published: July 2002

The methyl tunnel spectrum of copper acetate is studied at low temperatures by means of nuclear magnetic resonance level-crossing spectroscopy employing a field-cycling technique. The recovery of the proton magnetisation following saturation is measured as a function of magnetic field. Changing the magnetic field causes energy levels to cross when the methyl tunnel frequency is equal to one or two times the proton Larmor frequency, and abrupt changes in the recovered magnetisation, showing up as peaks or dips in a smooth background, reveal the positions of the level crossings. A variety of possible field cycles and sequences of cycles leads to a series of different experimental procedures which highlight different aspects of the thermodynamic properties of the system. In particular the dependence of the spectra on scanning schemes and on the thermodynamic preparation conditions is investigated. The experiments are understood in a semi-quantitative way in terms of a simple mathematical model for the thermal equilibration of three energy reservoirs, of which two are resonantly coupled at the level crossings. This simulation shows that, while the dominant processes have been clearly identified and incorporated in the model, some important factors remain to be explained. The methyl tunnel frequency in copper acetate is found to be (64+or-5) MHz.
Quadrupole interactions of muonium in α-quartz
Authors: V G Baryshevskii  , S A Kuten  , V I Rapoport
Published: July 2002

The general theory of the behaviour of the muonium atom of 'finite size' with an electric quadrupole moment in matter is presented. The experimental situation in alpha -quartz is discussed, and the constants of hyperfine and quadrupole interactions are derived.
A theoretical study of Compton scattering for MgO. I. Momentum density, Compton profiles, and B-functions
Authors: R Podloucky  , J Redinger
Published: July 2002

On the basis of augmented-plane-wave band-structure calculations for the insulating compound MgO the authors have calculated the momentum density. Compton profiles, and B(z) functions. In order to derive physical insight from the results they have put much effort into understanding the momentum density in terms of real-space wavefunctions and nearest-neighbour interactions. To this end they performed a backtransformation of the momentum densities into real space, thus obtaining Wannier-like functions. The Compton profile and the B(z) function along (100) are distinctly different from the ones along the other two main directions, and this is also revealed by the experimental results. However, there is a significant discrepancy between the results and experiment for the B(z) function along (100). A similar discrepancy is also observed by another calculation using a different model. The source of this discrepancy is not understood.
The frequency dependence of the phonon transmission from NaF into liquid4He
Authors: T W Bradshaw  , A F G Wyatt
Published: July 2002

An analysis of the energy emitted by a NaF crystal into the peak and background angular distributions in liquid4He shows that the measured values can be accounted for if a simple form is chosen for the frequency dependence of the transmission coefficient of the background channel, alphab( omega ). The model takes into account the various stages of phonon propagation from the heater, through the NaF and liquid4He to the bolometer. The phonon frequency spectra as a function of time are evaluated at each stage. The ratio of the energy in the peak and background as a function of temperature gives values of alphab(T) which are consistent with the general behaviour found for Kapitza conductances.
Internal field distribution in the infinite-range Ising spin glass
Authors: J R L de Almeida  , E J S Lage
Published: July 2002

The authors have studied the internal field distribution P(H) in the infinite-range Ising spin glass within the framework of the replica method. Their results show that breaking of replica symmetry in the spin-glass phase yields a non-gaussian internal field distribution. Using Parisi's scheme for symmetry breaking they derive a set of Fokker-Planck-like differential equations that are obeyed by both P(H) and the multiple correlation functions in replica space. For t=1-T/Tc<<1 the equations can be integrated perturbatively and the field distribution thus obtained deviates from a guassian form, exhibiting a second maximum which increases and moves toward the origin as t increases. The asymmetry factor for P(H) is shown to be negative and of the order of t5.
Point-defect mobility in thallous chloride doped with divalent cation and anion impurities
Authors: J Corish  , B M C Parker  , J M Quigley  , A R Allnatt  , D C A Mulcahy
Published: July 2002

A detailed study of the temperature dependence of the ionic conductance of single crystals of thallous chloride has been made. Twenty crystals were grown from the melt and detailed results are presented for ten of these: three doped with divalent cations, four doped with divalent anions and three which were nominally pure. Precautions were taken during the conductivity measurements to minimise the effects of sublimation at elevated temperatures. An analysis of the data using computer fitting techniques has provided values for the thermodynamic parameters which govern the formation, migration and interaction of the point defects in the host lattice. The conventional Schottky model with transport on both sublattices and taking account of both nearest-neighbour and long-range (Debye-Huckel) defect interactions was employed. The value for the enthalpy of formation of a Schottky defect was found to be 1.247 eV and that for the migration of the cation and anion vacancies to be 0.379 eV and 0.097 eV respectively. The defect parameters derived are compared with previous experimental and theoretical results and the effect of the changes of the dopant species on the overall conductivity, particularly at lower temperatures, is discussed. The anion vacancy is found to be more mobile than the cation vacancy with the transport number of the former being virtually unity at low temperatures except in the case of the cation-doped crystals. The overall conductivity is interpreted in terms of the concentrations and mobilities of the defects and the extent of the vacancy-impurity association.
The diffuse X-ray scattering of silver-chalcogenide-type fast-ion conductors
Authors: Y Tsuchiya
Published: July 2002

The diffuse scattering of silver-chalcogenide-type fast-ion conductors is examined. It is shown that in an actual crystal the correlation of cation-anion pairs produces the most prominent diffuse scattering. The contribution from anion-anion pairs is small unless the amplitude of the anion thermal vibration is very large. The results support previous analyses of the diffuse haloes for alpha -Ag2S and alpha -AgI by Tsuchiya and co-workers (1978-79).
Lattice dynamics of RbBr
Authors: S Rolandson  , G Raunio
Published: July 2002

Phonon frequencies in RbBr at 80 K have been obtained by inelastic scattering of thermal neutrons. The measurements were performed in the symmetry directions Delta , Sigma and Lambda and along the line Z. Some zone boundary phonons were also measured at 300 K. Four versions of the shell model were fitted to the experimental frequencies, and the elastic and dielectric constants were calculated from the model parameters. From an eleven parameter model the authors have also calculated the phonon frequency spectrum and the temperature variation of the Debye temperature.
Hartree-Fock renormalization of magnetic anisotropy in the basal-plane ferromagnets terbium and dysprosium
Authors: J Jensen
Published: July 2002

The application of the Holstein-Primakoff transformation in the spin-wave theory of an anisotropic ferromagnet implies contributions from the isotropic two-ion coupling to the energy of the uniform spin-wave mode. Including these contributions, the energies of the HF renormalized spin waves are deduced using the method of Lindgard and Danielsen (1974). The macroscopic resonance theory for the uniform mode is found to agree with the spin-wave theory if the magnetization is along a symmetry direction. Numerical results for the renormalization of the static anisotropy parameters of Tb and Dy are presented. The effect of the ellipticity of the moment precession is found to be smaller than reported previously.
Localized description of the electronic structure of covalent semiconductors. I. Perfect crystals
Authors: B G Cartling
Published: July 2002

A localized description of covalent semiconductors is discussed as an alternative to the conventional band structure description. Localized orbitals are defined as eigenfunctions of the one-electron Hamiltonian for a finite cluster of atoms in a simulated crystalline environment. The bound electronic states of the cluster are determined by the SCF X alpha scattered wave method. It is shown that the main features of the valence band structure emerge in the spectrum of occupied cluster states. The use of the localized orbitals for the interpretation of X-ray emission spectra is justified by the localized nature of the excitations. A local density of states is defined for the interpretation of spectra of localized excitations. The information on the electronic structure, which photoelectron spectroscopy and optical absorption spectroscopy provide, is also compared to the predictions of the model. The model is particularly investigated with respect to silicon, and its general applicability to perfect crystals is tested by similar studies of diamond and germanium. The obtained results correlate very well with experimental observations.
A multiplexed single-photon instrument for routine measurement of time-resolved fluorescence anisotropy
Authors: D J S Birch  , A S Holmes  , J R Gilchrist  , R E Imhof  , S M Al Alawi  , B Nadolski
Published: July 2002

The authors report a new type of instrument, the Edinburgh Instruments Model 2997 differential fluorometer, for the measurement of the decay of fluorescence anisotropy. The instrument incorporates three multiplexed detection channels for simultaneous measurement of two polarised fluorescence decays and the excitation pulse, using time-correlated single-photon counting. This arrangement corrects automatically for temporal and intensity fluctuations of the spark source. A study of the probe 1,6-diphenyl-1,3,5-hexatriene (DPH) in a white oil reveals that the instrument can measure rotational correlation times with subnanosecond time resolution in a third of the time of conventional methods.
A sensor based on silicon technology for turbulence measurements
Authors: L Lofdahl  , G Stemme  , B Johansson
Published: July 2002

A very small and highly sensitive flow velocity sensor has been designed and fabricated using silicon microelectronic technology. To determine the performance of this silicon sensor, comparisons with a conventional hot-wire sensor were made in a well defined two-dimensional turbulent flat-plate boundary layer at a constant Reynolds number of 4.2*106. The silicon sensor was found to have spatial and frequency resolutions that make it suitable for turbulence measurements. In the investigated flow field the new silicon sensor measures profiles of the mean velocity and the turbulence intensity with the same accuracy as the hot wire.
The energy dispersion effect in field ionization/field desorption quadrupole mass spectrometers
Authors: H J Heinen  , H H Gierlich  , H D Beckey
Published: July 2002

A method is described whereby field ionization/field desorption quadrupole mass spectrometers can be used for energy analysis and appearance potential determination of field ions. With this method no special instrumental modifications are necessary. When employed for measurements of ionization potentials of some rare gases and some organic molecules an accuracy of better than +or-0.2 eV could be achieved when Pt tips were used as field anodes. The accuracy of measurement decreased only slightly when field ionization was performed at high temperature activated tungsten wire emitters. The same method of measurement also could be applied successfully to ions generated by field desorption.
On the structure of the set of bounded solutions on a periodic Liénard equation
Authors: Campos Juan , Torres Pedro
Published: July 2002

We describe the dynamics of a class of second order periodic differential equations whose main feature is a monotone nonlinearity. It is proved that the set of bounded solutions is homeomorphic to the graph of a decreasing function.
Explicit error bounds in a conforming finite element method
Authors: Destuynder Philippe , Métivet Brigitte
Published: July 2002

The goal of this paper is to define a procedure for bounding the error in a conforming finite element method. The new point is that this upper bound is fully explicit and can be computed locally. Numerical tests prove the efficiency of the method. It is presented here for the case of the Poisson equation and a first order finite element approximation.
On Minuscule Representations and the Principal SL₂
Authors: Gross Benedict
Published: July 2002

We study the restriction of minuscule representations to the principal

S

L
2

SL_2

, and use this theory to identify an interesting test case for the Langlands philosophy of liftings.
Functional Characterization and Localization of theAspergillus nidulansFormin SEPA
Authors: Sharpless Kathryn E. , Harris Steven D.
Published: July 2002

Formins are a family of multidomain scaffold proteins involved in actin-dependent morphogenetic events. In Aspergillus nidulans, the formin SEPA participates in two actin-mediated processes, septum formation and polarized growth. In this study, we use a new null mutant to demonstrate that SEPA is required for the formation of actin rings at septation sites. In addition, we find that a functional SEPA::GFP fusion protein localizes simultaneously to septation sites and hyphal tips, and that SEPA colocalizes with actin at each site. Using live imaging, we show that SEPA localization at septation sites and hyphal tips is dynamic. Notably, at septation sites, SEPA forms a ring that constricts as the septum is deposited. Moreover, we demonstrate that actin filaments are required to maintain the proper localization pattern of SEPA, and that the amino-terminal half of SEPA is sufficient for localization at septation sites and hyphal tips. In contrast, only localization at septation sites is affected by loss of the sepH gene product. We propose that specific morphological cues activate common molecular pathways to direct SEPA localization to the appropriate morphogenetic site.
Decision tree-based formation of consensus protein secondary
structure prediction
Authors: Selbig Joachim , Mevissen Theo , Lengauer Thomas
Published: July 2002

Motivation: Prediction of protein secondary structure provides information that is useful for other prediction methods like fold recognition and ab initio 3D prediction. A consensus prediction constructed from the output of several methods should yield more reliable results than each of the individual methods.

Method: We present an approach that reveals subtle but systematic differences in the output of different secondary structure prediction methods allowing the derivation of coherent consensus predictions. The method uses a machine learning technique that builds decision trees from existing data.

Results: The first results of our analysis show that consensus prediction of protein secondary structure may be improved both quantitatively and qualitatively.

Availability: Our method for consensus secondary structure prediction CoDe (Consensus formation by Decision tree learning) is based on machine learning and will be integrated into the ToPLign system (Toolbox for Protein aLignment) which can be accessed at http://cartan.gmd.de/ToPLign.html.

Contact: {mevissen,selbig}@gmd.de
A simple probabilistic scoring method for protein domain

identification
Authors: Murvai János , Vlahovic̆ek Kristian , Pongor Sándor
Published: July 2002

Summary: A simple heuristic scoring method is described for assigning sequences to known domain types based on BLAST search outputs. The scoring is based on the score distribution of the known domain groups determined from a database versus database comparison and is directly applicable to BLAST output processing.

Availability: The scoring system will be incorporated into the server www.icgeb.trieste.it/sbase/

Contact: murvai@icgeb.trieste.it; pongor@icgeb.trieste.it
Net Nearest Neighbor Analysis (NNNA) summarizes non-compensated
dinucleotides within gene sequences
Authors: Lang Dorothy M.
Published: July 2002

*Address for correspondence: 2538 Great Highway, San Francisco, CA 94116, USA.

Motivation: Net Nearest Neighbor Analysis (NNNA) measures a previously unexamined aspect of dinucleotide frequency—the non-compensated, non-repetitive dinucleotides in a sequence. Non-compensated dinucleotides are those in excess of their corresponding reverse dinucleotides.

Results: NNNA regards dinucleotides as vector quantities, making it possible to summarize any sequence as a group of circuits and tags. The results of NNNA are found to be consistent with traditional analytic methods, yet reveal additional characteristics of the sequences. The NNNA circuits and tags uniquely identify each tRNA in Escherichia coli K-12 and certain structural components of each tRNA, extract function-specific characteristics for each of the sequences involved in the formation of insulin from preinsulin, and exhibit species-specific phylogenetic characterization (demonstrated with Monilinia ).

Availability: Nearest neighbor analysis software has been available for many years and is a component of most gene analysis software packages, including the Staden Package which is available at no charge to academic users (http://www.mrc-1mb.cam.ac.uk/pubseq/).
Combinatorial motif analysis and hypothesis generation on a
genomic scale
Authors: Hu Yuh-Jyh , Sandmeyer Suzanne , McLaughlin Calvin , Kibler Dennis
Published: July 2002

3Now with Tatung University, Taipei, Taiwan. To whom correspondence should be addressed.

Motivation: Computer-assisted methods are essential for the analysis of biosequences. Gene activity is regulated in part by the binding of regulatory molecules (transcription factors) to combinations of short motifs. The goal of our analysis is the development of algorithms to identify regulatory motifs and to predict the activity of combinations of those motifs.

Approach: Our research begins with a new motif-finding method, using multiple objective functions and an improved stochastic iterative sampling strategy. Combinatorial motif analysis is accomplished by constructive induction that analyzes potential motif combinations. The hypothesis is generated by applying standard inductive learning algorithms.

Results: Tests using 10 previously identified regulons from budding yeast and 14 artificial families of sequences demonstrated the effectiveness of the new motif-finding method. Motif combination and classification approaches were used in the analysis of a sample DNA array data set derived from genome-wide gene expression analysis.

Availability: Programs will be available as executable files upon request.

Contact: yhu@ics.uci.eduor yhu@cse.ttu.edu.tw
An ontology for biological function based on molecular
interactions
Authors: Karp Peter D.
Published: July 2002

Motivations: A number of important bioinformatics computations involve computing with function: executing computational operations whose inputs or outputs are descriptions of the functions of biomolecules. Examples include performing functional queries to sequence and pathway databases, and determining functional equality to evaluate algorithms that predict function from sequence. A prerequisite to computing with function is the existence of an ontology that provides a structured semantic encoding of function. Functional bioinformatics is an emerging subfield of bioinformatics that is concerned with developing ontologies and algorithms for computing with biological function.

Results: The article explores the notion of computing with function, and explains the importance of ontologies of function to bioinformatics. The functional ontology developed for the EcoCyc database is presented. This ontology can encode a diverse array of biochemical processes, including enzymatic reactions involving small-molecule substrates and macromolecular substrates, signal-transduction processes, transport events, and mechanisms of regulation of gene expression. The ontology is validated through its use to express complex functional queries for the EcoCyc DB.

Contact: pkarp@ai.sri.com
PRoMT: inferring demographic history from DNA sequences
Authors: Wooding Stephen
Published: July 2002

Summary: I describe a parallel implementation of Rogers’ mismatch algorithm, a method for making inferences about demographic history from DNA sequence data. The program is distributed on clusters of workstations, providing a substantial speedup and low execution times on large numbers of nodes.

Availability: Source code and documentation are available at http://mombasa.anthro.utah.edu/wooding/

Contact: stephen.wooding@anthro.utah.edu
On the convergence of a clustering algorithm for protein-coding
regions in microbial genomes
Authors: Baldi Pierre
Published: July 2002

Motivation: As the number of fully sequenced prokaryotic genomes continues to grow rapidly, computational methods for reliably detecting protein-coding regions become even more important. Audic and Claverie (1998) Proc. Natl Acad. Sci. USA , 95, 10026–10031, have proposed a clustering algorithm for protein-coding regions in microbial genomes. The algorithm is based on three Markov models of order k associated with subsequences extracted from a given genome. The parameters of the three Markov models are recursively updated by the algorithm which, in simulations, always appear to converge to a unique stable partition of the genome. The partition corresponds to three kinds of regions: (1) coding on the direct strand, (2) coding on the complementary strand, (3) non-coding.

Results: Here we provide an explanation for the convergence of the algorithm by observing that it is essentially a form of the expectation maximization (EM) algorithm applied to the corresponding mixture model. We also provide a partial justification for the uniqueness of the partition based on identifiability. Other possible variations and improvements are briefly discussed.

Contact: pfbaldi@ics.uci.edu
A browser for expression data
Authors: Pocock M. R. , Hubbard T. J. P.
Published: July 2002

Summary: We have written a fully extensible Java application for visually browsing expression data, and clusters of genes or experimental conditions calculated from that data. The application requires a runtime environment for Java2.

Availability: http://www.sanger.ac.uk/Users/mrp/java/ExpressionBrowser

Contact: mrp@sanger.ac.uk
RSDB: representative protein sequence databases have high
information content
Authors: Park Jong , Holm Liisa , Heger Andreas , Chothia Cyrus
Published: July 2002

Motivation: Biological sequence databases are highly redundant for two main reasons: 1. various databanks keep redundant sequences with many identical and nearly identical sequences 2. natural sequences often have high sequence identities due to gene duplication. We wanted to know how many sequences can be removed before the databases start losing homology information. Can a database of sequences with mutual sequence identity of 50% or less provide us with the same amount of biological information as the original full database?

Results: Comparisons of nine representative sequence databases (RSDB) derived from full protein databanks showed that the information content of sequence databases is not linearly proportional to its size. An RSDB reduced to mutual sequence identity of around 50% (RSDB50) was equivalent to the original full database in terms of the effectiveness of homology searching. It was a third of the full database size which resulted in a six times faster iterative profile searching. The RSDBs are produced at different granularity for efficient homology searching.

Availability: All the RSDB files generated and the full analysis results are available through internet: ftp://ftp.ebi.ac.uk/pub/contrib/jong/RSDB/http://cyrah.ebi.ac.uk:1111/Proj/Bio/RSDB

Contact: jong@biosophy.org
The PACRAT system: an extensible WWW-based system for

correlated sequence retrieval, storage and analysis
Authors: Ray William C. , Daniels Charles J.
Published: July 2002

Summary: With PACRAT (Patterns, Analyses, Correlations. Remote Archive Testbed) we present an online database solution to the problem of accessing high-confidence sequences with specific relationships to classes of genes, such as upstream intergenic regions attached to tRNA genes. In addition the software contains a data warehousing and analysis-facilitating suite to streamline the process of analyzing the collected data. An unexpected additional benefit of the system is that it also provides easy access to sequences of lower confidence, and may be of assistance in such things as resolving ORF-call conflicts in genomic annotation projects.

Availability: An instance of the PACRAT system, implemented on a set of archaeal genomes, an experimental version of a Yeast genome database, and a random sequence database, is available for use at http://www.biosci.ohio-state.edu/~pacrat/. The system is also available for download for installation of local project-oriented sites. See the online PACRAT ‘About’ page for details.

Contact: ray@biosci.ohio-state.edu; daniels.7@osu.edu

Supplemental information: Additional information regarding the PACRAT system, including sample datasets is available linked from the ‘About’ page of the PACRAT website at: http://www.biosci.ohio-state.edu/~pacrat/.

* To whom correspondence should be addressed.
What are the baselines for protein fold recognition?
Authors: McGuffin Liam J. , Bryson Kevin , Jones David T.
Published: July 2002

Motivation: What constitutes a baseline level of success for protein fold recognition methods? As fold recognition benchmarks are often presented without any thought to the results that might be expected from a purely random set of predictions, an analysis of fold recognition baselines is long overdue. Given varying amounts of basic information about a protein—ranging from the length of the sequence to a knowledge of its secondary structure—to what extent can the fold be determined by intelligent guesswork? Can simple methods that make use of secondary structure information assign folds more accurately than purely random methods and could these methods be used to construct viable hierarchical classifications?

Experiments performed: A number of rapid automatic methods which score similarities between protein domains were devised and tested. These methods ranged from those that incorporated no secondary structure information, such as measuring absolute differences in sequence lengths, to more complex alignments of secondary structure elements. Each method was assessed for accuracy by comparison with the Class Architecture Topology Homology (CATH) classification. Methods were rated against both a random baseline fold assignment method as a lower control and FSSP as an upper control. Similarity trees were constructed in order to evaluate the accuracy of optimum methods at producing a classification of structure.

Results: Using a rigorous comparison of methods with CATH, the random fold assignment method set a lower baseline of 11% true positives allowing for 3% false positives and FSSP set an upper benchmark of 47% true positives at 3% false positives. The optimum secondary structure alignment method used here achieved 27% true positives at 3% false positives. Using a less rigorous Critical Assessment of Structure Prediction (CASP)-like sensitivity measurement the random assignment achieved 6%, FSSP—59% and the optimum secondary structure alignment method—32%. Similarity trees produced by the optimum method illustrate that these methods cannot be used alone to produce a viable protein structural classification system.

Conclusions: Simple methods that use perfect secondary structure information to assign folds cannot produce an accurate protein taxonomy, however they do provide useful baselines for fold recognition. In terms of a typical CASP assessment our results suggest that approximately 6% of targets with folds in the databases could be assigned correctly by randomly guessing, and as many as 32% could be recognised by trivial secondary structure comparison methods, given knowledge of their correct secondary structures.

Contact: David.Jones@brunel.ac.uk

* To whom correspondence should be addressed.
Nucleosome formation potential of exons, introns, and Alu repeats
Authors: Levitsky Victor G. , Podkolodnaya Olga A. , Kolchanov Nikolay A. , Podkolodny Nikolay L.
Published: July 2002

A program for constructing nucleosome formation potential profile was applied for investigation of exons, introns, and repetitive sequences. The program is available at http://wwwmgs.bionet.nsc.ru/mgs/programs/recon/. We have demonstrated that introns and repetitive sequences exhibit higher nucleosome formation potentials than exons. This fact may be explained by functional saturation of exons with genetic code, hindering the localization of efficient nucleosome positioning sites.
Promoter Extraction from GenBank (PEG): automatic extraction of
eukaryotic promoter sequences in large sets of genes
Authors: Zhang Theresa , Zhang Michael
Published: July 2002

Summary: Promoter Extraction from GenBank (PEG) extracts promoter sequences for large sets of genes using information present in GenBank. For a gene whose promoter sequence is not found, PEG will attempt to extract promoter sequences of the orthologous genes instead.

Availability: It is freely available to academic users at ftp://cshl.org/pub/science/mzhanglab/theresa/.

Contact: zhangt@cshl.org; mzhang@cshl.org

* To whom correspondence should be addressed.
Picasso: generating a covering set of protein family profiles
Authors: Heger Andreas , Holm Liisa
Published: July 2002

Motivation: Evolutionary classification leads to an economical description of protein sequence data because attributes of function and structure are inherited in protein families. This paper presents Picasso, a procedure for deriving a minimal set of protein family profiles that cover all known protein sequences.

Results: Picasso starts from highly overlapping sequence neighbourhoods revealed by all-on-all pairwise Blast alignment. Overlaps are reduced by merging sequences or parts of sequences into multiple alignments. For maximum unification, the multiple alignments must reach into the twilight zone of sequence similarity. Sensitive and selective profile–profile comparison allows unification down to about 15% pairwise sequence identity. Families unified through a short conserved sequence motif are associated with multiple full-length alignments describing different subfamilies. Domains that are mobile modules are identified based on their association with different sets of neighbours. The result is 10000 unified domain families (excluding singletons) representing functionally related proteins and recovering classical prolific domain types in high numbers. The classification is useful, for example, in developing strategies for efficient database searching and for selecting targets to complete the map of all 3-D structures.

Availability: http://www.embl-ebi.ac.uk/picasso/picasso.html

Contact: {heger,holm}@embl-ebi.ac.uk