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J D Thompson

Publications and source records attributed to J D Thompson.

At least 19 recordsLinked to original sources
PubMed2006

SPINE bioinformatics and data-management aspects of high-throughput structural biology.

SPINE (Structural Proteomics In Europe) was established in 2002 as an integrated research project to develop new methods and technologies for high-throughput structural biology. Development areas were broken down into workpackages and this article gives an overview of ongoing activity in the bioinformatics workpackage. Developments cover target selection, target registration, wet and dry laboratory data management and structure annotation as they pertain to high-throughput studies. Some individual projects and developments are discussed in detail, while those that are covered elsewhere in this issue are treated more briefly. In particular, this overview focuses on the infrastructure of the software that allows the experimentalist to move projects through different areas that are crucial to high-throughput studies, leading to the collation of large data sets which are managed and eventually archived and/or deposited.

Computational Biology↗
PubMed2006

Observation of internal electron transfer in bulky allyl ytterbium complexes with substituted terpyridine ligands.

A series of new bulky allyl terpyridyl-ytterbium complexes have been synthesized to determine the effect of allyl ligands on the internal charge-transfer process that exists in these materials. Compared to the pentamethylcyclopentadienyl-ytterbocene compound Cp*2Yb(tpyCN) (nu(C(triple bond)N) = 2172 cm(-1)), the symmetrically substituted allyl complex [1,3-(SiMe3)2C3H3]2Yb(tpyCN) possesses a markedly lowered C(triple bond)N frequency of 2130 cm(-1). Furthermore, the electronic nature of these bulky allyl complexes can be tuned, as demonstrated by the C(triple bond)N frequency of the asymmetric derivatives [1-(SiMe3)C3H4]2Yb(tpyCN) and [1-(SiPh3)-3-(SiMe3)C3H3]2Yb(tpyCN) (2171 and 2164 cm(-1), respectively). The differences in these frequencies can be attributed to differences in the ligands' steric and electronic character. Single-crystal X-ray characterization of [1,3-(SiMe3)2C3H3]2Yb(tpy) reveals that the allyl moiety possesses shorter Yb-C and Yb-N bond distances than the Cp* analogue. The magnetic susceptibility data for [1,3-(SiMe3)2C3H3]2Yb(tpy) departs dramatically from the Curie law, with a room-temperature magnetic moment of 2.95 mu(B).

Journal Article↗
PubMed2006

Reversible tuning of the heavy-fermion ground state in CeCoIn5.

Cadmium doping the heavy-fermion superconductor CeCoIn(5) at the percent level acts as an electronic tuning agent, sensitively shifting the balance between superconductivity and antiferromagnetism and opening new ambient-pressure phase space in the study of heavy-fermion ground states.

Journal Article↗
PubMed2006

MAGOS: multiple alignment and modelling server.

UNLABELLED: MAGOS is a web server allowing automated protein modelling coupled to the creation of a hierarchical and annotated multiple alignment of complete sequences. MAGOS is designed for an interactive approach of structural information within the framework of the evolutionary relevance of mined and predicted sequence information. AVAILABILITY: The web server is freely available at http://pig-pbil.ibcp.fr/magos.

Algorithms↗
PubMed2006

Ytterbocene charge-transfer molecular wire complexes.

A systematic study of the novel charge-transfer [(f)14-(pi)0-(f)14 --> (f)13-(pi)2-(f)13] electronic state found in 2:1 metal-to-ligand adducts of the type [(Cp)2Yb](BL)[Yb(Cp)2] [BL = tetra(2-pyridyl)pyrazine (tppz) (1), 6',6' '-bis(2-pyridyl)-2,2':4',4'':2'',2'''-quaterpyridine (qtp) (2), 1,4-di(terpyridyl)-benzene (dtb) (3), Cp = (C5Me5)] has been conducted with the aim of determining the effects of increased Yb-Yb separation on the magnetic and electronic properties of these materials. The neutral [(f)13-(pi)2-(f)13], cationic [(f)13-(pi)1-(f)13] and dicationic [(f)13-(pi)0-(f)13] states of these complexes were studied by cyclic voltammetry, UV-vis-NIR electronic absorption spectroscopy, NMR, X-ray crystallography, and magnetic susceptibility measurements. The spectroscopic and magnetic data for the neutral bimetallic complexes is consistent with an [(f)13(pi)2(f)13] ground-state electronic configuration in which each ytterbocene fragment donates one electron to give a singlet dianionic bridging ligand with two paramagnetic Yb(III) centers. The voltammetric data demonstrate that the electronic interaction in the neutral molecular wires 1-3, as manifested in the separation between successive metal reduction waves, is large compared to analogous transition metal systems. Electronic spectra for the neutral and monocationic bimetallic species are dominated by pi-pi and pi-pi transitions, masking the f-f bands that are expected to best reflect the electronic metal-metal interactions. However, these metal-localized transitions are observed when the electrons are removed from the bridging ligand via chemical oxidation to yield the dicationic species, and they suggest very little electronic interaction between metal centers in the absence of pi electrons on the bridging ligands. Analysis of the magnetic data reveals that the qtp complex displays antiferromagnetic coupling of the type Yb(alpha)(alphabeta)Yb(beta) at approximately 13 K.

Journal Article↗
PubMed2006

Localized excitation in the hybridization gap in YbAl3.

The intermediate valence compound YbAl3 exhibits a broad magnetic excitation in the inelastic neutron scattering spectrum with characteristic energy E1 approximately 50 meV, equal to the Kondo energy (T(K) approximately 600-700 K). In the low temperature (T < T(coh) approximately 40 K) Fermi liquid state, however, a new peak in the scattering occurs at E2 approximately 33 meV, which lies in the hybridization gap that exists in this compound. We report inelastic neutron scattering results for a single-crystal sample. The scattering at energies near E1 qualitatively has the momentum (Q) dependence expected for interband scattering across the indirect gap. The scattering near E2 has a very different Q dependence: it is a weak function of Q over a large fraction of the Brillouin zone and is smallest near (1/2,1/2, 1/2). A possibility is that the peak at E2 arises from a spatially localized excitation in the hybridization gap.

Journal Article↗
PubMed2006

Pressure dependence of the Fulde-Ferrell-Larkin-Ovchinnikov state in CeCoIn5.

Pressure studies of the thermodynamics of CeCoIn5 under magnetic fields H parallel to c and H parallel to ab have been made up to P = 1.34 GPa. We recorded the signature of the Fulde-Ferrell-Larkin-Ovchinnikov (FFLO) state for all pressures when H parallel to ab. Also remarkably, the FFLO regime suddenly expands for P = 1.34 GPa. With the help of a microscopic theory for d-wave superconductivity, we have extracted the gyromagnetic ratio g and the Fermi velocities nu(a) and nu(c). Our study is the first evidence for the existence of the FFLO state away from the influence of the antiferromagnetic fluctuations. We find a close parallel between the T-P phase diagram of CeCoIn5 and the T-x phase diagram of the high-Tc cuprates, where x is the hole concentration.

Journal Article↗
PubMed2006

Structure of Ce2RhIn8: an example of complementary use of high-resolution neutron powder diffraction and reciprocal-space mapping to study complex materials.

The room-temperature crystal structure of the heavy fermion antiferromagnet Ce2RhIn8, dicerium rhodium octaindide, has been studied by a combination of high-resolution synchrotron X-ray reciprocal-space mapping of single crystals and high-resolution time-of-flight neutron powder diffraction. The structure is disordered, exhibiting a complex interplay of non-periodic, partially correlated planar defects, coexistence and segregation of polytypic phases (induced by periodic planar ;defects'), mosaicity (i.e. domain misalignment) and non-uniform strain. These effects evolve as a function of temperature in a complicated way, but they remain down to low temperatures. The room-temperature diffraction data are best represented by a complex mixture of two polytypic phases, which are affected by non-periodic, partially correlated planar defects, differ slightly in their tetragonal structures, and exhibit different mosaicities and strain values. Therefore, Ce2RhIn8 approaches the paracrystalline state, rather than the classic crystalline state and thus several of the concepts of conventional single-crystal crystallography are inapplicable. The structural results are discussed in the context of the role of disorder in the heavy-fermion state and in the interplay between superconductivity and magnetism.

Journal Article↗
PubMed2006

Hidden magnetism and quantum criticality in the heavy fermion superconductor CeRhIn5.

With only a few exceptions that are well understood, conventional superconductivity does not coexist with long-range magnetic order (for example, ref. 1). Unconventional superconductivity, on the other hand, develops near a phase boundary separating magnetically ordered and magnetically disordered phases. A maximum in the superconducting transition temperature T(c) develops where this boundary extrapolates to zero Kelvin, suggesting that fluctuations associated with this magnetic quantum-critical point are essential for unconventional superconductivity. Invariably, though, unconventional superconductivity masks the magnetic phase boundary when T < T(c), preventing proof of a magnetic quantum-critical point. Here we report specific-heat measurements of the pressure-tuned unconventional superconductor CeRhIn5 in which we find a line of quantum-phase transitions induced inside the superconducting state by an applied magnetic field. This quantum-critical line separates a phase of coexisting antiferromagnetism and superconductivity from a purely unconventional superconducting phase, and terminates at a quantum tetracritical point where the magnetic field completely suppresses superconductivity. The T --> 0 K magnetic field-pressure phase diagram of CeRhIn5 is well described with a theoretical model developed to explain field-induced magnetism in the high-T(c) copper oxides, but in which a clear delineation of quantum-phase boundaries has not been possible. These experiments establish a common relationship among hidden magnetism, quantum criticality and unconventional superconductivity in copper oxides and heavy-electron systems such as CeRhIn5.

Journal Article↗
PubMed2006

Anomalous pressure dependence of the Kadowaki-Woods ratio and crystal-field effects in mixed-valence YbInCu4.

The mixed-valence compound was investigated by electrical resistivity and ac specific heat at low temperatures and high pressures. At atmospheric pressure, its Kadowaki-Woods (KW) ratio A/gamma2 is 16 times smaller than the universal value RKW(=1.0x10(-5) microOmega.cm.mol2.K2.mJ-2), but sharply increases to 16.5RKW at 27 kbar. The pressure-induced change in the KW ratio and deviation from RKW are analyzed in terms of the change in f-orbital degeneracy N and carrier density n. This analysis is further supported by a dramatic change in residual resistivity rho0 near 25 kbar, where rho0 jumps by a factor of 7.

Journal Article↗
PubMed2005

Novel coexistence of superconductivity with two distinct magnetic orders.

The heavy fermion system exhibits properties that range from an incommensurate antiferromagnet for small to an exotic superconductor on the Ir-rich end of the phase diagram. At intermediate where antiferromagnetism coexists with superconductivity, two types of magnetic order are observed: the incommensurate one of and a new, commensurate antiferromagnetism that orders separately. The coexistence of -electron superconductivity with two distinct -electron magnetic orders is unique among unconventional superconductors, adding a new variety to the usual coexistence found in magnetic superconductors.

Journal Article↗
PubMed2005

Ligand substituent effect observed for ytterbocene 4'-cyano-2,2':6',2' '-terpyridine.

A new N-heterocyclic complex of ytterbocene (Cp(2)Yb(II), Cp = C(5)Me(5)) has been prepared by the addition of 4'-cyano-2,2':6',2' '-terpyridine (tpyCN) to Cp(2)Yb(II)(OEt(2)) in toluene to give a dark blue species designated as Cp(2)Yb(tpyCN). The effect of the electron-withdrawing group (-CN) on the redox potentials of the charge-transfer form of this complex [in which an electron is transferred from the f(14) metal center to the lowest unoccupied (pi) molecular orbital of the tpyCN ligand to give a 4f(13)-pi(1) electronic configuration] has been quantified by cyclic voltammetry. The tpyCN ligand stabilizes this configuration by 60 mV more than that in the unsubstituted tpy ligand complex and by 110 mV more than that in the unsubstituted bpy ligand complex. Magnetic susceptibility measurements corroborate the enhanced stabilization of the 4f(13)-pi(1) configuration by the substituted terpyridyl ligand complex. Furthermore, the temperature dependence of the magnetic data is most consistent with a thermally induced valence tautomeric equilibrium between this paramagnetic 4f(13)-pi(1) form that dominates near room temperature and the diamagnetic 4f(14)-pi(0) form that dominates at low temperature. Differing coordination modes for the tpyCN ligand to the ytterbocene center have also been confirmed by isolation and X-ray crystallographic characterization of complexes binding through either the cyano nitrogen of tpyCN or the three terpyridyl nitrogen atoms of tpyCN.

Journal Article↗
PubMed2005

Unconventional superconductivity in PuCoGa5.

In the Bardeen-Cooper-Schrieffer theory of superconductivity, electrons form (Cooper) pairs through an interaction mediated by vibrations in the underlying crystal structure. Like lattice vibrations, antiferromagnetic fluctuations can also produce an attractive interaction creating Cooper pairs, though with spin and angular momentum properties different from those of conventional superconductors. Such interactions have been implicated for two disparate classes of materials--the copper oxides and a set of Ce- and U-based compounds. But because their transition temperatures differ by nearly two orders of magnitude, this raises the question of whether a common pairing mechanism applies. PuCoGa5 has a transition temperature intermediate between those classes and therefore may bridge these extremes. Here we report measurements of the nuclear spin-lattice relaxation rate and Knight shift in PuCoGa5, which demonstrate that it is an unconventional superconductor with properties as expected for antiferromagnetically mediated superconductivity. Scaling of the relaxation rates among all of these materials (a feature not exhibited by their Knight shifts) establishes antiferromagnetic fluctuations as a likely mechanism for their unconventional superconductivity and suggests that related classes of exotic superconductors may yet be discovered.

Journal Article↗
PubMed2005

Superconductivity in CeCoIn5-xSnx: veil over an ordered state or novel quantum critical point?

Measurements of specific heat and electrical resistivity in magnetic fields up to 9 T along [001] and temperatures down to 50 mK of Sn-substituted CeCoIn5 are reported. The maximal -ln(T) divergence of the specific heat at the upper critical field Hc2 down to the lowest temperature characteristic of non-Fermi-liquid systems at the quantum critical point (QCP), the universal scaling of the Sommerfeld coefficient, and agreement of the data with spin-fluctuation theory provide strong evidence for quantum criticality at Hc2 for all x< or =0.12 in CeCoIn5-xSnx. These results indicate the "accidental" coincidence of the QCP located near Hc2 in pure CeCoIn5, in actuality, constitute a novel quantum critical point associated with unconventional superconductivity.

Journal Article↗
PubMed2005

GOAnno: GO annotation based on multiple alignment.

UNLABELLED: GOAnno is a web tool that automatically annotates proteins according to the Gene Ontology (GO) using evolutionary information available in hierarchized multiple alignments. GO terms present in the aligned functional subfamily can be cross-validated and propagated to obtain highly reliable predicted GO annotation based on the GOAnno algorithm. AVAILABILITY: The web tool and a reduced version for local installation are freely available at http://igbmc.u-strasbg.fr/GOAnno/GOAnno.html SUPPLEMENTARY INFORMATION: The website supplies a detailed explanation and illustration of the algorithm at http://igbmc.u-strasbg.fr/GOAnno/GOAnnoHelp.html.

Algorithms↗
PubMed2005

Novel dielectric anomaly in the hole-doped La(2)Cu(1-x)Li(x)O(4) and La(2-x)Sr(x)NiO(4) insulators: signature of an electronic glassy state.

The low-frequency dielectric response of hole-doped insulators La(2)Cu(1-x)Li(x)O(4) and La(2-x)Sr(x)NiO(4) shows a large dielectric constant epsilon(') at high temperature and a steplike drop by a factor of 100 at a material-dependent low temperature T(f). T(f) increases with frequency, and the dielectric response shows universal scaling in a Cole-Cole plot, suggesting that a charge-glass state is realized both in the cuprates and in the nickelates.

Journal Article↗
PubMed2005

Spatial structure of genetic variation and primary succession in the pioneer tree species Antirhea borbonica on La Réunion.

In habitats where colonization and extinction are recurrent, the distribution of gene frequencies among patches of suitable habitat may reflect the age structure of different populations. In this study, we quantify population genetic structure for a pioneer tree species, Antirhea borbonica, in a chrono-sequence of primary succession on the lava flows of the Piton de La Fournaise volcano (La Réunion). Using microsatellite loci and amplified fragment length polymorphism (AFLP) markers, we quantified genetic variation within and among populations for early- and late-succession populations in a landscape where extinction and recolonization are recurrent (the 'Grand Brûlé') and for late-succession populations in a more stable landscape. This study produced three main results. First, we detected no evidence that founder events increase genetic differentiation among colonizing populations; F(ST) values among early- and among late-succession populations were similar. Second, we found no evidence for isolation by distance; genetic distance was not correlated with spatial distance within and among populations. Third, F(IS) values are consistently high in all populations, despite the fact that A. borbonica populations are functionally close to dioecy and thus expected to have an outcrossing mating system. Multiple colonization events from different sources may limit differentiation among young populations and spatial isolation may enhance differentiation among late-succession populations. Ecological processes acting during colonization may create the conditions for spatial aggregation within pioneer populations, and thus contribute to the high F(IS) values.

DNA Primers↗