Correlation of interfacial bonding mechanism and equilibrium conductance of molecular junctions

We report theoretical investigations on the role of interfacial bonding mechanism and its resulting structures to quantum transport in molecular wires. Two bonding mechanisms for the Au-S bond in an Au(111)/1,4-benzenedithiol(BDT)/Au(111) junction were identified by ab initio calculation, confirmed by a recent experiment, which, we showed, critically control charge conduction. It was found, for Au/ BDT/Au junctions, the hydrogen atom, bound by a dative bond to the Sulfur, is energetically non-dissociative after the interface formation. The calculated conductance and junction breakdown forces of H-non-dissociative Au/BDT/Au devices are consistent with the experimental values, while the H-dissociated devices, with the interface governed by typical covalent bonding, give conductance more than an order of magnitude larger. By examining the scattering states that traverse the junctions, we have revealed that mechanical and electric properties of a junction have strong correlation with the bonding configuration. This work clearly demonstrates that the interfacial details, rather than previously believed many-body effects, is of vital importance for correctly predicting equilibrium conductance of molecular junctions; and manifests that the interfacial contact must be carefully understood for investigating quantum transport properties of molecular nanoelectronics.Comment: 18 pages, 6 figures, 2 tables, to be appeared in Frontiers of Physics 9(6), 780 (2014

Highly Conducting pi-Conjugated Molecular Junctions Covalently Bonded to Gold Electrodes

We measure electronic conductance through single conjugated molecules bonded to Au metal electrodes with direct Au-C covalent bonds using the scanning tunneling microscope based break-junction technique. We start with molecules terminated with trimethyltin end groups that cleave off in situ resulting in formation of a direct covalent sigma bond between the carbon backbone and the gold metal electrodes. The molecular carbon backbone used in this study consist of a conjugated pi-system that has one terminal methylene group on each end, which bonds to the electrodes, achieving large electronic coupling of the electrodes to the pi-system. The junctions formed with the prototypical example of 1,4-dimethylenebenzene show a conductance approaching one conductance quantum (G0 = 2e2/h). Junctions formed with methylene terminated oligophenyls with two to four phenyl units show a hundred-fold increase in conductance compared with junctions formed with amine-linked oligophenyls. The conduction mechanism for these longer oligophenyls is tunneling as they exhibit an exponential dependence of conductance with oligomer length. In addition, density functional theory based calculations for the Au-xylylene-Au junction show near-resonant transmission with a cross-over to tunneling for the longer oligomers.Comment: Accepted to the Journal of the American Chemical Society as a Communication

A hybrid-capture approach to reconstruct the phylogeny of Scleractinia (Cnidaria: Hexacorallia)

A well-supported evolutionary tree representing most major lineages of scleractinian corals is in sight with the development and application of phylogenomic approaches. Specifically, hybrid-capture techniques are shedding light on the evolution and systematics of corals. Here, we reconstructed a broad phylogeny of Scleractinia to test previous phylogenetic hypotheses inferred from a few molecular markers, in particular, the relationships among major scleractinian families and genera, and to identify clades that require further research. We analysed 449 nuclear loci from 422 corals, comprising 266 species spanning 26 families, combining data across whole genomes, transcriptomes, hybrid capture and low-coverage sequencing to reconstruct the largest phylogenomic tree of scleractinians to date. Due to the large number of loci and data completeness (less than 38% missing data), node supports were high across shallow and deep nodes with incongruences observed in only a few shallow nodes. The “Robust” and “Complex” clades were recovered unequivocally, and our analyses confirmed that Micrabaciidae Vaughan, 1905 is sister to the “Robust” clade, transforming our understanding of the “Basal” clade. Several families remain polyphyletic in our phylogeny, including Deltocyathiidae Kitahara, Cairns, Stolarski & Miller, 2012, Caryophylliidae Dana, 1846, and Coscinaraeidae Benzoni, Arrigoni, Stefani & Stolarski, 2012, and we hereby formally proposed the family name Pachyseridae Benzoni & Hoeksema to accommodate Pachyseris Milne Edwards & Haime, 1849, which is phylogenetically distinct from Agariciidae Gray, 1847. Results also revealed species misidentifications and inconsistencies within morphologically complex clades, such as Acropora Oken, 1815 and Platygyra Ehrenberg, 1834, underscoring the need for reference skeletal material and topotypes, as well as the importance of detailed taxonomic work. The approach and findings here provide much promise for further stabilising the topology of the scleractinian tree of life and advancing our understanding of coral evolution

Quantum Smoluchowski equation: Escape from a metastable state

We develop a quantum Smoluchowski equation in terms of a true probability distribution function to describe quantum Brownian motion in configuration space in large friction limit at arbitrary temperature and derive the rate of barrier crossing and tunneling within an unified scheme. The present treatment is independent of path integral formalism and is based on canonical quantization procedure.Comment: 10 pages, To appear in the Proceedings of Statphys - Kolkata I

Phylogenetic Codivergence Supports Coevolution of Mimetic Heliconius Butterflies

The unpalatable and warning-patterned butterflies _Heliconius erato_ and _Heliconius melpomene_ provide the best studied example of mutualistic Müllerian mimicry, thought – but rarely demonstrated – to promote coevolution. Some of the strongest available evidence for coevolution comes from phylogenetic codivergence, the parallel divergence of ecologically associated lineages. Early evolutionary reconstructions suggested codivergence between mimetic populations of _H. erato_ and _H. melpomene_, and this was initially hailed as the most striking known case of coevolution. However, subsequent molecular phylogenetic analyses found discrepancies in phylogenetic branching patterns and timing (topological and temporal incongruence) that argued against codivergence. We present the first explicit cophylogenetic test of codivergence between mimetic populations of _H. erato_ and _H. melpomene_, and re-examine the timing of these radiations. We find statistically significant topological congruence between multilocus coalescent population phylogenies of _H. erato_ and _H. melpomene_, supporting repeated codivergence of mimetic populations. Divergence time estimates, based on a Bayesian coalescent model, suggest that the evolutionary radiations of _H. erato_ and _H. melpomene_ occurred over the same time period, and are compatible with a series of temporally congruent codivergence events. This evidence supports a history of reciprocal coevolution between Müllerian co-mimics characterised by phylogenetic codivergence and parallel phenotypic change

Synthesis of accelerograms compatible with the Chinese GB 50011-2001 design spectrum via harmonic wavelets: artificial and historic records

A versatile approach is employed to generate artificial accelerograms which satisfy the compatibility criteria prescribed by the Chinese aseismic code provisions GB 50011-2001. In particular, a frequency dependent peak factor derived by means of appropriate Monte Carlo analyses is introduced to relate the GB 50011-2001 design spectrum to a parametrically defined evolutionary power spectrum (EPS). Special attention is given to the definition of the frequency content of the EPS in order to accommodate the mathematical form of the aforementioned design spectrum. Further, a one-to-one relationship is established between the parameter controlling the time-varying intensity of the EPS and the effective strong ground motion duration. Subsequently, an efficient auto-regressive moving-average (ARMA) filtering technique is utilized to generate ensembles of non-stationary artificial accelerograms whose average response spectrum is in a close agreement with the considered design spectrum. Furthermore, a harmonic wavelet based iterative scheme is adopted to modify these artificial signals so that a close matching of the signals’ response spectra with the GB 50011-2001 design spectrum is achieved on an individual basis. This is also done for field recorded accelerograms pertaining to the May, 2008 Wenchuan seismic event. In the process, zero-phase high-pass filtering is performed to accomplish proper baseline correction of the acquired spectrum compatible artificial and field accelerograms. Numerical results are given in a tabulated format to expedite their use in practice

Hydrophobically Modified Sulfobetaine Copolymers with Tunable Aqueous UCST through Postpolymerization Modification of Poly(pentafluorophenyl acrylate)

Polysulfobetaines, polymers carrying highly polar zwitterionic side chains, present a promising research field by virtue of their antifouling properties, hemocompatibility, and stimulus-responsive behavior. However, limited synthetic approaches exist to produce sulfobetaine copolymers comprising hydrophobic components. Postpolymerization modification of an activated ester precursor, poly(pentafluorophenyl acrylate), employing a zwitterionic amine, 3-((3-aminopropyl)dimethylammonio)propane-1-sulfonate, ADPS, is presented as a novel, one-step synthetic concept toward sulfobetaine (co)polymers. Modifications were performed in homogeneous solution using propylene carbonate as solvent with mixtures of ADPS and pentylamine, benzylamine, and dodecylamine producing a series of well-defined statistical acrylamido sulfobetaine copolymers containing hydrophobic pentyl, benzyl, or dodecylacrylamide comonomers with well-controllable molar composition as evidenced by NMR and FT-IR spectroscopy and size exclusion chromatography.This synthetic strategy was exploited to investigate, for the first time, the influence of hydrophobic modification on the upper critical solution temperature (UCST) of sulfobetaine copolymers in aqueous solution. Surprisingly, incorporation of pentyl groups was found to increase solubility over a wide composition range, whereas benzyl groups decreased solubility—an effect attributed to different entropic and enthalpic contributions of both functional groups. While UCST transitions of polysulfobetaines are typically limited to higher molar mass samples, incorporation of 0–65 mol % of benzyl groups into copolymers with molar masses of 25.5–34.5 kg/mol enabled sharp, reversible transitions from 6 to 82 °C in solutions containing up to 76 mM NaCl, as observed by optical transmittance and dynamic light scattering. Both synthesis and systematic UCST increase of sulfobetaine copolymers presented here are expected to expand the scope and applicability of these smart materials