@article{3388, abstract = {Background: Fragmentation of terrestrial ecosystems has had detrimental effects on metapopulations of habitat specialists. Maculinea butterflies have been particularly affected because of their specialized lifecycles, requiring both specific food-plants and host-ants. However, the interaction between dispersal, effective population size, and long-term genetic erosion of these endangered butterflies remains unknown. Using non-destructive sampling, we investigated the genetic diversity of the last extant population of M. arion in Denmark, which experienced critically low numbers in the 1980s. Results: Using nine microsatellite markers, we show that the population is genetically impoverished compared to nearby populations in Sweden, but less so than monitoring programs suggested. Ten additional short repeat microsatellites were used to reconstruct changes in genetic diversity and population structure over the last 77 years from museum specimens. We also tested amplification efficiency in such historical samples as a function of repeat length and sample age. Low population numbers in the 1980s did not affect genetic diversity, but considerable turnover of alleles has characterized this population throughout the time-span of our analysis. Conclusions: Our results suggest that M. arion is less sensitive to genetic erosion via population bottlenecks than previously thought, and that managing clusters of high quality habitat may be key for long-term conservation.}, author = {Ugelvig, Line V and Nielsen, Per and Boomsma, Jacobus and Nash, David}, journal = {BMC Evolutionary Biology}, number = {201}, publisher = {BioMed Central}, title = {{Reconstructing eight decades of genetic variation in an isolated Danish population of the large blue butterfly Maculinea arion}}, doi = {10.1186/1471-2148-11-201}, volume = {11}, year = {2011}, } @article{3389, abstract = {Kernel canonical correlation analysis (KCCA) is a general technique for subspace learning that incorporates principal components analysis (PCA) and Fisher linear discriminant analysis (LDA) as special cases. By finding directions that maximize correlation, KCCA learns representations that are more closely tied to the underlying process that generates the data and can ignore high-variance noise directions. However, for data where acquisition in one or more modalities is expensive or otherwise limited, KCCA may suffer from small sample effects. We propose to use semi-supervised Laplacian regularization to utilize data that are present in only one modality. This approach is able to find highly correlated directions that also lie along the data manifold, resulting in a more robust estimate of correlated subspaces. Functional magnetic resonance imaging (fMRI) acquired data are naturally amenable to subspace techniques as data are well aligned. fMRI data of the human brain are a particularly interesting candidate. In this study we implemented various supervised and semi-supervised versions of KCCA on human fMRI data, with regression to single and multi-variate labels (corresponding to video content subjects viewed during the image acquisition). In each variate condition, the semi-supervised variants of KCCA performed better than the supervised variants, including a supervised variant with Laplacian regularization. We additionally analyze the weights learned by the regression in order to infer brain regions that are important to different types of visual processing.}, author = {Blaschko, Matthew and Shelton, Jacquelyn and Bartels, Andreas and Lampert, Christoph and Gretton, Arthur}, journal = {Pattern Recognition Letters}, number = {11}, pages = {1572 -- 1583}, publisher = {Elsevier}, title = {{Semi supervised kernel canonical correlation analysis with application to human fMRI}}, doi = {10.1016/j.patrec.2011.02.011}, volume = {32}, year = {2011}, } @article{3390, abstract = {What determines the genetic contribution that an individual makes to future generations? With biparental reproduction, each individual leaves a 'pedigree' of descendants, determined by the biparental relationships in the population. The pedigree of an individual constrains the lines of descent of each of its genes. An individual's reproductive value is the expected number of copies of each of its genes that is passed on to distant generations conditional on its pedigree. For the simplest model of biparental reproduction analogous to the Wright-Fisher model, an individual's reproductive value is determined within ~10 generations, independent of population size. Partial selfing and subdivision do not greatly slow this convergence. Our central result is that the probability that a gene will survive is proportional to the reproductive value of the individual that carries it, and that conditional on survival, after a few tens of generations, the distribution of the number of surviving copies is the same for all individuals, whatever their reproductive value. These results can be generalized to the joint distribution of surviving blocks of ancestral genome. Selection on unlinked loci in the genetic background may greatly increase the variance in reproductive value, but the above results nevertheless still hold. The almost linear relationship between survival probability and reproductive value also holds for weakly favored alleles. Thus, the influence of the complex pedigree of descendants on an individual's genetic contribution to the population can be summarized through a single number: its reproductive value.}, author = {Barton, Nicholas H and Etheridge, Alison}, journal = {Genetics}, number = {4}, pages = {953 -- 973}, publisher = {Genetics Society of America}, title = {{The relation between reproductive value and genetic contribution}}, doi = {10.1534/genetics.111.127555}, volume = {188}, year = {2011}, } @article{3391, abstract = {Evolutionary biology shares many concepts with statistical physics: both deal with populations, whether of molecules or organisms, and both seek to simplify evolution in very many dimensions. Often, methodologies have undergone parallel and independent development, as with stochastic methods in population genetics. Here, we discuss aspects of population genetics that have embraced methods from physics: non-equilibrium statistical mechanics, travelling waves and Monte-Carlo methods, among others, have been used to study polygenic evolution, rates of adaptation and range expansions. These applications indicate that evolutionary biology can further benefit from interactions with other areas of statistical physics; for example, by following the distribution of paths taken by a population through time}, author = {de Vladar, Harold and Barton, Nicholas H}, journal = {Trends in Ecology and Evolution}, number = {8}, pages = {424 -- 432}, publisher = {Cell Press}, title = {{The contribution of statistical physics to evolutionary biology}}, doi = {10.1016/j.tree.2011.04.002}, volume = {26}, year = {2011}, } @article{3392, abstract = {Migrating lymphocytes acquire a polarized phenotype with a leading and a trailing edge, or uropod. Although in vitro experiments in cell lines or activated primary cell cultures have established that Rho-p160 coiled-coil kinase (ROCK)-myosin II-mediated uropod contractility is required for integrin de-adhesion on two-dimensional surfaces and nuclear propulsion through narrow pores in three-dimensional matrices, less is known about the role of these two events during the recirculation of primary, nonactivated lymphocytes. Using pharmacological antagonists of ROCK and myosin II, we report that inhibition of uropod contractility blocked integrin-independent mouse T cell migration through narrow, but not large, pores in vitro. T cell crawling on chemokine-coated endothelial cells under shear was severely impaired by ROCK inhibition, whereas transendothelial migration was only reduced through endothelial cells with high, but not low, barrier properties. Using three-dimensional thick-tissue imaging and dynamic two-photon microscopy of T cell motility in lymphoid tissue, we demonstrated a significant role for uropod contractility in intraluminal crawling and transendothelial migration through lymph node, but not bone marrow, endothelial cells. Finally, we demonstrated that ICAM-1, but not anatomical constraints or integrin-independent interactions, reduced parenchymal motility of inhibitor-treated T cells within the dense lymphoid microenvironment, thus assigning context-dependent roles for uropod contraction during lymphocyte recirculation.}, author = {Soriano, Silvia and Hons, Miroslav and Schumann, Kathrin and Kumar, Varsha and Dennier, Timo and Lyck, Ruth and Sixt, Michael K and Stein, Jens}, issn = {1550-6606}, journal = {Journal of Immunology}, number = {5}, pages = {2356 -- 2364}, publisher = {American Association of Immunologists}, title = {{In vivo analysis of uropod function during physiological T cell trafficking}}, doi = {10.4049/jimmunol.1100935}, volume = {187}, year = {2011}, } @article{3393, abstract = {Unlike unconditionally advantageous “Fisherian” variants that tend to spread throughout a species range once introduced anywhere, “bistable” variants, such as chromosome translocations, have two alternative stable frequencies, absence and (near) fixation. Analogous to populations with Allee effects, bistable variants tend to increase locally only once they become sufficiently common, and their spread depends on their rate of increase averaged over all frequencies. Several proposed manipulations of insect populations, such as using Wolbachia or “engineered underdominance” to suppress vector-borne diseases, produce bistable rather than Fisherian dynamics. We synthesize and extend theoretical analyses concerning three features of their spatial behavior: rate of spread, conditions to initiate spread from a localized introduction, and wave stopping caused by variation in population densities or dispersal rates. Unlike Fisherian variants, bistable variants tend to spread spatially only for particular parameter combinations and initial conditions. Wave initiation requires introduction over an extended region, while subsequent spatial spread is slower than for Fisherian waves and can easily be halted by local spatial inhomogeneities. We present several new results, including robust sufficient conditions to initiate (and stop) spread, using a one-parameter cubic approximation applicable to several models. The results have both basic and applied implications.}, author = {Barton, Nicholas H and Turelli, Michael}, issn = {1537-5323}, journal = {American Naturalist}, number = {3}, pages = {E48 -- E75}, publisher = {The University of Chicago Press}, title = {{Spatial waves of advance with bistable dynamics: Cytoplasmic and genetic analogues of Allee effects}}, doi = {10.1086/661246}, volume = {178}, year = {2011}, } @article{3394, abstract = {Random genetic drift shifts clines in space, alters their width, and distorts their shape. Such random fluctuations complicate inferences from cline width and position. Notably, the effect of genetic drift on the expected shape of the cline is opposite to the naive (but quite common) misinterpretation of classic results on the expected cline. While random drift on average broadens the overall cline in expected allele frequency, it narrows the width of any particular cline. The opposing effects arise because locally, drift drives alleles to fixation—but fluctuations in position widen the expected cline. The effect of genetic drift can be predicted from standardized variance in allele frequencies, averaged across the habitat: 〈F〉. A cline maintained by spatially varying selection (step change) is expected to be narrower by a factor of relative to the cline in the absence of drift. The expected cline is broader by the inverse of this factor. In a tension zone maintained by underdominance, the expected cline width is narrower by about 1 – 〈F〉relative to the width in the absence of drift. Individual clines can differ substantially from the expectation, and we give quantitative predictions for the variance in cline position and width. The predictions apply to clines in almost one-dimensional circumstances such as hybrid zones in rivers, deep valleys, or along a coast line and give a guide to what patterns to expect in two dimensions.}, author = {Polechova, Jitka and Barton, Nicholas H}, journal = {Genetics}, number = {1}, pages = {227 -- 235}, publisher = {Genetics Society of America}, title = {{Genetic drift widens the expected cline but narrows the expected cline width}}, doi = {10.1534/genetics.111.129817}, volume = {189}, year = {2011}, } @article{3395, abstract = {Defining population structure and genetic diversity levels is of the utmost importance for developing efficient conservation strategies. Overfishing has caused mean annual catches of the European spiny lobster (Palinurus elephas) to decrease alarmingly along its distribution area. In this context, there is a need for comprehensive studies aiming to evaluate the genetic health of the exploited populations. The present study is based on a set of ten nuclear markers amplified in 331 individuals from ten different localities covering most of P. elephas distribution area. Samples from Atlantic and Mediterranean basins showed small but significant differences, indicating that P. elephas populations do not behave as a single panmictic unit but form two partially-overlapping groups. Despite intense overfishing, our dataset did not recover a recent bottleneck signal, and instead showed a large and stable historical effective size. This result could be accounted for by specific life-history traits (reproduction and longevity) and the limitations of molecular markers in covering recent timescales for nontemporal samples. The findings of the present study emphasize the need to integrate information on effective population sizes and life-history parameters when evaluating population connectivity levels from genetic data.}, author = {Palero, Ferran and Abello, Pere and Macpherson, Enrique and Beaumont, Mark and Pascual, Marta}, journal = {Biological Journal of the Linnean Society}, number = {2}, pages = {407 -- 418}, publisher = {Wiley-Blackwell}, title = {{Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster Palinurus elephas}}, doi = {10.1111/j.1095-8312.2011.01728.x}, volume = {104}, year = {2011}, } @article{3396, abstract = {Facial branchiomotor neurons (FBMNs) in zebrafish and mouse embryonic hindbrain undergo a characteristic tangential migration from rhombomere (r) 4, where they are born, to r6/7. Cohesion among neuroepithelial cells (NCs) has been suggested to function in FBMN migration by inhibiting FBMNs positioned in the basal neuroepithelium such that they move apically between NCs towards the midline of the neuroepithelium instead of tangentially along the basal side of the neuroepithelium towards r6/7. However, direct experimental evaluation of this hypothesis is still lacking. Here, we have used a combination of biophysical cell adhesion measurements and high-resolution time-lapse microscopy to determine the role of NC cohesion in FBMN migration. We show that reducing NC cohesion by interfering with Cadherin 2 (Cdh2) activity results in FBMNs positioned at the basal side of the neuroepithelium moving apically towards the neural tube midline instead of tangentially towards r6/7. In embryos with strongly reduced NC cohesion, ectopic apical FBMN movement frequently results in fusion of the bilateral FBMN clusters over the apical midline of the neural tube. By contrast, reducing cohesion among FBMNs by interfering with Contactin 2 (Cntn2) expression in these cells has little effect on apical FBMN movement, but reduces the fusion of the bilateral FBMN clusters in embryos with strongly diminished NC cohesion. These data provide direct experimental evidence that NC cohesion functions in tangential FBMN migration by restricting their apical movement.}, author = {Stockinger, Petra and Heisenberg, Carl-Philipp J and Maître, Jean-Léon}, journal = {Development}, number = {21}, pages = {4673 -- 4683}, publisher = {Company of Biologists}, title = {{Defective neuroepithelial cell cohesion affects tangential branchiomotor neuron migration in the zebrafish neural tube}}, doi = {10.1242/dev.071233}, volume = {138}, year = {2011}, } @article{3397, abstract = {Recent advances in microscopy techniques and biophysical measurements have provided novel insight into the molecular, cellular and biophysical basis of cell adhesion. However, comparably little is known about a core element of cell–cell adhesion—the energy of adhesion at the cell–cell contact. In this review, we discuss approaches to understand the nature and regulation of adhesion energy, and propose strategies to determine adhesion energy between cells in vitro and in vivo.}, author = {Maître, Jean-Léon and Heisenberg, Carl-Philipp J}, journal = {Current Opinion in Cell Biology}, number = {5}, pages = {508 -- 514}, publisher = {Elsevier}, title = {{The role of adhesion energy in controlling cell-cell contacts}}, doi = {10.1016/j.ceb.2011.07.004}, volume = {23}, year = {2011}, } @article{3399, abstract = {Context-dependent adjustment of mating tactics can drastically increase the mating success of behaviourally flexible animals. We used the ant Cardiocondyla obscurior as a model system to study adaptive adjustment of male mating tactics. This species shows a male diphenism of wingless fighter males and peaceful winged males. Whereas the wingless males stay and exclusively mate in the maternal colony, the mating behaviour of winged males is plastic. They copulate with female sexuals in their natal nests early in life but later disperse in search for sexuals outside. In this study, we observed the nest-leaving behaviour of winged males under different conditions and found that they adaptively adjust the timing of their dispersal to the availability of mating partners, as well as the presence, and even the type of competitors in their natal nests. In colonies with virgin female queens winged males stayed longest when they were the only male in the nest. They left earlier when mating partners were not available or when other males were present. In the presence of wingless, locally mating fighter males, winged males dispersed earlier than in the presence of docile, winged competitors. This suggests that C. obscurior males are capable of estimating their local breeding chances and adaptively adjust their dispersal behaviour in both an opportunistic and a risk-sensitive way, thus showing hitherto unknown behavioural plasticity in social insect males.}, author = {Cremer, Sylvia and Schrempf, Alexandra and Heinze, Jürgen}, journal = {PLoS One}, number = {3}, publisher = {Public Library of Science}, title = {{Competition and opportunity shape the reproductive tactics of males in the ant Cardiocondyla obscurior}}, doi = {10.1371/journal.pone.0017323}, volume = {6}, year = {2011}, } @article{3401, abstract = {The Bicoid morphogen gradient directs the patterning of cell fates along the anterior-posterior axis of the syncytial Drosophila embryo and serves as a paradigm of morphogen-mediated patterning. The simplest models of gradient formation rely on constant protein synthesis and diffusion from anteriorly localized source mRNA, coupled with uniform protein degradation. However, currently such models cannot account for all known gradient characteristics. Recent work has proposed that bicoid mRNA spatial distribution is sufficient to produce the observed protein gradient, minimizing the role of protein transport. Here, we adapt a novel method of fluorescent in situ hybridization to quantify the global spatio-temporal dynamics of bicoid mRNA particles. We determine that >90% of all bicoid mRNA is continuously present within the anterior 20% of the embryo. bicoid mRNA distribution along the body axis remains nearly unchanged despite dynamic mRNA translocation from the embryo core to the cortex. To evaluate the impact of mRNA distribution on protein gradient dynamics, we provide detailed quantitative measurements of nuclear Bicoid levels during the formation of the protein gradient. We find that gradient establishment begins 45 minutes after fertilization and that the gradient requires about 50 minutes to reach peak levels. In numerical simulations of gradient formation, we find that incorporating the actual bicoid mRNA distribution yields a closer prediction of the observed protein dynamics compared to modeling protein production from a point source at the anterior pole. We conclude that the spatial distribution of bicoid mRNA contributes to, but cannot account for, protein gradient formation, and therefore that protein movement, either active or passive, is required for gradient formation.}, author = {Little, Shawn and Tkacik, Gasper and Kneeland, Thomas and Wieschaus, Eric and Gregor, Thomas}, journal = {PLoS Biology}, number = {3}, publisher = {Public Library of Science}, title = {{The formation of the Bicoid morphogen gradient requires protein movement from anteriorly localized source}}, doi = {10.1371/journal.pbio.1000596}, volume = {9}, year = {2011}, } @article{3405, abstract = {Glutamate is the major excitatory neurotransmitter in the mammalian central nervous system and gates non-selective cation channels. The origins of glutamate receptors are not well understood as they differ structurally and functionally from simple bacterial ligand-gated ion channels. Here we report the discovery of an ionotropic glutamate receptor that combines the typical eukaryotic domain architecture with the 'TXVGYG' signature sequence of the selectivity filter found in K+ channels. This receptor exhibits functional properties intermediate between bacterial and eukaryotic glutamate-gated ion channels, suggesting a link in the evolution of ionotropic glutamate receptors.}, author = {Janovjak, Harald L and Sandoz, Guillaume and Isacoff, Ehud}, journal = {Nature Communications}, number = {232}, pages = {1 -- 6}, publisher = {Nature Publishing Group}, title = {{Modern ionotropic glutamate receptor with a K+ selectivity signature sequence}}, doi = {10.1038/ncomms1231}, volume = {2}, year = {2011}, } @article{341, abstract = {An oriented attachment and growth mechanism allows an accurate control of the size and morphology of Cu2-xS nanocrystals, from spheres and disks to tetradecahedrons and dodecahedrons. The synthesis conditions and the growth mechanism are detailed here.}, author = {Li, Wenhua and Shavel, Alexey and Guzman, Roger and Rubio Garcia, Javier and Flox, Cristina and Fan, Jiandong and Cadavid, Doris and Ibáñez, Maria and Arbiol, Jordi and Morante, Joan and Cabot, Andreu}, journal = {Chemical Communications}, number = {37}, pages = {10332 -- 10334}, publisher = {Royal Society of Chemistry (RSC) }, title = {{Morphology evolution of Cu2−xS nanoparticles: from spheres to dodecahedrons}}, doi = {10.1039/c1cc13803k}, volume = {47}, year = {2011}, } @article{14305, abstract = {Understanding the mechanism of protein folding requires a detailed knowledge of the structural properties of the barriers separating unfolded from native conformations. The S-peptide from ribonuclease S forms its α-helical structure only upon binding to the folded S-protein. We characterized the transition state for this binding-induced folding reaction at high resolution by determining the effect of site-specific backbone thioxylation and side-chain modifications on the kinetics and thermodynamics of the reaction, which allows us to monitor formation of backbone hydrogen bonds and side-chain interactions in the transition state. The experiments reveal that α-helical structure in the S-peptide is absent in the transition state of binding. Recognition between the unfolded S-peptide and the S-protein is mediated by loosely packed hydrophobic side-chain interactions in two well defined regions on the S-peptide. Close packing and helix formation occurs rapidly after binding. Introducing hydrophobic residues at positions outside the recognition region can drastically slow down association.}, author = {Bachmann, Annett and Wildemann, Dirk and Praetorius, Florian M and Fischer, Gunter and Kiefhaber, Thomas}, issn = {1091-6490}, journal = {PNAS}, keywords = {Multidisciplinary}, number = {10}, pages = {3952--3957}, publisher = {Proceedings of the National Academy of Sciences}, title = {{Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction}}, doi = {10.1073/pnas.1012668108}, volume = {108}, year = {2011}, } @article{1467, abstract = {We propose a general conjecture for the mixed Hodge polynomial of the generic character varieties of representations of the fundamental group of a Riemann surface of genus g to GLn(C) with fixed generic semisimple conjugacy classes at k punctures. This conjecture generalizes the Cauchy identity for Macdonald polynomials and is a common generalization of two formulas that we prove in this paper. The first is a formula for the E-polynomial of these character varieties which we obtain using the character table of GLn(Fq). We use this formula to compute the Euler characteristic of character varieties. The second formula gives the Poincaré polynomial of certain associated quiver varieties which we obtain using the character table of gln(Fq). In the last main result we prove that the Poincaré polynomials of the quiver varieties equal certain multiplicities in the tensor product of irreducible characters of GLn(Fq). As a consequence we find a curious connection between Kac-Moody algebras associated with comet-shaped, and typically wild, quivers and the representation theory of GLn(Fq).}, author = {Tamas Hausel and Letellier, Emmanuel and Rodríguez Villegas, Fernando}, journal = {Duke Mathematical Journal}, number = {2}, pages = {323 -- 400}, publisher = {Duke University Press}, title = {{Arithmetic harmonic analysis on character and quiver varieties}}, doi = {10.1215/00127094-1444258}, volume = {160}, year = {2011}, } @article{1781, abstract = {Microwave cavities with high quality factors enable coherent coupling of distant quantum systems. Virtual photons lead to a transverse interaction between qubits when they are nonresonant with the cavity but resonant with each other. We experimentally investigate the inverse scaling of the interqubit coupling with the detuning from a cavity mode and its proportionality to the qubit-cavity interaction strength. We demonstrate that the enhanced coupling at higher frequencies is mediated by multiple higher-harmonic cavity modes. Moreover, we observe dark states of the coupled qubit-qubit system and analyze their relation to the symmetry of the applied driving field at different frequencies.}, author = {Filipp, Stefan and Göppl, M and Johannes Fink and Baur, Matthias P and Bianchetti, R and Steffen, L. Kraig and Wallraff, Andreas}, journal = {Physical Review A - Atomic, Molecular, and Optical Physics}, number = {6}, publisher = {American Physical Society}, title = {{Multimode mediated qubit-qubit coupling and dark-state symmetries in circuit quantum electrodynamics}}, doi = {10.1103/PhysRevA.83.063827}, volume = {83}, year = {2011}, } @article{18012, abstract = {We report the first concurrent determination of conductance (G) and thermopower (S) of single-molecule junctions via direct measurement of electrical and thermoelectric currents using a scanning tunneling microscope-based break-junction technique. We explore several amine-Au and pyridine-Au linked molecules that are predicted to conduct through either the highest occupied molecular orbital (HOMO) or the lowest unoccupied molecular orbital (LUMO), respectively. We find that the Seebeck coefficient is negative for pyridine-Au linked LUMO-conducting junctions and positive for amine-Au linked HOMO-conducting junctions. Within the accessible temperature gradients (<30 K), we do not observe a strong dependence of the junction Seebeck coefficient on temperature. From histograms of thousands of junctions, we use the most probable Seebeck coefficient to determine a power factor, GS2, for each junction studied, and find that GS2 increases with G. Finally, we find that conductance and Seebeck coefficient values are in good quantitative agreement with our self-energy corrected density functional theory calculations.}, author = {Widawsky, Jonathan R. and Darancet, Pierre and Neaton, Jeffrey B. and Venkataraman, Latha}, issn = {1530-6992}, journal = {Nano Letters}, number = {1}, pages = {354--358}, publisher = {American Chemical Society}, title = {{Simultaneous determination of conductance and thermopower of single molecule junctions}}, doi = {10.1021/nl203634m}, volume = {12}, year = {2011}, } @article{18014, abstract = {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 σ bond between the carbon backbone and the gold metal electrodes. The molecular carbon backbone used in this study consist of a conjugated π system that has one terminal methylene group on each end, which bonds to the electrodes, achieving large electronic coupling of the electrodes to the π 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 100-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 on oligomer length. In addition, density functional theory based calculations for the Au–xylylene–Au junction show near-resonant transmission, with a crossover to tunneling for the longer oligomers.}, author = {Chen, Wenbo and Widawsky, Jonathan R. and Vázquez, Héctor and Schneebeli, Severin T. and Hybertsen, Mark S. and Breslow, Ronald and Venkataraman, Latha}, issn = {1520-5126}, journal = {Journal of the American Chemical Society}, number = {43}, pages = {17160--17163}, publisher = {American Chemical Society}, title = {{Highly conducting π-conjugated molecular junctions covalently bonded to gold electrodes}}, doi = {10.1021/ja208020j}, volume = {133}, year = {2011}, } @article{18015, abstract = {We investigate the binding and energy level alignment of 2,3,5,6-tetramethyl-1,4-benzenediamine (TMBDA) on Au(111) through a combination of helium atom scattering (HAS), X-ray photoemission (XPS), and scanning tunneling microscopy (STM). We show that TMBDA binds to step edges and to flat Au (111) terraces in a nearly flat-lying configuration. Through combination of HAS and STM data, we determine that the molecules are bound on step edges with an adsorption energy of about 1.2 eV, which is about 0.2 eV stronger than the adsorption energy we measure on flat surface. Preferential bonding to the under-coordinated Au atoms on step edges suggests that the molecules bind to Au through the nitrogen lone pair. Finally, STM measurements on TMBDA in these two different adsorption configurations show that the highest-occupied molecular orbital is deeper relative to Fermi for the more strongly bound molecules on step edges, confirming that the nitrogen bonds through charge donation to the Au.}, author = {Kamenetska, M. and Dell’Angela, M. and Widawsky, J.R. and Kladnik, G. and Verdini, A. and Cossaro, A. and Cvetko, D. and Morgante, A. and Venkataraman, Latha}, issn = {1932-7455}, journal = {The Journal of Physical Chemistry C}, number = {25}, pages = {12625--12630}, publisher = {American Chemical Society}, title = {{Structure and energy level alignment of tetramethyl benzenediamine on Au(111)}}, doi = {10.1021/jp202555d}, volume = {115}, year = {2011}, }