@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}, } @article{18016, abstract = {Understanding the electrical properties of semiconducting quantum dot devices have been limited due to the variability of their size/composition and the chemistry of ligand/electrode binding. Furthermore, to probe their electrical conduction properties and its dependence on ligand/electrode binding, measurements must be carried out at the single dot/cluster level. Herein we report scanning tunneling microscope based break junction measurements of cobalt chalcogenide clusters with Te, Se and S to probe the conductance properties. Our measured conductance trends show that the Co–Te based clusters have the highest conductance while the Co-S clusters the lowest. These trends are in very good agreement with cyclic voltammetry measurements of the first oxidation potentials and with density functional theory calculations of their HOMO–LUMO gaps.}, author = {Boardman, Brycelyn M. and Widawsky, Jonathan R. and Park, Young S. and Schenck, Christine L. and Venkataraman, Latha and Steigerwald, Michael L. and Nuckolls, Colin}, issn = {1520-5126}, journal = {Journal of the American Chemical Society}, number = {22}, pages = {8455--8457}, publisher = {American Chemical Society}, title = {{Conductance of single cobalt chalcogenide cluster junctions}}, doi = {10.1021/ja201334s}, volume = {133}, year = {2011}, } @article{18017, abstract = {The conductance of individual 1,4-benzenediamine (BDA)–Au molecular junctions is measured in different solvent environments using a scanning tunneling microscope based point-contact technique. Solvents are found to increase the conductance of these molecular junctions by as much as 50%. Using first principles calculations, we explain this increase by showing that a shift in the Au contact work function is induced by solvents binding to undercoordinated Au sites around the junction. Increasing the Au contact work function reduces the separation between the Au Fermi energy and the highest occupied molecular orbital of BDA in the junction, increasing the measured conductance. We demonstrate that the solvent-induced shift in conductance depends on the affinity of the solvent to Au binding sites and also on the induced dipole (relative to BDA) upon adsorption. Via this mechanism, molecular junction level alignment and transport properties can be statistically altered by solvent molecule binding to the contact surface.}, author = {Fatemi, V. and Kamenetska, M. and Neaton, J. B. and Venkataraman, Latha}, issn = {1530-6992}, journal = {Nano Letters}, number = {5}, pages = {1988--1992}, publisher = {American Chemical Society}, title = {{Environmental control of single-molecule junction transport}}, doi = {10.1021/nl200324e}, volume = {11}, year = {2011}, } @article{18018, abstract = {Controlling electron transport through a single-molecule device is key to the realization of nanoscale electronic components. A design requirement for single molecule electrical devices is that the molecule must be both structurally and electrically connected to the metallic electrodes. Typically, the mechanical and electrical contacts are achieved by the same chemical moiety. In this study, we demonstrate that the structural role may be played by one group (for example, a sulfide) while the electrical role may be played by another (a conjugated chain of C═C π-bonds). We can specify the electrical conductance through the molecule by modulating to which particular site on the oligoene chain the electrode binds. The result is a device that functions as a potentiometer at the single-molecule level.}, author = {Meisner, Jeffrey S. and Kamenetska, Masha and Krikorian, Markrete and Steigerwald, Michael L. and Venkataraman, Latha and Nuckolls, Colin}, issn = {1530-6992}, journal = {Nano Letters}, number = {4}, pages = {1575--1579}, publisher = {American Chemical Society}, title = {{A single-molecule potentiometer}}, doi = {10.1021/nl104411f}, volume = {11}, year = {2011}, } @article{18019, abstract = {We simultaneously measure conductance and force across nanoscale junctions. A new, two-dimensional histogram technique is introduced to statistically extract bond rupture forces from a large data set of individual junction elongation traces. For the case of Au point contacts, we find a rupture force of 1.4 ± 0.2 nN, which is in good agreement with previous measurements. We then study systematic trends for single gold metal−molecule−metal junctions for a series of molecules terminated with amine and pyridine linkers. For all molecules studied, single molecule junctions rupture at the Au−N bond. Selective binding of the linker group allows us to correlate the N−Au bond-rupture force to the molecular backbone. We find that the rupture force ranges from 0.8 nN for 4,4′ bipyridine to 0.5 nN in 1,4 diaminobenzene. These experimental results are in excellent quantitative agreement with density functional theory based adiabatic molecular junction elongation and rupture calculations.}, author = {Frei, Michael and Aradhya, Sriharsha V. and Koentopp, Max and Hybertsen, Mark S. and Venkataraman, Latha}, issn = {1530-6992}, journal = {Nano Letters}, number = {4}, pages = {1518--1523}, publisher = {American Chemical Society}, title = {{Mechanics and chemistry: Single molecule bond rupture forces correlate with molecular backbone structure}}, doi = {10.1021/nl1042903}, volume = {11}, year = {2011}, } @article{18020, abstract = {Understanding electron transport across π−π-stacked systems will help to answer fundamental questions about biochemical redox processes and benefit the design of new materials and molecular devices. Herein we employed the STM break-junction technique to measure the single-molecule conductance of multiple π−π-stacked aromatic rings. We studied electron transport through up to four stacked benzene rings held together in an eclipsed fashion via a paracyclophane scaffold. We found that the strained hydrocarbons studied herein couple directly to gold electrodes during the measurements; hence, we did not require any heteroatom binding groups as electrical contacts. Density functional theory-based calculations suggest that the gold atoms of the electrodes bind to two neighboring carbon atoms of the outermost cyclophane benzene rings in η2 fashion. Our measurements show an exponential decay of the conductance with an increasing number of stacked benzene rings, indicating a nonresonant tunneling mechanism. Furthermore, STM tip−substrate displacement data provide additional evidence that the electrodes bind to the outermost benzene rings of the π−π-stacked molecular wires.}, author = {Schneebeli, Severin T. and Kamenetska, Maria and Cheng, Zhanling and Skouta, Rachid and Friesner, Richard A. and Venkataraman, Latha and Breslow, Ronald}, issn = {1520-5126}, journal = {Journal of the American Chemical Society}, number = {7}, pages = {2136--2139}, publisher = {American Chemical Society}, title = {{Single-molecule conductance through multiple π−π-stacked benzene rings determined with direct electrode-to-benzene ring connections}}, doi = {10.1021/ja111320n}, volume = {133}, year = {2011}, } @article{18021, abstract = {Charge transport across metal–molecule interfaces has an important role in organic electronics1. Typically, chemical link groups such as thiols2 or amines3 are used to bind organic molecules to metal electrodes in single-molecule circuits, with these groups controlling both the physical structure and the electronic coupling at the interface. Direct metal–carbon coupling has been shown through C60, benzene and π-stacked benzene4,5,6,7, but ideally the carbon backbone of the molecule should be covalently bonded to the electrode without intervening link groups. Here, we demonstrate a method to create junctions with such contacts. Trimethyl tin (SnMe3)-terminated polymethylene chains are used to form single-molecule junctions with a break-junction technique2,3. Gold atoms at the electrode displace the SnMe3 linkers, leading to the formation of direct Au–C bonded single-molecule junctions with a conductance that is ∼100 times larger than analogous alkanes with most other terminations. The conductance of these Au–C bonded alkanes decreases exponentially with molecular length, with a decay constant of 0.97 per methylene, consistent with a non-resonant transport mechanism. Control experiments and ab initio calculations show that high conductances are achieved because a covalent Au–C sigma (σ) bond is formed. This offers a new method for making reproducible and highly conducting metal–organic contacts.}, author = {Cheng, Z.-L. and Skouta, R. and Vazquez, H. and Widawsky, J. R. and Schneebeli, S. and Chen, W. and Hybertsen, M. S. and Breslow, R. and Venkataraman, Latha}, issn = {1748-3395}, journal = {Nature Nanotechnology}, number = {6}, pages = {353--357}, publisher = {Springer Nature}, title = {{In situ formation of highly conducting covalent Au–C contacts for single-molecule junctions}}, doi = {10.1038/nnano.2011.66}, volume = {6}, year = {2011}, } @article{1815, abstract = {Many membrane channels and receptors exhibit adaptive, or desensitized, response to a strong sustained input stimulus, often supported by protein activity-dependent inactivation. Adaptive response is thought to be related to various cellular functions such as homeostasis and enlargement of dynamic range by background compensation. Here we study the quantitative relation between adaptive response and background compensation within a modeling framework. We show that any particular type of adaptive response is neither sufficient nor necessary for adaptive enlargement of dynamic range. In particular a precise adaptive response, where system activity is maintained at a constant level at steady state, does not ensure a large dynamic range neither in input signal nor in system output. A general mechanism for input dynamic range enlargement can come about from the activity-dependent modulation of protein responsiveness by multiple biochemical modification, regardless of the type of adaptive response it induces. Therefore hierarchical biochemical processes such as methylation and phosphorylation are natural candidates to induce this property in signaling systems.}, author = {Tamar Friedlander and Brenner, Naama}, journal = {Mathematical Biosciences and Engineering}, number = {2}, pages = {515 -- 526}, publisher = {Arizona State University}, title = {{Adaptive response and enlargement of dynamic range}}, doi = {10.3934/mbe.2011.8.515}, volume = {8}, year = {2011}, } @article{18362, abstract = {Maximally stable component detection is a very popular method for feature analysis in images, mainly due to its low computation cost and high repeatability. With the recent advance of feature-based methods in geometric shape analysis, there is significant interest in finding analogous approaches in the 3D world. In this paper, we formulate a diffusion-geometric framework for stable component detection in non-rigid 3D shapes, which can be used for geometric feature detection and description. A quantitative evaluation of our method on the SHREC’10 feature detection benchmark shows its potential as a source of high-quality features.}, author = {Litman, Roee and Bronstein, Alexander and Bronstein, Michael M.}, issn = {0097-8493}, journal = {Computers & Graphics}, number = {3}, pages = {549--560}, publisher = {Elsevier}, title = {{Diffusion-geometric maximally stable component detection in deformable shapes}}, doi = {10.1016/j.cag.2011.03.011}, volume = {35}, year = {2011}, } @article{18363, abstract = {Natural objects can be subject to various transformations yet still preserve properties that we refer to as invariants. Here, we use definitions of affine-invariant arclength for surfaces in in order to extend the set of existing non-rigid shape analysis tools. We show that by re-defining the surface metric as its equi-affine version, the surface with its modified metric tensor can be treated as a canonical Euclidean object on which most classical Euclidean processing and analysis tools can be applied. The new definition of a metric is used to extend the fast marching method technique for computing geodesic distances on surfaces, where now, the distances are defined with respect to an affine-invariant arclength. Applications of the proposed framework demonstrate its invariance, efficiency, and accuracy in shape analysis.}, author = {Raviv, Dan and Bronstein, Alexander and Bronstein, Michael M. and Kimmel, Ron and Sochen, Nir}, issn = {0097-8493}, journal = {Computers & Graphics}, number = {3}, pages = {692--697}, publisher = {Elsevier}, title = {{Affine-invariant geodesic geometry of deformable 3D shapes}}, doi = {10.1016/j.cag.2011.03.030}, volume = {35}, year = {2011}, } @inproceedings{18377, abstract = {We introduce an (equi-)affine invariant diffusion geometry by which surfaces that go through squeeze and shear transformations can still be properly analyzed. The definition of an affine invariant metric enables us to construct an invariant Laplacian from which local and global geometric structures are extracted. Applications of the proposed framework demonstrate its power in generalizing and enriching the existing set of tools for shape analysis.}, author = {Raviv, Dan and Bronstein, Michael M. and Bronstein, Alexander and Kimmel, Ron and Sochen, Nir}, booktitle = {CVPR 2011}, isbn = {9781457703942}, issn = {1063-6919}, location = {Colorado Springs, CO, United States}, publisher = {IEEE}, title = {{Affine-invariant diffusion geometry for the analysis of deformable 3D shapes}}, doi = {10.1109/cvpr.2011.5995486}, year = {2011}, } @inproceedings{18394, abstract = {In this paper we present a novel approach for fast search of handwritten Arabic word-parts within large lexicons. The algorithm runs through three steps to achieve the required results. First it warps multiple appearances of each word-part in the lexicon for embedding into the same euclidean space. The embedding is done based on the warping path produced by the Dynamic Time Warping (DTW) process while calculating the similarity distance. In the next step, all samples of different word-parts are resampled uniformly to the same size. The kd-tree structure is used to store all shapes representing word parts in the lexicon. Fast approximation of k-nearest neighbors generates a short list of candidates to be presented to the next step. In the third step, the Active-DTW [15] algorithm is used to examine each sample in the short list and give final accurate results. We demonstrate our method on a database of 23,500 images of word-parts extracted from the IFN/ENIT database [6] and 22,000 images collected from 93 writers. Our method achieves a speedup of 5 orders of magnitude over the exact method, at the cost of only a 3.8% reduction in accuracy.}, author = {Saabni, Raid and Bronstein, Alexander}, booktitle = {2011 International Conference on Document Analysis and Recognition}, isbn = {9781457713507}, issn = {2379-2140}, location = {Beijing, China}, publisher = {IEEE}, title = {{Fast key-word searching via embedding and active-DTW}}, doi = {10.1109/icdar.2011.23}, year = {2011}, } @inproceedings{18406, abstract = {Defining a suitable metric is one of the biggest challenges in deformable image fusion from different modalities. In this paper, we propose a novel approach for multi-modal metric learning in the deformable registration framework that consists of embedding data from both modalities into a common metric space whose metric is used to parametrize the similarity. Specifically, we use image representation in the Fourier/Gabor space which introduces invariance to the local pose parameters, and the Hamming metric as the target embedding space, which allows constructing the embedding using boosted learning algorithms. The resulting metric is incorporated into a discrete optimization framework. Very promising results demonstrate the potential of the proposed method.}, author = {Michel, Fabrice and Bronstein, Michael and Bronstein, Alexander and Paragios, Nikos}, booktitle = {2011 IEEE International Symposium on Biomedical Imaging: From Nano to Macro}, isbn = {9781424441280}, issn = {1945-8452}, location = { Chicago, IL, United States}, publisher = {IEEE}, title = {{Boosted metric learning for 3D multi-modal deformable registration}}, doi = {10.1109/isbi.2011.5872619}, year = {2011}, } @article{18411, abstract = {Recent works have shown the use of diffusion geometry for various pattern recognition applications, including nonrigid shape analysis. In this paper, we introduce spectral shape distance as a general framework for distribution-based shape similarity and show that two recent methods for shape similarity due to Rustamov and Mahmoudi and Sapiro are particular cases thereof.}, author = {Bronstein, Michael M and Bronstein, Alexander}, issn = {0162-8828}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, number = {5}, pages = {1065--1071}, publisher = {Institute of Electrical and Electronics Engineers}, title = {{Shape recognition with spectral distances}}, doi = {10.1109/tpami.2010.210}, volume = {33}, year = {2011}, }