@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}, } @article{18433, abstract = {The computer vision and pattern recognition communities have recently witnessed a surge of feature-based methods in object recognition and image retrieval applications. These methods allow representing images as collections of “visual words” and treat them using text search approaches following the “bag of features” paradigm. In this article, we explore analogous approaches in the 3D world applied to the problem of nonrigid shape retrieval in large databases. Using multiscale diffusion heat kernels as “geometric words,” we construct compact and informative shape descriptors by means of the “bag of features” approach. We also show that considering pairs of “geometric words” (“geometric expressions”) allows creating spatially sensitive bags of features with better discriminative power. Finally, adopting metric learning approaches, we show that shapes can be efficiently represented as binary codes. Our approach achieves state-of-the-art results on the SHREC 2010 large-scale shape retrieval benchmark.}, author = {Bronstein, Alexander and Bronstein, Michael M. and Guibas, Leonidas J. and Ovsjanikov, Maks}, issn = {1557-7368}, journal = {ACM Transactions on Graphics}, number = {1}, pages = {1--20}, publisher = {Association for Computing Machinery}, title = {{Shape google: Geometric words and expressions for invariant shape retrieval}}, doi = {10.1145/1899404.1899405}, volume = {30}, year = {2011}, } @inproceedings{757, abstract = {Synchronous distributed algorithms are easier to design and prove correct than algorithms that tolerate asynchrony. Yet, in the real world, networks experience asynchrony and other timing anomalies. In this paper, we address the question of how to efficiently transform an algorithm that relies on synchronization into an algorithm that tolerates asynchronous executions. We introduce a transformation technique from synchronous algorithms to indulgent algorithms [1], which induces only a constant overhead in terms of time complexity in well-behaved executions. Our technique is based on a new abstraction we call an asynchrony detector, which the participating processes implement collectively. The resulting transformation works for a large class of colorless tasks, including consensus and set agreement. Interestingly, we also show that our technique is relevant for colored tasks, by applying it to the renaming problem, to obtain the first indulgent renaming algorithm.}, author = {Alistarh, Dan-Adrian and Gilbert, Seth and Guerraoui, Rachid and Travers, Corentin}, pages = {41 -- 52}, publisher = {Springer}, title = {{Generating fast indulgent algorithms}}, doi = {10.1007/978-3-642-17679-1_4}, volume = {6522 LNCS}, year = {2011}, } @inproceedings{759, abstract = {We study the complexity of renaming, a fundamental problem in distributed computing in which a set of processes need to pick distinct names from a given namespace. We prove an individual lower bound of Ω(k) process steps for deterministic renaming into any namespace of size sub-exponential in k, where k is the number of participants. This bound is tight: it draws an exponential separation between deterministic and randomized solutions, and implies new tight bounds for deterministic fetch-and-increment registers, queues and stacks. The proof of the bound is interesting in its own right, for it relies on the first reduction from renaming to another fundamental problem in distributed computing: mutual exclusion. We complement our individual bound with a global lower bound of Ω(k log (k/c)) on the total step complexity of renaming into a namespace of size ck, for any c ≥ 1. This applies to randomized algorithms against a strong adversary, and helps derive new global lower bounds for randomized approximate counter and fetch-and-increment implementations, all tight within logarithmic factors.}, author = {Alistarh, Dan-Adrian and Aspnes, James and Gilbert, Seth and Guerraoui, Rachid}, pages = {718 -- 727}, publisher = {IEEE}, title = {{The complexity of renaming}}, doi = {10.1109/FOCS.2011.66}, year = {2011}, } @inproceedings{760, abstract = {A randomized implementation is given of a test-and-set register with O(log log n) individual step complexity and O(n) total step complexity against an oblivious adversary. The implementation is linearizable and multi-shot, and shows an exponential complexity improvement over previous solutions designed to work against a strong adversary.}, author = {Alistarh, Dan-Adrian and Aspnes, James}, pages = {97 -- 109}, publisher = {Springer}, title = {{Sub-logarithmic test-and-set against a weak adversary}}, doi = {10.1007/978-3-642-24100-0_7}, volume = {6950 LNCS}, year = {2011}, } @inproceedings{761, abstract = {We give two new randomized algorithms for strong renaming, both of which work against an adaptive adversary in asynchronous shared memory. The first uses repeated sampling over a sequence of arrays of decreasing size to assign unique names to each of n processes with step complexity O(log3 n). The second transforms any sorting network into a strong adaptive renaming protocol, with an expected cost equal to the depth of the sorting network. Using an AKS sorting network, this gives a strong adaptive renaming algorithm with step complexity O(log k), where k is the contention in the current execution. We show this to be optimal based on a classic lower bound of Jayanti. We also show that any such strong renaming protocol can be used to build a monotone-consistent counter with logarithmic step complexity (at the cost of adding a max register) or a linearizable fetch-and-increment register (at the cost of increasing the step complexity by a logarithmic factor).}, author = {Alistarh, Dan-Adrian and Aspnes, James and Censor Hillel, Keren and Gilbert, Seth and Zadimoghaddam, Morteza}, pages = {239 -- 248}, publisher = {ACM}, title = {{Optimal-time adaptive strong renaming, with applications to counting}}, doi = {10.1145/1993806.1993850}, year = {2011}, } @article{7701, abstract = {During assembly of the Drosophila olfactory circuit, projection neuron (PN) dendrites prepattern the developing antennal lobe before the arrival of axons from their presynaptic partners, the adult olfactory receptor neurons (ORNs). We previously found that levels of transmembrane Semaphorin-1a, which acts as a receptor, instruct PN dendrite targeting along the dorsolateral-ventromedial axis. Here we show that two secreted semaphorins, Sema-2a and Sema-2b, provide spatial cues for PN dendrite targeting. Sema-2a and Sema-2b proteins are distributed in gradients opposing the Sema-1a protein gradient, and Sema-1a binds to Sema-2a-expressing cells. In Sema-2a and Sema-2b double mutants, PN dendrites that normally target dorsolaterally in the antennal lobe mistarget ventromedially, phenocopying cell-autonomous Sema-1a removal from these PNs. Cell ablation, cell-specific knockdown, and rescue experiments indicate that secreted semaphorins from degenerating larval ORN axons direct dendrite targeting. Thus, a degenerating brain structure instructs the wiring of a developing circuit through the repulsive action of secreted semaphorins.}, author = {Sweeney, Lora Beatrice Jaeger and Chou, Ya-Hui and Wu, Zhuhao and Joo, William and Komiyama, Takaki and Potter, Christopher J. and Kolodkin, Alex L. and Garcia, K. Christopher and Luo, Liqun}, issn = {0896-6273}, journal = {Neuron}, number = {5}, pages = {734--747}, publisher = {Elsevier}, title = {{Secreted semaphorins from degenerating larval ORN axons direct adult projection neuron dendrite targeting}}, doi = {10.1016/j.neuron.2011.09.026}, volume = {72}, year = {2011}, } @article{7702, abstract = {Longitudinal axon fascicles within the Drosophila embryonic CNS provide connections between body segments and are required for coordinated neural signaling along the anterior-posterior axis. We show here that establishment of select CNS longitudinal tracts and formation of precise mechanosensory afferent innervation to the same CNS region are coordinately regulated by the secreted semaphorins Sema-2a and Sema-2b. Both Sema-2a and Sema-2b utilize the same neuronal receptor, plexin B (PlexB), but serve distinct guidance functions. Localized Sema-2b attraction promotes the initial assembly of a subset of CNS longitudinal projections and subsequent targeting of chordotonal sensory afferent axons to these same longitudinal connectives, whereas broader Sema-2a repulsion serves to prevent aberrant innervation. In the absence of Sema-2b or PlexB, chordotonal afferent connectivity within the CNS is severely disrupted, resulting in specific larval behavioral deficits. These results reveal that distinct semaphorin-mediated guidance functions converge at PlexB and are critical for functional neural circuit assembly.}, author = {Wu, Zhuhao and Sweeney, Lora Beatrice Jaeger and Ayoob, Joseph C. and Chak, Kayam and Andreone, Benjamin J. and Ohyama, Tomoko and Kerr, Rex and Luo, Liqun and Zlatic, Marta and Kolodkin, Alex L.}, issn = {0896-6273}, journal = {Neuron}, number = {2}, pages = {281--298}, publisher = {Elsevier}, title = {{A combinatorial semaphorin code instructs the initial steps of sensory circuit assembly in the Drosophila CNS}}, doi = {10.1016/j.neuron.2011.02.050}, volume = {70}, year = {2011}, }