@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}, } @article{1863, abstract = {The Levene model is the simplest mathematical model to describe the evolution of gene frequencies in spatially subdivided populations. It provides insight into how locally varying selection promotes a population’s genetic diversity. Despite its simplicity, interesting problems have remained unsolved even in the diallelic case. In this paper we answer an open problem by establishing that for two alleles at one locus and J demes, up to 2J−1 polymorphic equilibria may coexist. We first present a proof for the case of stable monomorphisms and then show that the result also holds for protected alleles. These findings allow us to prove that any odd number (up to 2J−1) of equilibria is possible, before we extend the proof to even numbers. We conclude with some numerical results and show that for J>2, the proportion of parameter space affording this maximum is extremely small.}, author = {Sebastian Novak}, journal = {Theoretical Population Biology}, number = {3}, pages = {97 -- 101}, publisher = {Academic Press}, title = {{The number of equilibria in the diallelic Levene model with multiple demes}}, doi = {10.1016/j.tpb.2010.12.002}, volume = {79}, year = {2011}, } @article{12649, abstract = {Physically based hydrological models describe natural processes more accurately than conceptual models but require extensive data sets to produce accurate results. To identify the value of different data sets for improving the performance of the distributed hydrological model TOPKAPI we combine a multivariable validation technique with Monte Carlo simulations. The study is carried out in the snow and ice-dominated Rhonegletscher basin, as these types of mountainous basins are generally the most critical with respect to data availability and sensitivity to climate fluctuations. Each observational data set is used individually and in combination with the other data sets to determine a subset of best parameter combinations out of 10,000 Monte Carlos runs performed with randomly generated parameter sets. We validate model results against discharge, glacier mass balance, and satellite snow cover images for a 14 year time period (1994–2007). While the use of all data sets combined provides the best overall model performance (defined by the concurrent best agreement of simulated discharge, snow cover and mass balance with their respective measurements), the use of one or two variables for constraining the model results in poorer performance. Using only one data set for constraining the model glacier mass balance proved to be the most efficient observation leading to the best overall model performance. Our main result is that a combination of discharge and satellite snow cover images is best for improving model performance, since the volumetric information of discharge data and the spatial information of snow cover images are complementary.}, author = {Finger, David and Pellicciotti, Francesca and Konz, Markus and Rimkus, Stefan and Burlando, Paolo}, issn = {0043-1397}, journal = {Water Resources Research}, number = {7}, publisher = {American Geophysical Union}, title = {{The value of glacier mass balance, satellite snow cover images, and hourly discharge for improving the performance of a physically based distributed hydrological model}}, doi = {10.1029/2010wr009824}, volume = {47}, year = {2011}, } @inbook{12650, abstract = {Streamflow is a hydrological variable measured at a defined river cross-section; it spatially integrates the runoff generating processes in the contributing watershed, including precipitation and air temperature. Trends in streamflow are progressive changes in the time series of streamflow that can be detected with statistical methods and their statistical significance can be assessed. Mountainous regions are particularly vulnerable to streamflow change because of their high specific runoff and the sensitivity to the distribution of precipitation and air temperature, and the processes of snow accumulation and melt.}, author = {Molnar, Peter and Burlando, Paolo and Pellicciotti, Francesca}, booktitle = {Encyclopedia of Snow, Ice and Glaciers}, editor = {Singh, Vijay and Singh, Pratap and Haritashya, Umesh}, isbn = {978-90-481-2641-5}, issn = {1871-756X}, pages = {1084--1089}, publisher = {Springer Nature}, title = {{Streamflow Trends in Mountainous Regions}}, doi = {10.1007/978-90-481-2642-2_543}, year = {2011}, } @article{12651, abstract = {Temperature data from three Automatic Weather Stations and twelve Temperature Loggers are used to investigate the spatiotemporal variability of temperature over a glacier, its main atmospheric controls, the suitability of extrapolation techniques and their effect on melt modeling. We use data collected on Juncal Norte Glacier, central Chile, during one ablation season. We examine temporal and spatial variability in lapse rates (LRs), together with alternative statistical interpolation methods. The main control over the glacier thermal regime is the development of a katabatic boundary layer (KBL). Katabatic wind occurs at night and in the morning and is eroded in the afternoon. LRs reveal strong diurnal variability, with steeper LRs during the day when the katabatic wind weakens and shallower LRs during the night and morning. We suggest that temporally variable LRs should be used to account for the observed change. They tend to be steeper than equivalent constant LRs, and therefore result in a reduction in simulated melt compared to use of constant LRs when extrapolating from lower to higher elevations. In addition to the temporal variability, the temperature-elevation relationship varies also in space. Differences are evident between local LRs and including such variability in melt modeling affects melt simulations. Extrapolation methods based on the spatial variability of the observations after removal of the elevation trend, such as Inverse Distance Weighting or Kriging, do not seem necessary for simulations of gridded temperature data over a glacier.}, author = {Petersen, L. and Pellicciotti, Francesca}, issn = {0148-0227}, journal = {Journal of Geophysical Research: Atmospheres}, keywords = {Paleontology, Space and Planetary Science, Earth and Planetary Sciences (miscellaneous), Atmospheric Science, Earth-Surface Processes, Geochemistry and Petrology, Soil Science, Water Science and Technology, Ecology, Aquatic Science, Forestry, Oceanography, Geophysics}, number = {D23}, publisher = {American Geophysical Union}, title = {{Spatial and temporal variability of air temperature on a melting glacier: Atmospheric controls, extrapolation methods and their effect on melt modeling, Juncal Norte Glacier, Chile}}, doi = {10.1029/2011jd015842}, volume = {116}, year = {2011}, } @article{12652, abstract = {We explore the robustness and transferability of parameterizations of cloud radiative forcing used in glacier melt models at two sites in the Swiss Alps. We also look at the rationale behind some of the most commonly used approaches, and explore the relationship between cloud transmittance and several standard meteorological variables. The 2 m air-temperature diurnal range is the best predictor of variations in cloud transmittance. However, linear and exponential parameterizations can only explain 30–50% of the observed variance in computed cloud transmittance factors. We examine the impact of modelled cloud transmittance factors on both solar radiation and ablation rates computed with an enhanced temperature-index model. The melt model performance decreases when modelled radiation is used, the reduction being due to an underestimation of incoming solar radiation on clear-sky days. The model works well under overcast conditions. We also seek alternatives to the use of in situ ground data. However, outputs from an atmospheric model (2.2 km horizontal resolution) do not seem to provide an alternative to the parameterizations of cloud radiative forcing based on observations of air temperature at glacier automatic weather stations. Conversely, the correct definition of overcast conditions is important.}, author = {Pellicciotti, Francesca and Raschle, Thomas and Huerlimann, Thomas and Carenzo, Marco and Burlando, Paolo}, issn = {1727-5652}, journal = {Journal of Glaciology}, number = {202}, pages = {367--381}, publisher = {Cambridge University Press}, title = {{Transmission of solar radiation through clouds on melting glaciers: A comparison of parameterizations and their impact on melt modelling}}, doi = {10.3189/002214311796406013}, volume = {57}, year = {2011}, } @article{1299, abstract = {Recent experiments have shown that motion detection in Drosophila starts with splitting the visual input into two parallel channels encoding brightness increments (ON) or decrements (OFF). This suggests the existence of either two (ON-ON, OFF-OFF) or four (for all pairwise interactions) separate motion detectors. To decide between these possibilities, we stimulated flies using sequences of ON and OFF brightness pulses while recording from motion-sensitive tangential cells. We found direction-selective responses to sequences of same sign (ON-ON, OFF-OFF), but not of opposite sign (ON-OFF, OFF-ON), refuting the existence of four separate detectors. Based on further measurements, we propose a model that reproduces a variety of additional experimental data sets, including ones that were previously interpreted as support for four separate detectors. Our experiments and the derived model mark an important step in guiding further dissection of the fly motion detection circuit.}, author = {Eichner, Hubert and Maximilian Jösch and Schnell, Bettina and Reiff, Dierk F and Borst, Alexander}, journal = {Neuron}, number = {6}, pages = {1155 -- 1164}, publisher = {Elsevier}, title = {{Internal structure of the fly elementary motion detector}}, doi = {10.1016/j.neuron.2011.03.028}, volume = {70}, year = {2011}, } @article{1985, abstract = { In Escherichia coli, the pole-to-pole oscillation of the Min proteins directs septum formation to midcell, which is required for symmetric cell division. In vitro, protein waves emerge from the self-organization of MinD, a membrane-binding ATPase, and its activator MinE. For wave propagation, the proteins need to cycle through states of collective membrane binding and unbinding. Although MinD presumably undergoes cooperative membrane attachment, it is unclear how synchronous detachment is coordinated. We used confocal and single-molecule microscopy to elucidate the order of events during Min wave propagation. We propose that protein detachment at the rear of the wave, and the formation of the E-ring, are accomplished by two complementary processes: first, local accumulation of MinE due to rapid rebinding, leading to dynamic instability; and second, a structural change induced by membrane-interaction of MinE in an equimolar MinD-MinE (MinDE) complex, which supports the robustness of pattern formation.}, author = {Martin Loose and Fischer-Friedrich, Elisabeth and Herold, Christoph and Kruse, Karsten and Schwille, Petra }, journal = {Nature Structural and Molecular Biology}, number = {5}, pages = {577 -- 583}, publisher = {Nature Publishing Group}, title = {{Min protein patterns emerge from rapid rebinding and membrane interaction of MinE}}, doi = {10.1038/nsmb.2037}, volume = {18}, year = {2011}, }