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Background A protein's function is determined by the wide range of motions exhibited by its 3D structure. However, current experimental techniques are not able to reliably provide the level of detail required for elucidating the exact mechanisms of protein motion essential for effective drug screening and design. Computational tools are instrumental in the study of the underlying structure-function relationship. We focus on a special type of proteins called "hinge proteins" which exhibit a motion that can be interpreted as a rotation of one domain relative to another. Results This work proposes a computational approach that uses the geometric structure of a single conformation to predict the feasible motions of the protein and is founded in recent work from rigidity theory, an area of mathematics that studies flexibility properties of general structures. Given a single conformational state, our analysis predicts a relative axis of motion between two specified domains. We analyze a dataset of 19 structures known to exhibit this hinge-like behavior. For 15, the predicted axis is consistent with a motion to a second, known conformation. We present a detailed case study for three proteins whose dynamics have been well-studied in the literature: calmodulin, the LAO binding protein and the Bence-Jones protein. Conclusions Our results show that incorporating rigidity-theoretic analyses can lead to effective computational methods for understanding hinge motions in macromolecules. This initial investigation is the first step towards a new tool for probing the structure-dynamics relationship in proteins.

Efficient inverted polymer solar cell is reported upon by integrating with a small molecular 1,3,5-tri(phenyl-2-benzimi-dazolyl)-benzene (TPBi) electron extraction layer (EEL) at low processing temperature with thermal-evaporation and solution-process, resulting in the power conversion efficiencies of 3.70 and 3.47, respectively. The potential of TPBi as an efficient EEL is associated with its suitable electronic energy level for electron extraction and hole blocking from the active layer to the indium tin oxide cathode. © 2013 American Institute of Physics.

Shape descriptors have been used frequently to characterize an image for classification and retrieval tasks. For example, shape features are applied in medical imaging to classify whether an image shows a tumor or not. The patent office uses the similarity of shape to ensure that there are no infringements of copyrighted trademarks. This paper focuses on using machine learning and information retrieval techniques to classify an image as belonging to one of many classes based on its shape. In particular, we compare support vector machines, Naive Bayes, maximum entropy, linear discriminant analysis, and relevance-based language models for classification. Our results indicate that, on the standard MPEG-7 database, the relevance model outperforms the machine learning techniques and is competitive with prior work on shape-based retrieval with a classification rate of 79.8%. We also show that the relevance model can be easily extended to classify images with multiple labels. The relevance model approach may be used to perform shape retrieval using keywords. Experiments on the MPEG-7 database and a binary version of the COIL-100 database show that good retrieval performance may be obtained using a small number of examples even when there is a large amount of viewpoint change.

The enhanced performance of inverted polymer solar cells enabled by a plasmonic backscattering effect is reported upon. To produce localized surface plasmons (LSPs) at the rear anode, thermally deposited Ag nanoparticles (NPs) are embedded in the MoO 3 hole extraction layer. Upon optimizing the MoO 3/Ag NPs/MoO 3 sandwich structure, enhanced light harvesting is achieved via plasmonic backscattering into the photoactive layer of poly(3-hexylthiophene)/[6,6]-phenyl-C61 butyric acid methyl ester (P3HT:PCBM), resulting in an increase in photocurrent without sacrificing electrical properties, and ∼20% enhancement in power conversion efficiency, of 4.32% vs. 3.61% of the reference device. The performance improvement of the inverted PSCs is ascribed to the enhanced light absorption as a result of the light backscattering as well as the excitation of LSPs induced by Ag NPs embedded in the MoO 3 layer. The present method provides a promising pathway for the fabrication of high-efficiency PSCs in an inexpensive and scalable way. © 2012 The Royal Society of Chemistry.

The effect of gold nanoparticle (NP)-induced surface plasmons on the performance of polymer solar cells (PSCs) is investigated by blending the solution processable Au NP-adhered graphene oxide (Au-GO) into the anodic buffer layer of poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS). The incorporation of Au-GOs provides a simple method to introduce a plasmonic effect, which is helpful to avoid aggregation of Au NPs blended in PEDOT:PSS. The addition of Au-GOs increased the light absorption and exciton generation rate in the active layer, thereby enhancing the short-circuit current and power conversion efficiency of these PSCs. According to the experimental and simulated results, the improvement in device performance can be ascribed to the near-field enhancement arising from the excitation of the localized surface plasmon resonance of Au-GOs along the active layer/PEDOT:PSS interface. Our work indicates the great potential of Au-GOs for high-efficiency plasmonic-enhanced PSC applications. © 2012 The Royal Society of Chemistry.

The mechanism of charge recombination in transition metal oxide-based interconnectors for tandem organic photovoltaic cells is investigated, where the interconnector is composed of an abrupt heterointerface between a Mg-doped 4,7-diphenyl-1,10-phenanthroline (Mg:BPhen) layer and a MoO3 film. Based on the results of the interface energetics determined by ultraviolet photoelectron spectroscopy, as well as the corresponding device characteristics, it is revealed that the MoO3 layer pronouncedly modifies the energy level alignment of the interconnector, which is beneficial for the charge recombination process at the interface between MoO3 and the adjacent donor material for electrons and holes injected from stacked subcells. The incorporation of Mg:BPhen is essential for the conduction of the generated electrons from the bottom subcell into the conduction band of MoO3. © The Royal Society of Chemistry 2012.

Surface plasmon-enhanced electroluminescence (EL) in an organic light-emitting diode is demonstrated by incorporating the synthesized Au nanoparticles (NPs) in the hole injection layer of poly(3,4-ethylene dioxythiophene):polystyrene sulfonic acid. An increase of ∼25% in the EL intensity and efficiency are achieved for devices with Au NPs, whereas the spectral and electrical properties remain almost identical to the control device. Time-resolved photoluminescence spectroscopy reveals that the EL enhancement is ascribed to the increase in spontaneous emission rate due to the plasmonic near-field effect induced by Au NPs. © 2012 American Institute of Physics.

An efficient inverted polymer solar cell is enabled by incorporating an n-type doped wide-gap organic electron transporting layer (ETL) between the indium tin oxide cathode and the photoactive layer for electron extraction. The ETL is formed by a thermal-deposited cesium carbonate-doped 4,7-diphenyl-1,10- phenanthroline (Cs2CO3:BPhen) layer. The cell response parameters critically depended on the doping concentration and film thickness of the Cs2CO3:BPhen ETL. Inverted polymer solar cell with an optimized Cs2CO3:BPhen ETL exhibits a power conversion efficiency of 4.12% as compared to 1.34% for the device with a pristine BPhen ETL. The enhanced performance in the inverted device is associated with the favorable energy level alignment between Cs2CO3:BPhen and the electron-acceptor material, as well as increased conductivity in the doped organic ETL for electron extraction. The method reported here provides a facile approach to optimize the performance of inverted polymer solar cells in terms of easy control of film morphology, chemical composition, conductivity at low processing temperature, as well as compatibility with fabrication on flexible substrates. © 2012 Elsevier B.V. All rights reserved.

Given a weighted, undirected simple graph G = (V, E, d) (where \({d:E\to\mathbb{R}_+}\)), the distance geometry problem (DGP) is to determine an embedding \({x:V\to\mathbb{R}^K}\) such that \({\forall \{i,j\} \in E\;\|x_i-x_j\|=d_{ij}}\) . Although, in general, the DGP is solved using continuous methods, under certain conditions the search is reduced to a discrete set of points. We give one such condition as a particular order on V. We formalize the decision problem of determining whether such an order exists for a given graph and show that this problem is NP-complete in general and polynomial for fixed dimension K. We present results of computational experiments on a set of protein backbones whose natural atomic order does not satisfy the order requirements and compare our approach with some available continuous space searches.

We study the rigidity of body-and-cad frameworks which capture the majority of the geometric constraints used in 3D mechanical engineering CAD software. We present a combinatorial characterization of the generic minimal rigidity of a subset of body-and-cad frameworks in which we treat 20 of the 21 body-and-cad constraints, omitting only point-point coincidences. While the handful of classical combinatorial characterizations of rigidity focus on distance constraints between points, this is the first result simultaneously addressing coincidence, angular, and distance constraints. Our result is stated in terms of the partitioning of a graph into edge-disjoint spanning trees. This combinatorial approach provides the theoretical basis for the development of deterministic algorithms (that will not depend on numerical methods) for analyzing the rigidity of body-and-cad frameworks., Comment: 17 pages, 7 figures, version to appear in Symposium on Solid and Physical Modeling '12 and associated special issue of Computer Aided Design

Background Partner violence may interfere with a woman's ability to maintain continuous contraception and therefore contribute to increased risk of pregnancy among childbearing women. Study design A retrospective review of medical records (N=2000) was conducted from four family planning clinics in the northeast United States. Eligibility criteria for inclusion were as follows: (1) female, (2) reproductive age (menarche through menopause), (3) seeking reproductive services and (4) clinic visit for annual gynecologic exam between 2006 and 2011. Results Partner violence was documented in 28.5% (n=569) of medical records. Chronicity of violence influenced contraceptive patterns and pregnancy risk. Women reporting past year partner violence only [odds ratio (OR)=10.2] and violence during the last 5 years (OR=10.6) had the highest odds of not using a current method of contraception. Women reporting recent exposure to violence were most likely to change birth control methods and use emergency contraception (OR=6.5). Women experiencing any history of violence reported more frequent contraceptive method changes during the previous year. Conclusions A history of partner violence was common among women utilizing family planning services. The chronicity of violence appeared to play a significant role in contraceptive method changes, types of methods used and pregnancy risk. These results may be one explanation for increased pregnancies among women who experience partner violence.

Inverted polymer solar cell is developed using small molecular tris(8-hydroxyquinolinato) aluminum (Alq3) as an electron collection layer between the active layer and indium-tin-oxide bottom cathode. Upon post-processing light irradiation by simulated solar illumination, the open-circuit voltage of the inverted device increases from 0.52 V to 0.60 V, resulting in the enhancement of the power conversion efficiency from 2.54 to 3.33 with negligible change in the short-circuit current. The performance improvement is attributed to the removal of surface potential due to irradiation-induced molecular dipole reorientation in the Alq3 layer, which reduces the charge transport barrier and improves the charge collection efficiency. © 2011 American Institute of Physics.

Enhanced performance of a poly(3-hexylthiophene):(6,6)-phenyl C61 butyric acid methyl ester bulk heterojunction polymer photovoltaic cell is reported by modifying the indium tin oxide (ITO) anode with chloroform solution. Instead of the traditional UV-ozone treatment, the optimized chloroform modification on ITO anode can result in an enhancement in the power conversion efficiency of an identical device, originating from an increase in the photocurrent with negligible change in the open-circuit voltage. The performance enhancement is attributed to the work function modification of the ITO substrate through the surface incorporation of the chlorine, and thus improved charge collection efficiency. © 2011 American Institute of Physics.

An efficient inverted polymer solar cell (PSC) is reported by employing an atomic layer deposited (ALD) cadmium sulfide (CdS) film between the indium tin oxide (ITO) cathode and the photoactive layer as the electron collection layer (ECL), on which a active layer is composed of a blended poly(3-hexylthiophene) and [6,6]-phenyl C61 butyric acid methyl ester (P3HT:PCBM) bulk heterojunction. As determined by photoelectron spectroscopy, the sulfur vacancy induces an n-type semiconducting property in the ALD-grown CdS films, and suitable energy level alignment at the ITO/CdS/PCBM interface is favorable to electron extraction through CdS to the ITO electrode. With the optimized CdS film thickness, the power conversion efficiency increases to 3.33%, with short-circuit current of 8.94 mA/cm2, open-circuit voltage of 0.61 V, and fill factor of 61.1% under AM1.5G 100 mW/cm2 irradiation. © 2011 Elsevier B.V. All rights reserved.

Data exchange between different computer-aided design (CAD) systems is a major problem inhibiting information integration in collaborative engineering environments. Existing CAD data format standards such as STEP and IGES enable geometric data exchange. However, they ignore construction history, features, constraints, and other parametric-based CAD data. As a result, they are inadequate for supporting modification, extension and other important higher-level functionality when accessing an imported CAD model from another CAD system. Achieving such higher-level functionality therefore often requires a time-consuming, error-prone, tedious process of manually recreating the model in the target CAD system. Based on techniques adapted from programming language research, this paper presents an approach to exchanging parametric data between CAD systems using formally-defined conversion semantics. We have demonstrated the utility of our approach by developing a prototype implementation that automates the conversion of 2D sketches between two popular CAD systems: Pro/ENGINEER and SolidWorks. We present examples showing that our approach is able to accurately convert parametric CAD data even in cases where models were constructed using operations from the source CAD system that have no direct counterpart in the target CAD system. Although the case study focuses on 2D interoperability, our approach provides formal foundations for supporting 3D and semantic interoperability between CAD systems.Copyright © 2011 by ASME

This paper provides new worst-case bounds for the size and treewith of the result Q(D) of a conjunctive query Q to a database D. We derive bounds for the result size jQ(D)j in terms of structural properties of Q, both in the absence and in the presence of keys and functional dependencies. These bounds are based on a novel "coloring" of the query variables that associates a coloring number C(Q) to each query Q. Using this coloring number, we derive tight bounds for the size of Q(D) in case (i) no functional dependencies or keys are specified, and (ii) simple (one-attribute) keys are given. These results generalize recent size-bounds for join queries obtained by Atserias, Grohe, and Marx (FOCS 2008). An extension of our coloring technique also gives a lower bound for jQ(D)j in the general setting of a query with arbitrary functional dependencies. Our new coloring scheme also al-lows us to precisely characterize (both in the absence of keys and with simple keys) the treewidth-preserving queries the queries for which the output treewidth is bounded by a function of the input treewidth. Finally we characterize the queries that preserve the sparsity of the input in the general setting with arbitrary functional dependencies. Copyright 2009 ACM.

The proton-dependent redox chemistry of dyads comprised of a ferrocenyl electron donor directly linked to a hydroquinonyl electron donor or to a quinone electron acceptor by a single covalent bond has been characterized. Ferrocenyl-1,4-hydroquinone (2), ferrocenyl-1,4-benzoquinone (3), 3-ferrocenyl-l,2catechol (5), and the precursors ferrocenyl-1,4-dimethoxybenzene (1) and 3-ferrocenyl-l,2-dimethoxybenzene (4) were studied; also the unstable compound 3-ferrocenyl-l,2-benzoquinone (6) was observed in the spectroelectrochemistry of 5. Detailed cyclic voltammetry, coulommetry, and UV-vis-NIR spectroelectrochemistry experiments allied with EPR, NMR, and Mössbauer spectroscopy were used to probe the pH-dependent redox chemistry and electron distribution within the compounds. © 2006 American Chemical Society.