8,043 research outputs found

    Folding path and funnel scenarios for two small disulfide-bridged proteins

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    Reproducible protein folding with the stochastic tunneling method

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    Geometric reasoning via internet crowdsourcing

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    The ability to interpret and reason about shapes is a peculiarly human capability that has proven difficult to reproduce algorithmically. So despite the fact that geometric modeling technology has made significant advances in the representation, display and modification of shapes, there have only been incremental advances in geometric reasoning. For example, although today's CAD systems can confidently identify isolated cylindrical holes, they struggle with more ambiguous tasks such as the identification of partial symmetries or similarities in arbitrary geometries. Even well defined problems such as 2D shape nesting or 3D packing generally resist elegant solution and rely instead on brute force explorations of a subset of the many possible solutions. Identifying economic ways to solving such problems would result in significant productivity gains across a wide range of industrial applications. The authors hypothesize that Internet Crowdsourcing might provide a pragmatic way of removing many geometric reasoning bottlenecks.This paper reports the results of experiments conducted with Amazon's mTurk site and designed to determine the feasibility of using Internet Crowdsourcing to carry out geometric reasoning tasks as well as establish some benchmark data for the quality, speed and costs of using this approach.After describing the general architecture and terminology of the mTurk Crowdsourcing system, the paper details the implementation and results of the following three investigations; 1) the identification of "Canonical" viewpoints for individual shapes, 2) the quantification of "similarity" relationships with-in collections of 3D models and 3) the efficient packing of 2D Strips into rectangular areas. The paper concludes with a discussion of the possibilities and limitations of the approach

    Validation of purdue engineering shape benchmark clusters by crowdsourcing

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    The effective organization of CAD data archives is central to PLM and consequently content based retrieval of 2D drawings and 3D models is often seen as a "holy grail" for the industry. Given this context, it is not surprising that the vision of a "Google for shape", which enables engineers to search databases of 3D models for components similar in shape to a query part, has motivated numerous researchers to investigate algorithms for computing geometric similarity. Measuring the effectiveness of the many approaches proposed has in turn lead to the creation of benchmark datasets against which researchers can compare the performance of their search engines. However to be useful the datasets used to measure the effectiveness of 3D retrieval algorithms must not only define a collection of models, but also provide a canonical specification of their relative similarity. Because the objective of shape retrieval algorithms is (typically) to retrieve groups of objects that humans perceive as "similar" these benchmark similarity relationships have (by definition) to be manually determined through inspection

    Investigation of the parallel tempering method for protein folding

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    Disorder-driven doping activation in organic semiconductors

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    Conductivity doping of organic semiconductors is an essential prerequisite for many organic devices, but the specifics of dopant activation are still not well understood. Using many-body simulations that include Coulomb interactions and dopant ionization/de-ionization events explicitly we here show significant doping efficiency even before the electron affinity of the dopant exceeds the ionization potential of the organic matrix (p-doping), similar to organic salts. We explicitly demonstrate that the ionization of weak molecular dopants in organic semiconductors is a disorder-, rather than thermally induced process. Practical implications of this finding are a weak dependence of the ionized dopant fraction on the electron affinity of the dopant, and an enhanced ionization of the weak dopants upon increasing dopant molar fraction. As a result, strategies towards dopant optimization should aim for presently neglected goals, such as the binding energy in host-dopant charge-transfer states being responsible for the number of mobile charge carriers. Insights into reported effects are provided from the analysis of the density of states, where two novel features appear upon partial dopant ionization. The findings in this work can be used in the rational design of dopant molecules and devices

    Applying the extended molecule approach to correlated electron transport: important insight from model calculations

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    Theoretical approaches of electronic transport in correlated molecules usually consider an extended molecule, which includes, in addition to the molecule itself, parts of electrodes. In the case where electron correlations remain confined within the molecule, and the extended molecule is sufficiently large, the current can be expressed by means of Laudauer-type formulae. Electron correlations are embodied into the retarded Green function of a sufficiently large but isolated extended molecule, which represents the key quantity that can be accurately determined by means of ab initio quantum chemical calculations. To exemplify these ideas, we present and analyze numerical results obtained within full CI calculations for an extended molecule described by the interacting resonant level model. Based on them, we argue that for organic electrodes the transport properties can be reliably computed, because the extended molecule can be chosen sufficiently small to be tackled within accurate ab initio methods. For metallic electrodes, larger extended molecules have to be considered in general, but a (semi-)quantitative description of the transport should still be possible particularly in the typical cases where electron transport proceeds by off-resonant tunneling. Our numerical results also demonstrate that, contrary to the usual claim, the ratio between the characteristic Coulomb strength and the level width due to molecule-electrode coupling is not the only quantity needed to assess whether electron correlation effects are strong or weak
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