High-T c Josephson junctions

Seidel, P.

doi:10.1533/9780857091031.3.317

Cited by 3 publications

(1 citation statement)

References 122 publications

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“…In this article, we introduce the new conformer ensemble generation tool CONFORGE ( Confor mer Ge nerator). CONFORGE is fully open-source (GNU LGPL) and available as part of the Chemical Data Processing Toolkit (CDPKit) 52 in the form of a versatile command-line tool as well as a set of classes and functions provided by CDPKit’s C++/Python API. CONFORGE aims at delivering state-of-the-art performance for all types of organic molecules in the drug-like chemical space and builds upon proven concepts and algorithms for conformer ensemble generation which were all implemented from scratch with maximum correctness, robustness, and performance in mind.…”

Section: Introductionmentioning

confidence: 99%

High-Quality Conformer Generation with CONFORGE: Algorithm and Performance Assessment

Seidel,

Permann,

Wieder

et al. 2023

J. Chem. Inf. Model.

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Knowledge of the putative bound-state conformation of a molecule is an essential prerequisite for the successful application of many computer-aided drug design methods that aim to assess or predict its capability to bind to a particular target receptor. An established approach to predict bioactive conformers in the absence of receptor structure information is to sample the low-energy conformational space of the investigated molecules and derive representative conformer ensembles that can be expected to comprise members closely resembling possible bound-state ligand conformations. The high relevance of such conformer generation functionality led to the development of a wide panel of dedicated commercial and open-source software tools throughout the last decades. Several published benchmarking studies have shown that open-source tools usually lag behind their commercial competitors in many key aspects. In this work, we introduce the open-source conformer ensemble generator CONFORGE, which aims at delivering state-of-the-art performance for all types of organic molecules in drug-like chemical space. The ability of CONFORGE and several well-known commercial and open-source conformer ensemble generators to reproduce experimental 3D structures as well as their computational efficiency and robustness has been assessed thoroughly for both typical drug-like molecules and macrocyclic structures. For small molecules, CONFORGE clearly outperformed all other tested open-source conformer generators and performed at least equally well as the evaluated commercial generators in terms of both processing speed and accuracy. In the case of macrocyclic structures, CONFORGE achieved the best average accuracy among all benchmarked generators, with RDKit’s generator coming close in second place.

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Section: Introductionmentioning

confidence: 99%

High-Quality Conformer Generation with CONFORGE: Algorithm and Performance Assessment

Seidel,

Permann,

Wieder

et al. 2023

J. Chem. Inf. Model.

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Josephson Memories

Hilgenkamp

2020

J Supercond Nov Magn

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Some Important Points of the Josephson Effect via Two Superconductors in Complex Bases

et al. 2022

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In this paper, we study the extraction of some analytical solutions to the nonlinear perturbed sine-Gordon equation with the long Josephson junction properties. The model studied was formed to observe the long Josephson junction properties separated by two superconductors. Moreover, it is also used to explain the Josephson effect arising in the highly nonlinear nature of the Josephson junctions. This provides the shunt inductances to realize a Josephson left-handed transmission line. A powerful scheme is used to extract the complex function solutions. These complex results are used to explain deeper properties of Josephson effects in the frame of impedance. Various simulations of solutions obtained in this paper are also reported.

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High-T c Josephson junctions

Cited by 3 publications

References 122 publications

High-Quality Conformer Generation with CONFORGE: Algorithm and Performance Assessment

High-Quality Conformer Generation with CONFORGE: Algorithm and Performance Assessment

Josephson Memories

Some Important Points of the Josephson Effect via Two Superconductors in Complex Bases

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