The Experts below are selected from a list of 85995 Experts worldwide ranked by ideXlab platform
Richard Bonneau - One of the best experts on this subject based on the ideXlab platform.
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rotamer libraries for the high resolution design of β amino acid foldamers
Structure, 2017Co-Authors: Andrew M Watkins, Douglas P Renfrew, Timothy W Craven, Paramjit S. Arora, Richard BonneauAbstract:Summary β-Amino acids offer attractive opportunities to develop biologically active peptidomimetics, either employed alone or in conjunction with natural α-amino acids. Owing to their potential for unique conformational preferences that deviate considerably from α-peptide geometries, β-amino acids greatly expand the possible chemistries and physical properties available to polyamide foldamers. Complete in silico support for designing new molecules incorporating non-natural amino acids typically requires representing their side-chain conformations as sets of discrete rotamers for Model Refinement and sequence optimization. Such rotamer libraries are key components of several state-of-the-art design frameworks. Here we report the development, incorporation in to the Rosetta macromolecular Modeling suite, and validation of rotamer libraries for β 3 -amino acids.
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rotamer libraries for the high resolution design of beta amino acid foldamers
bioRxiv, 2016Co-Authors: Andrew W Watkins, Douglas P Renfrew, Timothy W Craven, Paramjit S. Arora, Richard BonneauAbstract:β-amino acids offer attractive opportunities to develop biologically active peptidomimetics, either employed alone or in conjunction with natural α-amino acids. Owing to their potential for unique conformational preferences that deviate considerably from α-peptide geometries, β-amino acids greatly expand the possible chemistries and physical properties available to polyamide foldamers. Complete in silico support for designing new molecules incorporating nonnatural amino acids typically requires representing their side chain conformations as sets of discrete rotamers for Model Refinement and sequence optimization. Such rotamer libraries are key components of several state of the art design frameworks. Here we report the development, incorporation in to the Rosetta macromolecular Modeling suite, and validation of rotamer libraries for β3-amino acids.
Laurent Krähenbühl - One of the best experts on this subject based on the ideXlab platform.
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Progressive Source and Reaction Fields for Magnetodynamic Model Refinement via a Finite Element Subproblem Method
2014Co-Authors: Patrick Dular, Mauricio Ferreira Da Luz, Patrick Kuo-peng, Laurent KrähenbühlAbstract:Magnetodynamic Models are split into a sequence of progressive finite element subproblems. The source fields generated by the active conductors alone are calculated at first via either finite elements or the Biot-Savart law. The associated reaction fields for each added magnetic and/or conductingregion, and in return for the source regions themselves when massive, are then calculated with finite element Models, possibly with initial perfect magnetic, conductor and/or impedance boundary conditions to be further corrected. The resulting subproblem method allows efficient solving of parameterized analyses thanks to a proper mesh for each subproblem and the reuse of previous solutions to be locally corrected. Accuracy improvements are obtained for local fields and global quantities, i.e. inductances, resistances, Joule losses and forces.
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Finite Element Magnetic Models via a Coupling of Subproblems of Lower Dimensions
IEEE Transactions on Magnetics, 2010Co-Authors: Patrick Dular, Ruth Sabariego, Christophe Geuzaine, Mauricio Ferreira Da Luz, Patrick Kuo-peng, Laurent KrähenbühlAbstract:Model Refinements of magnetic circuits are performed via a subdomain finite element method based on a perturbation technique. A complete problem is split into subproblems, some of lower dimensions, to allow a progression from 1-D to 3-D Models. Its solution is then expressed as the sum of the subproblem solutions supported by different meshes. A convenient and robust correction procedure is proposed allowing independent overlapping meshes for both source and reaction fields, the latter being free of cancellation error in magnetic materials. The procedure simplifies both meshing and solving processes, and quantifies the gain given by each Model Refinement on both local fields and global quantities.
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magnetic Model Refinement via a perturbation finite element method from 1d to 3d
Compel-the International Journal for Computation and Mathematics in Electrical and Electronic Engineering, 2009Co-Authors: Patrick Dular, Ruth Sabariego, Laurent KrähenbühlAbstract:Purpose - The purpose of this paper is to develop a sub-domain perturbation technique for refining magnetic circuit Models with finite element (FE) Models of different dimensions. Design/methodology/approach - A simplified problem considering ideal flux tubes is first solved, as either a 1D magnetic circuit or a simplified FE problem. Its solution is then corrected via FE perturbation problems considering the actual flux tube geometry and the exterior regions, that allow first 2D and then 3D leakage fluxes. Each of these sub-problems requires an appropriate proper volume mesh, with no need of interconnection. The solutions are transferred from one problem to the other through projections of source fields between meshes. Findings - The developed perturbation FE method allows to split magnetic circuit analyses into subproblems of lower complexity with regard to meshing operations and computational aspects. A natural progression from simple to more elaborate Models, from 1D to 3D geometries, is thus possible, while quantifying the gain given by each Model Refinement and justifying its utility. Originality/value - Approximate problems with ideal flux tubes are accurately corrected when accounting for leakage fluxes via surface sources of perturbations. The constraints involved in the subproblems are carefully defined in the resulting FE formulations, respecting their inherent strong and weak nature. As a result, an efficient and accurate computation of local fields and global quantities, i.e. flux, MMF, reluctance, is obtained. The method is naturally adapted to parameterized analyses on geometrical and material data.
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perturbation finite element method for magnetic Model Refinement of air gaps and leakage fluxes
IEEE Conference on Electromagnetic Field Computation, 2009Co-Authors: Patrick Dular, Ruth Sabariego, M V F Da Luz, Patrick Kuopeng, Laurent KrähenbühlAbstract:Model Refinements of magnetic circuits are performed via a subproblem finite element method based on a perturbation technique. An approximate problem considering ideal flux tubes and simplified air-gap Models is first solved. It gives the sources for a finite element perturbation problem considering the actual air gaps and flux tubes geometries with the exterior regions. The procedure simplifies both meshing and solving processes, and allows to quantify the gain given by each Model Refinement.
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Magnetic Model Refinement via a perturbation finite element method - from 1D to 3D
COMPEL: The International Journal for Computation and Mathematics in Electrical and Electronic Engineering, 2009Co-Authors: Patrick Dular, Ruth Sabariego, Laurent KrähenbühlAbstract:Purpose - The purpose of this paper is to develop a sub-domain perturbation technique for refining magnetic circuit Models with finite element (FE) Models of different dimensions. Design/methodology/approach - A simplified problem considering ideal flux tubes is first solved, as either a 1D magnetic circuit or a simplified FE problem. Its solution is then corrected via FE perturbation problems considering the actual flux tube geometry and the exterior regions, that allow first 2D and then 3D leakage fluxes. Each of these sub-problems requires an appropriate proper volume mesh, with no need of interconnection. The solutions are transferred from one problem to the other through projections of source fields between meshes. Findings - The developed perturbation FE method allows to split magnetic circuit analyses into subproblems of lower complexity with regard to meshing operations and computational aspects. A natural progression from simple to more elaborate Models, from 1D to 3D geometries, is thus possible, while quantifying the gain given by each Model Refinement and justifying its utility. Originality/value - Approximate problems with ideal flux tubes are accurately corrected when accounting for leakage fluxes via surface sources of perturbations. The constraints involved in the subproblems are carefully defined in the resulting FE formulations, respecting their inherent strong and weak nature. As a result, an efficient and accurate computation of local fields and global quantities, i.e. flux, MMF, reluctance, is obtained. The method is naturally adapted to parameterized analyses on geometrical and material data.
Mohamed Souhassou - One of the best experts on this subject based on the ideXlab platform.
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spin resolved atomic orbital Model Refinement for combined charge and spin density analysis application to the ytio3 perovskite
Acta Crystallographica Section A, 2019Co-Authors: Iurii Kibalin, Ariste Bolivard Voufack, Mohamed Souhassou, Beatrice Gillon, Jean Michel Gillet, Nicolas Claiser, A Gukasov, Florence PorcherAbstract:A new crystallographic method is proposed in order to refine a spin-resolved atomic orbital Model against X-ray and polarized neutron diffraction data. This atomic orbital Model is applied to the YTiO3 perovskite crystal, where orbital ordering has previously been observed by several techniques: X-ray diffraction, polarized neutron diffraction and nuclear magnetic resonance. This method gives the radial extension, orientation and population of outer atomic orbitals for each atom. The interaction term between Ti3+, Y3+ cations and O2− ligands has been estimated. The Refinement statistics obtained by means of the orbital method are compared with those obtained by the multipole Model previously published.
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spin density in ytio 3 i joint Refinement of polarized neutron diffraction and magnetic x ray diffraction data leading to insights into orbital ordering
Physical Review B, 2017Co-Authors: Iurii Kibalin, Ariste Bolivard Voufack, Beatrice Gillon, Nicolas Claiser, A Gukasov, Florence Porcher, S Gueddida, A M Bataille, F Morini, Mohamed SouhassouAbstract:Orbital ordering below 30 K was previously observed in the ferromagnetic YTiO 3 compound both by polarized neutron diffraction (PND) and x-ray magnetic diffraction (XMD). In this paper we report a procedure for the joint Refinement of a unique spin-density Model based on both PND and XMD data. The distribution of the unpaired 3d electron of titanium is clearly seen on the magnetization density reconstructed by the maximum entropy method from the PND data collection at 5 K. The Ti 3+ 3d orbital populations obtained by joint Model Refinement are discussed in terms of the orbital ordering scheme. Small but significant magnetic moments on apical oxygen O 1 and yttrium atoms are found. The agreement between experimental and theoretical spin densities obtained using density functional theory is discussed.
Iurii Kibalin - One of the best experts on this subject based on the ideXlab platform.
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spin resolved atomic orbital Model Refinement for combined charge and spin density analysis application to the ytio3 perovskite
Acta Crystallographica Section A, 2019Co-Authors: Iurii Kibalin, Ariste Bolivard Voufack, Mohamed Souhassou, Beatrice Gillon, Jean Michel Gillet, Nicolas Claiser, A Gukasov, Florence PorcherAbstract:A new crystallographic method is proposed in order to refine a spin-resolved atomic orbital Model against X-ray and polarized neutron diffraction data. This atomic orbital Model is applied to the YTiO3 perovskite crystal, where orbital ordering has previously been observed by several techniques: X-ray diffraction, polarized neutron diffraction and nuclear magnetic resonance. This method gives the radial extension, orientation and population of outer atomic orbitals for each atom. The interaction term between Ti3+, Y3+ cations and O2− ligands has been estimated. The Refinement statistics obtained by means of the orbital method are compared with those obtained by the multipole Model previously published.
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spin density in ytio 3 i joint Refinement of polarized neutron diffraction and magnetic x ray diffraction data leading to insights into orbital ordering
Physical Review B, 2017Co-Authors: Iurii Kibalin, Ariste Bolivard Voufack, Beatrice Gillon, Nicolas Claiser, A Gukasov, Florence Porcher, S Gueddida, A M Bataille, F Morini, Mohamed SouhassouAbstract:Orbital ordering below 30 K was previously observed in the ferromagnetic YTiO 3 compound both by polarized neutron diffraction (PND) and x-ray magnetic diffraction (XMD). In this paper we report a procedure for the joint Refinement of a unique spin-density Model based on both PND and XMD data. The distribution of the unpaired 3d electron of titanium is clearly seen on the magnetization density reconstructed by the maximum entropy method from the PND data collection at 5 K. The Ti 3+ 3d orbital populations obtained by joint Model Refinement are discussed in terms of the orbital ordering scheme. Small but significant magnetic moments on apical oxygen O 1 and yttrium atoms are found. The agreement between experimental and theoretical spin densities obtained using density functional theory is discussed.
Patrick Dular - One of the best experts on this subject based on the ideXlab platform.
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Progressive Source and Reaction Fields for Magnetodynamic Model Refinement via a Finite Element Subproblem Method
2014Co-Authors: Patrick Dular, Mauricio Ferreira Da Luz, Patrick Kuo-peng, Laurent KrähenbühlAbstract:Magnetodynamic Models are split into a sequence of progressive finite element subproblems. The source fields generated by the active conductors alone are calculated at first via either finite elements or the Biot-Savart law. The associated reaction fields for each added magnetic and/or conductingregion, and in return for the source regions themselves when massive, are then calculated with finite element Models, possibly with initial perfect magnetic, conductor and/or impedance boundary conditions to be further corrected. The resulting subproblem method allows efficient solving of parameterized analyses thanks to a proper mesh for each subproblem and the reuse of previous solutions to be locally corrected. Accuracy improvements are obtained for local fields and global quantities, i.e. inductances, resistances, Joule losses and forces.
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Magnetic Model Refinement via a coupling of finite element subproblems
Mathematics in Industry, 2013Co-Authors: Patrick Dular, Ruth Sabariego, Laurent Krähenbühl, Christophe GeuzaineAbstract:Model Refinements of magnetic circuits are performed via a subdomain finite element method. A complete problem is split into subproblems with overlapping meshes, to allow a progression from source to reaction fields, ideal to real flux tubes, 1-D to 3-D Models, perfect to real materials, statics to dynamics, with any coupling of these changes. Its solution is then the sum of the subproblem solutions. The procedure simplifies both meshing and solving processes, and quantifies the gain given by each Refinement on both local fields and global quantities.
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Finite Element Magnetic Models via a Coupling of Subproblems of Lower Dimensions
IEEE Transactions on Magnetics, 2010Co-Authors: Patrick Dular, Ruth Sabariego, Christophe Geuzaine, Mauricio Ferreira Da Luz, Patrick Kuo-peng, Laurent KrähenbühlAbstract:Model Refinements of magnetic circuits are performed via a subdomain finite element method based on a perturbation technique. A complete problem is split into subproblems, some of lower dimensions, to allow a progression from 1-D to 3-D Models. Its solution is then expressed as the sum of the subproblem solutions supported by different meshes. A convenient and robust correction procedure is proposed allowing independent overlapping meshes for both source and reaction fields, the latter being free of cancellation error in magnetic materials. The procedure simplifies both meshing and solving processes, and quantifies the gain given by each Model Refinement on both local fields and global quantities.
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magnetic Model Refinement via a perturbation finite element method from 1d to 3d
Compel-the International Journal for Computation and Mathematics in Electrical and Electronic Engineering, 2009Co-Authors: Patrick Dular, Ruth Sabariego, Laurent KrähenbühlAbstract:Purpose - The purpose of this paper is to develop a sub-domain perturbation technique for refining magnetic circuit Models with finite element (FE) Models of different dimensions. Design/methodology/approach - A simplified problem considering ideal flux tubes is first solved, as either a 1D magnetic circuit or a simplified FE problem. Its solution is then corrected via FE perturbation problems considering the actual flux tube geometry and the exterior regions, that allow first 2D and then 3D leakage fluxes. Each of these sub-problems requires an appropriate proper volume mesh, with no need of interconnection. The solutions are transferred from one problem to the other through projections of source fields between meshes. Findings - The developed perturbation FE method allows to split magnetic circuit analyses into subproblems of lower complexity with regard to meshing operations and computational aspects. A natural progression from simple to more elaborate Models, from 1D to 3D geometries, is thus possible, while quantifying the gain given by each Model Refinement and justifying its utility. Originality/value - Approximate problems with ideal flux tubes are accurately corrected when accounting for leakage fluxes via surface sources of perturbations. The constraints involved in the subproblems are carefully defined in the resulting FE formulations, respecting their inherent strong and weak nature. As a result, an efficient and accurate computation of local fields and global quantities, i.e. flux, MMF, reluctance, is obtained. The method is naturally adapted to parameterized analyses on geometrical and material data.
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perturbation finite element method for magnetic Model Refinement of air gaps and leakage fluxes
IEEE Conference on Electromagnetic Field Computation, 2009Co-Authors: Patrick Dular, Ruth Sabariego, M V F Da Luz, Patrick Kuopeng, Laurent KrähenbühlAbstract:Model Refinements of magnetic circuits are performed via a subproblem finite element method based on a perturbation technique. An approximate problem considering ideal flux tubes and simplified air-gap Models is first solved. It gives the sources for a finite element perturbation problem considering the actual air gaps and flux tubes geometries with the exterior regions. The procedure simplifies both meshing and solving processes, and allows to quantify the gain given by each Model Refinement.