The Experts below are selected from a list of 81 Experts worldwide ranked by ideXlab platform
Robert L Jernigan - One of the best experts on this subject based on the ideXlab platform.
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residue residue potentials with a favorable contact pair Term and an unfavorable high packing Density Term for simulation and threading
Journal of Molecular Biology, 1996Co-Authors: Sanzo Miyazawa, Robert L JerniganAbstract:Abstract Attractive inter-residue contact energies for proteins have been re-evaluated with the same assumptions and approximations used originally by us in 1985, but with a significantly larger set of protein crystal structures. An additional repulsive packing energy Term, operative at higher densities to prevent overpacking, has also been estimated for all 20 amino acids as a function of the number of contacting residues, based on their observed distributions. The two Terms of opposite sign are intended to be used together to provide an estimate of the overall energies of inter-residue interactions in simplified proteins without atomic details. To overcome the problem of how to utilize the many homologous proteins in the Protein Data Bank, a new scheme has been devised to assign different weights to each protein, based on similarities among amino acid sequences. A total of 1168 protein structures containing 1661 subunit sequences are actually used here. After the sequence weights have been applied, these correspond to an effective number of residue – residue contacts of 113,914, or about six times more than were used in the old analysis. Remarkably, the new attractive contact energies are nearly identical to the old ones, except for those with Leu and the rarer amino acids Trp and Met. The largest change found for Leu is surprising. The estimates of hydrophobicity from the contact energies for non-polar side-chains agree well with the experimental values. In an application of these contact energies, the sequences of 88 structurally distinct proteins in the Protein Data Bank are threaded at all possible positions without gaps into 189 different folds of proteins whose sequences differ from each other by at least 35% sequence identity. The native structures for 73 of 88 proteins, excluding 15 exceptional proteins such as membrane proteins, are all demonstrated to have the lowest alignment energies.
Efstathios E Michaelides - One of the best experts on this subject based on the ideXlab platform.
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the immersed boundary lattice boltzmann method for solving fluid particles interaction problems
Journal of Computational Physics, 2004Co-Authors: Zhi Gang Feng, Efstathios E MichaelidesAbstract:A new computational method, the immersed boundary-lattice Boltzmann method, is presented. This method is a combination and utilizes the most desirable features of the lattice Boltzmann and the immersed boundary methods. The method uses a regular Eulerian grid for the flow domain and a Lagrangian grid to follow particles that are contained in the flow field. The rigid body conditions for the fluid and the particles are enforced by a penalty method, which assumes that the particle boundary is deformable with a high stiffness constant. The velocity field of the fluid and particles is solved by adding a force Density Term into the lattice Boltzmann equation. This novel method preserves the advantages of LBM in tracking a group of particles and, at the same time, provides an alternative and better approach to treating the solid-fluid boundary conditions. The method also solves the problems of fluctuation of the forces and velocities on the particles when the "bounce-back" boundary conditions are applied. This method enables one to simulate problems with particle deformation and fluid-structure deformation. Its results are validated by comparison with results from other methods.
Sanzo Miyazawa - One of the best experts on this subject based on the ideXlab platform.
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residue residue potentials with a favorable contact pair Term and an unfavorable high packing Density Term for simulation and threading
Journal of Molecular Biology, 1996Co-Authors: Sanzo Miyazawa, Robert L JerniganAbstract:Abstract Attractive inter-residue contact energies for proteins have been re-evaluated with the same assumptions and approximations used originally by us in 1985, but with a significantly larger set of protein crystal structures. An additional repulsive packing energy Term, operative at higher densities to prevent overpacking, has also been estimated for all 20 amino acids as a function of the number of contacting residues, based on their observed distributions. The two Terms of opposite sign are intended to be used together to provide an estimate of the overall energies of inter-residue interactions in simplified proteins without atomic details. To overcome the problem of how to utilize the many homologous proteins in the Protein Data Bank, a new scheme has been devised to assign different weights to each protein, based on similarities among amino acid sequences. A total of 1168 protein structures containing 1661 subunit sequences are actually used here. After the sequence weights have been applied, these correspond to an effective number of residue – residue contacts of 113,914, or about six times more than were used in the old analysis. Remarkably, the new attractive contact energies are nearly identical to the old ones, except for those with Leu and the rarer amino acids Trp and Met. The largest change found for Leu is surprising. The estimates of hydrophobicity from the contact energies for non-polar side-chains agree well with the experimental values. In an application of these contact energies, the sequences of 88 structurally distinct proteins in the Protein Data Bank are threaded at all possible positions without gaps into 189 different folds of proteins whose sequences differ from each other by at least 35% sequence identity. The native structures for 73 of 88 proteins, excluding 15 exceptional proteins such as membrane proteins, are all demonstrated to have the lowest alignment energies.
Zhi Gang Feng - One of the best experts on this subject based on the ideXlab platform.
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the immersed boundary lattice boltzmann method for solving fluid particles interaction problems
Journal of Computational Physics, 2004Co-Authors: Zhi Gang Feng, Efstathios E MichaelidesAbstract:A new computational method, the immersed boundary-lattice Boltzmann method, is presented. This method is a combination and utilizes the most desirable features of the lattice Boltzmann and the immersed boundary methods. The method uses a regular Eulerian grid for the flow domain and a Lagrangian grid to follow particles that are contained in the flow field. The rigid body conditions for the fluid and the particles are enforced by a penalty method, which assumes that the particle boundary is deformable with a high stiffness constant. The velocity field of the fluid and particles is solved by adding a force Density Term into the lattice Boltzmann equation. This novel method preserves the advantages of LBM in tracking a group of particles and, at the same time, provides an alternative and better approach to treating the solid-fluid boundary conditions. The method also solves the problems of fluctuation of the forces and velocities on the particles when the "bounce-back" boundary conditions are applied. This method enables one to simulate problems with particle deformation and fluid-structure deformation. Its results are validated by comparison with results from other methods.
Qi Zhang - One of the best experts on this subject based on the ideXlab platform.
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Fluid flow through anisotropic and deformable double porosity media with ultra-low matrix permeability: A continuum framework
2020Co-Authors: Qi Zhang, Yan Xia, Shao JianliAbstract:Fractured porous media or double porosity media are common in nature. At the same time, accurate modeling remains a significant challenge due to bi-modal pore size distribution, anisotropy, multi-field coupling, and various flow patterns. This study aims to formulate a comprehensive coupled flow and solid deformation model of anisotropic and deformable double porosity media with ultra-low matrix permeability. Fluid in fissures is modeled with the generalized Darcy's law, while the liquid in much less permeable matrix follows a low-velocity non-Darcy flow characterized by threshold values and non-linearity, and fluid mass transfer is dependent on the shape factor, phase pressure difference, and interface permeability. The solid deformation relies on a thermodynamically consistent effective stress derived from the energy balance equation, and it is modeled following anisotropic poroelastic theory. Scaling analysis is performed to drop the negligible force Density Term under reasonable ranges of parameters. The discussion revolves around generic double porosity media. Numerical simulation of the initial boundary value problem reveals the capability of this framework to capture the crucial roles of coupling, anisotropy, and ultra-low matrix permeability in dictating the pressure and displacement fields.Comment: More concise submissio
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fluid flow through anisotropic and deformable double porosity media with ultra low matrix permeability a continuum framework
arXiv: Geophysics, 2020Co-Authors: Qi Zhang, Ronaldo I BorjaAbstract:Fractured porous media or double porosity media are common in nature. At the same time, accurate modeling remains a significant challenge due to bi-modal pore size distribution, anisotropy, multi-field coupling and various flow patterns. The purpose of this study is to formulate a comprehensive coupled flow and solid deformation model of anisotropic and deformable double porosity media with ultra-low matrix permeability. Fluid in fissures is modeled with the generalized Darcy's law with an equivalent permeability upscaled from the detailed geological characterizations while the liquid in much less permeable matrix follows a low velocity non-Darcy flow characterized by threshold values and non-linearity, and fluid mass transfer is dependent on the shape factor, phase pressure difference, and interface permeability. The solid deformation relies on a thermodynamically consistent effective stress derived from the energy balance equation, and it is modeled following poroelastic theory. Scaling analysis is performed to drop the negligible force Density Term under reasonable parameters' ranges. The discussion revolves around generic double porosity media. Numerical simulation of the initial boundary value problem reveals the capability of this framework to capture the crucial roles of coupling, anisotropy and ultra-low matrix permeability in dictating the pressure and displacement fields.