The Experts below are selected from a list of 6249 Experts worldwide ranked by ideXlab platform
Jianhan Chen - One of the best experts on this subject based on the ideXlab platform.
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Accelerating the Generalized Born with Molecular Volume and Solvent Accessible Surface Area Implicit Solvent Model Using Graphics Processing Units.
Journal of computational chemistry, 2019Co-Authors: Xiping Gong, Charles L. Brooks, Mara Chiricotto, Xiaorong Liu, Erik Nordquist, Michael Feig, Jianhan ChenAbstract:The generalized Born with Molecular Volume and solvent accessible surface area (GBMV2/SA) implicit solvent model provides an accurate description of Molecular Volume and has the potential to accurately describe the conformational equilibria of structured and disordered proteins. However, its broader application has been limited by the computational cost and poor scaling in parallel computing. Here, we report an efficient implementation of both the electrostatic and nonpolar components of GBMV2/SA on graphics processing unit (GPU) within the CHARMM/OpenMM module. The GPU-GBMV2/SA is numerically equivalent to the original CPU-GBMV2/SA. The GPU acceleration offers ~60- to 70-fold speedup on a single NVIDIA TITAN X (Pascal) graphics card for Molecular dynamic simulations of both folded and unstructured proteins of various sizes. The current implementation can be further optimized to achieve even greater acceleration with minimal reduction on the numerical accuracy. The successful development of GPU-GBMV2/SA greatly facilitates its application to bioMolecular simulations and paves the way for further development of the implicit solvent methodology. © 2019 Wiley Periodicals, Inc.
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Effective Approximation of Molecular Volume Using Atom-Centered Dielectric Functions in Generalized Born Models
Journal of chemical theory and computation, 2010Co-Authors: Jianhan ChenAbstract:The generalized Born (GB) theory is a prime choice for implicit treatment of solvent that provides a favorable balance between efficiency and accuracy for reliable simulation of protein conformational equilibria. In GB, the dielectric boundary is a key physical property that needs to be properly described. While it is widely accepted that the Molecular surface (MS) should provide the most physical description, most existing GB models are based on van der Waals (vdW)-like surfaces for computational simplicity and efficiency. A simple and effective approximation to Molecular Volume is explored here using atom-centered dielectric functions within the context of a generalized Born model with simple switching (GBSW). The new model, termed GBSW/MS2, is as efficient as the original vdW-like-surface-based GBSW model, but is able to reproduce the Born radii calculated from the “exact” Poisson−Boltzmann theory with a correlation of 0.95. More importantly, examination of the potentials of mean force of hydrogen-bond...
Marco Antonio Chaer Nascimento - One of the best experts on this subject based on the ideXlab platform.
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A Molecular dynamics study of the correlations between solvent-accessible surface, Molecular Volume, and folding state.
The journal of physical chemistry. B, 2007Co-Authors: Wely B. Floriano, Gilberto B. Domont, Marco Antonio Chaer NascimentoAbstract:We analyzed the correlations between Molecular Volume, solvent-accessible surface, and folding state (secondary structure content) for unfolded conformers of alpha (holo- and apomyoglobin) and beta (retinal-binding protein) proteins and a small water-soluble alanine-rich alpha-helical peptide. Conformers with different degrees of folding were obtained using Molecular dynamics at constant temperature and pressure with implicit solvent (dielectric constant adjustment) for all four systems and with explicit solvent for the single helix peptide. Our results support the view that unfolded conformations are not necessary extended, that Volume variation is not a good indication of folding state and that the simple model of water penetrating the interior of the protein does not explain the increase in Volume upon unfolding.
Harry J. Ploehn - One of the best experts on this subject based on the ideXlab platform.
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Self-consistent field theory for polymer adsorption: Molecular Volume effects
Colloids and Surfaces A: Physicochemical and Engineering Aspects, 1994Co-Authors: Harry J. PloehnAbstract:Abstract In this work, we develop a self-consistent field model for homopolymer adsorption as a special case of a general theoretical formulation reported previously (H. J. Ploehn, Macromolecules, 27 (1994) 1617). The model treats polymer molecules as chains of continuously-distributed, idealized segments, thereby avoiding the artificiality of lattice discretization. The continuum formulation properly accounts for polymer stiffness by allowing polymer segments and solvent molecules to have differing molar Volumes. We find that the polymer Molecular weight, solvent quality, and surface adsorption energy influence the polymer density distribution and adsorbed amount in ways that are consistent with experimental observations. Varying the ratio of solvent and polymer molar Volumes alters the polymer adsorbed amount by changing the balance of local mixing enthalpy and entropy. Using no adjustable parameters, the predicted variation of adsorbed amount with polymer Molecular weight agrees well with some published experimental results. We observe unsatisfactory agreement when both the polymer Molecular weight and its solution concentration are high.
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Structure of Adsorbed Polymer Layers: Molecular Volume Effects
Macromolecules, 1994Co-Authors: Harry J. PloehnAbstract:A new continuum model for homopolymer absorption is developed within the framework of self-consistent field theory. The model differs from previous lattice-based and continuum models in that it properly accounts for polymer stiffness in the idealization of a polymer molecule as a chain of segments and it allows segments and solvent molecules to have differing partial molar Volumes. The altered balance of mixing enthalpy and entropy has quantitative implications for the structure of adsorbed polymer layers. Beginning with a heuristic development of a free energy balance for the system, functional minimisation of the free energy determines the appropriate form of the self-consistent field. The field appear in a modified diffusion equation which governs the spatial distribution of polymer
Wely B. Floriano - One of the best experts on this subject based on the ideXlab platform.
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A Molecular dynamics study of the correlations between solvent-accessible surface, Molecular Volume, and folding state.
The journal of physical chemistry. B, 2007Co-Authors: Wely B. Floriano, Gilberto B. Domont, Marco Antonio Chaer NascimentoAbstract:We analyzed the correlations between Molecular Volume, solvent-accessible surface, and folding state (secondary structure content) for unfolded conformers of alpha (holo- and apomyoglobin) and beta (retinal-binding protein) proteins and a small water-soluble alanine-rich alpha-helical peptide. Conformers with different degrees of folding were obtained using Molecular dynamics at constant temperature and pressure with implicit solvent (dielectric constant adjustment) for all four systems and with explicit solvent for the single helix peptide. Our results support the view that unfolded conformations are not necessary extended, that Volume variation is not a good indication of folding state and that the simple model of water penetrating the interior of the protein does not explain the increase in Volume upon unfolding.
Neil L. Harrison - One of the best experts on this subject based on the ideXlab platform.
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Molecular Volume determines the activity of the halogenated alkane bromoform at wild-type and mutant GABAA receptors
Brain Research, 2003Co-Authors: Thomas L. Kash, Andrew Jenkins, Neil L. HarrisonAbstract:The GABAA receptor is an important target for a variety of general anesthetics, including halogenated ethers such as isoflurane and halogenated ethers such as chloroform. Bromoform is a halogenated alkane that exhibits anesthetic properties and has been shown by X-ray crystallography to bind to model anesthetic targets. In this study we report the ability of bromoform to potentiate GABA-induced current in recombinant GABAA receptors composed of α1β2γ2s subunits. Recent studies have shown that specific point mutations in the transmembrane (TM) region of the GABAA receptor α-subunit can selectively abolish the modulatory activity of specific general anesthetics, and that Molecular Volume is a key determinant of anesthetic activity. The action of bromoform was examined in a series of mutant receptors and compared with the activity profiles of three other volatile anesthetics. The pharmacological profile of bromoform at the mutant receptors used in this study was similar to that seen with halothane, and distinct from that observed for isoflurane and chloroform. The Molecular Volume of bromoform is closest to that of halothane, and therefore our data are consistent with the idea that Molecular Volume is an important determinant of inhaled anesthetic activity at the GABAA receptor.
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Molecular Volume determines the activity of the halogenated alkane bromoform at wild-type and mutant GABA(A) receptors.
Brain research, 2003Co-Authors: Thomas L. Kash, Andrew Jenkins, Neil L. HarrisonAbstract:The GABA(A) receptor is an important target for a variety of general anesthetics, including halogenated ethers such as isoflurane and halogenated ethers such as chloroform. Bromoform is a halogenated alkane that exhibits anesthetic properties and has been shown by X-ray crystallography to bind to model anesthetic targets. In this study we report the ability of bromoform to potentiate GABA-induced current in recombinant GABA(A) receptors composed of alpha(1)beta(2)gamma(2s) subunits. Recent studies have shown that specific point mutations in the transmembrane (TM) region of the GABA(A) receptor alpha-subunit can selectively abolish the modulatory activity of specific general anesthetics, and that Molecular Volume is a key determinant of anesthetic activity. The action of bromoform was examined in a series of mutant receptors and compared with the activity profiles of three other volatile anesthetics. The pharmacological profile of bromoform at the mutant receptors used in this study was similar to that seen with halothane, and distinct from that observed for isoflurane and chloroform. The Molecular Volume of bromoform is closest to that of halothane, and therefore our data are consistent with the idea that Molecular Volume is an important determinant of inhaled anesthetic activity at the GABA(A) receptor.
