The Experts below are selected from a list of 68118 Experts worldwide ranked by ideXlab platform
Andrew J Mccammon - One of the best experts on this subject based on the ideXlab platform.
-
variational implicit solvation with poisson boltzmann theory
Journal of Chemical Theory and Computation, 2014Co-Authors: Shenggao Zhou, Litien Cheng, Joachim Dzubiella, Bo Li, Andrew J MccammonAbstract:We incorporate the Poisson–Boltzmann (PB) theory of electrostatics into our variational implicit-solvent model (VISM) for the solvation of charged molecules in an aqueous solvent. In order to numerically relax the VISM free-energy functional by our level-set method, we develop highly accurate methods for solving the dielectric PB equation and for computing the dielectric Boundary Force. We also apply our VISM-PB theory to analyze the solvent potentials of mean Force and the effect of charges on the hydrophobic hydration for some selected molecular systems. These include some single ions, two charged particles, two charged plates, and the host–guest system Cucurbit[7]uril and Bicyclo[2.2.2]octane. Our computational results show that VISM with PB theory can capture well the sensitive response of capillary evaporation to the charge in hydrophobic confinement and the polymodal hydration behavior and can provide accurate estimates of binding affinity of the host–guest system. We finally discuss several issues ...
-
level set variational implicit solvent modeling of biomolecules with the coulomb field approximation
Journal of Chemical Theory and Computation, 2012Co-Authors: Zhongming Wang, Litien Cheng, Joachim Dzubiella, Jianwei Che, Andrew J MccammonAbstract:Central in the variational implicit-solvent model (VISM) [Dzubiella, Swanson, and McCammon Phys. Rev. Lett.2006, 96, 087802 and J. Chem. Phys.2006, 124, 084905] of molecular solvation is a mean-field free-energy functional of all possible solute-solvent interfaces or dielectric boundaries. Such a functional can be minimized numerically by a level-set method to determine stable equilibrium conformations and solvation free energies. Applications to nonpolar systems have shown that the level-set VISM is efficient and leads to qualitatively and often quantitatively correct results. In particular, it is capable of capturing capillary evaporation in hydrophobic confinement and corresponding multiple equilibrium states as found in molecular dynamics (MD) simulations. In this work, we introduce into the VISM the Coulomb-field approximation of the electrostatic free energy. Such an approximation is a volume integral over an arbitrary shaped solvent region, requiring no solutions to any partial differential equations. With this approximation, we obtain the effective Boundary Force and use it as the "normal velocity" in the level-set relaxation. We test the new approach by calculating solvation free energies and potentials of mean Force for small and large molecules, including the two-domain protein BphC. Our results reveal the importance of coupling polar and nonpolar interactions in the underlying molecular systems. In particular, dehydration near the domain interface of BphC subunits is found to be highly sensitive to local electrostatic potentials as seen in previous MD simulations. This is a first step toward capturing the complex protein dehydration process by an implicit-solvent approach.
Cyrus K Aidun - One of the best experts on this subject based on the ideXlab platform.
-
a method for direct simulation of flexible fiber suspensions using lattice boltzmann equation with external Boundary Force
International Journal of Multiphase Flow, 2010Co-Authors: Cyrus K AidunAbstract:Abstract The computational method presented here can be used to study the effect of volume fraction and particle deformation on the rheology and microstructure of deformable fibers suspended in Newtonian fluid. In this method, the flow is computed on a fixed regular ‘lattice’ using the lattice Boltzmann method, where each solid particle is mapped onto a Lagrangian frame moving continuously through the domain. Instead of the standard bounce-back method, an external Boundary Force is used to impose the no-slip Boundary condition at the fluid–solid interface for stationary or moving boundaries. The motion and orientation of the fiber are obtained from Newtonian dynamics equations. Although the external Boundary Force method is general, in this application it is used in conjunction with a flexible fiber model, which calculates the flexible fiber deformation by the real material properties. The methodology is validated by comparing with experimental and theoretical results.
-
simulating 3d deformable particle suspensions using lattice boltzmann method with discrete external Boundary Force
International Journal for Numerical Methods in Fluids, 2009Co-Authors: Cyrus K AidunAbstract:A method for direct numerical analysis of three-dimensional deformable particles suspended in fluid is presented. The flow is computed on a fixed regular ‘lattice’ using the lattice Boltzmann method (LBM), where each solid particle is mapped onto a Lagrangian frame moving continuously through the domain. Instead of the bounce-back method, an external Boundary Force (EBF) is used to impose the no-slip Boundary condition at the fluid–solid interface for stationary or moving boundaries. The EBF is added directly to the lattice Boltzmann equation. The motion and orientation of the particles are obtained from Newtonian dynamics equations. The advantage of this approach is outlined in comparison with the standard and higher-order interpolated bounce-back methods as well as the LBM immersed-Boundary and the volume-of-fluid methods. Although the EBF method is general, in this application, it is used in conjunction with the lattice–spring model for deformable particles. The methodology is validated by comparing with experimental and theoretical results. Copyright © 2009 John Wiley & Sons, Ltd.
Shenggao Zhou - One of the best experts on this subject based on the ideXlab platform.
-
the calculus of Boundary variations and the dielectric Boundary Force in the poisson boltzmann theory for molecular solvation
Journal of Nonlinear Science, 2021Co-Authors: Zhengfang Zhang, Shenggao ZhouAbstract:In a continuum model of the solvation of charged molecules in an aqueous solvent, the classical Poisson–Boltzmann (PB) theory for the electrostatics of an ionic solution is generalized to include the solute point charges and the dielectric Boundary that separates the high-dielectric solvent from the low-dielectric solutes. With such a setting, we construct an effective electrostatic free-energy functional of ionic concentrations. The functional admits a unique minimizer whose corresponding electrostatic potential is the unique solution to the Boundary-value problem of the nonlinear dielectric Boundary PB equation. The negative first variation of this minimum free energy with respect to variations of the dielectric Boundary defines the normal component of the dielectric Boundary Force. Together with the solute–solvent interfacial tension and van der Waals interaction Forces, such Boundary Force drives an underlying charged molecular system to a stable equilibrium, as described by a variational implicit-solvent model. We develop an $$L^2$$ -theory for Boundary variations and derive an explicit formula of the dielectric Boundary Force. Our results agree with a molecular-level prediction that the electrostatic Force points from the high-dielectric aqueous solvent to the low-dielectric charged molecules. Our method of analysis is general as it does not rely on any variational principles.
-
the calculus of Boundary variations and the dielectric Boundary Force in the poisson boltzmann theory for molecular solvation
arXiv: Optimization and Control, 2020Co-Authors: Zhengfang Zhang, Shenggao ZhouAbstract:In a continuum model of the solvation of charged molecules in an aqueous solvent, the classical Poisson-Boltzmann (PB) theory is generalized to include the solute point charges and the dielectric Boundary that separates the high-dielectric solvent from the low-dielectric solutes. With such a setting, we construct an effective electrostatic free-energy functional of ionic concentrations, where the solute point charges are regularized by a reaction field. We prove that such a functional admits a unique minimizer in a class of admissible ionic concentrations and that the corresponding electrostatic potential is the unique solution to the Boundary-value problem of the dielectric-Boundary PB equation. The negative first variation of this minimum free energy with respect to variations of the dielectric Boundary defines the normal component of the dielectric Boundary Force. Together with the solute-solvent interfacial tension and van der Waals interaction Forces, such Boundary Force drives an underlying charged molecular system to a stable equilibrium, as described by a variational implicit-solvent model. We develop an $L^2$-theory for the continuity and differentiability of solutions to elliptic interface problems with respect to Boundary variations, and derive an explicit formula of the dielectric Boundary Force. With a continuum description, our result of the dielectric Boundary Force confirms a molecular-level prediction that the electrostatic Force points from the high-dielectric and polarizable aqueous solvent to the charged molecules. Our method of analysis is general as it does not rely on any variational principles.
-
variational implicit solvation with poisson boltzmann theory
Journal of Chemical Theory and Computation, 2014Co-Authors: Shenggao Zhou, Litien Cheng, Joachim Dzubiella, Bo Li, Andrew J MccammonAbstract:We incorporate the Poisson–Boltzmann (PB) theory of electrostatics into our variational implicit-solvent model (VISM) for the solvation of charged molecules in an aqueous solvent. In order to numerically relax the VISM free-energy functional by our level-set method, we develop highly accurate methods for solving the dielectric PB equation and for computing the dielectric Boundary Force. We also apply our VISM-PB theory to analyze the solvent potentials of mean Force and the effect of charges on the hydrophobic hydration for some selected molecular systems. These include some single ions, two charged particles, two charged plates, and the host–guest system Cucurbit[7]uril and Bicyclo[2.2.2]octane. Our computational results show that VISM with PB theory can capture well the sensitive response of capillary evaporation to the charge in hydrophobic confinement and the polymodal hydration behavior and can provide accurate estimates of binding affinity of the host–guest system. We finally discuss several issues ...
Baozhu Guo - One of the best experts on this subject based on the ideXlab platform.
-
dynamic stabilization of an euler bernoulli beam under Boundary control and non collocated observation
Systems & Control Letters, 2008Co-Authors: Baozhu Guo, Junmin Wang, Kunyi YangAbstract:Abstract We study the dynamic stabilization of an Euler–Bernoulli beam system using Boundary Force control at the free end and bending strain observation at the clamped end. We construct an infinite-dimensional observer to track the state exponentially. A proportional output feedback control based on the estimated state is designed. The closed-loop system is shown to be non-dissipative but admits a set of generalized eigenfunctions, which forms a Riesz basis for the state space. As consequences, both the spectrum-determined growth condition and exponential stability are concluded.
Ulf D Schiller - One of the best experts on this subject based on the ideXlab platform.
-
a unified operator splitting approach for multi scale fluid particle coupling in the lattice boltzmann method
Computer Physics Communications, 2014Co-Authors: Ulf D SchillerAbstract:Abstract A unified framework to derive discrete time-marching schemes for the coupling of immersed solid and elastic objects to the lattice Boltzmann method is presented. Based on operator splitting for the discrete Boltzmann equation, second-order time-accurate schemes for the immersed Boundary method, viscous Force coupling and external Boundary Force are derived. Furthermore, a modified formulation of the external Boundary Force is introduced that leads to a more accurate no-slip Boundary condition. The derivation also reveals that the coupling methods can be cast into a unified form, and that the immersed Boundary method can be interpreted as the limit of Force coupling for vanishing particle mass. In practice, the ratio between fluid and particle mass determines the strength of the Force transfer in the coupling. The integration schemes formally improve the accuracy of first-order algorithms that are commonly employed when coupling immersed objects to a lattice Boltzmann fluid. It is anticipated that they will also lead to superior long-time stability in simulations of complex fluids with multiple scales.