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Register a new userA Nonlinear Boundary Condition for Continuum Models of Biomolecular Electrostatics
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Understanding the behavior of biomolecules such as proteins requires understanding the critical influence of the surrounding fluid (solvent) environment--water with mobile salt ions such as sodium. Unfortunately, for many studies, fully atomistic simulations of biomolecules, surrounded by thousands of water molecules and ions are too computationally slow. Continuum solvent models based on macroscopic dielectric theory (e.g. the Poisson equation) are popular alternatives, but their simplicity fails to capture well-known phenomena of functional significance. For example, standard theories predict that electrostatic response is symmetric with respect to the sign of an atomic charge, even though response is in fact strongly asymmetric if the charge is near the biomolecule surface. In this work, we present an asymmetric continuum theory that captures the essential physical mechanism--the finite size of solvent atoms--using a nonlinear boundary condition (NLBC) at the dielectric interface between the biomolecule and solvent. Numerical calculations using boundary-integral methods demonstrate that the new NLBC model reproduces a wide range of results computed by more realistic, and expensive, all-atom molecular-dynamics (MD) simulations in explicit water. We discuss model extensions such as modeling dilute-electrolyte solvents with Debye-Huckel theory (the linearized Poisson-Boltzmann equation) and opportunities for the electromagnetics community to contribute to research in this important area of molecular nanoscience and engineering.
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The structure and function of biological molecules are strongly influenced by the water and dissolved ions that surround them. This aqueous solution (solvent) exerts significant electrostatic forces in response to the biomolecules ubiquitous atomic charges and polar chemical groups. In this work, we investigate a simple approach to numerical calculation of this model using boundary-integral equation (BIE) methods and boundary-element methods (BEM). Traditional BEM discretizes the protein--solvent boundary into a set of boundary elements, or panels, and the approximate solution is defined as a weighted combination of basis functions with compact support. The resulting BEM matrix then requires integrating singular or near singular functions, which can be slow and challenging to compute. Here we investigate the accuracy and convergence of a simpler representation, namely modeling the unknown surface charge distribution as a set of discrete point charges on the surface. We find that at low resolution, point-based BEM is more accurate than panel-based methods, due to the fact that the protein surface is sampled directly, and can be of significant value for numerous important calculations that require only moderate accuracy, such as the preliminary stages of rational drug design and protein engineering.
Continuum solvation methods can provide an accurate and inexpensive embedding of quantum simulations in liquid or complex dielectric environments. Notwithstanding a long history and manifold applications to isolated systems in open boundary conditions, their extension to materials simulations --- typically entailing periodic-boundary conditions --- is very recent, and special care is needed to address correctly the electrostatic terms. We discuss here how periodic-boundary corrections developed for systems in vacuum should be modified to take into account solvent effects, using as a general framework the self-consistent continuum solvation model developed within plane-wave density-functional theory [O. Andreussi et al. J. Chem. Phys. 136, 064102 (2012)]. A comprehensive discussion of real-space and reciprocal-space corrective approaches is presented, together with an assessment of their ability to remove electrostatic interactions between periodic replicas. Numerical results for zero-dimensional and two-dimensional charged systems highlight the effectiveness of the different suggestions, and underline the importance of a proper treatement of electrostatic interactions in first-principles studies of charged systems in solution.
Molecular dynamics simulations of biomolecules have been widely adopted in biomedical studies. As classical point-charge models continue to be used in routine biomolecular applications, there have been growing demands on developing polarizable force fields for handling more complicated biomolecular processes. Here we focus on a recently proposed polarizable Gaussian Multipole (pGM) model for biomolecular simulations. A key benefit of pGM is its screening of all short-range electrostatic interactions in a physically consistent manner, which is critical for stable charge-fitting and is needed to reproduce molecular anisotropy. Another advantage of pGM is that each atoms multipoles are represented by a single Gaussian function or its derivatives, allowing for more efficient electrostatics than other Gaussian-based models. In this study we present an efficient formulation for the pGM model defined with respect to a local frame formed with a set of covalent basis vectors. The covalent basis vectors are chosen to be along each atoms covalent bonding directions. The new local frame allows molecular flexibility during molecular simulations and facilitates an efficient formulation of analytical electrostatic forces without explicit torque computation. Subsequent numerical tests show that analytical atomic forces agree excellently with numerical finite-difference forces for the tested system. Finally, the new pGM electrostatics algorithm is interfaced with the PME implementation in Amber for molecular simulations under the periodic boundary conditions. To validate the overall pGM/PME electrostatics, we conducted an NVE simulation for a small water box of 512 water molecules. Our results show that, to achieve energy conservation in the polarizable model, it is important to ensure enough accuracy on both PME and induction iteration.
Electrostatic forces play many important roles in molecular biology, but are hard to model due to the complicated interactions between biomolecules and the surrounding solvent, a fluid composed of water and dissolved ions. Continuum model have been surprisingly successful for simple biological questions, but fail for important problems such as understanding the effects of protein mutations. In this paper we highlight the advantages of boundary-integral methods for these problems, and our use of boundary integrals to design and test more accurate theories. Examples include a multiscale model based on nonlocal continuum theory, and a nonlinear boundary condition that captures atomic-scale effects at biomolecular surfaces.
In this paper we extend the familiar continuum electrostatic model with a perturbation to the usual macroscopic boundary condition. The perturbation is based on the mean spherical approximation (MSA), to derive a multiscale hydration-shell boundary condition (HSBC). We show that the HSBC/MSA model reproduces MSA predictions for Born ions in a variety of polar solvents, including both protic and aprotic solvents. Importantly, the HSBC/MSA model predicts not only solvation free energies accurately but also solvation entropies, which standard continuum electrostatic models fail to predict. The HSBC/MSA model depends only on the normal electric field at the dielectric boundary, similar to our recent development of an HSBC model for charge-sign hydration asymmetry, and the reformulation of the MSA as a boundary condition enables its straightforward application to complex molecules such as proteins.
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