ABSTRACT
The Linearized Poisson-Boltzmann (LPB) equation is a popular and widely accepted model for accounting solvent effects in computational (bio-) chemistry. In the present article, we derive the analytical forces using the domain-decomposition-based LPB-method with a van-der Waals or solvent-accessible surface. We present an efficient strategy to compute the forces and its implementation, allowing linear scaling of the method with respect to the number of atoms using the fast multipole method. Numerical tests illustrate the accuracy of the computation of the analytical forces and compare the efficiency with other available methods.
ABSTRACT
The NonCovalent Interaction index (NCI) enables identification of attractive and repulsive noncovalent interactions from promolecular densities in a fast manner. However, the approach remained up to now qualitative, only providing visual information. We present a new version of NCIPLOT, NCIPLOT4, which allows quantifying the properties of the NCI regions (volume, charge) in small and big systems in a fast manner. Examples are provided of how this new twist enables characterization and retrieval of local information in supramolecular chemistry and biosystems at the static and dynamic levels.
ABSTRACT
This paper builds on two previous studies [Lindgren et al., J. Comput. Phys. 371, 712 (2018) and Quan et al., "A domain decomposition method for the Poisson-Boltzmann solvation models," SIAM J. Sci. Comput. (to be published); e-print arXiv:1807.05384] to devise a new method to solve the problem of calculating electrostatic interactions in a system composed by many dielectric particles, embedded in a homogeneous dielectric medium, which in turn can also be permeated by charge carriers. The system is defined by the charge, size, position, and dielectric constant of each particle, as well as the dielectric constant and the Debye length of the medium. The effects of taking into account the dielectric nature of the particles are explored in selected scenarios where the presence of electrolytes in the medium can significantly influence the total undergoing interactions. The description of the mutual interactions between all particles in the system as being truly of many-body nature reveals how such effects can effectively influence the magnitudes and even directions of the resulting forces, especially those acting on particles that have a null net charge. Particular attention is given to a situation that can be related to colloidal particles in an electrolyte solution, where it is shown that polarization effects alone can substantially raise or lower-depending on the dielectric contrast between the particles and the medium-the energy barrier that divides particle coagulation and flocculation regions, when an interplay between electrostatic and additional van der Waals forces is considered. Overall, the results suggest that for an accurate description of the type of system in question, it is essential to consider particle polarization if the separation between the interacting particles are comparable to or smaller than the Debye length of the medium.
ABSTRACT
We develop an algorithm for meshing molecular surfaces that is based on patch-wise meshing using an advancing-front method adapted to the particular case of molecular surfaces. We focus on the solvent accessible surface (SAS) and the solvent excluded surface (SES). The essential ingredient is a newly developed analysis of such surfaces in [18] that allows to describe all SES-singularities a priori and therefore a complete characterization of the SES. In addition, an algorithm for filling molecular inner holes is proposed based on the pre-computed data structures of molecular surfaces.
