We design and implement numerical methods for the incompressible Stokes solvent flow and solute-solvent interface motion for nonpolar molecules in aqueous solvent. The balance of viscous force, surface tension, and van der Waals type dispersive force leads to a traction boundary condition on the solute-solvent interface. To allow the change of solute volume, we design special numerical boundary conditions on the boundary of a computational domain through a consistency condition. We use a finite difference ghost fluid scheme to discretize the Stokes equation with such boundary conditions. The method is tested to have a second-order accuracy. We combine this ghost fluid method with the level-set method to simulate the motion of the solute-solvent interface that is governed by the solvent fluid velocity. Numerical examples show that our method can predict accurately the blow up time for a test example of curvature flow and reproduce the polymodal (e.g., dry and wet) states of hydration of some simple model molecular systems.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4922513 | PMC |
| http://dx.doi.org/10.1007/s10915-015-0099-z | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Some Challenges of Diffused Interfaces in Implicit-Solvent Models.
J Comput Chem
January 2025
Department of Mechanical Engineering, Universidad Técnica Federico Santa María, Valparaíso, Chile.
The standard Poisson-Boltzmann (PB) model for molecular electrostatics assumes a sharp variation of the permittivity and salt concentration along the solute-solvent interface. The discontinuous field parameters are not only difficult numerically, but also are not a realistic physical picture, as it forces the dielectric constant and ionic strength of bulk in the near-solute region. An alternative to alleviate some of these issues is to represent the molecular surface as a diffuse interface, however, this also presents challenges.
View Article and Find Full Text PDF: A Command-Line Interface for Molecular Simulations and Multiscale Microsolvation Modeling.
J Chem Inf Model
May 2024
Chemistry and Physics Department, Federal University of Paraíba, Areia, Paraíba 58397-000, Brazil.
In this work, we introduce the , a comprehensive and modular command-line interface designed for molecular simulation and microsolvation modeling. The suite interfaces with widely used scientific software, streamlining computational experiments for liquid systems through the automated creation of simulation boxes and topology with adjustable simulation parameters. Furthermore, it has features for graphical and statistical analysis of simulated properties and extraction of trajectory configurations with various filters.
View Article and Find Full Text PDFLiquid-Liquid Interface-Assisted Self-Assembly of Ag-Doped ZnO Nanosheets for Atomic Switch Application.
J Phys Chem Lett
January 2024
Department of Physics, Indian Institute of Technology Patna, Patna 801106, India.
Developing facile and inexpensive methods for obtaining large-area two-dimensional semiconducting nanosheets is highly desirable for mass-scale device application. Here, we report a method for producing uniform and large-area films of a Ag-doped ZnO (AZO) nanosheet network via self-assembly at the hexane-water interface by controlling the solute/solvent ratio. The self-assembled film comprises of uniformly tiled nanosheets with size ∼1 μm and thicknesses∼60-100 nm.
View Article and Find Full Text PDFHow to measure work functions from aqueous solutions.
Chem Sci
September 2023
Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Sakyo-Ku 606-8502 Kyoto Japan
The recent application of concepts from condensed-matter physics to photoelectron spectroscopy (PES) of volatile, liquid-phase systems has enabled the measurement of electronic energetics of liquids on an absolute scale. Particularly, vertical ionization energies, VIEs, of liquid water and aqueous solutions, both in the bulk and at associated interfaces, can now be accurately, precisely, and routinely determined. These IEs are referenced to the local vacuum level, which is the appropriate quantity for condensed matter with associated surfaces, including liquids.
View Article and Find Full Text PDFMolecular Crowders Can Induce Collapse in Hydrophilic Polymers via Soft Attractive Interactions.
J Phys Chem B
July 2023
Department of Materials Science and Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India.
A comprehensive understanding of protein folding and biomolecular self-assembly in the intracellular environment requires obtaining a microscopic view of the crowding effects. The classical view of crowding explains biomolecular collapse in such an environment in terms of the entropic solvent excluded volume effects subjected to hard-core repulsions exerted by the inert crowders, neglecting their soft chemical interactions. In this study, the effects of nonspecific, soft interactions of molecular crowders in regulating the conformational equilibrium of hydrophilic (charged) polymers are examined.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!