A java application to characterize biomolecules and nanomaterials in electrolyte aqueous solutions

Published: 24 May 2019| Version 1 | DOI: 10.17632/4t8ybf93d5.1


The electrostatic, entropic and surface interactions between a macroion (nanoparticle or biomolecule), surrounding ions and water molecules play a fundamental role in the behavior and function of colloidal systems. However, the molecular mechanisms governing these phenomena are still poorly understood. One of the major limitations in procuring this understanding is the lack of appropriate computational tools. Additionally, only experts in the field with an extensive background in programming, who are trained in statistical mechanics, and have access to supercomputers are able to study these systems. To overcome these limitations, in this article, we present a free, multi-platform, portable Java software, which provides experts and non-experts in the field an easy and efficient way to obtain an accurate molecular characterization of electrical and structural properties of aqueous electrolyte mixture solutions around both cylindrical- and spherical-like rigid macroions under multiple conditions. These properties include the normalized ions and water density profile distributions, the mean electrostatic potential, the integrated charge, the zeta potential, the electrostatic potential energy, the particle crowding entropy energy, the ion–ion electrostatic direct correlation energy, and the ionic potential of mean force. The Java software does not require outstanding skills and comes with detailed user-guide documentation. The application is based on the so-called Classical Density Functional Theory Solver (CSDFTS), which was successfully applied to a variety of rod-like biopolymers, rigid-like globular proteins, nanoparticles, and nano-rods. CSDFTS implements several electrolyte and macroion models, uses different levels of approximation and takes advantage of high performance Fortran90 routines and optimized libraries. These features enable the software to run on single processor computers at low-to-moderate computational cost depending on the computer performance, the grid resolution, and the characterization of the macroion and the electrolyte solution, among other factors. As a unique feature, the software comes with a graphical user interface (GUI) that allows users to take advantage of the visually guided setup of the required input data to properly characterize the system and configure the solver. Several examples on nanomaterials and biomolecules are provided to illustrate the use of the GUI and the solver performance.



Software, Biophysics, Computational Physics, Biomolecules, Nanomaterials, Density Functional Theory, Polyelectrolyte, Electrical Double Layer Theory, Solvation