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

Abstract

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. Program summaryProgram Title: CSDFTSProgram Files doi:http://dx.doi.org/10.17632/4t8ybf93d5.1Licensing provisions: GPLv2.Programming language: Java 1.8.External routines/libraries: GNU gawk installation is required if the user wants to calculate the protein volume using the 3v application.Nature of problem: A rich and complex, yet not fully understood, electrical double layer (EDL) formation arises when a nanoparticle or biomolecule is immersed in a liquid solution.Solution method: The Java application is based on the Classical Density Functional Theory Solver (CSDFTS).Additional comments including unusual features: The software incorporates a graphical user interface which eliminates the arduous and error-prone manual entry of data, and substantially reduces the time spent on the setup of the information required to characterize the macroion and the electrolyte solution. Additionally, each GUI screen provides helpful information about how to fill out the input data by simply holding the mouse pointer over the corresponding text or blank box. the GUI tests all the input data before running the CSDFTS to avoid the incorrect use of the software and prevent meaningless results.The GUI requires a variety of the user’s computer applications, which are a part of the basic operating systems. The GUI uses “Activity Monitor”, “procexp.exe”, and “gnome-system-monitor” (or “top”) applications for Mac, Windows and Linux users, respectively, to monitor the user’s computer performance. It also uses “Terminal.app”, “cmd.exe” and “gnome-terminal” (or “xterm”) for Mac, Windows, and Linux users, respectively, to display the CSDFT calculations.