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

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.

宏观离子（纳米颗粒或生物大分子）与周围离子及水分子之间的静电、熵和表面相互作用在胶体系统的行为和功能中起着根本性作用。然而，支配这些现象的分子机制仍然理解不足。在获取这种理解的主要限制之一是缺乏适当的计算工具。此外，只有那些在编程方面具有广泛背景、接受过统计力学培训并能够访问超级计算机的该领域专家才能研究这些系统。为了克服这些限制，本文提出了一种免费、多平台、便携式的Java软件，为该领域的专家和非专家提供了一个简便、高效的方法，以获得在多种条件下，围绕圆柱形和球形刚性宏观离子周围的水合电解质混合溶液的电和结构性质的准确分子表征。这些性质包括归一化的离子和水密度分布、平均静电势、总电荷、ζ势、静电势能、粒子拥挤熵能、离子-离子静电直接关联能以及离子势的平均力。该Java软件无需卓越的技能，并附带详细的用户指南文档。该应用基于所谓的经典密度泛函理论求解器（CSDFTS），该求解器已成功应用于多种棒状生物大分子、刚性球状蛋白质、纳米颗粒和纳米棒。CSDFTS实现了多种电解质和宏观离子模型，采用不同的近似水平，并利用高性能Fortran90例程和优化库。这些特性使得该软件能够在单处理器计算机上运行，计算成本取决于计算机性能、网格分辨率、宏观离子和电解质溶液的表征等因素。作为一项独特功能，该软件配备了图形用户界面（GUI），使用户能够利用直观引导的输入数据设置，以正确表征系统和配置求解器。提供了关于纳米材料和生物大分子的几个示例，以说明GUI的使用和求解器性能。