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, multiplatform, 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 macroions under multiple conditions. 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, rigidlike globular proteins, nanoparticles, and nano-rods. CSDFTS implements several electrolyte and macroion models, uses different level 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. a

Electrical Propagation of Condensed and Diffuse Ions Along Actin Filaments

“…Following the approach for the EDL, we calculate the parameters b DL and C DL o /(2π a) using CSDFT (Marucho, 2019).…”

“…1) was developed to account for the charging mechanisms of residues in actin proteins, and the non-trivial contributions of the electrical double layer (EDL) to the ionic electrical conductivity along actin filaments(Fig. 2a) (Hunley, Uribe, and Marucho, 2018;Marucho, 2019). Results for in-vitro and intracellular conditions revealed changes in width, decay and velocity of propagation depending on the voltage input and conducting properties of actin filaments.…”

Electrical impulse characterization along actin filaments in pathological conditions

“…The electric charge was calculated using pdb2pqr webserver with an Amber force field (https://server.poissonboltzmann.org/pdb2pqr). A Java Application for Cytoskeleton Filament Characterization (JACFC) web application [24,25,26] was used to obtain the capacitance parameters for different temperatures and filament radii.…”

“…A Java Application for Cytoskeleton Filament Characterization (JACFC) web application [24, 25, 26] was used to obtain the capacitance parameters for different temperatures and filament radii.…”

“…To include these, CSDFT calculations were used for an accurate consideration of the surface electric potential ψ o = ϕ ( R ). This process was explained in the supplement of a previous work [9], and can easily be done by using JACFC web application [24, 25, 26]. . The differential capacitance representing a monomer is found to be For the total charge we integrate over the voltage drop and get where b characterizes the non-linear behavior of the capacitance.…”