Giant charge inversion and/or nanoscale phenomena for living cells are studied using the codes of fortran 2003, and molecular dynamics simulations are execcuted (Refs. 1-5). "DNA in nanopores" in Ref. 5 is simulated for DNA transportation through nanepores, where counterion condensation and coion depletion are the key of the nanoscale pores of human cells.
The molecular dynamics simulation codes are created in several settings, and they are discussed in the articles. Gaint charge inversion is about the macroions surrounded by the electrolyte of multivalent counterions and monovalent coions. The simulation code is @chginv3.f03 with the paramer file parm_inv13.h and the configure file CIMV13_config.START3. The equation of motion in Eq.(1) of Ref.1 has the Lengevin thermostat on top of Coulomb and Lennard-Jones forces of the righthand side. The first 40 lines of the code are the title, author, equation of motion, and structure of the code. Other important remarks are explained thereafter. Main subroutines are RUN_MD, moldyn, realteil, p3m_perform, and Gopen graphic packages.
The simulation code utilizes the MPI and FFTW3 packages, and PDF's of Ref. 1 are shown with figures. We can see the occurrence of giant charge inversion by looking at sharp peaks in charge distribution functions around the macroions. From the figures, there are two requirements for the giant inversion, namely, (1) the multivalent counterions and monovalent coions exist around macroions, and (2) the Coulomb energy is larger than thermal energy of macroions and counterions.
In the listed articles, the figures are best illustrated, partly in color pictures. The PDF file cimv13_773a.pdf in the Langevin thermostat shows a rather stationary macroion. The first peak of counterions at the top-left panels exists very close to the macroion's surface at R= Rmac to (Rmac+5 Ang) of cimv13_78.pdf - only the 20 Angstrom regime from the macroion is plotted. We use K^+ counterions with the radius 2.0 Ang and Cl^- coions with 5.2 Ang
(* CGS system: t_unit= 0.01d-12 s, a_unit= 1.00d-08 cm, w_unit= 1.6605d-24 g, e_unit= 4.803d-10 esu, and \epsilon=78).
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