This work presents Atomistic Topology Operations in MATLAB (atom), an open source library of modular MATLAB routines which comprise a general and flexible framework for manipulation of atomistic systems. The purpose of the atom library is simply to facilitate common operations performed for construction, manipulation, or structural analysis. Due to the data structure used, atoms and molecules can be operated upon based on different chemical names or attributes, such as atom- or molecule-ID, name, residue name, charge, positions, etc. Furthermore, the Bond Valence Method and a neighbor-distance analysis can be performed to assign many chemical properties of inorganic molecules. Apart from reading and writing common coordinate files (.pdb, .xyz, .gro, .cif) and trajectories (.dcd, .trr, .xtc; binary formats are parsed via third-party packages), the atom library can also be used to generate topology files with bonding and angle information taking the periodic boundary conditions into account, and supports basic Gromacs, NAMD, LAMMPS, and RASPA2 topology file formats. Focusing on clay-mineral systems, the library supports CLAYFF (Cygan, 2004) but can also generate topology files for the INTERFACE forcefield (Heinz, 2005, 2013) for Gromacs and NAMD.

A better understanding of the thermodynamics of radioactive cesium uptake at the surfaces of phyllosilicate minerals is needed to understand the mechanisms of selective adsorption and help guide the development of practical and inexpensive decontamination techniques. In this work, molecular dynamics simulations were carried out to determine the thermodynamics of Cs+ adsorption at the basal surface of six 2:1 phyllosilicate minerals, namely pyrophyllite, illite, muscovite, phlogopite, celadonite, and margarite. These minerals were selected to isolate the effects of the magnitude of the permanent layer charge (⩽2), its location (tetrahedral vs. octahedral sheet), and the octahedral sheet structure (dioctahedral vs. trioctahedral). Good agreement was obtained with the experiments in terms of the hydration free energy of Cs+ and the structure and thermodynamics of Cs+ adsorption at the muscovite basal surface, for which published data were available for comparison. With the exception of pyrophyllite, which did not exhibit an inner-sphere free energy minimum, all phyllosilicate minerals showed similar behavior with respect to Cs+ adsorption; notably, Cs+ adsorption was predominantly inner-sphere, whereas outer-sphere adsorption was very weak with the simulations predicting the formation of an extended outer-sphere complex. For a given location of the layer charge, the free energy of adsorption as an inner-sphere complex varied linearly with the magnitude of the layer charge. For a given layer charge location and magnitude, adsorption at phlogopite (trioctahedral sheet structure) was much less favorable than at muscovite (dioctahedral sheet structure) due to electrostatic repulsion between adsorbed Cs+ and the H atom of the OH- ion directly below the six-membered siloxane ring cavity. For a given layer charge magnitude and octahedral sheet structure, adsorption to celadonite (octahedral sheet layer charge) was favored over adsorption to muscovite (tetrahedral sheet layer charge) due to the increased distance to the surface K+ ions and the decreased distance to the O atom of the OH- ion directly below the surface cavity.