Investigation of structure and dynamics of water confined between hybrid layered materials of graphene, boron nitride, and molybdenum disulfide

Development, Validation, and Applications of Nonbonded Interaction Parameters between Coarse-Grained Amino Acid and Water Models

“…57,59 The Lorentz−Berthelot (LB) combining rule is a common method used to determine the parameters for crossinteractions between different types of beads in molecular Biomacromolecules pubs.acs.org/Biomac Article simulations. 63,64 Using this method, ε ij and σ ij between two atoms i and j can be calculated using equations…”

“…The nonbonded self- and cross-interactions are represented through the 12–6 Lennard Jones (LJ) potential as shown in the last term of eq . The variable ε ij is the potential well depth, which describes the strength of interaction energy between two beads, σ ij is the finite distance where the potential between two beads is equal to zero, and r ij represents the distance between the centers of two interacting beads. , The 12–6 LJ equation was utilized to represent the cross-interactions between CG amino acid and water beads to maintain consistency with their respective self-interaction FFs developed earlier. , The Lorentz–Berthelot (LB) combining rule is a common method used to determine the parameters for cross-interactions between different types of beads in molecular simulations. , Using this method, ε ij and σ ij between two atoms i and j can be calculated using equations ε ij = false( ε ii ε jj false) 1 / 2 σ ij = 1 / 2 ( σ ii + σ jj ) These values, calculated for the different interacting bead pairs in our amino acid–water systems, provided a good starting point for further optimization of cross-interactions in our study by reproducing Gibbs hydration free energy values of amino acid dipeptides.…”

“…simulations. 63,64 Using this method, ε ij and σ ij between two atoms i and j can be calculated using equations…”

A review of recent advances and applications of machine learning in tribology

“…233,234 Additionally, MD simulations provide insight into molecular-level interactions and the interfacial structural characteristics that are challenging to examine through experiments. 235,236 Besides, MD simulations also aid in the determination of a material's chemical, mechanical, and structural properties, as well as the validation of experimental data at the molecular-level. 233 Because quantum mechanical ab initio calculations are confined to systems of hundreds of atoms, atomistic tribology MD simulations have historically been approached using empirical classical models of atomic interactions.…”

Recent advances in computational materials design: methods, applications, algorithms, and informatics

“…The article by Uberuaga et al [7] investigates the complex interplay between the alloying elements and the diffusion behavior of atoms and defects at grain boundaries in Ni. The article by Sose et al [8] investigates the structure and dynamics of confined water in hybrid layered materials. The article by Nikolov et al [9] demonstrates new capabilities to investigate the interplay between phonon and magnetic spin contributions to the thermal conductivity of a-iron using a new spectral neighbor analysis potential.…”