O(N) continuous electrostatics solvation energies calculation method for biomolecules simulations

We report a development of a new fast surface-based method for numerical calculations of solvation energy of biomolecules with a large number of charged groups. The procedure scales linearly with the system size both in time and memory requirements, is only a few percent wrong for any molecular configurations of arbitrary sizes, gives explicit value for the reaction field potential at any point, provides both the solvation energy and its derivatives suitable for Molecular Dynamics simulations. The method works well both for large and small molecules and thus gives stable energy differences for quantities such as solvation energies of molecular complex formation.Comment: 6 pages, 4 figures, more results, examples and references adde

The dynamics of copper intercalated molybdenum ditelluride

Layered transition metal dichalcogenides are emerging as key materials in nanoelectronics and energy applications. Predictive models to understand their growth, thermomechanical properties and interactions with metals are needed in order to accelerate their incorporation into commercial products. Interatomic potentials enable large-scale atomistic simulations at the device level, beyond the range of applications of first principle methods. We present a ReaxFF reactive force field to describe molybdenum ditelluride and its interactions with copper. We optimized the force field parameters to describe the properties of layered MoTe2 in various phases, the intercalation of Cu atoms and clusters within its van der Waals gap, including a proper description of energetics, charges and mechanical properties. The training set consists of an extensive set of first principle calculations computed from density functional theory. We use the force field to study the adhesion of a single layer MoTe2 on a Cu(111) surface and the results are in good agreement with density functional theory, even though such structures were not part of the training set. We characterized the mobility of the Cu ions intercalated into MoTe2 under the presence of an external electric fields via molecular dynamics simulations. The results show a significant increase in drift velocity for electric fields of approximately 0.4 V/A and that mobility increases with Cu ion concentration.Comment: 21 pages, 9 Figure

Atomic radius and charge parameter uncertainty in biomolecular solvation energy calculations

Atomic radii and charges are two major parameters used in implicit solvent electrostatics and energy calculations. The optimization problem for charges and radii is under-determined, leading to uncertainty in the values of these parameters and in the results of solvation energy calculations using these parameters. This paper presents a new method for quantifying this uncertainty in implicit solvation calculations of small molecules using surrogate models based on generalized polynomial chaos (gPC) expansions. There are relatively few atom types used to specify radii parameters in implicit solvation calculations; therefore, surrogate models for these low-dimensional spaces could be constructed using least-squares fitting. However, there are many more types of atomic charges; therefore, construction of surrogate models for the charge parameter space requires compressed sensing combined with an iterative rotation method to enhance problem sparsity. We demonstrate the application of the method by presenting results for the uncertainties in small molecule solvation energies based on these approaches. The method presented in this paper is a promising approach for efficiently quantifying uncertainty in a wide range of force field parameterization problems, including those beyond continuum solvation calculations.The intent of this study is to provide a way for developers of implicit solvent model parameter sets to understand the sensitivity of their target properties (solvation energy) on underlying choices for solute radius and charge parameters