174,252 research outputs found
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
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
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
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