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Spherically-symmetric atom-centered descriptors of atomic environments have been widely used for constructing potential or free energy surfaces of atomistic and colloidal systems and to characterize local structures using machine learning…
Molecular-dynamics simulation can give atomistic information on the processes occurring in nanoindentation experiments. In particular, the nucleation of dislocation loops, their growth, interaction and motion can be studied. We investigate…
We report a straightforward, model-free approach for measuring pair potentials from particle-coordinate data, based on enforcing consistency between the pair distribution function measured separately by the distance-histogram and…
A semianalytical approach is developed to calculate the effective pair potential of rigid arbitrarily shaped macroions with a nonvanishing particle volume, valid within linear screening theory and the mean-field approximation. The essential…
We critically discuss and review the general ideas behind single- and multi-site coarse-grained (CG) models as applied to macromolecular solutions in the dilute and semi-dilute regime. We first consider single-site models with zero-density…
A dynamical atomistic chain to simulate mechanical properties of a one-dimensional material with zero temperature may be modelled by the molecular dynamics (MD) model. Because the number of particles (atoms) is huge for a MD model, in…
Variational quantum algorithms (VQAs) are increasingly being applied in simulations of strongly-bound (covalently bonded) systems using full molecular orbital basis representations. The application of quantum computers to the weakly-bound…
We use functional, Fr\'echet, derivatives to quantify how thermodynamic outputs of a molecular dynamics (MD) simulation depend on the potential used to compute atomic interactions. Our approach quantifies the sensitivity of the quantities…
Coarse-grained models are a core computational tool in theoretical chemistry and biophysics. A judicious choice of a coarse-grained model can yield physical insight by isolating the essential degrees of freedom that dictate the…
Unpolarized 800 MeV proton inelastic scatterings from an s-d shell nucleus $^{22}$Ne are analyzed using phenomenological optical potentials in the Dirac coupled channel formalism. The first-order rotational collective model is used to…
Molecular dynamics (MD) simulations provide detailed insight into atomic-scale mechanisms but are inherently restricted to small spatio-temporal scales. Coarse-grained molecular dynamics (CGMD) techniques allow simulations of much larger…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…
We derive exact expressions for the forces and torques between biaxial molecules interacting via the RE-squared potential, a recent variant of the Gay-Berne potential. Moreover, efficient routines have been provided for rigid body MD…
The use of an effective intermolecular potential often involves a compromise between more accurate, complex functional forms and more tractable simple representations. To study this choice in detail, we systematically derive coarse-grained…
We calculate the energy and wave functions of two particles confined to two spatial dimensions interacting via arbitrary anisotropic potentials with negative or zero net volume. The general rigorous analytic expressions are given in the…
A new pairwise hybrid machine-learning/molecular mechanics (ML/MM) potential is introduced that is conceived for application to large, heterogeneous condensed-phase systems. The PhysNet ML method describes monomers and short-range dimer…
We introduce a method to bring nearly atomistic resolution to coarse-grained models, and we apply the method to proteins. Using a small number of coarse-grained sites (about one per eight atoms) but assigning an independent…
Theories of solvation free energies often involve electrostatic potentials at the position of a solute charge. Simulation calculations that apply cutoffs and periodic boundary conditions based on molecular centers result in center-dependent…
A coarse-graining strategy, previously developed for polymer solutions, is extended here to mixtures of linear polymers and hard-sphere colloids. In this approach groups of monomers are mapped onto a single pseudoatom (a blob) and the…
Computer simulations can provide mechanistic insight into ionic liquids (ILs) and predict the properties of experimentally unrealized ion combinations. However, ILs suffer from a particularly large disparity in the time scales of atomistic…