Related papers: Fast and accurate multidimensional free energy int…
Accurate absolute binding free energy (ABFE) calculations can reduce the time and cost of identifying drug candidates from a diverse pool of molecules that may have been overlooked experimentally. These calculations typically employ…
Fluid-Structure Interaction (FSI) is a crucial problem in ocean engineering. The smoothed particle hydrodynamics (SPH) method has been employed recently for FSI problems in light of its Lagrangian nature and its advantage in handling…
We demonstrate how a prior assumption of smoothness can be used to enhance the reconstruction of free energy profiles from multiple umbrella sampling simulations using the Bayesian Gaussian process regression approach. The method we derive…
Atomic-scale phase-field modeling formulates the probability densities of atomic vibrations as Gaussian distributions and derives a free energy functional using variational Gaussian theory and interatomic potentials. This framework permits…
We describe a new, adaptive solver for the two-dimensional Poisson equation in complicated geometries. Using classical potential theory, we represent the solution as the sum of a volume potential and a double layer potential. Rather than…
Finding the stationary states of a free energy functional is an important problem in phase field crystal (PFC) models. Many efforts have been devoted for designing numerical schemes with energy dissipation and mass conservation properties.…
A modification of the Adaptive Biasing Force method is introduced, in which the free energy is approximated by a sum of tensor products of one-dimensional functions. This enables to handle a larger number of reaction coordinates than the…
We propose an adaptive biasing algorithm aimed at enhancing the sampling of multimodal measures by Langevin dynamics. The underlying idea consists in generalizing the standard adaptive biasing force method commonly used in conjunction with…
In most classical approaches of computational geophysics for seismic wave propagation problems, complex surface topography is either accounted for by boundary-fitted unstructured meshes, or, where possible, by mapping the complex…
We generalize the interpolative separable density fitting (ISDF) method, used for compressing the four-index electron repulsion integral (ERI) tensor, to incorporate adaptive real space grids for potentially highly localized single-particle…
The Poisson-Boltzmann equation is a widely used model to study the electrostatics in molecular solvation. Its numerical solution using a boundary integral formulation requires a mesh on the molecular surface only, yielding accurate…
The calculation of potential energy surfaces for quantum dynamics can be a time consuming task -- especially when a high level of theory for the electronic structure calculation is required. We propose an adaptive interpolation algorithm…
Existing adaptive bias techniques, which seek to estimate free energies and physical properties from molecular simulations, are limited by their reliance on fixed kernels or basis sets which hinder their ability to efficiently conform to…
Accurate phase diagram calculation from molecular dynamics requires systematic treatment and convergence of statistical averages. In this work we propose a Gaussian process regression based framework for reconstructing the free energy…
We present a simple modification of the direct-forcing immersed boundary method (IBM) proposed by Uhlmann [J. Comput. Phys, 2005] in order to enable it to be applied to particulate flows with solid-to-fluid density ratios around unity. The…
Free energy profiles serve as a fundamental bridge between microscopic atomic fluctuations and macroscopic thermodynamic observables. Estimating the free energy profile along a reaction coordinate, referred to as the potential of mean force…
Many biological processes involve numerous coupled degrees of freedom, yet free-energy estimation is often restricted to one-dimensional profiles to mitigate the high computational cost of multidimensional sampling. In this work, we extend…
A coherent state technique is used to generate an Interacting Boson Model (IBM) Hamiltonian energy surface that simulates a mean field energy surface. The method presented here has some significant advantages over previous work.…
A method based on the Gibbs' adsorption isotherm is developed to calculate the decrease in interfacial free energy resulting from solute segregation at an internal interface, built on measured concentration profiles. Utilizing atom-probe…
A family of fast sampling methods is introduced here for molecular simulations of systems having rugged free energy landscapes. The methods represent a generalization of a strategy consisting of adjusting a model for the free energy as a…