Related papers: Accelerating ab initio path integral molecular dyn…
This work proposes a new efficient approach for calculating the bending stiffness of two-dimensional materials using simple atomistic tests on small periodic unit cells. The tests are designed such that bending deformations are dominating…
We present a simple, yet general, end-to-end deep neural network representation of the potential energy surface for atomic and molecular systems. This methodology, which we call Deep Potential, is "first-principle" based, in the sense that…
We study the convergence and the stability of fictitious dynamical methods for electrons. First, we show that a particular damped second-order dynamics has a much faster rate of convergence to the ground-state than first-order steepest…
Accurate, global Potential Energy Surfaces (PES) expressed in sum-of-products (SOP) form are a prerequisite for efficient high-dimensional quantum dynamics simulations using the MCTDH method. This work introduces a methodology for…
We present a detailed comparison of computational efficiency and precision for several free energy difference ($\Delta F$) methods. The analysis includes both equilibrium and non-equilibrium approaches, and distinguishes between…
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…
Highly accurate methods such as coupled cluster (CC) techniques can be used for periodic systems within the framework of the method of increments. Its extension to low-dimensional conducting system is considered. To demonstrate the…
Geometry optimization is an important part of both computational materials and surface science because it is the path to finding ground state atomic structures and reaction pathways. These properties are used in the estimation of…
Path integral Monte Carlo (PIMC) simulations are used to calculate the momentum distribution of the homogeneous electron gas at finite temperature. This is done by calculating the off-diagonal elements of the real-space density matrix,…
Density-functional theory forces, stresses and energies comprise a database from which the optimal parameters of a spline-based empirical potential combining Stillinger-Weber and modified embedded-atom forms are determined. Accuracy of the…
Ab initio metadynamics enables extracting free-energy landscapes having the accuracy of first principles electronic structure methods. We introduce an interface between the PLUMED code that computes free-energy landscapes and…
We numericaly demonstrate that, in double well models, the autocorrelation time of open path integral Monte Carlo simulations can be much smaller compared to standard ones using ring polymers. We also provide an intuitive explanation based…
In this work the free energy of solid phases is computed for the Lennard-Jones potential and for a model of NaCl. The free energy is evaluated through the Einstein crystal/molecule methodologies using the Molecular Dynamics programs:…
We describe and implement iMapD, a computer-assisted approach for accelerating the exploration of uncharted effective Free Energy Surfaces (FES), and more generally for the extraction of coarse-grained, macroscopic information from…
In this work, we developed an interatomic potential for saturated hydrocarbons using the modified embedded-atom method (MEAM), a reactive semi-empirical many-body potential based on density functional theory and pair potentials. We…
We present a new simulation method to calculate the free energy and the chemical potential of hard particle systems. The method relies on the introduction of a parameter dependent potential to smoothly transform between the hard particle…
The determination of potentials of mean force for solute insertion in a membrane by means of all-atom molecular dynamics simulations is often hampered by sampling issues. A multiscale approach to conformational sampling was recently…
We propose a new multi-scale molecular dynamics simulation method which can achieve high accuracy and high sampling efficiency simultaneously without aforehand knowledge of the coarse grained (CG) potential and test it for a biomolecular…
We present a method to accurately predict the Helmholtz harmonic free energies of molecular crystals in high-throughput settings. This is achieved by devising a computationally efficient framework that employs a Gaussian Process Regression…
Performing full-resolution atomistic simulations of nucleic acid folding has remained a challenge for biomolecular modeling. Understanding how nucleic acids fold and how they transition between different folded structures as they unfold and…