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Ab initio molecular dynamics (AIMD) simulations employing density functional theory (DFT) and plane waves are routinely carried out using density functionals at the level of Generalized Gradient Approximation (GGA). AIMD simulations…
Efficient computational methods that are capable of supporting experimental measures obtained at constant values of pH and redox potential are important tools as they serve to, among other things, provide additional atomic level information…
The modeling of solid-state transformations, such as polymorphic transitions and chemical reactions in molecular crystals, is vital for many applications including drug design or the development of new synthesis methods. However, a…
Configuration-interaction-type calculations on electronic and vibrational structure are often the method of choice for the reliable approximation of many-particle wave functions and energies. The exponential scaling, however, limits their…
In this paper, a hybrid quasi-static atomistic simulation method at finite temperature is developed, which combines the advantages of MD for thermal equilibrium and atomic-scale finite element method (AFEM) for efficient equilibration. Some…
The development and implementation of increasingly accurate methods for electronic structure calculations mean that, for many atomistic simulation problems, treating light nuclei as classical particles is now one of the most serious…
Developing efficient path integral (PI) methods for atomistic simulations of vibrational spectra in heterogeneous condensed phases and interfaces has long been a challenging task. Here, we present the h-CMD method, short for hybrid centroid…
We describe an efficient quantum embedding framework for realistic ab initio density matrix embedding (DMET) calculations in solids. We discuss in detail the choice of orbitals and mapping to a lattice, treatment of the virtual space and…
We compare a newly developed hybrid simulation method which combines classical molecular dynamics (MD) and computational fluid dynamics (CFD) to a simulation consisting only of molecular dynamics. The hybrid code is composed of three…
We extend density matrix embedding theory to periodic systems, resulting in an electronic band structure method for solid-state materials. The electron correlation can be captured by means of a local impurity model using various choices of…
Intermolecular vibrations are extremely challenging to describe but are the most crucial part for determining entropy and hence free energies, and enable for instance the distinction between different crystal-packing arrangements of the…
We present a new molecular-dynamics algorithm for integrating the equations of motion for a system of particles interacting with mixed continuous/impulsive forces. This method, which we call Impulsive Verlet, is constructed using operator…
Ab initio molecular dynamics (AIMD) based on density functional theory (DFT) has become a workhorse for studying the structure, dynamics, and reactions in condensed matter systems. Currently, AIMD simulations are primarily carried out at…
Multichannel frequency estimation with incomplete data and miscellaneous noises arises in array signal processing, modal analysis, wireless communications, and so on. In this paper, we consider maximum-likelihood(-like) optimization methods…
Variational methods are used to calculate structural and thermodynamical properties of a titrating polyelectrolyte in a discrete representation. The Coulomb interactions are emulated by harmonic repulsive forces, the force constants being…
With the path integral approach, the thermal average in a multi-electronic-state quantum systems can be approximated by the ring polymer representation on an extended configuration space, where the additional degrees of freedom are…
Existing machine learning methods for molecular (e.g., gene) embeddings are restricted to specific tasks or data modalities, limiting their effectiveness within narrow domains. As a result, they fail to capture the full breadth of gene…
Obtaining the free energy of large molecules from quantum mechanical energy functions is a longstanding challenge. We describe a method that allows us to estimate, at the quantum mechanical level, the harmonic contributions to the…
A variational approach, based on a discrete representation of the chain, is used to calculate free energy and conformational properties in polyelectrolytes. The true bond and Coulomb potentials are approximated by a trial isotropic harmonic…
Including quantum mechanical effects on the dynamics of nuclei in the condensed phase is challenging, because the complexity of exact methods grows exponentially with the number of quantum degrees of freedom. Efforts to circumvent these…