Related papers: Using Metadynamics to Reveal Extractant Conformati…
We present a computational scheme for extracting the energy level alignment of a metal/molecule interface, based on constrained density functional theory and local exchange and correlation functionals. The method, applied here to benzene on…
A major challenge in nonadiabatic molecular dynamics is to automatically and objectively identify the key reaction coordinates that drive molecules toward distinct excited-state decay channels. Traditional manual analyses are inefficient…
Machine learning is used to approximate the kinetic energy of one dimensional diatomics as a functional of the electron density. The functional can accurately dissociate a diatomic, and can be systematically improved with training. Highly…
Coarse-graining of fully atomistic molecular dynamics simulations is a long-standing goal in order to allow the description of processes occurring on biologically relevant timescales. For example, the prediction of pathways, rates and…
The excess free energy functional of classical density functional theory depends upon the type of fluid model, specifically on the choice of (pair) potential, is unknown in general, and is approximated reliably only in special cases. We…
The molecular dynamics (MD) simulation study of solvation structure and free energetics in 1-ethyl-3-methylimidazolium chloride and 1-ethyl-3-methylimidazolium hexafluorophosphate using a probe solute in the preceding article [Y. Shim, M.…
In standard molecular junctions, a molecular structure is placed between and connected to metal leads. Understanding how mechanical tuning in such molecular junctions can change heat conductance has interesting applications in nanoscale…
Ensemble density functional theory (eDFT) is an exact time-independent alternative to time-dependent DFT (TD-DFT) for the calculation of excitation energies. Despite its formal simplicity and advantages in contrast to TD-DFT (multiple…
We demonstrate the accurate calculation of entropies and free energies for a variety of liquid metals using an extension of the two phase thermodynamic (2PT) model based on a decomposition of the velocity autocorrelation function into…
Metadynamics is a commonly used and successful enhanced sampling method. By the introduction of a history dependent bias which depends on a restricted number of collective variables(CVs) it can explore complex free energy surfaces…
The conversion of $\mathrm{CO_2}$ into useful products such as methanol is a key strategy for abating climate change and our dependence on fossil fuels. Developing new catalysts for this process is costly and time-consuming and can thus…
Supercooled liquids are metastable states realized by suppressing crystallization below the melting temperature. While it is well established that their dynamics slow down dramatically and become spatially heterogeneous upon cooling, the…
The aqueous solvent profoundly influences protein folding, yet its effects are relatively poorly understood. In this study, we investigate the impact of solvation on the folding of lattice proteins by using Monte Carlo simulations. The…
We use a free energy functional theory to elucidate general properties of heterogeneously ordering, fast folding proteins, and we test our conclusions with lattice simulations. We find that both structural and energetic heterogeneity can…
Active semiflexible filaments are crucial in various biophysical processes, yet insights into their single-filament behavior have predominantly relied on theory and simulations, owing to the scarcity of controllable synthetic systems. Here,…
Molecular fragment or embedding methods are powerful techniques for overcoming scalability limitations in electronic structure theory by dividing large molecular systems into individual units that are small enough to be treated using…
Kinetic Riemann simulations have been completed to explore particle heating during guide field reconnection in the low-$\beta$ environment of the inner heliosphere and the solar corona. The reconnection exhaust is bounded by two rotational…
We present a precise and general method to map the activity of electrocatalysts across multiple sites. Starting from a mean-field statistical mechanics model, we introduce an effective adsorption free energy descriptor that explicitly…
Because of consuming energy to drive their motion, systems of active colloids are intrinsically out of equilibrium. In the past decade, a variety of intriguing dynamic patterns have been observed in systems of active colloids, and they…
We present an Adaptively Biased Molecular Dynamics (ABMD) method for the computation of the free energy surface of a reaction coordinate using non-equilibrium dynamics. The ABMD method belongs to the general category of umbrella sampling…