Related papers: Using Metadynamics to Reveal Extractant Conformati…
The rational design of single molecule electrical components requires a deep and predictive understanding of structure-function relationships. Here we explore the relationship between chemical substituents and the conductance of…
Performing alchemical transformations, in which one molecular system is nonphysically changed to another system, is a popular approach adopted in performing free energy calculations associated with various biophysical processes, such as…
This paper presents the first implementation of a coupling between advanced wave function theories and molecular density functional theory (MDFT). This method enables the modeling of solvent effect into quantum mechanical (QM) calculations…
We present a family of alchemical perturbation potentials that enable the calculation of hydration free energies of small to medium-sized molecules in a concerted single alchemical coupling step instead of the commonly used sequence of two…
The knowledge of the Free Energy Landscape topology is the essential key to understand many biochemical processes. The determination of the conformers of a protein and their basins of attraction takes a central role for studying molecular…
Hypotheses: To correctly predict the aggregation number and size of wormlike micelles from ionic surfactants, the molecular-thermodynamic theory has to calculate the free energy per molecule in the micelle with accuracy better than 0.01 kT,…
We show that classical molecular density functional theory (MDFT), here in the homogeneous reference fluid approximation in which the functional is inferred from the properties of the bulk solvent, is a powerful new tool to study, at a…
We combine three-dimensional (3D) large-eddy simulations (LES) and resolvent analysis to design active separation control techniques on a NACA 0012 airfoil. Spanwise-periodic flows over the airfoil at a chord-based Reynolds number of…
A 2.5-dimensional magnetohydrodynamics simulation analysis of the energy release for three different reconnection regimes is presented. The system under investigation consists in a current-sheet located in a medium with a strong density…
The accurate prediction of solvation free energy is of significant importance as it governs the behavior of solutes in solution. In this work, we apply a variety of machine learning techniques to predict and analyze the alchemical free…
Low-energy excitations play a key role in all condensed-matter systems, yet there is limited understanding of their nature in glasses, where they correspond to local rearrangements of groups of particles. Here we introduce an algorithm to…
Accurate calculations of solvation free energies remain a central challenge in molecular simulations, often requiring extensive sampling and numerous alchemical intermediates to ensure sufficient overlap between phase-space distributions of…
This work examines the conformational ensemble involved in $\beta$-hairpin folding by means of advanced molecular dynamics simulations and dimensionality reduction. A fully atomistic description of the protein and the surrounding solvent…
Understanding lithium solvation and transport in ionic liquids is important due to their possible application in electrochemical devices. Using first-principles simulations aided by a metadynamics approach we study the free-energy landscape…
Trajectories provide dynamical information that is discarded in free energy calculations, for which we sought to design a scheme with the hope of saving cost for generating dynamical information. We first demonstrated that snapshots in a…
Despite the modern level of development of computational chemistry methods and techno-logical progress, fast and accurate determination of solvation free energy remains a huge problem for physical chemists. In this paper, we describe two…
Theoretical studies of protein folding on lattice models relie on the assumption that water close to amino-acids is always in thermal equilibrium all along the folding pathway. Within this framework, it has always been considered that…
We introduce multistate metadynamics for automatic exploration of conical intersection seams between adiabatic Born-Oppenheimer potential energy surfaces in molecular systems. By choosing the energy gap between the electronic states as a…
We present a method for determining the free energy dependence on a selected number of collective variables using an adaptive bias. The formalism provides a unified description which has metadynamics and canonical sampling as limiting…
We report molecular-dynamics simulation results performed for a model of molecular liquid orthoterphenyl in supercooled states, which we then compare with both experimental data and mode-coupling-theory (MCT) predictions, aiming at a better…