相关论文: Free energy calculations for atomic solids through…
Understanding how different classes of molecules move across biological membranes is a prerequisite to predicting a solute's permeation rate, which is a critical factor in the fields of drug design and pharmacology. We use biased Molecular…
An expression for the free energy of embryo formation is constructed and analyzed. The Gibbs dividing surfaces method is used to attain a coincidence between Laplace formula for critical embryo and integral definitions of concenterations…
We present a simulation scheme to calculate defect formation free energies at a molecular crystal/water interface based on force-field molecular dynamics (MD) simulations. To this end we adopt and modify existing approaches to calculate…
In this work, phase diagrams of a modified two-mode phase-field crystal (PFC) that show two-dimensional (2D) and three-dimensional (3D) crystallographic structures were determined by utilizing a free energy minimization method. In this…
We explore the recently introduced $\eta$-ensemble approach to compute the free energy directly from \emph{ab initio} path integral Monte Carlo (PIMC) simulations [T.~Dornheim \emph{et al.}, arXiv:2407.01044] and apply it to the archetypal…
We develop analytic approximations of thermodynamic functions of fully ionized nonideal electron-ion plasma mixtures. In the regime of strong Coulomb coupling, we use our previously developed analytic approximations for the free energy of…
We investigate relations between spatial properties of the free energy and the radius of Gaussian curvature of the underlying curved lattice geometries. For this purpose we derive recurrence relations for the analysis of the free energy…
Active nematics are influenced by alignment angle singularities called topological defects. The localization of these defects is of major interest for biological applications. The total distortion of alignment angles due to defects is…
The molecular distributions obtained from canonical Monte Carlo simulations can be used to find an approximate interaction energy. This serves as the basis of a method for estimating the binding free energy for a ligand to a protein which…
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…
The evaluation of Coulomb forces is a difficult task. The summations that are involved converge only conditionally and care has to be taken in selecting the appropriate procedure to define the limits. The Ewald method is a standard method…
The determination of the solvation free energy of ions and molecules holds profound importance across a spectrum of applications spanning chemistry, biology, energy storage, and the environment. Molecular dynamics simulations are a powerful…
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 study the phase behavior of a nematic liquid crystal confined between a flat substrate with strong anchoring and a patterned substrate whose structure and local anchoring strength we vary. By first evaluating an effective surface free…
Metadynamics is a powerful computational tool to obtain the free energy landscape of complex systems. The Monte Carlo algorithm has proven useful to calculate thermodynamic quantities associated with simplified models of proteins, and thus…
We have developed a class of idealized models of chromonic molecules which are miscible in water, but which can form aggregates which in turn organize into lyotropic liquid crystal (LC) phases. By carrying out Monte Carlo simulation in a…
Obtaining the free energies of condensed phase chemical reactions remains computationally prohibitive for high-level quantum mechanical methods. We introduce a hierarchical machine learning framework that bridges this gap by distilling…
In this work a method is proposed for computing step free energies for faceted solid-liquid interfaces based on atomistic simulations. The method is demonstrated in an application to (111) interfaces in elemental Si, modeled with the…
The self-consistent harmonic approximation is an effective harmonic theory to calculate the free energy of systems with strongly anharmonic atomic vibrations, and its stochastic implementation has proved to be an efficient method to study,…
The free energy of glasses cannot be estimated using thermodynamic integration, as glasses are intrinsically not in equilibrium. We present numerical simulations showing that, in contrast, plausible free-energy estimates of a Kob-Andersen…