Related papers: Single-Sweep Methods for Free Energy Calculations
To address the large gap between time scales that can be easily reached by molecular simulations and those required to understand protein dynamics, we propose a rapid self-consistent approximation of the side chain free energy at every…
We compute the energy levels of a 2D Hydrogen atom when a constant magnetic field is applied. With the help of a mixed-basis variational method and a genera lization of virial theorem, which consists in scaling the wave function, we…
We present an extension of Alchemical Transfer Method (ATM) for the estimation of relative binding free energies of molecular complexes applicable to conventional as well as scaffold-hopping alchemical transformations. The method, named…
Free energy functionals of Ginzburg-Landau type lie at the heart of a broad class of continuum dynamical models, such as the Cahn-Hilliard and Swift-Hohenberg equations. Despite the wide use of such models, the assumptions embodied in the…
We present a simple yet accurate numerical approach to compute the free energy of binding of multivalent objects on a receptor-coated surface. The method correctly accounts for the fact that one ligand can bind to at most one receptor. The…
We introduce a novel and powerful method for exploring the properties of the multidimensional free energy surfaces of complex many-body systems by means of a coarse-grained non-Markovian dynamics in the space defined by a few collective…
Thermodynamic phase transitions, a central concept in physics and chemistry, are typically controlled by an interplay of enthalpic and entropic contributions. In most cases, the estimation of the enthalpy in simulations is straightforward…
Atmospheric moist available potential energy (MAPE) has been traditionally defined as the potential energy of a moist atmosphere relative to that of the adiabatically sorted reference state defining a global potential energy minimum.…
The phase diagram of numerous materials of technological importance features high-symmetry high-temperature phases that exhibit phonon instabilities. Leading examples include shape-memory alloys, as well as ferroelectric, refractory, and…
In this paper we combine two powerful computational techniques, well-tempered metadynamics and time lagged independent component analysis. The aim is to develop a new tool for studying rare events and exploring complex free energy…
We formally extend the energy landscape approach for the thermodynamics of liquids to account for saddle points. By considering the extensive nature of macroscopic potential energies, we derive the scaling behavior of saddles with system…
We introduce a classical algorithm to approximate the free energy of local, translation-invariant, one-dimensional quantum systems in the thermodynamic limit of infinite chain size. While the ground state problem (i.e., the free energy at…
This paper develops the so-called Weighted Energy-Dissipation (WED) variational approach for the analysis of gradient flows in metric spaces. This focuses on the minimization of the parameter-dependent global-in-time functional of…
We propose a new numerical technique to deal with nonlinear terms in gradient flows. By introducing a scalar auxiliary variable (SAV), we construct efficient and robust energy stable schemes for a large class of gradient flows. The SAV…
The solid-liquid interface free energy \gamma sl is a key parameter controlling nucleation and growth during solidification and other phenomena. There are intrinsic difficulties in obtaining accurate experimental values, and the previous…
Recent developments in statistical mechanics have allowed the estimation of equilibrium free energies from the statistics of work measurements during processes that drive the system out of equilibrium. Here a different class of processes is…
We present a fast adaptive method for the evaluation of heat potentials, which plays a key role in the integral equation approach for the solution of the heat equation, especially in a non-stationary domain. The algorithm utilizes a…
First principles calculations based on density functional theory are having an incerasing impact on our understanding of molecule-surface interactions. For example, calculations of the multi-dimensional potential energy surface have…
We demonstrate how a prior assumption of smoothness can be used to enhance the reconstruction of free energy profiles from multiple umbrella sampling simulations using the Bayesian Gaussian process regression approach. The method we derive…
Targeted free energy perturbation uses an invertible mapping to promote configuration space overlap and the convergence of free energy estimates. However, developing suitable mappings can be challenging. Wirnsberger et al. (2020)…