Related papers: Single-Sweep Methods for Free Energy Calculations
The development and first applications of a new periodic energy decomposition analysis (pEDA) scheme for extended systems based on the Kohn-Sham approach to density functional theory are described. The pEDA decomposes the binding energy…
In recent years single molecule force spectroscopy has opened a new avenue to provide profiles of the complex energy landscape of biomolecules. In this field, quantitative analyses of the data employing sound theoretical models, have played…
Nested sampling is a Bayesian sampling technique developed to explore probability distributions lo- calised in an exponentially small area of the parameter space. The algorithm provides both posterior samples and an estimate of the evidence…
According to the mean-field glass theory, the (free) energy landscape of disordered systems is hierarchical and ultrametric if they belong to the full-replica-symmetry-breaking universality class. However, examining this theoretical picture…
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…
This paper introduces a method for computing the Helmholtz free energy using the flow matching technique. Unlike previous work that utilized flow-based models for variational free energy calculations, this method provides bounds for free…
The absolute free energy -- or partition function, equivalently -- of a molecule can be estimated computationally using a suitable reference system. Here, we demonstrate a practical method for staging such calculations by growing a molecule…
With the help of metadynamics it is possible to calculate efficiently the free energy of systems displaying high energy barriers as a function of few selected "collective variables". In doing this, the contribution of all the other degrees…
Determining accurate absolute surface energies for polar surfaces of semiconductors has been a great challenge in decades. Here, we propose pseudo-hydrogen passivation to calculate them, using density functional theory approaches. By…
A mixed basis approach based on density functional theory is extended to one-dimensional(1D) systems. The basis functions here are taken to be the localized B-splines for the two finite non-periodic dimensions and the plane waves for the…
We propose a method for estimating smooth real-frequency self-energy in the dynamical mean-field theory with the finite-temperature exact diagonalization (DMFT-ED). One of the benefits of DMFT-ED calculations is that one can obtain…
Free-energy differences between pairs of end-states can be estimated based on molecular dynamics (MD) simulations using standard pathway-dependent methods such as thermodynamic integration (TI), free-energy perturbation, or Bennett's…
A novel overlap histogramming method based on Dual-Topology Hamiltonian-Replica-Exchange simulation technique is presented to efficiently calculate relative free energy difference in rough energy landscape, in which multiple conformers…
In the last decade, the atomically focused beam of a scanning transmission electron microscope (STEM) was shown to induce a broad set of transformations of material structure, open pathways for probing atomic-scale reactions and…
Estimating the free energy in molecular simulation requires, implicitly or explicitly, counting how many times the system is observed in a finite region. If the simulation is biased by an external potential, the weight of the configurations…
We present a novel method for the calculation of the energy density of states D(E) for systems described by classical statistical mechanics. The method builds on an extension of a recently proposed strategy that allows the free energy…
A new method is proposed for the calculation of the free energy of an N-component Phi^4 theory at finite temperature. The method combines a perturbative treatment of the hard modes with a non-perturbative treatment in the effectively…
In this study, we carried out equilibrium molecular dynamics (EMD) simulations of the liquid-liquid interface between two different Lennard-Jones components with varying miscibility, where we examined the relation between the interfacial…
The bootstrap method has proven useful for a wide range of matrix models. Here, we show that the computed momenta can be used to reconstruct the underlying eigenvalue probability distribution, which in turn allows us to compute the free…
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…