Related papers: Bounding free energy difference with flow matching
We review uses of the generalized-ensemble algorithms for free-energy calculations in protein folding. Two of the well-known methods are multicanonical algorithm and replica-exchange method; the latter is also referred to as parallel…
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…
The computation of free energy differences through an exponential weighting of out of equilibrium paths (known as the Jarzynski equality) is often used for transitions between states described by an external parameter $\lambda$ in the…
Phonon frequency moments and thermodynamic functions (electrostatic and vibrational parts of the free energy, internal energy, and heat capacity) are calculated for bcc and fcc Coulomb crystals in the harmonic approximation with a…
We numerically calculate the energy and momentum transfer rates due to Coulomb scattering between two fluids moving with a relative velocity. The results are fitted by simple functions. The fitting formulae are useful to simulate outflows…
We present a machine-learning model based on normalizing flows that is trained to sample from the isobaric-isothermal ensemble. In our approach, we approximate the joint distribution of a fully-flexible triclinic simulation box and particle…
We report on a methodology for the treatment of the Coulomb energy and potential in Kohn-Sham density functional theory that is free from self-interaction effects. Specifically, we determine the Coulomb potential given as the functional…
The intrinsic Helmholtz free-energy functional, the centerpiece of classical density functional theory, is at best only known approximately for 3D systems. Here we introduce a method for learning a neuralnetwork approximation of this…
We propose a numerical technique to compute the equilibrium free energy of glasses that cannot be prepared quasi-reversibly. For such systems, standard techniques for estimating the free energy by extrapolation, cannot be used. Instead, we…
Free energies govern the behavior of soft and liquid matter, and improving their predictions could have a large impact on the development of drugs, electrolytes or homogeneous catalysts. Unfortunately, it is challenging to devise an…
We build a double quantum-dot system with Coulomb coupling and aim at studying the connections among the entropy production, free energy, and information flow. By utilizing the concepts in stochastic thermodynamics and graph theory…
A recently proposed extension of the interaction flow method is applied to exemplary cases of selected physical and methodical parameters for the two-dimensional Hubbard model away from half-filling and perfect nesting. In this scheme, the…
This paper determines the excess free energy associated with the formation of a spherical cavity in a hard sphere fluid. The solvation free energy can be calculated by integration of the structural changes induced by inserting the cavity…
We describe a method that focuses sampling effort on a user-defined selection of a large system, which can lead to substantial decreases in computational effort by speeding up the calculation of nonbonded interactions. A naive approach can…
We calculate the free energy of a hot gas of electrons and photons to three loops using the hard-thermal-loop perturbation theory reorganization of finite-temperature perturbation theory. We calculate the free energy through three loops by…
When a system is driven out of equilibrium by a time-dependent protocol that modifies the Hamiltonian, it follows a nonequilibrium path. Samples of these paths can be used in nonequilibrium work theorems to estimate equilibrium quantities,…
Excess contributions to the free energy due to interfaces occur for many problems encountered in the statistical physics of condensed matter when coexistence between different phases is possible (e.g. wetting phenomena, nucleation, crystal…
We propose a proof of convergence of an adaptive method used in molecular dynamics to compute free energy profiles. Mathematically, it amounts to studying the long-time behavior of a stochastic process which satisfies a non-linear…
Computing phase diagrams of model systems is an essential part of computational condensed matter physics. In this paper we discuss in detail the interface pinning (IP) method for calculation of the Gibbs free energy difference between a…
We use free energy lattice Boltzmann methods (FRE LBM) to simulate shear and extensional flow of a binary mixture in two and three dimensions. To this end, two classical configurations are digitally twinned, namely a parallel-band device…