Related papers: Multidimensional replica-exchange method for free-…
In 1986, Swendsen and Wang proposed a replica Monte Carlo algorithm for spin glasses [Phys. Rev. Lett. 57 (1986) 2607]. Two important ingredients are present, (1) the use of a collection of systems (replicas) at different of temperatures,…
A simple exact-exchange density-functional method for a quasi-two-dimensional electron gas with variable density is presented. An analytical expression for the exact-exchange potential with only one occupied subband is provided, without…
Nested sampling (NS) has emerged as a powerful tool for exploring thermodynamic properties in materials science. However, its efficiency is often hindered by the limitations of Markov chain Monte Carlo (MCMC) sampling. In strongly…
Free energies play a central role in characterising the behaviour of chemical systems and are among the most important quantities that can be calculated by molecular dynamics simulations. Solvation free energies in various organic solvents,…
Ligand-receptor interactions are ubiquitous in biology and have become popular in materials in view of their applications to programmable self-assembly. Although, complex functionalities often emerge from the simultaneous interaction of…
The replica exchange molecular dynamics (REMD) approach is applied to four oligomeric peptide systems. At physiologically relevant temperature values REMD samples conformation space and aggregation transitions more efficiently than constant…
We present a methodology for accelerating the estimation of the free energy from path integral Monte Carlo simulations by considering an intermediate artificial reference system where interactions are inexpensive to evaluate numerically.…
The principles behind the computation of protein-ligand binding free energies by Monte Carlo integration are described in detail. The simulation provides gas-phase binding free energies that can be converted to aqueous energies by solvation…
Algorithms based on the particle flow approach are becoming increasingly utilized in collider experiments due to their superior jet energy and missing energy resolution compared to the traditional calorimeter-based measurements. Such…
We demonstrate the use of a new algorithm called the Flat Histogram sampling algorithm for the simulation of lattice polymer systems. Thermodynamics properties, such as average energy or entropy and other physical quantities such as…
A central endeavor of thermodynamics is the measurement of free energy changes. Regrettably, although we can measure the free energy of a system in thermodynamic equilibrium, typically all we can say about the free energy of a…
Density-functional theory simplifies many-electron calculations by approximating the exchange and correlation interactions with a one-electron operator that is a functional of the density. Hybrid functionals incorporate some amount of exact…
We introduce a new sampling algorithm, the equi-energy sampler, for efficient statistical sampling and estimation. Complementary to the widely used temperature-domain methods, the equi-energy sampler, utilizing the temperature--energy…
Quasi-dynamic energy flow calculation is an indispensable tool for the heat and electricity integrated energy system (HE-IES) analysis. One solves the nonlinear partial differential algebraic equations to obtain thermal, hydraulic and…
High-temperature dimensional reduction provides a systematic effective field theory framework for studying finite-temperature thermodynamics and cosmological phase transitions. While the matching of super-renormalizable operators in the…
We present a new simulation method to calculate the free energy and the chemical potential of hard particle systems. The method relies on the introduction of a parameter dependent potential to smoothly transform between the hard particle…
Estimating the eigenvalue or energy gap of a Hamiltonian H is vital for studying quantum many-body systems. Particularly, many of the problems in quantum chemistry, condensed matter physics, and nuclear physics investigate the energy gap…
Accurate free-energy calculations are essential for predicting thermodynamic properties and phase stability, but existing methods are limited: phonon-based approaches neglect anharmonicity and liquids, while molecular dynamics (MD) is…
In a recent article (J. Comput. Chem. 2013, 34, 132-140), convective Replica-Exchange (convective-RE) has been presented as an alternative to the standard even-odd transition scheme. Computations on systems of various complexity have shown…
We propose a new method for calculating total energies of systems of interacting electrons, which requires little more computational resources than standard density-functional theories. The total energy is calculated within the framework of…