Related papers: Free energy calculations of a proton transfer reac…
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…
An efficient approach of measuring the absolute free energy in parallel tempering Monte Carlo using the exponential averaging method is discussed and the results are compared with those of population annealing Monte Carlo using the…
Using very long molecular dynamics simulation runs, temperature protocols spanning up to five orders of magnitude in time-scales are performed to investigate thermally activated structural relaxation in a model amorphous solid. The…
Machine learning potentials (MLPs) have become a popular tool in chemistry and materials science as they combine the accuracy of electronic structure calculations with the high computational efficiency of analytic potentials. MLPs are…
The uniform electron gas is a key model system in the description of matter, including dense plasmas and solid state systems. However, the simultaneous occurence of quantum, correlation, and thermal effects makes the theoretical description…
Heating of trapped ion clouds by interactions with free electrons crossing the trapping potential was observed. A model describing such process was proposed and discussed. The presented approach predicts two effects: pushing and heating of…
A vast array of phenomena, ranging from chemical reactions to phase transformations, are analysed in terms of a free energy surface defined with respect to a single or multiple order parameters. Enhanced sampling methods are typically used,…
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…
Free energy perturbation (FEP) is frequently used to evaluate the free energy change of a biological process, e.g. the drug binding free energy or the ligand solvation free energy. Due to the sampling inefficiency, FEP is often employed…
A general approach to calculate the diabatic surfaces for electron-transfer reactions is presented, based on first-principles molecular dynamics of the active centers and their surrounding medium. The excitation energy corresponding to the…
Modelling the sudden depressurisation of superheated liquids through nozzles is a challenge because the pressure drop causes rapid flash boiling of the liquid. The resulting jet usually demonstrates a wide range of structures, including…
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…
Free cooling of granular materials is analyzed on the basis of a pseudo-Liouville operator. Exchange of translational and rotational energy requires surface roughness for spherical grains, but occurs for non-spherical grains, like needles,…
We present a theoretical first-principles method to calculate the free energy of a magnetic system in its high-temperature paramagnetic phase, including vibrational, electronic, and magnetic contributions. The method for calculating free…
Replica exchange molecular dynamics (REMD) becomes more efficient as the frequency of swap between the temperatures is increased. Recently in [Plattner et al, J. Chem. Phys. 135, 134111 (2011)] a method was proposed to implement infinite…
We present a differentiable formalism for learning free energies that is capable of capturing arbitrarily complex model dependencies on coarse-grained coordinates and finite-temperature response to variation of general system parameters.…
Solvation free energy is an important design parameter in reaction kinetics and separation processes, making it a critical property to predict during process development. In previous research, directed message passing neural networks…
The high-temperature cubic-tetragonal phase transition of pure stoichiometric zirconia is studied by molecular dynamics (MD) simulations and within the framework of the Landau theory of phase transformations. The interatomic forces are…
Freezing of simple liquid metals and the relative stabilities of competing crystalline solids are investigated using thermodynamic perturbation theory, the interactions between ions being modeled by effective pair potentials derived from…
Temperature is a fundamental regulator of chemical and biochemical kinetics, yet capturing nonlinear thermal effects directly from experimental data remains a major challenge due to limited throughput and model flexibility. Recent advances…