Related papers: Computing Absolute Free Energy with Deep Generativ…
We present a calculation of the change of free energy of a solid surface upon bending of the solid. It is based on extracting the surface stress through a molecular dynamics simulation of a bent slab by using a generalized stress theorem…
Accurate calculations of solvation free energies remain a central challenge in molecular simulations, often requiring extensive sampling and numerous alchemical intermediates to ensure sufficient overlap between phase-space distributions of…
We analyse the finite-size corrections to the free energy of crystals with a fixed center of mass. When we explicitly correct for the leading ($\ln N/N$) corrections, the remaining free energy is found to depend linearly on 1/N.…
This paper provides a concise description of the free energy principle, starting from a formulation of random dynamical systems in terms of a Langevin equation and ending with a Bayesian mechanics that can be read as a physics of sentience.…
Fluctuation relations allow for the computation of equilibrium properties, like free energy, from an ensemble of non-equilibrium dynamics simulations. Computing them for quantum systems, however, can be difficult, as performing dynamic…
The free energy principle (FEP) from neuroscience provides a framework called active inference for the joint estimation and control of state space systems, subjected to colored noise. However, the active inference community has been…
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…
The accurate but fast calculation of molecular excited states is still a very challenging topic. For many applications, detailed knowledge of the energy funnel in larger molecular aggregates is of key importance requiring highly accurate…
We propose a method, Temperature Integration, which allows an efficient calculation of free energy differences between two systems of interest, with the same degrees of freedom, which may have rough energy landscapes. The method is based on…
Comparison of free energies between different phases and different compositions underlies the prediction of alloy phase diagrams. To allow direct comparison, consistent reference points for the energies or enthalpies are required, and the…
Computational modeling is an integral part of catalysis research. With it, new methodologies are being developed and implemented to improve the accuracy of simulations while reducing the computational cost. In particular, specific…
Calculating free energies is an important and notoriously difficult task for molecular simulations. The rapid increase in computational power has made it possible to probe increasingly complex systems, yet extracting accurate free energies…
The Free Energy Principle (FEP) states that under suitable conditions of weak coupling, random dynamical systems with sufficient degrees of freedom will behave so as to minimize an upper bound, formalized as a variational free energy, on…
The free energy principle from neuroscience provides a brain-inspired perception scheme through a data-driven model learning algorithm called Dynamic Expectation Maximization (DEM). This paper aims at introducing an experimental design to…
We show how thermodynamic properties of molecular models can be computed over a large, multidimensional parameter space by combining multistate reweighting analysis with a linear basis function approach. This approach reduces the…
Core-electron x-ray photoelectron spectroscopy is a powerful technique for studying the electronic structure and chemical composition of molecules, solids and surfaces. However, the interpretation of measured spectra and the assignment of…
Retrosynthesis -- the process of identifying a set of reactants to synthesize a target molecule -- is of vital importance to material design and drug discovery. Existing machine learning approaches based on language models and graph neural…
This report presents the application of polynomial regression for estimating free energy differences using thermodynamic integration. We employ linear regression to construct a polynomial that optimally fits the thermodynamic integration…
We have considered a model of a small finite system with internal particles and surface degrees of freedom. All the main statistical distributions were explicitly obtained, on a pre thermodynamic limit basis. The concept of temperature or…
We propose an approach for computing the Gibbs free energy difference between phases of a material. The method is based on the determination of the average force acting on interfaces that separate the two phases of interest. This force,…