Related papers: Multimap targeted free energy estimation
We present an approach that extends the theory of targeted free energy perturbation (TFEP) to calculate free energy differences and free energy surfaces at an accurate quantum mechanical level of theory from a cheaper reference potential.…
The Targeted Free Energy Perturbation (TFEP) method aims to overcome the time-consuming and computer-intensive stratification process of standard methods for estimating the free energy difference between two states. To achieve this, TFEP…
Free energy perturbation (FEP) was proposed by Zwanzig more than six decades ago as a method to estimate free energy differences, and has since inspired a huge body of related methods that use it as an integral building block. Being an…
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…
We introduce a new procedure to construct weight factors, which flatten the probability density of the overlap with respect to some pre-defined reference configuration. This allows one to overcome free energy barriers in the overlap…
Free energy profile (FE Profile) is an essential quantity for the estimation of reaction rate and the validation of reaction mechanism. For chemical reactions in condensed phase or enzymatic reactions, the computation of FE profile at ab…
Based on a generative model (GM) and beliefs over hidden states, the free energy principle (FEP) enables an agent to sense and act by minimizing a free energy bound on Bayesian surprise. Inclusion of prior beliefs in the GM about desired…
The minimum free-energy path (MFEP) is the most probable route of the nucleation process on the multidimensional free-energy surface. In this study, the phase-field equation is used as a mathematical tool to deduce the minimum free-energy…
Targeted free energy perturbation uses an invertible mapping to promote configuration space overlap and the convergence of free energy estimates. However, developing suitable mappings can be challenging. Wirnsberger et al. (2020)…
Finding optimal solutions to combinatorial optimization problems is pivotal in both scientific and technological domains, within academic research and industrial applications. A considerable amount of effort has been invested in the…
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…
Free energy profiles serve as a fundamental bridge between microscopic atomic fluctuations and macroscopic thermodynamic observables. Estimating the free energy profile along a reaction coordinate, referred to as the potential of mean force…
The free energy principle (FEP), as an encompassing framework and a unified brain theory, has been widely applied to account for various problems in fields such as cognitive science, neuroscience, social interaction, and hermeneutics. As a…
In QM/MM indirect free energy simulation, QM/MM corrections can be obtained from integration of partial derivatives of alchemical Hamiltonians or from perturbation-based estimators including free energy perturbation (FEP) and acceptance…
This paper presents a meta-theory of the usage of the free energy principle (FEP) and examines its scope in the modelling of physical systems. We consider the so-called `map-territory fallacy' and the fallacious reification of model…
The free energy principle (FEP) is a mathematical framework that describes how biological systems self-organize and survive in their environment. This principle provides insights on multiple scales, from high-level behavioral and cognitive…
A simple, efficient, and accurate method is proposed to map multi-dimensional free energy landscapes. The method combines the temperature-accelerated molecular dynamics (TAMD) proposed in [Maragliano & Vanden-Eijnden, Chem. Phys. Lett. 426,…
We present design and implementation of a novel neural network potential (NNP) and its combination with an electrostatic embedding scheme, commonly used within the context of hybrid quantum-mechanical/molecular-mechanical (QM/MM)…
In this paper we study multi-matrix models whose potentials are perturbations of the quadratic potential associated with independent GUE random matrices. More precisely, we compute the free energy and the expectation of the trace of…
Reinforcement Learning (RL) requires a large amount of exploration especially in sparse-reward settings. Imitation Learning (IL) can learn from expert demonstrations without exploration, but it never exceeds the expert's performance and is…