相关论文: Accurate Free Energy Estimations of Molecular Syst…
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.…
We present a new method to compute free energies at a quantum mechanical (QM) level of theory from molecular simulations using cheap reference potential energy functions, such as force fields. To overcome the poor overlap between the…
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…
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…
Free energy perturbation (FEP) is considered the gold-standard simulation method for estimating small molecule binding affinity, a quantity of vital importance to drug discovery. The accuracy of FEP critically depends on an accurate model…
The Free-Energy-Principle (FEP) is an influential and controversial theory which postulates a deep and powerful connection between the stochastic thermodynamics of self-organization and learning through variational inference. Specifically,…
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 (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…
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…
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)…
The free energy principle (FEP) states that any dynamical system can be interpreted as performing Bayesian inference upon its surrounding environment. In this work, we examine in depth the assumptions required to derive the FEP in the…
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…
Deep learning has revolutionised artificial intelligence (AI) by enabling automatic feature extraction and function approximation from raw data. However, it faces challenges such as a lack of out-of-distribution generalisation, catastrophic…
We have developed a thorough and accurate method of determining anharmonic free energies, the temperature dependent effective potential technique (TDEP). It is based on \emph{ab initio} molecular dynamics followed by a mapping onto a model…
This study examines a new formulation of non-equilibrium thermodynamics, which gives a conditional derivation of the ``maximum entropy production'' (MEP) principle for flow and/or chemical reaction systems at steady state. The analysis uses…
In this paper we show how The Free Energy Principle (FEP) can provide an explanation for why real-world networks deviate from scale-free behaviour, and how these characteristic deviations can emerge from constraints on information…
Thermodynamic phase transitions, a central concept in physics and chemistry, are typically controlled by an interplay of enthalpic and entropic contributions. In most cases, the estimation of the enthalpy in simulations is straightforward…
The accurate estimation of free energy differences between two states is a long-standing challenge in molecular simulations. Traditional approaches generally rely on sampling multiple intermediate states to ensure sufficient overlap in…
One reason that free energy difference calculations are notoriously difficult in molecular systems is due to insufficient conformational overlap, or similarity, between the two states or systems of interest. The degree of overlap is…