Related papers: Multi-Layer Free Energy Perturbation
The primary limitation for the application of alchemical free energy methods to a wider variety of complex molecular systems is achieving reasonable sampling. Flexible binding complexes often have high free energy barriers, which require…
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,…
The free energy landscapes of several fundamental processes are characterized by high barriers separating long-lived metastable states. In order to explore these type of landscapes enhanced sampling methods are used. While many such methods…
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…
Understanding how different classes of molecules move across biological membranes is a prerequisite to predicting a solute's permeation rate, which is a critical factor in the fields of drug design and pharmacology. We use biased Molecular…
High-throughput preclinical perturbation screens, where the effects of genetic, chemical, or environmental perturbations are systematically tested on disease models, hold significant promise for machine learning-enhanced drug discovery due…
Polymorphism rationalizes how processing can control the final structure of a material. The rugged free-energy landscape and exceedingly slow kinetics in the solid state have so far hampered computational investigations. We report for the…
In this paper, we present a study on how to develop an efficient multiscale simulation strategy for the dynamics of chemically active systems on low-dimensional supports. Such reactions are encountered in a wide variety of situations,…
We calculate the free energy of a hot gas of electrons and photons to three loops using the hard-thermal-loop perturbation theory reorganization of finite-temperature perturbation theory. We calculate the free energy through three loops by…
The 'free energy principle' (FEP) has been suggested to provide a unified theory of the brain, integrating data and theory relating to action, perception, and learning. The theory and implementation of the FEP combines insights from…
Relative Binding Free Energy (RBFE) calculations are a cornerstone of rational hit-to-lead and lead optimization in modern drug discovery. However, the high computational cost and limited reliability in tackling large or complex molecular…
Current theories of heteropolymers are inherently macrpscopic, but are applied to folding proteins which are only mesoscopic. In these theories, one computes the averaged free energy over sequences, always assuming that it is self-averaging…
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…
Given a chemical reaction going from reactant (R) to the product (P) on a potential energy surface (PES) and a collective variable (CV) that discriminates between R and P, one can define a free-energy profile (FEP) as the logarithm of the…
We describe and implement iMapD, a computer-assisted approach for accelerating the exploration of uncharted effective Free Energy Surfaces (FES), and more generally for the extraction of coarse-grained, macroscopic information from…
Relative free energy calculations are now widely used in academia and industry, but the accuracy is often limited by poor sampling of the complexes conformational ensemble. To address this, we have developed a novel method termed…
The free energetics of water density fluctuations in bulk water, at interfaces, and in hydrophobic confinement inform the hydration of hydrophobic solutes as well as their interactions and assembly. The characterization of such free…
In the last decade, the free energy principle (FEP) and active inference (AIF) have achieved many successes connecting conceptual models of learning and cognition to mathematical models of perception and action. This effort is driven by a…
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…
This paper reviews standard oversampling strategies as performed in the Multiscale Finite Element Method (MsFEM). Common to those approaches is that the oversampling is performed in the full space restricted to a patch but including coarse…