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A heuristic perspective on non-variational Free Energy modulation at the sleep-like edge
(Elsevier, 2021-10)
Background: The variational Free Energy Principle (FEP) establishes that a neural system minimizes a free energy function of their internal state through environmental sensing entailing beliefs about hidden states in their ...
Chemical potential and free energy of nanoconfined water in Newton black films
(Elsevier Science, 2018-09)
In this work we investigate possible approximations to the free energy and chemical potential of water within a Newton black film as a natural nanoconfinement. As a first step we explore the different approximations in a ...
Bending Lipid Bilayers: A Closed-Form Collective Variable for Effective Free-Energy Landscapes in Quantitative Biology
(American Chemical Society, 2018-04)
Curvature-related processes are of major importance during protein-membrane interactions. The illusive simplicity of membrane reshaping masks a complex molecular process crucial for a wide range of biological functions ...
Effect of intercalated water on potassium ion transport through Kv1.2 channels studied via on-the-fly free-energy parametrization
(American Chemical Society, 2018-05)
We introduce a two-dimensional version of the method called on-the-fly free energy parametrization (OTFP) to reconstruct free-energy surfaces using Molecular Dynamics simulations, which we name OTFP-2D. We first test the ...
Free energies divergences as statistical quantifiers
(Elsevier Science, 2021-02-15)
We describe differences between the statistical behavior of two distinct systems by appeal to a new quantifier that we call a free-energies divergence. Using it, new perspectives arise with regards to a comparative analysis ...
Piezoelectric and structural properties of bismuth sodium potassium titanate lead-free ceramics for energy harvesting
(Springer, 2021-07)
The development of piezoelectric ceramics with high energy conversion efficiency is of decisive importance for the requirements of the advanced energy harvesting devices toward miniaturization and integration. Lead ...
FAMBE-pH: a fast and accurate method to compute the total solvation free energies of proteins
(American Chemical Society, 2008-12)
A fast and accurate method to compute the total solvation free energies of proteins as a function of pH is presented. The method makes use of a combination of approaches, some of which have already appeared in the literature; ...
On the accurate estimation of free energies using the jarzynski equality
(John Wiley & Sons Inc, 2019-02)
The Jarzynski equality is one of the most widely celebrated and scrutinized nonequilibrium work theorems, relating free energy to the external work performed in nonequilibrium transitions. In practice, the required ensemble ...
Lessons learned about steered molecular dynamics simulations and free energy calculations
(Wiley Blackwell Publishing, Inc, 2019-01)
The calculation of free energy profiles is central in understanding differential enzymatic activity, for instance, involving chemical reactions that require QM-MM tools, ligand migration, and conformational rearrangements ...
Charting molecular free-energy landscapes with an atlas of collective variables
(American Institute of Physics, 2016-11)
Collective variables (CVs) are a fundamental tool to understand molecular flexibility, to compute free energy landscapes, and to enhance sampling in molecular dynamics simulations. However, identifying suitable CVs is ...