arXiv subjects

Gabriela B. Correa

Publications and source records attributed to Gabriela B. Correa.

3 recordsLinked to original sources

arXiv2026

Integrated Alchemical and Conformational Enhanced Sampling for Solvation Free Energy Calculations

Accurate solvation free energies from molecular dynamics simulations require efficient sampling of coupled slow variables, including solvent coordinates, solute conformational modes, and the alchemical coordinate $λ$. Here, we develop a $λ$-dynamics framework that combines mass scaling, on-the-fly probability enhanced sampling (OPES), and driven adiabatic free energy dynamics (d-AFED) to address these sampling challenges within a unified protocol. For rigid organic solutes, Hamiltonian replica exchange with mass scaling is first used to quantify the effect of octanol solvent relaxation. Reducing all octanol atomic masses by a factor of ten accelerates convergence by more than fivefold while preserving equilibrium solvation free energies. These calculations then provide reference benchmarks for $λ$-OPES, a dual-bias $λ$-dynamics strategy that combines the "standard" and "explore" variants of OPES to promote transitions along the alchemical coordinate. This approach reaches convergence on timescales comparable to replica exchange, but without predefined $λ$ windows or multiple parallel simulations. For flexible $N$-acetyl amino-acid amide solutes, $λ$-OPES is coupled with d-AFED on selected backbone and side-chain dihedrals to enable simultaneous alchemical and conformational enhanced sampling. This combined strategy improves agreement with experimental octanol-water partition coefficients and reduces the mean absolute error from 0.75 log units with $λ$-OPES alone to 0.30 log units with $λ$-OPES-d-AFED. Overall, this work establishes an integrated enhanced sampling protocol for solvation free energy calculations across rigid organic solutes and flexible peptide-like solutes, and provides a foundation for the application of alchemical free energy methods to larger and more conformationally complex systems.

physics.chem-ph↗

arXiv2024

Effects of the growth kinetics on solute diffusion in porous films

For the development of porous materials with improved transport properties, a key missing ingredient is to determine the relations between growth kinetics, structure, and transport parameters. Here, we address these relations by studying solute diffusion through three-dimensional porous films produced by simple deposition models with controlled thickness and porosity. We simulate growing films with competitive aggregation rules that incorporate lateral aggregation (relative rate proportional to $p$), which leads to pore formation, and surface relaxation ($1-p$) that favors compaction. By connecting a solute source at the basis and a drain at the top outer surface of the films, we extract the effective diffusion coefficients from steady-state simulations. We find that for a given film thickness, the larger the $p$, the larger the effective porosity and diffusivity, but the smaller the tortuosity. Keeping constant growth conditions (i.e., same $p$), the increase of thickness always leads to an increase of effective porosity, but a nontrivial behavior in the diffusivity occurs: for $p\leq 0.7$, the diffusion coefficient is larger in thicker films; this is accompanied by a decrease of the tortuosity with the thickness, thus indicating that growth continuously improves pore structure for diffusion. Microscopically, such a result is associated with narrower distributions of local solute currents at higher points of films. Particularly for $p\geq 0.9$, in which film porosity is $\sim 0.65-0.7$, the tortuosity is between $1.3$ and $2$, increases with the thickness, and has maximal changes near $25\%$. Pairs of values of porosity and tortuosity that we obtain here, for the thickest films, agree with those experimentally measured in some porous electrodes. Noteworthy, the increase of film thickness is generally favorable for diffusion in their pores, and exceptions have small losses in tortuosity.

cond-mat.stat-mech↗

arXiv2023

A New Formulation for the Concerted Alchemical Calculation of van der Waals and Coulomb Components of Solvation Free Energies

Alchemical free energy calculations via molecular dynamics have been widely used to obtain thermodynamic properties related to protein-ligand binding and solute-solvent interactions. Although soft-core modeling is the most common approach, the linear basis function (LBF) methodology [Naden, L. N.; et al. J. Chem. Theory Comput. 2014, 10 (3), 1128; 2015, 11 (6), 2536] has emerged as a suitable alternative. It overcomes the end-point singularity of the scaling method while maintaining essential advantages such as ease of implementation and high flexibility for postprocessing analysis. In the present work, we propose a simple LBF variant and formulate an efficient protocol for evaluating van der Waals and Coulomb components of an alchemical transformation in tandem, in contrast to the prevalent sequential evaluation mode. To validate our proposal, which results from a careful optimization study, we performed solvation free energy calculations and obtained octanol-water partition coefficients of small organic molecules. Comparisons with results obtained via the sequential mode using either another LBF approach or the soft-core model attest to the effectiveness and correctness of our method. In addition, we show that a reaction field model with an infinite dielectric constant can provide very accurate hydration free energies when used instead of a lattice-sum method to model solute-solvent electrostatics.

physics.comp-ph↗