arXiv subjects

Frederico W. Tavares

Publications and source records attributed to Frederico W. Tavares.

5 recordsLinked to original sources

arXiv2024

Synthesis of Polyglobalide by Enzymatic Ring Opening Polymerization Using Pressurized Fluids

Here, the synthesis of polyglobalide (PGl) by enzymatic ring-opening polymerization (e-ROP) is investigated, using pressurized carbon dioxide (CO2), pressurized CO2 + dichloromethane (DCM), and pressurized propane as solvents. Particularly, the effects of phase equilibrium on the course of e-ROP and PGl final properties are discussed. The partition coefficients of CO2, DCM, propane, globalide and PGl were calculated with help of thermodynamic models, providing proper understanding of monomer partitioning in the reaction system. Reactions performed in pure CO2 resulted in monomer conversions of 100%. Besides, when only one liquid phase was present inside the reactor, PGl samples presented low polydispersities and high average molecular weights. When carried out in CO2 + DCM, e-ROP resulted in lower monomer conversions and PGl samples with higher polydispersities and lower average molecular weights. Finally, reactions carried out in pressurized propane (200 bar) produced PGl samples with the highest average molecular weights among the analyzed products.

physics.chem-ph↗

arXiv2023

Classical Density Functional Theory Reveals Structural Information of H2 and CH4 Fluids Adsorbed in MOF-5

This study employs classical Density Functional Theory (cDFT) to investigate the adsorption isotherms and structural information of H2 and CH4 fluids inside MOF-5. The results indicate that the adsorption of both fluids is highly dependent on the fluid temperature and the shape of the MOF-5 structure. Specifically, the CH4 molecules exhibit stronger interactions with the MOF-5 framework, resulting in a greater adsorbed quantity compared to H2. Additionally, the cDFT calculations reveal that the adsorption process is influenced by the fluid-fluid spatial correlations between the fluid molecules and the external potential produced by the MOF-5 solid atoms. These findings are supported by comparison with experimental data of adsorbed amount and the structure factor of the adsorbed fluid inside the MOF-5. We demonstrate the importance of choosing the appropriate grid size in calculating the adsorption isotherm and the fluid structure factors within the MOF-5. Overall, this work provides valuable insights into the adsorption mechanism of H2 and CH4 in MOF-5, emphasizing the importance of considering the structural properties of the adsorbed fluids in MOFs for predicting and designing their gas storage capacity at different thermodynamic conditions.

physics.chem-ph↗

arXiv2023

Exponential Integrators for Phase-Field Equations using Pseudo-spectral Methods: A Python Implementation

In this paper, we implement exponential integrators, specifically Integrating Factor (IF) and Exponential Time Differencing (ETD) methods, using pseudo-spectral techniques to solve phase-field equations within a Python framework. These exponential integrators have showcased robust performance and accuracy when addressing stiff nonlinear partial differential equations. We compare these integrators to the well-known implicit-explicit (IMEX) Euler integrators used in phase-field modeling. The synergy between pseudo-spectral techniques and exponential integrators yields significant benefits for modeling intricate systems governed by phase-field dynamics, such as solidification processes and pattern formation. Our comprehensive Python implementation illustrates the effectiveness of this combined approach in solving phase-field model equations. The results obtained from this implementation highlight the accuracy and computational advantages of the ETD method compared to other numerical techniques.

math.NA↗

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↗

arXiv2012

Attractive double-layer forces between neutral hydrophobic and neutral hydrophilic surfaces

The interaction between surface patches of proteins with different surface properties has a vital role to play driving conformational changes of proteins in different salt solutions. We demonstrate the existence of ion-specific attractive double-layer forces between neutral hydrophobic and hydrophilic surfaces in the presence of certain salt solutions. This is done by solving a generalized Poisson-Boltzmann equation for two unequal surfaces. In the calculations we utilize parameterized ion-surface-potentials and dielectric-constant-profiles deduced from recent non-primitive-model molecular dynamics (MD) simulations that account partially for molecular structure and hydration effects.

cond-mat.soft↗