Fernando Luı́s B. da Silva

Electrostatics in macromolecular solutions

An aqueous solution containing biological molecules can be described in a general sense as an electrolyte solution. That is, it contains simple ions such as Na+, K+, Cl−, etc., but it can also include macromolecules with a net charge significantly different from unity. Proteins, polysaccharides and ...

A new algorithm for Reverse Monte Carlo simulations

We present a new algorithm for Reverse Monte Carlo (RMC) simulations of liquids. During the simulations, we calculate energy, excess chemical potentials, bond-angle distributions and three-body correlations. This allows us to test the quality and physical meaning of RMC-generated results and its limitations. It also indicates the possibility to explore orientational correlations from simple scattering experiments. The new technique has been applied to bulk hard-sphere and Lennard-Jones systems and compared to standard Metropolis Monte Carlo results.

Protein-Ion Binding Process on Finite Macromolecular Concentration. A Poisson-Boltzmann and Monte Carlo Study

Electrostatic interactions are one of the key driving forces for protein-ligands complexation. Different levels for the theoretical modeling of such processes are available on the literature. Most of the studies on the Molecular Biology field are performed within numerical solutions of the Poisson-Boltzmann Equation and the dielectric continuum models framework. In such dielectric continuum models, there are two pivotal questions: (a) how the protein dielectric medium should be modeled, and (b) what protocol should be used when solving this effective Hamiltonian. By means of Monte Carlo (MC) and Poisson-Boltzmann (PB) calculations, we define the applicability of the PB approach with linear and nonlinear responses for macromolecular electrostatic interactions in electrolyte solution, revealing some physical mechanisms and limitations behind it especially due the raise of both macromolecular charge and concentration out of the strong coupling regime. A discrepancy between PB and MC for binding constant shifts is shown and explained in terms of the manner PB approximates the excess chemical potentials of the ligand, and not as a consequence of the nonlinear thermal treatment and/or explicit ion-ion interactions as it could be argued. Our findings also show that the nonlinear PB predictions with a low dielectric response well reproduce the pK shifts calculations carried out with an uniform dielectric model. This confirms and completes previous results obtained by both MC and linear PB calculations.

Application of a new reverse Monte Carlo algorithm to polyatomic molecular systems. I. Liquid water

Using a new reverse Monte Carlo algorithm, we present simulations that reproduce very well several structural and thermodynamic properties of liquid water. Both Monte Carlo, molecular dynamics simulations and experimental radial distribution functions used as input are accurately reproduced using a small number of molecules and no external constraints. Ad hoc energy and hydrogen bond analysis show the physical consistency and limitations of the generated RMC configurations.

Response to "Comment on 'A new algorithm for reverse Monte Carlo simulations'" (J. Chem. Phys. 111, 5620 (1999))

We present here results obtained from numerical calculations in order to respond to a misreading of our previous work. Sampling properties of our reverse Monte Carlo (RMC) algorithm are discussed and several tests are used to evaluate its properties. Important details are stressed, hopefully contributing to a better understanding of the technique.