Exploring electrostatic patterns of human, murine, equine and canine TLR4/MD-2 receptors.

Electrostatic interactions between phosphate anions and Toll-like receptor 4 / Myeloid differentiation factor-2 (TLR4/MD-2) protein complexes of human, murine, equine and canine species were computed. Such knowledge can provide mechanistic information about recognising LPS-like ligands, since anionic phosphate groups belong to the structural features of LPS with their diphosphorylated diglucosamine backbone. Sequence composition analyses, electrostatic interaction potentials and docked energies as well as molecular dynamics studies evaluated the phosphate interactions within the triangular LPS binding site (wedge). According to electrostatic analyses, human, horse and dog wedges possess phosphate-binding sites with indistinct positive and negative charge distributions, but the murine wedge shows a unique strong negative net charge at the site where antagonists bind in other species (Pan). Docking of a phosphate mono-anion (probe) confirmed its repulsion at this Pan site, but the Pag site of the murine wedge attracted the probe. It is occupied by phosphate groups of agonists in other species (Pag). Molecular dynamics trajectories show a variable degree of random walk across the wedges, that is, not following electrostatic preferences (neither Pag nor Pan). In summary, two opposing electrostatic patterns exist -murine versus human, equine and canine species - all of which reflect the potential dual activity mode of under-acylated ligands such as lipid IVA.

Influence of pH on the formation of a polyelectrolyte complex by dissipative particle dynamics simulation: From an extended to a compact shape.

This work aims to investigate the influence of pH on the mechanism of assembly of macromolecules. We studied the effect of the pH on the interaction of two polyelectrolytes of opposed charge, having the same size, by means of dissipative particle dynamics method. The system consisted of a strong cationic and a weak anionic polyelectrolyte in an aqueous solution containing monovalent counterions. The analysis was made by varying the pH of the solution, which modifies the charge fraction of the weak anionic polyelectrolyte with a dissociation acid constant pKa of 5.5, while the polycation is fully charged in all the pH range used, characteristic of a strong polyelectrolyte. In order to describe the influence of pH on the complexation process, we have analyzed the pair radial distribution functions polyanion-counterion, polycation-counterion, and polyanion-polycation. The complex conformation was studied by means of the radius of gyration and the end-to-end distance of both chains as the pH varied from 1 to 14. A relevant finding obtained here was the relationship between the radial distribution functions and the counterion release from the polyelectrolytes, which leads to a reduction in the size of the complex when pH increased. Surprisingly, a transition from an extended to a compact polyelectrolyte complex was obtained when the pH reached the dissociation acid constant pKa of the weak polyelectrolyte. This systematic study can help to understand a large number of more realistic problems in biological systems such as protein complex, chromatin phase transition, or in complex systems applied in biomedical science.

Dopamine and Caffeine Encapsulation within Boron Nitride (14,0) Nanotubes: Classical Molecular Dynamics and First Principles Calculations.

Classical molecular dynamics (MD) and density functional theory (DFT) calculations are developed to investigate the dopamine and caffeine encapsulation within boron nitride (BN) nanotubes (NT) with (14,0) chirality. Classical MD studies are done at canonical and isobaric-isothermal conditions at 298 K and 1 bar in explicit water. Results reveal that both molecules are attracted by the nanotube; however, only dopamine is able to enter the nanotube, whereas caffeine moves in its vicinity, suggesting that both species can be transported: the first by encapsulation and the second by drag. Findings are analyzed using the dielectric behavior, pair correlation functions, diffusion of the species, and energy contributions. The DFT calculations are performed according to the BLYP approach and applying the atomic base of the divided valence 6-31g(d) orbitals. The geometry optimization uses the minimum-energy criterion, accounting for the total charge neutrality and multiplicity of 1. Adsorption energies in the dopamine encapsulation indicate physisorption, which induces the highly occupied molecular orbital-lower unoccupied molecular orbital gap reduction yielding a semiconductor behavior. The charge redistribution polarizes the BNNT/dopamine and BNNT/caffeine structures. The work function decrease and the chemical potential values suggest the proper transport properties in these systems, which may allow their use in nanobiomedicine.

Static dielectric constant of water within a bilayer using recent water models: a molecular dynamics study.

The water confined within a surfactant bilayer is studied using different water models via molecular dynamics simulations. We considered four representative rigid models of water: the SPC/E and the TIP4P/2005, which are commonly used in numerical calculations and the more recent TIP4Q and SPC/ε models, developed to reproduce the dielectric behaviour of pure water. The static dielectric constant of the confined water was analyzed as a function of the temperature for the four models. In all cases it decreases as the temperature increases. Additionally, the static dielectric constant of the bilayer-water system was estimated through its expression in terms of the fluctuations in the total dipole moment, usually applied for isotropic systems. The estimated dielectric was compared with the available experimental data. We found that the TIP4Q and the SPC/ε produce closer values to the experimental data than the other models, particularly at room temperature. It was found that the probability of finding the sodium ion close to the head of the surfactant decreases as the temperature increases, thus the head of the surfactant is more exposed to the interaction with water when the temperature is higher.

The line tension of two-dimensional ionic fluids.

Pressure tensor components are very useful in the calculation of the tension associated with a liquid-vapor interface. In this work, we present expressions for the pressure tensor components of two-dimensional ionic fluids, modeled at the level of the primitive model. As an application, we carried out molecular dynamics simulations of liquid-vapor interfaces to calculate the line tension of the 1:1 two-dimensional ionic fluid, whose liquid-vapor coexistence curve had already been obtained in a previous work. The pressure tensor components were validated by simulating states of one phase and reproducing the scalar pressure, previously obtained from bulk simulations and reported in the literature. The effects on the line tension and the coexisting densities, originated by the choice of the Ewald parameters, the cutoff radius, and the interfacial length were also evaluated.

The structure and interaction mechanism of a polyelectrolyte complex: a dissipative particle dynamics study.

The mechanism of complex formation of two oppositely charged linear polyelectrolytes dispersed in a solvent is investigated by using dissipative particle dynamics (DPD) simulation. In the polyelectrolyte solution, the size of the cationic polyelectrolyte remains constant while the size of the anionic chain increases. We analyze the influence of the anionic polyelectrolyte size and salt effect (ionic strength) on the conformational changes of the chains during complex formation. The behavior of the radial distribution function, the end-to-end distance and the radius of gyration of each polyelectrolyte is examined. These results showed that the effectiveness of complex formation is strongly influenced by the process of counterion release from the polyelectrolyte chains. The radius of gyration of the complex is estimated using the Fox-Flory equation for a wormlike polymer in a theta solvent. The addition of salts in the medium accelerates the complex formation process, affecting its radius of gyration. Depending on the ratio of chain lengths a compact complex or a loosely bound elongated structure can be formed.

Liquid-vapor phase diagram and cluster formation of two-dimensional ionic fluids.

Direct molecular dynamics simulations on interfaces at constant temperature are performed to obtain the liquid-vapor phase diagram of the two-dimensional soft primitive model, an equimolar mixture of equal size spheres carrying opposite charges. Constant temperature and pressure simulations are also carried out to check consistency with interface simulations results. In addition, an analysis of the cluster formation of mixtures of particles with charge asymmetry in the range 1:1 to 1:36 at low and high densities is performed. The number of free ions, when plotted as a function of the positive ion charge, Z(+), has an oscillatory behavior and is independent of the density. The formation of aggregates is analyzed in terms of the attraction and repulsion between ions.

Interfacial and coexistence properties of soft spheres with a short-range attractive Yukawa fluid: molecular dynamics simulations.

Molecular dynamics simulations have been carried out to obtain the interfacial and coexistence properties of soft-sphere attractive Yukawa (SAY) fluids with short attraction range, κ = 10, 9, 8, 7, 6, and 5. All our simulation results are new. These data are also compared with the recently reported results in the literature of hard-core attractive Yukawa (HAY) fluids. We show that the interfacial and coexistence properties of both potentials are different. For the surveyed systems, here we show that all coexistence curves collapse into a master curve when we rescale with their respective critical points and the surface tension curves form a single master curve when we plot γ* vs. T/T(c).

Equilibrium structure of the multi-component screened charged hard-sphere fluid.

The generalized mean spherical approximation of the structural properties of the binary charge-symmetric fluid of screened charged hard-spheres of the same diameter, i.e., the screened restricted primitive model, is extended to include binary charge-asymmetric and multi-component fluids. Molecular dynamics simulation data are generated to assess the accuracy of the corresponding theoretical predictions.

Effect of softness of the potential on the stress anisotropy in liquids.

We have performed molecular dynamics simulations of dense liquids using nonconformal and Gaussian potential models. We investigate the effect of the softness of the potential on the pressure tensor of liquids and dense fluids when the simulations are carried out using parallelepiped cells. The combination of periodic boundary conditions and small cross sectional areas induces an anisotropy in the diagonal components of the pressure tensor. This anisotropy results in an artificial stress in the system that has to be taken into account in simulations of explicit interfaces, where the artificial stress introduces errors in the computation of the surface tension. At high liquid densities the stress anisotropy exhibits an oscillatory dependence with the cross sectional area of the simulation box. We find that the softness of the potential has a dramatic effect on the amplitude of the oscillations, which can be significantly reduced in soft potentials, such as those used in the modeling of hydrocarbon liquids or polymers.

Electrostatic interactions in dissipative particle dynamics using the Ewald sums.

The electrostatic interactions in dissipative particle dynamics (DPD) simulations are calculated using the standard Ewald [Ann. Phys. 64, 253 (1921)] sum method. Charge distributions on DPD particles are included to prevent artificial ionic pair formation. This proposal is an alternative method to that introduced recently by Groot [J. Chem. Phys. 118, 11265 (2003)] where the electrostatic field was solved locally on a lattice. The Ewald method is applied to study a bulk electrolyte and polyelectrolyte-surfactant solutions. The structure of the fluid is analyzed through the radial distribution function between charged particles. The results are in good agreement with those reported by Groot for the same systems. We also calculated the radius of gyration of a polyelectrolyte in salt solution as a function of solution pH and degree of ionization of the chain. The radius of gyration increases with the net charge of the polymer in agreement with the trend found in static light scattering experiments of polystyrene sulfonate solutions.

Finite-size effects in dissipative particle dynamics simulations.

We have performed dissipative particle dynamics (DPD) simulations to evaluate the effect that finite size of transversal area has on stress anisotropy and interfacial tension. The simulations were carried out in one phase and two phases in parallelepiped cells. In one-phase simulations there is no finite-size effect on stress anisotropy when the simulation is performed using repulsive forces. However, an oscillatory function of stress anisotropy is found for attractive-repulsive interactions. In the case of liquid-liquid interfaces with repulsive interaction between molecules, there is only a small effect of surface area on interfacial tension when the simulations are performed using the Monte Carlo method at constant temperature and normal pressure. An important but artificial finite-size effect of interfacial area on surface tension is found in simulations in the canonical ensemble. Reliable results of interfacial tension from DPD simulations can be obtained using small systems, less than 2000 particles, when they interact exclusively with repulsive forces.

Stress anisotropy induced by periodic boundary conditions.

Finite size effects due to periodic boundary conditions are investigated using computer simulations in the canonical ensemble. We study liquids with densities corresponding to typical liquid coexistence densities, and temperatures between the triple and critical points. The components of the pressure tensor are computed in order to analyze the finite size effects arising from the size and geometry of the simulation box. Two different box geometries are considered: cubic and parallelepiped. As expected the pressure tensor is isotropic in cubic boxes, but it becomes anisotropic for small noncubic boxes. We argue this is the origin of the anomalous behavior observed recently in the computation of the surface tension of liquid-vapor interfaces. Otherwise, we find that the bulk pressure is sensitive to the box geometry when small simulation boxes are considered. These observations are general and independent of the model liquid considered. We report results for liquids interacting through short range forces, square well and Lennard-Jones, and also long range Coulombic interactions. The effect that small surface areas have on the surface tension is discussed, and some preliminary results at the liquid vapor-interface for the square well potential are given.

Molecular dynamics simulations of the surface tension of ionic liquids.

We report molecular dynamics computer simulations of the surface tension and interfacial thickness of ionic liquid-vapor interfaces modeled with a soft core primitive model potential. We find that the surface tension shows an anomalous oscillatory behavior with interfacial area. This observation is discussed in terms of finite size effects introduced by the periodic boundary conditions employed in computer simulations. Otherwise we show that the thickness of the liquid-vapor interface increases with surface area as predicted by the capillary wave theory. Data on the surface tension of size-asymmetric ionic liquids are reported and compared with experimental data of molten salts. Our data suggest that the surface tensions of size-asymmetric ionic liquids do not follow a corresponding states law.

Surface tension of the restrictive primitive model for ionic liquids.

Hybrid molecular dynamics and Monte Carlo simulations are performed to study the liquid-vapor interface of the restricted primitive model (RPM) of ionic fluids. We report for the first time simulation results of the surface tension associated to this interface. The RPM accurately predicts experimental surface tensions of ionic salts and good agreement with theoretical predictions that include the idea of ion association is found. The simulation results indicate that the structure of an ionic liquid-vapor interface is rather rough. This is reflected in the interfacial thickness, larger than that observed in simple fluids and water.