Distribution of neutral prilocaine in a phospholipid bilayer: Insights from molecular dynamics simulations

In this work, we report a 20-ns constant pressure molecular dynamics simulation of prilocaine (PLC), in amine-amide local anesthetic, in a hydrated liquid crystal bilayer of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine. The partition of PLC induces the lateral expansion of the bilayer and a concomitant contraction in its thickness. PLC molecules are preferentially found in the hydrophobic acyl chains region, with a maximum probability at similar to 12 angstrom from the center of the bilayer (between the C(4) and C(5) methylene groups). A decrease in the acyl chain segmental order parameter, vertical bar S-CD vertical bar, compared to neat bilayers, is found, in good agreement with experimental H-2-NMR studies. The decrease in vertical bar S-CD vertical bar induced by PLC is attributed to a larger accessible volume per lipid in the acyl chain region. (C) 2008 Wiley Periodicals, Inc.

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. (C) 1998 American Institute of Physics.

Simulations under Ideal and Nonideal Conditions for Characterization of a Passive Doppler Geographical Location System Using Extension of Data Reception Network

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Structure of acetone and dimethyl sulfoxide from Monte Carlo simulations and MM2 calculations

The structure of acetone and dimethyl sulfoxide in the liquid phase is investigated using Monte Carlo simulations and MM2 calculations. The principal site - site correlations and degree of structure in both liquids have been investigated. The results showed that dimethyl sulfoxide is more structured than acetone. At short distances the dipoles of neighboring molecules are found to be in antiparallel configurations, but further apart the molecules tend to be aligned predominantly as head to tail. In both liquids there is evidence of strong methyl - oxygen interaction, important to the structure of the liquids. The contacts suggest weak hydrogen bonds between methyl hydrogen and oxygen.

Time series analysis for minority game simulations of financial markets

The minority game (MG) model introduced recently provides promising insights into the understanding of the evolution of prices, indices and rates in the financial markets. In this paper we perform a time series analysis of the model employing tools from statistics, dynamical systems theory and stochastic processes. Using benchmark systems and a financial index for comparison, several conclusions are obtained about the generating mechanism for this kind of evolution. The motion is deterministic, driven by occasional random external perturbation. When the interval between two successive perturbations is sufficiently large, one can find low dimensional chaos in this regime. However, the full motion of the MG model is found to be similar to that of the first differences of the SP500 index: stochastic, nonlinear and (unit root) stationary. (C) 2002 Elsevier B.V. B.V. All rights reserved.

NOISE and ULTRAVIOLET DIVERGENCES IN SIMULATIONS of GINZBURG-LANDAU-LANGEVIN TYPE of EQUATIONS

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

SPH simulations of clumps formation by dissipative collisions of molecular clouds - II. Magnetic case

We performed computer simulations of interstellar cloud-cloud collisions using the three-dimensional smoothed particle magnetohydrodynamics method. In order to study the role of the magnetic field on the process of collision-triggered fragmentation, we focused our attention on head-on supersonic collisions between two identical spherical molecular-clouds. Two extreme configurations of the magnetic field were adopted: parallel and perpendicular to the initial clouds motion. The initial magnetic field strength was approximately 12.0 muG. In the parallel case, much more of the collision debris were retained in the shocking region than in the non-magnetic case where gas escaped freely throughout the symmetry plane. Differently from the non-magnetic case, eddy-like vortices were formed. The regions of highest vorticity and the the regions of highest density are offset. We found clumps formation only in the parallel case, however, they were larger, hotter and less dense than in the analogous non-magnetic case. In the perpendicular case, the compressed field works as a magnetic wall, preventing a stronger compression of the colliding clouds. This last effect inhibits direct contact of the two clouds. In both cases, we found that the field lines show a chaotic aspect in large scales. Also, the field magnitude is considerably amplified in the shock layer. However, the field distribution is almost coherent in the higher density regions.

SPH simulations of clumps formation by dissipative collision of molecular clouds - I. Non magnetic case

Computer experiments of interstellar cloud collisions were performed with a new smoothed-particle-hydrodynamics (SPH) code. The SPH quantities were calculated by using spatially adaptive smoothing lengths and the SPH fluid equations of motion were solved by means of a hierarchical multiple time-scale leapfrog. Such a combination of methods allows the code to deal with a large range of hydrodynamic quantities. A careful treatment of gas cooling by H, H(2), CO and H II, as well as a heating mechanism by cosmic rays and by H(2) production on grains surface, were also included in the code. The gas model reproduces approximately the typical environment of dark molecular clouds. The experiments were performed by impinging two dynamically identical spherical clouds onto each other with a relative velocity of 10 km s(-1) but with a different impact parameter for each case. Each object has an initial density profile obeying an r(-1)-law with a cutoff radius of 10 pc and with an initial temperature of 20 K. As a main result, cloud-cloud collision triggers fragmentation but in expense of a large amount of energy dissipated, which occurred in the head-on case only. Off-center collision did not allow remnants to fragment along the considered time (similar to 6 Myr). However, it dissipated a considerable amount of orbital energy. Structures as small as 0.1 pc, with densities of similar to 10(4) cm(-3), were observed in the more energetic collision.

Evaluating and classifying contaminated areas based on loss functions using annealing simulations

This paper presents a methodology based on geostatistical theory for quantifying the risks associated with heavy-metal contamination in the harbor area of Santana, Amapa State, Northern Brazil. In this area there were activities related to the commercialization of manganese ore from Serra do Navio. Manganese and arsenic concentrations at unsampled sites were estimated by postprocessing results from stochastic annealing simulations; the simulations were used to test different criteria for optimization, including average, median, and quantiles. For classifying areas as contaminated or uncontaminated, estimated quantiles based on functions of asymmetric loss showed better results than did estimates based on symmetric loss, such as the average or the median. The use of specific loss functions in the decision-making process can reduce the costs of remediation and health maintenance. The highest global health costs were observed for manganese. (c) 2008 Elsevier B.V. All rights reserved

A critical investigation of the Tanford-Kirkwood scheme by means of Monte Carlo simulations

Monte Carlo simulations are used to assess the adequacy of the Tanford-Kirkwood prescription for electrostatic interactions in macromolecules. Within a continuum dielectric framework, the approach accurately describes salt screening of electrostatic interactions for moderately charged systems consistent with common proteins at physiological conditions. The limitations of the Debye-Huckel theory, which forms the statistical mechanical basis for the Tanford-Kirkwood result, become apparent for highly charged systems. It is shown, both by an analysis of the Debye-Huckel theory and by numerical simulations, that the difference in dielectric permittivity between macromolecule and surrounding solvent does not play a significant role for salt effects if the macromolecule is highly charged. By comparison to experimental data, the continuum dielectric model (combined with either an approximate effective Hamiltonian as in the Tanford-Kirkwood treatment or with exact Monte Carlo simulations) satisfactorily predicts the effects of charge mutation on metal ion binding constants, but only if the macromolecule and solvent are assigned the same or similar permittivities.

Theoretical studies of liquids by computer simulations: the water-acetone mixture.

Monte Carlo simulation results for pure liquid acetone and water-acetone mixtures calculated in the isothermal and isobaric (NPT) ensemble at T=298K and p=1.0atm are presented. The TIP4P model was used for water and optimized potential for liquid simulation (OPLS) force field parameters used for acetone. The results obtained for the average configurational energy as a function of the mole fraction are in good accord with experimental data. Energy partitioning and co-ordination numbers results calculated for equimolar water-acetone solution are compared to similar data obtained for other water-organic liquid mixtures. These results show an increase in water-water interaction energy and co-ordination numbers when the interaction between water and organic liquid molecules decrease. Distribution functions for pure liquid acetone and water-acetone mixtures are presented. Dipole-dipole angular correlation functions obtained for pure liquid acetone show a predominance of dimers with parallel alignment of dipole moments. Radial distribution functions from water-acetone interaction show characteristic features of hydrogen bonded liquids. Radial and angular distribution functions for water-water correlation calculated in pure water and in equimolar water-acetone mixture are compared, showing very similar features in both systems. (C) 1999 Elsevier B.V. B.V. All rights reserved.

Molecular dynamics simulations on devitrification: the PbF2 case

In this work molecular dynamics simulations were performed to reproduce the kinetic and thermodynamic transformations occurring during melt crystallization, vitrification, and glass crystallization (devitrification) of PbF2. Two potential parameters were analyzed in order to access the possibility of modeling these properties. These interionic potentials are models developed to describe specific characteristic of PbF2, and thermodynamic properties were well reproduced by one of them, while the other proved well adapted to simulate the crystalline structure of this fluoride. By a modeled nonisothermal heat treatment of the glass, it was shown that the devitrification of a cubic structure in which the Pb-Pb distances are in good agreement with theory and experiment. (C) 2002 American Institute of Physics.