Extending the use of canonical and microcanonical Monte Carlo algorithms to spin models

We describe the canonical and microcanonical Monte Carlo algorithms for different systems that can be described by spin models. Sites of the lattice, chosen at random, interchange their spin values, provided they are different. The canonical ensemble is generated by performing exchanges according to the Metropolis prescription whereas in the microcanonical ensemble, exchanges are performed as long as the total energy remains constant. A systematic finite size analysis of intensive quantities and a comparison with results obtained from distinct ensembles are performed and the quality of results reveal that the present approach may be an useful tool for the study of phase transitions, specially first-order transitions. (C) 2009 Elsevier B.V. All rights reserved.

Emergence and loss of assortative mating in sympatric speciation

We have studied an agent model which presents the emergence of sexual barriers through the onset of assortative mating, a condition that might lead to sympatric speciation. In the model, individuals are characterized by two traits, each determined by a single locus A or B. Heterozygotes on A are penalized by introducing an adaptive difference from homozygotes. Two niches are available. Each A homozygote is adapted to one of the niches. The second trait, called the marker trait has no bearing on the fitness. The model includes mating preferences, which are inherited from the mother and subject to random variations. A parameter controlling recombination probabilities of the two loci is also introduced. We study the phase diagram by means of simulations, in the space of parameters (adaptive difference, carrying capacity, recombination probability). Three phases are found, characterized by (i) assortative mating, (ii) extinction of one of the A alleles and (iii) Hardy-Weinberg like equilibrium. We also make perturbations of these phases to see how robust they are. Assortative mating can be gained or lost with changes that present hysteresis loops, showing the resulting equilibrium to have partial memory of the initial state and that the process of going from a polymorphic panmictic phase to a phase where assortative mating acts as sexual barrier can be described as a first-order transition. (C) 2009 Published by Elsevier Ltd.

Soluble one-dimensional particle conservation models with infinitely many absorbing states

Particle conservation lattice-gas models with infinitely many absorbing states are studied on a one-dimensional lattice. As one increases the particle density, they exhibit a phase transition from an absorbing to an active phase. The models are solved exactly by the use of the transfer matrix technique from which the critical behavior was obtained. We have found that the exponent related to the order parameter, the density of active sites, is 1 for all studied models except one of them with exponent 2.

Antiferromagnetic spherical spin-glass model

We study the thermodynamic properties and the phase diagrams of a multi-spin antiferromagnetic spherical spin-glass model using the replica method. It is a two-sublattice version of the ferromagnetic spherical p-spin glass model. We consider both the replica-symmetric and the one-step replica-symmetry-breaking solutions, the latter being the most general solution for this model. We find paramagnetic, spin-glass, antiferromagnetic and mixed or glassy antiferromagnetic phases. The phase transitions are always of second order in the thermodynamic sense, but the spin-glass order parameter may undergo a discontinuous change.

Conservative ensembles for nonequilibrium lattice-gas systems

We show how to set up a constant particle ensemble for the steady state of nonequilibrium lattice-gas systems which originally are defined on a constant rate ensemble. We focus on nonequilibrium systems in which particles are created and annihilated on the sites of a lattice and described by a master equation. We consider also the case in which a quantity other than the number of particle is conserved. The conservative ensembles can be useful in the study of phase transitions and critical phenomena particularly discontinuous phase transitions.

Critical behavior of a contact process with aperiodic transition rates

We performed Monte Carlo simulations to investigate the steady-state critical behavior of a one-dimensional contact process with an aperiodic distribution of rates of transition. As in the presence of randomness, spatial fluctuations can lead to changes of critical behavior. For sufficiently weak fluctuations, we give numerical evidence to show that there is no departure from the universal critical behavior of the underlying uniform model. For strong spatial fluctuations, the analysis of the data indicates a change of critical universality class.

Shared information in stationary states at criticality

We consider bipartitions of one-dimensional extended systems whose probability distribution functions describe stationary states of stochastic models. We define estimators of the information shared between the two subsystems. If the correlation length is finite, the estimators stay finite for large system sizes. If the correlation length diverges, so do the estimators. The definition of the estimators is inspired by information theory. We look at several models and compare the behaviors of the estimators in the finite-size scaling limit. Analytical and numerical methods as well as Monte Carlo simulations are used. We show how the finite-size scaling functions change for various phase transitions, including the case where one has conformal invariance.

Preparation and characterization of Cd(2)Nb(2)O(7) thin films on Si substrates

Thin Cd(2)Nb(2)O(7) films were grown on single-crystal p-type SiO(2)/Si substrates by the metallo-organic decomposition (MOD) technique. The films were investigated by X-ray diffraction, X-ray energy-dispersive spectroscopy, and field emission scanning electron microscopy, and showed a single phase (cubic pyrochlore), a crack-free spherical grain structure, and nanoparticles with a mean size of about 68 nm. A Cauchy model was also used in order to obtain the thickness and index of refraction of the stack layers (transparent layer/SiO(2)/Si) by spectroscopic ellipsometry (SE). The dielectric constant (K) of the films was calculated to be about 25 from the capacitance-voltage (C-V) measurements. (c) 2008 Elsevier Ltd. All rights reserved.

Influence of super-ohmic dissipation on a disordered quantum critical point

We investigate the combined influence of quenched randomness and dissipation on a quantum critical point with O(N) order-parameter symmetry. Utilizing a strong-disorder renormalization group, we determine the critical behavior in one space dimension exactly. For super-ohmic dissipation, we find a Kosterlitz-Thouless type transition with conventional (power-law) dynamical scaling. The dynamical critical exponent depends on the spectral density of the dissipative baths. We also discuss the Griffiths singularities, and we determine observables.

Adsorption Behavior of 5-Fluorouracil on Au(111): An In Situ STM Study

The biological effects of chemical substitution of DNA bases triggered several investigations of their physicochemical properties This paper studies the adsorption behavior of a halogenated uracil, 5-fluorouracil (5FU). at the electrochemical interface of Au(111) and sulfuric acid solution. Upon modulation of the electric field across the interface, four distinct phases could be inferred by means of cyclic voltammetry (CV) At negative potentials relative to the SCE electrode, limited by the threshold of hydrogen evolution, no molecular species could be detected by scanning tunneling microscopy (STM) at the reconstructed Au(111)-(23 x root 3) surface, indicating that any physisorbed molecules are randomly distributed Incursion into more positive potentials increases the surface population but doer not form any two-dimensional (2D) physisorbed ordered structure Instead, we observed metastable structures that are only detectable. on surfaces with high defect density At sufficiently high positive potentials. limited by gold oxidation, the molecules are chemisorbed in a (3 x 2 root 3) ordered structure. with the aromatic ring perpendicular to the surface We report the densest chemisorbed monolayer for pyrimidine-derivative molecules (area per molecule 0 14 +/- 0 04 nm(2)). A comparison of the adsorption behavior of uracil derivatives has been made based on recent results of chemical substitution and solvent effects. We propose that pi-stacking is enhanced when halogens are incorporated in the uracil structure, in a similar fashion to what is observed in then crystal structure

Density-Profile Processes Describing Biological Signaling Networks: Almost Sure Convergence to Deterministic Trajectories

We introduce jump processes in R(k), called density-profile processes, to model biological signaling networks. Our modeling setup describes the macroscopic evolution of a finite-size spin-flip model with k types of spins with arbitrary number of internal states interacting through a non-reversible stochastic dynamics. We are mostly interested on the multi-dimensional empirical-magnetization vector in the thermodynamic limit, and prove that, within arbitrary finite time-intervals, its path converges almost surely to a deterministic trajectory determined by a first-order (non-linear) differential equation with explicit bounds on the distance between the stochastic and deterministic trajectories. As parameters of the spin-flip dynamics change, the associated dynamical system may go through bifurcations, associated to phase transitions in the statistical mechanical setting. We present a simple example of spin-flip stochastic model, associated to a synthetic biology model known as repressilator, which leads to a dynamical system with Hopf and pitchfork bifurcations. Depending on the parameter values, the magnetization random path can either converge to a unique stable fixed point, converge to one of a pair of stable fixed points, or asymptotically evolve close to a deterministic orbit in Rk. We also discuss a simple signaling pathway related to cancer research, called p53 module.

Characterization of DODAB/DPPC vesicles

Dioctadecyldimethylammonium bromide (DODA B)/dipalmitoylphosphatidylcholine (DPPC) large and cationic vesicles obtained by vortexing a lipid film in aqueous solution and above the mean phase transition temperature (T-m) are characterized by means of determination of phase behaviour, size distribution, zeta-potential analysis and colloid stability. The effect of increasing % DODAB over the 0-100% range was a nonmonotonic phase behaviour. At 50% DODAB, the mean phase transition temperature and the colloid stability were at maximum. There is an intimate relationship between stability of the bilayer structure and colloid stability. In 1, 50 and 150 mM NaCl, the colloid stability for pure DPPC or pure DODAB vesicles was very low as observed by sedimentation or flocculation, respectively. In contrast, at 50% DODAB, remarkable colloid stability was achieved in 1, 50 or 150 mM NaCl for the DODAB/DPPC composite vesicles. Vesicle size decreased but the zeta-potential remained constant with % DODAB, due to a decrease of counterion binding with vesicle size. This might be important for several biotechnological applications currently being attempted with cationic bilayer systems. (c) 2008 Elsevier Ireland Ltd. All rights reserved.

Membrane Morphology Modifications Induced by Hydroquinones

We synthesize and characterize alkylthiohydroquinones (ATHs) in order to investigate their interactions with lipid model membranes, POPE and POPC. We observe the formation of structures with different morphologies, or curvature of the lipid bilayer, depending on pH and increasing temperature. We attribute their formation to changes in the balance charge/polarity induced by the ATHs. Mixtures of ATHs with POPE at pH 4 form two cubic phases, P4(3)32 and Im3m, that reach a maximum lattice size at 40 degrees C while under basic conditions these phases only expand upon heating from room temperature. The cubic phases coexist with lamellar or hexagonal phases and are associated with inhomogeneous distribution of the ATH molecules over the lipid matrix. The zwitterionic POPC does not form cubic phases but instead shows lamellar structures with no clear influence of the 2,6-BATH.

Ab initio study of the electronic and optical properties of sillimanite (Al(2)SiO(5)) crystal

Ab initio calculations based on the density functional theory (DFT) are used to investigate the electronic and optical properties of sillimanite. The geometrical parameters of the unit cell, which contain 32 atoms, have been fully optimized and are in good agreement with the experimental data. The electronic structure shows that sillimanite has an indirect band gap of 5.18 eV. The complex dielectric function and optical constants, such as extinction coefficient, refractive index, reflectivity and energy-loss spectrum, are calculated. The optical properties of sillimanite are discussed based on the band structure calculations. It is shown that the O-2p states and Al-3s, Si-3s states play the major role in optical transitions as initial and final states, respectively. (C) 2011 Elsevier B.V. All rights reserved.