S. Coutinho

Dynamics of HIV Infection: A Cellular Automata Approach

We use a cellular automata model to study the evolution of HIV infection and the onset of AIDS. The model takes into account the global features of the immune response to any pathogen, the fast mutation rate of the HIV and a fair amount of spatial localization. Our results reproduce quite well the three-phase pattern observed in T cell and virus counts of infected patients, namely, the primary response, the clinical latency period and the onset of AIDS. We have also found that the infected cells may organize themselves into special spatial structures since the primary infection, leading to a decrease on the concentration of uninfected cells. Our results suggest that these cell aggregations, which can be associated to syncytia, leads to AIDS.

Robustness of a cellular automata model for the HIV infection

An investigation was conducted to study the robustness of the results obtained from the cellular automata model which describes the spread of the HIV infection within lymphoid tissues [R.M. Zorzenon dos Santos, S. Coutinho, Phys. Rev. Lett. 87 (2001) 168102]. The analysis focused on the dynamic behavior of the model when defined in lattices with different symmetries and dimensionalities. The results illustrated that the three-phase dynamics of the planar models suffered minor changes in relation to lattice symmetry variations and, while differences were observed regarding dimensionality changes, qualitative behavior was preserved. A further investigation was conducted into primary infection and sensitiveness of the latency period to variations of the model’s stochastic parameters over wide ranging values. The variables characterizing primary infection and the latency period exhibited power-law behavior when the stochastic parameters varied over a few orders of magnitude. The power-law exponents were approximately the same when lattice symmetry varied, but there was a significant variation when dimensionality changed from two to three. The dynamics of the three-dimensional model was also shown to be insensitive to variations of the deterministic parameters related to cell resistance to the infection, and the necessary time lag to mount the specific immune response to HIV variants. The robustness of the model demonstrated in this work reinforce that its basic hypothesis are consistent with the three-stage dynamic of the HIV infection observed in patients.

Ising model with competing random decorating D vector spins

The Ising model on the square lattice decorated with random annealed diluted competing D vector bond spins is studied. The exact phase diagrams of the critical temperature plotted against the concentration and the critical temperature plotted against the competing parameter are evaluated analytically and presented. Re-entrant behaviour for the ferromagnetic and the antiferromagnetic phases is observed for definite range of values of the concentration. A new bond percolation threshold equal to p+c=1/2(1+1/2)=0.8535. . . is achieved when local competing interactions are present in the system. Moreover p+c is independent of the dimensionality (D) of the decorating spins and therefore independent of the physical origin of the interactions, as it should be. In particular the D=1 (Ising), D=2 (XY), D=3 (Heisenberg) and D to infinity cases are analysed.

Reversible transport of interacting Brownian ratchets.

The transport of interacting Brownian particles in a periodic asymmetric (ratchet) substrate is studied numerically. In a zero-temperature regime, the system behaves as a reversible step motor, undergoing multiple sign reversals of the particle current as any of the following parameters are varied: the pinning potential parameters, the particle occupation number, and the excitation amplitude. The reversals are induced by successive changes in the symmetry of the effective ratchet potential produced by the substrate and the fraction of particles which are effectively pinned. At high temperatures and low frequencies, thermal noise assists delocalization of the pinned particles, rendering the system to recover net motion along the gentler direction of the substrate potential. The joint effect of high temperature and high frequency, on the other hand, induces an additional current inversion, this time favoring motion along the direction where the ratchet potential is steeper. The dependence of these properties on the ratchet parameters and particle density is analyzed in detail.

Universality in short-range Ising spin glasses

The role of the distribution of coupling constants in the critical exponents of the short-range Ising spin-glass model is investigated via real space renormalization group. A saddle-point spin glass critical point characterized by a fixed-point distribution is found in an appropriated parameter space. The critical exponents β and ν are directly estimated from the data of the local Edwards–Anderson order parameters for the model defined on a diamond hierarchical lattice of fractal dimension df=3. Four distinct initial distributions of coupling constants (Gaussian, bimodal, uniform and exponential) are considered; the results clearly indicate a universal behaviour.

Axial decorated Ising model with competing interaction

The phase diagram and the thermodynamics of the axial decorated Ising model on a square lattice with m-dimensional bond spins are studied for the m=1 (Ising), m=2 (XY), m=3 (Heisenberg) and m= infinity cases. Competing interactions between the site and decorating bond spins have been considered. The expressions for the partition function, the thermodynamics and the pair correlation functions of the decorated Ising chain have been analytically obtained. The effect of the dimensionality of the decorating bond spin on the thermodynamic behaviour of both models is analyzed.

Multifractal analysis of polyalanines time series

Multifractal properties of the energy time series of short α-helix structures, specifically from a polyalanine family, are investigated through the MF-DFA technique (multifractal detrended fluctuation analysis). Estimates for the generalized Hurst exponent h(q) and its associated multifractal exponents τ(q) are obtained for several series generated by numerical simulations of molecular dynamics in different systems from distinct initial conformations. All simulations were performed using the GROMOS force field, implemented in the program THOR. The main results have shown that all series exhibit multifractal behavior depending on the number of residues and temperature. Moreover, the multifractal spectra reveal important aspects of the time evolution of the system and suggest that the nucleation process of the secondary structures during the visits on the energy hyper-surface is an essential feature of the folding process.

Dihedral-angle Gaussian distribution driving protein folding

The proposal of this paper is to provide a simple angular random-walk model to build up polypeptide structures, which encompass properties of dihedral angles of folded proteins. From this model, structures will be built with lengths ranging from 125 up to 400 amino acids for the different fractions of secondary structure motifs, in which dihedral angles were randomly chosen according to narrow Gaussian probability distributions. In order to measure the fractal dimension of proteins three different cases were analyzed. The first contained α-helix structures only, the second β-strands structures and the third a mix of α-helices and β-sheets. The behavior of proteins with α-helix motifs are more compact than in other situations. The findings herein indicate that this model describes some structural properties of a protein and suggest that randomness is an essential ingredient but proteins are driven by narrow angular Gaussian probability distributions and not by random-walk processes.

Ferromagnetic Potts model under an external magnetic field: An exact renormalization group approach

The q-state ferromagnetic Potts model under a non-zero magnetic field coupled with the 0^th Potts state was investigated by an exact real-space renormalization group approach. The model was defined on a family of diamond hierarchical lattices of several fractal dimensions d_F. On these lattices, the renormalization group transformations became exact for such a model when a correlation coupling that singles out the 0^th Potts state was included in the Hamiltonian. The rich criticality presented by the model with q=3 and d_F=2 was fully analyzed. Apart from the Potts criticality for the zero field, an Ising-like phase transition was found whenever the system was submitted to a strong reverse magnetic field. Unusual characteristics such as cusps and dimensional reduction were observed on the critical surface.

Short-range Ising spin glasses: a critical exponent study

The critical properties of short-range Ising spin-glass models, defined on diamond hierarchical lattices of graph fractal dimensions df=2.58,3, and 4, and scaling factor 2, are studied via a method based on the Migdal–Kadanoff renormalization-group scheme. The order-parameter critical exponent β is directly estimated from the data of the local Edwards–Anderson (EA) order parameter, obtained through an exact recursion procedure. The scaling of the EA order parameter, leading to estimates of the ν exponent of the correlation length is also performed. Four distinct initial distributions of the quenched coupling constants (Gaussian, bimodal, uniform and exponential) are considered. Deviations from a universal behavior are observed and analysed in the framework of the renormalized flow in a two-dimensional appropriate parameter space.