International Journal of Modern Physics C

Conformational structures of two common repeat motifs Val¹-Pro²-Gly³-Val⁴-Gly⁵ and Gly¹-Leu²-Gly³-Gly⁴ of tropoelastin are investigated by using the multicanonical simulation procedure with solvation effects included energy force field. The effects of solvation energy term on the conformations are determined by analyzing Ramachandran plots. By minimizing the energy structures along the trajectory, the thermodynamically most stable low-energy microstates of the molecule in aqueous solution are determined and the root mean square deviations of these structures with respect to the global minimum are calculated.

The presence of log-periodic structures before and after stock market crashes is considered to be an imprint of an intrinsic discrete scale invariance (DSI) in this complex system. The fractal framework of the theory leaves open the possibility of observing self-similar log-periodic structures at different time scales. In the present work, we analyze the daily closures of four of the most important indices worldwide since 2000: the DAX for Germany and the NASDAQ-100, the S&P 500 and the Dow Jones for the United States. The qualitative behavior of these different markets is similar during the temporal frame studied. Evidence is found for decelerating log-periodic oscillations of duration about two years and starting in September 2000. Moreover, a nested sub-structure starting in May 2002 is revealed, bringing more evidence to support the hypothesis of self-similar, log-periodic behavior. Ongoing log-periodic oscillations are also revealed. A Lomb analysis over the aforementioned periods indicates a preferential scaling factor λ~2. Higher order harmonics are also present. The spectral pattern of the data has been found to be similar to that of a Weierstrass-type function, used as a prototype of a log-periodic fractal function.

We investigate boron and nitrogen substitutional doping single wall carbon nanotubes (SWCNTs) by first-principles calculations. The optimized geometres of boron and nitrogen substituted SWCNTs exhibit bamboo-like structures. Boron and nitrogen impurities form acceptor and donor states in semiconductor SWCNTs. The highest occupied molecular orbital (HOMO) indicates the trend of forming inter-tube bonds in doping SWCNTs. It may start a new way to form inter-tube bonds by doping in SWCNTs.

Junction formation in crossed C(10,0) single wall carbon nanotubes under pressure has been investigated, using classical molecular-dynamics simulations at 1 K. It has been found that a stable mechanical junction was formed by means of placing two crossed single wall carbon nanotubes between two rigid graphene layers which move toward each other.

In this study, we have calculated energy levels of an N-electron quantum dot. For this purpose, we have used two different techniques, matrix diagonalization and quantum genetic algorithm, to obtain simultaneous solutions of the coupled Schrödinger and Poisson equation in the Hartree approximation. We have determined single particle energy levels, total energy, chemical potential and capacitive energy. We have also compared the results, demonstrated the applicability of QGA to many-electron quantum systems and evaluated its effectiveness.

The electron method spectroscopy consists in the detection of very low energy electrons formed in electron–molecule collisions. The advantage of this method over the method of optical spectroscopy lies in the possibility to study optically forbidden states, so the complexity of spectrum rises steeply, which makes its analysis more difficult. Besides electron states, there are also a vibrational states in threshold spectra analysis, and those had to be identified and classified. This paper presents an expert system developed to automate, speed up and improve the N₂ threshold spectra analysis.

In this article, a lattice Boltzmann model for two immiscible fluids with same density but a large viscosity difference is developed. The effect of surface tension is included. An indicator function is used to model the interface motion and is updated by a lattice Boltzmann scheme. The macroscopic equation for this function is derived using multi-scale analysis. Numerical results are compared with theoretical and experimental ones for the problem of drop deformation under steady linear flows. A qualitative comparison with results given by a level contour reconstruction method for drop collision in three dimensions is also shown. Other numerical applications, such as flow past obstacles and a falling drop, are presented.

Stochastic forces or random noises have been greatly used in studying the control of chaos of random real systems, but little is reported for random complex systems. Chaotic limit cycles of a complex Duffing–Van der Pol system with a random excitation is studied. Generating chaos via adjusting the intensity of random phase is investigated. We consider the positive top Lyapunov exponent as a criterion of chaos for random dynamical systems. It is computed based on the Khasminskii's formulation and the extension of Wedig's algorithm for linear stochastic systems. We demonstrate the stable behavior of deterministic system when noise intensity is zero by means of the top (local) Lyapunov exponent. Poincaré surface analysis and phase plot are used to confirm our results. Later, random noise is used to generate chaos by adjusting the noise intensity to make the top (local) Lyapunov exponent changes from a negative sign to a positive one, and the Poincaré surface analysis is also applied to verify the obtained results and excellent agreement between these results is found.

A dynamical system falling in between the elementary binary cellular automata and the coupled map lattices is presented. It is composed by a one-dimensional cellular automaton in which the values within each cell are continuous instead of discrete. However, in this case, the coupling between cells is made through a logistic map instead of making the fuzzification of the disjunctive normal form describing the corresponding Boolean rule. The system resembles the CA rule 90 evolution, since the future value of a cell depends only on a combination of the values of the nearest neighbors cells. The basic dynamical and stability properties of the system are analyzed. The system displays different types from attractors (fixed points, cycles and chaotic attractors), depending on the growth rate parameter used for the logistic map coupling. If the cell values are binary, i.e., only values 0 and 1 are allowed within each cell, the dynamical evolution of the rule 90 automaton is recovered.

We have numerically investigated the effect of the delay times τ_f and τ_s of a mixture of fast and slow vehicles on the fundamental diagram (the current-density relation) of the optimal velocity model. The optimal velocity function of the fast cars depends not only on the headway of each car but also on the headway of the immediately preceding one. It is found that the small delay times have almost no effects, while, for sufficiently large delay time τ_s, the current profile displays qualitatively five different forms, depending on τ_f, τ_s and the fractions d_f and d_s of the fast and slow cars, respectively. The velocity (current) exhibits first-order transitions at low and/or high densities, from freely moving phase to the congested state, and from congested state to a jamming one, respectively. The minimal current appears in intermediate values of τ_s. Furthermore, there exist a critical value of τ_f above which the metastability and hysteresis appear. The spatial-temporal traffic patterns near the congested-jamming first-order transition is also presented.

A model of the opinion dynamics underlying the political decision is proposed. The analysis is restricted to a bipolar scheme with a possible third political area. The interaction among voters is local but the final decision strongly depends on global effects such as the rating of the governments. As in the realistic case, the individual decision making process is determined by the most relevant personal interests and problems. The phenomenological analysis of the national vote in Italy and Germany has been carried out and a prediction of the next Italian vote as a function of the government rating is presented.

We have simulated 10-residue polyalanine chain by multicanonical method to visualize the 3D topographic picture of the free energy landscape over the whole range of temperatures, hence to show the funnel along the folding pathway exhaustively. We have simulated and compared the system in vacuo and in solvent, and examined the changes in the free energy landscape due to the solvent effects, which are taken into account by commonly used model Accessible Surface Area.