Sharif Digital Repository

A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model of proteins, is used to carry out long (several microsecond) simulations in order to study transport of proteins in nanopores. We simulated single-domain proteins with the α-helical native structure. Both attractive and repulsive interaction potentials between the proteins and the pores' walls are considered. The diffusivity D of the proteins is computed not only under the bulk conditions but also as a function of their "length" (the number of the amino-acid groups), temperature T, pore size, and interaction potentials with the walls. Compared with the... 

Localization of electromagnetic waves in two-dimensional (2D) and three-dimensional (3D) media with random permittivities is studied by numerical simulations of the Maxwell's equations. Using the transfer-matrix method, the minimum positive Lyapunov exponent γm of the model is computed, the inverse of which is the localization length. Finite-size scaling analysis of γm is carried out in order to check the localization-delocalization transition in 2D and 3D. We show that in 3D disordered media γm exhibits two distinct types of frequency dependence over two frequency ranges, hence indicating the existence of a localization-delocalization transition at a critical frequency ωc. The critical... 

Discontinuous molecular dynamics simulations, together with the protein intermediate resolution model, an intermediate-resolution model of proteins, are used to carry out several microsecond-long simulations and study folding transition and stability of α -de novo-designed proteins in slit nanopores. Both attractive and repulsive interaction potentials between the proteins and the pore walls are considered. Near the folding temperature Tf and in the presence of the attractive potential, the proteins undergo a repeating sequence of folding/partially folding/unfolding transitions, with Tf decreasing with decreasing pore sizes. The unfolded states may even be completely adsorbed on the pore's... 

Localization of elastic waves in two-dimensional (2D) and three-dimensional (3D) media with random distributions of the Lamé coefficients (the shear and bulk moduli) is studied, using extensive numerical simulations. We compute the frequency dependence of the minimum positive Lyapunov exponent γ (the inverse of the localization length) using the transfer-matrix method, the density of states utilizing the force oscillator method, and the energy-level statistics of the media. The results indicate that all the states may be localized in the 2D media, up to the disorder width and the smallest frequencies considered, although the numerical results also hint at the possibility that there might be... 

Three distinct methods, namely, the spectral density, the multifractal random walk approach, and the multifractal detrended fluctuation analysis are utilized to study the properties of four distinct types of well logs from three oil and gas fields, namely, the natural gamma ray emission, neutron porosity, bulk density, and the sonic transient time logs. Such well logs have never been analyzed by the methods that we utilize in the present study. The results indicate that the well logs exhibit multifractal characteristics, and the estimated Hurst exponents by the three methods are close to each other. Using multifractal detrended fluctuation analysis and the shuffled and surrogated data, we... 

Three distinct methods, namely, the spectral density, the multifractal random walk approach, and the multifractal detrended fluctuation analysis are utilized to study the properties of four distinct types of well logs from three oil and gas fields, namely, the natural gamma ray emission, neutron porosity, bulk density, and the sonic transient time logs. Such well logs have never been analyzed by the methods that we utilize in the present study. The results indicate that the well logs exhibit multifractal characteristics, and the estimated Hurst exponents by the three methods are close to each other. Using multifractal detrended fluctuation analysis and the shuffled and surrogated data, we... 

Monodispersed semiconducting nanoparticles are usually synthesised in a liquid medium using injection of an appropriate solution. A key factor in attaining a narrow particle size distribution (PSD) is the temporal separation of the nucleation and growth stages, where the former takes place during the injection. Faster injection produces a larger number of nuclei and a narrower PSD. The injection speed is expected to affect the diffusion of the ions in the solution and to create uniformly high supersaturation for a short period of time. In this paper, we study the growth of CdS nanoparticles during the injection by molecular dynamics simulation. A solution of Cd ions is injected into the... 

This review addresses a central question in the field of complex systems: given a fluctuating (in time or space), sequentially measured set of experimental data, how should one analyze the data, assess their underlying trends, and discover the characteristics of the fluctuations that generate the experimental traces? In recent years, significant progress has been made in addressing this question for a class of stochastic processes that can be modeled by Langevin equations, including additive as well as multiplicative fluctuations or noise. Important results have emerged from the analysis of temporal data for such diverse fields as neuroscience, cardiology, finance, economy, surface science,... 

We study localization of elastic waves in two-dimensional heterogeneous solids with randomly distributed Lamé coefficients, as well as those with long-range correlations with a power-law correlation function. The Matin-Siggia-Rose method is used, and the one-loop renormalization group (RG) equations for the coupling constants are derived in the limit of long wavelengths. The various phases of the coupling constants space, which depend on the value ρ, the exponent that characterizes the power-law correlation function, are determined and described. Qualitatively different behaviors emerge for ρ<1 and ρ>1. The Gaussian fixed point (FP) is stable (unstable) for ρ<1 (ρ>1). For ρ<1, there is a... 

Statistical properties of interbeat intervals cascade in human hearts are evaluated by considering the joint probability distribution P(Δx 2, τ 2 Δx1, τ 1) for two interbeat increments Δx1 and Δx2 of different time scales τ 1 and τ 2. We present evidence that the conditional probability distribution P(Δx2, τ2|Δx1, τ 1 ) may be described by a Chapman-Kolmogorov equation. The corresponding Kramers-Moyal (KM) coefficients are evaluated. The analysis indicates that while the first and second KM coefficients take on well-defined and significant values, the higher-order coefficients in the KM expansion are small. As a result, the joint probability distributions of the increments in the interbeat... 

We propose a novel inverse method that utilizes a set of data to construct a simple equation that governs the stochastic process for which the data have been measured, hence enabling us to reconstruct the stochastic process. As an example, we analyze the stochasticity in the beat-to-beat fluctuations in the heart rates of healthy subjects as well as those with congestive heart failure. The inverse method provides a novel technique for distinguishing the two classes of subjects in terms of a drift and a diffusion coefficients which behave completely differently for the two classes of subjects, hence potentially providing a novel diagnostic tool for distinguishing healthy subjects from those... 

Large-scale ab initio molecular-dynamics simulations have been carried out to compute, at human-body temperature, the vibrational modes and lifetimes of pure and hydrated dipalmitoylphosphatidylcholine (DPPC) lipids. The projected atomic vibrations calculated from the spectral energy density are used to compute the vibrational modes and the lifetimes. All the normal modes of the pure and hydrated DPPC and their frequencies are identified. The computed lifetimes incorporate the full anharmonicity of the atomic interactions. The vibrational modes of the water molecules close to the head group of DPPC are active (possess large projected spectrum amplitudes) in the frequency range 0.5-55 THz,... 

Propagation of acoustic waves in the one-dimensional (1D) random-dimer (RD) medium is studied by three distinct methods. First, using the transfer-matrix method, we calculate numerically the localization length ξ of acoustic waves in a binary chain (one in which the elastic constants take on one of two values). We show that when there exists short-range correlation in the medium-which corresponds to the RD model-the localization-delocalization transition occurs at a resonance frequency ωc. The divergence of ξ near ωc is studied, and the critical exponents that characterize the power-law behavior of ξ near ωc are estimated for the regimes ω> ωc and ω< ωc. Second, an exact analytical analysis... 

A mapping is developed between the linearized equation of motion for the dynamics of the transverse modes at T=0 of the Heisenberg-Mattis model of one-dimensional (1D) spin glasses and the (discretized) random wave equation. The mapping is used to derive an exact expression for the Lyapunov exponent (LE) of the magnon modes of spin glasses and to show that it follows anomalous scaling at low magnon frequencies. In addition, through numerical simulations, the differences between the LE and the density of states of the wave equation in a discrete 1D model of randomly disordered media (those with a finite correlation length) and that of continuous media (with a zero correlation length) are... 

We carry out a series of cross-correlation analysis of raw well-log data, in order to study the possible connection between natural gamma ray (GR) logs and other types of well logs, such as neutron porosity (NPHI), sonic transient time (denoted usually by DT), and bulk density (RHOB) of oil and gas reservoirs. Three distinct, but complementary, methods are used to analyze the cross correlations, namely, the multifractal detrended cross-correlation analysis (MF-DXA), the so-called Qcc(m) test in conjunction with the statistical test-the χ2(m) distribution-and the cross-wavelet transform (XWT) and wavelet coherency. The Qcc(m) test and MF-DXA are used to identify and quantify the strength of... 

Using the Martin-Siggia-Rose method, we study propagation of acoustic waves in strongly heterogeneous media which are characterized by a broad distribution of the elastic constants. Gaussian-white distributed elastic constants, as well as those with long-range correlations with nondecaying power-law correlation functions, are considered. The study is motivated in part by a recent discovery that the elastic moduli of rock at large length scales may be characterized by long-range power-law correlation functions. Depending on the disorder, the renormalization group (RG) flows exhibit a transition to localized regime in any dimension. We have numerically checked the RG results using the... 

We consider chaperone-assisted translocation of biopolymers with two distinct monomers or bases A and B, with the size of the chaperones being λα, where α is a monomer's size. The probability that A and B are neighbors in the biopolymer is PAB. A master equation is used, together with the detailed-balanced condition, in order to derive analytical results for the statistics of the first-passage times of the biopolymer as a function of PAB, λ, and the biopolymer's configuration. Monte Carlo simulations have also been carried out in order to compute the same quantities for biopolymers with 100-900 monomers and several λ. The results indicate nontrivial dependence of the variance of the... 

We carry out an exact analysis of the average frequency ν+ αxi in the direction x i of positiveslope crossing of a given level α such that, h(x, t) h = α, of growing surfaces in spatial dimension d. Here, h(x, t) is the surface height at time t, and h is its mean value. We analyze the problem when the surface growth dynamics is governed by the Kardar-Parisi-Zhang (KPZ) equation without surface tension, in the time regime prior to appearance of cusp singularities (sharp valleys), as well as in the random deposition (RD) model. The total number N + of such level-crossings with positive slope in all the directions is then shown to scale with time as t d/2 for both the KPZ equation and the RD... 

We have used the dynamic method to calculate the frequency dependence of the localization length in a disordered medium, using the amplitude change and the redshift of the spectral density of the propagating incident pulse. The frequency dependence of the localization length in an effectively one-dimensional disordered medium is computed in terms of the strength of the disorder. The results obtained with the dynamic method are confirmed by computing the same results using the transfer-matrix method  

We describe and discuss the recent progress in the study of propagation and localization of acoustic and elastic waves in heterogeneous media. The heterogeneity is represented by a spatial distribution of the local elastic moduli. Both randomly distributed elastic moduli as well as those with long-range correlations with a nondecaying power-law correlation function, are considered. The motivation for the study is twofold. One is that recent analysis of experimental data for the spatial distribution of the elastic moduli of rock indicated that the distribution is characterized by the type of long-range correlations that we consider in this study. The second motivation for the problem is to...