Theoretical prediction of spectral and optical properties of bacteriochlorophylls in thermally disordered LH2 antenna complexes

A general approach for calculating spectral and optical properties of pigment-protein complexes of known atomic structure is presented. The method, that combines molecular dynamics simulations, quantum chemistry calculations and statistical mechanical modeling, is demonstrated by calculating the absorption and circular dichroism spectra of the B800-B850 BChls of the LH2 antenna complex from Rs. molischianum at room temperature. The calculated spectra are found to be in good agreement with the available experimental results. The calculations reveal that the broadening of the B800 band is mainly caused by the interactions with the polar protein environment, while the broadening of the B850 band is due to the excitonic interactions. Since it contains no fitting parameters, in principle, the proposed method can be used to predict optical spectra of arbitrary pigment-protein complexes of known structure.Comment: ReVTeX4, 11 pages, 9 figures, submitted to J. Chem. Phy

Kinetic Monte Carlo and Cellular Particle Dynamics Simulations of Multicellular Systems

Computer modeling of multicellular systems has been a valuable tool for interpreting and guiding in vitro experiments relevant to embryonic morphogenesis, tumor growth, angiogenesis and, lately, structure formation following the printing of cell aggregates as bioink particles. Computer simulations based on Metropolis Monte Carlo (MMC) algorithms were successful in explaining and predicting the resulting stationary structures (corresponding to the lowest adhesion energy state). Here we present two alternatives to the MMC approach for modeling cellular motion and self-assembly: (1) a kinetic Monte Carlo (KMC), and (2) a cellular particle dynamics (CPD) method. Unlike MMC, both KMC and CPD methods are capable of simulating the dynamics of the cellular system in real time. In the KMC approach a transition rate is associated with possible rearrangements of the cellular system, and the corresponding time evolution is expressed in terms of these rates. In the CPD approach cells are modeled as interacting cellular particles (CPs) and the time evolution of the multicellular system is determined by integrating the equations of motion of all CPs. The KMC and CPD methods are tested and compared by simulating two experimentally well known phenomena: (1) cell-sorting within an aggregate formed by two types of cells with different adhesivities, and (2) fusion of two spherical aggregates of living cells.Comment: 11 pages, 7 figures; submitted to Phys Rev

Algorithm Selection Framework for Cyber Attack Detection

The number of cyber threats against both wired and wireless computer systems and other components of the Internet of Things continues to increase annually. In this work, an algorithm selection framework is employed on the NSL-KDD data set and a novel paradigm of machine learning taxonomy is presented. The framework uses a combination of user input and meta-features to select the best algorithm to detect cyber attacks on a network. Performance is compared between a rule-of-thumb strategy and a meta-learning strategy. The framework removes the conjecture of the common trial-and-error algorithm selection method. The framework recommends five algorithms from the taxonomy. Both strategies recommend a high-performing algorithm, though not the best performing. The work demonstrates the close connectedness between algorithm selection and the taxonomy for which it is premised.Comment: 6 pages, 7 figures, 1 table, accepted to WiseML '2

Analysis of Transient Processes in a Radiophysical Flow System

Transient processes in a third-order radiophysical flow system are studied and a map of the transient process duration versus initial conditions is constructed and analyzed. The results are compared to the arrangement of submanifolds of the stable and unstable cycles in the Poincare section of the system studied.Comment: 3 pages, 2 figure

Symmetries and Fixed Point Stability of Stochastic Differential Equations Modeling Self-Organized Criticality

A stochastic nonlinear partial differential equation is built for two different models exhibiting self-organized criticality, the Bak, Tang, and Wiesenfeld (BTW) sandpile model and the Zhang's model. The dynamic renormalization group (DRG) enables to compute the critical exponents. However, the nontrivial stable fixed point of the DRG transformation is unreachable for the original parameters of the models. We introduce an alternative regularization of the step function involved in the threshold condition, which breaks the symmetry of the BTW model. Although the symmetry properties of the two models are different, it is shown that they both belong to the same universality class. In this case the DRG procedure leads to a symmetric behavior for both models, restoring the broken symmetry, and makes accessible the nontrivial fixed point. This technique could also be applied to other problems with threshold dynamics.Comment: 19 pages, RevTex, includes 6 PostScript figures, Phys. Rev. E (March 97?

Statistics of extremal intensities for Gaussian interfaces

The extremal Fourier intensities are studied for stationary Edwards-Wilkinson-type, Gaussian, interfaces with power-law dispersion. We calculate the probability distribution of the maximal intensity and find that, generically, it does not coincide with the distribution of the integrated power spectrum (i.e. roughness of the surface), nor does it obey any of the known extreme statistics limit distributions. The Fisher-Tippett-Gumbel limit distribution is, however, recovered in three cases: (i) in the non-dispersive (white noise) limit, (ii) for high dimensions, and (iii) when only short-wavelength modes are kept. In the last two cases the limit distribution emerges in novel scenarios.Comment: 15 pages, including 7 ps figure

A Method for Determining the Transient Process Duration in Dynamic Systems in the Regime of Chaotic Oscillations

We describe a method for determining the transient process duration in a standard two-dimensionaldynamic system with discrete time (Henon map), occurring in the regime of chaotic oscillationsComment: 4 pages, 2 figure

Simulation study of the inhomogeneous Olami-Feder-Christensen model of earthquakes

Statistical properties of the inhomogeneous version of the Olami-Feder-Christensen (OFC) model of earthquakes is investigated by numerical simulations. The spatial inhomogeneity is assumed to be dynamical. Critical features found in the original homogeneous OFC model, e.g., the Gutenberg-Richter law and the Omori law are often weakened or suppressed in the presence of inhomogeneity, whereas the characteristic features found in the original homogeneous OFC model, e.g., the near-periodic recurrence of large events and the asperity-like phenomena persist.Comment: Shortened from the first version. To appear in European Physical Journal

Effect of Trends on Detrended Fluctuation Analysis

Detrended fluctuation analysis (DFA) is a scaling analysis method used to estimate long-range power-law correlation exponents in noisy signals. Many noisy signals in real systems display trends, so that the scaling results obtained from the DFA method become difficult to analyze. We systematically study the effects of three types of trends -- linear, periodic, and power-law trends, and offer examples where these trends are likely to occur in real data. We compare the difference between the scaling results for artificially generated correlated noise and correlated noise with a trend, and study how trends lead to the appearance of crossovers in the scaling behavior. We find that crossovers result from the competition between the scaling of the noise and the ``apparent'' scaling of the trend. We study how the characteristics of these crossovers depend on (i) the slope of the linear trend; (ii) the amplitude and period of the periodic trend; (iii) the amplitude and power of the power-law trend and (iv) the length as well as the correlation properties of the noise. Surprisingly, we find that the crossovers in the scaling of noisy signals with trends also follow scaling laws -- i.e. long-range power-law dependence of the position of the crossover on the parameters of the trends. We show that the DFA result of noise with a trend can be exactly determined by the superposition of the separate results of the DFA on the noise and on the trend, assuming that the noise and the trend are not correlated. If this superposition rule is not followed, this is an indication that the noise and the superimposed trend are not independent, so that removing the trend could lead to changes in the correlation properties of the noise.Comment: 20 pages, 16 figure

Effect of nonstationarities on detrended fluctuation analysis

Detrended fluctuation analysis (DFA) is a scaling analysis method used to quantify long-range power-law correlations in signals. Many physical and biological signals are ``noisy'', heterogeneous and exhibit different types of nonstationarities, which can affect the correlation properties of these signals. We systematically study the effects of three types of nonstationarities often encountered in real data. Specifically, we consider nonstationary sequences formed in three ways: (i) stitching together segments of data obtained from discontinuous experimental recordings, or removing some noisy and unreliable parts from continuous recordings and stitching together the remaining parts -- a ``cutting'' procedure commonly used in preparing data prior to signal analysis; (ii) adding to a signal with known correlations a tunable concentration of random outliers or spikes with different amplitude, and (iii) generating a signal comprised of segments with different properties -- e.g. different standard deviations or different correlation exponents. We compare the difference between the scaling results obtained for stationary correlated signals and correlated signals with these three types of nonstationarities.Comment: 17 pages, 10 figures, corrected some typos, added one referenc