108 research outputs found
Recurrence quantification analysis as a tool for the characterization of molecular dynamics simulations
A molecular dynamics simulation of a Lennard-Jones fluid, and a trajectory of
the B1 immunoglobulin G-binding domain of streptococcal protein G (B1-IgG)
simulated in water are analyzed by recurrence quantification, which is
noteworthy for its independence from stationarity constraints, as well as its
ability to detect transients, and both linear and nonlinear state changes. The
results demonstrate the sensitivity of the technique for the discrimination of
phase sensitive dynamics. Physical interpretation of the recurrence measures is
also discussed.Comment: 7 pages, 8 figures, revtex; revised for review for Phys. Rev. E
(clarifications and expansion of discussion)-- addition of the 8 postscript
figures previously omitted, but unchanged from version
Extended Recurrence Plot Analysis and its Application to ERP Data
We present new measures of complexity and their application to event related
potential data. The new measures base on structures of recurrence plots and
makes the identification of chaos-chaos transitions possible. The application
of these measures to data from single-trials of the Oddball experiment can
identify laminar states therein. This offers a new way of analyzing
event-related activity on a single-trial basis.Comment: 21 pages, 8 figures; article for the workshop ''Analyzing and
Modelling Event-Related Brain Potentials: Cognitive and Neural Approaches``
at November 29 - December 01, 2001 in Potsdam, German
Recurrence Plot Based Measures of Complexity and its Application to Heart Rate Variability Data
The knowledge of transitions between regular, laminar or chaotic behavior is
essential to understand the underlying mechanisms behind complex systems. While
several linear approaches are often insufficient to describe such processes,
there are several nonlinear methods which however require rather long time
observations. To overcome these difficulties, we propose measures of complexity
based on vertical structures in recurrence plots and apply them to the logistic
map as well as to heart rate variability data. For the logistic map these
measures enable us not only to detect transitions between chaotic and periodic
states, but also to identify laminar states, i.e. chaos-chaos transitions. The
traditional recurrence quantification analysis fails to detect the latter
transitions. Applying our new measures to the heart rate variability data, we
are able to detect and quantify the laminar phases before a life-threatening
cardiac arrhythmia occurs thereby facilitating a prediction of such an event.
Our findings could be of importance for the therapy of malignant cardiac
arrhythmias
Diffraction from the beta-sheet crystallites in spider silk
We analyze the wide angle x-ray scattering from oriented spider silk fibers
in terms of a quantitative scattering model, including both structural and
statistical parameters of the -sheet crystallites of spider silk in the
amorphous matrix. The model is based on kinematic scattering theory and allows
for rather general correlations of the positional and orientational degrees of
freedom, including the crystallite's size, composition and dimension of the
unit cell. The model is evaluated numerically and compared to experimental
scattering intensities allowing us to extract the geometric and statistical
parameters. We show explicitly that for the experimentally found mosaicity
(width of the orientational distribution) inter-crystallite effects are
negligible and the data can be analyzed in terms of single crystallite
scattering, as is usually assumed in the literature.Comment: 15 pages, 14 figures, on average 0.93 figures per pag
Implications from a Network-Based Topological Analysis of Ubiquitin Unfolding Simulations
BACKGROUND: The architectural organization of protein structures has been the focus of intense research since it can hopefully lead to an understanding of how proteins fold. In earlier works we had attempted to identify the inherent structural organization in proteins through a study of protein topology. We obtained a modular partitioning of protein structures with the modules correlating well with experimental evidence of early folding units or "foldons". Residues that connect different modules were shown to be those that were protected during the transition phase of folding. METHODOLOGY/PRINCIPAL FINDINGS: In this work, we follow the topological path of ubiquitin through molecular dynamics unfolding simulations. We observed that the use of recurrence quantification analysis (RQA) could lead to the identification of the transition state during unfolding. Additionally, our earlier contention that the modules uncovered through our graph partitioning approach correlated well with early folding units was vindicated through our simulations. Moreover, residues identified from native structure as connector hubs and which had been shown to be those that were protected during the transition phase of folding were indeed more stable (less flexible) well beyond the transition state. Further analysis of the topological pathway suggests that the all pairs shortest path in a protein is minimized during folding. CONCLUSIONS: We observed that treating a protein native structure as a network by having amino acid residues as nodes and the non-covalent interactions among them as links allows for the rationalization of many aspects of the folding process. The possibility to derive this information directly from 3D structure opens the way to the prediction of important residues in proteins, while the confirmation of the minimization of APSP for folding allows for the establishment of a potentially useful proxy for kinetic optimality in the validation of sequence-structure predictions
A New Approach to Analyzing Convergence and Synchronicity in Growth and Business Cycles: Cross Recurrence Plots and Quantification Analysis
Convergence and synchronisation of business and growth cycles are important issues in the efficient formulation of euro area economic policies, and in particular European Central Bank (ECB) monetary policy. Although several studies in the economics literature address the issue of synchronicity of growth within the euro area, this is the first to address the issue using cross recurrence analysis. The main findings are that member state growth rates had largely converged before the introduction of the euro, but there is a wide degree of different synchronisation behaviours which appear to be non-linear in nature. Many of the euro area member states display what is termed here intermittency in synchronization, although this is not consistent across countries or members of the euro area. These differences in synchronization behaviors could introduce further challenges in managing the country-specific effects of the common monetary policy in the euro area
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