Recurrence analysis of hydration effects on nonlinear protein dynamics: multiplicative scaling and additive processes

Manetti, Cesare; Giuliani, Alessandro; Ceruso, Marc-Antoine; Webber, Charles L.; Zbilut, Joseph P.

doi:10.1016/s0375-9601(01)00147-5

Cited by 31 publications

(15 citation statements)

References 33 publications

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“…Scientists working in various fields have made use of RPs. Applications of RPs can be found in numerous fields of research such as astrophysics [3][4][5], earth sciences [6][7][8], engineering [9,10], biology [11,12], cardiology or neuroscience [13][14][15][16][17][18].…”

Section: Pablo Nerudamentioning

confidence: 99%

“…By means of JRPs, the synchronisation between electrochemical oscillators were studied [151]. Other applications in chemistry/molecular biology concern the dynamics of chemical processes, for example in molecular dynamics simulations of poly-peptides [11,12] or to detect chaotic transitions of Nicotinamide adenine dinucleotide [179]. Applying the RQA to glycoproteins of a virus has uncovered the interaction between specific glycoprotein partners [180].…”

Section: Applicationsmentioning

confidence: 99%

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Recurrence plots for the analysis of complex systems

et al. 2007

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Section: Pablo Nerudamentioning

confidence: 99%

Section: Applicationsmentioning

confidence: 99%

Recurrence plots for the analysis of complex systems

et al. 2007

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“…Recurrence plots (RP) and recurrence quantification analysis (RQA) have been used extensively to study proteins over the years . Most of the work investigated the sequence‐structure relationship in proteins.…”

Section: Introductionmentioning

confidence: 99%

“…Most of the work investigated the sequence‐structure relationship in proteins. A few works dealt with analyzing protein molecular dynamics simulations, and the Lennard–Jones systems of different fluid and solid states …”

Section: Introductionmentioning

confidence: 99%

Detecting protein atom correlations using correlation of probability of recurrence

Fataftah

Karain

2014

Proteins

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The dynamic cross-correlation Map(DCCM) technique has been used extensively to study protein dynamics. In this work, we introduce the use of the method of correlation of probability of recurrence (CPR) as a complementary method to detect correlations between protein residue atoms. Time series of the distances of the Cα atoms of the β-lactamase inhibitory protein (BLIP) from a reference position are analyzed using CPR and mutual information (MI). The results are compared to those provided by DCCM. In comparison to MI, CPR is found to detect more of the correlations present in DCCM. It is also able to detect a small number of significant correlations between distant residues that are not detected by DCCM.

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“…Since that time, scientists have been working in various fields have made use of the RPs. Applications of RPs can be found in numerous fields of research such as astrophysics [52], earth sciences [28], engineering [39,17,21,22,20,6,38], biology [11,23], cardiology, or neuroscience [29,30,46,51], and otolaryngology [41]. Damage detection of various mechanical structure is also analyzed with the help of the RP [34,35,42,33].…”

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confidence: 99%

A numerical-experimental study on damaged beams dynamics

Samborski

Wieczorkiewicz

Rusinek

2015

EiN

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Article citation info: IntroductionIn many contemporary structures various types of defects can appear leading to significant reduction of the element rigidity and changing its overall mechanical behaviour. A special challenge is detection and localization of hidden defects, which can have many forms depending on the scale of the problem, eg. dislocations, voids or inclusions in microscale [43,49,44,3] to macroscopic defects, such as delamination in laminated composites [31] or welds in metallic materials [53,50]. The current work is focused on testing the applicability of dynamic vibration-based, as well as the space analysis methods to defect detection and localization in 1D (beam) structures. The vibration-based methods have been widely used in the plates and beams dynamics. For example, Manoach et al. [25,26,27,24,48] analysed the frequencies and modes of free vibrations in order to identify damage in beam and plates. The most interesting aspect of these papers was introduction of the so-called Damage Index exploiting the information given by the Poincaré maps [19]. The authors of the current study aimed at testing other dynamical methods towards detection and localization of defects in structures, which led them to reach for time series analysis.Experimental time series, especially nonlinear, can be analyzed by means of the method of delay coordinates, which allows to reconstruct a phase space and Poincaré section. This procedure is precisely described in [2,32] and can be applied for analysis of experimental signals obtained from different kinds of real processes [12,5] and numerical simulations [40]. For instance, the delay coordinate technique is used for researching dynamics of robot joints [47] and to analyse nonlinear system with dry friction [40]. Interesting contribution in the field of phase space reconstruction is presented in [7,8,36] in which the method of delay coordinates is employed for experimental and numerically generated signals, also with noise. Another example can be an impact and a self-excited oscillator with CoulombAmontons friction [13].On the basis of delay coordinates method, a recurrence plot technique is introduced to analyse linear or non-linear stationary and also non-stationary time series [30]. The formal concept of recurrences was introduced by Henri Poincaré in his seminal work from 1890 [37], for which he won a prize sponsored by King Oscar II of Sweden and Norway [30]. Therein, Poincaré did not only discover the homoclinic tangl which lies at the root of the chaotic behaviour of orbits, but he also introduced (as a by-product) the concept of recurrences in conservative systems. Even though much mathematical work was carried out in the following years, Poincaré's pioneering work and his discovery of recurrence had to wait for more than 70 years for the development of fast and efficient computers to be exploited numerically. The use of powerful computers boosted chaos theory and allowed to study new and exciting systems. Some of the tedious computations needed to use the c...

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Recurrence analysis of hydration effects on nonlinear protein dynamics: multiplicative scaling and additive processes

Cited by 31 publications

References 33 publications

Recurrence plots for the analysis of complex systems

Recurrence plots for the analysis of complex systems

Detecting protein atom correlations using correlation of probability of recurrence

A numerical-experimental study on damaged beams dynamics

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