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Abstract: Estimation of configurational entropy from molecular dynamics trajectories is a difficult task which is often performed using quasi-harmonic or histogram analysis. An entirely different approach, proposed recently, estimates local density distribution around each conformational sample by measuring the distance from its nearest neighbors. In this work we show this theoretically well grounded the method can be easily applied to estimate the entropy from conformational sampling. We consider a set of systems that are representative of important biomolecular processes. In particular: reference entropies for amino acids in unfolded proteins are obtained from a database of residues not participating in secondary structure elements; the conformational entropy of folding of β2-microglobulin is computed from molecular dynamics simulations using reference entropies for the unfolded state; backbone conformational entropy is computed from molecular dynamics simulations of four different states of the EPAC protein and compared with order parameters (often used as a measure of entropy); the conformational and rototranslational entropy of binding is computed from simulations of 20 tripeptides bound to the peptide binding protein OppA and of β2-microglobulin bound to a citrate coated gold surface. This work shows the potential of the method in the most representative biological processes involving proteins, and provides a valuable alternative, principally in the shown cases, where other approaches are problematic.
Found in: ključnih besedah
Keywords: entropy, protein, molecular dynamics, simulations, MD
Published: 12.10.2016; Views: 3166; Downloads: 192
Fulltext (2,40 MB)

Abstract: This paper unwraps nanofluids’ particle dynamics with multi-walled carbon nanotubes (MWCNTs) in base fluids such as acetone, water, and ethylene glycol. Having confirmed the morphology and structure of the MWCNTs by field emission scanning electron microscopy, X-ray diffraction, and Raman spectroscopic analyses, the nanofluids are prepared in three different concentrations. The nonzero absorbance at the laser wavelength, revealed through the UV−visible spectrum, makes the thermal diffusivity study of the sample by the sensitive nondestructive single beam thermal lens (TL) technique possible. The TL signal analysis by time series and fractal techniques divulges the complex particle dynamics, through phase portrait, sample entropy, fractal dimension, and Hurst exponent. The study unveils the effect of the amount of nanoparticles and the viscosity of the medium on thermal diffusivity and particle dynamics. The observed inverse relation between thermal diffusivity and viscosity is in good agreement with the Sankar−Swapna model. The complexity of particle dynamics in MWCNT nanofluids reflected through sample entropy, and fractal dimension shows an inverse relation to the base fluid’s viscosity. This paper investigates the role of viscosity of the base fluid on particle dynamics and thermal diffusivity of the nanofluid to explore its applicability in various thermal systems, thereby suggesting a method to tune the sample entropy through proper selection of base fluid.
Found in: ključnih besedah
Summary of found: ...complex particle dynamics, through phase portrait, sample entropy, fractal dimension, and Hurst exponent. The study...
Keywords: MWCNT, thermal lens, fractals, nonlinear time series, phase portrait, sample entropy
Published: 28.06.2022; Views: 157; Downloads: 0
Fulltext (3,59 MB)

Abstract: The present work suggests a method of improving the thermal system efficiency, through entropy minimisation, and unveils the mechanism involved by analysing the molecular/particle dynamics in soot nanofluids (SNFs) using the time series, power spectrum, and wavelet analyses of the thermal lens signal (TLS). The photothermal energy deposition in the SNF lowers the refractive index due to the temperature rise. It triggers the particle dynamics that are investigated by segmenting the TLS and analysing the refractive index, phase portrait, fractal dimension (D), Hurst exponent (H), and sample entropy (SampEn). The wavelet analysis gives information about the relation between the entropy and the frequency components. When the phase portrait analysis reflects the complex dynamics from region 1 to 2 for all the samples, the SampEn analysis supports it. The decreasing value of D (from 1.59 of the base fluid to 1.55 and 1.52) and the SampEn (from 1.11 of the base fluid to 0.385 and 0.699) with the incorporation of diesel and camphor soot, indicate its ability to lower the complexity, randomness, and entropy. The increase of SampEn with photothermal energy deposition suggests its relation to the thermodynamic entropy (S). The lowering of thermal diffusivity value of the base fluid from 1.4 × 10−7 m2/s to 1.1 × 10−7 and 0.5 × 10−7 m2 /s upon diesel and camphor soot incorporation suggests the heat-trapping and reduced molecular dynamics in heat dissipation.
Found in: ključnih besedah
Keywords: soot, entropy, thermal system, photothermal, time series, nanofluid, fractal
Published: 30.06.2022; Views: 112; Downloads: 0
Fulltext (2,27 MB)

Abstract: Since the outbreak of the pandemic Coronavirus Disease 2019, the world is in search of novel non-invasive methods for safer and early detection of lung diseases. The pulmonary pathological symptoms refected through the lung sound opens a possibility of detection through auscultation and of employing spectral, fractal, nonlinear time series and principal component analyses. Thirty-fve signals of vesicular and expiratory wheezing breath sound, subjected to spectral analyses shows a clear distinction in terms of time duration, intensity, and the number of frequency components. An investigation of the dynamics of air molecules during respiration using phase portrait, Lyapunov exponent, sample entropy, fractal dimension, and Hurst exponent helps in understanding the degree of complexity arising due to the presence of mucus secretions and constrictions in the respiratory airways. The feature extraction of the power spectral density data and the application of principal component analysis helps in distinguishing vesicular and expiratory wheezing and thereby, giving a ray of hope in accomplishing an early detection of pulmonary diseases through sound signal analysis.
Found in: ključnih besedah
Summary of found: ...respiration using phase portrait, Lyapunov exponent, sample entropy, fractal dimension, and Hurst exponent helps in...
Keywords: auscultation, wheeze, fractals, nonlinear time series analysis, sample entropy
Published: 30.06.2022; Views: 113; Downloads: 0
Fulltext (2,46 MB)

Abstract: Cough signal analysis for understanding the pathological condition has become important from the outset of the exigency posed by the epidemic COVID-19. The present work suggests a surrogate approach for the classification of cough signals - croup cough (CC) and pertussis (PT) – based on spectral, fractal, and nonlinear time-series techniques. The spectral analysis of CC reveals the presence of more frequency components in the short duration cough sound compared to PT. The musical nature of CC is unveiled not only through the spectral analysis but also through the phase portrait features – sample entropy (S), maximal Lyapunov exponent (L), and Hurst exponent (Hb). The modifications in the internal morphology of the respiratory tract, giving rise to more frequency components associated with the complex airflow dynamics, get staged through the higher fractal dimension of CC. Among the two supervised classification tools, cubic KNN (CKNN) and neural net pattern recognition (NNPR), used for classifying the CC and PT signals based on nonlinear time series parameters, NNPR is found better. Thus, the study opens the possibility of identification of pulmonary pathological conditions through cough sound signal analysis.
Found in: ključnih besedah
Summary of found: ...through the phase portrait features – sample entropy (S), maximal Lyapunov exponent (L), and Hurst...
Keywords: Croup cough Pertussis Fractal dimension Phase portrait Sample entropy Machine learning techniques
Published: 04.07.2022; Views: 82; Downloads: 0
Fulltext (5,42 MB)