Erratum: “Spectral signatures of the diffusional anomaly in water” [J. Chem. Phys. 122, 104507 (2005)]

Mudi, Anirban; Chakravarty, Charusita; Ramaswamy, Ramakrishna

doi:10.1063/1.2167357

Cited by 24 publications

(35 citation statements)

References 3 publications

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“…In a series of recent papers, we showed that power spectral analysis could be used to understand the connections between the local order, hydrogen bond network dynamics and the kinetic anomalies in water 14,15,16,17,18,19 . The power spectral density of an observable A(t) as a function of time t is defined as follows 20 :…”

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confidence: 99%

Diffusional anomaly and network dynamics in liquid silica

Sharma

Mudi

Chakravarty

2006

The Journal of Chemical Physics

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The present study applies the power spectral analysis technique to understand the diffusional anomaly in liquid silica, modeled using the BKS potential. Molecular dynamics simulations have been carried out to show that power spectrum of tagged particle potential energy of silica shows a regime with 1/f α dependence on frequency f which is the characteristic signature of multiple time-scale behaviour in networks. As demonstrated earlier in the case of water (J. Chem. Phys., 122, 104507 (2005)), the variations in the mobility associated with the diffusional anomaly are mirrored in the scaling exponent α associated with this multiple time-scale behaviour. Our results indicate that in the anomalous regime, as the local tetrahedral order decreases with temperature or pressure, the coupling of local modes to network reorganisations increases and so does the diffusivity. This symmetry-dependence of the vibrational couplings is responsible for the connection between the structural and diffusional anomalies.

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confidence: 99%

Diffusional anomaly and network dynamics in liquid silica

Sharma

Mudi

Chakravarty

2006

The Journal of Chemical Physics

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“…As a consequence of a multiplicity of time scales, water as well as other network forming liquids show a 1/f R behavior in the S u (f) spectra. [21][22][23][24][25]63 Figure 6 shows that the key features of the S u (f) spectra of TIP3P and SPC/E water are S u (f) ) lim…”

Section: Resultsmentioning

confidence: 99%

Local Order, Energy, and Mobility of Water Molecules in the Hydration Shell of Small Peptides

2009

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The extent to which the presence of a biomolecular solute modifies the local energetics of water molecules, as measured by the tagged molecule potential energy (TPE), is examined using molecular dynamics simulations of the beta-hairpin of 2GB1 and the alpha-helix of deca-alanine in water. The CHARMM22 force field, in conjunction with the TIP3P solvent water model, is used for the peptides, with simulations of TIP3P and SPC/E water used as benchmarks for the behavior of bulk solvent. TIP3P water is shown to have significantly lower local tetrahedral order and higher binding energy than SPC/E at the same state point. The TIP3P and SPC/E water models show very similar dynamical correlations in the TPE fluctuations on frequency scales greater than 0.1 cm(-1). In addition, the two models show the same linear correlation between mean tetrahedral order and binding energy, suggesting that the relationship between choice of water models and simulated hydration behavior may involve a complex interplay of static and dynamic factors. The introduction of a peptide in water modifies the local TPE of water molecules as a function of distance from the biomolecular interface. There is an oscillatory variation in the TPE with distance from the peptide for water molecules lying outside a 3 A radius and extending to at least 10 A. These variations are of the order of 2-5% of the bulk TPE value and are anticorrelated with variations in local tetrahedral order in terms of locations of maxima and minima, which may be understood in terms of the relative contribution of van der Waals and Coulombic contributions to the TPE. The distance-dependent variations in local order and energetics are essentially the same for the beta-hairpin of 2GB1 as well as deca-alanine. Within a radius of 3 A, the perturbation of the solvent structure is very significant with local TPEs that are 10-15% lower than the bulk value. The chemical identity of side-chain residues and the secondary structure play an important role in determining residue-dependent variations in the TPEs. The variation in the residue-dependent tagged molecule potential energies is of the order of 3-5%, while the local residence times vary by a factor of approximately 5. The correlation of the local residence times with the local energetics within the innermost hydration layer is weak, though charged residues typically have low binding energies and large residence times.

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“…For example, long time fluctuations of the potential energy in water and silica exhibiting 1/f spectra have been reported in computer simulation studies [44,47,48]. The 1/f power spectrum of the potential energy fluctuations for water is related to the non-exponential relaxation of slow hydrogen bond dynamics [14,47]. A study of solvation dynamics in an ionic liquid at room temperature has also shown 1/f spectral behavior [50].…”

Section: Noise Power Spectral Analysismentioning

confidence: 99%

Widom line and noise-power spectral analysis of a supercritical fluid

Han

2012

Phys. Rev. E

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We have performed extensive molecular dynamics simulations to study noise-power spectra of density and potential energy fluctuations of a Lennard-Jones model of a fluid in the supercritical region. Emanating from the liquid-vapor critical point, there is a locus of isobaric specific heat maxima, called the Widom line, which is often regarded as an extension of the liquid-vapor coexistence line. Our simulation results show that the noise-power spectrum of the density fluctuations on the Widom line of the liquid-vapor transition exhibits three distinct 1/f^{γ} behaviors with exponents γ=0, 1.2, and 2, depending on the frequency f. We find that the intermediate frequency region with an exponent γ∼ 1 appears as the temperature approaches the Widom temperature from above or below. On the other hand, we do not find three distinct regions of 1/f^{γ} in the power spectrum of the potential energy fluctuations on the Widom line. Furthermore, we find that the power spectra of both the density and potential energy fluctuations at low frequency have a maximum on the Widom line, suggesting that the noise power can provide an alternative signature of the Widom line.

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Erratum: “Spectral signatures of the diffusional anomaly in water” [J. Chem. Phys. 122, 104507 (2005)]

Cited by 24 publications

References 3 publications

Diffusional anomaly and network dynamics in liquid silica

Diffusional anomaly and network dynamics in liquid silica

Local Order, Energy, and Mobility of Water Molecules in the Hydration Shell of Small Peptides

Widom line and noise-power spectral analysis of a supercritical fluid

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