Biomedical subjects

Charusita Chakravarty

Publications and source records attributed to Charusita Chakravarty.

9 recordsLinked to original sources

PubMed2006

Entropy, diffusivity, and structural order in liquids with waterlike anomalies.

The excess entropy, defined as the difference between the entropies of the liquid and the ideal gas under identical density and temperature conditions, is studied as a function of density and temperature for liquid silica and a two-scale ramp potential, both of which are known to possess waterlike liquid state anomalies. The excess entropy for both systems is evaluated using a fairly accurate pair correlation approximation. The connection between the excess entropy and the density and diffusional anomalies is demonstrated. Using the pair correlation approximation to the excess entropy, it can be shown that if the energetically favorable local geometries in the low and high density limits have different symmetries, then a structurally anomalous regime can be defined in terms of orientational and translational order parameters, as in the case of silica and the two-scale ramp system but not for the one-scale ramp liquid. Within the category of liquids with waterlike anomalies, we show that the relationship between the macroscopic entropy and internal energy is sufficient to distinguish between those with local anisotropy and consequent open packings at low densities and those with isotropic interactions but multiple length scales. Since it is straightforward to evaluate the pair correlation entropy and internal energy from simulations or experimental data, such plots should provide a convenient means to diagnose the existence as well as type of anomalous behavior in a range of liquids, including ionic and intermetallic melts and complex fluids with ultrasoft repulsions.

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PubMed2006

Spectral characterization of hydrogen bond network dynamics in water.

Some computational aspects of the characterization of the complex hydrogen bond network dynamics using power spectral analysis are discussed. In the case of hydrogen-bonded liquids, the tagged molecule potential energy is shown to be a useful quantity for capturing the behavior of the networked liquid on different lengths and time scales. The computation of the tagged potential energy for rigid-body effective pair potentials, such as the TIP5P-E and SPC-E models, is discussed. The more structured nature of the TIP5P-E potential, compared to the SPC/E potential, shows up as differences in the high-frequency librational band of the power spectra of the tagged molecule potential energies. The static distributions of the tagged molecule potential energies are also more structured in the case of TIP5P-E, rather than SPC/E, water. The overall behavior of the key power spectral features remains the same in both the models. The possibility of detailed characterization of the power spectrum, and therefore of the underlying dynamics, using a model-based parametric fitting procedure for the power spectra is also discussed. We show that a parametric fitting can allow one to test alternative models of the dynamics underlying the liquid state dynamics.

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PubMed2006

Diffusional anomaly and network dynamics in liquid silica.

The present study applies the power spectral analysis technique to understand the diffusional anomaly in liquid silica, modeled using the Beest-Kramer-van Santen (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 1f(alpha) 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 alpha associated with this multiple time scale behavior. 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 reorganizations 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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PubMed2006

Effect of ionic solutes on the hydrogen bond network dynamics of water: power spectral analysis of aqueous NaCl solutions.

To understand the modifications of the hydrogen bond network of water by ionic solutes, power spectra as well as static distributions of the potential energies of tagged solvent molecules and solute ions have been computed from molecular dynamics simulations of aqueous NaCl solutions. The key power spectral features of interest are the presence of high-frequency peaks due to localized vibrational modes, the existence of a multiple time scale or 1/falpha frequency regime characteristic of networked liquids, and the frequency of crossover from 1/falpha type behavior to white noise. Hydrophilic solutes, such as the sodium cation and the chloride anion, are shown to mirror the multiple time scale behavior of the hydrogen bond network fluctuations, unlike hydrophobic solutes which display essentially white noise spectra. While the power spectra associated with tagged H2O molecules are not very sensitive to concentration in the intermediate frequency 1/falpha regime, the crossover to white noise is shifted to lower frequencies on going from pure solvent to aqueous alkali halide solutions. This suggests that new and relatively slow time scales enter the picture, possibly associated with processes such as migration of water molecules from the hydration shell to the bulk or conversion of contact ion pairs into solvent-separated ion pairs which translate into variations in equilibrium transport properties of salt solutions with concentration. For anions, cations, and solvent molecules, the trends in the alpha exponents of the multiple time scale region and the self-diffusivities are found to be strongly correlated.

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PubMed2006

Diffusivity, excess entropy, and the potential-energy landscape of monatomic liquids.

The connection between thermodynamic, transport, and potential-energy landscape features is studied for liquids with Lennard-Jones-type pair interactions using both microcanonical molecular-dynamics and isothermal-isobaric ensemble Monte Carlo simulations. Instantaneous normal-mode and saddle-point analyses of two variants of the monatomic Lennard-Jones liquid have been performed. The diffusivity is shown to depend linearly on several key properties of instantaneous and saddle configurations-the energy, the fraction of negative curvature directions, and the mean, maximum, and minimum eigenvalues of the Hessian. Since the Dzugutov scaling relationship also holds for such systems [Nature (London) 381, 137 (1996)], the exponential of the excess entropy, within the two-particle approximation, displays the same linear dependence on energy landscape properties as the diffusivity.

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PubMed2005

Generating inherent structures of liquids: comparison of local minimization algorithms.

Properties of minima obtained by two different local minimization algorithms, the conjugate gradient and the limited-memory Broyden-Fletcher-Goldfarb-Shanno, are compared for a liquid whose particles interact via a modified Lennard-Jones pair interaction. The average properties of inherent structures obtained by the two minimization procedures are shown to agree within statistical error, though for a given starting configuration the two algorithms may not quench to identical minima.

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PubMed2005

Hybrid Monte Carlo implementation of the Fourier path integral algorithm.

This paper formulates a hybrid Monte Carlo implementation of the Fourier path integral (FPI-HMC) approach with partial averaging. Such a hybrid Monte Carlo approach allows one to generate collective moves through configuration space using molecular dynamics while retaining the computational advantages associated with the Fourier path integral Monte Carlo method. In comparison with the earlier Metropolis Monte Carlo implementations of the FPI algorithm, the present HMC method is shown to be significantly more efficient for quantum Lennard-Jones solids and suggests that such algorithms may prove useful for efficient simulations of a range of atomic and molecular systems.

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PubMed2005

Spectral signatures of the diffusional anomaly in water.

Power spectra for various tagged particle quantities in bulk extended simple point charge model water [H. J. C. Berendsen, J. R. Grigera, and T. P. Straatsma, J. Phys. Chem. 91, 6269 (1987)] are shown to have a regime with 1f(alpha) dependence on frequency f with alpha lying between 1 and 1.5 if the dynamical changes in the particular observable are sensitive to the multiple time-scale behavior of the hydrogen-bond network. The variations in mobility associated with the diffusional anomaly are mirrored in the scaling exponent alpha associated with this multiple time-scale behavior, suggesting that monitoring of 1f(alpha) behavior is a simple and direct method for linking phenomena on three distinctive length and time scales: the local molecular environment, hydrogen-bond network reorganizations, and the diffusivity. Our results indicate that experimental studies of supercooled water to probe the density dependence of 1f(alpha) spectral features, or equivalent stretched exponential behavior in time-correlation functions, will be of interest.

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PubMed2002

Potential-energy landscapes of simple liquids.

Changes in the potential-energy surface as a function of the range and curvature of the pair potential are studied using isothermal-isobaric ensemble Monte Carlo simulations of Morse liquids. The configurational energies of stationary points are found to be linear functions of the fraction of imaginary modes, with slopes that are proportional to the range of the potential. The relative energies of saddles, minima, and instantaneous configurations show qualitatively different behavior for short, long, and intermediate range potentials, which imply corresponding variations in liquid state relaxation dynamics.

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