Biomedical subjects

Nicolas Giovambattista

Publications and source records attributed to Nicolas Giovambattista.

16 recordsLinked to original sources

PubMed2006

Family of tunable spherically symmetric potentials that span the range from hard spheres to waterlike behavior.

We investigate the equation of state, diffusion coefficient, and structural order of a family of spherically symmetric potentials consisting of a hard core and a linear repulsive ramp. This generic potential has two characteristic length scales: the hard and soft core diameters. The family of potentials is generated by varying their ratio, lambda. We find negative thermal expansion (thermodynamic anomaly) and an increase of the diffusion coefficient upon isothermal compression (dynamic anomaly) for 0< or =lambda<6/7. As in water, the regions where these anomalies occur are nested domes in the (T, p) or (T, P) planes , with the thermodynamic anomaly dome contained entirely within the dynamic anomaly dome. We calculate translational and orientational order parameters (t and Q6), and project equilibrium state points onto the (t, Q6) plane, or order map. The order map evolves from waterlike behavior to hard-sphere-like behavior upon varying lambda between 4/7 and 6/7. Thus, we traverse the range of liquid behavior encompassed by hard spheres (lanbda=1) and waterlike (lambda approximately 4/7) with a family of tunable spherically symmetric potentials by simply varying the ratio of hard to soft-core diameters. Although dynamic and thermodynamic anomalies occur almost across the entire range 0< or=lambda< or=1, waterlike structural anomalies (i.e., decrease in both t and Q6 upon compression and strictly correlated T and Q6 in the anomalous region) occur only around lambda=4/7. Waterlike anomalies in structure, dynamics and thermodynamics arise solely due to the existence of two length scales, with their ratio lambda being the single control parameter, orientation-dependent interactions being absent by design.

Journal Article↗

PubMed2006

Effect of pressure on the phase behavior and structure of water confined between nanoscale hydrophobic and hydrophilic plates.

We perform systematic molecular dynamics simulations of water confined between two nanoscale plates at T = 300K. We investigate the effect of pressure (-0.15 GPa< or = P< or =0.2GPa) and plate separation (0.4 nm < or =d < or =1.6 nm) on the phase behavior of water when the plates are either hydrophobic or hydrophilic. When water is confined between hydrophobic plates, capillary evaporation occurs between the plates at low enough P. The threshold value of d at which this transition occurs decreases with P (e.g., 1.6 nm at P approximately equal to -0.05 GPa, 0.5 nm at P approximately equal to 0.1 GPa), until, at high P, no capillary evaporation occurs. For d approximately equal to 0.6 nm and P > or =0.1 GPa, the system crystallizes into a bilayer ice. A P-d phase diagram showing the vapor, liquid, and bilayer ice phases is proposed. When water is confined by hydrophilic (hydroxylated silica) plates, it remains in the liquid phase at all P and d studied. Interestingly, we observe for this case that even at the P at which bulk water cavitates, the confined water remains in the liquid state. We also study systematically the state of hydration at different P for both kinds of plates. For the range of conditions studied here, we find that in the presence of hydrophobic plates the effect of P is to enhance water structure and to push water molecules toward the plates. The average orientation of water molecules next to the hydrophobic plates does not change upon pressurization. In contrast, in the presence of hydrophilic plates, water structure is insensitive to P. Hence, our results suggest that upon pressurization, hydrophobic plates behave as "soft" surfaces (in the sense of accommodating pressure-dependent changes in water structure) while hydrophilic walls behave as "hard" surfaces.

Journal Article↗

PubMed2006

Relation between rotational and translational dynamic heterogeneities in water.

We use molecular dynamics simulations to probe the rotational dynamics of the extended simple point charge model of water for a range of temperatures down to 200 K, 6 K above the mode coupling temperature. We find that rotational dynamics is spatially heterogeneous; i.e., there are clusters of molecules that rotate significantly more than the average for a given time interval, and we study the size and the temporal behavior of these clusters. We find that the position of a rotational heterogeneity is strongly correlated with the position of a translational heterogeneity, and that the fraction of molecules belonging to both kinds of heterogeneities increases with decreasing temperature. We further find that although the two types of heterogeneities are not identical, they are related to the same physical picture.

Computer Simulation↗

PubMed2005

Thermodynamics, structure, and dynamics of water confined between hydrophobic plates.

We perform molecular dynamics simulations of 512 waterlike molecules that interact via the TIP5P potential and are confined between two smooth hydrophobic plates that are separated by 1.10 nm. We find that the anomalous thermodynamic properties of water are shifted to lower temperatures relative to the bulk by approximately 40 K. The dynamics and structure of the confined water resemble bulk water at higher temperatures, consistent with the shift of thermodynamic anomalies to lower temperature. Because of this T shift, our confined water simulations (down to T=220 K) do not reach sufficiently low temperature to observe a liquid-liquid phase transition found for bulk water at T approximately 215 K using the TIP5P potential, but we see inflections in isotherms at lower temperatures presumably due to the presence of a liquid-liquid critical point. We find that the different crystalline structures that can form for two different separations of the plates, 0.7 and 1.10 nm, have no counterparts in the bulk system, and we discuss the relevance to experiments on confined water.

Journal Article↗

PubMed2005

Phase diagram of amorphous solid water: low-density, high-density, and very-high-density amorphous ices.

We calculate the phase diagram of amorphous solid water by performing molecular dynamics simulations using the extended simple point charge (SPC/E) model. Our simulations follow different paths in the phase diagram: isothermal compression/decompression, isochoric cooling/heating, and isobaric cooling/heating. We are able to identify low-density amorphous (LDA), high-density amorphous (HDA), and very-high density amorphous (VHDA) ices. The density rho of these glasses at different pressure P and temperature T agree well with experimental values. We also study the radial distribution functions of glassy water. In agreement with experiments, we find that LDA, HDA, and VHDA are characterized by a tetrahedral hydrogen-bonded network and that, as compared to LDA, HDA has an extra interstitial molecule between the first and second shell. VHDA appears to have two such extra molecules. We obtain VHDA, as in experiment, by isobaric heating of HDA. We also find that "other forms" of glassy water can be obtained upon isobaric heating of LDA, as well as amorphous ices formed during the transformation of LDA to HDA. We argue that these other forms of amorphous ices, as well as VHDA, are not altogether new glasses but rather are the result of aging induced by heating. Samples of HDA and VHDA with different densities are recovered at normal P, showing that there is a continuum of glasses. Furthermore, the two ranges of densities of recovered HDA and recovered VHDA overlap at ambient P. Our simulations reproduce the experimental findings of HDA --> LDA and VHDA --> LDA transformations. We do not observe a VHDA --> HDA transformation, and our final phase diagram of glassy water together with equilibrium liquid data suggests that for the SPC/E model the VHDA --> HDA transformation cannot be observed with the present heating rates accessible in simulations. Finally, we discuss the consequences of our findings for the understanding of the transformation between the different amorphous ices and the two hypothesized phases of liquid water.

Journal Article↗

PubMed2005

Structural order for one-scale and two-scale potentials.

We perform molecular dynamics simulations to investigate the relationship between structural order and waterlike dynamic and thermodynamic anomalies in spherically symmetric potentials having either one or two characteristic length scales. Structural order is characterized by translational and orientational order parameters. We find that (i) dynamic and thermodynamic anomalies exist for both one-scale and two-scale ramp potentials, and (ii) waterlike structural order anomalies exist only for the two-scale ramp potential. Our findings suggest that the waterlike relationship between structural order and anomalies is related to the presence of two different length scales in the potential.

Journal Article↗

PubMed2005

Structural relaxation in the glass transition region of water.

We perform molecular dynamics (MD) simulations using the extended simple-point-charge (SPC/E) model for water to study the structural relaxation through the glass transition region. We follow the same standard protocol used in differential scanning calorimetry experiments. Specifically, we cool liquid configurations at different cooling rates to produce a glass, and then we heat the glass back to the liquid state. We also study aging effects in the glass before heating. We find that MD simulations can reproduce the phenomenology observed in experiments. We review the Tool-Narayanaswamy-Moynihan (TNM) phenomenological approach, introduced to describe the behavior of the specific heat upon heating glass to the liquid phase. The TNM approach requires, as an ansatz, an expression for the temperature dependence of the relaxation time. We compare the simulation results with the prediction of the TNM approach supplemented with two well-known expressions for the relaxation time: the Narayanaswamy-Moynihan (NM) and the Adam-Gibbs-Scherer (AGS) expressions. We find that, in the case of slow cooling rates, our simulations are well represented by the TNM approach, but only if the AGS expression is adopted. We also find that the TNM approach fails in the case of fast cooling rates for both NM and AGS expressions. Several attempts to provide more freedom to the fitting procedure by allowing the fitting parameters to depend on temperature, cooling, and/or heating rates do not improve the agreement between the simulation data and the TNM predictions.

Journal Article↗

PubMed2005

Clusters of mobile molecules in supercooled water.

We study the spatially heterogeneous dynamics in water via molecular dynamics simulations using the extended simple point charge potential. We identify clusters formed by mobile molecules and study their properties. We find that these clusters grow in size and become more compact as temperature decreases. We analyze the probability density function of cluster size, and we study the cluster correlation length. We find that clusters appear to be characterized by a fractal dimension consistent with that of lattice animals. We relate the cluster size and correlation length to the configurational entropy, S(conf). We find that these quantities depend weakly on 1/ S(conf). In particular, the linearity found between the cluster mass n(*) and 1/ S(conf) suggests that n(*) may be interpreted as the mass of the cooperatively rearranging regions that form the basis of the Adam-Gibbs approach to the dynamics of supercooled liquids. We study the motion of molecules within a cluster, and find that each molecule preferentially follows a neighboring molecule in the same cluster. Based on this finding we hypothesize that stringlike cooperative motion may be a general mechanism for molecular rearrangement of complex, as well as simple liquids. By mapping each equilibrium configuration onto its corresponding local potential energy minimum or inherent structure (IS), we are able to compare the mobile molecule clusters in the equilibrium system with the molecules forming the clusters identified in the transitions between IS. We find that (i) mobile molecule clusters obtained by comparing different system configurations and (ii) clusters obtained by comparing the corresponding IS are completely different for short time scales, but are the same on the longer time scales of diffusive motion.

Journal Article↗

PubMed2005

Structural order in glassy water.

We investigate structural order in glassy water by performing classical molecular dynamics simulations using the extended simple point charge (SPC/E) model of water. We perform isochoric cooling simulations across the glass transition temperature at different cooling rates and densities. We quantify structural order by orientational and translational order metrics. Upon cooling the liquid into the glassy state, both the orientational order parameter Q and translational order parameter tau increase. At T=0 K, the glasses fall on a line in the Q-tau plane or order map. The position of this line depends only on density and coincides with the location in the order map of the inherent structures (IS) sampled upon cooling. We evaluate the energy of the IS, eIS(T), and find that both order parameters for the IS are proportional to eIS. We also study the structural order during the transformation of low-density amorphous ice (LDA) to high-density amorphous ice (HDA) upon isothermal compression and are able to identify distinct regions in the order map corresponding to these glasses. Comparison of the order parameters for LDA and HDA with those obtained upon isochoric cooling indicates major structural differences between glasses obtained by cooling and glasses obtained by compression. These structural differences are only weakly reflected in the pair correlation function. We also characterize the evolution of structural order upon isobaric annealing, leading at high pressure to very-high density amorphous ice (VHDA).

Journal Article↗

PubMed2005

Relation between the high density phase and the very-high density phase of amorphous solid water.

It has been suggested that high-density amorphous (HDA) ice is a structurally arrested form of high-density liquid (HDL) water, while low-density amorphous ice is a structurally arrested form of low-density liquid (LDL) water. Recent experiments and simulations have been interpreted to support the possibility of a second distinct high-density structural state, named very high-density amorphous (VHDA) ice, questioning the LDL-HDL hypothesis. We test this interpretation using extensive computer simulations and find that VHDA is a more stable form of HDA and that, in fact, VHDA should be considered as the amorphous ice of the quenched HDL.

Journal Article↗

PubMed2005

Static and dynamic heterogeneities in water.

The thermodynamic behaviour of water seems to be related to static heterogeneities. These static heterogeneities are related to the local structure of water molecules and, when properly characterized, may offer an economical explanation of thermodynamic data. 'What matters' most in determining some of the unusual properties of liquid water may be the fact that the local geometry of the liquid molecules is not spherical or oblong, but rather tetrahedral. In respect to static heterogeneities, this local geometry is critical. The dynamic behaviour of water seems to be related to dynamic heterogeneities, which seem to explain the dynamics of supercooled liquid water well.

Anisotropy↗

PubMed2004

Glass-transition temperature of water: a simulation study.

We report a computer simulation study of the glass transition for water using the extended simple point charge potential. To mimic the difference between standard and hyperquenched glass, we generate glassy configurations with different cooling rates, and we calculate the temperature dependence of the specific heat on heating. The absence of crystallization phenomena allows us, for properly annealed samples, to detect in the specific heat the simultaneous presence of a weak prepeak ("shadow transition") and an intense glass transition peak at higher temperature. Our results support the view-point that the glass transition temperature is higher than the conventionally accepted value 136 K. We also compare our simulation results with the Tool-Narayanaswamy-Moynihan phenomenological model.

Journal Article↗

PubMed2004

Cooling rate, heating rate, and aging effects in glassy water.

We report a molecular dynamics simulation study of the properties of the potential energy landscape sampled by a system of water molecules during the process of generating a glass by cooling, and during the process of regenerating the equilibrium liquid by heating the glass. We study the dependence of these processes on the cooling/heating rates as well as on the role of aging (the time elapsed in the glass state). We compare the properties of the potential energy landscape sampled during these processes with the corresponding properties sampled in the liquid equilibrium state to elucidate under which conditions glass configurations can be associated with equilibrium liquid configurations.

Journal Article↗

PubMed2003

Potential-energy landscape study of the amorphous-amorphous transformation in H(2)O.

We study the potential energy landscape explored during a compression-decompression cycle for the simple point charge extended model of water. During the cycle, the system changes from low density amorphous (LDA) ice to high density amorphous ice. After the cycle, the system does not return to the same region of the landscape, supporting the interesting possibility that more than one significantly different configuration corresponds to LDA. We find that the regions of the landscape explored during this transition have properties remarkably different from those explored in thermal equilibrium in the liquid phase.

Journal Article↗

PubMed2003

Connection between Adam-Gibbs theory and spatially heterogeneous dynamics.

We investigate the spatially heterogeneous dynamics in the extended simple point charge model of water using molecular dynamics simulations. We relate the average mass n* of mobile particle clusters to the diffusion constant and the configurational entropy. Hence, n* can be interpreted as the mass of the "cooperatively rearranging regions" that form the basis of the Adam-Gibbs theory of the dynamics of supercooled liquids. We also examine the time and temperature dependence of these transient clusters.

Journal Article↗

PubMed2002

Transitions between inherent structures in water.

The energy landscape approach has been useful to help understand the dynamic properties of supercooled liquids and the connection between these properties and thermodynamics. The analysis in numerical models of the inherent structure (IS) trajectories-the set of local minima visited by the liquid-offers the possibility of filtering out the vibrational component of the motion of the system on the potential energy surface and thereby resolving the slow structural component more efficiently. Here we report an analysis of an IS trajectory for a widely studied water model, focusing on the changes in hydrogen bond connectivity that give rise to many IS's separated by relatively small energy barriers. We find that while the system travels through these IS's, the structure of the bond network is continuously modified, exchanging linear bonds for bifurcated bonds and usually reversing the exchange to return to nearly the same initial configuration. For the 216-molecule system we investigate, the time scale of these transitions is as small as the simulation time scale ( approximately 1 fs). Hence, for water, the transition between each of these IS's is relatively small and eventual relaxation of the system occurs only by many of these transitions. We find that during IS changes the molecules with the greatest displacements move in small "clusters" of 1-10 molecules with displacements of approximately 0.02-0.2 nm, not unlike simpler liquids. However, for water these clusters appear to be somewhat more branched than the linear "stringlike" clusters formed in a supercooled Lennard-Jones system found by Glotzer and her collaborators.

Journal Article↗