Biomedical subjects

Francis W Starr

Publications and source records attributed to Francis W Starr.

11 recordsLinked to original sources

PubMed2006

Polarizable contributions to the surface tension of liquid water.

Surface tension, gamma, strongly affects interfacial properties in fluids. The degree to which polarizability affects gamma in water is thus far not well established. To address this situation, we carry out molecular dynamics simulations to study the interfacial forces acting on a slab of liquid water surrounded by vacuum using the Gaussian charge polarizable (GCP) model at 298.15 K. The GCP model incorporates both a fixed dipole due to Gaussian distributed charges and a polarizable dipole. We find a well-defined bulklike region forms with a width of approximately 31 A. The average density of the bulklike region agrees with the experimental value of 0.997 g/cm3. However, we find that the orientation of the molecules in the bulklike region is strongly influenced by the interfaces, even at a distance five molecular diameters from the interface. Specifically, the orientations of both the permanent and induced dipoles show a preferred orientation parallel to the interface. Near the interface, the preferred orientation of the dipoles becomes more pronounced and the average magnitude of the induced dipoles decreases monotonically. To quantify the degree to which molecular orientation affects gamma, we calculate the contributions to gamma from permanent dipolar interactions, induced dipolar interactions, and dispersion forces. We find that the induced dipole interactions and the permanent dipole interactions, as well as the cross interactions, have positive contributions to gamma, and therefore contribute stability to the interface. The repulsive core interactions result in a negative contribution to gamma, which nearly cancels the positive contributions from the dipoles. The large negative core contributions to gamma are the result of small oxygen-oxygen separation between molecules. These small separations occur due to the strong attractions between hydrogen and oxygen atoms. The final predicted value for gamma (68.65 m/Nm) shows a deviation of approximately 4% of the experimental value of 71.972 m/Nm. The inclusion of polarization is critical for this model to produce an accurate value.

Journal Article↗

PubMed2006

Fractional Stokes-Einstein and Debye-Stokes-Einstein relations in a network-forming liquid.

We study the breakdown of the Stokes-Einstein (SE) and Debye-Stokes-Einstein (DSE) relations for translational and rotational motion in a prototypical model of a network-forming liquid, the ST2 model of water. We find that the emergence of fractional SE and DSE relations at low temperature is ubiquitous in this system, with exponents that vary little over a range of distinct physical regimes. We also show that the same fractional SE relation is obeyed by both mobile and immobile dynamical heterogeneities of the liquid.

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

Spatially heterogeneous dynamics and the Adam-Gibbs relation in the Dzugutov liquid.

We perform molecular dynamics simulations of a one-component glass-forming liquid and use the inherent structure formalism to test the predictions of the Adam-Gibbs (AG) theory and to explore the possible connection between these predictions and spatially heterogeneous dynamics. We calculate the temperature dependence of the average potential energy of the equilibrium liquid and show that it obeys the Rosenfeld-Tarazona T(3/5) law for low temperature T, while the average inherent structure energy is found to be inversely proportional to temperature at low T, consistent with a Gaussian distribution of potential energy minima. We investigate the shape of the basins around the local minima in configuration space via the average basin vibrational frequency and show that the basins become slightly broader upon cooling. We evaluate the configurational entropy S(conf), a measure of the multiplicity of potential energy minima sampled by the system, and test the validity of the AG relation between S(conf) and the bulk dynamics. We quantify the dynamically heterogeneous motion by analyzing the motion of particles that are mobile on short and intermediate time scales relative to the characteristic bulk relaxation time. These mobile particles move in one-dimensional "strings", and these strings form clusters with a well-defined average cluster size. The AG approach predicts that the minimum size of cooperatively rearranging regions (CRR) of molecules is inversely proportional to S(conf), and recently (Phys. Rev. Lett. 2003, 90, 085506) it has been shown that the mobile-particle clusters are consistent with the CRR envisaged by Adam and Gibbs. We test the possibility that the mobile-particle strings, rather than clusters, may describe the CRR of the Adam-Gibbs approach. We find that the strings also follow a nearly inverse relation with S(conf). We further show that the logarithm of the time when the strings and clusters are maximum, which occurs in the late-beta-relaxation regime of the intermediate scattering function, follows a linear relationship with 1/TS(conf), in agreement with the AG prediction for the relationship between the configurational entropy and the characteristic time for the liquid to undergo a transition to a new configuration. Since strings are the basic elements of the clusters, we propose that strings are a more appropriate measure of the minimum size of a CRR that leads to configurational transitions. That the cluster size also has an inverse relationship with S(conf) may be a consequence of the fact that the clusters are composed of strings.

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

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↗

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↗

PubMed2003

Recent results on the connection between thermodynamics and dynamics in supercooled water.

We review recent results on the connection between thermodynamics and dynamics in a model for water. We verify the Adam-Gibbs relation between entropy and dynamic properties using computer simulations, which allow direct access to the relevant properties. We combine experimental measurements of entropy with the Adam-Gibbs hypothesis to predict dynamic properties in deeply supercooled states, which are difficult to access experimentally. We find evidence suggesting that the glass transition temperature of water may be significantly higher than previously reported, but is still consistent with recent measurements. Finally, we discuss the hypothesis that the dynamical behavior of deeply supercooled water undergoes a crossover from 'fragile' to 'strong' behavior.

Cold Temperature↗

PubMed2002

What do we learn from the local geometry of glass-forming liquids?

We examine the local geometry of a simulated glass-forming polymer melt. Using the Voronoi construction, we find that the distributions of Voronoi volume P(v(V)) and asphericity P(a) appear to be universal properties of dense liquids, supporting the use of packing approaches to understand liquid properties. We also calculate the average free volume along a path of constant density and find that extrapolates to zero at the same temperature T0 that the extrapolated relaxation time diverges. We relate to the Debye-Waller factor, which is measurable by neutron scattering.

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↗