arXiv subjects

Francis W. Starr

Publications and source records attributed to Francis W. Starr.

At least 37 records · Page 2Linked to original sources

arXiv2005

Model for Assembly and Gelation of Four-Armed DNA Dendrimers

We introduce and numerically study a model designed to mimic the bulk behavior of a system composed of single-stranded DNA dendrimers. Complementarity of the base sequences of different strands results in the formation of strong cooperative intermolecular links. We find that in an extremely narrow temperature range the system forms a large-scale, low-density disordered network via a thermo-reversible gel transition. By controlling the strand length, the gel transition temperature can be made arbitrarily close to the percolation transition, in contrast with recent model systems of physical gelation. This study helps the understanding of self-assembly in this class of new biomaterials and provides an excellent bridge between physical and chemical gels.

cond-mat.soft↗

arXiv2005

Relation between Rotational and Translational Dynamic Heterogeneities in Water

We use molecular dynamics simulations to probe the rotational dynamics of the SPC/E model of water for a range of temperatures down to 200 K, 13 K above to 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.

cond-mat.soft↗

arXiv2005

Thermodynamics, Structure, and Dynamics of Water Confined between Hydrophobic Plates

We perform molecular dynamics simulations of 512 water-like 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 $\approx 40$ 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. Due to 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 $T\approx 215$ K using the TIP5P potential. We find that the different crystalline structures that can form for two different separations of the plates, 0.7 nm and 1.10 nm, have no counterparts in the bulk system, and discuss the relevance to experiments on confined water.

cond-mat.soft↗

arXiv2003

Structural Signatures of Vitrification in Hard Core Fluids

Computer simulations of hard spheres and disks are used to estimate the most probable cavity size, $ξ_{\rm cavity}$, and a ``rattle'' size, $ξ_{\rm rattle}$, over which a particle can translate holding all other particles fixed. Both of these measures of free volume appear to extrapolate to zero at the random close packed density, $ρ_{\rm rcp}$, close to the density where extrapolations of the viscosity diverge. We also identify the onset of caging as the density at which cavities cluster. These results suggest that vitrification in hard core fluids can be viewed as a geometrical phenomenon, and that {\em local} free volume measures can identify the location of the onset of liquid-like dynamics, the complex dynamics of caged liquids, and vitrification.

cond-mat.soft↗

arXiv2002

Connection between Adam-Gibbs Theory and Spatially Heterogeneous Dynamics

We investigate the spatially heterogeneous dynamics in the SPC/E model of water by 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. Finally, we examine the time and temperature dependence of these transient clusters.

cond-mat.soft↗

arXiv2002

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 $T_0$ that the extrapolated relaxation time diverges. We relate $ $ to the Debye-Waller factor.

cond-mat↗

arXiv2002

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 separated by relatively small energy barriers. We find that while the system \emph{travels} through these IS, the structure of the bond network continuously modifies, 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 ($\approx 1$ fs). Hence for water, the transitions between each of these IS 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 $\approx 0.02-0.2$ nm, not unlike simpler liquids. However, for water these clusters appear to be somewhat more branched than the linear ``string-like'' clusters formed in a supercooled Lennar d-Jones system found by Glotzer and her collaborators.

cond-mat.soft↗

arXiv2001

Static and Dynamic Properties of Stretched Water

We present the results of molecular dynamics simulations of the extended simple point charge (SPC/E) model of water to investigate thethermodynamic and dynamic properties of stretched and supercooled water. We locate the liquid-gas spinodal, and confirm that the spinodal pressure increases monotonically with $T$, supporting thermodynamic scenarios for the phase behavior of supercooled water involving a ``non-reentrant'' spinodal. The dynamics at negative pressure show a minimum in the diffusion constant $D$ when the density is decreased at constant temperature, complementary to the known maximum of $D$ at higher pressures. We locate the loci of minima of $D$ relative to the spinodal, showing that the locus is inside the thermodynamicaly metastable regions of the phase-diagram. These dynamical results reflect the initial enhancement and subsequent breakdown of the tetrahedral structure and of the hydrogen bond network as the density decreases.

cond-mat↗

arXiv2000

Thermodynamic and structural aspects of the potential energy surface of simulated water

Relations between the thermodynamics and dynamics of supercooled liquids approaching a glass transition have been proposed over many years. The potential energy surface of model liquids has been increasingly studied since it provides a connection between the configurational component of the partition function on one hand, and the system dynamics on the other. This connection is most obvious at low temperatures, where the motion of the system can be partitioned into vibrations within a basin of attraction and infrequent inter-basin transitions. In this work, we present a description of the potential energy surface properties of supercooled liquid water. The dynamics of this model has been studied in great details in the last years. Specifically, we locate the minima sampled by the liquid by ``quenches'' from equilibrium configurations generated via molecular dynamics simulations. We calculate the temperature and density dependence of the basin energy, degeneracy, and shape. The temperature dependence of the energy of the minima is qualitatively similar to simple liquids, but has anomalous density dependence. The unusual density dependence is also reflected in the configurational entropy, the thermodynamic measure of degeneracy. Finally, we study the structure of simulated water at the minima, which provides insight on the progressive tetrahedral ordering of the liquid on cooling.

cond-mat.soft↗

arXiv2000

Effects of a nanoscopic filler on the structure and dynamics of a simulated polymer melt and the relationship to ultra-thin films

We perform molecular dynamics simulations of an idealized polymer melt surrounding a nanoscopic filler particle to probe the effects of a filler on the local melt structure and dynamics. We show that the glass transition temperature $T_g$ of the melt can be shifted to either higher or lower temperatures by appropriately tuning the interactions between polymer and filler. A gradual change of the polymer dynamics approaching the filler surface causes the change in the glass transition. We also find that while the bulk structure of the polymers changes little, the polymers close to the surface tend to be elongated and flattened, independent of the type of interaction we study. Consequently, the dynamics appear strongly influenced by the interactions, while the melt structure is only altered by the geometric constraints imposed by the presence of the filler. Our findings show a strong similarity to those obtained for ultra-thin polymer films (thickness $\lesssim 100$ nm) suggesting that both ultra-thin films and filled-polymer systems might be understood in the same context.

cond-mat.soft↗

arXiv2000

Supercooled Water: Dynamics, Structure and Thermodynamics

The anomalous properties of water in the supercooled state are numerous and well-known. Particularly striking are the strong changes in dynamic properties that appear to display divergences at temperatures close to -- but beyond -- the lowest temperatures attainable either experimentally or in computer simulations. Recent work on slow or glassy dynamics in water suggests analogies with simple liquids not previously appreciated, and at the same time highlights some aspects that remain peculiar to water. A comparison of the behavior of water with normal liquids, with respect to its dynamic, thermodynamic and structural changes in the supercooled regime is made by analyzing, via computer simulations, the properties of local potential energy minima sampled by water in supercooled temperatures and pressures.

cond-mat.stat-mech↗

arXiv1999

Entropy and dynamic properties of water below the homogeneous nucleation temperature

Controversy exists regarding the possible existence of a transition between the liquid and glassy states of water. Here we use experimental measurements of the entropy, specific heat, and enthalpy of both liquid and glassy water to construct thermodynamically-plausible forms of the entropy in the difficult-to-probe region between 150 K and 236 K. We assume there is no discontinuity in the entropy of the liquid in this temperature range, and use the Adam-Gibbs theory -- which relates configurational entropy to dynamic behavior -- to predict that dynamic quantities such as the diffusion constant and the viscosity pass through an inflection where the liquid behavior changes from that of an extremely ``fragile'' liquid to that of a ``strong'' liquid.

cond-mat↗

arXiv1999

Configurational Entropy and Diffusivity of Supercooled Water

We calculate the configurational entropy S_conf for the SPC/E model of water for state points covering a large region of the (T,rho) plane. We find that (i) the (T,rho) dependence of S_conf correlates with the diffusion constant and (ii) that the line of maxima in S_conf tracks the line of density maxima. Our simulation data indicate that the dynamics are strongly influenced by S_conf even above the mode-coupling temperature T_MCT(rho).

cond-mat.soft↗

arXiv1999

Dynamics of simulated water under pressure

We present molecular dynamics simulations of the SPC/E model of water to probe the dynamic properties at temperatures from 350 K down to 190 K and pressures from 2.5GPa (25kbar) down to -300MPa (-3kbar). We compare our results with those obtained experimentally, both of which show a diffusivity maximum as a function of pressure. We find that our simulation results are consistent with the predictions of the mode-coupling theory (MCT) for the dynamics of weakly supercooled liquids -- strongly supporting the hypothesis that the apparent divergences of {\it dynamic} properties observed experimentally may be independent of a possible thermodynamic singularity at low temperature. The dramatic change in water's dynamic and structural properties as a function of pressure allows us to confirm the predictions of MCT over a much broader range of the von Schweidler exponent values than has been studied for simple atomic liquids. We also show how structural changes are reflected in the wave-vector dependence of dynamic properties of the liquid along a path of nearly constant diffusivity. For temperatures below the crossover temperature of MCT (where the predictions of MCT are expected to fail), we find tentative evidence for a crossover of the temperature dependence of the diffusivity from power-law to Arrhenius behavior, with an activation energy typical of a strong liquid.

cond-mat↗

arXiv1999

Instantaneous Normal Mode Analysis of Supercooled Water

We use the instantaneous normal mode approach to provide a description of the local curvature of the potential energy surface of a model for water. We focus on the region of the phase diagram in which the dynamics may be described by the mode-coupling theory. We find, surprisingly, that the diffusion constant depends mainly on the fraction of directions in configuration space connecting different local minima, supporting the conjecture that the dynamics are controlled by the geometric properties of configuration space. Furthermore, we find an unexpected relation between the number of basins accessed in equilibrium and the connectivity between them.

cond-mat↗

arXiv1999

Slow dynamics of water under pressure

We perform lengthy molecular dynamics simulations of the SPC/E model of water to investigate the dynamics under pressure at many temperatures and compare with experimental measurements. We calculate the isochrones of the diffusion constant $D$ and observe power-law behavior of $D$ on lowering temperature with an apparent singularity at a temperature $T_c(P)$, as observed for water. Additional calculations show that the dynamics of the SPC/E model are consistent with slowing down due to the transient caging of molecules, as described by the mode-coupling theory (MCT). This supports the hypothesis that the apparent divergences of dynamic quantities along $T_c(P)$ in water may be associated with ``slowing down'' as described by MCT.

cond-mat↗

arXiv1998

Structural evidence for the continuity of liquid and glassy water

An open question is whether the liquid and glassy phases of water are thermodynamically distinct or continuous. Here we address this question using molecular dynamics simulations in comparison with neutron scattering experiments to study the effect of temperature and pressure on the local structure of liquid water. From both simulations and experiments, we find that the liquid structure at high pressure is nearly independent of temperature, and remarkably similar to the known structure of the high-density amorphous ice (HDA). Further at low pressure, the liquid structure appears to approach the experimentally-measured structure of low-density amorphous ice (LDA) as temperature decreases. These results are consistent with continuity between the liquid and glassy phases of H$_2$O.

cond-mat↗

arXiv1998

Fast and slow dynamics of hydrogen bonds in liquid water

We study hydrogen-bond dynamics in liquid water at low temperatures using molecular dynamics simulations. We find that bond lifetime (``fast dynamics'') has Arrhenius temperature dependence. We also calculate the bond correlation function and find that the correlation time (``slow dynamics'') shows power-law behavior. This power-law behavior, as well as the decay of the bond correlations, is consistent with the predictions of the mode-coupling theory. The correlation time at the lowest temperature studied shows deviation from power-law behavior that suggests continuity of dynamic functions between the liquid and glassy states of water at low pressure.

cond-mat↗