arXiv subjects

David Chandler

Publications and source records attributed to David Chandler.

At least 55 records · Page 3Linked to original sources

arXiv2011

The Putative Liquid-Liquid Transition is a Liquid-Solid Transition in Atomistic Models of Water

We use numerical simulation to examine the possibility of a reversible liquid-liquid transition in supercooled water and related systems. In particular, for two atomistic models of water, we have computed free energies as functions of multiple order parameters, where one is density and another distinguishes crystal from liquid. For a range of temperatures and pressures, separate free energy basins for liquid and crystal are found, conditions of phase coexistence between these phases are demonstrated, and time scales for equilibration are determined. We find that at no range of temperatures and pressures is there more than a single liquid basin, even at conditions where amorphous behavior is unstable with respect to the crystal. We find a similar result for a related model of silicon. This result excludes the possibility of the proposed liquid-liquid critical point for the models we have studied. Further, we argue that behaviors others have attributed to a liquid-liquid transition in water and related systems are in fact reflections of transitions between liquid and crystal.

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arXiv2011

Extended surfaces modulate and can catalyze hydrophobic effects

Interfaces are a most common motif in complex systems. To understand how the presence of interfaces affect hydrophobic phenomena, we use molecular simulations and theory to study hydration of solutes at interfaces. The solutes range in size from sub-nanometer to a few nanometers. The interfaces are self-assembled monolayers with a range of chemistries, from hydrophilic to hydrophobic. We show that the driving force for assembly in the vicinity of a hydrophobic surface is weaker than that in bulk water, and decreases with increasing temperature, in contrast to that in the bulk. We explain these distinct features in terms of an interplay between interfacial fluctuations and excluded volume effects---the physics encoded in Lum-Chandler-Weeks theory [J. Phys. Chem. B 103, 4570--4577 (1999)]. Our results suggest a catalytic role for hydrophobic interfaces in the unfolding of proteins, for example, in the interior of chaperonins and in amyloid formation.

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arXiv2011

Quantifying density fluctuations in volumes of all shapes and sizes using indirect umbrella sampling

Water density fluctuations are an important statistical mechanical observable that is related to many-body correlations, as well as hydrophobic hydration and interactions. Local water density fluctuations at a solid-water surface have also been proposed as a measure of its hydrophobicity. These fluctuations can be quantified by calculating the probability, $P_v(N)$, of observing $N$ waters in a probe volume of interest $v$. When $v$ is large, calculating $P_v(N)$ using molecular dynamics simulations is challenging, as the probability of observing very few waters is exponentially small, and the standard procedure for overcoming this problem (umbrella sampling in $N$) leads to undesirable impulsive forces. Patel et al. [J. Phys. Chem. B, 114, 1632 (2010)] have recently developed an indirect umbrella sampling (INDUS) method, that samples a coarse-grained particle number to obtain $P_v(N)$ in cuboidal volumes. Here, we present and demonstrate an extension of that approach to other basic shapes, like spheres and cylinders, as well as to collections of such volumes. We further describe the implementation of INDUS in the NPT ensemble and calculate $P_v(N)$ distributions over a broad range of pressures. Our method may be of particular interest in characterizing the hydrophobicity of interfaces of proteins, nanotubes and related systems.

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arXiv2010

An improved coarse-grained model of solvation and the hydrophobic effect

We present a coarse-grained lattice model of solvation thermodynamics and the hydrophobic effect that implements the ideas of Lum-Chandler-Weeks (LCW) theory [J. Phys. Chem. B 103, 4570 (1999)] and improves upon previous lattice models based on it. Through comparison with molecular simulation, we show that our model captures the length-scale and curvature dependence of solvation free energies with near-quantitative accuracy and two to three orders of magnitude less computational effort, and further, correctly describes the large but rare solvent fluctuations that are involved in dewetting, vapor tube formation and hydrophobic assembly. Our model is intermediate in detail and complexity between implicit-solvent models and explicit-water simulations.

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arXiv2010

Corresponding States of Structural Glass Formers. II

The earlier paper of this same title demonstrated a collapse of relaxation data of fragile supercooled glass forming liquids [\textit{J. Phys. Chem. B} \textbf{113}, 5563-5567 (2009)]. For temperature $T$ below that of the onset to supercooled behavior, $T_{\mathrm{o}}$, the logarithm of structural relaxation time, $\log τ$, is given by the parabolic form $\log (τ/τ_{\mathrm{o}}) \, =\, J^2(1/T - 1/T_{\mathrm{o}})^{2}$, where $J$ and $τ_{\mathrm{o}}$ are temperature independent. This paper presents further applications of this formula. In particular, it is shown that the effects of attractive forces in numerical simulation of glass forming liquids can be logically organized in terms of $J$ and $T_{\mathrm{o}}$. Further, analysis of experimental data for several systems suggests that $J$ and $T_{\mathrm{o}}$ are material properties. In contrast, values of similar parameters for other fitting formulas are shown to depend not only upon the material but also upon the range of data used in fitting these formulas. Expressions demonstrated to fail in this way include the Vogel-Fulcher-Tammann formula, a double-exponential formula, and a fractional exponential formula.

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arXiv2010

Finite-temperature critical point of a glass transition

We generalize the simplest kinetically constrained model of a glass-forming liquid by softening kinetic constraints, allowing them to be violated with a small finite rate. We demonstrate that this model supports a first-order dynamical (space-time) phase transition, similar to those observed with hard constraints. In addition, we find that the first-order phase boundary in this softened model ends in a finite-temperature dynamical critical point, which we expect to be present in natural systems. We discuss links between this critical point and quantum phase transitions, showing that dynamical phase transitions in $d$ dimensions map to quantum transitions in the same dimension, and hence to classical thermodynamic phase transitions in $d+1$ dimensions. We make these links explicit through exact mappings between master operators, transfer matrices, and Hamiltonians for quantum spin chains.

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arXiv2009

Instantaneous Liquid Interfaces

We describe and illustrate a simple procedure for identifying a liquid interface from atomic coordinates. In particular, a coarse grained density field is constructed, and the interface is defined as a constant density surface for this coarse grained field. In applications to a molecular dynamics simulation of liquid water, it is shown that this procedure provides instructive and useful pictures of liquid-vapor interfaces and of liquid-protein interfaces.

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arXiv2009

Fluctuations of water near extended hydrophobic and hydrophilic surfaces

We use molecular dynamics simulations of the SPC-E model of liquid water to derive probability distributions for water density fluctuations in probe volumes of different shapes and sizes, both in the bulk as well as near hydrophobic and hydrophilic surfaces. To obtain our results, we introduce a biased sampling of coarse-grained densities, which in turn biases the actual solvent density. The technique is easily combined with molecular dynamics integration algorithms. Our principal result is that the probability for density fluctuations of water near a hydrophobic surface, with or without surface-water attractions, is akin to density fluctuations at the water-vapor interface. Specifically, the probability of density depletion near the surface is significantly larger than that in bulk. In contrast, we find that the statistics of water density fluctuations near a model hydrophilic surface are similar to that in the bulk.

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arXiv2009

Dynamics on the Way to Forming Glass: Bubbles in Space-time

We review a theoretical perspective of the dynamics of glass forming liquids and the glass transition. It is a perspective we have developed with our collaborators during this decade. It is based upon the structure of trajectory space. This structure emerges from spatial correlations of dynamics that appear in disordered systems as they approach non-ergodic or jammed states. It is characterized in terms of dynamical heterogeneity, facilitation and excitation lines. These features are associated with a newly discovered class of non-equilibrium phase transitions. Equilibrium properties have little if anything to do with it. The broken symmetries of these transitions are obscure or absent in spatial structures, but they are vivid in space-time (i.e., trajectory space). In our view, the glass transition is an example of this class of transitions. The basic ideas and principles we review were originally developed through the analysis of idealized and abstract models. Nevertheless, the central ideas are easily illustrated with reference to molecular dynamics of more realistic atomistic models, and we use that illustrative approach here.

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arXiv2008

Corresponding States of Structural Glass Formers

The variation with respect to temperature T of transport properties of 58 fragile structural glass forming liquids (68 data sets in total) are analyzed and shown to exhibit a remarkable degree of universality. In particular, super-Arrhenius behaviors of all super-cooled liquids appear to collapse to one parabola for which there is no singular behavior at any finite temperature. This behavior is bounded by an onset temperature To above which liquid transport has a much weaker temperature dependence. A similar collapse is also demonstrated, over the smaller available range, for existing numerical simulation data.

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arXiv2008

Negative differential mobility of weakly driven particles in models of glass formers

We study the response of probe particles to weak constant driving in kinetically constrained models of glassy systems, and show that the probe's response can be non-monotonic and give rise to negative differential mobility: increasing the applied force can reduce the probe's drift velocity in the force direction. Oth er significant non-linear effects are also demonstrated, such as the enhancement with increasing force of the probe's fluctuations away from the average path, a phenomenon known in other contexts as giant diffusivity. We show that these res ults can be explained analytically by a continuous-time random walk approximatio n where there is decoupling between persistence and exchange times for local dis placements of the probe. This decoupling is due to dynamic heterogeneity in the glassy system, which also leads to bimodal distributions of probe particle disp lacements. We discuss the relevance of our results to experiments.

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arXiv2008

Coarse Grained Modeling of The Interface Between Water and Heterogeneous Surfaces

Using coarse grained models we investigate the behavior of water adjacent to an extended hydrophobic surface peppered with various fractions of hydrophilic patches of different sizes. We study the spatial dependence of the mean interface height, the solvent density fluctuations related to drying the patchy substrate, and the spatial dependence of interfacial fluctuations. We find that adding small uniform attractive interactions between the substrate and solvent cause the mean position of the interface to be very close to the substrate. Nevertheless, the interfacial fluctuations are large and spatially heterogeneous in response to the underlying patchy substrate. We discuss the implications of these findings to the assembly of heterogeneous surfaces.

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arXiv2008

Water at an electrochemical interface - a simulation study

The results of molecular dynamics simulations of the properties of water in an aqueous ionic solution close to an interface with a model metallic electrode are described. In the simulations the electrode behaves as an ideally polarizable hydrophilic metal, supporting image charge interactions with charged species, and it is maintained at a constant electrical potential with respect to the solution so that the model is a textbook representation of an electrochemical interface through which no current is passing. We show how water is strongly attracted to and ordered at the electrode surface. This ordering is different to the structure that might be imagined from continuum models of electrode interfaces. Further, this ordering significantly affects the probability of ions reaching the surface. We describe the concomitant motion and configurations of the water and ions as functions of the electrode potential, and we analyze the length scales over which ionic atmospheres fluctuate. The statistics of these fluctuations depend upon surface structure and ionic strength. The fluctuations are large, sufficiently so that the mean ionic atmosphere is a poor descriptor of the aqueous environment near a metal surface. The importance of this finding for a description of electrochemical reactions is examined by calculating, directly from the simulation, Marcus free energy profiles for transfer of charge between the electrode and a redox species in the solution and comparing the results with the predictions of continuum theories. Significant departures from the electrochemical textbook descriptions of the phenomenon are found and their physical origins are characterized from the atomistic perspective of the simulations.

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arXiv2007

De-coupling of Exchange and Persistence Times in Atomistic Models of Glass Formers

With molecular dynamics simulations of a fluid mixture of classical particles interacting with pair-wise additive Weeks-Chandler-Andersen potentials, we consider the time series of particle displacements and thereby determine distributions for local persistence times and local exchange times. These basic characterizations of glassy dynamics are studied over a range of super-cooled conditions and shown to have behaviors, most notably de-coupling, similar to those found in kinetically constrained lattice models of structural glasses. Implications are noted.

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arXiv2007

Fluctuation-dissipation ratios in the dynamics of self-assembly

We consider two seemingly very different self-assembly processes: formation of viral capsids, and crystallization of sticky discs. At low temperatures, assembly is ineffective, since there are many metastable disordered states, which are a source of kinetic frustration. We use fluctuation-dissipation ratios to extract information about the degree of this frustration. We show that our analysis is a useful indicator of the long term fate of the system, based on the early stages of assembly.

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arXiv2007

Segue Between Favorable and Unfavorable Solvation

Solvation of small and large clusters are studied by simulation, considering a range of solvent-solute attractive energy strengths. Over a wide range of conditions, both for solvation in the Lennard-Jones liquid and in the SPC model of water, it is shown that the mean solvent density varies linearly with changes in solvent-solute adhesion or attractive energy strength. This behavior is understood from the perspective of Weeks' theory of solvation [Ann. Rev. Phys. Chem. 2002, 53, 533] and supports theories based upon that perspective.

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arXiv2007

Solvent coarse-graining and the string method applied to the hydrophobic collapse of a hydrated chain

Using computer simulations of over 100,000 atoms, the mechanism for the hydrophobic collapse of an idealized hydrated chain is obtained. This is done by coarse-graining the atomistic water molecule positions over 129,000 collective variables that represent the water density field and then using the string method in these variables to compute the minimum free energy pathway (MFEP) for the collapsing chain. The dynamical relevance of the MFEP (i.e. its coincidence with the mechanism of collapse) is validated a posteriori using conventional molecular dynamics trajectories. Analysis of the MFEP provides atomistic confirmation for the mechanism of hydrophobic collapse proposed by ten Wolde and Chandler. In particular, it is shown that lengthscale-dependent hydrophobic dewetting is the rate-limiting step in the hydrophobic collapse of the considered chain.

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arXiv2006

Space-time thermodynamics and subsystem observables in a kinetically constrained model of glassy systems

In a recent article [M. Merolle et al., Proc. Natl. Acad. Sci. USA 102, 10837 (2005)] it was argued that dynamic heterogeneity in $d$-dimensional glass formers is a manifestation of an order-disorder phenomenon in the $d+1$ dimensions of spacetime. By considering a dynamical analogue of the free energy, evidence was found for phase coexistence between active and inactive regions of spacetime, and it was suggested that this phenomenon underlies the glass transition. Here we develop these ideas further by investigating in detail the one-dimensional Fredrickson-Andersen (FA) model in which the active and inactive phases originate in the reducibility of the dynamics. We illustrate the phase coexistence by considering the distributions of mesoscopic spacetime observables. We show how the analogy with phase coexistence can be strengthened by breaking microscopic reversibility in the FA model, leading to a non-equilibrium theory in the directed percolation universality class.

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