CiteULike: kedmond's simulation

Self-assembly route for photonic crystals with a bandgap in the visible region

Antti-Pekka Hynninen — 2008-05-29T22:05:04-00:00

Nat Mater, Vol. 6, No. 3. (March 2007), pp. 202-205.

Three-dimensional photonic crystals, or periodic materials, that do not allow the propagation of photons in all directions with a wavelength in the visible region have not been experimentally fabricated, despite there being several potential structures and the interesting applications and physics that this would lead to1. We show using computer simulations that two structures that would enable a bandgap in the visible region, diamond and pyrochlore, can be self-assembled in one crystal structure from a binary colloidal dispersion. In our approach, these two structures are obtained as the large (Mg) and small (Cu) sphere components of the colloidal analogue of the MgCu2 Laves phase2, whose growth can be selected and directed using appropriate wall patterning. The method requires that the particles consist of different materials, so that one of them can be removed selectively after drying (for example, by burning or dissolution). Photonic calculations show that gaps appear at relatively low frequencies indicating that they are robust and open for modest contrast, enabling fabrication from more materials.

The shapes of cooperatively rearranging regions in glass-forming liquids

Jacob Stevenson — 2007-12-11T15:53:07-00:00

Nat Phys, Vol. 2, No. 4. (April 2006), pp. 268-274.

The cooperative rearrangement of groups of many molecules has long been thought to underlie the dramatic slowing of liquid dynamics on cooling towards the glassy state. For instance, there exists experimental evidence for cooperatively rearranging regions (CRRs) on the nanometre length scale near the glass transition. The random first-order transition (RFOT) theory of glasses predicts that, near the glass-transition temperature, these regions are compact, but computer simulations and experiments on colloids suggest CRRs are string-like. Here, we present a microscopic theory within the framework of RFOT, which unites the two situations. We show that the shapes of CRRs in glassy liquids should change from being compact at low temperatures to fractal or ‘stringy’ as the dynamical crossover temperature from activated to collisional transport is approached from below. This theory predicts a correlation of the ratio of the dynamical crossover temperature to the laboratory glass-transition temperature, and the heat-capacity discontinuity at the glass transition. The predicted correlation quantitatively agrees with experimental results for 21 materials.

Correlation between Dynamic Heterogeneity and Medium-Range Order in Two-Dimensional Glass-Forming Liquids

Takeshi Kawasaki — 2007-12-07T05:03:46-00:00

Physical Review Letters, Vol. 99, No. 21. (2007)

A glassy state of matter results if crystallization is avoided upon cooling or increasing density. However, the physical factors controlling the ease of vitrification and nature of the glass transition remain elusive. Using numerical simulations of polydisperse hard disks, we find a direct relation between medium-range crystalline ordering and the slow dynamics which characterizes the glass transition. This suggests an intriguing scenario that the strength of frustration controls both the ease of vitrification and nature of the glass transition. Vitrification may be a process of hidden crystalline ordering under frustration, at least in our system.

Confinement, entropy, and single-particle dynamics of equilibrium hard-sphere mixtures

Jeetain Mittal — 2007-12-01T12:11:26-00:00

The Journal of Chemical Physics, Vol. 127, No. 15. (2007)

Layering and Position-Dependent Diffusive Dynamics of Confined Fluids

Jeetain Mittal — 2008-05-02T15:47:32-00:00

Physical Review Letters, Vol. 100, No. 14. (2008)

We study the diffusive dynamics of a hard-sphere fluid confined between parallel smooth hard walls. The position-dependent diffusion coefficient normal to the walls is larger in regions of high local packing density. High density regions also have the largest available volume, consistent with the fast local diffusivity. Indeed, local and global diffusivities as a function of the Widom insertion probability approximately collapse onto a master curve. Parallel and average normal diffusivities are strongly coupled at high densities and deviate from bulk fluid behavior.

Does confining the hard-sphere fluid between hard walls change its average properties?

Jeetain Mittal — 2007-10-30T01:06:27-00:00

The Journal of Chemical Physics, Vol. 126, No. 24. (2007), pp. 244708-244708.

We use grand canonical transition-matrix Monte Carlo and discontinuous molecular dynamics simulations to generate precise thermodynamic and kinetic data for the equilibrium hard-sphere fluid confined between smooth hard walls. These simulations show that the pronounced inhomogeneous structuring of the fluid normal to the confining walls, often the primary focus of density functional theory studies, has a negligible effect on many of its average properties over a surprisingly broad range of conditions. We present one consequence of this insensitivity to confinement: a simple analytical equation relating the average density of the confined fluid to that of the bulk fluid with equal activity. Nontrivial implications of confinement for average fluid properties do emerge in this system, but only when the fluid is both (i) dense and (ii) confined to a gap smaller than approximately three particle diameters. For this limited set of conditions, we find that “in-phase” oscillatory deviations in excess entropy and self-diffusivity (relative to the behavior of the bulk fluid at the same average density) occur as a function of gap size. These paired thermodynamic/kinetic deviations from bulk behavior appear to reflect the geometric packing frustration that arises when the confined space cannot naturally accommodate an integer number of particle layers. ©2007 American Institute of Physics

Nature of the breakdown in the Stokes-Einstein relationship in a hard sphere fluid

Sanat Kumar — 2008-04-16T15:47:53-00:00

The Journal of Chemical Physics, Vol. 124, No. 21. (2006)

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Tuning Density Profiles and Mobility of Inhomogeneous Fluids

Gaurav Goel — 2008-04-04T21:36:07-00:00

Physical Review Letters, Vol. 100, No. 10. (2008)

Density profiles are the most common measure of inhomogeneous structure in confined fluids, but their connection to transport coefficients is poorly understood. We explore via simulation how tuning particle-wall interactions to flatten or enhance the particle layering of a model confined fluid impacts its self-diffusivity, viscosity, and entropy. Interestingly, interactions that eliminate particle layering significantly reduce confined fluid mobility, whereas those that enhance layering can have the opposite effect. Excess entropy helps to understand and predict these trends.

On the relationship between structure and dynamics in a supercooled liquid

Asaph Widmer-Cooper — 2008-02-15T14:48:10-00:00

Journal of Physics: Condensed Matter, Vol. 17, No. 49. (2005), pp. S4025-S4034.

We present the dynamic propensity distribution as an explicit measure of the degree to which the dynamics in a liquid over the time scale of structural relaxation is determined by the initial configuration. We then examine, for a binary mixture of soft discs in two dimensions, the correlation between the spatial distribution of propensity and that of two local measures of configuration structure: the local composition and local free volume. While the small particles dominate the high propensity population, we find no strong correlation between either the local composition or the local free volume and the propensity. It is argued that this is a generic failure of purely local structural measures to capture the inherently non-local character of collective behaviour.

How Reproducible Are Dynamic Heterogeneities in a Supercooled Liquid?

Asaph Widmer-Cooper — 2007-09-28T20:46:54-00:00

Physical Review Letters, Vol. 93, No. 13. (2004), pp. 135701-135701.

The particle dynamics in a liquid exhibits a transient spatial distribution of dynamic heterogeneities. The relationship between this kinetic structure and the underlying particle configuration remains an outstanding problem. In this Letter, we present a general simulation technique for identifying the features of the dynamic heterogeneity which arise due to a specific configuration, as distinct from the random spatial variation due to the intermittent particle dynamics.

Water in channel-like cavities: structure and dynamics.

MS Sansom — 2007-10-29T23:02:36-00:00

Biophys. J., Vol. 70, No. 2. (1 February 1996), pp. 693-702.

Ion channels contain narrow columns of water molecules. It is of interest to compare the structure and dynamics of such intrapore water with those of the bulk solvent. Molecular dynamics simulations of modified TIP3P water molecules confined within channel-like cavities have been performed and the orientation and dynamics of the water molecules analyzed. Channels were modeled as cylindrical cavities with lengths ranging from 15 to 60 A and radii from 3 to 12 A. At the end of the molecular dynamics simulations water molecules were observed to be ordered into approximately concentric cylindrical shells. The waters of the outermost shell were oriented such that their dipoles were on average perpendicular to the normal of the wall of the cavity. Water dynamics were analyzed in terms of self-diffusion coefficients and rotational reorientation rates. For cavities of radii 3 and 6 A, water mobility was reduced relative to that of simulated bulk water. For 9- and 12-A radii confined water molecules exhibited mobilities comparable with that of the bulk solvent. If water molecules were confined within an hourglass-shaped cavity (with a central radius of 3 A increasing to 12 A at either end) a gradient of water mobility was observed along the cavity axis. Thus, water within simple models of transbilayer channels exhibits perturbations of structure and dynamics relative to bulk water. In particular the reduction of rotational reorientation rate is expected to alter the local dielectric constant within a transbilayer pore.

Glass transition and layering effects in confined water: A computer simulation study

P Gallo — 2007-10-29T22:56:02-00:00

The Journal of Chemical Physics, Vol. 113, No. 24. (2000), pp. 11324-11335.

Single particle dynamics of water confined in a nanopore is studied through computer molecular dynamics. The pore is modeled to represent the average properties of a pore of Vycor glass. Dynamics is analyzed at different hydration levels and upon supercooling. At all hydration levels and all temperatures investigated a layering effect is observed due to the strong hydrophilicity of the substrate. The time density correlators show, already at ambient temperature, strong deviations from the Debye and the stretched exponential behavior. Both on decreasing hydration level and upon supercooling we find features that can be related to the cage effect typical of a supercooled liquid undergoing a kinetic glass transition. Nonetheless the behavior predicted by mode coupling theory can be observed only by carrying out a proper shell analysis of the density correlators. Water molecules within the first two layers from the substrate are in a glassy state already at ambient temperature (bound water). The remaining subset of molecules (free water) undergoes a kinetic glass transition; the relaxation of the density correlators agree with the main predictions of the theory. From our data we can predict the temperature of structural arrest of free water. ©2000 American Institute of Physics.

Glass transition in confinement: a Lennard-Jones binary mixture study

Paola Gallo — 2007-10-29T22:53:21-00:00

Computer Physics Communications, Vol. 169, No. 1-3. (1 July 2005), pp. 214-217.

We present results from an extensive study upon cooling on the behavior of a model glass former, a liquid Lennard-Jones binary mixture, confined in a model for Xerogels. Modification of the dynamical and thermodynamical behavior on approaching the glass transition with respect to the bulk are studied. The Mode Coupling Theory is able to account for the behavior of the liquid mixture also in confinement, but with important differences with respect to the bulk. A study of the thermodynamic behavior via inherent structure analysis is also performed and the Kauzmann temperature is evaluated from the behavior of the configurational entropy.

Connection of translational and rotational dynamical heterogeneities with the breakdown of the Stokes-Einstein and Stokes-Einstein-Debye relations in water

Marco Mazza — 2007-10-16T14:47:04-00:00

Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 76, No. 3. (2007)

We study the Stokes-Einstein (SE) and the Stokes-Einstein-Debye (SED) relations, Dt=kBT/6R and Dr=kBT/8R3, where Dt and Dr are the translational and rotational diffusivity, respectively, T is the temperature, the viscosity, kB the Boltzmann constant, and R the “molecular” radius. Our results are based on molecular dynamics simulations of the extended simple point charge model of water. We find that both the SE and SED relations break down at low temperature. To explore the relationship between these breakdowns and dynamical heterogeneities (DHs), we also calculate the SE and SED relations for subsets of the 7% “fastest” and 7% “slowest” molecules. We find that the SE and SED relations break down in both subsets, and that the breakdowns occur on all scales of mobility. Thus these breakdowns appear to be generalized phenomena, in contrast with a view where only the most mobile molecules are the origin of the breakdown of the SE and SED relations, embedded in an inactive background where these relations hold. At low temperature, the SE and SED relations in both subsets of molecules are replaced with “fractional” SE and SED relations, Dt~(/T)−t and Dr~(/T)−r, where t0.84(<1) and r0.75(<1). We also find that there is a decoupling between rotational and translational motion, and that this decoupling occurs in both the fastest and slowest subsets of molecules. Further, we find that, the decoupling increases upon cooling, but that the probability of a molecule being classified as both translationally and rotationally fastest also increases. To study the effect of time scale for SE and SED breakdown and decoupling, we introduce a time-dependent version of the SE and SED relations, and a time-dependent function that measures the extent of decoupling. Our results suggest that both the decoupling and SE and SED breakdowns originate at a time scale corresponding to the end of the cage regime, when diffusion starts. This is also the time scale when the DHs are more relevant. Our work also demonstrates that selecting DHs on the basis of translational or rotational motion more strongly biases the calculation of diffusion constants than other dynamical properties such as relaxation times.

Thermodynamics Predicts How Confinement Modifies the Dynamics of the Equilibrium Hard-Sphere Fluid

Jeetain Mittal — 2007-08-30T13:11:57-00:00

Physical Review Letters, Vol. 96, No. 17. (2006)

We study how confining the equilibrium hard-sphere fluid to restrictive one- and two-dimensional channels with smooth interacting walls modifies its structure, dynamics, and entropy using molecular dynamics and transition-matrix Monte Carlo simulations. Although confinement strongly affects local structuring, the relationships between self-diffusivity, excess entropy, and average fluid density are, to an excellent approximation, independent of channel width or particle-wall interactions. Thus, thermodynamics can be used to predict how confinement impacts dynamics.

Bifurcation of translational and rotational non-Gaussian behaviors in two-dimensional liquid

Genzou Matsui — 2007-08-09T17:16:08-00:00

Physics Letters A, Vol. 293, No. 3-4. (28 January 2002), pp. 156-160.

The dynamics of the rigid diatomic molecules in a supercooled liquid state is investigated by molecular dynamics simulations. We define two different non-Gaussian parameters for the translational and the rotational degrees of freedom, and we find that the two time scales bifurcate in the temperature higher than the critical temperature. The time scale of the translational motion diverges towards the critical temperature, while that of the rotational motion shows the Arrhenius like behavior in same temperature range. This fact indicates that obtained two different time scales are originated from the different relaxation processes related to the translational and the rotational degrees of freedom.

Fractional Stokes-Einstein and Debye-Stokes-Einstein Relations in a Network-Forming Liquid

Stephen Becker — 2007-06-30T17:34:58-00:00

Physical Review Letters, Vol. 97, No. 5. (2006)

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.

Dynamic Heterogeneities in Supercooled Water

N Giovambattista — 2007-06-27T18:37:19-00:00

J. Phys. Chem. B, Vol. 108, No. 21. (27 May 2004), pp. 6655-6662.

Abstract: We investigate dynamic heterogeneities in liquid water by performing molecular dynamics simulations of the SPC/E model. We find clusters of mobile molecules. We study the temperature and time dependence of the cluster size and find that clusters grow as temperature decreases and have a maximum size at the time scale corresponding to the escape of the molecules from the cage formed by neighboring molecules. We relate the average mass n* of mobile particle clusters to the diffusion constant, D, and the configurational entropy, Sconf. We find that n* can be interpreted as the mass of the "cooperatively rearranging regions" hypothesized in the Adam-Gibbs theory of the dynamics of supercooled liquids. In the context of the potential energy landscape (PEL) approach, the diffusion of molecules is related to the change of basins. By studying the dynamics of the system on the PEL, we identify clusters formed by the molecules with large displacements as the system visits consecutive local minima on the PEL. We relate the changing of basins with the restructuring of the hydrogen bond network.

Probes of heterogeneity in rotational dynamics: Application to supercooled liquid CS_2

Joohyun Kim — 2007-06-26T22:41:30-00:00

Physical Review E, Vol. 67, No. 2. (27 February 2003), 021506.

The distribution of individual molecular contributions to the second-rank rotational correlation function is introduced and used to construct probes of heterogeneity in rotational dynamics. The ideas are tested in a molecular dynamics simulation of supercooled liquid CS 2 . Both the quantity of heterogeneity and its lifetime or exchange time τ ex increase as the temperature is lowered through the supercooled state; and increase strongly as the mode-coupling temperature T c is approached. Crossover from Arrhenius to super-Arrhenius behavior of the rotational relaxation times τ 1 and τ 2 is observed; direct evidence of fragility in CS 2 . The T dependence of τ ex is stronger than that of the rotational times; and it may approach them from below at T c ; although the simulation is then very difficult. A detailed characterization of other aspects of the dynamical crossover is obtained; and the general implications of rotational heterogeneity for supercooled dynamics are discussed.

On the mechanism of reorientational and structural relaxation in supercooled liquids: The role of border dynamics and cooperativity

Joohyun Kim — 2007-06-26T21:45:18-00:00

The Journal of Chemical Physics, Vol. 121, No. 9. (2004), pp. 4237-4245.

Molecular dynamics simulation and analysis based upon the many-body potential energy landscape (PEL) are employed to characterize single molecule reorientation and structural relaxation, and their interrelation, in deeply supercooled liquid CS2. The rotational mechanism changes from small-step Debye diffusion to sudden large angle reorientation (SLAR) as the temperature falls below the mode-coupling temperature Tc. The onset of SLAR is explained in terms of the PEL; it is an essential feature of low-T rotational dynamics, along with the related phenomena of dynamic heterogeneity and the bifurcation of slow and fast relaxation processes. A long trajectory in which the system is initially trapped in a low energy local minimum, and eventually escapes, is followed in detail, both on the PEL and in real space. During the trapped period, "return" dynamics occurs, always leading back to the trap. Structural relaxation is identified with irreversible escape to a new trap. These processes lead to weak and strong SLAR, respectively; strong SLAR is a clear signal of structural relaxation. Return dynamics involves small groups of two to four molecules, while a string-like structure composed of all the active groups participates in the escape. It is proposed that, rather than simple, nearly instantaneous, one-dimensional barrier crossings, relaxation involves activation of the system to the complex, multidimensional region on the borders of the basins of attraction of the minima for an extended period. ©2004 American Institute of Physics.

Dynamics of the rotational degrees of freedom in a supercooled liquid of diatomic molecules

Stefan Kämmerer — 2007-06-26T13:22:47-00:00

Physical Review E, Vol. 56 (November 1997), 5450.

Using molecular-dynamics computer simulations; we investigate the dynamics of the rotational degrees of freedom in a supercooled system composed of rigid; diatomic molecules. The interaction between the molecules is given by the sum of interaction-site potentials of the Lennard-Jones type. In agreement with mode-coupling theory (MCT); we find that the relaxation times of the orientational time correlation functions C 1 ( s ) ( t ); C 2 ( s ) ( t ); and C 1 ( t ) show at low temperatures a power law with the same critical temperature T c ; which is also identical to the critical temperature for the translational degrees of freedom. In contrast to MCT; we find; however; that for these correlators the time-temperature superposition principle does not hold well and also the critical exponent γ depends on the correlator. For C l ( s ) with l =3;…;6 this principle does hold. We also study the temperature dependence of the rotational diffusion constant D r and demonstrate that at high temperatures D r is proportional to the translational diffusion constant D and when the system starts to become supercooled the former shows an Arrhenius behavior; whereas the latter exhibits a power-law dependence. We discuss the origin for the difference in the temperature dependence of D (or the relaxation times of C l ( s ) ) and D r . Finally; we present results that show that at low temperatures 180° flips of the molecule are an important component of the relaxation dynamics for the orientational degrees of freedom.

Relation between Rotational and Translational Dynamic Heterogeneities in Water

Marco Mazza — 2007-06-26T00:38:18-00:00

Physical Review Letters, Vol. 96, No. 5. (2006)

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.

Probe particles alter dynamic heterogeneities in simple supercooled systems

Ronen Zangi — 2007-06-25T01:40:09-00:00

The Journal of Chemical Physics, Vol. 126, No. 10. (2007)

The authors present results from molecular dynamics simulations on the effect of smooth and rough probes on the dynamics of a supercooled Lennard-Jones (LJ) mixture. The probe diameter was systematically varied from one to seven times the diameter of the large particles of the LJ mixture. Mean square displacements show that in the presence of a large smooth probe the supercooled liquid speeds up, while in the presence of a large rough probe, the supercooled liquid slows down. Non-Gaussian parameters indicate that with both smooth and rough probes, the heterogeneity of the supercooled system increases. From the analysis of local Debye-Waller factors, it is evident that the change in the dynamics of the LJ system is heterogeneous, with the largest perturbations close to the probes. Large smooth and rough probes appear to set up heterogeneities in these supercooled systems that would otherwise not occur, and these heterogeneities persist for long times. ©2007 American Institute of Physics

Dynamical Heterogeneities in a Supercooled Lennard-Jones Liquid

Walter Kob — 2007-05-18T06:48:08-00:00

Physical Review Letters, Vol. 79 (13 October 1997), 2827.

We present the results of a molecular dynamics computer simulation study in which we investigate whether a supercooled Lennard-Jones liquid exhibits dynamical heterogeneities. We evaluate the non-Gaussian parameter for the self part of the van Hove correlation function and use it to identify “mobile” particles. We find that these particles form clusters whose sizes grow with decreasing temperature. We also find that the relaxation time of the mobile particles is significantly shorter than that of the average particle; and that this difference increases with decreasing temperature.

Stringlike Cooperative Motion in a Supercooled Liquid

Claudio Donati — 2007-05-16T20:25:15-00:00

Physical Review Letters, Vol. 80, No. 11. (16 March 1998), 2338.

Extensive molecular dynamics simulations are performed on a glass-forming Lennard-Jones mixture to determine the nature of the cooperative motions occurring in this model fragile liquid. We observe stringlike cooperative molecular motion (“strings”) at temperatures well above the glass transition. The mean length of the strings increases upon cooling; and the string length distribution is found to be nearly exponential.

Computational probes of molecular motion in the Lewis-Wahnstr[o-umlaut]m model for ortho-terphenyl

Thomas Lombardo — 2007-05-15T20:53:34-00:00

The Journal of Chemical Physics, Vol. 125, No. 17. (2006)

We use molecular dynamics simulations to investigate translational and rotational diffusion in a rigid three-site model of the fragile glass former ortho-terphenyl, at 260 KT346 K and ambient pressure. An Einstein formulation of rotational motion is presented, which supplements the commonly used Debye model. The latter is shown to break down at supercooled temperatures as the mechanism of molecular reorientation changes from small random steps to large infrequent orientational jumps. We find that the model system exhibits non-Gaussian behavior in translational and rotational motion, which strengthens upon supercooling. Examination of particle mobility reveals spatially heterogeneous dynamics in translation and rotation, with a strong spatial correlation between translationally and rotationally mobile particles. Application of the Einstein formalism to the analysis of translation-rotation decoupling results in a trend opposite to that seen in conventional approaches based on the Debye formalism, namely, an enhancement in the effective rate of rotational motion relative to translation upon supercooling. ©2006 American Institute of Physics

A Precise Packing Sequence for Self-Assembled Convex Structures

T Chen — 2007-04-05T21:57:45-00:00

ArXiv Condensed Matter e-prints (August 2006)

Molecular simulations of the self-assembly of cone-shaped particles with specific, attractive interactions are performed. Upon cooling from random initial conditions, we find that the cones self assemble into clusters and that clusters comprised of particular numbers of cones (e.g. 4 - 17, 20, 27, 32, 42) have a unique and precisely packed structure that is robust over a range of cone angles. These precise clusters form a sequence of structures at specific cluster sizes- a precise packing sequence - that for small sizes is identical to that observed in evaporation-driven assembly of colloidal spheres. We further show that this sequence is reproduced and extended in simulations of two simple models of spheres self-assembling from random initial conditions subject to certain convexity constraints. This sequence contains six of the most common virus capsid structures obtained in vivo including large chiral clusters, and a cluster that may correspond to several non-icosahedral, spherical virus capsid structures obtained in vivo. Our findings suggest this precise packing sequence results from free energy minimization subject to convexity constraints and is applicable to a broad range of assembly processes.