arXiv subjects

Sharon C. Glotzer

Publications and source records attributed to Sharon C. Glotzer.

At least 109 records · Page 6Linked to original sources

arXiv2006

Structural signatures of strings and propensity for mobility in a simulated supercooled liquid above the glass transition

By molecular dynamics (MD) simulation of the one-component Dzugutov liquid in a metastable equilibrium supercooled state approaching the glass transition, we investigate the structural properties of highly mobile particles moving in strings at low temperature T where string-like particle motion (SLM) is well developed. We find that SLM occurs most frequently in the boundary regions between clusters of icosahedrally-ordered particles and disordered, liquid-like, domains. Further, we find that the onset T for significant SLM coincides with the T at which clusters of icosahedrally-ordered particles begin to appear in considerable amounts, which in turn coincides with the onset T for non-Arrhenius dynamics. We find a unique structural environment for strings that is different from the structure of the bulk liquid at any T. This unique string environment persists from the melting T upon cooling to the lowest T studied in the vicinity of the mode-coupling temperature, and is explained by the existence of rigid elongated cages. We also form a criterion based solely on structural features of the local environment that allow the identification of particles with an increased propensity for mobility.

cond-mat.soft↗

arXiv2006

Simulation studies of the self-assembly of cone-shaped particles

We systematically investigate the self-assembly of anisotropic cone-shaped particles decorated by ring-like attractive patches. We demonstrate that the self-assembled clusters, which arise due to the conical particle's anisotropic shape combined with directional attractive interactions, are precise for certain cluster sizes, resulting in a precise packing sequence of clusters of increasing sizes with decreasing cone angles. We thoroughly explore the dependence of cluster packing on cone angle and cooling rate, and categorize the resulting structures as stable and metastable clusters. We also discuss the implication of our simulation results in the context of the Israelachvili packing rule for surfactants, and a recent geometrical packing analysis on hard cones in the limit of large numbers of cones.

cond-mat.mtrl-sci↗

arXiv2006

Simulation Studies of A Phenomenological Model for the Assembly of Elongated Virus Capsids

We extend our previously developed general approach (1) to study a phenomenological model in which the simulated packing of hard, attractive spheres on a prolate spheroid surface with convexity constraints produces structures identical to those of prolate virus capsid structures. Our simulation approach combines the traditional Monte Carlo method with the method of random sampling on an ellipsoidal surface and a convex hull searching algorithm. Using this approach we study the assembly and structural origin of non-icosahedral, elongated virus capsids, such as two aberrant flock house virus (FHV) particles and the prolate prohead of bacteriophage phi29, and discuss the implication of our simulation results in the context of recent experimental findings.

q-bio.BM↗

arXiv2006

A Precise Packing Sequence for Self-Assembled Convex Structures

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.

cond-mat.mtrl-sci↗

arXiv2004

Dynamical heterogeneity and jamming in glass-forming liquids

The relationship between spatially heterogeneous dynamics (SHD) and jamming is studied in a glass-forming binary Lennard-Jones system via molecular dynamics simulations. It has been suggested that the probability distribution of interparticle forces $P(F)$ develops a peak at the glass transition temperature $T_g$, and that the large force inhomogeneities, responsible for structural arrest in granular materials, are related to dynamical heterogeneities in supercooled liquids that form glasses. It has been further suggested that ``force chains'' present in granular materials may exist in supercooled liquids, and may provide an order parameter for the glass transition. Our goal is to investigate the extent to which the forces experienced by particles in a glass-forming liquid are related to SHD, and compare these forces to those observed in granular materials and other glass-forming systems. We find no peak in $P(F)$ at any temperature in our system, even below $T_g$. We also find that particles that have been localized for a long time are less likely to experience high relative force and that mobile particles experience higher relative forces at shorter time scales, indicating a correlation between pairwise forces and particle mobility. We also discuss a possible relationship between force chains found here and the development of string-like motion found in other glass-forming liquids.

cond-mat.dis-nn↗

arXiv2004

Spatially heterogeneous dynamics and dynamic facilitation in a model of viscous silica

Performing molecular dynamics simulations, we find that the structural relaxation dynamics of viscous silica, the prototype of a strong glass former, are spatially heterogeneous and cannot be understood as a statistical bond breaking process. Further, we show that high particle mobility predominantly propagates continuously through the melt, supporting the concept of dynamic facilitation emphasized in recent theoretical work.

cond-mat.dis-nn↗

arXiv2003

Particle rearrangements during transitions between local minima of the potential energy landscape of a supercooled Lennard-Jones liquid

The potential energy landscape (PEL) of supercooled binary Lennard-Jones (BLJ) mixtures exhibits local minima, or inherent structures (IS), which are organized into meta-basins (MB). We study the particle rearrangements related to transitions between both successive IS and successive MB for a small 80:20 BLJ system near the mode-coupling temperature T_MCT. The analysis includes the displacements of individual particles, the localization of the rearrangements and the relevance of string-like motion. We find that the particle rearrangements during IS and MB transitions do not change significantly at T_MCT. Further, it is demonstrated that IS and MB dynamics are spatially heterogeneous and facilitated by string-like motion. To investigate the mechanism of string-like motion, we follow the particle rearrangements during suitable sequences of IS transitions. We find that most strings observed after a series of transitions do not move coherently during a single transition, but subunits of different sizes are active at different times. Several findings suggest that the occurrence of a successful string enables the system to exit a MB. Moreover, we show that the particle rearrangements during two consecutive MB transitions are basically uncorrelated. Specifically, different groups of particles are highly mobile during subsequent MB transitions. Finally, the relation between the features of the PEL and the relaxation processes in supercooled liquids is discussed.

cond-mat↗

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↗

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↗

arXiv1999

Theory of Non-linear Susceptibility and Correlation Length in Glasses and Liquids

Within the framework of the effective potential theory of the structural glass transition, we calculate for the p-spin model a static nonlinear susceptibility related to a four-point density correlation function, and show that it grows and diverges in mean field with exponent $γ=1/2$ as the mode coupling critical temperature T_c is approached from below. When T_c is approached from above, we calculate within the mode coupling framework a dynamic nonlinear susceptibility and show that there is a characteristic time where the susceptibility is a maximum, and that this time grows with decreasing T. We find that this susceptibility diverges as T_c is approached from above, and has key features in common with the ``displacement-displacement susceptibility'' recently introduced to measure correlated particle motion in simulations of glass-forming liquids.

cond-mat.dis-nn↗

arXiv1999

Crossover to Potential Energy Landscape Dominated Dynamics in a Model Glass-forming Liquid

An equilibrated model glass-forming liquid is studied by mapping successive configurations produced by molecular dynamics simulation onto a time series of inherent structures (local minima in the potential energy). Using this ``inherent dynamics'' approach we find direct numerical evidence for the long held view that below a crossover temperature, $T_x$, the liquid's dynamics can be separated into (i) vibrations around inherent structures and (ii) transitions between inherent structures (M. Goldstein, J. Chem. Phys. {\bf 51}, 3728 (1969)), i.e., the dynamics become ``dominated'' by the potential energy landscape. In agreement with previous proposals, we find that $T_x$ is within the vicinity of the mode-coupling critical temperature $T_c$. We further find that at the lowest temperature simulated (close to $T_x$), transitions between inherent structures involve cooperative, string like rearrangements of groups of particles moving distances substantially smaller than the average interparticle distance.

cond-mat.soft↗

arXiv1999

Dynamic Entropy as a Measure of Caging and Persistent Particle Motion in Supercooled Liquids

The length-scale dependence of the dynamic entropy is studied in a molecular dynamics simulation of a binary Lennard-Jones liquid above the mode-coupling critical temperature $T_c$. A number of methods exist for estimating the entropy of dynamical systems and we utilize an approximation based on calculating the mean first-passage time (MFPT) for particle displacement because of its tractability and its accessibility in real and simulation measurements. The MFPT dynamic entropy $S(ε)$ is defined to equal the inverse of the average first-passage time for a particle to exit a sphere of radius $ε$. This measure of the degree of chaotic motion allows us to identify characteristic time and space scales and to quantify the increasingly correlated particle motion and intermittency occurring in supercooled liquids. In particular, we identify a ``cage'' size defining the scale at which the particles are transiently localized, and we observe persistent particle motion at intermediate length scales beyond the scale where caging occurs. Furthermore, we find that the dynamic entropy at the scale of one interparticle spacing extrapolates to zero as the mode-coupling temperature $T_c$ is approached.

cond-mat.soft↗

arXiv1999

Filler-Induced Composition Waves in Phase-Separating Polymer Blends

The influence of immobile filler particles (spheres, fibers, platelets) on polymer blend phase separation is investigated computationally using a generalization of the Cahn-Hilliard-Cook (CHC) model. Simulation shows that the selective affinity of one of the polymers for the filler surface leads to the development of concentration waves about the filler particles at an early stage of phase separation in near critical composition blends. These "target" patterns are overtaken in late stage phase separation by a growing "background" spinodal pattern characteristic of blends without filler particles. The linearized CHC model is used to estimate the number of composition oscillations emanating from isolated filler particles. In far-off-critical composition blends, an "encapsulation layer" grows at the surface of the filler rather than a target pattern. The results of these simulations compare favorably with experiments on filled phase separating blend films.

cond-mat.stat-mech↗

arXiv1998

Quantifying Spatially Heterogeneous Dynamics in Computer Simulations of Glassforming Liquids

We examine the phenomenon of dynamical heterogeneity in computer simulations of an equilibrium, glass-forming liquid. We describe several approaches to quantify the spatial correlation of single-particle motion, and show that spatial correlations of particle displacements become increasingly long-range as the temperature decreases toward the mode coupling critical temperature.

cond-mat.soft↗

arXiv1998

Growing spatial correlations of particle displacements in a simulated liquid on cooling toward the glass transition

We define a correlation function that quantifies the spatial correlation of single-particle displacements in liquids and amorphous materials. We show for an equilibrium liquid that this function is related to fluctuations in a bulk dynamical variable. We evaluate this function using computer simulations of an equilibrium glass-forming liquid, and show that long range spatial correlations of displacements emerge and grow on cooling toward the mode coupling critical temperature.

cond-mat.soft↗

arXiv1998

Effect of Ordering on Spinodal Decomposition of Liquid-Crystal/Polymer Mixtures

Partially phase-separated liquid-crystal/polymer dispersions display highly fibrillar domain morphologies that are dramatically different from the typical structures found in isotropic mixtures. To explain this, we numerically explore the coupling between phase ordering and phase separation kinetics in model two-dimensional fluid mixtures phase separating into a nematic phase, rich in liquid crystal, coexisting with an isotropic phase, rich in polymer. We find that phase ordering can lead to fibrillar networks of the minority polymer-rich phase.

cond-mat.soft↗

arXiv1997

String-like Clusters and Cooperative Motion in a Model Glass-Forming Liquid

A large-scale molecular dynamics simulation is performed on a glass-forming Lennard-Jones mixture to determine the nature of dynamical heterogeneities which arise in this model fragile liquid. We observe that the most mobile particles exhibit a cooperative motion in the form of string-like paths (``strings'') whose mean length and radius of gyration increase as the liquid is cooled. The length distribution of the strings is found to be similar to that expected for the equilibrium polymerization of linear polymer chains.

cond-mat.dis-nn↗

arXiv1997

Dynamical heterogeneities in a supercooled Lennard-Jones liquid

We present the results of a large scale 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 size grows with decreasing temperature. We also find that the relaxation time of the mobile particles is significantly shorter than that of the bulk, and that this difference increases with decreasing temperature.

cond-mat.dis-nn↗