Equilibrium ultrastable glasses produced by random pinning

Ultrastable glasses have risen to prominence due to their potentially useful material properties and the tantalizing possibility of a general method of preparation via vapor deposition. Despite the importance of this novel class of amorphous materials, numerical studies have been scarce because achieving ultrastability in atomistic simulations is an enormous challenge. Here we bypass this difficulty and establish that randomly pinning the position of a small fraction of particles inside an equilibrated supercooled liquid generates ultrastable configurations at essentially no numerical cost, while avoiding undesired structural changes due to the preparation protocol. Building on the analogy with vapor-deposited ultrastable glasses, we study the melting kinetics of these configurations following a sudden temperature jump into the liquid phase. In homogeneous geometries, we find that enhanced kinetic stability is accompanied by large scale dynamic heterogeneity, while a competition between homogeneous and heterogeneous melting is observed when a liquid boundary invades the glass at constant velocity. Our work demonstrates the feasibility of large-scale, atomistically resolved, and experimentally relevant simulations of the kinetics of ultrastable glasses.Comment: 9 pages, 5 figure

Improved prediction of molecular response to pulling by combining force tempering with replica exchange methods

Small mechanical forces play important functional roles in many crucial cellular processes, including in the dynamical behavior of the cytoskeleton and in the regulation of osmotic pressure through membrane-bound proteins. Molecular simulations offer the promise of being able to design the behavior of proteins that sense and respond to these forces. However, it is difficult to predict and identify the effect of the relevant piconewton (pN) scale forces due to their small magnitude. Previously, we introduced the Infinite Switch Simulated Tempering in Force (FISST) method which allows one to estimate the effect of a range of applied forces from a single molecular dynamics simulation, and also demonstrated that FISST additionally accelerates sampling of a molecule's conformational landscape. For some problems, we find that this acceleration is not sufficient to capture all relevant conformational fluctuations, and hence here we demonstrate that FISST can be combined with either temperature replica exchange or solute tempering approaches to produce a hybrid method that enables more robust prediction of the effect of small forces on molecular systems.Comment: 15 Pages with 6 figures, plus 7 supplemental figures and one supplemental tabl

Correlation of Local Order with Particle Mobility in Supercooled Liquids is Highly System Dependent

We investigate the connection between local structure and dynamical heterogeneity in supercooled liquids. Through the study of four different models we show that the correlation between a particle's mobility and the degree of local order in nearby regions is highly system dependent. Our results suggest that the correlation between local structure and dynamics is weak or absent in systems that conform well to the mean-field picture of glassy dynamics and strong in those that deviate from this paradigm. Finally, we investigate the role of order-agnostic point-to-set correlations and reveal that they provide similar information content to local structure measures, at least in the system where local order is most pronounced.Comment: 6 pages, 3 figures and 6 page sup. with 5 figures and 1 tabl

Crossovers in the dynamics of supercooled liquids probed by an amorphous wall

We study the relaxation dynamics of a binary Lennard-Jones liquid in the presence of an amorphous wall generated from equilibrium particle configurations. In qualitative agreement with the results presented in Nature Phys. {\bf 8}, 164 (2012) for a liquid of harmonic spheres, we find that our binary mixture shows a saturation of the dynamical length scale close to the mode-coupling temperature $T_c$. Furthermore we show that, due to the broken symmetry imposed by the wall, signatures of an additional change in dynamics become apparent at a temperature well above $T_c$. We provide evidence that this modification in the relaxation dynamics occurs at a recently proposed dynamical crossover temperature $T_s > T_c$, which is related to the breakdown of the Stokes-Einstein relation. We find that this dynamical crossover at $T_s$ is also observed for a system of harmonic spheres as well as a WCA liquid, showing that it may be a general feature of glass-forming systems.Comment: 10 pages, 8 figure

Size-and-shape space Gaussian mixture models for structural clustering of molecular dynamics trajectories

Determining the optimal number and identity of structural clusters from an ensemble of molecular configurations continues to be a challenge. Recent structural clustering methods have focused on the use of internal coordinates due to the innate rotational and translational invariance of these features. The vast number of possible internal coordinates necessitates a feature space supervision step to make clustering tractable, but yields a protocol that can be system type specific. Particle positions offer an appealing alternative to internal coordinates, but suffer from a lack of rotational and translational invariance, as well as a perceived insensitivity to regions of structural dissimilarity. Here, we present a method, denoted shape-GMM, that overcomes the shortcomings of particle positions using a weighted maximum likelihood (ML) alignment procedure. This alignment strategy is then built into an expectation maximization Gaussian mixture model (GMM) procedure to capture metastable states in the free energy landscape. The resulting algorithm distinguishes between a variety of different structures, including those indistinguishable by RMSD and pair-wise distances, as demonstrated on several model systems. Shape- GMM results on an extensive simulation of the the fast-folding HP35 Nle/Nle mutant protein support a 4-state folding/unfolding mechanism which is consistent with previous experimental results and provides kinetic detail comparable to previous state of the art clustering approaches, as measured by the VAMP-2 score. Currently, training of shape-GMMs is recommended for systems (or subsystems) that can be represented by . 200 particles and . 100K configurations to estimate high-dimensional covariance matrices and balance computational expense. Once a shape-GMM is trained, it can be used to predict the cluster identities of millions of configurations.Chemistr

Computing equilibrium free energies through a nonequilibrium quench

Many methods to accelerate sampling of molecular configurations are based on the idea that temperature can be used to accelerate rare transitions. These methods typically compute equilibrium properties at a target temperature using reweighting or through Monte Carlo exchanges between replicas at higher temperatures. A recent paper demonstrated that accurate equilibrium densities of states can also be computed through a nonequilibrium ``quench'' process, where sampling is performed at a higher temperature to encourage rapid mixing and then quenched to lower energy states with dissipative dynamics. Here we provide an implementation of the quench dynamics in LAMMPS and evaluate a new formulation of nonequilibrium estimators for the computation of partition functions or free energy surfaces (FESs) of molecular systems. We show that the method is exact for a minimal model of $N$-independent harmonic springs, and use these analytical results to develop heuristics for the amount of quenching required to obtain accurate sampling.= We then test the quench approach on alanine dipeptide, where we show that it gives an FES that is accurate near the most stable configurations using the quench approach, but disagrees with a reference umbrella sampling calculation in high FE regions. We then show that combining quenching with umbrella sampling allows the efficient calculation of the free energy in all regions. Moreover, by using this combined scheme, we obtain the FES across a range of temperatures at no additional cost, making it much more efficient than standard umbrella sampling if this information is required. Finally, we discuss how this approach can be extended to solute tempering and demonstrate that it is highly accurate for the case of solvated alanine dipeptide without any additional modifications.Comment: 18 pages, with 8 figures, 1 table, and 9 supplemental figure