35 research outputs found
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 . 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 . We provide evidence that
this modification in the relaxation dynamics occurs at a recently proposed
dynamical crossover temperature , which is related to the breakdown
of the Stokes-Einstein relation. We find that this dynamical crossover at
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 -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