1,440 research outputs found
Evolution of the structure of amorphous ice - from low-density amorphous (LDA) through high-density amorphous (HDA) to very high-density amorphous (VHDA) ice
We report results of molecular dynamics simulations of amorphous ice for
pressures up to 22.5 kbar. The high-density amorphous ice (HDA) as prepared by
pressure-induced amorphization of Ih ice at T=80 K is annealed to T=170 K at
various pressures to allow for relaxation. Upon increase of pressure, relaxed
amorphous ice undergoes a pronounced change of structure, ranging from the
low-density amorphous ice (LDA) at p=0, through a continuum of HDA states to
the limiting very high-density amorphous ice (VHDA) regime above 10 kbar. The
main part of the overall structural change takes place within the HDA
megabasin, which includes a variety of structures with quite different local
and medium-range order as well as network topology and spans a broad range of
densities. The VHDA represents the limit to densification by adapting the
hydrogen-bonded network topology, without creating interpenetrating networks.
The connection between structure and metastability of various forms upon
decompression and heating is studied and discussed. We also discuss the analogy
with amorphous and crystalline silica. Finally, some conclusions concerning the
relation between amorphous ice and supercooled water are drawn.Comment: 11 pages, 12 postscript figures. To be published in The Journal of
Chemical Physic
Polyamorphism of ice at low temperatures from constant-pressure simulations
We report results of MD simulations of amorphous ice in the pressure range 0
- 22.5 kbar. The high-density amorphous ice (HDA) prepared by compression of Ih
ice at T = 80 K is annealed to T = 170 K at intermediate pressures in order to
generate relaxed states. We confirm the existence of recently observed
phenomena, the very high-density amorphous ice and a continuum of HDA forms. We
suggest that both phenomena have their origin in the evolution of the network
topology of the annealed HDA phase with decreasing volume, resulting at low
temperatures in the metastability of a range of densities.Comment: 11 pages, 5 postscript figures. To be published in Physical Review
Letter
Predicting crystal structures: the Parrinello-Rahman method revisited
By suitably adapting a recent approach [A. Laio and M. Parrinello, PNAS, 99,
12562 (2002)] we develop a powerful molecular dynamics method for the study of
pressure-induced structural transformations. We use the edges of the simulation
cell as collective variables. In the space of these variables we define a
metadynamics that drives the system away from the local minimum towards a new
crystal structure. In contrast to the Parrinello-Rahman method our approach
shows no hysteresis and crystal structure transformations can occur at the
equilibrium pressure. We illustrate the power of the method by studying the
pressure-induced diamond to simple hexagonal phase transition in a model of
silicon.Comment: 5 pages, 2 Postscript figures, submitte
Feedback Loops Between Fields and Underlying Space Curvature: an Augmented Lagrangian Approach
We demonstrate a systematic implementation of coupling between a scalar field
and the geometry of the space (curve, surface, etc.) which carries the field.
This naturally gives rise to a feedback mechanism between the field and the
geometry. We develop a systematic model for the feedback in a general form,
inspired by a specific implementation in the context of molecular dynamics (the
so-called Rahman-Parrinello molecular dynamics, or RP-MD). We use a generalized
Lagrangian that allows for the coupling of the space's metric tensor (the first
fundamental form) to the scalar field, and add terms motivated by RP-MD. We
present two implementations of the scheme: one in which the metric is only
time-dependent [which gives rise to ordinary differential equation (ODE) for
its temporal evolution], and one with spatio-temporal dependence [wherein the
metric's evolution is governed by a partial differential equation (PDE)].
Numerical results are reported for the (1+1)-dimensional model with a
nonlinearity of the sine-Gordon type.Comment: 5 pages, 3 figures, Phys. Rev. E in pres
Influence of Temperature and Anisotropic Pressure on the Phase Transitions in α-Cristobalite
The role of temperature and anisotropy of the applied load in the pressure–induced transformations of α -cristobalite is investigated by means of first principles molecular dynamics combined with the metadynamics algorithm for the study of solid-solid phase transitions. We reproduce the transition to α-PbO2 as found in experiments and we observe that the transition paths are qualitatively different and yield different products when a nonhydrostatic load is applied, giving rise to a new class of metastable structures with mixed tetrahedral and octahedral coordination
Metric tensor as the dynamical variable for variable cell-shape molecular dynamics
We propose a new variable cell-shape molecular dynamics algorithm where the
dynamical variables associated with the cell are the six independent dot
products between the vectors defining the cell instead of the nine cartesian
components of those vectors. Our choice of the metric tensor as the dynamical
variable automatically eliminates the cell orientation from the dynamics.
Furthermore, choosing for the cell kinetic energy a simple scalar that is
quadratic in the time derivatives of the metric tensor, makes the dynamics
invariant with respect to the choice of the simulation cell edges. Choosing the
densitary character of that scalar allows us to have a dynamics that obeys the
virial theorem. We derive the equations of motion for the two conditions of
constant external pressure and constant thermodynamic tension. We also show
that using the metric as variable is convenient for structural optimization
under those two conditions. We use simulations for Ar with Lennard-Jones
parameters and for Si with forces and stresses calculated from first-principles
of density functional theory to illustrate the applications of the method.Comment: 10 pages + 6 figures, Latex, to be published in Physical Review
Tautomeric equilibrium in condensed phases
We present an ab initio molecular dynamics (MD) investigation of the
tautomeric equilibrium for aqueous solutions of glycine and acetone at
realistic experimental conditions. Metadynamics is used to accelerate proton
migration among tautomeric centers. Due to the formation of complex water-ion
structures involved the proton dynamics in the aqueous environment, standard
enhanced sampling approaches may face severe limitations in providing a general
description of the phenomenon. Recently, we developed a set of Collective
Variables (CVs) designed to study protons transfer reactions in complex
condensed systems [Grifoni et al. PNAS, 2019, 116(10), 4054-4057]. In this work
we applied this approach to study proton dissociation dynamics leading to
tautomeric interconversion of biologically and chemically relevant prototypical
systems, namely glycine and acetone in water. Although relatively simple from a
chemical point of view, the results show that even for these small systems
complex reaction pathways and non-trivial conversion dynamics are observed. The
generality of our method allows obtaining these results without providing any
prior information on the dissociation dynamics but only the atomic species that
can exchange protons in the process. Our results agree with literature
estimates and demonstrate the general applicability of this method in the study
of tautomeric reactions
Reconstructing the Density of States by History-Dependent Metadynamics
We present a novel method for the calculation of the energy density of states
D(E) for systems described by classical statistical mechanics. The method
builds on an extension of a recently proposed strategy that allows the free
energy profile of a canonical system to be recovered within a pre-assigned
accuracy,[A. Laio and M. Parrinello, PNAS 2002]. The method allows a good
control over the error on the recovered system entropy. This fact is exploited
to obtain D(E) more efficiently by combining measurements at different
temperatures. The accuracy and efficiency of the method are tested for the
two-dimensional Ising model (up to size 50x50) by comparison with both exact
results and previous studies. This method is a general one and should be
applicable to more realistic model systems
Elastic Constants of Quantum Solids by Path Integral Simulations
Two methods are proposed to evaluate the second-order elastic constants of
quantum mechanically treated solids. One method is based on path-integral
simulations in the (NVT) ensemble using an estimator for elastic constants. The
other method is based on simulations in the (NpT) ensemble exploiting the
relationship between strain fluctuations and elastic constants. The strengths
and weaknesses of the methods are discussed thoroughly. We show how one can
reduce statistical and systematic errors associated with so-called primitive
estimators. The methods are then applied to solid argon at atmospheric
pressures and solid helium 3 (hcp, fcc, and bcc) under varying pressures. Good
agreement with available experimental data on elastic constants is found for
helium 3. Predictions are made for the thermal expectation value of the kinetic
energy of solid helium 3.Comment: 9 pages doublecolumn, 6 figures, submitted to PR
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