No Arabic abstract
Molecular dynamics simulation is used to study the time-scales involved in the homogeneous melting of a superheated crystal. The interaction model used is an embedded-atom model for Fe developed in previous work, and the melting process is simulated in the microcanonical $(N, V, E)$ ensemble. We study periodically repeated systems containing from 96 to 7776 atoms, and the initial system is always the perfect crystal without free surfaces or other defects. For each chosen total energy $E$ and number of atoms $N$, we perform several hundred statistically independent simulations, with each simulation lasting for between 500 ps and 10 ns, in order to gather statistics for the waiting time $tau_{rm w}$ before melting occurs. We find that the probability distribution of $tau_{rm w}$ is roughly exponential, and that the mean value $<tau_{rm w} >$ depends strongly on the excess of the initial steady temperature of the crystal above the superheating limit identified by other researchers. The mean $<tau_{rm w}>$ also depends strongly on system size in a way that we have quantified. For very small systems of $sim 100$ atoms, we observe a persistent alternation between the solid and liquid states, and we explain why this happens. Our results allow us to draw conclusions about the reliability of the recently proposed Z method for determining the melting properties of simulated materials, and to suggest ways of correcting for the errors of the method.
We extend the early time ordering theory of Cahn, Hilliard, and Cook (CHC) so that our generalized theory applies to solid-to-solid transitions. Our theory involves spatial symmetry breaking (the initial phase contains a symmetry not present in the final phase). The predictions of our generalization differ from those of the CHC theory in two important ways: exponential growth does not begin immediately following the quench, and the objects that grow exponentially are not necessarily Fourier modes. Our theory is consistent with simulation results for the long-range antiferromagnetic Ising model.
Estimating the homogeneous ice nucleation rate from undercooled liquid water is at the same time crucial for understanding many important physical phenomena and technological applications, and challenging for both experiments and theory. From a theoretical point of view, difficulties arise due to the long time scales required, as well as the numerous nucleation pathways involved to form ice nuclei with different stacking disorders. We computed the homogeneous ice nucleation rate at a physically relevant undercooling for a single-site water model, taking into account the diffuse nature of ice-water interfaces, stacking disorders in ice nuclei, and the addition rate of particles to the critical nucleus.We disentangled and investigated the relative importance of all the terms, including interfacial free energy, entropic contributions and the kinetic prefactor, that contribute to the overall nucleation rate.There has been a long-standing discrepancy for the predicted homogeneous ice nucleation rates, and our estimate is faster by 9 orders of magnitude compared with previous literature values. Breaking down the problem into segments and considering each term carefully can help us understand where the discrepancy may come from and how to systematically improve the existing computational methods.
In this paper we present a study of the early stages of unstable state evolution of systems with spatial symmetry changes. In contrast to the early time linear theory of unstable evolution described by Cahn, Hilliard, and Cook, we develop a generalized theory that predicts two distinct stages of the early evolution for symmetry breaking phase transitions. In the first stage the dynamics is dominated by symmetry preserving evolution. In the second stage, which shares some characteristics with the Cahn-Hilliard-Cook theory, noise driven fluctuations break the symmetry of the initial phase on a time scale which is large compared to the first stage for systems with long interaction ranges. To test the theory we present the results of numerical simulations of the initial evolution of a long-range antiferromagnetic Ising model quenched into an unstable region. We investigate two types of symmetry breaking transitions in this system: disorder-to-order and order-to-order transitions. For the order-to-order case, the Fourier modes evolve as a linear combination of exponentially growing or decaying terms with different time scales.
In this paper we discuss how the information contained in atomistic simulations of homogeneous nucleation should be used when fitting the parameters in macroscopic nucleation models. We show how the number of solid and liquid atoms in such simulations can be determined unambiguously by using a Gibbs dividing surface and how the free energy as a function of the number of solid atoms in the nucleus can thus be extracted. We then show that the parameters of a model based on classical nucleation theory can be fit using the information contained in these free-energy profiles but that the parameters in such models are highly correlated. This correlation is unfortunate as it ensures that small errors in the computed free energy surface can give rise to large errors in the extrapolated properties of the fitted model. To resolve this problem we thus propose a method for fitting macroscopic nucleation models that uses simulations of planar interfaces and simulations of three-dimensional nuclei in tandem. We show that when the parameters of the macroscopic model are fitted in this way the numerical errors for the final fitted model are smaller and that the extrapolated predictions for large nuclei are thus more reliable.
Nearly a quarter of genomic sequences and almost half of all receptors that are likely to be targets for drug design are integral membrane proteins. Understanding the detailed mechanisms of the folding of membrane proteins is a largely unsolved, key problem in structural biology. Here, we introduce a general model and use computer simulations to study the equilibrium properties and the folding kinetics of a $C_{alpha}$-based two helix bundle fragment (comprised of 66 amino-acids) of Bacteriorhodopsin. Various intermediates are identified and their free energy are calculated toghether with the free energy barrier between them. In 40% of folding trajectories, the folding rate is considerably increased by the presence of non-obligatory intermediates acting as traps. In all cases, a substantial portion of the helices is rapidly formed. This initial stage is followed by a long period of consolidation of the helices accompanied by their correct packing within the membrane. Our results provide the framework for understanding the variety of folding pathways of helical transmembrane proteins.