Lattice mold technique for the calculation of crystal nucleation rates

2016 ◽  
Vol 195 ◽  
pp. 569-582 ◽  
Author(s):  
Jorge R. Espinosa ◽  
Pablo Sampedro ◽  
Chantal Valeriani ◽  
Carlos Vega ◽  
Eduardo Sanz
Keyword(s):  
Rare Event ◽  
Simulation Method ◽  
Crystal Nucleation ◽  
Second Step ◽  
Complex Structures ◽  
Continuous Version ◽  
Event Simulation ◽  
Simulation Techniques ◽  
Dynamics Simulations ◽  
Good Agreement

We present a new simulation method for the calculation of crystal nucleation rates by computer simulation. The method is based on the use of molds to induce crystallization in state points where nucleation is a rare event. The mold is a cluster of potential energy wells placed in the lattice positions of the solid. The method has two distinct steps. In the first one the probability per unit volume of forming a sub-critical crystal cluster in the fluid is computed by means of thermodynamic integration. The thermodynamic route consists in gradually switching on an attractive interaction between the wells and the fluid particles. In the second step, the frequency with which such cluster becomes post-critical is computed in Molecular Dynamics simulations with the mold switched on. We validate our method with a continuous version of the hard sphere potential and with the sodium chloride Tosi–Fumi model. In all studied state points we obtain a good agreement with literature data obtained from other rare event simulation techniques. Our method is quite suitable for the study of both crystal nucleation of arbitrarily complex structures and the competition between different polymorphs in the nucleation stage.

Rare event simulation

2017 ◽  
Author(s):  
Michael P. Allen ◽  
Dominic J. Tildesley
Keyword(s):  
Rare Event ◽  
Path Sampling ◽  
Rapid Progress ◽  
Computationally Efficient ◽  
Transition Path ◽  
Transition Path Sampling ◽  
Event Simulation ◽  
Reaction Coordinates ◽  
Simulation Techniques ◽  
Transition Interface

The development of techniques to simulate infrequent events has been an area of rapid progress in recent years. In this chapter, we shall discuss some of the simulation techniques developed to study the dynamics of rare events. A basic summary of the statistical mechanics of barrier crossing is followed by a discussion of approaches based on the identification of reaction coordinates, and those which seek to avoid prior assumptions about the transition path. The demanding technique of transition path sampling is introduced and forward flux sampling and transition interface sampling are considered as rigorous but computationally efficient approaches.

scholarly journals Determination of sample size in a rare event simulation method

2006 ◽  
Vol 42 (1) ◽  
pp. 65-74
Author(s):  
V. P. Kharchenko ◽  
S. V. Nagaev ◽  
A. G. Kukush ◽  
E. A. Znakovskaya ◽  
S. I. Dotsenko
Keyword(s):  
Sample Size ◽  
Rare Event ◽  
Simulation Method ◽  
Rare Event Simulation ◽  
Event Simulation

scholarly journals Replicating $$\textsc {Restart}$$ with Prolonged Retrials: An Experimental Report

2021 ◽  
pp. 373-380
Author(s):  
Carlos E. Budde ◽  
Arnd Hartmanns
Keyword(s):  
Monte Carlo Simulation ◽  
Original Work ◽  
Ad Hoc ◽  
Rare Event ◽  
Statistical Model Checking ◽  
State Space Explosion ◽  
Event Simulation ◽  
Simulation Techniques ◽  
Independent Replication ◽  
Improved Performance

AbstractStatistical model checking uses Monte Carlo simulation to analyse stochastic formal models. It avoids state space explosion, but requires rare event simulation techniques to efficiently estimate very low probabilities. One such technique is $$\textsc {Restart}$$ R E S T A R T . Villén-Altamirano recently showed—by way of a theoretical study and ad-hoc implementation—that a generalisation of $$\textsc {Restart}$$ R E S T A R T to prolonged retrials offers improved performance. In this paper, we demonstrate our independent replication of the original experimental results. We implemented $$\textsc {Restart}$$ R E S T A R T with prolonged retrials in the and tools, and apply them to the models used originally. To do so, we had to resolve ambiguities in the original work, and refine our setup multiple times. We ultimately confirm the previous results, but our experience also highlights the need for precise documentation of experiments to enable replicability in computer science.

scholarly journals Ion dissolution mechanism and kinetics at kink sites on NaCl surfaces

2018 ◽  
Vol 115 (4) ◽  
pp. 656-661 ◽  
Author(s):  
Mark N. Joswiak ◽  
Michael F. Doherty ◽  
Baron Peters
Keyword(s):  
Rare Event ◽  
Alkali Halides ◽  
Collective Variable ◽  
Independent Study ◽  
Reaction Coordinate ◽  
Dissolution Mechanism ◽  
Enzyme Active Site ◽  
Event Simulation ◽  
Simulation Techniques ◽  
Desolvation Mechanism

Desolvation barriers are present for solute–solvent exchange events, such as ligand binding to an enzyme active site, during protein folding, and at battery electrodes. For solution-grown crystals, desolvation at kink sites can be the rate-limiting step for growth. However, desolvation and the associated kinetic barriers are poorly understood. In this work, we use rare-event simulation techniques to investigate attachment/detachment events at kink sites of a NaCl crystal in water. We elucidate the desolvation mechanism and present an optimized reaction coordinate, which involves one solute collective variable and one solvent collective variable. The attachment/detachment pathways for Na+ and Cl− are qualitatively similar, with quantitative differences that we attribute to different ion sizes and solvent coordination. The attachment barriers primarily result from kink site desolvation, while detachment barriers largely result from breaking ion–crystal bonds. We compute ion detachment rates from kink sites and compare with results from an independent study. We anticipate that the reaction coordinate and desolvation mechanism identified in this work may be applicable to other alkali halides.

Advances in Molecular Dynamics Simulations of Nanotribology

2008 ◽  
Author(s):  
Michael Chandross
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
State Of The Art ◽  
Simulation Method ◽  
Detailed Understanding ◽  
The Past ◽  
Simulation Techniques ◽  
Dynamics Simulations ◽  
The Individual ◽  
Made In

Molecular dynamics is the simulation method that is most amenable to the length and time scales of nanotribological experiments. The ability to track the individual motion of every atom in simulations has led to a detailed understanding of the underlying physics that is difficult to extract from experiment. While significant progress has been made in simulations over the past two decades, computational issues still limit the types of problems that can be approached, and the detailed understanding that results. Here we discuss recent advances in molecular dynamics simulations that push the bounds of simulation size, velocity, and chemistry. These state of the art simulation techniques have made great strides in allowing detailed comparisons to experimental results. These advances will be placed in context by addressing the barriers that remain and where future progress lies.

scholarly journals Transport Properties of the Lennard-Jones Truncated and Shifted Fluid from Non-equilibrium Molecular Dynamics Simulations

2021 ◽  
Author(s):  
Martin P. Lautenschläger ◽  
Hans Hasse
Keyword(s):  
Molecular Dynamics ◽  
Simulation Method ◽  
Self Diffusion ◽  
Lennard Jones ◽  
Wide Range ◽  
Data Correlations ◽  
Non Equilibrium Molecular Dynamics ◽  
Dynamics Simulations ◽  
Good Agreement ◽  
Non Equilibrium

The thermal conductivity λ, shear viscosity η, and self-diffusion coefficient D of the Lennard-Jones fluid truncated and shifted at the cut-off radius rc=2.5σ (LJTS fluid) are determined for a wide range of liquid and supercritical states (T*=[0.6,10.0] and ρ*=[0.2,1.2]). The simulations are carried out using a non-equilibrium molecular dynamics (NEMD) method that was introduced recently and in which two gradients are applied simultaneously. It is shown that the two-gradient method is well-suited for studies of liquid and supercritical states. Data for λ, η, and D for about 350 state points are reported. Two variants of the simulation method, which differ in the accuracy and efficiency, are explored and found to yield consistent data. Correlations for λ, η, and Dρ of the LJTS fluid are provided. The data and the correlations are compared to literature data of Lennard-Jones (LJ) type fluids and good agreement is observed. The truncation of the LJ potential causes a slight increase in D, while it has no significant effect on λ and η.

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