scholarly journals Computing long time scale biomolecular dynamics using quasi-stationary distribution kinetic Monte Carlo (QSD-KMC)

2019 ◽  
Vol 151 (7) ◽  
pp. 074109 ◽  
Author(s):  
Animesh Agarwal ◽  
Nicolas W. Hengartner ◽  
S. Gnanakaran ◽  
Arthur F. Voter
Keyword(s):  
Monte Carlo ◽  
Stationary Distribution ◽  
Time Scale ◽  
Kinetic Monte Carlo ◽  
Biomolecular Dynamics ◽  
Long Time ◽  
Quasi Stationary Distribution

scholarly journals Simulations of long time scale dynamics using the dimer method

2001 ◽  
Vol 677 ◽  
Author(s):  
Graeme Henkelman ◽  
Hannes Jónsson
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Method ◽  
Transition State ◽  
Time Scale ◽  
Transition State Theory ◽  
Kinetic Monte Carlo ◽  
Chem Phys ◽  
State Theory ◽  
Kinetic Monte Carlo Method ◽  
Long Time

We have carried out long time scale simulations where the “dimer method” [G. Henkelman and H. Jónsson, J. Chem. Phys. 111, 7010 (1999)] is used to find the mechanism and estimate the rate of transitions within harmonic transition state theory and time is evolved by using the kinetic Monte Carlo method. Unlike traditional applications of kinetic Monte Carlo, the atoms are not assigned to lattice sites and a list of all possible transitions does not need to be specified beforehand. Rather, the relevant transitions are found on the y during the simulation. An application to the diffusion and island formation of Al adatoms on an Al(100) surface is presented.

Examination of the Effect of Vacancy Detachment Rates on Kinetic Monte Carlo Simulations of bcc Metals

MRS Advances ◽  
2016 ◽  
Vol 1 (35) ◽  
pp. 2489-2494 ◽  
Author(s):  
Richard T Hoffman ◽  
Alexander P Moore ◽  
Chaitanya S Deo
Keyword(s):  
Monte Carlo ◽  
Kinetic Monte Carlo ◽  
Void Formation ◽  
Binding Energies ◽  
Size Dependent ◽  
Bcc Metals ◽  
Bcc Lattice ◽  
Long Time ◽  
Kinetic Monte Carlo Simulations ◽  
Dynamics Simulations

ABSTRACTA Kinetic Monte Carlo simulation, using a modified version of the SPPARKS code, of simple defects and complex vacancy clusters was run on a bcc lattice. In this simulation the complexity of void formation was varied by introducing a detachment rate for individual vacancies leaving the void and either treating this value as constant for all size voids or having this value be dependent on the size of the void. Molecular Dynamics simulations were used to determine the binding energies of vacancies for voids of varying size. The simulation was then run over long time periods to determine the number of defects in the simulation under irradiation conditions. It was found that the additional complexity of size dependent void detachment rates had little effect on the defect concentrations and thus a constant barrier should be sufficient for simulations of voids in bcc metals.

scholarly journals A derivation and scalable implementation of the synchronous parallel kinetic Monte Carlo method for simulating long-time dynamics

2017 ◽  
Vol 219 ◽  
pp. 246-254 ◽  
Author(s):  
Hye Suk Byun ◽  
Mohamed Y. El-Naggar ◽  
Rajiv K. Kalia ◽  
Aiichiro Nakano ◽  
Priya Vashishta
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Method ◽  
Kinetic Monte Carlo ◽  
Kinetic Monte Carlo Method ◽  
Time Dynamics ◽  
Long Time ◽  
Long Time Dynamics

Simulation of Atomistic Crystal Growth from the Vapor Phase

1986 ◽  
Vol 77 ◽  
Author(s):  
Paul A. Taylor ◽  
Brian W. Dodson
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Crystal Growth ◽  
Monte Carlo Method ◽  
Vapor Phase ◽  
Time Scale ◽  
Transient Dynamics ◽  
Strained Layer ◽  
The Monte Carlo Method ◽  
Long Time

ABSTRACTWe are in the process of studying strained-layer growth of two-dimensional Lennard-Jones lattices. To do so, we have developed three techniques, based on the Monte Carlo method and molecular dynamics, of simulating atomistic crystal growth from the vapor phase. The Monte Carlo method efficiently simulates the effects of long time-scale processes on the growth of strained-layer systems, but omits the transient dynamics of particle adsorption. The second technique, using molecular dynamics, gives results suggesting that epitaxial growth of strained-layer systems can occur on the picosecond timescales. However, this technique cannot capture the influence of the long time-scale processes on the growth process. In view of the shortcomings of the previous two techniques, A hybrid technique incorporating both the Monte Carlo method and molecular dynamics, has been developed. In principle, this technique models the transient dynamics of adsorption as well as the long term evolution of the system. This technique, however, is limited by artifacts that may only be eliminated by use of unwarrented amounts of supercomputer time.

scholarly journals Modeling the Sputter Deposition of Thin Film Photovoltaics using Long Time Scale Dynamics Techniques

2011 ◽  
Vol 1327 ◽  
Author(s):  
S. Blackwell ◽  
R. Smith ◽  
S. D. Kenny ◽  
J. M. Walls
Keyword(s):  
Thin Film ◽  
Time Scale ◽  
Plasma Deposition ◽  
Kinetic Monte Carlo ◽  
Void Formation ◽  
Substrate Bias ◽  
Time Dynamics ◽  
Experimental Parameters ◽  
Long Time ◽  
Crystalline Growth

ABSTRACTResults are presented for modeling the deposition of Ag and rutile TiO2. The model can be used to examine the effect of varying experimental parameters, such as the substrate bias in the magnetron and the stoichiometry of the deposition species. We illustrate how long time scale dynamics techniques can be used to model the process over experimental time scales. Long time dynamics is achieved through an on-the-fly Kinetic Monte Carlo (otf-KMC) method, which determines diffusion pathways and barriers, in parallel, with no prior knowledge of the involved transitions. Using this otf-KMC method we have modeled the deposition of Ag and TiO2 for various plasma deposition energies, in the range 1 eV to 100 eV. It was found that Ag {111} produces the most crystalline growth when deposited at 40 eV. TiO2 growth showed that at energies of 1 eV and 100 eV a porous structure occurs with void formation. At deposition energies of 30 eV and 40 eV, a more dense and crystalline rutile growth forms. The results show that deposition energy plays an important role in the resulting thin film quality and surface morphology.

scholarly journals Locally activated Monte Carlo method for long-time-scale simulations

2000 ◽  
Vol 61 (2) ◽  
pp. 980-987 ◽  
Author(s):  
M. Kaukonen ◽  
J. Peräjoki ◽  
R. M. Nieminen ◽  
G. Jungnickel ◽  
Th. Frauenheim
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Method ◽  
Time Scale ◽  
Long Time
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