Molecular Dynamics Simulations of Solid Phase Epitaxy of Si:Growth Mechanism and Defect Formation

1999 ◽  
Vol 584 ◽  
Author(s):  
T. Motooka ◽  
S. Munetoh ◽  
K. Nisihira ◽  
K. Moriguchi ◽  
A. Shintani
Keyword(s):  
Molecular Dynamics ◽  
Temperature Region ◽  
Defect Formation ◽  
Solid Phase ◽  
Md Simulations ◽  
Solid Phase Epitaxy ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Dynamics Simulations ◽  
Rate Limiting

AbstractWe have investigated crystal growth and defect formation processes during solid phase epitaxy (SPE) of Si in the [001] direction based on molecular dynamics (MD) simulations using the Tersoff potential. From the Arrhenius plot of the growth rates obtained by MD simulations, we have found that the activation energy of SPE at lower temperatures is in good agreement with the experimental value, approximately 2.7 eV, while it becomes lower at higher temperatures. This can be attributed to the difference in the amorphous/crystalline (a/c) interface structure. In the low temperature region, the a/c interface is essentially (001) and the rate-limiting step is two-dimensional nucleation on the (001) a/c interface. On the other hand, the a/c interface becomes rough due to (111) facets formation in the high temperature region and the rate-limiting step is presumably a diffusion process of Si to be trapped at the kink sites associated with these facets. Defect formation is found to be initiated by 5-membered rings created at the a/c interface. These mismatched configurations at the interface give rise to (111) stacking faults during further SPE growth.

Molecular dynamics simulations of solid-phase epitaxy of Si: Defect formation processes

2001 ◽  
Vol 64 (19) ◽  
Author(s):  
Shinji Munetoh ◽  
Koji Moriguchi ◽  
Akira Shintani ◽  
Ken Nishihira ◽  
Teruaki Motooka
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Defect Formation ◽  
Solid Phase ◽  
Formation Processes ◽  
Solid Phase Epitaxy ◽  
Dynamics Simulations

Molecular Dynamics Simulations to Evaluate the Effect of Applied Strain on Interstitial Cluster Formation and Orientation Under Collision Cascade Damage

2012 ◽  
Author(s):  
Satoshi Miyashiro ◽  
Satoshi Fujita ◽  
Mitsuhiro Itakura ◽  
Taira Okita
Keyword(s):  
Molecular Dynamics ◽  
Defect Formation ◽  
Cluster Formation ◽  
Md Simulations ◽  
Defect Cluster ◽  
Applied Strain ◽  
Collision Cascade ◽  
Defect Clusters ◽  
Dynamics Simulations ◽  
Cascade Damage

We conducted molecular dynamics (MD) simulations to analyze the strain influence on defect formation and orientation. Collision cascade damage was initiated under uniaxial applied strain with a PKA energy of 10 keV. The number of residual defects increased with applied strain because of the enhanced formation of larger defect cluster. We also applied uniaxial strain to the simulation cell which included an interstitial cluster and detected the change in its direction. The probability of a change in the defect cluster direction was significantly higher under strain. Results further showed that the probability of the change in direction is higher with smaller defect clusters, and that it is extremely low with clusters larger than a certain size.

scholarly journals Molecular Dynamics Simulations of Hexane Deposited onto Graphite: An Explicit–Hydrogen Model at ρ = 1

2007 ◽  
Vol 6 (1) ◽  
Author(s):  
M Connolly ◽  
M Roth ◽  
Carlos Wexler ◽  
Paul Gray
Keyword(s):  
Molecular Dynamics ◽  
Solid Phase ◽  
Orientational Order ◽  
Md Simulations ◽  
Thermal Fluctuations ◽  
Melting Behavior ◽  
Negative Energy ◽  
Graphite Substrate ◽  
Open Questions ◽  
Dynamics Simulations

We present the results of parallel Molecular Dynamics computer simulations of hexane (C6H14) adlayers physisorbed onto a graphite substrate in the density range 0.5 ≤ ρ ≤1 in units of monolayers, with emphasis on monolayer completion (ρ = 1). The hexane molecules are modeled to explicitly include hydrogens and the graphite is modeled as a six – layer all atom structure. In the explicit hydrogen simulations, the herringbone solid loses its orientational order at T1 = 140 °K, fairly consistent with results of UA simulations. However there is almost no nematic meso-phase or negative energy change at the loss of herringbone order. The explicit hydrogen melting temperature is T2 = 160 °K—somewhat lower than seen in experiment and in UA simulations. Generally, results for the all–atom model agree well with experiment, as the molecules remain overall flat on the substrate in the solid phase. At densities below about ρ = 0.875 the system supports a connected network which stabilizes it against thermal fluctuations and yields much more reasonable sub-monolayer- melting behavior. The united atom picture, on the other hand, departs significantly from experiment at most sub-monolayer- densities and gives melting temperatures several decades below what is experimentally observed. The purpose of this work is to compare the results of UA and explicit hydrogen MD simulations of hexane on graphite mainly at ρ = 1, to discuss cursory explorations at sub-monolayer- densities and mention open questions related to the system that are worth pursuing. Various structural and thermodynamic order parameters and distributions are presented in order to outline such differences.

scholarly journals The influence of active site conformations on the hydride transfer step of the thymidylate synthase reaction mechanism

2015 ◽  
Vol 17 (46) ◽  
pp. 30793-30804 ◽  
Author(s):  
Katarzyna Świderek ◽  
Amnon Kohen ◽  
Vicent Moliner
Keyword(s):  
Reaction Mechanism ◽  
Thymidylate Synthase ◽  
Active Site ◽  
Hydride Transfer ◽  
Md Simulations ◽  
Concerted Mechanism ◽  
X Ray ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Rate Limiting

QM/MM MD simulations from different X-ray structures support the concerted mechanism character in the rate limiting step of thymidylate synthase catalysis.

scholarly journals Revealing a hidden intermediate of rotatory catalysis with X-ray crystallography and Molecular simulations

2021 ◽  
Author(s):  
Mrinal Shekhar ◽  
Chitrak Gupta ◽  
Kano Suzuki ◽  
Abhishek Singharoy ◽  
Takeshi Murata
Keyword(s):  
Molecular Motors ◽  
Atp Hydrolysis ◽  
Structural Information ◽  
Hydrolysis Product ◽  
X Ray ◽  
X Ray Crystallography ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Dynamics Simulations ◽  
Rate Limiting

The mechanism of rotatory catalysis in ATP-hydrolyzing molecular motors remain an unresolved puzzle in biological energy transfer. Notwithstanding the wealth of available biochemical and structural information inferred from years of experiments, knowledge on how the coupling between the chemical and mechanical steps within motors enforces directional rotatory movements remains fragmentary. Even more contentious is to pinpoint the rate-limiting step of a multi-step rotation process. Here, using Vacuolar or V1-type hexameric ATPase as an exemplary rotational motor, we present a model of the complete 4-step conformational cycle involved in rotatory catalysis. First, using X-ray crystallography a new intermediate or 'dwell' is identified, which enables the release of an inorganic phosphate (or Pi) after ATP hydrolysis. Using molecular dynamics simulations, this new dwell is placed in a sequence with three other crystal structures to derive a putative cyclic rotation path. Free-energy simulations are employed to estimate the rate of the hexameric protein transfor-mations, and delineate allosteric effects that allow new reactant ATP entry only after hydrolysis product exit. An analysis of transfer entropy brings to light how the sidechain level interactions transcend into larger scale reorganizations, highlighting the role of the ubiquitous arginine-finger residues in coupling chemical and mechanical information. Inspection of all known rates encompassing the 4-step rotation mechanism implicates overcoming of the ADP interactions with V1-ATPase to be the rate-limiting step of motor action.

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