Observing reorientation dynamics with Time-Resolved fluorescence and molecular dynamics in varying periodic boundary conditions

2021 ◽  
pp. 1-15
Author(s):  
Gouri S. Jas ◽  
Ed W. Childs ◽  
C. Russell Middaugh ◽  
Krzysztof Kuczera
Keyword(s):  
Molecular Dynamics ◽  
Boundary Conditions ◽  
Periodic Boundary ◽  
Periodic Boundary Conditions ◽  
Time Resolved Fluorescence ◽  
Time Resolved ◽  
Reorientation Dynamics

Computer-Generated Structural Models for a-Si:H

1988 ◽  
Vol 141 ◽  
Author(s):  
Laurent J. Lewis ◽  
Normand Mousseau ◽  
FranÇois Drolet
Keyword(s):  
Molecular Dynamics ◽  
Boundary Conditions ◽  
Amorphous Silicon ◽  
Periodic Boundary ◽  
Hydrogenated Amorphous Silicon ◽  
Structural Models ◽  
Periodic Boundary Conditions ◽  
Dynamics Simulations ◽  
Hydrogenated Amorphous ◽  
Good Agreement

AbstractA new algorithm for generating fully-coordinated hydrogenated amorphous silicon models with periodic boundary conditions is presented. The hydrogen is incorporated into an a-Si matrix by a bond-switching process similar to that proposed by Wooten, Winer, and Weaire, making sure that four-fold coordination is preserved and that no rings with less than 5 members are created. After each addition of hydrogen, the structure is fully relaxed. The models so obtained, to be used as input to molecular dynamics simulations, are found to be in good agreement with experiment. A model with 12 at.% H is discussed in detail.

scholarly journals Investigation of Pressure Effect on Structure of 3Al2O3.2SiO2 System

2019 ◽  
Vol 35 (4) ◽  
Author(s):  
Pham Tri Dung ◽  
Nguyen Quang Bau ◽  
Nguyen Thi Thu Ha ◽  
Mai Thi Lan
Keyword(s):  
Molecular Dynamics ◽  
Distribution Function ◽  
Molecular Dynamics Simulation ◽  
Boundary Conditions ◽  
Periodic Boundary ◽  
Pressure Effect ◽  
Bond Angle ◽  
Periodic Boundary Conditions ◽  
Pair Interaction ◽  
Dynamics Simulation

The paper presents research results of structure of the Mullite system (3Al2O3.2SiO2) by  Molecular Dynamics simulation (MDs) using the Born–Mayer– Huggins pair interaction and periodic boundary conditions. The simulation is performed with model of 5250 atoms at different pressure and at 3500 K temperature. The structural properties of the system have been clarified through analysis of the pair radial distribution function, the distribution of coordination number, the bond angle and the link between adjacent TOx units.

scholarly journals SemiEmpirical Born-Oppenheimer Molecular Dynamics (SEBOMD) Within the Amber Biomolecular Package

2018 ◽  
Author(s):  
Antoine Marion ◽  
Hatice Gokcan ◽  
Gerald Monard
Keyword(s):  
Molecular Dynamics ◽  
Boundary Conditions ◽  
Liquid Water ◽  
Periodic Boundary ◽  
Molecular System ◽  
Periodic Boundary Conditions ◽  
Ewald Summation ◽  
Molecular Systems ◽  
Parallel Performance ◽  
Scaling Methods

<div>Semiempirical quantum methods from the Neglect of Differential Diatomic Overlap (NDDO) family such as MNDO, AM1, or PM3 are fast albeit approximate quantum methods. By combining them with linear scaling methods like the Divide & Conquer (D&C) method, it is possible to quickly evaluate the energy of systems containing hundreds to thousands of atoms. We here present our implementation in the Amber biomolecular package of a SEBOMD module that provides a way to run SemiEmpirical Born-Oppenheimer Molecular Dynamics. At each step of a SEBOMD molecular dynamics, a fully converged SCF calculation is performed to obtain the semiempirical quantum potential energy of a molecular system encaged or not in periodic boundary conditions. We describe the implementation and the features of our SEBOMD implementation. We show the equirements to conserve the total energy in NVE simulations, and how to accelerate SCF convergence through density matrix extrapolation. Specific ways of handling periodic boundary conditions using mechanical embedding or electrostatic embedding through a tailored quantum Ewald summation is developed. The parallel performance of SEBOMD simulations using the D&C scheme are presented for liquid water systems of various sizes, and a comparison between the traditional full diagonalization scheme and the D&C approach for the reproduction of the structure of liquid water illustrates the potentiality of SEBOMD to simulate molecular systems containing several hundreds of atoms for hundreds of picoseconds with a quantum mechanical potential in a reasonable amount of CPU time.</div>

scholarly journals Violations of the Clausius–Duhem inequality in Couette flows of granular media

2020 ◽  
Vol 476 (2244) ◽  
pp. 20200207
Author(s):  
Martin Ostoja-Starzewski ◽  
Rossella Laudani
Keyword(s):  
Molecular Dynamics ◽  
Boundary Conditions ◽  
Granular Media ◽  
Periodic Boundary ◽  
Periodic Boundary Conditions ◽  
Dissipation Function ◽  
Disc Diameter ◽  
Planar Systems ◽  
Micropolar Media ◽  
Energy Balances

Spontaneous violations of the Clausius–Duhem (CD) inequality in Couette-type collisional flows of model granular media are studied. Planar systems of monosized circular discs (with disc numbers from 10 to 204, and disc diameters from 0.001 m to 1 m) with frictional-Hookean contacts are simulated under periodic boundary conditions by a molecular dynamics. The scale-dependent homogenization of micropolar media is used to determine the energy balances and mechanical entropy production. The dissipation function exhibits spontaneous negative entropy increments described by the fluctuation theorem. The boundary between violations and non-violations of the CD inequality is mapped in the parameter space, where the probability of such events diminishes with the disc diameter, the disc number and the area fraction increasing. The dissipation function is a random process, tending to Gaussian as the number of discs increases, and possessing non-trivial fractal and anti-persistent Hurst properties.

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