Investigation of Possible Structures of Silicon Nanotubes via Density-Functional Tight-Binding Molecular Dynamics Simulations and ab Initio Calculations

2005 ◽  
Vol 109 (18) ◽  
pp. 8605-8612 ◽  
Author(s):  
R. Q. Zhang ◽  
Ho-Lam Lee ◽  
Wai-Kee Li ◽  
Boon K. Teo
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio Calculations ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Density Functional ◽  
Tight Binding ◽  
Silicon Nanotubes ◽  
Dynamics Simulations

scholarly journals Multiscale QM/MM Molecular Dynamics Simulations of the Trimeric Major Light-Harvesting Complex II

2021 ◽  
Author(s):  
Sayan Maity ◽  
Vangelis Daskalakis ◽  
Marcus Elstner ◽  
Ulrich Kleinekathöfer
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Chlorophyll A ◽  
Density Functional ◽  
Light Harvesting ◽  
Higher Plants ◽  
Tight Binding ◽  
Spectral Densities ◽  
Light Harvesting Complex ◽  
Dynamics Simulations

Photosynthetic processes are driven by sunlight. Too little of it and the photosynthetic machinery cannot produce the reductive power to drive the anabolic pathways. Too much sunlight and the machinery can get damaged. In higher plants, the major Light Harvesting Complex (LHCII) efficiently absorbs the light energy, but can also dissipate it when in excess (quenching). In order to study the dynamics related to the quenching process but also the exciton dynamics in general, one needs to accurately determine the so-called spectral density which describes the coupling between the relevant pigment modes and the environmental degrees of freedom. To this end, Born–Oppenheimer molecular dynamics simulations in a quantum mechanics/molecular mechanics (QM/MM) fashion utilizing the density functional based tight binding (DFTB) method have been performed for the ground state dynamics. Subsequently, the time-dependent extension of the long-range-corrected DFTB scheme has been employed for the excited state calculations of the individual chlorophyll-a molecules in the LHCII complex. The analysis of this data resulted in spectral densities showing an astonishing agreement with the experimental counterpart in this rather large system. This consistency with an experimental observable also supports the accuracy, robustness, and reliability of the present multi-scale scheme. In addition, the resulting spectral densities and site energies were used to determine the exciton transfer rate within a special pigment pair consisting of a chlorophyll-a and a carotenoid molecule which is assumed to play a role in the balance between the light harvesting and quenching modes.

Tight-Binding Molecular Dynamics Study of Liquid and Amorphous Carbon

1992 ◽  
Vol 291 ◽  
Author(s):  
C. Z. Wang ◽  
K. M. Ho ◽  
C. T. Chan
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Amorphous Carbon ◽  
Simulation Study ◽  
Tight Binding ◽  
Sufficient Accuracy ◽  
Complex Carbon ◽  
Dynamics Simulations

ABSTRACTTight-binding molecular-dynamics simulations are performed to study the structure of liquid and amorphous carbon. Comparisons of our results with ab initiomolecular dynamics (Car-Parrinello) results and experimental data show that the scheme has sufficient accuracy and efficiency for realistic simulation study of the structural properties of complex carbon systems.

Equation of state of water based on the SCAN meta-GGA density functional

2020 ◽  
Vol 22 (8) ◽  
pp. 4626-4631 ◽  
Author(s):  
Gang Zhao ◽  
Shuyi Shi ◽  
Huijuan Xie ◽  
Qiushuang Xu ◽  
Mingcui Ding ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Equation Of State ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Density Functional ◽  
State Of Water ◽  
Water Based ◽  
Dynamics Simulations ◽  
Better Than

By ab initio molecular dynamics simulations, the newly developed SCAN meta-GGA functional is proved better than the widely used PBE-GGA functional in describing the equation of state of water.

scholarly journals Surface energy of nanoparticles – influence of particle size and structure

2018 ◽  
Vol 9 ◽  
pp. 2265-2276 ◽  
Author(s):  
Dieter Vollath ◽  
Franz Dieter Fischer ◽  
David Holec
Keyword(s):  
Molecular Dynamics ◽  
Particle Size ◽  
Surface Energy ◽  
Ab Initio Calculations ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Definition Of ◽  
Dynamics Simulations ◽  
Classical Thermodynamics ◽  
A Minor

The surface energy, particularly for nanoparticles, is one of the most important quantities in understanding the thermodynamics of particles. Therefore, it is astonishing that there is still great uncertainty about its value. The uncertainty increases if one questions its dependence on particle size. Different approaches, such as classical thermodynamics calculations, molecular dynamics simulations, and ab initio calculations, exist to predict this quantity. Generally, considerations based on classical thermodynamics lead to the prediction of decreasing values of the surface energy with decreasing particle size. This phenomenon is caused by the reduced number of next neighbors of surface atoms with decreasing particle size, a phenomenon that is partly compensated by the reduction of the binding energy between the atoms with decreasing particle size. Furthermore, this compensating effect may be expected by the formation of a disordered or quasi-liquid layer at the surface. The atomistic approach, based either on molecular dynamics simulations or ab initio calculations, generally leads to values with an opposite tendency. However, it is shown that this result is based on an insufficient definition of the particle size. A more realistic definition of the particle size is possible only by a detailed analysis of the electronic structure obtained from initio calculations. Except for minor variations caused by changes in the structure, only a minor dependence of the surface energy on the particle size is found. The main conclusion of this work is that surface energy values for the equivalent bulk materials should be used if detailed data for nanoparticles are not available.

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