Sticking to (first) principles: quantum molecular dynamics and Bayesian probabilistic methods to simulate aquatic pollutant absorption spectra

2016 ◽  
Vol 18 (8) ◽  
pp. 1068-1077 ◽  
Author(s):  
Kasidet Trerayapiwat ◽  
Nathan Ricke ◽  
Peter Cohen ◽  
Alex Poblete ◽  
Holly Rudel ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Absorption Spectra ◽  
First Principles ◽  
Probabilistic Methods ◽  
Quantum Molecular Dynamics ◽  
Excitation Energies ◽  
Aquatic Photochemistry ◽  
The Relationship

This work explores the relationship between theoretically predicted excitation energies and experimental molar absorption spectra as they pertain to environmental aquatic photochemistry.

First-principles quantum molecular-dynamics study of the vibrations of icosahedralC60

1991 ◽  
Vol 44 (8) ◽  
pp. 4052-4055 ◽  
Author(s):  
G. B. Adams ◽  
J. B. Page ◽  
O. F. Sankey ◽  
K. Sinha ◽  
J. Menendez ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
First Principles ◽  
Quantum Molecular Dynamics

Theoretical studies of structural stability at high pressure

1995 ◽  
Vol 73 (5-6) ◽  
pp. 253-257 ◽  
Author(s):  
John S. Tse ◽  
Dennis D. Klug
Keyword(s):  
Molecular Dynamics ◽  
High Pressure ◽  
First Principles ◽  
High Pressures ◽  
Structural Phase ◽  
Md Simulations ◽  
Quantum Molecular Dynamics ◽  
First Principles Calculations ◽  
Quantum Mechanical Effects ◽  
Structural Memory

Theoretical methods are indispensible for the study of matter at high pressure. In the last decade the development of accurate intermolecular potentials and the methodologies in classical molecular dynamics (MD) simulations have greatly facililated the applications of these methods to the study of structural phase transformamtions of solids at high pressures. More recently, it has been possible to incorporate quantum mechanical effects into MD calculations. This method eliminates a great deal of empiricism. These first principles calculations have not only reproduced the experimental results for phase transformations but also provided detailed mechanisms and in some cases predicted new structures that may be found at high pressures. The success of MD calculations is illustrated through a review of our studies of pressure-induced amorphization and phase transitions in SiO2 and TiO2, and the structural memory effect in several materials. Current applications using quantum molecular dynamics on ice are discussed.

New insights into Li diffusion in Li–Si alloys for Si anode materials: role of Si microstructures

Nanoscale ◽  
2019 ◽  
Vol 11 (29) ◽  
pp. 14042-14049 ◽  
Author(s):  
Guoqing Wang ◽  
Bo Xu ◽  
Jing Shi ◽  
Musheng Wu ◽  
Haibin Su ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
First Principles ◽  
Diffusion Coefficients ◽  
Anode Materials ◽  
Molecular Dynamics Calculations ◽  
Si Anode ◽  
The Relationship ◽  
First Principles Molecular Dynamics

The effect of Si microstructures on Li diffusion in Li–Si alloys was studied by using first-principles molecular dynamics calculations. The relationship between aggregation degree of Si and Li diffusion coefficients is established.

Generalized Langevin Equation: An Introductory Review for Biophysicists

2019 ◽  
Vol 14 (04) ◽  
pp. 171-196
Author(s):  
Shin-Ho Chung ◽  
Michael Roper
Keyword(s):  
Molecular Dynamics ◽  
Differential Equations ◽  
Stochastic Differential Equations ◽  
Langevin Equation ◽  
First Principles ◽  
Generalized Langevin Equation ◽  
Biophysical Modeling ◽  
Open Problems ◽  
The Relationship ◽  
Introductory Review

An introductory, pedagogical review of the generalized Langevin equation (GLE) within the classical regime is presented. It is intended to be accessible to biophysicists with an interest in molecular dynamics (MD). Section 1 presents why the equation may be of interest within biophysical modeling. A detailed elementary first principles derivation of the (multidimensional) Kac–Zwanzig model is presented. The literature is reviewed with a focus on biophysical applications and representation by Markovian stochastic differential equations. The relationship with the Mori–Zwanzig formalism is discussed. The framework of model reduction and approximation is emphasized. Some open problems are identified.

Electronic Structure and X-ray Absorption Spectra of Rutile TiO2 Using First-Principles Calculations

2014 ◽  
Vol 52 (12) ◽  
pp. 1025-1029
Author(s):  
Min-Wook Oh ◽  
Tae-Gu Kang ◽  
Byungki Ryu ◽  
Ji Eun Lee ◽  
Sung-Jae Joo ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Absorption Spectra ◽  
First Principles ◽  
First Principles Calculations ◽  
Rutile Tio2 ◽  
X Ray ◽  
X Ray Absorption
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