Ab initio total energy calculations

Fig. 11.38 Lag ejfects in ab initio molecular dynamics. (Figure redrawn from Payne MC, M P Teter, D C Allan, R A Arias and D ] Joannopoidos 1992. Iterative Minimisaticm Techniques for Ab Initio Total-Energy Calculations Molecular Dynamics and Conjugate Gradients. Reviews of Modern Physics 64 1045-1097.)...

The precursor of such atomistic studies is a description of atomic interactions or, generally, knowledge of the dependence of the total energy of the system on the positions of the atoms. In principle, this is available in ab-initio total energy calculations based on the loc density functional theory (see, for example, Pettifor and Cottrell 1992). However, for extended defects, such as dislocations and interfaces, such calculations are only feasible when the number of atoms included into the calculation is well below one hundred. Hence, only very special cases can be treated in this framework and, indeed, the bulk of the dislocation and interfacial... 

In crystals with the LI2 structure (the fcc-based ordered structure), there exist three independent elastic constants-in the contracted notation, Cn, C12 and 044. A set of three independent ab initio total-energy calculations (i.e. total energy as a function of strain) is required to determine these elastic constants. We have determined the bulk modulus, Cii, and C44 from distortion energies associated with uniform hydrostatic pressure, uniaxial strain and pure shear strain, respectively. The shear moduli for the 001 plane along the [100] direction and for the 110 plane along the [110] direction, are G ooi = G44 and G no = (Cu — G12), respectively. The shear anisotropy factor, A = provides a measure of the degree of anisotropy of the electronic charge... 

Kresse G, Furthmuller J. 1996a. Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set. Comput Mater Sci 6 15-50. 

Payne, M. C., Teter, M. P., Allen, D. C., Arias, T. A., and Joanopolus, J. D. (1992). Iterative minimization techniques for ab initio total energy calculations Molecular dynamics and conjugate gradients. Rev. Mod. Phys. 64,1045-97. 

M.C. Payne, M.P. Teter, D.C. Allan, T.A. Arias, and J.D. Joannopoulos, "Iterative minimization techniques for Ab Initio total-energy calculations molecular dynamics and conjugate gradients," Rev. Mod. Phys. 64 (1992), 1045-1097. 

Kresse G, Furthmueller J (1996) Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set, Phys. Rev. B54 11169—11186... 

Iddir H, Ogiit S, Zapol P, Browing ND (2007) Diffusion mechanisms of native point defects in rutile TiO ab initio total-energy calculations. Phys Rev B 75 073203... 

We have described here, in detail, three different DNA CG models. Other examples, found in the literature, vary both in their approaches to coarse-graining and in the structural detail included in the corresponding models. For example, Hsu et al. developed a CG DNA model using a bottom-up approach from ab initio total-energy calculations based on density functional theory (DFT) (Hsu et al., 2012). This model reduces each nucleotide into two CG sites, where the Hamiltonian terms in the CG model include hydrogen bonding, stacking interactions, backbone-backbone and backbone-... 

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