Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userA van der Waals density functional mapping of attraction in DNA dimers
184
0
0.0
(
0
)
Ask ChatGPT about the research
No Arabic abstract
The dispersion interaction between a pair of parallel DNA double-helix structures is investigated by means of the van der Waals density functional (vdW-DF) method. Each double-helix structure consists of an infinite repetition of one B-DNA coil with 10 base pairs. This parameter-free density functional theory (DFT) study illustrates the initial step in a proposed vdW-DF computational strategy for large biomolecular problems. The strategy is to first perform a survey of interaction geometries, based on the evaluation of the van der Waals (vdW) attraction, and then limit the evaluation of the remaining DFT parts (specifically the expensive study of the kinetic-energy repulsion) to the thus identified interesting geometries. Possibilities for accelerating this second step is detailed in a separate study. For the B-DNA dimer, the variation in van der Waals attraction is explored at relatively short distances (although beyond the region of density overlap) for a 360 degrees rotation. This study highlights the role of the structural motifs, like the grooves, in enhancing or reducing the vdW interaction strength. We find that to a first approximation, it is possible to compare the DNA double strand at large wall-to-wall separations to the cylindrical shape of a carbon nanotube (which is almost isotropic under rotation). We compare our first-principles results with the atom-based dispersive interaction predicted by DFT-D2 [J. Comp. Chem. 27, 1787 (2006)] and find agreement in the asymptotic region. However, we also find that the differences in the enhancement that occur at shorter distances reveal characteristic features that result from the fact that the vdW-DF method is an electron-based (as opposed to atom-based) description.
rate research
Read More
The non-local van der Waals density functional (vdW-DF) has had tremendous success since its inception in 2004 due to its constraint-based formalism that is rigorously derived from a many-body starting point. However, while vdW-DF can describe binding energies and structures for van der Waals complexes and mixed systems with good accuracy, one long-standing criticism---also since its inception---has been that the $C_6$ coefficients that derive from the vdW-DF framework are largely inaccurate and can be wrong by more than a factor of two. It has long been thought that this failure to describe the $C_6$ coefficients is a conceptual flaw of the underlying plasmon framework used to derive vdW-DF. We prove here that this is not the case and that accurate $C_6$ coefficient can be obtained without sacrificing the accuracy at binding separations from a modified framework that is fully consistent with the constraints and design philosophy of the original vdW-DF formulation. Our design exploits a degree of freedom in the plasmon-dispersion model $omega_{mathbf{q}}$, modifying the strength of the long-range van der Waals interaction and the cross-over from long to short separations, with additional parameters tuned_ to reference systems. Testing the new formulation for a range of different systems, we not only confirm the greatly improved description of $C_6$ coefficients, but we also find excellent performance for molecular dimers and other systems. The importance of this development is not necessarily that particular aspects such as $C_6$ coefficients or binding energies are improved, but rather that our finding opens the door for further conceptual developments of an entirely unexplored direction within the exact same constrained-based non-local framework that made vdW-DF so successful in the first place.
Potassium intercalation in graphite is investigated by first-principles theory. The bonding in the potassium-graphite compound is reasonably well accounted for by traditional semilocal density functional theory (DFT) calculations. However, to investi
gate the intercalate formation energy from pure potassium atoms and graphite requires use of a description of the graphite interlayer binding and thus a consistent account of the nonlocal dispersive interactions. This is included seamlessly with ordinary DFT by a van der Waals density functional (vdW-DF) approach [Phys. Rev. Lett. 92, 246401 (2004)]. The use of the vdW-DF is found to stabilize the graphite crystal, with crystal parameters in fair agreement with experiments. For graphite and potassium-intercalated graphite structural parameters such as binding separation, layer binding energy, formation energy, and bulk modulus are reported. Also the adsorption and sub-surface potassium absorption energies are reported. The vdW-DF description, compared with the traditional semilocal approach, is found to weakly soften the elastic response.
We propose a second version of the van der Waals density functional (vdW-DF2) of Dion et al. [Phys. Rev. Lett. 92, 246401 (2004)], employing a more accurate semilocal exchange functional and the use of a large-N asymptote gradient correction in determining the vdW kernel. The predicted binding energy, equilibrium separation, and potential-energy curve shape are close to those of accurate quantum chemical calculations on 22 duplexes. We anticipate the enabling of chemically accurate calculations in sparse materials of importance for condensed-matter, surface, chemical, and biological physics.
The past few years has brought renewed focus on the physics behind the class of materials characterized by long-range interactions and wide regions of low electron density, sparse matter. There is now much work on developing the appropriate algorithms and codes able to correctly describe this class of materials within a parameter-free quantum physical description. In particular, van der Waals (vdW) forces play a major role in building up material cohesion in sparse matter. This work presents an application to the vanadium pentoxide (V2O5) bulk structure of t
Large biomolecular systems, whose function may involve thousands of atoms, cannot easily be addressed with parameter-free density functional theory (DFT) calculations. Until recently a central problem was that such systems possess an inherent sparseness, that is, they are formed from components that are mutually separated by low-electron-density regions where dispersive forces contribute significantly to the cohesion and behavior. The introduction of, for example, the van der Waals density functional (vdW-DF) method [PRL 92, 246401 (2004)] has addressed part of this sparse-matter system challenge. However, while a vdW-DF study is often as computationally efficient as a study performed in the generalized gradient approximation, the scope of large-sparse-matter DFT is still limited by computer time and memory. It is costly to self-consistently determine the electron wavefunctions and hence the kinetic-energy repulsion. In this paper we propose and evaluate an adaption of the Harris scheme [PRB 31, 1770 (1985)]. This is done to speed up non-selfconsistent vdW-DF studies of molecular-system interaction energies. Also, the Harris-type analysis establishes a formal link between dispersion-interaction effects on the effective potential for electron dynamics and the impact of including selfconsistency in vdW-DF calculations [PRB 76, 125112 (2007)].
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
