Aalto University, P.O. Box 11000, FI-00076 Aalto www.aalto.fi Author Andris Guļāns Name of the doctoral dissertation Van der Waals interactions in density-functional theory: implementation and applications Publisher School of Science Unit Applied Physics Series Aalto University publication series DOCTORAL DISSERTATIONS 6/2012 Field of research Electronic structure theory Manuscript submitted 3 ...

We present a dynamic van der Waals theory starting with entropy and energy functional with gradient contributions. The resultant hydrodynamic equations contain the stress arising from the density gradient. It provides a general scheme of two-phase hydrodynamics involving the gas-liquid transition in nonuniform temperature. Some complex hydrodynamic processes with evaporation and condensation ar...

Van der Waals materials have received a great deal of attention for their exceptional layered structures and exotic properties, which can open up various device applications in nanoelectronics. However, in situ epitaxial growth of dissimilar van der Waals materials remains challenging. Here we demonstrate a solution for fabricating van der Waals heterostructures. Graphene/hexagonal boron nitrid...

We use scanning tunneling microscopy to visualize and thermal desorption spectroscopy to quantitatively measure that the binding of naphthalene molecules to graphene, a case of pure van der Waals interaction, strengthens with n and weakens with p doping of graphene. Density-functional theory calculations that include the van der Waals interaction in a seamless, ab initio way accurately reproduc...

A detailed computational analysis of 32 protein-RNA complexes is presented. A number of physical and chemical properties of the intermolecular interfaces are calculated and compared with those observed in protein-double-stranded DNA and protein-single-stranded DNA complexes. The interface properties of the protein-RNA complexes reveal the diverse nature of the binding sites. van der Waals conta...

Vibrational relaxation of trapped molecules due to collisions with cold atoms is investigated using the results of quantum-mechanical scattering calculations. Trap loss is analyzed using an exactly solvable kinetic model that includes direct collisional quenching and an indirect process of vibrational predissociation. At low atom density, the relaxation is due primarily to collisional quenchin...

the internal structure of a molecule can be presented in terms of intra-molecular (i.e., inter atomic)and inter-molecular energies such as van der waals, bond and bending, torsion, and inversion energy.in this study, changes in molecular energies of individual asphalt components are evaluated as afunction of physical aging factors. the factors for physical aging such as temperature and pressure...

Implicit solvent hydration free energy models are an important component of most modern computational methods aimed at protein structure prediction, binding affinity prediction, and modeling of conformational equilibria. The nonpolar component of the hydration free energy, consisting of a repulsive cavity term and an attractive van der Waals solute-solvent interaction term, is often modeled usi...

Cystatin superfamily is a large group of evolutionarily related proteins involved in numerous physiological activities through their inhibitory activity towards cysteine proteases. Despite sharing the same cystatin fold, and inhibiting cysteine proteases through the same tripartite edge involving highly conserved N-terminal region, L1 and L2 loop; cystatins differ widely in their inhibitory aff...