Real-Time Propagation TDDFT and Density Analysis for Exciton Couplings Calculations in Large Systems

Photo-active systems are characterized by their capacity of absorbing light energy and transforming it. Usually, more than one chromophore is involved in the light absorption and excitation transport processes in complex systems. Linear-Response Time-Dependent Density Functional (LR-TDDFT) is commonly used to identify excitation energies and transition properties by solving well-known Casida's equation for single molecules. However, this methodology is not useful in practice when dealing with multichromophore systems. In this work, we extend our local density decomposition method that enables to disentangle individual contributions into the absorption spectrum to computation of exciton dynamic properties, such as exciton coupling parameters. We derive an analytical expression for the transition density from Real-Time Propagation TDDFT (P-TDDFT) based on Linear Response theorems. We demonstrate the validity of our method to determine transition dipole moments, transition densities and exciton coupling for systems of increasing complexity. We start from the isolated benzaldehyde molecule, perform a distance analysis for $\pi$-stacked dimers and finally map the exciton coupling for a 14 benzaldehyde cluster.Comment: 32 pages, 8 figures; added references in introductions, typos fixe

Nanotube-based scanning rotational microscope

A scheme of the scanning rotational microscope is designed. This scheme is based on using carbon nanotubes simultaneously as a probe tip and as a bolt/nut pair which converts translational displacements of two piezo actuators into pure rotation of the probe tip. First-principles calculations of the interaction energy between movable and rotational parts of the microscope confirms the capability for its operation. The scanning rotational microscope with a chemically functionalized nanotube-based tip can be used to study how the interaction between individual molecules or a molecule and a surface depends on their relative orientation.Comment: 4 pages, 3 figure

Dislocations in stacking and commensurate-incommensurate phase transition in bilayer graphene and hexagonal boron nitride

Dislocations corresponding to a change of stacking in two-dimensional hexagonal bilayers, graphene and boron nitride, and associated with boundaries between commensurate domains are investigated using the two-chain Frenkel-Kontorova model on top of ab initio calculations. Structural transformations of bilayers in which the bottom layer is stretched and the upper one is left to relax freely are considered for gradually increased elongation of the bottom layer. Formation energies of dislocations, dislocation width and orientation of the boundary between commensurate domains are analyzed depending on the magnitude and direction of elongation. The second-order phase transition from the commensurate phase to the incommensurate one with multiple dislocations is predicted to take place at some critical elongation. The order parameter for this transition corresponds to the density of dislocations, which grows continuously upon increasing the elongation of the bottom layer above the critical value. In graphene and metastable boron nitride with the layers aligned in the same direction, where elementary dislocations are partial, this transition, however, is preceded by formation of the first dislocation at the elongation smaller than the critical one. The phase diagrams including this intermediate state are plotted in coordinates of the magnitude and direction of elongation of the bottom layer.Comment: 15 pages, 9 figure

Transformation of amorphous carbon clusters to fullerenes

Transformation of amorphous carbon clusters into fullerenes under high temperature is studied using molecular dynamics simulations at microsecond times. Based on the analysis of both structure and energy of the system, it is found that fullerene formation occurs in two stages. Firstly, fast transformation of the initial amorphous structure into a hollow sp$^2$ shell with a few chains attached occurs with a considerable decrease of the potential energy and the number of atoms belonging to chains and to the amorphous domain. Then, insertion of remaining carbon chains into the sp$^2$ network takes place at the same time with the fullerene shell formation. Two types of defects remaining after the formation of the fullerene shell are revealed: 7-membered rings and single one-coordinated atoms. One of the fullerene structures obtained contains no defects at all, which demonstrates that defect-free carbon cages can be occasionally formed from amorphous precursors directly without defect healing. No structural changes are observed after the fullerene formation, suggesting that defect healing is a slow process in comparison with the fullerene shell formation. The schemes of the revealed reactions of chain atoms insertion into the fullerene shell just before its completion are presented. The results of the performed simulations are summarized within the paradigm of fullerene formation due to selforganization of the carbon system.Comment: 35 pages, 9 figure