Classical simulations from the atomistic to the mesoscale and back: coarse graining an azobenzene liquid crystal

Computationally connecting organic photovoltaic performance to atomistic arrangements and bulk morphology

“…We refer to the process of mapping atomistic coordinates into a coarse-grained model as "finegraining", which is has found extensive use in the investigation of complex proteins [66][67][68], as well as other molecular systems [69][70][71][72][73]. Here, we use fine-graining to inform electronic property calculations, which complement the aforementioned structural analysis.…”

“…The atomic positions are therefore adjusted to make the conformation of the molecule more realistic, by energetically relaxing the molecules over very short timescales. This can be performed on a molecule-by-molecule basis in isolation [67,68], or in situ using energetic minimization methodologies [69][70][71], or even full molecular dynamics simulations [72]. In some cases, particularly when polymer chains with high conformational disorder are being simulated, it is useful to apply additional geometrical constraints during the fine-graining process to maintain the original centers-of-mass of each group according to the fully equilibrated, corasegrained morphology generation.…”

“…These forces cause numerical instabilities, strongly disrupting the molecule's equilibrium formation determined by the coarse-grained molecular dynamics. It is therefore not uncommon to use a "soft", repulsive pair potential such as the dissipative particle dynamics (DPD) forcefield, which is finite and well-defined at short separations, to gradually spread apart atoms, while still permitting them to overlap [72]. Some flavors of this potential include random fluctuations to the inter-atomic force, providing thermal 'kicks' or damping [87], however in this investigation, the DPD forcefield is not being used to obtain the final molecular conformations and is instead used as a tool to reduce overlap, so these fluctuations are unnecessary.…”

“…In some cases, particularly when polymer chains with high conformational disorder are being simulated, it is useful to apply additional geometrical constraints during the fine-graining process to maintain the original centers-of-mass of each group according to the fully equilibrated, corasegrained morphology generation. This can be achieved by simulating harmonic bonds with strong spring constants and small equilibrium lengths between the average positions of the atoms and the corresponding coarse-grained site position [72], anchoring the functional group in place. Such constraints can also help to simulate non-equilibrium effects such as a significant shear force [83].…”

“…Such constraints can also help to simulate non-equilibrium effects such as a significant shear force [83]. A final relaxation stage is frequently performed with a longer molecular dynamics simulation, in order to fully relax the chains in the simulation volume and ensure that there are no atomic overlaps between molecules [69][70][71][72]. When a physically realistic, atomistic conformation for the molecule has been achieved, it can be used by QCCs to determine the electronic structure.…”