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the surface profile was read out using atom force microscopy.
The computational treatment comprised atomistic molecular
dynamics simulations explicitly taking into account the photoisomerization
dynamics and the light polarization 31 . This
combined approach allows for new insight into the mechanistic
aspects of the surface relief forming process. A particular
focus lies on the role of the light polarization direction relative
to the stripe pattern.
II.
COMPUTATIONAL DETAILS
Our atomistic computational model consists of a 20 nm
thick quasi-infinite periodic slab with a unit cell of size
19.3×32.1×50 nm 3 (z being the plane normal direction) containing
1944 16-meric PDO3M molecules (i.e., a total of
995 328 atoms and 31 104 AB chromophore units) that can
be partitioned into a bright (irradiated) half and a dark (not
irradiated) half, as shown in Fig.1. To maintain the shape of
the slab, the polymer backbone atoms at the bottom (i.e., with
z ≤0.9 nm) were fixed by constraints.
Laser-induced E ↔ Z photoswitching was then simulated
by repeatedly applying our molecular mechanics switch 31–33
(that we extended to include the Z → E direction (cf. SI)) every
50 ps to all chromophore units in the active region whose
transition dipole moment, D, was sufficiently aligned with
the polarisation vector, P, of the incident light. We chose
the two polarisation directions P = (1, 0, 0) (x-direction) and
P = (0, 1, 0) (y-direction).
The overall heating of the slab due to the energy uptake
of ≈ 2.8 eV per photoactivated chromophore was controlled
by a moderate heat bath of Nosé-Hoover type (τ = 80 ps,
T = 300 K) applied separately to the bright and dark regions,
respectively, in order to prevent the extreme temperatures observed
in our previous studies 31 .
In order to further probe orientation and finite size effects,
we carried out simulations with two different partitionings of
dark and bright regions as shown in Fig. 1. In the first partitioning,
the slab was divided into two halves along the y-
direction. With the two polarisations considered, this resulted
in the setups ’yy’ and ’yx’ (Fig. 1). The second partitioning
consisted in dividing the system in two halves in x-direction,
resulting in the ’xy’ and ’xx’ setups.
The molecular dynamics simulations were performed using
an in-house modified version Gromacs ?
III.
RESULTS AND DISCUSSION
In this section we describe the observed surface modifactions.
We first present the results from theory and experiment
in two separate sections and then discuss the implications on
the mechanistic aspects.
FIG. 1. Schematic representation of the different simulation setups.
A. Molecular dynamics simulations
The computer simulations mimick, due to the periodic
boundary conditions, alternating bright and dark stripes on
the thin film surface with the stripes oriented either parallel
to the x (’vertical’) or the y axis (’horizontal’), respectively
(cf. Fig. 1).
This general setup of the periodic MD box is visualised in
Fig. 2 together with the resulting surface profile.
FIG. 2. View of the periodic simulation box. Top row: complete box
with periodic continuation displayed for the first top layers (highlighted
via colour scheme) and ’bright’ area indicated by a yellow
rectangle. Bottom row: resulting final surface profile obtained after
photostimulation and re-cooling (see text).
The time evolution of the emerging height profiles for the
four different setups is shown in Fig. 3, where we have plotted
the maximum z-value of the molecules with a given position
along the axis perpendicular to the bright- dark separation,
or in other words, the profile seen when viewing the sample
parallel to the stripes.
Focussing first on Fig. 3a), it is seen that the photoirradiation
within the first 1 ns leads to a significant increase in height