Main_manuscript_JCP_template

Sample title 3
especially in the centre of the bright region (blue curve) due
to the energy input by repeated photoexcitation (note that the
centre of the dark region around y = 8 nm is nearly unaffected
throughout). In the time window 1–2 ns, the increase in the
centre comes to a halt and the elevation begins to shift to the
bright/dark boundary (red curve). This latter effect is dominant
in the remaining illumination time window (2–5 ns) and
is accompanied by a drop in height in the central bright region
(orange, black, yellow). After re-cooling to 300 K, a trench of
≈ 1 nm depth is clearly visible in the centre of the bright region
together with two hills (≈1 nm) formed at the bright/dark
boundary (green curve). The effect is similar when changing
the direction of polarisation as seen from Fig.3c), but is
significantly less pronounced upon changing the bright/dark
separation to ’horizontal’ (cf. Fig.3b), d)).
T / K
T / K
900
800
700
600
500
400
300
0 1 2 3 4 5 6
900
800
700
600
500
400
300
0 1 2 3 4 5 6
0 1 2 3 4 5 6 7 8 9 10 11
0 1 2 3 4 5 6 7 8 9 10 11
all
bright
dark
t / ps
t / ns
z / nm
20
18
FIG. 4. Time evoultion of global (bulk, bright and dark region) temperature
for the four different MD setups.
16
14
20
-15 -10 -5 0 5 10 15
-10 -5 0 5 10
0 ns
0.5 ns
1.0 ns
2.0 ns
3.0 ns
4.0 ns
5.0 ns
re-cooled
ter 1 ns. While the temperature bath manages to maintain a
bulk average temperature of about 600 K (see above), a hot
’bubble’ appearing in the bright region is clearly visible, with
peak temperatures of about 1400 K in the ’vertical’ setup and
roughly 200 K lower for the ’horizontal’ setup.
z / nm
18
16
14
-15 -10 -5 0 5 10 15
y / nm
-10 -5 0 5 10
x / nm
FIG. 3. Time evolution of the slab height profiles observed for the
four different MD setups.
The characteristics of the thermal energy uptake due to photoexcitation
is shown in Fig. 4, which presents the time evolution
of the overall bulk system temperature together with the
average values for the bright and dark regions, respectively.
In the first 1 ns, the system is seen to heat up from the initial
value of 300 K to a global average of roughyl 600 K in all
cases. Afterwards, the temperature remains stable for the remaining
duration. The pronounced fluctuations are due to the
photoexcitation cycles every 50 ps. A closer look at this analysis
reveals some subtle differences between the global average
temperatures of the ’vertical’ and ’horizontal’ setups. While
the overall system temperature of the ’vertical’ setups plateaus
at about 630 K, it converges to about 580 K for the ’horizontal’
setup. Furthermore, it is seen that the average temperature in
the bright region is ca. 100 K higher in the ’vertical’ setup as
compared to the ’horizontal’ partitioning (800 K vs. 700 K).
At the same time, the average temperature of the dark region is
lower for the ’vertical’ than for the ’horizontal’ setup. This is
attributed to the different widths of the bright and dark stripes
in the two setups, the narrower horizontal stripes allowing for
a more rapid exchange of heat between the two regions.
Going beyond temperature averages, Fig. 5 presents the
temperature distributions across the slab profile as reached af-
z / nm z / nm
FIG. 5. Temperature distribution of slab profile observed for the four
different MD setups after 1 ns.
The lower overall temperature reached in the two ’horizontal’
setups corresponds to a slightly lower (≈ 10 %) number of
activated chromophore units as can be seen from Fig. 6, where
the number of photoactivated E → Z and Z → E azo chromophore
units is shown, respectively, as a function of time
together with their sum (blue line). Here, it is seen that –
starting from an all-E situation – in each of the four setups a
kind of ’steady state’ is reached with about 58 % E → Z and
42 % Z → E excitation.
Next, we turn to the drift motion and the associated mass
transport (cf. Fig. ??), which is ultimately responsible for the
formation of a surface pattern. We begin our detailed analysis
of the molecular motion involved with Fig. 7, which presents
the average root mean square displacements (total rmsd and
cartesian components x, y and z) of the molecules represented