![](bg7.png)
simulation, and it is re-assembled for visualization
and further numerical analysis. A simple 2D graphi-
cal representation of the assembled complexes is also
generated, where one can track the ssDNAs within
the complex as well as all the binding interactions.
Different from other computational modeling
frameworks for DNA strand assembly, we can modify
some of the systems parameters, such as the temper-
ature of the system, during the system simulation.
Thus, we can model also an entire annealing process
for the formation of a DNA structure. The underlining
computational modeling engine used by VDNA-Lab,
namely NFsim, allows also for other parameters to be
adjusted mid-simulation: e.g., we can define specific
binding/un-binding kinetic rates for each different
length-3 subsequence. Currently, VDNA-Lab does
not have these features implemented.
ACKNOWLEDGEMENTS
This work was partially supported by the Academy of
Finland, project 311371/2017, and by the Romanian
National Authority for Scientific Research and Inno-
vation, PED grant 2391.
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