Summary: NEST Scientific Report 2007-2009
iological matter is characterized by an overwhelming complexity: In order to "live"
an organism must undergo a variety of events that occur on different scales of length
and time. These range from a few Å, the size of the active site of proteins, where the
ultra-fast triggering steps of the biochemical reactions take place, up to the level of the cells
and organs, where the macroscopic physiological effects are detectable by the naked eye,
and involve the nano- and micro- scale as intermediates. This hierarchical organization is
responsible for the complexity, because each single process inherently involves a cascade
of events occurring on different scales.
In the period 2005-2006 we developed and tested modeling methodologies tailored
to address the nano-micro scale typical of the macromolecular aggregates, namely the
Coarse Grained models. In the subsequent period (2007-2009), we extended those
models and applied them to specific problems (fundamental steps of HIV replication and in
general of DNA replication, and the Fluorescent Proteins structural and optical properties).
In addition, we started a process of integration of the CG models within a more general
multi-scale approach, which, we believe, is essential for a coherent description and a deep
understanding of any biological processes.