  No systematic method exists to derive intra-chromosomal potentials between
nucleosomes along a chromosome consistently across a given genome. Such
potentials can yield information on nucleosomal ordering, thermal as well as
mechanical properties of chromosomes. Thus, indirectly, they shed light on a
possible mechanical genomic code along a chromosome. To develop a method
yielding effective intra-chromosomal potentials between nucleosomes a
generalized Lennard-Jones potential for the parameterization is developed based
on nucleosomal positioning data. This approach eliminates some of the problems
that the underlying nucleosomal positioning data has, rendering the extraction
difficult on the individual nucleosomal level. Furthermore, patterns on which
to base a classification along a chromosome appear on larger domains, such as
hetero- and euchromatin. An intuitive selection strategy for the
noisy-optimization problem is employed to derive effective exponents for the
generalized potential. The method is tested on the Candida albicans genome.
Applying k-means clustering based on potential parameters and thermodynamic
compressibilities, a genome-wide clustering of nucleosome sequences is obtained
for Candida albicans. This clustering shows that a chromosome beyond the
classical dichotomic categories of hetero- and euchromatin, is more
feature-rich.
