In attempting to model chromosomes packed within a nucleus, I've decided that I
need a type of Monte Carlo Minimization routine. Scouring the Web has turned up
little in the way progress, so I've turned to you all in NG-Land...
Essentially I'm looking for an algorithm (in Fortran 77/90, preferably) where I
may enter a set of initial cartesian coordinates, the associated radii for each
"chromosome," and an objective function (i.e. Lennard-Jones potential
function). Let the program calculate the value of my objective function, Monte
Carlo (smartly) to re-position the chromosomes, recalculate the potential, etc.,
etc. until the function value is minimized.
Anyone's help (books, articles, URL's) would be greatly appreciated!! If anyone
in the realm of molecular dynamics, or packing theory (of non-uniform shapes)
have any ideas, I'd obviously welcome them as well.
Thanks in advance... (oh & as this is probably not of general interest to these
ng's please just e-mail me directly if you'd like)
-- Ryan D. Alexander
Ryan D. Alexander, CSU-LBNL NSCORT Ph.D. Trainee
Colorado State Univ., Dept. of Radiological Health Sciences
E-mail: ryanalex at lamar.colostate.edu
Office Ph: 970-491-0520, Dept. Fax: 970-491-0623