Basic Sciences Applications

Large-Scale Linear Programming Techniques for the Design of Protein Folding Potentials

  • Ron Elber
  • Jaroslaw Meller
  • Michael Wagner
    • Categories Basic Sciences Applications, Linear Programming, Parallel Algorithms Tags , , ,

    We present large-scale optimization techniques to model the energy function that underlies the folding process of proteins. Linear Programming is used to identify parameters in the energy function model, the objective being that the model predict the structure of known proteins correctly. Such trained functions can then be used either for {\em ab-initio} prediction or … Read more

    Improved linear programming bounds for antipodal spherical codes

  • Kurt M. Anstreicher
    • Categories Basic Sciences Applications, Linear Programming Tags , , , ,

    Let $S\subset[-1,1)$. A finite set $C=\{x_i\}_{i=1}^M\subset\Re^n$ is called a {\em spherical S-code} if $||x_i||=1$ for each $i$, and $x_i^T x_j\in S$, $i\ne j$. For $S=[-1,.5]$ maximizing $M=|C|$ is commonly referred to as the {\em kissing number} problem. A well-known technique based on harmonic analysis and linear programming can be used to bound $M$. We consider … Read more