Theoretical Models for Biopolymers
Pp. 478-507 (30)
J. Ginés Hernández Cifre and F. Guillermo Díaz Baños
Theoretical models play a very important role in experimental practice and
are essential for the development of current science and technology. They have been
accessible for many years, but their development in recent decades, in parallel with the
improvements in computation, has allowed the emergence of an important number of
methodologies to complement experimental measurements. In this chapter, we present
a brief overview of these methodologies. Among them, bead modeling has put a
significant step forward. For rigid molecules, programs like those contained in the
HYDRO suite have become very popular tools. For flexible molecules, computer
simulation of their behavior in solution, either with a detailed atomic description
(molecular dynamics) or based on coarse grain models for longer time scales
(Brownian dynamics), is now a usual tool with a variety of accessible programs for use
by scientists. Finally, a few examples of recent applications of these methodologies for
proteins and polysaccharides are included. With this, we seek to illustrate to nonspecialized
readers the possibilities available today and, hopefully, to encourage them
to find ways to incorporate theoretical models to complement their work.
Bead modeling, Brownian dynamics, Flexible models, HYDRO,
Molecular dynamics, Monte Carlo, Polysaccharides, Proteins, Rigid models.
Departamento de Química Física, Universidad de Murcia, Campus de Espinardo, 30100, Murcia, Spain.