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Methods and Tools for the Prediction of Hydrodynamic Coefficients and Other Solution Properties of Flexible Macromolecules in Solution. A Tutorial Minireview
Author(s) -
de la Torre José García,
Ortega Álvaro,
Amorós Diego,
Schmidt Ricardo Rodríguez,
Cifre José G. Hernández
Publication year - 2010
Publication title -
macromolecular bioscience
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.924
H-Index - 105
eISSN - 1616-5195
pISSN - 1616-5187
DOI - 10.1002/mabi.200900464
Subject(s) - monte carlo method , statistical physics , brownian dynamics , analytical ultracentrifugation , molecular dynamics , computer science , parallel tempering , brownian motion , monte carlo molecular modeling , chemistry , physics , computational chemistry , mathematics , markov chain monte carlo , ultracentrifuge , statistics , chromatography , quantum mechanics
The calculation of solution properties of flexible macromolecules and other nanoparticles requires, in addition to the hydrodynamic formalisms needed for the sedimentation coefficient and other transport properties, the consideration of the conformational statistics and internal dynamics. The latter aspects can be handled with simulation methods like Monte Carlo and Brownian dynamics. An example of a Monte Carlo simulation for a model specific of DNA is illustrated with results for the several solution properties over an extremely wide range of molecular weight. The convenience of having computational tools of a quite general applicability has prompted us to implement the simulation and hydrodynamic treatments in software packages, MONTEHYDRO for Monte Carlo, and SIMUFLEX for Brownian dynamics which—with a scope similar to the HYDRO suite for rigid particles—can handle a variety of situations. As an application of the new methodology to a yet unclear problem in analytical ultracentrifugation, in a simple application of the SIMUFLEX software, we present a simulation of the so‐called anomalous sedimentation of very long DNA molecules, obtaining results for the experimentally observable rotor‐speed‐dependence of the sedimentation coefficient.