We propose a continuum model for the description of the dynamics of isolated macromolecules. A second-rank tensor describes the macromolecular shape. We identify the action occurring along the molecular dynamics by imposing power equivalence between the discrete and continuum schemes, on the basis of a pertinet expression of the Cauchy-Born rule. We compare molecular dynamics stretching simulations with the continuum model starting from discrete toy schemes, going on with increasing complexity, and ending with the analysis of the Ubiquitin protein. We show that the proposed model is appropriate for the analysis of constrained dy- namics of interest in laboratory experiments, such as protein mechanical unfolding driven by atomic-force microscopy.
Protein dynamics: An approach based on the Cauchy–Born rule / Marco Bacci; Paolo Maria Mariano. - In: PHYSICA E-LOW-DIMENSIONAL SYSTEMS & NANOSTRUCTURES. - ISSN 1386-9477. - STAMPA. - 61:(2014), pp. 69-82. [10.1016/j.physe.2014.03.009]
Protein dynamics: An approach based on the Cauchy–Born rule
Paolo Maria Mariano
2014
Abstract
We propose a continuum model for the description of the dynamics of isolated macromolecules. A second-rank tensor describes the macromolecular shape. We identify the action occurring along the molecular dynamics by imposing power equivalence between the discrete and continuum schemes, on the basis of a pertinet expression of the Cauchy-Born rule. We compare molecular dynamics stretching simulations with the continuum model starting from discrete toy schemes, going on with increasing complexity, and ending with the analysis of the Ubiquitin protein. We show that the proposed model is appropriate for the analysis of constrained dy- namics of interest in laboratory experiments, such as protein mechanical unfolding driven by atomic-force microscopy.File | Dimensione | Formato | |
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