Coarse-grained molecular dynamics and continuum models for the transport of protein molecules

Marco Bacci (1)

1 DICeA - Dipartimento di Ingegneria Civile e Ambientale

We describe protein transport across nanopores in a coarse-grained modeling. Numerical results reproduce a rich phenomenology, from fast transport to long blockades. Main translocation features are maintained in a 1D description of the process in an appropriate potential of the mean force. A second-rank tensor is selected as descriptor of the molecular shape. Its dynamics is identified by a power-equivalence procedure and Cauchy-Born rule. The modeling is supplemented by heuristic approaches that appear adequate also in unconstrained dynamics.

Mots clés: complex materials; translocation; stall; molecular dynamics; free; energy; langevin; continuum model; complex materials.

Domaines: Analyse numérique [math.NA]; Mécanique [physics]; Sciences de l'ingénieur [physics]

Marco Bacci. Coarse-grained molecular dynamics and continuum models for the transport of protein molecules. 2nd ECCOMAS Young Investigators Conference (YIC 2013), Sep 2013, Bordeaux, France. ⟨hal-00855844⟩