  The atomistic mechanisms during lithiation and delithiation of amorphous Si
nanowires ($a$-SiNW) have been investigated over cycles by molecular dynamics
simulations. First, the Modified Embedded Atom Method (MEAM) potential from Cui
et al. [J. Power Sources. 2012, (207) 150] has been further optimized on static
(Li$_x$Si alloy phases and point defect energies) and on dynamic properties (Li
diffusion) to reproduce the lithiation of small crystalline Si nanowires
calculated at the {\it ab initio} level. The lithiation of $a$-SiNW reveals a
two-phase process of lithiation with a larger diffusion interface compared to
crystalline Si lithiation. Compressive axial stresses are observed in the
amorphous Si$_x$Li alloy outer shell. They are easily released thanks to the
soft glassy behavior of the amorphous alloy. Conversely, in crystalline SiNW,
the larger stress in the narrow crystalline lithiated interface is hardly
released and requires a phase transformation to amorphous to operate, which
delays the lithiation. The history of the charge-discharge cycles as well as
the temperature appear as driving forces for phase transformation from
amorphous Li$_x$Si alloy to the more stable crystalline phase counterpart. Our
work suggest that a full delithiation could heal the SiNWs to improve the life
cycles of Li-ion batteries with Si anode.
