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Is there any relationship between both definitions of minimal models? (the couple of definitions I know are the one mentioned in Lefèvre's thesis, in the sense that the differential is zero, and the other in Tamaroff's article, which agrees with Loday-Vallette's book Algebraic Operads). Of course the second definition is only restricted to dg algebras, while first one covers the more general concept of $A_{\infty}$-algebras.

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The two definitions are the same. The thesis of Lefèvre-Hasegawa does not require the differential to be zero, it requires the component $m_1$ of the differential to be equal to zero: minimality translates as not having linear part. This is of course the same definition as used in the article of Tamaroff and the book of Loday and Vallette.

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The way you can see the definitions are the same is by noting that one can pack up an $A_\infty$-algebra $(A,\mu_1,\mu_2,\ldots)$ into its bar construction $(BA,d)$ (or, dually, as in the article you refer to, pack up an $A_\infty$-coalgebra into a cobar construction, which is a free algebra).

Then the linear part of $d$ is precisely (a suspension) of $\mu_1$ and the condition that $d(V)\subseteq V^{\geqslant 2}$ is equivalent to the linear part of $d$ being zero. The $A_\infty$ interpretation is given by Lefèvre-Hasegawa, while the one using free (or cofree nilpotent co)algebras is in the book and article you refer to.

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