The endomorphism monoid of a model-theoretic structure carries two interesting topologies: on the one hand, the topology of pointwise convergence induced externally by the action of the endomorphisms on the domain via evaluation; on the other hand, the Zariski topology induced within the monoid by (non-)solutions to equations. For all concrete endomorphism monoids of $\omega $-categorical structures on which the Zariski topology has been analysed thus far, the two topologies were shown to coincide, in turn yielding that the pointwise topology is the coarsest Hausdorff semigroup topology on those endomorphism monoids.

We establish two systematic reasons for the two topologies to agree, formulated in terms of the model-complete core of the structure. Further, we give an example of an $\omega $-categorical structure on whose endomorphism monoid the topology of pointwise convergence and the Zariski topology differ, answering a question of Elliott, Jonušas, Mitchell, Péresse, and Pinsker.

We devise a fairly general sufficient condition ensuring that the endomorphism monoid of a countably infinite ultrahomogeneous structure (i.e. a Fraïssé limit) embeds all countable semigroups. This approach not only provides us with a framework unifying the previous scattered results in this vein, but actually yields new applications for endomorphism monoids of the (rational) Urysohn space and the countable universal ultrahomogeneous semilattice.

We show that if A is a stable basis algebra satisfying the distributivity condition, then B is a reduct of an independence algebra A having the same rank. If this rank is finite, then the endomorphism monoid of B is a left order in the endomorphism monoid of A.

In 1990, Howie and McFadden showed that every proper two-sided ideal of the full transformation monoid $T_n$, the set of all maps from an $n$-set to itself under composition, has a generating set, consisting of idempotents, that is no larger than any other generating set. This fact is a direct consequence of the same property holding in an associated finite $0$-simple semigroup. We show a correspondence between finite $0$-simple semigroups that have this property and bipartite graphs that satisfy a condition that is similar to, but slightly stronger than, Hall's condition. The results are applied in order to recover the above result for the full transformation monoid and to prove the analogous result for the proper two-sided ideals of the monoid of endomorphisms of a finite vector space.

If $A$ is a stable basis algebra of rank $n$, then the set $S_{n-1}$ of endomorphisms of rank at most $n-1$ is a subsemigroup of the endomorphism monoid of $A$. This paper gives a number of necessary and sufficient conditions for $S_{n-1}$ to be generated by idempotents. These conditions are satisfied by finitely generated free modules over Euclidean domains and by free left $T$-sets of finite rank, where $T$ is cancellative monoid in which every finitely generated left ideal is principal.