A three-dimensional memory device includes an alternating stack of insulating layers and electrically conductive layers located over a substrate, memory openings vertically extending through the alternating stack and having lateral protrusions at levels of the electrically conductive layers, and memory opening fill structures located in the memory openings. Each of the memory opening fill structures includes a vertical semiconductor channel, a dielectric material liner laterally surrounding the vertical semiconductor channel, and a vertical stack of discrete memory elements laterally surrounding the dielectric material liner and located within volumes of the lateral protrusions. Each discrete memory element includes a vertical inner sidewall and a convex or stepped outer sidewall.