Markopoulou is principal at ComplexReal, an interdisciplinary collective tracking sensitive intervention points (SIPs) in the interface between science, technology and culture.

Her Masters group project won the Deutsche Bank Award for Creative Enterprise (Design Category) 2014[2] and was exhibited at the John Lewis Future Store.

[3] In her interdisciplinary paper "The Internal Description of a Causal Set: What the Universe Looks Like from the Inside", Markopoulou instantiates some abstract terms from mathematical category theory to develop straightforward models of space-time.

In 2008, Markopoulou, Tomasz Konopka, Mohammad H. Ansari, and Simone Severini initiated the study of a new background independent model of evolutionary space called quantum graphity.

As described in George Musser's book, Spooky Action at a Distance, in the quantum graphity model, points in spacetime are represented by nodes on a graph connected by links that can be on or off.

[15] With Eric Beinhocker, Doyne Farmer and Steen Rasmussen, Markopoulou participated in the Working Group on The Growing Gap between Social and Physical Technologies.

She co-organized two workshops at SFI to bring together engineers, scientists, writers, historians, lawyers, futurists, economists, philosophers, founders, philanthropists, and policymakers, to identify tracking indicators for such transitions and create roadmaps of scenarios and options.