The MIT-Portugal Program has its intellectual foundations in engineering systems and systems thinking. Engineering systems is an emerging field that integrates engineering, management and social sciences to achieve the best possible understanding, design, and implementation of the highly complex, technology-based systems on which society is increasingly dependent. Further, Engineering Systems account for multiple stakeholder perspectives, by exploring flexibility, robustness, scalability, safety, security, durability, sustainability, reliability, quality, recyclability, and maintainability – the "ilities" often left out of traditional analysis, but critical to developing lasting solutions.

Research within fundamentals of Engineering Systems is grouped into the following four clusters of methodologies:

Design and Implementation: spans the disciplines of engineering, logistics, economics and finance, marketing, and human resources to enhance the ways in which ideas and concepts can be materialized into competitive new products or efficient large and multifunctional services and systems. Design research explicitly take into account these functional needs as well as the need to plan for future uncertainties. A holistic design further incorporates implementation and enterprise adoption challenges.

Research in this topic includes: 1) creating new methods and models for requirements development, product architecture and design, and program and project management; 2) improving the various processes associated with design and implementation, including requirements development, product architecture and design, program and project management, and new reliability/robustness/testing methods.

Uncertainty and Dynamics: deals with advanced methods and models to ensure flexibility in systems and thus make it possible to address rapid shifts in societal requirements, technical options, and markets. Large-scale systems inevitably face multidimensional uncertainty over their long lives, from ever-changing technologies to financial and political exigencies to economic globalization; this is part of what creates such great complexity. By building flexibility into the development of major products, adaptation becomes smooth and opportunities are not missed.

Research in this topic includes: 1) identifying the key sources of uncertainty in each particular engineering systems context; 2) modeling and quantifying these uncertainties so that they can be taken into account during design, implementation, and management of the systems; 3) using robust and flexible strategies to design systems in order to both mitigate downside risks and take advantage of upside opportunities; 4) maintaining properties such as safety and resilience as systems change over time. The basic approaches to tackling uncertainty include building in robustness and flexibility.

Networks and Flows: this research is based on the understanding that all engineering systems are characterized by technical, social, and managerial networks and flows. Consider a national electricity grid, or highway network, or air traffic control system. This research must help to create the big-picture view from which the best sustainable solutions to modern challenges can be derived — solutions that address the ongoing lifecycle of system interactions within the network by representing, analyzing, and designing systems as interdependent multilayered networks with multiple types of flows.

Research in this topic is focused on: 1) technical systems, such as power generation plants link to transformers, transmission lines, and consumers; 2) social systems, such as contractual relationships, government policies, and cultural needs affecting the flow of people, goods, and information; 3) or management systems, such as links connecting designers, suppliers, manufacturing plants, warehouses, distribution centers, and retail shops. This research into networks and flows must apply modern graph and network theory to complex systems, but doing so in a way that allows a representation of the dynamics and uncertainties that are most relevant to engineering systems.

Interface of Humans and Technology: examines the ways in which human attitudes and behaviors affect the successful use of technologies, as well as design methodologies that explicitly account for the human interface. The explosion of automated technology and the emergence of complex technological systems have greatly increased the need to support human interaction with these systems. Complex technologies, as the Internet to global positioning systems, are now integral to everyday life, affecting decisions across various domains. However, automated devices distance people from physical control of the action, which can change behaviors and affect safety. Technology can also put new demands on organizations, creating a need for restructuring.

Research in this topic is focused on: 1) illuminating the complex relationship between designers, users, and technology to facilitate the design improvements and effective operation of complex systems; 2) recognizing that human interaction with complex technology has both individual and group elements; 3) developing methodologies and investigating key questions ranging from system design, to human-in-the-loop modeling, to process interventions, and to organizational structures.