Research challenges, opportunities and synergism in systems engineering and computational biology

Abstract

During the last three decades, the research area of systems engineering has emerged as a domain of fundamental importance and major impact within chemical engineering, as well as a cornerstone area in interdisciplinary research initiatives with computer science, operations research, applied mathematics, materials and life sciences. This is attributed to the unique characteristics of systems engineering which are the combination of analysis and synthesis for the design, optimization, and operation of processes and products. The product and process discovery research efforts are founded on fundamental advances in mathematical modeling, optimization theory and algorithms, and insights derived either from existing operations and/or from biology, chemistry, and physics. The fundamental advances are epitomized through new theoretical, algorithmic, and modeling frameworks for (a) mixed-integer linear and nonlinear optimization, (b) deterministic global optimization, and (c) dynamic simulation and optimization. The proposed modeling and optimization approaches have multiscale applications ranging from macroscopic to mesoscopic to microscopic systems, and which provide a natural and fundamental link between systems engineering, computational chemistry, computational biology and systems biology. Approaches based on mixed-integer linear and nonlinear optimization which were typically identified with process synthesis, scheduling and planning applications, have entered the domains of gene regulatory networks, metabolic networks, signal transduction networks, beta-sheet topology prediction in proteins, de novo peptide and protein design, DNA recombination, phase problem in X-ray crystallography, side chain optimization in protein prediction, peptide identification via tandem mass spectroscopy. Approaches based on deterministic global optimization associated with process design, synthesis, scheduling, and pooling/blending applications, are now in the main stream of product design, structure prediction in protein folding, dynamics of protein folding, NMR protein structure refinement, and de novo protein design. Approaches based on dynamic models and large scale optimization which were identified with process models and their applications, are suited for metabolic and signal transduction networks. As a result, a synergism between systems engineering, computational biology, and systems biology has evolved gradually, opened new research avenues and has reached the stage where fascinating research contributions address important questions in computational biology with methods and tools from systems engineering which combine mathematical rigor with key biological insights. This article provides a perspective on the challenges and opportunities that emerge from the fundamental developments in the research fields of systems engineering and computational biology. The advances in the areas of deterministic global optimization and process scheduling are introduced first, followed by their respective research opportunities. The revolution of genomics is discussed next with a particular focus on the advances and challenges in the areas of structure prediction in protein folding, de novo peptide and protein design, and peptide and protein identification via tandem mass spectroscopy. This article is based on material presented as an invited talk at the session on “The Future of Chemical Engineering Research III” during the 2004 annual AIChE meeting.