The common thread of the research in the C. Maranas Chemical & Biological Systems Optimization Laboratory at PSU is the development of algorithmic and, in particular, optimization techniques to support the analysis and redesign of systems at different scales. On a micro-scale, the goal is to systematically analyze the organizational principles and redesign biological systems such as proteins, metabolic pathways, signaling networks and synthetic circuits. Additional areas of interest include the design of product molecules involving optimal levels of physical, chemical and physiological properties while accounting for process considerations. On a macro-scale, the objective is to optimally design, plan and operate manufacturing plants and their accompanying supply chains as well as use real option concepts in R&D pharma planning and emissions trading applications. A unifying feature of these seemingly disparate research targets is the need to systematically search through many network configurations, protein structures, molecular architectures, DNA sequences and/or chemical plant and supply chain configurations, etc. and identify the “best” one. To this end, the development of efficient theoretical, algorithmic and computational techniques for arriving at relevant as well as theoretically sound results while maximizing computational efficiency is pursued.

Computational Analyses in Protein Engineering

Computational Protein Library Design Using Atomistic Potential Energy Functions

Computational Protein Library Optimization Using Scoring Functions or Clash Maps

Modeling and Optimization of Directed Evolution Protocols

Analysis & Redesign of Biological Pathways and Networks

Computational Procedures for Strain Optimization Using Stoichiometric Models of Metabolism

Analysis of Network Properties of Metabolic Models

Elucidation of Metabolic Fluxes using Labeled Isotopes

Analysis and Redesign for Kinetic Models of Metabolism

Analysis and Redesign of Signaling Networks

Hierarchical methods for Regulatory Network Inference

Optimal Decision Making in Product & Process Planning

Design and Scheduling Real Options based Planning

Supply Chain Planning and CPI Design and Scheduling

Design of Molecular Products with Optimal Properties

Current Sponsors