Processes2015, 3(3), 607-618; doi:10.3390/pr3030607 - published 22 July 2015 Show/Hide Abstract
Abstract: The advent of high throughput -omics has made the accumulation of comprehensive data sets possible, consisting of changes in genes, transcripts, proteins and metabolites. Systems biology-inspired computational methods for translating metabolomics data into fluxomics provide a direct functional, dynamic readout of metabolic networks. When combined with appropriate experimental design, these methods deliver insightful knowledge about cellular function under diverse conditions. The use of computational models accounting for detailed kinetics and regulatory mechanisms allow us to unravel the control and regulatory properties of the fluxome under steady and time-dependent behaviors. This approach extends the analysis of complex systems from description to prediction, including control of complex dynamic behavior ranging from biological rhythms to catastrophic lethal arrhythmias. The powerful quantitative metabolomics-fluxomics approach will help our ability to engineer unicellular and multicellular organisms evolve from trial-and-error to a more predictable process, and from cells to organ and organisms.
Processes2015, 3(3), 568-606; doi:10.3390/pr3030568 - published 16 July 2015 Show/Hide Abstract
Abstract: This contribution concerns the development of generic methods and tools for robust optimal control of high-pressure liquid chromatographic separation processes. The proposed methodology exploits a deterministic robust formulation, that employs a linearization of the uncertainty set, based on Lyapunov differential equations to generate optimal elution trajectories in the presence of uncertainty. Computational tractability is obtained by casting the robust counterpart problem in the framework of bilevel optimal control where the upper level concerns forward simulation of the Lyapunov differential equation, and the nominal open-loop optimal control problem augmented with the robustified target component purity inequality constraint margin is considered in the lower level. The lower-level open-loop optimal control problem, constrained by spatially discretized partial differential equations, is transcribed into a finite dimensional nonlinear program using direct collocation, which is then solved by a primal-dual interior point method. The advantages of the robustification strategy are highlighted through the solution of a challenging ternary complex mixture separation problem for a hydrophobic interaction chromatography system. The study shows that penalizing the changes in the zero-order hold control gives optimal solutions with low sensitivity to uncertainty. A key result is that the robustified general elution trajectories outperformed the conventional linear trajectories both in terms of recovery yield and robustness.
Processes2015, 3(3), 541-567; doi:10.3390/pr3030541 - published 14 July 2015 Show/Hide Abstract
Abstract: A technique for optimizing large-scale differential-algebraic process models under uncertainty using a parallel embedded model approach is developed in this article. A combined multi-period multiple-shooting discretization scheme is proposed, which creates a significant number of independent numerical integration tasks for each shooting interval over all scenario/period realizations. Each independent integration task is able to be solved in parallel as part of the function evaluations within a gradient-based non-linear programming solver. The focus of this paper is on demonstrating potential computation performance improvement when the embedded differential-algebraic equation model solution of the multi-period discretization is implemented in parallel. We assess our parallel dynamic optimization approach on two case studies; the first is a benchmark literature problem, while the second is a large-scale air separation problem that considers a robust set-point transition under parametric uncertainty. Results indicate that focusing on the speed-up of the embedded model evaluation can significantly decrease the overall computation time; however, as the multi-period formulation grows with increased realizations, the computational burden quickly shifts to the internal computation performed within the non-linear programming algorithm. This highlights the need for further decomposition, structure exploitation and parallelization within the non-linear programming algorithm and is the subject for further investigation.
Processes2015, 3(3), 514-539; doi:10.3390/pr3030514 - published 13 July 2015 Show/Hide Abstract
Abstract: The water footprint of energy systems must be considered, as future water scarcity has been identified as a major concern. This work presents a general life cycle network modeling and optimization framework for energy-based products and processes using a functional unit of liters of water consumed in the processing pathway. We analyze and optimize the water-energy nexus over the objectives of water footprint minimization, maximization of economic output per liter of water consumed (economic efficiency of water), and maximization of energy output per liter of water consumed (energy efficiency of water). A mixed integer, multiobjective nonlinear fractional programming (MINLFP) model is formulated. A mixed integer linear programing (MILP)-based branch and refine algorithm that incorporates both the parametric algorithm and nonlinear programming (NLP) subproblems is developed to boost solving efficiency. A case study in bioenergy is presented, and the water footprint is considered from biomass cultivation to biofuel production, providing a novel perspective into the consumption of water throughout the value chain. The case study, optimized successively over the three aforementioned objectives, utilizes a variety of candidate biomass feedstocks to meet primary fuel products demand (ethanol, diesel, and gasoline). A minimum water footprint of 55.1 ML/year was found, economic efficiencies of water range from −$1.31/L to $0.76/L, and energy efficiencies of water ranged from 15.32 MJ/L to 27.98 MJ/L. These results show optimization provides avenues for process improvement, as reported values for the energy efficiency of bioethanol range from 0.62 MJ/L to 3.18 MJ/L. Furthermore, the proposed solution approach was shown to be an order of magnitude more efficient than directly solving the original MINLFP problem with general purpose solvers.
Processes2015, 3(3), 497-513; doi:10.3390/pr3030497 - published 25 June 2015 Show/Hide Abstract
Abstract: The introduction and removal of protecting groups is ubiquitous in multi-step synthetic schemes. From a green chemistry standpoint, however, alternative strategies that employ in situ and reversible protection and deprotection sequences would be attractive. The reversible reactions of CO2 with amines could provide a possible vehicle for realizing this strategy. Herein, we present (1) the products of reaction of benzylamines with CO2 in a variety of solvents with and without the presence of basic additives; (2) new adducts associated with CO2 protected benzylamine in acetonitrile containing 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU); and (3) the intermolecular competitive acylation of benzylamine and benzyl alcohol and the intramolecular competitive acylation of (4-aminomethyl)phenyl) methanol with isopropenyl acetate in acetonitrile containing DBU in the absence and presence of CO2.