Chaperonin-facilitated protein folding: optimization of rate and yield by an iterative annealing mechanism.

We develop a heuristic model for chaperonin-facilitated protein folding, the iterative annealing mechanism, based on theoretical descriptions of "rugged" conformational free energy landscapes for protein folding, and on experimental evidence that (i) folding proceeds by a nucleation mechanism whereby correct and incorrect nucleation lead to fast and slow folding kinetics, respectively, and (ii) chaperonins optimize the rate and yield of protein folding by an active ATP-dependent process. The chaperonins GroEL and GroES catalyze the folding of ribulose bisphosphate carboxylase at a rate proportional to the GroEL concentration. Kinetically trapped folding-incompetent conformers of ribulose bisphosphate carboxylase are converted to the native state in a reaction involving multiple rounds of quantized ATP hydrolysis by GroEL. We propose that chaperonins optimize protein folding by an iterative annealing mechanism; they repeatedly bind kinetically trapped conformers, randomly disrupt their structure, and release them in less folded states, allowing substrate proteins multiple opportunities to find pathways leading to the most thermodynamically stable state. By this mechanism, chaperonins greatly expand the range of environmental conditions in which folding to the native state is possible. We suggest that the development of this device for optimizing protein folding was an early and significant evolutionary event.

A novel hybrid simulation-optimization approach for the optimal design of multicomponent distillation columns

Póster presentado en Escape 22, European Symposium on Computer Aided Process Engineering, University College London, UK, 17-20 June 2012.

Combined simulation-optimization methodology for the design of environmental conscious absorption systems

This work addresses the optimization of ammonia–water absorption cycles for cooling and refrigeration applications with economic and environmental concerns. Our approach combines the capabilities of process simulation, multi-objective optimization (MOO), cost analysis and life cycle assessment (LCA). The optimization task is posed in mathematical terms as a multi-objective mixed-integer nonlinear program (moMINLP) that seeks to minimize the total annualized cost and environmental impact of the cycle. This moMINLP is solved by an outer-approximation strategy that iterates between primal nonlinear programming (NLP) subproblems with fixed binaries and a tailored mixed-integer linear programming (MILP) model. The capabilities of our approach are illustrated through its application to an ammonia–water absorption cycle used in cooling and refrigeration applications.

Some examples of modeling in chemical engineering: thermal treatment of polymers, phase equilibrium calculations and process design

Presentation submitted to PSE Seminar, Chemical Engineering Department, Center for Advanced Process Design-making (CAPD), Carnegie Mellon University, Pittsburgh (USA), October 2012.

A hybrid simulation-optimization approach for the design of internally heat-integrated distillation columns

Paper submitted to AIChE 2012 Annual Meeting: Energy Efficiency by Process Intensification, Pittsburgh, PA, October 28-November 2, 2012.

Hybrid simulation-optimization based approach for the optimal design of single-product biotechnological processes

In this work, we present a systematic method for the optimal development of bioprocesses that relies on the combined use of simulation packages and optimization tools. One of the main advantages of our method is that it allows for the simultaneous optimization of all the individual components of a bioprocess, including the main upstream and downstream units. The design task is mathematically formulated as a mixed-integer dynamic optimization (MIDO) problem, which is solved by a decomposition method that iterates between primal and master sub-problems. The primal dynamic optimization problem optimizes the operating conditions, bioreactor kinetics and equipment sizes, whereas the master levels entails the solution of a tailored mixed-integer linear programming (MILP) model that decides on the values of the integer variables (i.e., number of equipments in parallel and topological decisions). The dynamic optimization primal sub-problems are solved via a sequential approach that integrates the process simulator SuperPro Designer® with an external NLP solver implemented in Matlab®. The capabilities of the proposed methodology are illustrated through its application to a typical fermentation process and to the production of the amino acid L-lysine.

Logic hybrid simulation-optimization algorithm for distillation design

In this paper, we propose a novel algorithm for the rigorous design of distillation columns that integrates a process simulator in a generalized disjunctive programming formulation. The optimal distillation column, or column sequence, is obtained by selecting, for each column section, among a set of column sections with different number of theoretical trays. The selection of thermodynamic models, properties estimation etc., are all in the simulation environment. All the numerical issues related to the convergence of distillation columns (or column sections) are also maintained in the simulation environment. The model is formulated as a Generalized Disjunctive Programming (GDP) problem and solved using the logic based outer approximation algorithm without MINLP reformulation. Some examples involving from a single column to thermally coupled sequence or extractive distillation shows the performance of the new algorithm.

An alternative disjunctive optimization model for heat integration with variable temperatures

This paper presents an alternative model to deal with the problem of optimal energy consumption minimization of non-isothermal systems with variable inlet and outlet temperatures. The model is based on an implicit temperature ordering and the “transshipment model” proposed by Papoulias and Grossmann (1983). It is supplemented with a set of logical relationships related to the relative position of the inlet temperatures of process streams and the dynamic temperature intervals. In the extreme situation of fixed inlet and outlet temperatures, the model reduces to the “transshipment model”. Several examples with fixed and variable temperatures are presented to illustrate the model's performance.

Mathematical programming model for heat exchanger design through optimization of partial objectives

Mathematical programming can be used for the optimal design of shell-and-tube heat exchangers (STHEs). This paper proposes a mixed integer non-linear programming (MINLP) model for the design of STHEs, following rigorously the standards of the Tubular Exchanger Manufacturers Association (TEMA). Bell–Delaware Method is used for the shell-side calculations. This approach produces a large and non-convex model that cannot be solved to global optimality with the current state of the art solvers. Notwithstanding, it is proposed to perform a sequential optimization approach of partial objective targets through the division of the problem into sets of related equations that are easier to solve. For each one of these problems a heuristic objective function is selected based on the physical behavior of the problem. The global optimal solution of the original problem cannot be ensured even in the case in which each of the sub-problems is solved to global optimality, but at least a very good solution is always guaranteed. Three cases extracted from the literature were studied. The results showed that in all cases the values obtained using the proposed MINLP model containing multiple objective functions improved the values presented in the literature.

Simultaneous environmental and economic process synthesis of Isobutane Alkylation

This multidisciplinary study concerns the optimal design of processes with a view to both maximizing profit and minimizing environmental impacts. This can be achieved by a combination of traditional chemical process design methods, measurements of environmental impacts and advanced mathematical optimization techniques. More to the point, this paper presents a hybrid simulation-multiobjective optimization approach that at once optimizes the production cost and minimizes the associated environmental impacts of isobutane alkylation. This approach has also made it possible to obtain the flowsheet configurations and process variables that are needed to manufacture isooctane in a way that satisfies the above-stated double aim. The problem is formulated as a Generalized Disjunctive Programming problem and solved using state-of-the-art logic-based algorithms. It is shown, starting from existing alternatives for the process, that it is possible to systematically generate a superstructure that includes alternatives not previously considered. The optimal solution, in the form a Pareto curve, includes different structural alternatives from which the most suitable design can be selected. To evaluate the environmental impact, Life Cycle Assessment based on two different indicators is employed: Ecoindicator 99 and Global Warming Potential.

Fault tolerant embedded systems design by multi-objective optimization

The design of fault tolerant systems is gaining importance in large domains of embedded applications where design constrains are as important as reliability. New software techniques, based on selective application of redundancy, have shown remarkable fault coverage with reduced costs and overheads. However, the large number of different solutions provided by these techniques, and the costly process to assess their reliability, make the design space exploration a very difficult and time-consuming task. This paper proposes the integration of a multi-objective optimization tool with a software hardening environment to perform an automatic design space exploration in the search for the best trade-offs between reliability, cost, and performance. The first tool is commanded by a genetic algorithm which can simultaneously fulfill many design goals thanks to the use of the NSGA-II multi-objective algorithm. The second is a compiler-based infrastructure that automatically produces selective protected (hardened) versions of the software and generates accurate overhead reports and fault coverage estimations. The advantages of our proposal are illustrated by means of a complex and detailed case study involving a typical embedded application, the AES (Advanced Encryption Standard).

MINLP Optimization Algorithm for the Synthesis of Heat and Work Exchange Networks

This paper introduces a new optimization model for the simultaneous synthesis of heat and work exchange networks. The work integration is performed in the work exchange network (WEN), while the heat integration is carried out in the heat exchanger network (HEN). In the WEN synthesis, streams at high-pressure (HP) and low-pressure (LP) are subjected to pressure manipulation stages, via turbines and compressors running on common shafts and stand-alone equipment. The model allows the use of several units of single-shaft-turbine-compressor (SSTC), as well as helper motors and generators to respond to any shortage and/or excess of energy, respectively, in the SSTC axes. The heat integration of the streams occurs in the HEN between each WEN stage. Thus, as the inlet and outlet streams temperatures in the HEN are dependent of the WEN design, they must be considered as optimization variables. The proposed multi-stage superstructure is formulated in mixed-integer nonlinear programming (MINLP), in order to minimize the total annualized cost composed by capital and operational expenses. A case study is conducted to verify the accuracy of the proposed approach. The results indicate that the heat integration between the WEN stages is essential to enhance the work integration, and to reduce the total cost of process due the need of a smaller amount of hot and cold utilities.

MINLP Model for the Synthesis of Heat Exchanger Networks with Handling Pressure of Process Streams

This paper introduces a new mathematical model for the simultaneous synthesis of heat exchanger networks (HENs), wherein the handling pressure of process streams is used to enhance the heat integration. The proposed approach combines generalized disjunctive programming (GDP) and mixed-integer nonlinear programming (MINLP) formulation, in order to minimize the total annualized cost composed by operational and capital expenses. A multi-stage superstructure is developed for the HEN synthesis, assuming constant heat capacity flow rates and isothermal mixing, and allowing for streams splits. In this model, the pressure and temperature of streams must be treated as optimization variables, increasing further the complexity and difficulty to solve the problem. In addition, the model allows for coupling of compressors and turbines to save energy. A case study is performed to verify the accuracy of the proposed model. In this example, the optimal integration between the heat and work decreases the need for thermal utilities in the HEN design. As a result, the total annualized cost is also reduced due to the decrease in the operational expenses related to the heating and cooling of the streams.

Logic-Based Outer-Approximation Algorithm for Solving Discrete-Continuous Dynamic Optimization Problems

We present an extension of the logic outer-approximation algorithm for dealing with disjunctive discrete-continuous optimal control problems whose dynamic behavior is modeled in terms of differential-algebraic equations. Although the proposed algorithm can be applied to a wide variety of discrete-continuous optimal control problems, we are mainly interested in problems where disjunctions are also present. Disjunctions are included to take into account only certain parts of the underlying model which become relevant under some processing conditions. By doing so the numerical robustness of the optimization algorithm improves since those parts of the model that are not active are discarded leading to a reduced size problem and avoiding potential model singularities. We test the proposed algorithm using three examples of different complex dynamic behavior. In all the case studies the number of iterations and the computational effort required to obtain the optimal solutions is modest and the solutions are relatively easy to find.

X lberoamerican Conference on Phase Equilibria and Fluid Properties for Process Design (EQUIFASE): June 28-July 1, 2015 - Alicante (Spain): Book of Abstracts

The general purpose of the EQUIFASE Conference is to promote the Scientific and Technologic exchange between people from both the academic and the industrial environment in the field of Phase Equilibria and Thermodynamic Properties for the Design of Chemical Processes. Topics: Measurement of Thermodynamic Properties. Phase Equilibria and Chemical Equilibria. Theory and Modelling. Alternative Solvents. Supercritical Fluids. Ionic Liquids. Energy. Gas and oil. Petrochemicals. Environment and sustainability. Biomolecules and Biotechnology. Product and Process Design. Databases and Software. Education.