Pedro Castro - Academia.edu (original) (raw)

Papers by Pedro Castro

Cellular and molecular life sciences : CMLS, 2012

Protein post-translational modifications diversify the proteome and install new regulatory levels... more Protein post-translational modifications diversify the proteome and install new regulatory levels that are crucial for the maintenance of cellular homeostasis. Over the last decade, the ubiquitin-like modifying peptide small ubiquitin-like modifier (SUMO) has been shown to regulate various nuclear processes, including transcriptional control. In plants, the sumoylation pathway has been significantly implicated in the response to environmental stimuli, including heat, cold, drought, and salt stresses, modulation of abscisic acid and other hormones, and nutrient homeostasis. This review focuses on the emerging importance of SUMO in the abiotic stress response, summarizing the molecular implications of sumoylation and emphasizing how high-throughput approaches aimed at identifying the full set of SUMO targets will greatly enhance our understanding of the SUMO-abiotic stress association.

Computers & Chemical Engineering, 2008

This study addresses the work developed at Process Integration Group of CPQ to build a software t... more This study addresses the work developed at Process Integration Group of CPQ to build a software tool in the area of Pollution Prevention, regarding the Mass-Exchange Networks (MEN) targeting and design.Given a set of mass transfer operations and their limiting data, AquoMin can analyse different options to reduce fresh water consumption and minimise wastewater production. The available strategies to optimise

Insect Conservation and Diversity, 2008

1. A thorough inventory of a Mediterranean oak forest spider fauna carried out during 2 weeks is ... more 1. A thorough inventory of a Mediterranean oak forest spider fauna carried out during 2 weeks is presented. It used a semi-quantitative sampling protocol to collect comparable data in a rigorous, rapid and efficient way. Four hundred and eighty samples of one person-hour of work each were collected, mostly inside a delimited 1-ha plot.

Chemical Engineering Science, 1999

This paper addresses minimum utility cost mass-exchange network design by considering the special... more This paper addresses minimum utility cost mass-exchange network design by considering the special case of water minimisation. Two different situations are considered, re-use and regeneration re-use for single contaminants. For re-use, three different methods of targeting are presented, one of them being simultaneously a design method. This novel design method has the advantage of considering flowrate constraints only in the final stage of design. The concept of multiple pinches is introduced to prevent designing networks that do not lead to minimum cost distributed effluent treatment systems. For regeneration re-use, this paper presents the first known algorithm for targeting minimum water consumption in all possible situations. The targeted flowrate is then used to design the mass-exchange network, that almost always features splitting of operations.

Computers & Operations Research, 2015

ABSTRACT

Journal of Controlled Release, 2015

Therapeutic proteins and peptides demonstrate unique, peerless, pharmacological characteristics s... more Therapeutic proteins and peptides demonstrate unique, peerless, pharmacological characteristics such as high specificity to receptors and superior biological mimicking of physiological mechanisms, resulting in a better therapeutic index compared to conventional chemical-derived drugs. However, proteins also present inherent bioavailability limitations. Thus, this paper proposes several effective tools to improve protein/peptide drugs stability, permeability and pharmacokinetics with special emphasis on oral polymeric films as oral delivery platforms. Indeed, oral films present inherent characteristics that can greatly enhance biological performance of proteins and peptides and patient compliance along with other advantages that are critically discussed in this review. A rational choice of excipients addressed in and manufacture processes are also focused. In addition, possible toxicity issues to be overtaken and critical analysis regarding current market tendencies respecting oral films and protein/peptides along with future prospects are disclosed.

We propose two mixed-integer linear programming based approaches for the 2D orthogonal strip pack... more We propose two mixed-integer linear programming based approaches for the 2D orthogonal strip packing problem. Using knowledge from the alternative forms of time representation in scheduling formulations, we show how to efficiently combine three different concepts into the x-and y-dimensions. One model features a discrete representation on the x-axis (strip width) and a continuous representation with general precedence variables on the y-axis (strip height). The other features a full continuous-space representation with the same approach for the y-axis and a single non-uniform grid made up of slots for the x-axis. Through the solution of a set of twenty nine instances from the literature, we show that the former is a better approach, even when compared to three alternative MILP models ranging from a pure discretespace to a pure continuous-space with precedence variables in both dimensions. All models are available in www.minlp.org.

This paper present a dynamic model compiled in gPROMS that describes the hydrogen production via ... more This paper present a dynamic model compiled in gPROMS that describes the hydrogen production via the catalytic hydrolysis reactions of sodium borohydride (NaBH4) solutions. It extends our previous work for the self-hydrolysis of NaBH4 [1], with the addition of a modified version of Davis et al. [2] empirical correlation to describe the reaction mechanism limiting step rate. The kinetic parameters

This paper presents a new algorithm for the scheduling of batch plants with a large number of ord... more This paper presents a new algorithm for the scheduling of batch plants with a large number of orders and sequence-dependent changeovers. Such problems are either intractable or yield poor solutions with full-space approaches. We use decomposition on the entire set of orders and derive the complete schedule in several iterations. The key idea is to allow for partial rescheduling without altering the main decisions in terms of unit assignments and sequencing, so that the complexity is kept at a manageable level. It has been implemented with a unit-specific continuous-time model and tested for different decomposition settings. The results show that a real-life 50-order, 17-unit, 6stage problem can effectively be solved in roughly 6 minutes of computational time.

This work addresses the scheduling of continuous single-stage multiproduct plants with energy int... more This work addresses the scheduling of continuous single-stage multiproduct plants with energy intensive processing tasks and time-dependent electricity cost and power supply. A new rolling horizon algorithm is proposed that consists of a planning model to predict the production levels and a continuous-time model for detailed scheduling. The results from a set of test problems from the literature show that the algorithm can generate global optimal solutions much more rapidly than standalone discrete or continuous-time formulations in problems involving unlimited power availability.

Resources, Conservation and Recycling, 2007

This paper presents a new approach for the optimal design of wastewater treatment systems. An alg... more This paper presents a new approach for the optimal design of wastewater treatment systems. An algorithm that can be divided in two parts is proposed for finding global optimal solutions to the problem. The first part comprises a new linear program formulation that is used to generate good starting points for the solution of the general non-linear program (second part).

International Journal of Production Research, 2014

ABSTRACT Flowshop scheduling problems have been extensively studied by several authors using diff... more ABSTRACT Flowshop scheduling problems have been extensively studied by several authors using different approaches. A typical flowshop process consists of successive manufacturing stages arranged in a single production line where different jobs have to be processed following a predefined production recipe. In this work, the scheduling of a complex flowshop process involving automated wet-etch station from semiconductor manufacturing systems requires a proper synchronisation of processing and transport operations, due to stringent storage policies and fixed transfer times between stages. Robust hybrid solution strategies based on mixed integer linear programming formulations and heuristic-based approaches, such as aggregation and decomposition methods, are proposed and illustrated on industrial-scale problems. The results show significant improvements in solution quality coupled with a reduced computational effort compared to other existing methodologies.

Industrial & Engineering Chemistry Research, 2013

ABSTRACT In today’s energy markets, there is a growing effort toward the alignment of the industr... more ABSTRACT In today’s energy markets, there is a growing effort toward the alignment of the industrial sector and the power grid for the sake of efficient energy distribution and consumption. In this paper, the resource–task network is used to provide a generic modeling framework for production scheduling under energy constraints. Three alternative process models for the energy-intensive melt shop of a steel plant are proposed and linked to a discrete-time formulation. The results show a trade-off between accurate representation of problem data and computational performance. By keeping track of the total energy and power consumption through time, we study the impact of fluctuating energy prices on the scheduling of operations and the economic benefits that can be obtained from the plant’s participation in the price- and incentive-based industrial demand side management programs.

Computers & Chemical Engineering, 2014

ABSTRACT

Computers & Chemical Engineering, 2011

This work addresses the scheduling of continuous single stage multiproduct plants with parallel u... more This work addresses the scheduling of continuous single stage multiproduct plants with parallel units and shared storage tanks. Processing tasks are energy intensive and we consider timedependent electricity pricing and availability together with multiple intermediate due dates, handled as hard constraints. A new discrete-time aggregate formulation is proposed to rapidly plan the production levels. It is combined with a continuous-time model for detailed scheduling as the essential part of a rolling horizon algorithm. Their computational performance is compared to traditional discrete and continuous-time full-space formulations with all models relying on the Resource-Task Network (RTN) process representation. The results show that new models and algorithm can generate global optimal schedules much more efficiently than their counterparts in problems involving unlimited power availability. Under restricted power, the aggregate model  =amount continuously sent to storage by task i during interval t [ton]

AIChE Journal, 2011

This paper presents a new algorithm for the near optimal scheduling of multistage batch plants wi... more This paper presents a new algorithm for the near optimal scheduling of multistage batch plants with a large number of orders and sequence-dependent changeovers. Such problems are either intractable when solved with full-space approaches or poor solutions result. We use decomposition on the entire set of orders and derive the complete schedule in several iterations, by inserting a couple of orders at a time. The key idea is to allow for partial rescheduling of previously scheduled orders without altering the unit assignment and sequencing decisions, so that the combinatorial complexity is kept at a manageable level. The algorithm has been implemented for three alternative continuous-time mixed integer linear programming models and tested through the solution of ten 2 example problems for different decomposition settings. The results show that an industrial-size scheduling problem with 50-orders, 17-units distributed over 6-stages can effectively be solved in roughly 6 minutes of computational time.

AIChE Journal, 2009

... Email: Pedro M. Castro (pedro.castro@ineti.pt). *Correspondence: Pedro M. Castro, Dept. de Mo... more ... Email: Pedro M. Castro (pedro.castro@ineti.pt). *Correspondence: Pedro M. Castro, Dept. de Modelação e Simulação de Processos, Instituto Nacional de Engenharia, Tecnologia e Inovação, 1649-038 Lisboa, Portugal. Publication History. ...

ABSTRACT This paper gives a review on existing scheduling methodologies developed for process ind... more ABSTRACT This paper gives a review on existing scheduling methodologies developed for process industries. Above all, the aim of the paper is to focus on the industrial aspects of scheduling and discuss the main characteristics, including strengths and weaknesses of the presented approaches. It is claimed that optimization tools of today can effectively support the plant level production. However there is still clear potential for improvements, especially in transferring academic results into industry. For instance, usability, interfacing and integration are some aspects discussed in the paper. After the introduction and problem classification, the paper discusses some lessons learned from industry, provides an overview of models and methods and concludes with general guidelines and examples on the modeling and solution of industrial problems.

Cellular and molecular life sciences : CMLS, 2012

Protein post-translational modifications diversify the proteome and install new regulatory levels... more Protein post-translational modifications diversify the proteome and install new regulatory levels that are crucial for the maintenance of cellular homeostasis. Over the last decade, the ubiquitin-like modifying peptide small ubiquitin-like modifier (SUMO) has been shown to regulate various nuclear processes, including transcriptional control. In plants, the sumoylation pathway has been significantly implicated in the response to environmental stimuli, including heat, cold, drought, and salt stresses, modulation of abscisic acid and other hormones, and nutrient homeostasis. This review focuses on the emerging importance of SUMO in the abiotic stress response, summarizing the molecular implications of sumoylation and emphasizing how high-throughput approaches aimed at identifying the full set of SUMO targets will greatly enhance our understanding of the SUMO-abiotic stress association.

Computers & Chemical Engineering, 2008

This study addresses the work developed at Process Integration Group of CPQ to build a software t... more This study addresses the work developed at Process Integration Group of CPQ to build a software tool in the area of Pollution Prevention, regarding the Mass-Exchange Networks (MEN) targeting and design.Given a set of mass transfer operations and their limiting data, AquoMin can analyse different options to reduce fresh water consumption and minimise wastewater production. The available strategies to optimise

Insect Conservation and Diversity, 2008

1. A thorough inventory of a Mediterranean oak forest spider fauna carried out during 2 weeks is ... more 1. A thorough inventory of a Mediterranean oak forest spider fauna carried out during 2 weeks is presented. It used a semi-quantitative sampling protocol to collect comparable data in a rigorous, rapid and efficient way. Four hundred and eighty samples of one person-hour of work each were collected, mostly inside a delimited 1-ha plot.

Chemical Engineering Science, 1999

This paper addresses minimum utility cost mass-exchange network design by considering the special... more This paper addresses minimum utility cost mass-exchange network design by considering the special case of water minimisation. Two different situations are considered, re-use and regeneration re-use for single contaminants. For re-use, three different methods of targeting are presented, one of them being simultaneously a design method. This novel design method has the advantage of considering flowrate constraints only in the final stage of design. The concept of multiple pinches is introduced to prevent designing networks that do not lead to minimum cost distributed effluent treatment systems. For regeneration re-use, this paper presents the first known algorithm for targeting minimum water consumption in all possible situations. The targeted flowrate is then used to design the mass-exchange network, that almost always features splitting of operations.

Computers & Operations Research, 2015

ABSTRACT

Journal of Controlled Release, 2015

Therapeutic proteins and peptides demonstrate unique, peerless, pharmacological characteristics s... more Therapeutic proteins and peptides demonstrate unique, peerless, pharmacological characteristics such as high specificity to receptors and superior biological mimicking of physiological mechanisms, resulting in a better therapeutic index compared to conventional chemical-derived drugs. However, proteins also present inherent bioavailability limitations. Thus, this paper proposes several effective tools to improve protein/peptide drugs stability, permeability and pharmacokinetics with special emphasis on oral polymeric films as oral delivery platforms. Indeed, oral films present inherent characteristics that can greatly enhance biological performance of proteins and peptides and patient compliance along with other advantages that are critically discussed in this review. A rational choice of excipients addressed in and manufacture processes are also focused. In addition, possible toxicity issues to be overtaken and critical analysis regarding current market tendencies respecting oral films and protein/peptides along with future prospects are disclosed.

We propose two mixed-integer linear programming based approaches for the 2D orthogonal strip pack... more We propose two mixed-integer linear programming based approaches for the 2D orthogonal strip packing problem. Using knowledge from the alternative forms of time representation in scheduling formulations, we show how to efficiently combine three different concepts into the x-and y-dimensions. One model features a discrete representation on the x-axis (strip width) and a continuous representation with general precedence variables on the y-axis (strip height). The other features a full continuous-space representation with the same approach for the y-axis and a single non-uniform grid made up of slots for the x-axis. Through the solution of a set of twenty nine instances from the literature, we show that the former is a better approach, even when compared to three alternative MILP models ranging from a pure discretespace to a pure continuous-space with precedence variables in both dimensions. All models are available in www.minlp.org.

This paper present a dynamic model compiled in gPROMS that describes the hydrogen production via ... more This paper present a dynamic model compiled in gPROMS that describes the hydrogen production via the catalytic hydrolysis reactions of sodium borohydride (NaBH4) solutions. It extends our previous work for the self-hydrolysis of NaBH4 [1], with the addition of a modified version of Davis et al. [2] empirical correlation to describe the reaction mechanism limiting step rate. The kinetic parameters

This paper presents a new algorithm for the scheduling of batch plants with a large number of ord... more This paper presents a new algorithm for the scheduling of batch plants with a large number of orders and sequence-dependent changeovers. Such problems are either intractable or yield poor solutions with full-space approaches. We use decomposition on the entire set of orders and derive the complete schedule in several iterations. The key idea is to allow for partial rescheduling without altering the main decisions in terms of unit assignments and sequencing, so that the complexity is kept at a manageable level. It has been implemented with a unit-specific continuous-time model and tested for different decomposition settings. The results show that a real-life 50-order, 17-unit, 6stage problem can effectively be solved in roughly 6 minutes of computational time.

This work addresses the scheduling of continuous single-stage multiproduct plants with energy int... more This work addresses the scheduling of continuous single-stage multiproduct plants with energy intensive processing tasks and time-dependent electricity cost and power supply. A new rolling horizon algorithm is proposed that consists of a planning model to predict the production levels and a continuous-time model for detailed scheduling. The results from a set of test problems from the literature show that the algorithm can generate global optimal solutions much more rapidly than standalone discrete or continuous-time formulations in problems involving unlimited power availability.

Resources, Conservation and Recycling, 2007

This paper presents a new approach for the optimal design of wastewater treatment systems. An alg... more This paper presents a new approach for the optimal design of wastewater treatment systems. An algorithm that can be divided in two parts is proposed for finding global optimal solutions to the problem. The first part comprises a new linear program formulation that is used to generate good starting points for the solution of the general non-linear program (second part).

International Journal of Production Research, 2014

ABSTRACT Flowshop scheduling problems have been extensively studied by several authors using diff... more ABSTRACT Flowshop scheduling problems have been extensively studied by several authors using different approaches. A typical flowshop process consists of successive manufacturing stages arranged in a single production line where different jobs have to be processed following a predefined production recipe. In this work, the scheduling of a complex flowshop process involving automated wet-etch station from semiconductor manufacturing systems requires a proper synchronisation of processing and transport operations, due to stringent storage policies and fixed transfer times between stages. Robust hybrid solution strategies based on mixed integer linear programming formulations and heuristic-based approaches, such as aggregation and decomposition methods, are proposed and illustrated on industrial-scale problems. The results show significant improvements in solution quality coupled with a reduced computational effort compared to other existing methodologies.

Industrial & Engineering Chemistry Research, 2013

ABSTRACT In today’s energy markets, there is a growing effort toward the alignment of the industr... more ABSTRACT In today’s energy markets, there is a growing effort toward the alignment of the industrial sector and the power grid for the sake of efficient energy distribution and consumption. In this paper, the resource–task network is used to provide a generic modeling framework for production scheduling under energy constraints. Three alternative process models for the energy-intensive melt shop of a steel plant are proposed and linked to a discrete-time formulation. The results show a trade-off between accurate representation of problem data and computational performance. By keeping track of the total energy and power consumption through time, we study the impact of fluctuating energy prices on the scheduling of operations and the economic benefits that can be obtained from the plant’s participation in the price- and incentive-based industrial demand side management programs.

Computers & Chemical Engineering, 2014

ABSTRACT

Computers & Chemical Engineering, 2011

This work addresses the scheduling of continuous single stage multiproduct plants with parallel u... more This work addresses the scheduling of continuous single stage multiproduct plants with parallel units and shared storage tanks. Processing tasks are energy intensive and we consider timedependent electricity pricing and availability together with multiple intermediate due dates, handled as hard constraints. A new discrete-time aggregate formulation is proposed to rapidly plan the production levels. It is combined with a continuous-time model for detailed scheduling as the essential part of a rolling horizon algorithm. Their computational performance is compared to traditional discrete and continuous-time full-space formulations with all models relying on the Resource-Task Network (RTN) process representation. The results show that new models and algorithm can generate global optimal schedules much more efficiently than their counterparts in problems involving unlimited power availability. Under restricted power, the aggregate model  =amount continuously sent to storage by task i during interval t [ton]

AIChE Journal, 2011

This paper presents a new algorithm for the near optimal scheduling of multistage batch plants wi... more This paper presents a new algorithm for the near optimal scheduling of multistage batch plants with a large number of orders and sequence-dependent changeovers. Such problems are either intractable when solved with full-space approaches or poor solutions result. We use decomposition on the entire set of orders and derive the complete schedule in several iterations, by inserting a couple of orders at a time. The key idea is to allow for partial rescheduling of previously scheduled orders without altering the unit assignment and sequencing decisions, so that the combinatorial complexity is kept at a manageable level. The algorithm has been implemented for three alternative continuous-time mixed integer linear programming models and tested through the solution of ten 2 example problems for different decomposition settings. The results show that an industrial-size scheduling problem with 50-orders, 17-units distributed over 6-stages can effectively be solved in roughly 6 minutes of computational time.

AIChE Journal, 2009

... Email: Pedro M. Castro (pedro.castro@ineti.pt). *Correspondence: Pedro M. Castro, Dept. de Mo... more ... Email: Pedro M. Castro (pedro.castro@ineti.pt). *Correspondence: Pedro M. Castro, Dept. de Modelação e Simulação de Processos, Instituto Nacional de Engenharia, Tecnologia e Inovação, 1649-038 Lisboa, Portugal. Publication History. ...

ABSTRACT This paper gives a review on existing scheduling methodologies developed for process ind... more ABSTRACT This paper gives a review on existing scheduling methodologies developed for process industries. Above all, the aim of the paper is to focus on the industrial aspects of scheduling and discuss the main characteristics, including strengths and weaknesses of the presented approaches. It is claimed that optimization tools of today can effectively support the plant level production. However there is still clear potential for improvements, especially in transferring academic results into industry. For instance, usability, interfacing and integration are some aspects discussed in the paper. After the introduction and problem classification, the paper discusses some lessons learned from industry, provides an overview of models and methods and concludes with general guidelines and examples on the modeling and solution of industrial problems.