Set-based design of mechanical systems with design robustness integrated

This paper presents a method for parameter design of mechanical products based on a set-based approach. Set-based concurrent engineering emphasises on designing in a multi-stakeholder environment with concurrent involvement of the stakeholders in the design process. It also encourages flexibility in design through communication in terms of ranges instead of fixed point values and subsequent alternative solutions resulting from intersection of these ranges. These alternative solutions can then be refined and selected according to the designers’ preferences and clients’ needs. This paper presents a model and tools for integrated flexible design that take into account the manufacturing variations as well as the design objectives for finding inherently robust solutions using QCSP transformation through interval analysis. In order to demonstrate the approach, an example of design of rigid flange coupling with a variable number of bolts and a choice of bolts from ISO M standard has been resolved and demonstrated

Certainty Closure: Reliable Constraint Reasoning with Incomplete or Erroneous Data

Constraint Programming (CP) has proved an effective paradigm to model and solve difficult combinatorial satisfaction and optimisation problems from disparate domains. Many such problems arising from the commercial world are permeated by data uncertainty. Existing CP approaches that accommodate uncertainty are less suited to uncertainty arising due to incomplete and erroneous data, because they do not build reliable models and solutions guaranteed to address the user's genuine problem as she perceives it. Other fields such as reliable computation offer combinations of models and associated methods to handle these types of uncertain data, but lack an expressive framework characterising the resolution methodology independently of the model. We present a unifying framework that extends the CP formalism in both model and solutions, to tackle ill-defined combinatorial problems with incomplete or erroneous data. The certainty closure framework brings together modelling and solving methodologies from different fields into the CP paradigm to provide reliable and efficient approches for uncertain constraint problems. We demonstrate the applicability of the framework on a case study in network diagnosis. We define resolution forms that give generic templates, and their associated operational semantics, to derive practical solution methods for reliable solutions.Comment: Revised versio

Quantified Constraints in Twenty Seventeen

I present a survey of recent advances in the algorithmic and computational complexity theory of non-Boolean Quantified Constraint Satisfaction Problems, incorporating some more modern research directions

Verified Model Checking for Conjunctive Positive Logic

We formalize, in the Dafny language and verifier, a proof system PS for deciding the model checking problem of the fragment of first-order logic, denoted FOAE/\ , known as conjunctive positive logic (CPL). We mechanize the proofs of soundness and completeness of PS ensuring its correctness. Our formalization is representative of how various popular verification systems can be used to verify the correctness of rule-based formal systems on the basis of the least fixpoint semantics. Further, exploiting Dafny’s automatic code generation, from the completeness proof we achieve a mechanically verified prototype implementation of a proof search mechanism that is a model checker for CPL. The model checking problem of FOAE/\ is equivalent to the quantified constraint satisfaction problem (QCSP), and it is PSPACE-complete. The formalized proof system decides the general QCSP and it can be applied to arbitrary formulae of CPL.This research has been supported by the European Union (FEDER funds) under grant TIN2017-86727-C2-2-R, and by the University of the Basque Country under Project LoRea GIU18-182

QCSPScore: a new scoring function for driving protein-ligand docking with quantitative chemical shifts perturbations

Through the use of information about the biological target structure, the optimization of potential drugs can be improved. In this work I have developed a procedure that uses the quantitative change in the chemical perturbations (CSP) in the protein from NMR experiments for driving protein-ligand docking. The approach is based on a hybrid scoring function (QCSPScore) which combines traditional DrugScore potentials, which describe the interaction between protein and ligand, with Kendall’s rank correlation coefficient, which evaluates docking poses in terms of their agreement with experimental CSP. Prediction of the CSP for a specific ligand pose is done efficiently with an empirical model, taking into account only ring current effects. QCSPScore has been implemented in the AutoDock software package. Compared to previous methods, this approach shows that the use of rank correlation coefficient is robust to outliers. In addition, the prediction of native-like complex geometries improved because the CSP are already being used during the docking process, and not only in a post-filtering setting for generated docking poses. Since the experimental information is guaranteed to be quantitatively used, CSP effectively contribute to align the ligand in the binding pocket. The first step in the development of QCSPScore was the analysis of 70 protein-ligand complexes for which reference CSP were computed. The success rate in the docking increased from 71% without involvement of CSP to 100% if CSP were considered at the highest weighting scheme. In a second step QCSPScore was used in re-docking three test cases, for which reference experimental CSP data was available. Without CSP, i.e. in the use of conventional DrugScore potentials, none of the three test cases could be successfully re-docked. The integration of CSP with the same weighting factor as described above resulted in all three cases successfully re-docked. For two of the three complexes, native-like solutions were only produced if CSP were considered.Conformational changes in the binding pockets of up to 2 Å RMSD did not affect the success of the docking. QCSPScore will be particularly interesting in difficult protein-ligand complexes. They are in particular those cases in which the shape of the binding pocket does not provide sufficient steric restraints such as in flat protein-protein interfaces and in the virtual screening of small chemical fragments.Durch die Verwendung von Information über die biologische Zielstruktur kann die Optimierung potentieller Wirkstoffe verbessert werden. Im Rahmen dieser Arbeit habe ich ein Verfahren entwickelt, das quantitativ die Veränderung der Chemischen Verschieben (CSP) im Protein aus NMR-Experimenten für das Protein-Ligand-Docking verwendet. Der Ansatz basiert auf einer Hybridbewertungsfunktion (QCSPScore) und kombiniert herkömmliche DrugScore-Potentiale, welche die Wechselwirkung zwischen Protein und Ligand beschreiben, mit dem Rangkorrelationskoeffizienten nach Kendall, der die Dockingposen hinsichtlich ihrer Übereinstimmung mit experimentellen CSP. Die Vorhersage der CSP für einen bestimmten Liganden geschieht effizient mit einem empirischen Modell, wobei nur Ringstromeffekte berücksichtigt werden. QCSPScore wurde in das AutoDock Softwarepaket implementiert. Im Vergleich zu früheren Verfahren zeigt dieser Ansatz, dass die Verwendung des Rangkorrelationskoeffizienten robuster ist gegenüber Ausreißern in den vorhergesagten CSP. Außerdem ist die Vorhersage nativ-ähnlicher Komplexgeometrien verbessert, da die CSP bereits während des Docking-Prozesses eingesetzt werden, und nicht erst in einem nachträglichen Filter für generierte Dockingposen. Da die experimentelle Informationen quantitativ benutzt werden wird sichergestellt, dass die CSP effektiv dazu beitragen, den Liganden in der Bindetasche auszurichten. Der erste Schritt bei der Entwicklung des QCSPScore war die Analyse von 70 Protein-Ligand-Komplexen, für die als Referenz CSP vorhergesagt wurden. Die Erfolgsrate im Docking erhöhte sich von 71 %, ohne Einbeziehung von CSP, auf 100 %, wenn CSP mit höchster Gewichtung mit einbezogen wurden. Die globale Optimierung auf der kombinierten Docking-Energiehyperfläche ist also erfolgreich. In einem zweiten Schritt wurde QCSPScore zum Docking dreier Testfälle verwendet, für die als Referenz experimentelle CSP zur Verfügung standen. Ohne CSP, d.h. bei der Verwendung von herkömmlichen DrugScore-Potentialen, konnte keiner der drei Testfälle erfolgreich gedockt werden. Die Einbeziehung von CSP mit dem selben hohen Gewichtungsfaktor wie oben führte in allen drei Fällen zu erfolgreichen Docking-Ergebnissen. Für zwei der drei Komplexe wurden zudem nur bei Einbeziehung der experimentellen Information nativ-ähnliche Geometrien vorhergesagt. Konformationelle Änderungen der Bindetasche bis zu 2 Å RMSD beeinträchtigen den Erfolg des Dockings nicht. Ich bin davon überzeugt, dass mein Verfahren besonders für Protein-Ligand-Komplexe interessant sein wird, für die die Vorhersage nativ-ähnlicher Komplexe bislang schwierig war. Das sind insbesondere solche Fälle, in denen die Form der Bindetasche zur Vorhersage des Komplexes nicht ausreichend, wie das bei flachen Protein-Protein-Wechselwirkungsregionen oder beim virtuellen Screening kleiner Fragmente der Fall ist

Sea Container Terminals

Due to a rapid growth in world trade and a huge increase in containerized goods, sea container terminals play a vital role in globe-spanning supply chains. Container terminals should be able to handle large ships, with large call sizes within the shortest time possible, and at competitive rates. In response, terminal operators, shipping liners, and port authorities are investing in new technologies to improve container handling infrastructure and operational efficiency. Container terminals face challenging research problems which have received much attention from the academic community. The focus of this paper is to highlight the recent developments in the container terminals, which can be categorized into three areas: (1) innovative container terminal technologies, (2) new OR directions and models for existing research areas, and (3) emerging areas in container terminal research. By choosing this focus, we complement existing reviews on container terminal operations

From Complexity to Algebra and Back: Digraph Classes, Collapsibility, and the PGP

Inspired by computational complexity results for the quantified constraint satisfaction problem, we study the clones of idem potent polymorphisms of certain digraph classes. Our first results are two algebraic dichotomy, even "gap", theorems. Building on and extending [Martin CP'11], we prove that partially reflexive paths bequeath a set of idem potent polymorphisms whose associated clone algebra has: either the polynomially generated powers property (PGP), or the exponentially generated powers property (EGP). Similarly, we build on [DaMM ICALP'14] to prove that semi complete digraphs have the same property. These gap theorems are further motivated by new evidence that PGP could be the algebraic explanation that a QCSP is in NP even for unbounded alternation. Along the way we also effect a study of a concrete form of PGP known as collapsibility, tying together the algebraic and structural threads from [Chen Sicomp'08], and show that collapsibility is equivalent to its Pi2-restriction. We also give a decision procedure for k-collapsibility from a singleton source of a finite structure (a form of collapsibility which covers all known examples of PGP for finite structures). Finally, we present a new QCSP trichotomy result, for partially reflexive paths with constants. Without constants it is known these QCSPs are either in NL or Pspace-complete [Martin CP'11], but we prove that with constants they attain the three complexities NL, NP-complete and Pspace-complete

Quantified weighted constraint satisfaction problems.

Mak, Wai Keung Terrence.Thesis (M.Phil.)--Chinese University of Hong Kong, 2011.Includes bibliographical references (p. 100-104).Abstracts in English and Chinese.Chapter 1 --- Introduction --- p.1Chapter 1.1 --- Constraint Satisfaction Problems --- p.1Chapter 1.2 --- Weighted Constraint Satisfaction Problems --- p.2Chapter 1.3 --- Quantified Constraint Satisfaction Problems --- p.3Chapter 1.4 --- Motivation and Goal --- p.4Chapter 1.5 --- Outline of the Thesis --- p.6Chapter 2 --- Background --- p.7Chapter 2.1 --- Constraint Satisfaction Problems --- p.7Chapter 2.1.1 --- Backtracking Tree Search --- p.9Chapter 2.1.2 --- Local Consistencies for solving CSPs --- p.11Node Consistency (NC) --- p.13Arc Consistency (AC) --- p.14Searching by Maintaining Arc Consistency --- p.16Chapter 2.1.3 --- Constraint Optimization Problems --- p.17Chapter 2.2 --- Weighted Constraint Satisfaction Problems --- p.19Chapter 2.2.1 --- Branch and Bound Search (B&B) --- p.23Chapter 2.2.2 --- Local Consistencies for WCSPs --- p.25Node Consistency --- p.26Arc Consistency --- p.28Chapter 2.3 --- Quantified Constraint Satisfaction Problems --- p.32Chapter 2.3.1 --- Backtracking Free search --- p.37Chapter 2.3.2 --- Consistencies for QCSPs --- p.38Chapter 2.3.3 --- Look Ahead for QCSPs --- p.45Chapter 3 --- Quantified Weighted CSPs --- p.48Chapter 4 --- Branch & Bound with Consistency Techniques --- p.54Chapter 4.1 --- Alpha-Beta Pruning --- p.54Chapter 4.2 --- Consistency Techniques --- p.57Chapter 4.2.1 --- Node Consistency --- p.62Overview --- p.62Lower Bound of A-Cost --- p.62Upper Bound of A-Cost --- p.66Projecting Unary Costs to Cθ --- p.67Chapter 4.2.2 --- Enforcing Algorithm for NC --- p.68Projection Phase --- p.69Pruning Phase --- p.69Time Complexity --- p.71Chapter 4.2.3 --- Arc Consistency --- p.73Overview --- p.73Lower Bound of A-Cost --- p.73Upper Bound of A-Cost --- p.75Projecting Binary Costs to Unary Constraint --- p.75Chapter 4.2.4 --- Enforcing Algorithm for AC --- p.76Projection Phase --- p.77Pruning Phase --- p.77Time complexity --- p.79Chapter 5 --- Performance Evaluation --- p.83Chapter 5.1 --- Definitions of QCOP/QCOP+ --- p.83Chapter 5.2 --- Transforming QWCSPs into QCOPs --- p.90Chapter 5.3 --- Empirical Evaluation --- p.91Chapter 5.3.1 --- Random Generated Problems --- p.92Chapter 5.3.2 --- Graph Coloring Game --- p.92Chapter 5.3.3 --- Min-Max Resource Allocation Problem --- p.93Chapter 5.3.4 --- Value Ordering Heuristics --- p.94Chapter 6 --- Concluding Remarks --- p.96Chapter 6.1 --- Contributions --- p.96Chapter 6.2 --- Limitations and Related Works --- p.97Chapter 6.3 --- Future Works --- p.99Bibliography --- p.10

Mathematical Models of Seaside Operations in Container Ports and their Solution

Operational Research and Optimization are fundamental disciplines which, for decades, provided the real-world with tools for solving practical problems. Many such problems arise in container ports. Container terminals are important assets in modern economies. They constitute an important means of distributing goods made overseas to domestic markets in most countries. They are expensive to build and difficult to operate. We describe here some of the main operations which are faced daily by decision makers at those facilities. Decision makers often use Operational Research and Optimization tools to run these operations effectively. In this thesis, we focus on seaside operations which can be divided into three main problems: 1- the Berth Allocation Problem (BAP), 2- the Quay Crane Assignment Problem (QCAP), 3- the Quay Crane Scheduling Problem (QCSP). Each one of the above is a complex optimization problem in its own right. However, solving them individually without the consideration of the others may lead to overall suboptimal solutions. For this reason we will investigate the pairwise combinations of these problems and their total integration In addition, several important factors that affected on the final solution. The main contributions of this study are modelling and solving of the: 1- Robust berth allocation problem (RBAP): a new efficient mathematical model is formulated and a hybrid algorithm based on Branch-and-Cut and the Genetic Algorithm is used to find optimal or near optimal solutions for large scale instances in reasonable time. 2- Quay crane assignment and quay crane scheduling problem (QCASP): a new mathematical model is built to simultaneously solve QCASP and a heuristic based on the Genetic Algorithm is developed to find solutions to realistic instances in reasonable time. 3- Berth allocation, quay crane assignment and quay crane scheduling problem (BACASP): an aggregate model for all three seaside operations is proposed and to solve realistic instances of the problem, an adapted variant of the Genetic Algorithm is implemented. Keywords: berth allocation; quay crane assignment; quay crane scheduling; terminal operations; genetic algorith