Operations research: from computational biology to sensor network

In this dissertation we discuss the deployment of combinatorial optimization methods for modeling and solve real life problemS, with a particular emphasis to two biological problems arising from a common scenario: the reconstruction of the three-dimensional shape of a biological molecule from Nuclear Magnetic Resonance (NMR) data. The fi rst topic is the 3D assignment pathway problem (APP) for a RNA molecule. We prove that APP is NP-hard, and show a formulation of it based on edge-colored graphs. Taking into account that interactions between consecutive nuclei in the NMR spectrum are diff erent according to the type of residue along the RNA chain, each color in the graph represents a type of interaction. Thus, we can represent the sequence of interactions as the problem of fi nding a longest (hamiltonian) path whose edges follow a given order of colors (i.e., the orderly colored longest path). We introduce three alternative IP formulations of APP obtained with a max flow problem on a directed graph with packing constraints over the partitions, which have been compared among themselves. Since the last two models work on cyclic graphs, for them we proposed an algorithm based on the solution of their relaxation combined with the separation of cycle inequalities in a Branch & Cut scheme. The second topic is the discretizable distance geometry problem (DDGP), which is a formulation on discrete search space of the well-known distance geometry problem (DGP). The DGP consists in seeking the embedding in the space of a undirected graph, given a set of Euclidean distances between certain pairs of vertices. DGP has two important applications: (i) fi nding the three dimensional conformation of a molecule from a subset of interatomic distances, called Molecular Distance Geometry Problem, and (ii) the Sensor Network Localization Problem. We describe a Branch & Prune (BP) algorithm tailored for this problem, and two versions of it solving the DDGP both in protein modeling and in sensor networks localization frameworks. BP is an exact and exhaustive combinatorial algorithm that examines all the valid embeddings of a given weighted graph G=(V,E,d), under the hypothesis of existence of a given order on V. By comparing the two version of BP to well-known algorithms we are able to prove the e fficiency of BP in both contexts, provided that the order imposed on V is maintained

Constraint-Aware, Scalable, and Efficient Algorithms for Multi-Chip Power Module Layout Optimization

Moving towards an electrified world requires ultra high-density power converters. Electric vehicles, electrified aerospace, data centers, etc. are just a few fields among wide application areas of power electronic systems, where high-density power converters are essential. As a critical part of these power converters, power semiconductor modules and their layout optimization has been identified as a crucial step in achieving the maximum performance and density for wide bandgap technologies (i.e., GaN and SiC). New packaging technologies are also introduced to produce reliable and efficient multichip power module (MCPM) designs to push the current limits. The complexity of the emerging MCPM layouts is surpassing the capability of a manual, iterative design process to produce an optimum design with agile development requirements. An electronic design automation tool called PowerSynth has been introduced with ongoing research toward enhanced capabilities to speed up the optimized MCPM layout design process. This dissertation presents the PowerSynth progression timeline with the methodology updates and corresponding critical results compared to v1.1. The first released version (v1.1) of PowerSynth demonstrated the benefits of layout abstraction, and reduced-order modeling techniques to perform rapid optimization of the MCPM module compared to the traditional, manual, and iterative design approach. However, that version is limited by several key factors: layout representation technique, layout generation algorithms, iterative design-rule-checking (DRC), optimization algorithm candidates, etc. To address these limitations, and enhance PowerSynth’s capabilities, constraint-aware, scalable, and efficient algorithms have been developed and implemented. PowerSynth layout engine has evolved from v1.3 to v2.0 throughout the last five years to incorporate the algorithm updates and generate all 2D/2.5D/3D Manhattan layout solutions. These fundamental changes in the layout generation methodology have also called for updates in the performance modeling techniques and enabled exploring different optimization algorithms. The latest PowerSynth 2 architecture has been implemented to enable electro-thermo-mechanical and reliability optimization on 2D/2.5D/3D MCPM layouts, and set up a path toward cabinet-level optimization. PowerSynth v2.0 computer-aided design (CAD) flow has been hardware-validated through manufacturing and testing of an optimized novel 3D MCPM layout. The flow has shown significant speedup compared to the manual design flow with a comparable optimization result

Kinetic model construction using chemoinformatics

Kinetic models of chemical processes not only provide an alternative to costly experiments; they also have the potential to accelerate the pace of innovation in developing new chemical processes or in improving existing ones. Kinetic models are most powerful when they reflect the underlying chemistry by incorporating elementary pathways between individual molecules. The downside of this high level of detail is that the complexity and size of the models also steadily increase, such that the models eventually become too difficult to be manually constructed. Instead, computers are programmed to automate the construction of these models, and make use of graph theory to translate chemical entities such as molecules and reactions into computer-understandable representations. This work studies the use of automated methods to construct kinetic models. More particularly, the need to account for the three-dimensional arrangement of atoms in molecules and reactions of kinetic models is investigated and illustrated by two case studies. First of all, the thermal rearrangement of two monoterpenoids, cis- and trans-2-pinanol, is studied. A kinetic model that accounts for the differences in reactivity and selectivity of both pinanol diastereomers is proposed. Secondly, a kinetic model for the pyrolysis of the fuel “JP-10” is constructed and highlights the use of state-of-the-art techniques for the automated estimation of thermochemistry of polycyclic molecules. A new code is developed for the automated construction of kinetic models and takes advantage of the advances made in the field of chemo-informatics to tackle fundamental issues of previous approaches. Novel algorithms are developed for three important aspects of automated construction of kinetic models: the estimation of symmetry of molecules and reactions, the incorporation of stereochemistry in kinetic models, and the estimation of thermochemical and kinetic data using scalable structure-property methods. Finally, the application of the code is illustrated by the automated construction of a kinetic model for alkylsulfide pyrolysis