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An edited volume describing the latest developments in approaching the problem of polymer sequence analysis, with special emphasis on the most relevant biopolymers (peptides and DNA) but not limited to them. The chapters will include peptide sequence analysis, DNA sequence analysis, analysis of biopolymers and nonpolymers, sequence alignment problems, and more.
This first comprehensive overview of reactive extrusion technology for over a decade combines the views of contributors from both academia and industry who share their experiences and highlight possible applications and markets. They also provide updated information on the underlying chemical and physical concepts, summarizing recent developments in terms of the material and machinery used. As a result, readers will find here a compilation of potential applications for reactive extrusion to access new and cost-effective polymeric materials, while using existing compounding machines.
The idea of this book grew out of a symposium that was held at Stony Brook in September 2012 in celebration of David S.Warren's fundamental contributions to Computer Science and the area of Logic Programming in particular. Logic Programming (LP) is at the nexus of Knowledge Representation, Artificial Intelligence, Mathematical Logic, Databases, and Programming Languages. It is fascinating and intellectually stimulating due to the fundamental interplay among theory, systems, and applications brought about by logic. Logic programs are more declarative in the sense that they strive to be logical specifications of "what" to do rather than "how" to do it, and thus they are high-level and easier to understand and maintain. Yet, without being given an actual algorithm, LP systems implement the logical specifications automatically. Several books cover the basics of LP but focus mostly on the Prolog language with its incomplete control strategy and non-logical features. At the same time, there is generally a lack of accessible yet comprehensive collections of articles covering the key aspects in declarative LP. These aspects include, among others, well-founded vs. stable model semantics for negation, constraints, object-oriented LP, updates, probabilistic LP, and evaluation methods, including top-down vs. bottom-up, and tabling. For systems, the situation is even less satisfactory, lacking accessible literature that can help train the new crop of developers, practitioners, and researchers. There are a few guides onWarren’s Abstract Machine (WAM), which underlies most implementations of Prolog, but very little exists on what is needed for constructing a state-of-the-art declarative LP inference engine. Contrast this with the literature on, say, Compilers, where one can first study a book on the general principles and algorithms and then dive in the particulars of a specific compiler. Such resources greatly facilitate the ability to start making meaningful contributions quickly. There is also a dearth of articles about systems that support truly declarative languages, especially those that tie into first-order logic, mathematical programming, and constraint solving. LP helps solve challenging problems in a wide range of application areas, but in-depth analysis of their connection with LP language abstractions and LP implementation methods is lacking. Also, rare are surveys of challenging application areas of LP, such as Bioinformatics, Natural Language Processing, Verification, and Planning. The goal of this book is to help fill in the previously mentioned void in the LP literature. It offers a number of overviews on key aspects of LP that are suitable for researchers and practitioners as well as graduate students. The following chapters in theory, systems, and applications of LP are included.
This book is a collection of representative and novel works done in Data Mining, Knowledge Discovery, Clustering and Classification that were originally presented in French at the EGC'2012 Conference held in Bordeaux, France, on January 2012. This conference was the 12th edition of this event, which takes place each year and which is now successful and well-known in the French-speaking community. This community was structured in 2003 by the foundation of the French-speaking EGC society (EGC in French stands for ``Extraction et Gestion des Connaissances'' and means ``Knowledge Discovery and Management'', or KDM). This book is intended to be read by all researchers interested in these fields, including PhD or MSc students, and researchers from public or private laboratories. It concerns both theoretical and practical aspects of KDM. The book is structured in two parts called ``Knowledge Discovery and Data Mining'' and ``Classification and Feature Extraction or Selection''. The first part (6 chapters) deals with data clustering and data mining. The three remaining chapters of the second part are related to classification and feature extraction or feature selection.
Propositional logic has been recognized throughout the centuries as one of the cornerstones of reasoning in philosophy and mathematics. Over time, its formalization into Boolean algebra was accompanied by the recognition that a wide range of combinatorial problems can be expressed as propositional satisfiability (SAT) problems. Because of this dual role, SAT developed into a mature, multi-faceted scientific discipline, and from the earliest days of computing a search was underway to discover how to solve SAT problems in an automated fashion. This book, the Handbook of Satisfiability, is the second, updated and revised edition of the book first published in 2009 under the same name. The handbook aims to capture the full breadth and depth of SAT and to bring together significant progress and advances in automated solving. Topics covered span practical and theoretical research on SAT and its applications and include search algorithms, heuristics, analysis of algorithms, hard instances, randomized formulae, problem encodings, industrial applications, solvers, simplifiers, tools, case studies and empirical results. SAT is interpreted in a broad sense, so as well as propositional satisfiability, there are chapters covering the domain of quantified Boolean formulae (QBF), constraints programming techniques (CSP) for word-level problems and their propositional encoding, and satisfiability modulo theories (SMT). An extensive bibliography completes each chapter. This second edition of the handbook will be of interest to researchers, graduate students, final-year undergraduates, and practitioners using or contributing to SAT, and will provide both an inspiration and a rich resource for their work. Edmund Clarke, 2007 ACM Turing Award Recipient: "SAT solving is a key technology for 21st century computer science." Donald Knuth, 1974 ACM Turing Award Recipient: "SAT is evidently a killer app, because it is key to the solution of so many other problems." Stephen Cook, 1982 ACM Turing Award Recipient: "The SAT problem is at the core of arguably the most fundamental question in computer science: What makes a problem hard?"
Biomarker discovery is an important area of biomedical research that may lead to significant breakthroughs in disease analysis and targeted therapy. Biomarkers are biological entities whose alterations are measurable and are characteristic of a particular biological condition. Discovering, managing, and interpreting knowledge of new biomarkers are challenging and attractive problems in the emerging field of biomedical informatics. This volume is a collection of state-of-the-art research into the application of data mining to the discovery and analysis of new biomarkers. Presenting new results, models and algorithms, the included contributions focus on biomarker data integration, information retrieval methods, and statistical machine learning techniques. This volume is intended for students, and researchers in bioinformatics, proteomics, and genomics, as well engineers and applied scientists interested in the interdisciplinary application of data mining techniques.
Scientific theories that explain how physical systems behave are described by mathematical models which provide the basis for computer simulations of events that occur in the physical universe. These models, being only mathematical characterizations of actual phenomena, are obviously subject to error because of the inherent limitations of all mathematical abstractions. In this work, new theory and methodologies are developed to quantify such modeling error in a special way that resolves a fundamental and standing issue: multiscale modeling, the development of models of events that transcend many spatial and temporal scales. Specifically, we devise the machinery for a posteriori estimates of relative modeling error between a model of fine scale and another of coarser scale, and we use this methodology as a general approach to multiscale problems. The target application is one of critical importance to nanomanufacturing: imprint lithography of semiconductor devices. The development of numerical methods for multiscale modeling has become one of the most important areas of computational science. Technological developments in the manufacturing of semiconductors hinge upon the ability to understand physical phenomena from the nanoscale to the microscale and beyond. Predictive simulation tools are critical to the advancement of nanomanufacturing semiconductor devices. In principle, they can displace expensive experiments and testing and optimize the design of the manufacturing process. The development of such tools rest on the edge of contemporary methods and high-performance computing capabilities and is a major open problem in computational science. In this dissertation, a molecular model is used to simulate the deformation of polymeric materials used in the fabrication of semiconductor devices. Algorithms are described which lead to a complex molecular model of polymer materials designed to produce an etch barrier, a critical component in imprint lithography approaches to semiconductor manufacturing. Each application of this so-called polymerization process leads to one realization of a lattice-type model of the polymer, a molecular statics model of enormous size and complexity. This is referred to as the base model for analyzing the deformation of the etch barrier, a critical feature of the manufacturing process. To reduce the size and complexity of this model, a sequence of coarser surrogate models is generated. These surrogates are the multiscale models critical to the successful computer simulation of the entire manufacturing process. The surrogate involves a combination of particle models, the molecular model of the polymer, and a coarse-scale model of the polymer as a nonlinear hyperelastic material. Coefficients for the nonlinear elastic continuum model are determined using numerical experiments on representative volume elements of the polymer model. Furthermore, a simple model of initial strain is incorporated in the continuum equations to model the inherit shrinking of the A coupled particle and continuum model is constructed using a special algorithm designed to provide constraints on a region of overlap between the continuum and particle models. This coupled model is based on the so-called Arlequin method that was introduced in the context of coupling two continuum models with differing levels of discretization. It is shown that the Arlequin problem for the particle-tocontinuum model is well posed in a one-dimensional setting involving linear harmonic springs coupled with a linearly elastic continuum. Several numerical examples are presented. Numerical experiments in three dimensions are also discussed in which the polymer model is coupled to a nonlinear elastic continuum. Error estimates in local quantities of interest are constructed in order to estimate the modeling error due to the approximation of the particle model by the coupled multiscale surrogate model. The estimates of the error are computed by solving an auxiliary adjoint, or dual, problem that incorporates as data the quantity of interest or its derivatives. The solution of the adjoint problem indicates how the error in the approximation of the polymer model inferences the error in the quantity of interest. The error in the quantity of interest represents the relative error between the value of the quantity evaluated for the base model, a quantity typically unavailable or intractable, and the value of the quantity of interest provided by the multiscale surrogate model. To estimate the error in the quantity of interest, a theorem is employed that establishes that the error coincides with the value of the residual functional acting on the adjoint solution plus a higher-order remainder. For each surrogate in a sequence of surrogates generated, the residual functional acting on various approximations of the adjoint is computed. These error estimates are used to construct an adaptive algorithm whereby the model is adapted by supplying additional fine-scale data in certain subdomains in order to reduce the error in the quantity of interest. The adaptation algorithm involves partitioning the domain and selecting which subdomains are to use the particle model, the continuum model, and where the two overlap. When the algorithm identifies that a region contributes a relatively large amount to the error in the quantity of interest, it is scheduled for refinement by switching the model for that region to the particle model. Numerical experiments on several configurations representative of nano-features in semiconductor device fabrication demonstrate the effectiveness of the error estimate in controlling the modeling error as well as the ability of the adaptive algorithm to reduce the error in the quantity of interest. There are two major conclusions of this study: 1. an effective and well posed multiscale model that couples particle and continuum models can be constructed as a surrogate to molecular statics models of polymer networks and 2. an error estimate of the modeling error for such systems can be estimated with sufficient accuracy to provide the basis for very effective multiscale modeling procedures. The methodology developed in this study provides a general approach to multiscale modeling. The computational procedures, computer codes, and results could provide a powerful tool in understanding, designing, and optimizing an important class of semiconductormanufacturing processes. The study in this dissertation involves all three components of the CAM graduate program requirements: Area A, Applicable Mathematics; Area B, Numerical Analysis and Scientific Computation; and Area C, Mathematical Modeling and Applications. The multiscale modeling approach developed here is based on the construction of continuum surrogates and coupling them to molecular statics models of polymer as well as a posteriori estimates of error and their adaptive control. A detailed mathematical analysis is provided for the Arlequin method in the context of coupling particle and continuum models for a class of one-dimensional model problems. Algorithms are described and implemented that solve the adaptive, nonlinear problem proposed in the multiscale surrogate problem. Large scale, parallel computations for the base model are also shown. Finally, detailed studies of models relevant to applications to semiconductor manufacturing are presented.