Large-scale changes are taking place in the way modelling is performed within the US EPA, and a new generation of environmental models is currently under construction. The US EPA is engaging in several modelling efforts in response to Congressional mandates such as the Clean Air Act and the Clean Water Act. These mandates require the scientific modelling of the impact of pollutants on human health and the environment. The complexity of scale in environmental models has increased by several orders of magnitude, with a simultaneous demand for increased stability, accuracy and efficiency in the computed model solution. This book showcases numerical algorithms appropriate to the subject areas listed below and explores how new algorithmic methods would benefit the US EPA's environmental models and other environmental studies.

Introduces readers to core algorithmic techniques for next-generation sequencing (NGS) data analysis and discusses a wide range of computational techniques and applications This book provides an in-depth survey of some of the recent developments in NGS and discusses mathematical and computational challenges in various application areas of NGS technologies. The 18 chapters featured in this book have been authored by bioinformatics experts and represent the latest work in leading labs actively contributing to the fast-growing field of NGS. The book is divided into four parts: Part I focuses on computing and experimental infrastructure for NGS analysis, including chapters on cloud computing, modular pipelines for metabolic pathway reconstruction, pooling strategies for massive viral sequencing, and high-fidelity sequencing protocols. Part II concentrates on analysis of DNA sequencing data, covering the classic scaffolding problem, detection of genomic variants, including insertions and deletions, and analysis of DNA methylation sequencing data. Part III is devoted to analysis of RNA-seq data. This part discusses algorithms and compares software tools for transcriptome assembly along with methods for detection of alternative splicing and tools for transcriptome quantification and differential expression analysis. Part IV explores computational tools for NGS applications in microbiomics, including a discussion on error correction of NGS reads from viral populations, methods for viral quasispecies reconstruction, and a survey of state-of-the-art methods and future trends in microbiome analysis. Computational Methods for Next Generation Sequencing Data Analysis: Reviews computational techniques such as new combinatorial optimization methods, data structures, high performance computing, machine learning, and inference algorithms Discusses the mathematical and computational challenges in NGS technologies Covers NGS error correction, de novo genome transcriptome assembly, variant detection from NGS reads, and more This text is a reference for biomedical professionals interested in expanding their knowledge of computational techniques for NGS data analysis. The book is also useful for graduate and post-graduate students in bioinformatics.

Mathematical problems concerning time evolution of solutions related to nonlinear systems modelling dynamics of continuous media are of great interest both in wave propagation and in stability problems. During the last few decades many striking developments have taken place, especially in connection with the effects of nonlinearity of the equations describing physical situations. The articles in this book have been written by reputable specialists in the field and represent a valuable contribution to its advancement. The topics are: discontinuity and shock waves; linear and nonlinear stability in fluid dynamics; kinetic theories and comparison with continuum models; propagation and non-equilibrium thermodynamics; exact solutions via group methods; numerical applications.

This book provides concise, up-to-date and easy-to-follow information on an increasingly important area of hydro-environmental analysis and management. It covers important aspects of both surface and subsurface water quality management, as they are inseparable components of aquifers and the flow in physical domains occur in combination with the other. However, the main emphasis of the book is on the practical development and application of computer based algorithms, via appropriate schemes, to realistic problems. Mathematical theories are not discussed as they can be found in many expert books. All sections of the book include detailed descriptions of practical examples. It also, uniquely, gives explanations regarding the formulation of practical management schedules and tools for hydro-environmental systems. There is a lack of books dealing with the practical aspects of the application of computer modelling techniques to complex hydrodynamical phenomena, and this book has been written for professionals and researchers, especially those who are not trained mathematicians who, nevertheless, need to make managerial decisions. Computational Methods in the Management of Hydro-Environmental Systems will be an invaluable source of information for post-graduate level researchers and decision-makers who need to apply numerical modelling techniques to investigate hydrodynamic phenomena and pollutants dispersion in natural aquatic systems. Professionals and engineers, who now need to gain insights about the working of computer techniques for choosing appropriate schemes and applying them to realistic problems, will also value this work. Masters' level and final-year graduate students are also expected to benefit from the book.

This IMA Volume in Mathematics and its Applications RESOURCE RECOVERY, CONFINEMENT, AND REMEDIATION OF ENVIRONMENTAL HAZARDS contains papers presented at two successful one-week workshops: Confine ment and Remediation of Environmental Hazards held on January 15-19, 2000 and Resource Recovery, February 9-13, 2000. Both workshops were integral parts of the IMA annual program on Mathematics in Reactive Flow and Transport Phenomena, 1999-2000. We would like to thank John Chadam (University of Pittsburgh), Al Cunningham (Montana State Uni versity), Richard E. Ewing (Texas A&M University), Peter Ortoleva (In diana University), and Mary Fanett Wheeler (TICAM, The University of Texas at Austin) for their excellent work as organizers of the meetings and for editing the proceedings. We take this opportunity to thank the National Science Foundation for their support of the IMA. Series Editors Douglas N. Arnold, Director of the IMA Fadil Santosa, Deputy Director of the IMA v PREFACE Advances in resource recovery, and confinement/remediation of envi ronmental hazards requires a coordinated, interdisciplinary effort involving mathematicians, scientists and engineers. The intent of this collection of papers is to summarize recent theoretical, computational, and experimen tal advances in the theory of phenomena in porous media, with the intent to identify similarities and differences concerning applications related to both resource recovery and confinement and remediation of environmental hazards.

Contains papers presented at the October 1998 SIAM Workshop on Object Oriented Methods for Interoperable Scientific and Engineering Computing that covered a variety of topics and issues related to designing and implementing computational tools for science and engineering.

This book presents the fundamental principles, mathematical methods and applications of atmospheric chemistry models for graduate students and researchers.

In 1969 the North Atlantic Treaty Organization (NATO) established the Committee on Challenges of Modern Society (CCMS). The subject of air pollution was from the start, one of the priority problems under study within the framework of various pilot studies undertaken by this committee. The organization of a periodic conference dealing with air pollution modelling and its application has become one of the main activities within the pilot study relating to air pollution. These international conferences were successively organized by the United States (first five); Federal Republic of Germany (five); Belgium (five); The Netherlands (four) and Denmark (five). With this one Portugal takes over the duty. This volume contains the papers and poster abstracts presented at the NATO/CCMS International Technical Meeting on Air Pollution Modelling and Its Application held in Louvain-la-Neuve, Belgium, during 15-19 October 2001. This ITM was jointly organized by the University of Aveiro, Portugal (Pilot country) and by the Catholic University of Louvain, Belgium (host country). The ITM was attended by 78 participants representing 26 countries from Western and Eastern Europe, North and South America, Asia, Australia and Africa. The main topics of this ITM were : Role of Atmospheric Models in Air Pollution Policy and Abatement Strategies; Integrated Regional Modelling; Global and Long-Range Transport; Regional Air Pollution and Climate; New Developments; and Model Assessment and Verification.