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.

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.

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.

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.

Sediment Dynamics of Chinese Muddy Coasts and Estuaries: Physics, Biology and Their Interactions provides a forum for the latest research addressing the physics, sedimentary processes, biology, chemistry and ecological processes associated with these rapidly changing estuarine and coastal environments. The book explores the challenges and opportunities for future research in China's estuaries and coastal waters around the world, and uses China as a case study to provide answers to the causes of, and possible solutions to, these problems, presenting methodologies on working with observation and modelling analysis. China's coastal zone is facing many urgent issues in the environmental degradation and sustainable use of its marine resources. This book reviews and synthesizes papers from international research communities, including those from China, to exemplify and document their scientific approaches to manage and recover coastal ecological functions. - Presents spatio-temporal processes and multivariate dynamic modelling - Includes physical and biological feedback, along with marine ecosystem observation and modeling - Features multidisciplinary methodological approaches - Includes important information on the effects of climate change to the coasts and estuaries of China

Scour and Erosion IX contains the peer-reviewed scientific contributions presented at 9th International Conference on Scour and Erosion (ICSE 2018, Taipei, Taiwan, 5–8 November 2018), and includes recent accomplishments about scour and erosion in field observation, experimental laboratory work, theoretical development, numerical modeling and disaster management. The book covers fourteen topics: A. Internal erosion B. River, coastal, estuarine and marine scour and erosion C. Rock scour and erosion D. Sediment transport: grain scale and continuum scale E. Scour and erosion around structures F. Soil erosion, restoration mechanisms and conservation G. Hillslope conservation and debris flow H. Geotechnical issues related to scour and erosion I. Field observation and analyses J. Scour and erosion testing and experiment K. Remote sensing, instrumentation and monitoring L. Advanced numerical modelling of scour and erosion M. Natural hazards due to scour and erosion N. Management of scour/erosion and sediment.