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Bioinformatics and Computational Biology Solutions Using R and Bioconductor
Bioconductor is a widely used open source and open development software project for the analysis and comprehension of data arising from high-throughput experimentation in genomics and molecular biology. Bioconductor is rooted in the open source statistical computing environment R. This volume's coverage is broad and ranges across most of the key capabilities of the Bioconductor project, including: Importation and preprocessing of high-throughput data from microarray, proteomic, and flow cytometry platforms / Curation and delivery of biological metadata for use in statistical modeling and interpretation. / Statistical analysis of high-throughput data, including machine learning and visualization,modeling and visualization of graphs and networks. This book is a dynamic document. Code underlying all of the computations that are shown is made available on a companion website, and readers can reproduce every number, figure, and table on their own computers.
Bioarrays : From Basics to Diagnostics
Bioarrays: From Basics to Diagnostics provides an integrated and comprehensive collection of timely articles on the use of bioarray techniques in the fields of biotechnology and molecular medicine. The entire volume is broken into four sections – Bioarray Technology Platforms, Biomarkers and Clinical Genomics, Biomarker Identification Using Clinical Proteomics and Glycomics, and Emerging Technologies in Diagnostics – that create one well-integrated work. Particular emphasis is placed on DNA, protein, and carbohydrate biochips. The volume also looks extensively at oligonucleotides, cDNA, proteins, antibodies, and carbohydrate arrays.
Bioactive Heterocycles IV
This volume contains nine more contributions from expert researchers of the?eld, providing readers with in depth and current research results regarding therespective topics. In the?rst chapter, Flemming et al. review the chemistry, biosynthesis, metabolism and biological activities of tetrahydrocannabinol and its deri- tives. Hansch and Verma contribute to the quantitative structure-activity re- tionship (QSAR) analysis of heterocyclic topoisomerase I and II inhibitors. These inhibitors, knowntoinhibit either enzyme, actasantitumoragentsand are currently used in chemotherapy and in clinicaltrials. In the third chapter, Khan reviews some aspects of molecular modeling studies on biologically active alkaloids.
Atoms, molecules and photons : An introduction to atomic- molecular- and quantum physics
This introduction to Atomic and Molecular Physics explains how our present model of atoms and molecules has been developed over the last two centuries both by many experimental discoveries and, from the theoretical side, by the introduction of quantum physics to the adequate description of micro-particles. It illustrates the wave model of particles by many examples and shows the limits of classical description. The interaction of electromagnetic radiation with atoms and molecules and its potential for spectroscopy is outlined in more detail and in particular lasers as modern spectroscopic tools are discussed more thoroughly. Many examples and problems with solutions are offered to encourage readers to actively engage in experimentation.
Atomistic modeling of materials failure
Atomistic Modeling of Materials Failure is an introduction to molecular and atomistic modeling techniques applied to solid deformation and fracture. Focusing on a variety of brittle, ductile and geometrically confined materials, this detailed overview includes computational methods at the atomic scale, and describes how these techniques can be used to model the dynamics of cracks, dislocations and other deformation mechanisms.
Atomistic approaches in modern biology : From quantum chemistry to molecular simulations
This volume of Topics in Current Chemistry presents an overview of atomistic theoreticalmethodsapplied tomolecular biologicalsystems. Itthus repesents abottom-upview of chemistryonbiologyfroma theoreticalperspective. The chapters arearrangedsuchthat important issuesareconsidered startingfrom a quantum mechanical perspective and proceeding to a molecular mechanics and molecular dynamics descriptiono fthemotionoftheelementaryparticles involved.which are responsible for the properties and function of biomolecules. Depending on the length and time scales relevant for a given phenomenon to be investigated, tailored theoretical methods are required to account for these. If one is interested in large scale motions of molecules, a molecul- mechnanics-based description willbeappropriate.
Asphaltenes, heavy oils, and petroleomics
Petroleomics is the prediction of all properties of petroleum based on the Petroleome, or complete listing of all components in a given crude oil. As it is developed, petroleomics will lead petroleum science into a bright new future, and it is the major focus of this book. A necessary step has been to resolve the molecular size and structure of asphaltene and its hierarchical aggregate structures, as well as the dynamics of asphaltenes. This is especially important for heavy oils. Flow assurance concerns and interfacial science are also treated. The technological development of downhole fluid analysis addresses the most important issues in deepwater production of oil.
Analytical Methods for Problems of Molecular Transport
"This book is designed to serve a dual function. It is intended that it be capable of serving as a teaching instrument, either in a classroom environment or independently, for the study of basic analytical methods and mathematical techniques that may be used in the Kinetic Theory of Gases and is primarily suitable for use in graduate level physics and engineering courses on the subject. This book should also be useful as a reference for scientists and engineers working in the fields of Rarefied Gas Dynamics and Aerosol Mechanics. In addition, the material in this book may be of interest to individuals working in such areas as Physical Chemistry, Chemical Engineering, or any other applied discipline in which gas-surface interactions should play a significant role."-
Analysis, Modeling and Simulation of Multiscale Problems
This book reports recent mathematical developments in the Programme "Analysis, Modeling and Simulation of Multiscale Problems", which started as a German research initiative in 2006. Multiscale problems occur in many fields of science, such as microstructures in materials, sharp-interface models, many-particle systems and motions on different spatial and temporal scales in quantum mechanics or in molecular dynamics. The book presents current mathematical foundations of modeling, and proposes efficient numerical treatment.
Analysis of phylogenetics and evolution with R
This book integrates a wide variety of data analysis methods into a single and flexible interface: the R language. This open source language is available for a wide range of computer systems and has been adopted as a computational environment by many authors of statistical software. Adopting R as a main tool for phylogenetic analyses will ease the workflow in biologists' data analyses, ensure greater scientific repeatability, and enhance the exchange of ideas and methodological developments.
Analysis and Control of Ultrafast Photoinduced Reactions
The present monograph summarizes, in a comprehensive way, several years of joint experimental and theoretical frontier research on ultrafast laser-induced molecular dynamics and its control. Emphasis is set on the characterization of the nuclear dynamics within molecular systems in various environments (gas phase, surfaces, solids, solution, strong fields) triggered by optical excitations spanning from the infrared to the ultraviolet. Building on the converged analysis between experiment and theory, control of chemical reactions is established by means of optimally shaped laser pulses. This paves the road toward new applications and future challenges in this rapidly developing research field.
An Introduction To Chemoinformatics
This, the first text written specifically for this field, aims to provide an introduction to the major techniques of chemoinformatics. The first part of the book deals with the representation of 2D and 3D molecular structures, the calculation of molecular descriptors and the construction of mathematical models. The second part describes other important topics including molecular similarity and diversity, the analysis of large data sets, virtual screening, and library design. Simple illustrative examples are used throughout to illustrate key concepts, supplemented with case studies from the literature.
Alzheimers Disease
Alzheimer’s disease (AD) is a neurodegenerative disease that robs the minds of our elderly population. Approximately one in every eight adults over the age of 65 and nearly half of those over 85 are afflicted with this disease. The aging population in developed societies will impose an ever increasing socioeconomic threat in the future. Current medicines for AD patients are mainly symptomatic treatments and a huge unmet medical need exists to slow the progression of this disease. A great deal of research has been dedicated to understanding the pathogenesis of AD from which comes many ideas for intervening with its progression. Some of these ideas have been fast-tracked to clinical trials due to the availability of medicines with proven clinical efficacies for other diseases (e.g. atorvastatin, simvastatin, rosiglitazone and clioquinol) while others represent novel chemical entities (e.g. glycogen synthase kinase-3 inhibitors).
Advanced computer simulation approaches for soft matter sciences I
Soft matter science is nowadays an acronym for an increasingly important class of materials, which ranges from polymers, liquid crystals, colloids up to complex macromolecular assemblies, covering sizes from the nanoscale up the microscale. Computer simulations have proven as an indispensable, if not the most powerful, tool to understand properties of these materials and link theoretical models to experiments. In this first volume of a small series recognized leaders of the field review advanced topics and provide critical insight into the state-of-the-art methods and scientific questions of this lively domain of soft condensed matter research.
Adsorption and Diffusion
Molecular Sieves - Science and Technology covers, in a comprehensive manner, the science and technology of zeolites and all related microporous and mesoporous materials. Authored by renowned experts, the contributions to this handbook-like series are grouped together topically in such a way that each volume deals with a specific sub-field. Volume 7 is treating fundamentals and analyses of adsorption and diffusion in zeolites including single-file diffusion, i.e. phenomena of basic importance, especially with respect to separation processes and catalysis. Various methods of measuring adsorption and diffusion are described and discussed, i.e. techniques such as chromatographic, gravimetric and barometric uptake and desorption, nuclear magnetic resonance, infrared spectroscopy, interference microscopy, neutron scattering, frequency response as well as proton profiling.
Acidity and Basicity
This is the first handbook on zeolites and other microporous materials. It is an up-to-date, highly sophisticated collection of information for those who deal with zeolites in industry or at academic institutions as well as being a guide for newcomers.
