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Advancing Rna Circuitry Engineering With Guidance Of Mathematical And Computational Models
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Book Synopsis Advancing RNA Circuitry Engineering with Guidance of Mathematical and Computational Models by : Yongxi Hu
Download or read book Advancing RNA Circuitry Engineering with Guidance of Mathematical and Computational Models written by Yongxi Hu and published by . This book was released on 2018 with total page 424 pages. Available in PDF, EPUB and Kindle. Book excerpt: The main goal of synthetic biology is to harness the power of biological genetic expression in order to perform various tasks, which could often have an impact on many aspects of our lives ranging from healthcare, pharmaceutical, to renewable energy and environments. These tasks are often carried out through synthetic genetic circuits composed of genetic parts like promoters, RBS, terminators, and inducible gene regulators. Numerous studies have expanded the toolbox for synthetic circuitry and established the guideline of circuitry assembly in the past decade. As the field advances, regulatory sRNA is emerging as a powerful tool in synthetic biology. These regulatory sRNAs are versatile and designable, more importantly, they offer a fast dynamic in genetic circuitry due to the fast production rates and degradation rates of RNA molecules. However, little work has been done to create a theoretical foundation for RNA circuit design. With the ultimate goal of gaining full control of RNA circuitry dynamics, this work focuses on building the theoretical foundation to understand and guide the design of RNA synthetic circuitry. A prerequisite to building such a foundation is to create a modeling framework that accurately describes the dynamics of RNA circuits. In the first part of this work, we build an effective model composed of ordinary differential equations to describe transcriptional RNA genetic circuitry and validate the model using a three-level cascade as a test case. We develop a sensitivity analysis based parameterization procedure that requires only a handful of simple experiments that can be performed in parallel using rapid cell-free transcription-translation (TX-TL) reactions. This part of the work establishes a fundamental method to predict circuit dynamics, which allow us to build more complex systems. Next, we expand the repertoire of synthetic gene networks built from these regulators by constructing a transcriptional negative autoregulation (NAR) network out of small RNAs (sRNAs). Using parameter sensitivity analysis, we design a simple set of experiments that allow us to accurately predict the NAR circuit dynamic in TX-TL. We also transfer the successful network design into Escherichia coli and show that our sRNA transcriptional network is functional in vivo. In the third part of this work, we investigate into an interesting observation where the transfer functions of inducible systems are altered by small transcriptional activating RNAs (STARs). We combine theory, computational model and experimental results to uncover the underlying causes of this phenomenon. Based on which, we establish the design principle of transfer function manipulation and dynamic range amplification induced by STARs. Together the work presented here establishes a theoretical foundation of RNA circuitry design. We anticipate that this foundation would support the development of new mathematical and computational models that provide insights and guidance for RNA circuitry design -which ultimately contributes to the advancement of synthetic circuitry engineering.
Book Synopsis A Cell Biologist's Guide to Modeling and Bioinformatics by : Raquell M. Holmes
Download or read book A Cell Biologist's Guide to Modeling and Bioinformatics written by Raquell M. Holmes and published by John Wiley & Sons. This book was released on 2008-02-13 with total page 224 pages. Available in PDF, EPUB and Kindle. Book excerpt: A step-by-step guide to using computational tools to solve problems in cell biology Combining expert discussion with examples that can be reproduced by the reader, A Cell Biologist's Guide to Modeling and Bioinformatics introduces an array of informatics tools that are available for analyzing biological data and modeling cellular processes. You learn to fully leverage public databases and create your own computational models. All that you need is a working knowledge of algebra and cellular biology; the author provides all the other tools you need to understand the necessary statistical and mathematical methods. Coverage is divided into two main categories: Molecular sequence database chapters are dedicated to gaining an understanding of tools and strategies—including queries, alignment methods, and statistical significance measures—needed to improve searches for sequence similarity, protein families, and putative functional domains. Discussions of sequence alignments and biological database searching focus on publicly available resources used for background research and the characterization of novel gene products. Modeling chapters take you through all the steps involved in creating a computational model for such basic research areas as cell cycle, calcium dynamics, and glycolysis. Each chapter introduces a new simulation tooland is based on published research. The combination creates a rich context for ongoing skill and knowledge development in modeling biological research systems. Students and professional cell biologists can develop the basic skills needed to learn computational cell biology. This unique text, with its step-by-step instruction, enables you to test and develop your new bioinformatics and modeling skills. References are provided to help you take advantage of more advanced techniques, technologies, and training.
Book Synopsis Mammalian Synthetic Systems by : Francesca Ceroni
Download or read book Mammalian Synthetic Systems written by Francesca Ceroni and published by Springer Nature. This book was released on with total page 319 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis The lac Operon by : Benno Müller-Hill
Download or read book The lac Operon written by Benno Müller-Hill and published by Walter de Gruyter. This book was released on 2011-05-12 with total page 221 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Feedback Systems by : Karl Johan Åström
Download or read book Feedback Systems written by Karl Johan Åström and published by Princeton University Press. This book was released on 2021-02-02 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The essential introduction to the principles and applications of feedback systems—now fully revised and expanded This textbook covers the mathematics needed to model, analyze, and design feedback systems. Now more user-friendly than ever, this revised and expanded edition of Feedback Systems is a one-volume resource for students and researchers in mathematics and engineering. It has applications across a range of disciplines that utilize feedback in physical, biological, information, and economic systems. Karl Åström and Richard Murray use techniques from physics, computer science, and operations research to introduce control-oriented modeling. They begin with state space tools for analysis and design, including stability of solutions, Lyapunov functions, reachability, state feedback observability, and estimators. The matrix exponential plays a central role in the analysis of linear control systems, allowing a concise development of many of the key concepts for this class of models. Åström and Murray then develop and explain tools in the frequency domain, including transfer functions, Nyquist analysis, PID control, frequency domain design, and robustness. Features a new chapter on design principles and tools, illustrating the types of problems that can be solved using feedback Includes a new chapter on fundamental limits and new material on the Routh-Hurwitz criterion and root locus plots Provides exercises at the end of every chapter Comes with an electronic solutions manual An ideal textbook for undergraduate and graduate students Indispensable for researchers seeking a self-contained resource on control theory
Download or read book Computerworld written by and published by . This book was released on 2000-09-25 with total page 128 pages. Available in PDF, EPUB and Kindle. Book excerpt: For more than 40 years, Computerworld has been the leading source of technology news and information for IT influencers worldwide. Computerworld's award-winning Web site (Computerworld.com), twice-monthly publication, focused conference series and custom research form the hub of the world's largest global IT media network.
Book Synopsis Selected Water Resources Abstracts by :
Download or read book Selected Water Resources Abstracts written by and published by . This book was released on 1978 with total page 656 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Cell-Free Synthetic Biology by : Jian Li
Download or read book Cell-Free Synthetic Biology written by Jian Li and published by Frontiers Media SA. This book was released on 2022-01-13 with total page 205 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis ASEE ... Profiles of Engineering & Engineering Technology Colleges by :
Download or read book ASEE ... Profiles of Engineering & Engineering Technology Colleges written by and published by . This book was released on 1998 with total page 796 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Mathematical Modelling in Biomedicine by : Vitaly Volpert
Download or read book Mathematical Modelling in Biomedicine written by Vitaly Volpert and published by MDPI. This book was released on 2021-01-26 with total page 224 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mathematical modelling in biomedicine is a rapidly developing scientific discipline at the intersection of medicine, biology, mathematics, physics, and computer science. Its progress is stimulated by fundamental scientific questions and by the applications to public health. This book represents a collection of papers devoted to mathematical modelling of various physiological problems in normal and pathological conditions. It covers a broad range of topics including cardiovascular system and diseases, heart and brain modelling, tumor growth, viral infections, and immune response. Computational models of blood circulation are used to study the influence of heart arrhythmias on coronary blood flow and on operating modes for left-ventricle-assisted devices. Wave propagation in the cardiac tissue is investigated in order to show the influence of tissue heterogeneity and fibrosis. The models of tumor growth are used to determine optimal protocols of antiangiogenic and radiotherapy. The models of viral hepatitis kinetics are considered for the parameter identification, and the evolution of viral quasi-species is investigated. The book presents the state-of-the-art in mathematical modelling in biomedicine and opens new perspectives in this passionate field of research.
Book Synopsis An Introduction to Mathematical Modeling by : Edward A. Bender
Download or read book An Introduction to Mathematical Modeling written by Edward A. Bender and published by Courier Corporation. This book was released on 2012-05-23 with total page 273 pages. Available in PDF, EPUB and Kindle. Book excerpt: Employing a practical, "learn by doing" approach, this first-rate text fosters the development of the skills beyond the pure mathematics needed to set up and manipulate mathematical models. The author draws on a diversity of fields — including science, engineering, and operations research — to provide over 100 reality-based examples. Students learn from the examples by applying mathematical methods to formulate, analyze, and criticize models. Extensive documentation, consisting of over 150 references, supplements the models, encouraging further research on models of particular interest. The lively and accessible text requires only minimal scientific background. Designed for senior college or beginning graduate-level students, it assumes only elementary calculus and basic probability theory for the first part, and ordinary differential equations and continuous probability for the second section. All problems require students to study and create models, encouraging their active participation rather than a mechanical approach. Beyond the classroom, this volume will prove interesting and rewarding to anyone concerned with the development of mathematical models or the application of modeling to problem solving in a wide array of applications.
Book Synopsis Mathematical Modeling in Systems Biology by : Brian P. Ingalls
Download or read book Mathematical Modeling in Systems Biology written by Brian P. Ingalls and published by MIT Press. This book was released on 2022-06-07 with total page 423 pages. Available in PDF, EPUB and Kindle. Book excerpt: An introduction to the mathematical concepts and techniques needed for the construction and analysis of models in molecular systems biology. Systems techniques are integral to current research in molecular cell biology, and system-level investigations are often accompanied by mathematical models. These models serve as working hypotheses: they help us to understand and predict the behavior of complex systems. This book offers an introduction to mathematical concepts and techniques needed for the construction and interpretation of models in molecular systems biology. It is accessible to upper-level undergraduate or graduate students in life science or engineering who have some familiarity with calculus, and will be a useful reference for researchers at all levels. The first four chapters cover the basics of mathematical modeling in molecular systems biology. The last four chapters address specific biological domains, treating modeling of metabolic networks, of signal transduction pathways, of gene regulatory networks, and of electrophysiology and neuronal action potentials. Chapters 3–8 end with optional sections that address more specialized modeling topics. Exercises, solvable with pen-and-paper calculations, appear throughout the text to encourage interaction with the mathematical techniques. More involved end-of-chapter problem sets require computational software. Appendixes provide a review of basic concepts of molecular biology, additional mathematical background material, and tutorials for two computational software packages (XPPAUT and MATLAB) that can be used for model simulation and analysis.
Book Synopsis All of Statistics by : Larry Wasserman
Download or read book All of Statistics written by Larry Wasserman and published by Springer Science & Business Media. This book was released on 2013-12-11 with total page 446 pages. Available in PDF, EPUB and Kindle. Book excerpt: Taken literally, the title "All of Statistics" is an exaggeration. But in spirit, the title is apt, as the book does cover a much broader range of topics than a typical introductory book on mathematical statistics. This book is for people who want to learn probability and statistics quickly. It is suitable for graduate or advanced undergraduate students in computer science, mathematics, statistics, and related disciplines. The book includes modern topics like non-parametric curve estimation, bootstrapping, and classification, topics that are usually relegated to follow-up courses. The reader is presumed to know calculus and a little linear algebra. No previous knowledge of probability and statistics is required. Statistics, data mining, and machine learning are all concerned with collecting and analysing data.
Book Synopsis American Book Publishing Record by :
Download or read book American Book Publishing Record written by and published by . This book was released on 2003 with total page 724 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Sustainable Agriculture in the Era of the OMICs Revolution by : Channa S. Prakash
Download or read book Sustainable Agriculture in the Era of the OMICs Revolution written by Channa S. Prakash and published by Springer Nature. This book was released on 2023-01-01 with total page 511 pages. Available in PDF, EPUB and Kindle. Book excerpt: Access to food with enough calories and nutrients is a fundamental right of every human. The global population has exceeded 7.8 billion and is expected to pass 10 billion by 2055. Such rapid population increase presents a great challenge for food supply. More grain production is needed to provide basic calories for humans. Thus, it is crucial to produce 60-110% more food to fill the gap between food production and the demand of future generations. Meanwhile food nutritional values are of increasing interest to accommodate industrialized modern lives. The instability of food production caused by global climate change presents another great challenge. The global warming rate has become more rapid in recent decades, with more frequent extreme climate change including higher temperatures, drought, and floods. Our world faces various unprecedented scenarios such as rising temperatures, which causes melting glaciers and the resulting various biotic and abiotic stresses, ultimately leading to food scarcity. In these circumstances it is of utmost importance to examine the genetic basis and extensive utilization of germplasm to develop “climate resilient cultivars” through the application of plant breeding and biotechnological tools. Future crops must adapt to these new and unpredictable environments. Crop varieties resistant to biotic and abiotic stresses are also needed as plant disease, insects, drought, high- and low-temperature stresses are expected to be impacted by climate change. Thus, we need a food production system that can simultaneously satisfy societal demands and long-term development. Since the Green Revolution in the 1960s, farming has been heavily dependent on high input of nitrogen and pesticides. This leads to environmental pollution which is not sustainable in the long run. Therefore, a new breeding scheme is urgently needed to enable sustainable agriculture; including new strategies to develop varieties and crops that have high yield potential, high yield stability, and superior grain quality and nutrition while also using less consumption of water, fertilizer, and chemicals in light of environmental protection. While we face these challenges, we also have great opportunities, especially with flourishing developments in omics technologies. High-quality reference genomes are becoming available for a larger number of species, with some species having more than one reference genome. The genome-wide re-sequencing of diverse varieties enables the identification of core- and pan-genomes. An integration of omics data will enable a rapid and high-throughput identification of many genes simultaneously for a relevant trait. This will change our current research paradigm fundamentally from single gene analysis to pathway or network analysis. This will also expand our understanding of crop domestication and improvement. In addition, with the knowledge gained from omics data, in combination with new technologies like targeted gene editing, we can breed new varieties and crops for sustainable agriculture.
Book Synopsis Neuromechanical Modeling of Posture and Locomotion by : Boris I. Prilutsky
Download or read book Neuromechanical Modeling of Posture and Locomotion written by Boris I. Prilutsky and published by Springer. This book was released on 2015-12-30 with total page 371 pages. Available in PDF, EPUB and Kindle. Book excerpt: Neuromechanics is a new, quickly growing field of neuroscience research that merges neurophysiology, biomechanics and motor control and aims at understanding living systems and their elements through interactions between their neural and mechanical dynamic properties. Although research in Neuromechanics is not limited by computational approaches, neuromechanical modeling is a powerful tool that allows for integration of massive knowledge gained in the past several decades in organization of motion related brain and spinal cord activity, various body sensors and reflex pathways, muscle mechanical and physiological properties and detailed quantitative morphology of musculoskeletal systems. Recent work in neuromechanical modeling has demonstrated advantages of such an integrative approach and led to discoveries of new emergent properties of neuromechanical systems. Neuromechanical Modeling of Posture and Locomotion will cover a wide range of topics from theoretical studies linking the organization of reflex pathways and central pattern generating circuits with morphology and mechanics of the musculoskeletal system (Burkholder; Nichols; Shevtsova et al.) to detailed neuromechanical models of postural and locomotor control (Bunderson; Edwards, Marking et al., Ting). Furthermore, uniquely diverse modeling approaches will be presented in the book including a theoretical dynamic analysis of locomotor phase transitions (Spardy and Rubin), a hybrid computational modeling that allows for in vivo interactions between parts of a living organism and a computer model (Edwards et al.), a physical neuromechanical model of the human locomotor system (Lewis), and others.
Book Synopsis Molecular Modeling and Simulation by : Tamar Schlick
Download or read book Molecular Modeling and Simulation written by Tamar Schlick and published by Springer Science & Business Media. This book was released on 2013-04-18 with total page 669 pages. Available in PDF, EPUB and Kindle. Book excerpt: Very broad overview of the field intended for an interdisciplinary audience; Lively discussion of current challenges written in a colloquial style; Author is a rising star in this discipline; Suitably accessible for beginners and suitably rigorous for experts; Features extensive four-color illustrations; Appendices featuring homework assignments and reading lists complement the material in the main text