Download or read book Molecular Logic and Computational Synthetic Biology written by Madalena Chaves and published by Springer. This book was released on 2019-04-27 with total page 168 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book collects the revised selected proceedings of the First International Symposium in Molecular Logic and Computational Synthetic Biology ( MLCSB), held in Chile, Santiago, in December 2018. The volume contains 7 full revised papers along with 2 surveys from 19 submissions presented at the symposium. One of the goals of the MLCSB 2018 was to explore the potential of molecular logic frameworks to study the emerging behavioural patterns in biological networks, combining discrete, continuous and stochastic features, and resorting both to specific or general-purpose analysis and verification techniques.

Download or read book Molecular Logic based Computation written by A Prasanna de Silva and published by Royal Society of Chemistry. This book was released on 2016-01-13 with total page 417 pages. Available in PDF, EPUB and Kindle. Book excerpt: We all learn - in schools, factories, bars and streets. We gather, store, process and transmit information in society. Molecular systems involved in our senses and within our brains allow all this to happen and molecular systems allow living things of all kinds to handle information for the purpose of survival and growth. Nevertheless, the vital link between molecules and computation was not generally appreciated until a few decades ago. Semiconductor-based information technology had penetrated society at many levels and the interest in maintaining momentum of this revolution led to the consideration of molecules, among others, as possible information handlers. Such an overlap between the recent engineering-oriented revolution with the ancient biology-oriented success story is very interesting and George Boole's times in Ireland 150 years ago produced the logic ideas that provide the foundations of computation to this day. Molecular logic and computation is a field which is 17 years young, has had a healthy growth and is a story which deserves to be told. It is a growing branch of chemical science which highlights the connection between information technology (engineering and biological) and chemistry. The author and co-workers of this publication launched molecular logic as an experimental field by publishing the first research in the primary literature in 1993 and are uniquely placed to recount how the field has grown. There is no other book at present on molecular logic and computation and is more comprehensive than that found in any review available so far. It shows how designed molecules can play the role of information processors in a wide variety of situations, once we are educated by those information processors already available in the semiconductor electronics business and in the natural world. Following a short history of the field, is a set of primers on logic, computing and photochemical principles which are an essential basis in this field. The book covers all of the Boolean logic gates driven by a single input and all of those with double inputs and the wide range of designs which lie beneath these gates is a particular highlight. The easily-available diversity of chemical systems is another highlight, especially when it leads to reconfigurable logic gates. Further on in the book, molecular arithmetic and other more complex logic operations, including those with a memory and those which stray beyond binary are covered. Then follows molecular computing approaches which lie outside the Boolean blueprint, including quantum phenomena and finally, the book catalogues the useful real-life applications of molecular logic and computation which are already available. This book is an authoritative, state of the art, reference and a 'one-stop-shop' concerning the current state of the field for scientists, academics and postgraduate students.

Download or read book Computational Systems Biology written by Andres Kriete and published by Academic Press. This book was released on 2013-11-26 with total page 549 pages. Available in PDF, EPUB and Kindle. Book excerpt: This comprehensively revised second edition of Computational Systems Biology discusses the experimental and theoretical foundations of the function of biological systems at the molecular, cellular or organismal level over temporal and spatial scales, as systems biology advances to provide clinical solutions to complex medical problems. In particular the work focuses on the engineering of biological systems and network modeling. - Logical information flow aids understanding of basic building blocks of life through disease phenotypes - Evolved principles gives insight into underlying organizational principles of biological organizations, and systems processes, governing functions such as adaptation or response patterns - Coverage of technical tools and systems helps researchers to understand and resolve specific systems biology problems using advanced computation - Multi-scale modeling on disparate scales aids researchers understanding of dependencies and constraints of spatio-temporal relationships fundamental to biological organization and function.

Download or read book Algorithms in Structural Molecular Biology written by Bruce R. Donald and published by MIT Press. This book was released on 2023-08-15 with total page 497 pages. Available in PDF, EPUB and Kindle. Book excerpt: An overview of algorithms important to computational structural biology that addresses such topics as NMR and design and analysis of proteins.Using the tools of information technology to understand the molecular machinery of the cell offers both challenges and opportunities to computational scientists. Over the past decade, novel algorithms have been developed both for analyzing biological data and for synthetic biology problems such as protein engineering. This book explains the algorithmic foundations and computational approaches underlying areas of structural biology including NMR (nuclear magnetic resonance); X-ray crystallography; and the design and analysis of proteins, peptides, and small molecules. Each chapter offers a concise overview of important concepts, focusing on a key topic in the field. Four chapters offer a short course in algorithmic and computational issues related to NMR structural biology, giving the reader a useful toolkit with which to approach the fascinating yet thorny computational problems in this area. A recurrent theme is understanding the interplay between biophysical experiments and computational algorithms. The text emphasizes the mathematical foundations of structural biology while maintaining a balance between algorithms and a nuanced understanding of experimental data. Three emerging areas, particularly fertile ground for research students, are highlighted: NMR methodology, design of proteins and other molecules, and the modeling of protein flexibility. The next generation of computational structural biologists will need training in geometric algorithms, provably good approximation algorithms, scientific computation, and an array of techniques for handling noise and uncertainty in combinatorial geometry and computational biophysics. This book is an essential guide for young scientists on their way to research success in this exciting field.

Download or read book DNA Computing and Molecular Programming written by Chris Thachuk and published by Springer. This book was released on 2019-07-30 with total page 247 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 25th International Conference on DNA Computing and Molecular Programming, DNA 25, held in Seattle, WA, USA, in August 2019. The 12 full papers presented were carefully selected from 19 submissions. The papers cover a wide range of topics relating to biomolecular computing such as algorithms and models for computation on biomolecular systems; computational processes in vitro and in vivo; molecular switches, gates, devices, and circuits; molecular folding and self-assembly of nanostructures; analysis and theoretical models of laboratory techniques; molecular motors and molecular robotics; information storage; studies of fault-tolerance and error correction; software tools for analysis, simulation, anddesign; synthetic biology and in vitro evolution; and applications in engineering, physics, chemistry, biology, and medicine.

Download or read book The Science and Applications of Synthetic and Systems Biology written by Institute of Medicine and published by National Academies Press. This book was released on 2011-12-30 with total page 570 pages. Available in PDF, EPUB and Kindle. Book excerpt: Many potential applications of synthetic and systems biology are relevant to the challenges associated with the detection, surveillance, and responses to emerging and re-emerging infectious diseases. On March 14 and 15, 2011, the Institute of Medicine's (IOM's) Forum on Microbial Threats convened a public workshop in Washington, DC, to explore the current state of the science of synthetic biology, including its dependency on systems biology; discussed the different approaches that scientists are taking to engineer, or reengineer, biological systems; and discussed how the tools and approaches of synthetic and systems biology were being applied to mitigate the risks associated with emerging infectious diseases. The Science and Applications of Synthetic and Systems Biology is organized into sections as a topic-by-topic distillation of the presentations and discussions that took place at the workshop. Its purpose is to present information from relevant experience, to delineate a range of pivotal issues and their respective challenges, and to offer differing perspectives on the topic as discussed and described by the workshop participants. This report also includes a collection of individually authored papers and commentary.

Download or read book Computational Methods in Systems Biology written by Monika Heiner and published by Springer Science & Business Media. This book was released on 2008-10-07 with total page 413 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 6th International Conference on Computational Methods in Systems Biology, CMSB 2008, held in Rostock, Germany, in September 2008. The 21 revised full papers presented together with the summaries of 5 invited papers were carefully reviewed and selected from more than 60 submissions. The papers cover theoretical or applied contributions that are motivated by a biological question focusing on modeling approaches, including process algebra, simulation approaches, analysis methods, in particular model checking and flux analysis, and case studies.

Download or read book Digital Transformation and the World Economy written by Andrei Rudskoi and published by Springer Nature. This book was released on 2022-01-24 with total page 243 pages. Available in PDF, EPUB and Kindle. Book excerpt: Nanotechnology, biotechnology, information technology, and cognitive sciences are contributing to the emergence of intelligent computers and robots with elements of artificial intelligence and intelligent machines. This book postulates that these developments are accelerating the technological substitution of jobs and the shift in labor demand towards high qualification levels, putting the jobs of lower-skilled labor at risk. The digital economy is poised to increase the demand for highly qualified specialists in STEM fields (scientific research, innovative technologies, engineering, and mathematics serving digital technologies). In addition, highly skilled robotics engineers, AI and machine learning specialists, and virtual and augmented reality architects will be required. This book, using sector-focused mathematical models, explores how the demand for specialized human capital will play a decisive role in increasing the efficiency and productivity of labor in the digital economy. Success is guaranteed to those entrepreneurs who manage to establish a successful process of interaction with intelligent machines, which will require a deep restructuring of the training system for the digital economy.

Download or read book Computational Systems Biology of Pathogen Host Interactions written by Saliha Durmuş and published by Frontiers Media SA. This book was released on 2016-05-30 with total page 200 pages. Available in PDF, EPUB and Kindle. Book excerpt: A thorough understanding of pathogenic microorganisms and their interactions with host organisms is crucial to prevent infectious threats due to the fact that Pathogen-Host Interactions (PHIs) have critical roles in initiating and sustaining infections. Therefore, the analysis of infection mechanisms through PHIs is indispensable to identify diagnostic biomarkers and next-generation drug targets and then to develop strategic novel solutions against drug-resistance and for personalized therapy. Traditional approaches are limited in capturing mechanisms of infection since they investigate hosts or pathogens individually. On the other hand, the systems biology approach focuses on the whole PHI system, and is more promising in capturing infection mechanisms. Here, we bring together studies on the below listed sections to present the current picture of the research on Computational Systems Biology of Pathogen-Host Interactions: - Computational Inference of PHI Networks using Omics Data - Computational Prediction of PHIs - Text Mining of PHI Data from the Literature - Mathematical Modeling and Bioinformatic Analysis of PHIs Computational Inference of PHI Networks using Omics Data Gene regulatory, metabolic and protein-protein networks of PHI systems are crucial for a thorough understanding of infection mechanisms. Great advances in molecular biology and biotechnology have allowed the production of related omics data experimentally. Many computational methods are emerging to infer molecular interaction networks of PHI systems from the corresponding omics data. Computational Prediction of PHIs Due to the lack of experimentally-found PHI data, many computational methods have been developed for the prediction of pathogen-host protein-protein interactions. Despite being emerging, currently available experimental PHI data are far from complete for a systems view of infection mechanisms through PHIs. Therefore, computational methods are the main tools to predict new PHIs. To this end, the development of new computational methods is of great interest. Text Mining of PHI Data from Literature Despite the recent development of many PHI-specific databases, most data relevant to PHIs are still buried in the biomedical literature, which demands for the use of text mining techniques to unravel PHIs hidden in the literature. Only some rare efforts have been performed to achieve this aim. Therefore, the development of novel text mining methods specific for PHI data retrieval is of key importance for efficient use of the available literature. Mathematical Modeling and Bioinformatic Analysis of PHIs After the reconstruction of PHI networks experimentally and/or computationally, their mathematical modeling and detailed computational analysis is required using bioinformatics tools to get insights on infection mechanisms. Bioinformatics methods are increasingly applied to analyze the increasing amount of experimentally-found and computationally-predicted PHI data.

Download or read book Formal Methods for Computational Systems Biology written by Marco Bernardo and published by Springer. This book was released on 2008-05-31 with total page 533 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents a set of 14 papers accompanying the lectures of leading researchers given at the 8th edition of the International School on Formal Methods for the Design of Computer, Communication and Software Systems, SFM 2008, held in Bertinoro, Italy in June 2008. SFM 2008 was devoted to formal techniques for computational systems biology and covered several aspects of the field, including computational models, calculi and logics for biological systems, and verification and simulation methods. The first part of this volume comprises nine papers based on regular lectures, the second part of this volume comprises five papers based on talks given by people involved in the Italian BISCA research project on Bio-Inspired Systems and Calculi with Applications.

Download or read book Demystifying Computation A Hands on Introduction written by Apostolos Syropoulos and published by World Scientific Publishing Company. This book was released on 2017-04-19 with total page 214 pages. Available in PDF, EPUB and Kindle. Book excerpt: Problem solving in computing is referred to as computational thinking. The theory behind this concept is challenging in its technicalities, yet simple in its ideas. This book introduces the theory of computation from its inception to current form of complexity; from explanations of how the field of computer science was formed using classical ideas in mathematics by Gödel, to conceptualization of the Turing Machine, to its more recent innovations in quantum computation, hypercomputation, vague computing and natural computing. It describes the impact of these in relation to academia, business and wider society, providing a sound theoretical basis for its practical application.Written for accessibility, Demystifying Computation provides the basic knowledge needed for non-experts in the field, undergraduate computer scientists and students of information and communication technology and software development.

Download or read book Computational Matter written by Susan Stepney and published by Springer. This book was released on 2018-07-20 with total page 335 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is concerned with computing in materio: that is, unconventional computing performed by directly harnessing the physical properties of materials. It offers an overview of the field, covering four main areas of interest: theory, practice, applications and implications. Each chapter synthesizes current understanding by deliberately bringing together researchers across a collection of related research projects. The book is useful for graduate students, researchers in the field, and the general scientific reader who is interested in inherently interdisciplinary research at the intersections of computer science, biology, chemistry, physics, engineering and mathematics.

Download or read book Transactions on Computational Systems Biology VI written by Gordon Plotkin and published by Springer. This book was released on 2006-11-17 with total page 253 pages. Available in PDF, EPUB and Kindle. Book excerpt: The 5th Transactions on Computational Systems Biology volume, edited by Gordon Plotkin, features carefully selected and enhanced contributions initially presented at the 2005 IEEE International Conference on Granular Computing. The 9 papers selected for this special issue discuss various aspects of computational methods, algorithm and techniques in bioinformatics such as gene expression analysis, biomedical literature mining and natural language processing, protein structure prediction, biological database management and biomedical information retrieval.

Download or read book Synthetic Biology written by Madan L. Nagpal and published by BoD – Books on Demand. This book was released on 2020-02-12 with total page 208 pages. Available in PDF, EPUB and Kindle. Book excerpt: Synthetic biology gives us a new hope because it combines various disciplines, such as genetics, chemistry, biology, molecular sciences, and other disciplines, and gives rise to a novel interdisciplinary science. We can foresee the creation of the new world of vegetation, animals, and humans with the interdisciplinary system of biological sciences. These articles are contributed by renowned experts in their fields. The field of synthetic biology is growing exponentially and opening up new avenues in multidisciplinary approaches by bringing together theoretical and applied aspects of science.

Download or read book Nanoscience And Technology A Collection Of Reviews From Nature Journals written by Peter Rodgers and published by World Scientific. This book was released on 2009-08-21 with total page 367 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book contains 35 review articles on nanoscience and nanotechnology that were first published in Nature Nanotechnology, Nature Materials and a number of other Nature journals. The articles are all written by leading authorities in their field and cover a wide range of areas in nanoscience and technology, from basic research (such as single-molecule devices and new materials) through to applications (in, for example, nanomedicine and data storage).

Download or read book Logical Modeling of Biological Systems written by Luis Fariñas del Cerro and published by John Wiley & Sons. This book was released on 2014-08-08 with total page 328 pages. Available in PDF, EPUB and Kindle. Book excerpt: Systems Biology is the systematic study of the interactions between the components of a biological system and studies how these interactions give rise to the function and behavior of the living system. Through this, a life process is to be understood as a whole system rather than the collection of the parts considered separately. Systems Biology is therefore more than just an emerging field: it represents a new way of thinking about biology with a dramatic impact on the way that research is performed. The logical approach provides an intuitive method to provide explanations based on an expressive relational language. This book covers various aspects of logical modeling of biological systems, bringing together 10 recent logic-based approaches to Systems Biology by leading scientists. The chapters cover the biological fields of gene regulatory networks, signaling networks, metabolic pathways, molecular interaction and network dynamics, and show logical methods for these domains based on propositional and first-order logic, logic programming, answer set programming, temporal logic, Boolean networks, Petri nets, process hitting, and abductive and inductive logic programming. It provides an excellent guide for all scientists, biologists, bioinformaticians, and engineers, who are interested in logic-based modeling of biological systems, and the authors hope that new scientists will be encouraged to join this exciting scientific endeavor.

Download or read book Biodefense in the Age of Synthetic Biology written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2019-01-05 with total page 189 pages. Available in PDF, EPUB and Kindle. Book excerpt: Scientific advances over the past several decades have accelerated the ability to engineer existing organisms and to potentially create novel ones not found in nature. Synthetic biology, which collectively refers to concepts, approaches, and tools that enable the modification or creation of biological organisms, is being pursued overwhelmingly for beneficial purposes ranging from reducing the burden of disease to improving agricultural yields to remediating pollution. Although the contributions synthetic biology can make in these and other areas hold great promise, it is also possible to imagine malicious uses that could threaten U.S. citizens and military personnel. Making informed decisions about how to address such concerns requires a realistic assessment of the capabilities that could be misused. Biodefense in the Age of Synthetic Biology explores and envisions potential misuses of synthetic biology. This report develops a framework to guide an assessment of the security concerns related to advances in synthetic biology, assesses the levels of concern warranted for such advances, and identifies options that could help mitigate those concerns.