Hybrid Biomolecular Modeling

Author : Slavica Jonic,Osamu Miyashita,Isabelle Callebaut
Publisher : Frontiers Media SA
Page : 128 pages
File Size : 45,6 Mb
Release : 2019-01-24
Category : Electronic
ISBN : 9782889456994

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Hybrid Biomolecular Modeling by Slavica Jonic,Osamu Miyashita,Isabelle Callebaut Pdf

Models of biomolecular structure and dynamics are often obtained by combining simulation or prediction approaches (e.g., comparative modeling, Molecular Dynamics (MD) simulations, Normal Mode Analysis (NMA), etc.) with experimental approaches (e.g., Nuclear Magnetic Resonance (NMR), X-ray crystallography, Small-Angle X-ray Scattering (SAXS), Electron Microscopy (EM), etc.). Such hybrid modeling extends the capabilities of experimental techniques, by enriching structural information and facilitating dynamics studies of biomolecules. This eBook contains articles on methodological developments, applications, and challenges of hybrid biomolecular modeling that have been collected in the framework of the Frontiers Research Topic entitled “Hybrid Biomolecular Modeling”.

Author : Andrei L. Tchougréeff
Publisher : Springer Science & Business Media
Page : 360 pages
File Size : 49,9 Mb
Release : 2008-08-01
Category : Science
ISBN : 9781402081897

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Hybrid Methods of Molecular Modeling by Andrei L. Tchougréeff Pdf

This is a self-contained advanced review offering step by step derivation of the consistent theoretical picture of hybrid modeling methods and the thorough analysis of the concepts and current practical methods of hybrid modeling based on this theory. The book presents its material in a sequential way paying attention both to the physical soundness of the approximations used and to the mathematical rigor necessary for practical developing of the robust modeling code.

Author : Valentina Tozzini,Giulia Palermo,Matteo Dal Peraro,Alexandre M. J. J. Bonvin,Rommie E. Amaro
Publisher : Frontiers Media SA
Page : 235 pages
File Size : 46,9 Mb
Release : 2020-10-27
Category : Science
ISBN : 9782889661091

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Multiscale Modeling From Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations by Valentina Tozzini,Giulia Palermo,Matteo Dal Peraro,Alexandre M. J. J. Bonvin,Rommie E. Amaro Pdf

This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact.

Author : Jinhu Lü,Pei Wang
Publisher : Springer Nature
Page : 464 pages
File Size : 54,9 Mb
Release : 2020-12-06
Category : Science
ISBN : 9789811591440

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Modeling and Analysis of Bio-molecular Networks by Jinhu Lü,Pei Wang Pdf

This book addresses a number of questions from the perspective of complex systems: How can we quantitatively understand the life phenomena? How can we model life systems as complex bio-molecular networks? Are there any methods to clarify the relationships among the structures, dynamics and functions of bio-molecular networks? How can we statistically analyse large-scale bio-molecular networks? Focusing on the modeling and analysis of bio-molecular networks, the book presents various sophisticated mathematical and statistical approaches. The life system can be described using various levels of bio-molecular networks, including gene regulatory networks, and protein-protein interaction networks. It first provides an overview of approaches to reconstruct various bio-molecular networks, and then discusses the modeling and dynamical analysis of simple genetic circuits, coupled genetic circuits, middle-sized and large-scale biological networks, clarifying the relationships between the structures, dynamics and functions of the networks covered. In the context of large-scale bio-molecular networks, it introduces a number of statistical methods for exploring important bioinformatics applications, including the identification of significant bio-molecules for network medicine and genetic engineering. Lastly, the book describes various state-of-art statistical methods for analysing omics data generated by high-throughput sequencing. This book is a valuable resource for readers interested in applying systems biology, dynamical systems or complex networks to explore the truth of nature.

Author : Haruki Nakamura,Gerard Kleywegt,Stephen K. Burley,John L. Markley
Publisher : Springer
Page : 272 pages
File Size : 48,5 Mb
Release : 2019-01-08
Category : Science
ISBN : 9789811322006

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Integrative Structural Biology with Hybrid Methods by Haruki Nakamura,Gerard Kleywegt,Stephen K. Burley,John L. Markley Pdf

This book presents a new emerging concept of "Integrative Structural Biology". It covers current trends of the molecular and cellular structural biology, providing new methods to observe, validate, and keep the structural models of the large cellular machines with recent scientific results. Structures of very large macromolecular machines in cells are being determined by combining observations from complementary experimental methods. Thus, this volume presents the each methods such as X-ray crystallography, NMR spectroscopy, 3DEM, small-angle scattering (SAS), FRET, crosslinking, and enables the readers to understand the hybrid methods. This book discusses how those integrative models should be represented, validated and archived. A unique highlight of this book is discussion of the data validation and archive, which are big problems in this filed along with the progress of this field. The researchers in biology will be interested in this book as a guide book for learning the current structure biology, but also those in structure biology may use this book as a comprehensive reference to cover broad topics.

Author : Tamar Schlick
Publisher : Royal Society of Chemistry
Page : 381 pages
File Size : 45,6 Mb
Release : 2012
Category : Biomolecules
ISBN : 9781849734615

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Innovations in Biomolecular Modeling and Simulations by Tamar Schlick Pdf

This two volume set describes innovations in biomolecular modeling and simulation, in both the algorithmic and application fronts.

Author : Jarka Glassey,Moritz von Stosch
Publisher : CRC Press
Page : 219 pages
File Size : 42,7 Mb
Release : 2018-02-01
Category : Science
ISBN : 9781351184366

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Hybrid Modeling in Process Industries by Jarka Glassey,Moritz von Stosch Pdf

This title introduces the underlying theory and demonstrates practical applications in different process industries using hybrid modeling. It reviews hybrid modeling approach applicability in wide range of process industries, recommends how to increase hybrid model performance and throw Insights into cost efficient practices in modeling techniques Discusses advance process operation maximizing the benefits of available process knowledge and Includes real-life and practical case studies

Author : Tamar Schlick
Publisher : Royal Society of Chemistry
Page : 380 pages
File Size : 53,7 Mb
Release : 2012-05-24
Category : Science
ISBN : 9781849735049

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Innovations in Biomolecular Modeling and Simulations by Tamar Schlick Pdf

The chemical and biological sciences face unprecedented opportunities in the 21st century. A confluence of factors from parallel universes - advances in experimental techniques in biomolecular structure determination, progress in theoretical modeling and simulation for large biological systems, and breakthroughs in computer technology - has opened new avenues of opportunity as never before. Now, experimental data can be interpreted and further analysed by modeling, and predictions from any approach can be tested and advanced through companion methodologies and technologies. This two volume set describes innovations in biomolecular modeling and simulation, in both the algorithmic and application fronts. With contributions from experts in the field, the books describe progress and innovation in areas including: simulation algorithms for dynamics and enhanced configurational sampling, force field development, implicit solvation models, coarse-grained models, quantum-mechanical simulations, protein folding, DNA polymerase mechanisms, nucleic acid complexes and simulations, RNA structure analysis and design and other important topics in structural biology modeling. The books are aimed at graduate students and experts in structural biology and chemistry and the emphasis is on reporting innovative new approaches rather than providing comprehensive reviews on each subject.

Author : Rajeev Alur,George Pappas
Publisher : Springer
Page : 674 pages
File Size : 42,5 Mb
Release : 2004-02-24
Category : Computers
ISBN : 9783540247432

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Hybrid Systems: Computation and Control by Rajeev Alur,George Pappas Pdf

This volume contains the proceedings of the 7th Workshop on Hybrid Systems: Computation and Control (HSCC 2004) held in Philadelphia, USA, from March 25 to 27, 2004. The annual workshop on hybrid systems attracts researchers from academia and industry interested in modeling, analysis, and implemen- tion of dynamic and reactive systems involving both discrete and continuous behaviors. The previous workshops in the HSCC series were held in Berkeley, USA(1998),Nijmegen,TheNetherlands(1999),Pittsburgh,USA(2000),Rome, Italy (2001), Palo Alto, USA (2002), and Prague, Czech Republic (2003). This year’s HSCC was organized in cooperation with ACM SIGBED (Special Interest Group on Embedded Systems) and was technically co-sponsored by the IEEE Control Systems Society. The program consisted of 4 invited talks and 43 regular papers selected from 117 regular submissions. The program covered topics such as tools for analysis and veri?cation, control and optimization, modeling, and engineering applica- ons, as in past years, and emerging directions in programming language support and implementation. The program also contained one special session focusing on the interplay between biomolecular networks, systems biology, formal methods, andthecontrolofhybridsystems.

Author : Tamar Schlick
Publisher : Royal Society of Chemistry
Page : 354 pages
File Size : 49,9 Mb
Release : 2012-05-24
Category : Science
ISBN : 9781849735056

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Innovations in Biomolecular Modeling and Simulations by Tamar Schlick Pdf

The chemical and biological sciences face unprecedented opportunities in the 21st century. A confluence of factors from parallel universes - advances in experimental techniques in biomolecular structure determination, progress in theoretical modeling and simulation for large biological systems, and breakthroughs in computer technology - has opened new avenues of opportunity as never before. Now, experimental data can be interpreted and further analysed by modeling, and predictions from any approach can be tested and advanced through companion methodologies and technologies. This two volume set describes innovations in biomolecular modeling and simulation, in both the algorithmic and application fronts. With contributions from experts in the field, the books describe progress and innovation in areas including: simulation algorithms for dynamics and enhanced configurational sampling, force field development, implicit solvation models, coarse-grained models, quantum-mechanical simulations, protein folding, DNA polymerase mechanisms, nucleic acid complexes and simulations, RNA structure analysis and design and other important topics in structural biology modeling. The books are aimed at graduate students and experts in structural biology and chemistry and the emphasis is on reporting innovative new approaches rather than providing comprehensive reviews on each subject.

Author : Joseph W. Kurutz
Publisher : Unknown
Page : 376 pages
File Size : 46,5 Mb
Release : 1998
Category : Electronic
ISBN : WISC:89066549122

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Experimental and Theoretical Studies in Biomolecular Structure and Catalysis by Joseph W. Kurutz Pdf

Author : Bhaskar DasGupta,Jie Liang
Publisher : John Wiley & Sons
Page : 264 pages
File Size : 43,6 Mb
Release : 2016-01-07
Category : Science
ISBN : 9781119162278

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Models and Algorithms for Biomolecules and Molecular Networks by Bhaskar DasGupta,Jie Liang Pdf

By providing expositions to modeling principles, theories, computational solutions, and open problems, this reference presents a full scope on relevant biological phenomena, modeling frameworks, technical challenges, and algorithms. Up-to-date developments of structures of biomolecules, systems biology, advanced models, and algorithms Sampling techniques for estimating evolutionary rates and generating molecular structures Accurate computation of probability landscape of stochastic networks, solving discrete chemical master equations End-of-chapter exercises

Author : Maria D. Di Benedetto,Alberto L. Sangiovanni-Vincentelli
Publisher : Springer
Page : 516 pages
File Size : 49,6 Mb
Release : 2003-06-29
Category : Computers
ISBN : 9783540453512

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Hybrid Systems: Computation and Control by Maria D. Di Benedetto,Alberto L. Sangiovanni-Vincentelli Pdf

This volume contains the proceedings of the Fourth Workshop on Hybrid - stems: Computation and Control (HSCC 2001) held in Rome, Italy on March 28-30, 2001. The Workshop on Hybrid Systems attracts researchers from in- stry and academia interested in modeling, analysis, synthesis, and implemen- tion of dynamic and reactive systems involving both discrete (integer, logical, symbolic) and continuous behaviors. It is a forum for the discussion of the - test developments in all aspects of hybrid systems, including formal models and computational representations, algorithms and heuristics, computational tools, and new challenging applications. The Fourth HSCC International Workshop continues the series of workshops held in Grenoble, France (HART’97), Berkeley, California, USA (HSCC’98), N- megen, The Netherlands (HSCC’99), and Pittsburgh, Pennsylvania, USA (HSCC 2000). Proceedings of these workshops have been published in the Lecture Notes in Computer Science (LNCS) series by Springer-Verlag. In line with the beautiful work that led to the design of the palace in which the workshop was held, Palazzo Lancellotti in Rome, resulting from the col- boration of many artists and architects of di erent backgrounds, the challenge faced by the hybrid system community is to harmonize and extract the best from two main research areas: computer science and control theory.

Author : Garegin A. Papoian
Publisher : CRC Press
Page : 430 pages
File Size : 47,8 Mb
Release : 2017-10-30
Category : Science
ISBN : 9781466576179

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Coarse-Grained Modeling of Biomolecules by Garegin A. Papoian Pdf

"The chapters in this book survey the progress in simulating biomolecular dynamics.... The images conjured up by this work are not yet universally loved, but are beginning to bring new insights into the study of biological structure and function. The future will decide whether this scientific movement can bring forth its Picasso or Modigliani." –from the Foreword by Peter G. Wolynes, Bullard-Welch Foundation Professor of Science, Rice University This book highlights the state-of-art in coarse-grained modeling of biomolecules, covering both fundamentals as well as various cutting edge applications. Coarse-graining of biomolecules is an area of rapid advances, with numerous new force fields having appeared recently and significant progress made in developing a systematic theory of coarse-graining. The contents start with first fundamental principles based on physics, then survey specific state-of-art coarse-grained force fields of proteins and nucleic acids, and provide examples of exciting biological problems that are at large scale, and hence, only amenable to coarse-grained modeling. Introduces coarse-grained models of proteins and nucleic acids. Showcases applications such as genome packaging in nuclei and understanding ribosome dynamics Gives the physical foundations of coarse-graining Demonstrates use of models for large-scale assemblies in modern studies Garegin A. Papoian is the first Monroe Martin Associate Professor with appointments in the Department of Chemistry and Biochemistry and the Institute for Physical Science and Technology at the University of Maryland.

Author : Felipe A. La Porta,Carlton A. Taft
Publisher : Springer Nature
Page : 778 pages
File Size : 41,7 Mb
Release : 2021-05-17
Category : Technology & Engineering
ISBN : 9783030622268

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Functional Properties of Advanced Engineering Materials and Biomolecules by Felipe A. La Porta,Carlton A. Taft Pdf

This book shows how a small toolbox of experimental techniques, physical chemistry concepts as well as quantum/classical mechanics and statistical methods can be used to understand, explain and even predict extraordinary applications of these advanced engineering materials and biomolecules. It highlights how improving the material foresight by design, including the fundamental understanding of their physical and chemical properties, can provide new technological levels in the future.