Multiscale Theoretical And Computational Methods For Modelling Proteins And Protein Protein Interactions

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Multiscale Approaches to Protein Modeling

Author : Andrzej Kolinski
Publisher : Springer Science & Business Media
ISBN 13 : 144196889X
Total Pages : 360 pages
Book Rating : 4.4/5 (419 download)

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Book Synopsis Multiscale Approaches to Protein Modeling by : Andrzej Kolinski

Download or read book Multiscale Approaches to Protein Modeling written by Andrzej Kolinski and published by Springer Science & Business Media. This book was released on 2010-10-13 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book gives a comprehensive review of the most advanced multiscale methods for protein structure prediction, computational studies of protein dynamics, folding mechanisms and macromolecular interactions. It approaches span a wide range of the levels of coarse-grained representations, various sampling techniques and variety of applications to biomedical and biophysical problems. This book is intended to be used as a reference book for those who are just beginning their adventure with biomacromolecular modeling but also as a valuable source of detailed information for those who are already experts in the field of biomacromolecular modeling and in related areas of computational biology or biophysics.

Combining Simulations, Theory, and Experiments into Multiscale Models of Biological Events

Author : Fabio Trovato
Publisher : Frontiers Media SA
ISBN 13 : 2889740250
Total Pages : 322 pages
Book Rating : 4.8/5 (897 download)

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Book Synopsis Combining Simulations, Theory, and Experiments into Multiscale Models of Biological Events by : Fabio Trovato

Download or read book Combining Simulations, Theory, and Experiments into Multiscale Models of Biological Events written by Fabio Trovato and published by Frontiers Media SA. This book was released on 2022-01-11 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Computational Modelling of Nanoparticles

Author : Stefan T. Bromley
Publisher : Elsevier
ISBN 13 : 9780081022320
Total Pages : 0 pages
Book Rating : 4.0/5 (223 download)

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Book Synopsis Computational Modelling of Nanoparticles by : Stefan T. Bromley

Download or read book Computational Modelling of Nanoparticles written by Stefan T. Bromley and published by Elsevier. This book was released on 2018-09-14 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational Modelling of Nanoparticles highlights recent advances in the power and versatility of computational modelling, experimental techniques, and how new progress has opened the door to a more detailed and comprehensive understanding of the world of nanomaterials. Nanoparticles, having dimensions of 100 nanometers or less, are increasingly being used in applications in medicine, materials and manufacturing, and energy. Spanning the smallest sub-nanometer nanoclusters to nanocrystals with diameters of 10s of nanometers, this book provides a state-of-the-art overview on how computational modelling can provide, often otherwise unobtainable, insights into nanoparticulate structure and properties. This comprehensive, single resource is ideal for researchers who want to start/improve their nanoparticle modelling efforts, learn what can be (and what cannot) achieved with computational modelling, and understand more clearly the value and details of computational modelling efforts in their area of research.

Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes

Author : Adam Liwo
Publisher : Springer
ISBN 13 : 3319958437
Total Pages : 849 pages
Book Rating : 4.3/5 (199 download)

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Book Synopsis Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes by : Adam Liwo

Download or read book Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes written by Adam Liwo and published by Springer. This book was released on 2018-12-19 with total page 849 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a comprehensive overview of modern computer-based techniques for analyzing the structure, properties and dynamics of biomolecules and biomolecular processes. It is organized in four main parts; the first one deals with methodology of molecular simulations; the second one with applications of molecular simulations; the third one introduces bioinformatics methods and the use of experimental information in molecular simulations; the last part reports on selected applications of molecular quantum mechanics. This second edition has been thoroughly revised and updated to include the latest progresses made in the respective field of research.

Multiscale Modeling From Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations

Author : Valentina Tozzini
Publisher : Frontiers Media SA
ISBN 13 : 2889661091
Total Pages : 235 pages
Book Rating : 4.8/5 (896 download)

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Book Synopsis Multiscale Modeling From Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations by : Valentina Tozzini

Download or read book Multiscale Modeling From Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations written by Valentina Tozzini and published by Frontiers Media SA. This book was released on 2020-10-27 with total page 235 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Multiscale and Multiphysics Computational Frameworks for Nano- and Bio-Systems

Author : Hyungjun Kim
Publisher : Springer Science & Business Media
ISBN 13 : 1441976019
Total Pages : 191 pages
Book Rating : 4.4/5 (419 download)

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Book Synopsis Multiscale and Multiphysics Computational Frameworks for Nano- and Bio-Systems by : Hyungjun Kim

Download or read book Multiscale and Multiphysics Computational Frameworks for Nano- and Bio-Systems written by Hyungjun Kim and published by Springer Science & Business Media. This book was released on 2010-11-18 with total page 191 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume develops multiscale and multiphysics simulation methods to understand nano- and bio-systems by overcoming the limitations of time- and length-scales. Here the key issue is to extend current computational simulation methods to be useful for providing microscopic understanding of complex experimental systems. This thesis discusses the multiscale simulation approaches in nanoscale metal-insulator-metal junction, molecular memory, ionic transport in zeolite systems, dynamics of biomolecules such as lipids, and model lung system. Based on the cases discussed here, the author suggests various systematic strategies to overcome the limitations in time- and length-scales of the traditional monoscale approaches.

Drug Design Strategies

Author : Lee Banting
Publisher : Royal Society of Chemistry
ISBN 13 : 1849733406
Total Pages : 251 pages
Book Rating : 4.8/5 (497 download)

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Book Synopsis Drug Design Strategies by : Lee Banting

Download or read book Drug Design Strategies written by Lee Banting and published by Royal Society of Chemistry. This book was released on 2012-01-04 with total page 251 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book documents the latest research into the theory and application of force-fields, semi-empirical molecular orbital, density functional and ab initio calculations, Quantum Mechanical (QM) based modelling, Atoms in Molecules (AIM) approach, and biomolecular dynamics. It also covers theory and application of 2D cheminformatics, QSAR/QSPR, ADME properties of drugs, drug docking/scoring protocols and approaches, topological methodology, and modelling accurate inhibition constants of enzymes. Finally, the book gives the theory and applications of multiscale modelling of proteins and biomolecular systems. The information need for a book in this area is due to the continuing rapid advance of firstly theoretical approaches, secondly software/hardware and lastly the successful application of the technology and this book fills a gap in the literature. The co-editors have extensive experience of teaching and researching in the field and the book includes contributions from cutting-edge academic and industrial researchers in their respective fields. It is essential reading for medicinal chemists, computational chemists and those in the pharmaceutical industry.

Explainable AI: Interpreting, Explaining and Visualizing Deep Learning

Author : Wojciech Samek
Publisher : Springer Nature
ISBN 13 : 3030289540
Total Pages : 435 pages
Book Rating : 4.0/5 (32 download)

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Book Synopsis Explainable AI: Interpreting, Explaining and Visualizing Deep Learning by : Wojciech Samek

Download or read book Explainable AI: Interpreting, Explaining and Visualizing Deep Learning written by Wojciech Samek and published by Springer Nature. This book was released on 2019-09-10 with total page 435 pages. Available in PDF, EPUB and Kindle. Book excerpt: The development of “intelligent” systems that can take decisions and perform autonomously might lead to faster and more consistent decisions. A limiting factor for a broader adoption of AI technology is the inherent risks that come with giving up human control and oversight to “intelligent” machines. For sensitive tasks involving critical infrastructures and affecting human well-being or health, it is crucial to limit the possibility of improper, non-robust and unsafe decisions and actions. Before deploying an AI system, we see a strong need to validate its behavior, and thus establish guarantees that it will continue to perform as expected when deployed in a real-world environment. In pursuit of that objective, ways for humans to verify the agreement between the AI decision structure and their own ground-truth knowledge have been explored. Explainable AI (XAI) has developed as a subfield of AI, focused on exposing complex AI models to humans in a systematic and interpretable manner. The 22 chapters included in this book provide a timely snapshot of algorithms, theory, and applications of interpretable and explainable AI and AI techniques that have been proposed recently reflecting the current discourse in this field and providing directions of future development. The book is organized in six parts: towards AI transparency; methods for interpreting AI systems; explaining the decisions of AI systems; evaluating interpretability and explanations; applications of explainable AI; and software for explainable AI.

Computational Multiscale Modeling of Multiphase Nanosystems

Author : Alexander V. Vakhrushev
Publisher : CRC Press
ISBN 13 : 1771885297
Total Pages : 403 pages
Book Rating : 4.7/5 (718 download)

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Book Synopsis Computational Multiscale Modeling of Multiphase Nanosystems by : Alexander V. Vakhrushev

Download or read book Computational Multiscale Modeling of Multiphase Nanosystems written by Alexander V. Vakhrushev and published by CRC Press. This book was released on 2017-10-10 with total page 403 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational Multiscale Modeling of Multiphase Nanosystems: Theory and Applications presents a systematic description of the theory of multiscale modeling of nanotechnology applications in various fields of science and technology. The problems of computing nanoscale systems at different structural scales are defined, and algorithms are given for their numerical solutions by the quantum/continuum mechanics, molecular dynamics, and mesodynamics methods. Emphasis is given to the processes of the formation, movement, and interaction of nanoparticles; the formation of nanocomposites; and the processes accompanying the application of nanocomposites. The book concentrates on different types of nanosystems: solid, liquid, gaseous, and multi-phase, consisting of various elements interacting with each other, and with other elements of the nanosystem and with the environment. The book includes a large number of examples of numerical modeling of nanosystems. The valuable information presented here will be useful to engineers, researchers, and postgraduate students engaged in the design and research in the field of nanotechnology.

Chemical Theory and Multiscale Simulation in Biomolecules

Author : Guohui Li
Publisher : Elsevier
ISBN 13 : 0323959180
Total Pages : 399 pages
Book Rating : 4.3/5 (239 download)

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Book Synopsis Chemical Theory and Multiscale Simulation in Biomolecules by : Guohui Li

Download or read book Chemical Theory and Multiscale Simulation in Biomolecules written by Guohui Li and published by Elsevier. This book was released on 2024-03-29 with total page 399 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chemical Theory and Multiscale Simulation in Biomolecules: From Principles to Case Studies helps readers understand what simulation is, what information modeling of biomolecules can provide, and how to compare this information with experiments. Beginning with an introduction to computational theory for modeling, the book goes on to describe how to control the conditions of modeling systems and possible strategies for time-cost savings in computation. Part Two further outlines key methods, with step-by-step guidance supporting readers in studying and practicing simulation processes. Part Three then shows how these theories are controlled and applied in practice, through examples and case studies on varied applications. This book is a practical guide for new learners, supporting them in learning and applying molecular modeling in practice, whilst also providing more experienced readers with the knowledge needed to gain a deep understanding of the theoretical background behind key methods. - Presents computational theory alongside case studies to help readers understand the use of simulation in practice - Includes extensive examples of different types of simulation methods and approaches to result analysis - Provides an overview of the current academic frontier and research challenges, encouraging creativity and directing attention to current problems

Report of the Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics

Author : National Academies of Sciences, Engineering, and Medicine
Publisher : National Academies Press
ISBN 13 : 0309484936
Total Pages : 24 pages
Book Rating : 4.3/5 (94 download)

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Book Synopsis Report of the Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics by : National Academies of Sciences, Engineering, and Medicine

Download or read book Report of the Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2018-10-18 with total page 24 pages. Available in PDF, EPUB and Kindle. Book excerpt: This report describes the work of the Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics, Ninth Round. The committee evaluated submissions received in response to a Request for Proposals (RFP) for biomolecular simulation time on Anton 2, a supercomputer specially designed and built by D.E. Shaw Research (DESRES). Over the past 8 years, DESRES has made an Anton or Anton 2 system housed at the Pittsburgh Supercomputing Center (PSC) available to the non-commercial research community, based on the advice of previous National Research Council committees. As in prior rounds, the goal of the ninth RFP for simulation time on Anton 2 is to continue to facilitate breakthrough research in the study of biomolecular systems by providing a massively parallel system specially designed for molecular dynamics simulations. The program seeks to continue to support research that addresses important and high impact questions demonstrating a clear need for Anton's special capabilities. Report of the Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics, Ninth Round is the final report of the committee's evaluation of proposals based on scientific merit, justification for requested time allocation, and investigator qualifications and past accomplishments. This report identifies the proposals that best met the selection criteria.

Handbook of Materials Modeling

Author : Sidney Yip
Publisher : Springer Science & Business Media
ISBN 13 : 1402032862
Total Pages : 2903 pages
Book Rating : 4.4/5 (2 download)

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Book Synopsis Handbook of Materials Modeling by : Sidney Yip

Download or read book Handbook of Materials Modeling written by Sidney Yip and published by Springer Science & Business Media. This book was released on 2007-11-17 with total page 2903 pages. Available in PDF, EPUB and Kindle. Book excerpt: The first reference of its kind in the rapidly emerging field of computational approachs to materials research, this is a compendium of perspective-providing and topical articles written to inform students and non-specialists of the current status and capabilities of modelling and simulation. From the standpoint of methodology, the development follows a multiscale approach with emphasis on electronic-structure, atomistic, and mesoscale methods, as well as mathematical analysis and rate processes. Basic models are treated across traditional disciplines, not only in the discussion of methods but also in chapters on crystal defects, microstructure, fluids, polymers and soft matter. Written by authors who are actively participating in the current development, this collection of 150 articles has the breadth and depth to be a major contributor toward defining the field of computational materials. In addition, there are 40 commentaries by highly respected researchers, presenting various views that should interest the future generations of the community. Subject Editors: Martin Bazant, MIT; Bruce Boghosian, Tufts University; Richard Catlow, Royal Institution; Long-Qing Chen, Pennsylvania State University; William Curtin, Brown University; Tomas Diaz de la Rubia, Lawrence Livermore National Laboratory; Nicolas Hadjiconstantinou, MIT; Mark F. Horstemeyer, Mississippi State University; Efthimios Kaxiras, Harvard University; L. Mahadevan, Harvard University; Dimitrios Maroudas, University of Massachusetts; Nicola Marzari, MIT; Horia Metiu, University of California Santa Barbara; Gregory C. Rutledge, MIT; David J. Srolovitz, Princeton University; Bernhardt L. Trout, MIT; Dieter Wolf, Argonne National Laboratory.

Computational Methods for Complex Liquid-Fluid Interfaces

Author : Mohammad Taeibi Rahni
Publisher : CRC Press
ISBN 13 : 1498722091
Total Pages : 549 pages
Book Rating : 4.4/5 (987 download)

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Book Synopsis Computational Methods for Complex Liquid-Fluid Interfaces by : Mohammad Taeibi Rahni

Download or read book Computational Methods for Complex Liquid-Fluid Interfaces written by Mohammad Taeibi Rahni and published by CRC Press. This book was released on 2015-11-11 with total page 549 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational Methods for Complex Liquid-Fluid Interfaces highlights key computational challenges involved in the two-way coupling of complex liquid-fluid interfaces. The book covers a variety of cutting-edge experimental and computational techniques ranging from macro- to meso- and microscale approaches (including pivotal applications). As example

Simulations in Nanobiotechnology

Author : Kilho Eom
Publisher : CRC Press
ISBN 13 : 1439835047
Total Pages : 564 pages
Book Rating : 4.4/5 (398 download)

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Book Synopsis Simulations in Nanobiotechnology by : Kilho Eom

Download or read book Simulations in Nanobiotechnology written by Kilho Eom and published by CRC Press. This book was released on 2011-10-19 with total page 564 pages. Available in PDF, EPUB and Kindle. Book excerpt: Until the late 20th century, computational studies of biomolecules and nanomaterials had considered the two subjects separately. A thorough presentation of state-of-the-art simulations for studying the nanoscale behavior of materials, Simulations in Nanobiotechnology discusses computational simulations of biomolecules and nanomaterials together. The book gives readers insight into not only the fundamentals of simulation-based characterizations in nanobiotechnology, but also in how to approach new and interesting problems in nanobiotechnology using basic theoretical and computational frameworks. Presenting the simulation-based nanoscale characterizations in biological science, Part 1: Describes recent efforts in MD simulation-based characterization and CG modeling of DNA and protein transport dynamics in the nanopore and nanochannel Presents recent advances made in continuum mechanics-based modeling of membrane proteins Summarizes theoretical frameworks along with atomistic simulations in single-molecule mechanics Provides the computational simulation-based mechanical characterization of protein materials Discussing advances in modeling techniques and their applications, Part 2: Describes advances in nature-inspired material design; atomistic simulation-based characterization of nanoparticles’ optical properties; and nanoparticle-based applications in therapeutics Overviews of the recent advances made in experiment and simulation-based characterizations of nanoscale adhesive properties Suggests theoretical frameworks with experimental efforts in the development of nanoresonators for future nanoscale device designs Delineates advances in theoretical and computational methods for understanding the mechanical behavior of a graphene monolayer The development of experimental apparatuses has paved the way to observing physics at the nanoscale and opened a new avenue in the fundamental understanding of the physics of various objects such as biological materials and nanomaterials. With expert contributors from around the world, this book addresses topics such as the molecular dynamics of protein translocation, coarse-grained modeling of CNT-DNA interactions, multi-scale modeling of nanowire resonator sensors, and the molecular dynamics simulation of protein mechanics. It demonstrates the broad application of models and simulations that require the use of principles from multiple academic disciplines.

Multi-scale Quantum Models for Biocatalysis

Author : Darrin M. York
Publisher : Springer Science & Business Media
ISBN 13 : 1402099568
Total Pages : 426 pages
Book Rating : 4.4/5 (2 download)

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Book Synopsis Multi-scale Quantum Models for Biocatalysis by : Darrin M. York

Download or read book Multi-scale Quantum Models for Biocatalysis written by Darrin M. York and published by Springer Science & Business Media. This book was released on 2009-05-30 with total page 426 pages. Available in PDF, EPUB and Kindle. Book excerpt: “Multi-scale Quantum Models for Biocatalysis” explores various molecular modelling techniques and their applications in providing an understanding of the detailed mechanisms at play during biocatalysis in enzyme and ribozyme systems. These areas are reviewed by an international team of experts in theoretical, computational chemistry, and biophysics. This book presents detailed reviews concerning the development of various techniques, including ab initio molecular dynamics, density functional theory, combined QM/MM methods, solvation models, force field methods, and free-energy estimation techniques, as well as successful applications of multi-scale methods in the biocatalysis systems including several protein enzymes and ribozymes. This book is an excellent source of information for research professionals involved in computational chemistry and physics, material science, nanotechnology, rational drug design and molecular biology and for students exposed to these research areas.

Computer Simulations in Molecular Biology

Author : Hiqmet Kamberaj
Publisher : Springer Nature
ISBN 13 : 3031348397
Total Pages : 306 pages
Book Rating : 4.0/5 (313 download)

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Book Synopsis Computer Simulations in Molecular Biology by : Hiqmet Kamberaj

Download or read book Computer Simulations in Molecular Biology written by Hiqmet Kamberaj and published by Springer Nature. This book was released on 2023-07-31 with total page 306 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book covers a range of topics in quantum mechanics and molecular dynamics simulation, including computational modeling and machine learning approaches. The book also provides a Python GUI and tutorials for simulating molecular biological systems and presents case studies of quantum mechanics simulations for predicting electronic properties. Its pedagogical formatting makes it easy for students to understand and follow and has been praised for providing clear and detailed explanations of complex topics. This book is ideal for graduate students and researchers in theoretical and computational biophysics, physics, chemistry, and materials science, as well as postgraduates in applied mathematics, computer science, and bioinformatics.

Advanced Computational Approaches to Biomedical Engineering

Author : Punam K. Saha
Publisher : Springer Science & Business Media
ISBN 13 : 3642415393
Total Pages : 224 pages
Book Rating : 4.6/5 (424 download)

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Book Synopsis Advanced Computational Approaches to Biomedical Engineering by : Punam K. Saha

Download or read book Advanced Computational Approaches to Biomedical Engineering written by Punam K. Saha and published by Springer Science & Business Media. This book was released on 2014-01-23 with total page 224 pages. Available in PDF, EPUB and Kindle. Book excerpt: There has been rapid growth in biomedical engineering in recent decades, given advancements in medical imaging and physiological modelling and sensing systems, coupled with immense growth in computational and network technology, analytic approaches, visualization and virtual-reality, man-machine interaction and automation. Biomedical engineering involves applying engineering principles to the medical and biological sciences and it comprises several topics including biomedicine, medical imaging, physiological modelling and sensing, instrumentation, real-time systems, automation and control, signal processing, image reconstruction, processing and analysis, pattern recognition, and biomechanics. It holds great promise for the diagnosis and treatment of complex medical conditions, in particular, as we can now target direct clinical applications, research and development in biomedical engineering is helping us to develop innovative implants and prosthetics, create new medical imaging technologies and improve tools and techniques for the detection, prevention and treatment of diseases. The contributing authors in this edited book present representative surveys of advances in their respective fields, focusing in particular on techniques for the analysis of complex biomedical data. The book will be a useful reference for graduate students, researchers and industrial practitioners in computer science, biomedical engineering, and computational and molecular biology.