A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules
A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules

Author: Yong Wang

Publisher:

Published: 2023

Total Pages: 0

ISBN-13: 9780735425255

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Biomolecular modeling and simulation are becoming increasingly crucial for understanding the microscopic biological world with high time and spatial recognition. A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules offers guidance for advanced multiscale modeling and machine learning-aided molecular simulations. The book provides reproducible, step-by-step instructions on the scripts and codes needed to complete the simulations. It offers readers tips, tricks, and troubleshooting advice for the reader's real-life challenges. Topics in this book focus on the latest developments and: Provide an overview of current methods and techniques; Serve as a tutorial and an in-depth historical record of the topic; Contain step-by-step instructions for the methods used in molecular modeling and simulation of biomolecules. A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules is a key resource for students and researchers in biology, biophysics, biochemistry, and computational chemistry.

Chemical Theory and Multiscale Simulation in Biomolecules
Chemical Theory and Multiscale Simulation in Biomolecules

Author: Guohui Li

Publisher: Elsevier

Published: 2024-03-28

Total Pages: 399

ISBN-13: 0323959180

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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

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

Author: Valentina Tozzini

Publisher: Frontiers Media SA

Published: 2020-10-27

Total Pages: 235

ISBN-13: 2889661091

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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 Simulations and Mechanics of Biological Materials
Multiscale Simulations and Mechanics of Biological Materials

Author: Shaofan Li

Publisher: John Wiley & Sons

Published: 2013-03-19

Total Pages: 509

ISBN-13: 1118402944

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Multiscale Simulations and Mechanics of Biological Materials A compilation of recent developments in multiscale simulation and computational biomaterials written by leading specialists in the field Presenting the latest developments in multiscale mechanics and multiscale simulations, and offering a unique viewpoint on multiscale modelling of biological materials, this book outlines the latest developments in computational biological materials from atomistic and molecular scale simulation on DNA, proteins, and nano-particles, to meoscale soft matter modelling of cells, and to macroscale soft tissue and blood vessel, and bone simulations. Traditionally, computational biomaterials researchers come from biological chemistry and biomedical engineering, so this is probably the first edited book to present work from these talented computational mechanics researchers. The book has been written to honor Professor Wing Liu of Northwestern University, USA, who has made pioneering contributions in multiscale simulation and computational biomaterial in specific simulation of drag delivery at atomistic and molecular scale and computational cardiovascular fluid mechanics via immersed finite element method. Key features: Offers a unique interdisciplinary approach to multiscale biomaterial modelling aimed at both accessible introductory and advanced levels Presents a breadth of computational approaches for modelling biological materials across multiple length scales (molecular to whole-tissue scale), including solid and fluid based approaches A companion website for supplementary materials plus links to contributors’ websites (www.wiley.com/go/li/multiscale)

Biophysical Approaches for the Study of Membrane Structure Part B
Biophysical Approaches for the Study of Membrane Structure Part B

Author:

Publisher: Elsevier

Published: 2024-07-21

Total Pages: 630

ISBN-13: 0443295670

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Biophysical Approaches for the Study of Membrane Structure, Part B, Volume 701 explores lipid membrane asymmetry and lateral heterogeneity. A burst of recent research has shown that bilayers whose leaflets differ in their physical properties—such as composition, phase state, or lateral stress—exhibit many fascinating new characteristics, but also pose a host of challenges related to their creation, characterization, simulation, and theoretical description. Chapters in this new release include Characterization of domain formation in complex membranes: Analyzing the bending modulus from simulations of complex membranes, The density-threshold affinity: Calculating lipid binding affinities from unbiased Coarse-Grain Molecular Dynamics simulations, and much more. Additional sections cover Uncertainty quantification for trans-membrane stresses and moments from simulation, Using molecular dynamics simulations to generate small-angle scattering curves and cryo-EM images of proteoliposomes, Binary Bilayer Simulations for Partitioning Within Membranes, Modeling Asymmetric Cell Membranes at All-atom Resolution, Multiscale remodeling of biomembranes and vesicles, Building complex membranes with Martini 3, Predicting lipid sorting in curved bilayer membranes, Simulating asymmetric membranes using P21 periodic boundary conditions, and many other interesting topics. Explore the state-of-the-art of lipid membrane asymmetry Covers experimental, theoretical, and computational techniques to create and characterize asymmetric lipid membranes Teaches how these kinds of approaches create and characterize laterally inhomogeneous membranes

Molecular Modeling and Simulation
Molecular Modeling and Simulation

Author: Tamar Schlick

Publisher: Springer Science & Business Media

Published: 2013-04-18

Total Pages: 669

ISBN-13: 0387224645

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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

Innovations in Biomolecular Modeling and Simulations
Innovations in Biomolecular Modeling and Simulations

Author: Tamar Schlick

Publisher: Royal Society of Chemistry

Published: 2012-05-24

Total Pages: 381

ISBN-13: 1849735042

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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.

Multiscale Modeling of Particle Interactions
Multiscale Modeling of Particle Interactions

Author: Michael King

Publisher: John Wiley & Sons

Published: 2010-03-30

Total Pages: 398

ISBN-13: 047057982X

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Discover how the latest computational tools are building our understanding of particle interactions and leading to new applications With this book as their guide, readers will gain a new appreciation of the critical role that particle interactions play in advancing research and developing new applications in the biological sciences, chemical engineering, toxicology, medicine, and manufacturing technology The book explores particles ranging in size from cations to whole cells to tissues and processed materials. A focus on recreating complex, real-world dynamical systems helps readers gain a deeper understanding of cell and tissue mechanics, theoretical aspects of multiscale modeling, and the latest applications in biology and nanotechnology. Following an introductory chapter, Multiscale Modeling of Particle Interactions is divided into two parts: Part I, Applications in Nanotechnology, covers: Multiscale modeling of nanoscale aggregation phenomena: applications in semiconductor materials processing Multiscale modeling of rare events in self-assembled systems Continuum description of atomic sheets Coulombic dragging and mechanical propelling of molecules in nanofluidic systems Molecular dynamics modeling of nanodroplets and nanoparticles Modeling the interactions between compliant microcapsules and patterned surfaces Part II, Applications in Biology, covers: Coarse-grained and multiscale simulations of lipid bilayers Stochastic approach to biochemical kinetics In silico modeling of angiogenesis at multiple scales Large-scale simulation of blood flow in microvessels Molecular to multicellular deformation during adhesion of immune cells under flow Each article was contributed by one or more leading experts and pioneers in the field. All readers, from chemists and biologists to engineers and students, will gain new insights into how the latest tools in computational science can improve our understanding of particle interactions and support the development of novel applications across the broad spectrum of disciplines in biology and nanotechnology.