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

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.

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

This highly informative and carefully presented book comprises select proceedings of Foundation for Molecular Modelling and Simulation (FOMMS 2018). The contents are written by invited speakers centered on the theme Innovation for Complex Systems. It showcases new developments and applications of computational quantum chemistry, statistical mechanics, molecular simulation and theory, and continuum and engineering process simulation. This volume will serve as a useful reference to researchers, academicians and practitioners alike.

Molecular simulation is a powerful tool in materials science, physics, chemistry and biomolecular fields. This updated edition provides a pragmatic introduction to a wide range of techniques for the simulation of molecular systems at the atomic level. The first part concentrates on methods for calculating the potential energy of a molecular system, with new chapters on quantum chemical, molecular mechanical and hybrid potential techniques. The second part describes methods examining conformational, dynamical and thermodynamical properties of systems, covering techniques including geometry-optimization, normal-mode analysis, molecular dynamics, and Monte Carlo simulation. Using Python, the second edition includes numerous examples and program modules for each simulation technique, allowing the reader to perform the calculations and appreciate the inherent difficulties involved in each. This is a valuable resource for researchers and graduate students wanting to know how to use atomic-scale molecular simulations. Supplementary material, including the program library and technical information, available through www.cambridge.org/9780521852524.

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

The book presents select proceedings of Global meet on ‘Computational Modelling and Simulation, Recent Innovations, Challenges and Perspectives, 2020. This book covers leading-edge technologies from different domains such as computation in optimization and control, multiscale and multiphysics modeling and computation analysis, environmental modeling, modeling approaches to enterprise systems and services, finite element analysis, dependability and security, high-performance computation/cloud computing applications, computational biology and chemistry and computational mechanics. The primary goal of this book is to strengthen pre-eminence in computational modeling and simulation by catalyzing the transformative use of innovative developments in a wide range of disciplines to achieve lasting societal impact. The book discusses on how to perform simulation of large complex dynamic systems in an efficient manner using advanced computational analysis. The inter-disciplinary nature of the book would be a valuable reference for academicians and research scientists, industrialists interested in modelling and simulation driven by computational technology.

This textbook originated from the course 'Simulation, Modeling, and Computations in Biophysics' that I have taught at the University of Chicago since 2011. The students typically came from a wide range of backgrounds, including biology, physics, chemistry, biochemistry, and mathematics, and the course was intentionally adapted for senior undergraduate students and graduate students. This is not a highly technical book dedicated to specialists. The objective is to provide a broad survey from the physical description of a complex molecular system at the most fundamental level, to the type of phenomenological models commonly used to represent the function of large biological macromolecular machines.The key conceptual elements serving as building blocks in the formulation of different levels of approximations are introduced along the way, aiming to clarify as much as possible how they are interrelated. The only assumption is a basic familiarity with simple mathematics (calculus and integrals, ordinary differential equations, matrix linear algebra, and Fourier-Laplace transforms).

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”.

Molecular Dynamic Simulation: Fundamentals and Applications explains the basic principles of MD simulation and explores its recent developments and roles in advanced modeling approaches. The implementation of MD simulation and its application to various aspects of materials science and engineering including mechanical, thermal, mass transportation, and physical/chemical reaction problems are illustrated. Innovative modeling techniques that apply MD to explore the mechanics of typical nanomaterials and nanostructures and to characterize crystalline, amorphous, and liquid systems are also presented. The rich research experience of the authors in MD simulation will ensure that the readers are provided with both an in-depth understanding of MD simulation and clear technical guidance. - Provides a comprehensive overview of the underlying theories of molecular dynamics (MD) simulation - Presents application-based examples pertaining to a broad range of mechanical, thermal, and mass transport problems - Explores innovative modeling techniques for simulating typical nanomaterials and nanostructures and for characterizing crystalline, amorphous, and liquid systems