Download or read book Multiscale Dynamics Simulations written by Dennis R. Salahub and published by Royal Society of Chemistry. This book was released on 2021-09-24 with total page 411 pages. Available in PDF, EPUB and Kindle. Book excerpt: Over the past decade, great strides have been taken in developing methodologies that can treat more and more complex nano- and nano-bio systems embedded in complex environments. Multiscale Dynamics Simulations covers methods including DFT/MM-MD, DFTB and semi-empirical QM/MM-MD, DFT/MMPOL as well as Machine-learning approaches to all of the above. Focusing on key methodological breakthroughs in the field, this book provides newcomers with a comprehensive menu of multiscale modelling options so that they can better chart their course in the nano/bio world.

Download or read book Multiscale Dynamics Simulations Nano and Nano bio Systems in Complex Environments written by Dennis R. Salahub and published by Royal Society of Chemistry. This book was released on 2021-10-01 with total page 411 pages. Available in PDF, EPUB and Kindle. Book excerpt: Focusing on key methodological breakthroughs in the field, this book provides newcomers with a comprehensive menu of multiscale modelling options.

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.

Download or read book Cheminformatics and Bioinformatics at the Interface with Systems Biology written by Aman Chandra Kaushik and published by Royal Society of Chemistry. This book was released on 2023-09-08 with total page 304 pages. Available in PDF, EPUB and Kindle. Book excerpt: The cost of drug development is increasing, and investment returns are decreasing. The number of drugs approved by FDA is in decline in terms of the number of new molecular entities (NMEs). Amongst the reasons noted for this are the adverse side effects and reduced efficiency of many of the potential compounds. This is a problem both for the pharmaceutical industry and for those suffering from diseases for which there are no or few available treatments. Advances in computational chemistry, computer science, structural biology and molecular biology have all contributed to improved drug design strategies and reduced the time taken for drug discovery. By interfacing cheminformatics and bioinformatics with systems biology we can create a powerful tool for understanding the mechanisms of patho-physiological systems and identifying lead molecules for various diseases. This integration of drug design approaches can also play a crucial role in the prediction and rationalization of drug effects and side effects, improving safety and efficacy and leading to better approval rates. Addressing the lack of knowledge on the fundamental aspects of the various computational tools for drug discovery, this book is a compilation of recent bioinformatics and cheminformatics approaches, and their integration with systems biology. Written primarily for researchers and academics in chem- and bioinformatics, it may also be a useful resource for advanced-level students.

Download or read book Machine Learning and Hybrid Modelling for Reaction Engineering written by Dongda Zhang and published by Royal Society of Chemistry. This book was released on 2023-12-20 with total page 342 pages. Available in PDF, EPUB and Kindle. Book excerpt: Over the last decade, there has been a significant shift from traditional mechanistic and empirical modelling into statistical and data-driven modelling for applications in reaction engineering. In particular, the integration of machine learning and first-principle models has demonstrated significant potential and success in the discovery of (bio)chemical kinetics, prediction and optimisation of complex reactions, and scale-up of industrial reactors. Summarising the latest research and illustrating the current frontiers in applications of hybrid modelling for chemical and biochemical reaction engineering, Machine Learning and Hybrid Modelling for Reaction Engineering fills a gap in the methodology development of hybrid models. With a systematic explanation of the fundamental theory of hybrid model construction, time-varying parameter estimation, model structure identification and uncertainty analysis, this book is a great resource for both chemical engineers looking to use the latest computational techniques in their research and computational chemists interested in new applications for their work.

Download or read book Structural Dynamics with X ray and Electron Scattering written by Kasra Amini and published by Royal Society of Chemistry. This book was released on 2023-12-20 with total page 671 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Exploration on Quantum Chemical Potential Energy Surfaces written by Koichi Ohno and published by Royal Society of Chemistry. This book was released on 2022-12-12 with total page 255 pages. Available in PDF, EPUB and Kindle. Book excerpt: Written chemical formulas, such as C2H6O, can tell us the constituent atoms a molecule contains but they cannot differentiate between the possible geometrical arrangements (isomers) of these models. Yet the chemical properties of different isomers can vary hugely. Therefore, to understand the world of chemistry we need to ask what kind of isomers can be produced from a given atomic composition, how are isomers converted into each other, how do they decompose into smaller pieces, and how can they be made from smaller pieces? The answers to these questions will help us to discover new chemistry and new molecules. A potential energy surface (PES) describes a system, such as a molecule, based on geometrical parameters. The mathematical properties of the PES can be used to calculate probable isomer structures as well as how they are formed and how they might behave. Exploration on Quantum Chemical Potential Energy Surfaces focuses on the PES search based on quantum chemical calculations. It describes how to explore the chemical world on PES, discusses fundamental methods and specific techniques developed for efficient exploration on PES, and demonstrates several examples of the PES search for chemical structures and reaction routes.

Download or read book Multiscale Modeling of Particle Interactions written by Michael King and published by John Wiley & Sons. This book was released on 2010-03-30 with total page 398 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Multiscale Modeling of Complex Molecular Structure and Dynamics with MBN Explorer written by Ilia A. Solov’yov and published by Springer. This book was released on 2017-05-16 with total page 460 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book introduces readers to MesoBioNano (MBN) Explorer – a multi-purpose software package designed to model molecular systems at various levels of size and complexity. In addition, it presents a specially designed multi-task toolkit and interface – the MBN Studio – which enables the set-up of input files, controls the simulations, and supports the subsequent visualization and analysis of the results obtained. The book subsequently provides a systematic description of the capabilities of this universal and powerful software package within the framework of computational molecular science, and guides readers through its applications in numerous areas of research in bio- and chemical physics and material science – ranging from the nano- to the mesoscale. MBN Explorer is particularly suited to computing the system’s energy, to optimizing molecular structure, and to exploring the various facets of molecular and random walk dynamics. The package allows the use of a broad variety of interatomic potentials and can, e.g., be configured to select any subset of a molecular system as rigid fragments, whenever a significant reduction in the number of dynamical degrees of freedom is required for computational practicalities. MBN Studio enables users to easily construct initial geometries for the molecular, liquid, crystalline, gaseous and hybrid systems that serve as input for the subsequent simulations of their physical and chemical properties using MBN Explorer. Despite its universality, the computational efficiency of MBN Explorer is comparable to that of other, more specialized software packages, making it a viable multi-purpose alternative for the computational modeling of complex molecular systems. A number of detailed case studies presented in the second part of this book demonstrate MBN Explorer’s usefulness and efficiency in the fields of atomic clusters and nanoparticles, biomolecular systems, nanostructured materials, composite materials and hybrid systems, crystals, liquids and gases, as well as in providing modeling support for novel and emerging technologies. Last but not least, with the release of the 3rd edition of MBN Explorer in spring 2017, a free trial version will be available from the MBN Research Center website (mbnresearch.com).

Download or read book Multiscale Simulations and Mechanics of Biological Materials written by Shaofan Li and published by John Wiley & Sons. This book was released on 2013-03-19 with total page 509 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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)

Download or read book Multiscale Modeling of Nano scale Phenomena written by D. White and published by . This book was released on 2003 with total page 24 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this white paper, a road map is presented to establish a multiphysics simulation capability for the design and optimization of sensor systems that incorporate nanomaterials and technologies. The Engineering Directorate's solid/fluid mechanics and electromagnetic computer codes will play an important role in both multiscale modeling and integration of required physics issues to achieve a baseline simulation capability. Molecular dynamic simulations performed primarily in the BBRP, CMS and PAT directorates, will provide information for the construction of multiscale models. All of the theoretical developments will require closely coupled experimental work to develop material models and validate simulations. The plan is synergistic and complimentary with the Laboratory's emerging core competency of multiscale modeling. The first application of the multiphysics computer code is the simulation of a ''simple'' biological system (protein recognition utilizing synthesized ligands) that has a broad range of applications including detection of biological threats, presymptomatic detection of illnesses, and drug therapy. While the overall goal is to establish a simulation capability, the near-term work is mainly focused on (1) multiscale modeling, i.e., the development of ''continuum'' representations of nanostructures based on information from molecular dynamics simulations and (2) experiments for model development and validation. A list of LDRDER proposals and ongoing projects that could be coordinated to achieve these near-term objectives and demonstrate the feasibility and utility of a multiphysics simulation capability is given.

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.

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.

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.

Download or read book Molecular Dynamics of Nanostructures and Nanoionics written by Junko Habasaki and published by CRC Press. This book was released on 2020-11-30 with total page 314 pages. Available in PDF, EPUB and Kindle. Book excerpt: Nanostructured materials with multiple components and complex structures are the current focus of research and are expected to develop further for material designs in many applications in electrochemical, colloidal, medical, pharmaceutical, and several other fields. This book discusses complex nanostructured systems exemplified by nanoporous silicates, spontaneously formed gels from silica-nanocolloidal solutions, and related systems, and examines them using molecular dynamics simulations. Nanoporous materials, nanocolloidal systems, and gels are useful in many applications and can be used in electric devices and storage, and for gas, ion, and drug delivery. The book gives an overview of the history, current status, and frontiers of the field. It also discusses the fundamental aspects related to the common behaviors of some of these systems and common analytical methods to treat them.

Download or read book Multiscale Modeling of Particle Interactions written by Michael King and published by Wiley. This book was released on 2010-03-22 with total page 388 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Computational Multiscale Modeling of Multiphase Nanosystems written by ALEXANDER V. VAKHRUSHEV and published by Apple Academic Press. This book was released on 2021-03-31 with total page 0 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.