Multiscale Dynamics Simulations

Multiscale Dynamics Simulations

Author: Dennis R. Salahub

Publisher: Royal Society of Chemistry

Published: 2021-09-24

Total Pages: 411

ISBN-13: 1839164670

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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.


Cheminformatics and Bioinformatics at the Interface with Systems Biology

Cheminformatics and Bioinformatics at the Interface with Systems Biology

Author: Aman Chandra Kaushik

Publisher: Royal Society of Chemistry

Published: 2023-09-08

Total Pages: 304

ISBN-13: 1839166045

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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.


Machine Learning and Hybrid Modelling for Reaction Engineering

Machine Learning and Hybrid Modelling for Reaction Engineering

Author: Dongda Zhang

Publisher: Royal Society of Chemistry

Published: 2023-12-20

Total Pages: 342

ISBN-13: 1837670188

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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.


Exploration on Quantum Chemical Potential Energy Surfaces

Exploration on Quantum Chemical Potential Energy Surfaces

Author: Koichi Ohno

Publisher: Royal Society of Chemistry

Published: 2022-12-12

Total Pages: 255

ISBN-13: 1839167750

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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.


Modeling of Microscale Transport in Biological Processes

Modeling of Microscale Transport in Biological Processes

Author: Sid M. Becker

Publisher: Academic Press

Published: 2017-01-12

Total Pages: 0

ISBN-13: 9780128045954

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Modeling of Microscale Transport in Biological Processes provides a compendium of recent advances in theoretical and computational modeling of biotransport phenomena at the microscale. The simulation strategies presented range from molecular to continuum models and consider both numerical and exact solution method approaches to coupled systems of equations. The biological processes covered in this book include digestion, molecular transport, microbial swimming, cilia mediated flow, microscale heat transfer, micro-vascular flow, vesicle dynamics, transport through bio-films and bio-membranes, and microscale growth dynamics. The book is written for an advanced academic research audience in the fields of engineering (encompassing biomedical, chemical, biological, mechanical, and electrical), biology and mathematics. Although written for, and by, expert researchers, each chapter provides a strong introductory section to ensure accessibility to readers at all levels.


Computational Quantum Chemistry

Computational Quantum Chemistry

Author: Joseph J W McDouall

Publisher: Royal Society of Chemistry

Published: 2015-11-09

Total Pages: 252

ISBN-13: 1782625860

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Computational Quantum Chemistry presents computational electronic structure theory as practised in terms of ab initio waveform methods and density functional approaches. Getting a full grasp of the field can often prove difficult, since essential topics fall outside of the scope of conventional chemistry education. This professional reference book provides a comprehensive introduction to the field. Postgraduate students and experienced researchers alike will appreciate Joseph McDouall's engaging writing style. The book is divided into five chapters, each providing a major aspect of the field. Electronic structure methods, the computation of molecular properties, methods for analysing the output from computations and the importance of relativistic effects on molecular properties are also discussed. Links to the websites of widely used software packages are provided so that the reader can gain first hand experience of using the techniques described in the book.


Molecular Simulations and Biomembranes

Molecular Simulations and Biomembranes

Author: Mark S P Sansom

Publisher: Royal Society of Chemistry

Published: 2010-08-01

Total Pages: 331

ISBN-13: 1849732159

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The need for information in the understanding of membrane systems has been caused by three things - an increase in computer power; methodological developments and the recent expansion in the number of researchers working on it worldwide. However, there has been no up-to-date book that covers the application of simulation methods to membrane systems directly and this book fills an important void in the market. It provides a much needed update on the current methods and applications as well as highlighting recent advances in the way computer simulation can be applied to the field of membranes and membrane proteins. The objectives are to show how simulation methods can provide an important contribution to the understanding of these systems. The scope of the book is such that it covers simulation of membranes and membrane proteins, but also covers the more recent methodological developments such as coarse-grained molecular dynamics and multiscale approaches in systems biology. Applications embrace a range of biological processes including ion channel and transport proteins. The book is wide ranging with broad coverage and a strong coupling to experimental results wherever possible, including colour illustrations to highlight particular aspects of molecular structure. With an internationally respected list of authors, its publication is timely and it will prove indispensable to a large scientific readership.


Multiscale Modeling and Simulation of Composite Materials and Structures

Multiscale Modeling and Simulation of Composite Materials and Structures

Author: Young Kwon

Publisher: Springer Science & Business Media

Published: 2007-12-04

Total Pages: 634

ISBN-13: 0387363181

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This book presents the state-of-the-art in multiscale modeling and simulation techniques for composite materials and structures. It focuses on the structural and functional properties of engineering composites and the sustainable high performance of components and structures. The multiscale techniques can be also applied to nanocomposites which are important application areas in nanotechnology. There are few books available on this topic.