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Theoretical and Computational Chemistry Series
Multiscale Dynamics Simulations: Nano and Nano-bio Systems in Complex Environments
Edited by
Dennis R. Salahub;
Dennis R. Salahub
University of Calgary, Canada
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Dongqing Wei
Dongqing Wei
Shanghai Jiao Tong University, China
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Hardback ISBN:
978-1-83916-178-0
PDF ISBN:
978-1-83916-466-8
EPUB ISBN:
978-1-83916-467-5
Special Collection:
2021 ebook collection
No. of Pages:
388
Published online:
24 Sep 2021
Published in print:
01 Oct 2021
About this book
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.
Multiscale Dynamics Simulations: Nano and Nano-bio Systems in Complex Environments, The Royal Society of Chemistry, 2021.
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Digital access
$250.00
Print format
Multiscale Dynamics Simulations
$250.00
Table of contents
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Chapter 1: QM/MM with Auxiliary DFT in deMon2k1p1-54ByJuan D. Samaniego-Rojas;Juan D. Samaniego-RojasDepartamento de Química, Cinvestav, Avenida Instituto Politécnico Nacional 2508A.P. 14-740, CDMXC.P. 07360México[email protected]Search for other works by this author on:Luis-Ignacio Hernández-Segura;Luis-Ignacio Hernández-SeguraDepartamento de Química, Cinvestav, Avenida Instituto Politécnico Nacional 2508A.P. 14-740, CDMXC.P. 07360México[email protected]Search for other works by this author on:Luis López-Sosa;Luis López-SosaDepartamento de Química, Cinvestav, Avenida Instituto Politécnico Nacional 2508A.P. 14-740, CDMXC.P. 07360México[email protected]Search for other works by this author on:Rogelio I. Delgado-Venegas;Rogelio I. Delgado-VenegasDepartment of Chemistry, University of Calgary2500 University Dr. NWCalgaryAlbertaT2N 1N4CanadaSearch for other works by this author on:Badhin Gomez;Badhin GomezDepartamento de Farmacía, Bioquímica y Biotecnología, Universidad Católica de Santa MaríaArequipaPerúSearch for other works by this author on:Jean-Christophe Lambry;Jean-Christophe LambryLaboratoire d'Optique et Biosciences, Ecole Polytechnique, Institut Polytechnique de Paris, CNRS, INSERMRoute de Saclay91128 Palaiseau cedexFranceSearch for other works by this author on:Aurelien de la Lande;Aurelien de la LandeInstitut de Chimie Physique, Université Paris-Saclay, CNRS15 Avenue Jean Perrin91405 OrsayFranceSearch for other works by this author on:Tzonka Mineva;Tzonka MinevaICGM, Université Montpellier, CNRS, ENSCMMontpellierFranceSearch for other works by this author on:José Alejandre;José AlejandreDepartamento de Química, UAM-IztapalapaSan Rafael Atlixco 186, A.P. 55-534, CDMXC.P. 09340MéxicoSearch for other works by this author on:Bernardo A. Zúñiga-Gutiérrez;Bernardo A. Zúñiga-GutiérrezDepartamento de Química, Universidad de Guadalajara, CUCEIBlvd. Marcelino García Barragán 1421C.P. 44430 GuadalajaraJaliscoMéxicoSearch for other works by this author on:Roberto Flores-Moreno;Roberto Flores-MorenoDepartamento de Química, Universidad de Guadalajara, CUCEIBlvd. Marcelino García Barragán 1421C.P. 44430 GuadalajaraJaliscoMéxicoSearch for other works by this author on:Patrizia Calaminici;Patrizia CalaminiciDepartamento de Química, Cinvestav, Avenida Instituto Politécnico Nacional 2508A.P. 14-740, CDMXC.P. 07360México[email protected]Search for other works by this author on:Gerald Geudtner;Gerald GeudtnerDepartamento de Química, Cinvestav, Avenida Instituto Politécnico Nacional 2508A.P. 14-740, CDMXC.P. 07360México[email protected]Search for other works by this author on:Andreas M. KösterAndreas M. KösterDepartamento de Química, Cinvestav, Avenida Instituto Politécnico Nacional 2508A.P. 14-740, CDMXC.P. 07360México[email protected]Search for other works by this author on:
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Chapter 2: Computational Enzymology: A Challenge for Multiscale Approachesp55-78ByTiziana Marino;Tiziana MarinoDipartimento di Chimica e Tecnologie Chimiche, Università della CalabriaVia P. Bucci87036 Rende (CS)Italy[email protected][email protected]Search for other works by this author on:Marta E. Alberto;Marta E. AlbertoDipartimento di Chimica e Tecnologie Chimiche, Università della CalabriaVia P. Bucci87036 Rende (CS)Italy[email protected][email protected]Search for other works by this author on:Mario Prejanò;Mario PrejanòDipartimento di Chimica e Tecnologie Chimiche, Università della CalabriaVia P. Bucci87036 Rende (CS)Italy[email protected][email protected]Search for other works by this author on:Nino Russo;Nino RussoDipartimento di Chimica e Tecnologie Chimiche, Università della CalabriaVia P. Bucci87036 Rende (CS)Italy[email protected][email protected]Search for other works by this author on:Marirosa ToscanoMarirosa ToscanoDipartimento di Chimica e Tecnologie Chimiche, Università della CalabriaVia P. Bucci87036 Rende (CS)Italy[email protected][email protected]Search for other works by this author on:
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Chapter 3: QM/MM Simulations of Proteins: Is Explicit Inclusion of Polarization on the Horizon?1p79-116BySridhar B. Dwadasi;Sridhar B. DwadasiCMS – Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary2500 University DriveNW, CalgaryT2N 1N4Canada[email protected]Search for other works by this author on:K. Shudipto Amin;K. Shudipto AminCMS – Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary2500 University DriveNW, CalgaryT2N 1N4Canada[email protected]Search for other works by this author on:Dennis R. Salahub;Dennis R. SalahubDepartment of Chemistry, Department of Physics and Astronomy, CMS – Centre for Molecular Simulation, IQST – Institute for Quantum Science and Technology, Quantum Alberta, University of Calgary2500 University DriveNW, CalgaryT2N 1N4CanadaSearch for other works by this author on:Sergei Y. NoskovSergei Y. NoskovCMS – Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary2500 University DriveNW, CalgaryT2N 1N4Canada[email protected]Search for other works by this author on:
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Chapter 4: Electron and Molecular Dynamics Simulations with Polarizable Embeddingp117-143ByAurélio Alvarez-Ibarra;Aurélio Alvarez-IbarraInstitut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay91405 OrsayFrance[email protected]Search for other works by this author on:Karwan Ali Omar;Karwan Ali OmarInstitut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay91405 OrsayFrance[email protected]Department of Chemistry, College of Education, University of Sulaimani41005 KurdistanIraqSearch for other works by this author on:Karim Hasnaoui;Karim HasnaouiHigh Performance Computing User Support Team, Institut du Développement et des Ressources en Informatique Scientifique (IDRIS)91403 OrsayFranceMaison de la Simulation, CNRS, Commissariat à l'Energie Atomique et aux Énergies Alternatives (CEA), Université Paris-Saclay91191 Gif-sur-YvetteFranceSearch for other works by this author on:Aurélien de la LandeAurélien de la LandeInstitut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay91405 OrsayFrance[email protected]Search for other works by this author on:
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Chapter 5: DFTB and Hybrid-DFTB Schemes: Application to Metal Nanosystems, Isolated and in Environmentsp144-171ByMathias Rapacioli;Mathias RapacioliLaboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, CNRS and Université de Toulouse (UPS)118 Route de NarbonneF-31062 ToulouseFrance[email protected]Search for other works by this author on:Fernand Spiegelman;Fernand SpiegelmanLaboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, CNRS and Université de Toulouse (UPS)118 Route de NarbonneF-31062 ToulouseFrance[email protected]Search for other works by this author on:Nathalie TarratNathalie TarratCentre d'Elaboration de Matériaux et d'Etudes Structurales, CEMES, Université de Toulouse, CNRS29 rue Jeanne Marvig31055 ToulouseFranceSearch for other works by this author on:
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Chapter 6: From Atomic Orbitals to Nano-scale Charge Transport with Mixed Quantum/Classical Non-adiabatic Dynamics: Method, Implementation and Applicationp172-202BySamuele Giannini;Samuele GianniniDepartment of Physics and Astronomy and Thomas Young Centre, University College LondonLondon WC1E 6BTUK[email protected]Search for other works by this author on:Antoine Carof;Antoine CarofLaboratoire de Physique et Chimie Théoriques, CNRS, UMR No. 7019, Université de LorraineBP 239,54506 Vandoeuvre-lés-Nancy CedexFranceSearch for other works by this author on:Matthew Ellis;Matthew EllisDepartment of Physics and Astronomy and Thomas Young Centre, University College LondonLondon WC1E 6BTUK[email protected]Search for other works by this author on:Orestis G. Ziogos;Orestis G. ZiogosDepartment of Physics and Astronomy and Thomas Young Centre, University College LondonLondon WC1E 6BTUK[email protected]Search for other works by this author on:Jochen BlumbergerJochen BlumbergerDepartment of Physics and Astronomy and Thomas Young Centre, University College LondonLondon WC1E 6BTUK[email protected]Search for other works by this author on:
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Chapter 7: Modeling Nanocatalytic Reactions with DFTB/MM-MD and DFTB-NMDp203-226ByTingyu Lei;Tingyu LeiState Key Laboratory of Coal Conversion, Institute of Coal Chemistry, Chinese Academy of SciencesTaiyuan030001China[email protected][email protected]Institution State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical TechnologyBeijing100029ChinaSearch for other works by this author on:Xingchen Liu;Xingchen LiuState Key Laboratory of Coal Conversion, Institute of Coal Chemistry, Chinese Academy of SciencesTaiyuan030001China[email protected][email protected]Search for other works by this author on:Xiaodong WenXiaodong WenState Key Laboratory of Coal Conversion, Institute of Coal Chemistry, Chinese Academy of SciencesTaiyuan030001China[email protected][email protected]Search for other works by this author on:
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Chapter 8: Hohenberg–Kohn Theorems as a basis for Multi-scale Simulations: Frozen-density Embedding Theoryp227-253ByTomasz A. WesołowskiTomasz A. WesołowskiDepartment of Physical Chemistry, University of Geneva, 30, Quai Ernest-AnsermetCH-1211 Genève 4Switzerland[email protected]Search for other works by this author on:
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Chapter 9: 3D-RISM-KH Molecular Solvation Theoryp254-286ByDipankar Roy;Dipankar RoyDepartment of Mechanical Engineering, University of Alberta, 10-203 Donadeo Innovation Centre for Engineering9211-116 Street NWEdmontonAlberta T6G 1H9Canada[email protected]Search for other works by this author on:Andriy KovalenkoAndriy KovalenkoDepartment of Mechanical Engineering, University of Alberta, 10-203 Donadeo Innovation Centre for Engineering9211-116 Street NWEdmontonAlberta T6G 1H9Canada[email protected]Nanotechnology Research Centre, National Research Council of Canada11421 Saskatchewan DriveEdmontonAlberta T6G 2M9CanadaSearch for other works by this author on:
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Chapter 10: Free Energy Analysis Algorithms along Transition Paths and Transmembrane Ion Permeationp287-311ByXiao-Qing Guan;Xiao-Qing GuanShanghai University of Traditional Chinese Medicine, Institute of Interdisciplinary Integrative Medicine Research1200 Cailun RoadShanghai201203ChinaSearch for other works by this author on:Dong-Qing WeiDong-Qing WeiShanghai Jiao Tong University, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education800 Dongchuan Road200240ShanghaiChina[email protected]Search for other works by this author on:
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Chapter 11: Pathways in Classification Space: Machine Learning as a Route to Predicting Kinetics of Structural Transitions in Atomic Crystalsp312-348ByJutta Rogal;Jutta RogalDepartment of Chemistry, New York UniversityNew YorkNew York 10003USAFachbereich Physik, Freie Universität Berlin14195 BerlinGermanySearch for other works by this author on:Mark E. TuckermanMark E. TuckermanDepartment of Chemistry, New York UniversityNew YorkNew York 10003USACourant Institute of Mathematical Sciences, New York UniversityNew YorkNew York 10012USA[email protected][email protected]NYU-ECNU Center for Computational Chemistry at NYU Shanghai3663 Zhongshan Road NorthShanghai 200062ChinaSearch for other works by this author on:
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Chapter 12: Machine Learning Algorithms for the Analysis of Molecular Dynamics Trajectoriesp349-377ByAbbas Khan;Abbas KhanDepartment of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghaiP.R. China[email protected]Search for other works by this author on:Byu-Ri Sim;Byu-Ri SimDepartment of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghaiP.R. China[email protected]Search for other works by this author on:Dong-qing WeiDong-qing WeiDepartment of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghaiP.R. China[email protected]State Key Laboratory of Microbial Metabolism, Shanghai–Islamabad–Belgrade Joint Innovation Centre on Antibacterial Resistances, Joint International Research Laboratory of Metabolic & Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghai 200030P.R. ChinaPeng Cheng LaboratoryVanke Cloud City Phase I Building 8, Xili Street, Nashan DistrictShenzhenGuangdong, 518055P.R. ChinaSearch for other works by this author on:
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