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Overview

Eleven carefully selected, peer-reviewed contributions from the Virtual Conference on Computational Science (VCCS-2016) are featured in this edited book of proceedings. VCCS-2016, an annual meeting, was held online from 1st to 31st August 2016. The theme of the conference was "Computational Thinking for the Advancement of Society" and it matched the paradigm shift in the way we think. VCCS-2016 was attended by 100 participants from 20 countries. The chapters reflect a wide range of fundamental and applied research applying computational methods.

Product Details

ISBN-13: 9783110465365
Publisher: De Gruyter
Publication date: 10/23/2017
Pages: 248
Product dimensions: 6.69(w) x 9.45(h) x (d)
Age Range: 18 Years

About the Author

Ponnadurai Ramasami, University of Mauritius, Mauritius, Indian Ocean.

Table of Contents

Preface v

List of contributing authors xi

1 Addressing the challenges of standalone multi-core simulations in molecular dynamics R.O. Ocaya J.J. Terblans 1

1.1 Introduction 2

1.2 Standalone architectures 7

1.2.1 Classifications of parallelization paradigms 7

1.3 Getting started with standalone computation 8

1.3.1 To code or not to code 8

1.3.2 General tools 9

1.3.3 Parallelizable tools 9

1.4 Parallel processing paradigms in the C-language 10

1.4.1 Threads and message passing 10

1.4.2 Open multiprocessing programming 11

1.4.3 Message passing interface programming 13

1.4.4 The GPU approach 14

1.4.5 Cloud virtualization 15

1.5 Summary of results 17

1.6 Conclusions 17

References 18

2 Optical and magnetic properties of free-standing silicene, germanene and T-graphene system Suman Chowdhury Arka Bandyopadhyay Namrata Dhar Debnarayan Jana 23

2.1 Introduction 23

2.2 DFT study of the optical properties 27

2.2.1 Methodology 27

2.3 FS silicene monolayer 30

2.3.1 Optical properties 30

2.3.2 Magnetic properties of doped FS silicene monolayer 36

2.4 Elemental structure and synthesis of FS germanene 44

2.4.1 Electronic and magnetic properties of FS germanene 45

2.4.2 Optical properties of FS germanene 50

2.5 Structural properties of TG sheet 51

2.5.1 Electronic properties of pristine and functionalized TG sheet 52

2.5.2 TG nanoribbons (NRs) and clusters 54

2.5.3 Other allotropes beyond TG 57

2.6 Conclusions and future directions 59

References 61

3 Theoretical study of the electronic states of newly detected dications. Case of MgS2+ AND SiN2+ Toufik Khairat Mohammed Salah Khadija Marakchi Najia Komiha 71

3.1 Introduction 71

3.2 Computational details 72

3.3 Results and discussion 76

3.3.1 Neutral MgS 76

3.3.2 MgS2+ dication 79

3.3.3 SiN2+ dication study 83

3.4 Conclusion 88

References 90

4 Analytical Solution of Pantograph Equation with Incommensurate Delay Jayvant Patade Sachin Bhalekar 93

4.1 Introduction 93

4.2 Preliminaries 94

4.2.1 Basic definitions and results 94

4.2.2 Daftardar-Gejji and Jafari method 96

4.2.3 Existence, uniqueness and convergence 98

4.3 Stability analysis 101

4.4 The pantograph equation and its solution 102

4.5 Analysis 103

4.5.1 The relation between R(a, b, c, p, q, x) and Kummer's confluent hypergeometric function 108

4.6 Generalizations to fractional-order DDE 113

4.7 Conclusions 114

References 114

5 Computational chemistry applied to vibrational spectroscopy: A tool for characterization of nucleic acid bases and some of their 5-substituted derivatives M. Alcolea Palafox 117

5.1 Introduction 117

5.2 Molecules under study 118

5.3 Computational methods 120

5.4 Scaling 122

5.5 Applications of computational chemistry to vibrational spectroscopy 123

5.5.1 Characterization of all the normal modes of a molecule 123

5.5.2 Accurate assignment of all the bands of a spectrum 123

5.5.3 Identification of the tautomers present in the isolated state 135

5.5.4 Simulation of the crystal unit cell of a compound and the interpretation of its vibrational spectra 136

5.6 Summary and conclusions 147

References 149

6 Mechanism of nucleophilic substitution reactions of 4-(4'-nitro) phenylnitrobenzofurazan ether with aniline in acetonitrile K. Gbayo C. Isanbor K. Lobb O. Oloba-Whenu 153

6.1 Introduction 153

6.2 Results and discussion 154

6.3 Conclusion 158

6.4 Experimental section 159

References 160

7 Computational methods in preformulation study for pharmaceutical solid dosage forms of therapeutic proteins Sutapa Biswas Majee Gopa Roy Biswas 163

7.1 Introduction 163

7.2 Challenges to formulation development of therapeutic proteins 164

7.3 Aggregation of therapeutic proteins 165

7.3.1 Instrumental methods of analysis 166

7.3.2 Computational approaches in study of aggregation 169

7.4 Computational tools in assessment of immunogenicity of therapeutic proteins 170

7.5 Conclusion 170

References 171

8 Computational Investigation of Cationic, Anionic and Neutral Ag2AuN (N = 1-7) Nanoalloy Clusters Prabhat Ranjan Tanmoy Chakraborty Ajay Kumar 173

8.1 Introduction 173

8.2 Computational details 175

8.3 Results and discussion 176

8.3.1 Equilibrium geometries 176

8.3.2 Electronic properties and DFT-based descriptors 180

8.4 Conclusion 185

References 185

9 Evacuation simulation using Hybrid Space Discretisation and Application to Large Underground Rail Tunnel Station N Chooramun P. J. Lawrence E. R. Galea 191

9.1 Introduction 191

9.2 Software architecture for Hybrid Spatial Discretisation 193

9.2.1 Continuous region component 193

9.2.2 Coarse region component 195

9.2.3 Choice of discretisation strategies for using HSD 196

9.3 Large tunnel station complex case 196

9.4 Results and discussion 199

9.5 Conclusion 202

References 203

10 DFT study of anthocyanidin and anthocyanin pigments for Dye-Sensitized Solar Cells: Electron injecting from the excited states and adsorption onto TiO2 (anatase) surface Emildo Marcano 205

10.1 Introduction 205

10.2 Theory and computational details 206

10.3 Results and discussion 208

10.3.1 Geometric optimization and intramolecular charge transferences of anthocyanin dyes 208

10.3.2 Frontier molecular orbitals, absorption spectra and LHE 208

10.3.3 Free Energy Change of Electron Injection 211

10.3.4 Chemisorption on TiO2-anatase 213

Conclusions 215

References 215

11 Elemental Two-Dimensional Materials Beyond Graphene Udo Schwingenschlögl Jiajie Zhu Tetsuya Morishita Michelle J.S. Spencer Paola De Padova Amanda Generosi Barbara Paci Carlo Ottaviani Claudio Quaresima Bruno Olivieri Eric Salomon Thierry Angot Guy Le Lay Harold J.W. Zandvliet L. C. Lew Yan Voon 219

11.1 Silicene on substrates 219

11.2 Microscopic mechanism of the oxidation of silicene on Ag(111) 221

11.3 Multilayer silicene 222

11.4 Germanene 223

11.5 Summary 225

References 226

Index 229

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