Multiscale Simulations and Mechanics of Biological Materials

Shaofan Li is Professor of Applied and Computational Mechanics in the Department of Civil and Environmental Engineering at University of California, Berkeley, USA. He gained his PhD in Mechanical Engineering from Northwestern University, Illinois, in 1997, having previously earned his MSc in Aerospace Engineering. His current research interests include Meshfree Simulations of Adiabatic Shear Band and Spall Fracture, Simulations of Stem Cell Differentiations, and Multiscale Non-equilibrium Equilibrium Molecular Dynamics. Dr Li is the author of numerous articles and conference proceedings.

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 (wiley.com/go/li/multiscale)

This text offers a unique interdisciplinary approach to multiscale biomaterial modeling aimed at both accessible introductory and advanced levels. It presents a breadth of computational approaches for modeling biological materials across multiple length scales (molecular to whole-tissue scale), including solid and fluid based approaches.

About the Editors xv
 
List of Contributors xvii
 
Preface xxi
 
Part I MULTISCALE SIMULATION THEORY
 
1 Atomistic-to-Continuum Coupling Methods for Heat Transfer in Solids 3
Gregory J. Wagner
 
1.1 Introduction 3
 
1.2 The Coupled Temperature Field 5
 
1.3 Coupling the MD and Continuum Energy 7
 
1.4 Examples 9
 
1.5 Coupled Phonon-Electron Heat Transport 12
 
1.6 Examples: Phonon-Electron Coupling 14
 
1.7 Discussion 17
 
Acknowledgments 18
 
References 18
 
2 Accurate Boundary Treatments for Concurrent Multiscale Simulations 21
Shaoqiang Tang
 
2.1 Introduction 21
 
2.2 Time History Kernel Treatment 22
 
2.3 Velocity Interfacial Conditions: Matching the Differential Operator 27
 
2.4 MBCs: Matching the Dispersion Relation 30
 
2.5 Accurate Boundary Conditions: Matching the Time History Kernel Function 36
 
2.6 Two-Way Boundary Conditions 39
 
2.7 Conclusions 41
 
Acknowledgments 41
 
References 41
 
3 A Multiscale Crystal Defect Dynamics and Its Applications 43
Lisheng Liu and Shaofan Li
 
3.1 Introduction 43
 
3.2 Multiscale Crystal Defect Dynamics 44
 
3.3 How and Why the MCDD Model Works 47
 
3.4 Multiscale Finite Element Discretization 47
 
3.5 Numerical Examples 52
 
3.6 Discussion 54
 
Acknowledgments 54
 
Appendix 55
 
References 57
 
4 Application of Many-Realization Molecular Dynamics Method to Understand the Physics of Nonequilibrium Processes in Solids 59
Yao Fu and Albert C. To
 
4.1 Chapter Overview and Background 59
 
4.2 Many-Realization Method 60
 
4.3 Application of the Many-Realization Method to Shock Analysis 62
 
4.4 Conclusions 72
 
Acknowledgments 74
 
References 74
 
5 Multiscale, Multiphysics Modeling of Electromechanical Coupling in Surface-Dominated Nanostructures 77
Harold S. Park and Michel Devel
 
5.1 Introduction 77
 
5.2 Atomistic Electromechanical Potential Energy 79
 
5.3 Bulk Electrostatic Piola-Kirchoff Stress 84
 
5.4 Surface Electrostatic Stress 87
 
5.5 One-Dimensional Numerical Examples 89
 
5.6 Conclusions and Future Research 94
 
Acknowledgments 95
 
References 95
 
6 Towards a General Purpose Design System for Composites 99
Jacob Fish
 
6.1 Motivation 99
 
6.2 General Purpose Multiscale Formulation 103
 
6.3 Mechanistic Modeling of Fatigue via Multiple Temporal Scales 106
 
6.4 Coupling of Mechanical and Environmental Degradation Processes 107
 
6.5 Uncertainty Quantification of Nonlinear Model of Micro-Interfaces and Micro-Phases 111
 
References 113
 
Part II PATIENT-SPECIFIC FLUID-STRUCTURE INTERACTION MODELING, SIMULATION AND DIAGNOSIS
 
7 Patient-Specific Computational Fluid Mechanics of Cerebral Arteries with Aneurysm and Stent 119
Kenji Takizawa, Kathleen Schjodt, Anthony Puntel, Nikolay Kostov, and Tayfun E. Tezduyar
 
7.1 Introduction 119
 
7.2 Mesh Generation 120
 
7.3 Computational Results 124
 
7.4 Concluding Remarks 145
 
Acknowledgments 146
 
References 146
 
8 Application of Isogeometric Analysis to Simulate Local Nanoparticulate Drug Delivery in Patient-Specific Coronary Arteries 149
Shaolie S. Hossain and Yongjie Zhang
 
8.1 Introduction 149
 
8.2 Materials and Methods 151
 
8.3 Results 159
 
8.4 Conclusions and Future Work 165
 
Acknowledgments 166
 
References 166
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