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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…mehr
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)
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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. Dong Qian is Associate Professor of Mechanical Engineering and Director of Graduate Study for the Mechanical Engineering Program at the University of Cincinnati, USA. He obtained his BS degree in Bridge Engineering in 1994 from Tongji University in China. He came to US in 1996 and obtained M.S. degree in civil engineering at the University of Missouri-Columbia in 1998. Dr. Qian is a member of the US association for computational mechanics and ASME. He has published over 40 journal papers and book chapters. His research interests include nano-scale modeling, simulation and applications, meshfree methods, and development of multi-scale methods in solid mechanics.
Inhaltsangabe
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 9 Modeling and Rapid Simulation of High-Frequency Scattering Responses of Cellular Groups 169 Tarek Ismail Zohdi 9.1 Introduction 169 9.2 Ray Theory: Scope of Use and General Remarks 171 9.3 Ray Theory 173 9.4 Plane Harmonic Electromagnetic Waves 177 9.5 Summary 190 References 190 10 Electrohydrodynamic Assembly of Nanoparticles for Nanoengineered Biosensors 193 Jae-Hyun Chung, Hyun-Boo Lee, and Jong-Hoon Kim 10.1 Introduction for Nanoengineered Biosensors 193 10.2 Electric-Field-Induced Phenomena 193 10.3 Geometry Dependency of Dielectrophoresis 200 10.4 Electric-Field-Guided Assembly of Flexible Molecules in Combination with other Mechanisms 203 10.5 Selective Assembly of Nanoparticles 204 10.6 Summary and Applications 205 References 205 11 Advancements in the Immersed Finite-Element Method and Bio-Medical Applications 207 Lucy Zhang, Xingshi Wang, and Chu Wang 11.1 Introduction 207 11.2 Formulation 208 11.3 Bio-Medical Applications 211 11.4 Conclusions 217 References 217 12 Immersed Methods for Compressible Fluid-Solid Interactions 219 Xiaodong Sheldon Wang 12.1 Background and Objectives 219 12.2 Results and Challenges 222 12.3 Conclusion 234 References 234 Part III FROM CELLULAR STRUCTURE TO TISSUES AND ORGANS 13 The Role of the Cortical Membrane in Cell Mechanics: Model and Simulation 241 Louis Foucard, Xavier Espinet, Eduard Benet, and Franck J. Vernerey 13.1 Introduction 241 13.2 The Physics of the Membrane-Cortex Complex and Its Interactions 243 13.3 Formulation of the Membrane Mechanics and Fluid-Membrane Interaction 249 13.4 The Extended Finite Element and the Grid-Based Particle Methods 255 13.5 Examples 257 13.6 Conclusion 262 Acknowledgments 263 References 263 14 Role of Elastin in Arterial Mechanics 267 Yanhang Zhang and Shahrokh Zeinali-Davarani 14.1 Introduction 267 14.2 The Role of Elastin in Vascular Diseases 268 14.3 Mechanical Behavior of Elastin 269 14.4 Constitutive Modeling of Elastin 272 14.5 Conclusions 276 Acknowledgments 276 References 277 15 Characterization of Mechanical Properties of Biological Tissue: Application to the FEM Analysis of the Urinary Bladder 283 Eugenio Oñate, Facundo J. Bellomo, Virginia Monteiro, Sergio Oller, and Liz G. Nallim 15.1 Introduction 283 15.2 Inverse Approach for the Material Characterization of Biological Soft Tissues via a Generalized Rule of Mixtures 284 15.3 FEM Analysis of the Urinary Bladder 289 15.4 Conclusions 298 Acknowledgments 298 References 298 16 Structure Design of Vascular Stents 301 Yaling Liu, Jie Yang, Yihua Zhou, and Jia Hu 16.1 Introduction 301 16.2 Ideal Vascular Stents 303 16.3 Design Parameters that Affect the Properties of Stents 304 16.4 Main Methods for Vascular Stent Design 308 16.5 Vascular Stent Design Method Perspective 316 References 316 17 Applications of Meshfree Methods in Explicit Fracture and Medical Modeling 319 Daniel C. Simkins, Jr. 17.1 Introduction 319 17.2 Explicit Crack Representation 319 17.3 Meshfree Modeling in Medicine 327 Acknowledgments 331 References 331 18 Design of Dynamic and Fatigue-Strength-Enhanced Orthopedic Implants 333 Sagar Bhamare, Seetha Ramaiah Mannava, Leonora Felon, David Kirschman, Vijay Vasudevan, and Dong Qian 18.1 Introduction 333 18.2 Fatigue Life Analysis of Orthopedic Implants 335 18.3 LSP Process 338 18.4 LSP Modeling and Simulation 339 18.5 Application Example 342 18.6 Summary 348 Acknowledgments 348 References 349 Part IV BIO-MECHANICS AND MATERIALS OF BONES AND COLLAGENS 19 Archetype Blending Continuum Theory and Compact Bone Mechanics 353 Khalil I. Elkhodary, Michael Steven Greene, and Devin O'Connor 19.1 Introduction 353 19.2 ABC Formulation 358 19.3 Constitutive Modeling in ABC 361 19.4 The ABC Computational Model 367 19.5 Results and Discussion 368 19.6 Conclusion 373 Acknowledgments 374 References 374 20 Image-Based Multiscale Modeling of Porous Bone Materials 377 Judy P. Yang, Sheng-Wei Chi, and Jiun-Shyan Chen 20.1 Overview 377 20.2 Homogenization of Porous Microstructures 379 20.3 Level Set Method for Image Segmentation 387 20.4 Image-Based Microscopic Cell Modeling 391 20.5 Trabecular Bone Modeling 395 20.6 Conclusions 399 Acknowledgment 399 References 399 21 Modeling Nonlinear Plasticity of Bone Mineral from Nanoindentation Data 403 Amir Reza Zamiri and Suvranu De 21.1 Introduction 403 21.2 Methods 404 21.3 Results 407 21.4 Conclusions 408 Acknowledgments 408 References 408 22 Mechanics of Cellular Materials and its Applications 411 Ji Hoon Kim, Daeyong Kim, and Myoung-Gyu Lee 22.1 Biological Cellular Materials 411 22.2 Engineered Cellular Materials 421 References 431 23 Biomechanics of Mineralized Collagens 435 Ashfaq Adnan, Farzad Sarker, and Sheikh F. Ferdous 23.1 Introduction 435 23.2 Computational Method 438 23.3 Results 441 23.4 Summary and Conclusions 446 Acknowledgments 446 References 446 Index 449
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 9 Modeling and Rapid Simulation of High-Frequency Scattering Responses of Cellular Groups 169 Tarek Ismail Zohdi 9.1 Introduction 169 9.2 Ray Theory: Scope of Use and General Remarks 171 9.3 Ray Theory 173 9.4 Plane Harmonic Electromagnetic Waves 177 9.5 Summary 190 References 190 10 Electrohydrodynamic Assembly of Nanoparticles for Nanoengineered Biosensors 193 Jae-Hyun Chung, Hyun-Boo Lee, and Jong-Hoon Kim 10.1 Introduction for Nanoengineered Biosensors 193 10.2 Electric-Field-Induced Phenomena 193 10.3 Geometry Dependency of Dielectrophoresis 200 10.4 Electric-Field-Guided Assembly of Flexible Molecules in Combination with other Mechanisms 203 10.5 Selective Assembly of Nanoparticles 204 10.6 Summary and Applications 205 References 205 11 Advancements in the Immersed Finite-Element Method and Bio-Medical Applications 207 Lucy Zhang, Xingshi Wang, and Chu Wang 11.1 Introduction 207 11.2 Formulation 208 11.3 Bio-Medical Applications 211 11.4 Conclusions 217 References 217 12 Immersed Methods for Compressible Fluid-Solid Interactions 219 Xiaodong Sheldon Wang 12.1 Background and Objectives 219 12.2 Results and Challenges 222 12.3 Conclusion 234 References 234 Part III FROM CELLULAR STRUCTURE TO TISSUES AND ORGANS 13 The Role of the Cortical Membrane in Cell Mechanics: Model and Simulation 241 Louis Foucard, Xavier Espinet, Eduard Benet, and Franck J. Vernerey 13.1 Introduction 241 13.2 The Physics of the Membrane-Cortex Complex and Its Interactions 243 13.3 Formulation of the Membrane Mechanics and Fluid-Membrane Interaction 249 13.4 The Extended Finite Element and the Grid-Based Particle Methods 255 13.5 Examples 257 13.6 Conclusion 262 Acknowledgments 263 References 263 14 Role of Elastin in Arterial Mechanics 267 Yanhang Zhang and Shahrokh Zeinali-Davarani 14.1 Introduction 267 14.2 The Role of Elastin in Vascular Diseases 268 14.3 Mechanical Behavior of Elastin 269 14.4 Constitutive Modeling of Elastin 272 14.5 Conclusions 276 Acknowledgments 276 References 277 15 Characterization of Mechanical Properties of Biological Tissue: Application to the FEM Analysis of the Urinary Bladder 283 Eugenio Oñate, Facundo J. Bellomo, Virginia Monteiro, Sergio Oller, and Liz G. Nallim 15.1 Introduction 283 15.2 Inverse Approach for the Material Characterization of Biological Soft Tissues via a Generalized Rule of Mixtures 284 15.3 FEM Analysis of the Urinary Bladder 289 15.4 Conclusions 298 Acknowledgments 298 References 298 16 Structure Design of Vascular Stents 301 Yaling Liu, Jie Yang, Yihua Zhou, and Jia Hu 16.1 Introduction 301 16.2 Ideal Vascular Stents 303 16.3 Design Parameters that Affect the Properties of Stents 304 16.4 Main Methods for Vascular Stent Design 308 16.5 Vascular Stent Design Method Perspective 316 References 316 17 Applications of Meshfree Methods in Explicit Fracture and Medical Modeling 319 Daniel C. Simkins, Jr. 17.1 Introduction 319 17.2 Explicit Crack Representation 319 17.3 Meshfree Modeling in Medicine 327 Acknowledgments 331 References 331 18 Design of Dynamic and Fatigue-Strength-Enhanced Orthopedic Implants 333 Sagar Bhamare, Seetha Ramaiah Mannava, Leonora Felon, David Kirschman, Vijay Vasudevan, and Dong Qian 18.1 Introduction 333 18.2 Fatigue Life Analysis of Orthopedic Implants 335 18.3 LSP Process 338 18.4 LSP Modeling and Simulation 339 18.5 Application Example 342 18.6 Summary 348 Acknowledgments 348 References 349 Part IV BIO-MECHANICS AND MATERIALS OF BONES AND COLLAGENS 19 Archetype Blending Continuum Theory and Compact Bone Mechanics 353 Khalil I. Elkhodary, Michael Steven Greene, and Devin O'Connor 19.1 Introduction 353 19.2 ABC Formulation 358 19.3 Constitutive Modeling in ABC 361 19.4 The ABC Computational Model 367 19.5 Results and Discussion 368 19.6 Conclusion 373 Acknowledgments 374 References 374 20 Image-Based Multiscale Modeling of Porous Bone Materials 377 Judy P. Yang, Sheng-Wei Chi, and Jiun-Shyan Chen 20.1 Overview 377 20.2 Homogenization of Porous Microstructures 379 20.3 Level Set Method for Image Segmentation 387 20.4 Image-Based Microscopic Cell Modeling 391 20.5 Trabecular Bone Modeling 395 20.6 Conclusions 399 Acknowledgment 399 References 399 21 Modeling Nonlinear Plasticity of Bone Mineral from Nanoindentation Data 403 Amir Reza Zamiri and Suvranu De 21.1 Introduction 403 21.2 Methods 404 21.3 Results 407 21.4 Conclusions 408 Acknowledgments 408 References 408 22 Mechanics of Cellular Materials and its Applications 411 Ji Hoon Kim, Daeyong Kim, and Myoung-Gyu Lee 22.1 Biological Cellular Materials 411 22.2 Engineered Cellular Materials 421 References 431 23 Biomechanics of Mineralized Collagens 435 Ashfaq Adnan, Farzad Sarker, and Sheikh F. Ferdous 23.1 Introduction 435 23.2 Computational Method 438 23.3 Results 441 23.4 Summary and Conclusions 446 Acknowledgments 446 References 446 Index 449
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