Multiscale simulations and mechanics of biological materials / (Record no. 88862)

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International Standard Book Number 9781118452530
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International Standard Book Number 9781118402955 (electronic bk.)
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International Standard Book Number 1118402952 (electronic bk.)
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Title Multiscale simulations and mechanics of biological materials /
Statement of responsibility, etc edited by Shaofan Li, Dong Qian.
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Extent 1 online resource (475 pages)
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505 0# - CONTENTS
Formatted contents note Table of Contents<br/>About the Editors xv<br/><br/>List of Contributors xvii<br/><br/>Preface xxi<br/><br/>Part I MULTISCALE SIMULATION THEORY<br/><br/>1 Atomistic-to-Continuum Coupling Methods for Heat Transfer in Solids 3<br/>Gregory J. Wagner<br/><br/>1.1 Introduction 3<br/><br/>1.2 The Coupled Temperature Field 5<br/><br/>1.2.1 Spatial Reduction 5<br/><br/>1.2.2 Time Averaging 6<br/><br/>1.3 Coupling the MD and Continuum Energy 7<br/><br/>1.3.1 The Coupled System 7<br/><br/>1.3.2 Continuum Heat Transfer 8<br/><br/>1.3.3 Augmented MD 8<br/><br/>1.4 Examples 9<br/><br/>1.4.1 One-Dimensional Heat Conduction 9<br/><br/>1.4.2 Thermal Response of a Composite System 10<br/><br/>1.5 Coupled Phonon-Electron Heat Transport 12<br/><br/>1.6 Examples: Phonon–Electron Coupling 14<br/><br/>1.6.1 Equilibration of Electron/Phonon Energies 14<br/><br/>1.6.2 Laser Heating of a Carbon Nanotube 15<br/><br/>1.7 Discussion 17<br/><br/>Acknowledgments 18<br/><br/>References 18<br/><br/>2 Accurate Boundary Treatments for Concurrent Multiscale Simulations 21<br/>Shaoqiang Tang<br/><br/>2.1 Introduction 21<br/><br/>2.2 Time History Kernel Treatment 22<br/><br/>2.2.1 Harmonic Chain 22<br/><br/>2.2.2 Square Lattice 23<br/><br/>2.3 Velocity Interfacial Conditions: Matching the Differential Operator 27<br/><br/>2.4 MBCs: Matching the Dispersion Relation 30<br/><br/>2.4.1 Harmonic Chain 30<br/><br/>2.4.2 FCC Lattice 33<br/><br/>2.5 Accurate Boundary Conditions: Matching the Time History Kernel Function 36<br/><br/>2.6 Two-Way Boundary Conditions 39<br/><br/>2.7 Conclusions 41<br/><br/>Acknowledgments 41<br/><br/>References 41<br/><br/>3 A Multiscale Crystal Defect Dynamics and Its Applications 43<br/>Lisheng Liu and Shaofan Li<br/><br/>3.1 Introduction 43<br/><br/>3.2 Multiscale Crystal Defect Dynamics 44<br/><br/>3.3 How and Why the MCDD Model Works 47<br/><br/>3.4 Multiscale Finite Element Discretization 47<br/><br/>3.5 Numerical Examples 52<br/><br/>3.6 Discussion 54<br/><br/>Acknowledgments 54<br/><br/>Appendix 55<br/><br/>References 57<br/><br/>4 Application of Many-Realization Molecular Dynamics Method to Understand the Physics of Nonequilibrium Processes in Solids 59<br/>Yao Fu and Albert C. To<br/><br/>4.1 Chapter Overview and Background 59<br/><br/>4.2 Many-Realization Method 60<br/><br/>4.3 Application of the Many-Realization Method to Shock Analysis 62<br/><br/>4.4 Conclusions 72<br/><br/>Acknowledgments 74<br/><br/>References 74<br/><br/>5 Multiscale, Multiphysics Modeling of Electromechanical Coupling in Surface-Dominated Nanostructures 77<br/>Harold S. Park and Michel Devel<br/><br/>5.1 Introduction 77<br/><br/>5.2 Atomistic Electromechanical Potential Energy 79<br/><br/>5.2.1 Atomistic Electrostatic Potential Energy: Gaussian Dipole Method 80<br/><br/>5.2.2 Finite Element Equilibrium Equations from Total Electromechanical Potential Energy 83<br/><br/>5.3 Bulk Electrostatic Piola–Kirchoff Stress 84<br/><br/>5.3.1 Cauchy–Born Kinematics 84<br/><br/>5.3.2 Comparison of Bulk Electrostatic Stress with Molecular Dynamics Electrostatic Force 86<br/><br/>5.4 Surface Electrostatic Stress 87<br/><br/>5.5 One-Dimensional Numerical Examples 89<br/><br/>5.5.1 Verification of Bulk Electrostatic Stress 89<br/><br/>5.5.2 Verification of Surface Electrostatic Stress 91<br/><br/>5.6 Conclusions and Future Research 94<br/><br/>Acknowledgments 95<br/><br/>References 95<br/><br/>6 Towards a General Purpose Design System for Composites 99<br/>Jacob Fish<br/><br/>6.1 Motivation 99<br/><br/>6.2 General Purpose Multiscale Formulation 103<br/><br/>6.2.1 The Basic Reduced-Order Model 103<br/><br/>6.2.2 Enhanced Reduced-Order Model 104<br/><br/>6.3 Mechanistic Modeling of Fatigue via Multiple Temporal Scales 106<br/><br/>6.4 Coupling of Mechanical and Environmental Degradation Processes 107<br/><br/>6.4.1 Mathematical Model 107<br/><br/>6.4.2 Mathematical Upscaling 109<br/><br/>6.4.3 Computational Upscaling 110<br/><br/>6.5 Uncertainty Quantification of Nonlinear Model of Micro-Interfaces and Micro-Phases 111<br/><br/>References 113<br/><br/>Part II PATIENT-SPECIFIC FLUID-STRUCTURE INTERACTION MODELING, SIMULATION AND DIAGNOSIS<br/><br/>7 Patient-Specific Computational Fluid Mechanics of Cerebral Arteries with Aneurysm and Stent 119<br/>Kenji Takizawa, Kathleen Schjodt, Anthony Puntel, Nikolay Kostov, and Tayfun E. Tezduyar<br/><br/>7.1 Introduction 119<br/><br/>7.2 Mesh Generation 120<br/><br/>7.3 Computational Results 124<br/><br/>7.3.1 Computational Models 124<br/><br/>7.3.2 Comparative Study 131<br/><br/>7.3.3 Evaluation of Zero-Thickness Representation 142<br/><br/>7.4 Concluding Remarks 145<br/><br/>Acknowledgments 146<br/><br/>References 146<br/><br/>8 Application of Isogeometric Analysis to Simulate Local Nanoparticulate Drug Delivery in Patient-Specific Coronary Arteries 149<br/>Shaolie S. Hossain and Yongjie Zhang<br/><br/>8.1 Introduction 149<br/><br/>8.2 Materials and Methods 151<br/><br/>8.2.1 Mathematical Modeling 151<br/><br/>8.2.2 Parameter Selection 156<br/><br/>8.2.3 Mesh Generation from Medical Imaging Data 158<br/><br/>8.3 Results 159<br/><br/>8.3.1 Extraction of NP Wall Deposition Data 159<br/><br/>8.3.2 Drug Distribution in a Normal Artery Wall 160<br/><br/>8.3.3 Drug Distribution in a Diseased Artery Wall with a Vulnerable Plaque 160<br/><br/>8.4 Conclusions and Future Work 165<br/><br/>Acknowledgments 166<br/><br/>References 166<br/><br/>9 Modeling and Rapid Simulation of High-Frequency Scattering Responses of Cellular Groups 169<br/>Tarek Ismail Zohdi<br/><br/>9.1 Introduction 169<br/><br/>9.2 Ray Theory: Scope of Use and General Remarks 171<br/><br/>9.3 Ray Theory 173<br/><br/>9.4 Plane Harmonic Electromagnetic Waves 177<br/><br/>9.4.1 General Plane Waves 177<br/><br/>9.4.2 Electromagnetic Waves 177<br/><br/>9.4.3 Optical Energy Propagation 178<br/><br/>9.4.4 Reflection and Absorption of Energy 179<br/><br/>9.4.5 Computational Algorithm 183<br/><br/>9.4.6 Thermal Conversion of Optical Losses 187<br/><br/>9.5 Summary 190<br/><br/>References 190<br/><br/>10 Electrohydrodynamic Assembly of Nanoparticles for Nanoengineered Biosensors 193<br/>Jae-Hyun Chung, Hyun-Boo Lee, and Jong-Hoon Kim<br/><br/>10.1 Introduction for Nanoengineered Biosensors 193<br/><br/>10.2 Electric-Field-Induced Phenomena 193<br/><br/>10.2.1 Electrophoresis 194<br/><br/>10.2.2 Dielectrophoresis 195<br/><br/>10.2.3 Electroosmotic and Electrothermal Flow 198<br/><br/>10.2.4 Brownian Motion Forces and Drag Forces 199<br/><br/>10.3 Geometry Dependency of Dielectrophoresis 200<br/><br/>10.4 Electric-Field-Guided Assembly of Flexible Molecules in Combination with other Mechanisms 203<br/><br/>10.4.1 Dielectrophoresis in Combination with Fluid Flow 203<br/><br/>10.4.2 Dielectrophoresis in Combination with Binding Affinity 203<br/><br/>10.4.3 Dielectrophoresis in Combination with Capillary Action and Viscosity 203<br/><br/>10.5 Selective Assembly of Nanoparticles 204<br/><br/>10.5.1 Size-Selective Deposition of Nanoparticles 204<br/><br/>10.5.2 Electric-Property Sorting of Nanoparticles 205<br/><br/>10.6 Summary and Applications 205<br/><br/>References 205<br/><br/>11 Advancements in the Immersed Finite-Element Method and Bio-Medical Applications 207<br/>Lucy Zhang, Xingshi Wang, and Chu Wang<br/><br/>11.1 Introduction 207<br/><br/>11.2 Formulation 208<br/><br/>11.2.1 The Immersed Finite Element Method 208<br/><br/>11.2.2 Semi-Implicit Immersed Finite Element Method 210<br/><br/>11.3 Bio-Medical Applications 211<br/><br/>11.3.1 Red Blood Cell in Bifurcated Vessels 211<br/><br/>11.3.2 Human Vocal Folds Vibration during Phonation 214<br/><br/>11.4 Conclusions 217<br/><br/>References 217<br/><br/>12 Immersed Methods for Compressible Fluid–Solid Interactions 219<br/>Xiaodong Sheldon Wang<br/><br/>12.1 Background and Objectives 219<br/><br/>12.2 Results and Challenges 222<br/><br/>12.2.1 Formulations, Theories, and Results 222<br/><br/>12.2.2 Stability Analysis 227<br/><br/>12.2.3 Kernel Functions 228<br/><br/>12.2.4 A Simple Model Problem 231<br/><br/>12.2.5 Compressible Fluid Model for General Grids 231<br/><br/>12.2.6 Multigrid Preconditioner 232<br/><br/>12.3 Conclusion 234<br/><br/>References 234<br/><br/>Part III FROM CELLULAR STRUCTURE TO TISSUES AND ORGANS<br/><br/>13 The Role of the Cortical Membrane in Cell Mechanics: Model and Simulation 241<br/>Louis Foucard, Xavier Espinet, Eduard Benet, and Franck J. Vernerey<br/><br/>13.1 Introduction 241<br/><br/>13.2 The Physics of the Membrane–Cortex Complex and Its Interactions 243<br/><br/>13.2.1 The Mechanics of the Membrane–Cortex Complex 243<br/><br/>13.2.2 Interaction of the Membrane with the Outer Environment 247<br/><br/>13.3 Formulation of the Membrane Mechanics and Fluid–Membrane Interaction 249<br/><br/>13.3.1 Kinematics of Immersed Membrane 249<br/><br/>13.3.2 Variational Formulation of the Immersed MCC Problem 251<br/><br/>13.3.3 Principle of Virtual Power and Conservation of Momentum 253<br/><br/>13.4 The Extended Finite Element and the Grid-Based Particle Methods 255<br/><br/>13.5 Examples 257<br/><br/>13.5.1 The Equilibrium Shapes of the Red Blood Cell 257<br/><br/>13.5.2 Cell Endocytosis 259<br/><br/>13.5.3 Cell Blebbing 260<br/><br/>13.6 Conclusion 262<br/><br/>Acknowledgments 263<br/><br/>References 263<br/><br/>14 Role of Elastin in Arterial Mechanics 267<br/>Yanhang Zhang and Shahrokh Zeinali-Davarani<br/><br/>14.1 Introduction 267<br/><br/>14.2 The Role of Elastin in Vascular Diseases 268<br/><br/>14.3 Mechanical Behavior of Elastin 269<br/><br/>14.3.1 Orthotropic Hyperelasticity in Arterial Elastin 269<br/><br/>14.3.2 Viscoelastic Behavior 271<br/><br/>14.4 Constitutive Modeling of Elastin 272<br/><br/>14.5 Conclusions 276<br/><br/>Acknowledgments 276<br/><br/>References 277<br/><br/>15 Characterization of Mechanical Properties of Biological Tissue: Application to the FEM Analysis of the Urinary Bladder 283<br/>Eugenio Oñate, Facundo J. Bellomo, Virginia Monteiro, Sergio Oller, and Liz G. Nallim<br/><br/>15.1 Introduction 283<br/><br/>15.2 Inverse Approach for the Material Characterization of Biological Soft Tissues via a Generalized Rule of Mixtures 284<br/><br/>15.2.1 Constitutive Model for Material Characterization 284<br/><br/>15.2.2 Definition of the Objective Function and Materials Characterization Procedure 286<br/><br/>15.2.3 Validation of the Inverse Model for Urinary Bladder Tissue Characterization 287<br/><br/>15.3 FEM Analysis of the Urinary Bladder 289<br/><br/>15.3.1 Constitutive Model for Tissue Analysis 290<br/><br/>15.3.2 Validation. Test Inflation of a Quasi-incompressible Rubber Sphere 292<br/><br/>15.3.3 Mechanical Simulation of Human Urinary Bladder 293<br/><br/>15.3.4 Study of Urine–Bladder Interaction 295<br/><br/>15.4 Conclusions 298<br/><br/>Acknowledgments 298<br/><br/>References 298<br/><br/>16 Structure Design of Vascular Stents 301<br/>Yaling Liu, Jie Yang, Yihua Zhou, and Jia Hu<br/><br/>16.1 Introduction 301<br/><br/>16.2 Ideal Vascular Stents 303<br/><br/>16.3 Design Parameters that Affect the Properties of Stents 304<br/><br/>16.3.1 Expansion Method 305<br/><br/>16.3.2 Stent Materials 305<br/><br/>16.3.3 Structure of Stents 306<br/><br/>16.3.4 Effect of Design Parameters on Stent Properties 308<br/><br/>16.4 Main Methods for Vascular Stent Design 308<br/><br/>16.5 Vascular Stent Design Method Perspective 316<br/><br/>References 316<br/><br/>17 Applications of Meshfree Methods in Explicit Fracture and Medical Modeling 319<br/>Daniel C. Simkins, Jr.<br/><br/>17.1 Introduction 319<br/><br/>17.2 Explicit Crack Representation 319<br/><br/>17.2.1 Two-Dimensional Cracks 320<br/><br/>17.2.2 Three-Dimensional Cracks in Thin Shells 323<br/><br/>17.2.3 Material Model Requirements 323<br/><br/>17.2.4 Crack Examples 323<br/><br/>17.3 Meshfree Modeling in Medicine 327<br/><br/>Acknowledgments 331<br/><br/>References 331<br/><br/>18 Design of Dynamic and Fatigue-Strength-Enhanced Orthopedic Implants 333<br/>Sagar Bhamare, Seetha Ramaiah Mannava, Leonora Felon, David Kirschman, Vijay Vasudevan, and Dong Qian<br/><br/>18.1 Introduction 333<br/><br/>18.2 Fatigue Life Analysis of Orthopedic Implants 335<br/><br/>18.2.1 Fatigue Life Testing for Implants 335<br/><br/>18.2.2 Fatigue Life Prediction 337<br/><br/>18.3 LSP Process 338<br/><br/>18.4 LSP Modeling and Simulation 339<br/><br/>18.4.1 Pressure Pulse Model 339<br/><br/>18.4.2 Constitutive Model 340<br/><br/>18.4.3 Solution Procedure 341<br/><br/>18.5 Application Example 342<br/><br/>18.5.1 Implant Rod Design 342<br/><br/>18.5.2 Residual Stresses 342<br/><br/>18.5.3 Fatigue Tests and Life Predictions 344<br/><br/>18.6 Summary 348<br/><br/>Acknowledgments 348<br/><br/>References 349<br/><br/>Part IV BIO-MECHANICS AND MATERIALS OF BONES AND COLLAGENS<br/><br/>19 Archetype Blending Continuum Theory and Compact Bone Mechanics 353<br/>Khalil I. Elkhodary, Michael Steven Greene, and Devin O’Connor<br/><br/>19.1 Introduction 353<br/><br/>19.1.1 A Short Look at the Hierarchical Structure of Bone 354<br/><br/>19.1.2 A Background of Generalized Continuum Mechanics 355<br/><br/>19.1.3 Notes on the Archetype Blending Continuum Theory 356<br/><br/>19.2 ABC Formulation 358<br/><br/>19.2.1 Physical Postulates and the Resulting Kinematics 358<br/><br/>19.2.2 ABC Variational Formulation 359<br/><br/>19.3 Constitutive Modeling in ABC 361<br/><br/>19.3.1 General Concept 361<br/><br/>19.3.2 Blending Laws for Cortical Bone Modeling 363<br/><br/>19.4 The ABC Computational Model 367<br/><br/>19.5 Results and Discussion 368<br/><br/>19.5.1 Propagating Strain Inhomogeneities across Osteons 368<br/><br/>19.5.2 Normal and Shear Stresses in Osteons 369<br/><br/>19.5.3 Rotation and Displacement Fields in Osteons 370<br/><br/>19.5.4 Damping in Cement Lines 372<br/><br/>19.5.5 Qualitative Look at Strain Gradients in Osteons 372<br/><br/>19.6 Conclusion 373<br/><br/>Acknowledgments 374<br/><br/>References 374<br/><br/>20 Image-Based Multiscale Modeling of Porous Bone Materials 377<br/>Judy P. Yang, Sheng-Wei Chi, and Jiun-Shyan Chen<br/><br/>20.1 Overview 377<br/><br/>20.2 Homogenization of Porous Microstructures 379<br/><br/>20.2.1 Basic Equations of Two-Phase Media 379<br/><br/>20.2.2 Asymptotic Expansion of Two-Phase Medium 381<br/><br/>20.2.3 Homogenized Porous Media 386<br/><br/>20.3 Level Set Method for Image Segmentation 387<br/><br/>20.3.1 Variational Level Set Formulation 387<br/><br/>20.3.2 Strong Form Collocation Methods for Active Contour Model 389<br/><br/>20.4 Image-Based Microscopic Cell Modeling 391<br/><br/>20.4.1 Solution of Microscopic Cell Problems 391<br/><br/>20.4.2 Reproducing Kernel and Gradient-Reproducing Kernel Approximations 392<br/><br/>20.4.3 Gradient-Reproducing Kernel Collocation Method 393<br/><br/>20.5 Trabecular Bone Modeling 395<br/><br/>20.6 Conclusions 399<br/><br/>Acknowledgment 399<br/><br/>References 399<br/><br/>21 Modeling Nonlinear Plasticity of Bone Mineral from Nanoindentation Data 403<br/>Amir Reza Zamiri and Suvranu De<br/><br/>21.1 Introduction 403<br/><br/>21.2 Methods 404<br/><br/>21.3 Results 407<br/><br/>21.4 Conclusions 408<br/><br/>Acknowledgments 408<br/><br/>References 408<br/><br/>22 Mechanics of Cellular Materials and its Applications 411<br/>Ji Hoon Kim, Daeyong Kim, and Myoung-Gyu Lee<br/><br/>22.1 Biological Cellular Materials 411<br/><br/>22.1.1 Structure of Bone 411<br/><br/>22.1.2 Mechanical Properties of Bone 411<br/><br/>22.1.3 Failure of Bone 415<br/><br/>22.1.4 Simulation of Bone 417<br/><br/>22.2 Engineered Cellular Materials 421<br/><br/>22.2.1 Constitutive Models for Metal Foams 422<br/><br/>22.2.2 Structure Modeling of Cellular Materials 424<br/><br/>22.2.3 Simulation of Cellular Materials 428<br/><br/>References 431<br/><br/>23 Biomechanics of Mineralized Collagens 435<br/>Ashfaq Adnan, Farzad Sarker, and Sheikh F. Ferdous<br/><br/>23.1 Introduction 435<br/><br/>23.1.1 Mineralized Collagen 435<br/><br/>23.1.2 Molecular Origin and Structure of Mineralized Collagen 436<br/><br/>23.1.3 Bone Remodeling, Bone Marrow Microenvironment, and Biomechanics of Mineralized Collagen 438<br/><br/>23.2 Computational Method 438<br/><br/>23.2.1 Molecular Structure of Mineralized Collagen 438<br/><br/>23.2.2 The Constant-pH Molecular Dynamics Simulation 441<br/><br/>23.3 Results 441<br/><br/>23.3.1 First-Order Estimation of pH-Dependent TC–HAP Interaction Possibility 441<br/><br/>23.3.2 pH-Dependent TC–HAP Interface Interactions 443<br/><br/>23.4 Summary and Conclusions 446<br/><br/>Acknowledgments 446<br/><br/>References 446<br/><br/>Index 449
520 ## - SUMMARY, ETC.
Summary, etc 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.
545 0# - BIOGRAPHICAL OR HISTORICAL DATA
Biographical or historical note About the Author<br/>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.<br/><br/>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.
650 #0 - SUBJECT ADDED ENTRY--TOPICAL TERM
Topical term or geographic name as entry element Biomedical materials
Authority record control number http://id.loc.gov/authorities/subjects/sh85014239
General subdivision Computer simulation.
Authority record control number http://id.loc.gov/authorities/subjects/sh99005300.
650 #0 - SUBJECT ADDED ENTRY--TOPICAL TERM
Topical term or geographic name as entry element Biomedical materials
Authority record control number http://id.loc.gov/authorities/subjects/sh85014239
General subdivision Mechanical properties.
Authority record control number http://id.loc.gov/authorities/subjects/sh2002006407.
655 #4 - INDEX TERM--GENRE/FORM
Genre/form data or focus term Electronic books.
700 1# - ADDED ENTRY--PERSONAL NAME
Personal name Li, Shaofan.
Authority record control number http://id.loc.gov/authorities/names/no2004106433.
700 1# - ADDED ENTRY--PERSONAL NAME
Personal name Qian, Dong.
Authority record control number http://id.loc.gov/authorities/names/n2013002120.
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Uniform Resource Identifier https://onlinelibrary.wiley.com/doi/book/10.1002/9781118402955
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