Nano and Cell Mechanics

Horacio D. Espinosa, Northwestern University, USAHoracio D. Espinosa is the James and Nancy Farley Professor of Mechanical Engineering at Northwestern University, USA. He is a member of the European Academy of Arts and Sciences, and Fellow of AAM, ASME, and SEM. He served as Editor-in-chief of the Journal of Experimental Mechanics and Associate Editor of the Journal of Applied Mechanics. Currently, he is a co-editor of the Wiley Book Series in Micro and Nanotechnologies and serves in several journal editorial boards. His research interests include biomimetics, size scale electro-mechanical properties of nanomaterials, NEMS, in-situ microscopy testing of nanostructures, and the development of microdevices for tip-based nanofabrication and single cell studies. Gang Bao, Georgia Institute of Technology, USAGang Bao is Professor of Bioengineering at the Georgia Institute of Technology, USA. His research interests include biomolecular engineering, bionanotechnology, molecular imaging and molecular biomechanics.

• About the Editors xiiiList of Contributors xvForeword xixSeries Preface xxiPreface xxiiiPart One BIOLOGICAL PHENOMENA1 Cell–Receptor Interactions 3David Lepzelter and Muhammad Zaman1.1 Introduction 31.2 Mechanics of Integrins 41.3 Two-Dimensional Adhesion 71.4 Two-Dimensional Motility 91.5 Three-Dimensional Adhesion 111.6 Three-Dimensional Motility 121.7 Apoptosis and Survival Signaling 131.8 Cell Differentiation Signaling 131.9 Conclusions 14References 152 Regulatory Mechanisms of Kinesin and Myosin Motor Proteins: Inspiration for Improved Control of Nanomachines 19Sarah Rice2.1 Introduction 192.2 Generalized Mechanism of Cytoskeletal Motors 192.3 Switch I: A Controller of Motor Protein and G Protein Activation 212.4 Calcium-Binding Regulators of Myosins and Kinesins 232.5 Phospho-Regulation of Kinesin and Myosin Motors 262.6 Cooperative Action of Kinesin and Myosin Motors as a “Regulator” 282.7 Conclusion 29References 303 Neuromechanics: The Role of Tension in Neuronal Growth and Memory 35Wylie W. Ahmed, Jagannathan Rajagopalan, Alireza Tofangchi, and Taher A. Saif3.1 Introduction 353.1.1 What is a Neuron? 363.1.2 How Does a Neuron Function? 383.1.3 How Does a Neuron Grow? 403.2 Tension in Neuronal Growth 413.2.1 In Vitro Measurements of Tension in Neurons 413.2.2 In Vivo Measurements of Tension in Neurons 433.2.3 Role of Tension in Structural Development 453.3 Tension in Neuron Function 483.3.1 Tension Increases Neurotransmission 483.3.2 Tension Affects Vesicle Dynamics 483.4 Modeling the Mechanical Behavior of Axons 523.5 Outlook 58References 58Part Two NANOSCALE PHENOMENA4 Fundamentals of Roughness-Induced Superhydrophobicity 65Neelesh A. Patankar4.1 Background and Motivation 654.2 Thermodynamic Analysis: Classical Problem (Hydrophobic to Superhydrophobic) 674.2.1 Problem Formulation 684.2.2 The Cassie–Baxter State 714.2.3 Predicting Transition from Cassie–Baxter to Wenzel State 734.2.4 The Apparent Contact Angle of the Drop 774.2.5 Modeling Hysteresis 794.3 Thermodynamic Analysis: Classical Problem (Hydrophilic to Superhydrophobic) 844.4 Thermodynamic Analysis: Vapor Stabilization 864.5 Applications and Future Challenges 90Acknowledgments 91References 915 Multiscale Experimental Mechanics of Hierarchical Carbon-Based Materials 95Horacio D. Espinosa, Tobin Filleter, and Mohammad Naraghi5.1 Introduction 955.2 Multiscale Experimental Tools 975.2.1 Revealing Atomic-Level Mechanics: In-Situ TEM Methods 985.2.2 Measuring Ultralow Forces: AFM Methods 1015.2.3 Investigating Shear Interactions: In-Situ SEM/AFM Methods 1025.2.4 Collective and Local Behavior: Micromechanical Testing Methods 1035.3 Hierarchical Carbon-Based Materials 1065.3.1 Weak Shear Interactions between Adjacent Graphitic Layers 1065.3.2 Cross-linking Adjacent Graphitic Layers 1105.3.3 Local Mechanical Properties of CNT/Graphene Composites 1135.3.4 High Volume Fraction CNT Fibers and Composites 1155.4 Concluding Remarks 120References 1236 Mechanics of Nanotwinned Hierarchical Metals 129Xiaoyan Li and Huajian Gao6.1 Introduction and Overview 1296.1.1 Nanotwinned Materials 1306.1.2 Numerical Modeling of Nanotwinned Metals 1326.2 Microstructural Characterization and Mechanical Properties of Nanotwinned Materials 1346.2.1 Structure of Coherent Twin Boundary 1346.2.2 Microstructures of Nanotwinned Materials 1356.2.3 Mechanical and Physical Properties of Nanotwinned Metals 1376.3 Deformation Mechanisms in Nanotwinned Metals 1456.3.1 Interaction between Dislocations and Twin Boundaries 1466.3.2 Strengthening and Softening Mechanisms in Nanotwinned Metals 1476.3.3 Fracture of Nanotwinned Copper 1556.4 Concluding Remarks 156References 1577 Size-Dependent Strength in Single-Crystalline Metallic Nanostructures 163Julia R. Greer7.1 Introduction 1637.2 Background 1647.2.1 Experimental Foundation 1647.2.2 Models 1677.3 Sample Fabrication 1707.3.1 FIB Approach 1707.3.2 Directional Solidification and Etching 1727.3.3 Templated Electroplating 1737.3.4 Nanoimprinting 1737.3.5 Vapor–Liquid–Solid Growth 1747.3.6 Nanowire Growth 1757.4 Uniaxial Deformation Experiments 1757.4.1 Nanoindenter-Based Systems (Ex Situ) 1767.4.2 In-Situ Systems 1767.5 Discussion and Outlook on Size-Dependent Strength in Single-Crystalline Metals 1787.5.1 Cubic Crystals 1787.5.2 Non-Cubic Single Crystals 1837.6 Conclusions and Outlook 184References 185Part Three EXPERIMENTATION8 In-Situ TEM Electromechanical Testing of Nanowires and Nanotubes 193Horacio D. Espinosa, Rodrigo A. Bernal, and Tobin Filleter8.1 Introduction 1938.1.1 Relevance of Mechanical and Electromechanical Testing for One-Dimensional Nanostructures 1948.1.2 Mechanical and Electromechanical Characterization of Nanostructures: The Need for In-Situ TEM 1968.2 In-Situ TEM Experimental Methods 1978.2.1 Overview of TEM Specimen Holders 1998.2.2 Methods for Mechanical and Electromechanical Testing of Nanowires and Nanotubes 2008.2.3 Sample Preparation for TEM of One-Dimensional Nanostructures 2088.3 Capabilities of In-Situ TEM Applied to One-Dimensional Nanostructures 2128.3.1 HRTEM 2128.3.2 Diffraction 2168.3.3 Analytical Techniques 2178.3.4 In-Situ Specimen Modification 2188.4 Summary and Outlook 220Acknowledgments 221References 2219 Engineering Nano-Probes for Live-Cell Imaging of Gene Expression 227Gang Bao, Brian Wile, and Andrew Tsourkas9.1 Introduction 2279.2 Molecular Probes for RNA Detection 2299.2.1 Fluorescent Linear Probes 2299.2.2 Linear FRET Probes 2329.2.3 Quenched Auto-ligation Probes 2339.2.4 Molecular Beacons 2349.2.5 Dual-FRET Molecular Beacons 2369.2.6 Fluorescent Protein-Based Probes 2379.3 Probe Design, Imaging, and Biological Issues 2399.3.1 Specificity of Molecular Beacons 2399.3.2 Fluorophores, Quenchers, and Signal-to-Background 2419.3.3 Target Accessibility 2429.4 Delivery of Molecular Beacons 2449.4.1 Microinjection 2459.4.2 Cationic Transfection Agents 2459.4.3 Electroporation 2459.4.4 Chemical Permeabilization 2469.4.5 Cell-Penetrating Peptide 2469.5 Engineering Challenges and Future Directions 248Acknowledgments 249References 24910 Towards High-Throughput Cell Mechanics Assays for Research and Clinical Applications 255David R. Myers, Daniel A. Fletcher, and Wilbur A. Lam10.1 Cell Mechanics Overview 25510.1.1 Cell Cytoskeleton and Cell-Sensing Overview 25610.1.2 Forces Applied by Cells 25910.1.3 Cell Responses to Force and Environment 26010.1.4 General Principles of Combined Mechanical and Biological Measurements 26110.2 Bulk Assays 26210.2.1 Microfiltration 26210.2.2 Rheometry 26410.2.3 Ektacytometry 26610.2.4 Parallel-Plate Flow Chambers 26710.3 Single-Cell Techniques 26810.3.1 Micropipette Aspiration 26810.3.2 Atomic Force Microscopy 27010.3.3 Microplate Stretcher 27210.3.4 Optical Tweezers 27310.4 Existing High-Throughput Cell Mechanical-Based Assays 27410.4.1 Optical Stretchers 27410.4.2 Traction Force Microscopy via Bead-Embedded Gels 27510.4.3 Traction Force Microscopy via Micropost Arrays 27510.4.4 Substrate Stretching Assays 27710.4.5 Magnetic Twisting Cytometry 27710.4.6 Microfluidic Pore and Deformation Assays 27810.5 Cell Mechanical Properties and Diseases 280References 28411 Microfabricated Technologies for Cell Mechanics Studies 293Sri Ram K. Vedula, Man C. Leong, and Chwee T. Lim11.1 Introduction 29311.2 Microfabrication Techniques 29411.2.1 Photolithography and Soft Lithography 29411.2.2 Microphotopatterning (μPP) 29711.3 Applications to Cell Mechanics 29811.3.1 Micropatterned Substrates 29811.3.2 Micropillared Substrates 30111.3.3 Microfluidic Devices 30411.4 Conclusions 307References 307Part Four MODELING12 Atomistic Reaction Pathway Sampling: The Nudged Elastic BandMethod and Nanomechanics Applications 313Ting Zhu, Ju Li, and Sidney Yip12.1 Introduction 31312.1.1 Reaction Pathway Sampling in Nanomechanics 31412.1.2 Extending the Time Scale in Atomistic Simulation 31412.1.3 Transition-State Theory 31512.2 The NEB Method for Stress-Driven Problems 31512.2.1 The NEB method 31512.2.2 The Free-End NEB Method 31712.2.3 Stress-Dependent Activation Energy and Activation Volume 32012.2.4 Activation Entropy and Meyer–Neldel Compensation Rule 32212.3 Nanomechanics Case Studies 32412.3.1 Crack Tip Dislocation Emission 32412.3.2 Stress-Mediated Chemical Reactions 32612.3.3 Bridging Modeling with Experiment 32712.3.4 Temperature and Strain-Rate Dependence of Dislocation Nucleation 32912.3.5 Size and Loading Effects on Fracture 33012.4 A Perspective on Microstructure Evolution at Long Times 33212.4.1 Sampling TSP Trajectories 33312.4.2 Nanomechanics in Problems of Materials Ageing 334References 33613 Mechanics of Curvilinear Electronics 339Shuodao Wang, Jianliang Xiao, Jizhou Song, Yonggang Huang, and John A. Rogers13.1 Introduction 33913.2 Deformation of Elastomeric Transfer Elements during Wrapping Processes 34213.2.1 Strain Distribution in Stretched Elastomeric Transfer Elements 34213.2.2 Deformed Shape of Elastomeric Transfer Elements 34413.3 Buckling of Interconnect Bridges 34713.4 Maximum Strain in the Circuit Mesh 35113.5 Concluding Remarks 355Acknowledgments 355References 35514 Single-Molecule Pulling: Phenomenology and Interpretation 359Ignacio Franco, Mark A. Ratner, and George C. Schatz14.1 Introduction 35914.2 Force–Extension Behavior of Single Molecules 36014.3 Single-Molecule Thermodynamics 36414.3.1 Free Energy Profile of the Molecule Plus Cantilever 36514.3.2 Extracting the Molecular Potential of Mean Force φ(ξ ) 36614.3.3 Estimating Force–Extension Behavior from φ(ξ ) 36914.4 Modeling Single-Molecule Pulling Using Molecular Dynamics 37014.4.1 Basic Computational Setup 37014.4.2 Modeling Strategies 37114.4.3 Examples 37314.5 Interpretation of Pulling Phenomenology 37614.5.1 Basic Structure of the Molecular Potential of Mean Force 37714.5.2 Mechanical Instability 37814.5.3 Dynamical Bistability 38114.6 Summary 384Acknowledgments 385References 38515 Modeling and Simulation of Hierarchical Protein Materials 389Tristan Giesa, Graham Bratzel, and Markus J. Buehler15.1 Introduction 38915.2 Computational and Theoretical Tools 39115.2.1 Molecular Simulation from Chemistry Upwards 39115.2.2 Mesoscale Methods for Modeling Larger Length and Time Scales 39215.2.3 Mathematical Approaches to Biomateriomics 39415.3 Case Studies 40015.3.1 Atomistic and Mesoscale Protein Folding and Deformation in Spider Silk 40015.3.2 Coarse-Grained Modeling of Actin Filaments 40215.3.3 Category Theoretical Abstraction of a Protein Material and Analogy to an Office Network 40315.4 Discussion and Conclusion 406Acknowledgments 406References 40616 Geometric Models of Protein Secondary-Structure Formation 411Hendrik Hansen-Goos and Seth Lichter16.1 Introduction 41116.2 Hydrophobic Effect 41216.2.1 Variable Hydrogen-Bond Strength 41516.3 Prior Numerical and Coarse-Grained Models 41516.4 Geometry-Based Modeling: The Tube Model 41616.4.1 Motivation 41616.4.2 Impenetrable Tube Models 41716.4.3 Including Finite-Sized Particles Surrounding the Protein 41916.4.4 Models Using Real Protein Structure 42116.5 Morphometric Approach to Solvation Effects 42216.5.1 Hadwiger’s Theorem 42216.5.2 Applications 42416.6 Discussion, Conclusions, Future Work 42916.6.1 Results 42916.6.2 Discussion and Speculations 430Acknowledgments 433References 43317 Multiscale Modeling for the Vascular Transport of Nanoparticles 437Shaolie S. Hossain, Adrian M. Kopacz, Yongjie Zhang, Sei-Young Lee, Tae-Rin Lee, Mauro Ferrari, Thomas J.R. Hughes, Wing Kam Liu, and Paolo Decuzzi17.1 Introduction 43717.2 Modeling the Dynamics of NPs in the Macrocirculation 43817.2.1 The 3D Reconstruction of the Patient-Specific Vasculature 43917.2.2 Modeling the Vascular Flow and Wall Adhesion of NPs 44017.2.3 Modeling NP Transport across the Arterial Wall and Drug Release 44017.3 Modeling the NP Dynamics in the Microcirculation 44817.3.1 Semi-analytical Models for the NP Transport 44917.3.2 An IFEM for NP and Cell Transport 45217.4 Conclusions 456Acknowledgments 456References 457Index 461