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Nano and cell mechanics : fundamentals and frontiers

Author: H D Espinosa; Gang Bao
Publisher: Chichester, West Sussex : John Wiley & Sons, 2013.
Series: Wiley microsystem and nanotechnology series.
Edition/Format:   Print book : EnglishView all editions and formats



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Document Type: Book
All Authors / Contributors: H D Espinosa; Gang Bao
ISBN: 9781118460399 1118460391
OCLC Number: 801440772
Description: xxiv, 482 pages : illustrations (some color) ; 25 cm.
Contents: <p>About the Editors xiii <p>List of Contributors xv <p>Foreword xix <p>Series Preface xxi <p>Preface xxiii <p>Part One BIOLOGICAL PHENOMENA <p>1 Cell Receptor Interactions 3 David Lepzelter and Muhammad Zaman <p>1.1 Introduction 3 <p>1.2 Mechanics of Integrins 4 <p>1.3 Two-Dimensional Adhesion 7 <p>1.4 Two-Dimensional Motility 9 <p>1.5 Three-Dimensional Adhesion 11 <p>1.6 Three-Dimensional Motility 12 <p>1.7 Apoptosis and Survival Signaling 13 <p>1.8 Cell Differentiation Signaling 13 <p>1.9 Conclusions 14 <p>References 15 <p>2 Regulatory Mechanisms of Kinesin and Myosin Motor Proteins:Inspiration for Improved Control of Nanomachines 19 Sarah Rice <p>2.1 Introduction 19 <p>2.2 Generalized Mechanism of Cytoskeletal Motors 19 <p>2.3 Switch I: A Controller of Motor Protein and G ProteinActivation 21 <p>2.4 Calcium-Binding Regulators of Myosins and Kinesins 23 <p>2.5 Phospho-Regulation of Kinesin and Myosin Motors 262.6Cooperative Action of Kinesin and Myosin Motors as a Regulator 28 <p>2.7 Conclusion 29 <p>References 30 <p>3 Neuromechanics: The Role of Tension in Neuronal Growth andMemory 35 Wylie W. Ahmed, Jagannathan Rajagopalan, Alireza Tofangchi,and Taher A. Saif <p>3.1 Introduction 35 <p>3.1.1 What is a Neuron? 36 <p>3.1.2 How Does a Neuron Function? 38 <p>3.1.3 How Does a Neuron Grow? 40 <p>3.2 Tension in Neuronal Growth 41 <p>3.2.1 In Vitro Measurements of Tension in Neurons 41 <p>3.2.2 In Vivo Measurements of Tension in Neurons 43 <p>3.2.3 Role of Tension in Structural Development 45 <p>3.3 Tension in Neuron Function 48 <p>3.3.1 Tension Increases Neurotransmission 48 <p>3.3.2 Tension Affects Vesicle Dynamics 48 <p>3.4 Modeling the Mechanical Behavior of Axons 52 <p>3.5 Outlook 58 <p>References 58 <p>Part Two NANOSCALE PHENOMENA <p>4 Fundamentals of Roughness-Induced Superhydrophobicity65 Neelesh A. Patankar <p>4.1 Background and Motivation 65 <p>4.2 Thermodynamic Analysis: Classical Problem (Hydrophobic toSuperhydrophobic) 67 <p>4.2.1 Problem Formulation 68 <p>4.2.2 The Cassie Baxter State 71 <p>4.2.3 Predicting Transition from Cassie Baxter to WenzelState 73 <p>4.2.4 The Apparent Contact Angle of the Drop 77 <p>4.2.5 Modeling Hysteresis 79 <p>4.3 Thermodynamic Analysis: Classical Problem (Hydrophilic toSuperhydrophobic) 84 <p>4.4 Thermodynamic Analysis: Vapor Stabilization 86 <p>4.5 Applications and Future Challenges 90 <p>Acknowledgments 91 <p>References 91 <p>5 Multiscale Experimental Mechanics of HierarchicalCarbon-Based Materials 95 Horacio D. Espinosa, Tobin Filleter, and MohammadNaraghi <p>5.1 Introduction 95 <p>5.2 Multiscale Experimental Tools 97 <p>5.2.1 Revealing Atomic-Level Mechanics: In-Situ TEM Methods98 <p>5.2.2 Measuring Ultralow Forces: AFM Methods 101 <p>5.2.3 Investigating Shear Interactions: In-Situ SEM/AFM Methods102 <p>5.2.4 Collective and Local Behavior: Micromechanical TestingMethods 103 <p>5.3 Hierarchical Carbon-Based Materials 106 <p>5.3.1 Weak Shear Interactions between Adjacent Graphitic Layers106 <p>5.3.2 Cross-linking Adjacent Graphitic Layers 110 <p>5.3.3 Local Mechanical Properties of CNT/Graphene Composites113 <p>5.3.4 High Volume Fraction CNT Fibers and Composites 115 <p>5.4 Concluding Remarks 120 <p>References 123 <p>6 Mechanics of Nanotwinned Hierarchical Metals 129 Xiaoyan Li and Huajian Gao <p>6.1 Introduction and Overview 129 <p>6.1.1 Nanotwinned Materials 130 <p>6.1.2 Numerical Modeling of Nanotwinned Metals 132 <p>6.2 Microstructural Characterization and Mechanical Propertiesof Nanotwinned Materials 134 <p>6.2.1 Structure of Coherent Twin Boundary 134 <p>6.2.2 Microstructures of Nanotwinned Materials 135 <p>6.2.3 Mechanical and Physical Properties of Nanotwinned Metals137 <p>6.3 Deformation Mechanisms in Nanotwinned Metals 145 <p>6.3.1 Interaction between Dislocations and Twin Boundaries146 <p>6.3.2 Strengthening and Softening Mechanisms in NanotwinnedMetals 147 <p>6.3.3 Fracture of Nanotwinned Copper 155 <p>6.4 Concluding Remarks 156 <p>References 157 <p>7 Size-Dependent Strength in Single-Crystalline MetallicNanostructures 163 Julia R. Greer <p>7.1 Introduction 163 <p>7.2 Background 164 <p>7.2.1 Experimental Foundation 164 <p>7.2.2 Models 167 <p>7.3 Sample Fabrication 170 <p>7.3.1 FIB Approach 170 <p>7.3.2 Directional Solidification and Etching 172 <p>7.3.3 Templated Electroplating 173 <p>7.3.4 Nanoimprinting 173 <p>7.3.5 Vapor Liquid Solid Growth 174 <p>7.3.6 Nanowire Growth 175 <p>7.4 Uniaxial Deformation Experiments 175 <p>7.4.1 Nanoindenter-Based Systems (Ex Situ) 176 <p>7.4.2 In-Situ Systems 176 <p>7.5 Discussion and Outlook on Size-Dependent Strength inSingle-Crystalline Metals 178 <p>7.5.1 Cubic Crystals 178 <p>7.5.2 Non-Cubic Single Crystals 183 <p>7.6 Conclusions and Outlook 184 <p>References 185 <p>Part Three EXPERIMENTATION <p>8 In-Situ TEM Electromechanical Testing of Nanowires andNanotubes 193 Horacio D. Espinosa, Rodrigo A. Bernal, and TobinFilleter <p>8.1 Introduction 193 <p>8.1.1 Relevance of Mechanical and Electromechanical Testing forOne-Dimensional Nanostructures 194 <p>8.1.2 Mechanical and Electromechanical Characterization ofNanostructures: The Need for In-Situ TEM 196 <p>8.2 In-Situ TEM Experimental Methods 197 <p>8.2.1 Overview of TEM Specimen Holders 199 <p>8.2.2 Methods for Mechanical and Electromechanical Testing ofNanowires and Nanotubes 200 <p>8.2.3 Sample Preparation for TEM of One-DimensionalNanostructures 208 <p>8.3 Capabilities of In-Situ TEM Applied to One-DimensionalNanostructures 212 <p>8.3.1 HRTEM 212 <p>8.3.2 Diffraction 216 <p>8.3.3 Analytical Techniques 217 <p>8.3.4 In-Situ Specimen Modification 218 <p>8.4 Summary and Outlook 220 <p>Acknowledgments 221 <p>References 221 <p>9 Engineering Nano-Probes for Live-Cell Imaging of GeneExpression 227 Gang Bao, Brian Wile, and Andrew Tsourkas <p>9.1 Introduction 227 <p>9.2 Molecular Probes for RNA Detection 229 <p>9.2.1 Fluorescent Linear Probes 229 <p>9.2.2 Linear FRET Probes 232 <p>9.2.3 Quenched Auto-ligation Probes 233 <p>9.2.4 Molecular Beacons 234 <p>9.2.5 Dual-FRET Molecular Beacons 236 <p>9.2.6 Fluorescent Protein-Based Probes 237 <p>9.3 Probe Design, Imaging, and Biological Issues 239 <p>9.3.1 Specificity of Molecular Beacons 239 <p>9.3.2 Fluorophores, Quenchers, and Signal-to-Background 241 <p>9.3.3 Target Accessibility 242 <p>9.4 Delivery of Molecular Beacons 244 <p>9.4.1 Microinjection 245 <p>9.4.2 Cationic Transfection Agents 245 <p>9.4.3 Electroporation 245 <p>9.4.4 Chemical Permeabilization 246 <p>9.4.5 Cell-Penetrating Peptide 246 <p>9.5 Engineering Challenges and Future Directions 248 <p>Acknowledgments 249 <p>References 249 <p>10 Towards High-Throughput Cell Mechanics Assays for Researchand Clinical Applications 255 David R. Myers, Daniel A. Fletcher, and Wilbur A. Lam <p>10.1 Cell Mechanics Overview 255 <p>10.1.1 Cell Cytoskeleton and Cell-Sensing Overview 256 <p>10.1.2 Forces Applied by Cells 259 <p>10.1.3 Cell Responses to Force and Environment 260 <p>10.1.4 General Principles of Combined Mechanical and BiologicalMeasurements 261 <p>10.2 Bulk Assays 262 <p>10.2.1 Microfiltration 262 <p>10.2.2 Rheometry 264 <p>10.2.3 Ektacytometry 266 <p>10.2.4 Parallel-Plate Flow Chambers 267 <p>10.3 Single-Cell Techniques 268 <p>10.3.1 Micropipette Aspiration 268 <p>10.3.2 Atomic Force Microscopy 270 <p>10.3.3 Microplate Stretcher 272 <p>10.3.4 Optical Tweezers 273 <p>10.4 Existing High-Throughput Cell Mechanical-Based Assays274 <p>10.4.1 Optical Stretchers 274 <p>10.4.2 Traction Force Microscopy via Bead-Embedded Gels 275 <p>10.4.3 Traction Force Microscopy via Micropost Arrays 275 <p>10.4.4 Substrate Stretching Assays 277 <p>10.4.5 Magnetic Twisting Cytometry 277 <p>10.4.6 Microfluidic Pore and Deformation Assays 278 <p>10.5 Cell Mechanical Properties and Diseases 280 <p>References 284 <p>11 Microfabricated Technologies for Cell Mechanics Studies293 Sri Ram K. Vedula, Man C. Leong, and Chwee T. Lim <p>11.1 Introduction 293 <p>11.2 Microfabrication Techniques 294 <p>11.2.1 Photolithography and Soft Lithography 294 <p>11.2.2 Microphotopatterning ( PP) 297 <p>11.3 Applications to Cell Mechanics 298 <p>11.3.1 Micropatterned Substrates 298 <p>11.3.2 Micropillared Substrates 301 <p>11.3.3 Microfluidic Devices 304 <p>11.4 Conclusions 307 <p>References 307 <p>Part Four MODELING <p>12 Atomistic Reaction Pathway Sampling: The Nudged ElasticBandMethod and Nanomechanics Applications 313 Ting Zhu, Ju Li, and Sidney Yip <p>12.1 Introduction 313 <p>12.1.1 Reaction Pathway Sampling in Nanomechanics 314 <p>12.1.2 Extending the Time Scale in Atomistic Simulation 314 <p>12.1.3 Transition-State Theory 315 <p>12.2 The NEB Method for Stress-Driven Problems 315 <p>12.2.1 The NEB method 315 <p>12.2.2 The Free-End NEB Method 317 <p>12.2.3 Stress-Dependent Activation Energy and Activation Volume320 <p>12.2.4 Activation Entropy and Meyer Neldel CompensationRule 322 <p>12.3 Nanomechanics Case Studies 324 <p>12.3.1 Crack Tip Dislocation Emission 324 <p>12.3.2 Stress-Mediated Chemical Reactions 326 <p>12.3.3 Bridging Modeling with Experiment 327 <p>12.3.4 Temperature and Strain-Rate Dependence of DislocationNucleation 329 <p>12.3.5 Size and Loading Effects on Fracture 330 <p>12.4 A Perspective on Microstructure Evolution at Long Times332 <p>12.4.1 Sampling TSP Trajectories 333 <p>12.4.2 Nanomechanics in Problems of Materials Ageing 334 <p>References 336 <p>13 Mechanics of Curvilinear Electronics 339 Shuodao Wang, Jianliang Xiao, Jizhou Song, Yonggang Huang, andJohn A. Rogers <p>13.1 Introduction 339 <p>13.2 Deformation of Elastomeric Transfer Elements duringWrapping Processes 342 <p>13.2.1 Strain Distribution in Stretched Elastomeric TransferElements 342 <p>13.2.2 Deformed Shape of Elastomeric Transfer Elements 344 <p>13.3 Buckling of Interconnect Bridges 347 <p>13.4 Maximum Strain in the Circuit Mesh 351 <p>13.5 Concluding Remarks 355 <p>Acknowledgments 355 <p>References 355 <p>14 Single-Molecule Pulling: Phenomenology and Interpretation359 Ignacio Franco, Mark A. Ratner, and George C. Schatz <p>14.1 Introduction 359 <p>14.2 Force Extension Behavior of Single Molecules 360 <p>14.3 Single-Molecule Thermodynamics 364 <p>14.3.1 Free Energy Profile of the Molecule Plus Cantilever365 <p>14.3.2 Extracting the Molecular Potential of Mean Force ( ) 366 <p>14.3.3 Estimating Force Extension Behavior from ( ) 369 <p>14.4 Modeling Single-Molecule Pulling Using Molecular Dynamics370 <p>14.4.1 Basic Computational Setup 370 <p>14.4.2 Modeling Strategies 371 <p>14.4.3 Examples 373 <p>14.5 Interpretation of Pulling Phenomenology 376 <p>14.5.1 Basic Structure of the Molecular Potential of Mean Force377 <p>14.5.2 Mechanical Instability 378 <p>14.5.3 Dynamical Bistability 381 <p>14.6 Summary 384 <p>Acknowledgments 385 <p>References 385 <p>15 Modeling and Simulation of Hierarchical Protein Materials389 Tristan Giesa, Graham Bratzel, and Markus J. Buehler <p>15.1 Introduction 389 <p>15.2 Computational and Theoretical Tools 391 <p>15.2.1 Molecular Simulation from Chemistry Upwards 391 <p>15.2.2 Mesoscale Methods for Modeling Larger Length and TimeScales 392 <p>15.2.3 Mathematical Approaches to Biomateriomics 394 <p>15.3 Case Studies 400 <p>15.3.1 Atomistic and Mesoscale Protein Folding and Deformationin Spider Silk 400 <p>15.3.2 Coarse-Grained Modeling of Actin Filaments 402 <p>15.3.3 Category Theoretical Abstraction of a Protein Materialand Analogy to an Office Network 403 <p>15.4 Discussion and Conclusion 406 <p>Acknowledgments 406 <p>References 406 <p>16 Geometric Models of Protein Secondary-Structure Formation411 Hendrik Hansen-Goos and Seth Lichter <p>16.1 Introduction 411 <p>16.2 Hydrophobic Effect 412 <p>16.2.1 Variable Hydrogen-Bond Strength 415 <p>16.3 Prior Numerical and Coarse-Grained Models 415 <p>16.4 Geometry-Based Modeling: The Tube Model 416 <p>16.4.1 Motivation 416 <p>16.4.2 Impenetrable Tube Models 417 <p>16.4.3 Including Finite-Sized Particles Surrounding the Protein419 <p>16.4.4 Models Using Real Protein Structure 421 <p>16.5 Morphometric Approach to Solvation Effects 422 <p>16.5.1 Hadwiger s Theorem 422 <p>16.5.2 Applications 424 <p>16.6 Discussion, Conclusions, Future Work 429 <p>16.6.1 Results 429 <p>16.6.2 Discussion and Speculations 430 <p>Acknowledgments 433 <p>References 433 <p>17 Multiscale Modeling for the Vascular Transport ofNanoparticles 437 Shaolie S. Hossain, Adrian M. Kopacz, Yongjie Zhang, Sei-YoungLee, Tae-Rin Lee, Mauro Ferrari, Thomas J.R. Hughes, Wing Kam Liu,and Paolo Decuzzi <p>17.1 Introduction 437 <p>17.2 Modeling the Dynamics of NPs in the Macrocirculation438 <p>17.2.1 The 3D Reconstruction of the Patient-Specific Vasculature439 <p>17.2.2 Modeling the Vascular Flow and Wall Adhesion of NPs440 <p>17.2.3 Modeling NP Transport across the Arterial Wall and DrugRelease 440 <p>17.3 Modeling the NP Dynamics in the Microcirculation 448 <p>17.3.1 Semi-analytical Models for the NP Transport 449 <p>17.3.2 An IFEM for NP and Cell Transport 452 <p>17.4 Conclusions 456 <p>Acknowledgments 456 <p>References 457 <p>Index 461
Series Title: Wiley microsystem and nanotechnology series.
Responsibility: edited by Horacio D. Espinosa, Gang Bao.


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