Chapter 1 Atomistic to Continuum Modeling of DNA Molecules
1.1 Introduction
1.2 Statistical models for DNAs —— polymer elasticity
1.2.1 The freely jointed chain （FJC） model
1.2.2 The worm-like chain （WLC） model
1.2.3 Beyond the entropic regime
1.2.4 Long-range electrostatic effects
1.3 Atomistic modeling of DNA molecules
1.3.1 MD basic theory
1.3.2 Force fields for nucleic acids
1.3.3 Limitations and challenges
1.3.4 MD simulation of DNA stretching
1.4 Continuum DNA models
1.4.1 Kirchhoff's elastic Rod model for DNAs
1.4.2 Finite element （FE） analysis， of DNAs
1.4.3 Director field method for modeling of DNA viral packaging
1.5 Multiscale homogenization for simulation of DNA
molecules
1.5.1 Basics of multiscale wavelet projection method
1.5.2 First-level homogenization—— wavelet-based coarse-grained DNA model
1.5.3 Second-level homogenization—— hyperelastic beam formulation for DNA
1.5.4 Applications
1.6 Conclusion
Appendix： Wavelet and decomposition coefficients for linear spline function
References
Chapter 2 Computational Contact Formulations for SoftBody Adhesion
2.1 Introduction
2.2 Continuum contact formulation
2.3 Finite element formulations
2.4 Adhesion examples
2.5 Peeling contact .
2.6 Rough surface contact
2.7 Conclusion
References
Chapter 3 Soft Matter Modeling of Biological Cells
3.1 Introduction
3.2 Soft matter modeling of cells
3.2.1 The future is soft
3.2.2 The reasons to use liquid crystal elastomers tomodel cell and focal adhesion
3.2.3 Elasticity of soft contact/cell adhesion and surfacematerial property sensing
3.2.4 Cell and ECM modeling
3.3 A nanoscale adhesive contact model
3.4 Meshfree Galerkin formulation and the computationalalgorithm
3.5 Numerical simulations
3.5，1 Validation of the material models
3.5.2 Endothelial cell simulations
3.5.3 Stem cell simulations
3.6 Discussion and conclusionsReferences
Chapter 4 Modeling the Mechanics of Semifiexible Biopolymer Networks： Non-affine Deformation andPresence of Long-range Correlations
4.1 Introduction
4.2 Network representation and generation
4.3 Affine vs. non-affine deformation
4.4 Network microstructure： scaling properties of the fiberdensity function
4.5 Network elasticity： the equivalent continuum and itselastic moduli
4.6 Boundary value problems on dense fiber network domains .
4.6.1 Background： affine and non-affine theories
4.6.2Karhunen-Loeve decomposition
……
Chapter 5 Atomic Scale Monte-Carlo Studies of Entropic Elasticity Properties of Polymer Chain Molecules
Chapter 6 Continuum Models of Stimuli-responsive gels
Chapter 7 Micromechanics of 3D Crystallized Protein Structures
Chapter 8 Micromechanical Modeling of Three- dimensional Open-cell Foams
Chapter 9 Capillary Adhesion of Micro-beams and Plates： A Review
Color Plots
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