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 Soft Body
Adhesion
Chapter 3 Soft Matter Modeling of Biological Cells.
Chapter 4 Modeling the Mechanics of Semiflexible Biopoly- mer
Networks: Non-afIine Deformation and Presence of Long-range
Correlations
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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