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E-raamat: Advances in Cell Mechanics

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  • Formaat: PDF+DRM
  • Ilmumisaeg: 17-Nov-2011
  • Kirjastus: Springer-Verlag Berlin and Heidelberg GmbH & Co. K
  • Keel: eng
  • ISBN-13: 9783642175909
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Advances in Cell MechanicsSuurem pilt
  • Formaat: PDF+DRM
  • Ilmumisaeg: 17-Nov-2011
  • Kirjastus: Springer-Verlag Berlin and Heidelberg GmbH & Co. K
  • Keel: eng
  • ISBN-13: 9783642175909
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"Advances in Cell Mechanics" presents the latest developments in cell mechanics and biophysics, mainly focusing on interdisciplinary research in cell biology and the biophysics of cells. Moreover, a unique feature of the book is its emphasis on the molecular and complex continuum modeling and simulations of the cells. It may be the first work that brings rigorous and quantitative scientific analysis and state-of-the-art simulation technology into cell biology research.The book is intended for researchers and graduate students working in the fields of molecular cell biology, bio-engineering and bio-mechanics, soft matter physics, computational mechanics, bio-chemistry and bio-medicine.All contributors are leading scholars in their respective fields. Dr. Shaofan Li is a professor and an expert for computational mechanics at the University of California-Berkeley, USA; Dr. Bohua Sun is a professor at Cape Peninsula University of Technology, South Africa.

This book presents the latest developments in cell mechanics and biophysics, mainly focusing on interdisciplinary research in cell biology and the biophysics of cells. It emphasizes the molecular and complex continuum modeling and simulations of the cells.
Chapter 1 Modeling and Simulations of the Dynamics of Growing Cell Clusters
1(26)
1.1 Introduction
1(2)
1.2 Single cell geometry and kinematics
3(2)
1.2.1 The continuum model
4(1)
1.2.2 The numerical model for the cell geometry
5(1)
1.3 Single cell equilibrium and material model
5(3)
1.3.1 Cell equilibrium
5(1)
1.3.2 The material model
6(1)
1.3.3 Determination of material constants
6(2)
1.4 Modeling cell interactions
8(5)
1.4.1 Cell-to-cell contact
9(1)
1.4.2 Cell-to-cell adhesion
10(1)
1.4.3 Cell-to-cell interaction test
11(2)
1.5 Modeling the cell life cycle
13(2)
1.6 Details of the numerical implementation
15(2)
1.6.1 The finite element model
15(1)
1.6.2 Contact/adhesion interface detection
15(1)
1.6.3 Time integration
16(1)
1.6.4 Parallelization
17(1)
1.7 Numerical results
17(5)
1.8 Summary and conclusions
22(2)
References
24(3)
Chapter 2 Multiscale Biomechanical Modeling of Stem Cell-Extracellular Matrix Interactions
27(28)
2.1 Introduction
27(2)
2.2 Cell and ECM modeling
29(3)
2.2.1 Basic hypothesis and assumptions
29(1)
2.2.2 Hyperelastic model
30(1)
2.2.3 Liquid crystal model
31(1)
2.3 Contact and adhesion models for cell-substrate interactions
32(6)
2.3.1 The adhesive body force with continuum mechanics contact
33(3)
2.3.2 The cohesive contact model
36(2)
2.4 Meshfree Galerkin formulation and the computational algorithm
38(2)
2.5 Numerical simulations
40(10)
2.5.1 Validation of the material models
41(1)
2.5.2 Cell response in four different stiffness substrates
42(3)
2.5.3 Cell response to a stiffness-varying substrate
45(2)
2.5.4 Comparison of two different contact algorithms
47(1)
2.5.5 Three-dimensional simulation of cell spreading
47(3)
2.6 Discussion and conclusions
50(1)
References
51(4)
Chapter 3 Modeling of Proteins and Their Interactions with Solvent
55(62)
3.1 Introduction
55(3)
3.2 Classical molecular dynamics
58(4)
3.2.1 Coarse-grained model
59(3)
3.2.2 High performance computing
62(1)
3.3 Principal component analysis
62(12)
3.3.1 Three oscillators system analysis with PCA
64(8)
3.3.2 Quasi-harmonic analysis
72(1)
3.3.3 Equilibrium conformational analysis
73(1)
3.4 Methods and procedures
74(7)
3.4.1 Framework
74(1)
3.4.2 Overlap coefficients
74(1)
3.4.3 Correlation analysis
75(1)
3.4.4 PCA with MD simulation
76(3)
3.4.5 Kabsch algorithm
79(1)
3.4.6 Positional correlation matrix
80(1)
3.4.7 Cluster analysis
80(1)
3.5 MD simulation with T4 lysozyme
81(18)
3.5.1 Equilibration measures
83(1)
3.5.2 Fluctuation analysis
84(1)
3.5.3 Mode selection and evaluation
85(1)
3.5.4 Eigenvalue analysis
86(3)
3.5.5 Overlap evaluation
89(7)
3.5.6 Identification of slow conformational flexibility
96(1)
3.5.7 Correlation analysis of T4 lysozyme
96(3)
3.6 Hemoglobin and sickle cell anemia
99(13)
3.6.1 Molecular dynamic simulation with NAMD
103(3)
3.6.2 Conformational change analysis
106(3)
3.6.3 PCA analysis
109(1)
3.6.4 Correlation analysis with HbS interaction
110(2)
3.7 Conclusion
112(1)
References
112(5)
Chapter 4 Structural, Mechanical and Functional Properties of Intermediate Filaments from the Atomistic to the Cellular Scales
117(50)
4.1 Introduction
117(18)
4.1.1 Hierarchical structure of vimentin intermediate filaments
121(10)
4.1.2 The structural and physiological character of keratin
131(4)
4.2 Connecting filaments to cells level function and pathology
135(3)
4.2.1 Bending and stretching properties of IFs in cells
136(1)
4.2.2 IFs responding differently to tensile and shear stresses
137(1)
4.2.3 Mechanotransduction through the intermediate filament network
138(1)
4.3 Experimental mechanics
138(3)
4.3.1 Single filament mechanics
138(1)
4.3.2 Rheology of IF networks in vitro
139(1)
4.3.3 IF networks rheology in cells
140(1)
4.4 Case studies
141(17)
4.4.1 Single vimentin filament mechanics
141(11)
4.4.2 Network mechanics
152(4)
4.4.3 The mechanical role of intermediate filament in cellular system
156(2)
4.5 Conclusion
158(1)
References
159(8)
Chapter 5 Cytoskeletal Mechanics and Rheology
167(22)
5.1 Introduction
167(3)
5.2 Modelling semiflexible filament dynamics
170(3)
5.3 Experimental measurements
173(5)
5.3.1 Glass microneedles
174(1)
5.3.2 Cell poking
174(1)
5.3.3 Atomic force microscopy
175(1)
5.3.4 Micropipette aspiration
176(1)
5.3.5 Microplates
176(1)
5.3.6 Parallel-plate flow chambers
177(1)
5.3.7 Optical tweezers
177(1)
5.3.8 Magnetic traps
178(1)
5.4 Computational models
178(5)
5.5 Conclusion
183(1)
References
183(6)
Chapter 6 On the Application of Multiphasic Theories to the Problem of Cell-substrate Mechanical Interactions
189(36)
6.1 Introduction
190(2)
6.2 The physics of contractile fibroblasts and their interactions with an elastic substrate
192(5)
6.2.1 Cell spreading, contractility and substrate elasticity
192(2)
6.2.2 Molecular mechanisms of cell contractility
194(3)
6.3 Multiphasic mixture theory and cell contractility
197(15)
6.3.1 The cytoplasm as a quadriphasic medium
198(3)
6.3.2 Mass transport and mass exchange within the cell
201(4)
6.3.3 Contractility and force balance
205(4)
6.3.4 Model's prediction for simple cases
209(3)
6.4 Interaction between contractile cells and compliant substrates
212(6)
6.4.1 Two-dimensional plane stress formulation
212(1)
6.4.2 Numerical strategy: XFEM-level methods
213(3)
6.4.3 Analysis of mechanical interactions between a contractile cell and an elastic substrate
216(2)
6.5 Summary and conclusion
218(3)
6.5.1 Summary
218(1)
6.5.2 Limitations of the multiphasic approach
219(1)
6.5.3 Concluding remark
220(1)
References
221(4)
Chapter 7 Effect of Substrate Rigidity on the Growth of Nascent Adhesion Sites
225(14)
7.1 Introduction
225(2)
7.2 Model
227(4)
7.3 Results and Discussion
231(5)
7.4 Conclusion
236(1)
References
236(3)
Chapter 8 Opto-Hydrodynamic Trapping for Multiaxial Single-Cell Biomechanics
239(18)
8.1 Introduction
239(1)
8.2 Optical-hydrodynamic trapping
240(12)
8.2.1 Optical physics and microfluidics
240(2)
8.2.2 Theoretical stress analysis
242(4)
8.2.3 Experimental and computational flow validation
246(3)
8.2.4 Applied stresses and strain response
249(1)
8.2.5 Multiaxial single-cell biomechanics
250(2)
8.3 Discussion
252(2)
References
254(3)
Chapter 9 Application of Nonlocal Shell Models to Microtubule Buckling in Living Cells
257(18)
9.1 Introduction
257(2)
9.2 Nonlocal shell theories
259(6)
9.2.1 Constitutive relations
260(1)
9.2.2 Shear deformable shell model
261(3)
9.2.3 Thin shell model
264(1)
9.3 Bending buckling analysis
265(4)
9.4 Numerical results and discussion
269(5)
9.5 Conclusions
274(1)
Appendix A 275(1)
Appendix B 276(3)
Appendix C 279(2)
Appendix D 281(1)
References 282
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