Biophysical Approaches for the Study of Membrane Structure, Part B, Volume 701 explores lipid membrane asymmetry and lateral heterogeneity. A burst of recent research has shown that bilayers whose leaflets differ in their physical properties—such as composition, phase state, or lateral stress—exhibit many fascinating new characteristics, but also pose a host of challenges related to their creation, characterization, simulation, and theoretical description. Chapters in this new release include Characterization of domain formation in complex membranes: Analyzing the bending modulus from simulations of complex membranes, The density-threshold affinity: Calculating lipid binding affinities from unbiased Coarse-Grain Molecular Dynamics simulations, and much more.
Additional sections cover Uncertainty quantification for trans-membrane stresses and moments from simulation, Using molecular dynamics simulations to generate small-angle scattering curves and cryo-EM images of proteoliposomes, Binary Bilayer Simulations for Partitioning Within Membranes, Modeling Asymmetric Cell Membranes at All-atom Resolution, Multiscale remodeling of biomembranes and vesicles, Building complex membranes with Martini 3, Predicting lipid sorting in curved bilayer membranes, Simulating asymmetric membranes using P21 periodic boundary conditions, and many other interesting topics.
1. 1 Introduction - p. 176 2. 2 Shape remodeling of giant vesicles - p. 178 3. 3 Shape transformations of nanovesicles - p. 192 4. 4 Instabilities of lipid bilayers - p. 201 5. 5 Remodeling of vesicle topology - p. 206 6. 6 Summary and outlook - p. 223 7. Acknowledgements - p. 226 8. References - p. 236 9. Chapter Seven: Building complex membranes with Martini 3 - p. 279 10. Chapter Eight: Predicting lipid sorting in curved membranes - p. 288 11. Chapter Nine: Simulating asymmetric membranes using P21 periodic boundary conditions - p. 310 12. Chapter Ten: Free energy calculations for membrane morphological transformations and insights to physical biology and oncology - p. 360 13. Chapter Eleven: Modeling the mechanochemical feedback for membrane-protein interactions using a continuum mesh model - p. 388 14. Chapter Twelve: Lattice-based mesoscale simulations and mean-field theory of cell membrane adhesion - p. 426 15. Abstract - p. 426 16. 1 Introduction - p. 426 17. 2 Lattice-based mesoscale model for membrane adhesion - p. 429 18. 3 Mean-field theory - p. 432 19. 4 Implementation of the mean-field theory: Phase diagram - p. 436 20. 5 Monte Carlo simulations - p. 438 21. 6 Implementation of the Monte Carlo simulation: Algorithm - p. 439 22. 7 Parameter tuning - p. 448 23. 8 Examples - p. 449 24. 9 Performance - p. 450 25. 10 Summary and outlook - p. 451 26. 11 Connections - p. 452 27. Acknowledgements - p. 453 28. References - p. 453 29. Chapter Thirteen: Dynamic framework for large-scale modeling of membranes and peripheral proteins - p. 458 30. Abstract - p. 458 31. 1 Introduction - p. 458 32. 2 Main - p. 464 33. 3 Future directions - p. 500 34. References - p. 514 35. Chapter Fourteen: Computing the influence of lipids and lipid complexes on membrane mechanics - p. 516 36. Chapter Fifteen: Non-affine deformation analysis and 3D packing defects: A new way to probe membrane heterogeneity in molecular simulations - p. 542 37. Chapter Sixteen: Analyzing lipid distributions and curvature in molecular dynamics simulations of complex membranes - p. 580
Biophysical Approaches for the Study of Membrane Structure, Part B, Volume 701 explores lipid membrane asymmetry and lateral heterogeneity. A burst of recent research has shown that bilayers whose leaflets differ in their physical properties—such as composition, phase state, or lateral stress—exhibit many fascinating new characteristics, but also pose a host of challenges related to their creation, characterization, simulation, and theoretical description. Chapters in this new release include Characterization of domain formation in complex membranes: Analyzing the bending modulus from simulations of complex membranes, The density-threshold affinity: Calculating lipid binding affinities from unbiased Coarse-Grain Molecular Dynamics simulations, and much more.
Additional sections cover Uncertainty quantification for trans-membrane stresses and moments from simulation, Using molecular dynamics simulations to generate small-angle scattering curves and cryo-EM images of proteoliposomes, Binary Bilayer Simulations for Partitioning Within Membranes, Modeling Asymmetric Cell Membranes at All-atom Resolution, Multiscale remodeling of biomembranes and vesicles, Building complex membranes with Martini 3, Predicting lipid sorting in curved bilayer membranes, Simulating asymmetric membranes using P21 periodic boundary conditions, and many other interesting topics.
1. 1 Introduction - p. 176 2. 2 Shape remodeling of giant vesicles - p. 178 3. 3 Shape transformations of nanovesicles - p. 192 4. 4 Instabilities of lipid bilayers - p. 201 5. 5 Remodeling of vesicle topology - p. 206 6. 6 Summary and outlook - p. 223 7. Acknowledgements - p. 226 8. References - p. 236 9. Chapter Seven: Building complex membranes with Martini 3 - p. 279 10. Chapter Eight: Predicting lipid sorting in curved membranes - p. 288 11. Chapter Nine: Simulating asymmetric membranes using P21 periodic boundary conditions - p. 310 12. Chapter Ten: Free energy calculations for membrane morphological transformations and insights to physical biology and oncology - p. 360 13. Chapter Eleven: Modeling the mechanochemical feedback for membrane-protein interactions using a continuum mesh model - p. 388 14. Chapter Twelve: Lattice-based mesoscale simulations and mean-field theory of cell membrane adhesion - p. 426 15. Abstract - p. 426 16. 1 Introduction - p. 426 17. 2 Lattice-based mesoscale model for membrane adhesion - p. 429 18. 3 Mean-field theory - p. 432 19. 4 Implementation of the mean-field theory: Phase diagram - p. 436 20. 5 Monte Carlo simulations - p. 438 21. 6 Implementation of the Monte Carlo simulation: Algorithm - p. 439 22. 7 Parameter tuning - p. 448 23. 8 Examples - p. 449 24. 9 Performance - p. 450 25. 10 Summary and outlook - p. 451 26. 11 Connections - p. 452 27. Acknowledgements - p. 453 28. References - p. 453 29. Chapter Thirteen: Dynamic framework for large-scale modeling of membranes and peripheral proteins - p. 458 30. Abstract - p. 458 31. 1 Introduction - p. 458 32. 2 Main - p. 464 33. 3 Future directions - p. 500 34. References - p. 514 35. Chapter Fourteen: Computing the influence of lipids and lipid complexes on membrane mechanics - p. 516 36. Chapter Fifteen: Non-affine deformation analysis and 3D packing defects: A new way to probe membrane heterogeneity in molecular simulations - p. 542 37. Chapter Sixteen: Analyzing lipid distributions and curvature in molecular dynamics simulations of complex membranes - p. 580
