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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.
Contents
Preface
Tobias Baumgart and Markus Deserno
1. Characterization of domain formation in complex membranes: Analyzing the bending modulus from simulations of complex membranes
Rainer A. Böckmann and Marius F.W. Trollmann
2. The density-threshold affinity: Calculating lipid binding affinities from unbiased Coarse-Grain Molecular Dynamics simulations
Grace Brannigan, Jahmal Ennis, Ezry Santiago-McRae and Jesse W Sandberg
3. Uncertainty quantification for trans-membrane stresses and moments from simulation
Markus Deserno and Samuel Lincoln Foley
4. Binary Bilayer Simulations for Partitioning Within Membranes
Wonpil Im, Richard Walter Pastor and Soohyung Park
5. Modeling Asymmetric Cell Membranes at All-atom Resolution
Jeffrey Klauda, Jessica Bodosa and Anthony Pane
6. Multiscale remodeling of biomembranes and vesicles
Reinhard Lipowsky
7. Building complex membranes with Martini 3
Siewert-Jan Marrink, Helgi Ingolfur Ingolfsson, Tugba N. Ozturk, Melanie König, Timothy S. Carpenter, Kasper Busk Pedersen and Tsjerk A. Wassenaar
8. Predicting lipid sorting in curved bilayer membranes
Luca Monticelli, Cecile Hilpert and Jackson Crowley
9. Simulating asymmetric membranes using P21 periodic boundary conditions
Richard Walter Pastor, Amy Rice, Bernard Brooks and Samarjeet Prasad
10. Free Energy Calculations for Membrane Morphological Transformations and Insights to Physical Biology and Oncology
Ravi Radhakrishnan, Tobias Baumgart, Kshitiz Parihar, Seung-Hyun Brianna Ko, Wei Guo, Paul Janmey, Ryan Bradley, Phillip Taylor and Natesan Ramakrishnan
11. Modeling the mechanochemical feedback for membrane-protein interactions using a continuum mesh model
Padmini Rangamani and Christopher Lee
12. Lattice-based mesoscale simulations and mean-field theory of cell membrane adhesion
Bartosz Różycki, Jingeli Hu, Long Li, Lukasz Milewski and Jie Gao
13. Dynamic framework for large-scale modelling of membranes and peripheral proteins
Mohsen Sadeghi and David Rosenberger
14. Computing the spontaneous curvature of dynamic lipid complexes in molecular dynamics simulations
Alexander Sodt, Amirali Hossein and Kayla Sapp
15. Non-affine deformation analysis and 3D packing defects: A new way to probe membrane heterogeneity in molecular simulations
Anand Srivastava and Madhusmita Tripathy
16. Analyzing curvature and lipid distributions in molecular dynamics simulations of complex membranes
Peter Tieleman
