Biophysical Approaches for the Study of Membrane Structure Part B

Markus Deserno is a professor in the Department of Physics at Carnegie Mellon University, where he works in the field of theoretical and computational biophysics. He focuses on lipid membranes and proteins, using a wide spectrum of techniques that range from coarse-grained molecular dynamics simulations up to differential geometry, continuum elasticity, and statistical field theory. Deserno received his Ph.D. from the Max Planck Institute for Polymer Research (MPI-P) in Mainz, Germany, in 2000. After graduation, he held a postdoctoral research position in the Department of Chemistry and Biochemistry at UCLA, followed by a group leader position back at the MPI-P. In 2007 he joined the Department of Physics at Carnegie Mellon University, where he got tenured in 2011 and became Full Professor in 2016. Between 2014 and 2020 Deserno served on the Editorial Board of the Biophysical Journal. He is an elected Fellow of the American Physical Society and received the Thomas E. Thompson Award of the Biophysical Society. Edit Tobias Baumgart is a professor in the Chemistry Department of the University of Pennsylvania. An experimental biophysical chemist at heart, he focuses on understanding how both lipids and proteins, as well as the continuum mechanics of bilayer assemblies determine membrane function. Baumgart obtained his Ph.D. from the Max Planck Institute for Polymer Research (MPI-P) and the Johannes Gutenberg University in Mainz, Germany, in 2001. He was a postdoctoral research associate with Watt Webb, Gerald Feigenson, and Barbara Baird at Cornell University in Ithaca, before becoming an Assistant Professor in 2005, and a full professor in 2017. He was on the Biophysical Journal’s Editorial Board between 2013 and 2019. He is a recipient of the Alfred P. Sloan and NSF CAREER awards, as well as the Dennis M. DeTurck and Charles Ludwig awards for distinguished teaching. Edit

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 Rózycki, 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