Efficient Simulations of Solvent Asymmetry Across Lipid Membranes Using Flat-Bottom Restraints
D Biriukov, M Javanainen - Journal of Chemical Theory and …, 2023 - ACS Publications
The routinely employed periodic boundary conditions complicate molecular simulations of
physiologically relevant asymmetric lipid membranes together with their distinct solvent …
physiologically relevant asymmetric lipid membranes together with their distinct solvent …
Spontaneous curvature generation by peptides in asymmetric bilayers
1Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA,
USA, 2Department of Biochemistry and Biophysics, Washington University in St. Louis, St …
USA, 2Department of Biochemistry and Biophysics, Washington University in St. Louis, St …
Unraveling the Phase Behavior, Mechanical Stability, and Protein Reconstitution Properties of Polymer–Lipid Hybrid Vesicles
Hybrid vesicles consisting of natural phospholipids and synthetic amphiphilic copolymers
have shown remarkable material properties and potential for biotechnology, combining the …
have shown remarkable material properties and potential for biotechnology, combining the …
Building complex membranes with Martini 3
The Martini model is a popular force field for coarse-grained simulations. Membranes have
always been at the center of its development, with the latest version, Martini 3, showing great …
always been at the center of its development, with the latest version, Martini 3, showing great …
Effect of leaflet asymmetry on the stretching elasticity of lipid bilayers with phosphatidic acid
D Drabik, P Hinc, M Stephan, RRM Cavalcanti… - Biophysical …, 2024 - cell.com
The asymmetry of membranes has a significant impact on their biophysical characteristics
and behavior. This study investigates the composition and mechanical properties of …
and behavior. This study investigates the composition and mechanical properties of …
Non-affine deformation analysis and 3D packing defects: A new way to probe membrane heterogeneity in molecular simulations
M Tripathy, A Srivastava - Methods in enzymology, 2024 - pubmed.ncbi.nlm.nih.gov
Here, we discuss a new framework developed over the last 5 years in our group to probe
nanoscale membrane heterogeneity. The framework is based on the idea of characterizing …
nanoscale membrane heterogeneity. The framework is based on the idea of characterizing …
Simulating asymmetric membranes using P21 periodic boundary conditions
Molecular dynamics (MD) simulations of symmetric lipid bilayers are now well established,
while those of asymmetric ones are considerably less developed. This disjunction arises in …
while those of asymmetric ones are considerably less developed. This disjunction arises in …
Modeling asymmetric cell membranes at all-atom resolution
Molecular dynamics (MD) simulations are a useful tool when studying the properties of
membranes as they allow for a molecular view of lipid interactions with proteins, nucleic …
membranes as they allow for a molecular view of lipid interactions with proteins, nucleic …
Exploring the effects of emerging technologies on food processing through molecular dynamics simulations
WA Müller - 2023 - lume.ufrgs.br
Molecular dynamics simulations have proven to be an useful tool in the mechanistic analysis
of various phenomena in biomolecules. This technique is particularly promising in the study …
of various phenomena in biomolecules. This technique is particularly promising in the study …