OrganL: Dynamic triangulation of biomembranes using curved elements

. 2024 Jun 18 ; 123 (12) : 1553-1562. [epub] 20240503

Jazyk angličtina Země Spojené státy americké Médium print-electronic

Typ dokumentu časopisecké články, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/pmid38704638
Odkazy

PubMed 38704638
PubMed Central PMC11213972
DOI 10.1016/j.bpj.2024.04.028
PII: S0006-3495(24)00290-X
Knihovny.cz E-zdroje

We describe a method for simulating biomembranes of arbitrary shape. In contrast to other dynamically triangulated surface (DTS) algorithms, our method provides a rich, quasi-tangent-continuous, yet local description of the surface. We use curved Nagata triangles, which we generalize to cubic order to achieve the requisite flexibility. The resulting interpolation can be constructed locally without iterations, at the cost of having only approximate tangent continuity away from the vertices. This allows us to provide a parallelized and fine-tuned Monte Carlo implementation. As a first example of the potential benefits of the enhanced description, our method supports inhomogeneous lipid distributions as well as lipid mixing. It also supports restraints and constraints of various types and is constructed to be as easily extensible as possible. We validate the approach by testing its numerical accuracy, followed by reproducing the known Helfrich solutions for shapes with rotational symmetry. Finally, we present some example applications, including curvature-driven demixing and stylized effects of proteins. Input files for these examples, as well as the implementation itself, are freely available for researchers under the name OrganL (https://zenodo.org/doi/10.5281/zenodo.11204709).

Zobrazit více v PubMed

Noid W.G. Perspective: Advances, Challenges, and Insight for Predictive Coarse-Grained Models. J. Phys. Chem. B. 2023;127:4174–4207. PubMed

Evans E.A. Bending resistance and chemically induced moments in membrane bilayers. Biophys. J. 1974;14:923–931. PubMed PMC

Canham P.B. The minimum energy of bending as a possible explanation of the biconcave shape of the human red blood cell. J. Theor. Biol. 1970;26:61–81. PubMed

Helfrich W. Elastic Properties of Lipid Bilayers: Theory and Possible Experiments. Z. Naturforsch. C Biosci. 1973;28:693–703. PubMed

Golani G., Ariotti N., et al. Kozlov M.M. Membrane curvature and tension control the formation and collapse of caveolar superstructures. Dev. Cell. 2019;48:523–538.e4. PubMed

Bassereau P., Jin R., et al. Weikl T.R. The 2018 biomembrane curvature and remodeling roadmap. J. Phys. D Appl. Phys. 2018;51 PubMed PMC

Manor U., Bartholomew S., et al. Lippincott-Schwartz J. A mitochondria-anchored isoform of the actin-nucleating spire protein regulates mitochondrial division. Elife. 2015;4 PubMed PMC

Pezeshkian W., König M., et al. Marrink S.J. Backmapping triangulated surfaces to coarse-grained membrane models. Nat. Commun. 2020;11:2296. PubMed PMC

Fedosov D.A., Pan W., et al. Karniadakis G.E. Predicting human blood viscosity in silico. Proc. Natl. Acad. Sci. USA. 2011;108:11772–11777. PubMed PMC

Allolio C., Haluts A., Harries D. A Local Instantaneous Surface Method for Extracting Membrane Elastic Moduli from Simulation: Comparison with other Strategies. Chem. Phys. 2018;514:31–43.

Allolio C., Harries D. Calcium Ions Promote Membrane Fusion by Forming Negative-Curvature Inducing Clusters on Specific Anionic Lipids. ACS Nano. 2021;15:12880–12887. PubMed

Watson M.C., Brandt E.G., et al. Brown F.L.H. Determining Biomembrane Bending Rigidities from Simulations of Modest Size. Phys. Rev. Lett. 2012;109 PubMed

Khelashvili G., Harries D., Weinstein H. Modeling Membrane Deformations and Lipid Demixing upon Protein-Membrane Interaction: The {BAR} Dimer Adsorption. Biophys. J. 2009;97:1626–1635. PubMed PMC

Hu M., Diggins P., Deserno M. Determining the bending modulus of a lipid membrane by simulating buckling. J. Chem. Phys. 2013;138 PubMed

Gompper G., Kroll D.M. Random Surface Discretizations and the Renormalization of the Bending Rigidity. J. Phys. I France. 1996;6:1305–1320.

Gompper G., Kroll D.M. Membranes with Fluctuating Topology: Monte Carlo Simulations. Phys. Rev. Lett. 1998;81:2284–2287.

Gompper G., Kroll D.M. Network models of fluid, hexatic and polymerized membranes. J. Phys. Condens. Matter. 1997;9:8795–8834.

Jülicher F. The Morphology of Vesicles of Higher Topological Genus: Conformal Degeneracy and Conformal Modes. J. Phys. II France. 1996;6:1797–1824.

Kantor Y., Nelson D.R. Phase transitions in flexible polymeric surfaces. Phys. Rev. 1987;36:4020–4032. PubMed

Meyer M., Desbrun M., et al. Barr A.H. In: Visualization and Mathematics III. Hege H.-C., Polthier K., editors. Springer; Berlin Heidelberg, Berlin, Heidelberg: 2003. Discrete Differential-Geometry Operators for Triangulated 2-Manifolds; pp. 35–57.

McWhirter J.L., Noguchi H., Gompper G. Flow-induced clustering and alignment of vesicles and red blood cells in microcapillaries. Proc. Natl. Acad. Sci. USA. 2009;106:6039–6043. PubMed PMC

Tamemoto N., Noguchi H. Reaction-diffusion waves coupled with membrane curvature. Soft Matter. 2021;17:6589–6596. PubMed

Vutukuri H.R., Hoore M., et al. Vermant J. Active particles induce large shape deformations in giant lipid vesicles. Nature. 2020;586:52–56. PubMed

Ramakrishnan N., Sunil Kumar P.B., Radhakrishnan R. Mesoscale computational studies of membrane bilayer remodeling by curvature-inducing proteins. Phys. Rep. 2014;543:1–60. PubMed PMC

Bian X., Litvinov S., Koumoutsakos P. Bending models of lipid bilayer membranes: Spontaneous curvature and area-difference elasticity. Comput. Methods Appl. Mech. Eng. 2020;359

Siggel M., Kehl S., et al. Hummer G. TriMem: A parallelized hybrid Monte Carlo software for efficient simulations of lipid membranes. J. Chem. Phys. 2022;157:174801. PubMed

Sachin Krishnan T.V., Das S.L., Kumar P.B.S. Transition from curvature sensing to generation in a vesicle driven by protein binding strength and membrane tension. Soft Matter. 2019;15:2071–2080. PubMed

Brakke K.A. The Surface Evolver. Exp. Math. 1992;1:141–165.

Pezeshkian W., Ipsen J.H. Fluctuations and conformational stability of a membrane patch with curvature inducing inclusions. Soft Matter. 2019;15:9974–9981. PubMed

Chen J., Yu T., et al. Zigerelli A. Numerical methods for biomembranes: Conforming subdivision methods versus non-conforming PL methods. Math. Comput. 2020;90:471–516.

Barrett J.W., Garcke H., Nürnberg R. Finite element approximation for the dynamics of asymmetric fluidic biomembranes. Math. Comput. 2016;86:1037–1069.

Nagata T. Simple local interpolation of surfaces using normal vectors. Comput. Aided Geomet. Des. 2005;22:327–347.

Neto D., Oliveira M., et al. Alves J. Improving Nagata patch interpolation applied for tool surface description in sheet metal forming simulation. Comput. Aided Des. 2013;45:639–656.

Laursen M.E., Gellert M. Some criteria for numerically integrated matrices and quadrature formulas for triangles. Int. J. Numer. Methods Eng. 1978;12:67–76.

Seifert U., Berndl K., Lipowsky R. Shape transformations of vesicles: Phase diagram for spontaneous- curvature and bilayer-coupling models. Phys. Rev. 1991;44:1182–1202. PubMed

Miao L., Seifert U., et al. Döbereiner H.-G. Budding transitions of fluid-bilayer vesicles: The effect of area-difference elasticity. Phys. Rev. E. 1994;49:5389–5407. PubMed

Liu J.S., Liang F., Wong W.H. The Multiple-Try Method and Local Optimization in Metropolis Sampling. J. Am. Stat. Assoc. 2000;95:121–134.

Krauth W. Event-Chain Monte Carlo: Foundations, Applications, and Prospects. Front. Physiol. 2021;9

Khelashvili G., Kollmitzer B., et al. Harries D. Calculating the Bending Modulus for Multicomponent Lipid Membranes in Different Thermodynamic Phases. J. Chem. Theor. Comput. 2013;9:3866–3871. PubMed PMC

Kozlov M.M., Helfrich W. Effects of a cosurfactant on the stretching and bending elasticities of a surfactant monolayer. Langmuir. 1992;8:2792–2797.

Andelman D., Kozlov M.M., Helfrich W. Phase Transitions between Vesicles and Micelles Driven by Competing Curvatures. Europhys. Lett. 1994;25:231–236.

Konar S., Arif H., Allolio C. Mitochondrial Membrane Model: Lipids, Elastic Properties and the Changing Curvature of Cardiolipin. Biophys. J. 2023;122:4274–4287. PubMed PMC

Sunil Kumar P.B., Gompper G., Lipowsky R. Budding Dynamics of Multicomponent Membranes. Phys. Rev. Lett. 2001;86:3911–3914. PubMed

Ericson C. Crc Press; Boca Raton: 2004. Real-time Collision Detection.

Kurniawan R., Ko T.J. Surface topography analysis in three-dimensional elliptical vibration texturing (3D-EVT) Int. J. Adv. Manuf. Technol. 2019;102:1601–1621.

Landstorfer M., Prifling B., Schmidt V. Mesh generation for periodic 3D microstructure models and computation of effective properties. J. Comput. Phys. 2021;431

Mandal A., Chaudhuri P., Chaudhuri S. Interactive Physics-Based Virtual Sculpting with Haptic Feedback. Proc. ACM Comput. Graph. Interact. Tech. 2022;5:1–20.

Möller T. A fast triangle-triangle intersection test. J. Graph. Tool. 1997;2:25–30.

do Carmo M. Dover Publications; 2016. Differential Geometry of Curves and Surfaces: Revised and Updated Second Edition. Dover Books on Mathematics.

Max N. Weights for Computing Vertex Normals from Facet Normals. J. Graph. Tool. 1999;4:1–6.

Kitware Inc . Kitware Inc; Clifton Park: 2010. VTK User’s Guide.

Kitware Inc ParaView 5.11. 2022. www.paraview.org

Najít záznam

Citační ukazatele

Nahrávání dat ...

Možnosti archivace

Nahrávání dat ...