Structure of lateral heterogeneities in a coarse-grained model for multicomponent membranes

Soft Matter ◽  
2019 ◽  
Vol 15 (9) ◽  
pp. 1942-1952
Author(s):  
Sebastian Meinhardt ◽  
Friederike Schmid
Keyword(s):  
Molecular Simulation ◽  
Domain Structure ◽  
Lipid Bilayers ◽  
Coarse Grained ◽  
Simulation Studies ◽  
Coarse Grained Model ◽  
Lateral Heterogeneities

Coarse-grained molecular simulation studies of the lateral domain structure in multicomponent lipid bilayers reveal different morphological regimes.

scholarly journals Structural-Kinetic-Thermodynamic Relationships Identified from Physics-based Molecular Simulation Models

2017 ◽  
Author(s):  
Joseph F. Rudzinski ◽  
Tristan Bereau
Keyword(s):  
Thermodynamic Properties ◽  
Force Field ◽  
Molecular Simulation ◽  
Simulation Models ◽  
Coarse Grained ◽  
Kinetic Properties ◽  
Coarse Grained Model ◽  
Forbidden Configurations ◽  
Force Field Parameters ◽  
Representative System

Coarse-grained molecular simulation models have provided immense, often general, insight into the complex behavior of condensed-phase systems, but suffer from a lost connection to the true dynamical properties of the underlying system. In general, the physics that is built into a model shapes the free-energy landscape, restricting the attainable static and kinetic properties. In this work, we perform a detailed investigation into the property interrelationships resulting from these restrictions, for a representative system of the helix-coil transition. Inspired by high-throughput studies, we systematically vary force-field parameters and monitor their structural, kinetic, and thermodynamic properties. The focus of our investigation is a simple coarse-grained model, which accurately represents the underlying structural ensemble, i.e., effectively avoids sterically-forbidden configurations. As a result of this built-in physics, we observe a rather large restriction in the topology of the networks characterizing the simulation kinetics. When screening across force-field parameters, we find that structurally-accurate models also best reproduce the kinetics, suggesting structural-kinetic relationships for these models. Additionally, an investigation into thermodynamic properties reveals a link between the cooperativity of the transition and the network topology at a single reference temperature.

scholarly journals Understanding the Phase Behavior of Coarse-Grained Model Lipid Bilayers through Computational Calorimetry

2012 ◽  
Vol 116 (5) ◽  
pp. 1551-1569 ◽  
Author(s):  
Jocelyn M. Rodgers ◽  
Jesper Sørensen ◽  
Frédérick J.-M. de Meyer ◽  
Birgit Schiøtt ◽  
Berend Smit
Keyword(s):  
Phase Behavior ◽  
Lipid Bilayers ◽  
Coarse Grained ◽  
Coarse Grained Model

scholarly journals Characterizing the Liquid-liquid Phase Co-existence in Biomembrane: Insights from Local Non-affine Deformation and Topological Rearrangements

2017 ◽  
Author(s):  
Sahithya S. Iyer ◽  
Madhusmita Tripathy ◽  
Anand Srivastava
Keyword(s):  
Liquid Phase ◽  
Lipid Bilayers ◽  
Coarse Grained ◽  
Phase Boundaries ◽  
Dynamical Heterogeneity ◽  
Domain Boundaries ◽  
Liquid Ordered ◽  
Affine Deformation ◽  
Molecular Origin ◽  
Lateral Heterogeneities

AbstractLateral heterogeneities in bio-membranes play a crucial role in various physiological functions of the cell. Such heterogeneities lead to demixing of lipid constituents and formation of distinct liquid domains in the membrane. We study lateral heterogeneities in terms of the topological rearrangements of lipids, to identify liquid-liquid phase co-existence in model membranes. By quantifying the degree of non-affineness associated with individual lipid, we are able to characterize the liquid ordered (Lo) and liquid disordered (Ld) phases in model lipid bilayers, without any prior knowledge on chemical identity of the lipids. We explore the usage of this method on all atom and coarse-grained lipid bilayer trajectories. This method is helpful in defining the instantaneous Lo-Ld domain boundaries in complex multi-component bilayer systems. The characterization can also highlight the effect of line-active molecules on the phase boundaries and domain mixing. Overall, we propose a framework to explore the molecular origin of spatial and dynamical heterogeneity in bio-membranes systems, which can not only be exploited in computer simulation, but also in experiments.

scholarly journals Coarse-grained Force Fields from the Perspective of Statistical Mechanics: Better Understanding the Origins of a MARTINI Hangover

2020 ◽  
Author(s):  
Zack Jarin ◽  
James Newhouse ◽  
Gregory A. Voth
Keyword(s):  
Statistical Mechanics ◽  
Lipid Bilayers ◽  
Potential Of Mean Force ◽  
Distribution Functions ◽  
Coarse Grained ◽  
Test Case ◽  
Top Down ◽  
Coarse Grained Model ◽  
Potentials Of Mean Force ◽  
Dynamics Models

AbstractThe popular MARTINI coarse-grained model is used as a test case to analyze the adherence of top-down coarse-grained molecular dynamics models (i.e., models primarily parameterized to match experimental results) to the known features of statistical mechanics for the underlying all-atom representations. Specifically, the temperature dependence of various pair distribution functions, and hence their underlying potentials of mean force via the reversible work theorem, are compared between MARTINI 2.0, Dry MARTINI, and all-atom simulations mapped onto equivalent coarse-grained sites for certain lipid bilayers. It is found that the MARTINI models do not completely capture the lipid structure seen in atomistic simulations as projected onto the coarse-grained mappings, and that issues of accuracy and temperature transferability arise due to an incorrect enthalpy-entropy decomposition of these potentials of mean force. The potential of mean force for the association of two amphipathic helices in a lipid bilayer is also calculated and, especially at shorter ranges, the MARTINI and all-atom projection results differ substantially. The former is much less repulsive and hence will lead to a higher probability of MARTINI helix association in the MARTINI bilayer than occurs in the actual all-atom case. Additionally, the bilayer height fluctuation spectra are calculated for the MARTINI model and – compared to the all-atom results – it is found that the magnitude of thermally averaged amplitudes at intermediate length scales is quite different, pointing to a number of possible consequences for realistic modeling of membrane processes. Taken as a whole, the results presented here can point the way for future coarse-grained model parameterization efforts that might bring top-down coarse-grained models into better agreement with the statistical mechanics of the actual all-atom systems they aspire to represent.

scholarly journals Derivation of coarse-grained simulation models of chlorophyll molecules in lipid bilayers for applications in light harvesting systems

2015 ◽  
Vol 17 (34) ◽  
pp. 22054-22063 ◽  
Author(s):  
Ananya Debnath ◽  
Sabine Wiegand ◽  
Harald Paulsen ◽  
Kurt Kremer ◽  
Christine Peter
Keyword(s):  
Lipid Bilayers ◽  
Light Harvesting ◽  
Simulation Models ◽  
Coarse Grained ◽  
Light Harvesting Complex ◽  
Green Plants ◽  
Coarse Grained Model ◽  
Multi Scale ◽  
Harvesting Systems ◽  
Association Behavior

A coarse-grained model is derived for chlorophyll molecules in lipid bilayers using a multi-scale simulation ansatz aiming to understand the association behavior of the light harvesting complex (LHCII) of green plants.

Artifacts in dynamical simulations of coarse-grained model lipid bilayers

2005 ◽  
Vol 122 (20) ◽  
pp. 204901 ◽  
Author(s):  
Ask F. Jakobsen ◽  
Ole G. Mouritsen ◽  
Gerhard Besold
Keyword(s):  
Lipid Bilayers ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Dynamical Simulations

scholarly journals Peroxidised phospholipid bilayers: insight from coarse-grained molecular dynamics simulations

Soft Matter ◽  
2016 ◽  
Vol 12 (1) ◽  
pp. 263-271 ◽  
Author(s):  
Yachong Guo ◽  
Vladimir A. Baulin ◽  
Fabrice Thalmann
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Lipid Bilayers ◽  
Phospholipid Bilayers ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Dynamics Simulations ◽  
Coarse Grained Molecular Dynamics

We introduce a coarse-grained model for hydroperoxide lipid bilayers.

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