Biological membranes

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Table of contents

1 General Introduction 
1.1 Biological membranes
1.2 Transport of molecules in cells and membranes
1.3 Modeling anomalous diffusion
1.4 Recent simulation work
2 Concept of Molecular Dynamics Simulations 
2.1 Classical Molecular Dynamics Simulations
2.1.1 Concept and potential function
2.1.2 Periodic boundary conditions and treatment of electrostatic interactions
2.2 Treatment of thermodynamic conditions
3 Simulated systems and simulations 
3.1 System setup
3.1.1 All-atom OPLS force-field
3.1.2 Coarse-grained MARTINI force-field
3.2 Membrane simulations
3.2.1 OPLS-AA force-field
3.2.1.1 System equilibration
3.2.1.2 Short production run – 15 ns
3.2.1.3 Extended simulation – 150 ns
3.2.2 MARTINI force-field
3.2.2.1 System equilibration
3.2.2.2 600 ns production run in the canonical ensemble
3.2.2.3 600 ns production run in the NApzT ensemble
3.3 Bulk water reference simulation
4 Results 
4.1 Single molecule dynamics in a lipid bilayer
4.1.1 Mean Square Displacements
4.1.1.1 Atom-detailed simulations
4.1.1.2 Coarse-grained force-field results
4.1.1.3 Comparison between OPLS-AA and MARTINI force-fields
4.1.1.4 Bulk water comparison with membrane hydration water
4.1.2 Velocity autocorrelation function analysis
4.1.3 Density of States (DOS)
4.1.3.1 DOS as Fourier transform of VACF
4.1.3.2 Density of the States from the Autoregressive Model
4.1.4 Conclusions
4.2 Collective motions of lipids
4.2.1 Pair Correlation Function
4.2.2 Visualization of the cage e↵ect
4.2.3 Conclusions
5 Conclusions 
6 Publications 
References