The good, the bad and the user in soft matter simulations

Wong-ekkabut, Jirasak; Karttunen, Mikko

doi:10.1016/j.bbamem.2016.02.004

Cited by 113 publications

(97 citation statements)

References 193 publications

(294 reference statements)

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“…[48][49][50][51][52] Lorentz-Berthelot mixing rules were used to describe van der Waals interactions as required by the GAFF force field. 53 The topologies of the PLA and PHB monomer units were generated with the aid of the ACPYPE tool which is a wrapper for the antechamber module of Ambertools. 54, 55 The partial atomic charges were calculated using the Gaussian 09 software by the HF/6-31G*(RESP) method.…”

Section: Model and Simulation Methodsmentioning

confidence: 99%

Scale-Dependent Miscibility of Polylactide and Polyhydroxybutyrate: Molecular Dynamics Simulations

et al. 2017

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Miscibility of polylactide (PLA) and polyhydroxybutyrate (PHB) is studied by the microsecond atomistic molecular-dynamics (MD) simulations for the first time. The model and the simulation protocol were confirmed through comparison of the glass transition temperature (T g ) with experimental data. It was established that PLA and PHB are miscible on the basis of the 2 Flory-Huggins theory. Analysis of the mobilities of PLA and PHB subchains revealed that the blends have two transitions to a glassy state at the length scale of a few Kuhn segments, which is in line with the predictions of the self-concentration model. At the same time at the larger length scale, a single transition to a glassy state was observed suggesting scale-dependence of PLA and PHB miscibility. This scale-dependence was confirmed through the evaluation of the interchain pair correlation functions.

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Section: Model and Simulation Methodsmentioning

confidence: 99%

Scale-Dependent Miscibility of Polylactide and Polyhydroxybutyrate: Molecular Dynamics Simulations

et al. 2017

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“…These parameters and protocols have been extensively tested and optimized. [40][41][42] All visualizations were done using Visual Molecular Dynamic (VMD) software. 43 Free energy calculation: The potential of mean force (PMF) of an α-toc transferring into the lipid bilayer was calculated using the umbrella sampling technique 44 with the Weighted Histogram Analysis Method 45 (WHAM).…”

Section: Methodsmentioning

confidence: 99%

Alpha-tocopherol inhibits pore formation in oxidized bilayers

Boonnoy

Karttunen

Wong-ekkabut

2017

Phys. Chem. Chem. Phys.

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ABSTRACT:In biological membranes, alpha-tocopherols (α-toc; vitamin E) protect polyunsaturated lipids from free radicals. Although the interactions of α-toc with nonoxidized lipid bilayers have been studied, their on oxidized bilayers remain unknown. In this study, atomistic molecular dynamics (MD) simulations of oxidized lipid bilayers were performed with varying concentrations of α-toc. Bilayers with 1-palmitoyl-2-lauroyl-sn-glycero-3-phosphocholine (PLPC) lipids and its aldehyde derivatives at 1:1 ratio were studied. Our simulations show that oxidized lipids self-assemble into aggregates with a water pore rapidly developing across the lipid bilayer. The free energy of transporting an α-toc molecule in a lipid bilayer suggests that α-tocs can passively adsorb into the bilayer. When α-toc molecules were present at low concentrations in bilayers containing oxidized lipids, the formation of water pores was slowed down. At high α-toc concentrations, no pores were observed. Based on the simulations, we propose that the mechanism of how α-toc inhibits pore formation in bilayers with oxidized lipids is the following: α-tocs trap the polar groups of the oxidized lipids at the membrane-water interface resulting in a decreased probability for the oxidized lipids to reach contact with the two leaflets and initiate pore formation. This demonstrates that α-toc molecules not only protect the bilayer from oxidation but also help to stabilize the bilayer after lipid peroxidation occurs. These results will help in designing more efficient molecules to protect membranes from oxidative stress.Biological membranes serve as a partition between cells and their environment. Under oxidative stress, unsaturated lipids present in cell membranes may become exposed to attacks by free radicals, that is, oxidation. Oxidation transforms some of the membrane lipids to oxidized ones such as hydroperoxide and aldehyde lipids. 1,2It has also been suggested that internal, that is intra-leaflet, oxidation may be important in altering bilayer properties. 3Lipid peroxidation is an important mechanism of cell membrane damage. [4][5][6] Previous experiments and computer simulations 4,[7][8][9][10][11][12][13][14] have demonstrated how oxidized lipids disturb and deform bilayers. The polar chains in oxidized lipids are energetically unfavorable to stay in the bilayer's interior resulting in the reversal of the polar lipid chain to the bilayer interface. 4,11,15,16 This reversal causes major changes in bilayer properties such as increase of area per lipid, bilayer thinning, decrease of lipid tail order parameter, and increase in water permeability. 4,12,[15][16][17][18] Recently, we performed MD simulations of lipid bilayers with oxidized lipids at high concentrations. Two major oxidized lipid species including hydroperoxide and aldehyde were studied. The results showed that only aldehyde lipids were able to induce pore formation across a PLPC lipid bilayer and cause significant bilayer deformation. 13,15α-toc is well-known as an efficient antioxidant ...

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“…Meanwhile, MD simulations, like any technique, are also prone to errors and artifacts. This important topic is discussed by Wong-ekkabut and Karttunen [21] and also in the paper by Neale and Pomès [22], who consider problems resulting from sampling errors in free energy calculations.…”

Section: Development Of Simulation Methodology For Studies Of Membranesmentioning

confidence: 98%