Martini straight: Boosting performance using a shorter cutoff and GPUs

Jong, Djurre H. de; Baoukina, Svetlana; Ingólfsson, Helgi I.; Marrink, Siewert J.

doi:10.1016/j.cpc.2015.09.014

Cited by 374 publications

(362 citation statements)

References 19 publications

(22 reference statements)

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“…These parameters follow the standard “ new ” Martini set of run parameters. 76 All the evaporation simulations were run using the GROMACS 5.x package. 79 All the run parameter files, as well as the solvent evaporation protocol, implemented as a bash script (which assumes the use of GROMACS), are available for download as part of the Supporting Information and on the Martini portal .…”

Section: Methodsmentioning

confidence: 99%

Bulk Heterojunction Morphologies with Atomistic Resolution from Coarse-Grain Solvent Evaporation Simulations

Alessandri¹,

Uusitalo²,

Vries³

et al. 2017

J. Am. Chem. Soc.

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153

266

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Control over the morphology of the active layer of bulk heterojunction (BHJ) organic solar cells is paramount to achieve high-efficiency devices. However, no method currently available can predict morphologies for a novel donor–acceptor blend. An approach which allows reaching relevant length scales, retaining chemical specificity, and mimicking experimental fabrication conditions, and which is suited for high-throughput schemes has been proven challenging to find. Here, we propose a method to generate atom-resolved morphologies of BHJs which conforms to these requirements. Coarse-grain (CG) molecular dynamics simulations are employed to simulate the large-scale morphological organization during solution-processing. The use of CG models which retain chemical specificity translates into a direct path to the rational design of donor and acceptor compounds which differ only slightly in chemical nature. Finally, the direct retrieval of fully atomistic detail is possible through backmapping, opening the way for improved quantum mechanical calculations addressing the charge separation mechanism. The method is illustrated for the poly(3-hexyl-thiophene) (P3HT)–phenyl-C61-butyric acid methyl ester (PCBM) mixture, and found to predict morphologies in agreement with experimental data. The effect of drying rate, P3HT molecular weight, and thermal annealing are investigated extensively, resulting in trends mimicking experimental findings. The proposed methodology can help reduce the parameter space which has to be explored before obtaining optimal morphologies not only for BHJ solar cells but also for any other solution-processed soft matter device.

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Section: Methodsmentioning

confidence: 99%

Bulk Heterojunction Morphologies with Atomistic Resolution from Coarse-Grain Solvent Evaporation Simulations

Alessandri¹,

Uusitalo²,

Vries³

et al. 2017

J. Am. Chem. Soc.

Self Cite

153

266

View full text Add to dashboard Cite

show abstract

“…The neighbour list was updated after every 10 steps with a cutoff distance set to 1.4 nm. These parameters correspond to the ‘common' set of parameters for the MARTINI forcefield67. Repeat simulations were run by generating new random seeds for velocities.…”

Section: Methodsmentioning

confidence: 99%

Stability and dynamics of membrane-spanning DNA nanopores

et al. 2017

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Recently developed DNA-based analogues of membrane proteins have advanced synthetic biology. A fundamental question is how hydrophilic nanostructures reside in the hydrophobic environment of the membrane. Here, we use multiscale molecular dynamics (MD) simulations to explore the structure, stability and dynamics of an archetypical DNA nanotube inserted via a ring of membrane anchors into a phospholipid bilayer. Coarse-grained MD reveals that the lipids reorganize locally to interact closely with the membrane-spanning section of the DNA tube. Steered simulations along the bilayer normal establish the metastable nature of the inserted pore, yielding a force profile with barriers for membrane exit due to the membrane anchors. Atomistic, equilibrium simulations at two salt concentrations confirm the close packing of lipid around of the stably inserted DNA pore and its cation selectivity, while revealing localized structural fluctuations. The wide-ranging and detailed insight informs the design of next-generation DNA pores for synthetic biology or biomedicine.

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“…A time step of 15 fs was used and the Lennard-Jones and coulomb potential were cutoff at 11 Å. The Verlet neighbor scheme was used with a straight cutoff to keep track of particles within specified distances 32 . Coulomb interactions were treated using a reaction-field.…”

Section: Methodsmentioning

confidence: 99%

The Ebola virus protein VP40 hexamer enhances the clustering of PI(4,5)P₂ lipids in the plasma membrane

Jeevan

Gerstman

Stahelin

et al. 2016

Phys. Chem. Chem. Phys.

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The Ebola virus is a lipid-enveloped virus that obtains its lipid coat from the plasma membrane of the host cell it infects during the budding process. The Ebola virus protein VP40 localizes to the inner leaflet of the plasma membrane and forms the viral matrix, which provides the major structure for the Ebola virus particles. VP40 is initially a dimer that rearranges to a hexameric structure that mediates budding. VP40 hexamers and larger filaments have been shown to be stabilized by PI(4,5)P2 in the plasma membrane inner leaflet. Reduction in the plasma membrane levels of PI(4,5)P2 significantly reduce formation of VP40 oligomers and virus-like particles. We investigated the lipid-protein interactions in VP40 hexamers at the plasma membrane. We quantified lipid-lipid self-clustering by calculating the fractional interaction matrix and found that the VP40 hexamer significantly enhances the PI(4,5)P2 clustering. The radial pair distribution functions suggest a strong interaction between PI(4,5)P2 and the VP40 hexamer. The cationic Lys side chains are found to mediate the PIP2 clustering around the protein, with cholesterol filling the space between the interacting PIP2 molecules. These computational studies support recent experimental data and provide new insights into the mechanisms by which VP40 assembles at the plasma membrane inner leaflet, alters membrane curvature, and forms new virus-like particles.

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Martini straight: Boosting performance using a shorter cutoff and GPUs

Cited by 374 publications

References 19 publications

Bulk Heterojunction Morphologies with Atomistic Resolution from Coarse-Grain Solvent Evaporation Simulations

Bulk Heterojunction Morphologies with Atomistic Resolution from Coarse-Grain Solvent Evaporation Simulations

Stability and dynamics of membrane-spanning DNA nanopores

The Ebola virus protein VP40 hexamer enhances the clustering of PI(4,5)P₂ lipids in the plasma membrane

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Martini straight: Boosting performance using a shorter cutoff and GPUs

Cited by 374 publications

References 19 publications

Bulk Heterojunction Morphologies with Atomistic Resolution from Coarse-Grain Solvent Evaporation Simulations

Bulk Heterojunction Morphologies with Atomistic Resolution from Coarse-Grain Solvent Evaporation Simulations

Stability and dynamics of membrane-spanning DNA nanopores

The Ebola virus protein VP40 hexamer enhances the clustering of PI(4,5)P2 lipids in the plasma membrane

Contact Info

Product

Resources

About

The Ebola virus protein VP40 hexamer enhances the clustering of PI(4,5)P₂ lipids in the plasma membrane