Implicit-solvent dissipative particle dynamics force field based on a four-to-one coarse-grained mapping scheme

Wan, Mingwei; Ling, Gao; Fang, Wei‐Hai

doi:10.1371/journal.pone.0198049

Cited by 14 publications

(27 citation statements)

References 81 publications

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“…Therefore, Gao et al 28 have established the H-shape model on the basis of the four-to-one scheme with more detailed bead classification according to the MARTINI force field and calculated the repulsive parameters suitable for the explicit/implicit-solvent DPD simulation. 32 They have also verified that this new force field could well reproduce the structure and thermodynamic properties of the bimolecular membranes. 28 Although the above model can more It is inevitable that the simplified model may ignore many details of the cell membrane, so a huge amount of effort is obliged to ensure that the formed bimolecular membrane conforms to the morphological and mechanical properties of the real cell membrane.…”

Section: Modeling Methods Of Cell Membranementioning

confidence: 76%

Mechanism studies on the cellular internalization of nanoparticles using computer simulations: A review

et al. 2021

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Nanomaterial drug delivery systems have become one of the most important targeted therapy technologies. Although great efforts have been made to study the selfassembled mesoscopic structure of nanoparticles and understand drug loading and release mechanisms, the interaction between nanoparticles and cell membranes has not yet been clearly studied. Moreover, the research of experimental methods in this field has been greatly restricted due to its special time-space scale, so it is necessary to apply computer simulations to visualize the cell internalization of the nanoparticle. This review covers modeling methods and the current status and viewpoints of research on the influencing factors of the nanoparticle-biomembrane interaction mechanism. In particular, we discussed in detail the positive and negative effects of various nanoparticle properties. This article may assist researchers in rationally optimize the nanoparticle structure to improve therapeutic efficiency.

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Section: Modeling Methods Of Cell Membranementioning

confidence: 76%

Mechanism studies on the cellular internalization of nanoparticles using computer simulations: A review

et al. 2021

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“…These models emphasize the mapping of three heavy atoms into a coarse-grained bead, but this is not consistent with the conception of the MARTINI force field. Therefore, Gao 37 et al have established the H-shape model on the basis of the four-to-one scheme with more detailed bead classification according to the MARTINI force field and calculated the repulsive parameters suitable for the explicit / implicit-solvent DPD simulation 38 . They have also verified that this new force field could well reproduce the structure and thermodynamic properties of the bimolecular membranes 37 .…”

Section: Modelling Methods Of Cell Membranementioning

confidence: 99%

Mechanism studies on the cellular internalization of nanoparticles using computer simulations: A review

Feng

Chen

Fei

et al. 2021

Preprint

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Nanomaterial drug delivery systems have become one of the most important targeted therapy technologies. Although great efforts have been made to study the self-assembled mesoscopic structure of nanoparticles and understand drug loading and release mechanisms, the interaction between nanoparticles and cell membranes has not yet been clearly studied. Moreover, the research of experimental methods in this field has been greatly restricted due to its special time-space scale, so it is necessary to apply computer simulations to visualize the cell internalization of the nanoparticle. This review covers modelling methods and the current status and viewpoints of research on the influencing factors of the nanoparticle-biomembrane interaction mechanism. In particular, we discussed in detail the positive and negative effects of various nanoparticle properties. This article may assist researchers in rationally optimize the nanoparticle structure to improve therapeutic efficiency.

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“…In the case of DOPC, the equilibrium 4-5-6 and 8-9-10 angles are set to 120° to mimic the unsaturated hydrocarbon chains. 35 , 38 …”

Section: Simulation Detailsmentioning

confidence: 99%

How Ethanolic Disinfectants Disintegrate Coronavirus Model Membranes: A Dissipative Particle Dynamics Simulation Study

Zhou

Das

et al. 2022

J. Chem. Theory Comput.

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We have developed dissipative particle dynamics models for pure dipalmitoylphosphatidylcholine (DPPC), dioleoylphosphatidylcholine (DOPC), and dimyristoylphosphatidylcholine (DMPC) as well as their binary and ternary mixed membranes, as coronavirus model membranes. The stabilities of pure and mixed membranes, surrounded by aqueous solutions containing up to 70 mol % ethanol (alcoholic disinfectants), have been investigated at room temperature. We found that aqueous solutions containing 5–10 mol % ethanol already have a significant weakening effect on the pure and mixed membranes. The magnitude of the effect depends on the membrane composition and the ethanol concentration. Ethanol permeabilizes the membrane, causing its lateral swelling and thickness shrinking and reducing the orientational order of the hydrocarbon tail of the bilayer. The free energy barrier for the permeation of ethanol in the bilayers is considerably reduced by the ethanol uptake. The rupture-critical ethanol concentrations causing the membrane failure are 20.7, 27.5, and 31.7 mol % in the aqueous phase surrounding pure DMPC, DOPC, and DPPC membranes, respectively. Characterizing the failure of lipid membranes by a machine-learning neural network framework, we found that all mixed binary and/or ternary membranes disrupt when immersed in an aqueous solution containing a rupture-critical ethanol concentration, ranging from 20.7 to 31.7 mol %, depending on the composition of the membrane; the DPPC-rich membranes are more intact, while the DMPC-rich membranes are least intact. Due to the tight packing of long, saturated hydrocarbon tails in DPPC, increasing the DPPC content of the mixed membrane increases its stability against the disinfectant. At high DPPC concentrations, where the DOPC and DMPC molecules are confined between the DPPC lipids, the ordered hydrocarbon tails of DPPC also induce order in the DOPC and DMPC molecules and, hence, stabilize the membrane more. Our simulations on pure and mixed membranes of a diversity of compositions reveal that a maximum ethanol concentration of 32 mol % (55 wt %) in the alcohol-based disinfectants is enough to disintegrate any membrane composed of these three lipids.

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Implicit-solvent dissipative particle dynamics force field based on a four-to-one coarse-grained mapping scheme

Cited by 14 publications

References 81 publications

Mechanism studies on the cellular internalization of nanoparticles using computer simulations: A review

Mechanism studies on the cellular internalization of nanoparticles using computer simulations: A review

Mechanism studies on the cellular internalization of nanoparticles using computer simulations: A review

How Ethanolic Disinfectants Disintegrate Coronavirus Model Membranes: A Dissipative Particle Dynamics Simulation Study

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