Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userCoarse-grained molecular dynamics simulation for uptake of nanoparticles into a charged lipid vesicle dominated by electrostatic interactions
71
0
0.0
(
0
)
Ask ChatGPT about the research
No Arabic abstract
We use a coarse-grained molecular dynamics simulation to investigate the interaction between neutral or charged nanoparticles (NPs) and a vesicle consisting of neutral and negatively charged lipids. We focus on the interaction strengths of hydrophilic and hydrophobic attraction and electrostatic interactions between a lipid molecule and an NP. A neutral NP passes through the lipid membrane when the hydrophobic interaction is sufficiently strong. As the valence of the positively charged NP increases, the membrane permeation speed of the NP is increased compared with the neutral NP and charged lipids are accumulated around the charged NP. A charged NP with a high valence passes through the lipid membrane via a transient channel formed by charged lipids or transport-like endocytosis. These permeation processes can be classified based on analyses of the density correlation function. When the non-electrostatic interaction parameters are large enough, a negatively charged NP can be adsorbed on the membrane and a neutral lipid-rich region is formed directly below the NP. The NP is spontaneously incorporated into the vesicle under various conditions and the incorporation is mediated by the membrane curvature. We reveal how the NPs behavior depends on the NP valence, size, and the non-electrostatic interaction parameters.
rate research
Read More
This paper has been withdrawn.
During the last decade coarse-grained nucleotide models have emerged that allow us to DNA and RNA on unprecedented time and length scales. Among them is oxDNA, a coarse-grained, sequence-specific model that captures the hybridisation transition of DNA and many structural properties of single- and double-stranded DNA. oxDNA was previously only available as standalone software, but has now been implemented into the popular LAMMPS molecular dynamics code. This article describes the new implementation and analyses its parallel performance. Practical applications are presented that focus on single-stranded DNA, an area of research which has been so far under-investigated. The LAMMPS implementation of oxDNA lowers the entry barrier for using the oxDNA model significantly, facilitates future code development and interfacing with existing LAMMPS functionality as well as other coarse-grained and atomistic DNA models.
Integral equation theory is applied to a coarse-grained model of water to study potential of mean force between hydrophobic solutes. Theory is shown to be in good agreement with the available simulation data for methane-methane and fullerene-fullerene potential of mean force in water; the potential of mean force is also decomposed into its entropic and enthalpic contributions. Mode coupling theory is employed to compute self-diffusion coefficient of water, as well as diffusion coefficient of a dilute hydrophobic solute; good agreement with molecular dynamics simulation results is found.
A coarse-grained simulation model eliminates microscopic degrees of freedom and represents a polymer by a simplified structure. A priori, two classes of coarse-grained models may be distinguished: those which are designed for a specific polymer and reflect the underlying atomistic details to some extent, and those which retain only the most basic features of a polymer chain (chain connectivity, short-range excluded-volume interactions, etc.). In this review we mainly focus on the second class of generic polymer models, while the first class of specific coarse-grained models is only touched upon briefly.
A coarse-grained model is developed to allow large-scale molecular dynamics (MD) simulations of a branched polyetherimide derived from two backbone monomers [4,4-bisphenol A dianhydride (BPADA) and m-phenylenediamine (MPD)], a chain terminator [phthalic anhydride (PA)], and a branching agent [tris[4-(4-aminophenoxy)phenyl] ethane (TAPE)]. An atomistic model is first built for the branched polyetherimide. A systematic protocol based on chemistry-informed grouping of atoms, derivation of bond and angle interactions by direct Boltzmann inversion, and parameterization of nonbonded interactions by potential of mean force (PMF) calculations via gas-phase MD simulations of atomic group pairs, is used to construct the coarse-grained model. A six-pair geometry, with one atomic group at the center and six replicates of the other atomic group placed surrounding the central group in a NaCl structure, has been demonstrated to significantly speed up the PMF calculations and partially capture the many-body aspect of the PMFs. Furthermore, we propose a correction term to the PMFs that can make the resulting coarse-grained model transferable temperature-wise, by enabling the model to capture the thermal expansion property of the polymer. The coarse-grained model has been applied to explore the mechanical, structural, and rheological properties of the branched polyetherimide.
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
