In this paper, a novel method to construct MD simulation models of ultrafine and stable PE nanoparticles with different molecular architecture is introduced. The MD models are used to examine the compressive flat-punch behavior of PE nanoparticles with linear, branched, and AG-881 chemical structure cross-linked chains. It is shown that the chain architecture has a significant effect on the compression behavior of freestanding individual PE nanoparticles. Methods A combination of united-atom force fields [25–28] was used for the MD models of polymeric nanoparticles in which the CH, CH2, and CH3 groups were considered to be LY3039478 in vivo single spherical neutral interacting beads, resulting

in great saving in terms of the total number of atoms in the simulated systems. Each of these united-atom models has been shown to be applicable to entangled linear and branched

PE polymer systems. The total potential energy Blasticidin S research buy can be expressed as: (1) where the total potential energy (E total) includes two components: non-bonded (E nb) and bonded (E bond) interaction terms. For the non-bonded interaction term, all the inter-beads separated by more than three bonds only interact through a standard 12–6 Lennard-Jones potential. The cutoff distance was set to 12 Å in the simulations. Standard Lorentz-Berthelot’s combining rules were utilized for the unlike-pair interactions. The bonded term comprises three contributions: bond stretching (E b), angle bending (E θ), and dihedral torsion (E φ), in which dihedral torsion is expressed by a cosine polynomial and bond stretching and angle bending are described by Glutamate dehydrogenase harmonic functions. The detailed

potential function forms and their respective parameters are summarized in Table 1. Table 1 Potential functions and parameters of united atom force field Non-bond Bond Angle Torsion   ϵ (kcal/mol) σ (Å) r c (Å)   k b (kcal/(mol·Å 2 )) r 0 (Å)   k θ (kcal/mol) θ 0 (deg)   A 0 (kcal/mol) A 1 (kcal/mol) A 2 (kcal/mol) A 3 (kcal/mol) CH x … CH y (x = 1, 2, 3; y = 2, 3) [25] 0.1119 4.01 12 CH x -CH y 95.89 1.54 CH x -CH2-CH y 57.6 111.6 CH x -CH2-CH2-CH y 1.73 −4.493 0.776 6.99 (x, y = 1, 2, 3) [27] (x, y = 1, 2, 3) [27] (x, y = 1, 2, 3) [25] CH… CH [26] 0.0789 3.85 12       CH x -CH-CH y 62.1 109.74 CH x -CH-CH2-CH y 0.8143 1.7926 0.3891 3.6743 (x, y = 2) [26]                     (x, y = 2) [28]         Three distinct PE molecule structures were constructed to study the effect of chain architecture on the mechanical behavior. Figure 1a shows a schematic of the cross-linked, branched, and linear chains that were constructed using the united atoms. For each of the three PE systems, an MD simulation box with periodical boundary conditions was built based on the method of Theodorou and Suter [29]. Each simulation box had an initial bulk density of 0.5 g/cm3 composed of 30 of the corresponding systems shown in Figure 1a.