Simulation of chain folding in polyethylene: A comparison of united atom and explicit hydrogen atom models

Effect of Force Field Resolution on Membrane Mechanical Response and Mechanoporation Damage under Deformation Simulations

Damage induced by transient disruption and mechanoporation in an intact cell membrane is a vital nanoscale biomechanical mechanism that critically affects cell viability. To complement experimental studies of mechanical membrane damage and disruption, molecular dynamics (MD) simulations have been performed at different force field resolutions, each of which follows different parameterization strategies and thus may influence the properties and dynamics of membrane systems. Therefore, the current study performed tensile deformation MD simulations of bilayer membranes using all-atom (AA), united-atom (UA), and coarse-grained Martini (CG-M) models to investigate how the damage biomechanics differs across atomistic and coarse-grained (CG) simulations. The mechanical response and mechanoporation damage were qualitatively similar but quantitatively different in the three models, including some progressive changes based on the coarse-graining level. The membranes yielded and reached ultimate strength at similar strains; however, the coarser systems exhibited lower average yield stresses and failure strains. The average failure strain in the UA model was approximately 7% lower than the AA, and the CG-M was 20% lower than UA and 27% lower than AA. The CG systems also nucleated a higher number of pores and larger pores, which resulted in higher damage during the deformation process. Overall, the study provides insight on the impact of force field-a critical factor in modeling biomolecular systems and their interactions-in inspecting membrane mechanosensitive responses and serves as a reference for justifying the appropriate force field for future studies of more complex membranes and more diverse biomolecular assemblies.

Revealing the Effect of the Molecular Weight Distribution on the Chain Diffusion and Crystallization Process under a Branched Trimodal Polyethylene System

With the increasing demand for high-end materials, trimodal polyethylene (PE) has become a research hotspot in recent years due to its superior performance compared with bimodal PE. By means of molecular dynamics (MD) simulations, we aim to expound the effect of the molecular weight distribution (MWD) on the mechanism of nucleation and crystallization of trimodal PE. The crystallization rate is faster when short-chain branching is distributed on a single backbone compared to that on two backbones. In addition, as the content of high molecular weight backbone decreases, the time required for nucleation decreases, but the crystallization rate slows down. This is because low molecular weight backbones undergo intra-chain nucleation and crystallize earlier due to the high diffusion capacity, which leads to entanglement that prevents the movement of medium or high molecular weight backbones. Furthermore, crystallized short backbones hinder the movement and crystallization of other backbones. What is more, a small increase in the high molecular weight branched backbone of trimodal PE can make the crystallinity greater than that of bimodal PE, but when the content of high molecular weight backbone is too high, the crystallinity decreases instead, because the contribution of short and medium backbones to high crystallinity is greater than that of long backbones.

Unraveling the influential mechanism of short-chain branching on the crystallization of trimodal polyethylene by molecular dynamics simulation

Trimodal polyethylene (PE) has become the focus of research in recent years due to its excellent performance. By means of molecular dynamics simulations, we aim to expound the molecular mechanism of short-chain branching (SCB) in the nucleation process, crystallization process and chain entanglement of trimodal PE. In this study, a series of polyethylene models including different short-chain branching concentrations (SCBCs), short-chain branching lengths (SCBLs), and short-chain branching distributions (SCBDs) were considered. The increase of SCBCs greatly reduces the ability of flipping and movement of PE chains, resulting in more time for nucleation and crystallization and a significant reduction of crystallinity. In contrast, an increase in the SCBL only slightly slows down the diffusion rate of the chain, which leads to a little increase in crystallization time. Most important of all, in the study of SCBD, we find that the distribution of SCBs on a high molecular weight chain, which is the characteristic of trimodal PE, is conducive to the chain entanglement and prevents the occurrence of micro phase separation compared with the case where the SCBs are distributed on a medium molecular weight chain. The mechanism of chain entanglement is proposed to explain the effect of SCBs on tie chain entanglement.

Comparison of the United- and All-Atom Representations of (Halo)alkanes Based on Two Condensed-Phase Force Fields Optimized against the Same Experimental Data Set

The level of accuracy that can be achieved by a force field is influenced by choices made in the interaction-function representation and in the relevant simulation parameters. These choices, referred to here as functional-form variants (FFVs), include for example the model resolution, the charge-derivation procedure, the van der Waals combination rules, the cutoff distance, and the treatment of the long-range interactions. Ideally, assessing the effect of a given FFV on the intrinsic accuracy of the force-field representation requires that only the specific FFV is changed and that this change is performed at an optimal level of parametrization, a requirement that may prove extremely challenging to achieve in practice. Here, we present a first attempt at such a comparison for one specific FFV, namely the choice of a united-atom (UA) versus an all-atom (AA) resolution in a force field for saturated acyclic (halo)alkanes. Two force-field versions (UA vs AA) are optimized in an automated way using the CombiFF approach against 961 experimental values for the pure-liquid densities ρ_liq and vaporization enthalpies ΔH_vap of 591 compounds. For the AA force field, the torsional and third-neighbor Lennard-Jones parameters are also refined based on quantum-mechanical rotational-energy profiles. The comparison between the UA and AA resolutions is also extended to properties that have not been included as parameterization targets, namely the surface-tension coefficient γ, the isothermal compressibility κ_T, the isobaric thermal-expansion coefficient α_P, the isobaric heat capacity c_P, the static relative dielectric permittivity ϵ, the self-diffusion coefficient D, the shear viscosity η, the hydration free energy ΔG_wat, and the free energy of solvation ΔG_che in cyclohexane. For the target properties ρ_liq and ΔH_vap, the UA and AA resolutions reach very similar levels of accuracy after optimization. For the nine other properties, the AA representation leads to more accurate results in terms of η; comparably accurate results in terms of γ, κ_T, α_P, ϵ, D, and ΔG_che; and less accurate results in terms of c_P and ΔG_wat. This work also represents a first step toward the calibration of a GROMOS-compatible force field at the AA resolution.

Characterization of Cure Behavior in Epoxy Using Molecular Dynamics Simulation Compared with Dielectric Analysis and DSC

The curing behavior of a thermosetting material that influences the properties of the material is a key issue for predicting the changes in material properties during processing. An empirical equation can describe the reaction kinetics of the curing behavior of an investigated material, which is usually estimated using experimental methods. In this study, the curing process of an epoxy resin, the polymer matrix in an epoxy molding compound, is computed concerning thermal influence using molecular dynamics. Furthermore, the accelerated reaction kinetics, which are influenced by an increased reaction cutoff distance, are investigated. As a result, the simulated crosslink density with various cutoff distances increases to plateau at a crosslink density of approx. 90% for the investigated temperatures during curing time. The reaction kinetics are derived according to the numerical results and compared with the results using experimental methods (dielectric analysis and differential scanning calorimetry), whereby the comparison shows a good agreement between experiment and simulation.

Dominant Effects of Short-Chain Branching on the Initial Stage of Nucleation and Formation of Tie Chains for Bimodal Polyethylene as Revealed by Molecular Dynamics Simulation

The molecular mechanism of short-chain branching (SCB), especially the effects of methylene sequence length (MSL) and short-chain branching distribution (SCBD) on the initial stage of nucleation, the crystallization process, and particularly the tie chain formation process of bimodal polyethylene (BPE), were explored using molecular dynamics simulation. This work constructed two kinds of BPE models in accordance with commercial BPE pipe resins: SCB incorporated in the long chain or in the short chains. The initial stage of nucleation was determined by the MSL of the system, as the critical MSL for a branched chain to nucleate is about 60 CH2. SCB incorporated in the long chain led to a delay of the initial stage of nucleation relative to the case of SCB incorporated in the short chains. The increase of branch length could accelerate the delay to nucleation. The location of short chain relative to the long chain depended on the MSL of the short chain. As the MSL of the system decreased, the crystallinity decreased, while the tie chains concentration increased. The tie chains concentration of the BPE model with branches incorporated in the long chain was higher than that with branches incorporated in the short chain.

Molecular dynamics simulation of shish-kebab crystallization of polyethylene: Unraveling the effects of molecular weight distribution

By means of molecular dynamics simulations, extensional flow was performed on five polyethylene models with different molecular weight distributions (MWDs) precisely designed in view of Grubbs, metallocene, Ziegler-Natta, and chromium-based catalysts, while ignoring the sequence distributions of short branches to shed light on the molecular mechanism of MWD on shish-kebab formation. The formation of shish-kebab crystallites can be divided into three stages: the emergence of precursors, evolution from precursors to shish nuclei, and the formation of lamellar crystallites. The results demonstrated that the precursors initiated from trans-rich segments with local order and minor crystallinity grew into large shish nuclei and eventually evolved into lamellae. There were more inconsecutively trans-state bonds occurring in long chains rather than in short chains, which promoted an easier transformation from precursors to shish nuclei. Therefore, broader MWDs make positive contributions to the formation of shish nuclei, increase the crystallization speed, and the generation of a more regular, compact, and thicker lamella with less tie molecule fractions, while the final crystallinity is independent of MWD.

An accelerated united-atom molecular dynamics simulation on the fast crystallization of ring polyethylene melts

To investigate crystallinities based on trans-structures, we determined the differences in the crystallization properties of ring and linear polymers by performing united-atom-model molecular dynamics (MD) simulations of homogeneous polyethylene melts of equal length, N, which refers to the number of monomers per chain. Modified parameters based on the DREIDING force field for the CH₂ units were used in order to accelerate the crystallization process. To detect polymer crystallization, we introduced some local-order parameters that relate to trans-segments in addition to common crystallinities using neighboring bond orders. Through quenching MD simulations at 5 K/ns, we roughly determined temperature thresholds, T_th, at which crystallization is observed although it was hard to determine the precise T_th as observed in the laboratory time frame with the present computing resources. When N was relatively small (100 and 200), T_th was determined to be 320 and 350 K for the linear- and ring-polyethylene melts, respectively, while T_th was found to be 330 and 350 K, respectively, when N was 1000. Having confirmed that the crystallization of a ring-polyethylene melt occurs faster than that of the analogous linear melt, we conclude that the trans-segment-based crystallinities are effective for the analysis of local crystal behavior.

Molecular dynamics simulation of the folding of single alkane chains with different lengths on single-walled carbon nanotubes and graphene

Chain folding is an important step during polymer crystallization. In order to study the effects of the surface on chain folding, molecular dynamics simulations of the folding of different alkane chains on three kinds of single-walled carbon nanotubes (SWCNTs) and graphene were performed. The folding behaviors of the single alkane chains on these surfaces were found to be different from their folding behaviors in vacuum. The end-to-end distances of the chains were calculated to explore the chain folding. An increasing tendency to fold into two or more stems with increasing alkane chain length was observed. This result indicates that the occurrence and the stability of chain folding are related to the surface curvature, the diameter of the SWCNT, and surface texture. In addition, the angle between the direction of the alkane chain segment and the direction of the surface texture was measured on different surfaces.

Molecular Dynamics Simulation of Chain Folding for Polyethylene Subjected to Vibration Excitation

We propose a molecular dynamics method with vibration excitation, named as VEMD, to investigate the vibration effect on chain folding for polymer molecule. The VEMD method is based on the introduction of periodic force, the amplitude and frequency of which can be adjusted, and the method was applied to the folding simulation of a polyethylene chain. Simulation results show that the vibration excitation significantly affects the folding of the polyethylene, and frequency and amplitude of the vibration excitation play key roles in VEMD. Different frequencies and amplitudes will determine how and to what extent does the vibration excitation affect the folding process of the polyethylene structure.

Temperature dependent free energy surface of polymer folding from equilibrium and quench studies

Langevin dynamics simulation studies have been employed to calculate the temperature dependent free energy surface and folding characteristics of a 500 monomer long linear alkane (polyethylene) chain with a realistic interaction potential. Both equilibrium and temperature quench simulation studies have been carried out. Using the shape anisotropy parameter (S) of the folded molecule as the order parameter, we find a weakly first order phase transition between the high-temperature molten globule and low-temperature rodlike crystalline states separated by a small barrier of the order of k(B)T. Near the melting temperature (580 K), we observe an intriguing intermittent fluctuation with pronounced "1/f noise characteristics" between these two states with large difference in shape and structure. We have also studied the possibilities of different pathways of folding to states much below the melting point. At 300 K starting from the all-trans linear configuration, the chain folds stepwise into a very regular fourfold crystallite with very high shape anisotropy. Whereas, when quenched from a high temperature (900 K) random coil regime, we identify a two step transition from the random coiled state to a molten globulelike state and, further, to a anisotropic rodlike state. The trajectory reveals an interesting coupling between the two order parameters, namely, radius of gyration (R(g)) and the shape anisotropy parameter (S). The rodlike final state of the quench trajectory is characterized by lower shape anisotropy parameter and significantly larger number of gauche defects as compared to the final state obtained through equilibrium simulation starting from all-trans linear chain. The quench study shows indication of a nucleationlike pathway from the molten globule to the rodlike state involving an underlying rugged energy landscape.