Conformations and dynamics of adsorbed protein-like chains

Conformations and dynamics of adsorbed protein-like chains are investigated by using Monte Carlo simulation based on the modified orientation-dependent monomer-monomer interaction (ODI) model. The chain size and shape of adsorbed protein-like chains, such as mean-square end-to-end distance 〈R²〉, mean-square radius of gyration 〈S²〉_xy (or 〈S²〉_z), shape factors , and 〈δ^*〉 are discussed here. At the same time, fraction of adsorbed segment f_a and average orientation of bond 〈P₂(cos θ)〉 are also investigated. The adsorbed protein-like chains trend to be more flat when adsorption interaction energy becomes strong. Different kinds of interactions (such as contact interaction, sheet interaction, spin-spin interaction, helical interaction, and adsorbed interaction) are considered in detail. Dynamics of adsorbed protein-like chains are investigated by calculating their diffusion coefficients, and we find that there exist the relationships of Dxy∼N−γxyand Dz∼N−γz, and the values of γ_xy and γ_z are 4-5 times larger than that of general self-avoiding walk (SAW) chains. These investigations may provide some insights into adsorption of proteins.     

Computer simulations of the conformations of strongly adsorbed chains at the solid-liquid interface

We have utilized molecular dynamics simulations to critically study the conformation of isolated polymer chains adsorbed on surfaces in the presence of explicit solvent. The changes in conformations of the polymer chain in good solvent as it adsorbs onto a substrate is mapped. The quasi two-dimensional pancake conformation of a well adsorbed polymer chain is confirmed. The effect of wetting characteristics of the solvent on the adsorption transition of polymer chain is also studied. We found that a non-wetting solvent aids adsorption of the polymer chain even at low sticking energies compared to wetting solvent.     

Atomic-scale mechanical behaviors of polycrystalline graphene under biaxial loadings and high temperature

Graphene is widely utilized due to its excellent properties. Nevertheless, the failure mechanism previously acquired by uniaxial tension needs to be optimized urgently as its service conditions become more and more demanding. Here, the mechanical behaviors of polycrystalline graphene under tensile-shear biaxial strains and high temperature were investigated by molecular dynamics simulations. We proved that the shear strain dominated the failure of polycrystalline graphene when tensile and shear loading were applied simultaneously. As the temperature rises, the structural destruction of polycrystalline graphene changes from stress-dominated to temperature-dominated. Moreover, the ultimate shear stress increases with the increase of grain size, while the ultimate strain is the opposite. The polycrystalline graphene with a large grain size has better high temperature resistance. These results extend our understanding of the mechanical properties of polycrystalline graphene and guide the design of devices composed of 2D materials under extreme conditions.     

Molecular modeling of crosslinked epoxy polymers: The effect of crosslink density on thermomechanical properties

Molecular dynamics and molecular mechanics simulations are used to establish well-equilibrated, validated molecular models of the EPON 862-DETDA epoxy system with a range of crosslink densities using a united atom force field. Molecular dynamics simulations are subsequently used to predict the glass transition temperature, thermal expansion coefficients, and elastic properties of each of the crosslinked systems. The results indicate that glass transition temperature and elastic properties increase with increasing levels of crosslink density and the thermal expansion coefficient decreases with crosslink density, both above and below the glass transition temperature. The results demonstrate reasonable agreement with thermomechanical properties in the literature. The results also indicate that there may be a range of crosslink densities in epoxy systems beyond which there are limited changes in thermomechanical properties.     

Molecular dynamics simulation of diffusion and permeation of gases in polystyrene

Molecular dynamics simulations are performed to study the diffusion and permeation of gases, including argon, nitrogen, methane, carbon dioxide, and propane, in polystyrene over a wide range of temperatures. A jumping mechanism is observed for the diffusion of diffusants in polymer. The calculated diffusion coefficients agree well with the experimental data and with the results of former simulation studies. The relation between the diffusion coefficient and the molecular diameter is confirmed by the results. Our calculated results on the temperature-dependence of diffusion coefficients show that for some gases a break is seen, at the glass transition temperature, in the Arrhenius plot of ln (D) versus 1/T, while for some other light gases, argon and nitrogen, the plot is linear over the whole temperature range. We have also calculated the permeability coefficients, using the diffusion coefficients calculated in this work and our recently published solubility coefficients [Eslami and Müller-Plathe, Macromolecules 2007; 40:6413]. Our results show that the calculated permeability coefficients are higher than the experimental data by almost the same trend observed in the solubility calculations, but the ratios of calculated permeabilities are in a very good agreement with experiment.     

Molecular simulations of crosslinking process of thermosetting polymers

We use molecular dynamics (MD) with a procedure to describe chemical reactions to predict the atomic structure and properties of the thermosetting polymer epoxy EPON-862 and curing agent DETDA. The DREIDING force field is employed with environment-dependent atomic charges obtained self consistently during the dynamics. We propose a computationally efficient method to describe charge evolution based on the observation that atomic charges evolve significantly only during chemical reactions and in a repeatable manner. Two chemistry models with different relative rates for primary and secondary amine reactions are used to mimic the curing process in two extreme cases of processing conditions. The simulations show that differences in chemical reaction rates affect properties for intermediate conversion degrees (∼40-70%) but not for the higher conversion rates of interest in most applications. We also find that performing the polymerization at high temperatures leads to networks with lower internal strain energy due to increased molecular mobility. The predicted density, coefficient of thermal expansion, glass transition temperature and elastic constants of the resulting polymers are in excellent agreement with experiments.     

Different diffusion behavior of cyclic chains under confinement

Molecular dynamics simulations of merging process of two isolated cyclic chains and that of linear chains have been performed, in order to find the difference between the two kinds of chain in bulk and in vacuum, where surface of the system restrains thousands of configurations showing up. Analysis indicates that in such confinement the chain ends at most moments float on the surface layer, and their mobility is much larger than the mean value of all atoms in linear chains, or that in cyclic chains. Comparison of the merging processes of cyclic chains and their linear counterparts was intensively carried out by several means of analyzing the trajectory files in statics and in dynamics. It was found that the segments of cyclic chains showed almost the same behavior of motion with that of linear chains. This is different diffusion behavior from that in bulk systems, where the cyclic chain has much higher diffusion rate. This modeling therefore indicates that in these confined systems because of the surface energy, the end groups are involuntarily kept on the surface, and lost the capacity of leading chain reptation through the other polymer chains, which is possibly the origin that the difference of diffusion behavior between the linear chain and the cyclic chain in the bulk almost disappears in the case of the confinement.     

The phase behaviors of cylindrical diblock copolymers and rigid nanorods' mixtures

Mixtures of cylindrical forming diblock copolymers (DBCPs) and mobile nanorods (NRs) are systematically investigated via dissipative particle dynamics (DPD) simulations. Final morphology of such composites depends not only on the characteristics of the copolymers, but also on the physical or chemical features of NRs, such as NR number, length, and surface adsorption (neutral, A and B attractive). A consideration of enthalpic and entropic interactions is necessary when physically or chemically distinct NRs are introduced into the copolymer/nanorod composites. For the short NRs, the phase behavior is similar to that of spherical nanoparticles (NPs). For the long NRs, the self-assembly of NRs can influence both the orientation and morphology of diblock/nanorod mixtures. If more NRs are incorporated, under stronger confinement from the host phase separated domains, the long NRs will aggregate and self-assemble into a certain spatial organization, inducing the morphological transitions of the composites from one phase to another. This behavior is not encountered for a similar system doped with spherical particles, emphasizing the role of particle shape in the interaction between doping particles and the host phase.     

Role of entanglements and bond scission in high strain-rate deformation of polymer gels

A key factor that limits the practical implementation of polymer gels is low gel toughness. Here, we present coarse-grained molecular dynamics simulations of the effects of solvent molecular weight on the toughness of entangled and non-entangled polymer gels in the ballistic impact regime. Our results demonstrate that higher molecular weight solvents enhance gel toughness, and that mechanical properties including strength and toughness can be influenced by bond scission. Further, we find a remarkable two-step gel fracture mechanism on the molecular level: network chains undergo scission first (and well before fracture), followed by scission of solvent chains. For strain rates greater than inverse relaxation time of the solvent, long, highly entangled solvent chains provide fracture resistance even after the network chains break by effectively increasing the number of chains that must be broken as a crack propagates.     

The glass transition and thermoelastic behavior of epoxy-based nanocomposites: A molecular dynamics study

In this study, the glass transition and thermoelastic properties of cross-linked epoxy-based nanocomposites and their filler-size dependency are investigated through molecular dynamics simulations. In order to verify the size effect of nanoparticles, five different unit cells with different-sized silicon carbide (SiC) nanoparticles are considered under the same volume fraction. By considering a wide range of temperatures in isobaric ensemble simulations, the glass transition temperature is obtained from the specific volume-temperature relationship from the cooling-down simulation. In addition, the coefficient of thermal expansion (CTE) and the elastic stiffness of the nanocomposites at each temperature are predicted and compared with one another. As a result, the glass transition and thermoelastic properties of pure epoxy are found to be improved by embedding the SiC nanoparticles. Especially regarding the CTE and elastic moduli of nanocomposites, the particle-size dependency is clearly observed below and above the glass transition temperature.     

Molecular dynamics simulation of mixed matrix nanocomposites containing polyimide and polyhedral oligomeric silsesquioxane (POSS)

Mixed matrix blends containing polyimide (PI) and polyhedral oligomeric silsesquioxanes (POSS) are studied with atomistic molecular dynamics simulation. To examine the effect of functional group, two types of POSS are considered, either octahydrido silsesquioxane (OHS) or octaaminophenyl silsesquioxane (OAPS). The glass transition temperature of the model PI-OAPS blends increases with the incorporation of OAPS, an observation consistent with recent experiments on these systems. A decrease in glass transition temperature is shown for the model PI-OHS blends. Radial distribution functions for both blends are presented to show how packing between the inorganic (POSS) and organic (PI) species in the mixed matrix varies as a function of POSS loading and POSS functionalization. In addition, we report the mobility of the PI chains and POSS molecules in the material by calculating the mean square displacement. These results provide molecular insight about thermal property enhancements afforded by POSS-based additives.     

Non-equilibrium phase transitions in suspensions of oppositely driven inertial particles

The structural evolution of a two-specie suspension of inertial particles under opposite driving forces is investigated by molecular dynamics simulations. The effects of the driving force (F) and the total number density of the particles (ρ) on the final structure are explored. When F is increased under a high ρ, the system starts with a frozen phase, passes through an ordered phase characterized by two demixed lanes moving in opposite directions, and finally returns to a disorder phase. When ρ is increased under a low F, a novel re-entrant phase transition is found: more than two lanes parallel to the driving forces are observed first, followed by a disordered phase with different kinds of particles blocking each other, and then an ordered state with all particles separating into two demixed lanes. We comment on the possible mechanisms underlying these phase transitions in terms of the compromise between the directional driven motion and random thermal fluctuation.     

Cooperative behavior of poly(vinyl alcohol) and water as revealed by molecular dynamics simulations

An aqueous poly(vinyl alcohol) (PVA) model has been extensively studied by using the molecular dynamics (MD) simulation method. The employed molecular and force field models are validated against the available data in the literature. In particular, the glass transition temperature (T_g) is determined from the specific volume versus temperature, which compares well with the experimental observations. The diffusion coefficients of water (H₂O) through the PVA matrix follow the Arrhenius equations at both temperature regions separated by T_g, indicating the existence of free and bound water defined by hydrogen bonds (HBs). It has also been confirmed that HBs occur between PVA and H₂O, between PVA and PVA, between H₂O and H₂O, and all of them play the key roles in the glass transition. The local dynamics suggested by the decorrelations of various bond vectors can be well described by the Williams-Landel-Ferry (WLF) equation. This work demonstrates the cooperative behavior of PVA and H₂O which is responsible for the glass transition of the whole binary system.     

Molecular dynamics simulation of the structural and mechanical property changes in the Brill transition of nylon 10/10 crystal

In order to confirm the structural features in the Brill transition of aliphatic nylons, molecular dynamics calculation has been performed at the various temperatures for nylon 10/10 crystal as a model. With an increase in temperature, the torsional motions around the methylene-amide and methylene-methylene bonds were activated. These motions became more remarkable above 420 K and the interconversion between trans and gauche forms occurred frequently, resulting in the disordered conformation of the methylene sequences and the pseudo-hexagonal packing of these parts. During such a drastic structural disordering, however, the hydrogen bonds were kept alive although the bond strength became weaker. These calculations were found to be consistent with the experimental results by the temperature-dependent X-ray diffraction and infrared spectral measurements. The Young's modulus along the chain axis was also calculated as a function of temperature: it decreased remarkably from 250 GPa at 0 K to 180 GPa at 300 K due to a small contraction of the skeletal chain by only about 0.2-0.5% through the torsional motion of the skeletal chains, and the modulus decreased furthermore to 80 GPa at 550 K because of the larger conformational disordering of the skeletal chains. The Young's modulus in the direction perpendicular to the chain axis was also found to decrease remarkably in parallel to the change of the chain packing mode.     

Effect of polymer structure on the molecular dynamics and thermal behavior of poly(allyl acetoacetate) and copolymers

In this paper, dielectric and calorimetric studies of the small-molecule glass former allyl acetoacetate monomers as well as its newly synthetized homopolymer and copolymers with different styrene composition were performed in both the liquid and glassy states. The molecular dynamics studies by the broadband dielectric spectroscopy and the stochastic temperature modulated differential scanning calorimetry enabled us to explore relaxation processes of examined materials in the wide frequency range. We found that the copolymers reveal two co-existing glass transitions characterized by the glass transition temperatures, which are very close to those of the corresponding homopolymers. These results suggest that the copolymers exhibited some sequences of acetoacetate units with a microphase-separated morphology in agreement with the value of reactivity ratio previously determined. We investigated effects of copolymerization compositions on the glass transition temperature, the isobaric fragility index, the dielectric and calorimetric intensity, and the dynamic heterogeneity on the glass transitions of the materials.     

Molecular dynamics simulation of polar chains under an external electric field

By means of molecular dynamics simulation the effect of external electric field on charged chains in the liquid state is investigated. Three types of hypothetical chains with different charge and weight distributions are studied. External electric fields with different forms, field strength and frequency are examined. Results indicate that the populations of trans and gauche configuration, the dipole moment of the chain, the dihedral angle correlation function and the sequence of trans and gauche configuration are sensitive to the strength and form of applied external field. The result and significance of each of these properties are discussed.     

The role of adsorption in passivation phenomena modelled by discrete lattice gas automata

Simulation results are presented for a simple modification of recent lattice gas cellular automata model of passivation. In the previous model, the passive layer sites produced at the corroding surface, neither adhere to nor are repelled from the surface. As a result, no net adsorption or desorption, at equilibrium, is possible for this model. Nonetheless, the crucial features of passivation appear due to the kinetic crowding of the passive layer sites. This crowding effect is further enhanced by the aggregation of the passive layer sites introduced via asymmetric exclusion rules. The results of this model challenge a common view that adsorption is crucial for passivation. This analysis calls for the evaluation of the role of adsorption. Therefore, in this paper, the model takes into account the attraction of the passive layer sites with the metallic substrate. The present model is compared with the model examined in the previous paper. It demonstrates that although adsorption does not modify essentially the overall image of passivation, as seen in the polarization curves, there are important quantitative and qualitative new features in the passivation phenomenology introduced by adsorption. These new features result from the appearance of two regimes of passivation: a thin layer regime at the passivation transition followed by a thick layer regime at more anodic potentials.     

The structure and dynamics of adsorbed molecules in microporous solids; a comparison between experiments and computer simulations

A critical evaluation is made of the results of computer simulations of adsorbed molecules in microporous inorganic materials. Structural, thermochemical and dynamic data are compared with the corresponding experimental findings. The systems examined include inert gases and simple alkanes in zeolites Na-Y and silicalite, benzene and pyridine in Na-Y and K-L, respectively, andp-xylene in silicalite. Future developments in the area are also discussed.