Poly(Sitosterol)-Based Hydrophobic Blocks in Amphiphilic Block Copolymers for the Assembly of Hybrid Vesicles.

Amphiphilic block copolymer and lipids can be assembled into hybrid vesicles (HVs), which are an alternative to liposomes and polymersomes. Block copolymers that have either poly(sitostryl methacrylate) or statistical copolymers of sitosteryl methacrylate and butyl methacrylate as the hydrophobic part and a poly(carboxyethyl acrylate) hydrophilic segment are synthesized and characterized. These block copolymers assemble into small HVs with soybean L-α-phosphatidylcholine (soyPC), confirmed by electron microscopy and small-angle X-ray scattering. The membrane's hybrid nature is illustrated by fluorescence resonance energy transfer between labeled building blocks. The membrane packing, derived from spectra when using Laurdan as an environmentally sensitive fluorescent probe, is comparable between small HVs and the corresponding liposomes with molecular sitosterol, although the former show indications of transmembrane asymmetry. Giant HVs with homogenous distribution of the block copolymers and soyPC in their membranes are assembled using the electroformation method. The lateral diffusion of both building blocks is slowed down in giant HVs with higher block copolymer content, but their permeability toward (6)-carboxy-X-rhodamine is higher compared to giant vesicles made of soyPC and molecular sitosterol. This fundamental effort contributes to the rapidly expanding understanding of the integration of natural membrane constituents with designed synthetic compounds to form hybrid membranes.

Cooling-Rate Computer Simulations for the Description of Crystallization of Organic Phase-Change Materials.

A molecular-level insight into phase transformations is in great demand for many molecular systems. It can be gained through computer simulations in which cooling is applied to a system at a constant rate. However, the impact of the cooling rate on the crystallization process is largely unknown. To this end, here we performed atomic-scale molecular dynamics simulations of organic phase-change materials (paraffins), in which the cooling rate was varied over four orders of magnitude. Our computational results clearly show that a certain threshold (1.2 × 1011 K/min) in the values of cooling rates exists. When cooling is slower than the threshold, the simulations qualitatively reproduce an experimentally observed abrupt change in the temperature dependence of the density, enthalpy, and thermal conductivity of paraffins upon crystallization. Beyond this threshold, when cooling is too fast, the paraffin's properties in simulations start to deviate considerably from experimental data: the faster the cooling, the larger part of the system is trapped in the supercooled liquid state. Thus, a proper choice of a cooling rate is of tremendous importance in computer simulations of organic phase-change materials, which are of great promise for use in domestic heat storage devices.

Effect of Solvent Removal Rate and Annealing on the Interface Properties in a Blend of a Diketopyrrolopyrrole-Based Polymer with Fullerene.

We study the effect of solvent-free annealing and explicit solvent evaporation protocols in classical molecular dynamics simulations on the interface properties of a blend of a diketopyrrolopyrrole (DPP) polymer with conjugated substituents (DPP2Py2T) and PCBM[60]. We specifically analyze the intramolecular segmental mobility of the different polymer building blocks as well as intermolecular radial and angular distribution functions between donor and acceptor. The annealing simulations reveal an increase of the glass-transition temperature of 45 K in the polymer-fullerene blend compared to that of pure DPP2Py2T. Our results show that the effective solvent evaporation rates at room temperature only have a minor influence on the segmental mobility and intermolecular orientation, characterized in all cases by a preferential arrangement of PCBM[60] close to the electron-donating substituents in DPP2Py2T. In contrast, solvent-free annealing from a liquid yields clustering of the fullerene close to the electron-withdrawing DPP, generally considered to be detrimental for application in organic solar cells. We find that the difference can be attributed to differences in the behavior of 2-hexyldecyl side-chains, which collapse toward DPP when solvent is explicitly removed, thereby blocking access of PCBM[60].

Electro-osmotic Drag and Thermodynamic Properties of Water in Hydrated Nafion Membranes from Molecular Dynamics.

One of the important parameters in water management of proton exchange membranes is the electro-osmotic drag (EOD) coefficient of water. The value of the EOD coefficient is difficult to justify, and available literature data on this for Nafion membranes show scattering from in experiments and simulations. Here, we use a classical all-atom model to compute the EOD coefficient and thermodynamic properties of water from molecular dynamics simulations for temperatures between 330 and 420 K, and for different water contents between λ = 5 and λ = 20. λ is the ratio between the moles of water molecules to the moles of sulfonic acid sites. This classical model does not capture the Grotthuss mechanism; however, it is shown that it can predict the EOD coefficient within the range of experimental values for λ = 5 where the vehicular mechanism dominates proton transfer. For λ > 5, the Grotthuss mechanism becomes dominant. To obtain the EOD coefficient, average velocities of water and ions are computed by imposing different electric fields to the system. Our results show that the velocities of water and hydronium scale linearly with the electric field, resulting in a constant ratio of ca. 0.4 within the error bars. We find that the EOD coefficient of water linearly increases from 2 at λ = 5 to 8 at λ = 20 and the results are not sensitive to temperature. The EOD coefficient at λ = 5 is within the range of experimental values, confirming that the model can capture the vehicular transport of protons well. At λ = 20, due to the absence of proton hopping in the model, the EOD coefficient is overestimated by a factor of 3 compared to experimental values. To analyze the interactions between water and Nafion, the partial molar enthalpies and partial molar volumes of water are computed from molecular dynamics simulations. At different water uptakes, multiple linear regression is used on raw simulation data within a narrow composition range of water inside the Nafion membrane. The partial molar volumes and partial molar excess enthalpies of water asymptotically approach the molar volumes and molar excess enthalpies of pure water for water uptakes above 5. This confirms the model can capture the bulklike behavior of water in the Nafion at high water uptakes.

A coarse-grained model for capturing the helical behavior of isotactic polypropylene.

Understanding the process-property relations of helical polymers using molecular simulations has been an attractive research field over the years. Specifically, isotactic polypropylene still remains a challenge for current computational experimentation, as it exhibits phenomena such as crystallization that emerge on large spatial and temporal scales. Coarse-graining is an efficient technique for approaching such phenomena, although previous coarse-grained models lack in preserving important atomistic and structural details. In this paper we develop a new coarse-grained model, based on the popular MARTINI force field, that is able to reproduce the helical behavior of isotactic polypropylene. To test the model, the predicted statistical and structural properties (characteristic ratio, density, entanglement molecular weight, solubility parameter in the melt) are compared with previous simulation results and available experimental data. For the development of the new coarse-grained force field, a single unperturbed chain Monte Carlo algorithm has been implemented: an efficient algorithm which samples conformations representative of a melt by simulating just a single chain.

Development and Testing of an All-Atom Force Field for Diketopyrrolopyrrole Polymers with Conjugated Substituents.

We develop an all-atom force field for a series of diketopyrrolopyrrole polymers with two aromatic pyridine substituents and a variable number of π-conjugated thiophene units in the backbone (DPP2PymT), used as donor materials in organic photovoltaic devices. Available intrafragment parameterizations of the individual fragment building blocks are combined with interfragment bonded and nonbonded parameters explicitly derived from density functional theory calculations. To validate the force field, we perform classical molecular dynamics simulations of single polymer chains with m = 1, 2, 3 in good and bad solvents and of melts. We observe the expected dependence of the chain conformation on the solvent quality, with the chain collapsing in water, and swelling in chloroform. The glass-transition temperature for the polymer melts is found to be in the range of 340-370 K. Analysis of the mobility of the conjugated segments in the polymer backbone reveals two relaxation processes: a fast one with a characteristic time at room temperature on the order of 10 ps associated with nearly harmonic vibrations and a slow one on the order of 100 ns associated with temperature-activated cis-trans transitions.

Unveiling the Mechanism of the Location of the Grafted Nanoparticles in a Lamellar-Forming Block Copolymer.

Through coarse-grained molecular dynamics simulation of polymer-grafted nanoparticles (NPs) in a lamellar-forming diblock copolymer (BCP), we systematically study the effects of the grafting density (Ng), the compatibility between the grafted chains and the A-block of BCPs (εgA), and the NP number (N) on the distance (D) of the NPs from the interface by proposing novel characterization parameters of the orientation and distribution of the grafted chains. The NP gradually migrates away from the interface and into the A-block region with the increase of εgA for all studied Ng, while slightly returning toward the interface at high εgA and great Ng, which is the first observation of nonmonotonic migration at the molecular level. We ascribe the reason of this to the behavior of the grafted chains that are near the interface. Furthermore, we classify the grafted chains into three types along the normal direction of the interface and the migration process is illustrated by the distribution and orientation of the different types of grafted chains, together with the radial distribution function between the NP and the A-block chains. We observe the formation of the NP layers parallel to the interface for N < 20, and a similar nonmonotonic migration of the layers is as well observed. The D is the largest for a small N because of the excluded volume effects between the NPs. Increasing Ng and N pushes the neighboring NP layers toward the interface due to the mutual repulsion. Generally, this study may shed some light on how to better understand and design high-performance polymer nanocomposites with a tunable location of NPs.

Toward Predictive Molecular Dynamics Simulations of Asphaltenes in Toluene and Heptane.

The conventional definition of asphaltenes is based on their solubility in toluene and their insolubility in heptane. We have utilized this definition to study the influence of partial charge parametrization on the aggregation behavior of asphaltenes using classical atomistic molecular dynamics simulations performed on the microsecond time scale. Under consideration here are toluene- and heptane-based systems with different partial charges parametrized using the general AMBER force field (GAFF). Systems with standard GAFF partial charges calculated by the AM1-BCC and HF/6-31G*(RESP) methods were simulated alongside systems without partial charges. The partial charges implemented differ in terms of the resulting electrical negativity of the asphaltene polyaromatic core, with the AM1-BCC method giving the greatest magnitude of the total core charge. Based on our analysis of the molecular relaxation and orientation, and on the aggregation behavior of asphaltenes in toluene and heptane, we proposed to use the partial charges obtained by the AM1-BCC method for the study of asphaltene aggregates. A good agreement with available experimental data was observed on the sizes of the aggregates, their fractal dimensions, and the solvent entrainment for the model asphaltenes in toluene and heptane. From the results obtained, we conclude that for a better predictive ability, simulation parameters must be carefully chosen, with particular attention paid to the partial charges owing to their influence on the electrical negativity of the asphaltene core and on the asphaltenes aggregation.

Tailoring the mechanical properties of polymer nanocomposites via interfacial engineering.

The improvement of mechanical properties of polymer nanocomposites (PNCs) has been studied for many years, with the main focus on the structure of the nanofillers. Much less effort has been devoted to unraveling the factors controlling the structure of the grafted chains. Herein, through coarse-grained molecular-dynamics simulations, we have successfully fabricated an ideal, mechanically-interlocked composite structure composed of end-functionalized chains grafted to the nanoparticle surface forming rings and making the matrix chains thread through these rings. Depending on the details of the grafting, the reinforcement effect can be remarkable, improving the tensile stress of the system significantly up to 700%. Meanwhile, anisotropy of the system's mechanical response is also observed. Furthermore, the influence of the grafted chain distribution on the mechanical properties of the system has been investigated as well. We observe that the mechanical properties of the system are closely related to the total number of the beads in the grafted chains or the synergistic effect between the length and density of the grafted chains leads to no significant difference in the performance of systems. At constant grafting density, the mechanical properties of the systems correlate negatively to the grafted chain length. In general, our study should help to design and fabricate high-performance PNCs with excellent mechanical properties.

Molecular Modeling of Structure and Dynamics of Nafion Protonation States.

We present the results of the atomistic molecular dynamics modeling of different protonation states of Nafion at varying hydration levels. Previous experiments have shown that the degree of deprotonation (DDP) of the sulfonic acid groups in a Nafion membrane varies significantly upon hydration. Our goal is to provide insights into the effects of variable protonation states and water content on the internal structure and vehicular transport inside the Nafion membrane. The Nafion side chain lengths showed a weak increasing trend with increasing DDP at all hydration levels, exposing more of the sulfonic acid groups to the hydrophilic/water phase. The water-phase characteristic size/diameter decreased with increasing DDP, but, interestingly, the average number of water molecules per cluster increased. The probability of water-hydronium hydrogen bond formation decreased with increasing DDP, despite an increase in the total number of such hydrogen bonds. The water diffusion was largely unaffected by the state of deprotonation. In contrast to that, the hydronium ion diffusion slowed down with increasing DDP in the overall membrane. The hydronium ion residence times around the sulfonic acid group increased with increasing DDP. Our simulations show a strong connection between the morphology of the water domains and protonation states of Nafion. Such a connection can also be expected in polyelectrolyte membranes similar to Nafion.

Salt concentration dependence of the mechanical properties of LiPF6/poly(propylene glycol) acrylate electrolyte at a graphitic carbon interface: A reactive molecular dynamics study.

This reactive molecular dynamics study explores the salt concentration dependence of the viscoelastic and mechanical failure properties of a poly(propylene glycol)/LiPF6-based solid polymer electrolyte (SPE) at a graphitic carbon electrode interface. To account for the finite-size effect of interface-confined SPE films, the properties of two distinct film thicknesses are compared with the respective bulk properties. Additionally, the effect of uniaxial compression in the interface-normal direction on free energy profiles of Li-ion SPE-desolvation is studied. © 2018 The Authors. Journal of Polymer Science Part B: Polymer Physics Published by Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2018, 56, 718-730.

Molecular Dynamics Simulations of Substrate Hydrophilicity and Confinement Effects in Capped Nafion Films.

Nafion nanocomposites for energy-related applications are being used extensively because of the attractive properties such as enhanced water retention, low unwanted crossover of electrolytes, and high proton conductivity. We present the results of the molecular dynamics modeling of Nafion films confined between two walls (substrates) of different polymer-wall interaction strengths and of different separation distances to model Nafion nanocomposites. Our goal is to provide insights into the effects of varying hydrophilicity and volume fraction of fillers/nanoparticles on the internal structure and water transport inside the Nafion membrane. The sulfur-sulfur radial distribution function first peak distance and the sulfur-oxygen (water) coordination number in the first hydration shell were negligibly affected by the wall (substrate) hydrophilicity or the film thickness. The Nafion side chains were found to bend toward the substrates with high hydrophilicity which is in qualitative agreement with existing experiments. The amount of bending was observed to reduce with increasing film thickness. However, the side-chain length did not show any noticeable variation with wall (substrate) hydrophilicity or film thickness. The water clusters became smaller and more isolated clusters emerged for highly hydrophilic substrates. In addition, the water cluster sizes showed a decreasing trend with decreasing film thickness in the case of hydrophilic substrates, which has also been observed in experiments of supported Nafion films. The in-plane water diffusion was enhanced considerably for hydrophilic substrates, and this mechanism has also been proposed previously in experiments. The in-plane water diffusion was also found to be a strong function of the substrate selectivity toward the hydrophilic phase. Our simulations can help provide more insights to experimentalists for choosing or modifying nanoparticles for Nafion nanocomposites.

Structural Ordering in SWCNT-Polyimide Nanocomposites and Its Influence on Their Mechanical Properties.

Using fully-atomistic models, tens-microseconds-long molecular-dynamic modelling was carried out for the first time to simulate the kinetics of polyimides ordering induced by the presence of single-walled carbon nanotube (SWCNT) nanofillers. Three polyimides (PI) were considered with different dianhydride fragments, namely 3,3',4,4'-biphenyltetracarboxylic dianhydride (BPDA), 2,3',3,4'-biphenyltetracarboxylic dianhydride (aBPDA), and 3,3',4,4'-oxidiphthalic dianhydride (ODPA) and same diamine 1,4-bis[4-(4-aminophenoxy)phenoxy]benzene (diamine P3). Both crystallizable PI BPDA-P3 and two amorphous polyimides ODPA-P3 and aBPDA-P3 reinforced by SWCNTs were studied. The structural properties of the nanocomposites at temperature close to the bulk polymer melting point were studied. The mechanical properties were determined for the nanocomposites cooled down to the glassy state. It was found that the SWCNT nanofiller initiates' structural ordering not only in the crystallizable BPDA-P3 but also in the amorphous ODPA-P3 samples were in agreement with previously obtained experimental results. Two stages of the structural ordering were detected in the presence of SWCNTs, namely the orientation of the planar moieties followed by the elongation of whole polymer chains. The first type of local ordering was observed on the microsecond time scale and did not lead to the change of the mechanical properties of a polymer binder in considered nanocomposites. At the end of the second stage, both BPDA-P3 and ODPA-P3 PI chains extended completely along the SWCNT surface, which in turn led to enhanced mechanical characteristics in their glassy state.

Formation mechanism of bound rubber in elastomer nanocomposites: a molecular dynamics simulation study.

Bound rubber plays a key role in the mechanical reinforcement of elastomer nanocomposites. In the present work, we reveal the formation mechanism of bound rubber in elastomer nanocomposites, using the coarse-grained molecular dynamics simulations. For the polymer-nanoparticle system, the "chain bridge" connected with neighboring nanoparticles forms, once the gap between two neighboring nanoparticles is less than the polymer size. The polymer-nanoparticle-solvent systems, mimicking the oil-swollen rubber in the experiment, are simulated with three models. From the analysis of the potential energy, the static structure and dynamic diffusing processes, all the models indicate that the increase of the volume fraction of the nanoparticles and the polymer-nanoparticle interaction strength could promote the formation of the bound rubber. The existence of solvent disrupts the bound rubber, and eventually deteriorates the mechanical properties. These simulations could provide some theoretical guidance for a better understanding of the formation mechanism of the bound rubber, which is helpful for designing the elastomer materials with excellent mechanical properties.

Simulational insights into the mechanical response of prestretched double network filled elastomers.

This paper deals with molecular-dynamics simulations of the mechanical properties of prestretched double network filled elastomers. To this end, we firstly validated the accuracy of this method, and affirmed that the produced stress-strain characteristics were qualitatively consistent with Lesser's experimental results on the prestretched tri-block copolymers with a competitive double network. Secondly, we investigated the effect of the crosslinking network ratio on the mechanical properties of the prestretched double network homopolymers under uniaxial tension. We found that the prestretched double network contributes greatly to the enhanced tensile stress and ultimate strength at fracture, as well as to the lower permanent set (the residual strain) and dynamic hysteresis loss, both parallel and perpendicular to the prestretching direction. Notably, though, an anisotropic behavior was observed: in the parallel direction, both the first and the second crosslinked networks bore the external force; whereas in the perpendicular direction, only the second crosslinked network was relevantly effective. Finally, the polymer nanocomposites with a prestretched double network exhibited tensile mechanical properties similar to those of the studied homopolymers with prestretched double networks. Summing up the results, it can be concluded that the incorporation of prestretched double networks with a specified crosslinking network ratio seems to be a promising method for manipulating the mechanical properties of elastomers and their nanocomposites, as well as for introducing anisotropy in their mechanical response.

Self-Assembly of Block Copolymer Chains To Promote the Dispersion of Nanoparticles in Polymer Nanocomposites.

In this paper we adopt molecular dynamics simulations to study the amphiphilic AB block copolymer (BCP) mediated nanoparticle (NP) dispersion in polymer nanocomposites (PNCs), with the A-block being compatible with the NPs and the B-block being miscible with the polymer matrix. The effects of the number and components of BCP, as well as the interaction strength between A-block and NPs on the spatial organization of NPs, are explored. We find that the increase of the fraction of the A-block brings different dispersion effect to NPs than that of B-block. We also find that the best dispersion state of the NPs occurs in the case of a moderate interaction strength between the A-block and the NPs. Meanwhile, the stress-strain behavior is probed. Our simulation results verify that adopting BCP is an effective way to adjust the dispersion of NPs in the polymer matrix, further to manipulate the mechanical properties.

Designing polymer nanocomposites with a semi-interpenetrating or interpenetrating network structure: toward enhanced mechanical properties.

Using short polymer chains and through molecular dynamics simulation, we designed a well-dispersed nanoparticle (NP) network, which was then incorporated with the polymer matrix. First, we examined the effects of the dual-end grafted chains flexibility and density on the spatial distribution of this particular polymer nanocomposites system. By changing the interaction strength between the matrix polymer chains and the dual-end grafted chains in the semi-interpenetrating network system (NP network), we analyzed the interpenetration state between the linear polymer matrix and the NP network via calculating the total interfacial interaction energy. Moreover, the uniaxial tensile stress-strain and orientation behavior influenced by the interaction strength between the matrix polymer and the grafted chains were investigated for both the semi-interpenetrating network system and the interpenetrating network system (NP network and matrix network). Furthermore, for the interpenetrating network system, we modulated the integrity of the NP network ranging from 0% to 100%, corresponding to the gradual transition of the dispersion morphology of the NPs from the aggregation state to the uniform dispersion state, to examine the effect of the NP network on the tensile mechanical behavior. In particular, by simulating the dynamic shear process in the semi-interpenetrating network system, the composites were found to exhibit a lower non-linear behavior (the famous Payne effect), a higher storage modulus, and a lower tangent loss at large strain amplitude with increasing NP network integrity. In general, our results could provide a new approach for the design of high-performance polymer nanocomposites by taking advantage of the semi-interpenetrating or interpenetrating network reinforcing structure.

Interfacial and topological effects on the glass transition in free-standing polystyrene films.

United-atom molecular-dynamics computer simulations of atactic polystyrene (PS) were performed for the bulk and free-standing films of 2 nm-20 nm thickness, for both linear and cyclic polymers comprised of 80 monomers. Simulated volumetric glass-transition temperatures (Tg) show a strong dependence on the film thickness below 10 nm. The glass-transition temperature of linear PS is 13% lower than that of the bulk for 2.5 nm-thick films, as compared to less than 1% lower for 20 nm films. Our studies reveal that the fraction of the chain-end groups is larger in the interfacial layer with its outermost region approximately 1 nm below the surface than it is in the bulk. The enhanced population of the end groups is expected to result in a more mobile interfacial layer and the consequent dependence of Tg on the film thickness. In addition, the simulations show an enrichment of backbone aliphatic carbons and concomitant deficit of phenyl aromatic carbons in the interfacial film layer. This deficit would weaken the strong phenyl-phenyl aromatic (π-π) interactions and, hence, lead to a lower film-averaged Tg in thin films, as compared to the bulk sample. To investigate the relative importance of the two possible mechanisms (increased chain ends at the surface or weakened π-π interactions in the interfacial region), the data for linear PS are compared with those for cyclic PS. For the cyclic PS, the reduction of the glass-transition temperature is also significant in thin films, albeit not as much as for linear PS. Moreover, the deficit of phenyl carbons in the film interface is comparable to that observed for linear PS. Therefore, chain-end effects alone cannot explain the observed pronounced Tg dependence on the thickness of thin PS films; the weakened phenyl-phenyl interactions in the interfacial region seems to be an important cause as well.

Atomistic Molecular Dynamics Simulations of the Initial Crystallization Stage in an SWCNT-Polyetherimide Nanocomposite.

Crystallization of all-aromatic heterocyclic polymers typically results in an improvement of their thermo-mechanical properties. Nucleation agents may be used to promote crystallization, and it is well known that the incorporation of nanoparticles, and in particular carbon-based nanofillers, may induce or accelerate crystallization through nucleation. The present study addresses the structural properties of polyetherimide-based nanocomposites and the initial stages of polyetherimide crystallization as a result of single-walled carbon nanotube (SWCNT) incorporation. We selected two amorphous thermoplastic polyetherimides ODPA-P3 and aBPDA-P3 based on 3,3',4,4'-oxydiphthalic dianhydride (ODPA), 2,3',3,4'-biphenyltetracarboxylic dianhydride (aBPDA) and diamine 1,4-bis[4-(4-aminophenoxy)phenoxy]benzene (P3) and simulated the onset of crystallization in the presence of SWCNTs using atomistic molecular dynamics. For ODPA-P3, we found that the planar phthalimide and phenylene moieties show pronounced ordering near the CNT (carbon nanotube) surface, which can be regarded as the initial stage of crystallization. We will discuss two possible mechanisms for ODPA-P3 crystallization in the presence of SWCNTs: the spatial confinement caused by the CNTs and π⁻π interactions at the CNT-polymer matrix interface. Based on our simulation results, we propose that ODPA-P3 crystallization is most likely initiated by favorable π⁻π interactions between the carbon nanofiller surface and the planar ODPA-P3 phthalimide and phenylene moieties.

Influence of Morphology on the Mechanical Properties of Polymer Nanocomposites Filled with Uniform or Patchy Nanoparticles.

In this work we perform molecular-dynamics simulations, both on the coarse-grained and the chemistry-specific levels, to study the influence of morphology on the mechanical properties of polymer nanocomposites (PNCs) filled with uniform spherical nanoparticles (which means without chemical modification) and patchy spherical nanoparticles (with discrete, attractive interaction sites at prescribed locations on the particle surface). Through the coarse-grained model, the nonlinear decrease of the elastic modulus (G') and the maximum of the viscous modulus (G″) around the shear strain of 10% is clearly reproduced. By turning to the polybutadiene model, we examine the effect of the shear amplitude and the interaction strength among uniform NPs on the aggregation kinetics. Interestingly, the change of the G' as a function of the aggregation time exhibited a maximum value at intermediate time attributed to the formation of a polymer-bridged filler network in the case of strong interaction between NPs. By imposing a dynamic periodic shear, we probe the change of the G' as a function of the strain amplitude while varying the interaction strength between uniform NPs and its weight fraction. A continuous filler network is developed at a moderate shear amplitude, which is critically related to the interaction strength between NPs and the weight fraction of the fillers. In addition, we study the self-assembly of the patchy NPs, which form the typical chain-like and sheet-like structures. For the first time, the effect of these self-assembled structures on the viscoelastic and stress-strain behavior of PNCs is compared. In general, in the coarse-grained model we focus on the size effect of the rough NPs on the Payne effect, while some other parameters such as the dynamic shear flow, the interaction strength between NPs, the weight fraction, and the chemically heterogeneous surface of the NPs are explored for the chemistry-specific model.