United-atom Molecular Dynamics Research Articles

Unraveling the Mechanical Response of Short-Chain Branched Amorphous Polyethylene: Insights from Molecular Dynamics Simulations

The deformation behavior of short-chain branched, amorphous polyethylene (PE) was investigated using united atom molecular dynamics (MD) simulations under uniaxial stretching. Our research reported in this paper examined the internal mechanisms underlying the mechanical response of the PE by analyzing potential energies, dihedral angle distributions, chain orientation and entanglements. The findings indicated that the short-chain branching generally enhanced Young’s modulus, except for sample B60 with a critical ethyl branch content of 60/1000 (60 ethyl branches per 1000 backbone carbons). The Young’s modulus of B60 was the local minimum value in the various samples. Analysis of the evolution of dihedral angles shows that the short-chain branching hinders the transition from gauche to trans configurations, leading to a decrease in the trans population as the branch content increases. Regarding the sample B60 with critical branch content 60/1000, the orientation parameter and entanglement parameter of the molecular chains along the backbone were lowest in the initial structure, and the efficiency of chain disentanglement was at its lowest during deformation. The simulation results elucidated the deformation mechanism related to the conformational evolution of the molecular chains, which can provide atomic-scale insights into the mechanical properties and processability of branched polyethylene, thereby allowing for optimization in its design and application.

Effect of deformation ratio of flow-induced crystallization on polyethylene in crystalline behavior, thermal stability, and tensile loading: A molecular dynamics simulation

Since the physical and mechanical properties of semicrystalline polymers strongly depend on crystalline morphology, understanding the correlation between the crystallization kinetics and crystalline structure of polythene is beneficial for their rational processing and applications. In this study, united-atom (UA) molecular dynamics (MD) simulations were employed to elucidate the variations in crystalline structure, phase transition temperatures, and uniaxial tensile deformation among polyethylene (PE) with randomly oriented and flow-induced crystallization (FIC). The results showed that crystallization occurs in areas with low potential energy. For the FIC process, the entanglement parameter and interplanar spacing was less than for randomly oriented crystallization, and the crystallinity was higher. The relationship between the deformation and the crystallinity of PE with randomly oriented crystallization was expressed, which indicates that the crystalline structure promoted elongation at break of PE in tensile deformation. As PE was oriented to crystallize during the FIC process, the polymer stiffness is positively correlated with the deformation ratio of the PE model, so crystal conformation systems with higher deformation ratios produce higher ultimate stresses in tensile loading. From the visualization results, the crystalline phase was stable and does not easily transform into an amorphous phase during tensile loading. Additional results show that the fracture region of PE at tensile fracture tends to develop in the amorphous phase under tensile loading. Energy analysis showed that the elastic and yield regions were mainly dominated by intra-chain bonds, angles, and dihedral motion of PE, whereas interchain nonbonded interactions mainly dominated strain-hardening regions.

Solvent Isotherms and Structural Transitions in Nanoparticle Superlattice Assembly.

We introduce a Molecular Theory for Compressible Fluids (MOLT-CF) that enables us to compute free energies and other thermodynamic functions for nanoparticle superlattices with any solvent content, including the dry limit. Quantitative agreement is observed between MOLT-CF and united-atom molecular dynamics simulations performed to assess the reliability and precision of the theory. Among other predictions, MOLT-CF shows that the amount of solvent within the superlattice decreases approximately linearly with its vapor pressure and that in the late stages of drying, solvent-filled voids form at lattice interstitials. Applied to single-component superlattices, MOLT-CF predicts fcc-to-bcc Bain transitions for decreasing vapor pressure and for increasing ligand length, both in agreement with experimental results. We explore the stability of other single-component phases and show that the C14 Frank-Kasper phase, which has been reported in experiments, is not a global free-energy minimum. Implications for precise assembly and prediction of multicomponent nanoparticle systems are discussed.

Chain-Level Analysis of Reinforced Polyethylene through Stretch-Induced Crystallization.

Herein, we propose a large-scale simulation approach to perform the stretch-induced crystallization of entangled polyethylene (PE) melts. Sufficiently long (1000 ns) united-atom molecular dynamics (UAMD) simulations for 16000 chains of 1000 consecutive CH2 united-atom particles under periodic boundary conditions were performed to achieve the crystallinity observed in experiments. Before the isothermal crystallization process, we applied uniaxial stretching as pre-elongation to the embedded strain memory on the entangled PE melts. We confirmed significant differences in the morphologies of crystal domains and scattering patterns for pre-elongation ratios of 400% and 800%. The obtained scattering patterns were consistent with the experimental results. Uniaxial stretching MD simulations revealed that the elastic modulus at 800% pre-elongation was stronger than that at 400% pre-elongation. From this observation, we can derive the structure-property relationship, wherein the magnitude of the pre-elongation governs the crystal domain structures and mechanical properties.

Geometry-based cross-linking algorithm for modeling resorcinol resins through united-atom molecular dynamics simulations

The addition-condensation polymerization (ACP) of resorcinol with formaldehyde and the electrochemical polymerization (ECP) of resorcinol were desirable to improve the performances of resins. To achieve computational design, a new geometry-based cross-linking modeling algorithm for three-dimensional (3D) cross-linked network structures of resorcinol resins was developed for molecular dynamics (MD) simulations using a united-atom model. The ACP and ECP of resorcinol were successfully modeled using one algorithm by changing the parameters of the reaction rate constants of methylene, ether, and biphenyl bond formations. Furthermore, reaction judgment was performed under a reaction probability function comprising the Gaussian functions based on the interatomic distance of the reaction candidate atom pairs and interior angles regarding the spatial arrangement of two resorcinol rings. This geometry-based cross-linking algorithm successfully generated strainless 3D cross-linked network structures of the ACP and ECP resorcinol resins without the formation of highly bent unstable structures, such as U-shaped biphenyls. The MD simulation results indicated that the cross-linking of the ACP resin comprising methylene linkages proceeded with a network structure formation mechanism similar to that of phenolic resins, where the cross-linked network structure was determined at the gel point and the reactions after the gel point were to fix and freeze the network structure. For the ECP resins comprising ether and biphenyl linkages, the molar ratio of ether to biphenyl bonds affected the elastic property of the resins, and the incorporation of rigid biphenyl structures into ether-linkage networks increased the elastic modulus. Moreover, an increase in rigidity was observed as a decrease in the Poisson's ratio.

Aspirin-Induced Ordering and Faster Dynamics of a Cationic Bilayer for Drug Encapsulation.

The lipid dynamics and phase play decisive roles in drug encapsulation and delivery to the intracellular target. Thus, understanding the dynamic and structural alterations of membranes induced by drugs is essential for targeted delivery. To this end, united-atom molecular dynamics simulations of a model bilayer, dioctadecyldimethylammonium bromide (DODAB), are performed in the absence and presence of the usual nonsteroidal anti-inflammatory drug (NSAID), aspirin, at 298, 310, and 345 K. At 298 and 310 K, the bilayers are in the interdigitated two-dimensional square phases, which become rugged in the presence of aspirin, as evident from height fluctuations. At 345 K, the bilayer is in the fluid phase in both the absence and presence of aspirin. Aspirin is preferentially located near the oppositely charged headgroup and creates void space, which leads to an increase in the interdigitation and order parameters. Although the center of mass of lipids experiences structural arrest, they reach the diffusive regime faster and have higher lateral diffusion constants in the presence of aspirin. Results are found to be consistent with recent quasi-elastic neutron scattering studies that reveal that aspirin acts as a plasticizer and enhances lateral diffusion of lipids in both ordered and fluid phases. Different relaxation time scales of the bonds along the alkyl tails of DODAB due to the multitude of lipid motions become faster upon the addition of aspirin. Our results show that aspirin insertion is most favorable at physiological temperature. Thus, the ordered, more stable, and faster DODAB bilayer can be a potential drug carrier for the protected encapsulation of aspirin, followed by targeted and controlled drug release with antibacterial activity in the future.

Extension of the TraPPE Force Field for Battery Electrolyte Solvents.

Optimizing electrolyte formulations is key to improving performance of Li-/Na-ion batteries, where transport properties (diffusion coefficient, viscosity) and permittivity need to be predicted as functions of temperature, salt concentration and solvent composition. More efficient and reliable simulation models are urgently needed, owing to the high cost of experimental methods and the lack of united-atom molecular dynamics force fields validated for electrolyte solvents. Here the computationally efficient TraPPE united-atom force field is extended to be compatible with carbonate solvents, optimizing the charges and dihedral potential. Computing the properties of electrolyte solvents, ethylene carbonate (EC), propylene carbonate (PC), dimethyl carbonate (DMC), diethyl carbonate (DEC), and dimethoxyethane (DME), we observe that the average absolute errors in the density, self-diffusion coefficient, permittivity, viscosity, and surface tension are approximately 15% of the corresponding experimental values. Results compare favorably to all-atom CHARMM and OPLS-AA force fields, offering computational performance improvement of at least 80%. We further use TraPPE to predict the structure and properties of LiPF6 salt in these solvents and their mixtures. EC and PC form complete solvation shells around Li+ ions, while the salt in DMC forms chain-like structures. In the poorest solvent, DME, LiPF6 forms globular clusters despite DME's higher permittivity than DMC.

Molecular Dynamics of Topological Barriers on the Crystallization Behavior of Ring Polyethylene Melts with Trefoil Knots

Topological barriers in ring polyethylene (PE) melts of trefoil knots inhibit crystallization due to self-entanglement, as confirmed by united atom molecular dynamics (UAMD) simulations. In this study, we clarified the decrease in the topological barriers of self-entangled knots with increasing polymer chain length (N) and the localization of the knotted segments in the noncrystallized region. In the UAMD simulations, isothermal crystallization processes were performed at T = 300 K for the trefoil knots using a crystallization time tIC = 200 ns. Here, the trefoil knot gives the simplest nontrivial topology with nonzero crossing number. Crystallization was not observed in trefoil PE knots for N ≤ 120; however, crystallization did take place in the ring PE melt of the trivial knot with trivial topology and zero minimal crossing number. For N = 140, suppression of the growth of a crystalline phase (i.e., the polycrystalline phase) was observed in the trefoil PE melts, whereas such suppression was not detected in the trivial PE melts. In contrast, no significant differences in the crystallization behaviors of the trefoil and trivial PE melts were observed at N = 200. These results indicated that the topological barriers decreased with increasing N. Furthermore, to investigate the relationship between the chain conformation and degree of local crystallization, we developed a new mathematical method for searching the knotted segment of a trefoil knot in a crystallized trefoil PE melt. We found that trefoil knots with large subloops (“large-leaves”) exhibited localization of the knotted segment. In addition, the large leaves of the localized knots dominated in the crystallized region, and the knotted segments of the localized knots were located mainly in the noncrystallized region.

Molecular Insights into the Wall Slip Behavior of Pseudoplastic Polymer Melt in Nanochannels during Micro Injection Molding

Wall slip directly affects the molding quality of plastic parts by influencing the stability of the filling flow field during micro injection molding. The accurate modeling of wall slip in nanochannels has been a great challenge for pseudoplastic polymer melts. Here, an effective modeling method for polymer melt flow in nanochannels based on united-atom molecular dynamics simulations is presented. The effects of driving forces and wall–fluid interactions on the behavior of polyethylene melt under Poiseuille flow conditions were investigated by characterizing the slip velocity, dynamics information of the flow process, and spatial configuration parameters of molecular chains. The results indicated that the united-atom molecular dynamics model could better describe the pseudoplastic behavior in nanochannels than the commonly used finitely extensible nonlinear elastic (FENE) model. It was found that the slip velocity could be increased with increasing driving force and show completely opposite variation trends under different orders of magnitude of the wall–fluid interactions. The influence mechanism was interpreted by the density distribution and molecular chain structure parameters, including disentanglement and orientation, which also coincides with the change in the radius of gyration.

Polymer-Metal Interfacial Friction Characteristics under Ultrasonic Plasticizing Conditions: A United-Atom Molecular Dynamics Study.

Understanding the properties of polymer–metal interfacial friction is critical for accurate prototype design and process control in polymer-based advanced manufacturing. The transient polymer–metal interfacial friction characteristics are investigated using united-atom molecular dynamics in this study, which is under the boundary conditions of single sliding friction (SSF) and reciprocating sliding friction (RSF). It reflects the polymer–metal interaction under the conditions of initial compaction and ultrasonic vibration, so that the heat generation mechanism of ultrasonic plasticization microinjection molding (UPMIM) is explored. The contact mechanics, polymer segment rearrangement, and frictional energy transfer features of polymer–metal interface friction are investigated. The results reveal that, in both SSF and RSF modes, the sliding rate has a considerable impact on the dynamic response of the interfacial friction force, where the amplitude has a response time of about 0.6 ns to the friction. The high frequency movement of the polymer segment caused by dynamic interfacial friction may result in the formation of a new coupled interface. Frictional energy transfer is mainly characterized by dihedral and kinetic energy transitions in polymer chains. Our findings also show that the ultrasonic amplitude has a greater impact on polymer–metal interfacial friction heating than the frequency, as much as it does under ultrasonic plasticizing circumstances on the homogeneous polymer–polymer interface. Even if there are differences in thermophysical properties at the heterointerface, transient heating will still cause heat accumulation at the interface with a temperature difference of around 35 K.

Self-assembly of a CTAB surfactant on gold nanoparticles: a united-atom molecular dynamics study.

Self-assembly of a cetyltrimethyl ammonium bromide (CTAB) surfactant on gold nanoparticles (AuNPs) is studied using united-atom molecular dynamics (MD) simulations. For AuNPs in the size range of 1-3 nm, CTAB self-assembles such that the tail groups adsorb on the AuNP surface while the ionic head group is exposed to water, giving a net negative charge to the AuNPs. Near the AuNP surface, water molecules are depleted. The fraction of adsorbed CTAB molecules increased with AuNP size, while packing density decreased with size. Binding free energy also increased with AuNP size. The microscopic structural aspects of CTAB on AuNP and water-AuNP correlations are obtained from radial distribution functions. Contrary to the bilayer model proposed in the literature, the present simulations show the formation of a monolayer at CTAB concentrations equivalent to AuNP synthesis conditions. Even immobilizing bromide ions on the AuNP surface did not facilitate bilayer formation. Our simulation studies show that for very small nanoparticles, bilayer formation is unfavorable and instead a single monolayer of CTAB is formed around AuNPs.

Diffusing Diffusivityin Dynamics of Unentangled Polymer Melts

AbstractThe exact results for Rouse chain dynamics in the crowded environment modeled bydiffusing diffusivity(N. Ahamad and P. Debnath,Phys. A2020,549, 124335) in explaining polymer melt dynamics is explored. Theory for mode accounts for anomalous and non‐Gaussian diffusion in the center of mass (c.m.) and monomer dynamics of united atom molecular dynamics simulation trajectories of unentangled polyethylene melts, with excellent agreement. Accurate estimates of scaling relations for c.m. and monomer mean square displacement with time interval are obtained. The corresponding c.m. and monomer diffusion coefficients as a function of confirmdiffusing diffusivityin polymer melts. It is shown shown that the dependent parameters of the modified Rouse model expressed in terms of all modes are reducible to an identical set of per mode parameter values on application to real data. Analysis of velocity autocorrelation functions indicates that the theory is tested on simulation trajectories of polymer melts with friction. The theory estimates for additional power‐law exponents in the exponential of displacement distributions agree with the data. The results show fairly convincingly that the Rouse model withdiffusing diffusivitymay find scope as an alternate theoretical formalism for polymeric liquids.

United-Atom Molecular Dynamics Study of the Mechanical and Thermomechanical Properties of an Industrial Epoxy.

Epoxy resins are the most commonly used adhesives in industry due to their versatility, low cost, low toxicity, low shrinkage, high strength, resistance to moisture, and effective electrical resistance. These diverse properties can be tailored based on the chemical structure of the curing agent and the conditions of the curing process. Molecular simulations of epoxy resins have gained attention in recent years as a means to navigate the vast choice of chemical agents and conditions that will give the required properties of the resin. This work examines the statistical uncertainty in predicting thermodynamic and mechanical properties of an industrial epoxy resin using united atom molecular dynamics simulation. The results are compared with experimental measurements of the elastic modulus, Poisson’s ratio, and the glass transition temperature obtained at different temperatures and degrees of curing. The decreasing trend of the elastic modulus with increasing temperature is accurately captured by the simulated model, though the uncertainty in the calculated average is large. The glass transition temperature is expectedly overpredicted due to the high rates accessible to molecular simulations. We find that Poisson’s ratio is particularly sensitive to sample anisotropy as well as the method of evaluation, which explains the lack of consistent trends previously observed with molecular simulation at different degrees of crosslinking and temperatures.

Molecular modeling prediction of albumin-based nanoparticles and experimental preparation, characterization, and in-vitro release kinetics of prednisolone from the nanoparticles

Herein, ethanol's effect on the structure and dynamics of bovine serum albumin (BSA) and the nanoparticle formation was studied using united-atom and coarse-grained molecular dynamics (CG-MD) simulations. The results indicated that the BSA conformation remains stable both in pure water and ethanol/water environment. Molecular docking showed that ethanol-induced conformation changes do not reduce the drug loading. In the experimental approach, the prednisolone-loaded bovine serum albumin nanoparticles (PD-BSA NPs) were prepared using a desolvation technique. The nanoparticles were evaluated for nanocarrier production yield, particle size, shape, and surface morphology. The prepared BSA-NPs were then analyzed for their PD loading capacity, the adsorption profile, and in vitro release behavior. Our results showed the formation of spherical BSA-NPs of 200 nm average diameter and negative surface charge with a yield of 98%. The equilibrium isotherms of PD to BSA fitted to various models showed the best fit for the Langmuir model (R2 = 0.999). The kinetic data for prednisolone release from the BSA-NPs was slow (about 68% of the drug was released within 30 h) and followed the Gallagher-Corrigan equation (with R2 = 0.9957), which demonstrated the mechanism of Fickian diffusion and BSA-NPs matrix bulk erosion.

Spectroscopic, molecular dynamics simulation and biological studies of Flavin MonoNucleotide and Flavin Adenine Dinucleotide in biomimetic systems.

The present study describes a comprehensive investigation of the spectroscopic characteristics, stability and in vitro antioxidant and cytotoxic properties of the Flavin MonoNucleotide (FMN) and Flavin Adenine Dinucleotide (FAD) in Dextran70 (Dx70) and Dx70/phospatidylcholine (PC) biomimetic systems by means of the UV-Vis absorption, fluorescence spectroscopy, chemiluminescence and Neutral Red assay. The affinity of FMN, FAD and the precursor riboflavin (RF) to an unsaturated phospholipid bilayer model as well as the location of the probes within the lipid bilayer were assessed from united-atom molecular dynamics simulations carried out on an unsaturated phospholipid bilayer model system, and the theoretical and experimental characterization of the two probes within biomembranes was complemented with the light microscopy survey of the cell morphology of L929 fibroblast cells cultivated in the presence of various dosage of FAD/FMN. In lipid bilayers, FMN/FAD resulted in a noticeable improvement of the antioxidant activity (the scavenging of reactive oxygen species up to 40%) and a significant effect on cellular viability in the L929 fibroblast cells. The results are important in the oxidative stress process concerning the redox reactions of flavins in humans as well as in further studies on different systems belonging to the category of flavoenzymes/flavoproteins, required for cellular respiration.

Effect of Flow-Induced Nematic Order on Polyethylene Crystal Nucleation

We perform united atom molecular dynamics (MD) simulations to quantify the role of flow-induced nematic order in polyethylene (PE) crystal nucleation. Blends of periodic stretched and nonperiodic u...

Progressive Molecular Rearrangement and Heat Generation of Amorphous Polyethene Under Sliding Friction: Insight from the United-Atom Molecular Dynamics Simulations.

Frictional heat has been widely used in various polymer-based advanced manufacturing. The fundamental understanding of the thermodynamics of the interfacial friction of polymer bulk materials can help to avoid compromising the process controllability. In this work, we have performed united-atom molecular dynamics (MD) simulations to reveal the interfacial friction heating mechanism of amorphous polyethene (PE) in both the single sliding friction (SSF) and reciprocating sliding friction (RSF) modes. Different from the traditional view that the plastic deformation was the primary source of heat generation, the RSF process with no apparent plastic deformation in this work shows a better heat generation performance than SSF, where plastic deformation dominated the friction process. Our analysis uncovers that the mechanism of the interfacial friction heating enhancement in RSF can be attributed to the concentrated high-frequency chain motion related to molecular rearrangement, which is not clearly related to the deformation degree.

Surface anchoring behavior of 5CB liquid crystal confined between iron surfaces: A molecular dynamics study

To examine the anchoring behavior of 4-n-pentyl-4′-cyano biphenyl (5CB) liquid crystal (LC) on iron surfaces, united-atom molecular dynamics simulations were performed with a ~12 nm 5CB film composed of 1000 molecules under confinement between both the atomically-flat surfaces and sinusoidal grooved surfaces. The order parameter of 5CB is enhanced by the grooved surfaces, but diminished by the flat one. In both cases, 5CB molecules away from surfaces tend to align parallel to surfaces and along a certain direction. However, for the 5CB near surfaces, the flat surface yields a random planar anchoring and the grooved surface induces a unidirectional planar anchoring. The diffusion slows down when 5CB is confined between surfaces and the slowing down is mainly concentrated near surfaces, making 5CB solid-like. For the 5CB away from surfaces, the flat surface slows down the diffusion, while the grooved surface accelerates the diffusion, especially along the groove (and the director n) direction. The results provide a full description of the iron-LC interactions at the nanoscale and are important for the understanding of LC behaviors anchoring on surfaces with different morphologies.

The electric properties of AOT reverse micelles by molecular dynamics simulations

Reverse micelles (RMs) are the main component of a reverse microemulsion. The ionic RMs of sodium and calcium bis(2-ethylhexyl)sulfosuccinate (AOTNa and AOT2Ca, respectively), and water clusters of different size in isooctane were simulated by the united-atom molecular dynamics method. The radial density profiles characterized the local structure. The local electric potential and the electric field were calculated to describe the electric layer (EL). The behavior of these functions differs principally from the related quantities in the classical electric double layer. The decrease in the size of RMs leads to a noticeable compression of the EL. The value of the local electric field near the surface of the RM increases significantly with the replacement of Na+ counterions by Ca2+. The mutual compensation of the contributions from water and ions calculated separately was revealed, which results in poor sensitivity of the electric properties of the RMs to salt addition. The mean-square dipole moment was calculated for all considered aggregates. It was shown that this quantity strongly depends on the aggregate size as could be expected due to its fluctuation nature. Comparison of the mean-square dipole moment value obtained by the atomistic simulation with the one obtained within the primitive model witnesses that the strong overestimation of the dielectric permittivity of confined water in the primitive model of the RM leads to a significant decrease in the value of the micellar mean-square dipole moment.

Single-chain folding of a quenched isotactic polypropylene chain through united atom molecular dynamics simulations

The single-chain folding of an isotactic polypropylene (iPP) chain through united atom (UA) molecular dynamics simulations under quenching was investigated using force fields (FFs) based on TraPPE-UA. We estimated the degree of local rigidity of the folded chain along iPP undergoing single-chain folding. To maintain the tacticity of iPP, we introduced improper torsional angle potentials and/or explicit hydrogen atoms bonded to backbone carbon atoms. In the simulation using modified TraPPE-UA FFs with added hydrogen atoms, folded structures were observed. In the cases using modified TraPPE-UA FFs with only improper torsional potentials, folding of the quenched iPP chain was not observed. Moreover, to clarify the folding behavior of the iPP chain, we studied the chirality of a single iPP chain and subsequently observed spontaneous chirality selection during the quenched folding process. We also examined the effect of the angle and torsional potentials of the added hydrogen on the folding behavior of a single iPP chain into local crystals. Therefore, we confirmed that the strength of the angle and torsional potentials contributed to the acceleration of the folding behavior.