United-atom Molecular Dynamics Simulations Research Articles

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.

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.

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.

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.

Bilayer compositional asymmetry influences the nanoscopic to macroscopic phase domain size transition

The eukaryotic plasma membrane (PM) exhibits lipid mixing heterogeneities known as lipid rafts. These lipid rafts, the result of liquid-liquid phase separation, can be modeled by coexisting liquid ordered (Lo) and liquid disordered (Ld) domains. Four-lipid component systems with a high-melting lipid, a nanodomain-inducing low-melting lipid, a macrodomain-inducing low-melting lipid, and cholesterol (chol) can give rise to domains of different sizes. These four-component systems have been characterized in experiments, yet there are few studies that model the asymmetric distribution of lipids actually found in the PM. We used molecular dynamics (MD) simulations to analyze the transition from nanoscopic to macroscopic domains in symmetric and in asymmetric model membranes. Using coarse-grained MD simulations, we found that asymmetry promotes macroscopic domain growth in a case where symmetric systems exhibit nanoscopic domains. Also, macroscopic domain formation in symmetric systems is highly dependent on registration of like phases in the cytoplasmic and exoplasmic leaflets. Using united-atom MD simulations, we found that symmetric Lo domains are only slightly more ordered than asymmetric Lo domains. We also found that large Lo domains in our asymmetric systems induce a slight chain ordering in the apposed cytoplasmic regions. The chol fractions of phase-separated Lo and Ld domains of the exoplasmic leaflet were unchanged whether the system was symmetric or asymmetric.

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.

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.

Investigation of the properties of nanographene in polymer nanocomposites through molecular simulations: dynamics and anisotropic Brownian motion.

The dynamical behavior of nanographene sheets dispersed in polymer matrices is investigated through united-atom molecular dynamics simulations. The Brownian motion of the sheet and the anisotropy in its translational and orientational diffusion are the topics of the current study. Different polymer matrices and pristine and functionalized graphene constitute various nanocomposite systems. Interactions between the nanographene flake and the matrix determine the dynamics of the systems. The dynamics is reduced in polyethylene oxide compared to polyethylene matrix, whereas carboxylated sheets move considerably slower than the pristine nanographene in any matrix. Diffusion is anisotropic for short times, while it becomes isotropic in the long time limit. The in-plane motion of the nanographene sheet is faster than the out-of-plane component, in agreement with the diffusion of perfectly oblate ellipsoids. In functionalized graphene, the anisotropy is suppressed. By exploring the temperature effect on both the nanographene sheet and polymer close to the surface, indications for coupling in the motion of the two components are revealed. The strong effect of edge functional groups on the dynamics can be used as a way to control the Brownian motion of nanographene sheets in polymer nanocomposites and consequently tailor the properties of the materials.

Structure formation of a quenched single polyethylene chain with different force fields in united atom molecular dynamics simulations

The differences in the structure formations of a single polyethylene (PE) chain in united atom molecular dynamics (UAMD) simulations under quenching was investigated with varying force fields (FFs) that included torsional potential. We estimated the crystallinity of the folded structures undergoing local crystallization of the single PE chain. In simulations with DREIDING FF, highly folded structures were observed with fast quenching at the rate of 50 K/ns. From the viewpoint of crystallinity, we clarified that it was easy to achieve folding of the PE chains into local crystals with DREIDING FFs. With recent commonly used general FFs such as OPLS-UA and TraPPE-UA, highly folded structures were observed by quenching at the rate of 1 K/5 ns. In the present paper, we examine the Rigby–Roe (RR) FF optimized by Theodorou and coworkers and Paul–Yoon–Smith (PYS) FF optimized by Rutledge and coworkers. With the RR-Theodorou and PYS-Rutledge FFs, crystallization was observed with quenching at 1 K/ns and 1 K/5 ns, respectively. Consequently, it was relatively easier to achieve folding with the RR-Theodorou FF than with the PYS-Rutledge, OPLS-UA, and TraPPE-UA FFs.

Potential of mean force for two nanocrystals: Core geometry and size, hydrocarbon unsaturation, and universality with respect to the force field.

We present a detailed analysis of the interaction between two nanocrystals capped with ligands consisting of hydrocarbon chains by united atom molecular dynamics simulations. We analyze large cores (up to 10 nm in diameter) and ligands with unsaturated carbon bonds (oleic acid) and we investigate the accuracy of the computed potential of mean force by comparing different force fields. We also analyze the vortices that determine the bonding, including the case of asymmetric nanocrystals, and discuss effects related to the intrinsic anisotropy of the core. Overall our results are in agreement with the predictions of the recently proposed orbifold topological model.

Investigation of Dynamical Heterogeneities in Polymer Melts

In this paper, dynamical heterogeneities are characterized both at the monomer and centre-of-mass level, in polymer melts well above their glass transition temperature, responsible for anomalous dynamics in these systems. Microscopic analysis of united atom molecular dynamics simulations of unentangled polyethylene melts suggests a molecular mechanism for the observed heterogeneous dynamics based on local density fluctuations about a tagged polymer. These local density fluctuations are related to variations in entropy in a small volume about a polymer in the melt, which result in initial connections of the dynamical heterogeneities to entropy.

Capping Ligand Vortices as “Atomic Orbitals” in Nanocrystal Self-Assembly

We present a detailed analysis of the interaction between two nanocrystals capped with ligands consisting of hydrocarbon chains by united atom molecular dynamics simulations. We show that the bonding of two nanocrystals is characterized by ligand textures in the form of vortices. These results are generalized to nanocrystals of different types (differing core and ligand sizes) where the structure of the vortices depends on the softness asymmetry. We provide rigorous calculations for the binding free energy, show that these energies are independent of the chemical composition of the cores, and derive analytical formulas for the equilibrium separation. We discuss the implications of our results for the self-assembly of single-component and binary nanoparticle superlattices. Overall, our results show that the structure of the ligands completely determines the bonding of nanocrystals, fully supporting the predictions of the recently proposed Orbifold topological model.

Short-Time Dynamics Reveals Tg Suppression in Simulated Polystyrene Thin Films

Suppression of the glass transition temperature, Tg, in polymer thin films is of great practical importance and theoretical significance. It is widely believed that such Tg suppression results from enhanced segmental mobility at the free surface. To investigate these effects, we carry out united-atom molecular dynamics simulations on free-standing polystyrene thin films. Care has been taken to ensure consistent behavior between thin films and the bulk. The dilatometric Tg inferred from the density versus temperature shows substantial reduction in thin films compared to the bulk even at high cooling rates. Furthermore, we find that dynamical Tg shifts, obtained by collapsing temperature-dependent short-time dynamical properties onto a master curve, vary with film thickness just like the dilatometric Tg. We apply the same data collapse procedure to dynamics of segments within a given distance from the free surface to obtain the local Tg(z), which reveals a mobile surface layer of about 4 nm.

Effects of temperature, pH and counterions on the stability of peptide amphiphile nanofiber structures

Peptide amphiphiles are a class of self-assembling molecules that are widely used to form bioactive nanostructures for various applications in bionanomedicine. However, peptide molecules can exhibit distinct behaviors under different conditions, suggesting that environmental variables such as temperature, pH, electrolytes and the presence of biological factors may greatly affect the self-assembly process. In this work, we used united-atom molecular dynamics simulations to understand the effects of three counterions (Na+, Ca2+ at pH 7 and Cl− at pH 2) and temperature change on the stability of the lauryl-VVAGERGD peptide amphiphile self-assembly. This molecule contains a bioactive RGD peptide sequence and has been shown to support cellular adhesion and proliferation in vitro. A 19-layered peptide nanostructure, containing 12 peptide amphiphile molecules per layer, was previously shown to exhibit optimal stability and it was used as the model nanofiber system. Peptide backbone stability was studied under increasing temperatures (300–358 K) using the number of hydrogen bonds and root-mean-square deviations of nanofiber size. At higher temperatures, fiber disintegration was observed to be dependent on the type of counter-ion used for nanofiber formation. Interestingly, rapid heating to higher temperatures could sometimes reestablish the integrity of the nanofiber backbone, possibly by allowing the system to bypass an energy barrier and assuming a more thermodynamically stable configuration. As counterion identity was observed to exhibit remarkable effects on the thermal stability of peptide nanofibers, we suggest that these behaviors should be considered while developing new materials for potential applications.

A nonlinear continuum model of van der Waals interactions in crystalline polymers

A nonlinear continuum model of van der Waals interactions is established to relate the size-dependent nonlinear properties of crystalline polyethylene. The explicit formulas are derived from the Lennard-Jones potential function for the van der Waals force between any two polymer chains. The present results are in reasonable agreement with those from present united-atom molecular dynamics simulations. This work is a new effort to establish nonlinear analytical models of molecular mechanics for crystalline polymers, and it should be helpful to provide an efficient route for mechanical characterization of crystalline polymers and related materials.

Molecular dynamics simulations of self-assembled peptide amphiphile based cylindrical nanofibers

We carried out united-atom molecular dynamics simulations to understand the structural properties of peptide amphiphile (PA)-based cylindrical nanofibers and the factors that play a role in the “Self-Assembly” process on some specific nanofibers.

A comparative molecular dynamics study of crystalline, paracrystalline and amorphous states of cellulose

The quintessential form of cellulose in wood consists of microfibrils that have high aspect ratio crystalline domains embedded within an amorphous cellulose domain. In this study, we apply united-atom molecular dynamics simulations to quantify changes in different morphologies of cellulose. We compare the structure of crystalline cellulose with paracrystalline and amorphous phases that are both obtained by high temperature equilibration followed by quenching at room temperature. Our study reveals that the paracrystalline phase may be an intermediate, kinetically arrested phase formed upon amorphisation of crystalline cellulose. The quenched structures yield isotropic amorphous polymer domains consistent with experimental results, thereby validating a new computational protocol for achieving amorphous cellulose structure. The non-crystalline cellulose compared to crystalline structure is characterized by a dramatic decrease in elastic modulus, thermal expansion coefficient, bond energies, and number of hydrogen bonds. Analysis of the lattice parameters shows that Iβ cellulose undergoes a phase transition into high-temperature phase in the range of 450–550 K. The mechanisms of the phase transition elucidated here present an atomistic view of the temperature dependent dynamic structure and mechanical properties of cellulose. The paracrystalline state of cellulose exhibits intermediate mechanical properties, between crystalline and amorphous phases, that can be assigned to the physical properties of the interphase regions between crystalline and amorphous cellulose in wood microfibrils. Our results suggest an atomistic structural view of amorphous cellulose which is consistent with experimental data available up to date and provide a basis for future multi-scale models for wood microfibrils and all-cellulose nanocomposites.

Molecular Conformation and Bilayer Pores in a Nonionic Surfactant Lamellar Phase Studied with 1H–13C Solid-State NMR and Molecular Dynamics Simulations

The structure of the lamellar phase of aqueous pentaethylene glycol mono-n-dodecyl ether (C12E5) surfactant at various temperatures and molar fractions is studied by using united atom molecular dynamics simulations and nuclear magnetic resonance measurements. Namely, the simulation model is used to interpret the magnitude and temperature dependence of experimental C-H order parameter profiles in terms of the molecular conformation and orientation. Our simulations suggest that the low order parameters that are generally measured in poly(ethylene oxide) surfactant bilayers are due to the presence of bilayer pores throughout the entire lamellar phase region.