Molecular dynamics simulation of a flexible polymer network in a liquid crystalline solvent; dynamical properties

Molecular dynamics simulation was performed for the systems consisting of a flexible regular tetrafunctional polymer network and a low molecular liquid crystal (LC) solvent. The LC solvent comprises of anisotropic rod-like semiflexible linear molecules composed of beads bonded by a FENE potential. Rigidity was induced by a bending potential, proportional to the cosine of the angle between neighbouring valence bonds. All interactions between non-bonded beads are described by the repulsive part of the Lennard–Jones potential. For comparison the simulations of the system of flexible polymer chains in a low molecular LC solvent and a system of pure low molecular LC solvent were also carried out. The influence of the network and linear chain polymer on the translational and rotational mobility of low molecular LC solvent was studied. The influence of the LC solvent ordering on the local translational mobility of the polymer chains was also observed.     

Exploration of the transition temperatures and crystal structure of highly crystalline poly(1,3-cyclohexadiene): An experimental and computational investigation

Experimental determination of transition temperatures for highly crystalline polymers such as poly-1,3-cyclohexadiene (PCHD) can be difficult due to reduced solubility and thermalization processes which occur during data acquisition. In order to facilitate further understanding of these processes for PCHD, density functional theory (DFT) and molecular dynamics (MD) were used in conjunction with differential scanning calorimetry (DSC) and powder X-ray diffraction (XRD) to explore the oligomer microstructures, the crystal structure, and the temperature dependence of the specific volume (1/ρ). DFT geometry minimizations on isolated oligomers were used to identify the lowest energy confirmer; revealing that alternating R,R and S,S chiral bonds between monomer units afford the lowest energy structure. MD simulations of crystalline PCHD were constructed so as to replicate the experimental XRD pattern of crystalline PCHD, with the best fit producing a monoclinic crystal structure. The temperature dependence of the specific volume derived from MD simulations provided insight into the glass/vitrification (T_g) and melting (T_m) transition temperatures. Comparison of the simulation transition temperatures with differential scanning calorimetry data of PCHD polymerized with Ni(acac)₂/MAO shows good agreement and solidifies the fidelity of the newly defined PCHD crystalline structure.     

Structural Characterization of Poly-l-lactic Acid (P(L)LA) and Poly(glycolic acid)(PGA) Oligomers

Structural characterization of poly-l-lactic acid (P(L)LA) and poly(glycolic acid) (PGA) oligomers containing three units was carried out with an atomistic approach. Oligomer structures were first optimized through quantum chemical calculations, using density functional theory (DFT); rotational barriers concerning dihedral angles along the chain were then investigated. Diffusion coefficients of l-lactic acid and glycolic acid in pure water were estimated through molecular dynamic (MD) simulations. Monomer structures were obtained with quantum chemical computation in implicit water using DFT method; atomic charges were fitted with Restrained Electrostatic Potentials (RESP) formalism, starting from electrostatic potentials calculated with quantum chemistry. MD simulations were carried out in explicit water, in order to take into account solvent presence.     

PP/PA11共混物微、介观形态的分子模拟

采用分子动力学（MD）和介观动力学（MesoDyn）模拟方法研究了不同质量含量（10/90、30/70、50/50、70/30和90/10）PP/PA11共混物的相容性和介观形态结构。通过对MD模拟得到的Flory-Huggins相互作用参数（χ）和PP-PP、PA11-PA11及PP-PA11分子间C-C原子对径向分布函数的研究表明：当PP与PA含量为90/10时两者具有一定的相容性,而其它比例的相容性则较差。为了进一步研究共混物的介观形态结构,采用MesoDyn模拟方法在介观尺度对共混体系的介观形貌进行了研究,将通过MD模拟计算的分子间相互作用参数和其他结构参数（重复单元个数、聚合度和极限特征比等）转化为MesoDyn模拟的输入参数,实现了微、介观多尺度模拟的连接。     

Study on the gas permeabilities in styrene-butadiene rubber by molecular dynamics simulation

In this research, molecular dynamics (MD)simulations were used to study the transport properties of small gas molecules in the butadiene-styrene copolymer(SBR). The condensed-phase optimized molecular potentials for atomistic simulation studies (COMPASS) force field was applied. The diffusion coefficients were obtained from MD (NVT ensemble) and the relationship between gas permeability; the chemical structure and free volume of butadiene-styrene copolymer were investigated. The results indicated that the diffusion coefficient of oxygen declined with increasing styrene content. The fraction of free volume (FFV) in butadiene-styrene copolymer was calculated. It was concluded that diffusion coefficient increased as the FFV increases, which is in accordance with the analysis of the small molecular hop through the free volume in polymer matrix. Subsequently, the glass transition temperatures of these copolymers were calculated by MD. The result showed that the glass transition temperature increased with increasing styrene content in polymer.     

Study on the gas permeabilities in styrene-butadiene rubber by molecular dynamics simulation

In this research, molecular dynamics (MD) simulations were used to study the transport properties of small gas molecules in the butadiene-styrene copolymer (SBR). The condensed-phase optimized molecular potentials for atomistic simulation studies (COMPASS) force field was applied. The diffusion coefficients were obtained from MD (NVT ensemble) and the relationship between gas permeability; the chemical structure and free volume of butadiene-styrene copolymer were investigated. The results indicated that the diffusion coefficient of oxygen declined with increasing styrene content. The fraction of free volume (FFV) in butadiene-styrene copolymer was calculated. It was concluded that diffusion coefficient increased as the FFV increases, which is in accordance with the analysis of the small molecular hop through the free volume in polymer matrix. Subsequently, the glass transition temperatures of these copolymers were calculated by MD. The result showed that the glass transition temperature increased with increasing styrene content in polymer.     

Pyrolysis of vulcanized styrene-butadiene rubber via ReaxFF molecular dynamics simulation

Styrene-butadiene rubber (SBR) is widely used in tires in the automotive segment and vulcanization using sulfur is a common process to enhance its mechanical properties. However, the addition of sulfur as the cross-linking agent usually results in impurities in pyrolysis products during rubber recycling, and thus the desulfurization during tire pyrolysis attracts much attention. In this work, the pyrolysis of vulcanized SBR is studied in detail with the help of ReaxFF molecular dynamics simulation. A series of crosslinked SBR models were built with different sulfur contents and densities. The following ReaxFF MD simulations were performed to show products distributions at different pyrolysis conditions. The simulation results show that sulfur products distribution is mainly controlled by sulfur contents and temperatures. The reaction mechanism is proposed based on the analysis of sulfur products conversion pathway, where most sulfur atoms are bonded with hydrocarbon radicals and the rest transfer to H₂S. High sulfur contents tend to the formation of elemental sulfur intermediate, and temperature increase facilitates the release of H₂S.     

The effect of chain interpenetration on an ordering process in the early stage of polymer crystal nucleation

In the present study, the degree of chain interpenetration was considered as a structural attribute of the entanglements in polymer chain system. Inter-chain radial distribution function (RDF) was used to perform this measurement. We applied this method to a model system, in which an ordering process in the early stage of polymer crystal nucleation at the atomistic level was simulated by means of molecular dynamics (MD). Initial chain structures possessed different degrees of interpenetration and underwent the ordering process at 400 K. Obtained results indicated that at the nanosecond scale the degree of interpenetration impedes the ordering process remarkably, which agrees with the experimental observation at laboratory time scale. Such behavior among chains indicates that at the atomistic level a creeping polymer chain is able to recognize if the neighbor group on the ‘tube’ is from the same chain or other chains. This recognition manifests that the reptation time of a chain would be influenced by the ‘tube’ composition or the degree of interpenetration. It also showed that the degree of interpenetration changes little during the ordering process, which means that the motion of the chain segments is mainly predominated by the ordering process rather than further adjusting the entanglement extent under the conditions simulated.     

Refinement of protein cores and protein-peptide interfaces using a potential scaling approach

Refinement of side chain conformations in protein model structures and at the interface of predicted protein-protein or protein-peptide complexes is an important step during protein structural modelling and docking. A common approach for side chain prediction is to assume a rigid protein main chain for both docking partners and search for an optimal set of side chain rotamers to optimize the steric fit. However, depending on the target-template similarity in the case of comparative protein modelling and on the accuracy of an initially docked complex, the main chain template structure is only an approximation of a realistic target main chain. An inaccurate rigid main chain conformation can in turn interfere with the prediction of side chain conformations. In the present study, a potential scaling approach (PS-MD) during a molecular dynamics (MD) simulation that also allows the inclusion of explicit solvent has been used to predict side chain conformations on semi-flexible protein main chains. The PS-MD method converges much faster to realistic protein-peptide interface structures or protein core structures than standard MD simulations. Depending on the accuracy of the protein main chain, it also gives significantly better results compared with the standard rotamer search method.     

Automatic coarse graining of polymers

Several recently proposed semi-automatic and fully-automatic coarse-graining schemes for polymer simulations are discussed. All these techniques derive effective potentials for multi-atom units or super-atoms from atomistic simulations. These include techniques relying on single chain simulations in vacuum and self-consistent optimizations from the melt like the simplex method and the inverted Boltzmann method. The focus is on matching the polymer structure on different scales. Several ways to obtain a time-scale for dynamic mapping are discussed additionally. Finally, similarities to other simulation areas where automatic optimization are applied as well are pointed out.     

Edge effects control helical wrapping of carbon nanotubes by polysaccharides

Carbon nanotubes (CNTs) wrapped by polysaccharide chains via noncovalent interactions have been shown to be soluble and dispersed in aqueous environments, and have several potential chemical and biomedical applications. The wrapping mechanism, in particular the role played by the end of the CNT, remains, however, unknown. In this work, a hybrid complex formed by an amylose (AMYL) chain and a single-walled carbon nanotube (SWNT) has been examined by means of atomistic molecular dynamics (MD) simulations to assess its propensity toward self-assembly, alongside its structural characteristics in water. To explore edge effects, the middle and end regions of the SWNT have been chosen as two initial wrapping sites, to which two relative orientations have been assigned, i.e. parallel and orthogonal. The present results prove that AMYL can wrap spontaneously around the tubular surface, starting from the end of the SWNT and driven by both favorable van der Waals attraction and hydrophobic interactions, and resulting in a perfectly compact, helical conformation stabilized by an interlaced hydrogen-bond network. Principal component analysis carried out over the MD trajectories reveals that stepwise burial of hydrophobic faces of pyranose rings controlled by hydrophobic interactions is a key step in the formation of the helix. Conversely, if wrapping proceeds from the middle of the SWNT, self-organization into a helical structure is not observed due to strong van der Waals attractions preventing the hydrophobic faces of the AMYL chain generating enough contacts with the tubular surface.     

A systematic procedure to build a relaxed dense-phase atomistic representation of a complex amorphous polymer using a coarse-grained modeling approach

A systematic procedure has been developed to construct a relaxed dense-phase atomistic structure of a complex amorphous polymer. The numerical procedure consists of (1) coarse graining the atomistic model of the polymer into a mesoscopic model based on an iterative algorithm for potential inversion from distribution functions of the atomistic model, (2) relaxation of the coarse-grained chain using a molecular dynamics scheme, and (3) recovery of the atomistic structure by reverse mapping based on the superposition of atomistic counterparts on the corresponding coarse-grained coordinates. These methods are demonstrated by their application to construct a relaxed, dense-phase model of poly(DTB succinate), which is an amorphous tyrosine-derived biodegradable polymer that is being developed for biomedical applications. Both static and dynamic properties from the coarse-grained and atomistic simulations are analyzed and compared. The coarse-grained model, which contains the essential features of the DTB succinate structure, successfully described both local and global structural properties of the atomistic chain. The effective speedup compared to the corresponding atomistic simulation is substantially above 10², thus enabling simulation times to reach well into the characteristic experimental regime. The computational approach for reversibly bridging between coarse-grained and atomistic models provides an efficient method to produce relaxed dense-phase all-atom molecular models of complex amorphous polymers that can subsequently be used to study and predict the atomistic-level behavior of the polymer under different environmental conditions in order to optimally design polymers for targeted applications.     

Molecular Insight into the Self-Assembly Process of Cellulose Iβ Microfibril

The self-assembly process of β-D-glucose oligomers on the surface of cellulose Iβ microfibril involves crystallization, and this process is analyzed herein, in terms of the length and flexibility of the oligomer chain, by means of molecular dynamics (MD) simulations. The characterization of this process involves the structural relaxation of the oligomer, the recognition of the cellulose I microfibril, and the formation of several hydrogen bonds (HBs). This process is monitored on the basis of the changes in non-bonded energies and the interaction with hydrophilic and hydrophobic crystal faces. The oligomer length is considered a parameter for capturing insight into the energy landscape and its stability in the bound form with the cellulose I microfibril. We notice that the oligomer–microfibril complexes are more stable by increasing the number of hydrogen bond interactions, which is consistent with a gain in electrostatic energy. Our studies highlight the interaction with hydrophilic crystal planes on the microfibril and the acceptor role of the flexible oligomers in HB formation. In addition, we study by MD simulation the interaction between a protofibril and the cellulose I microfibril in solution. In this case, the main interaction consists of the formation of hydrogen bonds between hydrophilic faces, and those HBs involve donor groups in the protofibril.     

A coarse-grained model for polylactide: glass transition temperature and conformational properties

In this article, we present a coarse-grained (CG) model of poly(lactic acid) (PLA) developed by the iterative Boltzmann inversion (IBI) method. The coarse-grained potential was derived by matching the structural probability distribution functions to those of reference atomistic simulation. The resulting coarse-grained potential was found to be temperature-dependent when trying to reproduce the thermal expansion behavior of PLA. To satisfactory reproduce this behavior, the potential needs to be modified by a temperature factor of (T/T ₀)^0.3; T ₀ = 327 K is the temperature at which the potential has been derived. The glass transition temperature (T _g) as predicted by the modified CG potential compared favorably with those from experiment and atomistic simulation. Chain conformational properties were also evaluated in terms of a chain length (N)-radius of gyration (R _g) relation and the persistence length. The model we develop was also noted to provide a considerable speed-up of computer time compared to its atomistic counterpart.     

氧气和一氧化碳在人血红蛋白迁移过程研究

为了揭示CO和O₂竞争性结合人血红蛋白血红素位点的机制及其与人血红蛋白结构转换之间的关系，本文采用全原子分子动力学模拟（MD）结合马尔科夫状态模型（MSMs）研究氧气（O₂）和一氧化碳（CO）分子从水溶液迁移进入人血红蛋白四聚体α链和β链的全过程。分子动力学模拟揭示了O₂和CO结合α链和β链的稳态结合位点和瞬态结合位点、迁移通道以及α链的结构变化。结果显示，分子模拟不仅仅能够再现全部实验中所观察到的离散Xe结合位点和分子扩散通道，而且揭示了实验中无法观测的瞬态结合位点和多重气体迁移途径。上述结果表明人血红蛋白因其结构柔性所形成的瞬态通道对于气体分子迁移过程的重要性。除此之外，利用MSM和过渡路径理论（TPT）构建了人血红蛋白α链结构变化与气体分子迁移之间的关系，阐释了血红蛋白中影响气体迁移的关键结构及其微观机制。     

Effect of chain architecture on the compression behavior of nanoscale polyethylene particles

Polymeric particles with controlled internal molecular architectures play an important role as constituents in many composite materials for a number of emerging applications. In this study, classical molecular dynamics techniques are employed to predict the effect of chain architecture on the compression behavior of nanoscale polyethylene particles subjected to simulated flat-punch testing. Cross-linked, branched, and linear polyethylene chain architectures are each studied in the simulations. Results indicate that chain architecture has a significant influence on the mechanical properties of polyethylene nanoparticles, with the network configuration exhibiting higher compressive strengths than the branched and linear architectures. These findings are verified with simulations of bulk polyethylene. The compressive stress versus strain profiles of particles show four distinct regimes, differing with that of experimental micron-sized particles. The results of this study indicate that the mechanical response of polyethylene nanoparticles can be custom-tailored for specific applications by changing the molecular architecture.     

Atomistic understanding of surface wear process of sodium silicate glass in dry versus humid environments

Understanding surface reactions of silicate glass under interfacial shear is critical as it can provide physical insights needed for rational design of more durable glasses. Here, we performed reactive molecular dynamics (MD) simulations with ReaxFF potentials to study the mechanochemical wear of sodium silicate glass rubbed with amorphous silica in the absence and presence of interfacial water molecules. The effect of water molecules on the shear-induced chemical reaction at the sliding interface was investigated. The dependence of wear on the number of interfacial water molecules in ReaxFF-MD simulations was in reasonable agreement with the experimental data. Confirming this, the ReaxFF-MD simulation was used to find further details of atomistic reaction dynamics that cannot be obtained from experimental investigations only. The simulation showed that the severe wear in the dry condition is due to the formation of interfacial Si_substrate–O–Si_{counter_surface} bond that convey the interfacial shear stress to the subsurface and the presence of interfacial water reduces the interfacial bridging bond formation. The leachable sodium ions facilitate surface reactions with water-producing hydroxyl groups and their key role in the hydrolysis reaction is discussed.     

Carnosine Inhibits Aβ42 Aggregation by Perturbing the H‐Bond Network in and around the Central Hydrophobic Cluster

Aggregation of the amyloid‐β peptide (Aβ) into fibrillar structures is a hallmark of Alzheimer's disease. Thus, preventing self‐assembly of the Aβ peptide is an attractive therapeutic strategy. Here, we used experimental techniques and atomistic simulations to investigate the influence of carnosine, a dipeptide naturally occurring in the brain, on Aβ aggregation. Scanning force microscopy, circular dichroism and thioflavin T fluorescence experiments showed that carnosine does not modify the conformational features of Aβ42 but nonetheless inhibits amyloid growth. Molecular dynamics (MD) simulations indicated that carnosine interacts transiently with monomeric Aβ42 by salt bridges with charged side chains, and van der Waals contacts with residues in and around the central hydrophobic cluster (¹⁷LVFFA²¹). NMR experiments on the nonaggregative fragment Aβ12–28 did not evidence specific intermolecular interactions between the peptide and carnosine, in agreement with MD simulations. However, a close inspection of the spectra revealed that carnosine interferes with the local propensity of the peptide to form backbone hydrogen bonds close to the central hydrophobic cluster (residues E22, S26 and N27). Finally, MD simulations of aggregation‐prone Aβ heptapeptide segments show that carnosine reduces the propensity to form intermolecular backbone hydrogen bonds in the region 18–24. Taken together, the experimental and simulation results (cumulative MD sampling of 0.2 ms) suggest that, despite the inability of carnosine to form stable contacts with Aβ, it might block the pathway toward toxic aggregates by perturbing the hydrogen bond network near residues with key roles in fibrillogenesis.     

Multiscale Genome Modeling for Predicting the Thermal Conductivity of Silicon Carbide Ceramics

Silicon carbide (SiC) ceramics have been widely used in industry due to its high thermal conductivity. Understanding the relations between the microstructure and the thermal conductivity of SiC ceramics is critical for improving the efficiency of heat removal in heat sink applications. In this paper, a multiscale model is proposed to predict the thermal conductivity of SiC ceramics by bridging atomistic simulations and continuum model via a materials genome model. Interatomic potentials are developed using ab initio calculations to achieve more accurate molecular dynamics (MD) simulations. Interfacial thermal conductivities with various additive compositions are predicted by nonequilibrium MD simulations. A homogenized materials genome model with the calculated interfacial thermal properties is used in a continuum model to predict the effective thermal conductivity of SiC ceramics. The effects of grain size, additive compositions, and temperature are also studied. The good agreement found between prediction results and experimental measurements validates the capabilities of the proposed multiscale genome model in understanding and improving the thermal transport characteristics of SiC ceramics.     

Atomistic simulations of the structure and thermodynamic properties of poly(1,2-vinyl-butadiene) surfaces

Computer simulations play an important role in the design of new polymers and in the prediction of the properties of existing polymers. Atomistic modeling of amorphous poly(1,2-vinyl butadiene) using molecular mechanics and molecular dynamics simulations was carried out in three-dimensionally periodic and effective two-dimensionally periodic condensed phases. Sets of sample structures of two different periodicity (box edge lengths of 23.982 and 30.042 Å) were generated in order to explore the structural and energetic aspects as a function of the simulation cell size. The calculated surface energy for poly(1,2-vinyl-butadiene) compares very well with the experimental value reported in literature. The equilibrium structure of the films shows an interior region of mass density reasonably close to the value in the bulk state and an outer surface layer of approximately 20 Å across which the density falls rapidly but smoothly to zero at the outer limit of the free surface. The overall characteristics of the atomistic simulation approach is found to be similar to those presented in previous investigations for flexible polymers. In order to create the surface from the bulk state, energetic changes as a result of changes in the states of torsions and bond angles are favored, and these are opposite to the changes in the energies originating from non-bonded interactions. The dominant molecular energetic contribution to the formation of the surface is from dispersion forces (van der Waals).