Pathway of orientational symmetry breaking in crystallization of short n-alkane droplets: A molecular dynamics study.

We carry out molecular dynamics simulations by using an all-atom model to study the nucleation and crystallization of n-alkane droplets under three-dimensional and quasi-two-dimensional conditions. We focus on the development of orientational order of chains from a random state to a neatly ordered one. Two new methods, the map of symmetry breaking and the information entropy of chain orientations, are introduced to characterize the emerge and remelting phenomena of a primary nucleus at the early stage of crystallization. Stepwise nucleation, as well as the surface induced nucleation, of large droplets is observed. We elucidate the kinetic process of the formation of a primary nucleus and the rearrangement of every single molecule involved in a primary nucleus. We found that density fluctuation and orientational preordering are coupled together and occur simultaneously in nucleation. Our results show the pathway of orientational symmetry breaking in the crystallization of n-alkane droplets that are heuristic for the deeper understanding of the crystallization in more complex molecules such as polymers.

Frozen topology: entanglements control nucleation and crystallization in polymers.

Polymer chains form lamellar structures during crystallization which display a memory of thermal history. Using molecular dynamics simulations and primitive path analysis, we show a direct dependence of both density and crystalline stem length on the local entanglement length. The slow relaxation of the entanglement state after a change of external conditions can directly explain the role of thermal history for polymer crystallization, in particular memory effects. The analysis of the local entanglement state can be used to predict the occurrence of nucleation events. Our results present a fresh insight of the nonequilibrium properties of polymer crystals which might be identified as "frozen topology" of polymer melts.

Accumulation of Hydrogen Bonds and van der Waals Interactions Determines Force Response between Two Parallel Cellulose Chains: Steered Molecular Dynamics Simulations.

We investigated the response forces between two parallel cellulose chains during the shearing and tearing processes by using steered molecular dynamics simulations. It was found that there are two logarithmic dependencies between response force and pulling speed in shearing processes but only one in tearing, according to Bell's equation by fitting the f-ln v curve. The mechanism is that there are 2-fold interactions determining the force response between two parallel cellulose chains resisting chain separation during a shearing process. Our results indicate that hydrogen bonds dominate the interchain interactions in the fast pull mode (FPM) for shearing, while van der Waals interactions dominate in the slow pull mode (SPM). For tearing, the one-by-one breaking of hydrogen bonds and van der Waals interactions plays a main role.

State Transitions and Crystalline Structures of Single Polyethylene Rings: MD Simulations.

This study investigates the structural changes of cyclic polyethylene (PE) single chains during cooling through molecular dynamics simulations. The influence of topological constraint on a ring is examined by comparing it with the results of its linear counterpart. A pseudo phase diagram of state transition for PE rings based on length and temperature is constructed, revealing a consistent chain-folding transition during cooling. The shape anisotropy of short crystallized cyclic chains exhibits oscillations with chain length, leading to a more pronounced odd-even effect in single cyclic chains compared with the linear ones. A honeycomb model is proposed to elucidate the odd-even effect of chain folding in crystalline structures of single linear and cyclic chains, and we discuss its potential to predict surface tension. Analyses of the tight folding model and the re-entry modes demonstrate that a cyclic chain possesses a shorter average crystalline stem length and a more compact folded structure than its linear counterpart. The findings highlight the impact of topological change on crystallization and the odd-even effect of chain length, providing valuable insights for understanding polymer crystallization with different topologies.

Ferroelectricity of ice nanotube forests grown in three-dimensional graphene: the electric field effect.

Generating diverse ferroelectric ice nanotubes (NTs) efficiently has always been challenging, but matters in nanomaterial synthesis and processing technology. In the present work, we propose a method of growing ice NT forests in a single cooling process. A three-dimensional (3D) graphene structure was selected to behave as a representative container in which a batch of (5, 0) ice NTs was formed simultaneously under the cooling process from molecular dynamics simulation. Other similar 3D graphene structures but with different hole configurations, like uniform triangle or both triangle and pentagon, were also tested, revealing that ice NTs with different tube indices, i.e. both (3, 0) and (5, 0), could also be formed at the same time. Intriguingly, the orientations of the dipole moments of the water molecules of an ice NT formed were independent of each other, making the net ferroelectricity of the whole system weakened or even cancelled. An electric field could help change the orientation of the water molecules of the already obtained ice NTs and even twist the tube to be a spiral (5, 1) one if it was applied during the cooling process, such that the net ferroelectricity was greatly improved. The underlying physical mechanism of all phase transition phenomena, including the improvement of the ferroelectricity under an electric field, were explored in depth from the phase transition curves and structural point of view. The obtained results are of significant application value for improving the preparation efficiency of nano-ferroelectric materials, which are prosperous in nano-devices.

State Transitions and Crystalline Structures of a Single Polyethylene Chain: MD Simulations.

The structures of a single polyethylene chain were investigated using all-atom molecular dynamics simulations with a series of cutoff distances. We found that a long single chain with a short cutoff distance undergoes coil, globule, and crystal states during a continuous cooling process. The globule state vanishes for short chains less than a certain length where there is large conformational fluctuation. A tight-folding model was applied to analyze the folded structures, and the re-entry modes show that a shorter chain prefers the nearest folding while a longer one prefers the second or third nearest folding. Our results show that a single polyethylene chain can exhibit condensed phenomena of state transitions, which could be heuristic for single-chain physics and polymer crystallization.

D-arginine Enhances the Effect of Alpha-Amylase on Disassembling Actinomyces viscosus Biofilm.

Peri-implantitis is the leading cause of dental implant failure, initially raised by biofilm accumulation on the implant surface. During the development of biofilm, Actinomyces viscosus (A. viscosus) plays a pivotal role in initial attachment as well as the bacterial coaggregation of multispecies pathogens. Hence, eliminating the A. viscosus-associated biofilm is fundamental for the regeneration of the lost bone around implants. Whereas clinical evidence indicated that antimicrobials and debridement did not show significant effects on the decontamination of biofilm on the implant surface. In this study, alpha-amylase was investigated for its effects on disassembling A. viscosus biofilm. Then, in order to substantially disperse biofilm under biosafety concentration, D-arginine was employed to appraise its enhancing effects on alpha-amylase. In addition, molecular dynamics simulations and molecular docking were conducted to elucidate the mechanism of D-arginine enhancing alpha-amylase. 0.1-0.5% alpha-amylase showed significant effects on disassembling A. viscosus biofilm, with definite cytotoxicity toward MC3T3-E1 cells meanwhile. Intriguingly, 8 mM D-arginine drastically enhanced the eradication of A. viscosus biofilm biomass by 0.01% alpha-amylase with biosafety in 30 min. The exopolysaccharides of biofilm were also thoroughly hydrolyzed by 0.01% alpha-amylase with 8 mM D-arginine. The biofilm thickness and integrity were disrupted, and the exopolysaccharides among the extracellular matrix were elusive. Molecular dynamics simulations showed that with the hydrogen bonding of D-arginine to the catalytic triad and calcium-binding regions of alpha-amylase, the atom fluctuation of the structure was attenuated. The distances between catalytic triad were shortened, and the calcium-binding regions became more stable. Molecular docking scores revealed that D-arginine facilitated the maltotetraose binding process of alpha-amylase. In conclusion, these results demonstrate that D-arginine enhances the disassembly effects of alpha-amylase on A. viscosus biofilm through potentiating the catalytic triad and stabilizing the calcium-binding regions, thus providing a novel strategy for the decontamination of biofilm contaminated implant surface.

Molecular mechanics of coiled coils loaded in the shear geometry.

Coiled coils are important nanomechanical building blocks in biological and biomimetic materials. A mechanistic molecular understanding of their structural response to mechanical load is essential for elucidating their role in tissues and for utilizing and tuning these building blocks in materials applications. Using a combination of single-molecule force spectroscopy (SMFS) and steered molecular dynamics (SMD) simulations, we have investigated the mechanics of synthetic heterodimeric coiled coils of different length (3-4 heptads) when loaded in shear geometry. Upon shearing, we observe an initial rise in the force, which is followed by a constant force plateau and ultimately strand separation. The force required for strand separation depends on the coiled coil length and the applied loading rate, suggesting that coiled coil shearing occurs out of equilibrium. This out-of-equilibrium behaviour is determined by a complex structural response which involves helix uncoiling, uncoiling-assisted sliding of the helices relative to each other in the direction of the applied force as well as uncoiling-assisted dissociation perpendicular to the force axis. These processes follow a hierarchy of timescales with helix uncoiling being faster than sliding and sliding being faster than dissociation. In SMFS experiments, strand separation is dominated by uncoiling-assisted dissociation and occurs at forces between 25-45 pN for the shortest 3-heptad coiled coil and between 35-50 pN for the longest 4-heptad coiled coil. These values are highly similar to the forces required for shearing apart short double-stranded DNA oligonucleotides, reinforcing the potential role of coiled coils as nanomechanical building blocks in applications where protein-based structures are desired.

Role of Thermal History and Entanglement Related Thickness Selection in Polymer Crystallization.

Using molecular dynamics simulations and primitive path analysis, we show that hot entangled polymer melts can crystallize faster with higher crystallinities and larger crystalline stem lengths, as compared to cold melts under rapid quenching conditions or during cold-crystallization. This counterintuitive phenomenon similar to the so-called Mpemba effect observed for water can be explained by the temperature dependence of entanglements. Our results demonstrate the key role of the entanglement state for crystallization properties and provide a new approach to understand the role of thermal history and to the open question of thickness selection in polymer crystallization.

Disentanglement of Linear Polymer Chains Toward Unentangled Crystals.

Large scale and long time molecular dynamics simulations and primitive path analysis are used to investigate the disentanglement of long linear polymer chains during their crystallization from the melt state. In general, two competitive processes, a slow decrease of average entanglement length during cooling caused by stiffening of chains and a strong increase during crystallization, can be observed. In both homogeneous and heterogeneous nucleation, disentanglement occurs via forming folds from locally unentangled segments and continues in postcrystallization processes (slow reorganization), in particular, during annealing. Re-entanglement processes after melting are slow and can lead to memory effects in heating-recooling protocols such as self-seeding.

Coexistence of melting and growth during heating of a semicrystalline polymer.

The coexistence of melting and growth during heating is observed by molecular dynamics simulations of semicrystalline entangled polymers. During heating, some microcrystalline domains (MCDs) are melted while others are still growing, which can be associated with multiple-peaked melting endotherms. The growth of MCD's stability is related to the increase of molecular disorder. The increasing of the stem length during annealing close to the melting point is contributed by the orientational correlation in the semimelted surface regions while direct trans-trans states are decreasing which increases the flexibility and mobility of the crystalline stems.

Ferroelectric ordering in ice nanotubes confined in carbon nanotubes.

The ice nanotubes with odd number of side faces formed inside carbon nanotubes (CNTs) are found to exhibit spontaneous electric polarizations along their tube axes by means of molecular dynamics simulations. The physical mechanism underlying the quasi-one-dimensional (Q1D) ferroelectricity is an interplay between the Q1D geometrical confinement of CNTs and the distinct orientational ordering of the hydrogen bonds dictated by the "ice rule". This mechanism is fundamentally different from the conventional one seen in three-dimensional ferroelectric (FE) materials or in two-dimensional FE ice films. In addition, it is found that vacancies in the ice nanotubes can induce a net polarization normal to the tube axis.

Coexistence of ferroelectricity and ferromagnetism in tantalum clusters.

The atomic and electronic structures of Ta(N) (N=2-23) clusters have been determined in the framework of pseudopotential density-functional calculations, based upon an unbiased global search with guided simulated annealing to an empirical potential. It is found that the ground-state structures of Ta(N) are very similar to those of Nb(N), showing no preference for the icosahedral growth. Also, a size- and structure-dependent ferroelectricity is found in these tantalum clusters. More importantly, it is found that the ferroelectricity and ferromagnetism can coexist in the homogeneous transition-metal cluster, offering a possibility to obtain a new type of "multiferroic" materials composed of the clusters. Finally, the far-infrared spectroscopy is suggested to be an efficient tool to distinguish the ferroelectric clusters.

Adsorption of O2 on tubelike Au24 and Au24- clusters.

The nondissociative adsorptions of O(2) on the neutral and anionic Au(24) have been studied using the density functional theory (DFT) in the generalized gradient approximation. Their geometrical structures are optimized by using a combination of the relativistic effective core potential and all-electron potential with scalar relativistic corrections. It is found that the adsorptions of O(2) on the tubelike Au(24) and Au(24) (-) are more stable than it on their space-filled counterparts. Mulliken population analysis shows that the O(2) adsorbed on the tubelike Au(24) and Au(24) (-) got more electrons than on the amorphous ones, which may be a reason why the O(2) can be adsorbed more easily on the former rather than on the latter. Compared with the previous DFT studies of O(2) adsorbed on small Au(n) (n< or =10) clusters, we have shown that the O(2) can also be adsorbed on the neutral even Au(24) with an adsorption energy compatible with that on the small neutral odd gold clusters, but the adsorption energy of O(2) on the anionic Au(24) (-) is lower than that on the small anionic Au(n) with even n. In all the optimized geometrical structures of the O(2)-adsorbed Au(24) and Au(24) (-) clusters, including both tubelike and amorphous ones, we found that O(2) prefers its two O atoms to be attached to two near gold atoms with the least coordination number rather than only one O atom to be attached to one gold atom.