Self-Assembled Tetraphenylethene-Based Nanoaggregates with Tunable Electrochemiluminescence for the Ultrasensitive Detection of E. coli.

As an effective ECL emitter, tetraphenylethene (TPE)-based molecules have recently been reported with aggregation-induced electrochemiluminescence (AIECL) property, while it is still a big challenge to control its aggregation states and obtain uniform aggregates with intense ECL emission. In this study, we develop three TPE derivatives carrying a pyridinium group, an alkyl chain, and a quaternary ammonium group via the Menschutkin reaction. The resulting molecules exhibit significantly red-shifted FL and enhanced ECL emissions due to the tunable reduction of the energy gap between the highest occupied molecular orbitals (HOMOs) and the lowest unoccupied molecular orbitals (LUMOs). More importantly, the amphiphilicity of the as-developed molecules enables their spontaneous self-assembly into well-controlled spherical nanoaggregates, and the ECL intensity of nanoaggregates with 3 -CH2- (named as C3) is 17.0-fold higher compared to that of the original 4-(4-(1,2,2-triphenylvinyl)phenyl)pyridine (TPP) molecule. These cationic nanoaggregates demonstrate a high affinity toward bacteria, and an ECL sensor for the profiling of Escherichia coli (E. coli) was developed with a broad linear range and good selectivity in the presence of an E. coli-specific aptamer. This study provides an effective way to enhance the ECL emission of TPE molecules through their derivatization and a simple way to prepare well-controlled AIECL nanoaggregates for ECL application.

Influence of temperature on bend, twist and twist-bend coupling of dsDNA.

The temperature-dependent bend and twist elasticities of dsDNA, as well as their couplings, were explored through all-atom molecular dynamics simulations. Three rotational parameters, tilt, roll, and twist, were employed to assess the bend and twist elasticities through their stiffness matrix. Our analysis indicates that the bend and twist stiffnesses decrease as the temperature rises, primarily owing to entropic influences stemming from thermodynamic fluctuations. Furthermore, the couplings between these rotational parameters also exhibit a decline with increasing temperature, although the roll-twist coupling displays greater strength than the tilt-roll and tilt-twist couplings, attributed to its more robust correction component. We elucidated the influence of temperature on bend and twist elasticities based on the comparisons between various models and existing data.

Temperature dependence of DNA elasticity: An all-atom molecular dynamics simulation study.

We used all-atom molecular dynamics simulation to investigate the elastic properties of double-stranded DNA (dsDNA). We focused on the influences of temperature on the stretch, bend, and twist elasticities, as well as the twist-stretch coupling, of the dsDNA over a wide range of temperature. The results showed that the bending and twist persistence lengths, together with the stretch and twist moduli, decrease linearly with temperature. However, the twist-stretch coupling behaves in a positive correction and enhances as the temperature increases. The potential mechanisms of how temperature affects dsDNA elasticity and coupling were investigated by using the trajectories from atomistic simulation, in which thermal fluctuations in structural parameters were analyzed in detail. We analyzed the simulation results by comparing them with previous simulation and experimental data, which are in good agreement. The prediction about the temperature dependence of dsDNA elastic properties provides a deeper understanding of DNA elasticities in biological environments and potentially helps in the further development of DNA nanotechnology.

Sliding dynamics of multi-rings on a semiflexible polymer in poly[n]catenanes.

The sliding dynamics of one- or multi-ring structures along a semiflexible cyclic polymer in radial poly[n]catenanes is investigated using molecular dynamics simulations. The fixed and fluctuating (non-fixed) semiflexible central cyclic polymers are considered, respectively. With increasing bending energy of the central cyclic polymer, for the fixed case, the diffusion coefficient increases monotonically due to the reduction of the tortuous sliding path, while for the fluctuating case, the diffusion coefficient decreases. This indicates that the contribution of the polymer fluctuation is suppressed by a further increase in the stiffness of the central cyclic chain. Compared with the one ring case, the mean-square displacement of the multiple rings exhibits a unique sub-diffusive behavior at intermediate time scales due to the repulsion between two neighboring rings. In addition, for the multi-ring system, the whole set of rings exhibit relatively slower diffusion, but faster local dynamics of threading rings and rotational diffusion of the central cyclic polymer arise. These results may help us to understand the diffusion motion of rings in radial poly[n]catenanes from a fundamental point of view and control the sliding dynamics in molecular designs.

An attraction-repulsion transition of force on wedges induced by active particles.

Effective forces between two micro-wedges immersed in an active bath are investigated using Brownian dynamics simulations. Two anti-parallel and parallel wedge-like obstacles are considered respectively, and the effective forces between two wedges rely on the wedge-to-wedge distance, the apex angle of the wedge, as well as the particle density and aspect ratio. For two anti-parallel wedges, a transition from repulsion to attraction occurs by varying the apex angle, which is also sensitive to the particle density and aspect ratio. The optimal apex angle θr* (or θa*) and particle density ρ* are characterized by the saturated trapping of active particles inside a wedge. For two parallel wedges, the effective force also experiences a transition from repulsion to attraction as the wedge-to-wedge distance increases. These results originate from the collective trapping effect which is driven by the many-body dynamics of self-propelled particles in the confinement (near the boundary) of obstacles. Our results can provide insight into controlling the motion and assembly of microscopic objects through the suspension of active particles.

Self-assembly of phospholipid molecules in solutions under shear flows: Microstructures and phase diagrams.

Shear-induced microstructures and their phase diagrams were investigated for phospholipid molecules in aqueous solution by dissipative particle dynamic simulation. Self-assembled microstructures, including spherical and cylindrical micelles, spherical vesicles, lamellae, undulated lamellae, perforated lamellae, and continuous networks, were observed under various shear flows and phospholipid concentrations, where the spatial inhomogeneity and symmetry were analysed. A series of phase diagrams were constructed based on the chain lengths under various phospholipid concentrations. The phase distributions showed that the structures with spherical symmetry could be shear-induced to structures with cylindrical symmetry in the dilute solutions. In the semi-concentrated solutions, the lamellae were located in most spaces under zero shear flows, which could be shear-induced into undulated lamellae and then into cylindrical micelles. For the concentrated solutions, the strong shear flows oriented the directions of multilayer lamellae and phase transitions appeared between several cylindrical network structures. These observations on shear-induced microstructures and their distributions revealed a promising approach that could be used to design bio-microstructures based on phospholipid molecules under shear flows.

Phase diagrams of diblock copolymers in electric fields: a self-consistent field theory study.

We investigated the phase diagrams of diblock copolymers in external electrostatic fields by using real-space self-consistent field theory. The lamella, cylinder, sphere, and ellipsoid structures were observed and analyzed by their segment distributions, which were arranged to two types of phase diagrams to examine the phase behavior in weak and strong electric fields. One type was constructed on the basis of Flory-Huggins interaction parameter and volume fraction. We identified an ellipsoid structure with a body-centered cuboid arrangement as a stable phase and discussed the shift of phase boundaries in the electric fields. The other type of phase diagrams was established on the basis of the dielectric constants of two blocks in the electric fields. We then determined the regions of ellipsoid phase in the phase diagrams to examine the influence of dielectric constants on the phase transition between ellipsoidal and hexagonally packed cylinder phases. A general agreement was obtained by comparing our results with those described in previous experimental and theoretical studies.

Liquid crystalline assembly of rod-coil diblock copolymer and homopolymer blends by dissipative particle dynamics simulation.

Liquid crystalline assembly of rod-coil diblock copolymers blended with coil or rod homopolymers is investigated by dissipative particle dynamics simulation, considering systematically the effect of the interactions between rods and coils, the volume fraction and length of the added coil or rod homopolymers. The addition of coil or rod homopolymers induces disorder-order or order-liquid crystalline transition. In rod-coil/coil blends, the solubilization of homopolymers will saturate at a certain amount of homopolymers and then the excess homopolymers will be segregated into the central regions of coil block domains, forming "wet-dry mixture" lamellae. The solubility capacity decreases with increasing homopolymer length, determined by the competition between the mixing entropy and the elastic entropy. In rod-coil/rod blends, due to the orientational interactions between rods, the length matched rod homopolymers directly interdigitate with rod blocks with less entropy loss, thus prompting the formation of a bilayer liquid crystalline phase. The rod domain spacing Dr remains unchanged and conversely the coil domain spacing Dc becomes thin, to occupy more interfacial area. With the addition of shorter rod homopolymers, the overall lamellar spacing D of blends monotonically increases with the volume fraction of homopolymers, similar to the case of rod-coil/coil blends. Generally, rod homopolymers have a more significant impact on the liquid crystalline assembly of the blends, compared with the coil homopolymers. Our results indicate that blending with coil or rod homopolymers into a rod-coil system is an effective method to induce liquid crystal phase transition and control the phase spacing of the ordered structure.

Wrapping/unwrapping transition of double-stranded DNA in DNA-nanosphere complexes induced by multivalent anions.

Wrapping and unwrapping behaviors of double-stranded DNA around a positively charged nanosphere in solution are studied by using the coarse-grained molecular dynamics (CGMD) simulation method. When monovalent, divalent and trivalent anions are added to the DNA-nanosphere complex solution, double-stranded DNA binds with a nanosphere owing to strong electrostatic attraction. However, when tetravalent anions are added to the DNA-nanosphere complex solution, local charge inversion is observed for a high anion concentration of tetravalent anions and the double-stranded DNA can be unwrapped from the nanosphere because of the local charge inversion near the nanosphere. Moreover, the helical structure of DNA is damaged when double-stranded DNA wraps around the nanosphere and the helical structure can be rebuilt when the double-stranded DNA unwraps from the nanosphere. This study can help us understand how to control the release of DNA in DNA-nanosphere complexes.

Detection of respiratory syncytial virus fusion protein variants between 2009 and 2012 in China.

Respiratory syncytial virus (RSV) causes respiratory tract infection, particularly acute lower respiratory tract infection (ALRTI), in early childhood. The RSV fusion protein (F protein) is an important surface protein, and it is the target of both cytotoxic T lymphocytes (CTL) and neutralizing antibodies; thus, it may be useful as a candidate for vaccine research. This study investigated the genetic diversity of the RSV F protein. To this end, a total of 1800 nasopharyngeal aspirates from hospitalized children with ALRTI were collected for virus isolation between June 2009 and March 2012. There were 333 RSV-positive cases (277 cases of RSV A, 55 of RSV B, and 1 with both RSV A and RSV B), accounting for 18.5 % of the total cases. Next, 130 clinical strains (107 of RSV A, 23 of RSV B) were selected for F gene sequencing. Phylogenetic analysis revealed that the F gene sequence is highly conserved, with significant amino acid changes at residues 16, 25, 45, 102, 122, 124, 209, and 447. Mutations in human histocompatibility leukocyte antigen (HLA)-restricted CTL epitopes were also observed. Variations in RSV A F protein at the palivizumab binding site 276 (N→S) increased between 2009 and 2012 and became predominant. Western blot analysis and microneutralization data showed a substitution at residue 276 (N→S) in RSV A that did not cause resistance to palivizumab. In conclusion, the RSV F gene is geographically and temporally conserved, but limited genetic variations were still observed. These data could be helpful for the development of vaccines against RSV infection.

Self-assembly of cyclic rod-coil diblock copolymers.

The phase behavior of cyclic rod-coil diblock copolymer melts is investigated by the dissipative particle dynamics simulation. In order to understand the effect of chain topological architecture better, we also study the linear rod-coil system. The comparison of the calculated phase diagrams between the two rod-coil copolymers reveals that the order-disorder transition point (χN)ODT for cyclic rod-coil diblock copolymers is always higher than that of equivalent linear rod-coil diblocks. In addition, the phase diagram for cyclic system is more "symmetrical," due to the topological constraint. Moreover, there are significant differences in the self-assembled overall morphologies and the local molecular arrangements. For example, frod = 0.5, both lamellar structures are formed while rod packing is different greatly in cyclic and linear cases. The lamellae with rods arranged coplanarly into bilayers occurs in cyclic rod-coil diblocks, while the lamellar structure with rods arranged end by end into interdigitated bilayers appears in linear counterpart. In both the lamellar phases, the domain size ratio of cyclic to linear diblocks is ranged from 0.63 to 0.70. This is attributed to that the cyclic architecture with the additional junction increases the contacts between incompatible blocks and prevents the coil chains from expanding as much as the linear cases. As frod = 0.7, the hexagonally packed cylinder is observed for cyclic rod-coil diblocks, while liquid-crystalline smectic A lamellar phase is formed in linear system. As a result, the cyclization of a linear rod-coil block copolymer can induce remarkable differences in the self-assembly behavior and also diversify its physical properties and applications greatly.

Ordered structures of diblock nanorods induced by diblock copolymers.

The self-assembly of diblock copolymer (DBCP)/diblock nanorod (DBNR) mixtures are studied by using a dissipative particle dynamics simulation method. The microstructures of DBCP/DBNR blends depend on the type of DBCPs as well as the number of DBNRs. For the asymmetric DBCPs of A3B7, the morphological transition of DBCP/DBNR blends from cylinder phase to lamellar phase is observed for the DBNRs with suitable length and component. Meanwhile, for the symmetric DBCPs of A5B5, the lamellar morphologies of DBCP/DBNR blends can always maintain during the process of adding DBNRs to the blends except for the case of component length mismatch between the DBCPs and the DBNRs. On the other hand, DBCPs can also affect the orientation and the spatial distributions of DBNRs deeply, and the ordered structures of DBNRs are formed for the DBCP/DBNR blends with a large number of DBNRs. Comparisons with homopolymer/DBNR blends are made, and only the aggregation structures are observed in homopolymer/DBNR blends. This investigation can provide valuable assistance in exploring and designing complicated polymer/nanoparticle composites with the desired properties.

Asymmetric Lipid Membranes under Shear Flows: A Dissipative Particle Dynamics Study.

We investigate the phase behavior of the asymmetric lipid membranes under shear flows, using the dissipative particle dynamics simulation. Two cases, the weak and strong shear flows, are considered for the asymmetric lipid microstructures. Three typical asymmetric structures, the membranes, tubes, and vesicle, are included in the phase diagrams, where the effect of two different types of lipid chain length on the formation of asymmetric membranes is evaluated. The dynamic processes are demonstrated for the asymmetric membranes by calculating the average radius of gyration and shape factor. The result indicates that different shear flows will affect the shape of the second type of lipid molecules; the shape of the first type of lipid molecules is more stable than that of the second type of lipid molecules. The mechanical properties are investigated for the asymmetric membranes by analyzing the interface tension. The results reveal an absolute pressure at the junctions of different types of particles under the weak shear flow; the other positions are almost in a state of no pressure; there is almost no pressure inside the asymmetric lipid membrane structure under the strong shear flow. The findings will help us to understand the potential applications of asymmetric lipid microstructures in the biological and medical fields.

Predicting asymmetric phospholipid microstructures in solutions.

Asymmetric phospholipid microstructures, such as asymmetric phospholipid membranes, have potential applications in biological and medicinal processes. Here, we used the dissipative particle dynamics simulation method to predict the asymmetric phospholipid microstructures in aqueous solutions. The asymmetric phospholipid membranes, tubes and vesicles are determined and characterized by the chain density distributions and order parameters. The phase diagrams are constructed to evaluate the effects of the chain length on the asymmetric structure formations at equilibrium states, while the average radius of gyration and shape factors are calculated to analyze the asymmetric structure formations in the non-equilibrium processes. Meanwhile, we predicted the mechanical properties of the asymmetric membranes by analyzing the spatial distributions of the interface tensions and osmotic pressures in solutions.

Effects of Topological Constraints on Penetration Structures of Semi-Flexible Ring Polymers.

The effects of topological constraints on penetration structures of semi-flexible ring polymers in a melt are investigated using molecular dynamics simulations, considering simultaneously the effects of the chain stiffness. Three topology types of rings are considered: 01-knot (the unknotted), 31-knot and 61-knot ring polymers, respectively. With the improved algorithm to detect and quantify the inter-ring penetration (or inter-ring threading), the degree of ring threading does not increase monotonously with the chain stiffness, existing a peak value at the intermediate stiffness. It indicates that rings interpenetrate most at intermediate stiffness where there is a balance between coil expansion (favoring penetrations) and stiffness (inhibiting penetrations). Meanwhile, the inter-ring penetration would be suppressed with the knot complexity of the rings. The analysis of effective potential between the rings provides a better understanding for this non-monotonous behavior in inter-ring penetration.

An attraction-repulsion transition of force on two asymmetric wedges induced by active particles.

Effective interaction between two asymmetric wedges immersed in a two-dimensional active bath is investigated by computer simulations. The attraction-repulsion transition of effective force between two asymmetric wedges is subjected to the relative position of two wedges, the wedge-to-wedge distance, the active particle density, as well as the apex angle of two wedges. By exchanging the position of the two asymmetric wedges in an active bath, firstly a simple attraction-repulsion transition of effective force occurs, completely different from passive Brownian particles. Secondly the transition of effective force is symmetric for the long-range distance between two asymmetric wedges, while it is asymmetric for the short-range case. Our investigations may provide new possibilities to govern the motion and assembly of microscopic objects by taking advantage of the self-driven behaviour of active particles.

Interaction between Bottlebrush Polymers and Phospholipid Membranes in Solutions.

In this work, the interactions between bottlebrush polymers and phospholipid membranes were investigated using dissipative particle dynamics simulations. The weak and strong adsorption phenomena between the polymers and membranes were examined by calculating the system parameters. A spring model was introduced to explain the variances in the shape factors and the radius of gyration of the bottlebrush polymers, as well as the order parameters of the phospholipid membrane in the pulling processes. This work provides further understanding for the application of bottlebrush polymers in biological processes.

Effect of nanorods on the mesophase structure of diblock copolymers.

Mixtures of symmetric diblock copolymers and rigid nanorods (NRs) that are preferentially wetted by one of the blocks (A) are systematically investigated via dissipative particle dynamics simulations. The morphology of such composites depends not only on the characteristics of the copolymers, but also on the physical or chemical features of the NRs, such as NR volume fraction, size, and polymer-NR interaction. We find that the presence of NRs influences the phase behavior of copolymers and the phase-separated domains of copolymers in turn confine the NRs spatial distribution and positional orientation. The morphologies and phase transitions of hybrids and the corresponding NRs distributed and oriented regularities can be rationalized on the basis of the relative enthalpic and entropic effects involving all of the species, A and B blocks, and NRs. These results suggest that by choosing appropriate parameters, our model systems may provide a prediction to control and design the high-performance composites.

Entropy-induced Separation of Binary Semiflexible Ring Polymer Mixtures in Spherical Confinement.

Coarse-grained molecular dynamics simulations are used to investigate the conformations of binary semiflexible ring polymers (SRPs) of two different lengths confined in a hard sphere. Segregated structures of SRPs in binary mixtures are strongly dependent upon the number density of system (ρ), the bending energy of long SRPs (Kb, long), and the chain length ratio of long to short SRPs (α). With a low ρ or a weak Kb, long at a small ratio α, long SRPs are immersed randomly in the matrix of short SRPs. As ρ and bending energy of long SRPs (Kb, long) are increased up to a certain value for a large ratio α, a nearly complete segregation between long and short SRPs is observed, which can be further characterized by the ratio of tangential and radial components of long SRPs velocity. These explicit segregated structures of the two components in spherical confinement are induced by a delicate competition between the entropic excluded volume (depletion) effects and bending contributions.

Shear-induced microstructures and dynamics processes of phospholipid cylinders in solutions.

Shear-induced microstructures and their corresponding dynamic processes are investigated for phospholipid cylinders in aqueous solution by dissipative particle dynamic simulation. Various phospholipid cylinders with cross-sections, which are formed under shear-free flow, are selected to examine the effects of shear flow on their structures and dynamic processes. Shear flow induces the transition from cylinders into vesicles at weak rate and the transition into vesicle-lamella mixtures with increased shear rate and lamella structures at the strong shear rate. Then, the average radius of gyration and shape factors of the polymer chains in the dynamic processes are discussed in detail. Results show that shear flow causes the structure of the polymer chains to be elongated along the shear direction, and the configuration of the polymer chain can be rapidly transformed into an ellipsoid structure under strong shear.