Polymer Dynamics Research Articles

Mesoscale, long-time mixing of chromosomes and its connection to polymer dynamics

Mesoscale, long-time mixing of chromosomes and its connection to polymer dynamics

A mechanism of salt bridge-mediated resistance to FtsZ inhibitor PC190723 revealed by a cell-based screen.

Bacterial cell division proteins, especially the tubulin homologue FtsZ, have emerged as strong targets for developing new antibiotics. Here, we have utilized the fission yeast heterologous expression system to develop a cell-based assay to screen for small molecules that directly and specifically target the bacterial cell division protein FtsZ. The strategy also allows for simultaneous assessment of the toxicity of the drugs to eukaryotic yeast cells. As a proof-of-concept of the utility of this assay, we demonstrate the effect of the inhibitors sanguinarine, berberine, and PC190723 on FtsZ. Though sanguinarine and berberine affect FtsZ polymerization, they exert a toxic effect on the cells. Further, using this assay system, we show that PC190723 affects Helicobacter pylori FtsZ function and gain new insights into the molecular determinants of resistance to PC190723. On the basis of sequence and structural analysis and site-specific mutations, we demonstrate that the presence of salt bridge interactions between the central H7 helix and β-strands S9 and S10 mediates resistance to PC190723 in FtsZ. The single-step in vivo cell-based assay using fission yeast enabled us to dissect the contribution of sequence-specific features of FtsZ and cell permeability effects associated with bacterial cell envelopes. Thus, our assay serves as a potent tool to rapidly identify novel compounds targeting polymeric bacterial cytoskeletal proteins like FtsZ to understand how they alter polymerization dynamics and address resistance determinants in targets.

Editorial: Nanocomposites with interfaces controlled by grafted or adsorbed polymers

adsorbing polymer molecules can modify both the interfacial physics and the filler structure, giving access 14 to improved macroscopic (mechanical, electrical, or optical) material properties.It is the aim of the present topical collection to focus on some aspects of recent research in this 16 highly active and evolving area. We review and summarize state-of-the-art investigations of polymer 17 nanocomposite materials which promote at a better understanding and control of the complex behavior of 18 nanocomposites. Two articles with original experimental approaches have been contributed, one presenting 19 an innovative application of microgel-nanoparticle composites in solvent, the other an in-depth study of the 20 structure and dynamics of a bulk polymer nanocomposite. In parallel, we have reviewed the general field 21 of particle and polymer structure and dynamics using scattering techniques, in particular neutron scattering, 22 and highlighted the role of interfacial polymer layers in the specific case of polymer-grafted nanoparticles 23 in a second review.Nanocomposites can have many faces and may serve for fundamental studies as well as applications.

Influence of the molecular weight and physical properties of a thermoplastic polymer on its dynamic wetting behavior

The wetting dynamics of molten thermoplastic polymers, which are known to influence the force balance of the triple line, are not understood properly despite their importance in many industrial processes. In particular, the influence of the molecular weight Mn on the polymer dynamic wetting behavior is still unclear. In this work, we investigate how the dynamic equilibrium of the moving contact line between poly(ethylene glycol) and cellulosic substrates is influenced by Mn. After a careful assessment of the relevant material properties, dynamic wetting experiments are conducted using the Wilhelmy method. Our investigations reveal an influence of Mn on the evolution of all of the measured quantities. The dynamic wetting behavior is shown to relate to the polymer chain size, and to display a transition at the critical weight of entanglement Mc . This study should help defining guidelines for formulating and choosing polymers for various processes, such as composites manufacturing.

Simulation of polymeric mixed ionic and electronic conductors with a combined classical and quantum mechanical model.

In organic polymeric materials with mixed ionic and electronic conduction (OMIEC), the excess charge in doped polymers is very mobile and the dynamics of the polymer chain cannot be accurately described with a model including only fixed point charges. Ions and polymer are comparatively slower and a methodology to capture the correlated motions of excess charge and ions is currently unavailable. Considering a prototypical interface encountered in this type of materials, we constructed a scheme based on the combination of MD and QM/MM to evaluate the classical dynamics of polymer, water and ions, while allowing the excess charge of the polymer chains to rearrange following the external electrostatic potential. We find that the location of the excess charge varies substantially between chains. The excess charge changes across multiple timescales as a result of fast structural fluctuations and slow rearrangement of the polymeric chains. Our results indicate that such effects are likely important to describe the phenomenology of OMIEC, but additional features should be added to the model to enable the study of processes such as electrochemical doping.

Structure and dynamics of an active polymer chain inside a nanochannel grafted with polymers.

We use computer simulations to investigate the complex dynamics of a polymer, made of active Brownian particles, inside a channel grafted internally with passive polymer chains. Our simulations reveal that this probe-polymer, if passive, exhibits a compact structure when its interaction is repulsive with the grafted chains as it tends to stay within the hollow space created along the axis of the channel. On increasing the attractive interaction, the passive probe-polymer is pulled towards the grafted polymeric region and adopts an extended structure. By contrast, switching on the activity helps the probe-polymer to escape from the local traps caused by the sticky grafted chains. The interplay between the activity of the probe-polymer and its sticky interaction with the grafted chains results in shrinking, followed by swelling as the activity is increased. To elucidate the dynamics we compute the mean square displacement (MSD) of the center of mass of the probe-polymer, which increases monotonically with activity and displays superdiffusive behavior at an intermediate time and enhanced diffusion at a long time period. In addition, compared with the attractive interaction, the active probe-polymer shows faster dynamics when the interaction is repulsive to the grafted polymers. We believe that our current study will provide insights into the structural changes and dynamics of active polymers in heterogeneous media and will be useful in designing polymer-based drug delivery vehicles.

Crystallization and melting of unentangled poly(ε-caprolactone) cycles containing pendants.

The Rouse model provides a basic framework to understand the chain dynamics of polymers, which is confirmed to be more suitable for exploring the linear dynamics of unentangled polymers. The crystalline morphology governed by chain dynamics and crystallization kinetics is expected to differ in linear and cyclic polymers. Cyclic poly(ε-caprolactone)s (c-PCLs) containing two bi-anthracenyl group pendants with molecular weights close to the critical molecular weight (Mc) were synthesized to investigate the chain dynamics based crystallization and melting behavior by DSC, POM, and in situ simultaneous small-angle X-ray scattering/wide-angle X-ray scattering (SAXS/WAXS) investigations during heating of the isothermally crystallized samples. Double endothermic peaks were observed in the DSC curves with a low heating rate of c-PCLs without entanglement after isothermal crystallization, especially for c-PCLs with Mc. The structure evolution of the crystalline structures observed from the in situ investigations during the heating and double endothermic peaks in DSC heating curves of the c-PCLs indicate the role of pendants in the chain dynamics, which leads to the reorganization of the metastable structures. Banded spherulites of c-PCL without entanglement were observed for the first time, and the uneven growth of spherulites along the radial direction may be caused by the mismatch between chain dynamics and crystallization kinetics.

Dynamics of polymer electrolyte with LiTFSI via Quasi-Elastic Neutron Scattering

Most lithium batteries offer a wide range of applications. However, safety issues are still an unresolved issue for several applications. To solve the safety issue of Li-ion batteries, solid polymer electrolyte is a promising candidate to replace commercial liquid electrolyte. A 4-arm star poly(ethylene oxide) polymer with LiTFSI salt as an electrolyte was studied. The dynamics of this polymer were explored with the Quasi-Elastic Neutron Scattering technique. Furthermore, the influence of temperature and Li salt concentration on the polymer dynamics was investigated. The dynamics of the polymer ends of the arm show much higher flexibility than the core parts making those types of polymers attractive for further studies in battery research.

Molecular dynamics study of shear-induced lamellar alignment of ABA triblock copolymer thin films.

In this study, the shear-induced lamellar alignment of a thin-film ABA triblock copolymer melt was achieved via a non-equilibrium coarse-grained molecular dynamics simulation. The ABA triblock copolymer system displayed a slightly different phase behavior under different shear conditions compared to the AB diblock copolymer system. Unlike previous studies that only considered the wall velocity, the Flory-Huggins parameter was considered in our study as a factor that determines lamellar alignment. Pre-aligned lamellae and randomly mixed polymers were used as the initial states for the shear simulation to compare the shear-induced lamellar alignment on each. The two initial conditions displayed different alignment behaviors; specifically, in the pre-aligned lamellae, a tilted structure was observed when the system was not aligned in the shear direction. To explain the difference between the tilted and realigned structures, the potential energy over the simulation time, polymer dynamics from the Van Hove correlation function, and the directional order parameter were investigated. It was inferred that a tilted structure is induced by the energy barrier of realignment originating from the restricted movement of the local polymer chains. Once they cross the energy barrier, block copolymers tend to align in the shear direction to attain energy stabilization through the polymer flow.

Understanding the thermomechanical behavior of graphene-reinforced conjugated polymer nanocomposites via coarse-grained modeling.

Graphene-reinforced conjugated polymer (CP) nanocomposites are attractive for flexible and electronic devices, but their mechanical properties have been less explored at a fundamental level. Here, we present a predictive multiscale modeling framework for graphene-reinforced poly(3-alkylthiophene) (P3AT) nanocomposites via atomistically informed coarse-grained molecular dynamics simulations to investigate temperature-dependent thermomechanical properties at a molecular level. Our results reveal reduced graphene dispersion with increasing graphene loading. Nanocomposites with shorter P3AT side chains, lower temperatures, and higher graphene content exhibit stronger mechanical responses, which correlates with polymer dynamics. The elastic modulus increases linearly with the graphene content, which slightly deviates from the "Halpin-Tsai" micromechanical model prediction. Local stiffness analysis shows that graphene possesses the highest stiffness, followed by the P3AT backbone and side chains. Deformation-induced stronger chain alignment of the P3AT backbone compared to graphene may further promote conductive behavior. Our findings provide insights into the dynamical heterogeneity of nanocomposites, paving the way for understanding and predicting their thermomechanical properties.

PEG-fibrin conjugates: the PEG impact on the polymerization dynamics.

Fibrin and its modifications, particularly those with functionalized polyethylene glycol (PEG), remain highly attractive as a biomaterial in drug delivery and regenerative medicine. Despite the extensive knowledge of fibrinogenesis, there is little information on the processes occurring after its modification. Previously, we found structural differences between native fibrin and its conjugates with PEG that allows us to hypothesize that a combination of methods such as terahertz (THz) pulsed spectroscopy and rheology may contribute to the characterization of gelation and reveal the effect of PEG on the polymerization dynamics. Compared to native fibrin, PEGylated fibrins had a homogenously soft surface; PEGylation also led to a significant decrease in the gelation time: from 42.75 min for native fibrin to 31.26 min and 35.09 min for 5 : 1 and 10 : 1 PEGylated fibrin, respectively. It is worth noting that THz pulsed spectroscopy makes it possible to reliably investigate only the polymerization process itself, while it does not allow us to observe statistically significant differences between the distinct PEGylated fibrin gels. The polymerization time constant of native fibrin measured by THz pulsed spectroscopy was 14.4 ± 2.8 min. However, it could not be calculated for PEGylated fibrin because the structural changes were too rapid. These results, together with those previously reported, led us to speculate that PEG-fibrin conjugates formed homogenously distributed highly water-shelled aggregates without bundling compared to native fibrin, ensuring rapid gelation and stabilization of the system without increasing its complexity.

Non-Rouse behavior of short ring polymers in melts by molecular dynamics simulations.

Short ring polymers are expected to behave nearly Rouse-like due to the little effect of topological constraints of non-knot and non-concatenation. However, this notion is questioned because of several simulation and experiment findings in recent times, which requires a further more quantitative study. Therefore, we perform a deep investigation of statics and dynamics of flexible short ring polymers (N < 2Ne) in melts via molecular dynamics simulations by further taking linear analogues as well as all-crossing ring and linear polymers with switched off topological constraints for comparisons and demonstrate the noticeable deviations from the Rouse model in terms of local and global scales. Although the overall size is compact, the subchains are swollen, which is traced back to the deeper "segmental correlation hole" effect. The same scaling relationship of the non-Gaussian deviation of the static structure factor holds, but the deviation magnitude of rings is larger than that of linear analogues. By checking the non-Gaussian parameter and autocorrelation function of center-of-mass velocity, the physical origin of anomalous sub-diffusions of short rings is identified as unscreened viscoelastic hydrodynamic interactions and not correlation hole effects, like linear analogues.

Linear polymer chain diffusion in semi-flexible polymer network: A dissipative particle dynamics study

Linear polymer chains transport in the crowded biological environment is profoundly important to biomedical engineering and nanotechnology. Cytoskeleton, which can be modeled as a semi-flexible polymer network, acts as a barrier when linear polymers diffuse inside the cell. The diffusion of linear polymers with length N in this polymer network is investigated by the dissipative particle dynamics (DPD) in the present study. Rouse theory is applied to analyze the conformational dynamics of the linear polymers based on the numerical results. It is found that the geometric constraint length Na is a crucial parameter to describe the role of the network of the polymer diffusion. Analyses on Rouse modes show that, in a short wavelength regime, the relaxation time obtained in numerical simulation follows the prediction of the Rouse theory. With the increasing wavelength, the linear polymer exhibits a transition from reptation behavior to the spatially homogeneous behavior at critical length scale Na, which is illustrated by different scaling laws dependent on wavelength. Based on the analyses on the Rouse modes and mean square displacements of the linear polymer, we present a non-dimensional conformational dynamics function dependent on time, with which a scaling law is proposed to predict the long time diffusivity of the linear polymer in a semi-flexible polymer network with different mesh sizes. It is shown that the prediction is well consistent with our DPD simulation results.

The effect of the intramolecular disorder on hot exciton dynamics in polymer solar cells.

In polymer solar cells (PSCs), the contribution of hot excitons to charge generation is strongly limited by their relatively low yield and ultrafast internal conversion (IC) process. In recent years, different strategies have been proposed to modulate the hot exciton dynamics, but a direct correlation between the microscopic properties of the polymer and hot exciton dynamics is still not completely clear. Here, we theoretically investigate the effect of intramolecular disorder, including the diagonal disorder (DD) and off-diagonal disorder (ODD), on the hot exciton dynamics based on the tight-binding model calculations. We find that the effect of ODD on the hot exciton yield is more significant than that of DD. In addition, we find that the IC relaxation time of hot excitons depends nonmonotonically on the intensity of DD and ODD, indicating that the intramolecular disorder can modulate the competitive relationship between the spontaneous dissociation of hot excitons and the IC process. This work provides a guide for promoting charge generation in PSCs dominated by hot exciton dissociation.

Unpredictable polymeric flow dynamics with reaction between HPAM and Al3+ by comparison between pre- and post-reaction fluid properties.

A chemical reaction in the flow field affects the physical property of fluids, resulting in changing flow dynamics. The effect of the reaction on the flow dynamics is normally evaluated by comparison between the physical properties of the fluid between pre- and post-reaction. However, our group found a polymeric reacting flow in which a comparison between pre- and post-reaction fluid properties is insufficient to evaluate the influences of the reaction on the flow dynamics (T. Ueki et al., J. Phys. Chem. B, 2019, 123, 4587-4593). In the study, we examined the stirred flow by an impeller in a beaker with a chemical reaction between partially hydrolyzed polyacrylamide (HPAM) solution and Fe(NO3)3 solution. We found that a so-called Weissenberg effect, where the stirred solution climbs up the stirring shaft because of an increase in the viscoelasticity of the mixed solution, transiently appeared in only the halfway of the reaction, although the reaction slightly decreased the solution's viscosity at the final stage under a certain pH and we proposed the mechanism for the temporal increase in the viscoelasticity. In the present study, we conducted similar experiments as our previous study using HPAM solution at various pH and two concentrations of Al(NO3)3 solutions. The unpredictable flow dynamics by comparison between pre- and post-reaction fluid properties, i.e., the appearance and disappearance of the Weissenberg effect, has been observed under a certain pH and Al(NO3)3 concentration. We investigated the mechanism by means of the simultaneous measurement of pH and the stirring torque and the identification of the dominant species of aluminum aqua complexes by the Henderson-Hasselbalch equation. As a result, we proposed two mechanisms of dissapearance of the Weissenberg effect: one is the same for the Fe(NO3)3 case but the other is unique and novel for the Al(NO3)3 case. This study can contribute to the comprehensive understanding of the conditions for the occurrence of the unpredictable dynamics of polymeric reacting flow by comparison between the pre- and post-reaction fluid properties.

Universal features of the manifestation of the relationship between local and segmental dynamics of polymers at terahertz frequencies in IR spectra

Low-frequency IR- spectra of glassy polymers were obtained and analyzed at temperatures from 90 to 400 K. Temperature changes in the IR- spectra in the range from 10 to 140 cm-1 show three universal features: low-temperature, corresponding to the torsional-vibrational motion of monomer units, high-temperature, due to the influence of primary relaxation (glass transition) and intermediate, caused by the activation of conformational mobility in chains at a temperature of β-transition. This versatility extends both to polymers with universal chain-to-chain interactions and to those with hydrogen bonds. Keywords: IR spectra, excess density of vibrational states, bosonic peak, molecular dynamics, α- and β-relaxations.

Microscopic temperature-dependent structural dynamics in polymer nanocomposites: role of the graft-matrix chain interfacial entropic effect.

We present a systematic study of the structural dynamics in bulk entropic polymer nanocomposites (PNCs) with deuterated-polymer-grafted nanoparticles (DPGNPs) using quasi-elastic neutron scattering (QENS). We observe that the wave-vector-dependent relaxation dynamics depend on the entropic parameter f as well as the length scale being probed. The entropic parameter can be defined in terms of the grafted-to-matrix polymer molecular weight ratio and controls the extent of matrix chain penetration into the graft. Dynamical cross-over from Gaussian to non-Gaussian behavior at the wave vector Qc, which depends on temperature and f, was observed. Further insight into the underlying microscopic mechanism responsible for the observed behavior revealed that when interpreted using a jump-diffusion model, in addition to the speeding-up in local chain dynamics, the elementary distance over which sections of the chain hop is strongly dependent on f. Interestingly, we also observe dynamic heterogeneity (DH) in the studied systems, characterized by the non-Gaussian parameter α2, which reduces for a high-f (f = 0.225) sample compared with the pristine host polymer, indicating reduced dynamical heterogeneity, while it is mostly unchanged for the low-f sample. The results highlight that, unlike enthalpic PNCs, entropic PNCs with DPGNPs can modify the host polymer dynamics due to the subtle balance of interactions that occur at different length scales in the matrix.

Understanding creep suppression mechanisms in polymer nanocomposites through machine learning.

While recent efforts have shown how local structure plays an essential role in the dynamic heterogeneity of homogeneous glass-forming materials, systems containing interfaces such as thin films or composite materials remain poorly understood. It is known that interfaces perturb the molecular packing nearby, however, numerous studies show the dynamics are modified over a much larger range. Here, we examine the dynamics in polymer nanocomposites (PNCs) using a combination of simulations and experiments and quantitatively separate the role of polymer packing from other effects on the dynamics, as a function of distance from the nanoparticle surfaces. After showing good qualitative agreement between the simulations and experiments in glassy structure and creep compliance, we use a machine-learned structure indicator, softness, to decompose polymer dynamics in our simulated PNCs into structure-dependent and structure-independent processes. With this decomposition, the free energy barrier for polymer rearrangement can be described as a combination of packing-dependent and packing-independent barriers. We find both barriers are higher near nanoparticles and decrease with applied stress, quantitatively demonstrating that the slow interfacial dynamics is not solely due to polymer packing differences, but also the change of structure-dynamics relationships. Finally, we present how this decomposition can be used to accurately predict strain-time creep curves for PNCs from their static configuration, providing additional insights into the effects of polymer-nanoparticle interfaces on creep suppression in PNCs.

Dynamics-induced charge transfer in semiconducting conjugated polymers

Dynamics-induced interchain charge transfer in a polymer aggregate in stack configuration can be understood by single-oligomer polaron energy.

An energy minimization strategy based on an improved nonlinear conjugate gradient method for accelerating the charged polymer dynamics simulation.

Using a hybrid simulation method that combines a non-linear conjugate gradient (NCG) method for solving large-scale unconstrained optimization problems with a Brownian dynamics (BD) model for polymer chains, we investigate the pre-equilibrium simulation of charged polymers in different dielectric systems from an energy minimization perspective. We propose an improved NCG coefficient (βLPRPk) that satisfies a sufficient descent condition with a greater parameter under a strong Wolfe line search and converges globally for nonconvex minimization. Furthermore, preliminary numerical results show that the βLPRPk coefficient is more efficient than many existing NCG coefficients for a large number of practical test problems from our model. We further compare the performance of the improved NCG method with that of other mainstream numerical methods in energy minimization, and the simulation results suggest that the NCG method is more competitive in terms of cost-effectiveness. Importantly, we apply the geometrically optimized configuration obtained by performing the NCG method to the pre-equilibrium simulation, and the numerical results show that it increases the computational efficiency of a pure solvent and biomolecule-solution systems at most by about 32 and 70 times, respectively, with the relative energy errors being controlled below 1 × 10-2 and 4.5 × 10-3, respectively. More importantly, the final pre-equilibrium configuration of the BD simulation that performs energy minimization and the traditional BD simulation matched closely.