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Molecular chirality has traditionally been viewed as a binary property where a molecule is classified as either chiral or achiral, yet in recent decades, mathematical methods for quantifying chirality have been explored. Here, we use toy molecular systems to systematically compare the performance of two state-of-the-art chirality measures: (1) the Continuous Chirality Measure (CCM) and (2) the Chirality Characteristic (χ). We find that both methods exhibit qualitatively similar behavior when applied to simple molecular systems such as a four-site molecule or the polymer double-helix, but we show that the CCM may be more suitable for evaluating the chirality of arbitrary molecules or abstract structures such as normal vibrational modes. We discuss a range of considerations for applying these methods to molecular systems in general, and we provide links to user-friendly codes for both methods. We aim for this paper to serve as a concise resource for scientists attempting to familiarize themselves with these chirality measures or attempting to implement chirality measures in their own work. [ABSTRACT FROM AUTHOR]

Recent experiments by Brückner et al. [Science 380, 1357 (2023)] have observed an anomalous chain length dependence of the time of near approach of widely separated pairs of genomic elements on transcriptionally active chromosomal DNA. In this paper, I suggest that the anomaly may have its roots in internal friction between neighboring segments on the DNA backbone. The basis for this proposal is a model of chain dynamics formulated in terms of a continuum scaled Brownian walk (sBw) of polymerization index N. The sBw is an extension of the simple Brownian walk model widely used in path integral calculations of polymer properties, differing from it in containing an additional parameter H (the Hurst index) that can be tuned to produce varying degrees of correlation between adjacent monomers. A calculation using the sBw of the mean time τc for chain closure predicts-under the Wilemski-Fixman approximation for diffusion-controlled reactions-that at early times, τc varies as the 2/3 power of N, in close agreement with the findings of the Brückner et al. study. Other scaling relations of that study, including those related to the probability of loop formation and the mean square displacements of terminal monomers, are also satisfactorily accounted for by the model., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

Polymer models describing the statistics of biomolecules under confinement have applications to a wide range of single-molecule experimental techniques and give insight into biologically relevant processes in vivo. In this paper, we determine the transverse position and bending correlation functions for a wormlike chain confined within slits and cylinders (with one and two confined dimensions, respectively) using a mean-field approach that enforces rigid constraints on average. We show the theoretical predictions accurately capture the statistics of a wormlike chain from Monte Carlo simulations in both confining geometries for both weak and strong confinement. We also show that the longitudinal correlation function is accurately computed for a chain confined to a slit and leverages the accuracy of the model to suggest an experimental technique to infer the (often unobservable) transverse statistics from the (directly observable) longitudinal end-to-end distance. [ABSTRACT FROM AUTHOR]

Polymer crystallization has long been a fascinating problem and is still attracting many researchers. Most of the previous simulations are concentrated on clarifying the universal aspects of polymer crystallization using model linear polymers such as polyethylene. We are recently focusing on a nearly untouched but very interesting problem of chiral selecting crystallization in helical polymers. We previously proposed a stepwise approach using two kinds of helical polymers, simple "bare" helical polymers made of backbone atoms only such as polyoxymethylene (POM) and "general" helical polymers containing complicated side groups such as isotactic polypropylene. We have already reported on the crystallization in oligomeric POM-like helix but have observed only weak chiral selectivity during crystallization. In the present paper, we investigate the crystallization of sufficiently long POM-like polymer both from the isotropic melt and from the highly stretched melt. We find in both cases that the polymer shows a clear chiral selecting crystallization. Specifically, the observation of a single crystal growing from the isotropic melt is very illuminating. It shows that the crystal thickness and the crystal chirality are closely correlated; thicker crystals show definite chirality while thinner ones are mostly mixtures of the R- and the L-handed stems. The single crystal is found to have a marked lenticular shape, where the thinner growth front, since being made of the mixture, shows no chiral selectivity. The final chiral crystal is found to be completed through helix reversal processes within thicker regions. [ABSTRACT FROM AUTHOR]

The presence of gradient softer outer layers, commonly observed in biological systems (such as cartilage and ocular tissues), as well as synthetic crosslinked hydrogels, profoundly influences their interactions with opposing surfaces. Our prior research demonstrated that gradient-stiffness hydrogel layers, characterized by increasing elasticity with depth, control contact mechanics, particularly in proximity to the layer thickness. We postulate that the distribution of polymers within these gradient layers imparts extraordinary stretch and adhesion characteristics due to network adaptability and stress-induced reorganization. To investigate this phenomenon, we utilized Atomic Force Microscopy nanoindentation to assess the depth-dependent adhesion behavior of polyacrylamide hydrogels with varying gradient layer thicknesses. Two gradient layer thicknesses were achieved by employing different molding materials: glass and polyoxymethylene (POM). Glass-molded hydrogels exhibited a thinner gradient layer alongside a stiffer bulk layer compared to their POM-molded counterparts. In indentation experiments, the POM-molded hydrogel had larger adhesion compared to glass-molded hydrogel. We find that indenting within the gradient layer engenders increased load-unload hysteresis due to heightened fluid transport in the sparse outer polymer network. Consequently, this led to augmented adhesion and work of separation at shallow depths. We suggest that the prominent stretching capability of the sparse outer polymer network during probe retraction contributes to enhanced adhesion. The Maugis–Dugdale adhesive model only fits well to indentations on the thin layer or indentations which engage significantly with the bulk. These results facilitate a comprehensive characterization of adhesion mechanics in gradient-stiffness hydrogels, which could foster their application across emerging contexts in health science and environmental domains. [ABSTRACT FROM AUTHOR]

Mastering the manipulation of the electron spin plays a crucial role in comprehending the behavior of organic materials in several applications, such as asymmetric catalysis, chiroptical switches, and electronic devices. A promising avenue for achieving such precise control lies in the Chiral Induced Spin Selectivity (CISS) effect, where electrons with a favored spin exhibit preferential transport through chiral assemblies of specific handedness. Chiral supramolecular polymers emerge as excellent candidates for exploring the CISS effect due to their ability to modulate their helical structure through noncovalent interactions. In this context, systems capable of responding to external stimuli are particularly intriguing, sometimes even displaying chirality inversion. This study unveils spin selectivity in chiral supramolecular polymers, derived from single enantiomers, through scanning tunneling microscopy conducted in scanning tunneling spectroscopy mode. Following two distinct sample preparation protocols for each enantiomer, we generate supramolecular polymers with opposite handedness and specific spin transport characteristics. Our primary focus centers on chiral π-conjugated building blocks, with the aim of advancing novel systems that can inspire the organic spintronics community from a supramolecular chemistry level. [ABSTRACT FROM AUTHOR]

Comb-like polymers have shown potential as advanced materials for a diverse palette of applications due to the tunability of their polymer architecture. To date, however, it still remains a challenge to understand how the conformational properties of these polymers arise from the interplay of their architectural parameters. In this work, extensive simulations were performed using dissipative particle dynamics to investigate the effect of grafting density, backbone length, and sidechain length on the conformations of comb-like polymers immersed in a good solvent. To quantify the effect of these architectural parameters on polymer conformations, we computed the asphericity, radius of gyration, and backbone and sidechain end-to-end distances. Bond–bond correlation functions and effective Kuhn lengths were computed to quantify the topological stiffness induced by sidechain–sidechain interactions. Simulation results reveal that the effective Kuhn length increases as grafting density and sidechain length increase, in agreement with previous experimental and theoretical studies. This increase in stiffness results in comb-like polymers adopting extended conformations as grafting density and sidechain length increase. Simulation results regarding the radius of gyration of comb-like polymers as a function of grafting density are compared with scaling theory predictions based on a free energy proposed by Morozova and Lodge [ACS Macro Lett. 6, 1274–1279 (2017)] and scaling arguments by Tang et al. [Macromolecules 55, 8668–8675 (2022)]. [ABSTRACT FROM AUTHOR]

We analyze the shear response of grafted polymer chains in shear flow via coarse-grained molecular dynamics simulations with an explicit solvent. We find that the solvent flow penetrates into almost the whole brush for "mushroom"-type brushes but only a few bond distances for dense brushes. In all cases, the external stress on the wall equals the entropic stress associated with the distorted polymer conformations. We find that the external stress increases linearly with shear rate at low rates and sublinearly at high rates. The transition from linear to sublinear scaling occurs where chains react to flow by reorienting. Sublinear scaling with shear rate disappears if the shear rate is nondimensionalized with the effective relaxation time of chain subsegments located in the outer part of the brush that experiences flow. [ABSTRACT FROM AUTHOR]

Micelles of anionic or zwitterionic surfactants produced depletion interactions between nanofibrils leading to weak gels, while cationic surfactants adsorbed to the nanofibrils, screening repulsions leading to tough gels or phase separation. Are fundamentally and technologically interesting due to their diverse building blocks, network-supporting attractive forces, and gelation pathways. As described below, the 29 articles that appear in this issue shed new light on a wide variety of related topics, including limited valence networks, bridged colloidal networks and coagulant gels, depletant-mediated gels, I in situ i structural characterization of gel aging, mechanical and rheological properties of colloidal networks, hybrid and deformable particle assemblies, and nanocrystal gels with tunable optical response. Bridged networks and coagulant gels Colloidal networks formed by nonspecific bridging polymers represent another interesting class of gel formers, although it can be challenging to design dispersible systems with tunable polymer-colloid interactions. [Extracted from the article]

To examine the conventional idea that the gauche conformation of the OCCO dihedral angle promotes the dissolution of polyethylene glycol (PEG) in water through strong hydration, the thermodynamic properties of liquid mixtures of PEG and water were studied by means of polymer reference interaction site model (PRISM) theory. The intramolecular correlation functions required as input for PRISM theory were calculated by the generator matrix method, accompanied by changes in the distribution of dihedral angles. In the infinite dilution limit, the increased probability of gauche conformation of the OCCO dihedral angles stabilizes the hydration of PEG through enhanced hydrogen bonding between the ether oxygen of PEG and water. The mixing Gibbs energies of the liquid mixtures were also calculated in the whole concentration range based on the Gibbs–Duhem equation, as per our recent proposal. A liquid–liquid phase separation was observed when all the dihedral angles of PEG were in the trans conformation; for the liquid mixture to be miscible in the whole concentration range, the introduction of the OCCO gauche conformation was found to be indispensable. The above theoretical results support the conventional idea that the OCCO gauche conformation is important for the high miscibility of PEG and water. [ABSTRACT FROM AUTHOR]

The scattering functions of nine generations of ideal tri-functional comb and dendrimer polymers are computed by novel graph techniques. The properties of polymers having from 9 to 3069 branches are explored. The g-ratios and the scattering functions indicate that as the number of branches increases, comb polymers behave more and more like linear polymers with half the number of branches, whereas dendrimers become more like spherical objects. [ABSTRACT FROM AUTHOR]

Contemporary graph learning algorithms are not well-suited for large molecules since they do not consider the hierarchical interactions among the atoms, which are essential to determining the molecular properties of macromolecules. In this work, we propose Multiresolution Graph Transformers (MGT), the first graph transformer architecture that can learn to represent large molecules at multiple scales. MGT can learn to produce representations for the atoms and group them into meaningful functional groups or repeating units. We also introduce Wavelet Positional Encoding (WavePE), a new positional encoding method that can guarantee localization in both spectral and spatial domains. Our proposed model achieves competitive results on three macromolecule datasets consisting of polymers, peptides, and protein-ligand complexes, along with one drug-like molecule dataset. Significantly, our model outperforms other state-of-the-art methods and achieves chemical accuracy in estimating molecular properties (e.g., highest occupied molecular orbital, lowest unoccupied molecular orbital, and their gap) calculated by Density Functional Theory in the polymers dataset. Furthermore, the visualizations, including clustering results on macromolecules and low-dimensional spaces of their representations, demonstrate the capability of our methodology in learning to represent long-range and hierarchical structures. Our PyTorch implementation is publicly available at https://github.com/HySonLab/Multires-Graph-Transformer. [ABSTRACT FROM AUTHOR]

Following recent molecular dynamic simulations [M. Dinpajooh and A. Nitzan, J. Chem. Phys. 153, 164903 (2020)], we theoretically analyze how the phonon heat transport along a single polymer chain may be affected by varying the chain configuration. We suggest that phonon scattering controls the phonon heat conduction in strongly compressed (and tangled) chain when multiple random bends act as scattering centers for vibrational phonon modes, which results in the diffusive character of heat transport. As the chain is straightening up, the number of scatterers decreases, and the heat transport acquires nearly ballistic character. To analyze these effects, we introduce a model of a long atomic chain made out of identical atoms where some atoms are put in contact with scatterers and treat the phonon heat transfer through such a system as a multichannel scattering problem. We simulate the changes in the chain configurations by varying the number of the scatterers and mimic a gradual straightening of the chain by a gradual reducing of the number of scatterers attached to the chain atoms. It is demonstrated, in agreement with recently published simulation results, that the phonon thermal conductance shows a threshold-like transition from the limit where nearly all atoms are attached to the scatterers to the opposite limit where the scatterers vanish, which corresponds to a transition from the diffusive to the ballistic phonon transport. [ABSTRACT FROM AUTHOR]

Formation of base pairs between the nucleotides of a ribonucleic acid (RNA) sequence gives rise to a complex and often highly branched RNA structure. While numerous studies have demonstrated the functional importance of the high degree of RNA branching—for instance, for its spatial compactness or interaction with other biological macromolecules—RNA branching topology remains largely unexplored. Here, we use the theory of randomly branching polymers to explore the scaling properties of RNAs by mapping their secondary structures onto planar tree graphs. Focusing on random RNA sequences of varying lengths, we determine the two scaling exponents related to their topology of branching. Our results indicate that ensembles of RNA secondary structures are characterized by annealed random branching and scale similarly to self-avoiding trees in three dimensions. We further show that the obtained scaling exponents are robust upon changes in nucleotide composition, tree topology, and folding energy parameters. Finally, in order to apply the theory of branching polymers to biological RNAs, whose length cannot be arbitrarily varied, we demonstrate how both scaling exponents can be obtained from distributions of the related topological quantities of individual RNA molecules with fixed length. In this way, we establish a framework to study the branching properties of RNA and compare them to other known classes of branched polymers. By understanding the scaling properties of RNA related to its branching structure, we aim to improve our understanding of the underlying principles and open up the possibility to design RNA sequences with desired topological properties. [ABSTRACT FROM AUTHOR]

Mesogens, which are typically stiff rodlike or disklike molecules, are able to self-organize into liquid crystal (LC) phases in a certain temperature range. Such mesogens, or LC groups, can be attached to polymer chains in various configurations including within the backbone (main-chain LC polymers) or at the ends of side-chains attached to the backbone in an end-on or side-on configuration (side-chain LC polymers or SCLCPs), which can display synergistic properties arising from both their LC and polymeric character. At lower temperatures, chain conformations may be significantly altered due to the mesoscale LC ordering; thus, when heated from the LC ordered state through the LC to isotropic phase transition, the chains return from a more stretched to a more random coil conformation. This can cause macroscopic shape changes, which depend significantly on the type of LC attachment and other architectural properties of the polymer. Here, to study the structure–property relationships for SCLCPs with a range of different architectures, we develop a coarse-grained model that includes torsional potentials along with LC interactions of a Gay–Berne form. We create systems of different side-chain lengths, chain stiffnesses, and LC attachment types and track their structural properties as a function of temperature. Our modeled systems indeed form a variety of well-organized mesophase structures at low temperatures, and we predict higher LC-to-isotropic transition temperatures for the end-on side-chain systems than for analogous side-on side-chain systems. Understanding these phase transitions and their dependence on polymer architecture can be useful in designing materials with reversible and controllable deformations. [ABSTRACT FROM AUTHOR]

Many variants of RNA, DNA, and even proteins can be considered semiflexible polymers, where bending stiffness, as a type of energetic penalty, competes with attractive van der Waals forces in structure formation processes. Here, we systematically investigate the effect of the bending stiffness on ground-state conformations of a generic coarse-grained model for semiflexible polymers. This model possesses multiple transition barriers. Therefore, we employ advanced generalized-ensemble Monte Carlo methods to search for the lowest-energy conformations. As the formation of distinct versatile ground-state conformations, including compact globules, rod-like bundles, and toroids, strongly depends on the strength of the bending restraint, we also performed a detailed analysis of contact and distance maps. [ABSTRACT FROM AUTHOR]

Nonsolvent-induced phase separation (NIPS) is a popular method for creating polymeric particles with internal microstructure, but many fundamental questions remain surrounding the kinetics of the complex coupled mass transfer and phase separation processes. In this work, we use simulations of a phase-field model to examine how (i) finite domain boundaries of a polymer droplet and (ii) solvent/nonsolvent miscibility affect the NIPS process. To isolate the effects of phase separation kinetics and solvent/nonsolvent mass transfer on the NIPS process, we study two different cases. First, we investigate droplet concentrations that originate inside the two-phase region, where phase separation kinetics alone governs the microstructure. Second, we investigate the effects of solvent/nonsolvent mass transfer by studying droplet concentrations that begin outside the two-phase region, where both phase separation kinetics and mass transfer play a role. In both cases, we find that qualitative NIPS behavior is a strong function of the relative location of the initial droplet composition with respect to the phase diagram. We also find that polymer/nonsolvent miscibility competes with solvent/nonsolvent miscibility in driving NIPS kinetic behavior. Finally, we examine polymer droplets undergoing solvent/nonsolvent exchange and find that the model predicts droplets that shrink with nearly Fickian diffusion kinetics. We conclude with a brief perspective on the state of simulations of NIPS processes and some recommendations for future work. [ABSTRACT FROM AUTHOR]

Polymer cation exchange membranes (CEMs) are widely used in water treatment processes. The fundamental factors that control the separation and selectivity of cations with different valences in CEMs are not fully understood. In this study, we use atomistic molecular dynamics simulations to investigate the underlying molecular mechanisms that control the mobility of cations with different valences in Nafion membranes. Our results indicate structural differences in binding of monovalent and divalent cations, which gives rise to differences in ion diffusion in Nafion. Monovalent cations are shown to be "territorially" bound, i.e., bound while partially hydrated, to the fixed charge groups whereas divalent cations are shown to be "site" bound, i.e., bound while fully dehydrated, to the charge groups on the polymer. This difference in binding structure gives rise to differences in transport characteristics of cations in Nafion. [ABSTRACT FROM AUTHOR]

We develop a theory for the motion of a particle grafted with inhomogeneous bead-spring Rouse chains via the generalized Langevin equation (GLE), where individual grafted polymers are allowed to take different bead friction coefficients, spring constants, and chain lengths. An exact solution of the memory kernel K(t) is obtained for the particle in the time (t) domain in the GLE, which depends only on the relaxation of the grafted chains. The t-dependent mean square displacement g(t) of the polymer-grafted particle is then derived as a function of the friction coefficient γ0 of the bare particle and K(t). Our theory offers a direct way to quantify the contributions of the grafted chain relaxation to the mobility of the particle in terms of K(t). This powerful feature enables us to clarify the effect on g(t) of dynamical coupling between the particle and grafted chains, leading to the identification of a relaxation time of fundamental importance in polymer-grafted particles, namely, the particle relaxation time. This timescale quantifies the competition between the contributions of the solvent and grafted chains to the friction of the grafted particle and separates g(t) into the particle- and chain-dominated regimes. The monomer relaxation time and the grafted chain relaxation time further divide the chain-dominated regime of g(t) into subdiffusive and diffusive regimes. Analysis of the asymptotic behaviors of K(t) and g(t) provides a clear physical picture of the mobility of the particle in different dynamical regimes, shedding light on the complex dynamics of polymer-grafted particles. [ABSTRACT FROM AUTHOR]

Polymers contain functional groups that participate in hydrogen bond (H-bond) with water molecules, establishing a robust H-bond network that influences bulk properties. This study utilized molecular dynamics (MD) simulations to examine the H-bonding dynamics of water molecules confined within three poly(meth)acrylates: poly(2-methoxyethyl acrylate) (PMEA), poly(2-hydroxyethyl methacrylate) (PHEMA), and poly(1-methoxymethyl acrylate) (PMC1A). Results showed that H-bonding dynamics significantly slowed as the water content decreased. Additionally, the diffusion of water molecules and its correlation with H-bond breakage were analyzed. Our findings suggest that when the H-bonds between water molecules and the methoxy oxygen of PMEA are disrupted, those water molecules persist in close proximity and do not diffuse on a picosecond time scale. In contrast, the water molecules H-bonded with the hydroxy oxygen of PHEMA and the methoxy oxygen of PMC1A diffuse concomitantly with the breakage of H-bonds. These results provide an in-depth understanding of the impact of polymer functional groups on H-bonding dynamics. [ABSTRACT FROM AUTHOR]

Polymers conjugated with active agents have applications in biomedicine, anticorrosion, and smart agriculture. When the active agent is used as a drug, corrosion inhibitor, or pesticide, it can be released upon a specific stimulus. The efficiency and the sustainability of active agents are determined by the released kinetics. In this work, we study the fast-release kinetics of 8-hydroxyquinoline (8HQ) from a pH-responsive, random copolymer of methyl methacrylate and 8-quinolinyl-sulfide-ethyl acrylate [P(MMA-co-HQSEA)] by hydrolysis of the β-thiopropionate groups. We used contact angle measurements of sliding drops as an elegant way to characterize the release kinetics. Based on the results gained from 1H nuclear magnetic resonance measurement, fluorescent intensity measurement, and velocity-dependent contact angle measurement, we found that both the hydrolysis rate and polymer conformation affect the release kinetics of 8HQ from a P(MMA-co-HQSEA) film. Polymer chains collapse and further suppress the release from the inner layer in acidic conditions, while polymer chains in a stretched condition further facilitate the release from the inner layer. As a result, the cumulative release rate of 8HQ is higher in the basic condition than in the acidic condition. [ABSTRACT FROM AUTHOR]

We derive the non-adiabatic ring polymer molecular dynamics (RPMD) approach in the phase space of the SU(N) Lie Group. This method, which we refer to as the spin mapping non-adiabatic RPMD (SM-NRPMD), is based on the spin-mapping formalism for the electronic degrees of freedom (DOFs) and ring polymer path-integral description for the nuclear DOFs. Using the Stratonovich–Weyl transform for the electronic DOFs and the Wigner transform for the nuclear DOFs, we derived an exact expression of the Kubo-transformed time-correlation function (TCF). We further derive the spin mapping non-adiabatic Matsubara dynamics using the Matsubara approximation that removes the high frequency nuclear normal modes in the TCF and derive the SM-NRPMD approach from the non-adiabatic Matsubara dynamics by discarding the imaginary part of the Liouvillian. The SM-NRPMD method has numerical advantages compared to the original NRPMD method based on the Meyer–Miller–Stock–Thoss (MMST) mapping formalism due to a more natural mapping using the SU(N) Lie Group that preserves the symmetry of the original system. We numerically compute the Kubo-transformed position auto-correlation function and electronic population correlation function for three-state model systems. The numerical results demonstrate the accuracy of the SM-NRPMD method, which outperforms the original MMST-based NRPMD. We envision that the SM-NRPMD method will be a powerful approach to simulate electronic non-adiabatic dynamics and nuclear quantum effects accurately. [ABSTRACT FROM AUTHOR]

Polymer density functional theory (PDFT) is a computationally efficient and robust statistical mechanics theory for capturing the interfacial microstructure of grafted polymer brushes (PBs). Undoubtedly, the intramolecular and intermolecular interactions in PDFT (e.g., hard-core interactions and direct Coulomb interactions) are greatly affected by the grafting behavior of PBs. However, the combination of these interactions with the physical constraints on grafting behavior remains unclear and there is a remarkable difference in the density profile of grafted PB between PDFT and simulation. Herein, we propose a PDFT to study neutral and charged grafted PBs by incorporating the physical constraints of end-grafted PBs into the excess free energies due to intramolecular and intermolecular interactions. This PDFT has been successfully validated where the density distributions of neutral and weakly charged PBs predicted by the PDFT are in excellent agreement with the results of the Monte Carlo and molecular dynamics simulations. In addition, the significant contribution of grafting behavior to the free energy of PB systems is presented. Consequently, this work provides a powerful and accurate theoretical method to reveal the interfacial microstructure of grafted PBs. [ABSTRACT FROM AUTHOR]

We investigate the rheo-mechanical properties of Mebiol Gel®, a thermosensitive gel-forming polymer extensively used as a medium for cellular culture, using passive microrheology made either by standard dynamic light scattering or by photon correlation imaging. In the dilute limit, Mebiol displays a Newtonian behavior with an effective viscosity that decreases with temperature, consistent with a peculiar aggregation mechanism characterized by an increase of the molecular weight with a simultaneous reduction of the aggregate size. By increasing concentration and approaching gelation, both the storage and loss moduli show a nonmonotonic dependence with temperature, with a pronounced maximum around Tm ≃ 28–30 °C, the value above which, in the dilute limit, the individual Mebiol chains are fully compacted. Such a distinctive trend of the elastic and viscous properties persists within the gel, which, therefore, becomes "softer" above Tm. Although when temperature changes are performed adiabatically, the transition from the fluid to the gel phase takes place without any apparent discontinuity, a rapid T-jump leads to the formation of a hard gel at a concentration where a low heating rate conversely yields a fluid phase. This is a visible manifestation of the nonequilibrium nature of these physical gels. [ABSTRACT FROM AUTHOR]

We revisit a model of semiflexible Gaussian chains proposed by Winkler et al., solve the dynamics of the discrete description of the model, and derive exact algebraic expressions for some of the most relevant dynamical observables, such as the mean-square displacement of individual monomers, the dynamic structure factor, the end-to-end vector relaxation, and the shear stress relaxation modulus. The mathematical expressions for the dynamic structure factor are verified by comparing them with results from Brownian dynamics simulations, reporting an excellent agreement. Then, we generalize the model to linear polymer chains with arbitrary stiffness. In particular, we focus on the case of a linear polymer with stiffness that changes linearly from one end of the chain to the other, and we study the same dynamical functions previously presented. We discuss different approaches to check whether a polymer has constant or heterogeneous stiffness along its contour. Finally, we provide expressions for the Lagrangian multipliers for Gaussian chains with variable stiffness and bond length, as well as for chains with torsion-like interactions. Overall, this work presents a new insight into a well-known model for semiflexible chains and provides tools that can be exploited to explore a much broader class of polymers or compare the predictions of the model with simulations of coarse-grained semiflexible polymers. [ABSTRACT FROM AUTHOR]

We study the collective elastic behavior of semiflexible polymer solutions in a nematic liquid-crystalline state using polymer field theory. Our polymer field-theoretic model of semiflexible polymer solutions is extended to include second-order fluctuation corrections to the free energy, permitting the evaluation of the Frank elastic constants based on orientational order fluctuations in the nematic state. Our exact treatment of wormlike chain statistics permits the evaluation of behavior from the nematic state, thus accurately capturing the impact of single-chain behavior on collective elastic response. Results for the Frank elastic constants are presented as a function of aligning field strength and chain length, and we explore the impact of conformation fluctuations and hairpin defects on the twist, splay, and bend moduli. Our results indicate that the twist elastic constant Ktwist is smaller than both bend and splay constants (Kbend and Ksplay, respectively) for the entire range of polymer rigidity. Splay and bend elastic constants exhibit regimes of dominance over the range of chain stiffness, where Ksplay > Kbend for flexible polymers (large-N limit) while the opposite is true for rigid polymers. Theoretical analysis also suggests the splay modulus tracks exactly to that of the end-to-end distance in the transverse direction for semiflexible polymers at intermediate to large-N. These results provide insight into the role of conformation fluctuations and hairpin defects on the collective response of polymer solutions. [ABSTRACT FROM AUTHOR]

We present a simple mean-field theory to describe the polymer-mediated depletion attraction between colloidal particles that accounts for the polymer's chain stiffness. We find that for fixed polymer radius of gyration and volume fraction, the strength of this attraction increases with increasing chain stiffness in both dilute and semidilute concentration regimes. In contrast, the range of attraction monotonically decreases with chain stiffness in the dilute regime, while it attains a maximum in the semidilute regime. The obtained analytical expressions for the depletion interaction were compared with numerical self-consistent field lattice computations and shown to be in quantitative agreement. From the interaction potential between two spheres, we calculated the second osmotic virial coefficient B2, which appears to be a convex function of chain stiffness. A minimum of B2 as a function of chain stiffness was observed both in the numerical self-consistent field computations and the analytical theory. These findings help explain the general observation that semiflexible polymers are more effective depletants than flexible polymers and give insight into the phase behavior of mixtures containing spherical colloids and semiflexible polymers. [ABSTRACT FROM AUTHOR]

There are a variety of complementary descriptions of the temperature dependence of the structural relaxation time τ in glass-forming materials, which we interpret positively as suggesting an underlying unified description. We examine the inter-relation between the string model, an outgrowth of the Adam and Gibbs approach that emphasizes collective particle exchange motion, and the localization model, which emphasizes the volume explored by particles in their caged states, a kind of dynamic "free volume." Each model of liquid dynamics is described by a limited set of parameters that must be interrelated if both descriptions simultaneously describe the relaxation behavior. We pursue the consequences of this idea by performing coarse-grained molecular simulations of polymer melts with additives of variable size and interaction strength with the polymer matrix, thereby significantly altering the relaxation of the composite material. Both the string and localization models describe our relaxation time data well, and a comparison of the model parameters allows us to relate the local caging scale ⟨u2⟩ (the Debye-Waller parameter) to the entropy of activation for molecular rearrangements in the string model, thereby developing a bridge between these seemingly disparate approaches to liquid dynamics. [ABSTRACT FROM AUTHOR]

We report a colloid–polymer model system with tunable bridging interactions for microscopic studies of structure and dynamics using confocal imaging. The interactions between trifluoroethyl methacrylate-co-tert-butyl methacrylate copolymer particles and poly(acrylic acid) (PAA) polymers were controllable via polymer concentration and pH. The strength of adsorption of PAA on the particles, driven by pH-dependent interactions with polymer brush stabilizers on the particle surfaces, was tuned via solution pH. Particle–polymer suspensions formulated at low pH, where polymers strongly adsorbed to the particles, contained clusters or weak gels at particle volume fractions of ϕ = 0.15 and ϕ = 0.40. At high pH, where the PAA only weakly adsorbed to the particle surface, particles largely remained dispersed, and the suspensions behaved as a dense fluid. The ability to visualize the suspension structure is likely to provide insight into the role of polymer-driven bridging interactions in the behavior of colloidal suspensions. [ABSTRACT FROM AUTHOR]

Recent progress in establishing local order in polycarbonate-like glasses using rotational echo double resonance and centerband-only detection of exchange solid-state nuclear magnetic resonance (NMR) has stimulated a renewed attempt to connect molecular motion within glassy polymers and the mechanical properties of the glass. We have in fact established a correlation between molecular motion characterized by NMR and the mechanical secondary relaxation (tan δ) for nine polycarbonate-like glasses. All of the NMR and mechanical data are for T ≪ Tg. The resulting structural insights suggest that the chains of these polymers are simultaneously both Flory random coils and Vol'kenstein bundles. The cooperative motions of groups of bundles can be described qualitatively by a variety of constrained-kinetics models of the glass. All of the models share a common trait for large-amplitude motion: an exponential increase in the time required for an inter-bundle dilation event with a linear increase in bundle group size. This dependence and a locally ordered Vol'kenstein bundle lead to an understanding of the surprising 60° (K) shift of tan δ to higher temperature for ring-fluoro-polycarbonate relative to that of polycarbonate by the apparently minor substitution of a fluorine for a hydrogen on every fourth ring. [ABSTRACT FROM AUTHOR]

The artificial intelligence-based prediction of the mechanical properties derived from the tensile test plays a key role in assessing the application profile of new polymeric materials, especially in the design stage, prior to synthesis. This strategy saves time and resources when creating new polymers with improved properties that are increasingly demanded by the market. A quantitative structure–property relationship (QSPR) model for tensile strength at break is presented in this work. The QSPR methodology applied here is based on machine learning tools, visual analytics methods, and expert-in-the-loop strategies. From the whole study, a QSPR model composed of five molecular descriptors that achieved a correlation coefficient of 0.9226 is proposed. We applied visual analytics tools at two levels of analysis: a more general one in which models are discarded for redundant information metrics and a deeper one in which a chemistry expert can make decisions on the composition of the model in terms of subsets of molecular descriptors, from a physical-chemical point of view. In this way, with the present work, we close a contribution cycle to polymer informatics, providing QSPR models oriented to the prediction of mechanical properties related to the tensile test. [ABSTRACT FROM AUTHOR]

We investigate the local viscosity of a polymer glass around its glass transition temperature by using environment-sensitive fluorescent molecular rotors embedded in the polymer matrix. The fluorescence of the rotors depends on the local viscosity, and measuring the fluorescence intensity and lifetime of the probe therefore allows us to measure the local free volume in the polymer glass when going through the glass transition. This also allows us to study the local viscosity and free volume when the polymer film is put under an external stress. We find that the film does not flow homogeneously but undergoes shear banding that is visible as a spatially varying free volume and viscosity. [ABSTRACT FROM AUTHOR]

The ability of various cosolutes and cosolvents to enhance or quench solvent density fluctuations at solute–water interfaces has crucial implications on the conformational equilibrium of macromolecules such as polymers and proteins. Herein, we use an extended hydrophobic solute as a model system to study the effect of urea and methanol on the density fluctuations in the solute's solvation shell and the resulting thermodynamics. On strengthening the solute–water/cosolute repulsive interaction, we observe distinct trends in the mutual affinities between various species in, and the thermodynamic properties of, the solvation shell. These trends strongly follow the respective trends in the preferential adsorption of urea and methanol: solute–water/cosolute repulsion strengthens, urea accumulation decreases, and methanol accumulation increases. Preferential accumulation of urea is found to quench the density fluctuations around the extended solute, leading to a decrease in the compressibility of the solvation shell. In contrast, methanol accumulation enhances the density fluctuations, leading to an increase in the compressibility. The mode of action of urea and methanol seems to be strongly coupled to their hydration behavior. The observations from this simple model is discussed in relation to urea driven swelling and methanol induced collapse of some well-known thermo-responsive polymers. [ABSTRACT FROM AUTHOR]

Stretching of semicrystalline polymer materials is fundamentally important in their mechanical performance and industrial processing. By means of dynamic Monte Carlo simulations, we compared the parallel stretching processes between the initially bulk amorphous and semicrystalline polymers at various temperatures. In the early stage of stretching, semicrystalline polymers perform local and global melting-recrystallization behaviors at low and high temperatures, while the memory effects occur upon global melting-recrystallization at middle temperatures. However, the final crystallinities, crystalline bond orientations, chain-folding probabilities, residual stresses, and crystallite morphologies at high enough strains appear as the same at each temperature, irrelevant to the initially amorphous and semicrystalline polymers, indicating that the common post-growth melting-reorganization processes determine the final products. In addition, both final products harvest the highest crystallinities in the middle temperature region because the postgrowth stage yields the vast nuclei followed with less extent of crystal growth in the low temperature region and few nuclei followed with large extent of crystal growth in the high temperature region. Our observations imply that a large enough strain can effectively remove the thermal history of polymers, similar to the thermal treatment at a high enough temperature; therefore, the fracture strength of semicrystalline polymers depends upon their final structures in stretching, not related to their nascent semicrystalline structures. [ABSTRACT FROM AUTHOR]

In standard molecular junctions, a molecular structure is placed between and connected to metal leads. Understanding how mechanical tuning in such molecular junctions can change heat conductance has interesting applications in nanoscale energy transport. In this work, we use nonequilibrium molecular dynamics simulations to address the effect of stretching on the phononic contribution to the heat conduction of molecular junctions consisting of single long-chain alkanes and various metal leads, such as Ag, Au, Cu, Ni, and Pt. The thermal conductance of such junctions is found to be much smaller than the intrinsic thermal conductance of the polymer and significantly depends on the nature of metal leads as expressed by the metal–molecule coupling and metal vibrational density of states. This behavior is expected and reflects the mismatch of phonon spectra at the metal molecule interfaces. As a function of stretching, we find a behavior similar to what was observed earlier [M. Dinpajooh and A. Nitzan, J. Chem. Phys. 153, 164903 (2020)] for pure polymeric structures. At relatively short electrode distances, where the polyethylene chains are compressed, it is found that the thermal conductances of the molecular junctions remain almost constant as one stretches the polymer chains. At critical electrode distances, the thermal conductances start to increase, reaching the values of the fully extended molecular junctions. Similar behaviors are observed for junctions in which several long-chain alkanes are sandwiched between various metal leads. These findings indicate that this behavior under stretching is an intrinsic property of the polymer chain and not significantly associated with the interfacial structures. [ABSTRACT FROM AUTHOR]

Using analytical considerations and particle-based simulations of a coarse-grained model, we study the relaxation of a density modulation in a polymer system without nonbonded interactions. We demonstrate that shallow density modulations with identical amplitudes and wavevectors that have been prepared by different processes exhibit different nonexponential decay behaviors. Thus, in contrast to the popular assumption of dynamic self-consistent field theory, the density alone does not suffice to characterize the configuration of the polymer system. We provide an analytic description within Linear-Response Theory (LRT) and the Rouse model that quantitatively agree with the results of the particle-based simulations. LRT is equivalent to a generalized model-B dynamics with an Onsager coefficient that is nonlocal in space and time. Alternatively, the Rouse description can be cast into a dynamic density-functional theory that uses the full probability distribution of single-chain configurations as a dynamic variable and yields a memory-free description of the dynamics that quantitatively accounts for the dependence on the preparation process. An approximate scheme that only considers the joint distribution of the first two Rouse modes—the ellipsoid model—is also explored. [ABSTRACT FROM AUTHOR]

During fast diffusion-influenced polymerization, nonequilibrium behavior of the polymer chains and the surrounding reactive monomers has been reported recently. Based on the laws of thermodynamics, the emerging nonequilibrium structures should be characterizable by some "extra free energy" (excess over the equilibrium Helmholtz free energy). Here, we study the nonequilibrium thermodynamics of chain-growth polymerization of ideal chains in a dispersion of free reactive monomers, using off-lattice, reactive Brownian dynamics computer simulations in conjunction with approximative statistical mechanics and relative entropy (Gibbs–Shannon and Kullback–Leibler) concepts. In the case of fast growing polymers, we indeed report increased nonequilibrium free energies ΔFneq of several kBT compared to equilibrium and near-equilibrium, slowly growing chains. Interestingly, ΔFneq is a non-monotonic function of the degree of polymerization and thus also of time. Our decomposition of the thermodynamic contributions shows that the initial dominant extra free energy is stored in the nonequilibrium inhomogeneous density profiles of the free monomer gas (showing density depletion and wakes) in the vicinity of the active center at the propagating polymer end. At later stages of the polymerization process, we report significant extra contributions stored in the nonequilibrium polymer conformations. Finally, our study implies a nontrivial relaxation kinetics and "restoring" of the extra free energy during the equilibration process after polymerization. [ABSTRACT FROM AUTHOR]

The inclusion of nuclear quantum effects (NQEs) in molecular dynamics simulations is one of the major obstacles for an accurate modeling of molecular scattering processes involving more than a couple of atoms. An efficient method to incorporate these effects is ring polymer molecular dynamics (RPMD). Here, we extend the scope of our recently developed method based on non-equilibrium RPMD (NE-RPMD) from triatomic chemical reactions to reactions involving more atoms. We test the robustness and accuracy of the method by computing the integral cross sections for the H/F + CH4/CHD3 reactions where the methane molecule is either initially in its vibrational ground or excited state (C–H stretch). Furthermore, we analyze the extent to which NQEs are described by NE-RPMD. The method shows significant improvement over the quasiclassical trajectory approach while remaining computationally efficient. [ABSTRACT FROM AUTHOR]

Bottlebrush polymers are a class of highly branched macromolecules that show promise for applications such as self-assembled photonic materials and tunable elastomers. However, computational studies of bottlebrush polymer solutions and melts remain challenging due to the high computational cost involved in explicitly accounting for the presence of side chains. Here, we consider a coarse-grained molecular model of bottlebrush polymers where the side chains are modeled implicitly, with the aim of expediting simulations by accessing longer length and time scales. The key ingredients of this model are the size of a coarse-grained segment and a suitably coarse-grained interaction potential between the non-bonded segments. Prior studies have not focused on developing explicit forms of such potentials, instead, relying on scaling arguments to model non-bonded interactions. Here, we show how to systematically calculate an interaction potential between the coarse-grained segments of bottlebrush from finer grained explicit side chain models using Monte Carlo and Brownian dynamics and then incorporate it into an implicit side chain model. We compare the predictions from our coarse-grained implicit side chain model with those obtained from models with explicit side chains in terms of the potential of mean force, the osmotic second virial coefficient, and the interpenetration function, highlighting the range of applicability and limitations of the coarse-grained representation. Although presented in the context of homopolymer bottlebrushes in athermal solvents, our proposed method can be extended to other solvent conditions as well as to different monomer chemistries. We expect that our implicit side chain model will prove useful for accelerating large-scale simulations of bottlebrush solutions and assembly. [ABSTRACT FROM AUTHOR]

Although macromolecules such as polymers are in widespread industrial use, pure formulations rarely have precisely the properties new applications demand. Pure polymer is often too brittle and inflexible, necessitating plasticizers to soften or toughen films and bulk polymer materials. In practice, new formulations are developed by extensive trial-and-error methods, as no general molecular explanations exist for the mechanism of plasticization to aid in determining the optimal structure and concentration of plasticizers. Here, through atomistic molecular simulations augmented with advanced sampling techniques, we develop an atomic-level picture of the processes in plasticization by directly calculating free energies that govern the interaction between polymers and small-molecule plasticizers. This work focuses on the influence of two common plasticizer molecules—glycerol and sorbitol—interacting with polyvinyl alcohol (PVA), a frequently used component of polymer films. In particular, we focus on conformational and hydrogen bond structure changes induced in globules of PVA by the plasticizer molecules, with the hypothesis that hydrogen bonding plays a role in the incorporation of these plasticizers into PVA and, thus, in the observed mechanical properties. While we focus on nanoscopic systems, we observe distinct preferences in the conformational free energy that can be connected to the performance of polymer materials at laboratory and industrial scales. This work presents a new molecular perspective from which effective plasticizers can be developed and presents a firm basis from which important analyses of plasticization in complex chemical environments relevant to industry may be developed. [ABSTRACT FROM AUTHOR]