The translocation of biopolymers, such as DNA and proteins, across cellular or nuclear membranes is essential for numerous biological processes. The translocation dynamics are influenced by the properties of the polymers, such as polymer stiffness, and the geometry of the capsid. In our study, we aim to investigate the impact of polymer stiffness, activity, and different capsid geometries on the packing and ejection dynamics of both passive and active polymers. We employ Langevin dynamics simulations for a systematic investigation. We observe that flexible polymers exhibit packing times that are faster than those of their semi-flexible counterparts. Interestingly, for large polymers compared to the capsid size, sphere facilitates faster packing and unpacking compared to ellipsoid, mimicking the cell nucleus and suggesting a geometrical advantage for biopolymer translocation. In summary, we observe that increasing activity accelerates both the packing and ejection processes for both flexible and semi-flexible polymers. However, the effect is significantly more pronounced for semi-flexible polymers, highlighting the crucial role of polymer flexibility in these dynamics. These finding
The use of chemical warfare agents (CWAs) in modern warfare cannot be disregarded due to their ease of use and potential for large-scale incapacitation. An effective countermeasure involves the physical adsorption of these agents, preventing their entry through the respiratory tract by non-specific adsorption. In this study, we investigate the physical interaction between potential adsorbents and model gases mimicking CWAs, thereby identifying sufficient conditions for higher physical adsorption performance. Our findings reveal that the physical adsorption capacity is highly sensitive to the surface properties of the adsorbents, with uniform development of micropores, rather than solely high surface area, emerging as a critical factor. Additionally, we identified the potential of porous organic polymers as promising alternatives to conventional activated carbon-based adsorbents. Through a facile introduction of polar sulfone functional groups on the polymer surface, we demonstrated that these polar surface polymers exhibit physical adsorption capabilities for formaldehyde under ambient conditions comparable to high-performance activated carbons. Notably, the superior activated carb
The investigation of a dilute solution of phantom ideal ring polymers and ring polymers with excluded volume interactions (EVI) in a good solvent confined in a slit geometry of two parallel repulsive walls and in a solution of colloidal particles of big size was performed. Taking into account the correspondence between the field theoretical $φ^4$ $O(n)$-vector model in the limit $n\to 0$ and the behaviour of long-flexible polymers in a good solvent, the correspondent depletion forces and the forces which exert phantom ideal ring polymers and ring polymers with EVI on the walls were obtained in the framework of the massive field theory approach at fixed space dimensions $d$=3 up to one-loop order. Besides, taking into account the Derjaguin approximation, the depletion forces between big colloidal particle and a wall and in the case of two big colloidal particles were calculated. The obtained results indicate that phantom ideal ring polymers and ring polymers with EVI due to the complexity of chain topology and for entropical reasons demonstrate a completely different behaviour in confined geometries compared with linear polymers.
The structure and function of polymers in confined environments, e.g., biopolymers in the cytoplasm of a cell, are strongly affected by macromolecular crowding. To explore the influence of solvent quality on conformations of crowded polymers, we model polymers as penetrable ellipsoids, whose shape fluctuations are governed by the statistics of self-avoiding walks, appropriate for a polymer in a good solvent. Within this coarse-grained model, we perform Monte Carlo simulations of mixtures of polymers and hard-nanosphere crowders, including trial changes in polymer size and shape. Penetration of polymers by crowders is incorporated via a free energy cost predicted by polymer field theory. To analyze the impact of crowding on polymer conformations in different solvents, we compute average polymer shape distributions, radius of gyration, volume, and asphericity over ranges of polymer-to-crowder size ratio and crowder volume fraction. The simulation results are accurately predicted by a free-volume theory of polymer crowding. Comparison of results for polymers in good and theta solvents indicates that excluded-volume interactions between polymer segments significantly affect crowding, e
In this article, we review thermal transport in polymers with different morphologies from aligned fibers to bulk amorphous states. We survey early and recent efforts in engineering polymers with high thermal conductivity by fabricating polymers with large-scale molecular alignments. The experimentally realized extremely high thermal conductivity of polymer nanofibers are highlighted, and understanding of thermal transport physics from molecular simulations are discussed. We then transition to the discussion of bulk amorphous polymers with an emphasize on the physics of thermal transport and its relation with the conformation of molecular chains in polymers. We also discuss the current understanding of how the chemistry of polymers would influence thermal transport in amorphous polymers and some limited, but important chemistry-structural-property relationships. Lastly, challenges, perspectives and outlook of this field are presented. We hope this review will inspire more fundamental and applied research in the polymer thermal transport field to advance scientific understanding and engineering applications.
We focus on polymer-grafted nanoparticles (PGNP). A PGNP is composed of two different layers: the hard core of a nanoparticle and the soft corona of grafted polymers on the surface. It is predicted that PGNPs with these two distinct layers will have similar behaviors as star polymers and hard spheres. The interaction between PGNPs strongly depend upon their grafting density and the length of the grafted polymer chains, N. Thus, PGNP may exhibit polymorphism. Moreover, it is expected that crystals made from PGNPs will be structurally tough due to the entanglement of grafted polymers. The crystal polymorph of PGNP is explored using molecular dynamics simulations. We succeeded in finding FCC/HCP and BCC crystals depending on the length of the grafted polymer chain. When N is small, PGNPs behave like hard spheres. The crystals formed are arranged in FCC/HCP structure, much like the phase transition observed in an Alder transition. When N is large enough, the increase in the free energy of grafted polymers can no longer be neglected. Thus, the crystals formed in these systems are arranged in BCC structure, which has a lower density than FCC/HCP. When N is not too small or large, FCC/HCP
We present using simple scaling arguments and one step replica symmetry breaking a theory for the localization of semiflexible polymers in a quenched random environment. In contrast to completely flexible polymers, localization of semiflexible polymers depends not only on the details of the disorder but also on the ease with which polymers can bend. The interplay of these two effects can lead to the delocalization of a localized polymer with an increase in either the disorder density or the stiffness. Our theory provides a general criterion for the delocalization of polymers with varying degrees of flexibility and allows us to propose a phase diagram for the highly folded (localized) states of semiflexible polymers as a function of the disorder strength and chain rigidity.
Experiments using nanofluidic devices have proven effective in characterizing the physical properties of polymers confined to small cavities. Two recent studies using such methods examined the organization and dynamics of two DNA molecules in box-like cavities with strong confinement in one direction and with square and elliptical cross sections in the lateral plane. Motivated by these experiments, we employ Monte Carlo and Brownian dynamics simulations to study the physical behaviour of two polymers confined to small cavities with shapes comparable to those used in the experiments. We quantify the effects of varying the following polymer properties and confinement dimensions on the organization and dynamics of the polymers: the polymer width, the polymer contour length ratio, the cavity cross-sectional area, and the degree of cavity elongation for cavities with rectangular and elliptical cross sections. We find that the tendency for polymers to segregate is enhanced by increasing polymer width. For sufficiently small cavities, increasing cavity elongation promotes segregation and localization of identical polymers to opposite sides of the cavity along its long axis. A free-energy
We generalize the construction of connected branched polymers and the notion of the volume of the space of connected branched polymers studied by Brydges and Imbrie, and Kenyon and Winkler to any hyperplane arrangement A. The volume of the resulting configuration space of connected branched polymers associated to the hyperplane arrangement A is expressed through the value of the characteristic polynomial of A at 0. We give a more general definition of the space of branched polymers, where we do not require connectivity, and introduce the notion of q-volume for it, which is expressed through the value of the characteristic polynomial of A at -q. Finally, we relate the volume of the space of branched polymers to broken circuits and show that the cohomology ring of the space of branched polymers is isomorphic to the Orlik-Solomon algebra.
Due to their unique topology of having no chain ends, dilute solutions of ring polymers exhibit behaviour distinct from their linear chain counterparts. The universality of their static and dynamic properties, as a function of solvent quality $z$ in the thermal crossover regime between $θ$ and athermal solvents, is studied here using Brownian dynamics simulations. The universal ratio $U_{\text{RD}}$ of the radius of gyration $R_g$ to the hydrodynamic radius $R_H$ is determined, and a comparative study of the swelling ratio $α_g$ of the radius of gyration, the swelling ratio $α_H$ of the hydrodynamic radius, and the swelling ratio $α_X$ of the mean polymer stretch $X$ along the $x$-axis, for linear and ring polymers, is carried out. The ratio $U_{\text{RD}}$ for dilute ring polymer solutions is found to converge asymptotically to a constant value as $z \to \infty$, which is a major difference from the behaviour of solutions of linear chains, where no such asymptotic limit exists. Additionally, the ratio of the mean stretch along the $x$-axis to the hydrodynamic radius, $(X/R_H)$, is found to be independent of $z$ for polymeric rings, unlike in the case for linear polymers. These res
We show how to coarse grain polymers in a good solvent as single particles, interacting with density-independent or density-dependent interactions. These interactions can be between the centres of mass, the mid-points or end-points of the polymers. We also show how to extend these methods to polymers in poor solvents and mixtures of polymers. Treating polymers as soft colloids can greatly speed up the simulation of complex many-polymer systems, including polymer-colloid mixtures.
Polymers are widely used in industry and in our daily life because of their diverse functionality, light weight, low cost and excellent chemical stability. However, on some applications such as heat exchangers and electronic packaging, the low thermal conductivity of polymers is one of the major technological barriers. Enhancing the thermal conductivity of polymers is important for these applications and has become a very active research topic over the past two decades. In this review article, we aim to: 1). systematically summarize the molecular level understanding on the thermal transport mechanisms in polymers in terms of polymer morphology, chain structure and inter-chain coupling; 2). highlight the rationales in the recent efforts in enhancing the thermal conductivity of nanostructured polymers and polymer nanocomposites. Finally, we outline the main advances, challenges and outlooks for highly thermal-conductive polymer and polymer nanocomposites.
We review recent results of the field theoretical renormalization group analysis on the scaling properties of star polymers. We give a brief account of how the numerical values of the exponents governing the scaling of star polymers were obtained as well as provide some examples of the phenomena governed by these exponents. In particular we treat the interaction between star polymers in a good solvent, the Brownian motion near absorbing polymers, and diffusion-controlled reactions involving polymers.
Chain-like macromolecules (polymers) show characteristic adsorption properties due to their flexibility and internal degrees of freedom, when attracted to surfaces and interfaces. In this review we discuss concepts and features that are relevant to the adsorption of neutral and charged polymers at equilibrium, including the type of polymer/surface interaction, the solvent quality, the characteristics of the surface, and the polymer structure. We pay special attention to the case of charged polymers (polyelectrolytes) that have a special importance due to their water solubility. We present a summary of recent progress in this rapidly evolving field. Because many experimental studies are performed with rather stiff biopolymers, we discuss in detail the case of semi-flexible polymers in addition to flexible ones. We first review the behavior of neutral and charged chains in solution. Then, the adsorption of a single polymer chain is considered. Next, the adsorption and depletion processes in the many-chain case are reviewed. Profiles, changes in the surface tension and polymer surface excess are presented. Mean-field and corrections due to fluctuations and lateral correlations are dis
The conformational and dynamical properties of active polymers in solution are determined by the nature of the activity, and the behavior of polymers with self-propelled, active Brownian particle-type monomers differs qualitatively from that of polymers with monomers driven externally by colored noise forces. We present simulation and theoretical results for polymers in solution in the presence of external active noise. In simulations, a semiflexible bead-spring chain is considered, in analytical calculations, a continuous linear wormlike chain. Activity is taken into account by independent monomer/site velocities, with orientations changing in a diffusive manner. In simulations, hydrodynamic interactions (HI) are taken into account by the Rotne-Prager-Yamakawa tensor, or by an implementation of the active polymer in the multiparticle collision dynamics approach for fluids. To arrive at an analytical solution, the preaveraged Oseen tensor is employed. The active process implies a dependence of the stationary-state properties on HI via polymer relaxation times. With increasing activity, HI lead to an enhanced swelling of flexible polymers, and the conformational properties differ su
One of the grand challenges of utilizing machine learning for the discovery of innovative new polymers lies in the difficulty of accurately representing the complex structures of polymeric materials. Although a wide array of hand-designed polymer representations have been explored, there has yet to be an ideal solution for how to capture the periodicity of polymer structures, and how to develop polymer descriptors without the need for human feature design. In this work, we tackle these problems through the development of our periodic polymer graph representation. Our pipeline for polymer property predictions is comprised of our polymer graph representation that naturally accounts for the periodicity of polymers, followed by a message-passing neural network (MPNN) that leverages the power of graph deep learning to automatically learn chemically-relevant polymer descriptors. Across a diverse dataset of 10 polymer properties, we find that this polymer graph representation consistently outperforms hand-designed representations with a 20% average reduction in prediction error. Our results illustrate how the incorporation of chemical intuition through directly encoding periodicity into o
We investigate polymer partitioning from polymer mixtures into nanometer size cavities by formulating an equation of state for a binary polymer mixture assuming that only one (smaller) of the two polymer components can penetrate the cavity. Deriving the partitioning equilibrium equations and solving them numerically allows us to introduce the concept of "polymers-pushing-polymers" for the action of non-penetrating polymers on the partitioning of the penetrating polymers. Polymer partitioning into a pore even within a very simple model of a binary polymer mixture is shown to depend in a complicated way on the composition of the polymer mixture and/or the pore-penetration penalty. This can lead to enhanced as well as diminished partitioning, due to two separate energy scales that we analyse in detail.
We employ the recently introduced generalized microcanonical inflection point method for the statistical analysis of phase transitions in flexible and semiflexible polymers and study the impact of the bending stiffness upon the character and order of transitions between random-coil, globules, and pseudocrystalline conformations. The high-accuracy estimates of the microcanonical entropy and its derivatives required for this study were obtained by extensive replica-exchange Monte Carlo simulations. We observe that the transition behavior into the compact phases changes qualitatively with increasing bending stiffness. Whereas the $Θ$ collapse transition is less affected, the first-order liquid-solid transition characteristic for flexible polymers ceases to exist once bending effects dominate over attractive monomer-monomer interactions.
The interaction of polymers with small-scale velocity gradients can trigger a coil-stretch transition in the polymers. We analyze this transition within a direct numerical simulation of shear turbulence with an Oldroyd-B model for the polymer. In the coiled state the lengths of polymers are distributed algebraically with an exponent alpha=2 gamma-1/De, where gamma is a characteristic stretching rate of the flow and De the Deborah number. In the stretched state we demonstrate that the length distribution of the polymers is limited by the feedback to the flow.
We study an ensemble of branched polymers which are embedded on other branched polymers. This is a toy model which allows us to study explicitly the reaction of a statistical system on an underlying geometrical structure, a problem of interest in the study of the interaction of matter and quantized gravity. We find a phase transition at which the embedded polymers begin to cover the basis polymers. At the phase transition point the susceptibility exponent $γ$ takes the value 3/4 and the two-point function develops an anomalous dimension 1/2.