Semiflexible polymers under good solvent conditions interacting with repulsive walls

Adsorption-Driven Deformation and Footprints of the RBD Proteins in SARS-CoV-2 Variants on Biological and Inanimate Surfaces

Respiratory viruses, carried through airborne microdroplets, frequently adhere to surfaces, including plastics and metals. However, our understanding of the interactions between viruses and materials remains limited, particularly in scenarios involving polarizable surfaces. Here, we investigate the role of the receptor-binding domain (RBD) of the spike protein mutations on the adsorption of SARS-CoV-2 to hydrophobic and hydrophilic surfaces employing molecular simulations. To contextualize our findings, we contrast the interactions on inanimate surfaces with those on native biological interfaces, specifically the angiotensin-converting enzyme 2. Notably, we identify a 2-fold increase in structural deformations for the protein's receptor binding motif (RBM) onto inanimate surfaces, indicative of enhanced shock-absorbing mechanisms. Furthermore, the distribution of adsorbed amino acids (landing footprints) on the inanimate surface reveals a distinct regional asymmetry relative to the biological interface, with roughly half of the adsorbed amino acids arranged in opposite sites. In spite of the H-bonds formed at the hydrophilic substrate, the simulations consistently show a higher number of contacts and interfacial area with the hydrophobic surface, where the wild-type RBD adsorbs more strongly than the Delta or Omicron RBDs. In contrast, the adsorption of Delta and Omicron to hydrophilic surfaces was characterized by a distinctive hopping-pattern. The novel shock-absorbing mechanisms identified in the virus adsorption on inanimate surfaces show the embedded high-deformation capacity of the RBD without losing its secondary structure, which could lead to current experimental strategies in the design of virucidal surfaces.

Local and Global Order in Dense Packings of Semi-Flexible Polymers of Hard Spheres

The local and global order in dense packings of linear, semi-flexible polymers of tangent hard spheres are studied by employing extensive Monte Carlo simulations at increasing volume fractions. The chain stiffness is controlled by a tunable harmonic potential for the bending angle, whose intensity dictates the rigidity of the polymer backbone as a function of the bending constant and equilibrium angle. The studied angles range between acute and obtuse ones, reaching the limit of rod-like polymers. We analyze how the packing density and chain stiffness affect the chains' ability to self-organize at the local and global levels. The former corresponds to crystallinity, as quantified by the Characteristic Crystallographic Element (CCE) norm descriptor, while the latter is computed through the scalar orientational order parameter. In all cases, we identify the critical volume fraction for the phase transition and gauge the established crystal morphologies, developing a complete phase diagram as a function of packing density and equilibrium bending angle. A plethora of structures are obtained, ranging between random hexagonal closed packed morphologies of mixed character and almost perfect face centered cubic (FCC) and hexagonal close-packed (HCP) crystals at the level of monomers, and nematic mesophases, with prolate and oblate mesogens at the level of chains. For rod-like chains, a delay is observed between the establishment of the long-range nematic order and crystallization as a function of the packing density, while for right-angle chains, both transitions are synchronized. A comparison is also provided against the analogous packings of monomeric and fully flexible chains of hard spheres.

Depletion Interactions between Nanoparticles: The Effect of the Polymeric Depletant Stiffness

A Density Functional Theory is employed to study depletion interactions between nanoparticles mediated by semiflexible polymers. The four key parameters are the chain contour length and the persistence length of the polymeric depletant, its radius of gyration, and the nanoparticle radius. In the Density Functional Theory calculation of the depletion interaction between the nanoparticles mediated by semiflexible polymers, the polymer gyration radius is kept constant by varying the contour length and the persistence length simultaneously. This makes it possible to study the effect of the chain stiffness on the depletion potential of mean force between the nanoparticles for a given depletant size. It is found that the depletion attraction becomes stronger for stiffer polymer chains and larger colloids. The depletion potential of mean force is used as input to compute the phase diagram for an effective one-component colloidal system.

Depletion interaction mediated by semiflexible polymers

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.

Surface enrichment and interdiffusion in blends of semiflexible polymers of different stiffness

A model for a mixture of two kinds of semiflexible polymers (A and B) with the same chain length (N_A = N_B = 32), but different persistence lengths, confined between parallel planar repulsive walls in a common good solvent is studied by molecular dynamics simulations. In the isotropic phase at low polymer concentrations, both polymers are repelled by the walls, and the system is anisotropic near the walls over a range controlled by the polymer linear dimensions. Close to the concentrations where in the bulk nematic order sets in, precursors of thick nematic layers at the walls are observed, strongly enriched by a stiffer component, which hence is depleted in the center of the slit pore. At larger concentrations, where in the bulk a uniformly mixed nematic phase occurs, the enrichment of B-chains at the walls is rather minor, extending over the scale of the transverse correlation length of concentration fluctuations, which is of the order of a few monomeric diameters only for the present model. In this ordered phase, both self-diffusion and interdiffusion of chains (in the direction perpendicular to the director) are found to be significantly slowed down in comparison to dilute solutions. Since equilibration times scale with the square of the slit thickness, incomplete equilibration is predicted when polymeric coatings on substrate containing polymers differing in stiffness are produced.

The depletion thickness in solutions of semi-flexible polymers near colloidal surfaces: analytical approximations

We derive a simple, yet accurate approximate mean-field expression for the depletion thickness δ_sf of a solution of dilute semi-flexible polymers next to a hard surface. In the case of a hard wall this equation has the simple form δ_sf = δ₀[1 - tanh(p_sf/δ₀)], where p_sf accounts for the degree of flexibility and δ₀ is the depletion thickness in the case of fully flexible polymers. For fixed polymer coil size, increasing the chain stiffness leads to a decrease in the depletion thickness. The approach is also extended to include higher polymer concentrations in the semidilute regime. The analytical expressions are in quantitative agreement with numerical self-consistent field computations. A remarkable finding is that there is a maximum in the depletion thickness as a function of the chain stiffness in the semidilute concentration regime. This also means that depletion attractions between colloidal particles reach a maximum for a certain chain stiffness, which may have important implications for the phase stability of colloid-polymer mixtures. The derived equations could be useful for the description of interactions in- and phase stability of mixtures of colloids and semi-flexible polymers.

Bulk phase behavior and interfacial properties of binary mixtures of Lennard-Jones chains and solvent: a density functional theory study

A Density Functional Theory study is performed to analyze both bulk and interfacial properties of solvent-polymer binary mixtures. The effects of increasing polymer chain length on the bulk phase diagram morphology and interfacial tension are presented and compared to the prior simulation results. Good agreement between simulation and Density Functional Theory is found, including its ability to reproduce the density inversion phenomenon for highly asymmetric solvent-polymer binary mixtures. The data on the interfacial tensions is used to compute contact angles of the mixture at a planar wall, with particular focus on the wetting transition. The dependence of the wetting temperature on the polymer chain length and the mixture composition is analyzed in detail.

RNA Secondary Structures Regulate Adsorption of Fragments onto Flat Substrates

RNA is a functionally rich molecule with multilevel, hierarchical structures whose role in the adsorption to molecular substrates is only beginning to be elucidated. Here, we introduce a multiscale simulation approach that combines a tractable coarse-grained RNA structural model with an interaction potential of a structureless flat adsorbing substrate. Within this approach, we study the specific role of stem-hairpin and multibranch RNA secondary structure motifs on its adsorption phenomenology. Our findings identify a dual regime of adsorption for short RNA fragments with and without the secondary structure and underline the adsorption efficiency in both cases as a function of the surface interaction strength. The observed behavior results from an interplay between the number of contacts formed at the surface and the conformational entropy of the RNA molecule. The adsorption phenomenology of RNA seems to persist also for much longer RNAs as qualitatively observed by comparing the trends of our simulations with a theoretical approach based on an ideal semiflexible polymer chain.

Interactions between Sterically Stabilized Nanoparticles: The Effects of Brush Bidispersity and Chain Stiffness

Density Functional Theory is employed to study structural properties and interactions between solvent-free polymer-grafted nanoparticles. Both monodisperse and bidisperse polymer brushes with variable chain stiffness are considered. The three major control parameters are the grafting density, the grafted chain length, and its stiffness. The effect of these parameters on the brush-brush overlap and attractive interaction strength is analyzed. The Density Functional Theory results are compared with the available simulation data, and good quantitative agreement is found.

Multiscale Approaches for Confined Ring Polymer Solutions

We apply a hierarchy of multiscale modeling approaches to investigate the structure of ring polymer solutions under planar confinement. In particular, we employ both monomer-resolved (MR-DFT) and a coarse-grained (CG-DFT) density functional theories for fully flexible ring polymers, with the former based on a flexible tangent hard-sphere model and the latter based on an effective soft-colloid representation, to elucidate the ring polymer organization within slits of variable width in different concentration regimes. The predicted monomer and polymer center-of-mass densities in confinement, as well as the surface tension at the solution-wall interface, are compared to explicit molecular dynamics (MD) simulations. The approaches yield quantitative (MR-DFT) or semiquantitative (CG-DFT) agreement with MD. In addition, we provide a systematic comparison between confined linear and ring polymer solutions. When compared to their linear counterparts, the rings are found to feature a higher propensity to structure in confinement that translates into a distinct shape of the depletion potentials between two walls immersed into a polymer solution. The depletion potentials that we extract from CG-DFT and MR-DFT are in semiquantitative agreement with each other. Overall, we find consistency among all approaches as regards the shapes, trends, and qualitative characteristics of density profiles and depletion potentials induced on hard walls by linear and cyclic polymers.

Cylindrical confinement of solutions containing semiflexible macromolecules: surface-induced nematic order versus phase separation

Solutions of semiflexible polymers confined in cylindrical pores with repulsive walls are studied by Molecular Dynamics simulations for a wide range of polymer concentrations. Both the case where both lengths are of the same order and the case when the persistence length by far exceeds the contour length are considered, and the enhancement of nematic order along the cylinder axis is characterized. With increasing density the character of the surface effect changes from depletion to the formation of a layered structure. For binary 50 : 50 mixtures of the two types of polymers an interplay between surface enrichment of the stiffer component and the isotropic-nematic transition is found, and a phase separated structure with cylindrical symmetry occurs, with the isotropic phase located around the cylinder axis. For melt densities the mixed nematic phase forms at the wall a layer with a screw-like structure of a tilted smectic phase. The observed behavior is tentatively interpreted in terms of the competition of the chain orientational entropy with entropy of mixing and excluded volume due to the wall.

Phase Behavior of Lyotropic Liquid-Crystalline Polymers under Varying Solvent Conditions: Effect of External Fields on the Phase Diagram

In this work, we report a Density Functional Theory based study of phase behavior of lyotropic liquid-crystalline polymers under both good and varying solvent conditions in the presence of external electric or magnetic field. Our microscopic model for the good solvent case is based on the tangent hard-sphere chain with bond-bending potential to account for the chain stiffness; the variable solvent quality is modeled by adding attractive monomer-monomer interactions. The phase diagrams are constructed in three intensive variables (temperature, pressure, and field strength), and are characterized by the presence of critical and triple lines, which originate from the critical and triple points of the corresponding zero-field case. The merging of critical and triple lines results in the appearance of the "double critical" and "critical triple" points, already known from the earlier studies of the phase behavior of spin fluids in magnetic fields. The important difference of the present model from the spin fluids is due to the finite stiffness of the polymer chains (characterized by their persistence length), which adds an additional parameter controlling the morphology of the phase diagrams.

Semiflexible Polymers in Spherical Confinement: Bipolar Orientational Order Versus Tennis Ball States

Densely packed semiflexible polymers with contour length L confined in spheres with radius R of the same order as L cannot exhibit uniform nematic order. Depending on the chain stiffness (which we vary over a wide range), highly distorted structures form with topological defects on the sphere surface. These structures are completely different from previously observed ones of very long chains winding around the inner surface of spheres and from nematic droplets. At high densities, a thin shell of polymers close to the sphere surface exhibits a tennis ball texture due to the confinement-induced gradual bending of polymer bonds. In contrast, when the contour length of the chains is significantly smaller than the radius of the confining sphere, a few bent smectic layers form in the sphere. Molecular dynamics simulations demonstrate these complex structures, and suitable order parameters characterizing them are proposed.

Conformations and orientational ordering of semiflexible polymers in spherical confinement

Semiflexible polymers in lyotropic solution confined inside spherical nanoscopic "containers" with repulsive walls are studied by molecular dynamics simulations and density functional theory, as a first step to model confinement effects on stiff polymers inside of miniemulsions, vesicles, and cells. It is shown that the depletion effects caused by the monomer-wall repulsion depend distinctly on the radius R of the sphere. Further, nontrivial orientational effects occur when R, the persistence length ℓp, and the contour length L of the polymers are of similar magnitude. At intermediate densities, a "shell" of wall-attached chains is forming, such that the monomers belonging to those chains are in a layer at about the distance of one monomer from the container wall. At the same time, the density of the centers of mass of these chains is peaked somewhat further inside, but still near the wall. However, the arrangement of chains is such that the total monomer density is almost uniform in the sphere, apart from a small layering peak at the wall. It is shown that excluded volume effects among the monomers are crucial to account for this behavior, although they are negligible for comparable isolated single semiflexible chains of the same length.

Semiflexible polymers confined in a slit pore with attractive walls: two-dimensional liquid crystalline order versus capillary nematization

Semiflexible polymers under good solvent conditions interacting with attractive planar surfaces are investigated by Molecular Dynamics (MD) simulations and classical Density Functional Theory (DFT). A bead-spring type potential complemented by a bending potential is used, allowing variation of chain stiffness from completely flexible coils to rod-like polymers whose persistence length by far exceeds their contour length. Solvent is only implicitly included, monomer-monomer interactions being purely repulsive, while two types of attractive wall-monomer interactions are considered: (i) a strongly attractive Mie-type potential, appropriate for a strictly structureless wall, and (ii) a corrugated wall formed by Lennard-Jones particles arranged on a square lattice. It is found that in dilute solutions the former case leads to the formation of a strongly adsorbed surface layer, and the profile of density and orientational order in the z-direction perpendicular to the wall is predicted by DFT in nice agreement with MD. While for very low bulk densities a Kosterlitz-Thouless type transition from the isotropic phase to a phase with power-law decay of nematic correlations is suggested to occur in the strongly adsorbed layer, for larger densities a smectic-C phase in the surface layer is detected. No "capillary nematization" effect at higher bulk densities is found in this system, unlike systems with repulsive walls. This finding is attributed to the reduction of the bulk density (in the center of the slit pore) due to polymer adsorption on the attractive wall, for a system studied in the canonical ensemble. Consequently in a system with two attractive walls nematic order in the slit pore can occur only at a higher density than for a bulk system.

Concentration-induced planar-to-homeotropic anchoring transition of stiff ring polymers on hard walls

We study the structure and interfacial ordering of stiff ring polymers close to repulsive walls. For this purpose, we employ an anisotropic effective model in which the rings are pictured as soft, penetrable discs [P. Poier, C. N. Likos, A. J. Moreno and R. Blaak, Macromolecules, 2015, 48, 4983]. We have studied this model in the bulk and in the presence of a wall, employing Density Functional Theory and computer simulations. While the Ornstein-Zernike equation in combination with the Hypernetted Chain Approximation gives results that are in quantitative agreement with computer simulations, a simple Mean Field approximation strongly overestimates the interaction between the effective particles in the bulk. We discover that by increasing density one can induce a reorientation of the effective rings in the vicinity of a wall, which prefer to orient themselves parallel to the surface (face-on or planar) for low densities ρ and reorient orthogonal to the wall (edge-on or homeotropic) for higher values of ρ. This transition in the surface-structure can be observed in both computer simulations, as well as in an appropriate density functional theory. We trace its physical origin in the penetrable character of the rings, which allows for a reduction of the surface tension contribution due to ring-ring interactions upon the emergence of homeotropic ordering on the wall and increasing the density of the system.

Semiflexible Polymers in the Bulk and Confined by Planar Walls

Semiflexible polymers in solution under good solvent conditions can undergo an isotropic-nematic transition. This transition is reminiscent of the well-known entropically-driven transition of hard rods described by Onsager's theory, but the flexibility of the macromolecules causes specific differences in behavior, such as anomalous long wavelength fluctuations in the ordered phase, which can be understood by the concept of the deflection length. A brief review of the recent progress in the understanding of these problems is given, summarizing results obtained by large-scale molecular dynamics simulations and density functional theory. These results include also the interaction of semiflexible polymers with hard walls and the wall-induced nematic order, which can give rise to capillary nematization in thin film geometry. Various earlier theoretical approaches to these problems are briefly mentioned, and an outlook on the status of experiments is given. It is argued that in many cases of interest, it is not possible to describe the scaled densities at the isotropic-nematic transition as functions of the ratio of the contour length and the persistence length alone, but the dependence on the ratio of chain diameter and persistence length also needs to be considered.