Conformational phase diagram for polymers adsorbed on ultrathin nanowires

Supervised and unsupervised machine learning of structural phases of polymers adsorbed to nanowires

We identify configurational phases and structural transitions in a polymer nanotube composite by means of machine learning. We employ various unsupervised dimensionality reduction methods, conventional neural networks, as well as the confusion method, an unsupervised neural-network-based approach. We find neural networks are able to reliably recognize all configurational phases that have been found previously in experiment and simulation. Furthermore, we locate the boundaries between configurational phases in a way that removes human intuition or bias. This could be done before only by relying on preconceived, ad hoc order parameters.

Structure and dynamics of an active polymer adsorbed on the surface of a cylinder

The structure and dynamics of an active polymer on a smooth cylindrical surface are studied by Brownian dynamics simulations. The effect of an active force on the polymer adsorption behavior and the combined effect of chain mobility, length N, rigidity κ, and cylinder radius, R, on the phase diagrams are systemically investigated. We find that complete adsorption is replaced by the irregular alternative adsorption/desorption process at a large driving force. Three typical (spiral, helix-like, and rod-like) conformations of the active polymer are observed, dependent on N, κ, and R. Dynamically, the polymer shows rotational motion in the spiral state, snake-like motion in the intermediate state, and straight translational motion without turning back in the rod-like state. In the spiral state, we find that the rotation velocity ω and the chain length follow a power-law relation ω ∼ N^-0.42, consistent with the torque-balance theory of general Archimedean spirals. And the polymer shows super-diffusive behavior along the cylinder for a long time in the helix-like and rod-like states. Our results highlight that the mobility, rigidity, and curvature of surface can be used to regulate the polymer behavior.

Directed Assembly of Hybrid Nanomaterials and Nanocomposites

Hybrid nanomaterials are molecular or colloidal-level combinations of organic and inorganic materials, or otherwise strongly dissimilar materials. They are often, though not exclusively, anisotropic in shape. A canonical example is an inorganic nanorod or nanosheet sheathed in, or decorated by, a polymeric or other organic material, where both the inorganic and organic components are important for the properties of the system. Hybrid nanomaterials and nanocomposites have generated strong interest for a broad range of applications due to their functional properties. Generating macroscopic assemblies of hybrid nanomaterials and nanomaterials in nanocomposites with controlled orientation and placement by directed assembly is important for realizing such applications. Here, a survey of critical issues and themes in directed assembly of hybrid nanomaterials and nanocomposites is provided, highlighting recent efforts in this field with particular emphasis on scalable methods.

Polymer adsorption on curved surfaces

The conformational behavior of a coarse-grained finite polymer chain near an attractive spherical surface was investigated by means of multicanonical Monte Carlo computer simulations. In a detailed analysis of canonical equilibrium data over a wide range of sphere radius and temperature, we have constructed entire phase diagrams both for nongrafted and end-grafted polymers. For the identification of the conformational phases, we have calculated several energetic and structural observables such as gyration tensor based shape parameters and their fluctuations by canonical statistical analysis. Despite the simplicity of our model, it qualitatively represents in the considered parameter range real systems that are studied in experiments. The work discussed here could have experimental implications from protein-ligand interactions to designing nanosmart materials.

Subphase transitions in first-order aggregation processes

In this paper, we investigate the properties of aggregation transitions in the context of generic coarse-grained homopolymer systems. By means of parallel replica-exchange Monte Carlo methods, we perform extensive simulations of systems consisting of up to 20 individual oligomer chains with five monomers each. Using the tools of the versatile microcanonical inflection-point analysis, we show that the aggregation transition is a first-order process consisting of a sequence of subtransitions between intermediate structural phases. We unravel the properties of these intermediate phases by collecting and analyzing their individual contributions towards the density of states of the system. The central theme of this systematic study revolves around translational entropy and its role in the striking phenomena of missing intermediate phases. We conclude with a brief discussion of the scaling properties of the transition temperature and the latent heat.

Significance of bending restraints for the stability of helical polymer conformations

We performed parallel-tempering Monte Carlo simulations to investigate the formation and stability of helical tertiary structures for flexible and semiflexible polymers, employing a generic coarse-grained model. Structural conformations exhibit helical order with tertiary ordering into single helices, multiple helical segments organized into bundles, and disorganized helical arrangements. For both bending-restrained semiflexible and bending-unrestrained flexible helical polymers, the stability of the structural phases is discussed systematically by means of hyperphase diagrams parametrized by suitable order parameters, temperature, and torsion strength. This exploration lends insight into the restricted flexibility of biological polymers such as double-stranded DNA and proteins.

Structural phases of adsorption for flexible polymers on nanocylinder surfaces

By means of generalized-ensemble Monte Carlo simulations, we investigate the thermodynamic behavior of a flexible, elastic polymer model in the presence of an attractive nanocylinder. We systematically identify the structural phases that are formed by competing monomer-monomer and monomer-substrate interactions. The influence of the relative surface attraction strength on the structural phases in the hyperphase diagram, parameterized by cylinder radius and temperature, is discussed as well. In the limiting case of the infinitely large cylinder radius, our results coincide with previous outcomes of studies of polymer adsorption on planar substrates.

Confinement effects upon the separation of structural transitions in linear systems with restricted bond fluctuation ranges

By means of advanced parallel replica-exchange Monte Carlo methods we examine the influence of elasticity and confinement on the structural transitions of linear systems with restricted bonded interaction. For this purpose, we adopt a model for coarse-grained flexible polymers of finite length in the dilute regime. Hyperphase diagrams are constructed using energy-dependent canonical quantities to demonstrate the effects of the changes in the range of the confined interaction on the liquid and solid structural phases. With increasing bonded interaction range we observe the disappearance of the liquid phase and the fusion of the gas-liquid (or Θ) and the liquid-solid transitions. One of the most remarkable features, the liquid-gas transition, changes from second to first order if the confined interaction range exceeds a threshold that separates polymeric from nonpolymeric systems. The notoriously difficult sampling of the entropically suppressed conformations in the region of very strong first-order transitions is improved by using multiple Gaussian modified ensembles.

Inverted critical adsorption of polyelectrolytes in confinement

What are the fundamental laws for the adsorption of charged polymers onto oppositely charged surfaces, for convex, planar, and concave geometries? This question is at the heart of surface coating applications, various complex formation phenomena, as well as in the context of cellular and viral biophysics. It has been a long-standing challenge in theoretical polymer physics; for realistic systems the quantitative understanding is however often achievable only by computer simulations. In this study, we present the findings of such extensive Monte-Carlo in silico experiments for polymer-surface adsorption in confined domains. We study the inverted critical adsorption of finite-length polyelectrolytes in three fundamental geometries: planar slit, cylindrical pore, and spherical cavity. The scaling relations extracted from simulations for the critical surface charge density σc-defining the adsorption-desorption transition-are in excellent agreement with our analytical calculations based on the ground-state analysis of the Edwards equation. In particular, we confirm the magnitude and scaling of σc for the concave interfaces versus the Debye screening length 1/κ and the extent of confinement a for these three interfaces for small κa values. For large κa the critical adsorption condition approaches the known planar limit. The transition between the two regimes takes place when the radius of surface curvature or half of the slit thickness a is of the order of 1/κ. We also rationalize how σc(κ) dependence gets modified for semi-flexible versus flexible chains under external confinement. We examine the implications of the chain length for critical adsorption-the effect often hard to tackle theoretically-putting an emphasis on polymers inside attractive spherical cavities. The applications of our findings to some biological systems are discussed, for instance the adsorption of nucleic acids onto the inner surfaces of cylindrical and spherical viral capsids.

Adsorption and pattern recognition of polymers at complex surfaces with attractive stripelike motifs

We construct the complete structural phase diagram of polymer adsorption at substrates with attractive stripelike patterns in the parameter space spanned by the adsorption affinity of the stripes and temperature. Results were obtained by extensive generalized-ensemble Monte Carlo simulations of a generic model for the hybrid organic-inorganic system. By comparing with adhesion properties at homogeneous substrates, we find substantial differences in the formation of adsorbed polymer structures if translational invariance at the surface is broken by a regular pattern. Beside a more specific understanding of polymer adsorption processes, our results are potentially relevant for the design of macromolecular pattern recognition devices such as sensors.

Ground-state properties of a polymer chain in an attractive sphere

We analyze the structural formation of a polymer chain inside of an attractive sphere depending on the attraction strength. Our model is composed of a coarse-grained polymer and an attractive sphere potential. Within this frame, multicanonical Monte Carlo simulations are employed to identify the global minimum energies for a polymer chain interacting with the attractive inner wall of the sphere. Different compact structures are found with varying attraction strengths, among which are spherical, three/two, or monolayer. The conformational properties of these structures are presented.