Coupling of isotropic and directional interactions and its effect on phase separation and self-assembly

Theory of thermoreversible gelation and anomalous concentration fluctuations in polyzwitterion solutions

We present a theoretical framework to investigate thermoreversible phase transitions within polyzwitterion systems, encompassing macrophase separations (MPS) and gelation. In addition, we explore concentration fluctuations near critical points associated with MPS, as well as tricritical and bicritical points at the intersection of MPS and gelation. By utilizing mean-field percolation theory and field theory formalism, we derive the Landau free energy in terms of polyzwitterion concentration with fixed dipole strengths and other experimental variables, such as temperatures and salt concentrations. As the temperature decreases, the dipoles can form cross-links, resulting in polyzwitterion associations. The associations can grow to a gel network and enhance the propensity for MPS, including liquid-liquid, liquid-gel, and gel-gel phase separations. Remarkably, the associations also impact critical behaviors. Using the renormalization group technique, we find that the critical exponents of the polyzwitterion concentration correlation functions significantly deviate from those in the Ising universality class due to the presence of polyzwitterion associations, leading to crossover critical behaviors.

Influence of network defects on the conformational structure of nanogel particles: From "closed compact" to "open fractal" nanogel particles

We propose an approach to generate a wide range of randomly branched polymeric structures to gain general insights into how polymer topology encodes a configurational structure in solution. Nanogel particles can take forms ranging from relatively symmetric sponge-like compact structures to relatively anisotropic open fractal structures observed in some nanogel clusters and in some self-associating polymers in solutions, such as aggrecan solutions under physiologically relevant conditions. We hypothesize that this broad "spectrum" of branched polymer structures derives from the degree of regularity of bonding in the network defining these structures. Accordingly, we systematically introduce bonding defects in an initially perfect network having a lattice structure in three and two topological dimensions corresponding to "sponge" and "sheet" structures, respectively. The introduction of bonding defects causes these "closed" and relatively compact nanogel particles to transform near a well-defined bond percolation threshold into "open" fractal objects with the inherent anisotropy of randomly branched polymers. Moreover, with increasing network decimation, the network structure of these polymers acquires other configurational properties similar to those of randomly branched polymers. In particular, the mass scaling of the radius of gyration and its eigenvalues, as well as hydrodynamic radius, intrinsic viscosity, and form factor for scattering, all undergo abrupt changes that accompany these topological transitions. Our findings support the idea that randomly branched polymers can be considered to be equivalent to perforated sheets from a "universality class" standpoint. We utilize our model to gain insight into scattering measurements made on aggrecan solutions.

Comparative experimental and computational study of synthetic and natural bottlebrush polyelectrolyte solutions

We systematically investigate model synthetic and natural bottlebrush polyelectrolyte solutions through an array of experimental techniques (osmometry and neutron and dynamic light scattering) along with molecular dynamics simulations to characterize and contrast their structures over a wide range of spatial and time scales. In particular, we perform measurements on solutions of aggrecan and the synthetic bottlebrush polymer, poly(sodium acrylate), and simulations of solutions of highly coarse-grained charged bottlebrush molecules having different degrees of side-branch density and inclusion of an explicit solvent and ion hydration effects. While both systems exhibit a general tendency toward supramolecular organization in solution, bottlebrush poly(sodium acrylate) solutions exhibit a distinctive "polyelectrolyte peak" in their structure factor, but no such peak is observed in aggrecan solutions. This qualitative difference in scattering properties, and thus polyelectrolyte solution organization, is attributed to a concerted effect of the bottlebrush polymer topology and the solvation of the polymer backbone and counterions. The coupling of the polyelectrolyte topological structure with the counterion distribution about the charged polymer molecules along with direct polymer segmental hydration makes their solution organization and properties "tunable," a phenomenon that has significant ramifications for biological function and disease as well as for numerous materials applications.

Molecular recognition mechanisms directing the self-assembly of biological structures

Self-assembling may be defined as the spontaneous association of material units into structures that are often capable of cyclic reorganization and functional behavior. Various molecular recognition processes stabilize assemblies of polymers and biological structures. The present article analyzes cases in which chemical, shape and other recognition mechanisms are individually or cooperatively operative. Simpler self-assembling theories reported in the literature are highlighted. Detailed processes for which chemical recognition is the prevailing, enthalpy-driven, process include the non-ideal component of miscibility, supramolecular polymerization, host-guest complexes and template polymerization. Also discussed are systems such as liquid crystalline closed polymers, ternary mesogenic systems and rigid crystalline polymers for which shape recognition is the prevailing entropy-driven process. Other recognition mechanisms include ion condensation effects, hydrophobic bonding and growth-coupled-to-orientation. Combinations of various recognition mechanisms are particularly evident in biological structures. Self-assembling mechanisms involved in the genesis of some biological systems can be scientifically identified, but much more needs to be known to describe the "engineered" assembling modes that support complex functional organs.

Monte Carlo simulations of patch models with applications to soft matter

Patch models have been employed to describe anisotropic interactions in disparate soft matter systems. In this work, we present a unified study of a patch model to explore particle self-assembly in both monodisperse and polydisperse systems, with applications to both proteins and colloids. In the first case, we obtained a temperature-density phase diagram for a model of the protein polyglutamine from Monte Carlo simulations. These simulations evinced clusters in the gas phase and, via a comparison with the corresponding coarse-grained PLUM model for this system, we verified that dense clustering in the gas phase falls into the supersaturation region of the saturation curve. In the second case, we have investigated the effect of size polydispersity on the phase behavior of binary colloidal mixtures. It was found that the width of gas-liquid phase coexistence increases with increasing polydispersity and that, in addition to the aforementioned particle clustering, small particles decorate patches on large particles, thereby creating large-particle bridges. Our aim is to compare and contrast self-assembly in these two prototypical systems.

Phase diagram of two-patch colloids with competing anisotropic and isotropic interactions

Patchy particles are considered to be a good model for protein aggregation. We propose a novel method to generate different structures of glucose isomerase protein such as chains, crystals and bundles by utilising aggregation of two-patch colloidal particles in presence of competing isotropic and anisotropic potential. We calculate the equilibrium phase diagram of two-patch colloidal particles and demonstrates the coexistence of different phases like disordered clusters, chains, crystals and bundles depending on the relative strength of isotropic and anisotropic potential. We also show that the formation of network of bundles is metastable against the formation of thermodynamically favored finite sized bundles along with thermodynamically stable crystals. These bundles appear to be helical in structure similar to that observed in sickle cell hemoglobin. The simulation results show that the method can characterize phase behaviour of glucose isomerase protein, which provides a novel tool to unveil self-assembly mechanism of protein under different conditions.

Universal nature of dynamic heterogeneity in glass-forming liquids: A comparative study of metallic and polymeric glass-forming liquids

Glass-formation is a ubiquitous phenomenon that is often observed in a broad class of materials ranging from biological matter to commonly encountered synthetic polymer, as well as metallic and inorganic glass-forming (GF) materials. Despite the many regularities in the dynamical properties of GF materials, the structural origin of the universal dynamical properties of these materials has not yet been identified. Recent simulations of coarse-grained polymeric GF liquids have indicated the coexistence of clusters of mobile and immobile particles that appear to be directly linked, respectively, to the rate of molecular diffusion and structural relaxation. The present work examines the extent to which these distinct types of "dynamic heterogeneity" (DH) arise in metallic GF liquids (Cu-Zr, Ni-Nb, and Pd-Si alloys) having a vastly different molecular structure and chemistry. We first identified mobile and immobile particles and their transient clusters and found the DH in the metallic alloys to be remarkably similar in form to polymeric GF liquids, confirming the "universality" of the DH phenomenon. Furthermore, the lifetime of the mobile particle clusters was found to be directly related to the rate of diffusion in these materials, while the lifetime of immobile particles was found to be proportional to the structural relaxation time, providing some insight into the origin of decoupling in GF liquids. An examination of particles having a locally preferred atomic packing, and clusters of such particles, suggests that there is no one-to-one relation between these populations of particles so that an understanding of the origin of DH in terms of static fluid structure remains elusive.

Modeling the depletion effect caused by an addition of polymer to monoclonal antibody solutions

We present a theoretical study of colloidal stability of the model mixtures of monoclonal antibody molecules and non-adsorbing (no polymer-protein attraction) polymers. The antibodies are pictured as an assembly of seven hard spheres assuming a Y-like shape. Polymers present in the mixture are modeled as chain-like molecules having from 32 up to 128 monomers represented as hard spheres. We use Wertheim's thermodynamic perturbation theory to construct the two molecular species and to calculate measurable properties. The calculations are performed in the osmotic ensemble. In view that no direct attractive interaction is present in the model Hamiltonian, we only account for the entropic contribution to the phase equilibrium. We calculate chemical potentials and the equation of state for the model mixture to determine the liquid-liquid part of the phase diagram. We investigate how the critical antibody number density depends on the degree of polymerization and the bead size ratio of the polymer and protein components. The model mixture qualitatively correctly predicts some basic features of real systems. The effects of the model 'protein' geometry, that is the difference in results for the flexible Y-shaped protein versus the rigid spherical one, are also examined.

Aggregation kinetics of irreversible patches coupled with reversible isotropic interaction leading to chains, bundles and globules

In the present study we are performing simulation of simple model of two patch colloidal particles undergoing irreversible diffusion limited cluster aggregation using patchy Brownian cluster dynamics. In addition to the irreversible aggregation of patches, the spheres are coupled with isotropic reversible aggregation through the Kern–Frenkel potential. Due to the presence of anisotropic and isotropic potential we have also defined three different kinds of clusters formed due to anisotropic potential and isotropic potential only as well as both the potentials together. We have investigated the effect of patch size on self-assembly under different solvent qualities for various volume fractions. We will show that at low volume fractions during aggregation process, we end up in a chain conformation for smaller patch size while in a globular conformation for bigger patch size. We also observed a chain to bundle transformation depending on the attractive interaction strength between the chains or in other words depending on the quality of the solvent. We will also show that bundling process is very similar to nucleation and growth phenomena observed in colloidal system with short range attraction. We have also studied the bond angle distribution for this system, where for small patches only two angles are more probable indicating chain formation, while for bundling at very low volume fraction a tail is developed in the distribution. While for the case of higher patch angle this distribution is broad compared to the case of low patch angles showing we have a more globular conformation. We are also proposing a model for the formation of bundles which are similar to amyloid fibers using two patch colloidal particles.

Valence, loop formation and universality in self-assembling patchy particles

Patchy particles have emerged as an attractive model to mimic phase separation and self-assembly of globular proteins solutions, colloidal patchy particles, and molecular fluids where directional interactions are operative. In our previous work, we extensively explored the coupling of directional and isotropic interactions on both the phase separation and self-assembly in a system of patchy particles with five spots. Here, we extend this work to consider different patch valences and isotropic interaction strengths with an emphasis on self-assembly. Although the location of self-assembly transition lines in the temperature-density plane depend on a number of parameters, we find universal behavior of cluster size that is dependent only on the probability of a spot being bound, the patch valence, and the density. Using these principles, we quantify both the mass distribution and the shape for all clusters, as well as clusters containing loops. Following the logical implications of these results, combined with a simplified version of a mean-field theory that incorporates Flory-Stockmayer theory, we find a universal curve for the temperature dependence of cluster mass and a universal curve for the fraction of clusters that contain loops. As the curves are dependent on the particle valence, such results provide a method for parameterizing patchy particle models using experimental data.

Weak and Strong Gels and the Emergence of the Amorphous Solid State

Gels are amorphous solids whose macroscopic viscoelastic response derives from constraints in the material that serve to localize the constituent molecules or particles about their average positions in space. These constraints may either be local in nature, as in chemical cross-linking and direct physical associations, or non-local, as in case of topological "entanglement" interactions between highly extended fiber or sheet structures in the fluid. Either of these interactions, or both combined, can lead to "gelation" or "amorphous solidification". While gels are often considered to be inherently non-equilibrium materials, and correspondingly termed "soft glassy matter", this is not generally the case. For example, the formation of vulcanized rubbers by cross-linking macromolecules can be exactly described as a second order phase transition from an equilibrium fluid to an equilibrium solid state, and amorphous solidification also arises in diverse physical gels in which molecular and particle localization occurs predominantly through transient molecuar associations, or even topological interactions. As equilibrium, or near equilibrium systems, such gels can be expected to exhibit universal linear and non-linear viscoelastic properties, especially near the "critical" conditions at which the gel state first emerges. In particular, a power-law viscoelastic response is frequently observed in gel materials near their "gelation" or "amorphous solidification" transition. Another basic property of physical gels of both theoretical and practical interest is their response to large stresses at constant shear rate or under a fixed macrocopic strain. In particular, these materials are often quite sensitive to applied stresses that can cause the self-assembled structure to progressively break down under flow or deformation. This disintegration of gel structure can lead to "yield" of the gel material, i.e., a fluidization transition, followed by shear thinning of the resulting heterogeneous "jelly-like" fluid. When the stress is removed, however, the material can relax back to its former equilibrium gel state, i.e., gel rejuvenation. In constrast, a non-equilibrium material will simply change its form and properties in a way that depends on processing history. Physical gels are thus unique self-healing materials in which the existence of equilibrium ensures their eventual recovery. The existence of equilibrium also has implications for the nature of both the linear and non-linear rheological response of gel materials, and the present paper explores this phenomenon based on simple scaling arguments of the kind frequently used in describing phase transitions and the properties of polymer solutions.

Cluster Size and Quinary Structure Determine the Rheological Effects of Antibody Self-Association at High Concentrations

The question of how nonspecific reversible intermolecular protein interactions affect solution rheology at high concentrations is fundamentally rooted in the translation of nanometer-scale interactions into macroscopic properties. Well-defined solutions of purified monoclonal antibodies (mAbs) provide a useful system with which to investigate the manifold intricacies of weak protein interactions at high concentrations. Recently, characterization of self-associating IgG1 antibody (mAb2) solutions has established the direct role of protein clusters on concentrated mAb rheology. Expanding on our earlier work with three additional mAbs (mAb1, mAb3, and mAb4), the observed concentration-dependent static light scattering and rheological data present a substantially more complex relationship between protein interactions and solution viscosity at high concentrations. The four mAb systems exhibited divergent correlations between cluster formation (size) and concentrated solution viscosities dependent on mAb primary sequence and solution conditions. To address this challenge, well-established features of colloidal cluster phenomena could be applied as a framework for interpreting our observations. The initial stages of mAb cluster formation were investigated with small-angle X-ray scattering (SAXS) and ensemble-optimized fit methods, to uncover shifts in the dimer structure populations which are produced by changes in mAb interaction modes and association valence under the different solution conditions. Analysis of mAb average cluster number and effective hydrodynamic radii at high concentrations revealed cluster architectures can have a wide range of fractal dimensions. Collectively, the static light scattering, SAXS, and rheological characterization demonstrate that nonspecific and anisotropic attractive intermolecular interactions produce antibody clusters with different quinary structures to regulate the rheological properties of concentrated mAb solutions.

Mixtures of two self- and mutually-associating liquids: Phase behavior, second virial coefficients, and entropy-enthalpy compensation in the free energy of mixing

The theoretical description of the phase behavior of polymers dissolved in binary mixtures of water and other miscible solvents is greatly complicated by the self- and mutual-association of the solvent molecules. As a first step in treating these complex and widely encountered solutions, we have developed an extension of Flory-Huggins theory to describe mixtures of two self- and mutually-associating fluids comprised of small molecules. Analytic expressions are derived here for basic thermodynamic properties of these fluid mixtures, including the spinodal phase boundaries, the second osmotic virial coefficients, and the enthalpy and entropy of mixing these associating solvents. Mixtures of this kind are found to exhibit characteristic closed loop phase boundaries and entropy-enthalpy compensation for the free energy of mixing in the low temperature regime where the liquid components are miscible. As discussed by Widom et al. [Phys. Chem. Chem. Phys. 5, 3085 (2003)], these basic miscibility trends, quite distinct from those observed in non-associating solvents, are defining phenomenological characteristics of the "hydrophobic effect." We find that our theory of mixtures of associating fluids captures at least some of the thermodynamic features of real aqueous mixtures.

Universal interrelation between measures of particle and polymer size

The characterization of many objects involves the determination of a basic set of particle size measures derived mainly from scattering and transport property measurements. For polymers, these basic properties include the radius of gyration Rg, hydrodynamic radius Rh, intrinsic viscosity [η], and sedimentation coefficient S, and for conductive particles, the electric polarizability tensor αE and self-capacity C. It is often found that hydrodynamic measurements of size deviate from each other and from geometric estimates of particle size when the particle or polymer shape is complex, a phenomenon that greatly complicates both nanoparticle and polymer characterizations. The present work explores a general quantitative relation between αE, C, and Rg for nanoparticles and polymers of general shape and the corresponding properties η, Rh, and Rg using a hydrodynamic-electrostatic property interrelation.

Beyond histograms: efficiently estimating radial distribution functions via spectral Monte Carlo

Despite more than 40 years of research in condensed-matter physics, state-of-the-art approaches for simulating the radial distribution function (RDF) g(r) still rely on binning pair-separations into a histogram. Such methods suffer from undesirable properties, including subjectivity, high uncertainty, and slow rates of convergence. Moreover, such problems go undetected by the metrics often used to assess RDFs. To address these issues, we propose (I) a spectral Monte Carlo (SMC) quadrature method that yields g(r) as an analytical series expansion; and (II) a Sobolev norm that assesses the quality of RDFs by quantifying their fluctuations. Using the latter, we show that, relative to histogram-based approaches, SMC reduces by orders of magnitude both the noise in g(r) and the number of pair separations needed for acceptable convergence. Moreover, SMC reduces subjectivity and yields simple, differentiable formulas for the RDF, which are useful for tasks such as coarse-grained force-field calibration via iterative Boltzmann inversion.

Limiting the valence: advancements and new perspectives on patchy colloids, soft functionalized nanoparticles and biomolecules

Artistic representation of limited valance units consisting of a soft core (in blue) and a small number of flexible bonding patches (in orange).

Self-assembly of polymer-grafted nanoparticles in solvent-free conditions

Grafting of polymer chains onto the surface of spherical nanoparticles leads to a hybrid type of fluid that exhibits properties of both particle suspensions and melts of star polymers-these properties being controlled by the relative dimensions of the grafted polymer chains to the nanoparticle diameter, D, and the number of the number of chains grafted on the nanoparticle surface, f. While polymer-grafted nanoparticles (GNP) of this kind typically have a spherical average shape after grafting even a moderate number of chains, their instantaneous molecular shape can fluctuate significantly due to the deformation of the grafted chains. Both simulations and measurements have previously revealed that these "conformationally polarizable" particles can exhibit self-assembly into large scale polymeric structures in both solution and in polymer melts, and we simulate polymer-grafted nanoparticles with D and temperature (T) variations without a dispersing solvent to better understand the nature of this self-assembly process. We observe a reversible self-assembly into linear and branched dynamic GNP structures, where the extent of the assembly and geometry depend on D and T, and we constructed a map capturing the GNP structural behavior with D and T variations. Since the shape of the GNPs appeared to be correlated with the occurrence of the GNP self-assembly, we quantified the average shape and a measure of shape fluctuations to better understand how molecular shape influences their propensity to self-assemble into different structural forms. Based on this framework, we describe the clustering process of the GNPs as an equilibrium polymerization phenomenon and we calculate the order parameter governing the dynamic clustering behavior of GNPs, the average mass of the clusters, size distribution, and the apparent fractal dimension of the clusters.

Mechanical Response of DNA-Nanoparticle Crystals to Controlled Deformation

The self-assembly of DNA-conjugated nanoparticles represents a promising avenue toward the design of engineered hierarchical materials. By using DNA to encode nanoscale interactions, macroscale crystals can be formed with mechanical properties that can, at least in principle, be tuned. Here we present in silico evidence that the mechanical response of these assemblies can indeed be controlled, and that subtle modifications of the linking DNA sequences can change the Young's modulus from 97 kPa to 2.1 MPa. We rely on a detailed molecular model to quantify the energetics of DNA-nanoparticle assembly and demonstrate that the mechanical response is governed by entropic, rather than enthalpic, contributions and that the response of the entire network can be estimated from the elastic properties of an individual nanoparticle. The results here provide a first step toward the mechanical characterization of DNA-nanoparticle assemblies, and suggest the possibility of mechanical metamaterials constructed using DNA.

Modeling phase transitions in mixtures of β-γ lens crystallins

We analyze the experimentally determined phase diagram of a γD-βB1 crystallin mixture. Proteins are described as dumbbells decorated with attractive sites to allow inter-particle interaction. We use thermodynamic perturbation theory to calculate the free energy of such mixtures and, by applying equilibrium conditions, also the compositions and concentrations of the co-existing phases. Initially we fit the Tcloudversus packing fraction η measurements for a pure (x2 = 0) γD solution in 0.1 M phosphate buffer at pH = 7.0. Another piece of experimental data, used to fix the model parameters, is the isotherm x2vs. η at T = 268.5 K, at the same pH and salt content. We use the conventional Lorentz-Berthelot mixing rules to describe cross interactions. This enables us to determine: (i) model parameters for pure βB1 crystallin protein and to calculate; (ii) complete equilibrium surface (Tcloud-x2-η) for the crystallin mixtures. (iii) We present the results for several isotherms, including the tie-lines, as also the temperature-packing fraction curves. Good agreement with the available experimental data is obtained. An interesting result of these calculations is evidence of the coexistence of three phases. This domain appears for the region of temperatures just out of the experimental range studied so far. The input parameters, leading good description of experimental data, revealed a large difference between the numbers of the attractive sites for γD and βB1 proteins. This interesting result may be related to the fact that γD has a more than nine times smaller quadrupole moment than its partner in the mixture.