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G-quadruplexes (G4s) are helical four-stranded structures forming from guanine-rich nucleic acid sequences, which are thought to play a role in cancer development and malignant transformation. Most current studies focus on G4 monomers, yet under suitable and biologically relevant conditions, G4s undergo multimerization. Here, we investigate the stacking interactions and structural features of telomeric G4 multimers by means of a novel low-resolution structural approach that combines small-angle X-ray scattering (SAXS) with extremely coarse-grained (ECG) simulations. The degree of multimerization and the strength of the stacking interaction are quantitatively determined in G4 self-assembled multimers. We show that self-assembly induces a significant polydispersity of the G4 multimers with an exponential distribution of contour lengths, consistent with a step-growth polymerization. On increasing DNA concentration, the strength of the stacking interaction between G4 monomers increases, as well as the average number of units in the aggregates. We utilized the same approach to explore the conformational flexibility of a model single-stranded long telomeric sequence. Our findings indicate that its G4 units frequently adopt a beads-on-a-string configuration. We also observe that the interaction between G4 units can be significantly affected by complexation with benchmark ligands. The proposed methodology, which identifies the determinants that govern the formation and structural flexibility of G4 multimers, may be an affordable tool aiding in the selection and design of drugs that target G4s under physiological conditions.

An anisotropic colloidal shape in combination with an externally tunable interaction potential results in a plethora of self-assembled structures with potential applications toward the fabrication of smart materials. Here we present our investigation on the influence of an external magnetic field on the self-assembly of hematite-silica core-shell prolate colloids for two aspect ratios ρ = 2.9 and 3.69. Our study shows a rather counterintuitive but interesting phenomenon, where prolate colloids self-assemble into oblate liquid crystalline (LC) phases. With increasing concentration, particles with smaller ρ reveal a sequence of LC phases involving para-nematic, nematic, smectic, and oriented glass phases. The occurrence of a smectic phase for colloidal ellipsoids has been neither predicted nor reported before. Quantitative shape analysis of the particles together with extensive computer simulations indicate that in addition to ρ, a subtle deviation from the ideal ellipsoidal shape dictates the formation of this unusual sequence of field-induced structures. Particles with ρ = 2.9 exhibit a hybrid shape containing features from both spherocylinders and ellipsoids, which make their self-assembly behavior richer than that observed for either of the "pure" shapes. The shape of the particles with higher ρ matches closely with the ideal ellipsoids, as a result their phase behavior follows the one expected for a "pure" ellipsoidal shape. Using anisotropic building blocks and external fields, our study demonstrates the ramifications of the subtle changes in the particle shape on the field-directed self-assembled structures with externally tunable properties.

Amyloid fibrils offer the possibility of controlling their contour length, aspect ratio, and length distribution, without affecting other structural parameters. Here we show that a fine control in the contour length distribution of β-lactoglobulin amyloid fibrils, achieved by mechanical shear stresses of different levels, translates into the organization of tactoids of different shapes and morphologies. While longer fibrils lead to highly elongated nematic tactoids in an isotropic continuous matrix, only sufficiently shortened amyloid fibrils lead to cholesteric droplets. The progressive decrease in amyloid fibrils length leads to a linear decrease of the anchoring strength and homogeneous tactoid → bipolar tactoid → cholesteric droplet transitions. Upon fibrils length increase, we first find experimentally and predict theoretically a decrease of the cholesteric pitch, before full disappearance of the cholesteric phase. The latter is understood to arise from the decrease of the energy barrier separating cholesteric and nematic phases over thermal energy for progressively longer, semiflexible fibrils.

Unveiling the subtle rules that control the buildup of macroscopic chirality starting from chiral molecular elements is a challenge for theory and computations. In this context, a remarkable phenomenon is the formation of helically twisted nematic (cholesteric) phases, with pitch in the micrometer range, driven by self-assembly of relatively small chiral species into supramolecular semiflexible polymers. We have developed a theoretical framework to connect the cholesteric organization to the shape and chirality of the constituents, described with molecular detail, in this kind of system. The theory has been tested against new accurate measurements for solutions of short DNA duplexes. We show that the cholesteric organization is determined by steric repulsion between duplexes, and we identify distinctive features of linear self-assembly in the temperature and concentration dependence of the pitch.

The globular protein γB-crystallin exhibits a complex phase behavior, where liquid-liquid phase separation characterized by a critical volume fraction ϕc = 0.154 and a critical temperature Tc = 291.8 K coexists with dynamical arrest on all length scales at volume fractions around ϕ ≈ 0.3-0.35, and an arrest line that extends well into the unstable region below the spinodal. However, although the static properties such as the osmotic compressibility and the static correlation length are in quantitative agreement with predictions for binary liquid mixtures, this is not the case for the dynamics of concentration fluctuations described by the dynamic structure factor S(q,t). Using a combination of dynamic light scattering and neutron spin echo measurements, we demonstrate that the competition between critical slowing down and dynamical arrest results in a much more complex wave vector dependence of S(q,t) than previously anticipated.

The anisotropy of attractive interactions between particles can favor, through a self-assembly process, the formation of linear semi-flexible chains. In the appropriate temperatures and concentration ranges, the growing aspect ratio of the aggregates can induce formation of a nematic phase, as recently experimentally observed in several biologically relevant systems. We present here a numerical study of the isotropic-nematic phase boundary for a model of bifunctional polymerizing hard cylinders, to provide an accurate benchmark for recent theoretical approaches and to assess their ability to capture the coupling between self-assembly and orientational ordering. The comparison indicates the importance of properly modeling excluded volume and orientational entropy and provides a quantitative confirmation of some theoretical predictions.

In the diffusion model of chemical reactions, the encounter (reaction) rate between reactant particles is governed by the Smoluchowski equation, which is a diffusion equation in a field of forces. We consider crowded environments where the particles diffuse through a "liquid" of like particles. Assuming that the liquid-like short-range structure around the reactant gives rise to an effective (osmotic) barrier leads us to map a complicated many-body problem to a one-dimensional problem. This allows us to describe theoretically such complex systems that are encountered in many applications where crowding, intermolecular interactions, and flow are simultaneously present. A particularly important effect is discovered which is due to the interplay between shear and crowding. This effect is responsible for unexpected peaks in the reactivity at low flow intensity which may explain, among other things, the bizarre colloidal stability behavior of concentrated protein suspensions.

The analysis of realistic numerical simulations of a gel-forming irreversible aggregation process provides information on the role of cluster diffusion in controlling the late stages of the aggregation kinetics. Interestingly, the crossover from chemically controlled to diffusion-controlled aggregation takes place well beyond percolation, after most of the particles have aggregated in the spanning network and only small clusters remain in the sol. The simulation data are scrutinized to gain insight into the origin of this crossover. We show that a single additional time scale (related to the average diffusion time) is sufficient to provide an accurate description of the evolution of the extent of reaction at all times.

We report molecular dynamics simulations of a gel-forming mixture of ellipsoidal patchy particles with different functionality. We show that in this model, which disfavors the formation of bond-loops, elapsed time during irreversible aggregation--leading to the formation of an extended network--can be formally correlated with equilibrium temperature in reversible aggregation. We also show that it is possible to develop a parameter-free description of the self-assembly kinetics, bringing reversible and irreversible aggregation of loopless branched systems to the same level of understanding as equilibrium polymerization.

We report extensive Monte Carlo and event-driven molecular dynamics simulations of a liquid composed of particles interacting via hard-sphere interactions complemented by four tetrahedrally coordinated short-range attractive ("sticky") spots, a model introduced several years ago by Kolafa and Nezbeda (Kolafa, J.; Nezbeda, I. Mol. Phys. 1987, 87, 161). To access the dynamic properties of the model, we introduce and implement a new event-driven molecular dynamics algorithm suited to study the evolution of hard bodies interacting, beside the repulsive hard-core, with a short-ranged interpatch square well potential. We evaluate the thermodynamic properties of the model in deep supercooled states, where the bond network is fully developed, providing evidence of density anomalies. Different from models of spherically symmetric interacting particles, the liquid can be supercooled without encountering the gas-liquid spinodal in a wide region of packing fractions phi. Around an optimal phi, a stable fully connected tetrahedral network of bonds develops. By analyzing the dynamics of the model we find evidence of anomalous behavior: around the optimal packing, dynamics accelerate on both increasing and decreasing phi. We locate the shape of the isodiffusivity lines in the (phi - T) plane and establish the shape of the dynamic arrest line in the phase diagram of the model. Results are discussed in connection with colloidal dispersions of sticky particles and gel-forming proteins and their ability to form dynamically arrested states.