arXiv subjects

Jude Ann Vishnu

Publications and source records attributed to Jude Ann Vishnu.

4 recordsLinked to original sources

arXiv2026

Topological defect engineering enables size and shape control in self-assembly

The self-assembly of complex structures from engineered subunits is a major goal of nanotechnology, but controlling their size becomes increasingly difficult in larger assemblies. Existing strategies present significant challenges, among which the use of multiple subunit types or the precise control of their shape and mechanics. Here we introduce an alternative approach based on identical subunits whose interactions promote crystals, but also favor crystalline defects. We theoretically show that topological restrictions on the scope of these defects in large assemblies imply that the assembly size is controlled by the magnitude of the defect-inducing interaction. Using DNA origami, we experimentally demonstrate both size and shape control in two-dimensional disk- and fiber-like assemblies. Our basic concept of defect engineering could be generalized well beyond these simple examples, and thus provide a broadly applicable scheme to control self-assembly.

cond-mat.soft↗

arXiv2026

Designing corrugated surfaces to guide colloidal self-assembly

The self-assembly of colloidal particles enables the creation of structured materials with programmable functionalities; however, controlling interaction specificity and aggregate morphology in a reversible and scalable manner remains a major challenge. Here, we investigate the selective depletion-induced self-assembly of 3D-printed flat polygonal colloids, where nanoscale surface topography is engineered through precise modeling in two-photon polymerization. By designing anisotropic lateral surfaces, we direct specific interactions that govern aggregate morphology, yielding dimers, chains, zigzag, and honeycomb structures depending on the surface configuration. The specificity of interaction is tuned by varying the length scale of the topographic surfaces, the depletant concentration and the ionic strength of the solution, revealing a transition from selective to non-selective aggregation regimes. The relative placement of lateral interacting surfaces on the colloids enables assembly into aggregates spanning a broad range of sizes, while tuning the interaction strength selectively stabilizes distinct structural motifs. We demonstrate this interplay between geometric arrangement and interaction energy experimentally and corroborate through both theory and simulations for specifically hexagonal shaped colloids. This study establishes a versatile framework for programming colloidal interactions via micro-architectural design, offering new routes for fabricating reconfigurable and functional soft materials.

cond-mat.soft↗

arXiv2025

Sol-gel transition in heteroassociative RNA-protein solutions: A quantitative comparison of coarse-grained simulations and the Semenov-Rubinstein theory

Protein RNA-binding domains selectively interact with specific RNA sites, a key interaction that determines the emergent cooperative behaviors in RNA-protein mixtures. Through molecular dynamics simulations, we investigate the impact of the specific binding interactions on the phase transitions of an examplary RNA-protein system and compare it with predictions of the Semenov-Rubinstein theory of associative polymers. Our findings reveal a sol-gel (percolation) transition without phase separation, characterized by double reentrant behavior as the RNA or protein concentration increases. We highlight the crucial role of bridge formations in driving these transitions, particularly when binding sites are saturated. The theory quantitatively predicts the binding numbers at equilibrium in the semidilute regime, but it significantly overestimates the size of the concentration range where percolation is observed. This can partly be traced back to the fact that the mean-field assumption in the theory is not valid in the dilute regime, and that the theory neglects the existence of cycles in the connectivity graph of the percolating cluster at the sol-gel transition. Our study enriches the understanding of RNA-protein phase behaviors, providing valuable insights for the interpretation of experimental observations.

cond-mat.soft↗

arXiv2024

Structure and Dynamic Evolution of Interfaces between Polymer Solutions and Gels and Polymer Interdiffusion: A Molecular Dynamics Study

Letting free polymers diffuse from solution into a crosslinked polymer gel is often a crucial processing step in the synthesis of multiphase polymer-based gels, e.g., core-shell microgels. Here we use coarse-grained molecular dynamics simulations to obtain molecular insights into this process. We consider idealized situations where the gel is modeled as a regular polymer network with the topology of a diamond lattice, and all free polymers and strands have the same length and consist of the same type of monomer. After bringing the gel and the polymer solution into contact, two time regimes are observed: An initial compression of the gel caused by the osmotic pressure of the solution, followed by an expansion due to swelling. We characterize the time evolution of density profiles, the penetration of free polymers into the gel and the connection between the gel and solution phase. The interfacial structure locally equilibrates after roughly 100 chain relaxation times. At late times, the free chains inside the gel undergo a percolation transition if the polymer concentration in the gel exceeds a critical value, which is of the same order as the overlap concentration. The fluctuations of the interface can be described by a capillary wave model that accounts for the elasticity of the gel. Based on this, we extract the interfacial tension of the gel-solution interface. Interestingly, both the interfacial tension and the local interfacial width increase with increasing free polymer concentration - in contrast to liquid-liquid interfaces, where these two quantities are typically anticorrelated.

cond-mat.soft↗