Taming polymorphism of tubule self-assembly using templated growth

Sirui Liu; Thomas E. Videbæk; W. Benjamin Rogers

Home/Archive/arXiv

arXiv · 2511.02975

Taming polymorphism of tubule self-assembly using templated growth

Sirui Liu·Thomas E. Videbæk·W. Benjamin Rogers

View original source ↗Read source document ↗Export metadata ↓

Abstract

Self-closing assembly is prone to polymorphism due to thermally-excited bending fluctuations, which permit the formation of off-target assemblies at the point of self-closure. One way to overcome this source of polymorphism is to use templated growth, a process in which assembly initiates from a precisely-defined seed rather than by spontaneous nucleation. We explore this approach to quelling polymorphism in the self-closing assembly of cylindrical tubules assembled from DNA-origami subunits with user-specified inter-subunit binding angles and specific interactions. We develop two strategies to create seeds with precisely-defined diameters and helicity: 1) using multicomponent assembly; and 2) purifying a specific seed-type from a polymorphic mixture using gel electrophoresis and gel extraction. By tuning the seed and monomer concentrations, and adjusting the assembly temperature, we determine the conditions under which tubules grow from the seed while avoiding spontaneous nucleation. We observe that templated tubules tend to follow the guidance of the seed, thereby increasing the selectivity of the target geometry. Also, we find that by tuning the diameter of the seed, one can template the growth of monodisperse tubules over a range of target diameters, even while using a single monomer type with a single preferred local curvature. Our results demonstrate that employing precisely defined seeds to guide assembly can significantly decrease polymorphism in self-closing assembly in a controllable and economical way.

Explore related subjects

cond-mat.soft

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Sirui Liu, Thomas E. Videbæk, W. Benjamin Rogers. 2025-11-04. Taming polymorphism of tubule self-assembly using templated growth. https://arxiv.org/abs/2511.02975

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

Transient Elasticity -- A Unifying Framework for Thixotropy, Polymers, and Granular Media

Thixotropic yield stress fluids, such as paint or ketchup, are traditionally viewed as elastic structures that, under shear rates, break into viscous liquids with lumps, and reconnect at rest. An alternative framework is presented here: Upon shear, structural destruction is incomplete, leaving sufficient connections. As a result, elasticity fundamentally underlies their non-Newtonian behavior, though they do appear purely viscous under a steady shear, displaying little direct evidence of elastic rebound---same as granular media and polymers. Consequently, all three are described by the same set of evolution equations, differing only in their parameters. These equations are set up by starting from solid dynamics and allowing the elastic strain $\varepsilon^e$ to relax, which in effect interpolates between solid and fluid behavior, appropriate for systems that display both types of behavior. Incorporating in addition a two-temperature framework, tracking how energy is dissipated in two consecutive stages, yields the nonlinear model of Transient Elasticity (TE). It describes an elasticity that is transient in time yet persistent under shear. Previously validated for polymers and granular media, TE is here applied to thixotropic yield-stress fluids. As shown, it successfully accounts for a wide range of characteristic phenomena, including over- and undershoot, viscosity bifurcation, shear banding, and oscillatory rheography. Given its appropriateness across structurally diverse systems, TE offers a unified, surprisingly general account of non-Newtonian phenomena.

cond-mat.soft↗

arXiv2026

Linear and nonlinear active microrheology of viscous, viscoelastic, and elastic media: A fluid particle dynamics approach

Active microrheology is an effective tool to determine the rheological properties of viscous, viscoelastic, or elastic materials on microscopic length scales. The positional response of an embedded probe particle to an externally applied oscillating driving force allows to indirectly characterize the properties of the surrounding media. We aim to explore the linear and nonlinear response of probe particles in a microrheological setup of planar geometry. For this purpose, we extend the computational method of fluid particle dynamics from viscous fluid-like to viscoelastic and elastic media, including nonlinear regimes. We consider a system confined by solid walls. In this case, we validate the approach by quantifying the linear response in terms of a Jeffreys model. Increasing the amplitude of the driving force, we observe distinct nonlinear effects. They include distorted stress-strain curves and a gradual net drift of probe particles initially positioned close to a wall. This drift vanishes in the viscous fluid-like and elastic solid-like limits, but is manifest for intermediate viscoelastic systems. We further address a setup of two probe particles in the absence of walls. They experience reciprocal pairwise oscillatory forcing. Here, nonlinearities in viscoelastic systems induce a net drift gradually moving the particles further apart from each other. Comparing with real setups, our implementation of the driving force is in line with experimental setups of optical tweezers or active magnetic microrheology.

cond-mat.soft↗

arXiv2026

Reinterpreting ultrafast experiments on supercooled water: Glass transition versus liquid-liquid criticality

Water's anomalous properties have been hypothesized to originate from a liquid-liquid critical point in the supercooled regime, separating high- and low-density liquid states. Experimental verification remains challenging due to rapid crystallization under these conditions. A recent study reported evidence for such a transition, based primarily on a pronounced increase in the heat capacity of rapidly heated low-density amorphous ice. Here, we show that this heat capacity increase can be explained without invoking a liquid-liquid transition. By combining simulations using a machine-learning potential trained on the state-of-the-art MB-pol water model, combined with the Tool-Narayanaswamy-Moynihan (TNM) model of the glass transition, we demonstrate that the observed signal can arise instead from a dynamical effect induced by the mobilization of rotational and translational molecular degrees of freedom during ultrafast heating. We further show that our findings are fully consistent with recent electron diffraction measurements showing structural arrest of supercooled water close to our predicted glass-transition temperature. These results provide an alternative interpretation of the experimental observations and highlight the importance of nonequilibrium glassy dynamics in the interpretation of the behavior of supercooled water on ultra-short time scales.

cond-mat.soft↗