Related papers: Modelling DNA Origami Self-Assembly at the Domain …
Inspired by recent successes using single-stranded DNA tiles to produce complex structures, we develop a two-step coarse-graining approach that uses detailed thermodynamic calculations with oxDNA, a nucleotide-based model of DNA, to…
A foundational result in origami mathematics is Kawasaki and Justin's simple, efficient characterization of flat foldability for unassigned single-vertex crease patterns (where each crease can fold mountain or valley) on flat material. This…
Self-folding origami, structures that are engineered flat to fold into targeted, three-dimensional shapes, have many potential engineering applications. Though significant effort in recent years has been devoted to designing fold patterns…
We report model calculations on DNA single strands which describe the equilibrium dynamics and kinetics of hairpin formation and melting. Modeling is at the level of single bases. Strand rigidity is described in terms of simple polymer…
We discuss the phenomenon of spontaneous self-compactification in a model colloidal system, proposed in a recent work on DNA-mediated self-assembly. We focus on the effect of thermal fluctuations on the stability of membrane-like…
Establishing precise control over the shape and the interactions of the microscopic building blocks is essential for design of macroscopic soft materials with novel structural, optical and mechanical properties. Here, we demonstrate robust…
Programmable folding of elastic sheets typically relies on predefined flexible creases or active materials-enabled hinges, which lack intrinsic bistability and limit reprogrammability within a single structure. Here, we present a…
We report studies of the equilibrium and the dynamics of a general set of lattice models which capture the essence of the force-induced or mechanical DNA unzipping transition. Besides yielding the whole equilibrium phase diagram in the…
Controlling the size and shape of assembled structures is a fundamental challenge in self-assembly, and is highly relevant in material design and biology. Here, we show that specific, but promiscuous, short-range binding interactions make…
Origami and kirigami have emerged as potential tools for the design of mechanical metamaterials whose properties such as curvature, Poisson ratio, and existence of metastable states can be tuned using purely geometric criteria. A major…
We study the dynamics of DNA hairpin formation using oxDNA, a nucleotide-level coarse-grained model of DNA. In particular, we explore the effects of the loop stacking interactions and non-native base pairing on the hairpin closing times. We…
At the cutting edge of materials science, matter is designed to self-organize into structures that perform a wide range of functions. The past two decades have witnessed major innovations in the versatility of building blocks, ranging from…
Self-assembly is one of the most promising strategies for making functional materials at the nanoscale, yet new design principles for making self-limiting architectures, rather than spatially unlimited periodic lattice structures, are…
Experiments have reached a monumental capacity for designing and synthesizing microscopic particles for self-assembly, making it possible to precisely control particle concentrations, shapes, and interactions. However, more physical insight…
Self-assembly is traditionally described as the process through which an initially disordered system relaxes towards an equilibrium ordered phase only driven by local interactions between its building blocks. However, This definition is too…
In recent years there have been a number of proposals to utilize the specificity of DNA based interactions for potential applications in nanoscience. One interesting direction is the self-assembly of micro- and nanoparticle clusters using…
An oritatami system (OS) is a theoretical model of self-assembly via co-transcriptional folding. It consists of a growing chain of beads which can form bonds with each other as they are transcribed. During the transcription process, the…
A unified model is constructed to study the recently observed DNA entropic elasticity, cooperative extensibility, and supercoiling property. With the introduction of a new structural parameter (the folding angle $\phi$), bending…
Kirigami-inspired designs can enable self-folding three-dimensional materials from flat, two-dimensional sheets. Hierarchical designs of connected levels increase the diversity of possible target structures, yet they can lead to longer…
We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with…