Related papers: Computational complexity and pragmatic solutions f…
Developing construction methods of materials tailored for given applications with absolute control over building block placement poses an immense challenge. DNA-coated colloids offer the possibility of realising programmable self-assembly,…
DNA-coated colloids can crystallize into a multitude of lattices, ranging from face-centered cubic to diamond and thereby contribute to our understanding of crystallization and open avenues to producing structures with useful photonic…
In this paper we present a model containing modifications to the Signal-passing Tile Assembly Model (STAM), a tile-based self-assembly model whose tiles are capable of activating and deactivating glues based on the binding of other glues.…
With the continued improvement of sequencing technologies, the prospect of genome-based medicine is now at the forefront of scientific research. To realize this potential, however, we need a revolutionary sequencing method for the…
The programmable assembly of DNA strands is a promising tool for building tailored bottom-up nanostructures. Here, we present a plasmonic nanosystem obtained by the base-pairing mediated aggregation of gold nanoparticles (NPs) which are…
Curved structures in soft matter and biological systems commonly emerge as a result of self-assembly processes where building blocks aggregate in a controlled manner, giving rise to specific system structure and properties. Learning how to…
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…
Understanding chromatin dynamics across multiple spatiotemporal scales requires models that reconcile biological specificity with physics-based interactions and computational tractability. We present a modular, recognition-enabled…
Self-assembly processes are widespread in nature, and lie at the heart of many biological and physical phenomena. The characteristics of self-assembly building blocks determine the structures that they form. Two crucial properties are the…
Large protein complexes are assembled from protein subunits to form a specific structure. In our theoretic work, we propose that assembly into the correct structure could be reliably achieved through an assembly line with a specific…
We investigate general properties of non-deterministic self-assembly with asymmetric interactions, using a computational model and DNA tile assembly experiments. By contrasting symmetric and asymmetric interactions we show that the latter…
In this paper, we demonstrate a computationally efficient new approach based on deep learning (DL) techniques for analysis, design, and optimization of electromagnetic (EM) nanostructures. We use the strong correlation among features of a…
One of the frontiers of nanotechnology is advancing beyond the periodic self-assembly of materials. Icosahedral quasicrystals, aperiodic in all directions, represent one of the most challenging targets that have yet to be experimentally…
Photonic crystals -- a class of materials whose optical properties derive from their structure in addition to their composition -- can be created by self-assembling particles whose sizes are comparable to the wavelengths of visible light.…
In this paper we propose new solution methods for designing tag sets for use in universal DNA arrays. First, we give integer linear programming formulations for two previous formalizations of the tag set design problem, and show that these…
The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical…
We introduce staged self-assembly of Wang tiles, where tiles can be added dynamically in sequence and where intermediate constructions can be stored for later mixing. This model and its various constraints and performance measures are…
We propose generative neural network methods to generate DNA sequences and tune them to have desired properties. We present three approaches: creating synthetic DNA sequences using a generative adversarial network; a DNA-based variant of…
Self-organized complex structures in nature, e.g. viral capsids, hierarchical biopolymers, and bacterial flagella, offer efficiency, adaptability, robustness, and multi-functionality. Can we program the self-assembly of three-dimensional…
In the self-assembly process which drives the formation of cellular membranes, micelles, and capsids, a collection of separated subunits spontaneously binds together to form functional and more ordered structures. In this work, we study the…