Related papers: Self-Assembling DNA Complexes with a Wheel Graph S…
In order to optimize a self-assembly reaction, it is essential to understand the factors that govern its pathway. Here, we examine the influence of nucleation pathways in a model system for addressable, multicomponent self-assembly based on…
We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting…
We study theoretically a new generic scheme of programmable self-assembly of nanoparticles into clusters of desired geometry. The problem is motivated by the feasibility of highly selective DNA-mediated interactions between colloidal…
Graphs are often used to organize data because of their simple topological structure, and therefore play a key role in machine learning. And it turns out that the low-dimensional embedded representation obtained by graph representation…
Recently, Graph Neural Networks (GNNs) have greatly advanced the task of graph classification. Typically, we first build a unified GNN model with graphs in a given training set and then use this unified model to predict labels of all the…
We propose a general framework for solving inverse self-assembly problems, i.e. designing interactions between elementary units such that they assemble spontaneously into a predetermined structure. Our approach uses patchy particles as…
In equilibrium self-assembly, microscopic building blocks spontaneously self-organize into stable structures as dictated by their interaction potentials, which limits the accessible structural features to those that correspond to global…
The use of reduced models for investigating the self-assembly dynamics underlying protein shell formation in spherical viruses is described. The spontaneous self-assembly of these polyhedral, supramolecular structures, in which icosahedral…
DNA rearrangement processes recombine gene segments that are organized on the chromosome in a variety of ways. The segments can overlap, interleave or one may be a subsegment of another. We use directed graphs to represent segment…
We use Monte Carlo simulations and free-energy techniques to show that binary solutions of penta- and hexavalent two-dimensional patchy particles can form thermodynamically stable quasicrystals even at very narrow patch widths, provided…
The connection between self-assembly and computation suggests that a shape can be considered the output of a self-assembly ``program,'' a set of tiles that fit together to create a shape. It seems plausible that the size of the smallest…
In recent years significant attention has been attracted to proposals which utilize DNA for nanotechnological applications. Potential applications of these ideas range from the programmable self-assembly of colloidal crystals, to biosensors…
In this paper, we introduce the following problem in the theory of algorithmic self-assembly: given an input shape as the seed of a tile-based self-assembly system, design a finite tile set that can, in some sense, uniquely identify whether…
One of the challenges of self-assembling finite-sized colloidal aggregates with a sought morphology is the necessity of precisely sorting the position of the colloids at the microscopic scale to avoid the formation of off-target structures.…
The specificity and simplicity of the Watson-Crick base pair interactions make DNA one of the most versatile construction materials for creating nanoscale structures and devices. Among several DNA-based approaches, the DNA origami technique…
A major goal in nanoscience and nanotechnology is the self-assembly of any desired complex structure with a system of particles interacting through simple potentials. To achieve this objective, intense experimental and theoretical efforts…
There is a profound connection between copositive matrices and graph theory. Copositive matrices provide a powerful tool for formulating and solving various challenging graph-related problems. Conversely, graph theory provides a rich set of…
Concentrated solutions of short blunt-ended DNA duplexes, down to 6 base pairs, are known to order into the nematic liquid crystal phase. This self-assembly is due to the stacking interactions between the duplex terminals that promotes…
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…
Heterogeneous graphs offer powerful data representations for traffic, given their ability to model the complex interaction effects among a varying number of traffic participants and the underlying road infrastructure. With the recent advent…