Related papers: Analysis and Algorithmic Construction of Self-Asse…
In the standard DNA brick set-up, distinct 32-nucleotide strands of single-stranded DNA are each designed to bind specifically to four other such molecules. Experimentally, it has been demonstrated that the overall yield is increased if…
DNA plays a special role in polymer science not just because of the highly selective recognition of complementary single DNA strands but also because bacteria can express DNA chains that are very long yet perfectly monodisperse. The latter…
DNA tile self-assembly has emerged as a rich and promising primitive for nano-technology. This paper studies the problems of minimizing assembly time and error rate by changing the tile concentrations because changing the tile…
DNA origami consists of a long scaffold strand and short staple strands that self-assemble into a target 2D or 3D shape. It is a widely used construct in nucleic acid nanotechnology, offering a cost-effective way to design and create…
Understanding how highly symmetric, robust, monodisperse protein cages self-assemble can have major applications in various areas of bio-nanotechnology, such as drug delivery, biomedical imaging and gene therapy. We develop a model to…
The nucleotide sequence representation of DNA can be inadequate for resolving protein-DNA binding sites and regulatory substrates, such as those involved in gene expression and horizontal gene transfer. Considering that sequence-like…
Self assembly is a process by which supramolecular species form spontaneously from their components. This process is ubiquitous throughout the life chemistry and is central to biological information processing. It has been predicted that in…
Motivated by the question of how macromolecules assemble, the notion of an {\it assembly tree} of a graph is introduced. Given a graph $G$, the paper is concerned with enumerating the number of assembly trees of $G$, a problem that applies…
An approach that combines Self-Organizing maps, hierarchical clustering and network components is presented, aimed at comparing protein conformational ensembles obtained from multiple Molecular Dynamic simulations. As a first result the…
Designing molecular structures with desired chemical properties is an essential task in drug discovery and material design. However, finding molecules with the optimized desired properties is still a challenging task due to combinatorial…
Self-assembly is a process which is ubiquitous in natural, especially biological systems. It occurs when groups of relatively simple components spontaneously combine to form more complex structures. While such systems have inspired a large…
Fabrication of diamond structures by self-assembly is a fundamental challenge in making three-dimensional photonic crystals. We simulate a system of model hard particles with attractive patches and show that they can self-assemble into a…
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…
Our work is concerned with the generation and targeted design of RNA, a type of genetic macromolecule that can adopt complex structures which influence their cellular activities and functions. The design of large scale and complex…
This paper presents a novel graph-based deep learning model for tasks involving relations between two nodes (edge-centric tasks), where the focus lies on predicting relationships and interactions between pairs of nodes rather than node…
Inspired by biology's most sophisticated computer, the brain, neural networks constitute a profound reformulation of computational principles. Remarkably, analogous high-dimensional, highly-interconnected computational architectures also…
DNA sequencing is the basic workhorse of modern day biology and medicine. Shotgun sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are…
The evolution of multicellular organisms from monocellular ancestors represents one of the greatest advances of the history of life. The assembly of such multicellular organisms requires signalling and response between cells: over millions…
We introduce allostery-mimetic building blocks model for self-assembly of 3D structures. We represent the building blocks as patchy particles, where each binding site (patch) can be irreversibly activated or deactivated by binding of the…
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…