Related papers: Computational complexity and pragmatic solutions f…
De novo genome assembly is the process of stitching short DNA sequences to generate longer DNA sequences, without using any reference sequence for alignment. It enables high-throughput genome sequencing and thus accelerates the discovery of…
Genome assembly asks to reconstruct an unknown string from many shorter substrings of it. Even though it is one of the key problems in Bioinformatics, it is generally lacking major theoretical advances. Its hardness stems both from…
DNA origami is a novel self-assembly technique allowing one to form various 2D shapes and position matter with nanometer accuracy. It has been used to coordinate placement of nanoscale objects, both organic and inorganic; to make molecular…
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…
We present a new simulation scheme which allows an efficient sampling of reconfigurable supramolecular structures made of polymeric constructs functionalized by reactive binding sites. The algorithm is based on the configurational bias…
This is a review of a set of recent papers with some new data added. After a brief biological introduction a visualization scheme of the string composition of long DNA sequences, in particular, of bacterial complete genomes, will be…
Biomolecular computation has emerged as an important area of computer science research due to its high information density, immense parallelism opportunity along with potential applications in cryptography, genetic engineering and…
Intercalation of drug molecules into synthetic DNA nanostructures formed through self-assembled origami has been postulated as a valuable future method for targeted drug delivery. This is due to the excellent biocompatibility of synthetic…
Biomolecular graph analysis has recently gained much attention in the emerging field of geometric deep learning. Here we focus on organizing biomolecular graphs in ways that expose meaningful relations and variations between them. We…
In living cells, proteins self-assemble into large functional structures based on specific interactions between molecularly complex patches. Due to this complexity, protein self-assembly results from a competition between a large number of…
Polymer-grafted nanoparticles are versatile building blocks that self-assemble into a rich diversity of mesostructures. Coarse-grained molecular simulations have commonly accompanied experiments by resolving structure formation pathways and…
Despite tremendous progress in the research on self-assembled nanotechnological building blocks such as macromolecules, nanowires, and two-dimensional materials, synthetic self-assembly methods bridging nanoscopic to macroscopic dimensions…
We consider the problem of approximating a two-dimensional shape contour (or curve segment) using discrete assembly systems, which allow to build geometric structures based on limited sets of node and edge types subject to edge length and…
Controlled synthesis of materials with specified atomic structures underpins technological advances yet remains reliant on iterative, trial-and-error approaches. Nanoparticles (NPs), whose atomic arrangement dictates their emergent…
DNA self-assembly is a well-understood nanotechnology to obtain extremely ordered structures from the nanometer to up to the hundred of microns scale. By contrast, DNA hydrogels rely on the disordered assembly of DNA building blocks to…
In computational molecular biology, gene regulatory binding sites prediction in whole genome remains a challenge for the researchers. Now a days, the genome wide regulatory binding site prediction tools required either direct pattern…
The challenge of synthesizing graphene nanoribbons (GNRs) with atomic precision is currently being pursued along a one-way road, based on the synthesis of adequate molecular precursors that react in predefined ways through self-assembly…
Biomolecular condensates self-assemble when proteins and nucleic acids spontaneously demix to form droplets within the crowded intracellular milieu. This simple mechanism underlies the formation of a wide variety of membraneless…
Motivated by empirical observations of algebraic duplicated sequence length distributions in a broad range of natural genomes, we analytically formulate and solve a class of simple discrete duplication/substitution models that generate…
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…