Related papers: 3DNA: A Tool for DNA Sculpting
We report Monte Carlo simulations of a simple off-lattice patchy-particle model for DNA `bricks'. We relate the parameters that characterise this model with the binding free energy of pairs of single-stranded DNA molecules. We verify that…
In soft matter science, it is often the goal to design new materials with targeted properties. These materials can be used in many applications, each requiring specific features to be optimized for maximum fitness. The use of self-assembly…
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…
Printing custom DNA sequences is essential to scientific and biomedical research, but the technology can be used to manufacture plagues as well as cures. Just as ink printers recognize and reject attempts to counterfeit money, DNA…
DNA-coated particles are promising as building blocks for functional and finite-sized assemblies because they can be programmed with orthogonal interactions owing to the sequence-specific hybridization of DNA strands. To fully exploit this…
3D printing enables the fabrication of complex architectures by automating long sequences of additive steps. The increasing sophistication of printers, materials, and generative design promises to make geometric complexity a non-issue in…
The oxDNA model of DNA has been applied widely to systems in biology, biophysics and nanotechnology. It is currently available via two independent open source packages. Here we present a set of clearly-documented exemplar simulations that…
The central dogma of molecular biology is the principal framework for understanding how nucleic acid information is propagated and used by living systems to create complex biomolecules. Here, by integrating the structural and dynamic…
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…
It has been shown that genome spatial structures largely affect both genome activity and DNA function. Knowing this, many researchers are currently attempting to accurately model genome structures. Despite these increased efforts there…
Algorithmic self-assembly, a generalization of crystal growth processes, has been proposed as a mechanism for autonomous DNA computation and for bottom-up fabrication of complex nanostructures. A `program' for growing a desired structure…
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…
The study of DNA charge dynamics is a highly interdisciplinary field that bridges physics, chemistry, biology, and medicine, and plays a critical role in processes such as DNA damage detection, protein-DNA interactions, and DNA-based…
To make 3D human avatars widely available, we must be able to generate a variety of 3D virtual humans with varied identities and shapes in arbitrary poses. This task is challenging due to the diversity of clothed body shapes, their complex…
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…
Because of DNA appealing features as perfect material, including minuscule size, defined structural repeat and rigidity, programmable DNA-mediated processing is a promising computing paradigm, which employs DNAs as information storing and…
The Triander program is an interactive software package for nucleotide sequence visualization. The program was developed using the freeware Pascal RAD IDE Lazarus, and its source code and binaries compiled for Windows are freely accessible…
The availability of rich 3D datasets corresponding to the geometrical complexity of the built environments is considered an ongoing challenge for 3D deep learning methodologies. To address this challenge, we introduce GenScan, a generative…
Biological systems possess remarkable capabilities for self-recognition and morphological regeneration, often relying solely on local interactions. Inspired by these decentralized processes, we present a novel system of physical 3D…
This technical report deals with the concept of an artificial DNA which contains a blueprint of the structure and organization of an embedded system. This blueprint can be used to build up the embedded system in a self-organizing manner at…