Related papers: How we simulate DNA origami
In this paper, we provide assembly instructions for an easy to build experimental setup in order to gain practical experience with tomography. In view of this, this paper can be seen as a complementary work to excellent mathematical…
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…
Quantum effects are mainly used for the determination of molecular shapes in molecular biology, but quantum information theory may be a more useful tool to understand the physics of life. Organic molecules and quantum circuits/protocols can…
Colloidal particles grafted with single-stranded DNA (ssDNA) chains can self-assemble into a number of different crystalline structures, where hybridization of the ssDNA chains creates links between colloids stabilizing their structure.…
Programmable folding of elastic sheets typically relies on predefined flexible creases or active materials-enabled hinges, which lack intrinsic bistability and limit reprogrammability within a single structure. Here, we present a…
Origami design principles are scale invariant and enable direct miniaturization of origami structures provided the sheets used for folding have equal thickness to length ratios. Recently, seminal steps have been taken to fabricate…
Nanopore sequencing offers the ability for real-time analysis of long DNA sequences at a low cost, enabling new applications such as early detection of cancer. Due to the complex nature of nanopore measurements and the high cost of…
SIMD||DNA is a model of DNA strand displacement allowing parallel in-memory computation on DNA storage. We show how to simulate an arbitrary 3-symbol space-bounded Turing machine with a SIMD||DNA program, giving a more direct and efficient…
DNA nanoparticles with three-fold coordination have been observed to self-assemble in experiment into a network equivalent to the hexagonal (6.6.6) tiling, and a network equivalent to the 4.8.8 Archimedean tiling. Both networks are built…
Fabricating nanocavities in which optically-active single quantum emitters are precisely positioned, is crucial for building nanophotonic devices. Here we show that self-assembly based on robust DNA-origami constructs can precisely position…
Based on modern single molecule techniques, we devise a number of possible experimental setups to probe local properties of DNA such as the presence of DNA-knots, loops or folds, or to obtain information on the DNA-sequence. Similarly, DNA…
This study explores the use of origami composite structures as active aerodynamic control surfaces. Towards this goal, two origami concepts were designed leveraging a combination of analytical and finite element modeling, and computational…
We study the problem of the self-assembly of nanoparticles (NPs) into finite mesoscopic structures with a programmed local morphology and complex overall shape. Our proposed building blocks are NPs directionally-functionalized with DNA. The…
A cascaded phase-only mask architecture (or an optical diffractive neural network) can be employed for different optical information processing tasks such as pattern recognition, orbital angular momentum (OAM) mode conversion, image…
This paper introduces the use of cable dynamics models as a means to explore the mechanics of DNA on long-length scales. It is on these length scales that DNA forms twisted and curved three-dimensional shapes known as supercoils and loops.…
Electro-thermally actuated origami provides a novel method for creating 3-D systems with advanced morphing and functional capabilities. However, it is currently difficult to simulate the multi-physical behavior of such systems because the…
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…
We have functionalized the sides of fd bacteriophage virions with oligonucleotides to induce DNA hybridization driven self-assembly of high aspect ratio filamentous particles. Potential impacts of this new structure range from an entirely…
BioDynaMo is a biological processes simulator developed by an international community of researchers and software engineers working closely with neuroscientists. The authors have been working on gene expression, i.e. the process by which…
Although RNAs play many cellular functions little is known about the dynamics and thermodynamics of these molecules. In principle, all-atom molecular dynamics simulations can investigate these issues, but with current computer facilities,…