Related papers: Substrate-assisted 2D DNA lattices and algorithmic…
Spatial transcriptomics (ST) reveals spatial heterogeneity of gene expression, yet its resolution is limited by current platforms. Recent methods enhance resolution via H&E-stained histology, but three major challenges persist: (1)…
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…
Advanced composites are used in a variety of industrial applications and therefore attract much scientific interest. Here we describe the formation of novel carbon-based nanocomposites via incorporation of graphene oxide into the crystal…
Genetic information is stored in a linear sequence of base-pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we…
RNA secondary structures of increasing complexity are probed combining single molecule stretching experiments and stochastic unfolding/refolding simulations. We find that force-induced unfolding pathways cannot usually be interpretated by…
Self-assembly of structurally tunned nearly monodispersed HgTe - ssDNA nanostars of average size 1.4 nm have been achieved by manipulating HgTe nanoparticles using single stranded (ss) DNA under galvanostatic condition. The nanostars are…
For 3D spatial transcriptomics (ST), the high per-section acquisition cost of fully sampling every tissue section remains a significant challenge. Although recent approaches predict gene expression from histology images, these methods…
Harnessing the intrinsic dynamics of physical systems for information processing opens new avenues for computation embodied in matter. Using simulations of a model system, we show that assemblies of DNA tiles capable of self-organizing into…
In this paper, we propose a method to build molecular cages designed to capture a specific substrate. We model a cage as a graph of atoms with coordinates in space, and several constraints on their edges (degree, length and angle). We use a…
Solid texture synthesis (STS), an effective way to extend a 2D exemplar to a 3D solid volume, exhibits advantages in computational photography. However, existing methods generally fail to accurately learn arbitrary textures, which may…
A detailed description of the conformational plasticity of double stranded DNA (ds) is a necessary framework for understanding protein-DNA interactions. Until now, however structure and kinetics of the transition from the basic conformation…
In this paper we present the first known deterministic algorithm for the construction of multiple rank-1 lattices for the approximation of periodic functions of many variables. The algorithm works by converting a potentially large…
Dynamic stencil deposition (DSD) techniques offer a variety of fabrication advantages not possible with traditional lithographic processing, such as the the ability to directly deposit nanostructures with programmable height profiles.…
In the past decade, exemplar-based texture synthesis algorithms have seen strong gains in performance by matching statistics of deep convolutional neural networks. However, these algorithms require regularization terms or user-added spatial…
The computational modelling of DNA is becoming crucial in light of new advances in DNA nanotechnology, single-molecule experiments and in vivo DNA tampering. Here we present a mesoscopic model for double stranded DNA (dsDNA) at the single…
Efficient algorithms to generate candidate crystal structures with good stability properties can play a key role in data-driven materials discovery. Here we show that a crystal diffusion variational autoencoder (CDVAE) is capable of…
To obtain crystalline thin films of alpha-Quartz represents a challenge due to the tendency for the material towards spherulitic growth. Thus, understanding the mechanisms that give rise to spherulitic growth can help regulate the growth…
We here examine the nonlinear dynamics of artificial homogeneous DNA chain relying on the plain-base rotator model. It is shown that such dynamics can exhibit kink and antikink solitons of sine-Gordon type. In that respect we propose…
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…
A construction method for duplex cage structures with icosahedral sym- metry made out of single-stranded DNA molecules is presented and applied to an icosidodecahedral cage. It is shown via a mixture of analytic and computer techniques that…