Related papers: Inferring DNA sequences from mechanical unzipping …

Extracting the intrinsic kinetic information of biological molecule from its single-molecule kinetic data is of considerable biophysical interest. In this work, we theoretically investigate the feasibility of inferring single RNA's…

In this Letter, we investigate the link between thermal denaturation and mechanical unzipping for two models of DNA, namely the Dauxois-Peyrard-Bishop model and a variant thereof we proposed recently. We show that the critical line that…

Unbinding of a double-stranded DNA reduces to an unscreened long range interaction and maps on various problems. Heterogeneity renormalizes interaction. Renormalization is temperature dependent. At an unbinding transition it approaches…

When pulled along its axis, double-stranded DNA elongates abruptly at a force of about 65 pN. Two physical pictures have been developed to describe this overstretched state. The first proposes that strong forces induce a phase transition to…

This paper presents a new framework for analysing forensic DNA samples using probabilistic genotyping. Specifically it presents a mathematical framework for specifying and combining the steps in producing forensic casework electropherograms…

Gene expression and regulation rely on an apparently finely tuned set of reactions between some proteins and DNA. Such DNA-binding proteins have to find specific sequences on very long DNA molecules and they mostly do so in absence of any…

We introduce a probabilistic model for protein sliding motion along DNA during the search of a target sequence. The model accounts for possible effects due to sequence-dependent interaction between the nonspecific DNA and the protein. As an…

We study unzipping of a complementary RNA-DNA helix applied to an external force, focusing on the force-force correlations. While at the microscopic level these are given by the sequence, the experiment measures effective, macroscopic…

The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…

DNA supercoiling, the under or overwinding of DNA, is a key physical mechanism both participating to compaction of bacterial genomes and making genomic sequences adopt various structural forms. DNA supercoiling may lead to the formation of…

Efficient deep neural network (DNN) inference on mobile or embedded devices typically involves quantization of the network parameters and activations. In particular, mixed precision networks achieve better performance than networks with…

We consider the problem of assembling a sequence based on a collection of its substrings observed through a noisy channel. The mathematical basis of the problem is the construction and design of sequences that may be discriminated based on…

The yearly global production of data is growing exponentially, outpacing the capacity of existing storage media, such as tape and disk, and surpassing our ability to store it. DNA storage - the representation of arbitrary information as…

While measurement advances now allow extensive surveys of gene activity (large numbers of genes across many samples), interpretation of these data is often confounded by noise -- expression counts can differ strongly across samples due to…

There has recently been great progress in automatic segmentation of medical images with deep learning algorithms. In most works observer variation is acknowledged to be a problem as it makes training data heterogeneous but so far no…

This paper presents a novel method to segment/decode DNA sequences based on n-grams statistical language model. Firstly, we find the length of most DNA 'words' is 12 to 15 bps by analyzing the genomes of 12 model species. Then we design an…

We model unzipping of DNA/RNA molecules subject to an external force by a spin-oscillator system. The system comprises a macroscopic degree of freedom, represented by a one-dimensional oscillator, and internal degrees of freedom,…

We deduced the torque applied on a single stretched and twisted DNA by integrating with respect to force the change in the molecule's extension as it is coiled. While consistent with previous direct measurements of the torque at high forces…

Gel electrophoresis, a widely used technique to separate DNA according to their size and weight, generates images that can be analyzed automatically. Manual or semiautomatic image processing presents a bottleneck for further development and…

DNA is increasingly employed for bio and nanotechnology thanks to its exquisite versatility and designability. Most of its use is limited to linearised and torsionally relaxed DNA but non-trivial architectures and torsionally constrained --…