Related papers: Strand separation in negatively supercoiled dna

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…

We develop Bayesian inference methods for a recently-emerging type of epigenetic data to study the transmission fidelity of DNA methylation patterns over cell divisions. The data consist of parent-daughter double-stranded DNA methylation…

Using basic properties of p-adic numbers, we consider a simple new approach to describe main aspects of DNA sequence and genetic code. Central role in our investigation plays an ultrametric p-adic information space which basic elements are…

Strain-inducing deformations in graphene alter charge distributions and provide a new method to design specific features in the band structure and transport properties. Novel approaches implement engineered substrates to induce specifically…

Pinning and depinning of wave fronts are ubiquitous features of spatially discrete systems describing a host of phenomena in physics, biology, etc. A large class of discrete systems is described by overdamped chains of nonlinear oscillators…

We study the transmission of a disordered waveguide subjected to a finite bias field. The statisticaldistribution of transmission is analytically shown to take a universal form. It depends on a singleparameter, the system length expressed…

The melting transition of deoxyribonucleic acid (DNA), whereby the strands of the double helix structure completely separate at a certain temperature, has been characterized using neutron scattering. A Bragg peak from B-form fibre DNA has…

A weakly-supervised semantic segmentation framework with a tied deconvolutional neural network is presented. Each deconvolution layer in the framework consists of unpooling and deconvolution operations. 'Unpooling' upsamples the input…

DNA denaturation has long been a subject of intense study due to its relationship to DNA transcription and its fundamental importance as a nonlinear, structural transition. Many aspects of this phenomenon, however, remain poorly understood.…

Denoising is the essential step for distant supervision based named entity recognition. Previous denoising methods are mostly based on instance-level confidence statistics, which ignore the variety of the underlying noise distribution on…

Microarray-based genotyping is based on the high discrimination capability of oligonucleotide probes. For detection of Single Nucleotide Polymorphisms (SNPs) single-base discrimination is required. We investigate how various…

We propose a stochastic model for gene transcription coupled to DNA supercoiling, where we incorporate the experimental observation that polymerases create supercoiling as they unwind the DNA helix, and that these enzymes bind more…

We recently proposed a dynamical mesoscopic model for DNA, which is based, like statistical ones, on site-dependent finite stacking and pairing enthalpies. In the present article, we first describe how the parameters of this model are…

We theoretically investigate the effects of the weak magnetization on the local density of states of mesoscopic proximity structures, where two superconducting terminals are attached to a side surface of the diffusive ferromagnet wire with…

We provide an overview of current approaches to DNA-based storage system design and accompanying synthesis, sequencing and editing methods. We also introduce and analyze a suite of new constrained coding schemes for both archival and random…

We propose a model for the fluctuation dynamics of the local denaturation zones (bubbles) in double-stranded DNA. In our formulation, the DNA strand is model as a one dimensional Rouse chain confined at both the ends. The bubble is formed…

Learning-based image reconstruction models, such as those based on the U-Net, require a large set of labeled images if good generalization is to be guaranteed. In some imaging domains, however, labeled data with pixel- or voxel-level label…

In the present paper we study the impact of dispersion and nonlinearity on DNA dynamics. We rely on the helicoidal Peyrard-Bishop model and use the fact that nonlinear DNA dynamics represents an interplay between nonlinearity and…

A general theoretical framework is put forth to organize and understand various observed phenomena and mathematical relationships in the field of molecular biology. By modeling each cell in eukaryotic organisms as a processor having a…

Recent work has shown that using unlabeled data in semi-supervised learning is not always beneficial and can even hurt generalization, especially when there is a class mismatch between the unlabeled and labeled examples. We investigate this…