Related papers: Identify the stiffness of DNA via deep learning
DNA and other biopolymers differ from classical polymers due to their torsional stiffness. This property changes the statistical character of their conformations under tension from a classical random walk to a problem we call the `torsional…
The percentage and sequence of AT and GC base pairs and charges on the DNA backbone contribute significantly to the stiffness of DNA. This elastic property of DNA also changes with small interacting ligands. The single-molecule force…
It is well-established that many physical properties of DNA at sufficiently long length scales can be understood by means of simple polymer models. One of the most widely used elasticity models for DNA is the twistable worm-like chain…
As generative AI achieves hyper-realism, superficial artifact detection has become obsolete. While prevailing methods rely on resource-intensive fine-tuning of black-box backbones, we propose that forgery detection capability is already…
Many proteins interact with and deform double-stranded DNA in cells. Single-molecule experiments have studied the elasticity of DNA with helix-deforming proteins, including proteins that bend DNA. These experiments increase the need for…
Motivation Protein fold recognition is an important problem in structural bioinformatics. Almost all traditional fold recognition methods use sequence (homology) comparison to indirectly predict the fold of a tar get protein based on the…
In this paper, we consider a numerical homogenization of the poroelasticity problem with stochastic properties. The proposed method based on the construction of the deep neural network (DNN) for fast calculation of the effective properties…
In this note, we will present a specially designed deep neural network (DNN), which will target components of the solution of different time rate individually through perspective of the Laplace s-transform of the solution. Each segment of…
DNA supercoiling plays an important role in a variety of cellular processes. The torsional stress related with supercoiling may be also involved in gene regulation through the local structure and dynamics of the double helix. To check this…
Nonlinear bending phenomena of thin elastic structures arise in various modern and classical applications. Characterizing low energy states of elastic rods has been investigated by Bernoulli in 1738 and related models are used to determine…
We present a simple model which describes elastic response of single-stranded DNA (ssDNA) to stretching, including the regime of very high force (up to 1000 pN). ssDNA is modelled as a discreet persistent chain, whose ground state is a…
In this paper we develop a new perspective on generalization of neural networks by proposing and investigating the concept of a neural network stiffness. We measure how stiff a network is by looking at how a small gradient step in the…
Deoxyribonucleic acid (DNA) has shown great promise in enabling computational applications, most notably in the fields of DNA digital data storage and DNA computing. Information is encoded as DNA strands, which will naturally bind in…
Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…
Accurate estimation of shape thickness from medical images is crucial in clinical applications. For example, the thickness of myocardium is one of the key to cardiac disease diagnosis. While mathematical models are available to obtain…
DNA flexibility is a key determinant of biological function, from nucleosome positioning to transcriptional regulation, motivating a direct measurement of the bend-torque response of individual DNA molecules. In this work, DNA bending is…
Simple elastic network models of DNA were developed to reveal the structure-dynamics relationships for several nucleotide sequences. First, we propose a simple all-atom elastic network model of DNA that can explain the profiles of…
The competition between toroidal and rod-like conformations as possible ground states for DNA condensation is studied as a function of the stiffness, the length of the DNA and the form of the long-range interactions between neighboring…
Deep neural networks (DNNs) are widely used in real-world applications, yet they remain vulnerable to errors and adversarial attacks. Formal verification offers a systematic approach to identify and mitigate these vulnerabilities, enhancing…
We predict various detectable mechanical responses to the presence of local DNA defects which are defined as short DNA segments exhibiting mechanical properties obviously different from the 50 nm persistence length based semiflexible…