Related papers: Compound Poisson Statistics and Models of Clusteri…
DNA data storage offers a high-density, long-term alternative to traditional storage systems, addressing the exponential growth of digital data. Composite DNA extends this paradigm by leveraging mixtures of nucleotides to increase storage…
Healthcare data from patient or population cohorts are often characterized by sparsity, high missingness and relatively small sample sizes. In addition, being able to quantify uncertainty is often important in a medical context. To address…
Clustering analysis identifies samples as groups based on either their mutual closeness or homogeneity. In order to detect clusters in arbitrary shapes, a novel and generic solution based on boundary erosion is proposed. The clusters are…
A DNA palindrome is a segment of double-stranded DNA sequence with inver- sion symmetry which may form secondary structures conferring significant biolog- ical functions ranging from RNA transcription to DNA replication. To test if the…
We study the melting of a double stranded DNA in the presence of stretching forces, via 3D Monte-Carlo simulations, exactly solvable models and heuristic arguments. The resulting force-temperature phase diagram is dramatically different for…
Electron-impact ionization cross sections of atoms and molecules are essential for plasma modelling. However, experimentally determining the absolute cross sections is not easy, and ab initio calculations become computationally prohibitive…
The approach for the description of the DNA conformational transformations on the mesoscopic scales in the frame of the double helix is presented. Due to consideration of the joint motions of DNA structural elements along the conformational…
Bi-clustering is a useful approach in analyzing biological data when observations come from heterogeneous groups and have a large number of features. We outline a general Bayesian approach in tackling bi-clustering problems in moderate to…
DNA looping is important in DNA condensation and regulation. One method for forming a DNA loop, thought to be used by the condensing agent protamine, is bind-and-bend. In bind-and-bend, molecules bind all along the DNA, each creating a bend…
Using high-quality gas phase electron scattering calculations and multiple scattering theory, we attempt to gain insights on the radiation damage to DNA induced by secondary low-energy electrons in the condensed phase, and to bridge the…
Model of biological effects of ionizing particles, especially of protons and other ions, is proposed. The model is based on distinguishing the single-particle and collective effects of the underlying radiobiological mechanism. The…
The dynamics of the DNA denaturation is studied using the Peyrard-Bishop-Dauxois model. The denaturation rate of double stranded polymers decreases exponentially as function of length below the denaturation temperature. Above Tc, the rate…
Most of the anticancer drugs bind to double-stranded DNA (dsDNA) by intercalative-binding mode. Although experimental studies have become available recently, a molecular-level understanding of the interactions between the drug and dsDNA…
The model of the deformation of DNA macromolecule is developed with the accounting of two types of components of deformation: external and internal. External components describe the bend, twist and stretch of the double helix. The internal…
Galaxy clusters form through a sequence of mergers of smaller galaxy clusters and groups. Models of diffusive shock acceleration (DSA) suggest that in shocks that occur during cluster mergers, particles are accelerated to relativistic…
Most living systems rely on double-stranded DNA (dsDNA) to store their genetic information and perpetuate themselves. This biological information has been considered the main target of evolution. However, here we show that symmetries and…
The effect of heterogeneous sequence composition on the denaturation of double stranded DNA is investigated. The resulting pair-binding energy variation is found to have a negligible effect on the critical properties of the smooth second…
Deep neural networks are susceptible to poisoning attacks by purposely polluted training data with specific triggers. As existing episodes mainly focused on attack success rate with patch-based samples, defense algorithms can easily detect…
Complementary DNA strands in solution reliably hybridize to form stable duplexes. We study the kinetics of the hybridization process and the mechanisms by which two initially isolated strands come together to form a stable double helix. We…
We consider a model for strand separation in negatively supercoiled dna, and study the effect of supercoiling on the localization of denaturation, using notions from statistical mechanics. The model is based on on mean field Ising system,…