Related papers: A new Standard DNA damage (SDD) data format
Labeling of DNA molecules is a fundamental technique for DNA visualization and analysis. This process was mathematically modeled in [1], where the received sequence indicates the positions of the used labels. In this work, we develop error…
In [1], the authors proposed a new model of DNA storage system that integrates all three steps of retrieval and introduced the concept of DNA-correcting codes, which guarantees that the output of the storage system can be decoded to the…
The Geant4-DNA project proposes to develop an open-source simulation software based and fully included in the general-purpose Geant4 Monte Carlo simulation toolkit. The main objective of this software is to simulate biological damages…
This work applies concepts of artificial neural networks to identify the parameters of a mathematical model based on phase fields for damage and fracture. Damage mechanics is the part of the continuum mechanics that models the effects of…
Radiation damage induced by ion beams is traditionally treated at different levels of theoretical approaches, for the different scales and mechanisms involved.We present here details of a combined approach that, from a method at a…
The target theory is the most classical hypothesis explaining radiation-induced cell death, the physical or biological nature of the "target" remains ambiguous. This study hypothesizes that the distribution of DNA double-strand breaks…
DNA has immense potential as an emerging data storage medium. The principle of DNA storage is the conversion and flow of digital information between binary code stream, quaternary base, and actual DNA fragments. This process will inevitably…
In mammalian cells, repair centers for DNA double-strand breaks (DSBs) have been identified. However, previous researches predominantly rely on methods that induce specific DSBs by cutting particular DNA sequences. The clustering and its…
A major challenge in Structural Health Monitoring (SHM) is to accurately identify both the location and severity of damage using the dynamic response information acquired. While in theory the vibration-based and impedance-based methods may…
The failure of heterogeneous materials with microstructures is a complex process of damage nucleation, growth and localisation. This process spans multiple length scales and is challenging to simulate numerically due to its high…
How DNA repair enzymes find the relatively rare sites of damage is not known in great detail. Recent experiments and molecular data suggest that the individual repair enzymes do not work independently of each other, but rather interact with…
Cellular reprogramming, the conversion of one cell type to another, has fundamentally transformed our conception of cell types. Cellular reprogramming induces global changes in gene expression involving hundreds of transcription factors and…
Metropolis Monte Carlo simulation is used to investigate the elasticity of torsionally stressed double-stranded DNA, in which twist and supercoiling are incorporated as a natural result of base-stacking interaction and backbone bending…
Several neurodegenerative diseases involve the accumulation of cellular DNA damage. Comet assays are a popular way of estimating the extent of DNA damage. Current literature on the use of deep learning to quantify DNA damage presents an…
Data-Driven Product Development (DDPD) leverages data to learn the relationship between product design specifications and resulting properties. To discover improved designs, we train a neural network on past experiments and apply Projected…
We construct a theoretical model for the dynamics of a microscale colloidal particle, modeled as an interval, moving horizontally on a DNA-coated surface, modelled as a line coated with springs that can stick to the interval. Averaging over…
We employ a large scale molecular simulation based on bond-order ReaxFF to simulate the chemical reaction and study the damage to a large fragment of DNA-molecule in the solution by ionizing radiation. We illustrate that the randomly…
We present an integrated modeling framework that combines the Generalized Stochastic Microdosimetric Model (GSM2), used to predict cell survival fractions, with MINAS-TIRITH, a fast and efficient Geant4 DNA-based tool for simulating…
Point defects have a strong influence on the physical properties of materials, often dominating the electronic and optical behavior in semiconductors and insulators. The simulation and analysis of point defects is therefore crucial for…
According to the experimental evidence damage induced by densely ionizing radiation in mammalian cells is distributed along the DNA molecule in the form of clusters. The most critical constituent of DNA damage are double-strand breaks…