Related papers: A new Standard DNA damage (SDD) data format
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…
Damaged or mismatched bases in DNA can be repaired by Base Excision Repair (BER) enzymes that replace the defective base. Although the detailed molecular structures of many BER enzymes are known, how they colocalize to lesions remains…
Accurate Monte Carlo (MC) modelling in high-energy physics is challenging, particularly in complex scenarios where simulations fail to reproduce observed data. In practice, experimental information is often limited to one-dimensional (1D)…
DNA as a data storage medium has several advantages, including far greater data density compared to electronic media. We propose that schemes for data storage in the DNA of living organisms may benefit from studying the reconstruction…
Recent evidence highlights the usefulness of DNA methylation (DNAm) biomarkers as surrogates for exposure to risk factors for non-communicable diseases in epidemiological studies and randomized trials. DNAm variability has been demonstrated…
We present a detailed method to simulating sensor distortions using a photon and electron Monte Carlo method. We use three dimensional electrostatic simulations to parameterize the perturbed electric field profile for non-ideal sensor…
We present a novel strategy to uncover indirect signs of new physics in collider data using the Standard Model Effective Field Theory (SMEFT) framework, offering notably improved sensitivity compared to traditional global analyses. Our…
We study theoretically the in vitro evolution of a DNA sequence by binding to a transcription factor. Using a simple model of protein-DNA binding and available binding constants for the Mnt protein, we perform large-scale, realistic…
High performance sheet metals with a multi-phase microstructure suffer from deformation induced damage formation during forming in the constituent phases but importantly also where these intersect. To capture damage in terms of the physical…
Structural damage detection using non-contact sensing remains a challenging problem in structural health monitoring. This study presents a data-driven framework based on Dynamic Mode Decomposition (DMD) for extracting structural dynamics…
Comprehensive studies with the MARS15(2016) Monte-Carlo code are described on evaluation of prompt and residual radiation levels induced by nominal and accidental beam losses in the 5-MW, 2-GeV European Spallation Source (ESS) Linac. These…
As Deep Neural Networks (DNNs) are rapidly being adopted within large software systems, software developers are increasingly required to design, train, and deploy such models into the systems they develop. Consequently, testing and…
Infrastructure managers must maintain high standards to ensure user satisfaction during the lifecycle of infrastructures. Surveillance cameras and visual inspections have enabled progress in automating the detection of anomalous features…
Renaturation of complementary single strands of DNA is one of the important processes that requires better understanding in the view of molecular biology and biological physics. Here we develop a stochastic dynamical model on the DNA…
In this review paper, we delve into the nascent field of molecular data storage, focusing on system implementations and code constructions. We start by providing an overview of basic concepts in synthetic and computational biology.…
We propose a scar model to reproduce how double-strand breaks occur in the telomeric DNA damaged by the effect of the $\beta$-decay of tritium to helium. In this scar model, the two hydrogens bonded to the 5$^\prime$ carbon connecting the…
The phase field approach to modeling fracture uses a diffuse damage field to represent a crack. This addresses the singularities that arise at the crack tip in computations with sharp interface models, mollifying some of the difficulties…
Cells deploy robust mechanisms to repair DNA damage, safeguarding genomic stability and cellular health, but the physical principles underlying these processes remain incompletely understood. Experiments show \emph{in vitro} that upon a DNA…
Data-driven method for Structural Health Monitoring (SHM), that mine the hidden structural performance from the correlations among monitored time series data, has received widely concerns recently. However, missing data significantly…
A Monte Carlo model to simulate nuclear collisions in the energy range going from SPS to LHC, is presented. The model includes in its initial stage both soft and semihard components, which lead to the formation of color strings.…