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Cellular nuclei recognition serves as a fundamental and essential step in the workflow of digital pathology. However, with disparate source organs and staining procedures among histology image clusters, the scanned tiles inherently conform…
We consider error-correcting coding for deoxyribonucleic acid (DNA)-based storage using nanopore sequencing. We model the DNA storage channel as a sampling noise channel where the input data is chunked into $M$ short DNA strands, which are…
Structure-based drug design (SBDD) stands at the forefront of drug discovery, emphasizing the creation of molecules that target specific binding pockets. Recent advances in this area have witnessed the adoption of deep generative models and…
DNA-based data storage has been attracting significant attention due to its extremely high data storage density, low power consumption, and long duration compared to conventional data storage media. Despite the recent advancements in DNA…
DNA is emerging as an increasingly attractive medium for data storage due to a number of important and unique advantages it offers, most notably the unprecedented durability and density. While the technology is evolving rapidly, the…
Biomedical research increasingly relies on 3D cell culture models and AI-based analysis can potentially facilitate a detailed and accurate feature extraction on a single-cell level. However, this requires for a precise segmentation of 3D…
In regimes of low signal strengths and therefore a small signal-to-noise ratio, standard data analysis methods often fail to accurately estimate system properties. We present a method based on Monte Carlo simulations to effectively restore…
Diffusion Monte Carlo (DMC) based on fixed-node approximation has enjoyed significant developments in the past decades and become one of the go-to methods when accurate ground state energy of molecules and materials is needed. The remaining…
DNA has many valuable characteristics that make it suitable for a long-term storage medium, in particular its durability and high information density. DNA can be stored safely for hundreds of years with virtually no degradation, in contrast…
Over the past decade, experimental microscopy and spectroscopy have made significant progress in the study of the morphological, optical, electronic and transport properties of materials. These developments include higher spatial…
Recent advances in genomics have underscored the surprising ubiquity of DNA copy number variation (CNV). Fortunately, modern genotyping platforms also detect CNVs with fairly high reliability. Hidden Markov models and algorithms have played…
We propose a mathematical model for estimating biological damage caused by low-dose irradiation. We understand that the Linear Non Threshold (LNT) hypothesis is realized only in the case of no recovery effects. In order to treat the…
A mathematical model of genome degradation is proposed that takes into account a variable rate of mutation and increasing number of cells in a developing human organism. The model explains known properties of cancer development, in…
Context: The Monte Carlo method is probably the most widely used approach to solve the radiative transfer problem, especially in a general 3D geometry. The physical processes of emission, absorption, and scattering are easily incorporated…
Quantum Molecular Dynamics models (QMD) are Monte Carlo approaches targeted at the description of nucleon-ion and ion-ion collisions. We have developed a QMD code, which has been used for the simulation of the fast stage of ion-ion…
Biological genomes are divided into coding and non-coding regions. Introns are non-coding parts within genes, while the remaining non-coding parts are intergenic sequences. To study the evolutionary significance of recombination inside…
Quantum effects are mainly used for the determination of molecular shapes in molecular biology, but quantum information theory may be a more useful tool to understand the physics of life. Organic molecules and quantum circuits/protocols can…
DNA-based biodiversity surveys involve collecting physical samples from survey sites and assaying the contents in the laboratory to detect species via their diagnostic DNA sequences. DNA-based surveys are increasingly being adopted for…
Structural DNA nanotechnology has advanced to the extent that extremely complex structures can be designed. Much of this advancement has been due to the development of automated DNA design and simulation tools. Typically, the tools (e.g.…
The variation of the oxygen enhancement ratio (OER) across Linear Energy Transfer (LET) currently lacks a comprehensive mechanistic interpretation and a mechanistic model. Our earlier research revealed a significant correlation between the…