Related papers: Enhancing the performance of DNA surface-hybridiza…
The effect of target molecule depletion from the supernatant solution is incorporated into a physico-chemical model of hybridisation on oligonucleotide microarrays. Two possible regimes are identified: local depletion, in which depletion by…
Competitve hybridization, at the surface and in the bulk, lowers the sensitivity of DNA chips. Competitive surface hybridization occurs when different targets can hybridize with the same probe. Competitive bulk hybridization takes place…
We analyze a series of publicly available controlled experiments (Latin square) on Affymetrix high density oligonucleotide microarrays using a simple physical model of the hybridization process. We plot for each gene the signal intensity…
DNA adsorption and naturation is modeled via two interacting flexible homopolymers coupled to a solid surface. DNA denatures if the entropy gain for unbinding the two strands overcomes the loss of binding energy. When adsorbed to a surface,…
Denoising diffusion models achieved impressive results on several image generation tasks often outperforming GAN based models. Recently, the generative capabilities of diffusion models have been employed for perceptual image compression,…
High-density oligonucleotide arrays are among the most rapidly expanding technologies in biology today. In the {\sl GeneChip} system, the reconstruction of the target concentration depends upon the differential signal generated from…
Analysis of data from an Affymetrix Latin Square spike-in experiment indicates that measured fluorescence intensities of features on an oligonucleotide microarray are related to spike-in RNA target concentrations via a hyperbolic response…
Observing the hybridisation kinetics of DNA probes immobilised on plasmonic nanoparticles is key in plamon enhanced fluorescence detection from weak emitting species, and refractive index based single-molecule detection on optoplasmonic…
We consider a multi-object detection problem over a sensor network (SNET) with limited range multi-modal sensors. Limited range sensing environment arises in a sensing field prone to signal attenuation and path losses. The general problem…
DNA methylation (DNAme) is a critical component of the epigenetic regulatory machinery and aberrations in DNAme patterns occur in many diseases, such as cancer. Mapping and understanding DNAme profiles offers considerable promise for…
Background: Diagnostic DNA arrays for detection of point mutations as markers for cancer usually function in the presence of a large excess of wild type DNA. This excess can give rise to false positives due to competitive hybridization of…
Efficient capture and detection of minute amount of deoxyribonucleic acid (DNA) molecules are pivotal for an array of modern gene technologies which are widely utilized in medical, forensic and defense applications, including DNA…
We study DNA denaturation by integrating elasticity -- as described by the Gaussian network model -- with bond binding energies, distinguishing between different base-pair and stacking energies. We use exact calculation, within the model,…
Synchrotron-based X-ray computed tomography is widely used for investigating inner structures of specimens at high spatial resolutions. However, potential beam damage to samples often limits the X-ray exposure during tomography experiments.…
The melting of a homopolymer double-stranded (ds) deoxyribonucleic acid (DNA) in the dilute limit is studied numerically in the presence of an attractive and impenetrable surface on a simple cubic lattice. The two strands of the DNA are…
Dielectric metasurfaces have introduced a new paradigm for substance detection by exploiting their resonant properties to enhance light-matter interaction. This enhancement can be used for sensing either through refractive index changes or…
Hyperspectral imaging (HI) has emerged as a powerful tool in diverse fields such as medical diagnosis, industrial inspection, and agriculture, owing to its ability to detect subtle differences in physical properties through high spectral…
In DNA computing, it is impossible to decide whether a specific hybridization among complex DNA molecules is effective or not within acceptable time. In order to address this common problem, we introduce a new method based on the machine…
Accurate detection of target molecules at low concentrations in the presence of a high concentration of undesired molecules is a major challenge for End Point (EP) assays. Non-specific binding of undesired molecules to receptors limits the…
Surface defect detection is an extremely crucial step to ensure the quality of industrial products. Nowadays, convolutional neural networks (CNNs) based on encoder-decoder architecture have achieved tremendous success in various defect…