Related papers: DNA Circuits Based on Isothermal Constrained Loop …
Low-energy electrons (LEEs) are known to be effective in causing strand breaks in DNA. Recent experiments show that an important direct source of LEEs is the intermolecular Coulombic decay (ICD) process. Here we propose a new cascade…
This work proposes a new approach to study transport properties of highly correlated local structures. The method, dubbed the Logarithmic Discretization Embedded Cluster Approximation (LDECA), consists of diagonalizing a finite cluster…
As a non-linear extension of the classic Linear Discriminant Analysis(LDA), Deep Linear Discriminant Analysis(DLDA) replaces the original Categorical Cross Entropy(CCE) loss function with eigenvalue-based loss function to make a deep neural…
We calculate the equation of state of DNA under tension for the case that the DNA features loops. Such loops occur transiently during DNA condensation in the presence of multivalent ions or sliding cationic protein linkers. The…
DNA is an attractive medium for digital data storage. When data is stored on DNA, errors occur, which makes error-correcting coding techniques critical for reliable DNA data storage. To reduce the errors, a common technique is to include…
Deep learning-based methods have reached state of the art performances, relying on large quantity of available data and computational power. Such methods still remain highly inappropriate when facing a major open machine learning problem,…
Self-sustaining nonlinear oscillators of practically any type can function as latches and registers if Boolean logic states are represented physically as the phase of oscillatory signals. Combinational operations on such phase-encoded logic…
Canine cardiomegaly, marked by an enlarged heart, poses serious health risks if undetected, requiring accurate diagnostic methods. Current detection models often rely on small, poorly annotated datasets and struggle to generalize across…
We analyze the amplification processes occurring in a nonlinear fiber, either driven with one or two pumps. After determining the solution for the signal and idler fields resulting from these amplification processes, we analyze the physical…
Slot filling, a fundamental module of spoken language understanding, often suffers from insufficient quantity and diversity of training data. To remedy this, we propose a novel Cluster-to-Cluster generation framework for Data Augmentation…
Optical parametric amplification (OPA) comprises essentially a nonlinear four-wave mixing process in which a "pump" and a "signal" field give rise to an "idler" field under certain phase-matching conditions. Here we use a photonic crystal…
As a medium for cold data storage, DNA stands out as it promises significant gains in storage capacity and lifetime. However, it comes with its own data processing challenges to overcome. Constrained codes over the DNA alphabet…
We propose using graphene electrodes with hydrogenated edges for solid-state nanopore-based DNA sequencing, and perform molecular dynamics simulations in conjunction with electronic transport calculations to explore the potential merits of…
The purpose of this work is to extend the Geant4-DNA Monte Carlo toolkit to include electron interactions with the four DNA bases using a set of cross sections recently implemented in Geant-DNA CPA100 models and available for liquid water.…
This communication reports the increase in fluorescence resonance energy transfer (FRET) efficiency between two laser dyes in presence of Deoxyribonucleic acid (DNA). Two types of molecular logic gates have been designed where DNA acts as…
DNA is structurally and mechanically altered by the binding of intercalator molecules. Intercalation strongly affects the force-extension behavior of DNA, in particular the overstretching transition. We present a statistical model that…
Living cells provide a fluctuating, out-of-equilibrium environment in which genes must coordinate cellular function. DNA looping, which is a common means of regulating transcription, is very much a stochastic process; the loops arise from…
The concept of Dielectric Laser Acceleration (DLA) provides highest gradients among non-plasma particle accelerators. However, stable beam transport and staging have not been shown experimentally yet. We present a scheme that confines the…
Bending of DNA from a straight rod to a circular form in presence of any of the mono-, di-, tri- or tetravalent counterions has been simulated in strong Coulomb coupling environment employing a previously developed energy minimization…
We discuss possible mechanisms that may impact the order of the transition between denaturated and bound DNA states and lead to changes in the scaling laws that govern conformational properties of DNA strands. To this end, we re-consider…