Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Electronic transport in DNA.

ABSTRACT: We study the electronic properties of DNA by way of a tight-binding model applied to four particular DNA sequences. The charge transfer properties are presented in terms of localization lengths (crudely speaking, the length over which electrons travel). Various types of disorder, including random potentials, are employed to account for different real environments. We have performed calculations on poly(dG)-poly(dC), telomeric-DNA, random-ATGC DNA, and lambda-DNA. We find that random and lambda-DNA have localization lengths allowing for electron motion among a few dozen basepairs only. A novel enhancement of localization lengths is observed at particular energies for an increasing binary backbone disorder. We comment on the possible biological relevance of sequence-dependent charge transfer in DNA.

SUBMITTER: Klotsa D

PROVIDER: S-EPMC1366722 | biostudies-other | 2005 Oct

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Publications

Electronic transport in DNA.

Klotsa Daphne D Römer Rudolf A RA Turner Matthew S MS

Biophysical journal 20050722 4

We study the electronic properties of DNA by way of a tight-binding model applied to four particular DNA sequences. The charge transfer properties are presented in terms of localization lengths (crudely speaking, the length over which electrons travel). Various types of disorder, including random potentials, are employed to account for different real environments. We have performed calculations on poly(dG)-poly(dC), telomeric-DNA, random-ATGC DNA, and lambda-DNA. We find that random and lambda-D ...[more]

PMID: 16040753

Similar Datasets

Fast DNA sequencing via transverse electronic transport.

Project description:A rapid and low-cost method to sequence DNA would usher in a revolution in medicine. We propose and theoretically show the feasibility of a protocol for sequencing based on the distributions of transverse electrical currents of single-stranded DNA while it translocates through a nanopore. Our estimates, based on the statistics of these distributions, reveal that sequencing of an entire human genome could be done with very high accuracy in a matter of hours without parallelization, that is, orders of magnitude faster than present techniques. The practical implementation of our approach would represent a substantial advancement in our ability to study, predict, and cure diseases from the perspective of the genetic makeup of each individual.

| S-EPMC2556950 | biostudies-literature

Effect of noise on DNA sequencing via transverse electronic transport.

Project description:Previous theoretical studies have shown that measuring the transverse current across DNA strands while they translocate through a nanopore or channel may provide a statistically distinguishable signature of the DNA bases, and may thus allow for rapid DNA sequencing. However, fluctuations of the environment, such as ionic and DNA motion, introduce important scattering processes that may affect the viability of this approach to sequencing. To understand this issue, we have analyzed a simple model that captures the role of this complex environment in electronic dephasing and its ability to remove charge carriers from current-carrying states. We find that these effects do not strongly influence the current distributions due to the off-resonant nature of tunneling through the nucleotides--a result we expect to be a common feature of transport in molecular junctions. In particular, only large scattering strengths, as compared to the energetic gap between the molecular states and the Fermi level, significantly alter the form of the current distributions. Since this gap itself is quite large, the current distributions remain protected from this type of noise, further supporting the possibility of using transverse electronic transport measurements for DNA sequencing.

| S-EPMC2756358 | biostudies-literature

Electronic cigarettes

Project description:Electronic cigarettes (e-cigarettes) have gained their popularity as a substitute for cigarettes or cigars. Despite the widespread use of flavoring chemicals in e-cigarettes, the health impacts of the flavoring compounds, in particular their effects on critical cellular function in the lung, remain largely unknown. The goal of this study was to identify transcriptomic changes and impacted biological pathways in primary human bronchial epithelial cells (HBECs) exposed to flavoring chemicals (diacetyl or 2,3-pentanedione) and to flavored e-cigarette smoke. An airway-liquid interface culturing method was used to differentiate primary human bronchial epithelial cells (HBECs) into mature epithelial cells, which were then treated with 25 ppm diacetyl, 100 ppm 2,3 pentanedione, or e-cigarette smoke solution containing 2 ppm diacetyl. Poly(A)-selected RNA-Seq libraries were prepared with the PrepX RNA-Seq for Illumina Library kit. An Illumina HiSeq 2500 instrument was used to generate 50 base pair single-end reads. STAR was used to align sequencing reads to the hg38 reference genome, and HTSeq was used to quantify transcript levels. DESeq2 was used to perform differential expression analysis.

2019-08-21 | GSE118431 | GEO

Optimal Transport Distances to Characterize Electronic Excitations.

Project description:Understanding the character of electronic excitations is important in computational and reaction mechanistic studies, but their classification from simulations remains an open problem. Distances based on optimal transport have proven very useful in a plethora of classification problems and, therefore, seem a natural tool to try to tackle this challenge. We propose and investigate a new diagnostic Θ based on the Sinkhorn divergence from optimal transport. We evaluate a k-NN classification algorithm on Θ, the popular Λ diagnostic, and their combination, and assess their performance in labeling excitations, finding that (i) the combination only slightly improves the classification, (ii) Rydberg excitations are not separated well in any setting, and (iii) Θ breaks down for charge transfer in small molecules. We then define a length-scale-normalized version of Θ and show that the result correlates closely with Λ for results obtained with Gaussian basis functions. Finally, we discuss the orbital dependence of our approach and explore an orbital-independent version. Using an optimized combination of the optimal transport and overlap diagnostics together with a different metric is in our opinion the most promising for future classification studies.

| S-EPMC11238536 | biostudies-literature

Theoretical assessment of feasibility to sequence DNA through interlayer electronic tunneling transport at aligned nanopores in bilayer graphene.

Project description:Fast, cost effective, single-shot DNA sequencing could be the prelude of a new era in genetics. As DNA encodes the information for the production of proteins in all known living beings on Earth, determining the nucleobase sequences is the first and necessary step in that direction. Graphene-based nanopore devices hold great promise for next-generation DNA sequencing. In this work, we develop a novel approach for sequencing DNA using bilayer graphene to read the interlayer conductance through the layers in the presence of target nucleobases. Classical molecular dynamics simulations of DNA translocation through the pore were performed to trace the nucleobase trajectories and evaluate the interaction between the nucleobases and the nanopore. This interaction stabilizes the bases in different orientations, resulting in smaller fluctuations of the nucleobases inside the pore. We assessed the performance of a bilayer graphene nanopore setup for the purpose of DNA sequencing by employing density functional theory and non-equilibrium Green's function method to investigate the interlayer conductance of nucleobases coupling simultaneously to the top and bottom graphene layers. The obtained conductance is significantly affected by the presence of DNA in the bilayer graphene nanopore, allowing us to analyze DNA sequences.

| S-EPMC4669446 | biostudies-literature

Oral Epithelium Response of Electronic Cigarette Users to Electronic Cigarette

Project description:Electronic cigarettes (EC) are increasing in popularity, but there is only little information on their biologic effects on the oral epithelium, the initial site exposed to EC smoke. We assessed the oral epithelium response to EC by comparing the histology and RNA transcriptome (mRNA and miRNA) of healthy EC vapers to nonsmokers (NS). mRNA was assessed based on: (1) genome-wide; (2) genes previously identified as dysregulated in the oral epithelium of EC vapers vs NS; (3) immune and inflammatory-related genes previously identified as dysregulated in the nasal epithelium of EC vapers compared to NS; (4) genes previously identified as dysregulated in the small airway epithelium of NS following an acute exposure to EC; and (5) genes related to the initial steps of COVID-19 infection. In addition, miRNA was assessed genome-wide. Comparisons were performed using ANOVA, and Benajmini-Hochberg corrected p <0.05 was considered significant. The histology of the epithelium, lamina propria and basal layer in EC vapers appeared normal. Assessment of mRNA and miRNA, based on all gene lists, did not identify any genes significantly modified in the oral epithelium of EC vapers. Assessment of the oral epithelium of healthy EC vapers by histology, mRNA and miRNA demonstrated no abnormalities in response to EC smoke.

2025-06-05 | GSE176492 | GEO

Anomalous electronic transport in high-mobility Corbino rings.

Project description:We report low-temperature electronic transport measurements performed in two multi-terminal Corbino samples formed in GaAs/Al-GaAs two-dimensional electron gases (2DEG) with both ultra-high electron mobility ( ≳ 20 × 106 cm2/ Vs) and with distinct electron density of 1.7 and 3.6 × 1011 cm-2. In both Corbino samples, a non-monotonic behavior is observed in the temperature dependence of the resistance below 1 K. Surprisingly, a sharp decrease in resistance is observed with increasing temperature in the sample with lower electron density, whereas an opposite behavior is observed in the sample with higher density. To investigate further, transport measurements were performed in large van der Pauw samples having identical heterostructures, and as expected they exhibit resistivity that is monotonic with temperature. Finally, we discuss the results in terms of various lengthscales leading to ballistic and hydrodynamic electronic transport, as well as a possible Gurzhi effect.

| S-EPMC10318031 | biostudies-literature

Electronic transport in CdSe nanoplatelet based polymer fibres.

Project description:One of the most significant objectives in the field of nanotechnology is the transfer of specific properties of smaller nanoparticle building blocks into larger units. In this way, nanoscopic properties can be linked to the macroscopic addressability of larger systems. Such systems might find applications in fields like photoelectrochemical sensing or solar energy harvesting. Our work reports on the novel synthesis of hybrid semiconductor/polymer fibres, which are based on stacks of 4 monolayer (ML) thick CdSe nanoplatelets (NPLs) encapsulated into a polymer shell. The polymer encapsulation not only enables the water transfer of the NPL stacks but also allows the preparation of photoelectrodes by linking the fibres to surface modified indium tin oxide (ITO) glass slides. By applying electrochemical techniques like intensity modulated photocurrent spectroscopy (IMPS), it was possible to prove the motion of charge carriers inside the nanoplatelet stacks and by this the electronic addressibility of them.

| S-EPMC6333268 | biostudies-literature

Electronic Transport Modulation in Ultrastrained Silicon Nanowire Devices.

Project description:In this work, we explore the effect of ultrahigh tensile strain on electrical transport properties of silicon. By integrating vapor-liquid-solid-grown nanowires into a micromechanical straining device, we demonstrate uniaxial tensile strain levels up to 9.5%. Thereby the triply degenerated phonon dispersion relation at the Γ-point of silicon disentangle and the longitudinal phonon modes are used to precisely determine the extent of mechanical strain. Simultaneous electrical transport measurements showed a significant enhancement in the electrical conductance. Aside from considerable reduction of the Si bulk resistivity due to strain-induced band gap narrowing, comparison with quasi-particle GW calculations further reveals that the effective Schottky barrier height at the electrical contacts undergoes a substantial reduction. For these reasons, nanowire devices with ultrastrained channels may be promising candidates for future applications of high-performance silicon-based devices.

| S-EPMC11232017 | biostudies-literature