arXiv subjects

Thomas Heim

Publications and source records attributed to Thomas Heim.

5 recordsLinked to original sources

arXiv2006

Thermodynamics of RNA/DNA hybridization in high density oligonucleotide microarrays

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 versus the hybridization free energy of RNA/DNA duplexes in solution, for perfect matching and mismatching probes. Both values tend to align on a single master curve in good agreement with Langmuir adsorption theory, provided one takes into account the decrease of the effective target concentration due to target-target hybridization in solution. We give an example of a deviation from the expected thermodynamical behavior for the probe set 1091\_at due to annotation problems, i.e. the surface-bound probe is not the exact complement of the target RNA sequence, because of errors present in public databases at the time when the array was designed. We show that the parametrization of the experimental data with RNA/DNA free energy improves the quality of the fits and enhances the stability of the fitting parameters compared to previous studies.

q-bio.BM↗

arXiv2004

Ambipolar charge injection and transport in a single pentacene monolayer island

Electrons and holes are locally injected in a single pentacene monolayer island. The two-dimensional distribution and concentration of the injected carriers are measured by electrical force microscopy. In crystalline monolayer islands, both carriers are delocalized over the whole island. On disordered monolayer, carriers stay localized at their injection point. These results provide insight into the electronic properties, at the nanometer scale, of organic monolayers governing performances of organic transistors and molecular devices.

cond-mat.mtrl-sci↗

arXiv2004

Localization and delocalization of charges injected in DNA

The electrical properties of DNA molecules are investigated by charge injection and electric force microscopy experiments. Prior to injection, DNA molecules exhibit a weak positively charged state. We probe the electrical behaviour of DNA by measuring the localized or delocalized character of the DNA charge states upon injection of excess charges. We show that injected charges do not delocalize for overstretched DNA prepared by a receding meniscus technique, while the adjunction of spermidine during the deposition leads to relaxed DNA molecules exhibiting a charge delocalization over microns. The interplay between charge localization/delocalization and deposition techniques may explain that transport behaviors ranging from insulating to conductive have been reported for DNA deposited on surfaces.

cond-mat.mtrl-sci↗

arXiv2004

Conductivity of DNA probed by conducting-atomic force microscopy: effects of contact electrode, DNA structure, surface interactions

We studied the electrical conductivity of DNA molecules with conducting atomic force microscopy as a function of the chemical nature of the substrate surfaces, the nature of the electrical contact, and the number of DNA molecules (from a few molecules, to ropes and large fibers containing up to ~ 106 molecules). Independent of the chemical nature of the surface (hydrophobic or hydrophilic, electrically neutral or charged), we find that DNA is highly resistive. From a large number of current-voltage curves measured at several distance along the DNA, we estimate a conductivity of about 10-6-10-5 S.cm-1 per DNA molecule. For single DNA molecules, this highly resistive behavior is correlated with its flattened conformation on the surface (reduced thickness, \~0.5-1.5 nm, compared to its nominal value, ~2.4 nm). We find that intercalating an organic semiconductor buffer film between the DNA and the metal electrode improves the reliability of the contact, while direct metal evaporation usually destroys the DNA and prevents any current measurements. After long exposure under vacuum or dry nitrogen, the conductivity strongly decreases, leading to the conclusion that water molecules and ions in the hydration shell of the DNA play a major role.

cond-mat.mtrl-sci↗

arXiv2003

Charge transport in l-DNA probed by conducting-AFM, and relationship with its structure

We studied the electrical conductivity of DNA samples as function of the number of DNA molecules. We showed that the insulating gap (no current at low voltage) increases from ~1-2 V for bundles and large ropes to ~4-7 V for few DNA molecules. From the distance dependent variation of the current, a unique hopping distance of ~3 nm is calculated (polaron-hopping model) independently of the number of DNA in the sample. The highly resistive behavior of the single DNA is correlated with its flattened conformation on the surface (reduced thickness, ~0.5-1.5 nm, compared to its nominal value, ~2 nm).

cond-mat.soft↗