Alfredo D. Bobadilla

Current–voltage–temperature characteristics of DNA origami

The temperature dependences of the current-voltage characteristics of a sample of triangular DNA origami deposited in a 100 nm gap between platinum electrodes are measured using a probe station. Below 240 K, the sample shows high impedance, similar to that of the substrate. Near room temperature the current shows exponential behavior with respect to the inverse of temperature. Sweep times of 1 s do not yield a steady state; however sweep times of 450 s for the bias voltage secure a steady state. The thermionic emission and hopping conduction models yield similar barriers of approximately 0.7 eV at low voltages. For high voltages, the hopping conduction mechanism yields a barrier of 0.9 eV and the thermionic emission yields 1.1 eV. The experimental data set suggests that the dominant conduction mechanism is hopping in the range 280-320 K. The results are consistent with theoretical and experimental estimates of the barrier for related molecules.

Calculating the Hydrodynamic Volume of Poly(ethylene oxylated) Single-Walled Carbon Nanotubes and Hydrophilic Carbon Clusters

Poly(ethylene glycol) (PEG) functionalization of carbon nanotubes (CNTs) is widely used to render CNTs suitable as vectors for targeted drug delivery. One recently described PEGylated version uses an oxidized single-walled carbon nanotube called a hydrophilic carbon cluster (HCC). The resulting geometric dimension of the hybrid PEG-CNT or PEG-HCC is an important factor determining its ability to permeate the cellular membrane and to maintain its blood circulation. Molecular dynamics (MD) simulations were performed to estimate the maximum length and width dimensions for a PEGylated single-walled carbon nanotube in water solution as a model for the PEG-HCC. We ensured maximum PEGylation by functionalizing each carbon atom in a CNT ring with an elongated PEG molecule, avoiding overlapping between PEGs attached to different CNT rings. We suggest that maximum PEGylation is important to achieve an optimal drug delivery platform.

DNA origami impedance measurement at room temperature

The frequency response of triangular DNA origami is obtained at room temperature. The sample shows a high impedance at low frequencies, e.g., at zero frequency 20 Gohms, which decreases almost linearly with the logarithm of the frequency reaching a low and flat value at 100 kHz where the impedance turns from capacitive to resistive, concluding that DNA can be used for transmission of signals at frequencies larger than 100 kHz. It is also found that characteristics of DNA cannot be completely disentangled from the characteristics of the substrate on which it is deposited, making the design of molecular circuits more challenging than the design of circuits with present lumped devices; this is a natural feature at the nanoscale.

Self-assembly of DNA on a gapped carbon nanotube

AbstractWe perform molecular dynamics simulations to analyze the wrapping process of a single-stranded (ss) DNA around a gapped CNT immersed in a bath of water. We observe the formation of a stable molecular junction with the ssDNA adopting a helical or circular conformation around one CNT electrode and a linear conformation around the opposite electrode. We find that DNA undergoes several conformational changes during equilibration of the self-assembled molecular junction. This process would allow a higher yield of successful CNT-DNA interconnections, which constitutes a novel structure of interest in chemical and biological sensing at the single-molecule level. FigureEvolution from 0 K of a single-stranded DNA on a gapped CNT under water and sodium counter-ions (shown only in the initial conformation) as the temperature reaches 300 K after 44 ns.

PMMA-Assisted Plasma Patterning of Graphene

Microelectronic fabrication of Si typically involves high-temperature or high-energy processes. For instance, wafer fabrication, transistor fabrication, and silicidation are all above 500°C. Contrary to that tradition, we believe low-energy processes constitute a better alternative to enable the industrial application of single-molecule devices based on 2D materials. The present work addresses the postsynthesis processing of graphene at unconventional low temperature, low energy, and low pressure in the poly methyl-methacrylate- (PMMA-) assisted transfer of graphene to oxide wafer, in the electron-beam lithography with PMMA, and in the plasma patterning of graphene with a PMMA ribbon mask. During the exposure to the oxygen plasma, unprotected areas of graphene are converted to graphene oxide. The exposure time required to produce the ribbon patterns on graphene is 2 minutes. We produce graphene ribbon patterns with ∼50 nm width and integrate them into solid state and liquid gated transistor devices.

In Silico Assembly of Carbon-Based Nanodevices

Carbon nanostructures are 0D, 1D and 2D nanomaterials with potential to enable new markets in the electronic industry due to their novel properties which have been recognized recently with the awarding of Nobel Prizes in Physics and Chemistry. However their very small size constitutes a great challenge in the manufacturing industry, demanding extraordinary and expensive efforts in experimentation. Thus, the best way to avoid unneeded trial-and-error experimentation is by using theoretical-computational tools for the molecular analysis and simulation of prospective devices and systems, allowing us to observe properties at the nanoscale that are practically difficult and sometimes impossible to observe experimentally. We decided to review in this Chapter the use of these tools in order to analyze several scenarios on the assembly and characterization of carbon-based nanodevices. In an in silico experiment, by using molecular dynamics, we analyzed the outcome of bombarding carbon nanotubes with argon ions and we found that for very high energies the type of defects created were almost exclusively single vacancy, which is important in the development of spin-based electronics. On the other hand, combining carbon nanostructures with DNA molecules offers the possibility of exploiting the chemical sensitivity of DNA and the transduction of electrical signals. Therefore, by using molecular dynamics, we predicted a stable structure for a non-covalent DNA junction with a carbon nanotube (CNT) and graphene as interface electrodes. The electronic structure calculations predicted that the DNA electronic structure is coupled to the carbon electron nanodevices, which allow the sensing of a chemical environment. Finally, in the field of drug-delivery, biological barriers and the immune system constitute challenges for the effective delivery of drugs to targeted areas of the human organism. Therefore, by using molecular dynamics, we predicted the structure and stability of maximum PEGylated carbon nanotubes. We found the size of the PEG-CNT complex to be smaller at conditions of maximum PEGylation and in the nanosized regime, which is an important requirement for the effective delivery of drugs.