Identification of single nucleotides in MoS2 nanopores

Ultrathin membranes have drawn much attention due to their unprecedented spatial resolution for DNA nanopore sequencing. However, the high translocation velocity (3000-50000 nt/ms) of DNA molecules moving across such membranes limits their usability. To this end, we have introduced a viscosity gradient system based on room-temperature ionic liquids (RTILs) to control the dynamics of DNA translocation through a nanometer-size pore fabricated in an atomically thin MoS2 membrane. This allows us for the first time to statistically identify all four types of nucleotides with solid state nanopores. Nucleotides are identified according to the current signatures recorded during their transient residence in the narrow orifice of the atomically thin MoS2 nanopore. In this novel architecture that exploits high viscosity of RTIL, we demonstrate single-nucleotide translocation velocity that is an optimal speed (1-50 nt/ms) for DNA sequencing, while keeping the signal to noise ratio (SNR) higher than 10. Our findings pave the way for future low-cost and rapid DNA sequencing using solid-state nanopores.Comment: Manuscript 24 pages, 4 Figures Supporting Information 24 pages, 12 Figures, 2 Tables Manuscript in review Nature Nanotechnology since May 27th 201

Ionization-induced asymmetric self-phase modulation and universal modulational instability in gas-filled hollow-core photonic crystal fibers

We study theoretically the propagation of relatively long pulses with ionizing intensities in a hollow-core photonic crystal fiber filled with a Raman-inactive gas. Due to photoionization, previously unknown types of asymmetric self-phase modulation and `universal' modulational instabilities existing in both normal and anomalous dispersion regions appear. We also show that it is possible to spontaneously generate a plasma-induced continuum of blueshifting solitons, opening up new possibilities for pushing supercontinuum generation towards shorter and shorter wavelengths.Comment: 5 pages, 4 figure

Nanocapillaries combined with optical tweezers as a single molecule technique for studying DNA-protein complexes

Interactions of proteins with DNA are essential for carrying out DNA's biological functions and performing a cellular cycle. Such processes as DNA replication, expression and repair are performed by an organised action of various proteins. To better understand the function of protein machinery many methods have been developed over the years. They can be divided into two categories: single molecule and bulk techniques. In comparison to bulk experiments, where the effect of an ensemble of proteins is measured, single molecule techniques analyse each molecule one by one. This fact allows to detect rare events and avoid averaging over the population. Moreover, some single molecule techniques can be used for mechanical manipulation of biomolecules, i.e. twisting, stretching, etc. The objective of this thesis was to make a single molecule technique combining nanocapillaries and optical tweezers for the characterisation of DNA-protein complexes in physiological conditions. There were three main steps in this thesis: 1) building and characterisation of the setup 2) using it for detection and characterisation of DNA-protein complexes and 3) localisation and discrimination of DNA-protein complexes. On the first step of the project we combined two single molecule techniques: optical tweezers and glass nanocapillaries. We characterised the electrophoretic force acting on DNA in this setup by using nanocapillaries with openings of different sizes, at different applied voltages and with DNA molecules of different lengths. We observed that the position-dependent electrophoretic force acting on the DNA depends on all above-mentioned parameters. We modelled the system and found out that this effect is due to a non-uniform distribution of the potential inside the nanocapillary, which originates from its elongated shape. After having built and characterised the setup, we detected proteins bound to DNA during their controlled translocation through the opening. The proteins were visualised by a sudden decrease in the force acting on the bare DNA followed up by its slow restoration when the capillary was moved further away. We made a stochastic model to explain this force profile. From the fits of the model to experimental results we extracted the effective charges of DNA-protein complexes inside the nanocapillary. In the case of all three proteins (RecA, EcoRI and RNAP) the effective charge was of opposite sign than the one in solution. We attributed this fact to the dominant impact of the drag force in comparison to the electrostatic force inside the nanocapillary. On the last step of the project we showed the ability to localise and discriminate DNA-protein complexes in our setup using dCas9 and RNAP proteins. During controlled translocation of the DNA-protein complexes we measured multiple parameters, including protein's location on the DNA, work required to translocate the complex, and conductance change. We demonstrated that the measured location of the proteins is shifted from the designed binding site. We made a model that explained this phenomenon and that can account for the shift in our experiments. In addition, protein-specific work and conductance parameters allowed us to discriminate between RNAP and dCas9 proteins

Partial oxidation of toluene to benzaldehyde and benzoic acid over model vanadia/titania catalysts: Role of vanadia species

Pure and K-doped vanadia/titania prepared by different methods have been studied in order to elucidate the role of vanadia species (monomeric, polymeric, bulk) in catalytic toluene partial oxidation. The ratio of different vanadia species was controlled by treating the catalysts in diluted HNO3, which removes bulk vanadia and polymeric vanadia species, but not the monomeric ones, as was shown by FT-Raman spectroscopy and TPR in H2. Monolayer vanadia species (monomeric and polymeric) are responsible for the catalytic activity and selectivity to benzaldehyde and benzoic acid independently on the catalyst preparation method. Bulk V2O5 and TiO2 are considerably less active. Therefore, an increase of the vanadium concentration in the samples above the monolayer coverage results in a decrease of the specific rate in toluene oxidation due to the partial blockage of active monolayer species by bulk crystalline V2O5. Potassium diminishes the catalyst acidity resulting in a decrease of the total rate of toluene oxidation and suppression of deactivation. Deactivation due to coking is probably related to the Brønsted acid sites associated with the bridging oxygen in the polymeric species and bulk V2O5. Doping by K diminishes the amount of active monolayer vanadia leading to the formation of non-active K-doped monomeric vanadia species and KVO3

Towards sustainable production of formic acid

peer-reviewedFormic acid is a widely used commodity chemical. It can be applied as a safe, easily handled and transported source of hydrogen or CO for different reactions including those producing fuels. The review includes historical aspects of formic acid production. It shortly analyzes the production based on traditional sources such as toxic CO, methanol and methane. However, the main emphasis is done to the sustainable production of formic acid from biomass and biomass-derived products via hydrolysis, wet and catalytic oxidation processes. New strategies of low temperature synthesis from biomass may lead to utilization of formic acid for production of fuel additives such as methanol, upgraded bio-oil, γ-valerolactone and its derivatives, as well as synthesis gas used for Fischer-Tropsch synthesis of hydrocarbons. Some technological aspects are considered

Comparative analysis of results from experimental and numerical studies on concrete strength

Some results of numerical experiments of testing concrete cubes and prisms on unconfined compression, and the comparison of results obtained with experimental and specified data, are presented in the article. When performing calculations of structures in a nonlinear setting, it is very important to choose adequate deformation diagrams or material models. Because of the fact that there are no instructions how to use the diagrams of concrete and armature deformation in collaboration of steel and concrete, the simulation of reinforced concrete structures by finite elements of the same type without any assumptions is impossible. Numerical experiments have been performed in the LS-DYNA software package. This software package allows simulating the collaboration of concrete and steeling with the help of three-dimensional (for concrete) and rod (for the reinforcement) finite elements. As samples, a cube and a prism with dimensions of 150×150×150 mm and 150×150×600 mm, respectively, have been taken. The samples are simulated by solid finite elements. For the simulation of concrete, the non-linear CSCM (Continuous Surface Cap Model) material is used. The tests were carried out with samples of the following classes of concrete as for cylinder compressive strength: C12, C16, C20, C25, C30, C35. This corresponds to the following classes of cube compression strength: B15, B20, B25, B30, B37, B45. The tests have been carried out considering the friction coefficients between the plates of a testing machine, and a sample. The performed researches have shown that the destruction nature of the samples in a numerical experiment corresponds to the failure nature in real tests. The investigated model of CSCM concrete can be used in the calculation of concrete and reinforced concrete structures with acceptable accuracy for main classes of concrete

Relevance of the Drag Force during Controlled Translocation of a DNA–Protein Complex through a Glass Nanocapillary

Combination of glass nanocapillaries with optical tweezers allowed us to detect DNA-protein complexes in physiological conditions. In this system, a protein bound to DNA is characterized by a simultaneous change of the force and ionic current signals from the level observed for the bare DNA. Controlled displacement of the protein away from the nanocapillary opening revealed decay in the values of the force and ionic current. Negatively charged proteins EcoRI, RecA, and RNA polymerase formed complexes with DNA that experienced electrophoretic force lower than the bare DNA inside nanocapillaries. Force profiles obtained for DNA-RecA in our system were different than those in the system with nanopores in membranes and optical tweezers. We suggest that such behavior is due to the dominant impact of the drag force comparing to the electrostatic force acting on a DNA-protein complex inside nanocapillaries. We explained our results using a stochastic model taking into account the conical shape of glass nanocapillaries

Probing the size of proteins with glass nanopores

Single molecule studies using nanopores have gained attention due to the ability to sense single molecules in aqueous solution without the need to label them. In this study, short DNA molecules and proteins were detected with glass nanopores, whose sensitivity was enhanced by electron reshaping which decreased the nanopore diameter and created geometries with a reduced sensing length. Further, proteins having molecular weights (MW) ranging from 12 kDa to 480 kDa were detected, which showed that their corresponding current peak amplitude changes according to their MW. In the case of the 12 kDa ComEA protein, its DNA-binding properties to an 800 bp long DNA molecule was investigated. Moreover, the influence of the pH on the charge of the protein was demonstrated by showing a change in the translocation direction. This work emphasizes the wide spectrum of detectable molecules using nanopores from glass nanocapillaries, which stand out because of their inexpensive, lithography-free, and rapid manufacturing proces