Table of contents

The structure of native Champsocephalus gunnari icefish otoliths, scales, teeth, bones and pristine hydroxyapatite (HA) were examined using Near Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy. NEXAFS Cls-absorption spectra of the selected icefish hard tissues indicate that otoliths contain anion [CO₃]^2-. NEXAFS P2p-spectra clearly indicate the absence of phosphorus atoms only within otoliths and scales samples. However, the icefish teeth and bones P2p-spectra demonstrate identical spectral feature typical for the HA. NEXAFS Ca2p-spectra of the icefish hard tissues studied also shows features, which are in good correspondence with HA spectra. Interestingly, there is a red shift ≈ 0.1 eV of the 2p_1/2,3/2 → 3d transition energies in NEXAFS Ca2p-spectra of teethes and bones of the C. gunnari in comparison to HA.

The process of proton transport in cytochrome c oxidase is studied in the framework of stochastic modeling. The activation energies are calculated using Marcus theory. This model allows to define the key amino acid residues and water molecules which form the main H⁺ transduction pathway. According to the simulation results, Asn-207 and Asn-121 are not involved in direct proton translocation. The estimated rate of the proton transfer through the D-channel of cytochrome c oxidase is (1.43±0.18)·10⁴ s^-1.

Phantoms are imitations of biological tissue, which are used for modelling of the light propagation in biological tissues. Carrying out any biophysical experiments requires an indispensable constancy of the initial experiment conditions. The use of solid undegradable phantoms is the basis to obtain reliable reproducible experimental results. The fabrication of biological tissues phantoms containing high absorbance or fluorescence nanoparticles and corresponding to specific mechanical, optical properties is an actual task. This work describes development, fabrication and characterization of such solid tissue phantoms with embedded CdSe/ZnS quantum dots, gold and upconversion nanoparticles. Luminescence of samples with CdSe/ZnS quantum dots and upconversion nanoparticles were recorded. A sample of gold nanorods was analyzed using thermal gravimetric analysis. It can be concluded that the samples are well suited for experiments on laser thermolysis.

Implications of quantum-mechanical approach to the description of proton transport in biological systems are a tempting subject for an overlapping of fundamental physics and biology. The model of proton transport through the integrated membrane enzyme F_oF₁-ATP synthase responsible for ATP synthesis was developed. The estimation of the mathematical expectation of the proton transfer time through the half-channel was performed. Observed set of proton pathways through the inlet half-channel showed the nanosecond timescale highly dependable of some amino acid residues. There were proposed two types of crucial amino acids: critically localized (His245) and being a part of energy conserving system (Asp119).

The model presented in this work allows simulation of isotopic exchange reactions at chemical equilibrium catalyzed by a glutamine synthetase. To simulate the functioning of the enzyme the algorithm based on the stochastic approach was applied. The dependence of exchange rates for ¹⁴C and ³²P on metabolite concentration was estimated. The simulation results confirmed the hypothesis of the ascertained validity for preferred order random binding mechanism. Corresponding values of K_0.5 were also obtained.

Here we propose a simple label-free bio-electronic toxin detector based on nondestructive impedance spectroscopy (IS) method with a single living cell as a sensing element. The toxins distort cell membrane, which significantly affects on the impedance level of an electrode, which covered by a cell. This effect could be used for toxin detection. We believe that our bio-sensor will open a new roadmap in water purity purposes and will save many a one lives.

An application of the artificial immune system method for decomposition of complex spectra is presented. The results of decomposition of the model contour consisting of three components, Gaussian contours, are demonstrated. The method of artificial immune system is an optimization method, which is based on the behaviour of the immune system and refers to modern methods of search for the engine optimization.

The comparative research of silica, the magnetite and magnetite-silica nanoparticles modified with fluorescent dyes using gas-phase and liquid-phase methods was conducted. At the content of fluorescent dye comparable in size a particular spectrophotometric method, nanoparticles with fluorescein have up to 1000 times larger overall luminous efficiency. It is revealed that magnetic nanoparticles are characterized by a smaller light efficiency in comparison with silica particles, at the same time particles of a magnetite are most effective at modification with fluorescein, and magnetite-silica particles – at modification with indocyanine green.

In this work silica aminated nanoparticles were used to show capability for chemisorbing organic compound having a carboxyl group. Phosphocreatine (creatine phosphate) was used as an active ingredient. Since the method for determination of phosphocreatine with the sample analysis using Jaffe reaction didn't give a positive result, the definition of free phosphocreatine was carried out by the method of diacetyl in the presence of α-naphthol.

The application of a dynamic pin-photodiode as a recording device of the fluorescence radiation is considered. An experimental setup for registration of luminescence signals from biomolecules excited by laser radiation was developed. Rhodamine 6G and chlorophyll were investigated.

Investigation results of red blood cells (human erythrocytes) aligning and fixing inside the liquid crystal (LC) cell have been presented in the present paper. LC cells have been modified through the improved nanostructured relief and LC sensitized with intermolecular charge transfer complex COANP-C₇₀.

Creation of low-cost compact devices based on microfluidic platforms for biological and medical research depends on the degree of development and enhancement of prototyping technologies. Two designs of polymer and hybrid microfluidic devices fabricated by soft lithography and intended for isothermal amplification and polymerase chain reaction are presented in this paper. The digital helicase-dependent isothermal amplification was tested in the device containing a droplet generator. Polymerase chain reaction was carried out in the hybrid microfluidic device having ten reaction chambers. A synthesized cDNA fragment of GAPDH housekeeping gene was used as a target.

Single stranded DNA damage at photodynamic treatment with Radachlorin photosensitizer was investigated. Chemical trap method was used to evaluate generation of singlet oxygen in water solution. Interaction of singlet oxygen with ssDNA resulted into decrease of the replication activity of ssDNA. DNA stopped replicating during PCR at irradiation doses greater than 15 J/cm² and concentration of photosensitizer [PS] = 3.8 μM. The dependence of replication activity of ssDNA on generated singlet oxygen concentration was identified.

Currently several methods of super-resolution optical microscopy are known. One of them – super-resolution radial fluctuations (SRRF) microscopy – was successfully used in present work to study the structures, formed by FtsZ protein in living E.coli cells with a resolution well below the diffraction limit.

Emulsion dynamics is little-studied, but important subject for biological, medical and physical applications. In this work microfluidic droplet generator was used to experimentally study two-dimensional flow of monodispersed macroemulsion with 25 – 50 μm droplet size. Quantity of droplets, their trajectories and velocity profiles were studied. Obtained results showed, that velocity profile of droplets flow does not coincide with the Poiseuille profile of laminar oil flow in the channel. Droplet velocity decrease with the increasing of droplets concentration, which can be explained by the hydrodynamic interactions between droplets. The law of motion can be well described by the Greenberg's traffic flow model.

The numerical impact modeling of some external effects on the CVC of biosensors based on AlGaN/GaN heterostructures (HEMT) was carried out. The mathematical model was created that allowed to predict the behavior of the drain current depending on condition changes on the heterostructure surface in the gate region and to start the process of directed construction optimization of the biosensors based on AlGaN/GaN HEMT with the aim of improving their performance. The calculation of the drain current of the biosensor construction was carried out to confirm the reliability of the developed mathematical model and obtained results.

The new method for determining the components composition and their concentration in the express mode in biological objects and liquid suspensions is proposed. This method is based on the Bloch equations solutions for the components of the magnetization vector in case of registration of the NMR signal using a modulation technique in a weak magnetic field. It has allowed to measure not only the relaxation constants T₁ and T₂, using which it is possible determine the deviation degree of the medium from the standard state, but also the concentrations of the components included in mediums composition, at the site of sampling by a compact NMR spectrometer.

We present our recent development of new approach for compositional study of topography, nanomechanical and piezoelectric properties with nanometer spatial resolution and demonstrate it in application to two types of biopiezoelectrics: type I collagen and diphenylalanine peptide nanotubes.

The objective of this paper was to investigate whether it is possible to obtain biomimetic materials recreating the luminescent properties and molecular composition of intact dental tissues. Biomimetic materials were produced and their properties compared with native dental tissues. In addition, the overall contribution of the organic and non-organic components in the photoluminescence band was investigated. The results showed that it is possible to develop biomimetic materials with similar molecular composition and optical properties to native dental tissues for the early identification of dental caries.

The spectral-correlation method was described for diagnostics of optically inhomogeneous biological objects and materials of natural origin. The interrelation between parameters of the studied objects and parameters of the cross correlation function of speckle patterns produced by scattering of coherent light at different wavelengths is shown for thickness, optical density and internal structure of the material. A detailed study was performed for cellulose electric insulating paper with different parameters.

The load of a liquid sample into a measuring chamber is one of the stages of substance analysis in modern devices. Fluid flow is effectively calculated by numerical simulation using application packages, for example, COMSOL MULTIPHYSICS. In the same time it is often desirable to have an approximate analytical solution. The applicability of a submerged jet model for simulation the liquid sample load is considered for the chamber with sizes from hundreds micrometers to several millimeters. The paper examines the extent to which the introduction of amendments to the jet cutting and its replacement with an energy equivalent jet provide acceptable accuracy for evaluation of the loading process dynamics.

A scanning ion-conductance microscope was designed on the basis of scanning probe microscope NanoTutor. The optimal parameters of nanopipettes fabrication were found according to scanning electron microscopy diagnostics, current-distance I (Z) and current-voltage characteristics. A comparison of images of test objects, including biological samples, was carried out in the modes of optical microscopy, atomic force microscopy and scanning ion-conductance microscopy. Sphere-shaped nanopippettes probes were developed and tested to increase the stability of pipettes, reduce invasiveness and improve image quality of atomic force microscopy in tapping mode. The efficiency of sphere-shaped nanopippettes is shown.

To date, optogenetics is one of the most popular methods in the world in neuroscience. There are new equipment and devices created to keep the progress of this method. This article describes a light pulse generator developed at the Laboratory of Molecular Neurodegeneration, designed for optogenetic experiments.

Polyethylene glycol diacrylate (PEGDA) microparticles (MPs) have a great potential in a wider range of applications including cell carriers, drug delivery agents, and multiplexing assays. Among existing MP fabricating methods, only the microfluidic droplet-based methods provide both morphology complexity and substance diversity. This work is concerned with the production PEGDA-based droplets with the photoinitiator (Irgacure 2959) in a flow-focusing microfluidic generator. The kinetics of MPs solidification in mineral oil with various common surfactants (Abil EM 180, Span 80) were investigated. Also, the Young's modulus of solid PEGDA were obtained.

A model for chiral periodicity with alternating chiral sense in hierarchies of protein and nucleic acid structures is proposed and substantiated. Regular alternation of the chirality sense is revealed in transitions from the lowest to higher levels of structural-functional organization in proteins where it is L-D-L-D. The stratification principle combines the ideas of biomacromolecules folding and molecular biological machines.

Morphological features were visualized and the weight loss of chitosan microtubes during in vitro biodegradation was evaluated in two model media (an enzyme medium of lysozyme and the phosphate buffer) by means of scanning electron microscopy and gravimetry. It was observed that during incubation in the enzymatic medium, the relief and morphology of the microtube surface were changing, as expressed in the appearance of micropores, cracks and bulk defects. When keeping the samples in the phosphate buffer, no substantial defects were formed, only few micropores appeared. The weight loss of the samples after 180 days of storage in the lysozyme medium and phosphate buffer was 30 and 7%, respectively.

Transcription factor Oct4 is a marker of pluripotent stem cells and has a significant role in their self-renewal. Oct4 gene is controlled by three cis-regulatory elements – proximal promoter, proximal enhancer and distal enhancer. All of these elements are targets for binding of regulatory proteins. Distal enhancer is in our research focus because of its activity in early stages of embryonic development. There are two main sequences called site 2A and site 2B that are presented in distal enhancer. For this moment proteins which bind to a site 2A (CCCCTCCCCCC) remain unknown. Using combination of in vitro method electrophoretic mobility shift assay (EMSA) and mass spectromery we identified several candidates that can regulate Oct4 gene expression through site 2A.

Dense homogeneous fabric composed from continuous bead-free erbium-doped sodium potassium niobate (Er:NKN) 100 μm long and 100-200 nm in diameter nanofibers was sintered by sol-gel calcination assisted electrospinning technique. Er doping with the concentration of 2 at.% provides readily detectable room-temperature broad-band photoluminescence (PL) centered at λ_PL = 0.55 and 0.98 μm being pumped, respectively, with 532 and 785 nm lasers. Electric field induced resistance switching and strong electric rectification effect were found in nanoporous sandwich Au/Er:NKN/Pt capacitive cell. Memristor-type current-voltage I-V characteristics originate from the electrochemical migration of oxygen vacancies at the n-type Er:NKN oxide/high work function Pt cathode junction interface.