Igor V. Morozov

Applications of quartz tuning forks in spectroscopic gas sensing

A recently introduced approach to photoacoustic detection of trace gases utilizing a quartz tuning fork (TF) as a resonant acoustic transducer is described in detail. Advantages of the technique called quartz-enhanced photoacoustic spectroscopy (QEPAS) compared to conventional resonant photoacoustic spectroscopy include QEPAS sensor immunity to environmental acoustic noise, a simple absorption detection module design, and its capability to analyze gas samples ∼1mm3 in volume. Noise sources and the TF properties as a function of the sampled gas pressure, temperature and chemical composition are analyzed. Previously published results for QEPAS based chemical gas sensing are summarized. The achieved sensitivity of 5.4×10−9cm−1W∕√Hz is compared to recent published results of photoacoustic gas sensing by other research groups. An experimental study of the long-term stability of a QEPAS-based ammonia sensor is presented. The results of this study indicate that the sensor exhibits very low drift, which allows da...

Standards for molecular dynamics modelling and simulation of relaxation

An attempt is made to formulate a set of requirements for simulation and modelling of relaxation in dense media. Each requirement is illustrated by examples of numerical simulation of particles with different types of interaction given by soft-sphere, Lennard–Jones, embedded atom method or Coulomb potential. The approaches developed are expected to be universal for some classes of relaxation processes in liquids, fluids, crystals and plasmas.

Molecular dynamics simulations of the relaxation processes in the condensed matter on GPUs

Abstract We report on simulation technique and benchmarks for molecular dynamics simulations of the relaxation processes in solids and liquids using the graphics processing units (GPUs). The implementation of a many-body potential such as the embedded atom method (EAM) on GPU is discussed. The benchmarks obtained by LAMMPS and HOOMD packages for simple Lennard-Jones liquids and metals using EAM potentials are presented for both Intel CPUs and Nvidia GPUs. As an example the crystallization rate of the supercooled Al melt is computed.

Non-exponential dynamic relaxation in strongly nonequilibrium nonideal plasmas

Relaxation of kinetic energy to the equilibrium state is simulated by the molecular dynamics method for nonideal two-component non-degenerate plasmas. Three limiting examples of initial states of strongly nonequilibrium plasma are considered: zero electron velocities, zero ion velocities and zero velocities of both electrons and ions. The initial non-exponential stage, its duration τnB and subsequent exponential stages of the relaxation process are studied for a wide range of the nonideality parameter and the ion mass.

Double-resonance probe for near-field scanning optical microscopy

A surface-contact transducer is developed for scanning probe microscopes, whose operating principle is based on the coincidence between the resonance frequency of a 32kHz quartz tuning fork and that of the probe attached to it. This allows the transducer to have a high quality factor and, if the vibration amplitude of the probe tip exceeds that of the tuning fork prongs, materially improves its force sensitivity. The resonance transducer proposed by us has an experimentally verified force sensitivity of 8pN (rms) in the 300Hz frequency band, which is of the same order of magnitude as the sensitivity of atomic force microscope (AFM) cantilever sensors. The manufacture of such transducers equipped with optical-fiber probes for near-field scanning optical microscopy and with tungsten probes for AFM is described as an example.

A comparative study of cell-free apoptotic and genomic DNA using FISH and massive parallel sequencing

Objective : Study of circulating DNA (cirDNA) generation mechanisms with respect to their influence on the content of cirDNA is very important since it could indicate the best molecular targets for diagnostic applications. Since apoptosis was shown to be one of the main sources of cirDNA, we performed in vitro comparative study of cell-free apoptotic and genomic DNA (gDNA). Methods : DNA isolated from culture medium of apoptotic human umbilical vein endothelial cells (cm-apoDNA) and the gDNA from the same living cells was analyzed using FISH and sequenced on SOLiD 3 platform. Results/conclusions : FISH demonstrates overrepresentation of C-positive chromosome regions in cm-apoDNA. SOLiD 3 data show enrichment of cm-apoDNA for Alu repeats: the content of AluJ, AluS and AluY repeats was, respectively, 2.47-fold (standard deviation (SD) 3.6%), 2.45-fold (SD 5.5%) and 2.79-fold (SD 6.1%) higher in cm-apoDNA. By contrast, some of L1 elements were underrepresented in cm-apoDNA: the content of L1MA and L1ME was, respectively, 1.4-fold (SD 22%) and 1.45-fold (SD 9%) lower in cm-apoDNA. In contrast to FISH, these data and the predominant location of Alu repeats in euchromatic regions evidence the non-uniform gDNA degradation during apoptosis leading to the enrichment of cm-apoDNA with coding sequences.

Microbial communities of the discharge zone of oil- and gas-bearing fluids in low-mineral Lake Baikal

At the site of natural ingress of oil, microbial diversity in the Central Baikal bottom sediments differing in the chemical composition of pore waters was studied by molecular biological techniques. The sediments saturated with oil and methane were found to contain members of 10 bacterial and 2 archaeal phyla. The oxidized sediment layer contained methanotrophic bacteria belonging to the Alphaproteobacteria, which had a specific structure of the pmoA gene and clustered together with uncultured methanotrophs from cold ecosystems. The upper sediment layer also contained oil-oxidizing bacteria and the alkB genes most closely related to those of Rhodococcus. The microbial community of reduced sediments exhibited lower diversity and was represented mostly by the organisms involved in hydrocarbon biodegradation.

Spectrum and Frequency of the GJB2 Gene Pathogenic Variants in a Large Cohort of Patients with Hearing Impairment Living in a Subarctic Region of Russia (the Sakha Republic)

Pathogenic variants in the GJB2 gene, encoding connexin 26, are known to be a major cause of hearing impairment (HI). More than 300 allelic variants have been identified in the GJB2 gene. Spectrum and allelic frequencies of the GJB2 gene vary significantly among different ethnic groups worldwide. Until now, the spectrum and frequency of the pathogenic variants in exon 1, exon 2 and the flanking intronic regions of the GJB2 gene have not been described thoroughly in the Sakha Republic (Yakutia), which is located in a subarctic region in Russia. The complete sequencing of the non-coding and coding regions of the GJB2 gene was performed in 393 patients with HI (Yakuts—296, Russians—51, mixed and other ethnicities—46) and in 187 normal hearing individuals of Yakut (n = 107) and Russian (n = 80) populations. In the total sample (n = 580), we revealed 12 allelic variants of the GJB2 gene, 8 of which were recessive pathogenic variants. Ten genotypes with biallelic recessive pathogenic variants in the GJB2 gene (in a homozygous or a compound heterozygous state) were found in 192 out of 393 patients (48.85%). We found that the most frequent GJB2 pathogenic variant in the Yakut patients was c.-23+1G>A (51.82%) and that the second most frequent was c.109G>A (2.37%), followed by c.35delG (1.64%). Pathogenic variants с.35delG (22.34%), c.-23+1G>A (5.31%), and c.313_326del14 (2.12%) were found to be the most frequent among the Russian patients. The carrier frequencies of the c.-23+1G>A and с.109G>A pathogenic variants in the Yakut control group were 10.20% and 2.80%, respectively. The carrier frequencies of с.35delG and c.101T>C were identical (2.5%) in the Russian control group. We found that the contribution of the GJB2 gene pathogenic variants in HI in the population of the Sakha Republic (48.85%) was the highest among all of the previously studied regions of Asia. We suggest that extensive accumulation of the c.-23+1G>A pathogenic variant in the indigenous Yakut population (92.20% of all mutant chromosomes in patients) and an extremely high (10.20%) carrier frequency in the control group may indicate a possible selective advantage for the c.-23+1G>A carriers living in subarctic climate.

Nonideal plasmas as non-equilibrium media

Various aspects of the collective behaviour of non-equilibrium nonideal plasmas are studied. The relaxation of kinetic energy to the equilibrium state is simulated by the molecular dynamics (MD) method for two-component non-degenerate strongly non-equilibrium plasmas. The initial non-exponential stage, its duration and the subsequent exponential stage of the relaxation process are studied for a wide range of ion charge, nonideality parameter and ion mass. A simulation model of the nonideal plasma excited by an electron beam is proposed. An approach is developed to calculate the dynamic structure factor in non-stationary conditions. Instability increment is obtained from MD simulations.

Reflectivity and imaging capabilities of spherically bent crystals studied by ray-tracing simulations

Spherically bent crystals are widely used in focusing monochromators, spectrometers and other x-ray optical systems. In particular, they are used in focusing spectrometers with spatial resolution, applied in high energy density diagnostics and warm dense matter studies. In this case, plasma parameters are obtained via measurements of relative intensities of characteristic spectral emission lines for multiply charged ions, which are affected by an instrumental function. Here we develop and use the ray-tracing computer simulations to study reflectivity properties of spherically bent crystals in a particular experimental conditions and to provide the method to adjust and validate the measured spectral line intensities on quantitative basis.