Numeric analysis of reversibility of classic movement equations and constructive criteria of estimating quality of molecular dynamic simulations.

The fundamental criteria of the quality of molecular dynamics (MD) simulation represent a pivotal challenge, especially in the case of MD simulations of large systems (in particular, proteins).This work presents a simple theoretical analysis of time reversibility in classical mechanics that has allowed us to formulate a number of constructive criteria for evaluating the quality of the trajectories, generated in MD simulations. The results of testing the criteria on the structures of eight small proteins are presented.

[On Atomic Nuclear Fusion Processes at Low-Temperatures. An Enhancement of the Probability of Transition through a Potential Barrier Due to the So-Called Barrier Anti-Zeno Effect].

It is known that in quantum mechanics the act of observing the experiment can affect the experimental findings in some cases. In particular, it happens under the so-called Zeno effect. In this work it is shown that in contrast to the "standard" Zeno-effect where the act of observing a process reduces the probability of its reality, an inverse situation when a particle transmits through a potential barrier (a so-called barrier anti-Zeno effect) can be observed, the observation of the particle essentially increases the probability of its transmission through the barrier.

[A Compact Source of Terahertz Radiation Based on Interaction of Electrons in à Quantum Well with an Electromagnetic Wave of a Corrugated Waveguide].

Coherent sources of electromagnetic waves in the terahertz frequency range are very promising for various applications, including biology and medicine. In this paper we propose a scheme of a compact terahertz source, in which terahertz radiation is generated due to effective interaction of electrons in a quantum well with an electromagnetic wave of a corrugated waveguide. We have shown that the generation of electromagnetic waves with a frequency of 1012 sec(-1) and an output power of up to 25.

[Structural and Physicochemical Characteristics of Conformationally Stable alpha-Helical Oligopeptides].

The analysis of conformationally stable (conformational conservative) tetrapeptides selected from protein structures deposited in PDBSelect data bank has been fulfilled. The subset contained 943 tetrapeptide amino acid sequences and there were merely five 3D protein segment representatives for each sequence. As a result, the conclusion has been drawn on the basis of DSSP annotation analysis that in the majority of cases (900 of 943) alpha-helical conformation is obvious.

[Regular thermal waves in female mammary glands].

During experimental studies of thermal regime of female mammary glands tissues the existence of periodic thermal waves was discovered. At the same time, the space-amplitude relief of such waves can mask the space-amplitude relief of the thermal profile, projected to the skin surface of mammary glands by tumor, hidden in the thickness of the gland. The phenomenon observed would be taken into account upon diagnosing pathological states of mammary glands.

[On efficient in vitro purification of cell suspensions containing malignant cells].

We propose a method for magnetic sorting of cell suspensions able to differentiate not only cells with single specific antigen on their surface, but also cells with a group of pre-defined antigens. Individually, each antigen of this group may be present on surfaces of non-selected cells. However, only the simultaneous presence of all given antigens on the cell surface means that such a cell should be separated.

[Reparative and neoplastic spheroid cellular structures and their mathematical model].

Spheroid cell structures in the cell cultures have been described and are used for studying cell-cell and cell- matrix interactions. At the same time, spheroid cell structure participation in the repair and development of cancer in vivo remains unexplored. The aim of this study was to investigate the cellular composition of spherical structures and their functional significance in the repair of squamous epithelium in human papilloma virus-associated cervical pathology--chronic cervicitis and cervical intraepithelial neoplasia 1-3 degree, and also construct a mathematical model to explain the development and behavior of such spheroid cell structure.

[Conformationally stable segments in helical structures of polypeptide chains of proteins and their role in high level structures formation].

In the work the arguments are presented in favor of the idea on the role of conformationally stable oligo-peptides in specific long-distance interactions in phenomena of molecular recognition during various biological processes. Original authors' and literature data are taken into account. The examples of conformationally stable short oligopeptides participation in alpha-helix and collagen type structures formation are given simultaneously with theoretical approaches.

[On the possibility of improving the efficiency of cancer recognition and eradication in vivo when concurrently used two different types of nanodevices].

When using nanodevices in oncology, it is necessary to provide the efficiency of the performance of these nanodevices simultaneously with their safety for an organism. These are conflicting objectives to some extent. Nevertheless, as shown in this work, an approach that helps to eliminate this contradiction is offered.

[On general physical aspects of a problem of in vivo effective detection and recognition of malignant cells].

A fundamentally new recognition method of bio-objects (in particular malignant cells) that escape the immune system supervision control is suggested. Recognition of such bio-objects should be carried out by the unified complex consisting of several molecular groups (for example, antibodies) bound to each other, each group identifies on a surface of this bio-object its target binding site. The choice of such targets is determined by a specific surface-antigen expression profiling.

[Interconnection between architecture of protein globule and disposition of conformational conservative oligopeptides in proteins from one protein family].

It was shown that selective interactions between helical segments of macromolecules can realize in globular proteins in the segments characterized by the same periodicities of charge distribution i.e. between conformationally conservative oligopeptides.

[DNA sequencing using specific long-range interaction between macromolecules].

On the basis of the theory of specific long-range interaction between long molecules the approach has been elaborated for the "fast reading" of nucleotide sequences in sole DNA molecule. Firstly, a stretching force applies to the molecule that causes its unwinding from B-form to so called S-form. Then, a molecule disposes in a stretched state on the background.

[Nanotechnologies in medicine].

The paper deals with some of already available nanotechnology-based methods for struggle against oncological diseases. We discuss the potentialities of essentially new approaches within which devices built inside diseased cells could operate their behaviour. Conceptually, using these approaches one can force such "controlled" cells to fight against tumours.

[About the possibility of direct measurement of phases in X-ray diffraction analysis].

A method for direct experimental measurement of phases in X-ray diffraction analysis has been developed. The phases can be determined using a peculiar holographic filming (called here autoholography) in which the rays scattered on an object completely identical to the object under study but displaced, in a definite way, and turned in space relative to it serve as a reference beam. In principle, autoholography does not require any particularly good coherence of radiation since the reference bundle enables one to compensate to some extent for its absence.

[Ultraminiature electrochemical and photoelectric current sources and their possible use for controlled induction of immune system activity and in other medical applications].

The possibility of producing microparticles (10-1000 nm) suitable for the introduction into biological cells and tissues and producing the electrical field and electrical currents around them due to electrochemical and photoelectric processes is discussed. A number of phenomena related to antitumor immunity are discussed, and several hypotheses to explain them are invoked. Among them is the hypothesis that the antitumor activity of the immune system may be associated with some agents that are phagocytized by the cells of the macrophage series and promote their activation.

[How a long linear molecule can be straightened on a support].

A relatively simple means is proposed for fastening a macromolecule such as DNA in a straight line on a dielectric support (which is essential for "fast reading" of sequences by physical methods). A randomly coiled molecule in solution can be caused to align with a "straightening electrode" under the support, as in a phase transition. Conditions are envisaged that should ensure processive settling without defects.

[On the mechanisms of the influence of imino acids on the physical characteristics of collagens].

The influence of imino acids on the thermodynamic characteristics of collagen type structures in various collagens has been analyzed. It was shown that the basic mechanism of entropy increase in the protein-water system consists in the alteration in the number of cooperative segments accompanying the increase in imino acids content, which can be observed during the melting of the fibrous macromolecule. The range of variation in the physical characteristics of cooperative units is determined, in particular, by the variability of hydrogen bond parameters.

[On the periodicity in the fine structure of histograms during nuclear decay].

A possible explanation for the occurrence of periodicity in the fine structure of histograms during nuclear decay is proposed. The hypothesis states that, even in the absence of polarization, when the spin distribution of decaying nuclei over directions is, on the average, isotropic, the fine structure of histograms should depend, due to fluctuations, on the angles at which the sample is observed. There fore, when the Earth after some period would make a full furn, the distribution of fluctuations would return to the initial one, and, correspondingly, the fine structure of the histograms would repeat.

["Unpredictablity of the quantum world" and logical catastrophe].

The fundamental gnoseological question that is always present in a basic science is: Can this science adequately predict the future? In classical mechanics, we deal in many cases with dynamic chaos; therefore, this prediction is most often impossible. In the quantum theory, the dynamic chaos associated with the disturbances of initial conditions is formally absent. Nevertheless, as it was shown in this work, there are other reasons that directly relate to what is called the paradoxes of formal logic, which, in the case of quantum theory, too, do not enable one to precisely determine what will happen in the future.

[Long-range interactions between macromolecules, introduced into smectic liquid crystals].

Equations for the potentials of interactions between macromolecules of different shapes incorporated into smectic liquid crystals are presented. In addition to accurate equations, simple formula for estimation are given.

[Long-range interactions between macromolecules in ordered media].

The results of theoretical calculations of interactions between macromolecules dissolved in ordered media such as liquid crystals and biological membranes (lipid bilayers) are reviewed. Expressions for the potentials of interactions between macromolecules of different shape incorporated into nematic liquid crystals, thin films, and lipid mono- and bilayers were derived. In addition to exact expressions, simple evaluating formulae are given.

[A theoretical approach to "macroscopic fluctuations" effect].

At present there is no generally accepted theory of the effect of macroscopic fluctuations. It the article, an attempt is made to relate this effect to some basic properties of quantum systems, in particular, to the formal absence of dynamic chaos in these systems. Based on this approach, it was shown why the level of the effect must be of the same order of magnitude as the level of noise and cannot exceed this level as the number of experiments increases.

[A method for reconstruction of pathological changes in the volume of a living body].

A new method of contact thermography (intrograph) was developed. The method allows one to establish the temperature in any region of the body. The computer program provides an uninvasive and safe way of comparison of thermograms in time.

A new approach for the calculation of the energy of van der Waals interactions in macromolecules of globular proteins.

Van der Waals interaction energy in globular proteins is presented by the interaction energies between regions of protein spatial structure with homogenous medium density distribution. We introduce a notion of the local medium permittivity as a function of absorptance of molecular groups with particular conformation. Proposed theory avoids shortcomings which are typical for the calculations on the basis of the pairwise additive approximation.

Hierarchy of the interaction energy distribution in the spatial structure of globular proteins and the problem of domain definition.

An algorithm for determining of protein domain structure is proposed. Domain structures resulted from the algorithm application have been obtained and compared with available data. The method is based on entirely physical model of van der Waals interactions that reflects as illustrated in this work the distribution of electron density.