D. O. Sinitsyn

Possible Mechanisms Underlying the Therapeutic Effects of Transcranial Magnetic Stimulation

Transcranial magnetic stimulation (TMS) is an effective method used to diagnose and treat many neurological disorders. Although repetitive TMS (rTMS) has been used to treat a variety of serious pathological conditions including stroke, depression, Parkinson’s disease, epilepsy, pain, and migraines, the pathophysiological mechanisms underlying the effects of long-term TMS remain unclear. In the present review, the effects of rTMS on neurotransmitters and synaptic plasticity are described, including the classic interpretations of TMS effects on synaptic plasticity via long-term potentiation and long-term depression. We also discuss the effects of rTMS on the genetic apparatus of neurons, glial cells, and the prevention of neuronal death. The neurotrophic effects of rTMS on dendritic growth and sprouting and neurotrophic factors are described, including change in brain-derived neurotrophic factor concentration under the influence of rTMS. Also, non-classical effects of TMS related to biophysical effects of magnetic fields are described, including the quantum effects, the magnetic spin effects, genetic magnetoreception, the macromolecular effects of TMS, and the electromagnetic theory of consciousness. Finally, we discuss possible interpretations of TMS effects according to dynamical systems theory. Evidence suggests that a rTMS-induced magnetic field should be considered a separate physical factor that can be impactful at the subatomic level and that rTMS is capable of significantly altering the reactivity of molecules (radicals). It is thought that these factors underlie the therapeutic benefits of therapy with TMS. Future research on these mechanisms will be instrumental to the development of more powerful and reliable TMS treatment protocols.

Total lineshape analysis of high-resolution NMR spectra powered by simulated annealing.

The novel algorithm for a total lineshape analysis of high-resolution NMR spectra has been developed. A global optimization by simulated annealing has been applied that has allowed to overcome the main trouble of common approaches which had frequently returned solutions for local minima rather than for global ones. The algorithm has been verified for the four-spin test systems ABCD, and has been successfully used for analysis of experimental NMR spectra of proline. The approach has allowed to avoid a sophisticated manual setup of initial parameters and to conduct the analysis of complicated high-resolution NMR spectra nearly automatically.

Twisted quasiperiodic textures of biaxial nematic liquid crystals.

Textures (i.e., smooth space nonuniform distributions of the order parameter) in biaxial nematics turned out to be much more complex and interesting than expected. Scanning the literature we find only a very few publications on this topic. Thus, the immediate motivation of the present paper is to develop a systematic procedure to study, classify, and visualize possible textures in biaxial nematics. Based on the elastic energy of a biaxial nematic (written in the most simple form that involves the least number of phenomenological parameters) we derive and solve numerically the Lagrange equations of the first kind. It allows one to visualize the solutions and offers a deep insight into their geometrical and topological features. Performing Fourier analysis we find some particular textures possessing two or more characteristic space periods (we term such solutions quasiperiodic ones because the periods are not necessarily commensurate). The problem is not only of intellectual interest but also of relevance to optical characteristics of the liquid-crystalline textures.

New possibilities of X-ray nanocrystallography of biological macromolecules based on X-ray free-electron lasers

X-ray serial nanocrystallography is a new technique for determining the three-dimensional structure of biological macromolecules from data on the diffraction of ultrashort pulses generated by X-ray free-electron lasers. The maximum achievable resolution for a set of experimental data as a function of the sample sizes and parameters of the equipment is estimated based on simulations of the diffraction process with allowance for changes in the electronic structure of the atoms of the sample under the influence of X-rays. Estimates show that nanocrystallography greatly enhances the possibilities of X-ray analysis, reducing the requirements for the minimum permitted size of the crystals and enabling to explore poorly crystallizable molecular objects, such as many membrane proteins and complexes of macromolecules.

Elimination of signals tilting caused by B 0 field inhomogeneity using 2D-lineshape reference deconvolution

An efficient approach for reference deconvolution of two-dimensional spectra aiming at the correction of static field inhomogeneity was established. In comparison to known techniques, a great improvement was achieved using the cross-section along the diagonal of the reference peak instead of its full 2D line shape. The method is termed pseudo-2D diagonal deconvolution. The approach developed allows suppressing the two-dimensional peaks tilting caused by the magnetic field inhomogeneity, while keeping the signal-to-noise ratio constant. Long-known method of 2D reference deconvolution (true-2D reference deconvolution) was also applied for comparison. The neutral and resolution-enhancing pseudo-2D deconvolutions were successfully applied for the resolution of complex overlapping multiplets and for measuring small scalar coupling constants. The new algorithm for the elimination of shape distortion of two-dimensional peaks showed to be promising in the perspective of an automated analysis of 2D correlation NMR spectra.

Femtosecond X-ray free-electron lasers: A new tool for studying nanocrystals and single macromolecules

A brief overview of the design of femtosecond X-ray free-electron lasers (XFEL), characteristics of the emitted X-ray pulses, and potentialities of XFEL are presented. A concise analysis of the problems in modeling X-ray scattering patterns produced by ultraintense radiation sources is given.

Biocrystallization of bacterial nucleoid under stress

Structural, biochemical, and genetic changes caused by stress factors are known to be largely similar for cells of all modern organisms, which inherited the basic strategies of adaptation to different types of stress from their ancient ancestors. In the present work, the adaptation process is considered for the simplest example of the bacterial E. coli nucleoid. Experimental studies performed recently on prokaryotic bacterial cells, the simplest living organisms, have demonstrated that, under unfavorable environmental conditions (for example, starvation), bacterial cells can use biocrystallization, a special mechanism of protection of the genetic apparatus (nucleoid), generally untypical of living organisms. This mechanism helps to protect the nucleoid from damage and resume the activity of the bacterial cells later, upon improvement of the external conditions. The results of studying the structure of the nucleoid of E. coli bacteria (BL21-Gold strain (DE3)) subjected to starvation stress by using synchrotron radiation at the ESRF beamline ID23-1 are reported.

Variability of Neuronal Responses: Types and Functional Significance in Neuroplasticity and Neural Darwinism

HIGHLIGHTS We suggest classifying variability of neuronal responses as follows: false (associated with a lack of knowledge about the influential factors), “genuine harmful” (noise), “genuine neutral” (synonyms, repeats), and “genuine useful” (the basis of neuroplasticity and learning). The genuine neutral variability is considered in terms of the phenomenon of degeneracy. Of particular importance is the genuine useful variability that is considered as a potential basis for neuroplasticity and learning. This type of variability is considered in terms of the neural Darwinism theory. In many cases, neural signals detected under the same external experimental conditions significantly change from trial to trial. The variability phenomenon, which complicates extraction of reproducible results and is ignored in many studies by averaging, has attracted attention of researchers in recent years. In this paper, we classify possible types of variability based on its functional significance and describe features of each type. We describe the key adaptive significance of variability at the neural network level and the degeneracy phenomenon that may be important for learning processes in connection with the principle of neuronal group selection.

Asymptotic Hamiltonian reduction for the dynamics of a particle on a surface

We consider the motion of a particle on the surface generated by a small perturbation of the standard sphere. The key observation is that a trajectory of the particle has the shape of a coil, and one may qualitatively describe the turns of the latter as a precessing great circle of the sphere. Thus, we change the configuration space of the initial problem for the space of great circles on the sphere. The construction enables us to derive a subsidiary Hamiltonian system having the shape of equations for the top with a 4th order Hamiltonian. The subsidiary system provides a detailed asymptotic description of the particle’s motion in terms of graphs on the standard sphere.

ANATOLIA: NMR software for spectral analysis of total lineshape

In this paper we present a new fast and free open‐source software package ANATOLIA for the total lineshape analysis of NMR spectra. It performs fitting of experimental 1D NMR spectra based on quantum mechanical formalism. The program serves for the determination of J‐coupling constants and elucidation of complicated multiplet structures including strongly coupled systems. The program utilizes the Lorentzian broadening approach for local minima suppression. It is developed in the C++ language for standard personal computers. ANATOLIA is adapted to work with the Bruker NMR spectral format and could be conveniently integrated into the TopSpin software package. This tutorial contains a program description, 2 demonstration examples, and general recommendations for NMR spectra analysis.