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- Focusing effects of ballistic transverse-quantized excitons in metal nanofilmsPublication . Makarov, Vladimir; Khmelinskii, IgorNew type of behavior of transverse-quantized excitons was discovered in metal nanofilms. These excitons demonstrated ballistic properties, propagating along nanofilms in straight lines along centimeter distances, reflecting at the film patch boundaries, and refracting at the boundary separating films of different materials but with the same exciton energy. Exciton reflection and focusing was explored in elliptically shaped metal film patches, along with exciton refraction on the boundary line separating two different film patches with compatible transverse-confinementgenerated electronic structures. These transverse-quantized excitons interact with phonons very weakly, prohibited by symmetry selection rules. The latter statement was confirmed in timeresolved experiments. Weak interactions explain rectilinear trajectories and long lifetimes of excitons in thin metal films.
- Reversible and irreversible mitochondrial swelling in vitroPublication . Khmelinskii, Igor; Makarov, VladimirMitochondrial activity as regards ATP production strongly depends on mitochondrial swelling (MS) mode. Therefore, this work analyzes reversible and irreversible MS using a detailed biophysical model. The reported model includes mechanical properties of the inner mitochondrial membrane (IMM). The model describes MS dynamics for spherically symmetric, axisymmetric ellipsoidal and general ellipsoidal mitochondria. Mechanical stretching properties of the IMM were described by a second-rank rigidity tensor. The tensor components were estimated by fitting to the earlier reported results of in vitro experiments. The IMM rigidity constant of ca. 0.008 dyn/nm was obtained for linear deformations. The model also included membrane bending effects, which were small compared to those of membrane stretching. The model was also tested by simulation of the earlier reported experimental data and of the system dynamics at different initial conditions, predicting the system behavior. The transition criteria from reversible to irreversible swelling were determined and tested. The presently developed model is applicable directly to the analysis of in vitro experimental data, while additional improvements are necessary before it could be used to describe mitochondrial swelling in vivo. The reported theoretical model also provides an idea of physically consistent mechanism for the permeability transport pore (PTP) opening, which depends on the IMM stretching stress. In the current study, this idea is discussed briefly, but a detailed theoretical analysis of these ideas will be performed later. The currently developed model provides new understanding of the detailed MS mechanism and of the conditions for the transition between reversible and irreversible MS modes. On the other hand, the current model provides useful mathematical tools, that may be successfully used in mitochondrial biophysics research, and also in other applications, predicting the behavior of mitochondria in different conditions of the surrounding media in vitro or cellular cyto(sarco)plasm in vivo. These mathematical tools are based on real biophysical processes occurring in mitochondria. Thus, we note a significant progress in the theoretical approach, which may be used in real biological systems, compared to the earlier reported models. Significance of this study derives from inclusion of IMM mechanical properties, which directly impact the reversible and irreversible mitochondrial swelling dynamics. Reversible swelling corresponds to reversible IMM deformations, while irreversible swelling corresponds to irreversible deformations, with eventual membrane disruption. The IMM mechanical properties are directly dependent on the membrane biochemical composition and structure. The IMM deformationas are induced by osmotic pressure created by the ionic/neutral solute imbalance between the mitochondrial matrix media and the bulk solution in vitro, or cyto(sarco)plasm in vivo. The novelty of the reported model is in the biophysical mechanism detailing ionic and neutral solute transport for a large number of solutes, which were not taken into account in the earlier reported biophysical models of MS. Therefore, the reported model allows understanding response of mitochondria to the changes of initial concentration(s) of any of the solute(s) included in the model. Note that the values of all of the model parameters and kinetic constants have been estimated and the resulting complete model may be used for quantitative analysis of mitochondrial swelling dynamics in conditions of real in vitro experiments.
- Electron microscopy study of the central retinal fovea in Pied flycatcher: evidence of a mechanism of light energy transmission through the retinaPublication . Zueva, Lidia; Golubeva, Tatiana; Korneeva, Elena; Resto, Oscar; Inyushin, Mikhail; Khmelinskii, Igor; Makarov, VladimirWe present unique ultrastructural data on avian retinal cells. Presently and earlier (Zueva et al., 2016) we explored distribution of intermediate filaments (IFs) in retinal cells of the Pied flycatcher (Ficedula hypoleuca, Passeriformes, Aves) in the central foveolar zone. This retinal zone only contains single and double cone photoreceptors. Previously we found that continuous IFs span Müller cells (MC) lengthwise from the retinal inner limiting membrane (ILM) layer up to the outer limiting membrane (OLM) layer. Here we describe long cylindrical bundles of IFs (IFBs) inside the cone inner segments (CIS) adjoining the cone plasma membrane, with these IFBs following along the cone lengthwise, and surrounding the cone at equal spacing one from the other. Double cones form a combined unit, wherein they are separated by their respective plasma membranes. Double cones thus have a common external ring of IFBs, surrounding both cone components. In the layer of cilia, the IFBs that continue into the cone outer segment (COS) follow on to the cone apical tip along the direction of incident light, with single IFs separating from the IFB, touching, and sometimes passing in-between the light-sensitive lamellae of the COS. These new data support our previous hypothesis on the quantum mechanism of light energy propagation through the vertebrate retina (Zueva et al., 2016, 2019).
- On the effects of mechanical stress of biological membranes in modeling of swelling dynamics of biological systemsPublication . Khmelinskii, Igor; Makarov, VladimirWe highlight mechanical stretching and bending of membranes and the importance of membrane deformations in the analysis of swelling dynamics of biological systems, including cells and subcellular organelles. Membrane deformation upon swelling generates tensile stress and internal pressure, contributing to volume changes in biological systems. Therefore, in addition to physical (internal/external) and chemical factors, mechanical properties of the membranes should be considered in modeling analysis of cellular swelling. Here we describe an approach that considers mechanical properties of the membranes in the analysis of swelling dynamics of biological systems. This approach includes membrane bending and stretching deformations into the model, producing a more realistic description of swelling. We also discuss the effects of membrane stretching on swelling dynamics. We report that additional pressure generated by membrane bending is negligible, compared to pressures generated by membrane stretching, when both membrane surface area and volume are variable parameters. Note that bending deformations are reversible, while stretching deformation may be irreversible, leading to membrane disruption when they exceed a certain threshold level. Therefore, bending deformations need only be considered in reversible physiological swelling, whereas stretching deformations should also be considered in pathological irreversible swelling. Thus, the currently proposed approach may be used to develop a detailed biophysical model describing the transition from physiological to pathological swelling mode.
- Theoretical analysis of reversible and irreversible mitochondrial swelling in vivoPublication . Khmelinskii, Igor; Makarov, VladimirTheoretical biophysical model is reported for mitochondrial swelling (MS) dynamics in vivo. This newly developed model is based on the detailed biophysical model of MS dynamics in vitro, where mechanical properties of the inner mitochondrial membrane (IMM) were taken into account. The present model of MS dynamics in vivo is capable of analyzing MS dynamic transition from the reversible (physiological) to the irreversible (pathological) mode. This model was used to describe myocytes, assuming 1000 mitochondria distributed homogeneously over the sarcoplasm. Solute transport through the myocyte membrane was described by simplified phenomenological mechanisms of solute uptake and release. Biophysical processes occurring in mitochondria within cells were similar to those included in the earlier reported in vitro biophysical model of MS dynamics. Additionally, in vivo MS dynamics was simulated in different initial conditions, with results different from those of the in vitro model. Note that the presently reported model is the first attempt to develop a detailed biophysical model for the analysis of MS dynamics in vivo, capable of reproducing the transition between reversible and irreversible MS dynamics.
- Intermediate filaments are natural energy conductors in live cellsPublication . Khmelinskii, Igor; Makarov, VladimirTwo possible mechanisms describing intra-and inter-cell energy transfer in biological systems were analyzed. The first one is based on Davydov vibration soliton (DVS) theory, implying C=O vibrational energy transfer along alpha-helix polypeptides. According to Davydov, a certain vibration of one of the C=O groups somehow receives the entirety of ATP hydrolysis energy within an enzyme molecule. Next, dipole-dipole interactions of the C=O groups of neighboring amino acid residues should ensure propagation of the DVS along the polypeptide chain, transporting it to the site of catalytic reaction. Strong limitations of this theory when applied to energy transfer in living systems were underlined, accompanied by total lack of experimental evidence of DVS existence. The second, much more viable mechanism, based on electronic excited state (exciton) propagation along individual protein molecules and their assemblies - intermediate filaments (IFs) - was considered and discussed in detail. Excitons in IFs may be generated by photon absorption or by ATP hydrolysis energy transfer to IFs. Infrared (IR) excitons were generated in the latter case, which propagated along IFs, enabling energy transfer within and between cells, and inter-cellular communications. Earlier is has been noted that high-contrast vision of vertebrates is based on photon energy propagation along Muller cell (MC) IFs in the form of excitons, from the inner limiting membrane retinal layer to the outer fragments of cone cells, located in the outer limiting membrane retinal layer. Therefore, MC IFs operate as photon energy guides, transferring excitons from MC to cone cells, and thus communicating external visual information to the retinal cones and the brain. We finally conclude that apparently the mechanism based on the properties of IFs as natural energy guides plays the main role in communications within and between cells of live organisms.
- Stretching tension effects in permeability transition pores of inner mitochondrial membranePublication . Khmelinskii, Igor; Makarov, VladimirPresently a mechanism of permeability transition pore (PTP) opening was proposed and discussed. This mechanism is based on mechanical stretching of inner mitochondrial membrane (IMM) caused by mitochondrial swelling (MS). The latter is induced by osmotic pressure generated by solute imbalance between the matrix and the surrounding cyto(sarco)plasm. Modelled by the Monte-Carlo method, an IMM fragment of 350 simulated biological molecules exhibited formation of micro-domains containing two protein and seven phospholipid molecules. The energies (-0.191 eV per molecule) in these micro-domains were significantly larger than those (-0.375 eV per molecule) of other parts of the IMM fragment. Stretching forces applied to such domains expanded them much more than other parts of the IMM fragment. We identify these micro-domains as the PTPs. Both linear and nonlinear functions were used for the strain-stress relation of the IMM fragment, with nonlinear effects more important at large IMM stretching strains. Thus, two main factors are incorporated into the PTP opening mechanism: (1) presence of micro-domains in the IMM structure and (2) IMM stretching stress caused by MS. Taking into account both of these factors, the equation for the probability of PTP opening was deduced, with matrix Ca2+ and H+ ionic concentrations as its parameters. Note that the equation deduced was similar to an earlier reported empirical equation describing PTP opening dynamics. This correspondence provides support to the presently proposed mechanism. Thus, a new look at the PTP opening mechanism is provided, of interest to various research areas related to mitochondrial biophysics.
- Volt-ampere characteristics of porcine retinal Muller cell intermediate filamentsPublication . Makarov, Vladimir; Khmelinskii, IgorIn the current study we reported current-voltage (I/V) characteristics of Muller cell (MC) intermediate filaments (IFs) isolated from porcine retina. It was found that the measured I/V dependences demonstrate behavior of a semiconductor in contact with metal (Au) electrodes. The analysis of the temperature dependence of the experimental I/V curves produced estimates of the parameter values characterizing the electrical conductivity properties of the studied MC IFs. The I/V characteristics and the parameter values allowed to describe the MC IFs as a semiconducting material. The observed properties clarify the mechanism of high-contrast daylight vision of vertebrate eyes. This mechanism was extensively discussed earlier, and is directly dependent on the electric conductivity properties of MC IFs. Significance Statement: Retinal cones and rods are physically connected to glial Muller cells by intermediate filaments (IFs). Electric conductivity of IFs allows for a simple quantum mechanical description of light energy transmission through the retina, providing a convincing mechanism that achieves high-contrast vision in vertebrate eyes. Note that classic light transmission is hindered by light scattering on the retinal structures. Electric conductivity of IFs also opens the possibility for energy exchange within and between other cell types by way of IFs and microtubules, and the possibility that such structures may be used for signaling e.g. in the nervous system.
- Absorption spectra of Muler cell intermediate filaments: experimental results and theoretical modelsPublication . Khmelinskii, Igor; Makarov, VladimirExperimental spectra of Muller cell (MC) intermediate filaments (IFs) isolated from porcine retina are reported in this work. The absorption spectra recorded at different MC IF concentrations were used to estimate their absorption cross-sections at different wavelengths. The average absorption cross-section of a single MC IF was ca. (0.97...2.01) x 10(-1) cm(2) in the 650-445 nm spectral range. To interpret these experimental absorption spectra, we made ab initio calculations of the optical spectra of a-helix polypeptides, and also used a simplified theoretical approach that modeled an IF by a conductive wire. The energy spectra of the refractive index, extinction coefficient (absorption cross-section), energy loss and reflectivity functions for different photon polarizations, with strong anisotropy with respect to the system axis, were calculated ab initio for polyglycine a-helix molecule containing 1000 glycine residues. Strong anisotropy of these parameters was explained by photons interacting with different electronic transitions. Note that similarly strong anisotropy was also obtained for the optical absorption cross-sections in the simplified model. Both modeling approaches were used for calculating the absorption cross sections of interest. As a result, the absorption cross-section for photons propagating axially along MC IFs was much larger than their geometrical cross-section. The latter result was explained taking into account the density of electronic states, with numerous electrons contributing to the transition intensity at a given energy. We found that the simple conductive wire model describes the MC IF absorption spectrum better than the ab initio spectra. The latter conclusion was explained by the limitations of ab initio analysis, which only took into account one alpha-helix with 1000 aminoacids, whereas each porcine Muller cell IF is assembled of thousands of protein molecules, reaching the total length of ca. 100 mu m. The presently reported results contribute to the understanding of the quantum mechanism of high-contrast vision of vertebrate eyes. Published by Elsevier B.V.
- Current–voltage characteristics of a Co/Ni bilayer nanofilmPublication . Khmelinskii, Igor; Makarov, VladimirWidespread interest in optical and electrical properties of nanostructured systems began more than 20 years ago. Here, optical and electrical properties of Co/Ni bilayer nanofilms are explored. These optical and electrical properties were described in terms of a common confined wavefunction spanning both Co and Ni layers. The effective relative electron mass parameter f estimated for this bilayer film was about 0.1489. Temperature dependence of the current-voltage characteristics of the Co/Ni bilayer nanofilms was described as that of a Schottky diode with the Schottky barrier height of US = 24 cm-1, very small compared to other semiconducting materials. Therefore, Co/Ni bilayer nanofilms apparently had semiconducting properties, which may approxi-mately be described using Schottky diode theory. Such semiconducting properties of bilayer metal nanofilms could be used in special low-temperature low-consumption electronic devices.