Widespread 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.

Presently exciton activation of enzymatic oxidation of ethanol by human alcohol dehydrogenase (ADH) 1A enzyme is reported. The ADH1A enzyme was activated by infrared (IR) excitons transferred over Müller cell (MC) intermediate filaments (IFs). These IR excitons were generated by energy liberated upon enzymatic ATP hydrolysis and transferred to IFs. Also, the emission spectrum was recorded of the electronically excited ADH1A…NAD+…EtOH complexes obtained by energy transfer from IR excitons that traveled along IFs. These results support the hypothesis that ATP hydrolysis energy may be transmitted in vivo in the form of IR excitons, over the network of IFs, both within and between cells.

Low-energy (2500 cm(-1)) exciton transfer was explored in Muller cell (MC) intermediate filaments (IFs) isolated from porcine retina and filling a capillary matrix. Excitons were generated by absorption of IR radiation at 4 mu m. The effects of these excitons on ethanol oxidation by human alcohol dehydrogenase (ADH1A) enzyme were quantified. It was found that IR excitons transferred to the enzyme accelerated alcohol oxidation rate, which increased by the factor of 2.76 when exciting the IFs with 2.39 mu W/cm(2) of 4 mu m IR light. Power dependence of the oxidation rate was also explored. These results show that IFs may be transmitting energy to enzyme mole-cules in vivo, facilitating enzymatic reactions. The required excitons may be produced by cells at the cost of adenosine triphosphate (ATP) hydrolysis energy. Therefore, such control mechanism for enzymatic reactions may be operational in living systems. Direct activation of the enzyme by IR radiation with 4 mu m wavelength did not occur; instead, indirect activation of the IF...ADH1A...NAD (nicotinamide adenine dinucleotide)...EtOH complex occurred by energy transfer of the IR exciton to the ADH1A molecule of this complex. Considering that every living cell has a network of IFs, a similar reaction control mechanism may be operational in vivo, providing a much faster energy supply redirection within the cell than ATP diffusion, and justifying a closer inquiry.

•Excitons (electronic excited states) were generated by photons and propagated over Müller cell (MC) intermediate filaments (IFs).•Excitons traveled across macroscopic distances along IFs.•11-cis- to all-trans-retinal isomerization sensitized by excitons at a remote location.•Biphotonic processes in IFs reported for the first time at very low light intensities under steady-state excitation.

Flavins are a unique class of compounds that combine the features of singlet oxygen generators and redox-dependent fluorophores. From a broad family of flavin derivatives, deazaalloxazines are significantly underdeveloped from the point of view of photophysical properties. Herein, we report photophysics of 5-deazaalloxazine (1a) in water, acetonitrile, and some other solvents. In particular, triplet excited states of 1a in water and in acetonitrile were investigated using ultraviolet–visible (UV–Vis) transient absorption spectroscopy. The measured triplet lifetimes for 1a were all on the microsecond time scale (≈ 60 μs) in deoxygenated solutions. The quantum yield of S1 → T1 intersystem crossing for 1a in water was 0.43 based on T1 energy transfer from 1a to indicaxanthin (5) acting as acceptor and on comparative actinometric measurements using benzophenone (6). 1a was an efficient photosensitizer for singlet oxygen in aerated solutions, with quantum yields of singlet oxygen in methanol of about 0.76, compared to acetonitrile 0.74, dichloromethane 0.64 and 1,2-dichloroethane 0.54. Significantly lower singlet oxygen quantum yields were obtained in water and deuterated water (ФΔ 0.42 and 0.44, respectively). Human red blood cells (RBC) were used as a cell model to study the antioxidant capacity in vitro and cytotoxic activity of 1a. Fluorescence-lifetime imaging microscopy (FLIM) data were analyzed by fluorescence lifetime parameters and distribution for different parts of the emission spectrum. Comparison of multidimensional fluorescent properties of RBC under physiological-like and oxidative-stress conditions in the presence and absence of 1a suggests its dual activity as probe and singlet-oxygen generator and opens up a pathway for using FLIM to analyze complex intracellular behavior of flavin-like compounds. These new data on structure–property relationship contribute to the body of information required for a rational design of flavin-based tools for future biological and biochemical applications.

ATP production by mitochondria isolated from yeast cells (S. cerevisiae) was accelerated by exciton energy transfer from intermediate filaments (IFs). The effect was dependent on mitochondrial concentration and the intensity of light used to generate excitons. Presumably, mitochondrial cytochrome C (CC) was activated by IF exciton energy transfer to CC in the inner mitochondrial membrane (IMM), generating electronically excited CC, and the respective excitation energy was then used in the ATP production chain. A qualitative model was proposed describing observations, although more experiments are required before the detailed mechanisms could be deduced. The present results support the earlier proposed hypothesis of ATP production in vertebrate retina by excess photons in daytime, when retina needs extra energy for recovering the used opsins. Additionally, it shows that at early stages of evolution mitochondria could have been using solar radiation to produce ATP.

Existing theoretical approaches were considered that allow modelling of mitochondrial swelling (MS) dynamics. Simple phenomenological kinetic models were reviewed. Simple and extended biophysical and bioenergetic models that ignore mechanical properties of inner mitochondrial membrane (IMM), and similar models that include these mechanical properties were also reviewed. Limitations of these models we considered, as regards correct modelling of MS dynamics. It was found that simple phenomenological kinetic models have significant limitations, due to dependence of the kinetic parameter values estimated by fitting of the experimental data on the experimental conditions. Additionally, such simple models provide no understanding of the detailed mechanisms behind the MS dynamics, nor of the dynamics of various system parameters during MS. Thus, biophysical and bioenergetic models ignoring IMM mechanical properties can't be used to model the transition between reversible and irreversible MS. However, simple and extended biophysical models that include IMM mechanical properties allow modelling the transition to irreversible swelling. These latter models are still limited due to significantly simplified description of biochemistry, compared to those of bioenergetic models. Finally, a strategy of model development is proposed, towards correct interpretation of the mitochondrial life cycle, including the effects of MS dynamics.

ATP production by mitochondria isolated from Saccharomyces cerevisiae cells was accelerated upon both direct and indirect mitochondrial photo-activation (MPA). The extent of direct MPA was dependent on the wavelength of excitation light. Direct MPA was created by light in cytochrome c spectral absorption bands (440, 520 and 550 nm), this light was absorbed producing electronically excited cytochrome c, and the excitation energy of the latter was used in the ATP production chain. The activity of cytochrome c was tested with 600 nm light, where cytochrome c does not absorb, and thus ATP production rate remained the same as in darkness. Note that ATP production rates were significantly larger under light at 550, 520 and 440 nm. Therefore, photo-activation of cytochrome c was the first step of MPA synthesis of ATP. Indirect MPA of ATP production also proceeded via electronically excited cytochrome c, by energy transfer from electronically excited Co/BN film to cytochrome c located in the inner mitochondrial membrane (IMM). Co/BN excitons were generated by photons absorbed by the Co/BN film, which was not in contact with the mitochondrial sample. Next, these excitons propagated along the Co/BN film to the part of the film that was in contact with the mitochondrial sample. There the exciton energy was transferred to cytochrome c located in the IMM, producing electronically excited cytochrome c. Thus, excited cytochrome c was generated in a way different from that of direct MPA. Next, the energy of excited cytochrome c was used in activated ATP synthesis, with virtually the same effect for 519 and 427 nm excitation. Thus, the first step of ATP synthesis in indirect MPA was the exciton energy transfer from Co/BN film to cytochrome c located in the IMM, producing an electronically excited cytochrome c molecule. A phenomenological mechanism of direct and indirect MPA was proposed, and the model parameters were obtained by fitting the model to the experimental data. However, more information is needed before the detailed mechanism of ATP synthesis activation by electronically excited cytochrome c could be understood. The present results support the earlier proposed hypothesis of indirect MPA of ATP production in vertebrate retina in daylight.

The spectral and photophysical properties of two four-ring alloxazine derivatives, naphtho[2,3-g]pteridine-2,4(1H,3H)-dione (1a) and 1,3-dimethylnaphtho[2,3-g]pteridine-2,4(1H,3H)-dione, (1b) were studied. The propensity of 1a for excited-state proton transfer reactions in the presence of acetic acid as a catalyst was also studied, showing no signature of the reaction occurring. In addition, quenching of 1a fluorescence by acetic acid was investigated. Singlet and triplet states and spectral data for 1a and 1b were calculated using density functional theory TD-DFT at B3LYP/6-31G(d) and UB3LYP levels. Finally, fluorescence lifetime imaging microscopy (FLIM) using 1a and 1b as fluorescence probes was applied to in vitro human red blood cells (RBCs) with and without tert-butyl hydroperoxide (TB) as an oxidising agent. To evaluate and compare the effects of 1a and 1b on the redox properties of RBCs, the fluorescence lifetime, amplitude and fractional intensities were calculated, and phasor plot analysis was performed. The results obtained show the appearance of a new proximal cluster in the phasor fingerprint of RBCs in the presence of 1b and a shorter fluorescence lifetime of RBCs in the presence of 1a.

In the current study, we tested a possible mechanism of low- and high-contrast image component discrimination by the vertebrate eye-brain system. Apparently the eye-brain system has to discriminate between the low-contrast image component formed by light scattered within the retina, due to interaction of photons with cells and their parts, and the high-contrast image component transmitted by excitons via the quantum mechanism. Presently, effects of pulsed electric fields applied to Müller cell (MC) intermediate filaments (IFs) on the efficiency of exciton propagation were explored. The effects of both pulse duration and amplitude were recorded. These experimental results show that the eye-brain system may be using signal modulation to discriminate between high- and low-contrast image components, improving our understanding of high-contrast vision in vertebrates.

Temperature dependences of IR exciton properties in Muller cell (MC) intermediate filaments (IFs) isolated from porcine retina were studied. It was found that the widths of the spectral emission bands in the 2500 cm-1 and 5000 cm-1 energy ranges grow with temperature. It was found that temperature effects on the bandwidth may be described by thermal activation of the low-frequency vibrational modes of the IFs. The average activation energies for the two IR bands were estimated. Considering the dynamics of IR emission, its buildup time was independent on the sample temperature, while its decay time decreased with temperature. Thus, the emission decay rate increased exponentially with the sample temperature. The mechanisms explaining the observed temperature effects were proposed and discussed. Taking into account that MC IFs are capable of transmitting ATP hydrolysis energy within and between cells, with these properties being apparently common for all IFs, these IFs may be used by cells for physical energy transport and communications. As presently reported, temperature effects upon IR exciton spectra should not affect these proposed physiological functions to any significant extent. Therefore, the currently reported data are important for improving our understanding of the physical communication mechanisms operating within and between cells.

Two 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.

Presently a detailed biophysical model describing reversible and irreversible swelling dynamics of Müller cells (MC) is reported. The model includes a biophysical block of ionic and neutral species transport via MC membrane, water transport induced by osmotic pressure and pressure generated by membrane deformations, MC membrane potential and membrane mechanical properties. The model describes reversible and irreversible MC swelling (MCS) using the same set of parameters. The model was used in fitting available experimental data, and produced numerical values of previously unknown model parameters, including those describing mechanical properties of Müller cell membrane (MCM) with respect to bending and stretching. Numerical experiments simulating MC swelling showed complex oscillation dynamics of the relevant parameters in physiological initial conditions. In particular, MC membrane potential (ΔΨMC) demonstrated complex oscillation dynamics, which may be described by a superposition of several oscillations with their periods in the milliseconds, 100-ms and seconds time ranges. Dynamics of reversible and irreversible MCS, and the transition criteria from reversible to irreversible MCS modes were determined in model simulations.

Theoretical 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.

Presently 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.

In this chapter, the spectral properties of flavins are reviewed in the context of their catalytic applications. Optical spectroscopy of various types of flavin compounds is presented: iso- and alloxazines, 5-deazaisoalloxazines, 5-deazaalloxazines, and some of the flavinium salts, again with iso- and alloxazinic structures, together with 1,10-bridged 7,8-dimethyl-alloxazinium catalysts. Spectral properties of all of these compounds in the UV–Vis range are described, both in water and in organic solvents, and the spectral behavior of flavins as a function of pH is also discussed. Furthermore, different aspects of flavin optical spectroscopy not only in solutions, but also in gas phase and at low temperatures, are included in the discussion. Some results of theoretical calculations are presented alongside the experimental data.

Mitochondrial 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.

Presently we report that enzymatic oxidation of ethanol (EtOH) by ADH1A alcohol dehydrogenase is strongly accelerated in presence of adenosine triphosphate (ATP), by up to the factor of 20 in vitro. This result provides a different look on the role of ATP in functioning of alcohol dehydrogenases (ADH), which until presently were a textbook example of enzymes not requiring ATP and successfully operating without it. However, ATP is available in every living cell and will activate reactions conducted by ADH enzymes in vivo. Therefore, the body of published literature describing properties of numerous ADH enzymes requires a thorough revision.

Low-energy (IR -2500 cm-1) exciton transfer was explored in Muller cell (MC) intermediate filaments (IFs) isolated from porcine retina and filling a capillary matrix. IR excitons were generated either by absorption of IR radiation at 4 mu m, or by ATP hydrolysis energy transfer to the MC IFs. ATP hydrolysis was catalyzed by human alcohol dehydrogenase (ADH1A) in ADH1A...NAD+...IF complexes. Each exciton was generated by hydrolysis of one ATP molecule. Exciton energy was independent on ATP concentration. The emission spectra of IR excitons arriving to the other side of the capillary matrix were dependent on the exciton generation method. Timeresolved experiments with direct exciton generation by pulsed IR radiation allowed to measure exciton travel velocity, along with the exciton emission time. The results obtained support new ideas on ATP energy transfer along protein filaments in vivo. These unique experimental results provide for detailed understanding of the electronic state structure of the MC IFs. This study reports that MC IFs isolated from porcine retina have a longliving low-lying electronic excited state at 2500 cm-1 above the ground state.