Role of Bisolitons and their Correlations in Charge Transfer Processes

The charge transport processes in biological macromolecules are studied within the nonlinear electrosoliton mechanism. The interaction between few electrosolitons in a one-dimensional electron-phonon system is investigated. It is shown that in a singlet state the minimum of energy corresponds to a bisoliton. In a triplet state the autolocalized state is described by two electrosolitons which are separated from one another by some finite distance determined by the nonadiabatic terms of the Hamiltonian.     

3D Burgers Equation in Relativistic Plasma in the Presence of Electron and Negative Ion Trapping: Evolution of Shock Wave

The characteristics of shock waves in a relativistic plasma in the presence of nonisothermal electrons and nonisothermal negative ions is investigated by deriving the evolution equation in terms of a modified 3D Burgers equation, or trapped 3D Burgers equation. The solution of this equation is examined analytically to study the salient characteristics of shock waves in such plasma. The nonlinear coefficient is found to have the lowest (highest) value when the negative ions move toward thermal equilibrium with a dip-shaped electron distribution (when both electrons and negative ions follow a dip-shaped distribution) for a particular value of relativistic factor, and it remains in an intermediate state when both electrons and negative ions follow a flat-topped distribution. On the other hand, the dissipative coefficient is found to decrease (increase) with increasing relativistic parameter (viscous parameter). A profound effect of the trapped state of both electrons and negative ions and the temperature ratio between positive ions and electrons (negative ions and electrons) on the structure of the shock wave is also seen. However, it has been noticed that the trapped parameter of electrons has a dominating control over the shock potential profile than the trapped parameter of negative ions.     

Nonlinear dynamics of a nonisothermal collisionless plasma flow

It is shown that the two-fluid electrohydrodynamic equations for a transversely homogeneous flow of cold ions and Boltzmannian electrons in the ion-acoustic region are reduced to the Boussinesq equation. Using a two-soliton solution as an example, the nonlinear mechanism of collisionless relaxation of a supersonic plasma flow toward a steady state in the form of a double space charge layer is demonstrated.     

Skin Effects in a Dusty Plasma

A multifluid MHD model is applied to study the magnetic field dynamics in a dusty plasma. The motion of plasma electrons and ions is treated against the background of arbitrarily charged, immobile dust grains. When the dust density gradient is nonzero and when the inertia of the ions and electrons and the dissipation from their collisions with dust grains are neglected, we are dealing with a nonlinear convective penetration of the magnetic field into the plasma. When the dust density is uniform, the magnetic field dynamics is described by the nonlinear diffusion equations. The limiting cases of diffusion equations are analyzed for different parameter values of the problem (i.e., different rates of the collisions of ions and electrons with the dust grains and different ratios between the concentrations of the plasma components), and some of their solutions (including self-similar ones) are found. The results obtained can also be useful for research in solid-state physics, in which case the electrons and holes in a semiconductor may be analogues of plasma electrons and ions and the role of dust grains may be played by the crystal lattice and impurity atoms.     

Beam discharge excited by distributed virtual cathode

A new type of beam discharge, i.e., beam discharge with a distributed virtual cathode (VC) is proposed and considered by numerical simulation. The discharge is established during counter motion of high-current electron beams in a gas-filled equipotential cavity and is characterized by a state of hot dense electron plasma of primary electrons. The discharge temporal dynamics is studied. It is shown that the VC lifetime depends linearly from this sum in a wide range of the sum of beam currents, from the boundary current of two-beam instability to the critical current of Pierce instability. Generation of nonlinear electrostatic structures shaped as phase bubbles in the discharge is detected, and their dynamics is studied. The parameters are determined, at which the multiple coexistence of phase bubbles and their coalescence during collisions is observed.     

Irradiation by electrons of tubulin solution in vitro causes tubulin assembly in absence of a magnesium cofactor

It was shown that irradiation of a tubulin solution (5 x 10(-6) mol/l) with electrons makes tubulin assemble to microtubules. The response of the system was monitored by the femtosecond laser technique. The assembly under these conditions occurs without Mg2+ (magnesium cofactor) and GTP. At 730 (the first harmonic) and 365 nm (the second harmonic), a rise in signal intensity occurs during the first 60-70 ns followed by the onset of tubulin assembly to microtubules, which was registered by the methods of spectrophotometry and electron spectroscopy. Theoretically this effect can be explained by the appearance of hydrated electrons in the solvated tubulin shell. Hydrated electrons are mostly in a long-living polaron state, which can be considered as an ensemble of quasi-dipoles of the electron-H3O+ type. The interaction of quasi-dipoles with the weak internal electrostatic field of tubulin leads, due to nonlinear effects, to a manifold rise in the intensity of the electrostatic field of the solvated shell of initially nonpolymerized tubulin chains. Finally, the increased field makes separate tubulin chains aggregate to microtubules. The effect observed is identical to the action of Mg2+ on the GTP site of beta-tubulin, which transfers it to a slightly perturbed triplet state.     

Nonlinear inverse bremsstrahlung absorption in a photoionized plasma

Nonlinear inverse bremsstrahlung absorption is investigated for a plasma photoionized in the Bethe regime of suppression of the ionization barrier, in which case the electron velocity distribution coincides with the distribution of atomic electrons. A comparison is made between the characteristic features of absorption in the cases where atomic electrons before ionization are in the ns and np states. It is established that, in the case of np states, the effective high-frequency conductivity is always nonlinear; in particular, for weak pump fields, it is proportional to the square of the pump field strength. The maximum plasma conductivity associated with p electrons is one order of magnitude lower than the maximum effective conductivity associated with s electrons, which creates conditions for less efficient plasma heating through inverse bremsstrahlung absorption.     

Modulation of the electron redistribution in mixed valence cytochrome C oxidase by protein conformational changes

The redistribution of two electrons in the four redox centers of cytochrome c oxidase following photodissociation of CO from the CO-bound mixed valence species has been examined by resonance Raman spectroscopy. To account for both the kinetic data, obtained from 5 micros to 2 ms, and the equilibrium results, a model is proposed in which the electron redistribution is modulated by a protein conformation transition from a nascent P(1) state to a relaxed P(2) state in a time window longer than 2 ms. In this model, all six possible two-electron reduced species are considered. The high population of species with a one-electron reduced binuclear center, in which the spectrum of heme a(3) is perturbed by the redox state of Cu(B), accounts for the significant residuals in the fitting of the kinetic data with four standard spectra derived from redox species with either zero or two electrons in the binuclear center. Under equilibrium conditions, the conformational change to the P(2) state destabilizes the redox states with only one electron in the binuclear center with respect to those with either zero or two electrons. As a result, the redox equilibrium is perturbed, and the electrons are redistributed. A simulation based on the new kinetics scheme, in which the electron redistribution is modulated by the protein conformation, gives reasonable agreement with both the equilibrium and the kinetic data, demonstrating the validity of this model.     

Personal recollections of 40 years in photosynthesis research*

The major theme of my work in photosynthesis has been electron transport in green plant thylakoids. In particular, we investigated the properties and the role of the NADP-reducing flavoprotein and its possible function in cyclic electron transport, the regulation by protons of electron transport, and the redox system of ascorbate and monodehydroascorbate (the ascorbate free radical). The function of this system in providing ATP in the stoichiometric amount needed for carbon assimilation, and the regulation of the alternative transfer of electrons to NADP and to the ascorbate free radical were among the achievements of my collaborators and myself. Specifically, the early conviction that cyclic phosphorylation was essential part in photosynthesis was shattered as far as higher plants are concerned, and replaced by a modified Mehler reaction providing additional ATP to run the Calvin cycle. The situation seems to be different in unicellular green algae, where quantitatively much l arger changes of the relative size of Photosystem (PS) I and PS II antennae during the so-called state transitions have been reported, and these seem to be associated with a high activity of cyclic electron transport in state 2. Beyond the science, the friendly interactions with so many persons around the world sharing my interest in photosynthesis and in other aspects of human life have been most rewarding.     

Unsteady processes during stimulated emission from a relativistic electron beam in a quasi-longitudinal electrostatic pump field

The problem of stimulated emission from a relativistic electron beam in an external electrostatic pump field is studied. A set of nonlinear time-dependent equations for the spatiotemporal dynamics of the undulator radiation amplitude and the amplitude of the beam space charge field is derived. The beam electrons are described by a modified version of the macroparticle method. The regimes of the single-particle and collective Cherenkov effects during convective and absolute instabilities are considered. The nonlinear dynamics of radiation pulses emitted during the instabilities of the beam in its interaction with the forward and backward electromagnetic waves is investigated.     

A plea for ‘genealogical thinking’ in comparative biology – a rebuttal to the reply of Szucsich,Wirkner, and Pass to my article ‘Deconstructing Morphology’

Scholtz G. in press. A plea for ‘genealogical thinking’ in comparative biology – a rebuttal to the reply of Szucsich, Wirkner, and Pass to my article ‘Deconstructing Morphology’. —Acta Zoologica (Stockholm) 00 : 1–4. Szucsich et al. (in press) claim that – in contrast to my statement – morphological thinking has to be ‘cladistic.’ Based on this premise, they stress the difference between the relationships among states of characters versus those among structures assigned to the same character state as implemented in numerical cladistic reasoning. SEA claim that my approach to the homology concept only deals with the problem of the integration of various character states into the same character, whereas the necessary relationships among structures assigned to the same state are not covered. Based on this distinction, SEA also criticise the application of similarity in my definition of homology. Furthermore, they address the issue of evolutionarily independent units.     

Nonlinear theory of the collective Cherenkov interaction of a dense relativistic electron beam with a dense plasma in a waveguide

A nonlinear theory of the instability of a straight relativistic dense electron beam in a plasma waveguide is derived for conditions of the stimulated collective Cherenkov effect. A study is made of a waveguide with a dense plasma such that the plasma wave excited by the beam during the instability can be escribed, with a good degree of accuracy, as a potential wave. General relativistic nonlinear equations are btained that describe the temporal dynamics of beam-plasma instabilities with allowance for plasma nonlinearity and the generation of harmonics of the initial perturbation. Under the assumption that the resonant interaction between the beam waves and the plasma waves is weak, the general equations are reduced to relativistic equations with cubic nonlinearities by using the method of expansion in small perturbations of the trajectories and momenta of the beam and plasma electrons. The reduced equations are solved analytically, the time scales on which the instability saturates are determined, and the nonlinear saturation amplitudes are obtained. A comparison between analytical solutions to the reduced equations and numerical solutions to the general nonlinear equations shows them to be in good agreement. Nonlinear processes caused by the relativistic nature of the beam are found to prevent stochastization of the system in the nonlinear stage of the well-developed instability. In contrast, a nonrelativistic electron beam is found to be subject to significant anomalous nonlinear stochastization.     

Classical and quantum description of electron trapping during the Cherenkov beam instability in plasma

A nonlinear quantum theory of the Cherenkov instability of a nonrelativistic monoenergetic electron beam in a cold plasma is constructed. It is shown that the instability of a low-density beam is almost purely quantum in nature and results from the emission of one quantum of a plasma wave—a plasmon—by the beam electrons. The number of emitted (and absorbed) plasmons increases with beam density, so, in the limit of high-density beams, the instability becomes a classical Cherenkov beam instability in plasma. Some analytic solutions and estimates are found, detailed numerical results are obtained, and the evolution of the quantum distribution function of the beam electrons in different regimes of the beam instability is investigated.     

STANDARD CIRCUMSTANCES AND VITAL GOALS: COMMENTS ON VENKATAPURAM'S CRITIQUE

This article is a reply to Venkatapuram's critique in his article Health, Vital Goals, Capabilities, this volume. I take issue mainly with three critical points put forward by Venkatapuram with regard to my theory of health. (1) I deny that the contents of my vital goals are relative to each community or context, as Venkatapuram claims. There is no conceptual connection at all between standard circumstances and vital goals, as I understand these concepts. (2) Venkatapuram notes that I stop short of filling the framework of vital goals with any content and thereby make my concept of health less concrete. I reply that some vital goals are indeed universal, viz. the ones which are necessary conditions for survival. Many other vital goals are individual and cannot therefore be included in a universal list. (3) Venkatapuram claims that my definition of vital goals is too broad, since it entails that some persons without any disease can be regarded as ill. However, in my understanding health is a relational concept from a state of complete health to a state of maximal illness. In this framework, a minor reduction of a state of complete health does not entail illness. This article also contains a comparison between my theory of health and Martha Nussbaum's theory of capabilities for dignity.     

Mechanistic studies on the dehydrogenases of methylotrophic bacteria. 1. The influence of substrate binding to reduced trimethylamine dehydrogenase on the intramolecular electron transfer between its prosthetic groups.

The trimethylamine dehydrogenase of bacterium W3A1 is reduced with the formation of a triplet state in which two electrons, derived from the substrate, are distributed between the [4Fe-4S] cluster and 6-S-cysteinyl-FMN semiquinone. In titration experiments at pH 8.5 about 1.0 mol of dimethylamine or 0.5 mol of trimethylamine per mol of the enzyme is required to titrate the enzyme to an endpoint. At pH values less than 8.0, however, an excess of trimethylamine is required to obtain maximal yield of the g = 4 e.p.r. signal, characteristic of the triplet state, or maximal absorbance at 365 nm which indicates formation of the flavin semiquinone. The binding of 0.86 mol of trimethylamine per mol of the enzyme could be detected by a gel chromatographic method. When the enzyme is titrated with dithionite in the presence of tetramethylammonium chloride, an endpoint is reached after the uptake of two electrons which give rise to the triplet state, whereas three electrons are consumed in the absence of tetramethylammonium chloride to reduce the enzyme completely. The enzyme is inhibited noncompetitively by tetramethylammonium chloride and the slopes of double reciprocal plots are a concave upwards function of inhibitor concentration. The data indicate the presence of a binding site for the substrate and other amines on the reduced enzyme which enhances the proportion of enzyme in the triplet state.     

Time-dependent regimes of a Bursian diode I: Stability of steady solutions

A study is made of the physical phenomena characteristic of nonlinear oscillations in a Bursian diode in the regime with a virtual cathode. The question of how the shape of the oscillations varies as the beam current density increases is investigated for the first time. Sharp jumps in the time evolution of the convective current are revealed, and their causes are explained. The reason is found for the onset of long-lived electrons, and their properties are analyzed.     

Time-dependent regimes of a Bursian diode II: Characteristic features of nonlinear oscillations

A study is made of the physical phenomena characteristic of nonlinear oscillations in a Bursian diode in the regime with a virtual cathode. The question of how the shape of the oscillations varies as the beam current density increases is investigated for the first time. Sharp jumps in the time evolution of the convective current are revealed, and their causes are explained. The reason is found for the onset of long-lived electrons, and their properties are analyzed.     

Nonlinear mechanism for weak photon emission from biosystems

The nonlinear mechanism for the origin of the weak biophoton emission from biological systems is suggested. The mechanism is based on the properties of solitons that provide energy transfer and charge transport in metabolic processes. Such soliton states are formed in alpha-helical proteins. Account of the electron-phonon interaction in macromolecules results in the self-trapping of electrons in a localized soliton-like state, known as Davydov's solitons. The important role of the helical symmetry of macromolecules is elucidated for the formation, stability and dynamical properties of solitons. It is shown that the soliton with the lowest energy has an inner structure with the many-hump envelope. The total probability of the excitation in the helix is characterized by interspine oscillations with the frequency of oscillations, proportional to the soliton velocity. The radiative life-time of a soliton is calculated and shown to exceed the life-time of an excitation on an isolated peptide group by several orders of magnitude.     

Nonlinear ineraction of an annular electron beam with azimuthal surface waves

A nonlinear theory is developed that describes the interaction between an annular electron beam and an electromagnetic surface wave propagating strictly transverse to a constant external axial magnetic field in a cylindrical metal waveguide partially filled with a cold plasma. It is shown theoretically that surface waves with positive azimuthal mode numbers can be efficiently excited by an electron beam moving in the gap between the plasma column and the metal waveguide wall. Numerical simulations prove that, by applying a constant external electric field oriented along the waveguide radius, it is possible to increase the amplitude at which the surface waves saturate during the beam instability. The full set of equations consisting of the waveenvelope equation, the equation for the wave phase, and the equations of motion for the beam electrons is solved numerically in order to construct the phase diagrams of the beam electrons in momentum space and to determine their positions in coordinate space (in the radial variable-azimuthal angle plane).