The nature of phonons and solitary waves in alpha-helical proteins.

A parametric study of the Davydov model of energy transduction in alpha-helical proteins is described. Previous investigations have shown that the Davydov model predicts that nonlinear interactions between phonons and amide-I excitations can stabilize the latter and produce a long-lived combined excitation (the so-called Davydov soliton), which propagates along the helix. The dynamics of this solitary wave are approximately those of solitons described using the nonlinear Schr?dinger equation. The present study extends these previous investigations by analyzing the effect of helix length and nonlinear coupling efficiency on the phonon spectrum in short and medium length alpha-helical segments. The phonon energy accompanying amide-I excitation shows periodic variation in time with fluctuations that follow three different time scales. The phonon spectrum is highly dependent upon chain length but a majority of the energy remains localized in normal mode vibrations even in the long chain alpha-helices. Variation of the phonon-exciton coupling coefficient changes the amplitudes but not the frequencies of the phonon spectrum. The computed spectra contain frequencies ranging from 200 GHz to 6 THz, and as the chain length is increased, the long period oscillations increase in amplitude. The most important prediction of this study, however, is that the dynamics predicted by the numerical calculations have more in common with dynamics described by using the Frohlich polaron model than by using the Davydov soliton. Accordingly, the relevance of the Davydov soliton model was applied to energy transduction in alpha-helical proteins is questionable.(ABSTRACT TRUNCATED AT 250 WORDS)     

Influence of electromagnetic radiation on molecular solitons

The soliton model of charge and energy transport in biological macromolecules is used to suggest one of the possible mechanisms for electromagnetic radiation influence on biological systems. The influence of the electromagnetic field (EMF) on molecular solitons is studied both analytically and numerically. Numerical simulations prove the stability of solitons for fields of large amplitude, and allow the study of emission of phonons. It is shown that in the spectra of biological effects of radiation there are two characteristic frequencies of EMFs, one of which is connected with the most intensive energy absorption and emission of sound waves by the soliton, and the other of which is connected with the soliton photodissociation into a delocalized state.     

Electromagnetic Radiation Influence on Nonlinear Charge and Energy Transport in Biosystems

The influence of electromagnetic radiation (EMR) on charge and energy transport processes in biological systems is studied in the light of the soliton model. It is shown that in the spectrum of biological effects of EMR there are two frequency resonances corresponding to qualitatively different frequency dependent effects of EMR on solitons. One of them is connected with the quasiresonance dynamic response of solitons to the EMR. At EMR frequencies close to the dynamic resonance frequency the solitons absorb energy from the field and generate intensive vibrational modes in the macromolecule. The second EMR resonance is connected with soliton decay due to the quantum mechanical transition of the system from the bound soliton state into the excited unbound states.     

Thermodynamic properties of bulk knitted structures

The mechanism of interaction of an external magnetic field with liquid was proposed. The statistical integral and configurational contributions for a free energy, entropy and specific heat for the soliton model of bulk knitted structures in a magnetic field were calculated. It was shown that the concentration of solitons depends on the effect of external fields. In the specific case of bulk knitted structures (liquid water without magnetic field), the theoretical data are consistent with experimental. The memory effects in systems with hydrogen bonds in magnetic field was explained in the framework of the continuum soliton concept.     

The properties of bio-energy transport and influence of structure nonuniformity and temperature of systems on energy transport along polypeptide chains

A new theory of bio-energy transport along protein molecules in living systems, where the energy is released by hydrolysis of adenosine triphosphate (ATP), is proposed based on some physical and biological reasons. In the new theory, the Davydov's Hamiltonian and wave function of the systems are simultaneously modified and extended. A new interaction has been added into Davydov's Hamiltonian. The wave function of the excitation state of single particles for the excitons in the Davydov model is replaced by a new wave function of two-quanta quasicoherent state. In such a case, the bio-energy is transported by the new soliton, which differs from the Davydov's soliton. The soliton is formed through self- trapping of two excitons interacting amino acid residues. The exciton is generated by vibrations of amide-I (CO stretching) arising from the energy of hydrolysis of ATP. The properties of the new soliton are extensively studied by analytical method and its lifetime is calculated using the nonlinear quantum perturbation theory and a wide ranges of parameter values relevant to protein molecules. The lifetime of the new soliton at the biological temperature 300 K is enough large and belongs to the order of 10?1? s, or τ/τ?≥700, in which the soliton can transports over several hundreds amino acid residues. These studied results show clearly that the new soliton is thermally stable and has so larger lifetime that it can play an important role in biological processes. Thus the new model is a candidate of the bio-energy transport mechanism in protein molecules. In the meanwhile, the influences of structure nonuniformity in protein molecules and temperature of the systems on the states and properties of the soliton transport of bio-energy are numerically simulated and studied by the fourth-order Runge-Kutta method. The structure nonuniformity arises from the disorder distributions of masses of amino acid residues, side groups and impurities, which results also in the fluctuations of the spring constant of protein molecules, dipole-dipole interaction between the neighboring amides, exciton-phonon (vibration of amino acids)interaction, chain-chain interaction among the three channels and ground state energy of the systems. We investigated the behaviors and states of the new solitons in a single protein molecular chain and α-Helix protein molecules with three channels under influences of the structure nonuniformity. We prove first that the bio-energy is transported by a soliton, which can move without dispersion, retaining its shape, velocity and energy in a uniform and periodic protein molecule. When the structure nonuniformity exists, although the fluctuations of the spring constant, dipole-dipole interaction constant, exciton-phonon coupling constant and ground state energy and the nonuniformity distributions of masses of amino acid residues can change the states and properties of motion of new soliton, they are still quite stable and very robust against these structure nonuniformities, i.e., even there are a larger structure nonuniformity in the protein molecules, the new solitons cannot be still dispersed. If the effects of thermal perturbation of medium on the soliton in nonuniform proteins is considered again, the new soliton can transport also over a larger spacing of 400 amino acids and has a longer time period of 300 ps, it is still thermally stable up to 320 K under the influence of the above structure nonuniformities. However, the new soliton disperses in the case of a higher temperature of 325 K and in more large structure nonuniformity. Thus, we determine that the new soliton's lifetime and critical temperature are 300 ps and 320 K, respectively. These results are also consistent with analytical data obtained via quantum perturbed theory. For α-Helix protein molecules with three channels, the results obtained show that the structure nonuniformity and quantum fluctuation can change the states and features of the new solitons, for example, the amplitudes, energies and velocities of the new soliton are decreased, but the solitons have been not destroyed, they can still transport steadily along the molecular chains retaining energy and momentum. When the quantum fluctuations are larger, such as, structure disorders and quantum fluctuations of 0.67<α(K)<2, ΔW=±8%Wˉ, ΔJ=±1%Jˉ, Δ(χ?+χ?)=±3%(χˉ?+χˉ?) and ΔL=±1%Lˉ and Δ??=?|β(n)|, ?=0.1 meV, |β(n)|<0.5, the new soliton is still stable. Therefore, the new solitons are quite robust against these nonuniform effects. However, they will be dispersed or disrupted in cases of very large structure nonuniformity. When the influence of temperature on solitons is considered, we find that the new solitons can transport steadily over 333 amino acid residues in the case of a long time period of 120 ps, in which the soliton can retain its shape and energy to travel forward along protein molecules after their mutual collision at the biological temperature of 300 K. However, the soliton disperses in cases of higher temperatures 325 K under action of a larger structure disorder. Thus, its critical temperature is about 320 K. When the effects of structure nonuniformity and temperature are considered simultaneously, then the new soliton has still high thermal stability and can transport also along the protein molecular chains retaining its amplitude, energy and velocity, they will disperses in the larger fluctuations, for example, 0.67 Mˉ相似文献   

Slow electromagnetic solitons in electron-ion plasmas

A set of nonlinear differential equations that describe moving relativistic solitons is investigated analytically and solved numerically. The influence of the ion motion on the soliton structure is investigated. It is demonstrated that, depending on the propagation velocity, relativistic solitary waves can occur in the form of bright solitons, dark solitons, or collisionless electromagnetic shock waves. In the limit of a low propagation velocity, a dark soliton can trap the ions and accelerate them. In the case of a bright soliton, the effects of ion dynamics limit the soliton amplitude. The constraint on the maximum amplitude is related to either the breaking of ion motion or the intersection of electron trajectories. The soliton breaking provides a new mechanism for ion and electron acceleration in the interaction of high-intensity laser pulses with plasmas.     

Solitary fast magnetosonic waves propagating obliquely to the magnetic field in cold collisionless plasma

Solutions describing solitary fast magnetosonic (FMS) waves (FMS solitons) in cold magnetized plasma are obtained by numerically solving two-fluid hydrodynamic equations. The parameter domain within which steady-state solitary waves can propagate is determined. It is established that the Mach number for rarefaction FMS solitons is always less than unity. The restriction on the propagation velocity leads to the limitation on the amplitudes of the magnetic field components of rarefaction solitons. It is shown that, as the soliton propagates in plasma, the transverse component of its magnetic field rotates and makes a complete turn around the axis along which the soliton propagates.     

Nonlinear extraordinary wave in dense plasma

Conditions for the propagation of a slow extraordinary wave in dense magnetized plasma are found. A solution to the set of relativistic hydrodynamic equations and Maxwell’s equations under the plasma resonance conditions, when the phase velocity of the nonlinear wave is equal to the speed of light, is obtained. The deviation of the wave frequency from the resonance frequency is accompanied by nonlinear longitudinal-transverse oscillations. It is shown that, in this case, the solution to the set of self-consistent equations obtained by averaging the initial equations over the period of high-frequency oscillations has the form of an envelope soliton. The possibility of excitation of a nonlinear wave in plasma by an external electromagnetic pulse is confirmed by numerical simulations.     

Nonlinear ion acoustic waves in a quantum degenerate warm plasma with dust grains

A study is made of the propagation of ion acoustic waves in a collisionless unmagnetized dusty plasma containing degenerate ion and electron gases at nonzero temperatures. In linear theory, a dispersion relation for isothermal ion acoustic waves is derived and an exact expression for the linear ion acoustic velocity is obtained. The dependence of the linear ion acoustic velocity on the dust density in a plasma is calculated. An analysis of the dispersion relation reveals parameter ranges in which the problem has soliton solutions. In nonlinear theory, an exact solution to the basic equations is found and examined. The analysis is carried out by Bernoulli’s pseudopotential method. The ranges of the phase velocities of periodic ion acoustic waves and the velocities of solitons are determined. It is shown that these ranges do not overlap and that the soliton velocity cannot be lower than the linear ion acoustic velocity. The profiles of the physical quantities in a periodic wave and in a soliton are evaluated, as well as the dependence of the critical velocity of solitons on the dust density in a plasma.     

Energy transport mechanism in the form of proton soliton in a one-dimensional hydrogen-bonded polypeptide chain

The dynamics of protons in a one-dimensional hydrogen-bonded (HB) polypeptide chain (PC) is investigated theoretically. A new Hamiltonian is formulated with the inclusion of higher-order molecular interactions between peptide groups (PGs). The wave function of the excitation state of a single particle is replaced by a new wave function of a two-quanta quasi-coherent state. The dynamics is governed by a higher-order nonlinear Schrödinger equation and the energy transport is performed by the proton soliton. A nonlinear multiple-scale perturbation analysis has been performed and the evolution of soliton parameters such as velocity and amplitude is explored numerically. The proton soliton is thermally stable and very robust against these perturbations. The energy transport by the proton soliton is more appropriate to understand the mechanism of energy transfer in biological processes such as muscle contraction, DNA replication, and neuro-electric pulse transfer on biomembranes.     

High-order nonlinear excitations in the Joyeux-Buyukdagli model of DNA

By means of the semidiscrete multiple-scale method, we study the existence and properties of high-order envelope solitons and discrete breathers in a homogeneous DNA chain model that is based on pairing enthalpies and site-dependent finite stacking. We obtain the analytical solutions for an envelope soliton, and find that at the Brillouin zone center, discrete breather solutions can appear below the bottom of the phonon band. The behavior of two solitons in collisions and the stability of discrete breathers are confirmed by numerical simulations of the exact equations of the system.     

Investigation of low-frequency waves in plasma-filled microwave oscillators

The excitation of microwave oscillations by an electron beam in a hybrid plasma waveguide—a slow-wave structure (a sequence of inductively coupled resonators) with a plasma-filled transport channel—is studied both experimentally and theoretically. It is shown that the governing role in the generation of microwaves and their transmission to a feeder line is played by the spatial and temporal plasma-density variations associated with low-frequency ion plasma oscillations. The microwave pressure gives rise to low-frequency plasma oscillations with a rise time shorter than their period. This nonlinear mechanism for the excitation of low-frequency oscillations has a threshold in terms of the microwave power. The unsteady character of the spatial distribution of the plasma density results in intermittent microwave generation and shortens the duration of microwave pulses.     

Ion-acoustic soliton in a plasma with finite-temperature ions

The influence of the ion temperature on the properties of ion-acoustic solitons is considered. The critical parameters, the role of reflected ions, and the soliton profile are analyzed. The soliton evolution is studied using numerical simulations. The stability of stationary solutions is demonstrated. The results obtained are compared with the Korteweg-de Vries soliton and available experimental data.     

The lifetime of molecular (Davydov) solitons

The lifetime of Davydov solitons in a one-dimensional system is studied theoretically. The process of thermalization and the properties of solitons at finite temperature are investigated and the processes of soliton creation and disintegration are discussed.     

Channeling of high-power radio waves under conditions of strong anomalous absorption in the presence of an averaged electron heating source

Strong anomalous absorption of a high-power radio wave by small-scale plasma inhomogeneities in the Earth’s ionosphere can lead to the formation of self-consistent channels (solitons) in which the wave propagates along the magnetic field, but has a soliton-like intensity distribution across the field. The structure of a cylindrical soliton as a function of the wave intensity at the soliton axis is analyzed. Averaged density perturbations leading to wave focusing were calculated using the model proposed earlier by Vas’kov and Gurevich (Geomagn. Aéron. 16, 1112 (1976)), in which an averaged electron heating source was used. It is shown that, under conditions of strong electron recombination, the radii of individual solitons do not exceed 650 m.     

A theorem on Boussinesq solitons or why soliton formation sharpens resonant absorption and why this has nothing to do with real polymers

Soliton formation has been proposed as an explanation for anomalously sharp resonances observed in DNA microwave absorption. We give an elementary, physical explanation of why line narrowing occurs for Boussinesq solitons. We consider real atoms bound by realistic chemical bonds and show that even under the assumption of the most favorable possible conditions, the soliton narrowing mechanism is a maximum correction of only a few percent. At each step of the argument, the simple calculations we show are either exact-in the sense of following the Boussinesq equation - or err on the side of emphasizing the soliton lifetime enhancement. Thus our results serve as an upper bound to any enhancement effects.     

Ion-acoustic solitons in dusty plasma

The dynamics of dust ion-acoustic solitons is analyzed in a wide range of dusty plasma parameters. The cases of both a positive dust grain charge arising due to the photoelectric effect caused by intense electromagnetic radiation and a negative grain charge established in the absence of electromagnetic radiation are considered. The ranges of plasma parameters and Mach numbers in which ??conservative?? (nondissipative) solitons can exist are determined. It is shown that, in dusty plasma with negatively charged dust grains, both compression and rarefaction solitons can propagate, whereas in plasma with positively charged dust grains, only compression solitons can exist. The evolution of soliton-like compression and rarefaction perturbations is studied by numerically solving the hydrodynamic equations for ions and dust grains, as well as the equation for dust grain charging. The main dissipation mechanisms, such as grain charging, ion absorption by dust grains, momentum exchange between ions and dust grains, and ion-neutral collisions are taken into account. It is shown that the amplitudes of soliton-like compression and rarefaction perturbations decrease in the course of their evolution and their velocities (the Mach numbers) decrease monotonically in time. At any instant of time, the shape of an evolving soliton-like perturbation coincides with the shape of a conservative soliton corresponding to the current value of the Mach number. It is shown that, after the interaction between any types of soliton-like perturbations, their velocities and shapes are restored (with a certain phase shift) to those of the corresponding perturbations propagating without interaction; i.e., they are in fact weakly dissipative solitons.     

A Theorem on Boussinesq Solitons or Why Soliton Formation Sharpens Resonant Absorption and Why This Has Nothing to Do With Real Polymers

Abstract

Soliton formation has been proposed as an explanation for anomalously sharp resonances observed in DNA microwave absorption. We give an elementary, physical explanation of why line narrowing occurs for Boussinesq solitons. We consider real atoms bound by realistic chemical bonds and show that even under the assumption of the most favorable possible conditions, the soliton narrowing mechanism is a maximum correction of only a few percent. At each step of the argument, the simple calculations we show are either exact-in the sense of following the Boussinesq equation-or err on the side of emphasizing the soliton lifetime enhancement. Thus our results serve as an upper bound to any enhancement effects.     

Ion-acoustic solitons in Bi-Ion dusty plasma

The propagation of ion-acoustic solitons in a warm dusty plasma containing two ion species is investigated theoretically. Using an approach based on the Korteveg de Vries equation, it is shown that the critical value of the negative ion density that separates the domains of existence of compression and rarefaction solitons depends continuously on the dust density. A modified Korteveg de Vries equation for the critical density is derived in the higher order of the expansion in the small parameter. It is found that the nonlinear coefficient of this equation is positive for any values of the dust density and the masses of positive and negative ions. For the case where the negative ion density is close to its critical value, a soliton solution is found that takes into account both the quadratic and cubic nonlinearities. The propagation of a solitary wave of arbitrary amplitude is investigated by the quasi-potential method. It is shown that the range of dust densities around the critical value within which solitary waves with positive and negative potentials can exist simultaneously is relatively wide.     

Radiative damping of coronal-loop oscillations

A theoretical interpretation is given to the coronal-loop oscillations that have been recently detected by the UV telescope of the TRACE spacecraft. It is shown that the anomalously rapid damping of coronal-loop oscillations initiated by an external action (a shock wave from a solar flare) is completely explained in terms of the radiative damping mechanism. A coronal loop oscillating with a small but finite (observable) amplitude in an external magnetic field efficiently generates fast magnetosonic modes. As a result, the perturbation energy is completely dissipated during several periods of free oscillations of the loop. The problem is studied in the perfectly conducting plasma approximation. The effect is explained without making any hypotheses about anomalous properties of the plasma inside the coronal loops.