Investigation of Ion-Acoustic Solitons in Magnetosphere and Tokamak Warm Plasma with Two-Temperature Electrons

The properties of oblique propagation of small amplitude ion-acoustic soliton are investigated in a plasma containing weakly relativistic ions and two-temperature electrons (cold and hot electrons). The reductive perturbation method is used to derive the Korteweg?de Vries equation for the present plasma model. It is found that the parameters determining the nature of soliton are different for compressive or rarefactive structures. Moreover, the effects of weakly relativistic ions, the temperature ratio, and the density ratio of hot-to-cold electron species on soliton characters are studied. The theory is applied on the case of relativistic ions observed in the magnetosphere and in the case of nonrelativistic ions observed in tokamaks.     

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.     

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.     

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.     

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.     

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.     

电离辐射对蛋白质分子作用的量子孤波分析

本文运用量子力学方法对蛋白质分子中孤波传播的非线性动力学特征进行了探讨。研究表明：电离辐射产生的自由基对蛋白质分子的伤害将会对携带能量、信息的孤立子波传播产生较为显著的影响。     

Chirped dissipative ion-cyclotron solitons in the Earth’s low-altitude ionospheric plasma with two ion species

Conditions for the excitation of small-scale nonlinear ion-cyclotron gradient-drift dissipative structures in cold ionospheric plasma are considered. The solution for the wave electric field in this structure in the form of a chirped soliton satisfying the equation of the Ginzburg-Landau type is derived in the electrostatic approach. The dissipative structure as a whole represents the chirped soliton accompanied by the comoving quasineutral plasma hump. The possibility of the excitation of two modes of this type (the high- and low-frequency ones) in plasma containing light and heavy ion impurities is considered. The role of electromagnetic corrections and the possible contribution introduced by these structures to the transport processes in the ionosphere are discussed.     

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.     

Higher Dimensional Gaussian-Type Solitons of Nonlinear Schr?dinger Equation with Cubic and Power-Law Nonlinearities in PT-Symmetric Potentials

Two families of Gaussian-type soliton solutions of the (n+1)-dimensional Schrödinger equation with cubic and power-law nonlinearities in -symmetric potentials are analytically derived. As an example, we discuss some dynamical behaviors of two dimensional soliton solutions. Their phase switches, powers and transverse power-flow densities are discussed. Results imply that the powers flow and exchange from the gain toward the loss regions in the cell. Moreover, the linear stability analysis and the direct numerical simulation are carried out, which indicates that spatial Gaussian-type soliton solutions are stable below some thresholds for the imaginary part of -symmetric potentials in the defocusing cubic and focusing power-law nonlinear medium, while they are always unstable for all parameters in other media.     

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.     

Resonance Effects of Microwaves are Caused by their Interaction with Solitons in A-Helical Proteins

The frequency-dependent, resonance-type biological effects of electromagnetic radiation on a-helical protein macromolecules were treated in terms of Davydov soliton (DS) theory. We studied DS over the temperature range from 0 to 350 K. An important characteristic of the autolocalized state is the bond energy, which defines the soliton stability. As the DSs are stable, only a small probability exists of their energy dissipation into heat providing for the high efficiency of energy and charge transduction in bio-systems. However, under the influence of electromagnetic radiation (EMR), the DS decay (photodissociation) probability increases. This approach allows for the qualitative explanation of the resonant effects of low-intensity microwaves on living organisms found in a number of experiments. The dependence of resonance frequency on temperature was obtained this way. The direct charge transfer along the protein molecule may result from the capture of an extra electron by the moving acoustic soliton (electrosoliton). Decay of the electrosoliton under the influence of EMR (photodisintegration) is also examined.     

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.     

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.     

Is the arterial pulse a soliton?

The recent discovery of arterial smooth muscle contractions which are synchronized with the activity of the right atrial pacemaker in the rabbit heart gives support to the hypothesis that the arterial pulse wave is a soliton. The hypothesis is amenable to experimental tests.     

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 “Houston's horse” effect

The structure of an ion-acoustic forerunner excited by a shock wave in a weakly ionized plasma is studied. It is shown that, when the shock velocity exceeds the ion-acoustic speed, a soliton bunch is produced at the perturbation front. The increase in the shock velocity to a certain critical value is accompanied by an increase in the soliton amplitude. A further increase in velocity leads to an explosive-like collapse of the bunch, which results in a decrease in the medium resistance. This phenomenon is analogous to the “Houston's horse” effect in narrow-channel hydrodynamics.     

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)     

Air‐core fiber or photonic‐crystal rod,which is more suitable for energetic femtosecond pulse generation and three‐photon microscopy at the 1700‐nm window?

Energetic femtosecond pulses at the 1700‐nm window are a prerequisite for deep‐tissue three‐photon microscopy (3PM). Soliton self‐frequency shift (SSFS) in photonic‐crystal (PC) rod has been the only technique to generate such pulses suitable for 3PM. Here we demonstrate through SSFS in an air‐core fiber, we can generate most energetic femtosecond soliton pulses at the 1700‐nm window, 5.2 times higher than that from PC rod. However, the air‐core soliton pulse width is 5.9 times longer than that of PC rod soliton. Based on comparative 3PM excited with both air‐core and PC rod solitons, we propose the more suitable source for 3PM. We further elucidate the challenge of generating shorter soliton pulses from air‐core fibers through numerical simulation.