Bio-energy in s-Helix Protein Molecules with Three Properties of Soliton-Transported Channels

We study numerically the propagating properties of soliton-transported bio-energy excited in the a-helix protein molecules with three channels in the cases of the short-time and long-time motions and its features of collision at temperature T = 0 and biological temperature T = 300 K by the dynamic equations in the improved Davydov theory and fourth-order Runge-Kutta method, respectively. From these simulation experiments we see that the new solitons in the improved model can move without dispersion at a constant speed retaining its shape and energy in the cases of motion of both short-time or T = 0 and long time or T = 300 K and can go through each other without scattering in their collisions. In these cases its lifetime is, at least, 120 ps at 300 K, in which the soliton can travel over about 700 amino acid residues. This result is consistent with analytic result obtained by quantum perturbed theory in this model. In the meanwhile, the influences of structure disorder of a-helix protein molecules, including the inhomogeneous distribution of amino acids with different masses and fluctuations of spring constant, dipole-dipole interaction, exciton-phonon coupling constant and diagonal disorder, on the solitons are also studied by the fourth-order Runge-Kutta method. The results show that the soliton still is very robust against the structure disorders and thermal perturbation of proteins at biological temperature 300 K. Therefore we can conclude that the new soliton in the a-helix protein molecules with three channels is a possible carrier of bio-energy transport and the improved model is possibly a candidate for the mechanism of this transport.     

Properties of Soliton-Transported Bio-energy in α-Helix Protein Molecules with Three Channels

We study numerically the propagating properties of soliton-transported bio-energy excited in the α-helix protein molecules with three channels in the cases of the short-time and long-time motions and its features of collision at temperature T = 0 and biological temperature T = 300 K by the dynamic equations in the improved Davydov theory and fourth-order Runge-Kutta method, respectively. From these simulation experiments we see that the new solitons in the improved model can move without dispersion at a constant speed retaining its shape and energy in the cases of motion of both short-time or T = 0 and long time or T = 300 K and can go through each other without scattering in their collisions. In these cases its lifetime is, at least, 120 ps at 300 K, in which the soliton can travel over about 700 amino acid residues. This result is consistent with analytic result obtained by quantum perturbed theory in this model. In the meanwhile, the influences of structure disorder of α-helix protein molecules, including the inhomogeneous distribution of amino acids with different masses and fluctuations of spring constant, dipole-dipole interaction, exciton-phonon coupling constant and diagonal disorder, on the solitons are also studied by the fourth-order Runge-Kutta method. The results show that the soliton still is very robust against the structure disorders and thermal perturbation of proteins at biological temperature 300 K. Therefore we can conclude that the new soliton in the α-helix protein molecules with three channels is a possible carrier of bio-energy transport and the improved model is possibly a candidate for the mechanism of this transport.     

Changes of properties of the soliton with temperature under influences of structure disorder in the α-helix protein molecules with three channels

The changes of property of solitons in α-helix protein molecules with three channels under influences of fluctuations of structure parameters and thermal perturbation of medium are extensively investigated using dynamic equations in the improved theory, numerical simulation and Runge-Kutta method. In this investigation the peculiarities of the solitons are given first in the motions of short-time and long-time and its collision features at T = 0 K and biological temperature T = 300 K. This study shows that the solutions of dynamic equations are solitons, which are very stable at T = 0 and 300 K, although its amplitudes and velocity are somewhat decreased relative to that at T = 0 K, the soliton can transport over 1000 amino acid residues, its lifetime is, at least, 120 ps. Subsequently, studies are made of the changes of properties of the soliton with variations of temperature of the medium and fluctuations of structure parameters including mass sequence of amino acid residues and the coupling constant, force constant, dipole–dipole interaction, chain–chain interaction and ground state energy in the α-helix proteins. The investigations indicate that the soliton has high thermal stability and can transport along the molecular chains retaining amplitude, energy and velocity, although the fluctuations of the structure parameters and temperature of the medium increase continually. However, the solitons disperse in larger fluctuations at T = 300 K and higher temperatures than 315 K. Thus it is determined that the critical temperature of the soliton is 315 K. Finally reasons are given for the generation of high thermal stability of the soliton and the correctness of the improved model is demonstrated. It is concluded that the soliton in the improved model is very robust against structure disorder and thermal perturbation of the α-helix protein molecules at 300 K, and is a possible carrier of bio-energy transport, and the improved model is maybe a candidate for the mechanism of this transport.     

The theory of bio-energy transport in the protein molecules and its properties

The bio-energy transport is a basic problem in life science and related to many biological processes. Therefore to establish the mechanism of bio-energy transport and its theory have an important significance. Based on different properties of structure of α-helical protein molecules some theories of bio-energy transport along the molecular chains have been proposed and established, where the energy is released by hydrolysis of adenosine triphosphate (ATP). A brief survey of past researches on different models and theories of bio-energy, including Davydov's, Takeno's, Yomosa's, Brown et al.'s, Schweitzer's, Cruzeiro-Hansson's, Forner's and Pang's models were first stated in this paper. Subsequently we studied and reviewed mainly and systematically the properties, thermal stability and lifetimes of the carriers (solitons) transporting the bio-energy at physiological temperature 300 K in Pang's and Davydov's theories. From these investigations we know that the carrier (soliton) of bio-energy transport in the α-helical protein molecules in Pang's model has a higher binding energy, higher thermal stability and larger lifetime at 300 K relative to those of Davydov's model, in which the lifetime of the new soliton at 300 K is enough large and belongs to the order of 10(-10) s or τ/τ(0)≥700. Thus we can conclude that the soliton in Pang's model is exactly the carrier of the bio-energy transport, Pang's theory is appropriate to α-helical protein molecules.     

Influence of structure disorders and temperatures of systems on the bio-energy transport in protein molecules (II)

The influence of molecular structure disorders and physiological temperature on the states and properties of solitons as transporters of bio-energy are numerically studied through the fourth-order Runge-Kutta method and a new theory based on my paper [Front. Phys. China, 2007, 2(4): 469]. The structure disorders include fluctuations in the characteristic parameters of the spring constant, dipole-dipole interaction constant and exciton-phonon coupling constant, as well as the chain-chain interaction coefficient among the three channels and ground state energy resulting from the disorder distributions of masses of amino acid residues and impurities. In this paper, we investigate the behaviors and states of solitons in a single protein molecular chain, and in α-Helix protein molecules with three channels. In the former we prove first that the new solitons can move without dispersion, retaining its shape, velocity and energy in a uniform and periodic protein molecule. In this case of structure disorder, the fluctuations of the spring constant, dipole-dipole interaction constant and exciton-phonon coupling constant, as well as the ground state energy and the disorder distributions of masses of amino acid residues of the proteins influence the states and properties of motion of solitons. However, they are still quite stable and are very robust against these structure disorders, even in the presence of larger disorders in the sequence of masses, spring constants and coupling constants. Still, the solitons may disperse or be destroyed when the disorder distribution of the masses and fluctuations of structure parameters are quite great. If the effect of thermal perturbation of the environment on the soliton in nonuniform proteins is considered again, it is still thermally stable at the biological temperature of 300 K, and at the longer time period of 300 ps and larger spacing of 400 amino acids. The new soliton is also thermally stable in the case of motion over a long time period of 300 ps in the region of 300–320 K under the influence of the above structure disorders. However, the soliton disperses in the case of a higher temperature of 325 K and in larger structure disorders. Thus, we determine that the soliton’s lifetime and critical temperature are 300 ps and 300–320 K, respectively. These results are also consistent with analytical data obtained via quantum perturbed theory. In α-Helix protein molecules with three channels, results obtained show that these structure disorders and quantum fluctuations can change the states and features of solitons, decrease their amplitudes, energies and velocities, but they still cannot destroy the solitons, which can still transport steadily along the molecular chains while retaining energy and momentum when the quantum fluctuations are small, such as in structure disorders and quantum fluctuations of $ 0.67 < \alpha _k < 2,\Delta W = \pm 8\% \overline W ,\Delta J = \pm 1\% \overline J ,\Delta (\chi _1 + \chi _2 ) = \pm 3\% (\bar \chi _1 + \bar \chi _2 ) $ and $ \Delta L = \pm 1\% \bar L $ and $ \Delta \varepsilon _0 = \varepsilon \left| {\beta _n } \right|,\varepsilon = 0.1 meV,\left| {\beta _n } \right| < 0.5 $ . Therefore, the solitons in the improved model are quite robust against these disorder effects. However, the solitons may be dispersed or disrupted in cases of very large structure disorders. 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 motion over a long time period of 120 ps, and can retain their shapes and energies to travel forward along protein molecules after mutual collision of the solitons at the biological temperature of 300 K. Therefore, the soliton is also very robust against thermal perturbation of the α-helix protein molecules at 300 K. However, the soliton disperses in cases of higher temperatures at 325 K and in larger structure disorders. Thus, their critical temperature is about 320 K. When the effects of structure disorder and temperature are considered simultaneously, the soliton has high thermal stability and can transport for a long time along the protein molecular chains while retaining its amplitude, energy and velocity, even though the fluctuations of the structure parameters and temperature of the medium increase continually. However, the soliton disperses in the larger fluctuations of $ 0.67\overline M < M_k < 2\overline M , \Delta (\chi _1 + \chi _2 ) = \pm 2\% (\bar \chi _1 + \bar \chi _2 ), \Delta J = \pm 1.3\% \bar J, \Delta W = \pm 6\% \overline W , \Delta L = \pm 1.5\% \overline L $ and $ \Delta \varepsilon _0 = \varepsilon \left| {\beta _n } \right|, \varepsilon = 0.82 meV, \left| {\beta _n } \right| \leqslant 0.5 $ at T=300 K, and at temperatures higher than 315 K when the fluctuations are $ 0.67\overline M < M_k < 2\overline M , \Delta (\chi _1 + \chi _2 ) = \pm 1\% (\bar \chi _1 + \bar \chi _2 ), \Delta J = \pm 0.7\% \bar J, \Delta W = \pm 7\% \overline W , \Delta L = \pm 0.8\% \overline L $ and $ \Delta \varepsilon _0 = \varepsilon \left| {\beta _n } \right|, \varepsilon = 0.4 meV, \left| {\beta _n } \right| \leqslant 0.5 $ . This means that the critical temperature of the soliton is only 315 K in this condition. In a word, we can conclude from the above investigations that the soliton in the improved model is very robust against the structure disorders and thermal perturbation of proteins at the biological temperature of 300 K in α-helix protein molecules, and is a possible bio-energy transport carrier; the improved model is a possible candidate for the mechanism of this transport.     

Theory of bio-energy transport in protein molecules and its experimental evidences as well as applications ( I )

A new theory of bio-energy transport along protein molecules, where energy is released by the hydrolysis of adenosine triphosphate (ATP), has recently been proposed for some physical and biological reasons. In this theory, Davydov’s Hamiltonian and wave function of the systems are simultaneously improved and extended. A new interaction has been added into the original Hamiltonian. The original wave function of the excitation state of single particles has been replaced by a new wave function of the two-quanta quasi-coherent state. In such a case, bio-energy is carried and transported by the new soliton along protein molecular chains. The soliton is formed through the self-trapping of two excitons interacting with amino acid residues. The exciton is generated by the vibration of amide-I (C=O stretching) arising from the energy of the hydrolysis of ATP. The properties of the soliton are extensively studied by analytical methods and its lifetime for a wide range of parameter values relevant to protein molecules is calculated using the nonlinear quantum perturbation theory. The lifetime of the new soliton at the biological temperature of 300 K is large enough and belongs to the order of 10^-10 s or τ/τ₀ ≥ 700. The different properties of the new soliton are further studied. The results show that the new soliton in the new model is a better carrier of bio-energy transport and it can play an important role in biological processes. This model is a candidate of the bio-energy transport mechanism in protein molecules.     

Influence of structure disorders and temperaturesof systems on the bio-energy transport in proteinmolecules (Ⅱ)

The influence of molecular structure disorders and physiological temperature on the states and properties of solitons as transporters of bio-energy are numerically studied through the fourth-order Runge-Kutta method and a new theory based on my paper [Front. Phys. China, 2007, 2(4): 469]. The structure disorders include fluctuations in the characteristic parameters of the spring constant, dipole-dipole interaction constant and exciton-phonon coupling constant, as well as the chain-chain interaction coefficient among the three channels and ground state energy resulting from the disorder distributions of masses of amino acid residues and impurities. In this paper, we investigate the behaviors and states of solitons in a single protein molecular chain, and in α-Helix protein molecules with three channels. In the former we prove first that the new solitons can move without dispersion, retaining its shape, velocity and energy in a uniform and periodic protein molecule. In this case of structure disorder, the fluctuations of the spring constant, dipole-dipole interaction constant and exciton-phonon coupling constant, as well as the ground state energy and the disorder distributions of masses of amino acid residues of the proteins influence the states and properties of motion of solitons. However, they are still quite stable and are very robust against these structure disorders, even in the presence of larger disorders in the sequence of masses, spring constants and coupling constants. Still, the solitons may disperse or be destroyed when the disorder distribution of the masses and fluctuations of structure parameters are quite great. If the effect of thermal perturbation of the environment on the soliton in nonuniform proteins is considered again, it is still thermally stable at the biological temperature of 300 K, and at the longer time period of 300 ps and larger spacing of 400 amino acids. The new soliton is also thermally stable in the case of motion over a long time period of 300 ps in the region of 300–320 K under the influence of the above structure disorders. However, the soliton disperses in the case of a higher temperature of 325 K and in larger structure disorders. Thus, we determine that the soliton’s lifetime and critical temperature are 300 ps and 300–320 K, respectively. These results are also consistent with analytical data obtained via quantum perturbed theory. In α-Helix protein molecules with three channels, results obtained show that these structure disorders and quantum fluctuations can change the states and features of solitons, decrease their amplitudes, energies and velocities, but they still cannot destroy the solitons, which can still transport steadily along the molecular chains while retaining energy and momentum when the quantum fluctuations are small, such as in structure disorders and quantum fluctuations of and and . Therefore, the solitons in the improved model are quite robust against these disorder effects. However, the solitons may be dispersed or disrupted in cases of very large structure disorders. 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 motion over a long time period of 120 ps, and can retain their shapes and energies to travel forward along protein molecules after mutual collision of the solitons at the biological temperature of 300 K. Therefore, the soliton is also very robust against thermal perturbation of the α-helix protein molecules at 300 K. However, the soliton disperses in cases of higher temperatures at 325 K and in larger structure disorders. Thus, their critical temperature is about 320 K. When the effects of structure disorder and temperature are considered simultaneously, the soliton has high thermal stability and can transport for a long time along the protein molecular chains while retaining its amplitude, energy and velocity, even though the fluctuations of the structure parameters and temperature of the medium increase continually. However, the soliton disperses in the larger fluctuations of and at T=300 K, and at temperatures higher than 315 K when the fluctuations are and . This means that the critical temperature of the soliton is only 315 K in this condition. In a word, we can conclude from the above investigations that the soliton in the improved model is very robust against the structure disorders and thermal perturbation of proteins at the biological temperature of 300 K in α-helix protein molecules, and is a possible bio-energy transport carrier; the improved model is a possible candidate for the mechanism of this transport.      

Theory of bio-energy transport in protein molecules and its experimental evidences as well as applications (I)

A new theory of bio-energy transport along protein molecules, where energy is released by the hydrolysis of adenosine triphosphate (ATP), has recently been proposed for some physical and biological reasons. In this theory, Davydov’s Hamiltonian and wave function of the systems are simultaneously improved and extended. A new interaction has been added into the original Hamiltonian. The original wave function of the excitation state of single particles has been replaced by a new wave function of the two-quanta quasi-coherent state. In such case, bio-energy is carried and transported by the new soliton along protein molecular chains. The soliton is formed through the self-trapping of two excitons interacting with amino acid residues. The exciton is generated by the vibration of amide-I (C=O stretching) arising from the energy of the hydrolysis of ATP. The properties of the soliton are extensively studied by analytical methods and its lifetime for a wide range of parameter values relevant to protein molecules is calculated using the nonlinear quantum perturbation theory. The life-time of the new soliton at the biological temperature of 300 K is large enough and belongs to the order of 10⁻¹⁰ s or τ/τ ₀ ⩾ 700. The different properties of the new soliton are further studied. The results show that the new soliton in the new model is a better carrier of bio-energy transport and it can play an important role in biological processes. This model is a candidate of the bio-energy transport mechanism in protein molecules.      

The lifetime of the soliton in the improved Davydov model at the biological temperature 300 K for protein molecules

We study the effects of quantum fluctuations and thermal perturbations on the lifetime of the soliton in the improved Davydov model proposed by us with two-quanta and with an added interaction. By using quantum perturbation theory, we compute the soliton lifetime for a wide ranges of parameter values relevant for protein molecules. The lifetime of the new soliton at the biological temperature 300 K is of the order of 10^-10 second or τ/τ≥ 500 for parameters appropriate to α-helical protein molecules. This shows clearly that the new soliton in the improved model is a viable mechanism for the bio-energy transport in the α-helix region of proteins. Received 7 January 1999 and Received in final form 16 August 2000     

Properties of Proton Transfer in Hydrogen-Bonded Systems at Finite Temperature

The properties of proton transfer along hydrogen-bonded molecular systems are studied at finite temperature. The dynamic equations of the proton transport along the systems are obtained by using a completely quantum mechanics method. From the dynamic equations and its soliton solutions we find out specific heat arising from the motion of solitons in the systems with finite temperature and the critical temperature of the soliton in the protein molecules, which is about 318 K. This shows that we can continuously study some biological phenomena in the living systems by this model.     

温度对中心对称光折变稳态暗孤子演化的影响

为了得到温度对中心对称光折变晶体中空间暗孤子影响的结果,数值研究了中心对称光折变暗孤子动态演化的温度特性。结果表明,孤子强度包络演化强烈地依赖于晶体的温度和介电常数的温度特性。在290-320K的温度变化范围内,暗孤子的宽度随温度的增加而变大,孤子的峰值强度随温度的增加而变小。在300K的温度下,中心对称光折变介质中可以形成稳定的暗空间孤子,当温度从300K升高或降低时,孤子将克服较小的扰动而保持稳定的传播。通过调整温度可以改变孤子的空间形态。     

Influences of Quantum and Disorder Effects on Solitons Excited in Protein Molecules in Improved Model

Utilizing the improved model with quasi-coherent two-quantum state and new Hamiltonian containing an additional interaction term [Phys. Rev. E62 (2000) 6989 and Euro. Phys. J. B19 (2001) 297] we study numerically the influences of the quantum and disorder effects including distortion of the sequences of masses of amino acid molecules and fluctuations of force constant of molecular chains, and of exciton-phonon coupled constants and of the dipole-dipole interaction constant and of the ground state energy on the properties of the solitons transported the bio-energy in the protein molecules by Runge-Kutta method. The results obtained show that the new soliton is robust against these structure disorders, especially for stronger disorders in the sequence of masses spring constants and coupling constants, except for quite larger fluctuations of the ground state energy and dipole-dipole interaction constant. This means that the new soliton in the improved model is very stable in normal cases and is possibly a carrier of bio-energy transport in the protein molecules.     

Properties of Proton Transfer in Hydrogen-Bonded Systems at Finite Temperature

The properties of proton transfer along hydrogen-bonded molecular systems are studied at finite temperature. The dynamic equations of the proton transport along the systems are obtained by using a completely quantummechanics method. From the dynamic equations and its soliton solutions we find out specific heat arising from the motionof solitons in the systems with finite temperature and the critical temperature of the soliton in the protein molecules,which is about 318 K. This shows that we can continuously study some biological phenomena in the living systems bythis model.     

在三通道α-螺旋蛋白质中传递生物能量的孤子的特性

用庞小峰先生提出的生物能量传递的新理论和 Runge-Kutta数值模拟方法,研究了三通道α-螺旋蛋白质中激发的孤子的动力学特性,求出在0K和300K温度下该孤子稳定地沿蛋白质链传递.由此可见,它能担任在蛋白质分子中传递生物能量的功能.从而再次证实了新理论的可利用性.     

生物能量传递新模型中的孤立子特性研究

从庞提出的新的生物能量传递理论出发,用Runge-Kutta方法和蛋白质分子的特征参数值对该理论的基本动力学方程进行了数值模拟,求出了孤立子在自由运动下、在相互碰撞时以及它在长时间运动后的特征.研究表明,在这些运动过程中,这个孤立子始终保持稳定状态.于是看到它能真正承担起在蛋白质分子传递生物能量的功能.从而从数值模拟的角度证明了新理论的可利用性.     

Long-range effects on superdiffusive algebraic solitons in anharmonic chains

Studies on thermal diffusion of lattice solitons in Fermi-Pasta-Ulam (FPU)-like lattices were recently generalized to the case of dispersive long-range interactions (LRI) of the Kac-Baker form. The variance of the soliton position shows a stronger than linear time-dependence (superdiffusion) as found earlier for lattice solitons on FPU chains with nearest-neighbour interactions (NNI). Since the superdiffusion seems to be generic for nontopological solitons, we want to illuminate the role of the soliton shape on the superdiffusive mechanism. Therefore, we concentrate on an FPU-like lattice with a certain class of power-law long-range interactions where the solitons have algebraic tails instead of the exponential tails in the case of FPU-type interactions (with or without Kac-Baker LRI).Despite of structurally similar Langevin equations which hold for the soliton position and width of the two soliton types, the algebraic solitons reach the superdiffusive long-time limit with a characteristic t^3/2 time-dependence much faster than exponential solitons. The soliton shape determines the diffusion constant in the long-time limit that is approximately a factor of π smaller for algebraic solitons. Our results appear to be generic for nonlinear excitaitons in FPU-chains, because the same superdiffusive time-dependence was also observed in simulations with discrete breathers.     

Dynamics of matter-wave solitons in a ratchet potential

We study the dynamics of bright solitons formed in a Bose-Einstein condensate with attractive atomic interactions perturbed by a weak bichromatic optical lattice potential. The lattice depth is a biperiodic function of time with a zero mean, which realizes a flashing ratchet for matter-wave solitons. We find that the average velocity of a soliton and the soliton current induced by the ratchet depend on the number of atoms in the soliton. As a consequence, soliton transport can be induced through scattering of different solitons. In the regime when matter-wave solitons are narrow compared to the lattice period the dynamics is well described by the effective Hamiltonian theory.     

The effect of the negative particle velocity in a soliton gas within Korteweg–de Vries-type equations

The effect of changing the direction of motion of a defect (a soliton of small amplitude) in soliton lattices described by the Korteweg–de Vries and modified Korteweg–de Vries integrable equations (KdV and mKdV) was studied. Manifestation of this effect is possible as a result of the negative phase shift of a small soliton at the moment of nonlinear interaction with large solitons, as noted in [1], within the KdV equation. In the recent paper [2], an expression for the mean soliton velocity in a “cold” KdV-soliton gas has been found using kinetic theory, from which this effect also follows, but this fact has not been mentioned. In the present paper, we will show that the criterion of negative velocity is the same for both the KdV and mKdV equations and it can be obtained using simple kinematic considerations without applying kinetic theory. The averaged dynamics of the “smallest” soliton (defect) in a soliton gas consisting of solitons with random amplitudes has been investigated and the average criterion of changing the sign of the velocity has been derived and confirmed by numerical solutions of the KdV and mKdV equations.     

The Davydov Hamiltonian leads to stochastic energy transfer in proteins

A new set of equations of motion for the semiclassical Davydov model at finite temperature, which satisfy both the classical statistics of the lattice motion and the quantum statistics of the quasiparticle, is used. The Davydov soliton, defined as the exact one-quantum ground state of the Davydov Hamiltonian, is shown to disappear in the subpicosecond timescale. However, in contrast with previous simulations, the quasiparticle states are essentially localised at 310 K, and the Davydov model remains a possible mechanism for energy transfer in proteins. The dynamics at biological temperatures consists of a stochastic hopping of the quantum quasiparticle from site to site. The biological implications are discussed and in order to stimulate experimental tests of the theory the predicted absorption spectrum of the Davydov model is presented.     

线性塞曼劈裂对自旋-轨道耦合玻色-爱因斯坦凝聚体中亮孤子动力学的影响

利用变分近似及基于Gross-Pitaevskii方程的直接数值模拟方法,研究了自旋-轨道耦合玻色-爱因斯坦凝聚体中线性塞曼劈裂对亮孤子动力学的影响,发现线性塞曼劈裂将导致体系具有两个携带有限动量的静态孤子,以及它们在微扰下存在一个零能的Goldstone激发模和一个频率与线性塞曼劈裂有关的谐振激发模.同时给出了描述孤子运动的质心坐标表达式,发现线性塞曼劈裂明显影响孤子的运动速度和振荡周期.