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.     

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 The original wave function of the excitation state of single particles has been replaced by a new wave function of the two-quanta quasi-coherent state.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.      

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 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.     

The corrected Enskog theory and the transport properties of molecular liquids

Analytical expressions for the transport coefficients of liquids based on the corrected Enskog theory have been used in order to determine the self-diffusion coefficient (D) for molecular liquids as a function of density and temperature. The liquids considered are those composed of linear molecules and NH₃. The calculated D values agree with the experimental ones for those molecular liquids for which experimental self-diffusion data are available. The translational part of the thermal conductivity (λ_trans) has also been calculated and compared with the experimental thermal conductivity (λ). It turns out that λ_trans for diatomic molecular liquids practically represents the whole of λ in a substantial fraction of the liquid range, indicating that the internal degrees of freedom hardly contribute to the thermal conductivity in these dense liquids. A comparison is made with recently published results based on the modified Enskog theory.     

超晶格和层状结构传热特性的连续模型及其在能源材料设计中的应用

层状材料和超晶格结构为提高热电材料和隔热涂层提供了新的设计思路, 并成为最近的研究热点. 应用连续波动方程和线性阻尼理论, 本文研究了此类材料中的声子输运特性. 给出了在整个相空间里的界面调制和声子局域化效应, 得出了超晶格材料热导率的上极限和下极限; 同时, 分析表明界面锐化加强了声子带隙, 使得部分模态的声子局域化加强. 最后, 通过对石墨烯/氮化硼超晶格(G/hBN)和硅/锗超晶格的分子模拟(Si/Ge), 验证了该理论模型. 该方法适用于所有的层状材料和超晶格结构, 对此类新能源材料的设计提供了普适的设计思路.     

Investigation of a new mean temperature-dependent potential energy function for methane and its use for the prediction of transport properties

In this work an improved mean potential energy function for the interaction of an isolated pair of methane is obtained, from which the non-equilibrium properties of methane at zero pressure limit are calculated, accurately. The potential energy function of 21 different fixed orientations of (CH₄)₂ dimer has been obtained via the coupled cluster method. In order to obtain a mean potential energy function, the Boltzmann-average of the obtained potentials of the selected fixed orientations has been used. Unlike the full potential energy surface with the angle-dependent, the parameters of the mean potential are found to be temperature-dependent. The mean potential energy function is fitted well by an analytical expression at different temperatures. The mean absolute percentage deviation of analytical expression compare to the calculated value is about 0.6%. In studying a system with a great number of configurations, calculation of the potential energy function for all configurations is an impossible task; in the proposed model, 21 important fixed orientations have been selected. Introduction of a new approach for calculating the potential energy in methane and investigation of the temperature dependence of mean potential energy are the most important claims of this work. The mean potential function is used to calculate the viscosity, self-diffusion coefficient, and thermal conductivity at the zero pressure limit. The mean absolute percentage deviation in the calculated viscosity, self-diffusion coefficient and thermal conductivity is 3.1, 2.4, and 5.3%, respectively. Also, the second virial coefficient has been calculated for some temperatures.     

Interaction of RNA molecules: Binding energy and the statistical properties of random sequences

The free binding energy of two RNA molecules is determined and some statistical properties such as fluctuation of the mean binding energy between two RNA molecules and the distribution of loop lengths in the structure formed are discussed. An analysis of the dependence of the specific free energy of a complex of two long random RNA molecules on the number c of nucleotide types led us to suggest that the four-letter genetic alphabet used by nature plays a special role.