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 The original wave function of the excitation state of single particles has been replaced by a new wave function of the two-quanta quasi-coherent state.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 The original wave function of the excitation state of single particles has been replaced by a new wave function of the two-quanta quasi-coherent state.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

Temperature effects on the transport properties of molecules

Recent experiments found an unusual temperature-induced large shift in the resonant-tunneling voltage of certain molecules. We report first-principles calculations showing that such behavior can be caused by the excitation of rotational modes of ligands. These modes have classical characteristics, i.e., the maximum excursion is dominant, while at the same time they have a significant effect on the energy levels responsible for resonant tunneling. The proposed mechanism of ligand rotations is unique to molecules and accounts for the fact that the effect is not seen in semiconductor nanostructures.     

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.     

吐昔烯衍生物分子的电荷传输性质

根据爱因斯坦方程和Marcus电荷传输模型, 使用密度泛函理论B3lyp/6-31g^**理论水平计算6 个吐昔烯衍生物分子的结构和电荷传输性质. 结果显示: 6个吐昔烯的衍生物分子的空穴迁移速率为0.018–0.062 cm²·V^-1·s^-1, 电子迁移率为0.055–0.070 cm²·V^-1·s^-1, 其中3, 8, 13-辛烷氧基吐昔烯衍生物分子适合作为双极性传输材料. 三条烷氧基链的吐昔烯衍生物分子上引入三个甲氧基或羟基, 均使空穴和电子传输率降低. 引入给电子基团或共轭性基团可减小吐昔烯衍生物分子的能隙, 达到有机半导体的能隙要求. 关键词： 吐昔烯衍生物 空穴传输 电子传输 有机半导体     

Thermoelastic properties of helical protein molecules

The effect of stress on the helix-coil transition in a protein or polypeptide is investigated using the methods of statistical mechanics. A case is treated in which the helical sections are regarded as flexible chains withvery long, freely orienting segments and another in which they are considered to be rigid rods. Thermoelastic relations are derived; and it turns out that, depending upon conditions, stress can induce the helix-coil transition in one or another direction or do nothing at all. The most probable situations either involve stress applied to a molecule initially helical, in which case the helix is stabilized, or stress applied to the coil form, in which case transformation to the helical form is induced. The helical form exhibits a very low modulus of elasticity (which we also compute), and it is speculated that preservation of, or transition to, the helical form under stress aids in the protection of living tissue from disruption when subjected to large applied strain. Real tissues involve highly organized or quasirandom networks of protein chains. The results of this analysis suggest that, insofar as the mechanical properties of the networks are concerned, the chains can be treated as quasiharmonic strings whose configurations (weighted by potential energy) can be enumerated in order to include entropy effects in the calculation of the network modulus.Work performed as part of a 1970 summer study project in connection with the Advanced Research Projects Agency Materials Research Council.     

电子在蛋白质分子中的迁移机理及其特性

ATP水解作用所释放的能量能引起蛋白质分子中额外电子的激发,其激发与氨基酸残基晶格畸变相互作用,使额外电子自陷成孤子,这孤子在附着有供体(D)和受体(A)的蛋白质分子中运动时,由于孤子与供体电子的相互作用而"自局域"在孤子上进行迁移,从而可把电子供给受体.使用作者提出的孤子理论研究了这种迁移的特征,计算了在这种非平衡态过程中由孤子迁移电子的速率和动能系数,得到了一些有趣的结果,揭示了这种迁移的本质,求得了迁移的大小.     

分子链长对烷烃硫醇分子电输运性质的影响

在杂化密度泛函理论的基础上,利用弹性散射格林函数方法研究了烷烃硫醇系列分子的电输运性质,并同实验结果进行了比较。研究结果表明,在低的外加偏压下,烷烃硫醇分子电流值随着分子链长度的增加而指数减小,其衰减常数约为1.41/CH2,且衰减常数基本上与外加偏压值的大小无关。分子末端原子与探针的距离具有较大地自由度,不同的接触距离导致了分子的电流值有较大地差别。     

Nonequilibrium quantum transport properties of organic molecules on silicon

Electron transport properties of a Si/organic-molecule/Si junction are investigated by large-scale nonequilibrium Green function calculations. The results provide a qualitative picture and quantitative understanding of the importance of self-consistent screening, broadening of quasimolecular orbitals under large bias, and enhancement of transmission, which occurs when the broadened lowest unoccupied molecular orbital aligns with the conduction band edge of the negative lead. The varying coupling can lead to negative differential resistance for a large class of small molecules.     

The temperature-dependent electrical transport properties of liquid Sn using pseudopotential theory

We present the calculations of electrical resistivity, thermo-electric power and thermal conductivity based on the self-consistent approximation. The pseudopotential due to Hasegawa et al. [J. Non-Cryst. Solids 117/118, 300 (1990) M. Hasegawa, K. Hoshino, M. Watabe, and H. Young, J. Non-Cryst. Solids 117/118, 300 (1990).[Crossref], [Web of Science ®] , [Google Scholar]] for full electron–ion interaction, which is valid for all electrons and contains the repulsive delta function to achieve the necessary s-pseudisation, was used in the calculation. Temperature dependence of structure factor is achieved through temperature-dependent potential parameter in the pair-potential. The outcome of the present study is discussed in the light of other such results and with predictions of Wiedemann and Franz law up to moderately high temperature. Specially, high-temperature resistivity data necessitates the careful investigation of electron energy dispersion close to the Fermi level and possible metal to non-metal transition while going from dense-fluid to low density-fluid state. In the absence of experimental data at high temperature, these findings may serve as future guideline.