Pang Xiao-Feng

Stabilization of the soliton transported bio-energy in protein molecules in the improved model

We study the stabilization of the soliton transported bio-energy by the dynamic equations in the improved Davydov theory from four aspects containing the feature of free motion and states of the soliton at the long-time motion and at biological temperature 300 K and behaviors of collision of the solitons by Runge-Kutta method and physical parameter values appropriate to the alpha-helix protein molecules. We prove that the new solitons can move without dispersion at a constant speed retaining its shape and energy in free and long-time motions and can go through each other without, scattering. If considering further influence of the temperature effect of heat bath on the soliton, it is still thermally stable at biological temperature 300 K and in a time as long as 300 ps and amino acid spacings as large as 400, which shows that the lifetime of the new soliton is at least 300 ps, which is consistent with analytic result obtained by quantum perturbation theory. These results exhibit that, the new soliton is a possible carrier of bio-energy transport and the improved model is possibly a candidate for the mechanism of this transport.

Distribution of vibrational energy levels of protein molecular chains

The distributions of the quantum vibrational energy levels of the protein molecular chain are found by the discretely nonlinear Schrodinger equation appropriate to protein obtained from the Davydov theory. The results calculated by this method are basically consistent with the experimental values. Furthermore, the energy spectra at high excited states have also been obtained for the molecular chain which is helpful in researching the properties of infrared absorption and Raman scattering of the protein molecules.

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.

Nonlinearly vibrational energy-spectra of molecular crystals*

The nonlinear quantum vibrational energy spectra of amide-I in the molecular crystals acetanilide are calculated by using the discrete nonlinear Schrodinger equation appropriate to this kind of crystals. The numerical results obtained by this method are in good agreement with the experimental values. Meanwhile, the energy levels at high excited states have also been obtained for the acetanilide, which is helpful in researching the Raman scattering and infrared absorption properties of the this kind of crystals.

Features of Motion of Soliton Transported Bio-energy in Aperiodic α-Helix Protein Molecules with Three Channels

The structure aperiodicities can influence seriously the features of motion of soliton excited in the alpha-helix protein molecules with three channels. We study the influence of structure aperiodicities on the features of the soliton in the improved model by numerical simulation and Runge-Kulta method. The results obtained show that the new soliton is very robust against the structure aperiodicities including large disorder in the sequence of mass of the amino acids and fluctuations of spring constant, coupling constant, dipole-dipole interactional constant, ground state energy and chain-chain interaction. However, very strong structure aperiodicities can also destroy the stability of the soliton in the alpha-helix protein molecules.

Vibrational energy-spectra and infrared absorption of alpha-helical protein molecules

The quantum energy spectra, including high excited states, of vibrational amide-I or of intramolecular excitations in α-helical protein molecules, are calculated by the discrete nonlinear Schrodinger equation together with the parameters appropriate to the systems. The distribution of energy levels obtained is basically consistent with the experimental values obtained by infrared absorption and Raman scattering. Utilizing the energy spectra we explain the laser Raman spectrum from metabolically active escherichia coli and we present some further features of the infrared absorption of the protein molecules.

Influences of Structure Disorder and Temperature on Properties of Proton Conductivity in Hydrogen-Bond Molecular Systems

The dynamic properties of proton conductivity along hydrogen-bonded molecular systems,. for example, ice crystal, with structure disorder or damping and finite temperatures exposed in an externally applied electric-field have been numerically studied by Runge-Kutta way in our soliton model. The results obtained show that the proton-soliton is very robust against the structure disorder including the fluctuation of the force constant and disorder in the sequence of masses and thermal perturbation and damping of medium, the velocity of its conductivity increases with increasing of the externally applied electric-field and decreasing of the damping coefficient of medium, but the proton-soliton disperses for quite great fluctuation of the force constant and damping coefficient. In the numerical simulation we find that the proton-soliton in our model is thermally stable in a large region of temperature of T <= 273 K under influences of damping and externally applied electric-field in ice crystal. This shows that our model is available and appropriate to ice.

Influences of temperature on proton conductivity in the hydrogen-bond molecular systems with damping

Influences of temperature of medium on proton conductivity in hydrogen-bonded systems exposed in an electric-field are numerically studied by the fourth-order Runge-Kutta method with our model. The results obtained show that the proton soliton is very robust against thermal perturbation and damping of medium, and is thermally stable in the temperature range T <= 273 K. From the simulation we find out that the mobility (or velocity) of proton conduction in ice crystal is a nonmonotonic function of temperature in the temperature range 170-273 K: i.e., it increases initially, reaches a maximum at about 191 K, subsequently decreases to a minimum at about 211 K, and then increases again. This changed rule of mobility is qualitatively consistent with its experimental data in ice in the same temperature range. This result provides an evidence for existence of solitons in the hydrogen-bonded systems.