Increase a degree of freedom for one dimension dynamical system of the α-helix protein, obtaining the dynamical system model of double degree of freedom. In this new dynamical system there are the solution of double ...Increase a degree of freedom for one dimension dynamical system of the α-helix protein, obtaining the dynamical system model of double degree of freedom. In this new dynamical system there are the solution of double soliton on the polypeptide chain of α-helix protein, and the coupling intensity of the double soliton relate obviously with their center distance. The solution of the synchronous double soliton has been studied by the analytical method for two cases of the stronger and weaker coupling. The possible effect brought by tile double soliton for the protein property has been discussed.展开更多
We mainly investigate the variable-coefficient 3-coupled nonlinear Schrodinger(NLS)system,which describes soli- ton dynamics in the three-spineα-helical protein with inhomogeneous effect.The variable-coefficient NLS ...We mainly investigate the variable-coefficient 3-coupled nonlinear Schrodinger(NLS)system,which describes soli- ton dynamics in the three-spineα-helical protein with inhomogeneous effect.The variable-coefficient NLS equation is transformed into the constant coefficient NLS equation by similarity transformation firstly.The Hirota method is used to solve the constant coefficient NLS equation,and then we get the one-and two-breather solutions of the variable-coefficient NLS equation.The results show that,in the background of plane waves and periodic waves,the breather can be transformed into some forms of combined soliton solutions.The influence of different parameters on the soliton solution and the collision between two solitons are discussed by some graphs in detail.Our results are helpful to study the soliton dynamics inα-helical protein.展开更多
Proteins are important biological molecules whose structures are closely related to their specific functions. Understanding how the protein folds under physical principles, known as the protein folding problem, is one...Proteins are important biological molecules whose structures are closely related to their specific functions. Understanding how the protein folds under physical principles, known as the protein folding problem, is one of the main tasks in modern biophysics. Coarse-grained methods play an increasingly important role in the simulation of protein folding, especially for large proteins. In recent years, we proposed a novel coarse-grained method derived from the topological soliton model, in terms of the backbone Cα chain. In this review, we will first systematically address the theoretical method of topological soliton. Then some successful applications will be displayed, including the thermodynamics simulation of protein folding, the property analysis of dynamic conformations, and the multi-scale simulation scheme. Finally, we will give a perspective on the development and application of topological soliton.展开更多
The thermal stability of the soliton excited in the protein molecular system which work at finite temperature and a nonlinear vibration of the molecular chain have beed studied in our theory. The results obtained show...The thermal stability of the soliton excited in the protein molecular system which work at finite temperature and a nonlinear vibration of the molecular chain have beed studied in our theory. The results obtained show that the soliton moves in supersonic velocity and the amplitude of soliton depends on the temperature and the strengthen of nonlinear vibration. but the soliton excited is thermal stable in the case of the physiologic temperature 310K.展开更多
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 ...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.展开更多
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-ti...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 Range-Kutta method and physical parameter values appropriate to the ~-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 motious 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 result, s 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.展开更多
It is known that our theory is preferable and more justifiable to the protein compared with the Davydov theory. For example, the soliton energy （about 13—36cm）, the soliton lifetime at 310K (about 10<sup>-9&l...It is known that our theory is preferable and more justifiable to the protein compared with the Davydov theory. For example, the soliton energy （about 13—36cm）, the soliton lifetime at 310K (about 10<sup>-9</sup>—10<sup>-8</sup>s) and the specific heat resulting from the soliton （C<sub>v</sub>=A+BT and C<sub>1</sub>=10<sup>4</sup> erg/gK<sup>2</sup>） in our theory are basically consistent with the infrared and Raman spectral experimental datum (15cm<sup>-1</sup>), Auston’s picosecond freeelectron laser experimental value (about 10<sup>-10</sup>s) and Mrevishvil and Goldanskii’s measurement results （C<sub>v</sub>=a+rT and C<sub>1</sub>=10<sup>4</sup> erg/gK<sup>2</sup>）, respectively. These show that our theory for bio-energy transport by the soliton is correct and credible. The very reason is展开更多
The current geometric and thermodynamic approaches in protein folding studies do not provide a definite solution to understanding mechanisms of folding of biological proteins. A major problem is that the protein is fi...The current geometric and thermodynamic approaches in protein folding studies do not provide a definite solution to understanding mechanisms of folding of biological proteins. A major problem is that the protein is first synthesized as a linear molecule that subsequently must reach its native configuration in an extremely short time. Hydrophobicity-hydrophilicity models and random search mechanism cannot explain folding to the 3-D functional form in less than 1 second, as it occurs in the intact cell. We propose an integral approach, based on the embedding of proteins in the whole cellular context under the postulate: a life protein is never alone. In this concept the protein molecule is influenced by various long and short distance force fields of nature such as coherent electromagnetic waves and zero-point energy. In particular, the role of solitons is reviewed in relation to a novel GM-scale biophysical principle, revealed by us. This recent finding of a set of discrete EM frequency bands, that either promote or endanger life conditions, could be a key in further studies directed at the morphogenetic aspects of protein folding in a biological evolutionary context. In addition, an alternative hypothesis is presented in which each individual cell may store integral 3-D information holographically at the virtual border of a 4-D hypersphere that surrounds each living cell, providing a field receptive memory structure that is instrumental in guiding the folding process towards coherently oscillating protein networks that are crucial for cell survival.展开更多
Protein Secondary Structure Prediction (PSSP) is considered as one of the major challenging tasks in bioinformatics, so many solutions have been proposed to solve that problem via trying to achieve more accurate predi...Protein Secondary Structure Prediction (PSSP) is considered as one of the major challenging tasks in bioinformatics, so many solutions have been proposed to solve that problem via trying to achieve more accurate prediction results. The goal of this paper is to develop and implement an intelligent based system to predict secondary structure of a protein from its primary amino acid sequence by using five models of Neural Network (NN). These models are Feed Forward Neural Network (FNN), Learning Vector Quantization (LVQ), Probabilistic Neural Network (PNN), Convolutional Neural Network (CNN), and CNN Fine Tuning for PSSP. To evaluate our approaches two datasets have been used. The first one contains 114 protein samples, and the second one contains 1845 protein samples.展开更多
文摘Increase a degree of freedom for one dimension dynamical system of the α-helix protein, obtaining the dynamical system model of double degree of freedom. In this new dynamical system there are the solution of double soliton on the polypeptide chain of α-helix protein, and the coupling intensity of the double soliton relate obviously with their center distance. The solution of the synchronous double soliton has been studied by the analytical method for two cases of the stronger and weaker coupling. The possible effect brought by tile double soliton for the protein property has been discussed.
基金supported by the Scientific and Technological Innovation Programs of Higher Education Institution in Shanxi,China(Grant Nos.2020L0525 and 2019L0782)the National Natural Science Foundation of China(Grant Nos.11805141 and 12075210)+2 种基金Applied Basic Research Program of Shanxi Province,China(Grant No.201901D211424)“1331 Project”Key Innovative Research Team of Taiyuan Normal University(Grant No.I0190364)Key Research and Development program of Shanxi Province,China(Grant No.201903D421042).
文摘We mainly investigate the variable-coefficient 3-coupled nonlinear Schrodinger(NLS)system,which describes soli- ton dynamics in the three-spineα-helical protein with inhomogeneous effect.The variable-coefficient NLS equation is transformed into the constant coefficient NLS equation by similarity transformation firstly.The Hirota method is used to solve the constant coefficient NLS equation,and then we get the one-and two-breather solutions of the variable-coefficient NLS equation.The results show that,in the background of plane waves and periodic waves,the breather can be transformed into some forms of combined soliton solutions.The influence of different parameters on the soliton solution and the collision between two solitons are discussed by some graphs in detail.Our results are helpful to study the soliton dynamics inα-helical protein.
文摘Proteins are important biological molecules whose structures are closely related to their specific functions. Understanding how the protein folds under physical principles, known as the protein folding problem, is one of the main tasks in modern biophysics. Coarse-grained methods play an increasingly important role in the simulation of protein folding, especially for large proteins. In recent years, we proposed a novel coarse-grained method derived from the topological soliton model, in terms of the backbone Cα chain. In this review, we will first systematically address the theoretical method of topological soliton. Then some successful applications will be displayed, including the thermodynamics simulation of protein folding, the property analysis of dynamic conformations, and the multi-scale simulation scheme. Finally, we will give a perspective on the development and application of topological soliton.
文摘The thermal stability of the soliton excited in the protein molecular system which work at finite temperature and a nonlinear vibration of the molecular chain have beed studied in our theory. The results obtained show that the soliton moves in supersonic velocity and the amplitude of soliton depends on the temperature and the strengthen of nonlinear vibration. but the soliton excited is thermal stable in the case of the physiologic temperature 310K.
文摘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.
基金The project supported by National Natural Science Foundation of China under Grant No.19974034
文摘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 Range-Kutta method and physical parameter values appropriate to the ~-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 motious 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 result, s 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.
文摘It is known that our theory is preferable and more justifiable to the protein compared with the Davydov theory. For example, the soliton energy （about 13—36cm）, the soliton lifetime at 310K (about 10<sup>-9</sup>—10<sup>-8</sup>s) and the specific heat resulting from the soliton （C<sub>v</sub>=A+BT and C<sub>1</sub>=10<sup>4</sup> erg/gK<sup>2</sup>） in our theory are basically consistent with the infrared and Raman spectral experimental datum (15cm<sup>-1</sup>), Auston’s picosecond freeelectron laser experimental value (about 10<sup>-10</sup>s) and Mrevishvil and Goldanskii’s measurement results （C<sub>v</sub>=a+rT and C<sub>1</sub>=10<sup>4</sup> erg/gK<sup>2</sup>）, respectively. These show that our theory for bio-energy transport by the soliton is correct and credible. The very reason is
文摘The current geometric and thermodynamic approaches in protein folding studies do not provide a definite solution to understanding mechanisms of folding of biological proteins. A major problem is that the protein is first synthesized as a linear molecule that subsequently must reach its native configuration in an extremely short time. Hydrophobicity-hydrophilicity models and random search mechanism cannot explain folding to the 3-D functional form in less than 1 second, as it occurs in the intact cell. We propose an integral approach, based on the embedding of proteins in the whole cellular context under the postulate: a life protein is never alone. In this concept the protein molecule is influenced by various long and short distance force fields of nature such as coherent electromagnetic waves and zero-point energy. In particular, the role of solitons is reviewed in relation to a novel GM-scale biophysical principle, revealed by us. This recent finding of a set of discrete EM frequency bands, that either promote or endanger life conditions, could be a key in further studies directed at the morphogenetic aspects of protein folding in a biological evolutionary context. In addition, an alternative hypothesis is presented in which each individual cell may store integral 3-D information holographically at the virtual border of a 4-D hypersphere that surrounds each living cell, providing a field receptive memory structure that is instrumental in guiding the folding process towards coherently oscillating protein networks that are crucial for cell survival.
文摘Protein Secondary Structure Prediction (PSSP) is considered as one of the major challenging tasks in bioinformatics, so many solutions have been proposed to solve that problem via trying to achieve more accurate prediction results. The goal of this paper is to develop and implement an intelligent based system to predict secondary structure of a protein from its primary amino acid sequence by using five models of Neural Network (NN). These models are Feed Forward Neural Network (FNN), Learning Vector Quantization (LVQ), Probabilistic Neural Network (PNN), Convolutional Neural Network (CNN), and CNN Fine Tuning for PSSP. To evaluate our approaches two datasets have been used. The first one contains 114 protein samples, and the second one contains 1845 protein samples.
