Theoretical analysis of biomolecules using BSM models


1. Introduction 1

2. The new point of view of the BSM theory 2

3. Quantum loops and possible orbits for electron with optimal confined velocity. Embedded signature of the fine structure constant. 8

3.1 Quantum motion of the electron in closed loop trajectories. 8

3.2. Quantum orbits. Emission and absorption of photon. 10

3.3 Lifetime of the orbital motion of the electron 11

4. External shape and geometry of proton and neutron 12

5. Atlas of Atomic Nuclear Structures 14

5.1. Physical atomic models according to BSM concept. 14

5.2. Three-dimensional structure of atomic nuclei and limited angular freedom of the valence protons. 15

6. Electronic bonds between atoms in molecules 16

7. Vibrational motion of atoms connected in molecule by electronic bonds. Relation between optical and photoelectron spectra. 17

8. Method of determination of the molecular structure for diatomic molecules 19

9. Examples of some molecular structures 20

10. Rotational component in vibrational rotational spectra of molecules 21

11. Structural and angular restrictions of the atomic positions in the molecules when connected by electronic bonds 22

11.1. Restrictions from atomic nuclear configuration 22

11.2. Restrictions from spin-orbital interactions 22

12. New method for analysis of the biomolecules with identified structure and composition. 23

12.1. General considerations 23

12.2. Ring atomic structures in organic molecules. 23

12.3 Weak hydrogen bonds 25

12.4. Hypothesis of energy storage mechanism in molecules possessing ring atomic structures. 26

12.5 Hypothesis of energy flow through the chain structure of the biomolecule. 27

12.5.1. Energy flow in DNA molecule and its effect on the higher order structural characteristics. 27

12.5.2. Magnetic field conditions for proteins. 29

12.5.3. Environment considerations for preservation of the native shape of the biomolecules. 30

12.5.4. Magnetic field involved in the higher order structures of DNA. 31

12.6. Hypothesis about the role of DNA in the cell cycle synchronization mechanism 33

12.6.1 General considerations 33

12.6.2. Time sequence in the energy read-out process of DNA and its possible relation to the cell cycle synchronization. 36

11.6.3. Environment considerations for the efficiency of the avalanche process 37 Phase accuracy dependence of the cell cycle period 37 Physical factors of cell environment 38

12.7. Established features and experimental results supporting the hypothesis of the DNA involvement in the cell cycle synchronization 38

12.7.1 Absorption properties of DNA. 38

12.7.2 Increased binding ability of some simple organic molecules 39

12.7.3 Effects of the salt concentration in helical winding and DNA supercoiling 39

12.7.4 Role of intermolecular triplexes in genetic recombination 39

12.7.5. Electronic properties of DNA 39

13. Hypothesis of decoding process in some of the complexes aminoacyle-tRNA synthetases - tRNA. 40

13.1. General considerations and code analysis 40

13.2 Decoding algorithm 45

Discussion. 45

References: 46